18-FDOPA PET 1H-NMR 2-Piperidone urine assay 21-Day Fish Assay 24-hour urinary free cortisol 2D gel electrophoresis 2D gel electrophoresis plus anti-DNP immunoblotting 2D gel-electrophoresis with tandem mass spectrometry 2D gel-electrophoresis and tandem mass spectrometry 2D SDS-PAGE 2D SDS-PAGE and Immunofluorescence 3-nitrotyrosine assay 32P Post labelling 32P post-labeling, HPLC and immunologic detection 36Cl- uptake assay 3D CT scan 3D live imaging 3D Spheroid Invasion Assay 3D spheroid migration 3D-SIM immunofluorescence 3D-SPECT 3H-labeled ligand uptake assay 4-HNE assay 500-MHz proton nuclear magnetic resonance 53BP1 foci Detection with Time Course 5EU RNA labeling 5α-reductase inhibition assay 6-CF accumulation assay 6-hydroxychlorzoxazone/chlorzoxazone ratio 6-hydroxychlorzoxazone/chlorzoxazone ratio assay 8-nitroguanine (DNA) content 8-oxo-dG Assay [35S]t-butylbicyclophosphorothionate (TBPS) binding assay [3H]deoxycytidine or [3H]thymidine incorporation [3H]glutamate release assay [3H]thymidine incorporation 3H-thymidine incorporation 3H-thymidine incorporation assay [3H]-thymidine uptake ^31P NMR spectroscopy 31P NMR spectroscopy A280 Spectroscopy A280(Spectroscopy) AACCI Method 22-40.01 AB/PAS staining PAS staining Abcam MitoTox abdominal CT scan abdominal CT scan with histopathological biopsy Abell-Kendall technique ABRM contraction assay ACB-PCR ACE2 activity assay acellular tubulin polymerization assay acetylated tubulin immunofluorescence staining acetylcholine stimulation ACR criteria assessment acridine orange staining Acridine Orange/Ethidium Bromide staining Action potential recording activated partial thromboplastin time Activity assays activity assay enzymatic activity assays Adduct Analysis adenovirus expression system assay adenovirus-mediated overexpression adenylyl cyclase activity assay adhesion molecule expression assay Adp-Glo Kinase Assay ADP-Glo Kinase Assay ADP-to-O ratio assay adult bee count advanced oxidation protein products assay Aequorin-based bioluminescence assay AFB1-albumin adduct detection Affimetrix microarrays affinity assay affinity purification-mass spectrometry Affymetrix Genome U34A Array Genome U34A Array Affymetrix microarray Affymetrix Microarray AGD measurement Age of first forage AhR reporter assay air-liquid interface (ALI) epithelial model tracing airway microdissection Akinesia test Alamar Blue assay alanine dosimeters/NanoDots Albumin measurement Alcian blue staining with Clca3 Aldeflour kit Aldefluor assay ALDH1A2 mRNA measurement Alizarin red stain for calcium deposition Alizarin red staining alkali-labile phosphoprotein determination alkali-labile phosphoprotein alkali-labile phosphoprotein assay Alkaline Elution Assay Alkaline elution assay Alkaline Elution Assay with Time Course alkaline phosphatase assay Alkaline Unwinding Assay with Time Course Alkaline-labile phosphate assay alkaline-labile phosphate determination allele specific competitive blocker-polymerase chain reaction (ACB-PCR) ALP measurement ALP assay alpha diversity measurement AlphaLISA ALT measurement ambulatory blood pressure monitoring (ABPM) Ames test AMES assay Amino acid measurement assay amniocentesis Amperometry Amphibian Metamorphosis Assay Amplex UltraRed fluorescent assay Amplex Red Assay Amplex Red Ultra assay AmplexRed amplicon sequencing AMS AMS (Accelerated Mass Spectrometry) amylase release assay amylase secretion assay Amyloid A deposition staining Analysis of Volatile Organic Compounds in the Breath analytical ultracentrifuging anatomical examination angiogenesis assays Angiogenesis Imaging angiography animal model assay ankle-arm systolic blood pressure index Annexin V affinity assay annexin V – affinity assay Annexin V Binding Annexin V-FITC assay Annexin-V PI staining Anogenital distance (AGD) measurement antagonist compound assay Anti-glutathione immunoblotting Anti-Müllerian hormone (AMH) measurement Anti-nitrotyrosine immunoassays Antibody staining antibody staining Antibody staining of tissue sections Antibody-Based Assay antithrombin III AOPP assays aortic explant assay aortic pulse wave velocity measurement aortic ring assay ApoE-/- mouse model apoptosis inhibition assay Apoptosis PCR Microarray APR_HepG2_MitoMembPot APR_Mitochondrial_membrane_potential APTT aquatic tunnel assay AR dimerization assay AR Dimerization Assay AR Transactivation Assay AR activation assay ARE-Nrf2 Luciferase Assay Nrf2-ARE luciferase reporter assay area analysis of heart and edema area analysis of heart/edema area measurement Aromatase activity assay Aromatase activity assay (tritiated water release) Array Comparative Genomic Hybridization (aCGH) or SNP Microarray aCGH or SNP Microarray AS52 in vitro gene mutation assay ASC oligomer detection Asynchronous Development Assessment ATG_AR_TRANS ATG_LXRa_TRANS ATG_PXRE_CIS ATG_SREBF1_CIS_up assay atherosclerosis assessment Atomic force microscopy Atomic Force Microscopy atomic force microscopy ATP assay (CellTiter-Glo) ATP bioluminescent assay ATP assay ATP content assay ATP detection assay ATP modulation assay atRA formation assay Attagene GR TRANS Attagene reporter gene assay Attentional set-shifting (ATSET) task audiometry Auditory Brainstem Response (ABR) Auditory nerve electrophysiology Autobiographical Memory Task automated cell counters automated image-based system automated immunoassay automated observation and tracking system Autophagic flux measurement via radioactive protein turnover AV Node Tissue Slices avian morphological assessment avian sexual behavior frequency observation Axonal transport in mouse sciatic nerve backscatter electron microscopy balanopreputial separation assessment BALF cellularity assay BALF protein content BALF urea content BAP immunoassay Basophil Activation Test (BAT) BDNF level measurement BDNF quantitative real-time PCR Bead-Based Motility Assay Beck Depression Inventory (BDI) Bee health assessment bee health assessment Beekeeper Survey Behavior test Behavioral and cognitive performance assay Behavioral hearing test Behavioral audiometry Behavioral screening for auditory response defects behavioral studies Behavioral Tests Beta lactamase reporter gene assay Beta-catenin nuclear localization assay BG1luc BG1luc assay BG1luc estrogen receptor transactivation test BG1Luc Estrogen Receptor Transactivation Test BHAS 42 Cell Transformation Assay Bicinchoninic Acid Assay (BCA) Big Blue Big Blue assay Big Blue model Bilirubin measurement binding assay bioactivity assay biochemical compound quantification biochemical fluorometric assay Biochemistry assays Biolayer Interferometry (BLI) bioluminescent N-linked-glycosylation reporters bioluminescent reporter bioluminesence imaging BioMAP Systems Predictive Toxicology panel biomarker detection biomarker detection of ZEB1/2, SNAI1/2, and TWIST2 levels Biopsy biopsy biopsy with pathological examination BioSeek (ToxCast_BSK) multiplex assay Biotin affinity tag-based protein adduct detection Biotin labeling of glutathione Biotin-switch methods Birth dating procedures birth dating procedures bisulfite genomic sequencing Black-white preference test BLI Bioluminescence Imaging (BLI) bioluminescence imaging blood cell counts blood chemistry analysis Blood electrolyte and acid-base analysis blood gas analysis blood pressure measurement blood pressure measurement via pressure transducer blood serum metabolite measurement Blood Tests Blood tests blood tests Blood urea nitrogen measurement Blue-native polyacrylamide gel electrophoresis (BN-PAGE) BODIPY 581/591 C11 fluorescence assay body size measurement Bone connectivity modeling bone marrow aspirate for immunophenotypic analysis Bone mechanical resistance testing bone mineralisation assessment BoneTRAP assay Boronate-based indicators Boyden chamber BPDE protein adduct assay BQ assay Brain biopsy Brain-derived neurotrophic factor (BDNF) measurement BrdU BrdU immunostaining BRDU incorporation BrDU incorporation BrdU assay BrdU incorporation BrdU incorporation assay BrdU incorporation staining BrdU labeling BrdU or EdU incorporation assay BrdU staining BrdU, Ki67, IdU Quantification - Flow Cytometry Breathing parameters assessment BROD assay Bromodeoxyuridine (BrdU) labeling Bromodeoxyuridine (BrdU) labelling Bronchoalveolar lavage (BAL) fluid analysis Bronchoscopy brood assessment Brood cannibalism mapping Brood Care Behavior Brood care behavior filming BSEP inhibition assay BSK_3C_Proliferation BUN/creatinine assay C-banding C-reactive protein measurement C. elegans aneuploidy screening C. elegans screening C3 measurement Ca++ ATPase activity assay Calbindin-D9k (CaBP-9k) gene and protein expression Calcein AM assay Calcein green staining Calcium imaging Calcium Imaging calcium imaging Calcium influx assay calcium measurement assay Calcium stable isotope tracers Calcium staining (Xylenol orange, Calcein green, Tetracycline, Von Kossa, Alizarin red) Calcium-sensitive fluorescent dyes Calcofluor white staining calculation based on triglyceride and cholesterol levels Caliper measurement Caliper Mobility Shift Assay cAMP-Glo™ Assay candling cannibalism detection Capillary surfactometer Captive bubble surfactometer Capture-mark-recapture CAR null mouse assay CAR null mouse/rat experiments CAR reporter assay CAR signature analysis carbohydrate microarray carcinogenesis study Carcinogenicity assays Carotid Sinus Massage Caspase 1 FLICA Assay CASP1 Fluorescein Assay (FLICA) Caspase 8 fluorogenic substrate assay Caspase 8 enzymatic activity assay Caspase activity assay Caspase Activity Assay caspase activation assay caspase activity assay Caspase-3 and -8 colorimetric assay catalase activity assay CBA CBMN with Imaging Flow Cytometry CBMN with Microscopy CD/FTIR CD25 Phenotyping CD25 expression assay CE-MS Cell behaviour assays cell count assay Cell counting Cell Death Detection ELISA cell invasion assay cell layer diameter measurement Cell migration assay Cell morphology and size Cell Respiration Assay cell surface biotinylation cell transfection HPLC assay Cell Transformation Assays cell viability assay cell survival assay cell-based assay cell-based exogenous antioxidant assay Cell-based Phosphorylation Assay cell-based reporter gene assay cell-free decatenation assay Cell-free DNA sequencing Cellular glutathione (GSH) status assay Cellular oxygen consumption Oxygen consumption oxygen consumption measurement Ceramide synthase activity assay Ceratohyal angle measurement CFSE assay CFSE labeling CFSE proliferation assay Cytoplasmic proliferation dye (CFSE) CFSE staining (Microscopy) channel blockage by Ca2+ measurement CHART Chemiluminescence Chemiluminescence analysis chemiluminescence Chemotaxis assay chest x-ray chest X-ray Chick chorioallantoic membrane (CAM) vascularization assay Chick chorioallantoic membrane assay chick chorioallantoic membrane assay chorioallantoic membrane (CAM) assay Children’s Auditory Verbal Learning Test Children’s Auditory Verbal Learning Test (CAVLT) ChIP ChIPseq Chitin synthase activity assay radioactive chitin synthase activity assay chloride sweat test Chlorophyll fluorescence analysis chlorophyll a fluorescence Chlorzoxazone metabolism chorionic villus sampling ChREBP activation assay Chromatin immunoprecipitation (ChIP) Chromatin Immunoprecipitation (ChIP) Chromatin immunoprecipitation chromatin immunoprecipitation Chromatin Immunoprecipitation followed by qPCR or seq Chromatography and mass spectrometry chromatography-mass spectroscopy assay Chromium release assay Chromosomal aberration test Chromosomal Aberrations and Micronuclei Assays Chromosomal G-banding cilia length measurement Cl- sensitive fluorescent dye assay cleavage activity assay Cleaved caspase-3 assay Cleaved Caspase-3 Immunocytochemistry clinical examination clinical physical examination clinical interview scoring Clinical measurement and palpation clinical symptom observation clonal survival assay Club cell secretory protein expression CM-H2DCFDA Assay Co-culture myofibroblast differentiation assay co-immunoprecipitation co-precipitation Co-precipitation and gel shift assay Coagulation parameters measurement coagulation parameter measurement Coelenterazine chemiluminescence COG encoding proteins analysis collagen accumulation assessment Collagen Invasion Assay Colocalization of immunofluorescence colocalization of immunofluorescence Colony formation Colony-Forming Assay Colony loss survey Colony strength assessment Color Doppler sonography Colorimetric cholesterol assay Colorimetric H2O2 probe Colorimetric H2O2 probe assay colorimetric H2O2 assay colorimetry (DTNB) Colourimetric Dye Assay Colourimetric Dye Assays Comb visual inspection/digital imaging Combined PET-MRI Comet assay COMET assay Comet Assay Neutral Comet Assay comet assay modified comet assay Comet assay with Fpg and hOGG1 modifications Comet assay with Fpg and hOGG1 Comet Assay with Restriction Enzymes Comet Assay with Time-Course CometChip assay commercial enzyme assay commercial kit Commercial synaptogenesis assay kits CoMPARA CoMPARA computational model competitive [3H]colchicine tubulin-binding assay Competitive AR Binding Assay AR Competitive Binding Assay competitive binding assay radioligand competition binding assay Competitive inhibition binding assay Competitive PCR for cytokine mRNA quantification competitive radiometric binding assay by chemiluminescence Competitive T4-TTR fluorescence displacement assay competitive T4-TTR fluorescence displacement assay Complement 3 (C3) expression Complex I activity dipstick assay Complex I Enzyme Activity (Colorimetric) Complex I Enzyme Activity Assay (Colorimetric) colorimetric Complex I Enzyme Activity Assay Complex IV Activity Assay Complex sphingolipid measurement Complex V activity assay complex V activity assay Computational Model in silico computational models Computational Modeling Computational models computational modeling Computed Tomography (CT) Scans computer-assisted sperm analysis Concentration-response curves to vasodilators/vasoconstrictors condensed spermatid count Confocal Laser Scanning Microscopy Confocal laser scanning microscopy (CLSM) Confocal Microscopy confocal fluorescence microscopy confocal microscopy confocal microscopy with sox10 fluorescent reporter Connectivity density Connexin Analysis (Immunohistochemistry/Confocal Microscopy) Connexin Studies Constrained drop surfactometer Contextual Fear Conditioning contextual fear conditioning Continuous Visual Memory Test contractile factor detection assay Coomassie blue G250 binding method Corbiculae scoring Corneal neovascularization assay corneal neovascularization assay Corpus luteum counting Corrected Next Generation Sequencing cortisol measurement COX1 activity assay cpYFP CREB/CRE transcription activation assay CRP measurement CRP assay Cryogenic transmission electron microscopy crystallography CT Angiography computed tomography angiography CT scan CT CTL cytotoxicity assay CTX assays CV1-hGR CYP17A1 activity assay (microsomes) CYP17A1 inhibition assay CYP26B1 mRNA measurement Cyp2E1 knockout mouse metabolite measurement Humanized Cyp2E1 mouse metabolite measurement CYP2E1-dependent chemical oxidation in liver microsomes CYP7B knockout mouse model CyQuant cell Proliferation assay CyQuant Cell Proliferation Assay Cytochrome c binding domain determination Cytochrome c detection with metal nanoclusters Cytochrome c Reduction Assay Ferricytochrome c reduction assay cytochrome c reduction assay Cytogenetic analysis of oocytes cytogenetic assay cytogenetic assays Cytokeratin-18 fragment measurement cytokine bead array cytokine bead arrays cytokine bead arrays / cytokine PCR arrays Cytokine production assay Cytokine assay Cytokine measurement cytokine analysis cytokine release assay Cytokine secretion assay Cytological analysis cytological analysis cytometry Cytoplasmic Proliferation Dye Cytoplasmic Proliferation Dye Assays Cytotoxicity assay cytotoxicity assay D(-)-3-hydroxybutyric dehydrogenase assay D-dimer D-dimer concentration assay D-dimer measurement D1 protein degradation assay DAF-2 DA fluorescent indicator DAF-2 DA fluorescence DAF-2 DA fluorescent signal detection DAF-FM DAF-FM fluorescent probe Daphnia sp. Acute immobilization test DAPI Staining DAPI DAT immunostaining DCFH-DA assay DCFDA assay DCHF DCPIP reduction DCPIP reduction assay decylubiquinol/cytochrome c reductase assay Dendritic spine shrinkage quantification Density gradient subcellular fractionation DEXA DHE (dihydroethidium) diagnostic kits Dicentric Chromosome Assay Dicentric Chromosome Assay (DCA) differential display Differential scanning calorimetry differential scanning calorimetry Digital high-speed video imaging DiI fluorescent labelling Direct Costs Direct Costs assessment direct imaging of pancreatic secretion direct observation of embryonic heartbeats Direct observation of internal anatomic structures direct observation of phenotypic secondary sex characteristics phenotypic secondary sex characteristic observation Direct Peptide Reactivity Assay (DPRA) direct photolabeling disability-adjusted life year (DALY) assessment dissection and measurement Diverse Mobility assay Diverse Mobility assays DLCO DNA adduct quantitation DNA content measurement DNA DSB staining (γ-H2AX foci) DNA ladder assay DNA microarray analysis DNA microarray assay DNA sequencing DNA synthesis assay DNA-dependent radioligand binding assay DNA-methylation array DNPH derivatization with spectrophotometry Dominant Lethal test Dopamine depletion model Dopamine transporter staining dopaminergic terminal quantification Doppler optical coherence tomography (D-OCT) Dose-Response Curve for Alkyl Adducts/Mutations Dose-response modeling Drebrin immunocytochemistry drebrin immunocytochemistry droplet digital PCR Drug Study DSB repair assay DTNB assay spectrophotometry (DTNB) DXA dye exclusion assay dye transit test dye transport assay Dynamic bone histomorphometry Dynamic Energy Budget (DEB) modeling Dynamic energy budget model E. coli expressed 5α-reductase inhibition assay E2/P4 ratio EASZY assay ECG ECG (Electrocardiogram) Electrocardiogram (ECG) electrocardiogram ECG and blood pressure measurement in fish ECG recording Echocardiography ECIS ECoG ED1 immunolabeling EdU assay EdU incorporation EdU incorporation assay EEG EEG recording Electroencephalogram (EEG) Electroencephalography (EEG) electroencephalogram electroencephalography effects-based monitoring EGFR inhibition assay egg candling egg count Elastography Electric Cell-Substrate Impedance Sensing (ECIS) Electric Cell-Substrate Impedance Sensing Electrochemiluminescent immunoassay electrocorticogram electron energy loss analysis Electron Microscopy Electron microscopy electron microscopy light or electron microscopy Electron transport system (ETS) activity assay electrophoresis with DNA dye Electrophoretic Mobility Shift Assay (EMSA) Electrophoretic mobility shift assay Electrophoretic mobility shift assay (EMSA) electrophoretic mobility shift assay electrophoretic mobility shift assay (EMSA) electrophysiological recording of GABA-induced membrane currents Electrophysiology Electrophysiological measurements electrophysiology Electrophysiology Study (EPS) Electroretinography ELISA Enzyme-linked immunosorbent assay (ELISA) enzyme-linked immunosorbent assay (ELISA) immunoassay/ELISA ELISA (anti-DNA) ELISA for 8-oxodG 8-oxo-dG ELISA ELISA for angiogenic factors ELISA for Angiogenic Factors ELISA for beta-2-MG ELISA for cytokine quantification ELISA for endothelin ELISA for IFN-α ELISA for IL-2 ELISA for IL-6, IL-8, and Cox ELISA for inflammatory mediators ELISA for NF-κB activation ELISA for prostaglandin ELISA for STAT3 activation ELISA for TNF-α and IL-6 ELISA kit ELISA-based NRP1-VEGF-A165 protein binding assay ELISPOT EmA EmA assay embryo viability assessment Embryonic heart and great artery morphological assessment Embryonic swimming activity assay EMPO EMSA Endo H digestion endo H digestion analysis endogenous lifecycle model (ELM) Energy-absorbing bone capacity engineered microtissues assay enhanced polarizing microscopy Enhanced polarizing microscopy (Polscope/SpindleViewTM) enzymatic assay for glucose and ketone bodies enzymatic assay for glutamate and glutamine Enzymatic ATP synthase activity assay enzymatic method for filtrates Enzyme Activity Determination enzymatic activity assay enzymatic assay enzymatic assays enzyme activity assay enzyme activity measurement enzyme assay enzyme assays Enzyme Activity Determination (Complex I) Enzyme Activity Determination (Complex II) Enzyme Activity Determination (Complex III) enzyme activity/protein level measurement Enzyme immunoassay enzyme immunoassay enzyme immunoassay (EIA) enzyme inactivation assay Enzyme recycling assay enzyme-based microelectrode arrays enzyme-catalyzed activity assay enzyme-linked immunosorbent assay enzyme linked immunosorbent assay eosin-stained sperm morphology assessment EPH-receptor tyrosine kinase activity assay EPR (electron paramagnetic resonance spectroscopy) Electron Paramagnetic Resonance (EPR) EPR spectroscopy EPR spin-trapping EPSCs/IPSCs recording Equilibrium dialysis equilibrium dialysis Equilibrium dialysis and ultrafiltration ER ToxCast high-throughput screening assay panel ERa binding activity assay EROD EROD assay ERα CALUX ERα CALUX assay escape reflex assay Estradiol immunoassay Estrogen Receptor Binding Assay ER binding assay estrous cycle monitoring ETS activity assay (INT reduction) Euler’s characteristic Evans blue dye Evans Blue / sulforhodamine B uptake Evoked electrical activity measurements Evoked electrical activity measurements using D-AP5 D-AP5 evoked electrical activity measurement Ex vivo analysis of TLR stressors Ex vivo NMR with metabolomic profiling Ex vivo NMR and targeted metabolomics ex vivo quantification of 14C-labeled fatty acid oxidation to CO2 ex vivo steroidogenesis assay ex vivo stimulation ex vivo stimulation of PBMCs Ex vivo TLR function assay exhaled NO measurement exosomal marker analysis extended one generation test extended one-generation test Extracellular flux analysis extracellular flux analyzer assay Extracellular flux analysis (OCR/ECAR) Extracellular Matrix Composition Assay Extracellular recording (unit recording) Extracellular recordings extracellular recording extracellular recording (unit recording) eye color assessment F2-isoprostanes ELISA F4/80 immunolabeling FABO enzyme activity facial prominence measurement FACS analysis FACS-SCAN assay FAS gene expression analysis FasL/Fas binding assay fast-scan cyclic voltammetry FDG-PET Fe[DETC]2 and Fe[MGD]2 feather plumage assessment fecal egestion fecal egestion measurement Ferritin measurement fertility rate measurement fetal cell-free DNA analysis FEV1 FEV1 measurement Fiberoptic bronchoscope Fibrinogen concentration assay fibrinogen Fibrosis biomarker measurement Field Potential Recording Field potential recording Local field potential recording extracellular field potential recordings field potential recording FIGO 3-Grade Assessment Filipin staining filter insert assay Fin index calculation Fin ray length measurement Firmicutes/Bacteroidetes ratio measurement FISH Fish Auditory Evoked Potentials (AEP) fish behavioral test fish embryo heart rate observation Fish Lifecycle Toxicity Test fish ovarian tissue COX activity assay Fish Short Term Reproduction Assay FITC-dextran permeability assay FITC-dextran assay FITC-dextran serum assay flexiVent Flow cytometry FACS Flow Cytometry Flow-cytometry Flowcytometry flow cytometric method flow cytometry Flow Cytometry (alt-NHEJ) Flow Cytometry (R123 and Propidium Iodide) flow cytometry with Ca2+-sensitive fluorophores Flow Cytometry with DCFH-DA flow cytometry (DCFH-DA) Flow Cytometry with Dih123 flow cytometry (Dih123) Flow cytometry/microscopy of EGFP-degron flow cytommetry flow-mediated vasodilation (FMD) FLU-TTR FLU-TTR assay FLU-TTR (Fluorescent Probe Binding) Fluo3 AM fluorescence imaging Fluo3 AM imaging Fluorescence confocal microscopy fluorescence confocal microscopy Fluorescence Correlation Spectroscopy (FCS) Fluorescence Correlation Spectroscopy Fluorescence displacement assay fluorescence displacement assay Fluorescence in situ hybridization (FISH) Fluorescent In Situ Hybridization (FISH) fluorescence in situ hybridization (FISH) Fluorescence microscopy fluorescence microscopy fluorescent microscopy Fluorescence microscopy/spectroscopy fluorescence oxygen consumption assay Fluorescence Recovery After Photobleaching Fluorescence recovery after photobleaching Fluorescence videography/fluoroscopy fluorescence videography/fluoroscopy Fluorescence-based ROS detection Fluorescence/Substrate monitoring of autophagy-related proteins Fluorescent approaches Fluorescent AR Nuclear Translocation Assay AR Nuclear Translocation Assay Fluorescent binding assay fluorescence binding assay fluorescence binding assays Fluorescent Ca2+ imaging Fluorescent collagen reporter imaging Fluorescent displacement assay (FLU-TTR) fluorescence displacement assay (FLU-TTR) Fluorescent DNA immunostaining fluorescent dye transport Fluorescent dye uptake assay fluorescent microscopy using fluorescent collagen reporter zebrafish lines Fluorescent microscopy with Dil staining Fluorescent microscopy with MAP-2 immunohistochemistry Fluorescent Nuclear Track Detector (FNTD) fluorescent peptide substrate assay Fluorescent probe trafficking assay Fluorescent probes and imaging Fluorescent protein tagging Fluorescent reporter assay fluorescent reporter assay fluorescent reporter cell lines fluorescent reporter mouse imaging (CD11b promoter-driven fluorescent protein) Fluorescent tracer leakage assay fluorimetric analysis Fluoro-Jade staining Fluoro Jade stain Fluoro-Jade stain Fluorogenic H2O2 assay fluorogenic substrate assay Fluorometric analysis of total S-glutathionylated proteins Fluorometric assay for enzyme kinetics fluorometric enzyme kinetics assay fluorometry (H2O2 substrates) flux chamber assay FM-HCR foam cell formation assay Follicle counting Follicle counting (histological) follicle counting follicle culture food consumption measurement Food storage assessment food storage assessment Food store assessment force measurement forced oscillation Forepaw Stride length Forepaw stride length test Forward Electron Transfer assay FoxP3 expression assay fractional Ca2+ currents measurement FRAP FRET assay FRET FRET spectroscopy FRET-based assay Functional calcium imaging with light sheet microscopy Functional magnetic resonance imaging (fMRI) fMRI functional state analysis by MS G-banding gamma-H2AX Foci Staining with Time Course gamma-ray detection probe Gamma-scintigraphy gamma-scintigraphy GARD GC-MS GC/MS GC/MS or LC/MS gas chromatography mass spectrometry (GC-MS) gel filtration chromatography gel shift assay gel mobility shift assay Gene chips gene chips Gene expression analysis Gene Expression Analysis gene expression analysis gene expression assay gene expression profiling gene expression analysis (qPCR / microarray) gene expression sequencing gene set enrichment analysis Genetic Models (Knockout or Transgenic Mice) Genetic mouse model of angiogenesis Genetic Testing genomic approaches genomic, proteomic and metabolomic approaches genotyping germ cell marker probe/antibody assay germinal vesicle breakdown (GVBD) assessment GFP GFP assay GFP Reporter Assay GFP assays Green fluorescent protein reporter assay GFP fluorescence in transgenic zebrafish GFP imaging GFP technology and cofilin-F-actin quantification GFP-tagged protein trafficking assay GFP/calcium sensor imaging GGT measurement glucokinase expression assay Glucosamine quantification assay glucose flux assay glutamate assay Glutamate Assay Kit (Abcam ab83389) Glutamate-Glo™ Assay (Promega J7021) glutathione assay glycan microarray with scanning ellipsometry sensor GnRH mRNA quantification Golgi Stain Kit Golgi Staining Golgi-Cox Method Golgi-Cox and immunofluorescence confocal microscopy Golgi-Cox impregnation Gonadal examination gonado-somatic index GPx activity assay GR CALUX GR-GeneBlazer GR-regulated gene induction gradient gel electrophoresis Grid test Griess assay gross anatomical observation gross and histological examination GS-MS GS-MS-based steroid conversion assay GSH depletion GSH depletion assay glutathione depletion assay GSH:GSSG ratio detection assay GSH/GSSG Ratio Detection Assay GST pulldown guaiacol oxidation kinetic assay guaiacol oxidation assay guinea-pig occluded patch test H&E staining h-CLAT H2-DCF-DA fluorescent dye assay H295R cell-based assay H295R steroidogenesis assay H295R Steroidogenesis Assay H2DCF-DA fluorescence assay H2O2 generation assay H2O2 Production Assay with Scopoletin haematological methods haemocytometer HAI Halosperm kit Hamilton Depression Rating Scale (HAM-D) Hang test HDAC activity assay HE staining Heart developmental defect assessment heart rate measurement heartbeat rate measurement Heart Rate Monitoring heartbeat monitor Hebb-Williams Maze helium dilution Hemagglutination assay (HAI) hemagglutination assay hemagglutination inhibition (HAI) assay hemagglutination assay, receptor binding assay using sialylglycopolymers, biolayer interferometry analysis, carbohydrate microarray analysis, crystallography Hematocrit test hematocrit hematocrit test hematoxylin and eosin and Alcian blue-PAS staining Hematoxylin and eosin staining Haematoxylin and eosin staining Hematoxylin Eosin staining Hematoxylin and Eosin Staining Hematoxylin and Eosin staining Hematoxylin and eosin (H&E) staining Hematoxylin-eosin (HE) staining haematoxylin and eosin staining hematoxylin and eosin staining Hemorrhage frequency or severity index Hepatic elastography HepG2 cytotoxicity assay HepG2/HepG2-E47 comparison hERG fluorescence polarization kit Hershberger Bioassay Hershberger Bioassay in Rats hESC/iPSC differentiation system Hestrin method High content image analysis with RNAi screening High content imaging High content image analysis high content imaging high performance liquid chromatography (HPLC) high-performance liquid chromatography high throughput enzymatic analyses high-performance capillary electrophoresis (HPCE) High-resolution respirometry high-resolution respirometry High-throughput biomarker assays Hippocampal synaptic plasticity assay Histochemical and immunofluorescent imaging histological analysis of altered hepatic foci Histological examination of reproductive organs histological examination of the gonad Histological staining Histochemical Staining Histological examination Histology histochemical staining histochemistry histological assessment histological exam histological examination histological observation histological staining histology Histological staining for myelin histological staining of lung tissue Histological vitellogenin assessment Histomorphometry histone methyltransferase activity assay histopathological analysis with Ashcroft scoring Histopathological assessment of cuticle maturity Histopathology Histopathological evaluation Histopathological examination histopathologic examination histopathological analysis histopathological evaluation histopathological examination histopathological methods histopathology HLA typing HLA-binding assay HLA-DQ–gluten tetramer flow cytometry Flow cytometry with HLA-DQ–gluten tetramers HMG-CoA reductase activity assay Hoechst 33342 and propidium iodide double staining Hoechst 33342 staining Hoechst 33342 Staining Holter Monitoring Holter Monitor HOMA-IR Homeostatic Model for Insulin Resistance (HOMA-IR) home blood pressure monitoring (HBPM) Homogeneous proximity assay hormone level analysis hormone level measurement Horseradish peroxidase (HRP) microinjection HPA axis dysfunction (cortisol measurement) HPCE HPLC HPLC-based assay HPLC analysis of liver microsome metabolites HPLC analysis of recombinant CYP7B protein HPLC and capillary electrophoresis for dopamine metabolites HPLC for adenosine phosphates HPLC or HPLC-MS for total dopamine HPLC quantification of neopterin HPLC sequencing HPLC with electrochemical and fluorescence detection HPLC with electrochemical detector HPLC with fluorescence detector HPLC with fluorescence detection HPLC with fluorometric detection HPLC/fluorescence HPLC with radiolabeled steroid precursor HPLC-based CYP7B activity assay in liver microsomes HPLC-based iodothyronine synthesis assay HPLC-based SelR activity assay HPLC-based TPO activity assay HPLC-EC HPLC-ECD (in vitro) HPLC-LSS HPLC-MS HPLC-ESI-MS/MS HPLC-MS/MS HPLC/ICP-mass spectrometry HPLC-UV HPLC with UV-detection HPLC/Capillary Electrophoresis for GSH/GSSH HPLC/fluorescence detector-based assay using dihydroethidium HPPD enzyme inhibition assay HPRT Mutation Assay HPRT/XPRT gene mutation test hPSC-derived GnRH neuron characterization HRE reporter gene assay HRER assay HRIPT HRP-oxidizing substrates assay Human Androgen NHR Cell Based Antagonist Translocation LeadHunter Assay human capital approach human cardiovascular monitoring human cell-based in vitro tubulogenesis assay human epidemiological studies Human neurological rating scales Human Repeat Insult Patch Test HUVEC-based angiogenesis assay Hydrocyanine dye fluorescence assay Hydrocyanine dyes assay Hydrogel-based fibroblast culture Hydrogen peroxide detection assay Hydroxyapatite binding assay Hydroxyapatite (HAP) binding assay hydroxyapatite (HAP) binding assay Hydroxylysine glycosides assay Hydroxyproline assay Hydroxyproline Assay HyPer Probe HyPer hyperglycemia measurement hyperinsulineamic euglycaemic clamp (HEC) hyperinsulineamic euglycaemic clamp Hypopharyngeal gland development hypothalamic explants Hypronosticon assay I-O curve measurement I-O curve (input-output curve) Iba1 immunolabeling ICH or Western blot ICP-MS ICTP assay IdU incorporation IdU labeling IFNγ ELISPOT assay Igfbp3 gene expression assay IL-18 induction assay IL-1β neutralization assay IL-6 blood level measurement IL-6 immunoassay IL-8 ELISA IL-8 induction assay IL17 protein measurement IL1β measurement IL6 measurement ImageJ quantification Imaging flow cytometry imaging flow cytometry Imaging procedures imaging techniques Imaging tests immune-based assays immune based assays Immuno staining Immunoassay immunoassay immunological methods Immunoassay/microscopy Immunoassays for non-collagenous matrix proteins Immunobead-based multiplex assay ImmunoCAP Immunoblotting Immunoblot immunoblot analysis immunoblotting Immunoblotting for phospho-GSK3beta Immunocyto/histochemistry for UPS immunocyto/histochemistry/immunofluorescence Immunocytochemical assays for cathepsin K Immunocytochemistry immunocytochemistry immunocytochemistry (cofilin/phospho-cofilin) Immunocytochemistry and Western blot for DAT and VMAT2 Immunocytochemistry for C3 Immunocytochemistry for GFAP Immunocytochemistry with automated high content imaging immunodetection with anti-acetylated histone antibodies Immunofluorescence and microscopy immunofluorescence and microscopy immunofluorescent microscopy Immunofluorescence microscopy Immunofluorescence Immunofluorescence (IF) Immunofluorescence Microscopy Immunofluorescence staining Immunofluorescent staining immunofluorescence immunofluorescence assay immunofluorescence microscopy immunofluorescence staining Immunofluorescent ERK phosphorylation assay Immunofluorescent staining for α-SMA α-SMA immunohistochemistry Immunogold EM Immunohistochemical staining for olfactory marker protein Immunohistochemistry IHC IHC/IF Immunohistochemical staining Immunohistochemistry (IHC) immunohistochemical methods immunohistochemical staining immunohistochemistry immunohistochemistry (dendritic and lymphocyte markers) Immunohistochemistry detection of senescence markers (Ki67, Lamin B1) Immunohistochemistry for IgG and C3 Immunohistochemistry for Mef2c Immunohistochemistry/Immunoblotting immunohistocytological staining Immunological detection of histone acetylation immunophenotypic analyses immunophenotyping Immunoprecipitation immunoprecipitation immunoprecipitation and immunoblotting immunoprecipitation-HPLC immunoprecipitation-HPLC assay immunoslot blot assay Immunostaining immunostaining Immunostaining for excitatory synapses Immunostaining for synaptic proteins Immunostaining for α-synuclein (AS) aggregates Immunostaining for α-synuclein and ubiquitin Immunostaining of junctional markers immunostaining of lysosomal membrane proteins immunostaining with anti-5-methylcytosine antibodies immunostaining/flow cytometry of cell cycle proteins in silico analysis In silico computational modeling of angiogenesis in silico homology modeling In silico homology modeling and molecular docking in silico models In silico NMDA receptor targeting prediction NMDA receptor targeting prediction In situ hybridization In Situ Hybridization In-situ hybridization (ISH) in situ hybridization in-situ hybridization In vitro assessment of gluconeogenic capacity in vitro gluconeogenic capacity assay In Vitro DNA Cleavage Assay In vitro fibroblast proliferation assay in vitro human T cell proliferation and cytokine profile assay In vitro IKK kinase assay In vitro mammalian cell gene mutation test (HPRT) In vitro marker expression analysis in vitro neurotransmitter release assay in vitro phagocytosis assay In vitro polyadenylation assay In vitro reconstitution system in vitro T-cell-based assays (co-culture) in vivo 125I uptake assay In vivo anal fin elongation assay (western mosquitofish) In vivo cholinesterase activity measurement in vivo complex enzyme assay (ICE) in vivo complex of enzyme (ICE) assay in vivo deiodinase activity assay in vivo GCaMP imaging in vivo phototoxicity testing In vivo rodent phagocytosis and clearance assay In vivo substrate and metabolite measurement in vivo transgenic assay In vivo vessel density in fat pads In vivo zebrafish endothelial reporter assay Transgenic endothelial reporter zebrafish assay In-Cell Western Indigo Biosciences PXR activation assay Indigo hGR Indirect Immunofluorescence (IF) Indirect immunofluorescence assay (IIFA) Indirect immunohistochemistry indirect immunohistochemistry Indirect quantification of L-Glu transporter activity Inductively coupled plasma mass spectrometry (ICP-MS) Inductively coupled plasma mass spectrometry (ICPMS) indwelling dorsal aortic cannula Infectivity assay Inflammatory cytokine arrays cytokine arrays inflammatory marker quantification inflammatory mediator release assay Infrared gas analysis (IRGA) Inhibitory Synaptic Transmission probe initiation-promotion studies Intact ovarian tissue explant assay for testosterone intra-arterial pharmacologic stimulation Intracellular ATP levels assay intracellular electrode recording intracellular recordings intracellular nitric oxide assay Intracellular recording (sharp electrode) Intracranial pressure monitoring intraoperative ultrasound Intravital microscopy invasive electrophysiological auditory nerve recording Invasive fish electrophysiology invasive vasodilation measurement Ion Channel Expression Studies ion channel flux measurement ion chromatography IP3R activation assay IPA IRF7-GFP splicing reporter Ishak fibrosis score ISO 14902:2001 isolated perfused lung Isolated Tissue Studies isothermal titration calorimetry Isotope dilution mass spectrometry isotope-dilution gas chromatography-mass spectrometry Jaffé method JAK3 kinase activity assay JC-1 JC-1 assay Karyotype analysis karyotype analysis KeratinoSens KeratinoSens™ Ki-67 staining Ki-67 immunofluorescent staining Ki-67 immunohistochemistry Ki-67 immunostaining Ki67 immunostaining Ki67 probe Ki67 assay Kidney Dysfunction Assay Kidney Function Assay Kidney function assay Kinase assay Kinase assays Kinesin-driven microtubule gliding assay L-arginine to L-citrulline conversion assay L-arginine to L-citrulline assay L-arginine to L-citrulline conversion L-Glu residue quantification assay L-Glu transporter uptake assay Direct quantification of L-Glu transporter activity (Radioligand uptake) L-type Wako ALP J2 assay Labeled Probe pXRCC1 Labeled Probes for Double Strand Breaks labeled probes for oxidative damage and base excision repair Laboratory toxicity tests with population modeling laboratory-based reproduction assay lactate colorimetric assay Lactate dehydrogenase measurement Langendorff-Perfused Hearts Langmuir-Blodgett films Larval Amphibian Growth and Development Assay latex immunoassay LC-inductively coupled plasma–mass spectrometry LC-ICP-MS LC-MRM/MS LC-MS glutamate measurement LC-MS lipidomics LC-MS/MS LC-MS LC/MS LC/MS-MS LC/MS/MS Liquid chromatography-tandem mass spectrometry liquid chromatography mass spectrometry (LC–MS) liquid chromatography-tandem mass spectrometry (LC-MS/MS) liquid chromatography/mass spectrometry liquid chromatography/tandem mass spectrometry LC-MS/MS (in vivo) LC-MS/MS in vivo tissue microsome assay LC-MS/MS shotgun proteomics LC-MS/MS TH distribution analysis LC-MS/MS thyroid hormone distribution assay LC-MS/MS thyroid hormone measurement LC/MS-based methods LC3-I to LC3-II conversion assay LDH and LDH-X activity LDH release assay LDH assay LDH cytotoxicity assay LDH leakage assay LDL cholesterol assay lectin microarray length measurement Lens opacification grading systems Lentiviral NF-kB GFP reporter with flow cytometry Lentiviral NF-κB-GFP reporter with flow cytometry Leukocyte Surface Markers Leydig Cell-enriched Cultures LFP light microscopy morphometry Light microscopy or flow cytometry Light-dark transition assay line crossing assay lipid accumulation Lipid hydroperoxide assay lipid peroxidation assay Lipid peroxidation assay (TBARS) Lipidomics lipidomics Lipoprotein cholesterol assay Liquid chromatography–mass spectrometry liquid scintillation spectrometry Live cell imaging with fluorescent dyes Live-cell and confocal imaging assay Live-Cell Imaging live-cell imaging Liver biopsy LLNA LLNA: BrdU-ELISA LLNA:DA Local Lymph Node Assay (LLNA) Locomotor activity assay (birds) locomotor activity measurement Long-term potentiation (LTP) induction LTP induction long-term potentiation (LTP) induction and measurement low-temperature scanning electron microscopy Lowry Assay LPC measurement LPC membrane integration assay LPS-induced TNFα protein expression assay Lucifer Yellow leakage assay Lucifer Yellow (LY) leakage assay Luciferase reporter gene (LRG) assay Luciferase Reporter Assay Luciferase assay Luciferase reporter assay Luciferase reporter gene assay luciferase assay luciferase reporter assay luciferase reporter gene assay Luciferase-based ATP assay Luciferin-based GSH assay Luciferin-luciferase assay Luminometric luciferase/luciferin assay Lucigenin chemiluminescence assay lucigenin-enhanced chemiluminescence lung compliance and airway resistance lung tissue culture lung wet weight: dry weight ratio lung-on-a-chip Lymphocyte count Lysosomal Trapping assay LysoTracker Red staining Lysotracker green staining MA-10 assay Macromolecular permeability (Papp) Macroscopic examination macroscopic assessment macroscopic examination for malformations Magnusson-Kligman guinea pig maximization test MALDI-TOF MS MALDI-TOF/MS Male pubertal assay Male sexual behavior assay (birds) Male sexual behavior assay (newts) malformation incidence mammalian two-hybrid assay mammogram Mapping studies mapping studies MARCM fluorescent labelling Mark-recapture method Markers of leukocyte activation Mass Spectrometry Mass spectrometry mass spectrometry mass spectrometry analysis of thioredoxin/glutaredoxin system Masson Trichrome staining Masson's trichrome staining Mathematical modeling Matrigel assay Matrigel plug assay mature ova assessment MCM-2 assay MCM2 immunostaining MCT8-transfected cell uptake MDA-TBA assay MDC staining MEA Meiotic factor expression analysis Meiotic markers expression meiotic progression monitoring MELN MELN assay membrane integrity assessment Membrane SUnSET assay metabolomic approaches metabolomics metabolomics analysis metacholine challenge test metagenomic functional composition prediction metaproteomics Metatranscriptomics metatranscriptomics Methoxyresorufin O-demethylation (MROD) methyl-DIP methylated DNA immunoprecipitation (methyl-DIP) methylation-specific PCR Methylene blue-mediated enzyme biosensor MethyLight micro-electrode array micro-optical coherence tomography Microarray Micro-array micro-array microarray microarray analysis microarray profiling Microarray / RNAseq transcriptomics microarray expression profiling Microarray or RNAseq for CAR-responsive genes Microdialysis In vivo microdialysis in vivo microdialysis microdialysis microdialysis/high-performance liquid chromatography Microelectrode array (MEA) Micro-electrode array (MEA) recording Microelectrode Array (MEA) Microelectrode array (MEA) recordings micro-electrode array (MEA) recording micro-electrode arrays microelectrode array (MEA) microelectrode array (MEA) recordings Microelectrode Studies microelectrode technique Microfluidic assay microfluidic device assay Microfluidic Invasion Assays microfluidic lung-on-a-chip Micronucleus Assay by Microscopy in vivo Micronuclei (MN) Assay via Microscopy Micronucleus (MN) microscopy Micronucleus assay micronuclei assay Micronucleus assay with centromere-specific probes micronucleus formation microscale thermophoresis microscopic area analysis microscopic examination of tissue Microscopic techniques microscopy and staining Microscopy Examination Microscopy light microscopy microscope microscopy microscopy with labeled probes microsomal enzyme activity assay microsome assay mitochondria and membrane integrity assessment mitochondria assessment Mitochondrial Dye Staining Mitochondrial dynamics imaging mitochondrial function assay mitochondrial morphology assessment Mitochondrial membrane potential assay Mitochondrial Membrane Potential Assay mitochondrial membrane potential assay mitochondrial transmembrane potential measurement Mitochondrial membrane potential assay (TMRE/TMRM) Mitochondrial permeability transition pore (PTP) opening assay Mitochondrial trafficking assay MitoPy1 MitoSox MitoSOX mitotic index measurement mixed function oxidase assay MMP assay MMP activity assay MMP/TIMP measurement Modified Ellman method molecular biological techniques Molecular Markers molecular modelling molecular modeling molecular modelling; docking simulation molecular docking molecular probes Molecular Profiling Molecular Profiling (qPCR, Western Blot, Immunostaining) Monochlorobimane assay monochlorobimane assay monocyte adhesion assay monocytes migration Monte Carlo Simulations Morgan-Elson assay morphological analysis morphological analysis with electromicroscopy morphological live imaging Morphological live imaging + Aqueous outflow tract visualization Morphometric Analysis Morphometry morphometric analysis morphometric measurement morphometrics morphometric growth measurement morphometric measurement of posterior chamber size Morris Water Maze Morris water maze Mortality observation mouse IgM/IgG ELISA Mouse MPO ELISA Mouse SLT Mouse Specific Locus Test (SLT) MPO ELISA MRC scale and dynamometer MRI MRI Scan MRI scan Magnetic Resonance Imaging (MRI) Magnetic resonance imaging magnetic resonance imaging MRI-PDFF MRI/CT Scans MRI or CT Scans MRI/PET mRNA and protein level measurement mRNA and protein measurement mRNA and protein quantification using probes and antibodies mRNA expression analysis mRNA analysis mRNA measurement mRNA expression of ovulation markers mRNA quantification mRNA/protein expression assay MROD MS/MS MSD electrochemiluminescent immunoassay MSD multiplex electrochemiluminescent immunoassay MST mt-cpYFP mtDNA damage assay (QPCR) MTT assay MTT MTT Assay MTT reduction MTT/MTS/BrdU MUC5 antibody staining multicolour fluorescence in situ hybridization (FISH) Multiplex bead assay multiplex immunobead-based assay multiplex immunoassay murine Local Lymph Node Assay MUSST mutagenesis Mutant frequency assay mutation frequency analysis Mutation Spectrum mutational analysis MUTZ-3 migration assay Myc-tagged SMO activation assay Na/K ATPase activity assay NAD+/NADH ratio measurement NADH formation assay NAD reduction assay NADH/NAD+ ratio imaging NAG Assay NAG assay nasal potential difference nasal potential difference (NPD) NBT reduction assay NBT assay NCCT_HEK293T_CellTiterGLO NCI-H295 cell assay necropsy Nectar load measurement Nephelometric assay Nerve conduction studies Neurohistopathology Neutral red uptake assay Neutral red uptake Neutralization assay Neutrophil accumulation measurement Neutrophil to lymphocyte ratio newt tail-vibrating behavior count Next Generation Sequencing (NGS) NGS Next generation sequencing Next-generation sequencing Next Generation Sequencing (NGS): Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WES) NF-κB p65 (Total/Phospho) ELISA NF-κB-luciferase reporter gene assay NFkB reporter gene activation assay Nicoletti Assay Nipple retention assessment NIS-Elements image analysis NIS_HEK293T_CTG_Cytotoxicity Nitrate/Nitrite colorimetric assay Nitrate/Nitrite determination nitrate/nitrite determination Nitric oxide/nitrate/nitrite (NOx) assay kit (Griess assay) Nitroblue Tetrazolium Assay nitroblue tetrazolium nitrogen washout Nitrotyrosine and specific residue assays NMDA receptor radioligand competition binding assay (MK801 site) NMDA receptor (MK801 site) radioligand competition binding assay NMR studies NMR analysis NNF assay nocodazole treatment with electron microscopy non-contrasted head computed tomogram (CT) non-contrasted head CT Nonesterified fatty acids measurement nonesterified fatty acids measurement norepinephrine assay Northern Blot Northern blot Northern blotting northern blot Northern/Southern blotting NovaScreen (ToxCast_NVS) Novascreen assay NovaScreen biochemical profile NovaScreen NR hGR NovaScreen VEGFR2 enzymatic assay Novel Object Recognition novel object recognition Nrf2 gene expression Nrf2 qPCR assay NTE inhibition assay NTX assays Nuclear Magnetic Resonance NMR Nuclear protein extracts analysis nuclear receptor reporter assay nuclear receptor reporter assays Nuclear run-on assay Nuclear signaling assay Nuclear signaling assays nuclear signaling activation / inhibition assay nuclear signaling activation/inhibition assay nuclear signaling assay Nuclear Translocation Assay (NTA) nucleoside incorporation Nucleoside/nucleoside analog labeling Nucleotide Analog Incorporation Assays (e.g. BrdU, EdU) NVS_IC_rNaCh_site 2 NVS_IC_rNaCh_site2 NVS_NR_hAR NVS_NR_hPXR NVS_TR_rSERT OAT inhibition assay (renal tubule cells) OAT1/OAT3 inhibition assay observation Observational sampling observational study ocular biometry odor testing OECD 202 Daphnia sp. Acute immobilization test OECD 211 reproduction test OECD 416 two generation reproductive toxicity study OECD 458 OECD TG 230 OECD TG 250 OECD TG 440 Uterotrophic bioassay OECD TG 451 OECD TG 451 Carcinogenicity Study OECD TG 456 OECD TG 456 H295R Steroidogenesis Assay OECD TG 458 OECD TG 489 (Alkaline Comet Assay) OECD TG 493 offspring production assessment Oil Red O staining olfactory sensory neuron characterization Oligodendrocyte death assay Olink oocyte electrical state measurement oocyte maturation assay Oocyte size measurement Open field test Operant Responding OPPTS 890.1200 Aromatase assay Optical coherence tomography (OCT) optical coherence tomography Optical detection of neuronal spikes optical detection of neuronal spikes Optical Mapping Optical measurement (ion-sensitive dyes) optical oxygen sensor assay Opto Kinetic Response (OKR) Opto Motor Response (OMR) ORAC assay organ breakdown product analysis organ breakdown product examination organ examination organ weight measurement organism fat content measurement Organs-on-a-chip OSCAtest osteocalcin assay osmometer Osteoblast numbers and surface Osteomark Ntx urine or serum ELISA assay Ostk-PR assay OT_AR_ARELUC_AG_1440 Ovarian follicle count (OECD 416) ovarian granulosa cell assay ovarian tissue explant assay ovarian tissue explant steroidogenesis assay Ovary histology assessment Oviduct flushing oxidative biomarkers measurement oxidative burst assay oxygen consumption assay Oxygen consumption assay (Clark electrode) Clark electrode oxygen consumption assay Oxygen evolution measurement p-methoxy-phenol derivative fluorescent probe P3NP measurement PAH transport assay paired-pulse inhibition assay Pancreatic acinar cell proliferation assay pancreatic content analysis Pancreatic enzyme activity assay pancreatic enzyme activity assay pancreatic homogenate enzyme assay pancreatic exocrine secretion measurement pancreatic exocrine secretion assay pancreatic juice collection pancreatic weight measurement papillary process development para-nitrophenol oxidation para-nitrophenol oxidation assay Partial hepatectomy Passive avoidance Patch Clamp Patch clamp Patch clamp recording Patch clamping Patch-Clamp Recording Patch-Clamp Technique patch clamp patch clamp electrophysiology patch clamping patch-clamp patch-clamp recording patch-clamping patch clamp (brain slices) Patch clamp recording (current clamp configuration) pathological examination Patient Health Questionnaire-9 (PHQ-9) PCNA assay PCNA staining PCNA immunohistochemistry PCNA immunostaining PCR Assay PCR PCR assay PCR for microsatellite instability (MSI) PCR quantification of inflammatory factors PD-L1 expression analysis PEGylated bilirubin-coated iron oxide nanoparticles assay Peptide binding assay peptide binding assay perforin/granzyme assay perfused rat heart metabolic flux perfusion imaging Pericardial or tissue edema scoring Periodic acid-Schiff staining Peripheral biomarker measurement Permeability assay Permeability Assays membrane permeability assay peroxidase co-substrate oxidation assay Pest and disease assessment PET imaging with [11C]-PK 11195 PET scan PET PET imaging Positron emission tomography Positron emission tomography (PET) PET with L-[18F]-fluorodopa PET-MRI PET/CT PFC assay pH-sensitive dye assay pH sensitive dye assay PH3 immunostaining phagocytic receptor expression analysis Pharmacologic inhibition Pharmacological inhibition assay Pharmacologic inhibitor assay Pharmacological Testing Pharyngeal arch analysis Phenotypic enzyme activity assay phenotypic masculinization in fish Phenotypic sex ratio assessment Phenotyping PhiPhiLux Assay Phosphatase assay phosphatase assay photoaffinity labeling photobeam activity box photobeam activity chamber photobeam interruption Photocolorimetric assay Photocolorimetric ROS assay photometric enzyme activity assay photometric GSH quantification method Photometric method Photometry photopatch test Photosynthetic oxygen evolution physical exam physical examination physical manifestation assessment physical measurements of heart Picro-sirius red staining Pig-a assay pigmentation grade assessment Pin perception test Pirijinorin ICTP via RIA2 antibody assay Plaque assay plasma membrane permeability assay plasmid linearization assay plasticine spherical ball Platelet count platelet count plethysmography PMN measurement in BAL Pocket refractometer polarizing microscopy Pole test Pollen load assessment Pollen load scoring Pollen weight measurement population count (observational) Population growth rate measurement Portal blood sampling portal blood sampling potentiometric fluorescent probes PPAR-induced fatty acid oxidation of C14-labeled fatty acids to CO2 PPARα reporter gene assay PPARalpha nuclear-receptor activation/inhibition assay PPARalpha signaling assay PPARγ (mouse/rat) Reporter Assay Kit PPARγ reporter assay kit PPARγ antagonist assay PPARγ antagonism assay PPARγ transcription factor assay Precision cut lung slices (PCLS) precision cut lung slices Precision cut tissue slices Precision cut tissue slices (ex vivo) Prediscreen Assay Prediscreen In-Cell Western γH2AX preference test Premature Chromosome Condensation (PCC) Premature sister chromatid separation (PSCS) assessment Prenatal Developmental Toxicity Study Pressure transducer blood pressure and pulse rate measurement Primary Rat Hepatocyte DNA Repair Assay Pro-inflammatory cytokine measurement proboscis extension reflex Proboscis Extension Reflex Conditioning Procollagen PICP assay PROD assay Proliferation assay proliferation assay proliferation proteins (PCNA, Ki67, MCM-2) Promoter-reporter plasmid assay promoter-reporter assay promoter-reporter plasmid assay Promoter-reporter plasmid assay (human M-CPT I) promoter-reporter assay for M-CPT I Promoter-reporter plasmid assay (human MCAD) Propidium iodide staining propidium iodide staining Propidium Iodide Uptake prostaglandin detection assay Proteasome activity assay Protein carbonyl assays protein carbonyl content assay protein carbonyl content (PCC) assay protein content Protein Detection protein expression analysis protein level analysis protein analysis protein level quantification Protein Mass Spectrometry Mass spectrometry-based proteomics Protein quantification protein-DNA ratio Proteinuria measurement proteolytic enzyme assay proteomic approaches proteomics analysis Proteomics proteomic analysis proteomics Prothrombin time (PT) Prothrombin time measurement prothrombin time Proton magnetic resonance spectrometry Proximity Ligation Assay Proximity Ligation Assay (PLA) Pseudo-typed vesicular stomatitis virus infection assay pseudovirus infection assay PTEN activity assay pulmonary lavage pulse rate measurement Pulse wave velocity (PWV) Pulse-chase co-localization assay Co-localization pulse-chase Pulsed Field Gel Electrophoresis Pulsed Field Gel Electrophoresis (PFGE) Pulsed Field Gel Electrophoresis (PFGE) with Time-Course Pupil constriction observation Pupil diameter observation Pupil examination puromycin incorporation puromycin incorporation assay Pyrilinks assay pyrolysis-gas chromatography pyrosequencing qNPA qPCR (human surgical samples) qPCR for angiogenic markers qPCR for Keap1/Nrf2/ARE/EpRE pathway genes QSAR modelling QSAR model QSAR models for ER interaction QSAR/SAR modeling qualitative histological assessment histological analysis histological section analysis qualitative ovarian analysis quality-adjusted life year (QALY) assessment Quantikine Rat/Mouse Cytochrome c Immunoassay Quantitative Adverse Outcome Pathway (qAOP) modeling Quantitative autoradiography Autoradiography autoradiography Quantitative computed tomography Quantitative nuclease protection assay (qNPA) quantitative nuclease protection assay (qNPA) quantitative nuclease protection assays (qNPA) Quantitative polymerase chain reaction (QPCR) QPCR Quantitative PCR Quantitative PCR (qPCR) q-PCR qPCR quantitative PCR Quantitative proteomic analysis quantitative proteomic analysis Quantitative reverse transcription PCR (qRT-PCR) Quantitative Real-Time PCR (qRT-PCR) quantitative real-time PCR quantitative reverse transcription polymerase chain reaction (qRT-PCR) Quantitative RT-PCR q-RT PCR q-rtPCR qRT PCR qRT-PCR quantitative RT-PCR quantitative real-time RT-PCR Quantitative rtPCR Quantitative sensory testing of thermal threshold Quantitative sensory testing of vibratory threshold Quantitative stereology quantitative stereology stereology Queen egg laying pattern evaluation RADAR assay Radial Arm Maze Radial maze radio isotopes radio receptor assay Radio-frequency identification tagging radio-labeled alkylating agents radio-labeled chemical exposure followed by HPLC Radio-labeled fatty acid beta oxidation assay Fatty Acid Beta Oxidation Assay Mitochondrial fatty acid beta oxidation assay radio-labeled fatty acid substrate reaction Radio-labeled substrate flux assay radioactive iodine release assay radioactive iodine uptake test (RAIU) Radioactive nucleoside labeling Radioactive precursor incorporation assay Radioactive precursor incorporation Radioimmuno Assay Radioimmunoassay RIA (Radioimmunoassay) Radioimmunoassay (RIA) radioimmunoassay radioimmunoassay (RIA) radioimmunoassay (RIA) for cAMP Radioimmunoassay for pregnenolone Radioiodide uptake assay radioactive iodine uptake test radioisotope uptake radiolabel assay radiolabel incorporation radiolabeled tracer incorporation radiolabeled compounds Radiolabeled ligand binding Radiolabeled nAChR agonist binding Radiolabeled palmitate assay radiolabeled steroid assay radiolabeled T3/T4 uptake assay radiolabeled thymidine incorporation radiolabeled tracer efflux radiolabeled uptake assay Radiolabeling / Immunostaining Radioligand binding assay radioligand binding radioligand binding assay radioligand-binding assay Radioligand binding assay for thyroid hormone displacement Radioligand competition binding assay using [3H]-CGP 39653 radioligand competition binding assay ([3H]-CGP 39653) Radiometric AChE inhibition assay Radiometric methods Radiometric assay Radioreceptor assay Radiotracer flux radiotracer flux RAGE RAIU assay (hNIS-HEK293TEPA) RAIU test rapid test kits RAR transactivation assay RAR reporter gene assay RAR-RXR-RARE/RXR-RXR-RARE reporter assay RAR-RXR-RARE reporter assay Rat aortic explant assay rat aortic explant assay rat fetal aortic explant assay rat whole embryo culture ratio of reduced to oxidized glutathione or cysteine ratiometric NIR fluorescent probe assay Ratiometric or single-wavelength dyes reactive oxygen species assay Real-time fluorescent microscopy real-time fluorescent microscopy Real-time PCR Real time PCR Real-time polymerase chain reaction real time PCR real-time PCR real-time quantitative PCR receptor binding receptor phosphorylation assay Redox proteomics RelA-GFP reporter assay relative Ca2+ permeability measurement relative eye size analysis renal histopathology Reporter assay Reporter Assay Reporter Assays Reporter gene assay reporter assay reporter gene assay resistance mutant analysis Respiratory chain complex activity assay respiratory parameter measurement Respirometer-metabolism chamber respirometer metabolism chambers respirometry Retention of Alkyl Adducts retention of alkyl adducts Retrospective patient interview Retrospective symptom interview Reverse Electron Transfer assay Reverse-phase HPLC assay reverse-phase HPLC Rey Osterrieth Complex Figure Test Rey Osterieth Complex Figure Test Rhodamine 123 assay rhodamine 123 assay RIA RiboQuant MultiProbe RPA system RIP assay RNA content measurement RNA in situ hybridization RNA in situ hybridization (RNA-ISH) RNA measurement assays RNase protection assay RNAseq RNA sequence analysis RNA sequencing RNA-Seq RNA-seq Rodent Two-Year Cancer Bioassays roGFP or FRET ROS detection assay ROS production assay intracellular ROS assay ROS/RNS Assay rosette formation assay Rotarod test Rotation test RT-PCR / qPCR qPCR and RT-PCR quantitative reverse transcription-polymerase chain reaction (RT-PCR) RT-PCR for CAR-responsive genes RT-PCR gene expression assay RT-PCR with LDI-PCR RT-qPCR RT-PCR RT-PCR/RT-qPCR RT-qPCR (viral replication) Rubisco activity assay Running Fisher test SA-beta-gal staining Saccharin transit test (STT) Sadavongvivad (1970) biogenic amine estimation SAGE Saline infusion sonography Saline infusion sonography and Color Doppler sonography salivary cortisol assay Salmonella mutagenicity test (Ames Test) SAMDI-MS Assay Sandell-Kolthoff colorimetric assay Sandell-Kolthoff method Sandell-Kolthoff reaction assay Sandell-Kolthoff spectrophotometry sandwich enzyme-linked immunoassay SARS-CoV-2 spike protein neutralizing antibodies in saliva Saturation binding of radioligands sBLISS scanning electron microscopy SCD1 induction assay Scheimpflug imaging Scintillation counting scintillation counting Scintillation proximity binding assay scintillation proximity binding assay Scratch wound assay scratch assay scratch/wound healing assay scRNA-seq SDH activity assay (MTT/PMS) MTT assay for SDH activity SDS-PAGE Seahorse assay Seahorse XF analyzer Seahorse XF analysis Seahorse XFp Analyzer secondary ion emission semi-quantitative severity grading semiquantitative histological assessment SENSIS SEP ER transcriptional activation assay (HeLa-9903) SeqAPASS Sequencing assays Sequencing assays for oxidative DNA damage Serial sectioning with stereo microscopy, imaging, morphometric analysis Serial sectioning with stereo microscopy Serologic markers of fibrosis Serological typing & ASO probes serotonin concentration measurement Serotonin, dopamine, and norepinephrine level measurement Serum amyloid A measurement Serum Biomarkers Serum Biomarker Analysis Serum estrogen analysis estrogen serum levels serum FSH assay serum hormone measurement serum marker analysis Serum β-hydroxybutyrate measurement blood serum β-hydroxybutyrate measurement sex ratio determination sex steroid synthesis measurement Sexual behavior observation (Birds) SH2 domain binding assay silver degeneration stain Single molecule FRET Single-Cell Tracking Single-energy x-ray absorptiometry Single energy x-ray absorptiometry Single-molecule PCR Singlet oxygen bleaching assay Singlet Oxygen Spectrophotometry Sircol Collagen Assay Sirius Red staining size assessment size exclusion chromatography skin biopsy skin prick test skull ossification assessment Slit Lamp Grading System slot blotting SMART micro-FPLC SMART micro-FPLC with enzymatic assay Smith-modified Kernahan 'Y' classification revised Smith-modified Kernahan ‘Y’ classification SNP array SOD-inhibitable reduction of cytochrome c Sodium [3H]acetate labeling solid-phase receptor binding assay soluble CD163 measurement Sonography spawning observation SPECT (Single Photon Emission Computed Tomography) SPECT with [123I]-β-CIT Spectral karyotyping Spectrofluorometric biogenic amine assay Spectrophotofluorimetry Spectrophotometric Enzyme Activity Assay Spectrophotometric hemoglobin assay spectrophotometric kit Spectrophotometry spectrophotometry spectroscopic analysis Spectroscopic analysis of fatty acid substrates and products sperm density measurement sperm morphology and motility sperm quality assessment sperm-zona pellucida interaction assay Sphinganine (Sa) quantification assay sphygmomanometer spiggin expression assay spike-pseudotyped viral particles assay Spinal tap spinal tap Spinning Disk Confocal Microscopy-IVM SPION-based biosensor spirometry Split-signal FISH split-signal FISH Spontaneous alternation Spontaneous movement observation Sputum Analysis Sputum cytology sputum cytology SQR activity assay (DCPIP/UQ2) Stable isotope labeling stable isotope labeling Stably Transfected Human Androgen Receptor Transcriptional Activation Assay Staged AM Task Staining techniques Stanbio Laboratory enzymatic assay standard cytogenetic methods STAT5 phosphorylation inhibition assay STAT5 tyrosine phosphorylation assay Static bone histomorphometry stereological cell counting stereological cell counts stereomicroscopy Stereomicroscopy for anterior swim bladder inflation Stereomicroscopy for swim bladder inflation stomach contents analysis stomach content analysis Stra8 mRNA quantification Stra8 promoter-GFP reporter assay Stra8 promoter reporter assay strength measurement stress marker detection assay Stress Testing Stress-strain curve STRIDE Assay STRIDE assay stroke volume measurement structure-activity relationships (SARs) STTA assay Subcellular Fractionation subtype-specific antisera assay Sucrose Density Gradient Centrifugation Sucrose density gradient centrifugation Sucrose Density Gradient Centrifugation with Time Course Sucrose pelleting binding assay Sulfotransferase kinetic assay superoxide dismutase assay Sural nerve biopsy surface biolayer interferometry Surface Plasmon Resonance (SPR) Surface plasmon resonance surface plasmon resonance surface plasmon resonance (SPR) Surface plasmon resonance (SPR) biosensor Surface Plasmon Resonance (SPR) biosensor assay Surface plasmon resonance (SPR) biosensor assay Surface plasmon resonance (SPR)-based biosensor Surface plasmon resonance biosensor assay surface plasmon resonance (SPR) biosensor assay surface plasmon resonance (SPR)-based biosensor assay surface plasmon resonance-based biosensor assay Surfactant adsorption test surfactant adsorption test surgical excision Sustentacular cell count Swim bladder inflation assay swim tunnel Swimming pattern comparison Synaptogenesis assay kit synaptogenesis assay kit synchrotron phase contrast x-ray imaging SYNPLA T cell isolation from intestinal biopsies T cell phenotyping T cell stimulation assay T-cell proliferation assay T cell proliferation assay T cell proliferation assays T-Lymphocyte & Innate Immune Cell Activation Assays T/B-cell cooperation assay T3 level measurement T3 measurement T4 glucuronidation and sulfation assay T47D-Kbluc assay T47D-Kbluc TAC assay Tandem repeat mutation assay Tandem-R Ostase assay targeted gene expression assay targeted qPCR TBA assay for lipid peroxidation TBARS (thiobarbituric acid reactive substance) TBARS assay TBA Assay TBA assay TBA reactive substances assay TBARS TBARS Assay TBPS binding assay TBXA2 receptor binding assay TCA precipitation TCID50 assay TCR sequencing TEER telemetry-based distance measurement TEM/AFM Testicular Organ and Tissue Culture Systems testicular sperm count testicular volume measurement testosterone 6-β-hydroxylase activity assay testosterone radioimmunoassay Tetracycline staining Tetramer staining TG2-Ab ELISA TGF-β gene expression TGF-β-dependent gene expression TGx-HDACi transcriptomic biomarker TH immunocytochemistry immunocytochemistry for TH TH level/enzyme activity measurement THBD protein expression assay Thin-layer chromatography thiobarbituric acid assay Thiol oxidation assays thoracoscopic lung biopsy Three-dimensional sonography Three-point bending test Thymidine incorporation thymidine analogue incorporation Thymidine incorporation assay Thymidine kinase gene mutation test thymidine kinase gene mutation assay Thyroid hormone uptake analysis Tie2 activity assay Time-lapse microscopy Time-Lapse Microscopy time-lapse imaging time-lapse microscopy time-lapse recording time-lapse recording of blood flow TIQDT (Thyroxine-immunofluorescence quantitative disruption test) Tissue equivalent proportional counter Tissue equivalent proportional counter (TEPC) TK Mutation Assay TLR knock-out mice TLR polymorphism analysis TLR Reporter assay TMRE Staining TMRM assay TMRM/TMRE/JC-1 fluorescent probes TNF-alpha ELISA TNF-α blood level measurement TNFα measurement Toll-like receptor simulation assays Toll-like receptor stimulation assay Top-down proteomic approach Topoisomerase II assay Topoisomerase II decantation assay Total Dpy assay Total fin area measurement Total nitrate and nitrite concentration determination total nitrate and nitrite concentration determination Total T4 diagnostic kit TOX21 GR BLA TOX21 GR BLA Agonist Ratio Tox21_AR_BLA_Agonist_ratio tox21-mitotox-p1 TOX21_PXR_agonist Toxcast AR Transactivation Assay ToxCast assay NVS_IC_rNaCh_site 2 ToxCast ATG_SREBF1_CIS_up ToxCast Estrogen Receptor Agonist Pathway Model ToxCast HTS assay platform ToxCast NVS_IC_hKhERGCh ToxCast proliferation assay ToxCast SeqAPASS ToxCast/Tox21 mitochondrial membrane potential HTS assay TOXCAST: NVS_ENZ_hAChE TPO mRNA measurement Trabeculae measurements Trabecular microarchitecture analysis trace fear conditioning Trans-Endothelial Electrical Resistance (TEER) Transepithelial electrical resistance (TEER) transactivation assay Transbronchial Needle Aspiration Transcript expression analysis transcription assay Transcription factor level assay Transcription profiling of BAL samples Transcriptional profiling transcriptional profiling Transcriptomics Transcriptomic analyses transcription profiling transcriptomic analysis transcriptomics Transfection of reporter genes with RT-qPCR transgenic reporter assay Transgenic Rodent Mutation Assay Transgenic rodent mutation assay transgenic zebrafish reporter embryos transgenic zebrafish with fluorescent thyroid follicles Transient elastography (FibroScan) Transient transfection transactivation Transmission electron microscopy (TEM) Transmission electron microscopy transmission electron microscopy transmission electron microscopy (TEM) Transvaginal ultrasound Transwell Invasion Assay Transwell Migration Assay Transwell migration assay TRAP Treg/Th17 cell ratio assessment TRIFMA triglyceride accumulation assay triglyceride measurement Tritiated thymidine (³H) incorporation assay Tritiated water release assay tritium release assay Trout GR1 TRPA1 activation assay TrxR activity assay Trypan Blue Exclusion Trypan Blue Uptake Trypan blue exclusion assay trypan blue exclusion assay trypan blue exclusion test trypsin activity assay trypsin inhibitor activity assay Tube formation assay tube formation assay TUNEL and cleaved caspase-3 for apoptosis TUNEL staining TUNEL TUNEL Assay TUNEL assay Turbidimetric assay two-photon Ca2+ imaging Two-photon imaging Two-photon Microscopy Two photon-intravital microscopy Two-photon intravital microscopy Two-photon microscopy two-photon released caged neurotransmitters Two-photon time-lapse imaging tyrosine hydroxylase (TH) detection Tyrosine hydroxylase staining tyrosine phosphorylation assay U-SENS Ubiquitin accumulation assay ubiquitin and sequestosome-1 accumulation assay UHPLC-ESI-MS/MS Ultrafiltration Ultrasound Ultrasound imaging ultrasonography ultrasound ultrasound examination ultrasound imaging Ultrasound (quantitative bone ultrasonography) ultrasound biomicroscopy Unified Parkinson's Disease Rating Scale Unscheduled DNA synthesis test Unwinding Assay uPA/uPAR assay UPLC-MS (with immunomagnetic beads) UPLC-MS competitive binding assay isotope-free competitive binding assay with UPLC-MS UPLC-MS/MS UPLC-MS UPLC-MS/MS screening urethral internalization quantification urinary zinc excretion urinary zinc excretion and testicular zinc content Urinary β2-microglobulin assay urine analysis Urine and stool tests Urine biochemistry Urine ketone test strip urine test strips Urine test strips (reflectometry) Urine test strips with reflectometry UROD enzyme assay with HPLC UROD enzyme assay Uroporphyrinogen Oxidation (UROX) Spectrofluorimetry US EPA AR pathway model US EPA Estrogen Receptor Binding Assay (Rat Uterine Cytosol) US EPA OPPTS 890.1200 US EPA ToxCast COX2 activity assay Ussing chamber uterine weight measurement Uterotrophic bioassay Uterotrophic Bioassay UV light exposure assay UV meters or radiometers Vaginal cytology Vaginal Smear Cytology Vaginal smear cytology vaginal cytology vaginal smear cytology vaginal smear/cytology vaginal smear Vaginal wall impedance Valsalva Maneuver various trityl probes Vascular Imaging Vascular resistance calculation Vascular sprouting assay (mouse embryonic stem cells) vasoactive peptide detection assay VCAM1 expression assay vectorial transport assay VEGFR kinase activity assay Verhoeff-van Gieson staining Vesicle motility assay vessel density measurement viability assay (PI/TUNEL) viable offspring production Vibration and position sensation test video feeding rate video observation video or photograph monitoring of muscular waves video recording Video tracking video-based swimming speed assay Videomicroscopy video microscopy videomicroscopy videomicroscopy of frog palate Vimentin/S100beta staining Viral whole genome sequencing virtual screening Virus neutralization test (VNT) Virus-like particles Virus-like particles formation assay Virus-specific immunoglobulin characterization viscoelastic haemostatic assay viscometer visual assessment Visual assessment of estrous cycle Visual assessment of vaginal opening vaginal opening assessment visual identification of testes vs ovaries Visual inspection Visual observation physical (visual) observation visual observation visual observation or palpation visualized scoring of blood flow vitellogenin synthesis in primary fish liver cells VITOSENS VM7Luc ER TA assay Voltage-clamp voltage clamp voltage-clamp recordings voltage-sensitive dye assay voltage-sensitive dye imaging voltage-sensitive dyes / FRET volume measurement Von Kossa staining Voxel-based morphometry (VBM) VSV-SARS-S2 infection assay Waggle dance measurement Wako Chemicals D-3-hydroxybutyric acid kit Watanabe rabbit model water transport rate assay water-filled aquarium line crossing Wechsler Adult Intelligence Scale (WAIS) Wechsler Memory Scale Logical Memory Test Battery Wechsler Memory Scale Logical Memory Test Western blot Immunoblotting (western blotting) Western Blot Western Blotting Western blotting Western blotting/immunoblotting Western immunoblot Western immunoblotting western blot western immunoblot Western blot (4-hydroxynonenal) Western Blot and ELISA Western blot for cleaved caspase-3 Western blot for cytochrome c Western blot for cytochrome c release Western Blot for Nrf2 Western immunoblot quantification WGA-ELISA (sandwich-ELISA) White blood cell count Whole blood assay Whole blood coagulation and complement activation assay Whole blood fibrinolysis assay Whole blood stimulation assay whole body measurement whole body TH level measurement Whole body weight measurement Body weight measurement body weight measurement weight measurement Whole cell filtration binding assay whole cell filtration binding assay whole cell patch-clamp recording whole-cell patch clamp whole-cell patch-clamp whole genome sequencing (WGS) Whole human blood model whole human blood model Whole Transcriptome Profiling Whole-cell electrophysiology Whole-cell voltage clamp Window Chamber Models Wire myography WISC Wnt/beta-catenin activity assay Wound Healing Assay wound healing assay WST-1 assay X-ray and imaging options X-ray crystallography x-ray crystallography X-ray emission X-ray microanalysis Xenograft Assays XPRT Mutation Assay XTT Xylenol orange staining y-H2AX foci staining Yeast estrogen screen (YES) yeast estrogen screen (YES) YES YFP-based fluorescence assay YFP-based iodide efflux zebrafish Ca2+ imaging assay zebrafish embryotoxicity assay zebrafish embryotoxicity Zebrafish epigenetic biomarker assessment zebrafish epigenetic biomarker assessment zebrafish facial cartilage morphology zebrafish GFP reporter assay zebrafish reporter assay Zebrafish Larvae Morphological Examination zinc measurement Zymography ³¹P nuclear magnetic resonance spectroscopy ¹⁴C-bicarbonate uptake assay β-galactosidase reporter gene assay β-galactosidase staining γ-H2AX foci formation γ-H2AX Foci Quantification - Flow Cytometry γ-H2AX foci assay γH2AX analysis γH2AX assay γH2AX foci quantification ELISA Quantifies estradiol released by ovarian tissue explants into media. in_vitro estradiol concentration decrease http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI high Estradiol released by ovarian tissue explants into media can be quantified by radioimmunoassay (e.g., Jensen et al. 2001), ELISA, or analytical methods such as LC-MS (e.g., Owen et al. 2014) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0032570 GO ELISA Quantification of estradiol (E2) released by ovarian tissue explants into media using Enzyme-Linked Immunosorbent Assay. ex_vivo ovarian tissue estradiol released not_specified http://purl.obolibrary.org/obo/CHEBI_24829 CHEBI not_specified Estradiol released by ovarian tissue explants into media can be quantified by radioimmunoassay (e.g., Jensen et al. 2001), ELISA http://purl.obolibrary.org/obo/CHEBI_24829 CHEBI http://purl.obolibrary.org/obo/GO_0009414 GO LC-MS Quantifies estradiol released by ovarian tissue explants into media using liquid chromatography-mass spectrometry. in_vitro estradiol concentration decrease http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/OBI_0001047 OBI medium Estradiol released by ovarian tissue explants into media can be quantified by radioimmunoassay (e.g., Jensen et al. 2001), ELISA, or analytical methods such as LC-MS (e.g., Owen et al. 2014) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0032570 GO LC-MS Quantification of estradiol (E2) released by ovarian tissue explants into media using Liquid Chromatography-Mass Spectrometry. ex_vivo ovarian tissue estradiol released not_specified http://purl.obolibrary.org/obo/CHEBI_24829 CHEBI not_specified analytical methods such as LC-MS (e.g., Owen et al. 2014) http://purl.obolibrary.org/obo/CHEBI_24829 CHEBI http://purl.obolibrary.org/obo/GO_0009414 GO OECD TG 456 In vitro screen for chemical effects on steroidogenesis, specifically measuring the production of 17ß-estradiol (E2) and testosterone (T). in_vitro production of 17ß-estradiol (E2) and testosterone (T) not_specified http://purl.obolibrary.org/obo/CHEBI_24829 CHEBI http://purl.obolibrary.org/obo/CHEBI_24831 CHEBI OECD TG 456 not_specified OECD TG 456 (OECD 2011) is the validated test guideline for an in vitro screen for chemical effects on steroidogenesis, specifically the production of 17ß-estradiol (E2) and testosterone (T). http://purl.obolibrary.org/obo/CHEBI_24829 CHEBI http://purl.obolibrary.org/obo/GO_0009414 GO ovarian tissue explant steroidogenesis assay Measures estradiol (E2) production by intact ovarian tissue explants exposed to chemicals either in vitro or ex vivo. ex_vivo ovary estradiol production decrease http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/UBERON_0000992 UBERON http://purl.obolibrary.org/obo/GO_0006694 GO OECD TG 456 medium this key event can be evaluated by examining E2 production by intact ovarian tissue explants either exposed to chemicals in vitro (e.g., (Villeneuve et al. 2007; McMaster ME 1995) or in vivo (i.e., via ex vivo steroidogenesis assay; e.g., (Ankley et al. 2007)) OECD TG 456 (OECD 2011) is the validated test guideline for an in vitro screen for chemical effects on steroidogenesis, specifically the production of 17ß-estradiol (E2) and testosterone (T) http://purl.obolibrary.org/obo/CL_0000471 CL http://purl.obolibrary.org/obo/GO_0006704 GO radioimmunoassay Quantifies estradiol released by ovarian tissue explants into media. in_vitro estradiol concentration decrease http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI medium Estradiol released by ovarian tissue explants into media can be quantified by radioimmunoassay (e.g., Jensen et al. 2001) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0032570 GO radioimmunoassay Quantification of estradiol (E2) released by ovarian tissue explants into media using radioimmunoassays. ex_vivo ovarian tissue estradiol released not_specified http://purl.obolibrary.org/obo/CHEBI_24829 CHEBI not_specified Estradiol released by ovarian tissue explants into media can be quantified by radioimmunoassay http://purl.obolibrary.org/obo/CHEBI_24829 CHEBI http://purl.obolibrary.org/obo/GO_0009414 GO Hestrin method A colorimetric measurement of esterase activity where the rate of hydrolysis of acetylcholine with hydroxylamine to form hydroxamic acid is measured to determine acetylcholine levels. in_vitro acetylcholine levels not_specified http://purl.obolibrary.org/obo/GO_0016788 GO low Hestrin’s method involves a colorimetric measurement of esterase activity. The rate of hydrolysis of acetylcholine with hydroxylamine to form hydroxamic acid is measured to determine the amount of acetylcholine: RCOOR’ + H2NOH -> RCONHOH + R’OH This method is performed at alkaline pH in water and is applicable over a wide range of ester concentrations (Hestrin 1949). http://purl.obolibrary.org/obo/CHEBI_15718 CHEBI http://purl.obolibrary.org/obo/GO_0016810 GO Hestrin method The Hestrin method is a colorimetric measurement of esterase activity. It measures the rate of hydrolysis of acetylcholine with hydroxylamine to form hydroxamic acid to determine the amount of acetylcholine. in_vitro brain esterase activity increase low Hestrin’s method involves a colorimetric measurement of esterase activity. The rate of hydrolysis of acetylcholine with hydroxylamine to form hydroxamic acid is measured to determine the amount of acetylcholine: RCOOR’ + H2NOH -> RCONHOH + R’OH http://purl.obolibrary.org/obo/CHEBI_5905 CHEBI http://purl.obolibrary.org/obo/GO_0005576 GO HPLC-EC High-pressure liquid chromatography coupled to electrochemical detection, based on enzymatic conversion of acetylcholine into choline and acetate by acetylcholinesterase, and subsequent oxidation of choline to betaine and hydrogen peroxide for detection. in_vitro acetylcholine levels not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI medium High-pressure liquid chromatography coupled to electrochemical detection (HPLC-EC) is based on enzymatic conversion of acetylcholine into choline and acetate by acetylcholinesterase, and subsequent oxidation of choline by choline oxidase to betaine and hydrogen peroxide, which can be oxidized on a platinum electrode. This method permits detection of dialysate acetylcholine concentrations in the 5-10 nM range (Zapata, 2009). http://purl.obolibrary.org/obo/CHEBI_15718 CHEBI http://purl.obolibrary.org/obo/GO_0016810 GO LC-MS/MS Liquid chromatography - tandem mass spectrometer used to measure acetylcholine levels. in_vitro acetylcholine levels not_specified http://purl.obolibrary.org/obo/OBI_0000473 OBI medium liquid chromatography - tandem mass spectrometer LC-MS/MS (Gómez-Canela et al., 2017). http://purl.obolibrary.org/obo/CHEBI_15718 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO microdialysis A technique used to quantify nanomolar concentrations of acetylcholine in extracellular fluid using chromatographic mass spectrometric techniques. in_vivo brain acetylcholine levels in extracellular fluid not_specified http://purl.obolibrary.org/obo/OBI_0000218 OBI low Brain microdialysate studies quantify nanomolar concentrations of acetylcholine in extracellular fluid using chromatographic mass spectrometric techniques (Nirogi 2009). http://purl.obolibrary.org/obo/CHEBI_15718 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO pyrolysis-gas chromatography A technique used for quantification of acetylcholine through pyrolysis followed by gas chromatography. in_vitro acetylcholine levels not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI low Other microdialysis techniques for quantification of acetylcholine are liquid chromatography mass spectrometry (Nirogi 2009) and pyrolysis-gas chromatography (Szilagyi 1968). http://purl.obolibrary.org/obo/CHEBI_15718 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO In vivo cholinesterase activity measurement Measures cholinesterase activity levels in relevant tissues such as the brain and red blood cells after in vivo exposure. in_vivo brain red blood cells mammals cholinesterase activity levels decrease http://purl.obolibrary.org/obo/GO_0003990 GO low A direct measure of cholinesterase activity levels can be made within the relevant tissues after in vivo exposure, specifically the brain as well as red blood cells in mammals. http://purl.obolibrary.org/obo/PR_000001544 PR http://purl.obolibrary.org/obo/GO_0042136 GO Modified Ellman method Measures AChE activity levels using a modified version of the Ellman method, requiring selective inhibitors to remove other cholinesterases. in_vitro AChE activity levels decrease http://purl.obolibrary.org/obo/GO_0003990 GO medium Direct measures of AChE activity levels can be made using the modified Ellman method, although selective inhibitors that remove other cholinesterases not directly related to cholinergic responses (e.g., butyrylcholinesterase) are required [45,46]. For measuring AChE levels, the Ellman method is recommended with some modifications (Ellman et al., 1961; Wilson et al., 1996) http://purl.obolibrary.org/obo/PR_000001544 PR http://purl.obolibrary.org/obo/GO_0042136 GO Radiometric AChE inhibition assay A method that measures the inhibition of AChE activity using radiolabeled substrates, which is more sensitive to carbamylation caused by carbamate exposure compared to the Ellman method. in_vitro brain red blood cells mammals AChE inhibition increase http://purl.obolibrary.org/obo/GO_0008205 GO OECD TG 487 low Radiometric methods have been identified as better for measuring inhibition because of carbamylation (carbamate exposure) [20,46,47]. Radiometric methods have been identified as better for measuring inhibition because of carbamylation (carbamate exposure) (see Wilson 2010; Wilson et al., 1996; Johnson and Russell 1975). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0007268 GO Radiometric methods Measures AChE inhibition using radiometric techniques, particularly suitable for carbamate exposure. in_vitro AChE inhibition increase http://purl.obolibrary.org/obo/GO_0003990 GO low Radiometric methods have been identified as better for measuring inhibition because of carbamylation (carbamate exposure) [20,46,47]. radiometric methods have been identified as better for measuring inhibition due to carbamylation (carbamate exposure) (see Wilson 2010; Wilson et al., 1996; Johnson and Russell 1975). http://purl.obolibrary.org/obo/PR_000001544 PR http://purl.obolibrary.org/obo/GO_0042136 GO TOXCAST: NVS_ENZ_hAChE A high-throughput in vitro assay measuring human AChE activity levels. in_vitro Homo sapiens AChE activity levels decrease http://purl.obolibrary.org/obo/GO_0003990 GO high TOXCAST: NVS_ENZ_hAChE http://purl.obolibrary.org/obo/PR_000001544 PR http://purl.obolibrary.org/obo/GO_0042136 GO gene expression analysis Measures the expression levels of AHR/ARNT pathway-dependent genes, such as VEGF, to assess disruption in ARNT-dependent cellular functions. not_specified gene expression change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0050918 GO not_specified Sustained AHR/ARNT dimerization induced by DLCs may sequester ARNT from its other dimerization partners at inappropriate times during embryonic cardiomorphogenesis, disrupting ARNT-dependent cellular functions Dimerization between ARNT and HIF-1α forms a transcription factor complex (HIF-1) that binds to hypoxia response enhancer sequences on DNA to activate the expression of genes such as vascular endothelial growth factor (VEGF), which is involved in angiogenesis http://purl.obolibrary.org/obo/GO_0001525 GO chromatin immunoprecipitation Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo by crosslinking proteins and DNA, immunoprecipitation with an antibody, and DNA sequencing. in_vivo DNA sequence enrichment increase http://purl.obolibrary.org/obo/OBI_0000722 OBI low Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo [28]. It involves the treatment of cells with formaldehyde to crosslink neighboring protein-protein and protein-DNA molecules [28]. Enrichment of specific DNA sequences represents regions on the genome that the protein of interest is associated with in vivo [28]. http://purl.obolibrary.org/obo/CL_0000726 CL Chromatin immunoprecipitation This assay measures the interaction of the AHR complex with specific genomic regions in vivo by crosslinking, shearing DNA, and immunoprecipitating with an antibody against the AHR. in_vivo protein-DNA interaction increase http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0003677 GO low Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo. It involves the treatment of cells with formaldehyde to crosslink neighboring protein-protein and protein-DNA molecules. Nuclear fractions are isolated, the genomic DNA is sheared, and nuclear lysates are used in immunoprecipitations with an antibody against the protein of interest. After reversal of the crosslinking, the associated DNA fragments are sequenced. Enrichment of specific DNA sequences represents regions on the genome that the protein of interest is associated with in vivo. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0003677 GO Electrophoretic mobility shift assay This assay measures the binding of the AHR complex to DNA in vitro by detecting the slower migration of protein-DNA complexes through a polyacrylamide gel. in_vitro protein-DNA binding increase http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0003677 GO medium Electrophoretic mobility shift assay (EMSA) provides a rapid method to study DNA-binding protein interactions in vitro. This relies on the fact that complexes of protein and DNA migrate through a nondenaturing polyacrylamide gel more slowly than free DNA fragments. The protein-DNA complex components are then identified with appropriate antibodies. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0003677 GO Electrophoretic mobility shift assay (EMSA) An in vitro assay used to study DNA-binding protein interactions by migrating protein-DNA complexes through a polyacrylamide gel. in_vitro chicken hepatoma cells Gallus gallus migration of protein-DNA complexes change not_specified Electrophoretic mobility shift assay (EMSA) provides a rapid method to study DNA-binding protein interactions in vitro The EMSA assay was found to be consistent with the LRG assay in chicken hepatoma cells dosed with dioxin-like compounds Hydroxyapatite (HAP) binding assay Uses in vitro transcription/translation to synthesize AHR protein, incubated with radiolabeled TDCPP and a HAP pellet; radioactivity is measured to determine saturation or competitive binding. in_vitro radioactivity change not_specified The HAP binding assay makes use of an in vitro transcription/translation method to synthesize the AHR protein, which is then incubated with radiolabeled TDCPP and a HAP pellet. The occupied protein adsorbs to the HAP and the radioactivity is measured to determine saturation binding. This assay is simple, repeatable and reproducible; however, it is insensitive to weak ligand-receptor interactions hydroxyapatite (HAP) binding assay The HAP binding assay uses an in vitro transcription/translation method to synthesize AHR protein, which is incubated with radiolabeled TDCPP and a HAP pellet to measure saturation binding. in_vitro saturation binding (radioactivity) increase low The HAP binding assay makes use of an in vitro transcription/translation method to synthesize the AHR protein, which is then incubated with radiolabeled TDCPP and a HAP pellet [25]. The occupied protein adsorbs to the HAP and the radioactivity is measured to determine saturation binding [25]. This assay is simple, repeatable and reproducible [25]. Hydroxyapatite binding assay This assay measures the binding affinity of ligands to the AHR by synthesizing the AHR protein in vitro, incubating it with radiolabeled ligands, and using hydroxyapatite to separate bound from unbound ligand. in_vitro ligand binding increase http://purl.obolibrary.org/obo/GO_0005488 GO http://purl.obolibrary.org/obo/PR_000000001 PR low The HAP binding assay makes use of an in vitro transcription/translation method to synthesize the AHR protein, which is then incubated with radiolabeled TDCPP and a HAP pellet. The occupied protein adsorbs to the HAP and the radioactivity is measured to determine saturation binding. An additional ligand can also be included in the mixture in order to determine its binding affinity relative to TCDD (competitive binding). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005488 GO in silico homology modeling In silico homology modeling of the ligand binding domain of the AHR, combined with molecular docking simulations, provides insight into the transactivation-potential of AHR ligands. in_silico ligand potency prediction change http://purl.obolibrary.org/obo/OBI_0000694 OBI high In silico homology modeling of the ligand binding domain of the AHR in combination with molecular docking simulations can provide valuable insight into the transactivation-potential of a diverse array of AHR ligands. Such models have been developed for multiple AHR isoforms and ligands (high/low affinity, endogenous and synthetic, agonists and antagonists), and can accurately predict ligand potency based on their structure and physicochemical properties. Bonati et al 2017; Hirano et al 2015; Sovadinova et al 2006 In silico homology modeling and molecular docking This assay uses computational methods to model the ligand binding domain of the AHR and predict the binding affinity and transactivation potential of ligands based on their structure and physicochemical properties. in_silico ligand binding affinity increase http://purl.obolibrary.org/obo/OBI_0000215 OBI http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005488 GO high In silico homology modeling of the ligand binding domain of the AHR in combination with molecular docking simulations can provide valuable insight into the transactivation-potential of a diverse array of AHR ligands. Such models have been developed for multiple AHR isoforms and ligands (high/low affinity, endogenous and synthetic, agonists and antagonists), and can accurately predict ligand potency based on their structure and physicochemical properties. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005488 GO Luciferase reporter gene assay This assay measures AHR activation by transfecting cells with an AHR clone and a luciferase reporter construct, then exposing them to test compounds and measuring luminescence as a proxy for AHR activation. in_vitro Cos-7 Homo sapiens Gallus gallus Phasianus colchicus Coturnix japonica Sterna hirundo Phoebastria nigripes Phalacrocorax carbo Alligator mississippiensis Xenopus laevis Ambystoma mexicanum Salmo salar Microgadus tomcod Acipenser transmontanus Onchorhynchys mykiss Pagrus major Acipenser fulvescens Danio rerio luciferase activity increase http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0001223 GO high A monkey kidney cell line (Cos-7) that has low endogenous AHR1 expression was transfected with the appropriate avian AHR1 clone, cormorant ARNT1, a CYP1A5 firefly luciferase reporter construct and a Renilla luciferase vector to control for transfection efficiency. After seeding, the cells were exposed to DLC and luciferase activity was measured using a luminometer. Luminescence, which is proportional to the extent of AHR activation, is expressed as the ratio of firefly luciferase units to Renilla luciferase units. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006351 GO Transient transfection transactivation A method for evaluating nuclear receptor activation where AHR cDNAs are cloned into an expression vector with a reporter gene (e.g., luciferase, P-lactamase, or CAT) and transfected into recipient cells. in_vitro CV-1 HuH7 FLC-7 LS174T LS180 MCF-7 HEC1 LLC-PK1 HEK293 HepG2 Caco-2 nuclear receptor activation change not_specified Transient transfection transactivation is the most common method for evaluating nuclear receptor activation Full-length AHR cDNAs are cloned into an expression vector along with a reporter gene construct (chimeric luciferase, P-lactamase or CAT reporter vectors containing the appropriate response elements for the gene of interest). Transient transfection transactivation This assay evaluates nuclear receptor activation by cloning full-length AHR cDNAs into an expression vector along with a reporter gene construct, then transfecting into various cell lines to measure induction. in_vitro CV-1 HuH7 FLC-7 LS174T LS180 MCF-7 HEC1 LLC-PK1 HEK293 HepG2 Caco-2 reporter gene induction increase http://purl.obolibrary.org/obo/GO_0001223 GO http://www.bioassayontology.org/bao#BAO_0000416 BAO http://purl.obolibrary.org/obo/PR_000000001 PR medium Transient transfection transactivation is the most common method for evaluating nuclear receptor activation. Full-length AHR cDNAs are cloned into an expression vector along with a reporter gene construct (chimeric luciferase, P-lactamase or CAT reporter vectors containing the appropriate response elements for the gene of interest). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006351 GO Whole cell filtration binding assay This assay measures the binding of radiolabeled ligands to the AHR in whole cells by incubating cells with the ligand, filtering them, and measuring the retained radioactivity. in_vitro ligand binding increase http://purl.obolibrary.org/obo/GO_0005488 GO http://purl.obolibrary.org/obo/PR_000000001 PR medium Dold and Greenlee developed a method to detect specific binding of TCDD to whole mammalian cells in culture and was later modified by Farmahin et al. for avian species. The cultured cells are incubated with radiolabeled TCDD with or without the presence of a competing ligand and filtered. The occupied protein adsorbs onto the filter and the radioactivity is measured to determine saturation binging and/or competitive binding. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005488 GO Whole cell filtration binding assay Cultured cells are incubated with radiolabeled TCDD with or without a competing ligand and filtered; radioactivity on the filter is measured to determine saturation or competitive binding. in_vitro mammalian cells avian species cells radioactivity change not_specified The cultured cells are incubated with radiolabeled TCDD with or without the presence of a competing ligand and filtered. The occupied protein adsorbs onto the filter and the radioactivity is measured to determine saturation binging and/or competitive binding. This assay is able to detect weak ligand-receptor interactions that are below the detection limit of the HAP assay whole cell filtration binding assay Cultured cells are incubated with radiolabeled TCDD with or without a competing ligand and filtered; the occupied protein adsorbs onto the filter and radioactivity is measured to determine saturation and/or competitive binding. in_vitro mammalian cells avian species saturation/competitive binding (radioactivity) increase medium Dold and Greenlee [27] developed a method to detect specific binding of TCDD to whole mammalian cells in culture and was later modified by Farmahin et al. [21] for avian species. The cultured cells are incubated with radiolabeled TCDD with or without the presence of a competing ligand and filtered [21]. This assay is able to detect weak ligand-receptor interactions that are below the detection limit of the HAP assay [21]. ATG_AR_TRANS A cell-based assay that can differentiate agonism from antagonism of the androgen receptor. in_vitro androgen receptor activation not_specified high ATG_AR_TRANS A cell based assay that can differentiate agonism from antagonism ATG_AR_TRANS A cell-based high-throughput screening assay designed to differentiate androgen receptor agonism from antagonism. in_vitro AR agonism or antagonism change high ATG_AR_TRANS A cell based assay that can differentiate agonism from antagonism ATG_AR_TRANS A cell based assay that can differentiate agonism from antagonism. in_vitro cells transcriptional activation change high ATG_AR_TRANS A cell based assay that can differentiate agonism from antagonism http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0006355 GO CoMPARA Computational models to predict androgen receptor binding and agonist/antagonist activity. in_silico predicted binding/activity change high CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. The US EPA lead consortium has developed consensus computational models that can be used to predict androgen receptor binding, agonist or antagonist activity (Mansouri et al., 2020). http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON CoMPARA computational model Consensus computational models to predict androgen receptor binding, agonist or antagonist activity. in_silico androgen receptor binding/activity not_specified high CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. The US EPA lead consortium has developed consensus computational models that can be used to predict androgen receptor binding, agonist or antagonist activity (Mansouri et al., 2020). competitive binding assay Measures binding to the androgen receptor in cell-free systems based on displacement of a radio-labeled standard (testosterone or DHT). in_vitro androgen receptor binding not_specified not_specified Binding to the androgen receptor can be directly measured in cell free systems based on displacement of a radio-labeled standard (generally testosterone or DHT) in a competitive binding assay (e.g., (Olsson et al. 2005; Sperry and Thomas 1999; Wilson et al. 2007; Tilley et al. 1989; Kim et al. 2010). competitive binding assay Directly measures binding to the androgen receptor in cell-free systems by displacement of a radio-labeled standard. in_vitro receptor binding decrease low Binding to the androgen receptor can be directly measured in cell free systems based on displacement of a radio-labeled standard (generally testosterone or DHT) in a competitive binding assay (e.g., (Olsson et al. 2005; Sperry and Thomas 1999; Wilson et al. 2007; Tilley et al. 1989; Kim et al. 2010). http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON In vivo anal fin elongation assay (western mosquitofish) Measurement of anal fin elongation in female western mosquitofish as evidence of AR activation. in_vivo anal fin Gambusia affinis anal fin elongation increase low Anal fin elongation in female western mosquitofish ( Gambusia affinis ) has similarly been viewed as evidence of AR activation (Raut et al. 2011; Sone et al. 2005). NVS_NR_hAR A cell-free assay using recombinant human androgen receptor to detect binding, but cannot distinguish agonism from antagonism. in_vitro androgen receptor binding not_specified high NVS_NR_hAR A cell free assay using recombinant human AR. Can detect binding, but cannot distinguish agonism from antagonism. NVS_NR_hAR A cell free assay using recombinant human AR. Can detect binding, but cannot distinguish agonism from antagonism. in_vitro human receptor binding decrease high NVS_NR_hAR A cell free assay using recombinant human AR. Can detect binding, but cannot distinguish agonism from antagonism. http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON OECD 458 Stably transfected human androgen receptor transcriptional activation assay to detect androgen agonists and antagonists. in_vitro human cells transcriptional activation increase OECD TG 458 medium OECD Test No. 458: Stably transfected human androgen receptor transcriptional activation assay for detection of androgen agonists and antagonists has been reviewed and validated by OECD and is well suited for detection of this key event (OECD 2016). http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0006355 GO OECD TG 458 A stably transfected human androgen receptor transcriptional activation assay for detection of androgen agonists and antagonists. in_vitro androgen receptor transcriptional activation not_specified OECD TG 458 not_specified OECD Test No. 458: Stably transfected human androgen receptor transcriptional activation assay for detection of androgen agonists and antagonists has been reviewed and validated by OECD and is well suited for detection of this key event (OECD 2016). OT_AR_ARELUC_AG_1440 A cell-based assay that measures expression of a reporter gene under control of androgen-responsive elements, distinguishing agonism from antagonism. in_vitro androgen-responsive reporter gene expression not_specified high OT_AR_ARELUC_AG_1440 A cell based assay that measures expression of a reporter gene under control of androgen-responsive elements. Can distinguish agonism from antagonism. papillary process development Development of papillary processes in medaka as an indirect measure of androgen receptor agonism. in_vivo fin medaka papillary process development increase OECD 2012 low In medaka, development of papillary processes, which normally only appear on the second to seventh or eighth fin aray of the anal fin, has also been used as an indirect measure of androgen receptor agonism (OECD 2012). http://purl.obolibrary.org/obo/UBERON_0004824 UBERON http://purl.obolibrary.org/obo/GO_0008533 GO phenotypic masculinization in fish In vivo measurement of phenotypic masculinization in female fish as an indirect measure of androgen receptor agonism. in_vivo fathead minnow western mosquitofish medaka three-spined stickleback phenotypic masculinization increase low In fish, phenotypic masculinization of females has frequently been used as an indirect measurement of in vivo androgen receptor agonism. Development of nuptial tubercles, a dorsal fatpad, and a characteristic banding pattern has been observed in female fathead minnows exposed to androgen agonists (Ankley et al. 2003; Jensen et al. 2006; Ankley et al. 2010; LaLone et al. 2013; OECD 2012). Anal fin elongation in female western mosquitofish (Gambusia affinis) has similarly been viewed as evidence of AR activation (Raut et al. 2011; Sone et al. 2005). In medaka, development of papillary processes, which normally only appear on the second to seventh or eighth fin aray of the anal fin, has also been used as an indirect measure of androgen receptor agonism (OECD 2012). reporter gene assay Cell-based assays using reporter genes to screen chemicals for AR agonist and/or antagonist activity. in_vitro cells reporter gene expression change medium Cell based transcriptional activation assays are typically required to differentiate agonists from antagonists, in vitro. A number of reporter gene assays have been developed and used to screen chemicals for AR agonist and/or antagonist activity (e.g., (Wilson et al. 2002; van der Burg et al. 2010; Mak et al. 1999; Araki et al. 2005). http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0006355 GO spiggin expression assay Measures expression of androgen-responsive proteins like spiggin in primary cell cultures to detect AR agonist activity. in_vitro spiggin expression increase not_specified Expression of androgen responsive proteins like spiggin in primary cell cultures has also been used to detect AR agonist activity (Jolly et al. 2006). Tox21_AR_BLA_Agonist_ratio A cell-based assay with an inducible reporter to distinguish androgen receptor agonists from antagonists. in_vitro androgen receptor agonist activity not_specified high Tox21_AR_BLA_Agonist_ratio A cell based assay with an inducible reporter. Can distinguish agonists from antagonists. Tox21_AR_BLA_Agonist_ratio A cell based assay with an inducible reporter. Can distinguish agonists from antagonists. in_vitro cells reporter gene expression change high Tox21_AR_BLA_Agonist_ratio A cell based assay with an inducible reporter. Can distinguish agonists from antagonists. http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0006355 GO Toxcast AR Transactivation Assay ATG_AR_TRANS A cell based assay that can differentiate agonism from antagonism. in_vitro human cells not specified human androgen receptor transactivation increase not specified high Measures of AR agonism have been included in high throughput screening programs, such as US EPA's Toxcast program. Toxcast assays relevant for screening chemicals for their ability to bind and/or activate the AR include: ATG_AR_TRANS A cell based assay that can differentiate agonism from antagonism. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0032774 GO US EPA AR pathway model Includes 11 in vitro assays measuring receptor binding, coregulator recruitment, nuclear translocation, transactivation or cell proliferation to provide an AUC value for AR agonism/antagonism. in_vitro cells AUC value change medium US EPA Androgen receptor pathway model. The model includes 11 in vitro assays measuring receptor binding, coregulator recruitment, nuclear translocation, transactivation or cell proliferation. A “reduced” model that include fewer assays also exists. http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0007165 GO AR Competitive Binding Assay Competitive binding assays measure the ability of test compounds to displace a labeled ligand from the androgen receptor (AR) binding site, providing information on relative potency but not downstream effects. in_vitro Human binding affinity decrease http://purl.obolibrary.org/obo/GO_0005515 GO http://purl.obolibrary.org/obo/GO_0005488 GO medium Additional information on AR interaction can be obtained employing competitive AR binding assays, which can also inform on relative potency of the compounds, though not on downstream effect of the AR binding. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005515 GO AR dimerization assay Measures potential stressor-mediated disruption of AR dimerization/activation. in_vitro AR dimerization decrease low The recently developed AR dimerization assay provides an assay with an improved ability to measure potential stressor-mediated disruption of dimerization/activation (Lee et al, 2021). http://purl.obolibrary.org/obo/GO_0005518 GO AR Dimerization Assay The AR dimerization assay measures the ability of compounds to disrupt the dimerization and activation of the androgen receptor (AR), providing an improved ability to detect stressor-mediated disruption. in_vitro Human dimerization not_specified http://purl.obolibrary.org/obo/GO_0051258 GO medium The recently developed AR dimerization assay provides an assay with an improved ability to measure potential stressor-mediated disruption of dimerization/activation. http://purl.obolibrary.org/obo/PR_000000001 PR AR Nuclear Translocation Assay Fluorescent-based assays monitor the nuclear translocation of the androgen receptor (AR) in living cells in response to agonists or antagonists, indicating AR activation. in_vitro HEK293 other transfected cell lines Human Rat nuclear translocation increase http://purl.obolibrary.org/obo/GO_0006915 GO medium AR nuclear translocation can be monitored by various assays, for example by monitoring fluorescent rat AR movement in living cells. with several human AR translocation assays being commercially available; e.g. Fluorescent AR Nuclear Translocation Assay (tGFP-hAR/HEK293) http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006915 GO AR Transactivation Assay Transient or stable transactivation assays measure nuclear receptor activation of the androgen receptor (AR) in vitro. These assays use reporter gene constructs to evaluate AR-mediated transcriptional activity in response to agonists or antagonists. in_vitro HEK293 other transfected cell lines Human transcriptional activation change http://purl.obolibrary.org/obo/GO_0030521 GO http://purl.obolibrary.org/obo/GO_0006355 GO OECD TG 458 medium AR antagonism can be measured in vitro by transient or stable transactivation assays to evaluate nuclear receptor activation. This test guideline contains three different methods. More information on limitations, advantages, protocols, and availability, and description of cells are given in the test guideline. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0030521 GO Competitive AR Binding Assay Measures the binding of compounds to the androgen receptor, providing information on relative potency. in_vitro androgen receptor binding change medium Additional information on AR interaction can be obtained employing competitive AR binding assays (Freyberger et al 2010, Shaw et al 2018), which can also inform on relative potency of the compounds, though not on downstream effect of the AR binding. Fluorescent AR Nuclear Translocation Assay Monitors AR nuclear translocation by tracking fluorescently tagged AR movement in living cells. in_vitro HEK293 human androgen receptor nuclear translocation change medium AR nuclear translocation can be monitored by various assays (Campana et al 2015), for example by monitoring fluorescent rat AR movement in living cells (Tyagi et al 2020), with several human AR translocation assays being commercially available; e.g. Fluorescent AR Nuclear Translocation Assay (tGFP-hAR/HEK293) Human Androgen NHR Cell Based Antagonist Translocation LeadHunter Assay Detects androgen receptor translocation in response to antagonists using a cell‑based LeadHunter format with human AR‑NHR constructs. in_vitro human androgen receptor NHR cell based human AR nuclear translocation decrease http://purl.obolibrary.org/obo/GO_0008104 GO http://purl.obolibrary.org/obo/GO_0006913 GO not_specified Human Androgen NHR Cell Based Antagonist Translocation LeadHunter Assay http://purl.obolibrary.org/obo/GO_0008104 GO Stably Transfected Human Androgen Receptor Transcriptional Activation Assay Measures AR agonism and antagonism using stably transfected cells to evaluate nuclear receptor activation. in_vitro stably transfected human cells human androgen receptor transcriptional activation change OECD TG 458 medium AR antagonism can be measured in vitro by transient or stable transactivation assays to evaluate nuclear receptor activation. There is already a validated test guideline for AR (ant)agonism adopted by the OECD, Test No. 458: Stably Transfected Human Androgen Receptor Transcriptional Activation Assay for Detection of Androgenic Agonist and Antagonist Activity of Chemicals transactivation assay Evaluates nuclear receptor activation using transient or stable transfection. This assay measures AR antagonism. in_vitro nuclear receptor activation decrease OECD TG 458 medium AR antagonism can be measured in vitro by transient or stable transactivation assays to evaluate nuclear receptor activation. There is already a validated test guideline for AR (ant)agonism adopted by the OECD, Test No. 458: Stably Transfected Human Androgen Receptor Transcriptional Activation Assay for Detection of Androgenic Agonist and Antagonist Activity of Chemicals http://purl.obolibrary.org/obo/GO_0001228 GO aortic explant assay Cultured aortic explants from developing chick embryos or mouse/rat fetuses are used to evaluate microvessel outgrowth and sprouting behaviors, including cell migration, proliferation, tube formation, branching, and perivascular recruitment. in_vitro aorta chick mouse rat microvessel outgrowth and sprouting behaviors change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0016479 GO http://purl.obolibrary.org/obo/GO_0008283 GO low Aortic explants cultured from developing chick embryos or mouse/rat fetuses have been used as a source for evaluating drug/chemical effects on microvessel outgrowth [Baker et al. 2011; Beedie et al. 2015; Ellis-Hutchings et al. 2017; Kapoor et al. 2020; Katakia et al. 2020]. Microvascular streams from these explants are amenable to morphometric analysis of many sprouting behaviors, including cell migration, proliferation tube formation, branching, perivascular recruitment and remodeling. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0001525 GO Chick chorioallantoic membrane (CAM) vascularization assay The chick chorioallantoic membrane is used as an in vivo model to assess vascularization and angiogenic responses, allowing visualization and quantification of neovascularization in response to test agents. in_vivo endothelial cells chorioallantoic membrane blood vessel chick vascularization and angiogenic neovascularization change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/NCBITaxon_11908 NCBITAXON low in vivo measures with endothelial reporter zebrafish lines, chick chorioallantoic membrane vascularization, and genetic mouse models; http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0001525 GO Computational models In silico mathematical simulations used to probe molecular control of tip/stalk switching and predict toxicological effects on tubulogenesis. in_silico Danio rerio tip/stalk switching dynamics change not_specified These aspects of angiogenic sprouting have been modelled in silico mathematically or computationally simulating cell-cell interactions in a self-organizing computer model of tubulogenesis for predictive toxicology http://purl.obolibrary.org/obo/CL_0000294 CL http://purl.obolibrary.org/obo/GO_0001526 GO engineered microtissues assay Uses induced pluripotent stem cell-derived endothelial cells (iPSC-EC) cultured in 3D hydrogel microspheres or microfluidic devices to evaluate VEGF-dependent vascular network formation and sprouting behaviors. in_vitro iPSC-EC fibroblasts human vascular network formation and sprouting behaviors increase http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/CHEBI_17689 CHEBI medium Engineered microtissues: To better recapitulate angiogenesis in vivo, in vitro assays for drug and chemical screening must adopt physiological relevant culture conditions with robustness and scalability. Human endothelial lines have been derived from induced pluripotent stem cells (iPSC-EC) and cultured in engineered platforms that mimic the 3D microenvironment [Belair et al. 2015]. They formed VEGF-dependent 3D perfusable vascular networks when co-cultured with fibroblasts and aligned with flow in microfluidic devices [Belair et al. 2015]. Encapsulating endothelial cells at controlled densities in hydrogel microspheres surrounded by a synthetic ECM [Belair et al. 2016a] or VEGF-binding peptides [Belair et al. 2016b] can be used to evaluate the activation by ECM and ECM-sequestered VEGF and other angiogenic factors. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0001525 GO Genetic mouse model of angiogenesis Genetic mouse models are used to measure in vivo angiogenesis and vascular development, enabling assessment of endothelial cell behavior, sprouting and vessel formation in the context of intact mammalian physiology. in_vivo endothelial cells blood vessel microvasculature mouse angiogenesis and vascular development in vivo change http://purl.obolibrary.org/obo/GO_0001525 GO low in vivo measures with endothelial reporter zebrafish lines, chick chorioallantoic membrane vascularization, and genetic mouse models; http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0001525 GO human cell-based in vitro tubulogenesis assay Uses human umbilical vein endothelial cells (HUVEC) co-cultured with fibroblasts to form endothelial networks resembling a microvascular bed upon VEGF stimulation, quantified by immunochemical biomarkers and image analysis. in_vitro HUVEC fibroblasts human endothelial network formation increase http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/PR_000001519 PR http://purl.obolibrary.org/obo/CHEBI_17689 CHEBI OECD Guidance Document 34 for the Validation and International Acceptance of New or Updated Test Methods for Hazard Assessment medium Human cell-based in vitro tubulogenesis assay: Angiogenic sprouts convert into endothelial tubules and form connections with other vessels, which requires the local suppression of motility and the formation of new cell-cell junctions. In vitro assays for this assembly, commonly referred to as tubulogenesis, use human umbilical vein endothelial cells (HUVEC) co-cultured with fibroblasts [Bishop et al. 1999]. Routine cell culture methods support the organization of isolated HUVEC cells into endothelial networks that resemble a microvascular bed upon stimulation with VEGF. The standardized assay detects pro-angiogenic and anti-angiogenic activities that are tracked with with immunochemical biomarkers (eg, PECAM-1) and quantified by image analysis [Bishop et al. 1999]. http://purl.obolibrary.org/obo/CL_0000115 CL In silico computational modeling of angiogenesis Mathematical and computational models simulate angiogenic sprouting, including molecular control of tip/stalk switching dynamics linked to VEGF-Notch-DLL4 signaling, EC-tip and EC-stalk differentiation, and tubulogenesis for predictive toxicology. in_silico EC-tip cells EC-stalk cells microvasculature zebrafish angiogenic sprouting dynamics, tip/stalk switching and tubulogenesis simulation change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/OBI_0000011 OBI high in silico computational models for quantitative simulation and biological integration. These aspects of angiogenic sprouting have been modelled in silico mathematically or computationally, probing deeply into the molecular control of tip/stalk switching dynamics linked to the VEGF-Notch-DLL4 signaling [Venkataraman et al. 2016], uncovering the critical determinants of EC-tip and EC-stalk differentiation that influence the morphology of sprout progression [Palm et al. 2016], establishing canonical growth trajectories in normal and chemical-disrupted zebrafish embryos [Shirinifard et al. 2013], and simulating cell-cell interactions in a self-organizing computer model of tubulogenesis for predictive toxicology [Kleinstreuer et al. 2013]. http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0001525 GO in silico computational models Mathematical or computational models to simulate molecular control of tip/stalk switching dynamics, EC-tip and EC-stalk differentiation, and tubulogenesis for predictive toxicology. in_silico molecular control of angiogenic sprouting change http://purl.obolibrary.org/obo/GO_0001525 GO high Computational models: These aspects of angiogenic sprouting have been modelled in silico mathematically or computationally, probing deeply into the molecular control of tip/stalk switching dynamics linked to the VEGF-Notch-DLL4 signaling [Venkataraman et al. 2016], uncovering the critical determinants of EC-tip and EC-stalk differentiation that influence the morphology of sprout progression [Palm et al. 2016], establishing canonical growth trajectories in normal and chemical-disrupted zebrafish embryos [Shirinifard et al. 2013], and simulating cell-cell interactions in a self-organizing computer model of tubulogenesis for predictive toxicology [Kleinstreuer et al. 2013]. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0001525 GO In vivo zebrafish endothelial reporter assay Endothelial reporter zebrafish lines are used to measure vascularization and angiogenic sprouting in living embryos, allowing observation of EC-tip cell selection, migration, proliferation and tubulogenesis in the context of whole-organism development. in_vivo endothelial cells EC-tip cells blood vessel microvasculature zebrafish vascularization and angiogenic sprouting in vivo change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/NCBITaxon_7272 NCBITAXON low in vivo measures with endothelial reporter zebrafish lines, chick chorioallantoic membrane vascularization, and genetic mouse models; establishing canonical growth trajectories in normal and chemical-disrupted zebrafish embryos [Shirinifard et al. 2013] http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0001525 GO Vascular sprouting assay (mouse embryonic stem cells) A microsystem using mouse embryonic stem cells differentiated into vascularized embryoid bodies on 3D-collagen gels to recapitulate in vivo sprouting. in_vitro mouse embryonic stem cells embryoid bodies mouse sprouting behaviors (tip cell selection, migration, proliferation, tubulogenesis, mural cell recruitment) change http://purl.obolibrary.org/obo/GO_0001525 GO not_specified A vascular sprouting assay that utilizes mouse embryonic stem cells differentiated into vascularized embryoid bodies has been described, where the microsystem cultured onto 3D-collagen gels recapitulates key features of in vivo sprouting including endothelial EC-tip cell selection, migration and proliferation, polarized guidance, tubulogenesis, and mural cell recruitment http://purl.obolibrary.org/obo/CL_0000070 CL http://purl.obolibrary.org/obo/GO_0001525 GO Aromatase activity assay Aromatase activity is measured by evaluating the production of tritiated water released upon the aromatase catalyzed conversion of radio-labeled androstenedione to estrone. in_vitro human placental JEG-3 cells JAR choriocarcinoma cells H295R human adrenocortical carcinoma cells tritiated water production decrease OECD Test Guideline No. 456 high Aromatase activity is typically measured by evaluating the production of tritiated water released upon the aromatase catalyzed conversion of radio-labeled androstenedione to estrone (Lephart and Simpson 1991). Aromatase activity can be measured in cell lines exposed in vitro (e.g., human placental JEG-3 cells and JAR choriocarcinoma cells, (Letcher et al. 1999); H295R human adrenocortical carcinoma cells (Sanderson et al. 2000)). OECD Test Guideline No. 456 H295R Steroidogenesis Assay can be used to indirectly assess aromatase activity by measuring estradiol production by the H295R cells (OECD, 2013). http://purl.obolibrary.org/obo/GO_0006275 GO Aromatase activity assay (tritiated water release) Measures aromatase activity by evaluating the production of tritiated water released upon the conversion of radio-labeled androstenedione to estrone. in_vitro JEG-3 cells JAR choriocarcinoma cells H295R human adrenocortical carcinoma cells human aromatase activity decrease http://purl.obolibrary.org/obo/GO_0004009 GO high Aromatase activity is typically measured by evaluating the production of tritiated water released upon the aromatase catalyzed conversion of radio-labeled androstenedione to estrone (Lephart and Simpson 1991). Aromatase activity can be measured in cell lines exposed in vitro (e.g., human placental JEG-3 cells and JAR choriocarcinoma cells, (Letcher et al. 1999); H295R human adrenocortical carcinoma cells (Sanderson et al. 2000)). http://purl.obolibrary.org/obo/GO_0004009 GO http://purl.obolibrary.org/obo/GO_0006704 GO OECD TG 456 H295R Steroidogenesis Assay Indirectly assesses aromatase activity by measuring estradiol production by H295R cells. in_vitro H295R human adrenocortical carcinoma cells human estradiol production decrease OECD Test Guideline No. 456 medium OECD Test Guideline No. 456 H295R Steroidogenesis Assay can be used to indirectly assess aromatase activity by measuring estradiol production by the H295R cells (OECD, 2013). http://purl.obolibrary.org/obo/GO_0004009 GO http://purl.obolibrary.org/obo/GO_0006704 GO OPPTS 890.1200 Aromatase assay Measures aromatase activity using recombinant microsomes containing human aromatase and quantifies the 3H20 released by conversion of 3H-androstenedione to estrone, following the US EPA test guideline OPPTS 890.1200. in_vitro human 3H20 production increase OPPTS 890.1200 not_specified Aromatase activity can be measured using the US EPA test guideline assay OPPTS 890.1200. The assay uses recombinant microsomes containing human aromatase and measures 3H20 that is released by conversion of 3H-androstenedione to estrone (EPA, 2009) http://purl.obolibrary.org/obo/CHEBI_16239 CHEBI http://purl.obolibrary.org/obo/GO_0008406 GO Tritiated water release assay Measures aromatase activity by quantifying the production of tritiated water released during the conversion of radio-labeled androstenedione to estrone in vitro. in_vitro JEG-3 JAR H295R Homo sapiens tritiated water production decrease not_specified Aromatase activity is typically measured by evaluating the production of tritiated water released upon the aromatase catalyzed conversion of radio-labeled androstenedione to estrone (Lephart and Simpson 1991). Aromatase activity can be measured in cell lines exposed in vitro (e.g., human placental JEG-3 cells and JAR choriocarcinoma cells, (Letcher et al. 1999); H295R human adrenocortical carcinoma cells (Sanderson et al. 2000)). US EPA OPPTS 890.1200 Uses recombinant microsomes containing human aromatase and measures tritiated water released by conversion of tritiated androstenedione to estrone. in_vitro human aromatase activity decrease http://purl.obolibrary.org/obo/GO_0004009 GO US EPA OPPTS 890.1200 medium The assay uses recombinant microsomes containing human aromatase and measures 3H20 that is released by conversion of 3H-androstenedione to estrone (EPA, 2009). http://purl.obolibrary.org/obo/GO_0004009 GO http://purl.obolibrary.org/obo/GO_0006704 GO Embryonic swimming activity assay Measurement of embryonic swimming activity in fish and frog larvae by counting the number of times a larva crosses a grid line during a 1-min interval. in_vivo larva Danio rerio Xenopus number of grid line crossings change http://purl.obolibrary.org/obo/GO_0007626 GO http://purl.obolibrary.org/obo/GO_0048598 GO medium Embryonic swimming activity in fish and frogs was measured at 5 dpf by placing larvae-containing dishes above an 8-wedged pie chart grid and counting the number of times a larvae crossed a grid line during a 1-min interval http://purl.obolibrary.org/obo/UBERON_0002564 UBERON http://purl.obolibrary.org/obo/GO_0040011 GO Pupil constriction observation Clinical observation of pupil constriction in human patients experiencing cholinergic poisoning. in_vivo eye Homo sapiens pupil size decrease low human patients experiencing cholinergic poisoning constricted or pinpointed pupils are frequently reported in clinical cohort studies covering organophosphate exposure http://purl.obolibrary.org/obo/UBERON_0001753 UBERON http://purl.obolibrary.org/obo/GO_0007200 GO Pupil diameter observation Clinical observation of pupil size to detect constriction or pinpointing in humans. in_vivo eye human pupil constriction decrease http://purl.obolibrary.org/obo/DOID_11442 DOID low Pupils - human patients experiencing cholinergic poisoning constricted or pinpointed pupils are frequently reported http://purl.obolibrary.org/obo/UBERON_0000644 UBERON Pupil examination Clinical observation of pupil size in human patients. Constricted or pinpointed pupils are indicative of cholinergic poisoning. in_vivo eye Homo sapiens Pupil size decrease low In humans Pupils - human patients experiencing cholinergic poisoning constricted or pinpointed pupils are frequently reported in clinical cohort studies covering organophosphate exposure (Wadia, 1974, Peter, 2014). http://purl.obolibrary.org/obo/GO_0003878 GO Spontaneous movement observation Observation of spontaneous movements in developing fish and frog embryos under a dissection microscope, recording the number of movements per minute. in_vivo embryo Danio rerio Xenopus number of movements per minute change http://purl.obolibrary.org/obo/GO_0009790 GO medium Spontaneous movements in developing fish and frog embryos are defined as flexing or side-to-side motion of the trunk or tail and free-swimming activity, defined as bilateral rhythmic flexing of the tail. Embryos were observed under a dissection microscope and the number of movements per minute was recorded. http://purl.obolibrary.org/obo/UBERON_0000922 UBERON http://purl.obolibrary.org/obo/GO_0040011 GO BSEP inhibition assay In vitro assays designed to measure the inhibition of the Bile Salt Export Pump (ABCB11) to assess the cholestasis-inducing potential of drugs. in_vitro BSEP inhibition decrease not_specified A number of in vitro assays for measuring BSEP inhibition have been developed and successfully applied to demonstrate the cholestasis-inducing potential of drugs (Dawson et al., 2011; Kis et al., 2012; Morgan et al., 2010). http://purl.obolibrary.org/obo/PR_000001419 PR http://purl.obolibrary.org/obo/GO_0015721 GO Ca++ ATPase activity assay Measures the activity of Ca++ ATPase, which regulates intracellular calcium levels. not_specified Ca++ ATPase activity decrease http://purl.obolibrary.org/obo/GO_0004012 GO http://purl.obolibrary.org/obo/GO_0005509 GO not_specified Decreased Ca++ ATPase activity leads to an increase in intracellular calcium http://purl.obolibrary.org/obo/GO_0004012 GO http://purl.obolibrary.org/obo/GO_0006816 GO calcium measurement assay This assay measures intracellular calcium levels to determine increases in Ca++ concentration within cells. in_vitro intracellular calcium concentration increase http://purl.obolibrary.org/obo/GO_0005509 GO http://purl.obolibrary.org/obo/GO_0005622 GO not_specified KE title: Increase, Ca++ (intracellular) Decreased Ca++ ATPase activity leads to an increase in intracellular calcium http://purl.obolibrary.org/obo/CHEBI_25073 CHEBI http://purl.obolibrary.org/obo/GO_0005509 GO Ca++ ATPase activity assay Measures the activity of Ca++ ATPase, which is inhibited by Pb(II), leading to increased intracellular calcium. not_specified Ca++ ATPase activity decrease not_specified Pb(II) has been shown to decrease Ca++ ATPase activity, leading to an increase in intracellular calcium. channel blockage by Ca2+ measurement Measures channel blockage by Ca2+ in NMDA receptors. in_vitro channel blockage by Ca2+ not_specified low there are three methods for measuring Ca2+ influx in NMDA receptors that involve the measurement of 1) relative Ca2+ permeability, 2) channel blockage by Ca2+, and 3) fractional Ca2+ currents from whole-cell currents determined in the presence of high concentrations of intracellular Fura-2 (Traynelis et al., 2010). flow cytometry Flow cytometry uses fluorescent dyes (Ca2+-sensitive fluorophores) to determine intracellular Ca2+ concentration. in_vitro intracellular Ca2+ concentration decrease medium In vitro, well-established flow cytometric or high content imaging analysis with specific fluorescent dyes (Ca2+-sensitive fluorophores) such as Fura-2, Oregon Green-BAPTA, Fluo-4 and X-Rhod exist for determination of intracellular Ca2+ concentration. http://purl.obolibrary.org/obo/CL_0000273 CL http://purl.obolibrary.org/obo/GO_0006815 GO flow cytometry with Ca2+-sensitive fluorophores Uses fluorescent dyes such as Fura-2, Oregon Green-BAPTA, Fluo-4, and X-Rhod to measure intracellular Ca2+ concentration. in_vitro intracellular Ca2+ concentration not_specified high In vitro, well-established flow cytometric or high content imaging analysis with specific fluorescent dyes (Ca2+-sensitive fluorophores) such as Fura-2, Oregon Green-BAPTA, Fluo-4 and X-Rhod exist for determination of intracellular Ca2+ concentration. fluorescence microscopy Intra-cellular calcium concentration is measured using the calcium sensitive fluorescent dye Fura-2 AM and fluorescence microscopy. in_vitro intracellular calcium concentration decrease low Intra-cellular calcium concentration can be measured in cell cultures with the calcium sensitive fluorescent dye Fura-2 AM and fluorescence microscopy. http://purl.obolibrary.org/obo/CL_0000273 CL http://purl.obolibrary.org/obo/GO_0006815 GO fractional Ca2+ currents measurement Measures fractional Ca2+ currents from whole-cell currents in the presence of high concentrations of intracellular Fura-2. in_vitro fractional Ca2+ currents not_specified low there are three methods for measuring Ca2+ influx in NMDA receptors that involve the measurement of 1) relative Ca2+ permeability, 2) channel blockage by Ca2+, and 3) fractional Ca2+ currents from whole-cell currents determined in the presence of high concentrations of intracellular Fura-2 (Traynelis et al., 2010). high content imaging High content imaging uses fluorescent dyes (Ca2+-sensitive fluorophores) to determine intracellular Ca2+ concentration. in_vitro intracellular Ca2+ concentration decrease medium In vitro, well-established flow cytometric or high content imaging analysis with specific fluorescent dyes (Ca2+-sensitive fluorophores) such as Fura-2, Oregon Green-BAPTA, Fluo-4 and X-Rhod exist for determination of intracellular Ca2+ concentration. http://purl.obolibrary.org/obo/CL_0000273 CL http://purl.obolibrary.org/obo/GO_0006815 GO patch clamp electrophysiology This is the gold standard method for measuring Ca2+ current through NMDA receptors using electrophysiological techniques. in_vitro brain Ca2+ current decrease http://purl.obolibrary.org/obo/GO_0006814 GO low The gold standard method for measuring Ca2+ current through NMDA receptor is patch clamp electrophysiology (Blanke and VanDongen, 2009). http://purl.obolibrary.org/obo/GO_0006814 GO patch clamp electrophysiology Measures Ca2+ current through NMDA receptors using electrophysiological techniques. in_vitro Ca2+ current through NMDA receptor not_specified low The gold standard method for measuring Ca2+ current through NMDA receptor is patch clamp electrophysiology (Blanke and VanDongen, 2009). relative Ca2+ permeability measurement Measures relative Ca2+ permeability in NMDA receptors. in_vitro relative Ca2+ permeability not_specified low there are three methods for measuring Ca2+ influx in NMDA receptors that involve the measurement of 1) relative Ca2+ permeability, 2) channel blockage by Ca2+, and 3) fractional Ca2+ currents from whole-cell currents determined in the presence of high concentrations of intracellular Fura-2 (Traynelis et al., 2010). two-photon Ca2+ imaging Uses Ca2+-sensitive fluorescent indicators to measure changes in intracellular Ca2+ concentration in vivo. in_vivo brain rodents zebrafish intracellular Ca2+ concentration not_specified low In vivo, two-photon Ca2+ imaging using Ca2+-sensitive fluorescent indicators that measure changes in intracellular Ca2+ concentration as a readout for suprathreshold and subthreshold neuronal activity has also been used to study learning and memory in live rodents (Chen et al., 2013). The last two decades the neuronal function of the larval and adult zebrafish has been extensively studied using Ca2+ imaging methods. two-photon released caged neurotransmitters Uses two-photon released caged neurotransmitters to measure Ca2+ in dendritic spines. in_vitro Ca2+ concentration in dendritic spines not_specified low For quantitative estimation of Ca2+ in dendritic spines, besides of Ca2+-sensitive fluorophores the use of two-photon released caged neurotransmitters has been suggested as it allows direct stimulation of visualized spines (Higley and Sabatini, 2012). zebrafish Ca2+ imaging assay Measures intracellular Ca2+ concentration changes in zebrafish using fluorescent indicators in a transparent model. in_vivo zebrafish intracellular Ca2+ concentration change http://purl.obolibrary.org/obo/CHEBI_18357 CHEBI http://purl.obolibrary.org/obo/GO_0006874 GO not_specified The last two decades the neuronal function of the larval and adult zebrafish has been extensively studied using Ca2+ imaging methods. By applying simple Ca2+ indicators such as dextran or acetoxymethyl esters to more powerful genetically encoded Ca2+ indicators, zebrafish provides a transparent model where live Ca2+ imaging can be successfully achieved (Kettunen, 2012). http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0006874 GO gene expression analysis Measures changes in CD36 gene expression levels. not_specified CD36 gene expression increase not_specified CD36 is measured by changes in gene expression gene expression analysis Measurement of the transcription levels of the CD36 gene to assess up-regulation. not_specified gene expression change http://purl.obolibrary.org/obo/GO_0010467 GO not_specified CD36 is measured by changes in gene expression http://purl.obolibrary.org/obo/GO_0010467 GO protein level analysis Measures changes in CD36 protein levels. not_specified CD36 protein levels increase not_specified CD36 is measured by changes in [...] protein levels protein level quantification Measurement of the abundance of CD36 protein to assess up-regulation. not_specified protein levels change not_specified CD36 is measured by changes in ... protein levels qPCR This assay measures changes in gene expression of CD36. not_specified gene expression increase not_specified CD36 is measured by changes in gene expression and protein levels. http://purl.obolibrary.org/obo/GO_0010468 GO western blot This assay measures changes in protein levels of CD36. not_specified protein levels increase not_specified CD36 is measured by changes in gene expression and protein levels. http://purl.obolibrary.org/obo/GO_0006454 GO Acridine Orange/Ethidium Bromide staining A fluorescent microscopy assay that visualizes nuclear changes and apoptotic body formation characteristic of apoptosis. in_vitro apoptotic body formation increase http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/GO_0071840 GO low Acridine Orange/Ethidium Bromide staining is used to visualize nuclear changes and apoptotic body formation that are characteristic of apoptosis. Cells are viewed under a fluorescence microscope and counted to quantify apoptosis. http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0006915 GO Alamar Blue assay Uses the fluorescent dye resazurin which is reduced to a pink fluorescent dye by cell activity. in_vitro cell activity change http://purl.obolibrary.org/obo/GO_0008150 GO not_specified The oxidized blue non fluorescent Alamar blue is reduced to a pink fluorescent dye in the medium by cell activity http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008152 GO Alamar Blue assay A fluorescent assay that measures cell viability by detecting the reduction of resazurin (blue, non-fluorescent) to resorufin (pink, fluorescent) by metabolically active cells. in_vitro cell viability decrease http://purl.obolibrary.org/obo/GO_0008563 GO http://purl.obolibrary.org/obo/GO_0055114 GO medium Alamar Blue (resazurin) is a fluorescent dye. The oxidized blue non fluorescent Alamar blue is reduced to a pink fluorescent dye in the medium by cell activity (O'Brien et al., 2000) (12). http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008563 GO ATP assay Quantification of ATP, signaling the presence of metabolically active cells. in_vitro ATP concentration increase http://purl.obolibrary.org/obo/GO_0009266 GO medium Moreover, quantification of ATP, signaling the presence of metabolically active cells, can be performed (CellTiter-Glo; Promega). ATP assay: Quantification of ATP, signaling the presence of metabolically active cells (CellTiter-Glo; Promega). http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0009266 GO ATP assay (CellTiter-Glo) Quantifies ATP levels as an indicator of metabolically active cells using a luminescent assay. in_vitro ATP levels decrease http://purl.obolibrary.org/obo/GO_0046034 GO http://purl.obolibrary.org/obo/GO_0008563 GO high Moreover, quantification of ATP, signaling the presence of metabolically active cells, can be performed (CellTiter-Glo; Promega). ATP assay: Quantification of ATP, signaling the presence of metabolically active cells (CellTiter-Glo; Promega). http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0045333 GO Caspase activity assay Measures caspase-3 and -7 activity, which cleave PARP during apoptosis, using fluorescence or immunofluorescence to detect cleaved PARP fragments. in_vitro caspase activity increase http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/GO_0008656 GO medium Caspase activity assays measured by fluorescence. During apoptosis, mainly caspase-3 and -7 cleave PARP to yield an 85 kDa and a 25 kDa fragment. PARP cleavage is considered to be one of the classical characteristics of apoptosis. Antibodies to the 85 kDa fragment of cleaved PARP or to caspase-3 both serve as markers for apoptotic cells that can be monitored using immunofluorescence (Li, Peng et al., 2004). http://purl.obolibrary.org/obo/PR_000001000 PR http://purl.obolibrary.org/obo/GO_0006915 GO Hoechst 33342 staining A fluorescent assay that stains condensed or fragmented DNA in live or fixed cells, serving as a marker of apoptosis. in_vitro DNA condensation/fragmentation increase http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/GO_0003677 GO medium Hoechst 33342 staining: Hoechst dyes are cell-permeable and bind to DNA in live or fixed cells. Therefore, these stains are often called supravital, which means that cells survive a treatment with these compounds. The stained, condensed or fragmented DNA is a marker of apoptosis (Loo, 2002; Kubbies and Rabinovitch, 1983). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO LDH assay Measures the release of lactate dehydrogenase (LDH) into cell culture medium as an indicator of plasma membrane damage and necrosis. LDH catalyzes the oxidation of lactate to pyruvate, producing NADH, which then reduces a tetrazolium salt to a colored formazan product quantified by spectroscopy. in_vitro LDH release increase http://purl.obolibrary.org/obo/GO_0004456 GO http://purl.obolibrary.org/obo/GO_0008219 GO http://purl.obolibrary.org/obo/GO_0070265 GO medium Lactate dehydrogenase (LDH) is a soluble cytoplasmic enzyme that is present in almost all cells and is released into extracellular space when the plasma membrane is damaged. To detect the leakage of LDH into cell culture medium, a tetrazolium salt is used in this assay. The amount of formazan product can be colorimetrically quantified by standard spectroscopy. Because of the linearity of the assay, it can be used to enumerate the percentage of necrotic cells in a sample (Chan et al., 2013). http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0070265 GO LDH leakage assay Measures the release of the soluble cytoplasmic enzyme lactate dehydrogenase (LDH) into the extracellular space due to plasma membrane damage using a tetrazolium salt colorimetric method. in_vitro percentage of necrotic cells increase http://purl.obolibrary.org/obo/GO_0004402 GO not_specified Lactate dehydrogenase (LDH) is a soluble cytoplasmic enzyme that is present in almost all cells and is released into extracellular space when the plasma membrane is damaged. The amount of formazan product can be colorimetrically quantified by standard spectroscopy. it can be used to enumerate the percentage of necrotic cells in a sample http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0006911 GO MTT assay A colorimetric assay that measures cell viability by quantifying the reduction of the tetrazolium dye MTT to insoluble formazan by NAD(P)H-dependent cellular oxidoreductase enzymes. in_vitro cell viability decrease http://purl.obolibrary.org/obo/GO_0008563 GO medium The MTT assay is a colorimetric assay for assessing cell viability. NAD(P)H-dependent cellular oxidoreductase enzymes may reflect the number of viable cells present. Tetrazolium dye assays can also be used to measure cytotoxicity (loss of viable cells) or cytostatic activity (shift from proliferation to quiescence) of potential medicinal agents and toxic materials. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008563 GO MTT assay The MTT assay is a colorimetric assay that assesses cell viability by measuring the reduction of MTT dye to formazan by NAD(P)H-dependent cellular oxidoreductase enzymes. It can also measure cytotoxicity or cytostatic activity. in_vitro formazan production decrease http://purl.obolibrary.org/obo/GO_0005829 GO medium The MTT assay is a colorimetric assay for assessing cell viability. Tetrazolium dye assays can also be used to measure cytotoxicity or cytostatic activity (loss of viable cells) or cytostatic activity (shift from proliferation to quiescence) of potential medicinal agents and toxic materials. MTT assays are usually done in the dark since the MTT reagent is sensitive to light (Berridgeet al.,2005). http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0005829 GO Neutral red uptake A colorimetric assay that measures cell viability by quantifying the ability of viable cells to incorporate and bind the supravital dye neutral red in lysosomes. in_vitro cell viability / lysosomal integrity decrease http://purl.obolibrary.org/obo/GO_0030154 GO http://purl.obolibrary.org/obo/GO_0005762 GO low Neutral red uptake, which is based on the ability of viable cells to incorporate and bind the supravital dye neutral red in lysosomes (Repetto et al., 2008)(13). http://purl.obolibrary.org/obo/GO_0005764 GO http://purl.obolibrary.org/obo/GO_0030154 GO Neutral red uptake assay Measures the ability of viable cells to incorporate and bind the supravital dye neutral red within their lysosomes. in_vitro lysosomal uptake of neutral red change http://purl.obolibrary.org/obo/GO_0005748 GO not_specified Neutral red uptake, which is based on the ability of viable cells to incorporate and bind the supravital dye neutral red in lysosomes http://purl.obolibrary.org/obo/GO_0005748 GO Propidium iodide staining A fluorescent assay that stains necrotic cells by binding to nucleic acids when the cell membrane is compromised, with excitation at 535 nm and emission at 617 nm. in_vitro necrotic cell count increase http://purl.obolibrary.org/obo/GO_0070265 GO http://purl.obolibrary.org/obo/GO_0003677 GO medium Propidium iodide (PI) is an intercalating agent and a fluorescent molecule used to stain necrotic cells. It is cell membrane impermeant so it stains only those cells where the cell membrane is destroyed. http://purl.obolibrary.org/obo/GO_0016020 GO http://purl.obolibrary.org/obo/GO_0070265 GO TUNEL assay Detects DNA fragmentation characteristic of apoptosis by labeling nicks in the DNA with terminal deoxynucleotidyl transferase (TdT) and labeled dUTPs. in_vitro DNA fragmentation increase http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/GO_0006309 GO medium TUNEL is a common method for detecting DNA fragmentation that results from apoptotic signalling cascades. The assay relies on the presence of nicks in the DNA which can be identified by terminal deoxynucleotidyl transferase or TdT, an enzyme that will catalyze the addition of dUTPs that are secondarily labeled with a marker. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO 36Cl- uptake assay Measures the alteration in muscimol-stimulated or GABA-induced uptake of 36Cl- in cortical and cerebellar membranes or primary cerebellar granule cell cultures. in_vitro primary cerebellar granule cells cortical membranes cerebellar membranes 36Cl- uptake decrease http://purl.obolibrary.org/obo/GO_0044326 GO http://purl.obolibrary.org/obo/GO_0004890 GO medium The change in membrane conductance can be measured by determining the alteration (i.e., inhibition) in muscimol-stimulated (Banerjee et al. 1999) or GABA-induced uptake (Babot et al. 2007) of 36Cl- in cortical and cerebellar membranes or primary cerebellar granule cell cultures http://purl.obolibrary.org/obo/PR_000001179 PR http://purl.obolibrary.org/obo/GO_0006821 GO Cl- sensitive fluorescent dye assay Measures real-time changes in intracellular chloride concentration using a Cl- sensitive fluorescent dye with UV laser scanning confocal microscopy. in_vitro intracellular chloride concentration change http://purl.obolibrary.org/obo/GO_0044326 GO medium Inglefield and Schwartz-Bloom (1998) reported a Cl- sensitive fluorescent dye-based method where to measure real-time changes in intracellular chloride concentration with UV laser scanning confocal microscopy. http://purl.obolibrary.org/obo/CHEBI_17996 CHEBI http://purl.obolibrary.org/obo/GO_0006821 GO ChREBP activation assay Measures the activation of ChREBP, a transcription factor that enhances lipogenic gene expression, through the up-regulation of target genes such as L-PK. not_specified liver mice ChREBP activation increase not_specified ChREBP is an LXR target that independently enhances the up-regulation of select lipogenic genes. activation of LXR not only increases ChREBP mRNA via enhanced transcription but also modulates its activity ChREBP mediates activation of several regulatory enzymes of glycolysis and lipogenesis including L-PK, acetyl CoA carboxylase (ACC), and fatty acid synthase (FAS). enzyme activity measurement This assay measures the activity of regulatory enzymes of glycolysis and lipogenesis, including L-PK, ACC, and FAS, to assess ChREBP-mediated activation in the liver. in_vivo liver mouse activity of L-PK, ACC, and FAS increase low However, according to the study of Denechaud increase in the glucose flux in the cell is a prerequisite for ChREBP activation from T0901317 in mice In the liver, ChREBP mediates activation of several regulatory enzymes of glycolysis and lipogenesis including L-PK, acetyl CoA carboxylase (ACC), and fatty acid synthase (FAS). glucose flux assay Measures the increase in glucose flux within cells, which is a prerequisite for ChREBP activation. not_specified mice glucose flux increase not_specified increase in the glucose flux in the cell is a prerequisite for ChREBP activation from T0901317 in mice mRNA quantification This assay measures the mRNA levels of ChREBP, a lipogenic gene, to assess its up-regulation following LXR activation. The study focuses on the enhanced transcription of ChREBP mRNA. in_vivo liver mouse ChREBP mRNA levels increase low ChREBP is an LXR target that independently enhances the up-regulation of select lipogenic genes. The up-regulation of the ChREBP target gene is through liver-type pyruvate kinase (L-PK). activation of LXR not only increases ChREBP mRNA via enhanced transcription http://purl.obolibrary.org/obo/GO_0006955 GO histological staining Histological staining with Masson Trichrome or Picro-sirius red is used to identify and quantify collagen distribution using morphometric analysis. in_vivo collagen distribution and quantity increase http://purl.obolibrary.org/obo/CHEBI_24804 CHEBI low Histological staining with stains such as Masson Trichrome, Picro-sirius red are used to identify the tissue/cellular distribution of collagen, which can be quantified using morphometric analysis both in vivo and in vitro. http://purl.obolibrary.org/obo/GO_0031012 GO http://purl.obolibrary.org/obo/GO_0031012 GO Hydroxyproline assay Colorimetric methods to quantify collagen using the presence of hydroxyproline, a non-proteinogenic amino acid found only in collagen. in_vitro collagen content increase http://purl.obolibrary.org/obo/CHEBI_28872 CHEBI high Hydroxyproline is a non-proteinogenic amino acid formed by the prolyl-4-hydroxylase. Hydroxyproline is only found in collagen and thus, it serves as a direct measure of the amount of collagen present in cells or tissues. Colorimetric methods are readily available and have been extensively used to quantify collagen using this assay http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0032990 GO Hydroxyproline assay Quantifies collagen by measuring hydroxyproline, a non-proteinogenic amino acid unique to collagen, using colorimetric methods. in_vitro hydroxyproline content increase http://purl.obolibrary.org/obo/CHEBI_17257 CHEBI http://purl.obolibrary.org/obo/GO_0005581 GO high Hydroxyproline is a non-proteinogenic amino acid formed by the prolyl-4-hydroxylase. Hydroxyproline is only found in collagen and thus, it serves as a direct measure of the amount of collagen present in cells or tissues. Colorimetric methods are readily available and have been extensively used to quantify collagen using this assay http://purl.obolibrary.org/obo/GO_0005581 GO http://purl.obolibrary.org/obo/GO_0032964 GO Masson Trichrome staining Histological staining to identify tissue/cellular distribution of collagen, quantified using morphometric analysis. in_vivo collagen distribution and quantity increase http://purl.obolibrary.org/obo/OBI_0000385 OBI http://purl.obolibrary.org/obo/GO_0005581 GO medium Histological staining with stains such as Masson Trichrome, Picro-sirius red are used to identify the tissue/cellular distribution of collagen, which can be quantified using morphometric analysis both in vivo and in vitro http://purl.obolibrary.org/obo/GO_0005581 GO http://purl.obolibrary.org/obo/GO_0030198 GO Nuclear run-on assay Determines the transcriptional regulation of alpha1(I) collagen. in_vitro transcriptional activity of alpha1(I) collagen gene increase http://purl.obolibrary.org/obo/OBI_0000623 OBI http://purl.obolibrary.org/obo/GO_0006351 GO low methods to determine the transcriptional regulation of alpha1(I) collagen using a nuclear run-on assay http://purl.obolibrary.org/obo/GO_0006351 GO Picro-sirius red staining Histological staining to identify tissue/cellular distribution of collagen, quantified using morphometric analysis. in_vivo collagen distribution and quantity increase http://purl.obolibrary.org/obo/GO_0005581 GO medium Histological staining with stains such as Masson Trichrome, Picro-sirius red are used to identify the tissue/cellular distribution of collagen, which can be quantified using morphometric analysis both in vivo and in vitro http://purl.obolibrary.org/obo/GO_0005581 GO http://purl.obolibrary.org/obo/GO_0030198 GO Precision cut tissue slices Ex vivo technique using precision cut tissue slices to mimic whole organ response and allow histological assessment. ex_vivo histological changes not_specified low Ex vivo precision cut tissue slices mimic the whole organ response and allow histological assessment, an endpoint of interest in regulatory decision making Precision cut tissue slices (ex vivo) Prepares thin slices of tissue that maintain organ-like architecture, enabling histological assessment of collagen deposition as an endpoint for regulatory decision-making. ex_vivo tissue histological assessment of collagen in tissue slices increase not_specified Ex vivo precision cut tissue slices Precision cut tissue slices mimic the whole organ response and allow histological assessment, an endpoint of interest in regulatory decision making. http://purl.obolibrary.org/obo/GO_0032964 GO Real-time polymerase chain reaction Measures alpha1(I) collagen mRNA levels using real-time PCR. in_vitro alpha1(I) collagen mRNA levels increase http://purl.obolibrary.org/obo/OBI_0000274 OBI medium the measurement of alpha1(I) collagen mRNA levels using real-time polymerase chain reaction http://purl.obolibrary.org/obo/GO_0032964 GO Sircol Collagen Assay Quantifies collagen using Sirius Red F3BA dye that selectively binds to collagen, with signal read at 540 nm. in_vitro collagen quantity increase http://purl.obolibrary.org/obo/GO_0005581 GO high The Serius dye has been used for many decades to detect collagen in histology samples. The Serius Red F3BA selectively binds to collagen and the signal can be read at 540 nm http://purl.obolibrary.org/obo/GO_0005581 GO http://purl.obolibrary.org/obo/GO_0030198 GO Western immunoblotting Measures intact alpha1(I) collagen using antibodies directed to alpha1(I) collagen amino and carboxyl propeptides. in_vitro alpha1(I) collagen protein levels increase http://purl.obolibrary.org/obo/PR_P02452 PR low Western immunoblotting of intact alpha1(I) collagen using antibodies directed to alpha1(I) collagen amino and carboxyl propeptides http://purl.obolibrary.org/obo/PR_P02452 PR http://purl.obolibrary.org/obo/GO_0032964 GO egg count Cumulative fecundity is directly measured through daily egg counts. in_vitro gonad egg count decrease OECD Test No. 240 low In laboratory-based reproduction assays (e.g., OECD Test No. 229; OECD Test No. 240), spawning and cumulative fecundity can be directly measured through daily observation of egg deposition and egg counts. http://purl.obolibrary.org/obo/UBERON_0004648 UBERON http://purl.obolibrary.org/obo/GO_0000003 GO gonado-somatic index Fecundity may be estimated based on gonado-somatic index. in_vivo gonad gonado-somatic index change OECD 2008 low In some cases, fecundity may be estimated based on gonado-somatic index (OECD 2008). http://purl.obolibrary.org/obo/UBERON_0004648 UBERON laboratory-based reproduction assay Measures spawning and cumulative fecundity through daily observation of egg deposition and egg counts. in_vivo cumulative fecundity and spawning decrease OECD Test No. 229; OECD Test No. 240 low In laboratory-based reproduction assays (e.g., OECD Test No. 229; OECD Test No. 240), spawning and cumulative fecundity can be directly measured through daily observation of egg deposition and egg counts. http://purl.obolibrary.org/obo/UBERON_0000991 UBERON http://purl.obolibrary.org/obo/GO_0000003 GO spawning observation Spawning is directly measured through daily observation of egg deposition. in_vitro gonad egg deposition decrease OECD Test No. 229 low In laboratory-based reproduction assays (e.g., OECD Test No. 229; OECD Test No. 240), spawning and cumulative fecundity can be directly measured through daily observation of egg deposition and egg counts. http://purl.obolibrary.org/obo/UBERON_0004648 UBERON http://purl.obolibrary.org/obo/GO_0000003 GO COX1 activity assay Measures COX1 activity using the US EPA ToxCast assay with ID NVS_ENZ_oCOX1. in_vitro ovarian tissue fish COX1 activity decrease http://purl.obolibrary.org/obo/GO_0004122 GO http://purl.obolibrary.org/obo/GO_0006694 GO not_specified COX1 activity - US EPA ToxCast assay id: NVS_ENZ_oCOX1 http://purl.obolibrary.org/obo/PR_000000000 PR http://purl.obolibrary.org/obo/GO_0006694 GO fish ovarian tissue COX activity assay Measures COX activity in prepared fish ovarian tissue. ex_vivo ovary fish COX activity decrease http://purl.obolibrary.org/obo/GO_0004666 GO http://purl.obolibrary.org/obo/UBERON_0000992 UBERON not_specified The preparation of fish ovarian tissue for COX activity assay is described by Lister and Van der Kraak (2008). http://purl.obolibrary.org/obo/PR_000001126 PR http://purl.obolibrary.org/obo/GO_0006693 GO oxygen consumption assay Monitors COX activity by measuring oxygen consumption during the cyclooxygenase reaction. in_vitro oxygen consumption decrease http://purl.obolibrary.org/obo/GO_0004666 GO not_specified the cyclooxygenase (COX) reaction can be monitored by measurement of oxygen consumption http://purl.obolibrary.org/obo/PR_000001126 PR http://purl.obolibrary.org/obo/GO_0006693 GO peroxidase co-substrate oxidation assay Monitors COX activity by measuring peroxidase co-substrate oxidation during the cyclooxygenase reaction. in_vitro peroxidase co-substrate oxidation decrease http://purl.obolibrary.org/obo/GO_0004666 GO http://purl.obolibrary.org/obo/GO_0004601 GO not_specified the cyclooxygenase (COX) reaction can be monitored by measurement of ... peroxidase co-substrate oxidation http://purl.obolibrary.org/obo/PR_000001126 PR http://purl.obolibrary.org/obo/GO_0006693 GO prostaglandin detection assay Monitors COX activity by detecting prostaglandin production during the cyclooxygenase reaction. in_vitro prostaglandin levels decrease http://purl.obolibrary.org/obo/GO_0004666 GO http://purl.obolibrary.org/obo/CHEBI_26225 CHEBI not_specified the cyclooxygenase (COX) reaction can be monitored by ... prostaglandin (PG) detection http://purl.obolibrary.org/obo/PR_000001126 PR http://purl.obolibrary.org/obo/GO_0006693 GO US EPA ToxCast COX2 activity assay Measures COX2 activity using the US EPA ToxCast assay protocol. in_vitro COX2 activity decrease http://purl.obolibrary.org/obo/GO_0004666 GO http://purl.obolibrary.org/obo/PR_000001127 PR US EPA ToxCast assay id: NVS_ENZ_oCOX2 high COX2 activity - US EPA ToxCast assay id: NVS_ENZ_oCOX2 http://purl.obolibrary.org/obo/PR_000001127 PR http://purl.obolibrary.org/obo/GO_0006693 GO ELISA Measures plasma levels of pro-inflammatory cytokines or levels in cell supernatants using enzyme-linked immunosorbent assay (ELISA) with commercial kits. in_vitro plasma levels of pro-inflammatory cytokines not_specified http://purl.obolibrary.org/obo/GO_0001817 GO medium Plasma levels of pro-inflammatory cytokines, or levels in cell supernatants can be analysed by enzyme linked immunosorbent assay (ELISA) using commercial kits [6][3]. http://purl.obolibrary.org/obo/GO_0006954 GO In Situ Hybridization In Situ Hybridization of mRNA in liver tissue is used to measure mRNA levels. ex_vivo liver mRNA levels increase low Equally, In Situ Hybridization of mRNA in liver tissue can be used [5]. http://purl.obolibrary.org/obo/CHEBI_50889 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO In Situ Hybridization Detects mRNA of inflammatory cytokines in liver tissue using In Situ Hybridization. in_vivo liver mRNA levels of inflammatory cytokines in liver tissue not_specified http://purl.obolibrary.org/obo/OBI_0000558 OBI http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low Equally, In Situ Hybridization of mRNA in liver tissue can be used [5]. http://purl.obolibrary.org/obo/GO_0010467 GO MSD multiplex electrochemiluminescent immunoassay Analyzes blood, urine, and breath samples for pro-inflammatory cytokines using a multiplex electrochemiluminescent immunoassay system in a 96-well plate format. in_vitro human levels of pro-inflammatory cytokines in blood, urine, and breath samples not_specified http://purl.obolibrary.org/obo/CHMO_0000620 CHMO high A more advanced system was described recently by using a multiplex immunoassay platform. In a 96 well plate format the authors describe the analysis of blood, urine and breath samples of human volunteers in a Meso Scale Discovery (MSD) multiplex electrochemiluminescent immunoassay system [7]. http://purl.obolibrary.org/obo/GO_0006954 GO multiplex immunoassay Analysis of blood, urine and breath samples using a multiplex electrochemiluminescent immunoassay system (Meso Scale Discovery - MSD). in_vitro blood urine human cytokine levels increase high A more advanced system was described recently by using a multiplex immunoassay platform. In a 96 well plate format the authors describe the analysis of blood, urine and breath samples of human volunteers in a Meso Scale Discovery (MSD) multiplex electrochemiluminescent immunoassay system [7]. http://purl.obolibrary.org/obo/GO_0008568 GO http://purl.obolibrary.org/obo/GO_0006954 GO real-time PCR mRNA expression levels of inflammatory cytokines are determined using real-time PCR. in_vitro mRNA expression levels increase medium mRNA expression levels of inflammatory cytokines can be determined by using real-time PCR as described in [4]. http://purl.obolibrary.org/obo/CHEBI_50889 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO real-time PCR Measures mRNA expression levels of inflammatory cytokines using real-time PCR. in_vitro mRNA expression levels of inflammatory cytokines not_specified medium mRNA expression levels of inflammatory cytokines can be determined by using real-time PCR as described in [4]. http://purl.obolibrary.org/obo/GO_0010467 GO analytical ultracentrifuging Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase medium common techniques include high throughput enzymatic analyses, analytical ultracentrifuging http://purl.obolibrary.org/obo/CHEBI_15841 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO biochemical compound quantification Quantification of triglycerides, cholesterols, fatty acids, and related compounds in cells to assess levels in control versus potentially affected individuals. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase http://purl.obolibrary.org/obo/CHEBI_17783 CHEBI http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/CHEBI_15489 CHEBI high Increases in fatty acid synthesis are generally measured by increases in triglycerides, fatty acids, cholesterols, and similar compounds in cells. Concentrations of triglycerides, cholesterols, fatty acids, and related compounds are measured biochemically to assess levels in control versus potentially affected individuals; common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis, Nuclear Magnetic Resonance, lipidomics, and other direct assessment techniques (Schaefer et al. 2016; Yang and Han 2016). http://purl.obolibrary.org/obo/CHEBI_15489 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO gene expression analysis Assesses gene expression levels to attribute plausibility to changes in influx, efflux, synthesis, and/or breakdown pathways. in_vitro gene expression levels increase http://purl.obolibrary.org/obo/GO_0006633 GO high Analysis is often performed to look at gene expression levels to see which pathway(s) have increased expression levels, to attribute plausibility to changes in influx, eflux, synthesis, and/or breakdown pathways http://purl.obolibrary.org/obo/GO_0006633 GO gene expression assay Measures mRNA expression levels of genes involved in fatty acid synthesis (e.g., fatty acid synthase) to attribute changes in lipid levels to increased synthesis. in_vitro gene expression levels of fatty acid synthesis-associated genes increase http://purl.obolibrary.org/obo/GO_0010467 GO medium Analysis is often performed to look at gene expression levels to see which pathway(s) have increased expression levels, to attribute plausibility to changes in influx, eflux, synthesis, and/or breakdown pathways (Nguyen et al. 2008; Mellor et al. 2016, Aguayo-Orozco et al. 2018). http://purl.obolibrary.org/obo/GO_0006633 GO gradient gel electrophoresis Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase medium common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis http://purl.obolibrary.org/obo/CHEBI_15841 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO high throughput enzymatic analyses Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase high Concentrations of triglycerides, cholesterols, fatty acids, and related compounds are measured biochemically to assess levels in control versus potentially affected individuals; common techniques include high throughput enzymatic analyses http://purl.obolibrary.org/obo/CHEBI_15841 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO lipidomics Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase high common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis, Nuclear Magnetic Resonance, lipidomics http://purl.obolibrary.org/obo/CHEBI_15841 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO membrane integrity assessment Assesses cellular membrane integrity to evaluate alteration of normal function within cells. in_vitro membrane integrity change http://purl.obolibrary.org/obo/GO_0005886 GO medium Assessment of cellular components including mitochondria and membrane integrity can also be used as evidence of alteration of normal function within cells http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0061024 GO mitochondria assessment Assesses cellular components including mitochondria to evaluate alteration of normal function within cells. in_vitro mitochondrial integrity and function change http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0008108 GO medium Assessment of cellular components including mitochondria and membrane integrity can also be used as evidence of alteration of normal function within cells http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0008108 GO Nuclear Magnetic Resonance Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase medium common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis, Nuclear Magnetic Resonance http://purl.obolibrary.org/obo/CHEBI_15841 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO 32P post-labeling, HPLC and immunologic detection A combination method using 32P post-labeling, HPLC, and immunologic detection to quantify DNA adducts. in_vitro somatic cells DNA adducts increase http://purl.obolibrary.org/obo/GO_0016291 GO not_specified a combination of 32P post-labeling, HPLC and immunologic detection (Kang et al. 1992) http://purl.obolibrary.org/obo/CHEBI_36645 CHEBI http://purl.obolibrary.org/obo/GO_0016291 GO HPLC High performance liquid chromatography methods are used to measure alkyl adducts in somatic cells. in_vitro alkyl adducts not_specified medium High performance liquid chromatography (HPLC) methods can be used to measure whether an agent is capable of alkylating DNA in somatic cells. Alkyl adducts in somatic cells can be measured using immunological methods (described in Nehls et al. 1984), as well as HPLC (methods in de Groot et al. 1994) or a combination of 32P post-labeling, HPLC and immunologic detection (Kang et al. 1992). HPLC DNA adduct formation is determined after neutral and acid hydrolysis of DNA followed by separation of the various ethylation products using HPLC. in_vitro germ cells testis rodent ethylation products increase medium DNA adduct formation is determined after neutral and acid hydrolysis of DNA followed by separation of the various ethylation products using HPLC (described in van Zeeland et al. 1990). http://purl.obolibrary.org/obo/CHEBI_0001367 CHEBI http://purl.obolibrary.org/obo/GO_0006306 GO immunohistocytological staining Fixed testes are incubated with O6-EtGua-specific mouse monoclonal antibody and subsequently with a labeled anti-mouse IgG F antibody. Nuclear DNA is counterstained with DAPI. Fluorescence signals from immunostained O6-EtGua residues in DNA are visualized by fluorescence microscopy and quantitated using an image analysis system. in_vivo testes rodent O6-EtGua residues not_specified low In rodent testes, studies have detected adducts in situ by immuhistocytological staining. For example, fixed testes are incubated with O6-EtGua -specific mouse monoclonal antibody and subsequently with a labeled anti-mouse IgG F antibody. Nuclear DNA is counterstained with DAPI 4,6-diamidino- 2-phenylindole. Fluorescence signals from immunostained O6-EtGua residues in DNA are visualized by fluorescence microscopy and quantitated using an image analysis system. Methods are described in (Seiler et al. 1997). immunological methods Immunological methods are used to measure alkyl adducts in somatic cells. in_vitro alkyl adducts not_specified medium Alkyl adducts in somatic cells can be measured using immunological methods (described in Nehls et al. 1984), as well as HPLC (methods in de Groot et al. 1994) or a combination of 32P post-labeling, HPLC and immunologic detection (Kang et al. 1992). immunoslot blot assay An immunoslot blot assay for detection of O6-EtGua. in_vivo testes rodent O6-EtGua residues not_specified medium An immunoslot blot assay for detection of O6-EtGua has been described previously in (Mientjes et al. 1996). mass spectrometry Provides structural specificity and confirmation of DNA adduct structures by measuring mass-to-charge ratios of adducted nucleotides. in_vitro somatic cells DNA adduct structure increase medium We note that mass spectrometry provides structural specificity and confirmation of the structure of DNA adducts. modified comet assay A modified comet assay involving digestion of alkylated DNA bases with 3-methyladenine DNA glycosylase followed by the standard comet assay to detect alkyl adducts. in_vivo alkyl adducts not_specified OECD guideline for the alkaline version of the comet assay medium DNA alkylation can also be measured using a modified comet assay. This method involves the digestion of alkylated DNA bases with 3–methyladenine DNA glycosylase (Collins et al., 2001; Hasplova et al., 2012) followed by the standard comet assay to detect where alkyl adducts occur. The advantage of this method is that the alkaline version of the comet assay, as a core method, has an in vivo OECD guideline. radio-labeled alkylating agents Rodents are exposed to radio-labeled alkylating agents, and DNA adduct formation is determined after neutral and acid hydrolysis of DNA followed by separation of the various ethylation products using HPLC. in_vivo germ cells testes rodent DNA adduct formation not_specified low Alternatively, rodents have also been exposed to radio-labeled alkylating agents. Examples from the literature include [2-3H] ENU, [1-3H]di-ethyl sulfate, or [1-3H]ethyl-methane sulfonate. Following treatment with the labeled chemical, testis and other tissues of interest are removed. Germ cells are released from tubuli by pushing out the contents with forceps. Using this procedure all germ-cell stages are liberated from the tubuli, with the possible exception of part of the population of stem-cell spermatogonia that remain attached to the walls of the tubuli. DNA is then extracted from germ cells, empty testis tubuli and other tissues of interest. DNA adduct formation is determined after neutral and acid hydrolysis of DNA followed by separation of the various ethylation products using HPLC (described in van Zeeland et al. 1990). radio-labeled chemical exposure followed by HPLC Exposure of rodents to radio-labeled alkylating agents, followed by DNA extraction and separation of ethylation products using HPLC. in_vivo germ cells testis rodent DNA adduct formation increase http://purl.obolibrary.org/obo/GO_0016291 GO low Alternatively, rodents have also been exposed to radio-labeled alkylating agents. ... DNA adduct formation is determined after neutral and acid hydrolysis of DNA followed by separation of the various ethylation products using HPLC (described in van Zeeland et al. 1990). http://purl.obolibrary.org/obo/CHEBI_36645 CHEBI http://purl.obolibrary.org/obo/GO_0016291 GO structure-activity relationships (SARs) Structure-activity relationships are used to predict the possibility that a chemical will alkylate DNA. in_silico probability of DNA alkylation not_specified high Structure-activity relationships (SARs) have been developed to predict the possibility that a chemical will alkylate DNA (e.g., Vogel and Ashby, 1994; Benigni, 2005; Dai et al., 1989; Lewis and Griffith, 1987). Cell Respiration Assay Measures cellular oxygen consumption and uptake using a Clark oxygen electrode in a thermostatic water-jacketed vessel. in_vitro PC12 cells oxygen consumption decrease http://purl.obolibrary.org/obo/GO_0045333 GO low Cell respiration is determined polarographically with the help of a Clark oxygen electrode in a thermostatic water-jacketed vessel with magnetic stirring at 37°C. PC12 cells (10^7 cells) were incubated in 10 mL of the complete DMEM medium (with serum) in Petri dishes for different lengths of time with various concentrations of the corresponding heavy metal, then collected by centrifugation and transferred to the DMEM medium without serum. http://purl.obolibrary.org/obo/CL_0000189 CL http://purl.obolibrary.org/obo/GO_0045333 GO Cytochrome c binding domain determination Measures the identification of the inhibitory site of Cd in mitochondrial complex III by assessing cytochrome c binding. in_vitro mitochondria cytochrome c binding change http://purl.obolibrary.org/obo/GO_0005506 GO http://purl.obolibrary.org/obo/GO_0005750 GO medium Cytochrome c binding domain determination was performed in 2 ml of an assay mixture containing 30 mM phosphate, 100 mM KCl, 2 mM KCN, and 0.1% DM, pH 7.0. The reaction was started with addition of cytochrome c. http://purl.obolibrary.org/obo/GO_0005750 GO http://purl.obolibrary.org/obo/GO_0022900 GO Cytochrome c binding domain determination Identifies the inhibitory site of Cadmium (Cd) in Complex III by measuring the binding of DBH2 or the reaction with cytochrome c in an assay mixture. in_vitro identification of the inhibitory site not_specified not_specified Cytochrome c binding domain determination was performed in 2 ml of an assay mixture containing 30 mM phosphate, 100 mM KCl, 2 mM KCN, and 0.1% DM, pH 7.0. The final concentration of the mitochondrial protein was 13.7 mg/ml. The reaction was started with addition of cytochrome c. DBH2 binding determination was done in the same reaction system as described above. Enzyme Activity Determination Measures the enzymatic activities of mitochondrial complexes I to IV using dual wavelength spectrophotometry. in_vitro mitochondria enzyme activity decrease http://purl.obolibrary.org/obo/GO_0005747 GO http://purl.obolibrary.org/obo/GO_0005749 GO http://purl.obolibrary.org/obo/GO_0005750 GO http://purl.obolibrary.org/obo/GO_0005751 GO low Enzymatic activities of the complexes I to IV were determined by dual wavelength spectrophotometry with an Aminco Dual Wavelength 2 ATM UV-VIS spectrophotometer. Complex I (NADH:ubiquinone oxidoreductase) activity was determined at 340 nm with 380 nm as reference wavelength. Complex II (succinate dehydrogenase) activity was determined by the difference in absorbency between 270 and 330 nm. Complex III (Ubiquinol-cytochrome c reductase) activity was determined by the difference in absorbency between 550 and 580 nm. Complex IV (cytochrome c oxidase) activity was determined by the difference in absorbency between 550 and 580 nm. http://purl.obolibrary.org/obo/GO_0005746 GO http://purl.obolibrary.org/obo/GO_0022900 GO Enzyme Activity Determination (Complex I) Determines Complex I (NADH:ubiquinone oxidoreductase) activity by measuring the rate of decrease of NADH at 340 nm. in_vitro rate of decrease of NADH decrease not_specified Complex I (NADH:ubiquinone oxidoreductase) activity was determined at 340 nm with 380 nm as reference wavelength The activity was calculated from the rate of decrease of NADH http://purl.obolibrary.org/obo/GO_0006117 GO Enzyme Activity Determination (Complex II) Determines Complex II (succinate dehydrogenase) activity by measuring the difference in absorbency between 270 and 330 nm due to the rate of decrease in ubiquinone. in_vitro rate of decrease in ubiquinone decrease not_specified Complex II (succinate dehydrogenase) activity was determined by the difference in absorbency between 270 and 330 nm The activity was calculated from the rate of decrease in ubiquinone http://purl.obolibrary.org/obo/GO_0006117 GO Enzyme Activity Determination (Complex III) Determines Complex III (Ubiquinol-cytochrome c reductase) activity by measuring the rate of reduction of cytochrome cIII between 550 and 580 nm. in_vitro rate of reduction of cytochrome cIII change not_specified Complex III (Ubiquinol-cytochrome c reductase) activity was determined by the difference in absorbency between 550 and 580 nm The activity was calculated from the rate of reduction of cytochrome cIII http://purl.obolibrary.org/obo/GO_0006117 GO Luciferin-luciferase assay Measures ATP content of cells using a bioluminescent assay where luciferin and luciferase are used to quantify ATP levels. in_vitro HL-60 cells ATP content decrease http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0003684 GO high For ATP measurement, a commercially available luciferin-luciferase assay kit was used. HL-60 cells were treated with various concentrations of rotenone for 24 h and then collected. Whole-cell ATP content was determined by running an internal standard. http://purl.obolibrary.org/obo/CL_0000195 CL http://purl.obolibrary.org/obo/GO_0046034 GO MTT Measures the enzymatic activity of mitochondrial complex II by the reduction of MTT to a blue formazan compound, indicating mitochondrial metabolic activity. in_vitro mitochondrial suspensions mitochondria not_specified mitochondrial complex II activity decrease medium The metabolic activity of mitochondrial complex II was assayed by measuring the reduction of MTT to a blue formazan compound. Mitochondrial suspensions were incubated with different concentrations of uranyl acetate prior to addition of MTT. The product of formazan crystals were dissolved in DMSO and the absorbance at 570nm was measured with an ELISA reader. MTT assay Measures the enzymatic activity of the electron transport system by assessing the reduction of MTT to a blue formazan compound, indicating mitochondrial complex II activity. in_vitro mitochondria MTT reduction to formazan decrease http://purl.obolibrary.org/obo/GO_0022900 GO medium The metabolic activity of mitochondrial complex II was assayed by measuring the reduction of MTT to a blue formazan compound. Mitochondrial suspensions were incubated with different concentrations of uranyl acetate prior to addition of MTT. http://purl.obolibrary.org/obo/GO_0005749 GO http://purl.obolibrary.org/obo/GO_0022900 GO Spectrophotometric Enzyme Activity Assay Determines enzymatic activities of mitochondrial respiratory chain complexes I to IV using dual wavelength spectrophotometry to measure substrate reduction or product oxidation rates. in_vitro enzymatic activities of complexes I to IV decrease not_specified Enzyme Activity Determination Enzymatic activities of the complexes I to IV were determined by dual wavelength spectrophotometry with an Aminco Dual Wavelength 2 ATM UV-VIS spectrophotometer (Silver Spring, MD). Complex I (NADH:ubiquinone oxidoreductase) activity was determined at 340 nm with 380 nm as reference wavelength, with a slit width of 3.0 nm according to Estornell et al. (1993). AhR reporter assay An in vitro assay that measures Aryl Hydrocarbon Receptor (AhR) activity using a reporter gene. in_vitro not specified AhR activity change http://purl.obolibrary.org/obo/PR_000000047 PR medium The pVDC signature includes features for the basic helix-loop-helix transcription factors Aryl Hydrocarbon Receptor (AhR) [...] that are upstream regulators of VEGF gene expression during ischemia or hypoxia. [...] are measured in reporter assays (Attagene). http://purl.obolibrary.org/obo/PR_000000047 PR http://purl.obolibrary.org/obo/GO_0006351 GO angiogenesis assays In vitro cell-based assays that score various parameters of endothelial cell movement and network formation. in_vitro human umbilical endothelial cells HUVECs endothelial cells derived from human induced pluripotent stem cells iPSC-ECs human endothelial cell migration, cell counts, tubule counts, tubule length, tubule area, tubule intensity, and node counts change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/GO_0050853 GO medium Endothelial network formation can be monitored quantitatively in vitro using different human cell-based angiogenesis assays that score endothelial cell migration, cell counts, tubule counts, tubule length, tubule area, tubule intensity, and node counts http://purl.obolibrary.org/obo/CL_0000071 CL http://purl.obolibrary.org/obo/GO_0001525 GO Attagene reporter gene assay A reporter gene assay used to measure nuclear factor-kappa B (NFkB) activation, HIF1a, AhR, and ERa trans-activation. in_vitro reporter gene activation change http://purl.obolibrary.org/obo/GO_0006359 GO not_specified nuclear factor-kappa B (NFkB) mediated reporter gene activation (Attagene; cis- configuration) http://purl.obolibrary.org/obo/GO_0006351 GO Beta-catenin nuclear localization assay An in vitro assay that measures nuclear localization of beta-catenin (CTNB) in HUVEC cells. in_vitro HUVECs human beta-catenin nuclear localization change http://purl.obolibrary.org/obo/PR_000000660 PR medium Assays for nuclear localization of beta-catenin (CTNB) are based on the principle that nuclear translocation activates pathways important for endothelial cell migration, proliferation and survival during capillary network formation in HUVEC cells http://purl.obolibrary.org/obo/PR_000000660 PR http://purl.obolibrary.org/obo/GO_0016477 GO BioMAP Systems Predictive Toxicology panel An in vitro assay that measures chemical disruption of endothelial VCAM1 expression following stimulation by cytokines-growth factors. in_vitro HUVECs primary human coronary artery smooth muscle cells human dermal fibroblasts human VCAM1 expression change http://purl.obolibrary.org/obo/PR_000001859 PR http://purl.obolibrary.org/obo/CL_0000115 CL medium the pVDC signature aggregates assays from the BioMAP Systems Predictive Toxicology panel [Kunkel et al., 2004; Houck et al., 2009] focusing here on chemical disruption of endothelial VCAM1 expression following stimulation by cytokines-growth factors. http://purl.obolibrary.org/obo/PR_000001859 PR http://purl.obolibrary.org/obo/GO_0006954 GO Caspase 8 enzymatic activity assay An in vitro assay that measures caspase 8 enzymatic activity. in_vitro not specified caspase 8 enzymatic activity change http://purl.obolibrary.org/obo/PR_000001011 PR medium the pVDC signature aggregates features for caspase 8 enzymatic activity http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0006915 GO chick chorioallantoic membrane assay An animal model used to preserve biological complexity in studying vascular processes. in_vivo chorioallantoic membrane chick biological complexity of vascular processes not_specified low Animal models, including the chick chorioallantoic membrane assay, corneal neovascularization assay, and 3D embedded matrices preserve biological complexity but are costly and low throughput Chick chorioallantoic membrane assay An in vivo assay to study angiogenesis and vascular disruption in the chick chorioallantoic membrane. in_vivo chorioallantoic membrane chick neovascularization change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/UBERON_0000987 UBERON low Animal models, including the chick chorioallantoic membrane assay, corneal neovascularization assay, and 3D embedded matrices preserve biological complexity but are costly and low throughput http://purl.obolibrary.org/obo/UBERON_0000987 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO Chick chorioallantoic membrane assay An animal model assay used to preserve biological complexity for studying vascular disruption, noted as costly and low throughput. in_vivo chorioallantoic membrane Gallus gallus vascular disruption change low Animal models, including the chick chorioallantoic membrane assay, corneal neovascularization assay, and 3D embedded matrices preserve biological complexity but are costly and low throughput corneal neovascularization assay An animal model used to study the formation of new blood vessels in the cornea. in_vivo cornea corneal neovascularization not_specified low Animal models, including the chick chorioallantoic membrane assay, corneal neovascularization assay, and 3D embedded matrices preserve biological complexity but are costly and low throughput Corneal neovascularization assay An in vivo assay to study angiogenesis and vascular disruption in the cornea. in_vivo cornea not specified neovascularization change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/UBERON_0001798 UBERON low Animal models, including the chick chorioallantoic membrane assay, corneal neovascularization assay, and 3D embedded matrices preserve biological complexity but are costly and low throughput http://purl.obolibrary.org/obo/UBERON_0001798 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO EPH-receptor tyrosine kinase activity assay An in vitro assay that measures EPH-receptor tyrosine kinase activity. in_vitro not specified EPH-receptor tyrosine kinase activity change http://purl.obolibrary.org/obo/PR_000001215 PR medium The ToxCast pVDC signature included features for EPH-receptor tyrosine kinase biochemical activity (increased or decreased) for receptors EPHA1, EPHA2, EPHB1 and EPHB2 via their cognate cell membrane-anchored ligands (EFNAs). http://purl.obolibrary.org/obo/PR_000001215 PR http://purl.obolibrary.org/obo/GO_0001525 GO ERa binding activity assay An in vitro assay that measures estrogen receptor alpha (ERa) binding activity. in_vitro human ERa binding activity change http://purl.obolibrary.org/obo/PR_000000130 PR medium The pVDC signature has features for the estrogen receptor alpha (ERa), also a trans-activator of VEGF expression. This included human ERa binding activity (NovaScreen), ERa reporter trans-activation (Attagene) and ERE (estrogen responsive element) reporter cis-activation (Attagene). http://purl.obolibrary.org/obo/PR_000000130 PR http://purl.obolibrary.org/obo/GO_0006351 GO HUVEC-based angiogenesis assay Quantitatively monitors endothelial network formation in vitro by scoring endothelial cell migration, cell counts, tubule counts, tubule length, tubule area, tubule intensity, and node counts. in_vitro human umbilical endothelial cells (HUVECs) endothelial cells derived from human induced pluripotent stem cells (iPSC-ECs) human endothelial network formation change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/CL_0000115 CL medium Endothelial network formation can be monitored quantitatively in vitro using different human cell-based angiogenesis assays that score endothelial cell migration, cell counts, tubule counts, tubule length, tubule area, tubule intensity, and node counts http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0001525 GO LPS-induced TNFα protein expression assay An in vitro assay that measures LPS-induced TNFα protein expression. in_vitro not specified TNFα protein expression change http://purl.obolibrary.org/obo/PR_000000959 PR medium the pVDC signature aggregates features for LPS-induced TNFα protein expression http://purl.obolibrary.org/obo/PR_000000959 PR http://purl.obolibrary.org/obo/GO_0006954 GO MMP activity assay An in vitro assay that measures matrix metalloproteinases (MMPs) 1/2/9 activity. in_vitro not specified MMP activity change http://purl.obolibrary.org/obo/PR_000001575 PR medium Matrix metalloproteinases (MMPs) 1/2/9 aggregate features on biochemical activity and cellular function of zinc-dependent endopeptidases MMP1, MMP2 and MMP9 that facilitate angiogenesis through ECM degradation by activated endothelial cells. http://purl.obolibrary.org/obo/PR_000001575 PR http://purl.obolibrary.org/obo/GO_0022617 GO NFkB reporter gene activation assay An in vitro assay that measures NFkB-mediated reporter gene activation. in_vitro not specified NFkB-mediated reporter gene activation change http://purl.obolibrary.org/obo/PR_000001236 PR medium the pVDC signature aggregates features for nuclear factor-kappa B (NFkB) mediated reporter gene activation http://purl.obolibrary.org/obo/PR_000001236 PR http://purl.obolibrary.org/obo/GO_0003700 GO NovaScreen biochemical profile A biochemical assay platform used to measure caspase 8 enzymatic activity, receptor tyrosine kinase activity, and estrogen receptor binding/trans-activation. in_vitro enzymatic activity and receptor binding change not_specified caspase 8 enzymatic activity (NovaScreen; inhibition or activation) based on receptor kinase activity (RTK, inhibition or activation) from the NovaScreen biochemical profile http://purl.obolibrary.org/obo/GO_0006915 GO PTEN activity assay An in vitro assay that measures phosphatase and tensin homolog (PTEN) activity. in_vitro not specified PTEN activity change http://purl.obolibrary.org/obo/PR_000001645 PR medium The signature has features for the anti-angiogenic phosphatases PTEN (phosphatase and tensin homolog), PTPN11 (tyrosine-protein phosphatase non-receptor type 11) and PTPN12, and endothelial-specific receptor tyrosine protein phosphatase beta (PTPRB). http://purl.obolibrary.org/obo/PR_000001645 PR http://purl.obolibrary.org/obo/GO_0001525 GO rat fetal aortic explant assay An ex vivo assay measuring microvessel outgrowth in rat fetal aortic tissues. ex_vivo aortic explants rat microvessel outgrowth change not_specified microvessel outgrowth in rat fetal aortic explants [Ellis-Hutchings et al. 2017] http://purl.obolibrary.org/obo/GO_0001525 GO TBXA2 receptor binding assay An in vitro assay that measures thromboxane A2 (TBXA2) receptor binding. in_vitro not specified TBXA2 receptor binding change http://purl.obolibrary.org/obo/PR_000001875 PR medium TBXA2 was assayed for ligand binding in the NovaScreen platform. http://purl.obolibrary.org/obo/PR_000001875 PR http://purl.obolibrary.org/obo/GO_0001525 GO THBD protein expression assay An in vitro assay that measures thrombomodulin (THBD) protein expression. in_vitro HUVECs primary human coronary artery smooth muscle cells human THBD protein expression change http://purl.obolibrary.org/obo/PR_000001796 PR medium THBD protein expression was monitored in the 3C and CASM3C BioMAP systems http://purl.obolibrary.org/obo/PR_000001796 PR Tie2 activity assay An in vitro assay that measures Tie2 receptor tyrosine kinase activity. in_vitro not specified Tie2 activity change http://purl.obolibrary.org/obo/PR_000001610 PR medium The signature has features for [...] Tie2 - a receptor tyrosine kinase activated by the angiopoietins (ANG1, ANG2) that function stabilize nascent vasculature. http://purl.obolibrary.org/obo/PR_000001610 PR http://purl.obolibrary.org/obo/GO_0001525 GO Transgenic endothelial reporter zebrafish assay Use of endothelial-specific transgenic zebrafish reporter embryos to combine biological complexity with automated high-throughput screening for vascular disruption. in_vivo vasculature Danio rerio endothelial network formation change high Endothelial-specific transgenic zebrafish reporter embryos thus provide a test system that combines the biological complexity of in vivo models with automated high-throughput screening (HTS). transgenic endothelial reporter zebrafish lines transgenic zebrafish reporter embryos Endothelial-specific transgenic zebrafish models used for automated high-throughput screening of vascular development. in_vivo endothelial cells zebrafish vascular development/complexity not_specified high Endothelial-specific transgenic zebrafish reporter embryos thus provide a test system that combines the biological complexity of in vivo models with automated high-throughput screening (HTS). http://purl.obolibrary.org/obo/CL_0000071 CL http://purl.obolibrary.org/obo/GO_0001525 GO uPA/uPAR assay An in vitro assay that measures urokinase-type plasminogen activator (uPA) and its receptor (uPAR) activity. in_vitro HUVECs primary human coronary artery smooth muscle cells human dermal fibroblasts human bronchial epithelial cells human keratinocytes fibroblasts human uPA/uPAR activity change http://purl.obolibrary.org/obo/PR_000001709 PR http://purl.obolibrary.org/obo/PR_000001710 PR medium a number of chemicals had activity on diverse assays for urokinase-type plasminogen activator (uPA). That system, consisting of uPA (4 features) and its GPI-anchored receptor, uPAR (8 features) - both assayed in the BioMAP System http://purl.obolibrary.org/obo/GO_0022617 GO VCAM1 expression assay Measures chemical disruption of endothelial VCAM1 expression following stimulation by cytokines-growth factors in several cell systems. in_vitro HUVECs human coronary artery smooth muscle cells human dermal fibroblasts endothelium human VCAM1 expression decrease medium This assay endpoint is an in vitro surrogate for inflammatory cell recruitment per endothelial dysfunction and has been probed across five different cell systems...focusing here on chemical disruption of endothelial VCAM1 expression following stimulation by cytokines-growth factors. http://purl.obolibrary.org/obo/GO_0006954 GO VEGFR kinase activity assay An in vitro assay that measures VEGFR kinase activity. in_vitro not specified VEGFR kinase activity change http://purl.obolibrary.org/obo/PR_000001214 PR medium The pVDC signature has features for liganding VEGFR1, VEGFR2, and VEGFR3 based on receptor kinase activity http://purl.obolibrary.org/obo/PR_000001214 PR http://purl.obolibrary.org/obo/GO_0001525 GO zebrafish reporter assay Endothelial-specific transgenic zebrafish reporter embryos provide a test system that combines the biological complexity of in vivo models with automated high-throughput screening (HTS). in_vivo endothelial cells embryo zebrafish reporter gene expression change high Endothelial-specific transgenic zebrafish reporter embryos thus provide a test system that combines the biological complexity of in vivo models with automated high-throughput screening (HTS). http://purl.obolibrary.org/obo/CL_0002049 CL http://purl.obolibrary.org/obo/GO_0001545 GO BG1Luc Estrogen Receptor Transactivation Test A transactivation in vitro assay used to identify estrogen receptor agonists and antagonists. in_vitro transcriptional activation change OECD Test No. 457 not_specified OECD Test No. 457: BG1Luc Estrogen Receptor Transactivation Test Method for Identifying Estrogen Receptor Agonists and Antagonists (OECD 2012). http://purl.obolibrary.org/obo/GO_0045903 GO ER ToxCast high-throughput screening assay panel Panel of 18 high-throughput assays measuring ER binding, dimerization, chromatin binding, transcriptional activation, and ER-dependent cell proliferation to predict ER agonist/antagonist activity. in_vitro ER binding, dimerization, chromatin binding, transcriptional activation, ER-dependent cell proliferation change high Browne et al. (2015) integrated 18 ER ToxCast high-throughput screening (HTS) assays, measuring ER binding, dimerization, chromatin binding, transcriptional activation and ER-dependent cell proliferation, into the ToxCast ER pathway model. http://purl.obolibrary.org/obo/GO_0007165 GO ERα CALUX ER-based transactivation assay using ERα CALUX cell line to detect ER agonists and antagonists. in_vitro ERα CALUX estrogen receptor transactivation change not_specified ER-based transactivation assays that have been used to detect ER agonists and antagonist using cell lines include T47D-Kbluc assay (Wehmas et al., 2011), the ERα CALUX assay (Van et al.); MELN assay (Berckmans et al., 2007); and the yeast estrogen screen (YES; (De Boever et al., 2001)). ERα CALUX assay Measures ERα-mediated transcriptional activation using luciferase reporter to detect agonists and antagonists. in_vitro luciferase activity change medium ERα CALUX assay (Van et al.) http://purl.obolibrary.org/obo/GO_0006355 GO ERα CALUX assay ER-based transactivation assay used to detect ER agonists and antagonists. in_vitro transactivation increase not_specified ER-based transactivation assays that have been used to detect ER agonists and antagonist using cell lines include... the ERα CALUX assay (Van et.) MELN ER-based transactivation assay using MELN cell line to detect ER agonists and antagonists. in_vitro MELN estrogen receptor transactivation change not_specified ER-based transactivation assays that have been used to detect ER agonists and antagonist using cell lines include T47D-Kbluc assay (Wehmas et al., 2011), the ERα CALUX assay (Van et al.); MELN assay (Berckmans et al., 2007); and the yeast estrogen screen (YES; (De Boever et al., 2001)). MELN assay ER-based transactivation assay used to detect ER agonists and antagonists. in_vitro transactivation increase not_specified ER-based transactivation assays that have been used to detect ER agonists and antagonist using cell lines include... MELN assay (Berckmans et al., 2007) SEP ER transcriptional activation assay (HeLa-9903) Measures estrogen receptor-mediated transcriptional activation in HeLa-9903 human cells to detect agonists and antagonists. in_vitro HeLa-9903 Homo sapiens transcriptional activation change medium Standard Evaluation Procedure (SEP) for estrogen receptor transcriptional activation (Human Cell Line HeLa-9903) assay was developed by the U.S. Environmental Protection Agency (EPA). http://purl.obolibrary.org/obo/GO_0006355 GO T47D-Kbluc assay The T47D-Kbluc assay detects ER agonists and antagonists and responds to both ERα and ERß agonists. in_vitro T47D-Kbluc reporter gene expression increase http://purl.obolibrary.org/obo/GO_0005694 GO high ER-based transactivation assays that have been used to detect ER agonists and antagonist using cell lines include T47D-Kbluc assay (Wehmas et al., 2011), the ERα CALUX assay (Van et al.); MELN assay (Berckmans et al., 2007); and the yeast estrogen screen (YES; (De Boever et al., 2001)). The T47D-Kbluc assay responds to both ERα and ERß agonists but support the assumption that ERα is inducing more reporter expression than ERß. http://purl.obolibrary.org/obo/CHEBI_51523 CHEBI http://purl.obolibrary.org/obo/GO_0005694 GO Uterotrophic Bioassay An in vivo screening test to detect estrogenic properties in rodents by observing uterine response. in_vivo uterus estrogenic activity change OECD TG 440 not_specified OECD Test No. 440: Uterotrophic Bioassay in Rodents: A Short-Term Screenign Test for Oestrogenic Properties. OCED Publishing. 2018. has been used to detect in vivo estrogenic activity. http://purl.obolibrary.org/obo/UBERON_0000233 UBERON yeast estrogen screen (YES) A screening assay using yeast to detect estrogenic activity. in_vitro yeast estrogen receptor activity change http://purl.obolibrary.org/obo/GO_0005484 GO not_specified yeast estrogen screen (YES; (De Boever et al., 2001)) http://purl.obolibrary.org/obo/CHEBI_15453 CHEBI http://purl.obolibrary.org/obo/GO_0006355 GO Yeast estrogen screen (YES) Uses yeast engineered with estrogen receptor and reporter gene to detect estrogenic agonists/antagonists via reporter gene activity. in_vitro reporter gene activity change medium yeast estrogen screen (YES; (De Boever et al., 2001)) http://purl.obolibrary.org/obo/GO_0006355 GO Yeast estrogen screen (YES) ER-based transactivation assay using yeast to detect ER agonists and antagonists. in_vitro yeast Saccharomyces cerevisiae transactivation increase not_specified ER-based transactivation assays that have been used to detect ER agonists and antagonist using cell lines include... the yeast estrogen screen (YES; (De Boever et al., 2001)). BG1luc The BG1luc estrogen receptor transactivation test method identifies estrogen receptor agonists and antagonists by measuring transactivation. in_vitro estrogen receptor transactivation change OECD TG 457 medium The BG1luc estrogen receptor transactivation test method for identifying estrogen receptor agonists and antagonists (OECD Test Guideline 457) has been validated http://purl.obolibrary.org/obo/CHEBI_51523 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO BG1luc estrogen receptor transactivation test An in vitro assay for identifying estrogen receptor agonists and antagonists using the BG1luc cell line. in_vitro BG1luc human estrogen receptor transactivation change OECD Test Guideline 457 medium The BG1luc estrogen receptor transactivation test method for identifying estrogen receptor agonists and antagonists (OECD Test Guideline 457) has been validated by the National Toxicology Program Interagency Center for Evaluation of Alternative Toxicological Methods (NICEATM) and Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) as an appropriate assay for detecting ER antagonism. ERα CALUX The ERα CALUX assay detects ERα antagonism. in_vitro ERα antagonism decrease medium Other human ER-based transactivation assays that have been used to detect ERα antagonism include the ERα CALUX assay (van der Burg et al. 2010); http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0005102 GO ERα CALUX assay An in vitro assay for detecting ERα antagonism using the CALUX cell line. in_vitro CALUX human ERα transactivation change medium ERα CALUX assay (van der Burg et al. 2010); MELN The MELN assay detects ERα antagonism. in_vitro ERα antagonism decrease medium Other human ER-based transactivation assays that have been used to detect ERα antagonism include the MELN assay (Witters et al. 2010); http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0005102 GO MELN assay An in vitro assay for detecting ERα antagonism using the MELN cell line. in_vitro MELN human ERα transactivation change medium MELN assay (Witters et al. 2010); T47D-Kbluc The T47D-Kbluc assay detects ERα antagonism using a transactivation assay. in_vitro T47D ERα antagonism decrease medium Other human ER-based transactivation assays that have been used to detect ERα antagonism include the T47D-Kbluc assay (Wilson et al. 2004); http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0005102 GO T47D-Kbluc assay An in vitro assay for detecting ERα antagonism using the T47D-Kbluc cell line. in_vitro T47D-Kbluc human ERα transactivation change medium Other human ER-based transactivation assays that have been used to detect ERα antagonism include the T47D-Kbluc assay (Wilson et al. 2004); vitellogenin synthesis in primary fish liver cells An ex vivo assay for screening anti-estrogenic activity by measuring vitellogenin synthesis in primary fish liver cells. ex_vivo primary fish liver cells liver fish vitellogenin synthesis decrease low In aquatic ecotoxicology, vitellogenin synthesis in primary fish liver cells and liver slices has also been used to screen for anti-estrogenic activity (e.g., (Bickley et al. 2009; Navas and Segner 2006; Schmieder et al. 2000; Schmieder et al. 2004; Sun et al. 2010). yeast estrogen screen (YES) The yeast estrogen screen (YES) measures estrogen receptor (ER) antagonism by assessing the ability of test compounds to inhibit ER-mediated transcriptional activity in yeast cells. in_vitro yeast cells ER antagonism decrease http://purl.obolibrary.org/obo/GO_0033594 GO http://purl.obolibrary.org/obo/GO_0010628 GO not_specified not_specified Other human ER-based transactivation assays that have been used to detect ERα antagonism include the T47D-Kbluc assay (Wilson et al. 2004); ERα CALUX assay (van der Burg et al. 2010); MELN assay (Witters et al. 2010); and the yeast estrogen screen (YES; (De Boever et al. 2001)). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0033594 GO yeast estrogen screen (YES) An in vitro assay for detecting ERα antagonism using yeast cells. in_vitro yeast yeast ERα transactivation change medium yeast estrogen screen (YES; (De Boever et al. 2001)). YES Measures estrogen receptor transactivation using yeast cells expressing human estrogen receptor α. in_vitro http://purl.obolibrary.org/obo/NCBITaxon_559292 estrogen receptor α transactivation decrease http://purl.obolibrary.org/obo/GO_0006351 GO not_specified yeast estrogen screen (YES; (De Boever et al. 2001)) http://purl.obolibrary.org/obo/PR_000015750 PR http://purl.obolibrary.org/obo/GO_0006351 GO analytical ultracentrifuging Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically to assess levels in control versus potentially affected individuals. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase medium common techniques include high throughput enzymatic analyses, analytical ultracentrifuging http://purl.obolibrary.org/obo/CHEBI_15904 CHEBI http://purl.obolibrary.org/obo/GO_0015908 GO gene expression analysis Assesses gene expression levels to attribute plausibility to changes in influx, efflux, synthesis, and/or breakdown pathways. in_vitro gene expression levels increase high Analysis is often performed to look at gene expression levels to see which pathway(s) have increased expression levels, to attribute plausibility to changes in influx, eflux, synthesis, and/or breakdown pathways http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO gradient gel electrophoresis Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically to assess levels in control versus potentially affected individuals. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase medium common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis http://purl.obolibrary.org/obo/CHEBI_15904 CHEBI http://purl.obolibrary.org/obo/GO_0015908 GO high throughput enzymatic analyses Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically to assess levels in control versus potentially affected individuals. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase high Concentrations of triglycerides, cholesterols, fatty acids, and related compounds are measured biochemically to assess levels in control versus potentially affected individuals; common techniques include high throughput enzymatic analyses http://purl.obolibrary.org/obo/CHEBI_15904 CHEBI http://purl.obolibrary.org/obo/GO_0015908 GO lipidomics Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically to assess levels in control versus potentially affected individuals. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase high common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis, Nuclear Magnetic Resonance, lipidomics, and other direct assessment techniques http://purl.obolibrary.org/obo/CHEBI_15904 CHEBI http://purl.obolibrary.org/obo/GO_0015908 GO membrane integrity assessment Assessment of plasma membrane stability to provide evidence of altered cellular function. in_vitro plasma membrane stability change http://purl.obolibrary.org/obo/GO_0030606 GO not_specified assessment is generally made for plasma membrane stability Assessment of cellular components including mitochondria and membrane integrity can also be used as evidence of alteration of normal function within cells. http://purl.obolibrary.org/obo/UBERON_0000187 UBERON http://purl.obolibrary.org/obo/GO_0030606 GO mitochondria and membrane integrity assessment Assesses cellular components including mitochondria and membrane integrity as evidence of alteration of normal function within cells. in_vitro mitochondria and membrane integrity change medium Assessment of cellular components including mitochondria and membrane integrity can also be used as evidence of alteration of normal function within cells http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0008217 GO Nuclear Magnetic Resonance Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically to assess levels in control versus potentially affected individuals. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase medium common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis, Nuclear Magnetic Resonance http://purl.obolibrary.org/obo/CHEBI_15904 CHEBI http://purl.obolibrary.org/obo/GO_0015908 GO FAS gene expression analysis Measures the induction of fatty acid synthase (FAS) gene expression in response to LXR agonist treatment. in_vivo Mus musculus FAS gene expression increase http://purl.obolibrary.org/obo/GO_0004312 GO http://purl.obolibrary.org/obo/GO_0010467 GO not_specified LXR agonist treatment has been shown to induce the genes encoding fatty acid synthase (FAS) in SREBP-1c-deficient mice This finding shows that in parallel with the increase of FAS expression from the SREBP-1c and the ChREBP the enzyme is also directly induced from the LXR. http://purl.obolibrary.org/obo/GO_0010467 GO gene expression analysis This assay measures the expression levels of genes encoding fatty acid synthase (FAS) following LXR agonist treatment. The method is not further specified in the text. in_vivo mouse FAS gene expression increase not_specified LXR agonist treatment has been shown to induce the genes encoding fatty acid synthase (FAS) in SREBP-1c-deficient mice This finding shows that in parallel with the increase of FAS expression the enzyme is also directly induced from the LXR. http://purl.obolibrary.org/obo/CHEBI_16644 CHEBI http://purl.obolibrary.org/obo/GO_0010505 GO Attagene GR TRANS Measures glucocorticoid receptor activation in human liver cells, reported in Dexamethasone-equivalents (DEX-EQ). in_vitro Liver Human GR activation increase http://purl.obolibrary.org/obo/GO_0031965 GO high Attagene GR TRANS Human Liver Martin et al., 2010; Medvedev et al., 2018; Romanov et al., 2008 http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO CV1-hGR Measures glucocorticoid receptor activation in human kidney cells, reported in Dexamethasone-equivalents (DEX-EQ). in_vitro Kidney Human GR activation increase http://purl.obolibrary.org/obo/GO_0031965 GO high CV1-hGR Human Kidney Medlock Kakaley et al., 2019 http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO GR CALUX Measures glucocorticoid receptor activation in human osteosarcoma cells, reported in Dexamethasone-equivalents (DEX-EQ). in_vitro Osteosarcoma Human GR activation increase http://purl.obolibrary.org/obo/GO_0031965 GO high GR CALUX Human Osteosarcoma Been et al., 2021; Macikova et al., 2014; Schriks et al., 2010; Suzuki et al., 2015 http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO GR-GeneBlazer Measures glucocorticoid receptor activation in human kidney cells, reported in Dexamethasone-equivalents (DEX-EQ). in_vitro Kidney Human GR activation increase http://purl.obolibrary.org/obo/GO_0031965 GO high GR-GeneBlazer Human Kidney Jia et al., 2016 http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO GR-regulated gene induction Measures induction of GR-regulated genes as an indicator of GR agonism in vivo. in_vivo GR-regulated gene induction increase http://purl.obolibrary.org/obo/GO_0031963 GO http://purl.obolibrary.org/obo/GO_0010467 GO low induction of GR-regulated genes are also indicative of GR agonism in vivo (Cavallin et al., 2021; Cole et al., 2025; Garland et al., 2019) http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO Indigo hGR Measures glucocorticoid receptor activation in human cells, reported in Dexamethasone-equivalents (DEX-EQ). in_vitro Human GR activation increase http://purl.obolibrary.org/obo/GO_0031965 GO high Indigo hGR Human N/A Cavaillin et al., 2021; Cole et al., 2025 http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO NovaScreen NR hGR Measures glucocorticoid receptor activation in human cells, reported in Dexamethasone-equivalents (DEX-EQ). in_vitro Human GR activation increase http://purl.obolibrary.org/obo/GO_0031965 GO high NovaScreen NR hGR Human N/A Knudsen et al., 2011; Sipes et al., 2013 http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO TOX21 GR BLA This assay measures glucocorticoid receptor agonist ratio. in_vitro Cervix Human GR agonist ratio increase not_specified TOX21 GR BLA Agonist Ratio Human Cervix Huang et al., 2011 TOX21 GR BLA Agonist Ratio Measures glucocorticoid receptor activation in human cervical cells, reported in Dexamethasone-equivalents (DEX-EQ). in_vitro Cervix Human GR activation increase http://purl.obolibrary.org/obo/GO_0031965 GO high TOX21 GR BLA Agonist Ratio Human Cervix Huang et al., 2011 http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO Trout GR1 Measures glucocorticoid receptor activation in trout kidney cells, reported in Dexamethasone-equivalents (DEX-EQ). in_vitro Kidney Trout GR activation increase http://purl.obolibrary.org/obo/GO_0031965 GO high Trout GR1 Trout Kidney Kugathas & Sumpter, 2011 http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0031963 GO ELISA Measures circulating concentrations of gonadotropins using enzyme-linked immunosorbent assays. in_vitro human rodents livestock species gonadotropin concentration decrease http://purl.obolibrary.org/obo/CHEBI_38648 CHEBI medium Circulating concentrations of gonadotropins in humans and common mammalian models (e.g., rodents, many livestock species) can be directly measured using either commercial or custom immunoassays (e.g., enzyme-linked immunosorbent assays, radioimmunoassays, etc.) http://purl.obolibrary.org/obo/CHEBI_38648 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO mRNA expression analysis Measures expression levels of mRNAs coding for luteinizing hormone beta subunit (lhb) and follicle-stimulating hormone beta subunit (fshb). in_vivo gonad fish mRNA expression level change low Expression of mRNAs coding for luteinizing hormone beta subunit (lhb) and follicle-stimulating hormone beta subunit (fshb) tend to fluctuate in parallel in repeat-spawning fish and plasma concentrations LH and FSH in tilapia were also shown to fluctuate in parallel (reviewed in (Levavi-Sivan et al. 2010)). http://purl.obolibrary.org/obo/GO_0010468 GO quantitative reverse transcription polymerase chain reaction (qRT-PCR) Measures expression levels of mRNAs coding for luteinizing hormone beta subunit (lhb) and follicle-stimulating hormone beta subunit (fshb) in fish tissues using quantitative reverse transcription polymerase chain reaction. in_vitro gonad pituitary fish tilapia lhb and fshb mRNA expression levels change http://purl.obolibrary.org/obo/GO_0016075 GO http://purl.obolibrary.org/obo/UBERON_0000945 UBERON http://purl.obolibrary.org/obo/UBERON_0000968 UBERON medium Expression of mRNAs coding for luteinizing hormone beta subunit (lhb) and follicle-stimulating hormone beta subunit (fshb) tend to fluctuate in parallel in repeat-spawning fish http://purl.obolibrary.org/obo/GO_0010468 GO radioimmunoassay Measures circulating concentrations of gonadotropins using radioimmunoassays. in_vitro human rodents livestock species gonadotropin concentration decrease http://purl.obolibrary.org/obo/CHEBI_38648 CHEBI medium Circulating concentrations of gonadotropins in humans and common mammalian models (e.g., rodents, many livestock species) can be directly measured using either commercial or custom immunoassays (e.g., enzyme-linked immunosorbent assays, radioimmunoassays, etc.) http://purl.obolibrary.org/obo/CHEBI_38648 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO commercial kit Measures the depletion of glutathione (GSH) using commercial kits purchased from specialized companies. in_vitro GSH concentration decrease http://purl.obolibrary.org/obo/CHEBI_15377 CHEBI not_specified Photocolorimetric assays (Rahman 2007; Massarsky, Kozal, and Di Giulio 2017), HPLC (Afzal et al. 2002; J. Liu et al. 2010) http://purl.obolibrary.org/obo/CHEBI_15377 CHEBI http://purl.obolibrary.org/obo/GO_0006749 GO HPLC High-performance liquid chromatography used to quantify glutathione (GSH) levels by separating and detecting components in a sample. in_vitro glutathione levels decrease http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI medium HPLC (Afzal et al. 2002; J. Liu et al. 2010) http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0006750 GO Photocolorimetric assay A colorimetric method used to measure glutathione (GSH) levels based on color changes detected photometrically. in_vitro glutathione levels decrease http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI medium Photocolorimetric assays (Rahman 2007; Massarsky, Kozal, and Di Giulio 2017) http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0006750 GO Affymetrix Microarray Measures the transcript levels of Kupffer cell marker genes (Lyz, Gzmb, Il1b) using the Genome U34A Array platform. not_specified Kupffer cells expression of Lyz, Gzmb, and Il1b genes increase high increase in expression of Kupffer cell marker genes such as Lyz, Gzmb, and Il1b, (Genome U34A Array, Affymetrix); [16] ELISA Measures IL-6 expression to assess Kupffer cell activation. not_specified IL-6 expression increase not_specified IL-6 expression, measured by immunoassays or Elisa ELISA Measures cytokine concentrations (TNF-a, IL-6) in tissue samples using enzyme-linked immunosorbent assay. not_specified TNF-a and IL-6 concentrations increase not_specified immunoassays or Elisa (offered by various companies) tissue levels of TNF-a [13], IL-6 expression http://purl.obolibrary.org/obo/GO_0006954 GO Genome U34A Array Measures expression of Kupffer cell marker genes such as Lyz, Gzmb, and Il1b to assess Kupffer cell activation. not_specified expression of Kupffer cell marker genes increase high increase in expression of Kupffer cell marker genes such as Lyz, Gzmb, and Il1b, (Genome U34A Array, Affymetrix) Genome U34A Array Genome U34A Array (Affymetrix) measures the expression of Kupffer cell marker genes such as Lyz, Gzmb, and Il1b. in_vitro liver Expression of Lyz, Gzmb, and Il1b increase high increase in expression of Kupffer cell marker genes such as Lyz, Gzmb, and Il1b, (Genome U34A Array, Affymetrix); http://purl.obolibrary.org/obo/GO_0001972 GO IL-6 immunoassay Measures IL-6 expression in tissue as a marker of Kupffer cell activation using immunoassays or ELISA. in_vivo liver not_specified IL-6 concentration increase http://purl.obolibrary.org/obo/GO_0032501 GO not_specified Kupffer cell activation can be measured by means of expressed cytokines, e.g. tissue levels of TNF-a http://purl.obolibrary.org/obo/CL_0000632 CL http://purl.obolibrary.org/obo/GO_0006954 GO immunoassay Measures tissue levels of TNF-a to assess Kupffer cell activation. not_specified TNF-a levels increase not_specified Kupffer cell activation can be measured by means of expressed cytokines, e.g. tissue levels of TNF-a immunoassay/ELISA Measurement of soluble CD163 protein levels using immunoassays or ELISA. in_vitro soluble CD163 levels increase http://purl.obolibrary.org/obo/CHEBI_70436 CHEBI medium soluble CD163 [14][15] http://purl.obolibrary.org/obo/CL_0000183 CL immunoassay/ELISA Measurement of cytokine protein levels, specifically TNF-alpha and IL-6, using immunoassays or Enzyme-Linked Immunosorbent Assays. in_vitro liver tissue levels of TNF-a and IL-6 expression increase http://purl.obolibrary.org/obo/CHEBI_35445 CHEBI http://purl.obolibrary.org/obo/CHEBI_35451 CHEBI medium expressed cytokines, e.g. tissue levels of TNF-a [13], IL-6 expression, measured by immunoassays or Elisa http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0006954 GO soluble CD163 measurement Measures soluble CD163 levels to assess Kupffer cell activation. not_specified soluble CD163 levels increase not_specified soluble CD163 TNF-alpha ELISA Quantifies the tissue levels of TNF-alpha, a cytokine indicative of Kupffer cell activation. in_vivo liver not_specified TNF-alpha concentration increase http://purl.obolibrary.org/obo/GO_0032501 GO not_specified Kupffer cell activation can be measured by means of expressed cytokines, e.g. tissue levels of TNF-a http://purl.obolibrary.org/obo/CL_0000632 CL http://purl.obolibrary.org/obo/GO_0006954 GO histopathological examination This assay evaluates tissue samples for microscopic signs of liver damage, including necrosis, inflammation, and other cytotoxic effects in hepatocytes. in_vivo liver presence and severity of histopathological changes increase low Necrosis and inflammation are not observed after 52 weeks of DLC administration but occur during the second year of treatment and are observed at the 2-year termination of the NTP cancer bioassays. Damage to hepatocytes and cytotoxicity are common features of these histopathological changes. http://purl.obolibrary.org/obo/CL_0000068 CL http://purl.obolibrary.org/obo/GO_0072376 GO histopathology Histopathological analysis is used to observe necrosis and inflammation in liver tissues after DLC or TCDD administration. These effects are observed at lower doses than those at which tumors were observed. in_vivo liver necrosis and inflammation increase http://purl.obolibrary.org/obo/GO_0008625 GO http://purl.obolibrary.org/obo/GO_0006954 GO low Necrosis and inflammation are not observed after 52 weeks of DLC administration but occur during the second year of treatment and are observed at the 2-year termination of the NTP cancer bioassays. Necrosis and inflammation are observed at lower doses than those at which tumors were observed (Hailey et al., 2005). http://purl.obolibrary.org/obo/CL_0002056 CL http://purl.obolibrary.org/obo/GO_0006954 GO CRP assay Measurement of C-reactive protein (CRP) levels as a biomarker of inflammation. in_vivo blood C-reactive protein levels increase http://purl.obolibrary.org/obo/CHEBI_16994 CHEBI low Biomarkers (white cell count, CRP) ratios, and predictive score using http://purl.obolibrary.org/obo/CHEBI_16994 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO DCFDA assay Measurement of reactive oxygen species (ROS) using DCFDA. in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI medium Measuring ROS (DCFDA http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO ELISA Measurement of chemokines such as interleukins (IL1, IL6), TNF, and interferon in blood or histopathology samples. in_vitro chemokine levels increase http://purl.obolibrary.org/obo/PR_000000984 PR http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/PR_000001658 PR http://purl.obolibrary.org/obo/PR_000000042 PR medium Measuring chemokines in the blood (ELISA, multiplex bead assays: interleukines (IL1, IL6), TNF, interferon… ) (Brenner) and histopathology samples http://purl.obolibrary.org/obo/CHEBI_23723 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO ELISA ELISA is used to measure Prostaglandin levels and COX-2. in_vitro Prostaglandin levels, COX-2 levels increase http://purl.obolibrary.org/obo/CHEBI_5983 CHEBI medium Measuring Prostaglandin levels, COX-2 (ELISA, Liquid chromatography/tandem mass spectrometry , IHC) http://purl.obolibrary.org/obo/GO_0005238 GO http://purl.obolibrary.org/obo/GO_0005239 GO ELISA Measurement of transcription factor activation such as STAT3 and NF-κB. in_vitro transcription factor activation increase http://purl.obolibrary.org/obo/PR_000016098 PR http://purl.obolibrary.org/obo/PR_000005980 PR medium Transcription factors: STAT3 Activation, NF-κB Activation (ELISA http://purl.obolibrary.org/obo/GO_0003700 GO http://purl.obolibrary.org/obo/GO_0006954 GO ELISA for NF-κB activation Enzyme-linked immunosorbent assay to measure activation of the transcription factor NF-κB. in_vivo NF-κB activation increase medium Transcription factors : NF-κB Activation http://purl.obolibrary.org/obo/PR_00000087 PR http://purl.obolibrary.org/obo/GO_0006954 GO ELISA for prostaglandin Enzyme-linked immunosorbent assay to measure prostaglandin levels associated with inflammation. in_vivo Prostaglandin levels increase medium Measuring Prostaglandin levels, COX-2 (ELISA http://purl.obolibrary.org/obo/CHEBI_15928 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO ELISA for STAT3 activation Enzyme-linked immunosorbent assay to measure activation of the transcription factor STAT3. in_vivo STAT3 activation increase medium Transcription factors : STAT3 Activation http://purl.obolibrary.org/obo/PR_00000114 PR http://purl.obolibrary.org/obo/GO_0006954 GO histopathology Detection of inflammation through histopathological examination of organs such as liver and intestines. in_vivo liver intestines inflammation increase http://purl.obolibrary.org/obo/GO_0006954 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/UBERON_0000160 UBERON low Inflammation is generally detected in histopathological examination of organs (ex. liver, intestines) http://purl.obolibrary.org/obo/UBERON_0000062 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO HRP-oxidizing substrates assay Measurement of reactive oxygen species (ROS) using horseradish peroxidase (HRP)-oxidizing substrates. in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI medium horseradish peroxidase (HRP)-oxidizing substrates http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO IHC Detection of COX-2 expression as a marker of inflammation using immunohistochemistry. in_vivo COX-2 expression increase http://purl.obolibrary.org/obo/PR_000001002 PR low Measuring Prostaglandin levels, COX-2 (ELISA, Liquid chromatography/tandem mass spectrometry, IHC) http://purl.obolibrary.org/obo/PR_000001002 PR http://purl.obolibrary.org/obo/GO_0006954 GO liquid chromatography/tandem mass spectrometry Measurement of prostaglandin levels as a marker of inflammation. in_vitro prostaglandin levels increase medium Measuring Prostaglandin levels, COX-2 (ELISA, Liquid chromatography/tandem mass spectrometry, IHC) http://purl.obolibrary.org/obo/CHEBI_26289 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO Multiplex bead assay Multiplex bead-based immunoassay to measure chemokines and cytokines such as IL1, IL6, TNF, and interferon in blood. in_vivo blood Chemokines and cytokine levels in blood increase http://purl.obolibrary.org/obo/CHEBI_15907 CHEBI http://purl.obolibrary.org/obo/CHEBI_16162 CHEBI http://purl.obolibrary.org/obo/CHEBI_16243 CHEBI http://purl.obolibrary.org/obo/CHEBI_16018 CHEBI high Measuring chemokines in the blood (ELISA, multiplex bead assays: interleukines (IL1, IL6), TNF, interferon… ) (Brenner) http://purl.obolibrary.org/obo/PR_00400172 PR http://purl.obolibrary.org/obo/GO_0006954 GO RT-PCR Measurement of mRNA levels of transcription factors such as STAT3 and NF-κB. in_vitro mRNA levels increase http://purl.obolibrary.org/obo/SO_0000234 SO medium RtPCR to measure mRNA http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO SOD-inhibitable reduction of cytochrome c Measurement of reactive oxygen species (ROS) using SOD-inhibitable reduction of cytochrome c. in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI medium SOD-inhibitable reduction of cytochrome c http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO White blood cell count Measurement of white blood cell count as a biomarker of inflammation. in_vivo white blood cells blood White blood cell count increase http://purl.obolibrary.org/obo/CL_0000000 CL low Biomarkers (white cell count, CRP) ratios, and predictive score using http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0006954 GO 53BP1 foci Detection with Time Course 53BP1 is recruited to the site of DNA damage; the rate at which its level decreases over time is used to measure DNA repair. in_vitro 53BP1 foci level over time decrease medium 53BP1 is recruited to the site of DNA damage, the rate at which its level decreases over time is used to measure DNA repair Alkaline Elution Assay with Time Course DNA with strand breaks elute faster than DNA without, plotted against time intervals to determine the rate at which strand breaks repair. in_vitro DNA elution rate decrease low DNA with strand breaks elute faster than DNA without, plotted against time intervals to determine the rate at which strand breaks repair Alkaline Unwinding Assay with Time Course DNA is stored in alkaline solutions with DNA-specific dye and allowed to unwind following removal from tissue; increased strand damage associated with increased unwinding. Samples analyzed at different time points to compare remaining damage following repair opportunities. in_vitro DNA unwinding decrease OECD TG 489 low DNA is stored in alkaline solutions with DNA-specific dye and allowed to unwind following removal from tissue, increased strand damage associated with increased unwinding. Samples analyzed at different time points to compare remaining damage following repair opportunities Comet Assay with Time-Course Comet assay is performed with a time-course under alkaline conditions to detect SSBs and DSBs; quantity of DNA in the tail should decrease as DNA repair progresses. in_vitro DNA in comet tail decrease OECD TG 489 medium Comet assay is performed with a time-course under alkaline conditions to detect SSBs and DSBs. Quantity of DNA in the tail should decrease as DNA repair progresses Dose-Response Curve for Alkyl Adducts/Mutations Creation of a curve plotting the stressor dose and the abundance of adducts/mutations; characteristics of the resulting curve can provide information on the efficiency of DNA repair. in_vitro somatic cells spermatogenic cells abundance of adducts/mutations increase not_specified Creation of a curve plotting the stressor dose and the abundance of adducts/mutations; Characteristics of the resulting curve can provide information on the efficiency of DNA repair DSB repair assay Transfection of a GFP reporter construct where GFP signal is detected if the DSB is repaired; GFP signal is quantified using fluorescence microscopy or flow cytometry. in_vitro GFP signal increase http://purl.obolibrary.org/obo/GO_0006294 GO medium DSB Repair Assay (Reporter constructs) Mao et al., 2011 Transfection of a GFP reporter construct (and DsRed control) where the GFP signal is only detected if the DSB is repaired; GFP signal is quantified using fluorescence microscopy or flow cytometry http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006294 GO Flow Cytometry (alt-NHEJ) The alt-NHEJ flow cytometer method involves utilizing an extrachromosomal substrate; green fluorescent protein (GFP) expression is indicative of successful alt-NHEJ activity. in_vitro GFP expression increase high The alt-NHEJ flow cytometer method involves utilizing an extrachromosomal substrate. Green fluorescent protein (GFP) expression is indicative of successful alt-NHEJ activity, contingent on the removal of 10 nucleotides from each end of the DNA and subsequent rejoining within a 9-nucleotide microhomology region. FM-HCR Measures the ability of human cells to repair plasmid reporters, which contain different types and amounts of DNA damage. in_vitro human cells human repair of plasmid reporters increase medium Nagel et al. (2014) we developed a fluorescence-based multiplex flow-cytometric host cell reactivation assay (FM-HCR) to measures the ability of human cells to repair plasmid reporters. gamma-H2AX Foci Staining with Time Course Measures the rate of disappearance of phosphorylated histone H2AX over time as a proxy for DNA strand break repair. not_specified rate of disappearance of phosphorylated H2AX decrease not_specified Histone H2AX is phosphorylated in the presence of DNA strand breaks, the rate of its disappearance over time is used as a measure of DNA repair http://purl.obolibrary.org/obo/GO_0006281 GO Mutation Spectrum Shifts in the mutation spectrum after exposure to a chemical/mutagen relative to an unexposed subject can provide an indication of DNA repair efficiency. in_vitro mutation spectrum change not_specified Shifts in the mutation spectrum after exposure to a chemical/mutagen relative to an unexposed subject can provide an indication of DNA repair efficiency, and can inform as to the type of DNA lesions present Primary Rat Hepatocyte DNA Repair Assay Measurement of DNA synthesis in rat primary hepatocytes using 3H-thymidine to assess unscheduled DNA synthesis in response to damage. in_vitro primary hepatocytes liver rat 3H incorporated in the DNA change not_specified Rat primary hepatocytes are cultured with a 3H-thymidine solution in order to measure DNA synthesis in response to a stressor in non-replicating cells; Autoradiography is used to measure the amount of 3H incorporated in the DNA post-repair http://purl.obolibrary.org/obo/GO_0006281 GO Pulsed Field Gel Electrophoresis (PFGE) with Time-Course PFGE assay with a time-course; quantity of small DNA fragments should decrease as DNA repair progresses. in_vitro small DNA fragments decrease low PFGE assay with a time-course; Quantity of small DNA fragments should decrease as DNA repair progresses retention of alkyl adducts Examination of DNA for alkylation after exposure to an alkylating agent; presence of alkylation suggests a lack of repair. in_vivo spermatogenic cells spermatogonia hamster rat alkylation increase low RETENTION OF ALKYL ADDUCTS: Alkylated DNA can be found in cells long after exposure has occurred. This indicates that repair has not effectively removed the adducts. http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Retention of Alkyl Adducts Examination of DNA for alkylation after exposure to an alkylating agent; presence of alkylation suggests a lack of repair. in_vivo spermatogonia hamster rat presence of alkyl adducts increase not_specified Examination of DNA for alkylation after exposure to an alkylating agent; Presence of alkylation suggests a lack of repair Sucrose Density Gradient Centrifugation with Time Course Strand breaks alter the molecular weight of the DNA piece. DNA in alkaline solution centrifuged into sugar density gradient, repeated set time apart. The less DNA breaks identified in the assay repeats, the more repair occurred. in_vitro DNA breaks decrease low Strand breaks alter the molecular weight of the DNA piece. DNA in alkaline solution centrifuged into sugar density gradient, repeated set time apart. The less DNA breaks identified in the assay repeats, the more repair occurred y-H2AX foci staining Histone H2AX is phosphorylated in the presence of DNA strand breaks, the rate of its disappearance over time is used as a measure of DNA repair not_specified y-H2AX foci decrease low y-H2AX Foci Staining with Time Course Mariotti et al. 2013 Penninckx et al. 2021 Histone H2AX is phosphorylated in the presence of DNA strand breaks, the rate of its disappearance over time is used as a measure of DNA repair http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Dose-response modeling Uses the sustained AHR activation index as the dose term and measures of KEs or biomarkers as the response to model dose-response relationships. in_silico ED50/EC50 value not_specified high Dose-response modeling can be performed using the sustained AHR activation index as the dose term and the measures of the various KEs or biomarkers as the response. One of the model parameters is the ED50 or EC50 value e in other words, the effective dose or concentration sufficient to produce a 50% of the maximal response. EROD assay Measures the activity of 7-Ethoxyresorufin-O-deethylase (EROD) as an indicator of AHR activation and CYP1A1 induction. in_vivo liver EROD activity increase http://purl.obolibrary.org/obo/GO_0047040 GO http://purl.obolibrary.org/obo/GO_0001621 GO low Dose-response of CYP1A1 activation measured by EROD as a measure of AHR activation in response to an AUC measure of dose. shows plots of the increase in 7-Ethoxyresorufin-O-deethylase (EROD) versus the area-under-the-curve (AUC) of the hepatic concentration of three dioxin-like chemicals, TCDD, 4-PeCDF and PCB-126 occurring during lifetime dosing. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0001621 GO ATG_LXRa_TRANS This ToxCast assay evaluates gene expression changes. in_vitro gene expression change high Relevent ToxCast assays are ATG_LXRa_TRANS; ATG_LXRb_TRANS; ATG_DR4_LXR_CIS (U.S. EPA 2024). http://purl.obolibrary.org/obo/GO_0010505 GO ATG_LXRa_TRANS A targeted ToxCast assay measuring LXRa transcriptional activity. in_vitro LXRa transcriptional activity change http://purl.obolibrary.org/obo/GO_0003700 GO http://purl.obolibrary.org/obo/PR_000001150 PR high Relevent ToxCast assays are ATG_LXRa_TRANS; ATG_LXRb_TRANS; ATG_DR4_LXR_CIS (U.S. EPA 2024). http://purl.obolibrary.org/obo/PR_000001150 PR http://purl.obolibrary.org/obo/GO_0006351 GO metabolomics Measures changes in metabolite levels to infer LXR activation and downstream effects. in_vitro metabolite levels change http://purl.obolibrary.org/obo/OBI_0000368 OBI http://purl.obolibrary.org/obo/CHMO_0000000 CHMO high Effects of LXR on expression of downstream genes can be investigating using metabolomics and RT-qPCR approaches. http://purl.obolibrary.org/obo/CHEBI_25833 CHEBI http://purl.obolibrary.org/obo/GO_0008152 GO RT-qPCR Measures changes in gene expression levels of downstream genes regulated by LXR. in_vitro gene expression change http://purl.obolibrary.org/obo/GO_0010467 GO medium Effects of LXR on expression of downstream genes can be investigating using metabolomics and RT-qPCR approaches. http://purl.obolibrary.org/obo/SO_0000341 SO http://purl.obolibrary.org/obo/GO_0010467 GO RT-qPCR Quantitative reverse transcription PCR measuring changes in gene expression of downstream LXR target genes to assess liver X receptor activation. in_vitro gene expression levels of downstream LXR target genes change http://purl.obolibrary.org/obo/GO_0010468 GO medium Effects of LXR on expression of downstream genes can be investigating using metabolomics and RT-qPCR approaches. http://purl.obolibrary.org/obo/GO_0010468 GO SeqAPASS Evaluates gene expression changes from chemical exposure in model species to assess LXR activation. in_vitro model species gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO high targeted ToxCast assays using SeqAPASS evaluations can evaluate gene expression changes from chemical exposure for model species (e.g. Lalone et al. 2018). http://purl.obolibrary.org/obo/SO_0000341 SO http://purl.obolibrary.org/obo/GO_0010467 GO ToxCast SeqAPASS Evaluates chemical-induced gene expression changes for LXR using targeted assays. in_vitro not_specified model species gene expression changes increase http://purl.obolibrary.org/obo/GO_0010467 GO high In addition, targeted ToxCast assays using SeqAPASS evaluations can evaluate gene expression changes from chemical exposure for model species (e.g. Lalone et al. 2018). Relevent ToxCast assays are ATG_LXRa_TRANS; ATG_LXRb_TRANS; ATG_DR4_LXR_CIS (U.S. EPA 2024). http://purl.obolibrary.org/obo/GO_0010467 GO ADP-to-O ratio assay Measures the number of ADP molecules phosphorylated per oxygen atom reduced, providing information on the efficacy of mitochondrial function. in_vitro ADP-to-O ratio decrease http://purl.obolibrary.org/obo/GO_0042776 GO low One approach measures the ADP-to-O ratio (the number of ADP molecules phosphorylated per oxygen atom reduced (Hinkle, 1995 and Hafner et al., 1990). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0042776 GO Aequorin-based bioluminescence assay Measures mitochondrial calcium influx using aequorin as a calcium sensor in conjunction with GFP for bioluminescence resonance energy transfer (BRET). in_vitro mitochondrial calcium influx increase http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0070063 GO low Together with GFP, the aequorin moiety acts as Ca2+ sensor in vivo, which delivers emission energy to the GFP acceptor molecule in a BRET (Bioluminescence Resonance Energy Transfer) process; the Ca2+ can then be visualized with fluorescence microscopy. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0070063 GO ATP content assay Measures ATP levels using commercially available kits based on luciferin and luciferase activity, or via electrodes or luminometric methods for isolated mitochondria. in_vitro ATP content decrease http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI high For the evaluation of ATP levels, various commercially-available ATP assay kits are offered based on luciferin and luciferase activity. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0042775 GO Cellular glutathione (GSH) status assay Measures the levels of reduced (GSH) and oxidized (GSSG) glutathione, often using DTNB (Ellman’s reagent), to assess the cellular redox potential. in_vitro GSH/GSSG ratio decrease http://purl.obolibrary.org/obo/CHEBI_16957 CHEBI high GSH is regenerated from its oxidized form (GSSH) by the action of an NADPH dependent reductase (GSSH + NADPH + H+ à 2 GSH + NADP+). The ratio of GSH/GSSG is therefore a good indicator for the cellular NADH+/NADPH ratio (i.e. the redox potential). GSH and GSSH levels can be determined by HPLC, capillary electrophoresis, or biochemically with DTNB (Ellman’s reagent). http://purl.obolibrary.org/obo/CL_0000003 CL http://purl.obolibrary.org/obo/GO_0034599 GO Cellular oxygen consumption Measures the oxygen consumption rate in cells or isolated mitochondria, often combined with other endpoints to derive specific information on mitochondrial function. in_vitro oxygen consumption rate decrease http://purl.obolibrary.org/obo/GO_0009060 GO medium Cellular oxygen consumption. The oxygen consumption parameter can be combined with other endpoints to derive more specific information on the efficacy of mitochondrial function. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0009060 GO Electron transport system (ETS) activity assay Measures the activity of the mitochondrial electron transport system using a cell-free homogenate incubated with NADH and an artificial electron acceptor (INT). in_vitro electron transport system activity decrease http://purl.obolibrary.org/obo/GO_0006120 GO low Determination of ETS activity can be dene following Owens and King's assay (1975). The technique is based on a cell-free homogenate that is incubated with NADH to saturate the mitochondrial ETS and an artificial electron acceptor [l - (4 -iodophenyl) -3 - (4 -nitrophenyl) -5-phenylte trazolium chloride (INT)] to register the electron transmission rate. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006120 GO ETS activity assay (INT reduction) Determines electron transport system activity in cell-free homogenates by incubating with NADH and an artificial electron acceptor (INT), measuring INT-formazan production spectrophotometrically. in_vitro Electron transmission rate / INT-formazan production decrease low The technique is based on a cell-free homogenate that is incubated with NADH to saturate the mitochondrial ETS and an artificial electron acceptor [l - (4 -iodophenyl) -3 - (4 -nitrophenyl) -5-phenylte trazolium chloride (INT)] to register the electron transmission rate. The oxygen consumption rate is calculated from the molar production rate of INT-formazan which is determined spectrophotometrically Extracellular flux analysis Measures mitochondrial ATP production based on oxygen consumption rate (OCR) and extracellular acidification rate (ECAR), with inhibitors used to dissect ATP-linked OCR. in_vitro mitochondrial ATP production rate decrease http://purl.obolibrary.org/obo/GO_0042776 GO medium Determination of mitochondrial ATP production based on extracellular flux analysis The method is based on the detection of OCR (Oxygen Consumption Rate) that represents mitochondrial respiration as well as on the detection of ECAR (extracellular acidification rate) / proton efflux rate (PER): reflects extracellular acidification, a proxy for glycolysis (lactate release) plus contributions from CO₂/HCO₃⁻. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0042776 GO Extracellular flux analysis (OCR/ECAR) Uses Oxygen Consumption Rate (OCR) and Extracellular Acidification Rate (ECAR) to determine mitochondrial respiration and ATP-linked OCR. in_vitro OCR and ECAR change http://purl.obolibrary.org/obo/OBI_0001234 OBI medium Determination of mitochondrial ATP production based on extracellular flux analysis. The method is based on the detection of OCR (Oxygen Consumption Rate) that represents mitochondrial respiration as well as on the detection of ECAR (extracellular acidification rate) http://purl.obolibrary.org/obo/CL_0000001 CL http://purl.obolibrary.org/obo/GO_0006116 GO Flow Cytometry (R123 and Propidium Iodide) Combines R123 fluorescence (for mitochondrial membrane potential) and propidium iodide (for cell viability) using a flow cytometer. in_vitro membrane potential and viability decrease http://purl.obolibrary.org/obo/CHEBI_35538 CHEBI http://purl.obolibrary.org/obo/GO_0008263 GO medium Dc and viability were determined by analyzing the R123 and propidium iodide fluorescence intensity with a FACScan flow cytometer R123 is a cationic dye that accumulates in the negatively charged inner side of the mitochondria. When the potential drops, less R123 accumulates in the mitochondria, which results in a lower fluorescence signal. http://purl.obolibrary.org/obo/CL_0000001 CL http://purl.obolibrary.org/obo/CHEBI_35538 CHEBI Hydrogen peroxide detection assay Detects hydrogen peroxide (H2O2) production using fluorogenic substrates (diacetyldichlorofluorescein, homovanillic acid, Amplex® Red) in conjunction with horseradish peroxidase (HRP). Increasing amounts of H2O2 produce increasing fluorescent product. in_vitro Hydrogen peroxide (H2O2) production increase not_specified e. Detection of hydrogen peroxide (H2O2) production. There are a number of fluorogenic substrates, which serve as hydrogen donors that have been used in conjunction with horseradish peroxidase (HRP) enzyme to produce intensely fluorescent products in the presence of hydrogen peroxide (Zhou et al., 1997: Ruch et al., 1983). The more commonly used substrates include diacetyldichloro-fluorescein, homovanillic acid, and Amplex® Red. In these examples, increasing amounts of H2O2 form increasing amounts of fluorescent product (Tarpley et al., 2004). Lipid peroxidation assay (TBARS) Measures the formation of thiobarbituric acid-reactive substances (TBARS), such as malondialdehyde, as an indicator of lipid peroxidation. in_vitro lipid peroxidation increase http://purl.obolibrary.org/obo/GO_0006687 GO http://purl.obolibrary.org/obo/CHEBI_15355 CHEBI high Measurement of lipid peroxidation has historically relied on the detection of thiobarbituric acid (TBA)-reactive compounds such as malondialdehyde generated from the decomposition of cellular membrane lipid under oxidative stress (Pryor et al., 1976). http://purl.obolibrary.org/obo/CHEBI_18434 CHEBI http://purl.obolibrary.org/obo/GO_0006687 GO Mitochondrial membrane potential assay (TMRE/TMRM) Uses fluorescent probes like TMRE or TMRM to measure the mitochondrial membrane potential in living cells, with detection via flow cytometry, microscopy, or plate readers. in_vitro mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0086014 GO http://purl.obolibrary.org/obo/CHMO_0000625 CHMO high Quantitative assessment of ΔΨm in living cells is most commonly achieved through the use of cationic, lipophilic fluorescent probes that accumulate within the mitochondrial matrix in proportion to the electrochemical gradient (Leonard et al., 2014). Among these, tetramethylrhodamine derivatives such as TMRE (tetramethylrhodamine ethyl ester) and TMRM (tetramethylrhodamine methyl ester) are widely employed due to their reversible, potential-dependent distribution across the inner mitochondrial membrane (Scaduto and Grotyohann, 1999; Creed and McKenzie, 2019). http://purl.obolibrary.org/obo/GO_0005739 GO Mitochondrial permeability transition pore (PTP) opening assay Detects PTP opening through the translocation of cytochrome c, adenylate kinase, or AIF, or via calcein fluorescence quenching in permeabilized cells. in_vitro cytochrome c translocation / calcein quenching increase http://purl.obolibrary.org/obo/GO_0031645 GO medium The opening of the PTP is associated with a permeabilization of mitochondrial membranes, so that different compounds and cellular constituents can change intracellular localization. This can be measured by assessment of the translocation of cytochrome c, adenylate kinase or AIF from mitochondria to the cytosol or nucleus. http://purl.obolibrary.org/obo/GO_0005741 GO http://purl.obolibrary.org/obo/GO_0031645 GO Mitochondrial permeability transition pore (PTP) opening assay Measures the opening of the mitochondrial permeability transition pore by assessing the translocation of cytochrome c, adenylate kinase, or AIF, or using a calcein fluorescence quenching assay. in_vitro mitochondrial permeability transition pore opening increase http://purl.obolibrary.org/obo/PR_000000034 PR medium The opening of the PTP is associated with a permeabilization of mitochondrial membranes, so that different compounds and cellular constituents can change intracellular localization. This can be measured by assessment of the translocation of cytochrome c, adenylate kinase or AIF from mitochondria to the cytosol or nucleus. An alternative approach is to measure the accessibility of cobalt to the mitochondrial matrix in a calcein fluorescence quenching assay in live permeabilized cells (Petronilli et al., 1999). http://purl.obolibrary.org/obo/GO_0005739 GO mtDNA damage assay (QPCR) Detects changes in DNA structure and sequence in the mitochondrial genome using quantitative polymerase chain reaction (QPCR)-based assays. in_vitro mtDNA damage increase http://purl.obolibrary.org/obo/GO_0003990 GO http://purl.obolibrary.org/obo/GO_0006974 GO medium Various quantitative polymerase chain reaction (QPCR)-based assays have been developed to detect changes of DNA structure and sequence in the mitochondrial genome. http://purl.obolibrary.org/obo/GO_0003990 GO http://purl.obolibrary.org/obo/GO_0006974 GO Quantikine Rat/Mouse Cytochrome c Immunoassay Measures cytochrome c release using a monoclonal antibody specific for rat/mouse cytochrome c in a microplate-based immunoassay. in_vitro Mus musculus Rattus norvegicus cytochrome c release increase http://purl.obolibrary.org/obo/PR_000000034 PR http://purl.obolibrary.org/obo/GO_0001836 GO medium Cytochrome C release was measured a monoclonal antibody specific for rat/mouse cytochrome c was precoated onto the microplate. http://purl.obolibrary.org/obo/PR_000000034 PR http://purl.obolibrary.org/obo/GO_0001836 GO Rhodamine 123 assay Measures mitochondrial membrane potential using the cationic fluorescent dye rhodamine 123, with fluorescence monitored using a spectrophotometer. in_vitro mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0086014 GO medium Mitochondrial uptake of cationic fluorescent dye, rhodamine 123, is used for estimation of mitochondrial membrane potential. The fluorescence was monitored using Schimadzou RF-5000U fluorescence spectrophotometer at the excitation and emission wavelength of 490 nm and 535 nm, respectively. http://purl.obolibrary.org/obo/GO_0005739 GO ROS production assay Measures the generation of reactive oxygen species (ROS) such as superoxide anions and hydroxyl radicals using direct or indirect assays. in_vitro ROS production increase http://purl.obolibrary.org/obo/GO_0000002 GO http://purl.obolibrary.org/obo/CHEBI_26622 CHEBI high Electrons from the mitochondrial ETS may be transferred ‘erroneously’ to molecular oxygen to form superoxide anions. This type of side reaction can be strongly enhanced upon mitochondrial damage. As superoxide may form hydrogen peroxide, hydroxyl radicals or other reactive oxygen species, a large number of direct ROS assays and assays assessing the effects of ROS (indirect ROS assays) are available (Adam-Vizi, 2005; Fan and Li 2014). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0072593 GO TBARS Assay Quantifies lipid peroxidation by measuring malondialdehyde (MDA) content through its reaction with thiobarbituric acid. in_vitro kidney cells kidney MDA content increase http://purl.obolibrary.org/obo/GO_0006644 GO medium MDA content, a product of lipid peroxidation, was measured using a thiobarbituric acid reactive substances (TBARS) assay. Briefly, the kidney cells were collected in 1 ml PBS buffer solution (pH 7.4) and sonicated. http://purl.obolibrary.org/obo/CHEBI_16251 CHEBI http://purl.obolibrary.org/obo/GO_0006644 GO western blot Examines the redistribution of Cyto c in cytosolic and mitochondrial cellular fractions. in_vitro cytochrome c release increase http://purl.obolibrary.org/obo/CHEBI_16861 CHEBI low Examining the redistribution of Cyto c in cytosolic and mitochondrial cellular fractions. http://purl.obolibrary.org/obo/CHEBI_16861 CHEBI http://purl.obolibrary.org/obo/GO_0008219 GO Western blot for cytochrome c release Measures the redistribution of cytochrome c in cytosolic and mitochondrial cellular fractions using immunoblotting. in_vitro cytochrome c release increase http://purl.obolibrary.org/obo/PR_000000034 PR http://purl.obolibrary.org/obo/GO_0001836 GO low Examining the redistribution of Cyto c in cytosolic and mitochondrial cellular fractions. Cells are homogenized and centrifuged, then prepared for immunoblots. http://purl.obolibrary.org/obo/PR_000000034 PR http://purl.obolibrary.org/obo/GO_0001836 GO PPARalpha signaling assay This assay measures the effects of PPARalpha signaling on fatty acid oxidation through various approaches. not_specified fatty acid β-oxidation decrease http://purl.obolibrary.org/obo/GO_0006635 GO not_specified A variety of approaches establishing the effects of PPARalpha signaling on fatty acid oxidation are reviewed in Evans et al (2004). http://purl.obolibrary.org/obo/CHEBI_15884 CHEBI http://purl.obolibrary.org/obo/GO_0006635 GO ACB-PCR This PCR technique detects single base pair substitution mutations by selectively amplifying specific point mutations. in_vitro point mutations increase http://purl.obolibrary.org/obo/OBI_0000272 OBI medium Using this PCR technique, single base pair substitution mutations within oncogenes or tumour suppressor genes can be detected by selectively amplifying specific point mutations within an allele and selectively blocking amplification of the wild-type allele http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006468 GO Corrected Next Generation Sequencing NGS technique with error-correction strategies to detect rare subclonal mutations in heterogeneous DNA samples through clonal expansion or family analysis. in_vitro human rare subclonal mutations increase http://purl.obolibrary.org/obo/CHMO_0000901 CHMO high This technique detects rare subclonal mutations within a pool of heterogeneous DNA samples through the application of new error-correction strategies to NGS; At present, few laboratories in the world are capable of doing this, but commercial services are becoming available (e.g., Duplex sequencing at TwinStrand BioSciences) Corrected Next Generation Sequencing (NGS) Salk 2018 (Review) http://purl.obolibrary.org/obo/GO_0006284 GO HPRT Mutation Assay This assay measures X-linked HPRT mutations through colony formation in the presence of 6-TG or 8-azoguanine. in_vitro HPRT gene mutations increase http://purl.obolibrary.org/obo/SO_0000704 SO OECD TG 476 medium Similar to TK Mutation Assay above, X-linked HPRT mutations produced in response to chemical/mutagen exposure can be measured through colony formation in the presence of 6-TG or 8-azoguanine; Only HPRT-/- cells are able to form colonies http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006468 GO In vitro mammalian cell gene mutation test (HPRT) This assay identifies substances that induce gene mutations at the hprt gene using specific cell lines. in_vitro CHO CHL V79 L5178Y TK6 Chinese hamster mouse human gene mutations increase http://purl.obolibrary.org/obo/SO_0000704 SO OECD TG 476 medium A variety of in vitro mammalian cell gene mutation tests are described in OECD’s Test Guidelines 476 (2016) and 490 (2015). TG 476 (2016) is used to identify substances that induce gene mutations at the hprt (hypoxanthine-guanine phosphoribosyl transferase) gene, or the transgenic xprt (xanthine-guanine phosphoribosyl transferase) reporter locus. http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006468 GO Next-generation sequencing This technique detects rare subclonal mutations within a pool of heterogeneous DNA samples using error-correction strategies. in_vitro human other species mutations increase http://purl.obolibrary.org/obo/OBI_0002145 OBI medium Mutations can be directly measured in humans (and other species) through the application of next-generation sequencing. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006468 GO Pig-a assay This assay measures mutations in the Pig-a gene by flow cytometry of red blood cells expressing or not expressing the Pig-a gene. in_vivo blood human rat mouse monkey Pig-a gene mutations increase medium Thus, flow cytometry of red blood cells expressing or not expressing the Pig-a gene has been developed for mutation analysis in blood cells from humans, rats, mice, and monkeys. http://purl.obolibrary.org/obo/GO_0006468 GO Salmonella mutagenicity test (Ames Test) A bacterial reverse mutation test used to determine if a chemical can cause gene mutations by analyzing the growth capacity of different bacterial strains in the presence and absence of metabolic activation systems. in_vitro bacterial strains mutagenic potency increase http://purl.obolibrary.org/obo/GO_0007088 GO OECD TG 471 medium The Salmonella mutagenicity test (Ames Test) is generally used as part of a first tier screen to determine if a chemical can cause gene mutations. A variety of bacterial strains are used, in the presence and absence of a metabolic activation system (e.g., rat liver microsomal S9 fraction), to determine the mutagenic potency of chemicals by dose-response analysis. http://purl.obolibrary.org/obo/CHEBI_33157 CHEBI http://purl.obolibrary.org/obo/GO_0007101 GO Single-molecule PCR This PCR technique uses a single DNA template for detection of mutations in microsatellites or recombination studies. in_vitro sperm bone marrow tandem repeat mutations increase http://purl.obolibrary.org/obo/OBI_0000272 OBI low Tandem repeat mutations can be measured in bone marrow, sperm, and other tissues using single-molecule PCR. http://purl.obolibrary.org/obo/GO_0006468 GO TK Mutation Assay This assay detects mutations at the thymidine kinase (TK) loci by measuring resistance to triflurothymidine (TFT). in_vitro L5178Y wild-type mouse lymphoma TK (+/-) cells mouse TK gene mutations increase http://purl.obolibrary.org/obo/SO_0000704 SO OECD TG 490 medium After exposure to a chemical/mutagen, mutations are detected at the thymidine kinase (TK) loci of L5178Y wild-type mouse lymphoma TK (+/-) cells by measuring resistance to lethaltriflurothymidine (TFT); Only TK-/- cells are able to form colonies http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006468 GO Transgenic rodent mutation assay This in vivo test detects gene mutations using transgenic rodents that possess transgenes and reporter genes. in_vivo various tissues mouse rat gene mutations increase OECD TG 488 low The transgenic rodent mutation assay (OECD TG 488, 2020) is the only assay capable of measuring gene mutation in virtually all tissues in vivo. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006468 GO Transgenic Rodent Mutation Assay An in vivo assay measuring gene mutations, chromosomal deletions, and rearrangements in transgenic rodents by extracting genomic DNA from tissues and analyzing transgenes in bacteria. in_vivo virtually all tissues mouse rat mutant frequency increase http://purl.obolibrary.org/obo/GO_0007087 GO OECD TG 488 low The transgenic rodent mutation assay (OECD TG 488, 2020) is the only assay capable of measuring gene mutation in virtually all tissues in vivo. The transgenic reporter genes are used for detection of gene mutations and/or chromosomal deletions and rearrangements resulting in DNA size changes http://purl.obolibrary.org/obo/CHEBI_33157 CHEBI http://purl.obolibrary.org/obo/GO_0007087 GO XPRT Mutation Assay In vitro mammalian cell gene mutation test using transgenic xprt reporter locus in AS52 cells to detect gene mutations by colony formation. in_vitro AS52 cells not specified xprt transgene mutations increase http://purl.obolibrary.org/obo/GO_0006284 GO OECD TG 476 medium TG 476 (2016) is used to identify substances that induce gene mutations at the hprt (hypoxanthine-guanine phosphoribosyl transferase) gene, or the transgenic xprt (xanthine-guanine phosphoribosyl transferase) reporter locus. The only cells suitable for the XPRT test are AS52 cells containing the bacterial xprt (or gpt) transgene (from which the hprt gene was deleted). http://purl.obolibrary.org/obo/GO_0006284 GO birth dating procedures Specialized techniques to determine the timing of cell generation in brain regions, often using thymidine analogs. in_vivo neocortex cell generation timing change http://purl.obolibrary.org/obo/GO_0022008 GO low birth dating procedures and staining techniques http://purl.obolibrary.org/obo/CL_0000097 CL http://purl.obolibrary.org/obo/GO_0022008 GO birth dating procedures Specialized staining and procedures used to track cellular lineage and developmental timing in the neocortex. not_specified neocortex cytoarchitecture/cell lineage change not_specified Subtle changes in cytoarchitecure such as seen in the neocortex depend on more specialized birth dating procedures and staining techniques. http://purl.obolibrary.org/obo/UBERON_0001133 UBERON Birth dating procedures Tracks the developmental timing of neuronal birth and migration to detect subtle changes in cytoarchitecture, particularly in the neocortex. not_specified neocortex brain neuronal birth timing and cytoarchitecture change http://purl.obolibrary.org/obo/GO_0022008 GO low more specialized birth dating procedures and staining techniques Subtle changes in cytoarchitecure such as seen in the neocortex depend on more specialized birth dating procedures Imaging procedures Visualizes structural alterations in brain tissue using microscopy or other imaging modalities. not_specified brain neocortex anatomical structure not_specified http://purl.obolibrary.org/obo/UBERON_0000955 UBERON not_specified imaging procedures http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO immunohistochemical staining Uses antibodies to detect specific proteins in tissue sections, allowing visualization of cellular structures and their distribution. ex_vivo http://purl.obolibrary.org/obo/UBERON_0002037 anatomical abnormalities change http://purl.obolibrary.org/obo/OBI_0002629 OBI medium Data in support of this key event have been collected using a wide variety of standard biochemical, histological and anatomical methods (eg., morphometrics, immunohistochemical staining, in situ hybridation) http://purl.obolibrary.org/obo/UBERON_0001952 UBERON http://purl.obolibrary.org/obo/GO_0021987 GO immunohistochemical staining Staining of tissue sections using antibodies to detect specific proteins, revealing cellular and structural features. in_vivo brain protein expression and localization change http://purl.obolibrary.org/obo/OBI_0000659 OBI medium immunohistochemical staining http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0008104 GO in situ hybridization Detection of specific nucleic acid sequences in tissue sections to assess gene expression patterns. in_vivo brain mRNA expression and localization change medium in situ hybridation http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO In situ hybridization Detects specific nucleic acid sequences in tissue sections to assess spatial gene expression patterns related to brain structure. not_specified brain spatial gene expression patterns change http://purl.obolibrary.org/obo/OBI_0000451 OBI low anatomical methods (eg., morphometrics, immunohistochemical staining, in situ hybridation) morphometrics Quantitative measurement of anatomical structures to assess neuroanatomy. in_vivo brain anatomical structure dimensions change low morphometrics http://purl.obolibrary.org/obo/UBERON_0000955 UBERON morphometrics Quantitative analysis of the form, shape, size, and structure of biological entities. not_specified brain anatomical structure/morphology change http://purl.obolibrary.org/obo/OBI_0000144 OBI not_specified morphometrics http://purl.obolibrary.org/obo/UBERON_0000847 UBERON Neurohistopathology Routine neurohistopathological procedures to reveal anatomical abnormalities in the brain, following EPA and OECD developmental neurotoxicity guidelines. in_vivo brain not_specified anatomical abnormalities increase http://purl.obolibrary.org/obo/UBERON_0000955 UBERON EPA and OECD developmental neurotoxicity guidelines low Data in support of this key event have been collected using a wide variety of standard biochemical, histological and anatomical methods (eg., morphometrics, immunohistochemical staining, in situ hybridation) and imaging procedures. Many of methods applied to reveal anatomical abnormalities are routine neurohistopatholgical procedures similar to those recommended in EPA and OECD developmental neurotoxicity guidelines. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON Staining techniques General histological staining (e.g., Nissl) to visualize cellular structures and cytoarchitecture. not_specified brain neocortex cellular morphology not_specified http://purl.obolibrary.org/obo/GO_0030030 GO not_specified staining techniques http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0000902 GO ED1 immunolabeling Use of ED1 antibodies to detect phagocytic microglia in rat tissue. not_specified phagocytic microglia rat tissue rat phagocytic microglia presence not_specified http://purl.obolibrary.org/obo/CL_0000016 CL not_specified phagocytic microglia in rat tissue (ED1) http://purl.obolibrary.org/obo/CL_0000016 CL ELISA Measurement of inflammatory mediators using ELISA-related immuno-quantification. not_specified mediator concentration change medium Activation of glial cells can be assessed in tissue or cell culture models also by quantification of sets of activation markers. This can for instance be done by PCR quantification of inflammatory factors, by measurement of the respective mediators, e.g. by ELISA-related immuno-quantification. http://purl.obolibrary.org/obo/GO_0006950 GO ELISA for inflammatory mediators Quantifies inflammatory mediators such as cytokines using ELISA-related immuno-quantification methods. in_vitro brain tissue protein levels of inflammatory mediators increase http://purl.obolibrary.org/obo/GO_0006954 GO medium by measurement of the respective mediators, e.g. by ELISA-related immuno-quantification. http://purl.obolibrary.org/obo/CL_0000127 CL http://purl.obolibrary.org/obo/GO_0006954 GO F4/80 immunolabeling Use of F4/80 antibodies to detect microglia in mouse tissue. not_specified microglia mouse tissue mouse microglia presence not_specified http://purl.obolibrary.org/obo/CL_0000016 CL not_specified various well-established antibodies are available to detect microglia in mouse tissue (F4/80) http://purl.obolibrary.org/obo/CL_0000016 CL fluorescent reporter mouse imaging (CD11b promoter-driven fluorescent protein) Quantification of microglial cells in transgenic mice expressing fluorescent proteins under the control of the CD11b promoter, enabling direct visualization and counting of microglia without the need for specific stains. in_vivo microglia brain mouse microglial cell count increase http://purl.obolibrary.org/obo/CL_0000129 CL http://purl.obolibrary.org/obo/NCIT_C12427 NCIT http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Transgenic mice are available with fluorescent proteins under the control of the CD11b promoter to easily quantify microglia without the need for specific stains. http://purl.obolibrary.org/obo/CL_0000129 CL http://purl.obolibrary.org/obo/GO_0001773 GO Iba1 immunolabeling Use of Iba1 antibodies to detect microglia across species. not_specified microglia microglia presence not_specified http://purl.obolibrary.org/obo/CL_0000016 CL not_specified more generally microglia across species (Iba1). http://purl.obolibrary.org/obo/CL_0000016 CL Immunocytochemistry for C3 Detects A1 neurotoxic reactive astrocytes by staining for complement component 3 (C3), a marker highly upregulated in these astrocytes. in_vitro brain tissue C3 expression increase http://purl.obolibrary.org/obo/PR_000001000 PR http://purl.obolibrary.org/obo/GO_0001773 GO medium Antibodies for complement component 3 (C3), the most characteristic and highly upregulated marker of A1 neurotoxic reactive astrocytes are commercially available. http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0001773 GO Immunocytochemistry for GFAP Detects astrocyte activation by staining for GFAP, which is upregulated in reactive astrocytes. in_vitro brain tissue GFAP expression increase http://purl.obolibrary.org/obo/PR_000008383 PR http://purl.obolibrary.org/obo/GO_0001773 GO US EPA 40 CFR 79.67 medium The most frequently used astrocyte marker is GFAP (99% of all studies) (Eng et al., 2000). Measurement of glial fibrillary acidic protein (GFAP) in brain tissue, whose increase is a marker of astrocyte reactivity, is required by the US EPA in rodent toxicity studies for fuel additives (40 CFR 79.67). http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0001773 GO PCR Quantification of inflammatory factors and phenotype markers (e.g., Itgam, CD86, Arg1, MRC1) via gene expression analysis. in_vitro brain mRNA expression of inflammatory factors increase medium This can for instance be done by PCR quantification of inflammatory factors http://purl.obolibrary.org/obo/GO_0042090 GO PCR quantification of inflammatory factors Quantifies expression of inflammatory factors such as cytokines and immunostimulatory proteins using PCR. in_vitro brain tissue mRNA expression of inflammatory factors increase http://purl.obolibrary.org/obo/GO_0006954 GO high Activation of glial cells can be assessed in tissue or cell culture models also by quantification of sets of activation markers. This can for instance be done by PCR quantification of inflammatory factors http://purl.obolibrary.org/obo/CL_0000127 CL http://purl.obolibrary.org/obo/GO_0006954 GO PET imaging Monitoring microglial accumulation in patients using [11C]-PK 11195 as a microglial marker. in_vivo brain human microglial accumulation increase medium In patients, microglial accumulation can be monitored by PET imaging, using [11C]-PK 11195 as a microglial marker (Banati et al., 2002). http://purl.obolibrary.org/obo/CL_0000578 CL http://purl.obolibrary.org/obo/GO_0006950 GO PET imaging with [11C]-PK 11195 Positron emission tomography (PET) imaging using the microglial marker [11C]-PK 11195 to monitor microglial accumulation in patients. in_vivo microglia brain human microglial accumulation increase http://purl.obolibrary.org/obo/CL_0000016 CL low In patients, microglial accumulation can be monitored by PET imaging, using [11C]-PK 11195 as a microglial marker (Banati et al., 2002). http://purl.obolibrary.org/obo/CL_0000016 CL Vimentin/S100beta staining Staining of astrocytes using alternative markers such as vimentin or S100beta protein. not_specified astrocytes astrocytic marker expression not_specified http://purl.obolibrary.org/obo/CL_0000130 CL not_specified Occasionally, alternative astrocytic markers, such as vimentin of the S100beta protein, have been used for staining of astrocytes (Struzynska et al., 2007). http://purl.obolibrary.org/obo/CL_0000130 CL enzymatic assays Measures the activity of enzymes involved in neurotransmitter synthesis, such as choline acetyltransferase and glutamic acid decarboxylase. in_vitro enzyme activity change http://purl.obolibrary.org/obo/GO_0003824 GO medium enzymatic assays (e.g.: choline acetyltransferase, glutamic acid decarboxylase) http://purl.obolibrary.org/obo/CHEBI_35224 CHEBI http://purl.obolibrary.org/obo/GO_0006836 GO genomic approaches Non-targeted analysis of genomic changes relevant to neuronal dysfunction. in_vitro genomic changes change http://purl.obolibrary.org/obo/SO_0001026 SO high Genomic, proteomic and metabolomic approaches are also suitable for a non targeted approach. http://purl.obolibrary.org/obo/SO_0001026 SO genomic, proteomic and metabolomic approaches Non-targeted high-throughput technologies used to profile global changes in genes, proteins, or metabolites. in_vitro global molecular profiles change http://purl.obolibrary.org/obo/ENVO_01000434 ENVO high Genomic, proteomic and metabolomic approaches are also suitable for a non targeted approach. http://purl.obolibrary.org/obo/GO_0008152 GO immunoblotting Measures changes in protein levels of neuronal cytoskeleton markers, synapses, neurotransmitters, or enzymes involved in neurotransmitter synthesis. in_vitro protein level change http://purl.obolibrary.org/obo/GO_0019538 GO medium look for changes at the protein level, with immunoblotting http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0019538 GO Immunoblotting Detects and quantifies protein levels of specific neuronal markers such as tyrosine hydroxylase and neurofilament proteins. not_specified protein levels of neuronal markers change medium at the protein level, with immunoblotting (ex. thyrosine hydroxylase, NF-L,-M,-H) immunocytochemistry Immunocytochemistry is used to measure protein levels, followed by quantification. not_specified neurons protein levels change low immunocytochemistry followed by a quantification http://purl.obolibrary.org/obo/GO_0005576 GO http://purl.obolibrary.org/obo/GO_0005249 GO immunocytochemistry Detects and quantifies neuronal cytoskeleton markers, synapses, neurotransmitters, or enzymes involved in neurotransmitter synthesis at the cellular level. in_vitro protein localization and expression change http://purl.obolibrary.org/obo/GO_0008104 GO low immunocytochemistry followed by a quantification http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0008104 GO metabolomic approaches Non-targeted analysis of metabolomic changes relevant to neuronal dysfunction. in_vitro metabolomic changes change http://purl.obolibrary.org/obo/CHEBI_85725 CHEBI high Genomic, proteomic and metabolomic approaches are also suitable for a non targeted approach. http://purl.obolibrary.org/obo/CHEBI_85725 CHEBI http://purl.obolibrary.org/obo/GO_0008152 GO proteomic approaches Non-targeted analysis of proteomic changes relevant to neuronal dysfunction. in_vitro proteomic changes change http://purl.obolibrary.org/obo/PR_000000001 PR high Genomic, proteomic and metabolomic approaches are also suitable for a non targeted approach. http://purl.obolibrary.org/obo/PR_000000001 PR quantitative RT-PCR Measures changes in mRNA levels of neuronal cytoskeleton markers, synapses, neurotransmitters, or enzymes involved in neurotransmitter synthesis. in_vitro mRNA level change http://purl.obolibrary.org/obo/GO_0010467 GO medium look for changes at the mRNA level with quantitative RT-PCR http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO Quantitative RT-PCR Measures changes in mRNA levels of neuronal cytoskeleton proteins, synapses, or enzymes involved in neurotransmitter synthesis. not_specified mRNA levels of neuronal markers change medium look for changes at the mRNA level with quantitative RT-PCR electroencephalogram Measurement of electrical activity along large anatomical pathways in the brain. not_specified brain electrical activity in anatomical pathways change http://purl.obolibrary.org/obo/OBI_0001138 OBI not_specified to the very large anatomical pathways (e.g., electroencephalograms) http://purl.obolibrary.org/obo/UBERON_0000847 UBERON http://purl.obolibrary.org/obo/GO_0048167 GO field potential recording Measures synaptic transmission and neural circuit activity by recording extracellular field potentials in hippocampal regions. in_vivo hippocampus field potential amplitude/frequency change http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0007268 GO low field potentials in the hippocampus, an area critical for certain forms of learning and memory, to probe functional integrity after TH insufficiency Field potentials have been recorded following thyroid disruption both in vivo and in vitro, at two discrete hippocampal synaptic regions, area CA1 and the dentate gyrus http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0007268 GO field potential recording Field potentials are recorded to probe functional integrity after thyroid hormone insufficiency. Recordings are taken at two discrete hippocampal synaptic regions, area CA1 and the dentate gyrus. in_vivo hippocampus functional integrity of synaptic transmission change http://purl.obolibrary.org/obo/GO_0006508 GO http://purl.obolibrary.org/obo/UBERON_0002026 UBERON low A number of studies on TH and brain function have incorporated field potentials in the hippocampus, an area critical for certain forms of learning and memory, to probe functional integrity after TH insufficiency Field potentials have been recorded following thyroid disruption both in vivo and in vitro at two discrete hippocampal synaptic regions, area CA1 and the dentate gyrus. http://purl.obolibrary.org/obo/CL_0000279 CL http://purl.obolibrary.org/obo/GO_0006508 GO ion channel flux measurement Measurement of the movement of ions through individual ion channels. not_specified individual ion channel fluxes change http://purl.obolibrary.org/obo/GO_0004425 GO not_specified The scale of neurophysiological techniques that can be used ranges along a broad continuum from the very small (e.g., individual ion channel fluxes) http://purl.obolibrary.org/obo/GO_0004425 GO http://purl.obolibrary.org/obo/GO_0006811 GO microelectrode array (MEA) Measures electrical activity in cultured neurons in response to NMDA receptor activation or inactivation. in_vitro cultured neurons electrical activity change http://purl.obolibrary.org/obo/GO_0009056 GO http://purl.obolibrary.org/obo/GO_0015276 GO high Microelectrode array (MEA) recordings are used to measure electrical activity in cultured neurons in response to NMDA receptor activation or inactivation. MEAs can also be applied in higher throughput platforms to facilitate screening of numerous chemical compounds based on electrical activity measurements. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0042391 GO patch clamp Measures the activation or inhibition of NMDA receptors by recording ion channels selective to Na+, K+, and Ca2+ in neuronal cells. in_vitro neuronal cells brain slices ion channel conductance change http://purl.obolibrary.org/obo/GO_0005216 GO http://purl.obolibrary.org/obo/GO_0015276 GO low The measurement of the activation or the inhibition of NMDA receptors is done indirectly by recording the individual ion channels that are selective to Na+, K+ and Ca+2 by the patch clamp technique. The whole-cell patch clamp recording techniques have also been used to study synaptically-evoked NMDA receptor-mediated excitatory or inhibitory postsynaptic currents (EPSCs and IPSCs, respectively) in brain slices and neuronal cells, allowing the evaluation of the activated or inhibited state of the receptor. http://purl.obolibrary.org/obo/PR_000001240 PR http://purl.obolibrary.org/obo/GO_0006811 GO patch clamp (brain slices) Whole-cell patch clamp recording techniques are used to study synaptically-evoked NMDA receptor-mediated excitatory or inhibitory postsynaptic currents (EPSCs and IPSCs) in brain slices and neuronal cells, evaluating the activated or inhibited state of the receptor. ex_vivo neuronal cells brain postsynaptic currents (EPSCs and IPSCs) change http://purl.obolibrary.org/obo/GO_0007614 GO low The whole-cell patch clamp recording techniques have also been used to study synaptically-evoked NMDA receptor-mediated excitatory or inhibitory postsynaptic currents (EPSCs and IPSCs, respectively) in brain slices and neuronal cells, allowing the evaluation of the activated or inhibited state of the receptor (Ogdon and Stanfield, 2009; Zhao et al., 2009). http://purl.obolibrary.org/obo/CHEBI_59838 CHEBI http://purl.obolibrary.org/obo/GO_0007268 GO whole-cell patch clamp Measures NMDA receptor ion channel activity by recording ionic currents (e.g., EPSCs/IPSCs) through selective Na+, K+, Ca2+ channels using the patch clamp technique, assessing channel open/closed states. not_specified neuronal cells brain NMDA receptor-mediated ion channel current (EPSC/IPSC) decrease http://purl.obolibrary.org/obo/GO_0005216 GO http://purl.obolibrary.org/obo/GO_0007268 GO low The measurement of the activation or the inhibition of NMDA receptors is done indirectly by recording the individual ion channels that are selective to Na+, K+ and Ca+2 by the patch clamp technique. The whole-cell patch clamp recording techniques have also been used to study synaptically-evoked NMDA receptor-mediated excitatory or inhibitory postsynaptic currents (EPSCs and IPSCs, respectively) in brain slices and neuronal cells This method relies on lack of measurable ion flux when NMDA ion channel is closed, whereas constant channel specific conductance is recorded at the open state of the receptor http://purl.obolibrary.org/obo/GO_0007268 GO Evoked electrical activity measurements This assay measures the electrical activity evoked by NMDA receptor activation, using D-AP5 to study the activity of NMDA receptors. ex_vivo brain evoked electrical activity not_specified http://purl.obolibrary.org/obo/OBI_0000219 OBI low D-AP5, a selective N-methyl-D-aspartate (NMDA) receptor antagonist that competitively inhibits the glutamate binding site of NMDA receptors, can be studied by evoked electrical activity measurements. http://purl.obolibrary.org/obo/PR_00000122 PR http://purl.obolibrary.org/obo/GO_0007268 GO In silico NMDA receptor targeting prediction This assay uses computational methods such as molecular docking, pharmacophore searching, and chemical similarity searching to predict NMDA receptor targeting. in_silico predicted NMDA receptor targeting not_specified http://purl.obolibrary.org/obo/OBI_0001823 OBI http://purl.obolibrary.org/obo/OBI_0001824 OBI high The prediction of NMDA receptor targeting is achievable by combining database mining, molecular docking, structure-based pharmacophore searching, and chemical similarity searching methods together (Korkut and Varnali, 2003; Koutsoukos et al., 2011; Gao et al., 2013; Mazumder and Borah, 2014; Chtitaa et al., 2015). NMDA receptor (MK801 site) radioligand competition binding assay An ex vivo assay using the antagonist MK801 to detect and differentiate agonists and antagonists that bind to the MK801 site of the NMDA receptor. ex_vivo binding of agonists and antagonists to the MK801 site change http://purl.obolibrary.org/obo/OBI_0000057 OBI http://purl.obolibrary.org/obo/PR_000000001 PR not_specified The most common assay used is the NMDA receptor (MK801 site) radioligand competition binding assays This assay is based on the use of the most potent and specific antagonist of this receptor, MK801 that is used to detect and differentiate agonists and antagonists (competitive and non-competitive) that bind to this specific site of the receptor. NMDA receptor radioligand competition binding assay (MK801 site) This assay uses the radioligand MK801 to measure the binding of antagonists to the MK801 site of NMDA receptors, allowing differentiation of agonists and antagonists. ex_vivo brain binding of antagonists to NMDA receptors not_specified http://purl.obolibrary.org/obo/OBI_0000477 OBI medium The most common assay used is the NMDA receptor (MK801 site) radioligand competition binding assays (Reynolds, 2001; Gao et al., 2013; http://pdsp.med.unc.edu/UNC-CH%20Protocol%20Book.pdf; http://www.currentprotocols.com/WileyCDA/CPUnit/refId-ph0120.html). This assay is based on the use of the most potent and specific antagonist of this receptor, MK801 that is used to detect and differentiate agonists and antagonists (competitive and non-competitive) that bind to this specific site of the receptor. http://purl.obolibrary.org/obo/PR_00000122 PR http://purl.obolibrary.org/obo/GO_0015276 GO radioligand competition binding assay ([3H]-CGP 39653) A quantitative autoradiography technique using [3H]-CGP 39653, a high affinity selective antagonist at the glutamate site of the NMDA receptor. ex_vivo binding at the glutamate site of NMDA receptor change http://purl.obolibrary.org/obo/CHMO_0000647 CHMO not_specified Also radioligand competition binding assay can be performed using D, L-(E)-2-amino-4-[3H]-propyl-5-phosphono-3-pentenoic acid ([3H]-CGP 39653), a high affinity selective antagonist at the glutamate site of NMDA receptor, which is a quantitative autoradiography technique Beta lactamase reporter gene assay Measures NF-κB transcriptional activity using a beta lactamase reporter gene. in_vitro NF-κB transcriptional activity not_specified http://purl.obolibrary.org/obo/GO_0004879 GO http://purl.obolibrary.org/obo/GO_0008964 GO medium NF-κB transcriptional activity: Beta lactamase reporter gene assay (Miller et al. 2010) http://purl.obolibrary.org/obo/PR_000005852 PR http://purl.obolibrary.org/obo/GO_0006351 GO ELISA This assay measures NF-κB p65 (Total/Phospho) and levels of IL-6, IL-8, and Cox using ELISA. in_vitro protein levels (IL-6, IL-8, Cox, NF-κB p65) change medium NF-κB p65 (Total/Phospho) ELISA ： ELISA for IL-6, IL-8, and Cox http://purl.obolibrary.org/obo/GO_0043088 GO http://purl.obolibrary.org/obo/GO_0006954 GO ELISA for IL-6, IL-8, and Cox Measures levels of IL-6, IL-8, and Cox using ELISA. in_vitro IL-6, IL-8, and Cox levels not_specified http://purl.obolibrary.org/obo/PR_000001049 PR http://purl.obolibrary.org/obo/PR_000001050 PR medium ELISA for IL-6, IL-8, and Cox flow cytometry This assay measures NF-κB transcription using a lentiviral NF-κBGFP reporter and flow cytometry. in_vitro NF-κB transcription change high NF-κB transcription: Lentiviral NF-κBGFP reporter with flow cytometry (Moujalled et al. 2012) http://purl.obolibrary.org/obo/GO_0043087 GO http://purl.obolibrary.org/obo/GO_0006955 GO Lentiviral NF-κB-GFP reporter with flow cytometry Measures NF-κB transcription using a lentiviral GFP reporter and flow cytometry. in_vitro NF-κB transcription not_specified http://purl.obolibrary.org/obo/GO_0004879 GO medium NF-κB transcription: Lentiviral NF-κBGFP reporter with flow cytometry (Moujalled et al. 2012) http://purl.obolibrary.org/obo/PR_000005852 PR http://purl.obolibrary.org/obo/GO_0006351 GO NF-κB p65 (Total/Phospho) ELISA Measures total and phosphorylated NF-κB p65 using ELISA. in_vitro NF-κB p65 (Total/Phospho) not_specified http://purl.obolibrary.org/obo/GO_0004879 GO medium NF-κB p65 (Total/Phospho) ELISA http://purl.obolibrary.org/obo/PR_000005852 PR http://purl.obolibrary.org/obo/GO_0006468 GO Western blotting Measures IκBα phosphorylation using western blotting. in_vitro IκBα phosphorylation not_specified http://purl.obolibrary.org/obo/GO_0007249 GO http://purl.obolibrary.org/obo/GO_0006468 GO low IκBα phosphorylation: Western blotting (Miller et al. 2010) http://purl.obolibrary.org/obo/PR_000008496 PR http://purl.obolibrary.org/obo/GO_0006468 GO colorimetry (DTNB) Total glutathione can be determined colorimetrically by reacting GSH with DTNB (Ellman’s reagent) in the presence of glutathione reductase, producing a yellow colored product measured at 412 nm. in_vitro glutathione concentration increase http://purl.obolibrary.org/obo/CHEBI_5063 CHEBI http://purl.obolibrary.org/obo/OBI_0000269 OBI medium Total glutathione can be determined colorimetrically by reacting GSH with DTNB (Ellman’s reagent) in the presence of glutathione reductase. http://purl.obolibrary.org/obo/CHEBI_5063 CHEBI http://purl.obolibrary.org/obo/GO_0009484 GO F2-isoprostanes ELISA Measures F2-isoprostanes (IsoP) as a specific marker of lipid peroxidation using ELISA, often requiring sample purification. in_vitro F2-isoprostanes levels increase http://purl.obolibrary.org/obo/CHEBI_25485 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO medium The formation of F2-like prostanoid derivatives of arachidonic acid, termed F2-isoprostanes (IsoP) has been shown to be specific for lipid peroxidation. http://purl.obolibrary.org/obo/CHEBI_25485 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO Ferricytochrome c reduction assay Measures superoxide formation by monitoring the reduction of ferricytochrome c to ferrocytochrome c colorimetrically. in_vitro superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_26934 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium The reduction of ferricytochrome c to ferrocytochrome c has been used in a number of situations to assess the rate of superoxide formation. http://purl.obolibrary.org/obo/CHEBI_26934 CHEBI http://purl.obolibrary.org/obo/GO_0006801 GO Fluorescence-based ROS detection Measures oxidative stress using fluorescence-based agents to detect reactive oxygen species (ROS). in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO medium Agents for ROS detection are primarily fluorescence based, but recently luminescent based detections have been introduced. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Fluorogenic H2O2 assay Measures hydrogen peroxide levels using fluorogenic substrates in conjunction with horseradish peroxidase (HRP) enzyme. in_vitro hydrogen peroxide levels increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/OBI_0000221 OBI medium There are a number of fluorogenic substrates, which serve as hydrogen donors that have been used in conjunction with horseradish peroxidase (HRP) enzyme to produce intensely fluorescent products. http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0042744 GO fluorometry (H2O2 substrates) Hydrogen peroxide levels can be measured using fluorogenic substrates (diacetyldichloro-fluorescein, homovanillic acid, Amplex® Red) in conjunction with horseradish peroxidase (HRP), resulting in increased fluorescence with increasing H2O2. in_vitro fluorescent product formation increase http://purl.obolibrary.org/obo/CHEBI_28992 CHEBI medium There are a number of fluorogenic substrates, which serve as hydrogen donors that have been used in conjunction with horseradish peroxidase (HRP) enzyme to produce intensely fluorescent products. http://purl.obolibrary.org/obo/CHEBI_28992 CHEBI http://purl.obolibrary.org/obo/GO_0009484 GO GC/MS GC/MS is used to measure F2-isoprostanes (IsoP) as a specific indicator of lipid peroxidation, but requires sample purification and limits throughput. in_vitro F2-isoprostanes increase http://purl.obolibrary.org/obo/GO_0032934 GO low The only reliable means for detection is through the use of GC/MS, which makes it expensive and limits throughput. http://purl.obolibrary.org/obo/CL_0234040 CL http://purl.obolibrary.org/obo/GO_0009484 GO HPLC/Capillary Electrophoresis for GSH/GSSH Measures levels of reduced glutathione (GSH) and oxidized glutathione (GSSH) using HPLC or capillary electrophoresis. in_vitro GSH/GSSH ratio change http://purl.obolibrary.org/obo/CHEBI_16042 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO low GSH and GSSH levels can be determined by HPLC, capillary electrophoresis, or biochemically in microplates. http://purl.obolibrary.org/obo/CHEBI_16042 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Hydrocyanine dye fluorescence assay Uses hydrocyanine dyes (e.g., Hydro-Cy3, Hydro-Cy5) as fluorogenic sensors that increase fluorescence upon oxidation by superoxide or hydroxyl radicals. in_vitro fluorescence intensity increase medium Hydrocyanine dyes are fluorogenic sensors for superoxide and hydroxyl radical. While weakly fluorescent, upon oxidation their fluorescence intensity increases 100 fold. http://purl.obolibrary.org/obo/CHEBI_43150 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Hydrocyanine dyes assay Measures superoxide and hydroxyl radical levels using fluorogenic hydrocyanine dyes, which become highly fluorescent upon oxidation. in_vitro superoxide and hydroxyl radical levels increase http://purl.obolibrary.org/obo/CHEBI_26934 CHEBI http://purl.obolibrary.org/obo/CHEBI_25706 CHEBI medium Hydrocyanine dyes are fluorogenic sensors for superoxide and hydroxyl radical. These dyes are synthesized by reducing the iminium cation of the cyanine (Cy) dyes with sodium borohydride. http://purl.obolibrary.org/obo/CHEBI_26934 CHEBI http://purl.obolibrary.org/obo/GO_0006801 GO Luciferin-based GSH assay Measures glutathione levels using a luciferin derivative and glutathione S-transferase enzyme, with luminescent signal detection. in_vitro GSH levels increase http://purl.obolibrary.org/obo/CHEBI_16042 CHEBI http://purl.obolibrary.org/obo/OBI_0000220 OBI medium By using a luciferin derivative in conjunction with glutathione S-transferase enzyme the amount of GSH would be proportional to the luminescent signal generated when luciferase is added in a subsequent step. http://purl.obolibrary.org/obo/CHEBI_16042 CHEBI http://purl.obolibrary.org/obo/GO_0006749 GO Lucigenin chemiluminescence assay Measures superoxide levels using the chemiluminescent substrate Lucigenin. in_vitro superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_26934 CHEBI http://purl.obolibrary.org/obo/OBI_0000223 OBI medium Chemiluminescent reactions have been used for their potential increase in sensitivity over absorbance-based detection methods. The most widely used chemiluminescent substrate is Lucigenin http://purl.obolibrary.org/obo/CHEBI_26934 CHEBI http://purl.obolibrary.org/obo/GO_0006801 GO Nitrate/Nitrite colorimetric assay Measures nitric oxide production indirectly by detecting nitrate and nitrite colorimetrically using the Griess reaction. in_vitro nitrate and nitrite levels increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/CHEBI_17632 CHEBI http://purl.obolibrary.org/obo/CHEBI_16670 CHEBI medium A commonly used method for the indirect determination of •NO is the determination of its composition products nitrate and nitrite colorimetrically. http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006809 GO TBA Assay Detection of thiobarbituric acid (TBA) reactive compounds like malondialdehyde (MDA) via colorimetric or fluorescence measurement to determine lipid peroxidation. in_vitro malondialdehyde (MDA) increase http://purl.obolibrary.org/obo/GO_0008244 GO not_specified Measurement of lipid peroxidation has historically relied on the detection of thiobarbituric acid (TBA) reactive compounds such as malondialdehyde generated from the decomposition of lipid peroxidation products. http://purl.obolibrary.org/obo/GO_0005515 GO http://purl.obolibrary.org/obo/GO_0008244 GO TBA assay for lipid peroxidation Measures lipid peroxidation by detecting thiobarbituric acid (TBA) reactive compounds such as malondialdehyde (MDA) colorimetrically or fluorometrically. in_vitro lipid peroxidation increase http://purl.obolibrary.org/obo/GO_0006633 GO http://purl.obolibrary.org/obo/CHEBI_15787 CHEBI medium Measurement of lipid peroxidation has historically relied on the detection of thiobarbituric acid (TBA) reactive compounds such as malondialdehyde generated from the decomposition of lipid peroxidation products. http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/GO_0006633 GO enzyme-linked immunosorbent assay Measures total concentrations of 17β-estradiol in plasma using enzyme-linked antibodies. in_vitro plasma 17β-estradiol concentration decrease high Total concentrations of 17β-estradiol in plasma can be measured by [...] enzyme-linked immunosorbent assay (available through many commercial vendors) http://purl.obolibrary.org/obo/CHEBI_16469 CHEBI http://purl.obolibrary.org/obo/GO_0046887 GO GFP assay Uses a transgenic zebrafish line with GFP under control of estrogen response elements to measure estrogen levels, with decreased GFP signal indicating reduced estrogen. in_vivo liver ovary pituitary brain Danio rerio GFP signal decrease low A line of transgenic zebrafish employing green fluorescence protein under control of estrogen response elements could also be used to provide direct evidence of altered estrogen, with decreased GFP signal in estrogen responsive tissues like liver, ovary, pituitary, and brain indicating a reduction in circulating estrogens (Gorelick and Halpern 2011). GFP fluorescence in transgenic zebrafish Uses a transgenic zebrafish line with GFP under estrogen response element control to indicate altered estrogen levels via decreased GFP signal in estrogen-responsive tissues. in_vivo liver ovary pituitary brain Danio rerio GFP fluorescence decrease medium A line of transgenic zebrafish employing green fluorescence protein under control of estrogen response elements could also be used to provide direct evidence of altered estrogen, with decreased GFP signal in estrogen responsive tissues like liver, ovary, pituitary, and brain indicating a reduction in circulating estrogens (Gorelick and Halpern 2011) http://purl.obolibrary.org/obo/GO_0030521 GO LC/MS Measures total concentrations of 17β-estradiol in plasma using liquid chromatography-mass spectrometry. in_vitro plasma 17β-estradiol concentration decrease http://purl.obolibrary.org/obo/OBI_0000474 OBI medium Total concentrations of 17β-estradiol in plasma can be measured by [...] analytical chemistry (e.g., LC/MS; Owen et al. 2014) http://purl.obolibrary.org/obo/CHEBI_16469 CHEBI http://purl.obolibrary.org/obo/GO_0046887 GO proteomic analysis Analysis of protein levels of targets regulated by estrogen response elements to indirectly measure estrogen concentration. in_vitro protein levels of estrogen-regulated targets decrease not_specified targeted qPCR or proteomic analysis of appropriate targets could also be used as an indirect measure of reduced circulating estrogen concentrations. http://purl.obolibrary.org/obo/GO_0006415 GO qPCR Measures gene expression levels of estrogen-regulated genes as an indirect indicator of reduced circulating estrogen concentrations. in_vitro gene expression decrease http://purl.obolibrary.org/obo/OBI_0000662 OBI medium targeted qPCR or proteomic analysis of appropriate targets could also be used as an indirect measure of reduced circulating estrogen concentrations http://purl.obolibrary.org/obo/GO_0010467 GO radioimmunoassay Measures total concentrations of 17β-estradiol in plasma using radioactive isotopes and antibodies. in_vitro plasma 17β-estradiol concentration decrease medium Total concentrations of 17β-estradiol in plasma can be measured by radioimmunoassay (e.g., (Jensen et al. 2001)) http://purl.obolibrary.org/obo/CHEBI_16469 CHEBI http://purl.obolibrary.org/obo/GO_0046887 GO targeted qPCR Quantification of mRNA levels of specific estrogen-regulated genes (e.g., vitellogenins, cyp19a1b) as an indirect measure of estrogen levels. in_vitro gene expression of estrogen-regulated targets decrease http://purl.obolibrary.org/obo/GO_0010468 GO not_specified targeted qPCR or proteomic analysis of appropriate targets could also be used as an indirect measure of reduced circulating estrogen concentrations. http://purl.obolibrary.org/obo/GO_0006351 GO alkali-labile phosphoprotein assay Measures vitellogenin concentration via determination of alkali-labile phosphoprotein, a less specific/sensitive assay that detects phosphoprotein moieties of vitellogenin. in_vitro plasma vitellogenin concentration increase not_specified Less specific and/or sensitive assays such as determination of alkali-labile phosphoprotein (e.g., Kramer et al., 1998) and Western blotting (e.g., Heppell et al., 1995) may also be used. http://purl.obolibrary.org/obo/GO_0006083 GO alkali-labile phosphoprotein determination Measures alkali-labile phosphoprotein as a less specific/sensitive indicator of vitellogenin. in_vitro plasma alkali-labile phosphoprotein increase low Less specific and/or sensitive assays such as determination of alkali-labile phosphoprotein (e.g., Kramer et al., 1998) http://purl.obolibrary.org/obo/GO_0007594 GO ELISA Measures vitellogenin concentrations in plasma using enzyme-linked immunosorbent assay. in_vitro plasma vitellogenin concentration increase medium Vitellogenin concentrations in plasma are typically measured using enzyme linked immunosorbent assay (ELISA; e.g., Denslow et al., 1999; Holbech et al., 2001). http://purl.obolibrary.org/obo/GO_0007594 GO Fish Short Term Reproduction Assay Standardized assay measuring vitellogenin as part of a short-term fish reproduction test. in_vivo plasma fish vitellogenin concentration increase OECD TG 229 low Fish Short Term Reproduction Assay (OECD, 2009a) http://purl.obolibrary.org/obo/GO_0007594 GO Larval Amphibian Growth and Development Assay Standardized assay where vitellogenin measurement is an optional parameter in a larval amphibian growth and development test. in_vivo plasma amphibian vitellogenin concentration increase OECD TG 241 low Measurement of vtg is also an optional parameter in the Larval Amphibian Growth and Development Assay (OECD, 2015b). http://purl.obolibrary.org/obo/GO_0007594 GO Western blot Detects vitellogenin protein in plasma using Western blotting. in_vitro plasma vitellogenin protein increase low Western blotting (e.g., Heppell et al., 1995) http://purl.obolibrary.org/obo/GO_0007594 GO Alkaline-labile phosphate assay Alkaline-labile phosphate determination is used as a less specific and/or sensitive method to assess vitellogenin concentrations in plasma. in_vitro plasma vitellogenin concentrations decrease not_specified Although less specific and/or sensitive, determination of alkaline-labile phosphate or Western blotting has also been employed. alkaline-labile phosphate determination Measures alkaline-labile phosphate as an indirect indicator of vitellogenin levels. in_vitro plasma alkaline-labile phosphate not_specified medium determination of alkaline-labile phosphate http://purl.obolibrary.org/obo/GO_0007292 GO ELISA Detects vitellogenin concentrations in plasma using enzyme-linked immunosorbent assay. in_vitro plasma vitellogenin concentration not_specified medium Vitellogenin concentrations in plasma are typically detected using enzyme linked Immunosorbent assay (ELISA http://purl.obolibrary.org/obo/GO_0007292 GO western blot Detects vitellogenin protein levels in plasma using Western blotting. in_vitro plasma vitellogenin protein level not_specified low Western blotting has also been employed http://purl.obolibrary.org/obo/GO_0007292 GO binding assay Measures binding of ligands to PPARα in vitro and in silico. in_vitro ligand binding increase http://purl.obolibrary.org/obo/GO_0005694 GO not_specified Binding of ligands to PPARα is measured using binding assays in vitro and in silico http://purl.obolibrary.org/obo/GO_0005102 GO binding assay Measures the binding of ligands to PPARα in vitro and in silico. in_vitro ligand binding to PPARα not_specified not_specified Binding of ligands to PPARα is measured using binding assays in vitro and in silico Electrophoretic Mobility Shift Assay (EMSA) Determines if a protein or protein mixture will bind to a specific DNA or RNA sequence, measuring cofactor binding by changes in gel mobility. in_vitro cofactor binding not_specified not_specified Electrophoretic Mobility Shift Assay (EMSA) or commercially available PPARα transcription factor assay kits Electrophoretic Band Shift determines if a protein or protein mixture will bind to a specific DNA or RNA sequence Measures cofactor binding by changes in gel mobility EMSA Determines if a protein or protein mixture will bind to a specific DNA or RNA sequence, measuring cofactor binding by changes in gel mobility. in_vitro protein-DNA/RNA binding change low There are also other methods that have been used to measure PPARα activity, such as the Electrophoretic Mobility Shift Assay (EMSA) http://purl.obolibrary.org/obo/GO_0005695 GO microarray profiling Develops MIE-specific sets of gene expression biomarkers using microarray profiles from livers of wild-type and PPARα-null mice. in_vivo liver mouse gene expression signature not_specified not_specified The most direct measure of this MIE is microarray profiling from large gene expression databases TG-GATEs and DrugMatrix coupled with t statistical analysis of whole genome expression profiles A gene expression signature of 131 PPARα-dependent genes was built using microarray profiles from the livers of wild-type and PPARα-null mice molecular modelling; docking simulation Computational simulation of ligand binding to predict binding interactions. in_silico binding interaction prediction not_specified not_specified molecular modelling; docking simulation Computational simulation of ligand binding Prediction off binding interaction PPARα reporter gene assay Quantifies changes in PPARα activation via a sensitive surrogate, measuring changes in activity of genes linked to a PPARα receptor element. in_vitro changes in activity of genes linked to a PPARα receptor element not_specified http://purl.obolibrary.org/obo/OBI_0000725 OBI high Quantify changes in in PPARα activation via a sensitive surrogate Measures changes in activity of genes linked to a PPARα receptor element Quantitative in vitro screening http://purl.obolibrary.org/obo/GO_0001669 GO http://purl.obolibrary.org/obo/GO_0006351 GO PPARα reporter gene assay Quantifies changes in PPARα activation via a sensitive surrogate in vitro or ex vivo. in_vitro PPARα activation increase not_specified PPARα reporter gene assay Quantify changes in in PPARα activation via a sensitive surrogate Measures changes in activity of genes linked to a PPARα receptor element Running Fisher test Provides a quantitative measure of similarity/correlation between the PPARα gene expression signature and positive/negative test sets. in_silico similarity/correlation of gene expression signature not_specified not_specified A quantitative measure of this expression signature is a measure of similarity/correlation between the PPARα signature and positive and negative test sets is provided by the Running Fisher test scintillation proximity binding assay Direct binding of ligand, identifies compounds that bind to PPARα. in_vitro ligand binding increase http://purl.obolibrary.org/obo/GO_0005694 GO not_specified Scintillation proximity binding assay Direct binding of ligand In vitro Identifies compouds that bind to PPARα http://purl.obolibrary.org/obo/GO_0005102 GO Scintillation proximity binding assay Direct binding assay to identify compounds that bind to PPARα. in_vitro ligand binding to PPARα not_specified not_specified Scintillation proximity binding assay Direct binding of ligand Identifies compouds that bind to PPARα transactivation assay Measures functional activation of PPARα using transient or stably transfected cells with PPARα expression and reporter plasmids. in_vitro PPARα activation increase OECD Level 2 assay not_specified the information about functional activation is derived from transactivation assays (e.g. transactivation assay with reporter gene) that demonstrate functional activation of a nuclear receptor by a specific compound Transactivation assays are performed using transient or stably transfected cells with the PPARα expression plasmid and a reporter plasmid, respectively The transactivation (stable transfection) assay provides the most applicable OECD Level 2 assay (i.e. In vitro assays providing mechanistic data) aimed at identifying the initiating event leading to an adverse outcome Electrophoretic Mobility Shift Assay (EMSA) Measures protein:DNA binding activity, identifying sequence-specific DNA-binding proteins such as transcription factors. in_vitro DNA binding activity not_specified http://purl.obolibrary.org/obo/GO_0003677 GO low Electrophoretic Mobility Shift Assay (EMSA) Gene regulation and determining protein: DNA interactions are the detected by the EMSA. http://purl.obolibrary.org/obo/PR_000001336 PR http://purl.obolibrary.org/obo/GO_0003677 GO luciferase reporter gene assay Quantifies changes in luciferase expression in treated reporter cells as a surrogate measure of PPAR functional activity. in_vitro COS-1 C2C12 human mouse luciferase expression increase http://purl.obolibrary.org/obo/GO_0001077 GO OECD Level 2 assay medium luciferase reporter gene assay Quantifying changes in luciferase expression in the treated reporter cells provides a sensitive surrogate measure of the changes in PPAR functional activity. http://purl.obolibrary.org/obo/PR_000001336 PR http://purl.obolibrary.org/obo/GO_0001077 GO luciferase reporter gene assay Transactivation assay quantifying changes in luciferase expression in treated reporter cells as a surrogate measure of PPARγ functional activity. in_vitro COS-7 cells C2C12 cells human mouse luciferase reporter gene expression / PPARγ transcriptional activity change http://www.bioassayontology.org/bao#BAO_0000193 BAO http://purl.obolibrary.org/obo/GO_0006357 GO medium luciferase reporter gene assay Test environment: In vitro Quantifying changes in luciferase expression in the treated reporter cells provides a sensitive surrogate measure of the changes in PPAR functional activity. Transactivation assays are performed using the transient or stably transfected cells with the PPARγ expression plasmid and a reporter plasmid, correspondingly. PPARγ COS-1cell transactivation assay (transient transfection with human or mouse PPARγ expression plasmid and pHD(x3)-Luc reporter plasmid (PPRE)3- luciferase reporter construct C2C12 http://purl.obolibrary.org/obo/GO_0006357 GO molecular modelling Computational simulation of a candidate ligand binding to a receptor, predicting the strength of association or binding affinity. in_silico binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI high molecular modelling; docking Computational simulation of a candidate ligand binding to a receptor, Predicts the strength of association or binding affinity. http://purl.obolibrary.org/obo/PR_000001336 PR http://purl.obolibrary.org/obo/GO_0042379 GO PPARγ (mouse/rat) Reporter Assay Kit Commercially available assay to measure PPARγ transcriptional activity. in_vitro Proprietary rodent cell line mouse rat transcriptional activity increase http://purl.obolibrary.org/obo/GO_0001077 GO medium PPARγ (mouse/rat) Reporter Assay Kit Transcriptional activity of PPARγ can be assessed using commercially available kits like e.g. PPARγ transcription factor assay kit (Abcam, Cambridge, USA or Cayman Chemical, USA). http://purl.obolibrary.org/obo/PR_000001336 PR http://purl.obolibrary.org/obo/GO_0001077 GO PPARγ reporter assay kit Commercial transcription factor assay measuring PPARγ transcriptional activity using a proprietary rodent cell line expressing mouse/rat PPARγ. in_vitro proprietary rodent cell line expressing mouse/rat PPARγ mouse rat PPARγ transcriptional activity change http://www.bioassayontology.org/bao#BAO_0000192 BAO http://purl.obolibrary.org/obo/GO_0006357 GO medium PPARγ (mouse/rat) Reporter Assay Kit Test environment: In vitro, ex vivo Transcriptional activity of PPARγ can be assessed using commercially available kits like e.g. PPARγ transcription factor assay kit (Abcam, Cambridge, USA or Cayman Chemical, USA). Proprietary rodent cell line expressing the mouse/rat PPARγ http://purl.obolibrary.org/obo/GO_0006357 GO PPARγ transcription factor assay Commercially available kit to assess transcriptional activity of PPARγ by measuring protein: DNA binding. in_vitro mouse rat DNA binding activity increase http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0003677 GO not_specified Transcriptional activity of PPARγ can be assessed using commercially available kits like e.g. PPARγ transcription factor assay kit (Abcam, Cambridge, USA or Cayman Chemical, USA). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0003677 GO Scintillation proximity binding assay Direct binding assay indicating the mode of action for PPARα/γ. in_vitro ligand binding not_specified http://purl.obolibrary.org/obo/OBI_0000475 OBI medium Scintillation proximity binding assay direct binding indicating the mode of action for PPARα/γ http://purl.obolibrary.org/obo/PR_000001336 PR http://purl.obolibrary.org/obo/GO_0042379 GO scintillation proximity binding assay Direct in vitro binding assay measuring the interaction of compounds with PPARγ to identify modulators and assess binding mode of action. in_vitro ligand binding to PPARγ change http://www.bioassayontology.org/bao#BAO_0000191 BAO http://purl.obolibrary.org/obo/GO_0005515 GO medium Scintillation proximity binding assay Test environment: In vitro direct binding indicating the mode of action for PPARα/γ This assay determines whether compounds interact directly with PPARγ. Assess the ability of compounds to bind to PPARγ. Identifies the modulators of PPARγ. http://purl.obolibrary.org/obo/GO_0005488 GO gene expression analysis Measures changes in gene expression levels to investigate PPAR-gamma activation. in_vitro gene expression levels decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/PR_P37231 PR medium Peroxisome proliferation-activated receptors are investigated by changes in gene expression and protein levels. http://purl.obolibrary.org/obo/PR_P37231 PR http://purl.obolibrary.org/obo/GO_0010467 GO metabolomics Investigates the effects of PPAR-gamma on downstream gene expression using metabolomics. in_vitro metabolite levels not_specified http://purl.obolibrary.org/obo/OBI_0000366 OBI http://purl.obolibrary.org/obo/PR_P37231 PR high Effects of PPAR gamma on expression of downstream genes can be investigating using metabolomics and RT-qPCR approaches. http://purl.obolibrary.org/obo/CHEBI_25834 CHEBI http://purl.obolibrary.org/obo/GO_0008152 GO metabolomics Profiles small-molecule metabolites to investigate the downstream metabolic consequences of altered PPAR gamma activation. in_vitro metabolite levels downstream of PPAR gamma change http://purl.obolibrary.org/obo/GO_0035624 GO medium Effects of PPAR gamma on expression of downstream genes can be investigating using metabolomics and RT-qPCR approaches. http://purl.obolibrary.org/obo/CHEBI_25212 CHEBI http://purl.obolibrary.org/obo/GO_0008152 GO protein level analysis Measures changes in protein levels to investigate PPAR-gamma activation. in_vitro protein levels decrease http://purl.obolibrary.org/obo/GO_0045184 GO http://purl.obolibrary.org/obo/PR_P37231 PR medium Peroxisome proliferation-activated receptors are investigated by changes in gene expression and protein levels. http://purl.obolibrary.org/obo/PR_P37231 PR http://purl.obolibrary.org/obo/GO_0019538 GO RT-qPCR Measures the expression of downstream genes affected by PPAR-gamma. in_vitro gene expression levels not_specified http://purl.obolibrary.org/obo/GO_0010467 GO medium Effects of PPAR gamma on expression of downstream genes can be investigating using metabolomics and RT-qPCR approaches. http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO western blot Protein levels are investigated to assess PPAR activation. in_vitro protein levels change low Peroxisome proliferation-activated receptors are investigated by changes in gene expression and protein levels. X-ray crystallography Determines the molecular structure of PPAR-gamma. in_vitro molecular structure not_specified http://purl.obolibrary.org/obo/CHMO_0000000 CHMO http://purl.obolibrary.org/obo/PR_P37231 PR low X-ray crystallography can be used to determine molecular structure. http://purl.obolibrary.org/obo/PR_P37231 PR http://purl.obolibrary.org/obo/GO_0006457 GO ATG_PXRE_CIS Measures PXR activation using a cis-reporting assay. in_vitro PXR activation increase high The following ToxCast assays measure PXR activation: ATG_PXRE_CIS; ATG_PXR_TRANS; TOX21_PXR_agonist; ATG_mPXR_XSP2; NVS_NR_hPXR (U.S. EPA 2024). http://purl.obolibrary.org/obo/PR_000001216 PR http://purl.obolibrary.org/obo/GO_0002430 GO Indigo Biosciences PXR activation assay Measures human PXR activation using a commercial assay. in_vitro Homo sapiens PXR activation increase medium Indigo Biosciences sells a commercial assay for human PXR activation (INDIGO Biosciences 2024). http://purl.obolibrary.org/obo/PR_000001216 PR http://purl.obolibrary.org/obo/GO_0002430 GO NVS_NR_hPXR Measures human PXR activation using a specific assay. in_vitro Homo sapiens PXR activation increase high The following ToxCast assays measure PXR activation: ATG_PXRE_CIS; ATG_PXR_TRANS; TOX21_PXR_agonist; ATG_mPXR_XSP2; NVS_NR_hPXR (U.S. EPA 2024). http://purl.obolibrary.org/obo/PR_000001216 PR http://purl.obolibrary.org/obo/GO_0002430 GO RT-qPCR RT-qPCR is used to investigate the effects of Pregnane X receptor (PXR) activation on expression of downstream genes. in_vitro expression of downstream genes increase medium Effects of Pregnane X receptor (PXR) activation on expression of downstream genes can be investigating using transcriptomics and/or RT-qPCR approaches. http://purl.obolibrary.org/obo/GO_0010468 GO RT-qPCR Measures the effects of PXR activation on downstream gene expression using reverse transcription quantitative polymerase chain reaction. in_vitro gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO medium Effects of Pregnane X receptor (PXR) activation on expression of downstream genes can be investigating using transcriptomics and/or RT-qPCR approaches. http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0006351 GO TOX21_PXR_agonist Measures PXR activation using an agonist assay. in_vitro PXR activation increase high The following ToxCast assays measure PXR activation: ATG_PXRE_CIS; ATG_PXR_TRANS; TOX21_PXR_agonist; ATG_mPXR_XSP2; NVS_NR_hPXR (U.S. EPA 2024). http://purl.obolibrary.org/obo/PR_000001216 PR http://purl.obolibrary.org/obo/GO_0002430 GO Transcriptomics Investigates effects of PXR activation on expression of downstream genes using genome-wide RNA sequencing or microarray approaches. not_specified expression of downstream genes increase http://purl.obolibrary.org/obo/GO_0010467 GO high Effects of Pregnane X receptor (PXR) activation on expression of downstream genes can be investigating using transcriptomics and/or RT-qPCR approaches. http://purl.obolibrary.org/obo/GO_0010467 GO transcriptomics Measures the effects of PXR activation on downstream gene expression using high-throughput sequencing. in_vitro gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO high Effects of Pregnane X receptor (PXR) activation on expression of downstream genes can be investigating using transcriptomics and/or RT-qPCR approaches. http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0006351 GO HPLC-ESI-MS/MS High Performance Liquid Chromatography coupled with electrospray tandem mass spectrometry used to separate and detect polar molecules, including peptides and proteins, based on their mass-to-charge ratio. in_vitro mass-to-charge ratio of polar molecules not_specified http://purl.obolibrary.org/obo/CHMO_0000524 CHMO not_specified High Performance Liquid Chromatography – electrospray tandem mass spectrometry (HPLC-ESI-MS/MS) is the most popular MS technique. It combines the separation ability of HPLC along with the sensitivity and specificity of detection from MS. Typically high molecular weight compounds have multiple charges i.e. peptides and proteins. http://purl.obolibrary.org/obo/PR_000000001 PR HPLC-ESI-MS/MS High Performance Liquid Chromatography – electrospray tandem mass spectrometry combines the separation ability of HPLC with the sensitivity and specificity of detection from MS, particularly suited for analysing polar molecules of mass <2000 Dalton. in_vitro protein alkylation not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI medium High Performance Liquid Chromatography – electrospray tandem mass spectrometry (HPLC-ESI-MS/MS) is the most popular MS technique. It combines the separation ability of HPLC along with the sensitivity and specificity of detection from MS. This technique is particularly suited to analysing polar molecules of mass <2000 Dalton and requires no prior derivatisation in most applications. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006491 GO MALDI-TOF/MS Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization technique used in mass spectrometry for analyzing biomolecules like DNA, proteins, peptides, and sugars. It involves mixing the sample with a matrix, laser irradiation, and ionization of the analyte molecules. in_vitro biomolecule analysis change medium Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules (biopolymers such as DNA, proteins, peptides and sugars) and large organic molecules MALDI methodology is a three-step process. Finally, the analyte molecules are ionized by being protonated or deprotonated in the hot plume of ablated gases, and can then be accelerated into whichever mass spectrometer is used to analyse them. MALDI-TOF/MS A soft ionization mass spectrometry technique that uses a pulsed laser to ablate and ionize biomolecules mixed with a matrix, allowing the analysis of large, fragile molecules like proteins and peptides without fragmentation. not_specified mass-to-charge ratio of biomolecules and large organic molecules change not_specified Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules (biopolymers such as DNA, proteins, peptides and sugars) and large organic molecules (such as polymers, dendrimers and other macromolecules), which tend to be fragile and fragment when ionized by more conventional ionization methods. MALDI methodology is a three-step process. First, the sample is mixed with a suitable matrix material and applied to a metal plate. Second, a pulsed laser irradiates the sample, triggering ablation and desorption of the sample and matrix material. Finally, the analyte molecules are ionized by being protonated or deprotonated in the hot plume of ablated gases, and can then be accelerated into whichever mass spectrometer is used to analyse them. MALDI-TOF/MS Matrix-assisted laser desorption/ionization time of flight mass spectrometry is a soft ionization technique used to analyze biomolecules such as proteins, peptides, and other large organic molecules. in_vitro protein alkylation not_specified medium Matrix-assisted laser desorption/ionization (MALDI) is a soft ionization technique used in mass spectrometry, allowing the analysis of biomolecules (biopolymers such as DNA, proteins, peptides and sugars) and large organic molecules (such as polymers, dendrimers and other macromolecules), which tend to be fragile and fragment when ionized by more conventional ionization methods. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006491 GO histopathology This assay involves fixing, dehydrating, and embedding tissues in wax, cutting sections to 3–5 μm thickness, staining, and examining under a microscope to identify tissue changes. in_vivo renal tissue renal pathology increase OECD Test No. 123 low Histopathology focuses on the changes in tissues and is a technique used for identifying correlations with biochemical markers. Generally renal pathology is measured after either whole organism or specific tissue of interest is fixed, dehydrated, and then embedded in wax, commonly paraffin wax. Sections are then cut to approximately 3–5 μm in thickness and stained before being examined under a microscope (e.g., Folmar et al., 2001; Mihaich et al., 2012; Zha et al., 2007). OECD Test No. 123: Guidance document on the diagnosis of endocrine-related histopathology in fish gonads (OECD 2010). Crissman et al. (2004) describes best practice guidelines for toxicologic histopathology. http://purl.obolibrary.org/obo/UBERON_0002113 UBERON http://purl.obolibrary.org/obo/GO_0009605 GO histopathology Histopathology examines tissue changes after fixation, dehydration, embedding, sectioning, and staining, then microscopic examination to identify correlations with biochemical markers. It is used to measure renal pathology. in_vivo kidney fish tissue morphology change http://purl.obolibrary.org/obo/OBI_0000043 OBI OECD Test No. 123 low Histopathology focuses on the changes in tissues and is a technique used for identifying correlations with biochemical markers. Generally renal pathology is measured after either whole organism or specific tissue of interest is fixed, dehydrated, and then embedded in wax, commonly paraffin wax. Sections are then cut to approximately 3–5 μm in thickness and stained before being examined under a microscope (e.g., Folmar et al., 2001; Mihaich et al., 2012; Zha et al., 2007). http://purl.obolibrary.org/obo/CL_0000086 CL renal histopathology This assay measures renal tissue pathology, specifically vitellogenin (VTG) deposition, by fixing, dehydrating, embedding tissue in paraffin wax, sectioning to 3–5 μm, staining, and examining sections under a microscope. ex_vivo kidney fish renal pathology (VTG deposition) increase http://purl.obolibrary.org/obo/UBERON_0002113 UBERON http://purl.obolibrary.org/obo/OBI_0000047 OBI OECD TG 123; OECD TG 227; Crissman et al. 2004; Fiedler et al. 2023 low Generally renal pathology is measured after either whole organism or specific tissue of interest is fixed, dehydrated, and then embedded in wax, commonly paraffin wax. OECD Test No. 123: Guidance document on the diagnosis of endocrine-related histopathology in fish gonads (OECD 2010). Fiedler et al. (2023) have written standardized tissue sampling guidelines for histopathological analyses using rainbow trout. http://purl.obolibrary.org/obo/UBERON_0002113 UBERON http://purl.obolibrary.org/obo/GO_0000154 GO gene expression analysis Quantifies SCD1 mRNA levels in liver tissue of SREBP-1c-deficient mice to assess direct transcriptional induction by LXR activation. in_vivo liver mouse SCD1 mRNA expression increase http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low In addition to the FAS gene induction LXR activation leads to the direct induction of the stearoyl-CoA desaturase 1 (SCD1) in SREBP-1c-deficient mice SCD-1 deficient mice are completely protected against hypertriglyceridemia and TG accumulation in liver is decreased after treatment with T0901317 http://purl.obolibrary.org/obo/GO_0010467 GO lipid accumulation This assay measures the triglyceride (TG) accumulation in the liver of SCD1-deficient mice after treatment with T0901317. in_vivo liver mouse triglyceride accumulation decrease http://purl.obolibrary.org/obo/CHEBI_17850 CHEBI http://purl.obolibrary.org/obo/GO_0043593 GO not_specified SCD-1 deficient mice are completely protected against hypertriglyceridemia and TG accumulation in liver is decreased after treatment with T0901317 http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0043593 GO SCD1 induction assay Measures the direct induction of stearoyl-CoA desaturase 1 (SCD1) in SREBP-1c-deficient mice following LXR activation. in_vivo liver mouse SCD1 expression increase http://purl.obolibrary.org/obo/GO_0006633 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/NCBITaxon_10090 NCBITAXON low LXR activation leads to the direct induction of the stearoyl-CoA desaturase 1 (SCD1) in SREBP-1c-deficient mice SCD-1 deficient mice are completely protected against hypertriglyceridemia and TG accumulation in liver is decreased after treatment with T0901317 http://purl.obolibrary.org/obo/GO_0008610 GO triglyceride measurement This assay measures triglyceride (TG) accumulation in the liver, assessing the effect of SCD-1 deficiency and T0901317 treatment. in_vivo liver mouse triglyceride accumulation decrease low there are data supporting that SCD-1 deficient mice are completely protected against hypertriglyceridemia and TG accumulation in liver is decreased after treatment with T0901317 http://purl.obolibrary.org/obo/CHEBI_30759 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO adenovirus-mediated overexpression Uses adenovirus to overexpress SREBP-1c in the liver of STZ diabetic mice to study its effects on lipogenic enzyme expression and triglyceride content. in_vivo liver mice lipogenic enzyme expression and triglyceride hepatic content increase not_specified in STZ diabetic mice, adenovirus-mediated over-expression of SREBP-1c in the liver resulted in an increase of lipogenic enzyme expression with an increase of the triglyceride hepatic content and a marked decrease in the hyperglycaemia of diabetic mice mimicking perfectly the effect of an insulin injection glucokinase expression assay Measures the expression of glucokinase (GK) to study the role of SREBP-1c in its regulation. not_specified glucokinase (GK) expression not_specified not_specified there are a number of studies that demonstrated that SREBP-1c is essential for glucokinase (GK) expression and that it is a mediator of insulin action hyperglycemia measurement Measurement of blood glucose levels in diabetic mice. Overexpression of SREBP-1c reduces hyperglycemia. in_vivo liver mouse blood glucose levels decrease low in STZ diabetic mice, adenovirus-mediated over-expression of SREBP-1c in the liver resulted in an increase of lipogenic enzyme expression with an increase of the triglyceride hepatic content and a marked decrease in the hyperglycaemia of diabetic mice http://purl.obolibrary.org/obo/CHEBI_5986 CHEBI http://purl.obolibrary.org/obo/GO_0042424 GO mRNA quantification Measurement of mRNA levels for SREBP-1c and lipogenic enzymes such as acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS). not_specified mRNA levels increase http://purl.obolibrary.org/obo/OBI_0000117 OBI not_specified An increase on the mRNA of the SREBP-1c is responsible for an increase of the mRNA of lipogenic enzymes like acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS) http://purl.obolibrary.org/obo/GO_0006351 GO mRNA quantification Measurement of glucokinase (GK) mRNA levels. SREBP-1c is essential for GK expression. in_vivo liver mouse mRNA levels of glucokinase (GK) increase low Finally there are a number of studies that demonstrated that SREBP-1c is essential for glucokinase (GK) expression http://purl.obolibrary.org/obo/GO_0006715 GO http://purl.obolibrary.org/obo/GO_0006081 GO mRNA quantification Measures the mRNA levels of SREBP-1c and lipogenic enzymes such as acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS). not_specified mice mRNA levels of SREBP-1c, ACC, and FAS increase not_specified An increase on the mRNA of the SREBP-1c is responsible for an increase of the mRNA of lipogenic enzymes like acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS) (Foretz et al. 1999, Foretz et al. 2000). qPCR This assay measures the mRNA levels of SREBP-1c and lipogenic enzymes like acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS) using quantitative PCR. in_vitro liver mouse mRNA levels of SREBP-1c and lipogenic enzymes increase http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/OBI_0000727 OBI medium An increase on the mRNA of the SREBP-1c is responsible for an increase of the mRNA of lipogenic enzymes like acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS) (Foretz et al. 1999, Foretz et al. 2000). http://purl.obolibrary.org/obo/PR_000025555 PR http://purl.obolibrary.org/obo/GO_0006631 GO triglyceride accumulation assay Assesses triglyceride accumulation in mice, particularly in the context of SREBP-1c deficiency. in_vivo liver mice triglyceride accumulation not_specified not_specified This finding is demonstrated from the absence of triglyceride accumulation on SREBP-1c (-/-) mice gene expression profiling This assay measures the expression levels of genes related to HSC activation, including alpha smooth muscle actin (Acta2), lysyl oxidase (Lox), and collagen, type I, alpha 1 (Col1a1). not_specified hepatic stellate cells liver gene expression levels of Acta2, Lox, and Col1a1 change medium Gene expression profiling confirmed early changes for known genes related to HSC activation such as alpha smooth muscle actin (Acta2), lysyl oxidase (Lox) and collagen, type I, alpha 1 (Col1a1). http://purl.obolibrary.org/obo/GO_0010468 GO gene expression profiling Measures mRNA levels of genes associated with hepatic stellate cell activation, such as Acta2, Lox, Col1a1, and Igfbp3. in_vitro hepatic stellate cells liver mRNA expression of HSC activation markers increase http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0030308 GO high Gene expression profiling confirmed early changes for known genes related to HSC activation such as alpha smooth muscle actin (Acta2), lysyl oxidase (Lox) and collagen, type I, alpha 1 (Col1a1). Insulin-like growth factor binding protein 3 (Igfbp3) was identified as a gene strongly affected and as marker for culture-activated HSCs and plays a role in HSC migration (Morini et al., 2005; Mannaerts et al., 2013). http://purl.obolibrary.org/obo/CL_0000182 CL http://purl.obolibrary.org/obo/GO_0030308 GO Igfbp3 gene expression assay Measurement of insulin-like growth factor binding protein 3 (Igfbp3) gene expression as a marker for culture-activated hepatic stellate cells and to assess its role in HSC migration. in_vitro culture-activated hepatic stellate cells liver Igfbp3 gene expression change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0016478 GO http://purl.obolibrary.org/obo/CHMO_0000282 CHMO medium Insulin-like growth factor binding protein 3 (Igfbp3) was identified as a gene strongly affected and as marker for culture-activated HSCs and plays a role in HSC migration (Morini et al., 2005; Mannaerts et al., 2013). http://purl.obolibrary.org/obo/GO_0016478 GO α-SMA immunohistochemistry Detects alpha-smooth muscle actin (α-SMA) protein expression as a marker of hepatic stellate cell activation using the anti-alpha smooth muscle Actin [1A4] monoclonal antibody. in_vitro hepatic stellate cells liver α-SMA protein expression increase http://purl.obolibrary.org/obo/GO_0030308 GO medium Alpha-smooth muscle actin (α-SMA) is a well-known marker of hepatic stellate cells activation. Anti-alpha smooth muscle Actin [1A4] monoclonal antibody reacts with the alpha smooth muscle isoform of actin. http://purl.obolibrary.org/obo/CL_0000182 CL http://purl.obolibrary.org/obo/GO_0030308 GO RT-PCR Measures mRNA expression levels of the Steroidogenic acute regulatory protein (STAR). in_vitro Leydig cells testis STAR mRNA expression decrease medium The StAR expression can be measured by RT-PCR (mRNA) http://purl.obolibrary.org/obo/GO_0010467 GO western blot Measures protein expression levels of the Steroidogenic acute regulatory protein (STAR). in_vitro Leydig cells testis STAR protein expression decrease http://purl.obolibrary.org/obo/OBI_0000272 OBI low The StAR expression can be measured by RT-PCR (mRNA) and on the protein level (western blot) http://purl.obolibrary.org/obo/GO_0010485 GO in vitro human T cell proliferation and cytokine profile assay An in vitro assay measuring human T cell proliferation and dendritic cell and T cell cytokine profiles in response to chemical respiratory stimuli. in_vitro T cells dendritic cells lymphoid tissue human T cell proliferation and cytokine profiles change http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/CL_0000010 CL http://purl.obolibrary.org/obo/GO_0051726 GO http://purl.obolibrary.org/obo/CHEBI_53029 CHEBI http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON not_specified Human T cell proliferation and DC and T cell cytokine profiles produced in response to chemical respiratory stimuli have been measured in vitro. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0042110 GO in vitro T-cell-based assays (co-culture) Co-culture assays involving allergen-treated dendritic cells and modified T-lymphocytes to measure biomarker expression or T-cell proliferation. in_vitro dendritic cells T-lymphocytes interferon gamma expression or T-cell proliferation change http://purl.obolibrary.org/obo/GO_0008283 GO not_specified in vitro T-cell-based assays are typically co-cultures of allergen-treated dendritic cells and modified T-lymphocytes with expression of selected biomarkers (e.g. interferon gamma), or T-cell proliferation being the reported outcome. http://purl.obolibrary.org/obo/CL_0000182 CL http://purl.obolibrary.org/obo/GO_0008283 GO LLNA: BrdU-ELISA A non-radioactive modification of the LLNA assay using BrdU-ELISA to measure lymph node cell proliferation in mice for skin sensitization assessment. in_vivo lymph node mouse lymph node cell proliferation increase OECD TG 442B low together with its two non-radioactive modifications (LLNA-DA TG442A and LLNA-BrdU ELISA TG 442B http://purl.obolibrary.org/obo/GO_0008283 GO LLNA:DA A non-radioactive modification of the LLNA assay, measuring lymph node cell proliferation in mice to assess skin sensitization. in_vivo lymph node mouse lymph node cell proliferation increase OECD TG 442A low together with its two non-radioactive modifications (LLNA-DA TG442A http://purl.obolibrary.org/obo/GO_0008283 GO Local Lymph Node Assay (LLNA) An in vivo assay measuring lymph node cell proliferation in mice to assess skin sensitization. in_vivo lymph node mouse lymph node cell proliferation increase OECD TG 429 low lymph node cell proliferation is the basis for the in vivo mouse Local Lymph Node Assay (LLNA). OECD TG 429 is the validated test guideline for the Skin Sensitisation: Local Lymph Node Assay http://purl.obolibrary.org/obo/GO_0008283 GO T-cell proliferation assay Measures T-cell proliferation in co-cultures of allergen-treated dendritic cells and modified T-lymphocytes, often with biomarker expression (e.g., interferon gamma). in_vitro T-lymphocytes dendritic cells human T-cell proliferation increase http://purl.obolibrary.org/obo/GO_0042129 GO http://purl.obolibrary.org/obo/GO_0032606 GO medium in vitro T-cell-based assays are typically co-cultures of allergen-treated dendritic cells and modified T-lymphocytes with expression of selected biomarkers (e.g. interferon gamma), or T-cell proliferation being the reported outcome. Human T cell proliferation and DC and T cell cytokine profiles produced in response to chemical respiratory stimuli have been measured in vitro. http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042129 GO enzyme linked immunosorbent assay Measures steroid production by isolated primary theca cells using enzyme-linked antibodies. in_vitro primary theca cells ovary testosterone production decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006707 GO medium Steroid production by isolated primary theca cells can be measured using radioimmunoassay or enzyme linked immunosorbent assay approaches http://purl.obolibrary.org/obo/CL_0000068 CL http://purl.obolibrary.org/obo/GO_0006704 GO ex vivo steroidogenesis assay An in vivo evaluation of testosterone production using intact ovarian tissue explants. ex_vivo ovarian tissue T production decrease not_specified in vivo (i.e., via ex vivo steroidogenesis assay; e.g., (Ankley et al. 2007)) Reductions in T production by ovarian tissue explants ex vivo steroidogenesis assay Measures testosterone production by intact ovarian tissue explants following in vivo chemical exposure. ex_vivo ovary testosterone production decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/UBERON_0000982 UBERON low this key event is perhaps best evaluated by examining T production by intact ovarian tissue explants either exposed to chemicals in vitro (e.g., (Villeneuve et al. 2007; McMaster ME 1995) or in vivo (i.e., via ex vivo steroidogenesis assay; e.g., (Ankley et al. 2007)) http://purl.obolibrary.org/obo/UBERON_0000982 UBERON http://purl.obolibrary.org/obo/GO_0006704 GO Intact ovarian tissue explant assay for testosterone Measures testosterone production by intact ovarian tissue explants, either exposed to chemicals in vitro or in vivo. in_vitro the ovarian tissue explants ovary not_specified testosterone concentration decrease low However, the isolation and culture methods are not trivial. Similarly, development of immortalized theca cell lines has proven challenging (Havelock et al. 2004). Consequently, this key event is perhaps best evaluated by examining T production by intact ovarian tissue explants either exposed to chemicals in vitro (e.g., (Villeneuve et al. 2007; McMaster ME 1995) or in vivo (i.e., via ex vivo steroidogenesis assay; e.g., (Ankley et al. 2007)). http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006694 GO ovarian tissue explant assay Measures testosterone production by intact ovarian tissue explants exposed to chemicals in vitro. ex_vivo ovary testosterone production decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/UBERON_0000982 UBERON low this key event is perhaps best evaluated by examining T production by intact ovarian tissue explants either exposed to chemicals in vitro http://purl.obolibrary.org/obo/UBERON_0000982 UBERON http://purl.obolibrary.org/obo/GO_0006704 GO radioimmunoassay Measures steroid production by isolated primary theca cells using radioactive isotopes and antibodies. in_vitro primary theca cells ovary testosterone production decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006707 GO low Steroid production by isolated primary theca cells can be measured using radioimmunoassay http://purl.obolibrary.org/obo/CL_0000068 CL http://purl.obolibrary.org/obo/GO_0006704 GO ELISA Measures thyroid hormone levels (e.g., T4) using enzyme-linked immunosorbent assay. not_specified T4 levels decrease http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI medium ELISA http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO ELISA Enzyme-linked immunosorbent assay used to quantify the amount of thyroid hormone. in_vitro thyroid hormone concentration not_specified http://purl.obolibrary.org/obo/CHEBI_35221 CHEBI not_specified Methods used to assess TH synthesis include, incorporation of radiolabeled tracer compounds, radioimmunoassay, ELISA, and analytical detection. http://purl.obolibrary.org/obo/CHEBI_35221 CHEBI http://purl.obolibrary.org/obo/GO_0006639 GO HPLC/ICP-mass spectrometry Quantifies thyroid hormones using high-performance liquid chromatography coupled with inductively coupled plasma mass spectrometry. not_specified thyroid gland amphibian TH levels decrease http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI low THs was measured by HPLC/ICP-mass spectometry http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO LC-MS Analytical determination of thyroid hormone levels using liquid chromatography-mass spectrometry. not_specified TH levels decrease http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI http://purl.obolibrary.org/obo/OBI_0000475 OBI medium Analytical determination of TH levels by LC-MS http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO radioimmunoassay Quantifies thyroid hormone levels (e.g., T4) using antibody-based detection. not_specified T4 levels decrease http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI http://purl.obolibrary.org/obo/OBI_0000415 OBI not_specified radioimmunoassay http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO radioimmunoassay An immunological assay used to quantify thyroid hormone levels or synthesis. in_vitro thyroid hormone concentration not_specified http://purl.obolibrary.org/obo/CHEBI_35221 CHEBI not_specified Methods used to assess TH synthesis include, incorporation of radiolabeled tracer compounds, radioimmunoassay, ELISA, and analytical detection. http://purl.obolibrary.org/obo/CHEBI_35221 CHEBI http://purl.obolibrary.org/obo/GO_0006639 GO radiolabeled tracer incorporation Measures incorporation of radiolabeled compounds to assess thyroid hormone synthesis. not_specified thyroid gland incorporation of radiolabeled tracer compounds decrease http://purl.obolibrary.org/obo/GO_0042402 GO not_specified incorporation of radiolabeled tracer compounds http://purl.obolibrary.org/obo/UBERON_0002046 UBERON http://purl.obolibrary.org/obo/GO_0042402 GO TIQDT (Thyroxine-immunofluorescence quantitative disruption test) Provides an immunofluorescent-based estimate of thyroxine levels in the thyroid gland of zebrafish. in_vivo thyroid gland zebrafish thyroxine levels decrease http://purl.obolibrary.org/obo/CHEBI_18262 CHEBI http://purl.obolibrary.org/obo/OBI_0000515 OBI medium TIQDT (Thyroxine-immunofluorescence quantitative disruption test) is a method that provides an immunofluorescent based estimate of thyroxine in the gland of zebrafish http://purl.obolibrary.org/obo/CHEBI_18262 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO transgenic zebrafish with fluorescent thyroid follicles Visualizes compensatory proliferation of thyroid follicles following inhibition of TH synthesis using fluorescent markers. in_vivo thyroid follicles zebrafish thyroid follicle proliferation increase http://purl.obolibrary.org/obo/UBERON_0005600 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO low transgenic zebrafish with fluorescent thyroid follicles are being used to visualize the compensatory proliferation of the thyroid follicles following inhibition of TH synthesis http://purl.obolibrary.org/obo/UBERON_0005600 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO whole body TH level measurement Measures thyroid hormone levels in whole fish early life stages as indirect evidence of decreased TH synthesis. in_vivo fish whole body TH levels decrease http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI medium whole body TH level measurements in fish early life stages are used as indirect evidence of decreased TH synthesis http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO Amplex UltraRed fluorescent assay Measures TPO activity using a fluorescent substrate (Amplex UltraRed) that produces a stable fluorescent product proportional to TPO activity. in_vitro rodent thyroid glands porcine thyroid glands human thyroid glands rodent porcine human TPO activity decrease http://purl.obolibrary.org/obo/GO_0004797 GO high More recently, higher-throughput methods using commercial fluorescent and luminescent substrates with rodent, porcine, and human microsomal TPO have been developed (Vickers et al., 2012; Paul et al., 2013; 2014; Kaczur et al., 1997). This assay substitutes a pre-fluorescent substrate (Amplex UltraRed) for guaiacol, that when incubated with a source of peroxidase and excess hydrogen peroxidase, results in a stable fluorescent product proportional to TPO activity (Vickers et al., 2012). The stability of the fluorescent reaction product allows this assay to be used in a higher throughput format (Paul-Friedman et al., 2016). http://purl.obolibrary.org/obo/PR_000001729 PR http://purl.obolibrary.org/obo/GO_0006468 GO guaiacol oxidation assay Measures TPO activity via kinetic measurement of the oxidation of guaiacol. in_vitro porcine thyroid glands human goiter samples rat thyroid glands porcine human rat TPO activity decrease http://purl.obolibrary.org/obo/GO_0004797 GO low TPO activity has been measured for decades via indirect assessment by kinetic measurement of the oxidation of guaiacol (Chang & Doerge 2000; Hornung et al., 2010; Schmutzler et al., 2007). This method is a low-throughput assay due to the very rapid kinetics of the guaiacol oxidation reaction. http://purl.obolibrary.org/obo/PR_000001729 PR http://purl.obolibrary.org/obo/GO_0006468 GO guaiacol oxidation kinetic assay An indirect assessment of TPO activity via kinetic measurement of the oxidation of guaiacol. in_vitro thyroid glands follicles porcine human rat oxidation of guaiacol change low TPO activity has been measured for decades via indirect assessment by kinetic measurement of the oxidation of guaiacol This method is a low-throughput assay due to the very rapid kinetics of the guaiacol oxidation reaction. HPLC-based iodothyronine synthesis assay Uses HPLC to measure TPO activity by quantifying formation of MIT, DIT, T3, and T4 in a reaction mixture containing TPO or a surrogate enzyme. in_vitro thyroid gland not_specified monoiodotyrosine, diiodotyrosine, T3, and T4 formation decrease http://purl.obolibrary.org/obo/GO_0004775 GO http://purl.obolibrary.org/obo/CHMO_0000433 CHMO low HPLC has been used to measure the activity of TPO via formation of the precursors monoiodotyrosine (MIT), diiodotyrosine (DIT), and both T3 and T4, in a reaction mixture containing TPO, or a surrogate enzyme such as lactoperoxidase (Divi & Doerge 1994). However, HPLC or other analytical chemistry techniques make this a low throughput assay, depending on the level of automation. HPLC-based TPO activity assay Measures TPO activity via formation of MIT, DIT, T3, and T4 using HPLC. in_vitro formation of MIT, DIT, T3, and T4 decrease http://purl.obolibrary.org/obo/GO_0004797 GO http://purl.obolibrary.org/obo/CHEBI_17954 CHEBI http://purl.obolibrary.org/obo/CHEBI_17955 CHEBI http://purl.obolibrary.org/obo/CHEBI_18257 CHEBI http://purl.obolibrary.org/obo/CHEBI_18258 CHEBI low HPLC has been used to measure the activity of TPO via formation of the precursors monoiodotyrosine (MIT), diiodotyrosine (DIT), and both T3 and T4, in a reaction mixture containing TPO, or a surrogate enzyme such as lactoperoxidase (Divi & Doerge 1994). However, HPLC or other analytical chemistry techniques make this a low throughput assay, depending on the level of automation. http://purl.obolibrary.org/obo/PR_000001729 PR http://purl.obolibrary.org/obo/GO_0006468 GO TPO mRNA measurement Measures TPO mRNA levels as indirect evidence of TPO inhibition. in_vivo fish TPO mRNA levels increase http://purl.obolibrary.org/obo/GO_0010467 GO not_specified In fish, increases of TPO mRNA levels are often used as indirect evidence of TPO inhibition in in vivo experiments (Baumann et al., 2016; Nelson et al., 2016; Wang et al., 2020). http://purl.obolibrary.org/obo/PR_000001729 PR http://purl.obolibrary.org/obo/GO_0006468 GO LC-ICP-MS Liquid chromatography coupled with inductively coupled plasma mass spectrometry used to measure low levels of thyroid hormones in whole-body homogenates. in_vitro whole-body frog tadpoles brain concentrations of TH not_specified low Two analytical techniques, LC- and HPLC-inductively coupled plasma–mass spectrometry have recently been used to measure brain concentrations of TH. These techniques have proven capable of measuring very low levels in whole-body homogenates of frog tadpoles http://purl.obolibrary.org/obo/CHEBI_15212 CHEBI LC-inductively coupled plasma–mass spectrometry LC-inductively coupled plasma–mass spectrometry is used to measure brain concentrations of thyroid hormones, capable of detecting very low levels in whole-body homogenates. in_vitro brain frog tadpoles thyroid hormone levels not_specified http://purl.obolibrary.org/obo/CHEBI_18397 CHEBI http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Two analytical techniques, LC- and HPLC-inductively coupled plasma–mass spectrometry have recently been used to measure brain concentrations of TH. These techniques have proven capable of measuring very low levels in whole-body homogenates of frog tadpoles at different developmental stages (e.g., Simon et al., 2002; Tietge et al., 2010). http://purl.obolibrary.org/obo/CHEBI_18397 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO LC-MS/MS Liquid chromatography-tandem mass spectrometry used for simultaneous analysis of multiple thyroid hormones in serum and tissues including the brain. in_vitro brain serum simultaneous analysis of five THs not_specified low used liquid chromatography-tandem mass spectrometry for the simultaneous analysis of five THs including thyroxine (T4)... in serum and a variety of tissues including brain. http://purl.obolibrary.org/obo/CHEBI_15212 CHEBI LC-MS/MS Liquid chromatography-tandem mass spectrometry measures brain concentrations of I–, MIT, DIT, T4, T3, and rT3. It can measure very low levels in whole-body homogenates. in_vivo brain frog THs concentration (I–, MIT, DIT, T4, T3, and rT3) change http://purl.obolibrary.org/obo/CHEBI_50799 CHEBI http://purl.obolibrary.org/obo/CHEBI_50800 CHEBI medium Two analytical techniques, LC- and HPLC-inductively coupled plasma–mass spectrometry have recently been used to measure brain concentrations of TH. These techniques have proven capable of measuring very low levels in whole-body homogenates of frog tadpoles at different developmental stages The assay detects I–, MIT, DIT, T4, T3, and rT3. http://purl.obolibrary.org/obo/CHEBI_50799 CHEBI http://purl.obolibrary.org/obo/GO_0001952 GO liquid chromatography-tandem mass spectrometry (LC-MS/MS) A technique for the simultaneous analysis of multiple thyroid hormones in serum and various tissues, including the brain. in_vitro serum brain thyroid hormone concentration not_specified http://purl.obolibrary.org/obo/CHEBI_35103 CHEBI low used liquid chromatography-tandem mass spectrometry for the simultaneous analysis of five THs including thyroxine (T4), 3,3′,5-triidothyronine (T3), 3,3′,5′-triiodothyronine (rT3; reverse T3), 3,3′-diiodothyronine (3,3′-T2), and 3,5-diiodothyronine (3,5-T2) in serum and a variety of tissues including brain. http://purl.obolibrary.org/obo/CHEBI_35103 CHEBI Radioimmunoassay (RIA) Radioimmunoassays are used to detect thyroid hormones (TH) in neuronal tissue, measuring levels of I–, MIT, DIT, T4, T3, and rT3. in_vitro brain thyroid hormone levels decrease http://purl.obolibrary.org/obo/CHEBI_18397 CHEBI http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Radioimmunoassays (RIAs) are commonly used to detect TH in the brain (e.g., Obregon et al., 1982; Calvo et al., 1990; Morse et al., 1996; Bansal et al., 2005; Gilbert et al., 2013). The assay detects I–, MIT, DIT, T4, T3, and rT3. http://purl.obolibrary.org/obo/CHEBI_18397 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO RIA Radioimmunoassays (RIAs) detect tyrosine hydroxylase (TH) in the brain. The method requires technical knowledge of RIAs and is not available as a simple kit. in_vivo brain TH concentration decrease http://purl.obolibrary.org/obo/CHEBI_59748 CHEBI low Radioimmunoassays (RIAs) are commonly used to detect TH in the brain The method (and minor variants) is well established in the published literature. Evaluations in neuronal tissue are complicated by the difficulty of the fatty matrix, heterogeneity of regions within the brain, and low tissue concentrations and small tissue amounts especially in immature brain. http://purl.obolibrary.org/obo/CHEBI_59748 CHEBI http://purl.obolibrary.org/obo/GO_0008743 GO ELISA An indirect methodology commonly used as a human clinical test method to measure thyroid hormone concentrations. in_vitro serum human thyroid hormone concentrations not_specified not_specified The ELISA method is commonly used as a human clinical test method. Both RIA and ELISA measure THs by an indirect methodology ELISA Measures total T3 and T4 concentrations in serum using enzyme-linked immunosorbent assay. in_vitro serum total T3 and T4 concentrations decrease high The ELISA method is commonly used as a human clinical test method. Both RIA and ELISA measure THs by an indirect methodology http://purl.obolibrary.org/obo/CHEBI_17803 CHEBI http://purl.obolibrary.org/obo/GO_0035767 GO HPLC Measures iodothyronines and their conjugates using high-performance liquid chromatography. in_vitro serum iodothyronines and their conjugates change http://purl.obolibrary.org/obo/OBI_0000215 OBI low Analytical determination of iodothyronines (T3, T4, rT3, T2) and their conjugates, through methods employing HPLC, liquid chromatography, immuno luminescence, and mass spectrometry are less common, but are becoming increasingly available (Hornung et al., 2015; DeVito et al., 1999; Baret and Fert, 1989; Spencer, 2013; Samanidou V.F et al., 2000; Rathmann D. et al., 2015 ). http://purl.obolibrary.org/obo/CHEBI_17803 CHEBI http://purl.obolibrary.org/obo/GO_0042404 GO LC-MS Measures thyroid hormone levels in whole body or serum using liquid chromatography-mass spectrometry. in_vitro whole body serum fish thyroid hormone levels decrease http://purl.obolibrary.org/obo/OBI_0001073 OBI low In fish early life stages most evidence for the ontogeny of thyroid hormone synthesis comes from measurements of whole body thyroid hormone levels using LC-MS techniques (Hornung et al., 2015) which are increasingly used to accurately quantify whole body thyroid hormone levels as a proxy for serum thyroid hormone levels (Nelson et al., 2016; Stinckens et al., 2016; Stinckens et al., 2020). http://purl.obolibrary.org/obo/CHEBI_17803 CHEBI http://purl.obolibrary.org/obo/GO_0035767 GO Radioimmunoassay (RIA) Measures total T3 and T4 concentrations in serum using radioactive labels and antibodies. in_vitro serum total T3 and T4 concentrations decrease medium the radioimmunoassay (RIA). The method is routinely used in rodent endocrine and toxicity studies. Both RIA and ELISA measure THs by an indirect methodology http://purl.obolibrary.org/obo/CHEBI_17803 CHEBI http://purl.obolibrary.org/obo/GO_0035767 GO ELISA Measures the relative abundance of vitellogenin protein in liver tissue or whole body using enzyme-linked immunosorbent assay. in_vivo liver whole body relative abundance of vitellogenin protein not_specified medium Relative abundance of vitellogenin transcripts or protein can be readily measured in liver tissue (e.g., (Biales et al. 2007)) or whole body (H Holbech et al. 2001) from organisms exposed in vivo, or in liver slices (e.g., (Schmieder et al. 2000) or hepatocytes (e.g., (Navas and Segner 2006) exposed in vitro, using real-time quantitative polymerase chain reaction (PCR; transcripts) or enzyme linked immunosorbent assay (ELISA; protein). http://purl.obolibrary.org/obo/GO_0043043 GO real-time quantitative PCR Measures the relative abundance of vitellogenin transcripts in liver tissue or whole body using polymerase chain reaction. in_vivo liver whole body relative abundance of vitellogenin transcripts not_specified medium Relative abundance of vitellogenin transcripts or protein can be readily measured in liver tissue (e.g., (Biales et al. 2007)) or whole body (H Holbech et al. 2001) from organisms exposed in vivo, or in liver slices (e.g., (Schmieder et al. 2000) or hepatocytes (e.g., (Navas and Segner 2006) exposed in vitro, using real-time quantitative polymerase chain reaction (PCR; transcripts) http://purl.obolibrary.org/obo/GO_0010467 GO RT-qPCR Measures the transcriptional level of known downstream target genes of the androgen receptor (AR). in_vitro transcriptional level of AR target genes change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0030521 GO medium Altered transcription of genes by the AR can be measured by measuring the transcriptional level of known downstream target genes by RT-qPCR or other transcription analysis approaches http://purl.obolibrary.org/obo/PR_000001149 PR http://purl.obolibrary.org/obo/GO_0006351 GO RT-qPCR Quantification of the transcriptional levels of known downstream target genes using reverse transcription quantitative polymerase chain reaction. in_vitro transcriptional level of known downstream target genes change http://purl.obolibrary.org/obo/GO_0051272 GO http://purl.obolibrary.org/obo/GO_0006351 GO medium measuring the transcriptional level of known downstream target genes by RT-qPCR http://purl.obolibrary.org/obo/GO_0003677 GO transcriptomics Analyzes genome-wide transcriptional patterns to identify AR-mediated gene expression changes. in_vitro genome-wide transcriptional patterns change http://purl.obolibrary.org/obo/GO_0005669 GO http://purl.obolibrary.org/obo/OBI_0000369 OBI high other transcription analysis approaches, e.g. transcriptomics http://purl.obolibrary.org/obo/GO_0005669 GO http://purl.obolibrary.org/obo/GO_0010467 GO transcriptomics High-throughput transcriptome profiling used to assess AR-mediated transcriptional patterns of effect across many genes, followed by downstream bioinformatics analyses to identify and compare effect footprints. in_vitro transcriptional patterns of AR-mediated genes change http://purl.obolibrary.org/obo/GO_0006350 GO http://www.ebi.ac.uk/efo/EFO_0002810 EFO high Altered transcription of genes by the AR can be measured by measuring the transcriptional level of known downstream target genes by RT-qPCR or other transcription analysis approaches, e.g. transcriptomics. Since this KE aims to capture AR-mediated transcriptional patterns of effect, downstream bioinformatics analyses will typically be required to identify and compare effect footprints. http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006350 GO qPCR Measures gene expression levels of TSPO using quantitative polymerase chain reaction. in_vitro Leydig cells testis TSPO gene expression levels decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/PR_000001779 PR medium TSPO levels can be assayed by standard methods for assessment of gene expression levels like qPCR http://purl.obolibrary.org/obo/PR_000001779 PR http://purl.obolibrary.org/obo/GO_0010467 GO Western blot Measures protein levels of TSPO using antibody-based detection. in_vitro Leydig cells testis TSPO protein levels decrease http://purl.obolibrary.org/obo/GO_0032355 GO http://purl.obolibrary.org/obo/PR_000001779 PR low direct protein levels by Western blot http://purl.obolibrary.org/obo/PR_000001779 PR http://purl.obolibrary.org/obo/GO_0008104 GO analytical ultracentrifuging Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds using analytical ultracentrifugation. in_vitro concentration of triglycerides, cholesterols, fatty acids, and related compounds not_specified low common techniques include high throughput enzymatic analyses, analytical ultracentrifuging http://purl.obolibrary.org/obo/GO_0006995 GO http://purl.obolibrary.org/obo/GO_0006869 GO gene expression analysis Measures gene expression levels to assess changes in influx, efflux, synthesis, and/or breakdown pathways. in_vitro gene expression levels increase http://purl.obolibrary.org/obo/OBI_0000622 OBI high Analysis is often performed to look at gene expression levels to see which pathway(s) have increased expression levels, to attribute plausibility to changes in influx, eflux, synthesis, and/or breakdown pathways http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO gradient gel electrophoresis Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds using gradient gel electrophoresis. in_vitro concentration of triglycerides, cholesterols, fatty acids, and related compounds not_specified http://purl.obolibrary.org/obo/OBI_0000207 OBI medium common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis http://purl.obolibrary.org/obo/GO_0006995 GO http://purl.obolibrary.org/obo/GO_0006869 GO high throughput enzymatic analyses Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentration of triglycerides, cholesterols, fatty acids, and related compounds not_specified high Concentrations of triglycerides, cholesterols, fatty acids, and related compounds are measured biochemically to assess levels in control versus potentially affected individuals; common techniques include high throughput enzymatic analyses http://purl.obolibrary.org/obo/CHEBI_16468 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO lipidomics Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds using lipidomics techniques. in_vitro concentration of triglycerides, cholesterols, fatty acids, and related compounds not_specified high common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis, Nuclear Magnetic Resonance, lipidomics http://purl.obolibrary.org/obo/CHEBI_18055 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO lipidomics Large-scale study of pathways and concentrations of lipids including triglycerides and fatty acids. in_vitro lipid profiles change high common techniques include ... lipidomics http://purl.obolibrary.org/obo/GO_0006688 GO membrane integrity assessment Assesses membrane integrity to evaluate alteration of normal function within cells. in_vitro membrane integrity not_specified http://purl.obolibrary.org/obo/GO_0005886 GO medium Assessment of cellular components including mitochondria and membrane integrity can also be used as evidence of alteration of normal function within cells http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0008332 GO mitochondria assessment Assesses cellular components including mitochondria to evaluate alteration of normal function within cells. in_vitro mitochondrial function not_specified http://purl.obolibrary.org/obo/GO_0005739 GO medium Assessment of cellular components including mitochondria and membrane integrity can also be used as evidence of alteration of normal function within cells http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0008152 GO Nuclear Magnetic Resonance Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds using Nuclear Magnetic Resonance. in_vitro concentration of triglycerides, cholesterols, fatty acids, and related compounds not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI medium common techniques include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis, Nuclear Magnetic Resonance http://purl.obolibrary.org/obo/CHEBI_16468 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO computational modeling Predicts vascular insufficiency for potential vascular disrupting chemicals using pathway analysis. in_silico predicted vascular disruption not_specified high Computational models: Critical pathways for developmental angiogenesis and potential disruptions have critical signal-response systems embedded in three types of receptors that play key roles in a number of morphoregulatory processes: receptor tyrosine kinases (e.g., growth factor-signaling), G-protein coupled receptors (e.g., chemokine signaling), and GPI-anchored receptors (e.g., uPAR system). Computational approaches have been used to predict vascular insufficiency for potential vascular disrupting chemicals (pVDCs) that are developmental toxicants or non-toxicants [Kleinstreuer et al. 2011; Knudsen and Kleinstreuer, 2011]. This has been applied to the ToxCast inventory to rank order over a thousand chemicals for validation testing [McCollum et al. 2017; Tal et al. 2017; Saili et al. 2019; Zurlinden et al. 2020]. Live-cell and confocal imaging assay A quantitative imaging assay using live-cell and confocal microscopy to detect trajectory dynamics and subtle morphological changes in vascular patterning in zebrafish embryos during chemical exposure. in_vivo blood vessel Danio rerio vascular patterning trajectory dynamics change http://purl.obolibrary.org/obo/GO_0048538 GO medium Live-cell imaging has been used to quantitatively detect the trajectory dynamics of vascular patterning [Clendenon et al. 2013; Shirinfard et al. 2013] and confocal cell imaging has been used to develop a quantitative assay capable of detecting relatively subtle changes (~8%) in relative to controls during chemical exposure [Tal et al. 2017]. Rat aortic explant assay A functional assay using cultured rat aortic tissue explants to evaluate angiogenesis and vascular development in response to chemical exposure. in_vitro aorta Rattus norvegicus angiogenesis and vascular development decrease http://purl.obolibrary.org/obo/GO_0001525 GO low Complex functional assays such as the rat aortic explant assay, rat whole embryo culture, and the zebrafish embryotoxicity along with transcriptomic signatures provide a tiered approach to evaluate HTS signatures and their taxonomic implications for conserved pathways to prioritize further in vivo testing studies [Ellis-Hutchings et al. 2017]. anchored the results to complex in vitro functional assays: the rat aortic explant assay, rat whole embryo culture, and zebrafish embryotoxicity [Saili et al. 2019]. Both compounds disrupted angiogenesis and embryogenesis in the functional assays, with differences in potency and adverse effects. http://purl.obolibrary.org/obo/GO_0001525 GO rat aortic explant assay Evaluates angiogenesis and embryogenesis using rat aortic tissue. ex_vivo aorta Rattus norvegicus angiogenesis disruption decrease http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/UBERON_0000947 UBERON low Complex functional assays such as the rat aortic explant assay, rat whole embryo culture, and the zebrafish embryotoxicity along with transcriptomic signatures provide a tiered approach to evaluate HTS signatures and their taxonomic implications for conserved pathways to prioritize further in vivo testing studies [Ellis-Hutchings et al. 2017]. ToxCast: A study evaluated two anti-angiogenic agents, 5HPP-33, a synthetic Thalidomide analog [Noguchi et al. 2005] and TNP-470, a synthetic Fumagillan analog [Ingber et al. 1990] across the ToxCast HTS assay platform and anchored the results to complex in vitro functional assays: the rat aortic explant assay, rat whole embryo culture, and zebrafish embryotoxicity [Saili et al. 2019]. Both compounds disrupted angiogenesis and embryogenesis in the functional assays, with differences in potency and adverse effects. http://purl.obolibrary.org/obo/UBERON_0000947 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO rat whole embryo culture This assay involves culturing rat embryos to assess developmental toxicity. It is used to evaluate HTS signatures and prioritize in vivo testing. ex_vivo embryo rat embryonic development change medium Complex functional assays such as the rat aortic explant assay, rat whole embryo culture, and the zebrafish embryotoxicity along with transcriptomic signatures provide a tiered approach to evaluate HTS signatures ToxCast : A study evaluated two anti-angiogenic agents... and anchored the results to complex in vitro functional assays: the rat aortic explant assay, rat whole embryo culture, and zebrafish embryotoxicity http://purl.obolibrary.org/obo/CL_0000178 CL http://purl.obolibrary.org/obo/GO_0009555 GO ToxCast HTS assay platform A high-throughput screening platform used to evaluate the effects of chemicals on various biological pathways and endpoints. in_vitro chemical effects on biological pathways not_specified high ToxCast: A study evaluated two anti-angiogenic agents, 5HPP-33, a synthetic Thalidomide analog [Noguchi et al. 2005] and TNP-470, a synthetic Fumagillan analog [Ingber et al. 1990] across the ToxCast HTS assay platform and anchored the results to complex in vitro functional assays: the rat aortic explant assay, rat whole embryo culture, and zebrafish embryotoxicity [Saili et al. 2019]. zebrafish embryotoxicity This assay assesses toxicity in zebrafish embryos, often using transgenic lines expressing GFP under the control of the Vegfr2 promoter to visualize blood vessel development. in_vivo embryo blood vessels zebrafish blood vessel development decrease high Complex functional assays such as the rat aortic explant assay, rat whole embryo culture, and the zebrafish embryotoxicity along with transcriptomic signatures provide a tiered approach to evaluate HTS signatures Phenotypic readouts have been used to screen and validate anti-angiogenic compounds ToxCast : A study evaluated two anti-angiogenic agents... and anchored the results to complex in vitro functional assays: the rat aortic explant assay, rat whole embryo culture, and zebrafish embryotoxicity http://purl.obolibrary.org/obo/CL_0000136 CL http://purl.obolibrary.org/obo/GO_0001525 GO zebrafish embryotoxicity An in vivo assay assessing developmental toxicity and angiogenic effects in zebrafish embryos. in_vivo embryo zebrafish embryotoxicity change low the rat aortic explant assay, rat whole embryo culture, and zebrafish embryotoxicity along with transcriptomic signatures provide a tiered approach Both compounds disrupted angiogenesis and embryogenesis in the functional assays http://purl.obolibrary.org/obo/UBERON_0000115 UBERON http://purl.obolibrary.org/obo/GO_0044335 GO zebrafish embryotoxicity assay Evaluates vascular development and embryotoxicity in zebrafish embryos using GFP reporter lines. in_vivo embryo Danio rerio vascular patterning disruption decrease http://purl.obolibrary.org/obo/GO_0001568 GO http://purl.obolibrary.org/obo/NCBITaxon_7955 NCBITAXON medium Zebrafish reporter assays: Blood flow begins in the zebrafish embryo at ∼24 h postfertilization. Shortly after this, the angiogenic vessels that perfuse the trunk of the embryo (intersegmental vessels) sprout from the vasculogenic vessels [Tran et al. 2007]. These effects can be visualized in automated, quantitative screening assays using transgenic zebrafish expressing green fluorescent protein (GFP) under the control of the vascular endothelial growth factor receptor (VEGFR) Vegfr2 promoter that restricts reporter gene expression to developing blood vessels. Complex functional assays such as the rat aortic explant assay, rat whole embryo culture, and the zebrafish embryotoxicity along with transcriptomic signatures provide a tiered approach to evaluate HTS signatures and their taxonomic implications for conserved pathways to prioritize further in vivo testing studies [Ellis-Hutchings et al. 2017]. ToxCast: A study evaluated two anti-angiogenic agents, 5HPP-33, a synthetic Thalidomide analog [Noguchi et al. 2005] and TNP-470, a synthetic Fumagillan analog [Ingber et al. 1990] across the ToxCast HTS assay platform and anchored the results to complex in vitro functional assays: the rat aortic explant assay, rat whole embryo culture, and zebrafish embryotoxicity [Saili et al. 2019]. Both compounds disrupted angiogenesis and embryogenesis in the functional assays, with differences in potency and adverse effects. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0001568 GO zebrafish GFP reporter assay Uses transgenic zebrafish with GFP under VEGFR promoter to visualize and quantify vascular development. in_vivo blood vessels Danio rerio vascular patterning change http://purl.obolibrary.org/obo/GO_0001568 GO http://purl.obolibrary.org/obo/CHMO_0002700 CHMO http://purl.obolibrary.org/obo/NCBITaxon_7955 NCBITAXON high Zebrafish reporter assays: Blood flow begins in the zebrafish embryo at ∼24 h postfertilization. Shortly after this, the angiogenic vessels that perfuse the trunk of the embryo (intersegmental vessels) sprout from the vasculogenic vessels [Tran et al. 2007]. These effects can be visualized in automated, quantitative screening assays using transgenic zebrafish expressing green fluorescent protein (GFP) under the control of the vascular endothelial growth factor receptor (VEGFR) Vegfr2 promoter that restricts reporter gene expression to developing blood vessels. Phenotypic readouts have been used to screen and validate anti-angiogenic compounds [Tran et al. 2007; Yano et al. 2012; Yozzo et al. 2013; Tal et al. 2014; McCollum et al. 2017]. Live-cell imaging has been used to quantitatively detect the trajectory dynamics of vascular patterning [Clendenon et al. 2013; Shirinfard et al. 2013] and confocal cell imaging has been used to develop a quantitative assay capable of detecting relatively subtle changes (~8%) in relative to controls during chemical exposure [Tal et al. 2017]. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0001568 GO zebrafish reporter assay A quantitative screening assay using transgenic zebrafish expressing GFP under the control of the VEGFR2 promoter to visualize and quantify angiogenic vessel development. in_vivo embryo Danio rerio angiogenic vessel development change http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/GO_0001568 GO medium Zebrafish reporter assays: Blood flow begins in the zebrafish embryo at ~24 h postfertilization. Shortly after this, the angiogenic vessels that perfuse the trunk of the embryo (intersegmental vessels) sprout from the vasculogenic vessels [Tran et al. 2007]. These effects can be visualized in automated, quantitative screening assays using transgenic zebrafish expressing green fluorescent protein (GFP) under the control of the vascular endothelial growth factor receptor (VEGFR) Vegfr2 promoter that restricts reporter gene expression to developing blood vessels. Phenotypic readouts have been used to screen and validate anti-angiogenic compounds [Tran et al. 2007; Yano et al. 2012; Yozzo et al. 2013; Yozzo et al. 2013; Tal et al. 2014; McCollum et al. 2017]. Live-cell imaging has been used to quantitatively detect the trajectory dynamics of vascular patterning [Clendenon et al. 2013; Shirinfard et al. 2013] and confocal cell imaging has been used to develop a quantitative assay capable of detecting relatively subtle changes (~8%) in relative to controls during chemical exposure [Tal et al. 2017]. http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0001525 GO BioSeek (ToxCast_BSK) multiplex assay A cell-based co-culture assay that measures levels of VEGFR2-immunoreactive protein using ELISA in conditioned primary human umbilical vein cells (HUVEC). in_vitro primary human umbilical vein cells (HUVEC) human VEGFR2-immunoreactive protein levels change not_specified Also, in ToxCast, a multiplex assay described under the ‘BioSeek’ (ToxCast_BSK) platform exists for VEGFR2 bioactivity in a cell-based co-culture system [Kleinstreuer et al. 2014]. This assay measures increased or decreased levels of VEGFR2-immunoreactive protein by ELISA in primary human umbilical vein cells (HUVEC) conditioned to simulate proinflammation with histamine and IL4. http://purl.obolibrary.org/obo/GO_0012536 GO cell-based reporter gene assay A high-throughput reporter gene assay that measures cellular VEGF-secretion as a genetic response to hypoxia-induced Vegf expression. in_vitro ME-180 cervical carcinoma HRE reporter cell line cellular VEGF-secretion change high a cell-based reporter gene assay has screened approximately 73,000 compounds in a quantitative high-throughput screening (HTS) approach [Xia et al. 2009]. That assay measures cellular VEGF-secretion in an ME-180 cervical carcinoma HRE (hypoxia-response element) reporter cell line as a genetic response to hypoxia-induced Vegf expression. http://purl.obolibrary.org/obo/GO_0051235 GO HRE reporter gene assay Measures cellular VEGF-secretion in an ME-180 cervical carcinoma HRE reporter cell line as a genetic response to hypoxia-induced Vegf expression. in_vitro ME-180 cervical carcinoma HRE reporter cell line human VEGF secretion increase high a cell-based reporter gene assay has screened approximately 73,000 compounds in a quantitative high-throughput screening (HTS) approach [Xia et al. 2009]. That assay measures cellular VEGF-secretion in an ME-180 cervical carcinoma HRE (hypoxia-response element) reporter cell line as a genetic response to hypoxia-induced Vegf expression. http://purl.obolibrary.org/obo/CHEBI_18366 CHEBI http://purl.obolibrary.org/obo/GO_0001666 GO NovaScreen (ToxCast_NVS) A cell-free biochemical assay measuring VEGFR2 enzymatic activity via electrophoretic shift of a fluorescein-peptide substrate. in_vitro VEGFR2 enzymatic activity change high This biochemical (cell-free) assay is one of 331 enzymatic and receptor signaling assays under the ‘NovaScreen’ (ToxCast_NVS) platform VEGFR2 enzymatic activity is measured as an electrophoretic shift in migration of a specific fluorescein-peptide substrate NovaScreen VEGFR2 enzymatic assay Measures VEGFR2 enzymatic activity as an electrophoretic shift in migration of a fluorescein-peptide substrate to fluorescein-phosphopeptide after incubation with ATP. in_vitro human VEGFR2 enzymatic activity change http://purl.obolibrary.org/obo/GO_0004672 GO high VEGFR2 enzymatic activity is measured as an electrophoretic shift in migration of a specific fluorescein-peptide substrate to the fluorescein-phosphopeptide upon 1-hour incubation with ATP. Concentration response to a test chemical is detected by a change in activity, which may be decreased or increased depending on the nature of a drug or chemical’s effect on VEGFR2 catalysis or autophosphorylation, respectively with automated curve-fits [Knudsen et al. 2011; Sipes et al. 2013]. http://purl.obolibrary.org/obo/CHEBI_18366 CHEBI http://purl.obolibrary.org/obo/GO_0006468 GO Proximity Ligation Assay PLAs are used to evaluate small molecule inhibitors of VEGF-A165 binding to solubilized VEGFRs, monitoring the kinetics of formation and inhibition of ligand–receptor complexes. in_vitro ligand–receptor complex formation/inhibition decrease medium Proximity Ligation Assays (PLAs) have been used to evaluate small molecule inhibitors of VEGF-A165 binding to solubilized VEGFRs [Gustafsdottir et al. 2008]. PLAs are fit for the purpose of monitoring the kinetics of formation and inhibition of ligand–receptor complexes through different mechanisms of interference with VEGF-A165 or its cognate binding site. http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0005654 GO Proximity Ligation Assay (PLA) Evaluates small molecule inhibitors of VEGF-A binding to solubilized VEGFRs by monitoring the kinetics of ligand-receptor complex formation and inhibition. in_vitro VEGF-A binding to VEGFR2 decrease http://purl.obolibrary.org/obo/GO_0043022 GO medium Proximity Ligation Assays (PLAs) have been used to evaluate small molecule inhibitors of VEGF-A binding to solubilized VEGFRs [Gustafsdottir et al. 2008]. PLAs are fit for the purpose of monitoring the kinetics of formation and inhibition of ligand–receptor complexes through different mechanisms of interference with VEGF-A or its cognate binding site. http://purl.obolibrary.org/obo/CHEBI_18366 CHEBI http://purl.obolibrary.org/obo/GO_0038084 GO receptor phosphorylation assay This assay measures receptor phosphorylation following exposure to molecular probes or pharmacological reagents specific to VEGF-VEGFR2 receptor capacity and kinase activity. in_vitro receptor phosphorylation decrease medium The inhibition of VEGF-A165 binding to VEGFR2 correlated well in these assays with results obtained by measuring receptor phosphorylation following exposure to molecular probes or pharmacological reagents specific to VEGF-VEGFR2 receptor capacity and kinase activity [Gustafsdottir et al. 2008]. http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0006468 GO alkali-labile phosphoprotein Protein quantification can be measured using alkali-labile phosphoprotein. in_vivo liver protein quantification increase low protein quantification can be measured using alkali-labile phosphoprotein http://purl.obolibrary.org/obo/GO_0006457 GO alkali-labile phosphoprotein assay Measures the relative abundance of vitellogenin protein using alkali-labile phosphoprotein methods. not_specified liver vitellogenin protein abundance increase low protein quantification can be measured using alkali-labile phosphoprotein (e.g., Kramer et al., 1998) http://purl.obolibrary.org/obo/GO_0043043 GO ELISA Protein quantification can be measured using enzyme linked immunosorbent assay (ELISA). in_vivo liver protein quantification increase high protein quantification can be measured using enzyme linked immunosorbent assay (ELISA) http://purl.obolibrary.org/obo/GO_0006457 GO ELISA Measures the relative abundance of vitellogenin protein using enzyme-linked immunosorbent assay. not_specified liver vitellogenin protein abundance increase medium protein quantification can be measured using immunochemical methods such as enzyme linked immunosorbent assay (ELISA; e.g., Denslow et al., 1999) http://purl.obolibrary.org/obo/GO_0043043 GO qPCR mRNA transcripts are measured using real-time quantitative polymerase chain reaction (qPCR). in_vitro hepatocytes liver mRNA transcript abundance increase medium mRNA transcripts can be measured using real-time quantitative polymerase chain reaction (qPCR) http://purl.obolibrary.org/obo/GO_0010468 GO qPCR Measures the relative abundance of vitellogenin mRNA transcripts using real-time quantitative polymerase chain reaction. in_vitro hepatocytes liver vitellogenin mRNA abundance increase http://purl.obolibrary.org/obo/OBI_0000273 OBI medium mRNA transcripts can be measured using real-time quantitative polymerase chain reaction (qPCR) http://purl.obolibrary.org/obo/GO_0010467 GO radioimmunoassay (RIA) Measures the relative abundance of vitellogenin protein using radioimmunoassay. not_specified liver vitellogenin protein abundance increase http://purl.obolibrary.org/obo/OBI_0000274 OBI low protein quantification can be measured using immunochemical methods such as radioimmunoassay (RIA; e.g., Tyler & Sumpter, 1990) http://purl.obolibrary.org/obo/GO_0043043 GO RIA Protein quantification can be measured using radioimmunoassay (RIA). in_vivo liver protein quantification increase medium protein quantification can be measured using radioimmunoassay (RIA) http://purl.obolibrary.org/obo/GO_0006457 GO western blot Protein quantification can be measured using Western blotting. in_vitro hepatocytes liver protein quantification increase low protein quantification can be measured using Western blotting http://purl.obolibrary.org/obo/GO_0006457 GO Western blotting Measures the relative abundance of vitellogenin protein using Western blotting. not_specified liver vitellogenin protein abundance increase http://purl.obolibrary.org/obo/OBI_0000275 OBI low protein quantification can be measured using immunochemical methods such as Western blotting (e.g., Heppell et al., 1995) http://purl.obolibrary.org/obo/GO_0043043 GO histological analysis Evaluates relative vitellogenin accumulation qualitatively using routine histological approaches. in_vivo oocytes vitellogenin accumulation not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI low Relative vitellogenin accumulation can be evaluated qualitatively using routine histological approaches (Leino et al. 2005; Wolf et al. 2004). http://purl.obolibrary.org/obo/CL_0000044 CL http://purl.obolibrary.org/obo/GO_0007296 GO Histological vitellogenin assessment Qualitative evaluation of vitellogenin accumulation in oocytes using routine histological techniques. in_vitro ovary fish vitellogenin accumulation increase http://purl.obolibrary.org/obo/CL_0000018 CL low Relative vitellogenin accumulation can be evaluated qualitatively using routine histological approaches (Leino et al. 2005; Wolf et al. 2004). Oocyte size can be evaluated qualitatively or quantitatively using routine histological and light microscopy and/or imaging approaches. http://purl.obolibrary.org/obo/GO_0007283 GO light microscopy Evaluates oocyte size qualitatively or quantitatively using routine light microscopy and/or imaging approaches. in_vivo oocytes oocyte size not_specified http://purl.obolibrary.org/obo/CL_0000044 CL medium Oocyte size can be evaluated qualitatively or quantitatively using routine histological and light microscopy and/or imaging approaches. http://purl.obolibrary.org/obo/CL_0000044 CL http://purl.obolibrary.org/obo/GO_0048477 GO Oocyte size measurement Qualitative or quantitative assessment of oocyte size using histological, light microscopy, and/or imaging techniques. in_vitro ovary fish oocyte size change http://purl.obolibrary.org/obo/CL_0000018 CL low Oocyte size can be evaluated qualitatively or quantitatively using routine histological and light microscopy and/or imaging approaches. http://purl.obolibrary.org/obo/CL_0000018 CL http://purl.obolibrary.org/obo/GO_0007283 GO Basophil Activation Test (BAT) Measures basophil degranulation by detecting CD63 translocation to the membrane using flow cytometry. in_vitro basophils blood human basophil degranulation increase http://purl.obolibrary.org/obo/PR_000001120 PR medium Basophils degranulate in response to IgE cross-links bound to the high-affinity IgE receptor, much like mast cells. In fresh blood samples (less than 24 hours old) this can be measured by the translocation of CD63 to the membrane using flow cytometry. http://purl.obolibrary.org/obo/CL_0000783 CL http://purl.obolibrary.org/obo/GO_0045088 GO Basophil Activation Test (BAT) Flow cytometry-based assay measuring the translocation of CD63 to the membrane in basophils in response to allergen-induced IgE cross-linking. in_vitro basophils blood human translocation of CD63 to the membrane increase http://purl.obolibrary.org/obo/CL_0000138 CL http://purl.obolibrary.org/obo/GO_0006432 GO medium Basophils degranulate in response to IgE cross-links bound to the high-affinity IgE receptor In fresh blood samples (less than 24 hours old) this can be measured by the translocation of CD63 to the membrane using flow cytometry. http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0006432 GO Breathing parameters assessment Quantitative assessment of airway hyperreactivity through various respiratory measurements including tidal volume and peak expiratory flow. in_vivo lung human respiratory rate, minute volume, tidal volume, peak expiratory flow, inspiratory and expiratory times, Penh change http://purl.obolibrary.org/obo/NCIT_C15528 NCIT low In vivo, alterations in breathing parameters such as respiratory rate, minute volume, tidal volume, peak expiratory flow, inspiratory and expiratory times and a flow-derived estimation of airflow restriction (enhanced pause, Penh) have been used for quantitative assessment of allergen induced airway hyperreactivity http://purl.obolibrary.org/obo/UBERON_0000676 UBERON http://purl.obolibrary.org/obo/GO_0051035 GO Bronchoalveolar lavage (BAL) fluid analysis Measures polymorphonuclear neutrophils (PMN) in bronchoalveolar lavage fluid to confirm elicitation of airway response after inhalation challenge. in_vivo polymorphonuclear neutrophils lung Rattus norvegicus PMN in bronchoalveolar lavage fluid increase low In rats, respiratory exposure to diisocyanites leads to immediate and delayed airway response. Elicitation is confirmed measuring PMN in bronchoalveolar lavage fluid (BAL) one day after inhalation challenge and exhaled NO (Pauluhn 2014). ELISA Measures allergen-specific antibody isotype profiles using immune assays. in_vitro blood human allergen-specific antibody isotype profiles change http://purl.obolibrary.org/obo/PR_000001958 PR high Immune assays such as ELISA or ImmunoCAP are also used to investigate allergen-specific antibody isotype profiles http://purl.obolibrary.org/obo/PR_000001958 PR http://purl.obolibrary.org/obo/GO_0006955 GO exhaled NO measurement Measures exhaled nitric oxide (NO) as a marker of airway inflammation. in_vivo lung rat exhaled NO increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI low Elicitation is confirmed measuring PMN in bronchoalveolar lavage fluid (BAL) one day after inhalation challenge and exhaled NO http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO FEV1 measurement Airflow obstruction and bronchoconstriction are measured using serial measures of airflow (usually FEV1) about 12 hours after exposure to test for immediate or delayed bronchoconstriction. in_vivo lung human airflow (FEV1) decrease medium Airflow obstruction and bronchoconstriction are measured using serial measures of airflow (usually FEV1) about 12 hours after exposure to test for immediate or delayed bronchoconstriction (Beckett, 2008). http://purl.obolibrary.org/obo/UBERON_0000085 UBERON FEV1 measurement Measures airflow obstruction and bronchoconstriction using serial measures of airflow (FEV1) to test for immediate or delayed bronchoconstriction. in_vivo lung human airflow obstruction decrease http://purl.obolibrary.org/obo/GO_0043028 GO low Airflow obstruction and bronchoconstriction are measured using serial measures of airflow (usually FEV1) about 12 hours after exposure to test for immediate or delayed bronchoconstriction http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0043028 GO ImmunoCAP Measures allergen-specific IgE using a commercially available immune assay. in_vitro blood human allergen-specific IgE increase http://purl.obolibrary.org/obo/PR_000001958 PR high blood testing using immune assays such as ELISAs and commercially available tests such as ImmunoCAP™ http://purl.obolibrary.org/obo/PR_000001958 PR http://purl.obolibrary.org/obo/GO_0006955 GO PMN measurement in BAL Measures polymorphonuclear cells (PMN) in bronchoalveolar lavage fluid (BAL) to confirm elicitation of airway response. in_vivo polymorphonuclear cells lung rat PMN count in BAL increase http://purl.obolibrary.org/obo/CL_0000763 CL http://purl.obolibrary.org/obo/OBI_0000471 OBI low Elicitation is confirmed measuring PMN in bronchoalveolar lavage fluid (BAL) one day after inhalation challenge http://purl.obolibrary.org/obo/CL_0000763 CL http://purl.obolibrary.org/obo/GO_0006954 GO respiratory parameter measurement Measures alterations in breathing parameters such as respiratory rate, minute volume, tidal volume, peak expiratory flow, and enhanced pause (Penh) to assess airway hyperreactivity. in_vivo lung rat airway hyperreactivity increase http://purl.obolibrary.org/obo/GO_0043029 GO low In vivo, alterations in breathing parameters such as respiratory rate, minute volume, tidal volume, peak expiratory flow, inspiratory and expiratory times and a flow-derived estimation of airflow restriction (enhanced pause, Penh) have been used for quantitative assessment of allergen induced airway hyperreactivity http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0043029 GO skin prick test Detects allergen-specific IgE through intradermal or subcutaneous skin prick testing. in_vivo skin human allergen-specific IgE increase http://purl.obolibrary.org/obo/OBI_0000218 OBI http://purl.obolibrary.org/obo/PR_000001958 PR medium Allergen-specific IgE detection and measurement techniques include skin tests (intradermal and subcutaneous skin prick testing) http://purl.obolibrary.org/obo/PR_000001958 PR http://purl.obolibrary.org/obo/GO_0006955 GO area analysis of heart and edema Quantifies heart area, pericardial edema area, or yolk sac edema area using a microscope-linked digital camera and image software, measuring the area in pixels. in_vivo heart pericardium yolk sac area in pixels increase http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/MP_0002058 MP http://purl.obolibrary.org/obo/UBERON_0001045 UBERON medium As heart area, pericardial edema area, or yolk sac edema area quantified with area analysis by use of a microscope linked digital camera and conventional image software (Dong et al 2010; Teraoka et al 2008; 2014; Yamauchi et al 2006). Images at the same magnification are used to obtain the area measured as number of pixels (Teraoka et al 2008; 2014). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0007507 GO area analysis of heart/edema Quantifies heart area, pericardial edema area, or yolk sac edema area by measuring pixel counts from microscope-linked digital images; applicable to live individuals or histologic sections. not_specified heart pericardial edema area yolk sac edema area area measured as number of pixels (heart area, pericardial edema area, yolk sac edema area) change medium As heart area, pericardial edema area, or yolk sac edema area quantified with area analysis by use of a microscope linked digital camera and conventional image software (Dong et al 2010; Teraoka et al 2008; 2014; Yamauchi et al 2006). Images at the same magnification are used to obtain the area measured as number of pixels (Teraoka et al 2008; 2014). This method can use either live individuals or histologic samples. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0007507 GO heartbeat rate measurement Measures heartbeat rate by direct observation using a microscope. in_vivo heart heartbeat rate change http://purl.obolibrary.org/obo/UBERON_0000948 UBERON medium As heartbeat rate measured by direct observation by use of a microscope (Park et al 2014). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0060047 GO malformation incidence Measures the incidence of malformations as a percentage occurrence among individuals. in_vivo percentage of malformation occurrence increase http://purl.obolibrary.org/obo/MP_0000001 MP high As incidence of malformation measured as percent occurrence among individuals (Buckler et al 2015; Dong et al 2010; Park et al 2014; Yamauchi et al 2006). http://purl.obolibrary.org/obo/UBERON_0000922 UBERON http://purl.obolibrary.org/obo/GO_0009790 GO microscopic area analysis Heart area, pericardial edema area, or yolk sac edema area are quantified using area analysis with a microscope linked to a digital camera and image software. Area is measured as the number of pixels. in_vivo heart pericardium yolk sac area change medium As heart area, pericardial edema area, or yolk sac edema area quantified with area analysis by use of a microscope linked digital camera and conventional image software (Dong et al 2010; Teraoka et al 2008; 2014; Yamauchi et al 2006). Images at the same magnification are used to obtain the area measured as number of pixels (Teraoka et al 2008; 2014). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0008533 GO microscopic area analysis Quantifies heart area, pericardial edema area, or yolk sac edema area using a microscope linked digital camera and conventional image software, measuring areas as number of pixels. in_vivo heart pericardium yolk sac heart area, pericardial edema area, or yolk sac edema area (pixels) change low As heart area, pericardial edema area, or yolk sac edema area quantified with area analysis by use of a microscope linked digital camera and conventional image software (Dong et al 2010; Teraoka et al 2008; 2014; Yamauchi et al 2006). Images at the same magnification are used to obtain the area measured as number of pixels (Teraoka et al 2008; 2014). This method is described in detail by Teraoka et al (2003). physical measurements of heart Measures basic physical parameters such as heart weight, heart aspect ratio, and heart weight to body weight ratio. in_vivo heart heart weight, aspect ratio, or weight-to-body ratio change http://purl.obolibrary.org/obo/UBERON_0000948 UBERON high As basic physical measurements such as heart weight, heart aspect ratio (horizontal length versus vertical length), heart weight to body weight ratio (Fujisawa et al 2014). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0003207 GO time-lapse recording Blood flow in the mesencephalic vein is measured using time-lapse recording with a digital video camera. Blood flow is quantified as the number of red blood cells passing the mesencephalic vein per second. in_vivo mesencephalic vein blood flow change low As blood flow in the mesencephalic vein by use of time-lapse recording using a digital video camera (Teraoka et al 2008; 2014). Blood flow is measured as the number of red blood cells passing the mesencephalic vein per second (Teraoka et al 2008; 2014). http://purl.obolibrary.org/obo/UBERON_0000959 UBERON http://purl.obolibrary.org/obo/GO_0008201 GO time-lapse recording of blood flow Measures blood flow in the mesencephalic vein by counting the number of red blood cells passing a specific point per second using a digital video camera. in_vivo mesencephalic vein number of red blood cells passing the mesencephalic vein per second change http://purl.obolibrary.org/obo/UBERON_0001171 UBERON low As blood flow in the mesencephalic vein by use of time-lapse recording using a digital video camera Blood flow is measured as the number of red blood cells passing the mesencephalic vein per second http://purl.obolibrary.org/obo/CHEBI_16357 CHEBI http://purl.obolibrary.org/obo/GO_0007533 GO visualized scoring of blood flow Assesses blood flow through the mesencephalic vein using a microscope and scores it as (1) same rate as control, (2) slower rate than control, or (3) no flow. in_vivo mesencephalic vein blood flow rate score decrease http://purl.obolibrary.org/obo/GO_0008015 GO http://purl.obolibrary.org/obo/UBERON_0003550 UBERON medium some studies have assessed blood flow through visualized scoring techniques by use of a microscope as (1) same rate as control, (2) slower rate than control, or (3) no flow (Henry et al 1997). http://purl.obolibrary.org/obo/UBERON_0003550 UBERON http://purl.obolibrary.org/obo/GO_0008016 GO Dominant Lethal test Measures the effects of DNA damage in sperm on the dominant lethality in the offspring. in_vivo sperm dominant lethality in the offspring change http://purl.obolibrary.org/obo/GO_0008451 GO OECD TG 478 not_specified The Dominant Lethal test (OECD TG 478) is used to measure the effects of DNA damage in sperm on dominant lethality in the offspring. http://purl.obolibrary.org/obo/CL_0000393 CL http://purl.obolibrary.org/obo/GO_0008451 GO Mouse SLT The Mouse Specific Locus Test (SLT) assesses heritable mutations by examining visible trait markers in mice. Male mice are exposed to a mutagen and mated with females carrying recessive alleles to identify functional mutations at dominant loci, resulting in expression of the recessive phenotype in offspring. in_vivo spermatogenesis coat skeleton mouse expression of recessive phenotype in offspring increase http://purl.obolibrary.org/obo/GO_0001928 GO low The Oak Ridge National Laboratory's SLT test, established by William and Lianne Russell, was the gold standard for heritable mutation screening for several decades. Male mice are exposed to the mutagen and mated at varying times post-exposure to evaluate effects on different stages of spermatogenesis. Functional mutations at the dominant (male) locus results in expression of the recessive phenotype in the offspring. http://purl.obolibrary.org/obo/GO_0000438 GO Mouse Specific Locus Test (SLT) Measures heritable mutations in mice using seven dominant visible trait markers. Male mice are exposed to a mutagen and mated with females carrying recessive alleles, and mutations are detected by expression of recessive phenotypes in offspring. in_vivo Mus musculus heritable mutations increase http://purl.obolibrary.org/obo/GO_0043984 GO http://purl.obolibrary.org/obo/GO_0007283 GO low The SLT is based on the use of seven dominant visible trait markers in mice (Davis and Justice, 1998; Russell et al., 1979). Male mice are exposed to the mutagen and mated at varying times post-exposure to evaluate effects on different stages of spermatogenesis. Functional mutations at the dominant (male) locus results in expression of the recessive phenotype in the offspring. http://purl.obolibrary.org/obo/GO_0007281 GO http://purl.obolibrary.org/obo/GO_0007283 GO Next generation sequencing Measures heritable mutations by whole genome sequencing of offspring and parents to identify de novo mutations. in_vivo Mus musculus de novo mutations increase http://purl.obolibrary.org/obo/OBI_0002127 OBI http://purl.obolibrary.org/obo/SO_0001483 SO high Whole genome sequencing is applied to compare the genome sequences of parents and offspring to identify and haplotype (i.e., determine the parental origin) of de novo mutations (identified as mutations occurring in offspring but not their parents). Studies such as these have demonstrated that increasing paternal age causes an increase in both single nucleotide variants and tandem repeats in the offspring (Kong et al., 2012; Sun et al., 2012). http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006281 GO Tandem repeat mutation assay Measures changes in tandem repeat length in offspring relative to parents using DNA fingerprinting after exposing males to a mutagen. in_vivo mouse changes in repeat length in offspring relative to their parents change http://purl.obolibrary.org/obo/SO_0000433 SO low Transmission of mutations from exposed males to their offspring can also be measured by analysis of tandem repeat mutations DNA fingerprinting is used to measure changes in repeat length in offspring relative to their parents. http://purl.obolibrary.org/obo/SO_0000433 SO http://purl.obolibrary.org/obo/GO_0007626 GO Tandem repeat mutation assay Measures mutations in tandem repeat sequences in offspring of exposed males using DNA fingerprinting to detect changes in repeat length. in_vivo Mus musculus tandem repeat mutations increase http://purl.obolibrary.org/obo/SO_0000706 SO http://purl.obolibrary.org/obo/GO_0043984 GO medium Tandem repeat mutations can be measured in offspring using a similar approach. DNA fingerprinting is used to measure changes in repeat length in offspring relative to their parents. http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO Attentional set-shifting (ATSET) task A task measuring the ability to relearn cues over various schedules of reinforcement. in_vivo brain humans ability to relearn cues change low Attentional set-shifting (ATSET) task. Measures the ability to relearn cues over various schedules of reinforcement Autobiographical Memory Task Tests the recollection of specific personal events in humans, including episodic and semantic autobiographical memory. in_vivo hippocampus humans autobiographical memory performance change http://purl.obolibrary.org/obo/UBERON_0001954 UBERON low Autobiographical memory (AM) is the recollection of specific personal events in a multifaceted higher order cognitive process. http://purl.obolibrary.org/obo/UBERON_0001954 UBERON Children’s Auditory Verbal Learning Test Tests verbal learning and memory in children through free recall of presented word lists. in_vivo brain humans verbal learning and memory performance change http://purl.obolibrary.org/obo/GO_0007613 GO low Children’s Auditory Verbal Learning Test (CAVLT) is a free recall of presented word lists that yields measures of Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, and Total Intrusions. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0007613 GO Children’s Auditory Verbal Learning Test (CAVLT) A free recall test of presented word lists in children measuring various memory parameters including immediate and delayed recall. in_vivo brain humans Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, and Total Intrusions change low Children’s Auditory Verbal Learning Test (CAVLT) is a free recall of presented word lists that yields measures of Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, and Total Intrusions. Contextual Fear Conditioning Tests hippocampal-based learning in rodents by associating a novel environment with an aversive stimulus and measuring suppression of activity upon reintroduction to the environment. in_vivo hippocampus rodents fear memory retention change http://purl.obolibrary.org/obo/GO_0001994 GO http://purl.obolibrary.org/obo/UBERON_0001954 UBERON low Contextual Fear conditioning is a hippocampal based learning task in which animals are placed in a novel environment and allowed to explore for several minutes before delivery of an aversive stimulus, typically a mild foot shock. http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0001994 GO contextual fear conditioning Animals are placed in a novel environment and receive a foot shock. Later, re-exposure to the environment is used to measure memory retention based on suppression of activity. in_vivo hippocampus rodents suppression of activity increase http://purl.obolibrary.org/obo/GO_0007613 GO low Contextual Fear conditioning is a hippocampal based learning task in which animals are placed in a novel environment and allowed to explore for several minutes before delivery of an aversive stimulus, typically a mild foot shock. The degree of suppression of activity after training is taken as evidence of retention, i.e., memory (Curzon et al., 2009). http://purl.obolibrary.org/obo/UBERON_0001970 UBERON Continuous Visual Memory Test Tests visual learning and memory in children through free recall of presented pictures/objects. in_vivo brain humans visual learning and memory performance change http://purl.obolibrary.org/obo/GO_0007613 GO low Continuous Visual Memory Test (CVMT) measures visual learning and memory. It is a free recall of presented pictures/objects rather than words but that yields similar measures of Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, and Total Intrusions. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0007613 GO Hebb-Williams Maze Tests problem-solving abilities in rodents by providing no spatial cues to find the target. in_vivo hippocampus rodents problem-solving performance change http://purl.obolibrary.org/obo/GO_0035170 GO http://purl.obolibrary.org/obo/UBERON_0001954 UBERON low The Hebb-Williams maze measures an animal’s problem solving abilities by providing no spatial cues to find the target http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0035170 GO Morris water maze The Morris water maze (MWM) assesses spatial learning by requiring animals to learn the location of a hidden platform submerged in a tank of water. in_vivo hippocampus rodents time to find hidden platform decrease http://purl.obolibrary.org/obo/GO_0007613 GO low These include tests of spatial learning like the radial arm maze (RAM), the Barnes maze, Hebb-Williams maze, passive avoidance and Spontaneous alternation and most commonly, the Morris water maze (MWM). an escape hole to enter a preferred dark tunnel from a brightly lit open field area (Barnes maze), or a hidden platform submerged below the surface of the water in a large tank of water (MWM) (Vorhees and Williams, 2014). http://purl.obolibrary.org/obo/UBERON_0001970 UBERON Novel Object Recognition Tests recognition memory in rodents by measuring time spent interacting with a novel object versus a familiar one. in_vivo hippocampus rodents recognition memory performance change http://purl.obolibrary.org/obo/GO_0050955 GO http://purl.obolibrary.org/obo/UBERON_0001954 UBERON medium Novel Object recognition. This is a simpler task that can be used to probe recognition memory. http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0050955 GO novel object recognition This task assesses recognition memory by presenting animals with two objects, then replacing one with a novel object and measuring time spent interacting with the novel object. in_vivo hippocampus rodents time spent interacting with novel object increase http://purl.obolibrary.org/obo/GO_0007613 GO medium Test of novelty such as novel object recognition, and fear based context learning are also sensitive to hippocampal disruption. On trial 2, one object is replaced with a novel object and time spent interacting with the novel object is taken evidence of memory retention – I have seen one of these objects before, but not this one (Cohen and Stackman, 2015). http://purl.obolibrary.org/obo/UBERON_0001970 UBERON Operant Responding Tests the cortex's ability to organize processes in rodents through operant conditioning tasks. in_vivo cortex rodents operant responding performance change http://purl.obolibrary.org/obo/GO_0030855 GO http://purl.obolibrary.org/obo/UBERON_0001094 UBERON low Operant Responding. Performance on operant responding reflects the cortex’ ability to organize processes http://purl.obolibrary.org/obo/UBERON_0001094 UBERON http://purl.obolibrary.org/obo/GO_0030855 GO proboscis extension reflex This assay evaluates appetitive learning and memory in honey bees by pairing an odor with sucrose and measuring the proboscis extension reflex (PER). in_vivo honey bee proboscis extension increase http://purl.obolibrary.org/obo/GO_0008430 GO http://purl.obolibrary.org/obo/GO_0007613 GO medium For over 50 years an assay for evaluating olfactory conditioning of the proboscis extension reflex (PER) has been used as a reliable method for evaluating appetitive learning and memory in honey bees (Guirfa and Sandoz, 2012; LaLone et al., 2017). After conditioning, the odor alone will lead to the conditioned PER. Proboscis Extension Reflex Conditioning Tests appetitive learning and memory in honey bees by pairing an odor with a sucrose reward and measuring proboscis extension to the odor alone. in_vivo brain honey bees olfactory memory performance change http://purl.obolibrary.org/obo/GO_0035635 GO http://purl.obolibrary.org/obo/GO_0007613 GO medium For over 50 years an assay for evaluating olfactory conditioning of the proboscis extension reflex (PER) has been used as a reliable method for evaluating appetitive learning and memory in honey bees These experiments pair a conditioned stimulus (e.g., an odor) with an unconditioned stimulus (e.g., sucrose) provided immediately afterward, which elicits the proboscis extension http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0035635 GO Radial Arm Maze Tests spatial learning in rodents by requiring them to learn the location of a food reward. in_vivo hippocampus rodents spatial learning performance change http://purl.obolibrary.org/obo/GO_0048570 GO http://purl.obolibrary.org/obo/UBERON_0001954 UBERON low RAM, Barnes, MWM, Hebb-Williams maze are examples of spatial tasks, animals are required to learn the location of a food reward (RAM); http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0048570 GO Rey Osterieth Complex Figure Test Tests visuospatial abilities, memory, attention, planning, and working memory in humans. in_vivo brain humans visuospatial and memory performance change http://purl.obolibrary.org/obo/GO_0007613 GO low Rey Osterieth Complex Figure test (RCFT) which probes a variety of functions including as visuospatial abilities, memory, attention, planning, and working memory http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0007613 GO trace fear conditioning Fear conditioning with a delay between the conditioned stimulus and the unconditioned stimulus, requiring engagement of both the amygdala and hippocampus, measured by freezing behavior. in_vivo hippocampus amygdala rodents freezing behavior increase http://purl.obolibrary.org/obo/GO_0008430 GO low Introducing a brief delay between presentation of the neutral CS and the aversive US, a trace period, requires the engagement of the amygdala and the hippocampus (Shors et al., 2001). The unconditioned response (CR) that is elicited upon delivery of the footshock US is freezing behavior. http://purl.obolibrary.org/obo/UBERON_0001970 UBERON Wechsler Memory Scale Logical Memory Test Tests memory functions in humans through story recall. in_vivo brain humans memory performance change http://purl.obolibrary.org/obo/GO_0007613 GO low Story Recall from Wechsler Memory Scale (WMS) Logical Memory Test Battery, a standardized neurospychological test designed to measure memory functions http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0007613 GO Hepatic elastography Hepatic elastography is a noninvasive method for estimating liver stiffness, used to measure hepatic fibrosis. in_vivo liver human liver stiffness increase http://purl.obolibrary.org/obo/MP_0004700 MP http://purl.obolibrary.org/obo/UBERON_0002107 UBERON medium Hepatic elastography, a method for estimating liver stiffness, is a recent development in the noninvasive measurement of hepatic fibrosis Currently, elastography can be accomplished by ultrasound or magnetic resonance http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO Ishak fibrosis score The Ishak fibrosis score is a more sensitive grading system for liver fibrosis with six stages, ranging from no fibrosis (stage 0) to cirrhosis (stage 6). in_vivo liver human fibrosis stage increase http://purl.obolibrary.org/obo/MP_0004700 MP http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low the more sensitive Ishak fibrosis score with six stages - from no fibrosis (stage 0) over increasing fibrous expansion on portal areas (stages 1-2), bridging fibrosis (stages 3-4), and nodules (stage 5) to cirrhosis (stage 6) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO Liver biopsy Liver biopsy is used to assess the severity of liver diseases, including the stage of liver fibrosis, by evaluating the quantity and location of fibrous tissue, septa, and nodules. in_vivo liver human fibrosis stage increase http://purl.obolibrary.org/obo/MP_0004700 MP http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low Liver biopsy is an important part of the evaluation of patients with a variety of liver diseases. the biopsy is often used to assess the severity of the disease the stages are determined by both the quantity and location of the fibrosis, with the formation of septa and nodules as major factors in the transition from one stage to the next http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO MMP/TIMP measurement This assay measures the levels of matrix metalloproteinases 2 and 3 (MMP-2, MMP-3) and tissue inhibitors of metalloproteinases 1 and 2 (TIMP-1, TIMP-2), direct markers of fibrosis associated with matrix degradation. in_vitro liver MMP/TIMP levels change medium Other direct markers of fibrosis are those associated with matrix degradation, ie, matrix metalloproteinases 2 and 3 (MMP-2, MMP- 3) and tissue inhibitors of metalloproteinases 1 and 2 (TIMP-1, TIMP-2). http://purl.obolibrary.org/obo/CL_0000284 CL http://purl.obolibrary.org/obo/GO_0007259 GO P3NP measurement This assay measures the levels of procollagen type III amino-terminal peptide (P3NP) in serum, a direct serologic marker of hepatic fibrosis associated with matrix deposition. in_vitro liver P3NP levels increase medium Direct serologic markers of fibrosis include those associated with matrix deposition — e.g.procollagen type III amino-terminal peptide (P3NP), type I and IV collagens, laminin, hyaluronic acid, and chondrex. P3NP is the most widely studied marker of hepatic fibrosis. http://purl.obolibrary.org/obo/CL_0000284 CL http://purl.obolibrary.org/obo/GO_0007259 GO Serologic markers of fibrosis Measurement of direct biochemical markers in serum associated with matrix deposition (e.g., P3NP, collagens, laminin) or matrix degradation (e.g., MMPs, TIMPs). in_vitro liver concentration of matrix-related proteins increase http://purl.obolibrary.org/obo/UBERON_0002461 UBERON medium Direct serologic markers of fibrosis include those associated with matrix deposition — e.g.procollagen type III amino-terminal peptide (P3NP), type I and IV collagens, laminin, hyaluronic acid, and chondrex. Other direct markers of fibrosis are those associated with matrix degradation, ie, matrix metalloproteinases 2 and 3 (MMP-2, MMP- 3) and tissue inhibitors of metalloproteinases 1 and 2 (TIMP-1, TIMP-2). http://purl.obolibrary.org/obo/GO_0030198 GO http://purl.obolibrary.org/obo/GO_0030198 GO Anogenital distance (AGD) measurement Measurement of the distance from the anus to the genitals as a biomarker of prenatal androgen exposure and reproductive health risks. in_vivo genital tubercle anus rat anogenital distance decrease OECD TG 443 medium The anogenital distance (AGD) is a sexual dimorphism that results from the sex difference in foetal androgen (DHT) levels (Rhees et al., 1997). Measurement of AGD has also been proposed as a quantitative biomarker of foetal endocrine disruptor exposure in humans (Arbuckle et al. 2008), (Dean and Sharpe 2013). Decreased AGD in male rats is a hallmark of exposure to antiandrogenic substances (Noriega et al, 2009; Christiansen et al, 2010). The extended one-generation in vivo reproductive toxicity study OECD TG 443 is used to investigate adverse effects of chemical substances on fertility and developmental toxicity in the rat, in which AGD is measured. Macroscopic examination Detection of structural abnormalities or pathological changes in the male reproductive tract through visual inspection. in_vivo male reproductive tract structural abnormality or pathological change not_specified low Malformations are detected by macroscopically for any structural abnormality or pathological change. The Congenital malformation of the genitalia is a medical term referring to a broad category of conditions that for humans is classified by International Classification of Diseases (ICD) in chapter "Congenital malformations of genital organs" (Q50-Q56) e.g.Q54 Hypospadias, Q53 Undescended testicle. macroscopic examination for malformations Macroscopic visual inspection of the male reproductive tract to detect any structural abnormality or pathological change associated with congenital malformations of the genitalia. in_vivo male reproductive tract genitalia structural abnormalities or pathological changes in male reproductive tract change http://purl.obolibrary.org/obo/UBERON_0000073 UBERON http://purl.obolibrary.org/obo/GO_0036370 GO low Malformations are detected by macroscopically for any structural abnormality or pathological change. The Congenital malformation of the genitalia is a medical term referring to a broad category of conditions that for humans is classified by International Classification of Diseases (ICD) in chapter "Congenital malformations of genital organs" (Q50-Q56) e.g.Q54 Hypospadias, Q53 Undescended testicle. http://purl.obolibrary.org/obo/UBERON_0000073 UBERON http://purl.obolibrary.org/obo/GO_0001541 GO Daphnia sp. Acute immobilization test This assay measures the immobilization of Daphnia sp. as an indicator of acute toxicity. in_vivo Daphnia sp. immobilization increase OECD 202 medium the OECD 202 Daphnia sp. Acute immobilization test (OECD 2004) which can also be modified depending on the effect one expects. http://purl.obolibrary.org/obo/NCBITaxon_35525 NCBITAXON http://purl.obolibrary.org/obo/GO_0007626 GO Capture-mark-recapture A method used in ecology to estimate animal population size by capturing, marking, and recapturing individuals. in_vivo population size not_specified http://www.ebi.ac.uk/efo/EFO_0000532 EFO low in the field, for example by determining age structure after one capture, or by capture-mark-recapture efforts. The latter is a method commonly used in ecology to estimate an animal population's size where it is impractical to count every individual. http://purl.obolibrary.org/obo/ENVO_00000015 ENVO http://purl.obolibrary.org/obo/GO_0048565 GO Mortality observation Mortality is measured by observing the cessation of heart beat, breathing, and locomotory movements. The metric reported is the mortality rate. in_vivo mortality rate increase http://purl.obolibrary.org/obo/GO_0060048 GO http://purl.obolibrary.org/obo/GO_0007585 GO low Mortality of animals is generally observed as cessation of the heart beat, breathing (gill or lung movement) and locomotory movements. The reported metric is mostly the mortality rate: the number of deaths in a given area or period, or from a particular cause. http://purl.obolibrary.org/obo/NCBITaxon_1 NCBITAXON http://purl.obolibrary.org/obo/GO_0016265 GO Fluoro-Jade staining Fluoro-Jade staining is used to detect degenerating neurons by binding to anionic components of degenerating cells, providing a fluorescent marker for neurodegeneration. in_vivo brain presence of degenerating neurons increase http://purl.obolibrary.org/obo/GO_0097184 GO low Fluoro-Jade, an anionic fluorescent dye, is a good marker of degenerating neurons. Fluoro-Jade and Fluoro-Jade B were found to stain all degenerating neurons, regardless of specific insult or mechanism of cell death Fluoro-Jade C was shown to be highly resistant to fading and compatible with virtually all histological processing and staining protocols Fluoro-Jade C is a good tool for detecting acutely and chronically degenerating neurons http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0097502 GO Dynamic Energy Budget (DEB) modeling Uses a modeling framework to link stressor effects on growth, reproduction, and survival to energy acquisition and processing, informing population growth rate estimates. in_silico population growth rate change medium Dynamic energy budget (DEB) models offer a methodology that reverse engineers stressor effects on growth, reproduction, and/or survival into modular characterizations related to the acquisition and processing of energy resources (Nisbet et al. 2000, Nisbet et al. 2011). effects-based monitoring Combines field-based effects monitoring data informed by an AOP with a population model to project declines in population growth rate. ex_vivo white sucker population growth rate decrease medium A model construct could be based upon a combination of effects-based monitoring at field sites (informed by an AOP) and a population model. Miller et al. (2015) applied a population model informed by an AOP to project declines in population growth rate for white suckers (Catostomus commersoni) using observed changes in sex steroid synthesis in fish exposed to a complex pulp and paper mill effluent in Jackfish Bay, Ontario, Canada. endogenous lifecycle model (ELM) Integrates endogenous lifecycle processes of growth, development, survival, and reproduction to estimate fitness and predict effects of chemical stressors on vital rates. in_silico expected fitness (vital rates) decrease medium ● Endogenous Lifecycle Models (ELMs), capture the endogenous lifecycle processes of growth, development, survival, and reproduction and integrate these to estimate and predict expected fitness (Etterson and Ankley, 2021). AOPs can be used to inform ELMs of effects of chemical stressors on the vital rates that determine fitness, and to decide what hierarchical models of endogenous systems should be included within an ELM (Etterson and Ankley, 2021). Laboratory toxicity tests with population modeling Combines laboratory toxicity data (e.g., reproductive assays) with population models to estimate declines in population growth rate. in_silico Pimephales promelas population growth rate decrease medium A modeling construct could be based upon laboratory toxicity tests to determine effect(s) that are then linked to the population model and used to estimate decline in population growth rate. Miller et al. (2007) used concentration–response data from short term reproductive assays with fathead minnow (Pimephales promelas) exposed to endocrine disrupting chemicals in combination with a population model to examine projected alterations in population growth rate. Mark-recapture method Estimates population size by marking individuals (e.g., tags, bands, transmitters) and recapturing them at a later time to determine population growth rate. in_vivo population size change low For species that are mobile throughout a large range, a strategy such as using a mark-recapture method may be employed (i.e. tags, bands, transmitters) to determine a count over a time interval (at time = 0 and again at time =1). Mathematical modeling Uses mathematical constructs (e.g., differential equations, matrix projection models) to estimate population growth rate based on experimental or field data. in_silico population growth rate change high Population growth rate can also be estimated using mathematical model constructs (for example, ranging from simple differential equations to complex age or stage structured matrix projection models and individual based modeling approaches), and may assume a linear or nonlinear population increase over time. Observational sampling Measures population size by dividing a habitat into units and counting organisms within selected units at two time points to estimate population growth rate. in_vivo population size change low For stationary species an observational strategy may involve dividing a habitat into units. After setting up the units, samples are performed throughout the habitat at a select number of units (determined using a statistical sampling design) over a time interval (at time t = 0 and again at time t = 1), and the total number of organisms within each unit are counted. population count (observational) Measures population size at two time points by counting organisms within sampled habitat units to estimate population growth rate over the interval. in_vivo population size (count) decrease low For stationary species an observational strategy may involve dividing a habitat into units. After setting up the units, samples are performed throughout the habitat at a select number of units (determined using a statistical sampling design) over a time interval (at time t = 0 and again at time t = 1), and the total number of organisms within each unit are counted. Population growth rate measurement Population growth rate (instantaneous growth rate) is measured by sampling a population over a time interval and calculating the difference between the initial and final population sizes, divided by the initial size. This can be done using observational strategies for stationary species or mark-recapture methods for mobile species. in_vivo population growth rate decrease not_specified The population growth rate, r, can be determined by taking the difference (subtracting) between the initial population size, Nt=0 (population size at time t=0), and the population size at the end of the interval, Nt=1 (population size at time t = 1), and then subsequently dividing by the initial population size. For stationary species an observational strategy may involve dividing a habitat into units. After setting up the units, samples are performed throughout the habitat at a select number of units (determined using a statistical sampling design) over a time interval (at time t = 0 and again at time t = 1), and the total number of organisms within each unit are counted. For species that are mobile throughout a large range, a strategy such as using a mark-recapture method may be employed (i.e. tags, bands, transmitters) to determine a count over a time interval (at time = 0 and again at time =1). Quantitative Adverse Outcome Pathway (qAOP) modeling Uses a mathematical framework to model dose-response relationships of key events in an AOP to predict population-level impacts, including declines in population growth rate. in_silico Pimephales promelas population growth rate decrease medium A quantitative adverse outcome pathway (qAOP) has been defined as a mathematical construct that models the dose–response or response–response relationships of all KERs described in an AOP (Conolly et al. 2017, Perkins et al. 2019). Conolly et al. (2017) developed a qAOP using data generated with the aromatase inhibitor fadrozole as a stressor and then used it to predict potential population‐level impacts (including decline in population growth rate). sex steroid synthesis measurement Measuring changes in sex steroid synthesis in fish exposed to effluent to project declines in population growth rate. in_vivo gonad white sucker sex steroid levels decrease http://purl.obolibrary.org/obo/GO_0001583 GO low Miller et al. (2015) applied a population model informed by an AOP to project declines in population growth rate for white suckers (Catostomus commersoni) using observed changes in sex steroid synthesis in fish exposed to a complex pulp and paper mill effluent in Jackfish Bay, Ontario, Canada. http://purl.obolibrary.org/obo/CHEBI_5088 CHEBI http://purl.obolibrary.org/obo/GO_0001583 GO HPLC with fluorescence detection Quantifies levels and patterns of excreted porphyrins in urine or fecal samples using high-performance liquid chromatography with fluorescence detection. in_vitro urine feces levels and pattern of excreted porphyrins not_specified http://purl.obolibrary.org/obo/CHEBI_30116 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium Porphyria is easily confirmed through a urinary or fecal analysis to measure the levels and pattern of excreted porphyrins. Samples are quantified using a high-performance liquid chromatograph equipped with a fluorescence detector http://purl.obolibrary.org/obo/CHEBI_30116 CHEBI http://purl.obolibrary.org/obo/GO_0006778 GO AMS Accelerated mass spectrometry for highly sensitive detection of AFB1-specific DNA adducts using radiolabelled test material. in_vitro AFB1-specific DNA adducts increase http://purl.obolibrary.org/obo/OBI_0000475 OBI low More sensitivity is reported with accelerated mass spectrometry (AMS) approaches; these require the use of radiolabelled (14C) test material but can detect adducts down into the attomolar range. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0032408 GO AMS This assay detects adducts down into the attomolar range using accelerated mass spectrometry (AMS) approaches, requiring the use of radiolabelled (14C) test material. in_vitro tissues cells DNA adduct levels increase low More sensitivity is reported with accelerated mass spectrometry (AMS) approaches; these require the use of radiolabelled (14C) test material but can detect adducts down into the attomolar range. http://purl.obolibrary.org/obo/CHEBI_0001367 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO AMS (Accelerated Mass Spectrometry) Highly sensitive mass spectrometry approach using radiolabelled (14C) materials to detect DNA adducts at extremely low concentrations. in_vitro adducts in the attomolar range not_specified not_specified More sensitivity is reported with accelerated mass spectrometry (AMS) approaches; these require the use of radiolabelled (14C) test material but can detect adducts down into the attomolar range. http://purl.obolibrary.org/obo/GO_0006281 GO http://purl.obolibrary.org/obo/GO_0008455 GO HPLC-MS/MS High pressure liquid chromatography coupled with tandem mass spectrometry for definitive identification and quantification of AFB1-specific DNA adducts. in_vitro AFB1-specific DNA adducts increase http://purl.obolibrary.org/obo/OBI_0000475 OBI low Techniques include high pressure liquid chromatography (HPLC) or liquid chromatography (LC) separation coupled with tandem mass spectrometry (HPLC-MS/MS or LC-MS/MS). These techniques allow for definitive identification of the AFB1-related adducts using authentic standards. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0032408 GO ACB-PCR Allele specific competitive blocker-polymerase chain reaction (ACB-PCR) is used to detect specific chemical-induced mutations in critical cancer genes. in_vitro presence of specific mutations in critical genes increase http://purl.obolibrary.org/obo/GO_0006304 GO http://purl.obolibrary.org/obo/OBI_0000274 OBI low A newly developed method, allele specific competitive blocker-polymerase chain reaction (ACB-PCR) has proven useful in providing such information, and data on specific chemical-induced mutations are available for a very small number of chemicals (Parsons et al., 2010). http://purl.obolibrary.org/obo/GO_0006304 GO allele specific competitive blocker-polymerase chain reaction (ACB-PCR) A method used to detect specific chemical-induced mutations in critical cancer genes. in_vitro specific chemical-induced mutations change http://purl.obolibrary.org/obo/GO_0001088 GO not_specified A newly developed method, allele specific competitive blocker-polymerase chain reaction (ACB-PCR) has proven useful in providing such information, and data on specific chemical-induced mutations are available http://purl.obolibrary.org/obo/GO_0003696 GO http://purl.obolibrary.org/obo/GO_0001088 GO AS52 in vitro gene mutation assay The AS52 in vitro gene mutation assay uses the gpt gene and 6-thioguanine selection to measure mutation frequency (MF) induced by chemical exposure. in_vitro AS52 mutation frequency at the gpt gene increase http://purl.obolibrary.org/obo/GO_0006304 GO medium The AS52 in vitro gene mutation assay using the gpt gene, and 6-thioguanine selection has been used to demonstrate that AFB1 exposure increases the MF at the gpt gene. http://purl.obolibrary.org/obo/GO_0006304 GO DNA sequencing DNA sequencing is used to determine the presence of mutations in specific genes, such as the Codon 249 p53 mutation in human tumors. in_vivo tumors human presence of mutations in specific genes increase http://purl.obolibrary.org/obo/OBI_0000627 OBI http://purl.obolibrary.org/obo/GO_0006304 GO low DNA from tumors can be sequenced to determine the presence of mutations in specific genes. DNA sequencing has been used on human tumors to detect the presence of the Codon 249 p53 mutation. http://purl.obolibrary.org/obo/GO_0006304 GO in vivo transgenic assay In vivo transgenic assays use molecular methods to recover the transgene from isolated DNA and evaluate the mutation frequency (MF) in the transgene. in_vivo mutation frequency in the transgene increase http://purl.obolibrary.org/obo/GO_0006304 GO low In vivo transgenic assays use molecular methods to recover the transgene from isolated DNA and to evaluate the MF in the transgene. http://purl.obolibrary.org/obo/GO_0006304 GO clinical examination Detection of hepatocellular carcinoma in humans through clinical examination. in_vivo liver human presence of hepatocellular carcinoma not_specified http://purl.obolibrary.org/obo/MONDO_0005071 MONDO low Hepatocellular carcinoma is detected in humans by clinical examination confirmed by pathological examination http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/MONDO_0005071 MONDO pathological examination Confirmation of hepatocellular carcinoma in humans through pathological examination. in_vivo liver human presence of hepatocellular carcinoma not_specified http://purl.obolibrary.org/obo/MONDO_0005071 MONDO low Hepatocellular carcinoma is detected in humans by clinical examination confirmed by pathological examination http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/MONDO_0005071 MONDO ELISA Measures BDNF protein levels using commercial antibody sandwich ELISA kits. in_vitro brain tissue cerebro-spinal fluid whole blood serum plasma platelets BDNF protein levels not_specified http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI medium BDNF protein levels can be measured by commercial available antibody sandwich ELISA kits There are available commercial antibody sandwich ELISA kits (Trajkovska et al., 2007) There are several commercial double antibody sandwich ELISA kits that can be used for identification of BDNF levels in biological fluids (Trajkovska et al., 2007) http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI http://purl.obolibrary.org/obo/GO_0048011 GO Immunobead-based multiplex assay Measures BDNF protein levels using immunobead-based multiplex assays for high throughput screening. in_vitro cerebro-spinal fluid BDNF protein levels not_specified http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI high There are available commercial antibody sandwich ELISA kits (Trajkovska et al., 2007) and immunobead-based multiplex assays for high throughput screening (Zhang et al., 2008) http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI http://purl.obolibrary.org/obo/GO_0048011 GO Immunofluorescence Measures BDNF protein levels using immunofluorescence technique. in_vitro brain tissue BDNF protein levels not_specified http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI low BDNF protein levels can be measured by commercial available antibody sandwich ELISA kits, Western blotting, immunohistochemistry and immunofluorescence http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI http://purl.obolibrary.org/obo/GO_0048011 GO Immunohistochemistry Measures BDNF protein levels using immunohistochemistry technique. in_vitro brain tissue BDNF protein levels not_specified http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI low BDNF protein levels can be measured by commercial available antibody sandwich ELISA kits, Western blotting, immunohistochemistry and immunofluorescence http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI http://purl.obolibrary.org/obo/GO_0048011 GO RT-PCR Measures BDNF mRNA levels using reverse transcription polymerase chain reaction (RT-PCR). in_vitro brain tissue BDNF mRNA levels not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI medium BDNF primers for different exons are available to determine mRNA levels by RT-PCR http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Measures BDNF protein levels using Western blotting technique. in_vitro brain tissue BDNF protein levels not_specified http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI http://purl.obolibrary.org/obo/OBI_0000272 OBI low BDNF protein levels can be measured by commercial available antibody sandwich ELISA kits, Western blotting, immunohistochemistry and immunofluorescence http://purl.obolibrary.org/obo/CHEBI_17754 CHEBI http://purl.obolibrary.org/obo/GO_0048011 GO DiI fluorescent labelling Visualizes dendritic arborizations and spines in cell culture and tissue sections using the fluorescent marker DiI, enabling quantitative analysis. in_vitro neurons brain dendritic arborization and spine density change http://purl.obolibrary.org/obo/CHEBI_37977 CHEBI http://purl.obolibrary.org/obo/GO_0043195 GO http://purl.obolibrary.org/obo/OBI_0000296 OBI medium The morphological analysis of neurons, include the use of fluorescent markers, such as DiI (1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate) that permits not only the visualisation of detailed dendritic arborizations and spines in cell culture and tissue sections but also permits the quantitative analysis of dendritic spines (Cheng et al., 2014). http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/GO_0016358 GO Electron microscopy Measures dendritic processes using electron micrographs, identifying them by the presence of microtubule associated protein 2 (MAP-2) and absence of axonal/glial components. in_vitro brain dendritic process elaboration change http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/PR_000001110 PR low Elaboration of dendritic processes is measured from electron and fluorescent micrographs. These processes are identified primarily by the presence of microtubule associated protein 2 (MAP-2) and the absence of components characteristic of axons and glia (e.g. small vesicles, myelin, glial filaments). http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/GO_0016358 GO Fluorescent microscopy with MAP-2 immunohistochemistry Measures dendritic processes using fluorescent micrographs of cells stained with antibodies against microtubule associated protein 2 (MAP-2), often automated. in_vitro neurons dendritic process elaboration change http://purl.obolibrary.org/obo/PR_000001110 PR http://purl.obolibrary.org/obo/OBI_0000296 OBI medium These measurements can also be carried out by automated imaging systems in cells prepared for immunohistochemistry with specific antibodies that recognise MAP-2 (Harrill and Mundy, 2011). http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/GO_0016358 GO Golgi Stain Kit Measures dendrites and dendritic spines using Golgi staining, often combined with confocal microscopy. ex_vivo brain rodents non-human primates dendrite and dendritic spine morphology change http://purl.obolibrary.org/obo/GO_0043195 GO medium Golgi Stain Kit is used to measure both dendrites and dendritic spines. A combination of Golgi-Cox and immunofluorescence using confocal microscopy has also been suggested for the visualisation of dendrites in brain slices derived either from rodents or non-human primates (Levine et al., 2013). http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/GO_0016358 GO Golgi-Cox and immunofluorescence confocal microscopy A combination of Golgi-Cox staining and immunofluorescence using confocal microscopy to visualise dendrites in brain slices. ex_vivo brain slices rodents non-human primates visualisation of dendrites change low A combination of Golgi-Cox and immunofluorescence using confocal microscopy has also been suggested for the visualisation of dendrites in brain slices derived either from rodents or non-human primates (Levine et al., 2013). http://purl.obolibrary.org/obo/UBERON_0000683 UBERON http://purl.obolibrary.org/obo/GO_0043041 GO MARCM fluorescent labelling Fluorescent labelling for the Mosaic Analysis with a Repressible Cell Marker (MARCM) system, used in transparent larval body walls. in_vivo larval body wall Drosophila cell marker visualization change low Fluorescent labelling for MARCM (mosaic analysis with a repressible cell marker) system can also be used but only in case of transparent larval body wall found in Drosophila. MARCM fluorescent labelling Visualizes dendrites in Drosophila neurons using fluorescent labelling in the MARCM (mosaic analysis with a repressible cell marker) system. in_vivo neurons nervous system Drosophila dendrite morphology change http://purl.obolibrary.org/obo/NCBITaxon_7227 NCBITAXON http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/OBI_0000296 OBI low Fluorescent labelling for MARCM (mosaic analysis with a repressible cell marker) system can also be used but only in case of transparent larval body wall found in Drosophila. http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/GO_0016358 GO Two-photon time-lapse imaging Visualizes dendrites in GFP-transfected neurons using two-photon microscopy. in_vitro neurons dendrite morphology change http://purl.obolibrary.org/obo/PR_000008301 PR http://purl.obolibrary.org/obo/GO_0030425 GO low Two-photon time-lapse images can be used to visualise dendrites in GFP-transfected neurons http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/GO_0016358 GO [3H]glutamate release assay Measures the release of radioactive glutamate from presynaptic terminals using tritiated glutamate. in_vitro glutamate release decrease low There are radioactive assays like [3H]glutamate release assay HPLC with fluorescence detector Measures neurotransmitters, including glutamate, using high-performance liquid chromatography with a fluorescence detector. in_vitro glutamate concentration decrease medium neurotransmitters including glutamate can be measured by HPLC with fluorescence detector HPLC with fluorescence detector High-performance liquid chromatography coupled with a fluorescence detector to measure neurotransmitters, including glutamate. in_vitro neurotransmitter concentration not_specified not_specified neurotransmitters including glutamate can be measured by HPLC with fluorescence detector LC-MS Glutamate levels are measured in cell culture medium (release) or intracellularly (cell lysate) using liquid chromatography-mass spectrometry (LC-MS). in_vitro glutamate levels decrease http://purl.obolibrary.org/obo/CHEBI_591 CHEBI http://purl.obolibrary.org/obo/GO_0008470 GO medium spectrophotometric commercially available kits to measure glutamate in cell culture medium (release) or intracellular (cell lysate) using LC-MS. http://purl.obolibrary.org/obo/CHEBI_591 CHEBI http://purl.obolibrary.org/obo/GO_0022038 GO LC-MS glutamate measurement Measures glutamate levels in cell culture medium or cell lysate using liquid chromatography-mass spectrometry. in_vitro glutamate concentration decrease medium spectrophotometric commercially available kits to measure glutamate in cell culture medium (release) or intracellular (cell lysate) using LC-MS spectrophotometric kit Commercially available spectrophotometric kits used to measure glutamate levels in either cell culture medium or cell lysate. in_vitro glutamate concentration not_specified not_specified spectrophotometric commercially available kits to measure glutamate in cell culture medium (release) or intracellular (cell lysate) Commercial synaptogenesis assay kits Relies on the immunostaining of cells with MAP-2, PSD-95, and synaptophysin to assess synaptogenesis. in_vitro cells synaptic marker expression decrease not_specified There are commercial available synaptogenesis assay kits that rely on the immunostaining of cells with MAP-2, PSD-95 and synaptophysin. Electron microscopy Assesses the prevalence of excitatory and inhibitory synapses amongst convergent contacts using ultrastructural analysis. in_vitro prevalence of excitatory and inhibitory synapses decrease http://purl.obolibrary.org/obo/GO_0035205 GO http://purl.obolibrary.org/obo/OBI_0000219 OBI low Electron microscopy can also be applied to assess the prevalence of excitatory and inhibitory synapses amongst convergent contacts http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0050808 GO High content image analysis Uses RNAi screening protocols and imaging algorithms to analyze synaptic punctae in vitro and in vivo. in_vitro synaptic punctae decrease high a high content image analysis based on RNAi screening protocols has been suggested as a useful tool to create imaging algorithm for use in both in vitro and in vivo synaptic punctae analysis http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0050808 GO Immunostaining Immunostaining with specific antibodies to recognize vesicular glutamate transporters (VGLUTs) and postsynaptic density protein-95 kDa (PSD-95) for excitatory synapses, and vesicular GABA (VGAT) and vesicular inhibitory amino acid (VIAAT) transporters and gephryin (Gephyrin) for inhibitory synapses. in_vitro cultured hippocampus primary cells hippocampus not_specified number of excitatory or inhibitory synapses decrease http://purl.obolibrary.org/obo/GO_0044403 GO http://purl.obolibrary.org/obo/GO_0099536 GO http://purl.obolibrary.org/obo/GO_0099535 GO low Immunostaining can be employed with specific antibodies that recognize vesicular glutamate transporters (VGLUTs) and the postsynaptic density protein-95 kDa (PSD-95) that are characteristic of excitatory synapses, while inhibitory synapses are identified by the presence of the vesicular GABA (VGAT) and vesicular inhibitory amino acid (VIAAT) transporters and the postsynaptic adaptor protein gephryin (Gatto and Broadie, 2010). Some other presynaptic (Bassoon) and postsynaptic (ProSAP1/Shank2) markers have been suggested and showed to correlate well with the ultrastructural studies in cultured hippocampus primary cells (Grabrucker et al., 2009). http://purl.obolibrary.org/obo/GO_0044403 GO http://purl.obolibrary.org/obo/GO_0034156 GO Immunostaining for excitatory synapses Uses antibodies to detect vesicular glutamate transporters (VGLUTs) and postsynaptic density protein-95 kDa (PSD-95) to identify excitatory synapses. in_vitro number of excitatory synapses decrease http://purl.obolibrary.org/obo/GO_0035205 GO medium Immunostaining can be employed with specific antibodies that recognize vesicular glutamate transporters (VGLUTs) and the postsynaptic density protein-95 kDa (PSD-95) that are characteristic of excitatory synapses http://purl.obolibrary.org/obo/GO_0035205 GO http://purl.obolibrary.org/obo/GO_0050808 GO synaptogenesis assay kit Commercial kits rely on immunostaining of cells with MAP-2, PSD-95 and synaptophysin to assess synaptogenesis. not_specified protein expression levels of MAP-2, PSD-95 and synaptophysin change http://purl.obolibrary.org/obo/OBI_0000232 OBI medium There are commercial available synaptogenesis assay kits that rely on the immunostaining of cells with MAP-2, PSD-95 and synaptophysin. http://purl.obolibrary.org/obo/CL_0000568 CL ECoG Electrocorticography (ECoG) records brain activity generated by multiple neuronal cell networks, allowing quantification of neuronal network function. in_vivo brain brain activity decrease not_specified The recording of brain activity by using electroencephalography (EEG), electrocorticography (ECoG) and local field potentials (LFP) assists towards the collection of signals generated by multiple neuronal cell networks. http://purl.obolibrary.org/obo/GO_0099529 GO EEG Electroencephalography (EEG) records brain activity generated by multiple neuronal cell networks, allowing quantification of neuronal network function. in_vivo brain brain activity decrease http://purl.obolibrary.org/obo/OBI_0000269 OBI not_specified The recording of brain activity by using electroencephalography (EEG), electrocorticography (ECoG) and local field potentials (LFP) assists towards the collection of signals generated by multiple neuronal cell networks. http://purl.obolibrary.org/obo/GO_0099529 GO EPSCs/IPSCs recording Recording excitatory and inhibitory postsynaptic currents (EPSCs or IPSCs) by variably clamping the membrane potential to determine the number of excitatory or inhibitory synapses. in_vivo brain number of excitatory or inhibitory synapses change http://purl.obolibrary.org/obo/GO_0045202 GO not_specified The number of excitatory or inhibitory synapses can be functionally studied at an electrophysiological level by examining the contribution of glutamatergic and GABAergic synaptic inputs. The number of them can be determined by variably clamping the membrane potential and recording excitatory and inhibitory postsynaptic currents (EPSCs or IPSCs) (Liu, 2004). http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0007268 GO LFP Local field potentials (LFP) record brain activity generated by multiple neuronal cell networks, allowing quantification of neuronal network function. in_vivo brain brain activity decrease not_specified The recording of brain activity by using electroencephalography (EEG), electrocorticography (ECoG) and local field potentials (LFP) assists towards the collection of signals generated by multiple neuronal cell networks. http://purl.obolibrary.org/obo/GO_0099529 GO MEA Microelectrode array (MEA) recordings measure electrical activity in cultured neurons, facilitating high-throughput screening of chemical compounds. in_vitro cultured neurons electrical activity decrease high Microelectrode array (MEA) recordings are also used to measure electrical activity in cultured neurons (Keefer et al., 2001, Gramowski et al., 2000; Gopal, 2003; Johnstone et al., 2010). MEAs can be applied in high throughput platforms to facilitate screening of numerous chemical compounds (McConnell et al., 2012). http://purl.obolibrary.org/obo/CL_0000540 CL microelectrode array (MEA) recordings Microelectrode array (MEA) recordings measure electrical activity in cultured neurons, which can be applied in high throughput platforms to screen numerous chemical compounds and evaluate their response using selective agonists and antagonists of different classes of receptors. in_vitro cultured neurons not_specified not_specified electrical activity in cultured neurons decrease http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0002376 GO high Microelectrode array (MEA) recordings are also used to measure electrical activity in cultured neurons (Keefer et al., 2001, Gramowski et al., 2000; Gopal, 2003; Johnstone et al., 2010). MEAs can be applied in high throughput platforms to facilitate screening of numerous chemical compounds (McConnell et al., 2012). http://purl.obolibrary.org/obo/CL_0000540 CL Patch clamping Patch clamping technique measures ionic currents across neuronal membranes to assess neuronal network activity. in_vitro ionic currents across neuronal membrane decrease http://purl.obolibrary.org/obo/CHMO_0000047 CHMO not_specified Patch clamping technique can also be used to measure neuronal network activity. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0050801 GO patch clamping Patch clamping technique measures neuronal network activity by recording electrical currents across the cell membrane. in_vitro neurons neuronal network activity decrease http://purl.obolibrary.org/obo/OBI_0000278 OBI low Patch clamping technique can also be used to measure neuronal network activity. http://purl.obolibrary.org/obo/GO_0099529 GO Dendritic spine shrinkage quantification Quantification of cofilin and phospho-cofilin in neurons expressing eGFP, combined with immunocytochemical techniques, measures NMDAR overactivation-induced long lasting LTD and dendritic spine shrinkage. in_vitro neurons expressing eGFP brain rodents dendritic spine shrinkage decrease http://purl.obolibrary.org/obo/UBERON_0002300 UBERON http://purl.obolibrary.org/obo/GO_0008102 GO low NMDAR overactivation-induced long lasting LTD can be measured by the dendritic spine shrinkage by quantification of cofilin and phospho-cofilin in neurons expressing eGFP and combined with immunocytochemical techniques. http://purl.obolibrary.org/obo/UBERON_0002300 UBERON http://purl.obolibrary.org/obo/GO_0008102 GO drebrin immunocytochemistry Evaluates the degradation of drebrin, a marker of excitotoxicity induced by NMDAR overactivation, by detecting proteolytic fragments or reduction in full-length drebrin using immunocytochemistry. in_vitro cultured rodent neurons rodent drebrin degradation decrease http://purl.obolibrary.org/obo/GO_0006508 GO low Drebrin immunocytochemistry: drebrin, a major actin-filament-binding protein localized in mature dendritic spines is a target of calpain mediated proteolysis under excitotoxic conditions induced by the overactivation of NMDARs. Degradation of drebrin can be evaluated quantitatively by Western blot analysis (mRNA evel) or by immunocytochemistry (at protein level) http://purl.obolibrary.org/obo/GO_0006508 GO enzyme-based microelectrode arrays Measures extracellular glutamate levels in vivo or in brain slices using glutamate oxidase-coated ceramic MEAs coupled with constant voltage amperometry to assess hyperexcitability modulators on glutamate release. in_vivo brain slices extracellular glutamate levels increase http://purl.obolibrary.org/obo/CHEBI_18337 CHEBI http://purl.obolibrary.org/obo/GO_0014047 GO low Excessive excitability can be also measured directly by evaluating the level of the extracellular glutamate using the enzyme-based microelectrode arrays. Using glutamate oxidase coated ceramic MEAs coupled with constant voltage amperometry, it is possible to measure resting glutamate levels and synaptic overflow of glutamate after K(+) stimulation in brain slices http://purl.obolibrary.org/obo/CHEBI_18337 CHEBI http://purl.obolibrary.org/obo/GO_0014047 GO immunocytochemistry Immunocytochemistry is used to evaluate the degradation of drebrin at the protein level and to quantify dendritic spine shrinkage by measuring cofilin and phospho-cofilin levels. in_vitro neurons drebrin protein levels, dendritic spine size decrease low Degradation of drebrin can be evaluated quantitatively by ... or by immunocytochemistry. NMDAR overactivation-induced long lasting LTD can be measured by the dendritic spine shrinkage by quantification of cofilin and phospho-cofilin in neurons expressing eGFP and combined with immunocytochemical techniques http://purl.obolibrary.org/obo/CL_0007426 CL http://purl.obolibrary.org/obo/GO_0052506 GO immunocytochemistry (cofilin/phospho-cofilin) Measures dendritic spine shrinkage and NMDAR overactivation-induced long-lasting LTD by quantifying cofilin and phospho-cofilin in neurons expressing eGFP. in_vitro neurons cofilin and phospho-cofilin levels change http://purl.obolibrary.org/obo/GO_0043197 GO low NMDAR overactivation-induced long lasting LTD can be measured by the dendritic spine shrinkage by quantification of cofilin and phospho-cofilin in neurons expressing eGFP and combined with immunocytochemical techniques http://purl.obolibrary.org/obo/GO_0043197 GO http://purl.obolibrary.org/obo/GO_0060293 GO microelectrode array (MEA) Measures spontaneous or evoked network activity of cultured neurons, including glutamatergic receptor function, using specific agonists and antagonists. in_vitro cultured neurons network activity change http://purl.obolibrary.org/obo/GO_0004970 GO medium Microelectrode array (MEA) recordings are used to measure mainly spontaneous network activity of cultured neurons (Keefer et al., 2001, Gramowski et al., 2000 and Gopal, 2003; Johnstone et al., 2010). using specific agonists and antagonists of a receptor, including NMDAR, MEA technology can be used to measure evoked activity, including glutamatergic receptor function http://purl.obolibrary.org/obo/GO_0044476 GO http://purl.obolibrary.org/obo/GO_0007268 GO optical detection of neuronal spikes Measures neuronal network function by optically detecting neuronal spikes in vivo or in vitro. in_vivo neuronal spikes change http://purl.obolibrary.org/obo/GO_0019228 GO low Neuronal network function can be also measured using optical detection of neuronal spikes both in vivo and in vitro (Wilt et al., 2013). http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0001508 GO patch clamp Records individual ion channels selective to Na+, K+, and Ca2+ to indirectly measure the activation or inhibition of NMDA receptors by detecting ion flux when the channel is open or closed. in_vitro neuronal cells brain slices ion channel conductance change http://purl.obolibrary.org/obo/GO_0005216 GO http://purl.obolibrary.org/obo/GO_0004972 GO low The measurement of the activation or the inhibition of NMDA receptors is done indirectly by recording the individual ion channels that are selective to Na+, K+ and Ca2+ by the patch clamp technique. This method relies on lack of measurable ion flux when NMDA ion channel is closed, whereas constant channel specific conductance is recorded at the open state of the receptor http://purl.obolibrary.org/obo/PR_000001206 PR http://purl.obolibrary.org/obo/GO_0006811 GO Patch clamp Patch clamp technique records individual ion channels selective to Na+, K+ and Ca2+ to indirectly measure activation or inhibition of NMDA receptors. It relies on lack of measurable ion flux when the NMDA ion channel is closed and constant channel specific conductance is recorded at the open state of the receptor. in_vitro neuronal cells brain rodents NMDA receptor activation state change http://purl.obolibrary.org/obo/PR_000001123 PR http://purl.obolibrary.org/obo/GO_0005217 GO low The measurement of the activation or the inhibition of NMDA receptors is done indirectly by recording the individual ion channels that are selective to Na+, K+ and Ca2+ by the patch clamp technique. The whole-cell patch clamp recording techniques have also been used to study synaptically-evoked NMDA receptor-mediated excitatory or inhibitory postsynaptic currents (EPSCs and IPSCs, respectively) in brain slices and neuronal cells, allowing the evaluation of the activated or inhibited state of the receptor. http://purl.obolibrary.org/obo/PR_000001123 PR http://purl.obolibrary.org/obo/GO_0005217 GO Western blot Evaluates the degradation of drebrin by detecting proteolytic fragments or reduction in full-length drebrin at the protein level. in_vitro cultured rodent neurons rodent drebrin degradation decrease http://purl.obolibrary.org/obo/GO_0006508 GO low Degradation of drebrin can be evaluated quantitatively by Western blot analysis (mRNA evel) or by immunocytochemistry (at protein level) http://purl.obolibrary.org/obo/GO_0006508 GO whole-cell patch clamp Records synaptically-evoked NMDA receptor-mediated excitatory or inhibitory postsynaptic currents (EPSCs and IPSCs) in brain slices and neuronal cells to evaluate the activated or inhibited state of the receptor. ex_vivo neuronal cells brain slices postsynaptic currents change http://purl.obolibrary.org/obo/GO_0086010 GO http://purl.obolibrary.org/obo/GO_0004972 GO low The whole-cell patch clamp recording techniques have also been used to study synaptically-evoked NMDA receptor-mediated excitatory or inhibitory postsynaptic currents (EPSCs and IPSCs, respectively) in brain slices and neuronal cells, allowing the evaluation of the activated or inhibited state of the receptor. http://purl.obolibrary.org/obo/PR_000001206 PR http://purl.obolibrary.org/obo/GO_0007268 GO Calcium influx assay Measures the influx of calcium ions into cells, often used to assess intracellular calcium overload. in_vitro intracellular calcium levels increase http://purl.obolibrary.org/obo/GO_0006816 GO not_specified Calcium influx http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0006816 GO Direct Peptide Reactivity Assay (DPRA) Chemicals are incubated with synthetic peptides containing lysine or cysteine, and the depletion of the peptides is quantified, indicating reactivity towards these amino acids. in_vitro peptide depletion decrease http://purl.obolibrary.org/obo/OBI_0100046 OBI http://purl.obolibrary.org/obo/CL_0000218 CL http://purl.obolibrary.org/obo/CL_0000217 CL OECD TG 442C not_specified Protocols and Databases: While methionine, histidine, and serine all possess nucleophilic groups that are found in skin proteins, the –SH group of cysteine and the ε-NH2 group of lysine are the most often studied. Soft electrophilic interactions involving the thiol group can be modelled with small molecules. Glutathione (GSH; L-γ-glutamyl-L-cysteinyl-glycine) is the most widely used model nucleophile in soft electrophilic reactivity assays. [...] Recently, OECD adopted the new Test Guideline (TG) No442C: In chemico skin sensitisation – Direct Peptide Reactivity Assay (DPRA). This method quantifies the reactivity of chemicals towards model synthetic peptides containing either lysine or cysteine [15]. The DPRA protocol can be found in the EURL ECVAM Database Service on Alternative Methods to animal experimentation (DB-ALM): Protocol No154 for Direct Peptide Reactivity Assay (DPRA) for skin sensitisation testing [16]. http://purl.obolibrary.org/obo/OBI_0100046 OBI Direct Peptide Reactivity Assay (DPRA) Quantifies the reactivity of chemicals towards synthetic peptides containing lysine or cysteine. not_specified peptide reactivity not_specified OECD TG 442C medium Recently, OECD adopted the new Test Guideline (TG) No442C: In chemico skin sensitisation – Direct Peptide Reactivity Assay (DPRA). This method quantifies the reactivity of chemicals towards model synthetic peptides containing either lysine or cysteine [15]. http://purl.obolibrary.org/obo/CHEBI_16650 CHEBI http://purl.obolibrary.org/obo/GO_0018193 GO ELISA Enzyme-linked immunosorbent assay used to investigate the binding of diisocyanates. in_vitro binding of diisocyanates not_specified not_specified investigate the binding of diisocyanates in vapor and liquid phases with LC/MS, MS/MS, and ELISA glutathione depletion assay Chemicals are incubated with glutathione (GSH), and the concentration of free thiol groups is measured to assess reactivity. not_specified free thiol group concentration decrease medium Glutathione (GSH; L-γ-glutamyl-L-cysteinyl-glycine) is the most widely used model nucleophile in soft electrophilic reactivity assays. Typically, chemicals are incubated with GHS and, after a defined reaction time, the concentration of free thiol groups is measured. http://purl.obolibrary.org/obo/CHEBI_5798 CHEBI http://purl.obolibrary.org/obo/GO_0006805 GO GSH depletion assay Chemicals are incubated with glutathione (GSH), and the concentration of free thiol groups is measured after a defined reaction time. Depletion of GSH is assumed to indicate adduct formation. in_vitro GSH concentration decrease not_specified Typically, chemicals are incubated with GHS and, after a defined reaction time, the concentration of free thiol groups is measured. Such depletion based assays assume adduct formation, which is typically not confirmed. http://purl.obolibrary.org/obo/CHEBI_2882 CHEBI http://purl.obolibrary.org/obo/GO_0055114 GO HPLC-MS/MS High-performance liquid chromatography mass spectrometry (MS) analysis is used to analyze reaction products, improving predictive capacity. in_vitro reaction products change not_specified Dik et al. modified the DPRA protocol to include two peptide depletion measurement time points, and added high-performance liquid chromatography mass spectrometry (MS) analysis of reaction products, which improved predictive capacity. (Dik et al., 2016) http://purl.obolibrary.org/obo/GO_0003024 GO in silico models Computational techniques to predict chemical reactivity, ranging from simple structural alerts to quantitative QSAR models. in_silico chemical reactivity not_specified high Computational or in silico techniques to predict chemical reactivity have been developed; they vary in complexity from the relatively simple approach of forming chemical categories from 2D structural alerts (i.e. SARs for qualitative identification of chemical sub-structures with the potential of being reactive), such as used in the Organisation for Economic Co-Operation and Development (OECD)QSAR Toolbox [10] to QSAR models (i.e. quantitative prediction of relative reactivity) as described by Schwöbel et al. [11]. QSAR/SAR modeling Computational techniques using 2D structural alerts (SAR) or quantitative structure-activity relationships (QSAR) to predict chemical reactivity and covalent binding potential. in_silico chemical reactivity change http://purl.obolibrary.org/obo/OBI_0000467 OBI not_specified Computational or in silico techniques to predict chemical reactivity have been developed; they vary in complexity from the relatively simple approach of forming chemical categories from 2D structural alerts (i.e. SARs for qualitative identification of chemical sub-structures with the potential of being reactive), such as used in the Organisation for Economic Co-Operation and Development (OECD)QSAR Toolbox [10] to QSAR models (i.e. quantitative prediction of relative reactivity) as described by Schwöbel et al. [11]. Western blot A laboratory method used to detect specific protein binding, such as diisocyanates. in_vitro binding of diisocyanates not_specified not_specified investigate the binding of diisocyanates in vapor and liquid phases with LC/MS, MS/MS, and ELISA, as well as, Western blot. http://purl.obolibrary.org/obo/PR_000000001 PR Western blot Used to detect protein binding of diisocyanates in respiratory sensitization studies. in_vitro protein binding not_specified http://purl.obolibrary.org/obo/GO_0005515 GO low Other authors have worked to investigate the binding of diisocyanates in vapor and liquid phases with LC/MS, MS/MS, and ELISA, as well as, Western blot. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0018193 GO ELISA Enzyme Linked Immunosorbent Assay to quantify IL-8 levels. in_vitro IL-8 concentration increase http://purl.obolibrary.org/obo/PR_000008899 PR high Quantification of IL-8 can be performed by Enzyme Linked Immunosorbent Assay, a technique that is far simpler and amenable to high throughput screening than the flow cytometry technique used to measure CD86 expression http://purl.obolibrary.org/obo/PR_000008899 PR http://purl.obolibrary.org/obo/GO_0006954 GO GARD Genomic Allergen Rapid Detection test based on the human myelomonocytic cell line MUTZ-3 to assess chemical sensitizers using genomic biomarker prediction signatures. in_vitro MUTZ-3 human genomic biomarker signature change not_specified a biomarker signature, the Genomic Allergen Rapid Detection test (GARD) based on the human myelomonocytic cell line MUTZ-3 http://purl.obolibrary.org/obo/GO_0006955 GO h-CLAT Human Cell Line Activation Test measuring CD86 and CD54 expression in THP-1 cells by flow cytometry. in_vitro THP-1 human CD86 and CD54 expression increase draft TG under discussion at OECD medium The human Cell Line Activation Test (h-CLAT) reported flow cytometry results for CD86 and CD54 expression in THP-1 cells http://purl.obolibrary.org/obo/GO_0001775 GO IL-8 ELISA Quantifies IL-8 chemokine levels using Enzyme Linked Immunosorbent Assay to distinguish sensitisers from non-sensitisers. in_vitro human IL-8 concentration increase high Quantification of IL-8 can be performed by Enzyme Linked Immunosorbent Assay, a technique that is far simpler and amenable to high throughput screening than the flow cytometry technique used to measure CD86 expression MUSST An assay measuring CD86 responses by U937 cells, similar to h-CLAT. in_vitro U937 human CD86 expression increase not_specified Several assays similar to the h-CLAT have emerged over time and are currently in the process of being validated (e.g., the MUSST measuring CD86 responses by U937 cells) http://purl.obolibrary.org/obo/GO_0001775 GO MUTZ-3 migration assay An assay using MUTZ-3 cells to assess chemical-induced migration, distinguishing between irritant-induced (CCL5-dependent) and sensitizer-induced (CXCL12-dependent) migration. in_vitro MUTZ-3 human migration ratio (CXCL12/CCL5) change http://purl.obolibrary.org/obo/GO_0016477 GO not_specified The MUTZ-3 cell line is also being investigated for the potential to assess the capacity of a chemical to induce LC migration. The discriminating feature of the assay is that irritant-induced migration is CCL5 dependent, while sensitizer-induced migration is CXCL12 dependent. The readout of the test is the ratio between migration toward CXCL12 or to CCL5. http://purl.obolibrary.org/obo/GO_0016477 GO SENSIS A genomic platform measuring the over-expression of 3 sets of genes to assess the sensitising potential of a compound. in_vitro gene over-expression increase http://purl.obolibrary.org/obo/GO_0010467 GO not_specified a genomic platform, SENSIS, which consists of measuring the over-expression of 3 sets of genes, that may allow the in vitro assessment of the sensitising potential of a compound http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0006351 GO U-SENS Myeloid U937 skin sensitisation test measuring CD86 by flow cytometry. in_vitro U937 human CD86 expression increase not_specified Another assay, the myeloid U937 skin sensitisation test (U-SENS), is based as well on the measurement of CD86 by flow cytometry http://purl.obolibrary.org/obo/GO_0001775 GO VITOSENS An assay using human CD34+ progenitor-derived dendritic cells to measure differential expression of CREM and CCR2. in_vitro CD34+ progenitor-derived dendritic cells human CREM and CCR2 expression change http://purl.obolibrary.org/obo/CL_0000451 CL not_specified VITOSENS, an assay that uses human CD34+ progenitor-derived dendritic cells (CD34-DC), is based on the differential expression of the cAMP-responsive element modulator (CREM) and monocyte chemotactic protein-1 receptor (CCR2) http://purl.obolibrary.org/obo/CL_0000451 CL http://purl.obolibrary.org/obo/GO_0001775 GO Autobiographical Memory Task Tests episodic autobiographical memory in humans by measuring recollection of specific personal events. in_vivo hippocampus humans autobiographical memory performance decrease http://purl.obolibrary.org/obo/UBERON_0001954 UBERON low Autobiographical memory (AM) is the recollection of specific personal events in a multifaceted higher order cognitive process. http://purl.obolibrary.org/obo/UBERON_0001954 UBERON Children’s Auditory Verbal Learning Test Children’s Auditory Verbal Learning Test (CAVLT) measures immediate memory span, level of learning, immediate recall, delayed recall, recognition accuracy, and total intrusions through free recall of presented word lists. not_specified brain humans Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, Total Intrusions decrease http://purl.obolibrary.org/obo/GO_0007613 GO medium Children’s Auditory Verbal Learning Test (CAVLT) is a free recall of presented word lists that yields measures of Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, and Total Intrusions. (Lezak 1994; Talley, 1986). http://purl.obolibrary.org/obo/UBERON_0000002 UBERON http://purl.obolibrary.org/obo/GO_0008430 GO Children’s Auditory Verbal Learning Test Tests verbal learning and memory in children by measuring free recall of presented word lists. in_vivo brain humans verbal memory performance decrease http://purl.obolibrary.org/obo/GO_0007613 GO low Children’s Auditory Verbal Learning Test (CAVLT) is a free recall of presented word lists that yields measures of Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, and Total Intrusions. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON Contextual Fear Conditioning Tests hippocampal-based learning in rodents by measuring suppression of activity upon reintroduction to an environment previously associated with an aversive stimulus. in_vivo hippocampus rodents fear memory retention decrease http://purl.obolibrary.org/obo/GO_0001995 GO http://purl.obolibrary.org/obo/UBERON_0001954 UBERON low Contextual Fear Conditioning is a hippocampal based learning task in which animals are placed in a novel environment and allowed to explore for several minutes before delivery of an aversive stimulus, typically a mild foot shock. http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0001995 GO Continuous Visual Memory Test Continuous Visual Memory Test (CVMT) measures visual learning and memory through free recall of presented pictures/objects, yielding similar measures to CAVLT. not_specified brain humans Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, Total Intrusions decrease http://purl.obolibrary.org/obo/GO_0007613 GO medium Continuous Visual Memory Test (CVMT) measures visual learning and memory. It is a free recall of presented pictures/objects rather than words but that yields similar measures of Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, and Total Intrusions. (Lezak, 1984; 1994). http://purl.obolibrary.org/obo/UBERON_0000002 UBERON http://purl.obolibrary.org/obo/GO_0008430 GO Continuous Visual Memory Test Tests visual learning and memory in humans by measuring free recall of presented pictures/objects. in_vivo brain humans visual memory performance decrease http://purl.obolibrary.org/obo/GO_0007613 GO low Continuous Visual Memory Test (CVMT) measures visual learning and memory. It is a free recall of presented pictures/objects rather than words but that yields similar measures of Immediate Memory Span, Level of Learning, Immediate Recall, Delayed Recall, Recognition Accuracy, and Total Intrusions. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON Morris Water Maze A spatial learning task where rodents must locate a hidden platform submerged in a large tank of water, testing hippocampal function. in_vivo hippocampus rodents time to locate hidden platform decrease http://purl.obolibrary.org/obo/GO_0008345 GO http://purl.obolibrary.org/obo/GO_0061564 GO OECD TG 426 low Tests such as novel object recognition, and fear-based context learning are also sensitive to hippocampal disruption. RAM, Barnes Maze, and MWM are examples of spatial tasks in which animals are required to learn: the location of a food reward (RAM); an escape hole to enter a preferred dark tunnel from a brightly lit open field area (Barnes maze); or a hidden platform submerged below the surface of the water in a large tank of water (MWM) (Vorhees and Williams, 2014). http://purl.obolibrary.org/obo/UBERON_0001950 UBERON http://purl.obolibrary.org/obo/GO_0008345 GO Novel Object Recognition Tests recognition memory in rodents by measuring time spent interacting with a novel object after familiarization with two objects. in_vivo dorsal hippocampus rodents recognition memory performance decrease http://purl.obolibrary.org/obo/GO_0050804 GO http://purl.obolibrary.org/obo/UBERON_0002406 UBERON medium Novel Object Recognition (NOR) and its variants are widely used in neuroscience... time spent interacting with the novel object is taken evidence of memory retention http://purl.obolibrary.org/obo/UBERON_0002406 UBERON http://purl.obolibrary.org/obo/GO_0050804 GO Novel Object Recognition A recognition memory task where rodents explore two objects, and later one familiar object is replaced with a novel object to assess memory retention. in_vivo hippocampus rodents time spent interacting with novel object decrease http://www.bioassayontology.org/bao#BAO_0000027 BAO http://purl.obolibrary.org/obo/GO_0007616 GO http://purl.obolibrary.org/obo/UBERON_0001950 UBERON medium Novel Object Recognition (NOR) and its variants are widely used in neuroscience, although their suitability for safety assessment remains unclear (Vorhees and Williams, 2024). NOR and novel place recognition (NPR) are examples of ‘incidental learning’ and rely on the dorsal hippocampus. http://purl.obolibrary.org/obo/UBERON_0001950 UBERON http://purl.obolibrary.org/obo/GO_0007616 GO Radial Arm Maze Tests spatial learning in rodents by requiring them to learn the location of a food reward. in_vivo hippocampus rodents spatial learning performance decrease http://purl.obolibrary.org/obo/GO_0008544 GO http://purl.obolibrary.org/obo/UBERON_0001954 UBERON low RAM, Barnes Maze, and MWM are examples of spatial tasks in which animals are required to learn: the location of a food reward (RAM); http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO Rey Osterrieth Complex Figure Test Tests visuospatial abilities, memory, attention, planning, and working memory in humans by copying and recalling a complex figure. in_vivo brain humans visuospatial memory performance decrease http://purl.obolibrary.org/obo/GO_0007612 GO low Rey Osterieth Complex Figure (RCFT) which probes a variety of functions including visuospatial abilities, memory, attention, planning, and working memory http://purl.obolibrary.org/obo/UBERON_0000955 UBERON Staged AM Task Staged AM Task involves children participating in a staged event and subsequent interviews to assess autobiographical memory. not_specified brain humans autobiographical memory decrease http://purl.obolibrary.org/obo/GO_0007613 GO low Staged AM Task. In this version of the AM test, children participate in a staged event involving a tour of the hospital, perform a series of tasks (counting footprints in the hall, identifying objects in wall display, buying lunch, watched a video). http://purl.obolibrary.org/obo/UBERON_0002061 UBERON http://purl.obolibrary.org/obo/GO_0007613 GO trace fear conditioning Trace Fear Conditioning assesses learning by associating a neutral stimulus with an aversive stimulus with a delay, requiring engagement of both the amygdala and hippocampus. in_vivo hippocampus amygdala rodents freezing behavior change low Finally, trace fear conditioning which incorporates a temporal component upon traditional amygdala-based fear learning engages the hippocampus. Introducing a brief delay between presentation of the neutral CS and the aversive US, a trace period, requires the engagement of the amygdala and the hippocampus (Shors et al., 2004). http://purl.obolibrary.org/obo/UBERON_0002061 UBERON http://purl.obolibrary.org/obo/GO_0008430 GO Wechsler Adult Intelligence Scale (WAIS) A standardized neuropsychological test used to calculate composite scores for various cognitive domains including verbal comprehension, perceptual reasoning, working memory, and processing speed. in_vivo brain human cognitive ability change http://purl.obolibrary.org/obo/GO_0051322 GO low Wechsler Adult Intelligence Scale (WAIS) which calculates four composite scores that examine various domains within an individual’s overall cognitive ability http://purl.obolibrary.org/obo/UBERON_0000848 UBERON Wechsler Memory Scale Logical Memory Test Battery Tests memory functions in humans by measuring recall of stories. in_vivo brain humans memory performance decrease http://purl.obolibrary.org/obo/GO_0007613 GO low Story Recall from Wechsler Memory Scale (WMS) Logical Memory Test Battery, a standardized neuropsychological test designed to measure memory functions http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0007613 GO estrous cycle monitoring Monitoring the pattern of events in the estrous cycle to assess reproductive neuroendocrine and ovarian function in rodents. in_vivo ovary vagina rat mouse estrous cycle parameters change OECD TG 407, OECD TG 416, OECD TG 443, EPA OCSPP 890.1450 medium The pattern of events in the estrous cycle may provide a useful indicator of the normality of reproductive neuroendocrine and ovarian function in the nonpregnant female. Regular cyclicity is one of the key parameters in assessment of female reproductive function in rodents. Estrous cyclicity provides a method for evaluating the endocrine disrupting activity of each test chemical under physiologic conditions where endogenous concentrations of estrogen vary. http://purl.obolibrary.org/obo/UBERON_0000993 UBERON http://purl.obolibrary.org/obo/GO_0042698 GO follicle culture In vitro culture of follicles to study folliculogenesis and oogenesis, producing mature oocytes. in_vitro follicle ovary follicle development and oocyte maturation change http://purl.obolibrary.org/obo/GO_0001545 GO http://purl.obolibrary.org/obo/GO_0048496 GO low The follicle culture models were developed for the in-vitro production of mature oocytes and used to study the process of folliculogenesis and oogenesis in vitro. These in vitro cultures demonstrate near-identical effects to those found in vivo, therefore might be able to acquire a place in fertility testing, replacing some in-vivo studies for ovarian function and female gamete quality testing. http://purl.obolibrary.org/obo/GO_0048557 GO http://purl.obolibrary.org/obo/GO_0001545 GO serum FSH assay Measures follicle-stimulating hormone concentration in blood to evaluate ovarian function and endocrine status. in_vivo serum FSH level change not_specified The observation that animals do not ovulate while exhibiting estrous cycles indicates that estrous cyclicity alone may not be a sufficient surrogate of healthy function of ovaries; the measurements of serum hormones and particularly FSH can contribute to more sensitivity indicators of healthy function of ovaries (Davis, Maronpot, & Heindel, 1994). serum hormone measurement Measurement of serum hormone levels, particularly FSH, to assess ovarian function. This is used in conjunction with estrous cyclicity assessment for increased sensitivity. in_vivo ovary pituitary gland rat mouse serum hormone levels (e.g., FSH) change low The observation that animals do not ovulate while exhibiting estrous cycles indicates that estrous cyclicity alone may not be a sufficient surrogate of healthy function of ovaries; the measurements of serum hormones and particularly FSH can contribute to more sensitivity indicators of healthy function of ovaries (Davis, Maronpot, & Heindel, 1994). the measurements of serum hormones and particularly FSH can contribute to more sensitivity indicators of healthy function of ovaries http://purl.obolibrary.org/obo/CHEBI_50785 CHEBI http://purl.obolibrary.org/obo/GO_0008753 GO Vaginal Smear Cytology Monitoring of estrous cycle normality by observing changes in vaginal smear cytology to identify cycle stages and regularity. in_vivo vagina rat mouse estrous cycle length and stage distribution change http://purl.obolibrary.org/obo/GO_0009011 GO OECD TG 407, OECD TG 416, OECD TG 443 low Estrous cycle normality can be monitored in the rat and mouse by observing the changes in the vaginal smear cytology. Parameters assessed for cyclicity: - Number of cycling females - Number of females with regular cycles - Number of cycles - Estrous cycle length - Percentage of time spent in the various estrous cycle stages http://purl.obolibrary.org/obo/UBERON_0001945 UBERON http://purl.obolibrary.org/obo/GO_0009011 GO vaginal smear cytology Microscopic examination of vaginal smears to assess the stage of the estrous cycle based on cellular morphology. Visual observation is a quick method for identifying proestrus or estrus stages. in_vivo vaginal epithelial cells vagina rat mouse estrous cycle stage (proestrus, estrus, etc.) change OECD guidelines medium Estrous cycle normality can be monitored in the rat and mouse by observing the changes in the vaginal smear cytology. Visual observation of the vagina is the quickest method, requires no special equipment, and is best used when only proestrus or estrus stages need to be identified. For details see: (Westwood, 2008), (Byers, Wiles, Dunn, & Taft, 2012) http://purl.obolibrary.org/obo/CL_0002125 CL http://www.ebi.ac.uk/efo/EFO_0004797 EFO vaginal smear cytology Monitoring estrous cycle normality by observing changes in vaginal smear cytology in rats and mice. in_vivo vagina rat mouse vaginal cytology changes change OECD guidelines high Estrous cycle normality can be monitored in the rat and mouse by observing the changes in the vaginal smear cytology. Visual observation of the vagina is the quickest method, requires no special equipment, and is best used when only proestrus or estrus stages need to be identified. http://purl.obolibrary.org/obo/UBERON_0000996 UBERON http://purl.obolibrary.org/obo/GO_0042698 GO fertility rate measurement Measures the number of offspring born per mating pair, individual, or population. in_vivo number of offspring decrease low fertility rate, is the number of offspring born per mating pair, individual or population. ELISA Measures protein levels of aromatase (Cyp19a1) using enzyme-linked immunosorbent assay. in_vitro ovarian granulosa cells ovary aromatase protein level not_specified http://purl.obolibrary.org/obo/GO_0004049 GO high direct protein levels: Western blot or ELISA http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010457 GO ELISA ELISA is used to measure direct protein levels of aromatase (Cyp19a1). in_vitro ovarian cells ovary protein levels decrease medium Aromatase levels can be assayed by standard methods for assessment of gene expression levels like: q-PCR or direct protein levels: Western blot or ELISA. http://purl.obolibrary.org/obo/GO_0006454 GO q-PCR Measures gene expression levels of aromatase (Cyp19a1) using quantitative polymerase chain reaction. in_vitro ovarian granulosa cells ovary aromatase gene expression level not_specified http://purl.obolibrary.org/obo/GO_0004049 GO http://purl.obolibrary.org/obo/GO_0010467 GO medium Aromatase levels can be assayed by standard methods for assessment of gene expression levels like: q-PCR http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010467 GO q-PCR q-PCR is used to assess gene expression levels of aromatase (Cyp19a1). in_vitro ovarian cells ovary gene expression levels decrease medium Aromatase levels can be assayed by standard methods for assessment of gene expression levels like: q-PCR http://purl.obolibrary.org/obo/GO_0010468 GO Western blot Measures protein levels of aromatase (Cyp19a1) using antibody-based detection. in_vitro ovarian granulosa cells ovary aromatase protein level not_specified http://purl.obolibrary.org/obo/GO_0004049 GO low direct protein levels: Western blot http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010457 GO western blot Western blot is used to measure direct protein levels of aromatase (Cyp19a1). in_vitro ovarian cells ovary protein levels decrease low Aromatase levels can be assayed by standard methods for assessment of gene expression levels like: q-PCR or direct protein levels: Western blot http://purl.obolibrary.org/obo/GO_0006454 GO whole body measurement Measures tissue-specific expression of aromatase (Cyp19a1) in early life stage zebrafish embryos using whole body measurements. in_vivo whole body Danio rerio aromatase expression level not_specified http://purl.obolibrary.org/obo/GO_0004049 GO http://purl.obolibrary.org/obo/GO_0010467 GO medium In those cases, whole body measurements can be used as an indicator of this key event. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010467 GO Adduct Analysis Detection of AFB1-albumin adducts in human blood samples as a proxy for the presence of the reactive AFB1 exo-epoxide. ex_vivo blood Homo sapiens AFB1-albumin adducts increase not_specified Samples of blood from humans in AFB1-endemic regions have demonstrated presence of AFB1-albumin adducts, which are formed from the AFB1 exo-epoxide. http://purl.obolibrary.org/obo/PR_0000017 PR AFB1-albumin adduct detection Detects the presence of AFB1-albumin adducts in blood samples from humans in AFB1-endemic regions, indicating exposure to AFB1 exo-epoxide. in_vivo blood humans presence of AFB1-albumin adducts increase medium Samples of blood from humans in AFB1-endemic regions have demonstrated presence of AFB1-albumin adducts, which are formed from the AFB1 exo-epoxide. LC-MS/MS Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) is used to detect AFB1-albumin adducts in blood samples from humans in AFB1-endemic regions. in_vivo blood human AFB1-albumin adducts increase medium Samples of blood from humans in AFB1-endemic regions have demonstrated presence of AFB1-albumin adducts, which are formed from the AFB1 exo-epoxide. http://purl.obolibrary.org/obo/CHEBI_32883 CHEBI LC-MS/MS Detects and quantifies AFB1 metabolites, including the exo-epoxide, using liquid chromatography coupled with tandem mass spectrometry. in_vitro microsomes cellular homogenates cells in culture formation of AFB1 exo-epoxide increase http://purl.obolibrary.org/obo/OBI_0000473 OBI medium Formation of the exo-epoxide can be produced with in vitro systems and detected using techniques for structural quantitation of AFB1 metabolites (Himmelstein et al., 2009), including liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). By using subcellular fractions (e.g., microsomes), cellular homogenates, or cells in culture, it is possible to measure formation of AFB1 exo-epoxide. http://purl.obolibrary.org/obo/GO_0008152 GO LC-MS An analytical method to measure testosterone levels indirectly. in_vitro Leydig cells testosterone levels not_specified http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/OBI_0000473 OBI not_specified Testosterone synthesis in vitro cultured cells can be measured indirectly by testosterone radioimmunoassay or analytical methods such as LC-MS. http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006734 GO Leydig Cell-enriched Cultures A method for culturing Leydig cells to measure testosterone synthesis. in_vitro Leydig cells testis testosterone synthesis not_specified http://purl.obolibrary.org/obo/CL_0000185 CL http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI not_specified The methods for culturing Leydig cells can be found in the Database Service on Alternative Methods to animal experimentation (DB-ALM): Leydig Cell-enriched Cultures [2]. http://purl.obolibrary.org/obo/CL_0000185 CL http://purl.obolibrary.org/obo/GO_0006734 GO OECD TG 456 A validated in vitro screen for chemical effects on steroidogenesis, specifically the production of 17ß-estradiol (E2) and testosterone (T). in_vitro production of 17ß-estradiol and testosterone not_specified http://purl.obolibrary.org/obo/GO_0006694 GO http://purl.obolibrary.org/obo/CHEBI_16469 CHEBI http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI OECD TG 456 not_specified OECD TG 456 is the validated test guideline for an in vitro screen for chemical effects on steroidogenesis, specifically the production of 17ß-estradiol (E2) and testosterone (T). http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006694 GO radioimmunoassay Testosterone synthesis is measured indirectly using a testosterone radioimmunoassay. in_vitro Leydig cells testis testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_5905 CHEBI OECD TG 456 medium Testosterone synthesis in vitro cultured cells can be measured indirectly by testosterone radioimmunoassay OECD TG 456 is the validated test guideline for an in vitro screen for chemical effects on steroidogenesis, specifically the production of 17ß-estradiol (E2) and testosterone (T). The testosterone syntheis can be measured in vitro cultured Leydig cells. http://purl.obolibrary.org/obo/CHEBI_5905 CHEBI http://purl.obolibrary.org/obo/GO_0001583 GO Testicular Organ and Tissue Culture Systems A method for culturing testicular organ and tissue to measure testosterone synthesis. in_vitro testis testosterone synthesis not_specified http://purl.obolibrary.org/obo/UBERON_0000473 UBERON http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI not_specified The methods for culturing Leydig cells can be found in the Database Service on Alternative Methods to animal experimentation (DB-ALM): Testicular Organ and Tissue Culture Systems [3]. http://purl.obolibrary.org/obo/UBERON_0000473 UBERON http://purl.obolibrary.org/obo/GO_0006734 GO testosterone radioimmunoassay An analytical method to measure testosterone levels indirectly. in_vitro Leydig cells testosterone levels not_specified http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI not_specified Testosterone synthesis in vitro cultured cells can be measured indirectly by testosterone radioimmunoassay or analytical methods such as LC-MS. http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006734 GO cell viability assay Assay used to assess cytotoxicity to ensure observed effects are not due to cell death rather than specific NIS inhibition. in_vitro hNIS-HEK293TEPA cell viability decrease high Cell viability assays were performed to assess any confounding effects of cytotoxicity. in vivo 125I uptake assay An in vivo method measuring radioactive iodine uptake in rat thyroid glands via immunofluorescence and gamma counting after administration of Ci Na 125I. in_vivo thyroid gland rat percentage of 125I in the thyroid gland change low 125 I uptake assays is based on immunofluorescence analyses of thyroid glands after the treatment of rat with excess I −, injected with Ci Na 125 I Then the thyroid glands are removed and weighed, and the amount of 125 I in the thyroid gland is measured in a γ-counter Radioiodide uptake assay Measures the uptake of radioiodide (125I-) in NIS-expressing cells, commonly using the FRTL5 cell line or NIS-transfected cell lines. in_vitro FRTL5 NIS-transfected cell lines radioiodide uptake decrease http://purl.obolibrary.org/obo/GO_0015107 GO high Measurement of radioiodide uptake (125I-) in NIS expressing cells. This method has been also adapted in a high throughput format and has been already used for the screening of a chemical library of 17.020 compounds (Lecat-Guillet et al., 2008b). http://purl.obolibrary.org/obo/PR_000015773 PR http://purl.obolibrary.org/obo/GO_0015107 GO RAIU assay (hNIS-HEK293TEPA) Uses a novel cell line expressing human NIS to measure radioactive iodide uptake (RAIU) and identify inhibitors of NIS-mediated iodide uptake. in_vitro hNIS-HEK293TEPA human radioactive iodide uptake decrease http://purl.obolibrary.org/obo/GO_0015107 GO high A novel cell line expressing human NIS, hNIS-HEK293TEPA, was used in a radioactive iodide uptake (RAIU) assay to identify inhibitors of NIS-mediated iodide uptake. Strong assay performance and highly reproducible results support the utilization of this approach to screen large chemical libraries for inhibitors of NIS-mediated iodide uptake (Hallinger et al., 2017). http://purl.obolibrary.org/obo/PR_000015773 PR http://purl.obolibrary.org/obo/GO_0015107 GO Sandell-Kolthoff reaction assay A spectrophotometric assay that measures iodide uptake using the catalytic effect of iodide on the reduction of cerium(IV) to cerium(III) in the presence of arsenious acid. in_vitro FRTL5 rat iodide uptake decrease http://purl.obolibrary.org/obo/GO_0015107 GO http://purl.obolibrary.org/obo/OBI_0000218 OBI high It is a simple spectrophotometric assay for the determination of iodide uptake using rat thyroid-derived cells (FRTL5) based on the catalytic effect of iodide on the reduction of yellow cerium(IV) to colorless cerium(III) in the presence of arsenious acid (Sandell-Kolthoff reaction). http://purl.obolibrary.org/obo/PR_000015773 PR http://purl.obolibrary.org/obo/GO_0015107 GO YFP-based fluorescence assay Uses the YFP-H148Q/I152L variant to detect iodide efflux in FRTL5 cells, with fluorescence changes indicating NIS activity. in_vitro FRTL5 rat fluorescence changes change http://purl.obolibrary.org/obo/GO_0015107 GO not_specified A fluorescence-based method has been developed, which uses the variant YFP-H148Q/I152L of the Yellow Fluorescent Protein (YFP) in order to detect the efflux of iodide into the rat FRTL5 cells. http://purl.obolibrary.org/obo/PR_000015773 PR http://purl.obolibrary.org/obo/GO_0015107 GO YFP-based iodide efflux A fluorescence-based method using a YFP variant (YFP-H148Q/I152L) to detect iodide efflux in rat FRTL5 cells. Fluorescence changes are Na+-dependent. in_vitro FRTL5 thyroid rat iodide efflux change http://purl.obolibrary.org/obo/OBI_0000269 OBI not_specified A fluorescence-based method has been developed, which uses the variant YFP-H148Q/I152L of the Yellow Fluorescent Protein (YFP) in order to detect the efflux of iodide into the rat FRTL5 cells. Fluorescence changes in FRTL-5 cells are Na+-dependent, consistent with the Na+-dependence of NIS activity. radioactive iodine uptake test This test measures the absorption of radioactive iodine by the thyroid gland over 4-6 hours and 24 hours using a gamma scintillation counter. The percentage of uptake at 24 hours is the primary measurement. in_vivo thyroid gland percentage of radioactive iodine uptake decrease low The radioactive iodine uptake test, or RAIU test, is a type of scan used in the diagnosis of thyroid gland dysfunction The patient swallows radioactive iodine in the form of capsule or fluid, and its absorption by the thyroid is studied after 4–6 hours and after 24 hours with the aid of a gamma scintillation counter. The percentage of RAIU 24 hours after the administration of radioiodide is the most useful, since this is the time when the thyroid gland has reached the plateau of isotope accumulation, and because it has been shown that at this time, the best separation between high, normal, and low uptake is obtained. http://purl.obolibrary.org/obo/UBERON_0004778 UBERON radioactive iodine uptake test (RAIU) A diagnostic scan that measures the thyroid gland's avidity for iodide by quantifying the absorption of swallowed radioactive iodine using a gamma scintillation counter at specific time intervals. in_vivo thyroid gland human percentage of RAIU 24 hours after administration of radioiodide change low The radioactive iodine uptake test, or RAIU test, is a type of scan used in the diagnosis of thyroid gland dysfunction The patient swallows radioactive iodine in the form of capsule or fluid, and its absorption by the thyroid is studied after 4–6 hours and after 24 hours with the aid of a gamma scintillation counter. The percentage of RAIU 24 hours after the administration of radioiodide is the most useful The test does not measure hormone production and release but merely the avidity of the thyroid gland for iodide and its rate of clearance relative to the kidney. RAIU test The radioactive iodine uptake test measures the absorption of radioactive iodine by the thyroid gland using a gamma scintillation counter after 4–6 hours and 24 hours. in_vivo thyroid gland human percentage of radioactive iodine uptake decrease http://purl.obolibrary.org/obo/UBERON_0002046 UBERON low The radioactive iodine uptake test, or RAIU test, is a type of scan used in the diagnosis of thyroid gland dysfunction The patient swallows radioactive iodine in the form of capsule or fluid, and its absorption by the thyroid is studied after 4–6 hours and after 24 hours with the aid of a gamma scintillation counter The percentage of RAIU 24 hours after the administration of radioiodide is the most useful http://purl.obolibrary.org/obo/UBERON_0002046 UBERON ECG Measures atrioventricular block and heart rate using electrical activity of the heart. in_vivo heart atrioventricular block and heart rate increase http://purl.obolibrary.org/obo/GO_0002088 GO high Atrioventricular block and heart rate can be measured with an electrocardiogram (ECG). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO airway microdissection An in vitro test involving the microdissection of airways to study their structure and function. ex_vivo airway airway structure and function change low In vitro tests such as isolated perfused lung, airway microdissection, and lung tissue culture (Leikauf). http://purl.obolibrary.org/obo/UBERON_0001043 UBERON blood gas analysis Measures the arterial partial pressure of oxygen and carbon dioxide to determine gas exchange in humans. in_vivo blood human arterial partial pressure of oxygen and carbon dioxide change low Blood gas analysis measures the arterial partial pressure of oxygen and carbon dioxide to determine gas exchange (Leikauf). http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0008643 GO gross and histological examination Examines the nasal passages, larynx, bronchi, and parenchyma for inflammation or structural damage in animals. in_vivo nasal passages larynx bronchi parenchyma inflammation or structural damage not_specified low Morphological techniques include gross and histological examination of the nasal passages, larynx, bronchi, and parenchyma for inflammation or structural damage (Leikauf). http://purl.obolibrary.org/obo/UBERON_0001004 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO isolated perfused lung An in vitro test involving the perfusion of an isolated lung to study pulmonary function. ex_vivo lung pulmonary function change low In vitro tests such as isolated perfused lung, airway microdissection, and lung tissue culture (Leikauf). http://purl.obolibrary.org/obo/UBERON_0002048 UBERON lung compliance and airway resistance Measures lung compliance and airway resistance in animals by inflating and deflating the lung with incremental volumes and recording pressure. in_vivo lung lung compliance and airway resistance change low In animals, common pulmonary function measurements include tests of lung compliance and airway resistance. The lung is deflated and then inflated with incremental volumes and pressure is recorded; the lung is then deflated with incremental volumes and again recorded. Compliance is calculated as the slope of the volume-pressure curve, and indicates the properties of the lung parenchyma. Airway resistance, a measure of bronchoconstriction, can be measured by plethysmography (Leikauf). http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0007586 GO lung tissue culture An in vitro test involving the culture of lung tissue to study pulmonary function and responses. in_vitro lung tissue lung pulmonary responses change low In vitro tests such as isolated perfused lung, airway microdissection, and lung tissue culture (Leikauf). http://purl.obolibrary.org/obo/UBERON_0002048 UBERON lung wet weight: dry weight ratio Measures pulmonary edema in animals by comparing the wet weight of the lung to its dry weight after dessication. in_vivo lung lung wet weight: dry weight ratio increase low In animals, pulmonary edema is measured by lung wet weight: dry weight ratio. Lung water content, expressed as the wet (undessicated) weight of the whole lung or that of a single lobe, is normalized to the weight of the lung or the animal after dessication. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON metacholine challenge test Tests airway hyperreactivity in humans by measuring airway resistance following inhalation of increasing doses of a metacholine aerosol. in_vivo lung human airway resistance decrease low Airway hyperreactivity, a lowered threshold dose of a toxicant needed to induce bronchoconstriction, is tested by measuring airway resistance following inhalation of increasing doses of a metacholine aerosol (Leikauf). http://purl.obolibrary.org/obo/UBERON_0001043 UBERON plethysmography Airway resistance, a measure of bronchoconstriction, can be measured by plethysmography. in_vivo lung animal airway resistance increase low Airway resistance, a measure of bronchoconstriction, can be measured by plethysmography (Leikauf). http://purl.obolibrary.org/obo/UBERON_0002482 UBERON pulmonary lavage Detects pulmonary edema in animals by recovering and analyzing the fluid lining the pulmonary epithelium for signs of inflammation or damage. in_vivo lung fluid composition in pulmonary lavage change low Pulmonary edema can also be detected by pulmonary lavage, in which the fluid lining the pulmonary epithelium is recovered and analyzed for signs of inflammation or damage (Leikauf). http://purl.obolibrary.org/obo/UBERON_0005202 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO pulmonary lavage Pulmonary lavage recovers fluid lining the pulmonary epithelium and analyzes it for signs of inflammation or damage. in_vivo lung animal signs of inflammation or damage increase http://purl.obolibrary.org/obo/GO_0006954 GO low Pulmonary edema can also be detected by pulmonary lavage, in which the fluid lining the pulmonary epithelium is recovered and analyzed for signs of inflammation or damage (Leikauf). http://purl.obolibrary.org/obo/GO_0006954 GO respirometer metabolism chambers Measures cardio-respiratory function in fish by monitoring ventilation rate, cough response, ventilation volume, oxygen consumption, and oxygen utilization. in_vivo gill blood fish ventilation rate, cough response, ventilation volume, oxygen consumption, oxygen utilization change low Measurements of cardio-respiratory function in fish exposed to aqueous solutions of toxic chemicals may be conducted in respirometer metabolism chambers. Anesthetized fish are immobilized by spinal transection, and inserted with a urine catheter, dorsal aortic cannula, electrodes, and attachment of an oral membrane. Predose measurements are taken before chemical exposure. Fish are monitored for 24 to 48 hours, and measurements taken every 2 hours. Ventilation rate (VR) and cough response (CR) are determined using freestanding stainless steel electrodes. Ventilation volume (V), oxygen consumption (VO), and oxygen utilization (U) may be obtained using dissolved oxygen (DO) concentrations in inspired and expired water from the chambers (McKim 1987). http://purl.obolibrary.org/obo/UBERON_0003100 UBERON http://purl.obolibrary.org/obo/GO_0007586 GO respirometry Ventilation rate (VR), ventilation volume (V), oxygen consumption (VO), and oxygen utilization (U) are determined using dissolved oxygen (DO) concentrations in inspired and expired water. in_vivo lung fish ventilation rate, ventilation volume, oxygen consumption, oxygen utilization change http://purl.obolibrary.org/obo/GO_0002047 GO low Ventilation rate (VR) and cough response (CR) are determined using freestanding stainless steel electrodes. Ventilation volume (V), oxygen consumption (VO), and oxygen utilization (U) may be obtained using dissolved oxygen (DO) concentrations in inspired and expired water from the chambers (McKim 1987). http://purl.obolibrary.org/obo/UBERON_0000094 UBERON http://purl.obolibrary.org/obo/GO_0002097 GO spirometry Measures lung function in humans by assessing the ratio of volume of air expired in one second (FEV1) to forced vital capacity (FVC). in_vivo lung human FEV1/FVC ratio decrease low In humans, spirometry is used to measure lung function. The ratio of volume of air expired in one second (FEV1) to forced vital capacity (FVC) should be close to 80%. A decreased FEV 1/FVC is indicative of impaired ventilation. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0043588 GO Fish Lifecycle Toxicity Test Measures testosterone levels in fish during a full lifecycle exposure test. in_vivo fish testosterone concentration not_specified http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI US EPA OPPTS 850.1500 low Testosterone levels are measured i.a. in: Fish Lifecycle Toxicity Test (FLCTT) (US EPA OPPTS 850.1500) http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI Hershberger Bioassay Measures testosterone levels in rats following exposure to endocrine disruptors. in_vivo rat testosterone concentration not_specified http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI OECD TG 441 low Testosterone levels are measured i.a. in: OECD TG 441: Hershberger Bioassay in Rats (H Assay) http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI immunoassay Measures testosterone levels in serum using antibody-based detection. in_vitro serum testosterone concentration not_specified http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/UBERON_0000178 UBERON medium Testosterone can be measured by immunoassays http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI isotope-dilution gas chromatography-mass spectrometry Measures testosterone levels in serum using gas chromatography coupled with mass spectrometry with isotope dilution for quantification. in_vitro serum testosterone concentration not_specified http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/UBERON_0000178 UBERON low Testosterone can be measured by isotope-dilution gas chromatography-mass spectrometry in serum http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI Male pubertal assay Measures testosterone levels in male rats during pubertal development. in_vivo rat testosterone concentration not_specified http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI US EPA OPPTS 890.1500 low Testosterone levels are measured i.a. in: Male pubertal assay (PP Male Assay) (US EPA OPPTS 890.1500) http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI Filipin staining Qualitatively assesses intracellular cholesterol distribution using a fluorescent detergent that binds selectively to cholesterol. in_vitro intracellular cholesterol distribution not_specified http://purl.obolibrary.org/obo/CHEBI_16566 CHEBI medium Filipin staining is one of the most widely used tools for studying intracellular cholesterol distribution. The fluorescent detergent filipin binds selectively to cholesterol (and not to cholesterol esters) (Schroeder, Holland, and Bieber 1971). Filipin can be only used for the qualitative analysis of cholesterol distribution, since its fluorescence intensity is not necessarily linearly related to cholesterol content. http://purl.obolibrary.org/obo/CHEBI_16566 CHEBI http://purl.obolibrary.org/obo/GO_0032381 GO qPCR Quantitative Polymerase Chain Reaction used to measure the expression levels of mRNA for proteins involved in cholesterol transport. in_vitro mRNA expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Expression of the proteins involved in cholesterol transport by qPCR qPCR Measures the expression of proteins involved in cholesterol transport at the mRNA level. in_vitro mRNA expression of cholesterol transport proteins not_specified http://purl.obolibrary.org/obo/GO_0010467 GO medium Expression of the proteins involved in cholesterol transport by qPCR or Western blot. http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0032349 GO qPCR Measures the expression of proteins involved in cholesterol transport using quantitative PCR. in_vitro protein expression levels change http://purl.obolibrary.org/obo/GO_0006925 GO medium Expression of the proteins involved in cholesterol transport by qPCR or Western blot. http://purl.obolibrary.org/obo/CHEBI_5923 CHEBI http://purl.obolibrary.org/obo/GO_0006925 GO radioimmunoassay Measures pregnenolone concentration, which indirectly reflects cholesterol transport to the mitochondrial inner membrane. in_vitro pregnenolone concentration increase http://purl.obolibrary.org/obo/CHEBI_16241 CHEBI medium Indirectly as pregnenolone formation by cells. The pregnenolone concentration is assayed by commercially available radioimmunoassays and reflects the amount of cholesterol transported to the mitochondrial inner membrane (Charman et al. 2010). http://purl.obolibrary.org/obo/CHEBI_29984 CHEBI http://purl.obolibrary.org/obo/GO_0006834 GO Radioimmunoassay for pregnenolone Measures pregnenolone concentration as an indirect indicator of cholesterol transport to the mitochondrial inner membrane. in_vitro Leydig cells testis pregnenolone concentration decrease http://purl.obolibrary.org/obo/CHEBI_17558 CHEBI http://purl.obolibrary.org/obo/OBI_0000468 OBI medium Cholesterol transport to the mitochondrial inner membrane in intact cells: Indirectly as pregnenolone formation by cells. The pregnenolone concentration is assayed by commercially available radioimmunoassays and reflects the amount of cholesterol transported to the mitochondrial inner membrane (Charman et al. 2010). http://purl.obolibrary.org/obo/CHEBI_16566 CHEBI http://purl.obolibrary.org/obo/GO_0032349 GO western blot Measures the expression of proteins involved in cholesterol transport using western blot. in_vitro protein expression levels change http://purl.obolibrary.org/obo/OBI_0000233 OBI low Expression of the proteins involved in cholesterol transport by qPCR or Western blot. http://purl.obolibrary.org/obo/CHEBI_5923 CHEBI http://purl.obolibrary.org/obo/GO_0006925 GO Western blot Measures the expression of proteins involved in cholesterol transport at the protein level. in_vitro protein expression of cholesterol transport proteins not_specified http://purl.obolibrary.org/obo/GO_0010485 GO low Expression of the proteins involved in cholesterol transport by qPCR or Western blot. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0032349 GO analytical ultracentrifuging Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase http://purl.obolibrary.org/obo/CHEBI_16545 CHEBI http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/CHEBI_15347 CHEBI medium Concentrations of triglycerides, cholesterols, fatty acids, and related compounds are measured biochemically include high throughput enzymatic analyses, analytical ultracentrifuging http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO gradient gel electrophoresis Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase http://purl.obolibrary.org/obo/CHEBI_16545 CHEBI http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/CHEBI_15347 CHEBI medium Concentrations of triglycerides, cholesterols, fatty acids, and related compounds are measured biochemically include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO high throughput enzymatic analyses Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase http://purl.obolibrary.org/obo/CHEBI_16545 CHEBI http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/CHEBI_15347 CHEBI high Concentrations of triglycerides, cholesterols, fatty acids, and related compounds are measured biochemically include high throughput enzymatic analyses http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO histology Assesses steatosis through tissue examination. in_vivo liver steatosis increase http://purl.obolibrary.org/obo/MP_0001553 MP http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low Steatosis is measured by lipidomics approaches (e.g. Yang and Han 2016) that measure lipid levels, or by histology. http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0019915 GO lipidomics Measures lipid levels to assess steatosis. in_vitro liver lipid levels increase http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/MP_0001553 MP high Steatosis is measured by lipidomics approaches (e.g. Yang and Han 2016) that measure lipid levels http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0019915 GO Nuclear Magnetic Resonance Measures concentrations of triglycerides, cholesterols, fatty acids, and related compounds biochemically. in_vitro concentrations of triglycerides, cholesterols, fatty acids, and related compounds increase http://purl.obolibrary.org/obo/CHEBI_16545 CHEBI http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/CHEBI_15347 CHEBI medium Concentrations of triglycerides, cholesterols, fatty acids, and related compounds are measured biochemically include high throughput enzymatic analyses, analytical ultracentrifuging, gradient gel electrophoresis, Nuclear Magnetic Resonance http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO inflammatory mediator release assay Measures the release of inflammatory mediators into the circulation due to systemic inflammation. not_specified release of inflammatory mediators increase not_specified Systemic inflammation causes release of inflammatory mediators into the circulation that have autocrine and paracrine effects. Quantitative stereology Quantitative stereology is used to quantify the growth of altered hepatic foci (AHF). in_vivo liver growth of altered hepatic foci increase http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO low Quantitative stereology has been used to quantify the growth of AHF. http://purl.obolibrary.org/obo/CL_0000082 CL http://purl.obolibrary.org/obo/GO_0008283 GO stereology Quantitative stereology is used to quantify the growth of Altered Hepatic Foci (AHF). This involves a quantitative analysis of tissue structure to determine the size and number of AHF. in_vivo liver growth of AHF increase low Quantitative stereology has been used to quantify the growth of AHF. http://purl.obolibrary.org/obo/CL_0002046 CL http://purl.obolibrary.org/obo/GO_0008283 GO DNA adduct quantitation Quantifies chemical-specific DNA adducts (e.g., N7-AFB1-G, AFB1-FAPy) before and after DNA repair to assess repair efficiency and correctness. in_vitro DNA adduct levels decrease http://purl.obolibrary.org/obo/GO_0006281 GO low quantitation of chemical-specific DNA adducts, such as the N7-AFB1-G and AFB1-FAPy DNA adducts, before and after DNA repair occurs combined with DNA sequence data to determine whether the decrease in adducts were correctly repaired or not. specialized analytical chemistry techniques conducted on DNA isolated from tissues or cells and subjected to neutral thermal or enzyme or acid hydrolysis; this releases the adducted bases, which are then further analyzed with specialized approaches http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Mutant frequency assay Measures mutations in yeast strains with DNA repair deficiencies compared to wild type to infer insufficient or mis-repair of AFB1 DNA adducts. in_vitro yeast Saccharomyces cerevisiae mutant frequency increase http://purl.obolibrary.org/obo/GO_0006281 GO medium Measurement of mutations following AFB1 treatment of yeast with a variety of DNA repair deficiencies has been used to elucidate the role of DNA repair (Guo et al., 2005) by comparing mutant frequency (MF) in wild type vs. DNA repair deficient strains. MF serves as a marker for the insufficient or mis-repair of the AFB1 DNA adducts http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Calcium imaging Monitoring calcium levels in acute brain-slice preparations using calcium sensors. ex_vivo brain Calcium levels change low or calcium sensors in acute brain-slice preparations (Jasoni et al., 2007). http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0007165 GO GFP imaging Detection of living cells tagged with green fluorescent protein (GFP) to monitor cellular activity. in_vivo brain GFP fluorescence change medium detect living cells tagged with green fluorescent protein (GFP) (Spergel et al., 1999; Kato et al., 2003) http://purl.obolibrary.org/obo/CL_0000004 CL GFP/calcium sensor imaging Detection of living GnRH neurons tagged with GFP or calcium sensors in acute brain-slice preparations. ex_vivo brain rat GnRH neuron activity not_specified http://purl.obolibrary.org/obo/CL_0000606 CL low detect living cells tagged with green fluorescent protein (GFP) (Spergel et al., 1999; Kato et al., 2003) or calcium sensors in acute brain-slice preparations (Jasoni et al., 2007) http://purl.obolibrary.org/obo/CL_0000606 CL http://purl.obolibrary.org/obo/GO_0001503 GO GnRH mRNA quantification In situ hybridization to examine total GnRH mRNA and the primary GnRH heterogeneous nuclear RNA transcript. in_vitro GnRH neurons hypothalamus not_specified GnRH mRNA levels decrease low in situ hybridization was performed to examine total GnRH mRNA and the primary GnRH heterogeneous nuclear RNA transcript. hPSC-derived GnRH neuron characterization Development and functional characterization of GnRH-secreting neurons differentiated from human pluripotent stem cells to assess their pulsatile secretory properties. in_vitro human pluripotent stem cell-derived GnRH neurons human pulsatile secretory properties of GnRH neurons change http://purl.obolibrary.org/obo/GO_0001711 GO low The development of GnRH-secreting neurons from human pluripotent stem cell (hPSC) could be relevant in the future, but these new cells require characterization of their pulsatile secretory properties (Lund et al., 2016 and Lund et al., 2020). hypothalamic explants Use of hypothalamic explants to study GnRH release in vitro. ex_vivo hypothalamus rat GnRH release decrease http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI low Hypothalamic explants http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO immunohistochemistry Immunohistochemistry to measure GnRH immunoreactivity in hypothalamic tissue. in_vivo hypothalamus rat GnRH immunoreactivity decrease http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI medium GnRH immunoreactivity and total peptide levels were measured in hypothalamic tissue http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI in situ hybridization In situ hybridization to examine total GnRH mRNA and primary GnRH heterogeneous nuclear RNA transcript. in_vivo hypothalamus rat GnRH mRNA levels decrease low in situ hybridization was performed to examine total GnRH mRNA and the primary GnRH heterogeneous nuclear RNA transcript http://purl.obolibrary.org/obo/GO_0010467 GO microdialysis Samples extracellular fluid in hypothalamic tissue to measure GnRH release. in_vivo hypothalamus rat extracellular GnRH concentration change not_specified microdialysis in rat (Sisk, et al., 2001) microdialysis Microdialysis in rat to measure GnRH release. in_vivo brain rat GnRH release decrease http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI http://purl.obolibrary.org/obo/OBI_0000218 OBI low microdialysis in rat (Sisk, et al., 2001) http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO portal blood sampling Collects portal blood at high temporal resolution to measure GnRH pulses released into circulation. in_vivo portal blood GnRH concentration in portal blood change not_specified sampling of portal blood on a minute-by-minute basis (Evans, 1995) portal blood sampling Sampling of portal blood on a minute-by-minute basis to measure GnRH release. in_vivo blood rat GnRH release decrease http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI low sampling of portal blood on a minute-by-minute basis (Evans, 1995) http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO Portal blood sampling Sampling of portal blood on a minute-by-minute basis to measure hormone levels. in_vivo portal vein Hormone concentration change low sampling of portal blood on a minute-by-minute basis (Evans, 1995). RIA Commercial radioimmunoassay (RIA) kit to measure GnRH levels in vitro. in_vitro hypothalamus rat GnRH levels decrease http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI http://purl.obolibrary.org/obo/OBI_0000275 OBI medium In vitro: commercial RIA kit, sensitivity of the assay was 1 pg/tube http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO UPLC-MS/MS Ultra-performance liquid chromatography–tandem mass spectrometry to measure total GnRH peptide levels in hypothalamic tissue. in_vivo hypothalamus rat GnRH peptide levels decrease http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI http://purl.obolibrary.org/obo/OBI_0000474 OBI medium ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS) http://purl.obolibrary.org/obo/CHEBI_18280 CHEBI http://purl.obolibrary.org/obo/GO_0006508 GO β-galactosidase staining Selective visualization of GnRH neurons using β-galactosidase staining. in_vivo brain rat GnRH neuron visualization not_specified http://purl.obolibrary.org/obo/CL_0000606 CL low selective visualization of GnRH neurons with β-galactosidase (Skinner et al., 1999) http://purl.obolibrary.org/obo/CL_0000606 CL ELISA Measures circulating concentrations of gonadotropins using enzyme-linked immunosorbent assays. in_vitro humans rodents livestock species fish gonadotropin concentration decrease medium Circulating concentrations of gonadotropins in humans and common mammalian models (e.g., rodents, many livestock species) can be directly measured using either commercial or custom immunoassays (e.g., enzyme-linked immunosorbent assays, radioimmunoassay, etc.). Similar immunoassay-based methods have been developed for quantifying gonadotropins in fish (e.g., (Govoroun et al., 1998; Amano et al., 2000; Kah et al., 1989; Prat et al., 1996)). http://purl.obolibrary.org/obo/CHEBI_35347 CHEBI http://purl.obolibrary.org/obo/GO_0046883 GO ELISA Measures LH and FSH synthesis and secretion in LbT2 cells using ELISA. in_vitro LbT2 cells LH and FSH secretion decrease medium LbT2 cells is the major homologous cell line available for the study of FSH and LH synthesis and secretion ➔ELISA is used. http://purl.obolibrary.org/obo/CHEBI_38921 CHEBI http://purl.obolibrary.org/obo/GO_0046883 GO in vivo GCaMP imaging Measures pulsatile LH secretion using in vivo calcium imaging. in_vivo pulsatile LH secretion decrease http://purl.obolibrary.org/obo/OBI_0001940 OBI low in vivo GCaMP imaging (McQuillan, et al., 2019) http://purl.obolibrary.org/obo/CHEBI_38921 CHEBI http://purl.obolibrary.org/obo/GO_0046883 GO radioimmunoassay Measures circulating concentrations of gonadotropins using radioimmunoassay. in_vitro humans rodents livestock species gonadotropin concentration decrease low Circulating concentrations of gonadotropins in humans and common mammalian models (e.g., rodents, many livestock species) can be directly measured using either commercial or custom immunoassays (e.g., enzyme-linked immunosorbent assays, radioimmunoassay, etc.). http://purl.obolibrary.org/obo/CHEBI_35347 CHEBI http://purl.obolibrary.org/obo/GO_0046883 GO TRIFMA Measures serum LH using a time-resolved immunofluorometric assay. in_vitro serum LH concentration decrease medium serum LH ➔a time-resolved immunofluorometric assay (TRIFMA) (Bang 2017) http://purl.obolibrary.org/obo/CHEBI_38921 CHEBI http://purl.obolibrary.org/obo/GO_0046883 GO Radiolabeled ligand binding Uses radiolabeled nAChR agonists (e.g., [3H] imidacloprid) to detect the location and subunit composition of nicotinic acetylcholine receptors. in_vitro honey bees nAChR location and subunit composition not_specified http://purl.obolibrary.org/obo/PR_000001340 PR http://purl.obolibrary.org/obo/GO_0005488 GO low Radiolabeled nAChR agonists, (e.g., [3H] imidacloprid) or nAChR subunit specific antibodies to detect location and subunit composition of nAChR http://purl.obolibrary.org/obo/PR_000001340 PR Radiolabeled nAChR agonist binding Uses radiolabeled agonists, such as [3H] imidacloprid, to detect the location and subunit composition of the nicotinic acetylcholine receptor. in_vitro nAChR location and subunit composition not_specified http://purl.obolibrary.org/obo/CHEBI_35153 CHEBI not_specified Radiolabeled nAChR agonists, (e.g., [3H] imidacloprid) or nAChR subunit specific antibodies to detect location and subunit composition of nAChR http://purl.obolibrary.org/obo/CHEBI_35153 CHEBI http://purl.obolibrary.org/obo/GO_0044297 GO Radiolabeling / Immunostaining Use of radiolabeled nAChR agonists or subunit-specific antibodies to identify the location and subunit composition of the nicotinic acetylcholine receptor. in_vitro honey bees location and subunit composition of nAChR not_specified low Radiolabeled nAChR agonists, (e.g., [3H] imidacloprid) or nAChR subunit specific antibodies to detect location and subunit composition of nAChR http://purl.obolibrary.org/obo/CHEBI_24453 CHEBI http://purl.obolibrary.org/obo/GO_0030488 GO Radioligand binding assay This assay uses radiolabeled nicotinic acetylcholine receptor (nAChR) agonists, such as [3H] imidacloprid, to detect the location and subunit composition of nAChR. in_vitro brain honey bee Receptor binding increase low • Radiolabeled nAChR agonists, (e.g., [3H] imidacloprid) or nAChR subunit specific antibodies to detect location and subunit composition of nAChR http://purl.obolibrary.org/obo/CHEBI_6324 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO Whole-cell voltage clamp Electrophysiological measurements with agonists to measure nicotinic acetylcholine receptor activation. in_vitro honey bees nAChR activation increase http://purl.obolibrary.org/obo/PR_000001340 PR http://purl.obolibrary.org/obo/GO_0051899 GO low Whole-cell voltage clamp electrophysiological measurements with agonists to measure nAChR activation http://purl.obolibrary.org/obo/PR_000001340 PR http://purl.obolibrary.org/obo/GO_0006811 GO Comb visual inspection/digital imaging Estimating food storage by visual inspection or digital imaging of combs to determine the percentage of cells filled with nectar, honey, or pollen. in_vivo comb honey bees percent of cells filled with nectar (uncapped), honey (capped), or pollen change low Food storage can be measured by visual inspection or digital imaging of the combs with the objective to estimate the percent of cells filled with nectar (uncapped), honey (capped), or pollen Corbiculae scoring Assessment of pollen load by scoring the size/amount of pollen in the forager's pollen baskets relative to bee size. in_vivo honey bee amount of pollen in the forager’s corbiculae change medium Pollen load can also be assessed by scoring the size of amount of pollen in the forager’s corbiculae (pollen basket) relative to the size of the worker bee http://purl.obolibrary.org/obo/NCBITaxon_3502 NCBITAXON Food storage assessment Measures the amount of food stored in the hive by visual inspection or digital imaging of the combs to estimate the percent of cells filled with nectar, honey, or pollen. in_vivo combs honey bees food storage change http://purl.obolibrary.org/obo/UBERON_0002390 UBERON medium Food storage can be measured by visual inspection or digital imaging of the combs with the objective to estimate the percent of cells filled with nectar (uncapped), honey (capped), or pollen http://purl.obolibrary.org/obo/UBERON_0002390 UBERON food storage assessment Food storage is measured by visual inspection or digital imaging of the combs to estimate the percent of cells filled with nectar, honey, or pollen. in_vivo comb honey bee percent of cells filled with food decrease low Food storage can be measured by visual inspection or digital imaging of the combs with the objective to estimate the percent of cells filled with nectar (uncapped), honey (capped), or pollen Nectar load measurement Measures the amount of nectar collected by individual foragers using a pocket refractometer after inducing regurgitation. in_vivo honey bees nectar load change low Nectar loads from individual forager bees can be measured with a pocket refractometer after inducing regurgitation http://purl.obolibrary.org/obo/NCBITaxon_7460 NCBITAXON Pocket refractometer Measuring nectar loads from individual forager bees using a pocket refractometer after inducing regurgitation. in_vivo honey bees nectar loads change low Nectar loads from individual forager bees can be measured with a pocket refractometer after inducing regurgitation http://purl.obolibrary.org/obo/GO_0051023 GO Pollen load assessment Measures the amount of pollen collected by foragers either by weighing pollen from hive entrance traps or scoring the size of pollen in the corbiculae. in_vivo corbiculae honey bees pollen load change http://purl.obolibrary.org/obo/UBERON_0011252 UBERON medium Weigh bee-collected pollen from hive entrance trap Pollen load can also be assessed by scoring the size of amount of pollen in the forager’s corbiculae (pollen basket) relative to the size of the worker bee http://purl.obolibrary.org/obo/UBERON_0011252 UBERON Pollen load scoring Visual assessment of pollen amount in the corbiculae (pollen basket) relative to the worker bee size. in_vivo corbiculae honey bees size of amount of pollen in the forager’s corbiculae relative to the size of the worker bee change low Pollen load can also be assessed by scoring the size of amount of pollen in the forager’s corbiculae (pollen basket) relative to the size of the worker bee http://purl.obolibrary.org/obo/GO_0051023 GO Pollen weight measurement Measuring the weight of pollen collected by bees from a hive entrance trap. in_vivo honey bees weight of bee-collected pollen change low Weigh bee-collected pollen from hive entrance trap http://purl.obolibrary.org/obo/NCBITaxon_7469 NCBITAXON http://purl.obolibrary.org/obo/GO_0051023 GO Radio-frequency identification tagging Uses RFID tags to track individual foraging events, including frequency, duration, flight time, homing ability, and feeding behavior. in_vivo honey bees foraging behavior metrics change http://purl.obolibrary.org/obo/GO_0008156 GO http://purl.obolibrary.org/obo/GO_0007610 GO low Radio-frequency identification tagging technology to track the frequency and duration of individual foraging events, flight time, foragers homing ability, duration of time spent at a feeder, and duration between feeding http://purl.obolibrary.org/obo/NCBITaxon_7460 NCBITAXON http://purl.obolibrary.org/obo/GO_0008156 GO Radio-frequency identification tagging Uses RFID technology to monitor individual foraging events, flight time, homing ability, and feeding patterns. in_vivo honey bees frequency and duration of foraging events, flight time, homing ability, time at feeder, and time between feeding change http://purl.obolibrary.org/obo/GO_0051023 GO medium Radio-frequency identification tagging technology to track the frequency and duration of individual foraging events, flight time, foragers homing ability, duration of time spent at a feeder, and duration between feeding http://purl.obolibrary.org/obo/NCBITaxon_7469 NCBITAXON http://purl.obolibrary.org/obo/GO_0051023 GO Video tracking Uses video tracking software to measure total distance traveled and time spent in social interaction. in_vivo honey bees distance traveled and social interaction time change http://purl.obolibrary.org/obo/GO_0007626 GO http://purl.obolibrary.org/obo/GO_0035176 GO medium Video tracking software for measures of total distance traveled and time spent in social interaction http://purl.obolibrary.org/obo/NCBITaxon_7460 NCBITAXON http://purl.obolibrary.org/obo/GO_0007626 GO Waggle dance measurement Uses video recording to measure the number of waggle dance circuits performed by foragers returning to the hive. in_vivo honey bees waggle dance circuits change low Video foragers returning to hive and measure waggle dance circuits performed http://purl.obolibrary.org/obo/NCBITaxon_7460 NCBITAXON Beekeeper Survey Surveying commercial, sideline, and small scale beekeepers to identify trends and rates of honey bee colony losses. in_vivo honey bee average annual colony losses increase not_specified From surveying commercial (>300 colonies), sideline (25–300 colonies), and small scale <25 colonies) beekeepers, average annual colony losses (both summer and winter losses) per operation in the US during 2014–2015 were 49% Colony loss survey This assay measures the annual loss of managed honey bee colonies through surveys of beekeepers, quantifying the percentage of colonies lost. not_specified Apis mellifera colony loss percentage increase not_specified From surveying commercial (>300 colonies), sideline (25–300 colonies), and small scale <25 colonies) beekeepers, average annual colony losses (both summer and winter losses) per operation in the US during 2014–2015 were 49%, compared to 18.7% that has been identified by beekeepers as an acceptable loss rate (Seitz et al., 2015). NVS_IC_rNaCh_site 2 Measures binding to the sodium channel receptor, indicating potential inhibition of sodium channel function. in_vitro binding to sodium channel receptor not_specified http://purl.obolibrary.org/obo/GO_0035235 GO high ToxCast assay NVS_IC_rNaCh_site 2 also measures binding to the sodium channel receptor. http://purl.obolibrary.org/obo/PR_000001396 PR http://purl.obolibrary.org/obo/GO_0006811 GO ToxCast assay NVS_IC_rNaCh_site 2 A high-throughput screening assay designed to measure the binding affinity or inhibition at site 2 of the sodium channel receptor. in_vitro binding to the sodium channel receptor change http://purl.obolibrary.org/obo/GO_0005515 GO high ToxCast assay NVS_IC_rNaCh_site 2 also measures binding to the sodium channel receptor. http://purl.obolibrary.org/obo/GO_0005515 GO voltage-clamp recordings Measures sodium currents by recording ionic currents through sodium channels in response to voltage changes. in_vitro sodium currents not_specified http://purl.obolibrary.org/obo/GO_0005248 GO low Voltage-clamp recordings of sodium currents is a general means of detection. http://purl.obolibrary.org/obo/PR_000001396 PR http://purl.obolibrary.org/obo/GO_0006811 GO Action potential recording Measures the quick rise and fall of an electrical membrane potential of a cell, known as an action potential, to detect if it is diminished or eliminated. not_specified action potential decrease not_specified The quick rise and fall of an electrical membrane potential of a cell, known as an action potential, is either diminished or eliminated. electrophysiology Measures the electrical membrane potential changes of a cell, specifically the action potential. not_specified action potential amplitude decrease http://purl.obolibrary.org/obo/GO_0001508 GO http://purl.obolibrary.org/obo/GO_0001662 GO not_specified The quick rise and fall of an electrical membrane potential of a cell, known as an action potential, is either diminished or eliminated. http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0001508 GO aquatic tunnel assay Measures swimming speed by controlling water flow speed in an aquatic tunnel. in_vivo swimming speed decrease http://purl.obolibrary.org/obo/GO_0008345 GO http://purl.obolibrary.org/obo/GO_0007626 GO low The swimming speed may be measured by the use of an aquatic tunnel, wherein the researcher controls the speed of the water flow (see Tierney, 2001) http://purl.obolibrary.org/obo/GO_0040011 GO video recording Measurement of swimming speed by using video equipment to record the distance covered by an organism over a specific period. in_vivo distance swam within a period of time change not_specified using video equipment to record the distance the organism swims within a period of time http://purl.obolibrary.org/obo/GO_0050853 GO video recording Swimming speed is measured by recording the distance the organism swims within a period of time using video equipment. in_vivo swimming speed decrease medium or by using video equipment to record the distance the organism swims within a period of time (e.g., Kavitha and Rao, 2007). http://purl.obolibrary.org/obo/GO_0040012 GO video-based swimming speed assay Measures swimming speed by recording the distance swum within a period of time using video equipment. in_vivo swimming speed decrease http://purl.obolibrary.org/obo/GO_0008345 GO http://purl.obolibrary.org/obo/GO_0007626 GO medium by using video equipment to record the distance the organism swims within a period of time (e.g., Kavitha and Rao, 2007) http://purl.obolibrary.org/obo/GO_0040011 GO fecal egestion Feeding rates are determined by measuring the amount of fecal matter egested by the organism. not_specified feeding rate decrease not_specified Depending upon the organism and situation (lab or field), feeding rates may be determined by [...] fecal egestion (e.g., Bernot et al., 2005) http://purl.obolibrary.org/obo/GO_0007631 GO fecal egestion measurement Feeding rates are determined by measuring fecal egestion, as described by Bernot et al. (2005). in_vivo intestine fecal egestion rate decrease low Depending upon the organism and situation (lab or field), feeding rates may be determined by … fecal egestion (e.g., Bernot et al., 2005). stomach content analysis Feeding rates are determined by analyzing stomach contents, as reviewed by Cortes (1997). in_vivo stomach stomach content quantity decrease low Depending upon the organism and situation (lab or field), feeding rates may be determined by … stomach contents (review by Cortes 1997). http://purl.obolibrary.org/obo/UBERON_0002228 UBERON stomach contents analysis Feeding rates are determined by analyzing the contents of the organism's stomach. not_specified stomach feeding rate decrease http://purl.obolibrary.org/obo/UBERON_0000945 UBERON not_specified Depending upon the organism and situation (lab or field), feeding rates may be determined by [...] stomach contents (review by Cortes 1997) http://purl.obolibrary.org/obo/GO_0007631 GO video feeding rate Feeding rates are determined by video recording the organism's feeding behavior. not_specified feeding rate decrease http://purl.obolibrary.org/obo/GO_0007631 GO not_specified Depending upon the organism and situation (lab or field), feeding rates may be determined by video (e.g., Nassef et al., 2010) http://purl.obolibrary.org/obo/GO_0007631 GO video observation Feeding rates are determined by video observation, as described by Nassef et al. (2010). in_vivo stomach feeding rate decrease low Depending upon the organism and situation (lab or field), feeding rates may be determined by video (e.g., Nassef et al., 2010) hERG fluorescence polarization kit A commercially available kit that measures inhibition of the human ERG (hERG) channel using fluorescence polarization. in_vitro human hERG channel inhibition decrease http://purl.obolibrary.org/obo/GO_0005249 GO medium There is also a commercially available hERG fluorescence polarization kit. http://purl.obolibrary.org/obo/PR_000002020 PR http://purl.obolibrary.org/obo/GO_0006813 GO patch clamp electrophysiology Measures inhibition of the Ether-a-go-go (ERG) voltage-gated potassium channel using electrophysiological recordings. in_vitro ERG channel inhibition decrease http://purl.obolibrary.org/obo/GO_0005249 GO http://purl.obolibrary.org/obo/OBI_0000218 OBI low Generally, inhibition is mmeasured using patch clamp electrophysiology. http://purl.obolibrary.org/obo/PR_000002020 PR http://purl.obolibrary.org/obo/GO_0006813 GO patch clamp electrophysiology This assay measures ion channel activity using patch clamp electrophysiology to assess inhibition. in_vitro ion channel inhibition decrease low Generally, inhibition is mmeasured using patch clamp electrophysiology. http://purl.obolibrary.org/obo/GO_0006825 GO ToxCast NVS_IC_hKhERGCh A high-throughput assay that measures inhibition of the human ERG (hERG) channel. in_vitro human hERG channel inhibition decrease http://purl.obolibrary.org/obo/GO_0005249 GO high ToxCast assay NVS_IC_hKhERGCh also measures human ERG (hERG) inhibition. http://purl.obolibrary.org/obo/PR_000002020 PR http://purl.obolibrary.org/obo/GO_0006813 GO Novascreen assay Detects binding to the sodium channel 1A receptor site 2. in_vitro rat sodium channel 1A receptor binding not_specified http://purl.obolibrary.org/obo/GO_0005244 GO http://purl.obolibrary.org/obo/GO_0035255 GO medium The Novascreen assay, NVS_IC_rNaCh_site2, detects sodium channel 1A receptor binding. http://purl.obolibrary.org/obo/PR_000001396 PR http://purl.obolibrary.org/obo/GO_0022839 GO NVS_IC_rNaCh_site2 The Novascreen assay detects sodium channel 1A receptor binding. in_vitro sodium channel 1A receptor binding not_specified medium The Novascreen assay, NVS_IC_rNaCh_site2, detects sodium channel 1A receptor binding. http://purl.obolibrary.org/obo/GO_0005102 GO voltage clamp This technique studies changes in nerve membrane permeability and kinetic properties of ionic channels by controlling the membrane potential. in_vitro nerve nerve membrane permeability and kinetic properties of ionic channels change low Changes in nerve membrane permeability and kinetic properties of ionic channels can be studied using the voltage clamp or patch clamp technique. http://purl.obolibrary.org/obo/GO_0006825 GO voltage clamp Measures changes in nerve membrane permeability and kinetic properties of ionic channels by controlling membrane voltage and recording ionic currents. in_vitro nerve sodium tail current duration increase http://purl.obolibrary.org/obo/GO_0035725 GO http://purl.obolibrary.org/obo/GO_0005248 GO low Changes in nerve membrane permeability and kinetic properties of ionic channels can be studied using the voltage clamp or patch clamp technique. Pyrethroid action resulting in prolonged opening of the voltage-gated sodium ion channel is evidenced by the prolonged sodium tail current and subsequent repetitive nerve impulses. http://purl.obolibrary.org/obo/PR_000001396 PR http://purl.obolibrary.org/obo/GO_0006811 GO Electrophysiological measurements Measures epileptic seizure-related effects through electrophysiological recordings. in_vivo brain electrophysiological activity change http://purl.obolibrary.org/obo/HP_0001250 HP low Electrophysiological measurements and physical (visual) observation (for mortality) are the methods often used to detect epileptic seizure-related effects http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0050896 GO Electrophysiological measurements Records electrical activity to detect epileptic seizure-related effects. not_specified epileptic seizure-related effects change not_specified Electrophysiological measurements and physical (visual) observation (for mortality) are the methods often used to detect epileptic seizure-related effects (Ulate-Campos et al . 2016). Micro-electrode array (MEA) recording Uses microfabricated devices with spatially arranged microelectrodes to record field potentials and action potentials from multiple neurons. in_vitro brain tissue electrophysiological activity change http://purl.obolibrary.org/obo/NBO_0000358 NBO http://purl.obolibrary.org/obo/GO_0001508 GO medium a new technique called micro-electrode array (MEA) recording has been developed and tested both in vitro MEAs recordings constitute an excellent tool for studying the spatio-temporal patterns of spontaneous interictal and evoked seizure-like events http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0050896 GO micro-electrode array (MEA) recording MEA recording uses microfabricated devices with microelectrodes to simultaneously stimulate and record field potentials and action potentials of multiple neurons. in_vitro neurons brain field potentials, action potentials change http://purl.obolibrary.org/obo/GO_0005845 GO medium Recently, a new technique called micro-electrode array (MEA) recording has been developed and tested both in vitro (Novellino et al. 2011) and ex vivo (Dossi et al. 2014). MEAs, which are microfabricated devices embedding an array of spatially arranged microelectrodes, provide a unique opportunity to simultaneously stimulate and record field potentials, as well as action potentials of multiple neurons from different areas of the tissue (Dossi et al. 2014). http://purl.obolibrary.org/obo/CL_0000706 CL http://purl.obolibrary.org/obo/GO_0005843 GO micro-electrode array (MEA) recording A technique using microfabricated devices to simultaneously stimulate and record field potentials and action potentials of multiple neurons to study seizure-like events and electrophysiological activity. in_vitro neurons spatio-temporal patterns of spontaneous interictal and evoked seizure-like events and electrophysiological activity change medium micro-electrode array (MEA) recording has been developed and tested both in vitro (Novellino et al. 2011) and ex vivo (Dossi et al. 2014). MEAs, which are microfabricated devices embedding an array of spatially arranged microelectrodes, provide a unique opportunity to simultaneously stimulate and record field potentials, as well as action potentials of multiple neurons from different areas of the tissue (Dossi et al. 2014). MEAs recordings constitute an excellent tool for studying the spatio-temporal patterns of spontaneous interictal and evoked seizure-like events, the mechanisms underlying seizure onset and propagation, and electrophysiological activity of the neurons in response to chemical exposures physical (visual) observation Visual assessment used to detect mortality or physical signs associated with epileptic seizures. in_vivo mortality change low physical (visual) observation (for mortality) are the methods often used to detect epileptic seizure-related effects electroencephalography Detects paroxysmal depolarizing shifts in vivo using electroencephalography techniques. in_vivo brain paroxysmal depolarizing shifts not_specified medium PDS can be detected in vivo using electroencephalography techniques (Niedermeyer and da Silva 2005). http://purl.obolibrary.org/obo/UBERON_0000955 UBERON micro-electrode array This assay measures paroxysmal depolarizing shifts in vitro using micro-electrode arrays to determine effects of chemicals on action potential patterns of neurons. in_vitro neurons paroxysmal depolarizing shifts change medium using patch-clamp recording technique (Kapur 2009) or micro-electrode arrays (Novellino et al . 2011) to determine effects of chemicals on action potential patterns of neurons. http://purl.obolibrary.org/obo/CL_0000706 CL http://purl.obolibrary.org/obo/GO_0005864 GO micro-electrode arrays Measures action potential patterns of neurons using micro-electrode arrays to detect paroxysmal depolarizing shifts. in_vitro neurons action potential patterns not_specified http://purl.obolibrary.org/obo/GO_0001508 GO medium Paroxysmal depolarizing shifts can be measured in vitro using patch-clamp recording technique (Kapur 2009) or micro-electrode arrays (Novellino et al. 2011) to determine effects of chemicals on action potential patterns of neurons. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0001508 GO patch-clamp recording Measures action potential patterns of neurons using patch-clamp technique to detect paroxysmal depolarizing shifts. in_vitro neurons action potential patterns not_specified http://purl.obolibrary.org/obo/GO_0001508 GO low Paroxysmal depolarizing shifts can be measured in vitro using patch-clamp recording technique (Kapur 2009) or micro-electrode arrays (Novellino et al. 2011) to determine effects of chemicals on action potential patterns of neurons. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0001508 GO patch-clamp recording This assay measures paroxysmal depolarizing shifts in vitro using the patch-clamp recording technique to determine effects of chemicals on action potential patterns of neurons. in_vitro neurons paroxysmal depolarizing shifts change low using patch-clamp recording technique (Kapur 2009) or micro-electrode arrays (Novellino et al . 2011) to determine effects of chemicals on action potential patterns of neurons. http://purl.obolibrary.org/obo/CL_0000706 CL http://purl.obolibrary.org/obo/GO_0005864 GO Combined PET-MRI Combines positron emission tomography and magnetic resonance imaging to study functional processes in the brain, including vascular and oxygenation changes. in_vivo brain functional brain activity change low Combined positron emission tomography (PET) and magnetic resonance imaging (MRI) is a new tool to study functional processes in the brain, including the response to a stimulus simultaneously using PET. These results demonstrate the feasibility of combined PET-MRI for the simultaneous study of the brain at activation and rest, revealing comprehensive and complementary information to further decode brain function and brain networks (Wehrl et al., 2013). FDG-PET Uses [18F]fluorodeoxyglucose positron emission tomography to identify cerebral networks in rats by analyzing differences in images between resting and activation states. in_vivo brain rat cerebral network activity change low Seed-based correlative analysis of [18F]fluorodeoxyglucose (FDG)-PET (FDG-PET) differences in images (resting state minus activation) is suitable to identify cerebral networks in rats. GFP technology and cofilin-F-actin quantification Measures NMDAR overactivation-induced long-term depression and spine density changes in vitro using GFP technology and cofilin-F-actin quantification. in_vitro brain spine density decrease low NMDAR overactivation-induced LTD that decrease number of spine density can be measured in vitro using GFP technology and by cofilin-F-actin quantification (Calabrese et al., 2014). Microelectrode array (MEA) recordings Assesses neuronal network activity in primary cultures using microelectrode arrays to record spontaneous electrical activity. in_vitro primary neuronal cultures brain neuronal spontaneous activity change medium Microelectrode array (MEA) recordings in primary cultures. Neuronal spontaneous activity evaluation is already used for screening purposes (Valdivia et al., 2014). Morris water maze Evaluates spatial orientation and memory in rats by measuring their ability to find a hidden or visible platform in a pool of water. in_vivo brain rat spatial orientation change low The Morris water maze: this test is developed to measure spatial orientation in rats The rat has to swim around the pool to search for a platform onto which he can escape from the water. Optical detection of neuronal spikes Detects neuronal spikes in vivo and in vitro by measuring calcium transients associated with action potentials. in_vivo brain neuronal spikes change low Optical detection of neuronal spikes both in vivo and in vitro. Assuming action potential (AP) as the only trigger of calcium influx, spike patterns are directly reflected in the trains of calcium transients. Passive avoidance Evaluates fear-motivated avoidance in rats using electric current as a source of punishment. in_vivo brain rat avoidance behavior change low Passive avoidance: fear-motivated avoidance tests are usually based on electric current as source of punishment. PET-MRI Combined positron emission tomography (PET) and magnetic resonance imaging (MRI) studies functional processes in the brain, assessing vascular and oxygenation changes during activation. in_vivo brain vascular and oxygenation changes change http://purl.obolibrary.org/obo/GO_0006028 GO low Combined positron emission tomography (PET) and magnetic resonance imaging (MRI) is a new tool to study functional processes in the brain. Functional MRI (fMRI), is used to assesses at the same time fast vascular and oxygenation changes during activation. http://purl.obolibrary.org/obo/UBERON_0000988 UBERON Radial maze Assesses working memory in rats by requiring them to remember multiple items in a radial arm maze. in_vivo brain rat working memory change low Radial maze: In the T-maze version of working memory, the animal has to remember only a single item for each trial. In the radial arm version of the working memory procedure rats have to learn multiple items. Spontaneous alternation Quantifies innate, unlearned spatial alternation behavior in rats using T-maze, Y-maze, or radial maze. in_vivo brain rat spatial alternation change low Spontaneous alternation: spontaneous alternation is spatial alternation and represents a tendency to avoid stimulus re-exposure during exploratory behaviour. T-maze (simple or multiple), Y-maze, and radial maze are used to quantify an innate, unlearned response in rats. Two-photon imaging Measures neuronal network activity in vivo using fluorescent calcium indicators to visualize neural circuits. in_vivo brain calcium transients change low Two-photon imaging of cell populations in vivo that are labelled with fluorescent calcium indicators. The basic aspects of in vivo calcium imaging and recent developments that allow evaluation of the neural circuits activity are described by Göbel et al., (2007a). Two-photon imaging Two-photon imaging of cell populations in vivo that are labelled with fluorescent calcium indicators to measure neuronal network activity. in_vivo adult brain not_specified neuronal network function decrease low Two-photon imaging of cell populations in vivo that are labelled with fluorescent calcium indicators. Two-photon imaging relies on fluorescence excitation and, in general, necessitates staining of cells with fluorescent dyes. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0098982 GO fast-scan cyclic voltammetry Measures serotonin concentrations using fast-scan cyclic voltammetry. in_vivo serotonin concentration not_specified http://purl.obolibrary.org/obo/CHEBI_28806 CHEBI not_specified Serotonin concentrations can be measured via microdialysis/high-performance liquid chromatography, fast-scan cyclic voltammetry, N-Shaped Multiple Cyclic Square Wave Voltammetry, and Fast-Scan Controlled-Adsorption Voltammetry (Rojas Cabrera et al. 2023). http://purl.obolibrary.org/obo/CHEBI_28806 CHEBI http://purl.obolibrary.org/obo/GO_0014059 GO Fluorescent dye uptake assay A method to measure SERT activity using the uptake of fluorescent dyes. in_vitro uptake of fluorescent dyes change not_specified development of fluorescent dyes a recent development (Persson et al. 2023) microdialysis/high-performance liquid chromatography Measures serotonin concentrations using microdialysis coupled with high-performance liquid chromatography. in_vivo serotonin concentration not_specified http://purl.obolibrary.org/obo/CHEBI_28806 CHEBI not_specified Serotonin concentrations can be measured via microdialysis/high-performance liquid chromatography, fast-scan cyclic voltammetry, N-Shaped Multiple Cyclic Square Wave Voltammetry, and Fast-Scan Controlled-Adsorption Voltammetry (Rojas Cabrera et al. 2023). http://purl.obolibrary.org/obo/CHEBI_28806 CHEBI http://purl.obolibrary.org/obo/GO_0014059 GO NVS_TR_rSERT Assays targeting the serotonin transporter (5-HTT; SERT) gene SLC6A4. in_vitro SERT activity not_specified http://purl.obolibrary.org/obo/GO_0008514 GO not_specified Toxcast assays that target the serotonin transporter (5-HTT; SERT) gene SLC6A4 include: NVS_TR_rSERT,NVS_TR_rSERT. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0015878 GO radiolabeled uptake assay Measures the rate of uptake of radiolabeled compounds into cells to assess SERT activity. in_vitro SERT activity not_specified http://purl.obolibrary.org/obo/GO_0008514 GO not_specified SERT activity can be measured by the rate of uptake of radiolabeled compounds into cells, with development of fluorescent dyes a recent development (Persson et al. 2023). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0015878 GO radiolabeled uptake assay This assay measures SERT activity by the rate of uptake of radiolabeled compounds into cells. in_vitro uptake rate of radiolabeled compounds decrease not_specified SERT activity can be measured by the rate of uptake of radiolabeled compounds into cells, with development of fluorescent dyes a recent development (Persson et al. 2023). Real time PCR This assay measures transcript abundance of genes for SERT, providing an indirect indicator of protein abundance. in_vitro transcript abundance decrease http://purl.obolibrary.org/obo/GO_0006925 GO medium Real time PCR can be used to measure transcript abundance of genes for SERT, which is an indirect – and only semi-quantitative indicator of protein abundance. http://purl.obolibrary.org/obo/GO_0006925 GO real time PCR Measures transcript abundance of genes for SERT as an indirect indicator of protein abundance. in_vitro transcript abundance of SERT not_specified http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Real time PCR can be used to measure transcript abundance of genes for SERT, which is an indirect – and only semi-quantitative indicator of protein abundance. http://purl.obolibrary.org/obo/GO_0010467 GO video microscopy Measures cilia beat frequency (CBF) using video microscopy techniques. in_vitro cilia beat frequency increase low Cilia beat frequency (CBF) may be measured by use of video microscopy. Schmid et al., 2006 measured CBF by infrared differential interference contrast (IR-DIC) video microscopy. http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0003341 GO video observation This assay monitors muscular wave action and locomotion in gastropods by recording videos or taking photographs of the snail crawling up a vertical, transparent wall. Waves are visible as alternating dark and light transverse bands. in_vivo foot gastropods muscular wave action and locomotion increase low In gastropods, muscular wave action and locomotion may be monitored by video or (or photographs)of the snail crawling up a vertical, transparent wall. Waves and interwaves are visible as alternating dark and light transverse bands (Pavlova, 2011. http://purl.obolibrary.org/obo/UBERON_0002366 UBERON http://purl.obolibrary.org/obo/GO_0006936 GO video or photograph monitoring of muscular waves This assay monitors muscular wave action and locomotion in gastropods by recording video or photographs of the snail crawling up a vertical, transparent wall, where waves and interwaves are visible as alternating dark and light transverse bands. in_vivo muscle gastropods muscular wave frequency or pattern increase http://purl.obolibrary.org/obo/GO_0006936 GO http://purl.obolibrary.org/obo/GO_0040011 GO low In gastropods, muscular wave action and locomotion may be monitored by video or (or photographs)of the snail crawling up a vertical, transparent wall. Waves and interwaves are visible as alternating dark and light transverse bands (Pavlova, 2011. http://purl.obolibrary.org/obo/UBERON_0002387 UBERON http://purl.obolibrary.org/obo/GO_0006936 GO serotonin concentration measurement Measures the concentration of serotonin (5-HT) in neuronal junctions, which can be increased due to enhanced release or diminished reuptake. not_specified neuronal junctions serotonin concentration increase http://purl.obolibrary.org/obo/CHEBI_28821 CHEBI not_specified Increased concentration of serotonin in neuronal junctions either due to increased release of serotonin or diminished reuptake. http://purl.obolibrary.org/obo/CHEBI_28821 CHEBI http://purl.obolibrary.org/obo/GO_0007268 GO enzyme immunoassay (EIA) Measures steroid protein levels directly using enzyme immunoassay techniques. in_vitro steroid protein levels not_specified medium Steroid protein levels can be directly measured by immunoassay (including enzyme immunoassays (EIA) http://purl.obolibrary.org/obo/GO_0008202 GO gas chromatography mass spectrometry (GC-MS) Measures steroid protein levels directly using gas chromatography mass spectrometry. in_vitro steroid protein levels not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI low Steroid protein levels can be directly measured by mass spectrometry (including gas chromatography mass spectrometry (GC-MS) http://purl.obolibrary.org/obo/GO_0008202 GO mRNA expression analysis Measures mRNA expression levels of steroidogenic proteins as an indirect assessment of protein levels. in_vitro mRNA expression levels not_specified http://purl.obolibrary.org/obo/GO_0010608 GO not_specified mRNA expression an indirect assessment of protein levels (Qin et al. 2008; van den Driesche et al. 2012; Mendoza-Villarroel et al. 2014) http://purl.obolibrary.org/obo/SO_0000674 SO http://purl.obolibrary.org/obo/GO_0010467 GO enzyme immunoassay Measures changes in COUP-TFII protein levels. in_vitro Leydig cells COUP-TFII protein levels decrease medium COUP-TFII is measured by changes in gene expression (via real time PCR) and protein (via Western blotting or enzyme immunoassays) levels http://purl.obolibrary.org/obo/GO_0010457 GO enzyme immunoassay COUP-TFII protein levels are measured using enzyme immunoassays. in_vitro Leydig cells protein levels decrease medium COUP-TFII is measured by … protein (via enzyme immunoassays) levels. http://purl.obolibrary.org/obo/GO_0006457 GO real time PCR Measures changes in COUP-TFII gene expression levels. in_vitro Leydig cells COUP-TFII gene expression decrease medium COUP-TFII is measured by changes in gene expression (via real time PCR) http://purl.obolibrary.org/obo/GO_0010467 GO real time PCR Gene expression of COUP-TFII is measured using real time PCR. in_vitro Leydig cells gene expression levels decrease medium COUP-TFII is measured by changes in gene expression (via real time PCR) http://purl.obolibrary.org/obo/GO_0010468 GO western blot COUP-TFII protein levels are measured using Western blotting. in_vitro Leydig cells protein levels decrease low COUP-TFII is measured by … protein (via Western blotting) levels. http://purl.obolibrary.org/obo/GO_0006457 GO Western blotting Measures changes in COUP-TFII protein levels. in_vitro Leydig cells COUP-TFII protein levels decrease low COUP-TFII is measured by changes in gene expression (via real time PCR) and protein (via Western blotting or enzyme immunoassays) levels http://purl.obolibrary.org/obo/GO_0010457 GO immunoblotting Determines the phosphotyrosine content of purified nicotinic acetylcholine receptors. in_vitro phosphotyrosine content not_specified http://purl.obolibrary.org/obo/OBI_0000659 OBI http://purl.obolibrary.org/obo/PR_000001378 PR medium Immunoblotting to determine phosphotyrosine content of purified nAChR http://purl.obolibrary.org/obo/PR_000001378 PR http://purl.obolibrary.org/obo/GO_0016310 GO immunoblotting Immunoblotting assay to determine the phosphotyrosine content of purified nicotinic acetylcholine receptors, assessing post-translational modification status. in_vitro phosphotyrosine content of purified nAChR change http://purl.obolibrary.org/obo/CHEBI_25978 CHEBI http://purl.obolibrary.org/obo/OBI_0000684 OBI low Immunoblotting to determine phosphotyrosine content of purified nAChR http://purl.obolibrary.org/obo/GO_0004888 GO http://purl.obolibrary.org/obo/GO_0004674 GO patch-clamp Measures the number of channel openings per unit time to investigate desensitization of nicotinic acetylcholine receptors. in_vitro number of channel openings per unit time not_specified http://purl.obolibrary.org/obo/PR_000001378 PR low Patch-clamp, number of channel openings per unit time http://purl.obolibrary.org/obo/PR_000001378 PR [35S]t-butylbicyclophosphorothionate (TBPS) binding assay A radioligand binding assay used to determine the binding properties and inhibition at the convulsant binding site of the iGABAR chloride channel. in_vitro binding properties (i.e., inhibition by TBPS, picrotoxin, loreclezole and pentobarbital and modulation by GABA) change http://purl.obolibrary.org/obo/OBI_0000117 OBI not_specified Atack et al. (2007) chose the radioligand [35S]t-butylbicyclophosphorothionate (TBPS) binding assay to determine the binding properties (i.e., inhibition by TBPS, picrotoxin, loreclezole and pentobarbital and modulation by GABA) at the convulsant binding site. http://purl.obolibrary.org/obo/GO_0005515 GO molecular modeling Molecular modeling is used to determine binding to a specific site on iGABAR. in_silico protein-ligand interaction change http://purl.obolibrary.org/obo/OBI_0000703 OBI medium Binding to a specific site on iGABAR can be determined using a variety of methods including mutagenesis, pore structure studies, ligand binding, and molecular modeling (more details on methods can be found in Chen et al. 2006). http://purl.obolibrary.org/obo/GO_0046968 GO mutagenesis Mutagenesis is used to determine binding to a specific site on the iGABAR chloride channel. not_specified binding change http://purl.obolibrary.org/obo/GO_0005102 GO http://purl.obolibrary.org/obo/GO_0005488 GO not_specified mutagenesis http://purl.obolibrary.org/obo/GO_0005102 GO radioligand binding assay This assay measures the binding properties of ligands to the iGABAR convulsant binding site using a radioligand. Specifically, it determines inhibition by TBPS, picrotoxin, loreclezole and pentobarbital and modulation by GABA. in_vitro ligand binding change http://purl.obolibrary.org/obo/OBI_0000489 OBI low Atack et al. (2007) chose the radioligand [35S]t-butylbicyclophosphorothionate (TBPS) binding assay to determine the binding properties (i.e., inhibition by TBPS, picrotoxin, loreclezole and pentobarbital and modulation by GABA) at the convulsant binding site. http://purl.obolibrary.org/obo/GO_0005102 GO TBPS binding assay The radioligand [35S] TBPS binding assay determines the binding properties (i.e., inhibition by TBPS, picrotoxin, loreclezole and pentobarbital and modulation by GABA) at the convulsant binding site of the iGABAR chloride channel. not_specified binding inhibition change http://purl.obolibrary.org/obo/GO_0005102 GO http://purl.obolibrary.org/obo/GO_0005254 GO http://purl.obolibrary.org/obo/GO_0004889 GO not_specified radioligand [35S] t-butylbicyclophosphorothionate (TBPS) binding assay http://purl.obolibrary.org/obo/GO_0005254 GO electrophysiological recording of GABA-induced membrane currents Measures the inhibition of GABA-induced membrane currents in primary cultured neurons in a concentration-dependent manner. in_vitro primary cultured neurons small intestine guinea-pig GABA-induced membrane currents decrease http://purl.obolibrary.org/obo/GO_0043257 GO low used primary cultured neurons obtained from the guinea-pig small intestine to detect picrotoxin concentration-dependent (and reversible) inhibition of GABA-induced membrane currents. electrophysiology Measures inhibition of GABA-induced membrane currents using electrophysiological recording in primary cultured neurons. in_vitro primary cultured neurons small intestine guinea-pig GABA-induced membrane current amplitude decrease low Juarez et al. (2013) used primary cultured neurons obtained from the guinea-pig small intestine to detect picrotoxin concentration-dependent (and reversible) inhibition of GABA-induced membrane currents. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0060079 GO whole-cell patch-clamp Measures spontaneous inhibitory postsynaptic currents (sIPSCs) and GABA-evoked postsynaptic currents in rat basolateral amygdala (BLA) neurons. in_vitro neurons basolateral amygdala rat frequency and amplitude of GABA_A receptor mediated sIPSCs and amplitude of GABA-evoked postsynaptic currents decrease http://purl.obolibrary.org/obo/OBI_0001850 OBI low whole-cell in vitro recordings in the rat basolateral amygdala (BLA) to detect the reduced frequency and amplitude of GABA_A receptor mediated spontaneous inhibitory postsynaptic currents (sIPSCs) and the amplitude of GABA-evoked postsynaptic currents, both of which were induced by RDX http://purl.obolibrary.org/obo/PR_000000296 PR http://purl.obolibrary.org/obo/GO_0051965 GO whole-cell patch-clamp Measures membrane currents in primary cultured neurons from guinea-pig small intestine, detecting inhibition of GABA-induced currents by picrotoxin. in_vitro primary cultured neurons small intestine guinea-pig GABA-induced membrane currents decrease http://purl.obolibrary.org/obo/OBI_0001850 OBI low primary cultured neurons obtained from the guinea-pig small intestine to detect picrotoxin concentration-dependent (and reversible) inhibition of GABA-induced membrane currents http://purl.obolibrary.org/obo/PR_000000296 PR http://purl.obolibrary.org/obo/GO_0051965 GO EEG recording Records extracellular electrical activity or potential using >20 electroencephalogram (EEG) electrodes. in_vivo brain extracellular electrical activity change http://purl.obolibrary.org/obo/GO_0001964 GO medium recording extracellular electrical activity or potential using >20 electroencephalogram (EEG) electrodes (often in clinical settings) (Bromfield et al. 2006) http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0007268 GO intracellular electrode recording Measures electrical responses and changes in intracellular calcium concentration using intracellular electrodes. ex_vivo brain electrical responses and intracellular calcium concentration change http://purl.obolibrary.org/obo/GO_0001964 GO http://purl.obolibrary.org/obo/GO_0005509 GO low EPSPs are usually recorded by measuring electrical responses and changes in intracellular calcium concentration using intracellular electrodes (Miura et al. 1997) http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0007268 GO voltage-sensitive dye imaging Measures voltage responses from large neuronal populations in acute brain slice preparations using voltage-sensitive dyes. ex_vivo brain voltage responses change http://purl.obolibrary.org/obo/GO_0001964 GO medium voltage-sensitive dyes have been successfully used for measuring voltage responses from large neuronal populations in acute brain slice preparations (Popovic et al. 2015; Acker et al. 2016) http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0007268 GO Caspase-3 and -8 colorimetric assay Measures apoptosis initiation and execution via caspases 3 and 8 activity using colorimetric substrates. in_vitro caspase-3 and -8 activity increase low 10 µL of the supernatant was incubated with 80 µL of the caspase assay buffer and 10 µL of the colorimetric caspase-3 (Acetyl-asp-glu-val-asp-p-nitroanilide) or caspase-8 (Acetyl-ile-glu-thr-asp-p-nitroaniline) substrate. Coomassie blue G250 binding method A method used to determine total urinary protein concentration via Coomassie blue G250 binding. not_specified kidney total urinary protein not_specified not_specified Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. Kidney function assay Measures total urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, and serum and urinary creatinine to assess kidney function. in_vivo kidney human urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, serum and urinary creatinine increase low Measuring total urinary protein, albumin, transferrin, b2-microglobulin, retinolbinding protein, brush border tubular antigens, N-acetyl-b-Dglucosaminidase activity, serum and urinary creatine Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies. The total activity of N-acetyl-β-Dglucosaminidase (NAG-T-U) in urine was determined colorimetrically using a kit (PPR Diagnostics Ltd.). Serum and urinary creatinine (Creat-U) were measured by the methods of Heinegard and Tiderström (1973), and Jaffé, respectively (Henry, 1965). latex immunoassay Quantification of urinary albumin, transferrin, β2-microglobulin, and retinol-binding protein using latex immunoassay. not_specified kidney albumin, transferrin, β2-microglobulin, and retinol-binding protein levels not_specified not_specified Albumin (Alb-U), transferrin (Transf-U), β2-microglobulin (β2m-U), and retinolbinding protein (RBP-U) in urine were quantified by latex immunoassay (Bernard & Lauwerys, 1983). LDH cytotoxicity assay Measures necrosis via lactate dehydrogenase release into the extracellular space, quantified using a tetrazolium salt. in_vitro lactate dehydrogenase release increase high LDH is released into extracellular space when the plasma membrane is damaged. LDH oxidizes lactate to generate NADH, which then reacts with WST to generate a yellow colour. MTT assay Measures cell viability by detecting the reduction of MTT to formazan crystals by mitochondrial dehydrogenases. in_vitro cell viability decrease high This assay is a quantitative and sensitive method of detection of cell proliferation, measuring the growth rate of cells via activity and absorbance. It relies on the reduction of MTT (yellow, water-soluble tetrazolium dye) by mitochondrial dehydrogenases, to purple colored formazan crystals. NAG assay Measures urinary N-acetyl-β-D-glucosaminidase (NAG) activity using a colorimetric kit. in_vivo kidney human urinary NAG activity increase medium Urinary NAG activity was measured by using NAG Quantitative Kit (Shionogi, Osaka, Japan). sandwich enzyme-linked immunoassay Detection and analysis of brush border tubular antigens using monoclonal antibodies via sandwich ELISA. not_specified kidney brush border tubular antigens not_specified not_specified The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies (Mutti et al., 1985). Urinary β2-microglobulin assay Measures urinary β2-microglobulin levels using a solid-phase enzyme-linked immunosorbent assay (ELISA) with monoclonal antibodies, quantifying color intensity at 450 nm. in_vivo kidney Urinary β2-microglobulin concentration increase medium Urinary β2-MG was measured by using Enzygnost β2-MG Micro Kit (Behring Institute, Mannheim, Germany). Its method used the principle of solid phase enzyme-linked immunosorbent assay (ELISA). Monoclonal anti-β2-MG antibody and anti-2-MG-horseradish peroxidase conjugate solution were used. After that, color intensities were measured with a wavelength of 450 nm by using a spectrophotometer CAR null mouse assay An in vivo assay using CAR null mice or rats to provide definitive evidence that a substance is a CAR activator by demonstrating absence of responses in CAR null animals and presence of responses in wild-type animals. in_vivo not specified liver mouse rat gene expression, CYP2B enzyme induction, liver hepatocellular hypertrophy, liver weight not_specified http://purl.obolibrary.org/obo/GO_0010467 GO not_specified More definitive evidence that a substance is a CAR activator, can be attained in vivo by experiments in CAR null mice or rats, which lack the gene for the CAR molecule. Absence of responses in CAR null mice or rats for the gene expression, CYP2B enzyme induction, liver hepatocellular hypertrophy and increases in liver weight, and presence of these responses in treated wild-type animals, is a convincing proof that these effects were mediated by activation of CAR in the wild-type animals. CAR null mouse/rat experiments Compares responses in CAR null mice or rats versus wild-type animals to confirm CAR-mediated effects. in_vivo liver mouse rat absence of responses in CAR null animals not_specified low More definitive evidence that a substance is a CAR activator, can be attained in vivo by experiments in CAR null mice or rats, which lack the gene for the CAR molecule. Absence of responses in CAR null mice or rats for the gene expression, CYP2B enzyme induction, liver hepatocellular hypertrophy and increases in liver weight, and presence of these responses in treated wild-type animals, is a convincing proof that these effects were mediated by activation of CAR in the wild-type animals. CAR reporter assay Measures activation of CAR using a luciferase-based reporter construct transiently transfected into model cell lines. in_vitro model cell line mouse rat human dog luciferase activity increase medium Activation of CAR by a chemical substance is often detected in an in vitro system, using a reporter construct that is transiently transfected into a model cell line. The reporter readouts are typically luminescent (e.g. luciferase-based). Omiecinski et al. (2011b) were able to develop a successful reporter assay for CAR from mouse, rat, human and dogs by inserting a 5 amino acid modification into the different species' CAR, in conjunction with a luciferase reporter construct driven by a human CYP2B6 response element. CAR signature analysis Compares gene expression changes to a predefined 83-gene CAR signature derived from multiple CAR activating compounds. in_vivo liver mouse gene signature match change high Oshida et al. (2015a) have developed a CAR signature in mice that represents the combined change in an 83-gene signature derived from multiple CAR activating compounds given to groups of mice for 30 days. A compound's response compared to the CAR signature can be compared for both the direction and magnitude of all 83 genes, and a statistically significant match evaluated via Correlation Engine (Illumina). http://purl.obolibrary.org/obo/GO_0006351 GO enzyme activity/protein level measurement This assay looks for increases in enzyme activity or protein levels for CAR-responsive enzymes, such as CYP2B or CYP3A. in_vivo liver enzyme activity/protein levels increase http://purl.obolibrary.org/obo/GO_0004372 GO http://purl.obolibrary.org/obo/GO_0005576 GO low A more generic in vivo measurement approach that may be applicable in a wider array of species, is to look for increases in enzyme activity or protein levels for CAR-responsive enzymes, such as CYP2B or CYP3A induction (Burke et al., 1985; Burke et al., 1994; Sun et al., 2006). http://purl.obolibrary.org/obo/GO_0000128 GO luciferase reporter assay This assay uses a reporter construct transiently transfected into a model cell line to detect CAR activation. The readout is luminescent, typically luciferase-based. in_vitro model cell line mouse rat human dog luminescence increase http://purl.obolibrary.org/obo/GO_0003723 GO http://purl.obolibrary.org/obo/GO_0006956 GO medium Activation of CAR by a chemical substance is often detected in an in vitro system, using a reporter construct that is transiently transfected into a model cell line. The reporter readouts are typically luminescent (e.g. luciferase-based) (Omiecinski et al., 2011b; Stanley et al., 2006). http://purl.obolibrary.org/obo/GO_0005102 GO Microarray / RNAseq transcriptomics Whole-animal transcriptome analysis using microarrays or RNAseq is used to assess global gene expression changes in liver tissue of animals treated with test compounds versus controls, to identify CAR activation signatures. in_vivo liver mouse Whole transcriptome gene expression profile change http://www.bioassayontology.org/bao#BAO_0000087 BAO http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0009984 GO high or for the whole animal transcriptome by microarrays or RNAseq methodologies treatment of animals for 7 or 14 days and comparison of the response in control vs. treated tissue is assessed Oshida et al. (2015a) have developed a CAR signature in mice that represents the combined change in an 83-gene signature derived from multiple CAR activating compounds given to groups of mice for 30 days http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0006351 GO Microarray or RNAseq for CAR-responsive genes Measures whole animal transcriptome changes in CAR-responsive genes using microarray or RNAseq methodologies. in_vivo liver transcriptome changes change http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/OBI_0000368 OBI high With in vivo testing, activation of CAR by a chemical substance is most readily detected by indirect methods, considering the complex set of processes that are involved. Typically, expression of a small subset of genes in a tissue of interest (e.g. liver) that are known to be regulated by CAR can be measured via RT-PCR methods (reverse transcripase - polymerase chain reaction), or for the whole animal transcriptome by microarrays or RNAseq methodologies. http://purl.obolibrary.org/obo/GO_0006351 GO RT-PCR RT-PCR measures the expression of a small subset of genes known to be regulated by CAR in a tissue of interest. in_vivo liver mice gene expression increase http://purl.obolibrary.org/obo/GO_0006955 GO medium Typically, expression of a small subset of genes in a tissue of interest (e.g. liver) that are known to be regulated by CAR can be measured via RT-PCR methods (reverse transcripase - polymerase chain reaction) CAR-responsive genes in mice might include Cyp2b10, Gadd45b, Ki67, Cyp2c55 and Gstm3 (Oshida et al., 2015a; Peffer et al., 2018a; Tojima et al., 2012) http://purl.obolibrary.org/obo/GO_0006955 GO RT-PCR for CAR-responsive genes Measures expression of CAR-responsive genes in tissues via reverse transcriptase-polymerase chain reaction. in_vivo liver gene expression increase http://purl.obolibrary.org/obo/GO_0010467 GO low With in vivo testing, activation of CAR by a chemical substance is most readily detected by indirect methods, considering the complex set of processes that are involved. Typically, expression of a small subset of genes in a tissue of interest (e.g. liver) that are known to be regulated by CAR can be measured via RT-PCR methods (reverse transcripase - polymerase chain reaction). http://purl.obolibrary.org/obo/GO_0006351 GO RT-PCR gene expression assay RT-PCR is used to measure expression levels of CAR-responsive genes (e.g. Cyp2b10, Gadd45b, Ki67, Cyp2c55, Gstm3) in liver tissue of treated animals compared to controls, to detect CAR activation indirectly in vivo. in_vivo liver mouse Expression levels of CAR-responsive genes change http://purl.obolibrary.org/obo/OBI_0000682 OBI http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON not_specified Typically, expression of a small subset of genes in a tissue of interest (e.g. liver) that are known to be regulated by CAR can be measured via RT-PCR methods (reverse transcripase - polymerase chain reaction) CAR-responsive genes in mice might include Cyp2b10, Gadd45b, Ki67, Cyp2c55 and Gstm3 treatment of animals for 7 or 14 days and comparison of the response in control vs. treated tissue is assessed http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0010467 GO BrdU incorporation Detects DNA synthesis by incorporating the thymidine analog 5-bromo-2-deoxyuridine (BrdU) into newly synthesized DNA, followed by immunohistochemical detection of proliferating cells. in_vivo hepatocytes liver rat DNA synthesis increase http://purl.obolibrary.org/obo/GO_0006260 GO http://purl.obolibrary.org/obo/CHEBI_16104 CHEBI low Nucleoside analogs may also be incorporated into the newly-synthesized DNA, including 5-bromo-2-deoxyuridine (BrdU) or 5-ethyl-2’-deoxy uridine (EdU), which may be detected using standard immunohistochemical and biolabeling techniques, respectively A direct comparison of BrdU, Ki67 and PCNA labeling in various proliferating tissues of male Sprague-Dawley rats http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO Ki-67 immunohistochemistry Detects the endogenous proliferation marker Ki-67 in hepatocytes using standard immunohistochemical techniques; Ki-67 is expressed in actively cycling cells (G1, S, G2, M) but not in quiescent cells. in_vivo hepatocytes liver rat cell proliferation increase http://purl.obolibrary.org/obo/GO_0051726 GO low the detection of endogenous markers of proliferation such as antigen Ki-67 or proliferating cell nuclear antigen (PCNA) Ki-67 and PCNA are endogenous proteins expressed by mammalian cells that are in active phases of the cell cycle (G1, S, G2, M) and are not expressed in quiescent (G0) cells They are detected in hepatocytes using standard immunohistochemical techniques A direct comparison of BrdU, Ki67 and PCNA labeling in various proliferating tissues of male Sprague-Dawley rats Ki67 immunohistochemistry methods gave similar labelling index results http://purl.obolibrary.org/obo/PR_000036263 PR http://purl.obolibrary.org/obo/GO_0051726 GO Ki-67 immunohistochemistry Detection of actively proliferating cells by immunohistochemical staining of the endogenous protein Ki-67, which is expressed by mammalian cells in active phases of the cell cycle (G1, S, G2, M) and not expressed in quiescent (G0) cells. in_vitro hepatocytes liver rat fraction of labeled cell population/total number of cells in population increase http://purl.obolibrary.org/obo/GO_0007049 GO http://purl.obolibrary.org/obo/GO_0008283 GO low Ki-67 and PCNA are endogenous proteins expressed by mammalian cells that are in active phases of the cell cycle (G1, S, G2, M) and are not expressed in quiescent (G0) cells (Dietrich, 1993; Eldrige et al., 1993; Scholzen and Gerdes, 2000). They are detected in hepatocytes using standard immunohistochemical techniques. The advantage of using endogenous markers is that they do not require administration of exogenous markers for labeling, and they can be used for both prospective and retrospective cell proliferation analysis. A direct comparison of BrdU, Ki67 and PCNA labeling in various proliferating tissues of male Sprague-Dawley rats (Muskhelishvili et al., 2003) has indicated that Ki67 and BrdU immunohistochemistry methods gave similar labelling index results, whereas PCNA immunohistochemistry was not concordant with these methods and gave highly variable results. These authors suggested that PCNA is less accurate as a measure of cell proliferation because it has a long half-life and can be retained in cells that are not dividing, and is more involved in DNA repair mechanisms than Ki67. As a result, Ki67 has emerged as a more preferred endogenous marker for assessing cell proliferation in hepatocytes in recent years compared to PCNA. http://purl.obolibrary.org/obo/PR_003407 PR http://purl.obolibrary.org/obo/GO_0008283 GO Ki-67 immunohistochemistry Detects the endogenous proliferation marker Ki-67 in hepatocytes using immunohistochemical techniques, indicating cells in active phases of the cell cycle (G1, S, G2, M). in_vivo hepatocytes liver Sprague-Dawley rat Ki-67 expression increase http://purl.obolibrary.org/obo/GO_0008283 GO medium Ki-67 and PCNA are endogenous proteins expressed by mammalian cells that are in active phases of the cell cycle (G1, S, G2, M) and are not expressed in quiescent (G0) cells (Dietrich, 1993; Eldrige et al., 1993; Scholzen and Gerdes, 2000). Ki67 has emerged as a more preferred endogenous marker for assessing cell proliferation in hepatocytes in recent years compared to PCNA. http://purl.obolibrary.org/obo/CL_0000038 CL http://purl.obolibrary.org/obo/GO_0007049 GO Ki-67 immunohistochemistry Detects the endogenous proliferation marker protein Ki-67 in hepatocytes using immunohistochemical techniques to assess cells in active cell cycle phases. in_vivo hepatocytes liver Rattus norvegicus labeling index increase http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/GO_0007049 GO medium Ki-67 and PCNA are endogenous proteins expressed by mammalian cells that are in active phases of the cell cycle... They are detected in hepatocytes using standard immunohistochemical techniques. For each of these methods, a labeling index (fraction of labeled cell population/total number of cells in population) is calculated http://purl.obolibrary.org/obo/CL_0000182 CL http://purl.obolibrary.org/obo/GO_0008283 GO nucleoside incorporation Measures proliferation by quantifying the incorporation of labeled nucleosides or nucleoside analogs (e.g., 3H-thymidine, BrdU, EdU) into newly synthesized DNA. Detection is performed using autoradiography or immunohistochemical/biolabeling techniques. in_vitro hepatocytes liver rat incorporation of labeled nucleosides/analogs increase http://purl.obolibrary.org/obo/GO_0006260 GO low Mitogenic proliferation in vitro and in vivo is measured by the incorporation of labeled nucleosides or nucleoside analogs into newly synthesized DNA (Peffer et al., 2018b) Once the DNA of a cell is replicated during S phase, the cell undergoes mitosis. Nucleoside analogs may also be incorporated into the newly-synthesized DNA, including 5-bromo-2-deoxyuridine (BrdU) or 5-ethyl-2’-deoxy uridine (EdU) http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO Nucleoside/nucleoside analog labeling Measures DNA synthesis by detecting the incorporation of radiolabeled nucleosides (e.g., 3H-thymidine) or nucleoside analogs (e.g., BrdU, EdU) into newly synthesized DNA. in_vitro liver DNA synthesis / labeling index increase http://purl.obolibrary.org/obo/GO_0006260 GO http://purl.obolibrary.org/obo/GO_0008283 GO not_specified Mitogenic proliferation in vitro and in vivo is measured by the incorporation of labeled nucleosides or nucleoside analogs into newly synthesized DNA The DNA replication that occurs in S phase may be detected by the incorporation radiolabeled (e.g., 3H-thymidine) into the newly synthesized DNA Nucleoside analogs may also be incorporated into the newly-synthesized DNA, including 5-bromo-2-deoxyuridine (BrdU) or 5-ethyl-2’-deoxy uridine (EdU) http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO PCNA immunohistochemistry Detects the endogenous proliferation marker proliferating cell nuclear antigen (PCNA) in hepatocytes using standard immunohistochemical techniques; PCNA is expressed in active phases of the cell cycle but is less accurate due to its long half-life and involvement in DNA repair. in_vivo hepatocytes liver rat cell proliferation increase http://purl.obolibrary.org/obo/GO_0051726 GO low the detection of endogenous markers of proliferation such as antigen Ki-67 or proliferating cell nuclear antigen (PCNA) Ki-67 and PCNA are endogenous proteins expressed by mammalian cells that are in active phases of the cell cycle (G1, S, G2, M) and are not expressed in quiescent (G0) cells They are detected in hepatocytes using standard immunohistochemical techniques A direct comparison of BrdU, Ki67 and PCNA labeling in various proliferating tissues of male Sprague-Dawley rats PCNA immunohistochemistry was not concordant with these methods and gave highly variable results http://purl.obolibrary.org/obo/PR_000053318 PR http://purl.obolibrary.org/obo/GO_0051726 GO PCNA immunohistochemistry Detects the endogenous proliferation marker protein PCNA in hepatocytes using immunohistochemical techniques to assess cells in active cell cycle phases. in_vivo hepatocytes liver Rattus norvegicus labeling index increase http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/GO_0007049 GO medium Ki-67 and PCNA are endogenous proteins expressed by mammalian cells that are in active phases of the cell cycle... They are detected in hepatocytes using standard immunohistochemical techniques. For each of these methods, a labeling index (fraction of labeled cell population/total number of cells in population) is calculated http://purl.obolibrary.org/obo/CL_0000182 CL http://purl.obolibrary.org/obo/GO_0008283 GO PCNA immunohistochemistry Detects the endogenous proliferation marker PCNA in hepatocytes using immunohistochemical techniques, indicating cells in active phases of the cell cycle (G1, S, G2, M). in_vivo hepatocytes liver Sprague-Dawley rat PCNA expression increase http://purl.obolibrary.org/obo/GO_0008283 GO medium Ki-67 and PCNA are endogenous proteins expressed by mammalian cells that are in active phases of the cell cycle (G1, S, G2, M) and are not expressed in quiescent (G0) cells (Dietrich, 1993; Eldrige et al., 1993; Scholzen and Gerdes, 2000). PCNA immunohistochemistry was not concordant with these methods and gave highly variable results. http://purl.obolibrary.org/obo/CL_0000038 CL http://purl.obolibrary.org/obo/GO_0007049 GO radiolabeled thymidine incorporation Measures DNA synthesis by incorporating radiolabeled thymidine (e.g., 3H-thymidine) into newly synthesized DNA during the S phase of the cell cycle, detected via autoradiography in isolated livers. in_vivo hepatocytes liver rat DNA synthesis increase http://purl.obolibrary.org/obo/GO_0006260 GO http://purl.obolibrary.org/obo/CHEBI_17270 CHEBI low the incorporation of labeled nucleosides or nucleoside analogs into newly synthesized DNA The DNA replication that occurs in S phase may be detected by the incorporation radiolabeled (e.g., 3H-thymidine) into the newly synthesized DNA, which can be detected from isolated livers using standard autoradiographic techniques. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO competitive [3H]colchicine tubulin-binding assay Measures the inhibition of colchicine binding to tubulin by a test agent using radiolabeled [3H]colchicine and a scintillation counter. in_vitro brain radioactivity of [3H]colchicine-bound tubulin decrease http://purl.obolibrary.org/obo/GO_0015631 GO http://purl.obolibrary.org/obo/CHEBI_27899 CHEBI medium a competitive [3H]colchicine tubulin-binding assay is conducted in vitro to measure whether the binding of colchicine is inhibited by the presence of the test agent the radioactivity of [3H]colchicine-bound tubulin is measured using a scintillation counter The reduction of [3H]colchicine-bound tubulin value is inversely proportional to the test agent binding affinity http://purl.obolibrary.org/obo/PR_000008759 PR http://purl.obolibrary.org/obo/GO_0007017 GO acellular tubulin polymerization assay Measures microtubule depolymerization by assessing turbidity development at 350 nm in a reaction mixture containing tubulin and a test agent, with GTP added to initiate polymerization. in_vitro tubulin polymerization inhibition decrease http://purl.obolibrary.org/obo/GO_0046785 GO http://purl.obolibrary.org/obo/GO_0015631 GO medium Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay [Salmon et al., 1984; Wilson et al., 1984; Wallin and Hartley-Asp, 1993; Ibanez et al., 2003; Liu et al., 2010]. A reaction mixture containing tubulin and a test agent, after preincubation, is chilled on ice. GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer. The extent of the reaction is then measured and the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50) [Hamel, 2003]. http://purl.obolibrary.org/obo/GO_0005874 GO http://purl.obolibrary.org/obo/GO_0046785 GO acellular tubulin polymerization assay An assay that measures the inhibition of tubulin polymerization by monitoring the development of turbidity at 350 nm in a spectrophotometer following the addition of GTP to a tubulin and test agent mixture. in_vitro turbidity development (IC50 for tubulin polymerization inhibition) decrease http://purl.obolibrary.org/obo/GO_0008272 GO not_specified Microtubule depolymerization is generally assessed by an acellular tubulin polymerization assay GTP is added, and turbidity development is followed at 350 nm in a temperature-controlled recording spectrophotometer. The extent of the reaction is then measured and the area under the curve is used to determine the concentration that inhibited tubulin polymerization by 50% (IC50) http://purl.obolibrary.org/obo/GO_0008272 GO 3D live imaging Uses cells expressing fluorescent-tagged proteins to follow spindle function and measure abnormal parameters in real-time. in_vitro spindle morphology and dynamics change http://purl.obolibrary.org/obo/GO_0051225 GO low 3D live imaging of cells expressing fluorescent-tagged proteins provides the possibility to follow spindle function at high resolution, and to describe and measure abnormal parameters (e.g., spindle morphology, altered distance between the two poles, mono- or multipolarity) [Schuh and Ellenberg, 2007]. http://purl.obolibrary.org/obo/GO_0045172 GO http://purl.obolibrary.org/obo/GO_0051225 GO Enhanced polarizing microscopy (Polscope/SpindleViewTM) Detects reduction in birefringency and light retardance of the spindle, indicating loss of organization. in_vitro spindle birefringency and light retardance decrease http://purl.obolibrary.org/obo/GO_0051225 GO medium the use of enhanced polarizing microscope (Polscope/SpindleViewTM) allows the detection of reduction in the birefringency and reduced light retardance of the spindle, which are indicators of loss of organization, at doses below which spindle abnormalities are detected with more conventional immunofluorescence methods [Shen et al., 2005]. http://purl.obolibrary.org/obo/GO_0045172 GO http://purl.obolibrary.org/obo/GO_0051225 GO Immunofluorescence microscopy Assesses spindle organization by fluorescent immunodetection of spindle components using confocal microscopy. in_vitro spindle morphology and organization change http://purl.obolibrary.org/obo/GO_0051225 GO http://purl.obolibrary.org/obo/GO_0005874 GO low Spindle organization is generally assessed by fluorescent immunodetection of its components and confocal microscopy [Ibanez et al., 2003; Shen et al., 2005; Eichenlaub-Ritter et al., 2007; Xu et al., 2012]. http://purl.obolibrary.org/obo/GO_0045172 GO http://purl.obolibrary.org/obo/GO_0051225 GO polarizing microscopy Enhanced polarizing microscope (Polscope/SpindleViewTM) allows the detection of reduction in the birefringency and reduced light retardance of the spindle, which are indicators of loss of organization. in_vitro birefringency and light retardance decrease low In addition, the use of enhanced polarizing microscope (Polscope/SpindleViewTM) allows the detection of reduction in the birefringency and reduced light retardance of the spindle, which are indicators of loss of organization, at doses below which spindle abnormalities are detected with more conventional immunofluorescence methods [Shen et al., 2005]. http://purl.obolibrary.org/obo/CL_0000315 CL C-banding Identifies centromeres using traditional C-banding to improve the accuracy of chromosome counting. ex_vivo oocytes ovary rodents human centromere identification not_specified http://purl.obolibrary.org/obo/GO_0000775 GO low To improve the accuracy of counting, identification of the centromeres can be done using traditional C-banding [Salamanca and Armendares, 1974] http://purl.obolibrary.org/obo/GO_0000775 GO http://purl.obolibrary.org/obo/GO_0051276 GO C. elegans aneuploidy screening Measures aneugenicity by fluorescently marking aneuploid eggs and embryos in C. elegans. in_vivo Caenorhabditis elegans aneugenicity increase http://purl.obolibrary.org/obo/GO_0002228 GO high Aneugenicity can also be measured using a C. elegans screening platform for rapid assessment [Allard et al., 2013]. This methodology fluorescently marks aneuploid eggs and embryos. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007126 GO C. elegans screening A C. elegans screening platform is used for rapid assessment of aneugenicity. This methodology fluorescently marks aneuploid eggs and embryos. in_vivo C. elegans Aneuploid eggs and embryos increase high Aneugenicity can also be measured using a C. elegans screening platform for rapid assessment [Allard et al., 2013]. This methodology fluorescently marks aneuploid eggs and embryos. http://purl.obolibrary.org/obo/CL_0000134 CL http://purl.obolibrary.org/obo/GO_0009555 GO Cytogenetic analysis of oocytes Analyzes metaphases under a microscope to count the number of chromosomes in oocytes, with optional centromere identification techniques. ex_vivo oocytes ovary rodents human chromosome number change low Methods for handling either single oocytes [Tarkowski, 1966] or multiple oocytes [Mailhes and Yuan, 1987] are available. Metaphases are then analyzed under a microscope to count the number of chromosomes. Oocytes of several rodent species [reviewed in Mailhes and Marchetti, 2005; Pacchierotti et al., 2007] and human oocytes [Pellestor et al., 2005] have been analyzed for assessing aneuploidy. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007126 GO flow cytometry Flow cytometry approaches using multiple endpoints to discriminate aneugens from other chemical classes. in_vitro aneugenicity discrimination change high Recently, flow cytometry approaches have been developed that are using multiple endpoints to discriminate aneugens from other classes of chemicals [Bryce et al., 2014]. Flow cytometry Flow cytometry approaches are used with multiple endpoints to discriminate aneugens from other classes of chemicals. not_specified Multiple endpoints related to aneuploidy change high Recently, flow cytometry approaches have been developed that are using multiple endpoints to discriminate aneugens from other classes of chemicals [Bryce et al., 2014]. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0007049 GO Fluorescent DNA immunostaining Identifies centromeres using fluorescent DNA immunostaining to improve the accuracy of chromosome counting. ex_vivo oocytes ovary rodents human centromere identification not_specified http://purl.obolibrary.org/obo/GO_0000775 GO low identification of the centromeres can be done using ... fluorescent DNA immunostaining [Leland et al., 2009] http://purl.obolibrary.org/obo/GO_0000775 GO http://purl.obolibrary.org/obo/GO_0051276 GO Micronucleus assay Detects aneugens by assessing the formation of micronuclei, though not specific to aneugens. not_specified micronucleus formation increase http://purl.obolibrary.org/obo/GO_0000818 GO OECD TG 487 medium Aneugens can be detected using the micronucleus assay [OECD, 2016c,d], but these methods are not specific to aneugens. http://purl.obolibrary.org/obo/GO_0000818 GO http://purl.obolibrary.org/obo/GO_0007049 GO Micronucleus assay with centromere-specific probes Assesses aneugenicity by integrating centromere-specific probes in micronucleus assays to distinguish aneugens. not_specified aneugenicity increase http://purl.obolibrary.org/obo/GO_0000775 GO medium Integration of centromere-specific probes in micronucleus assays enables assessment of aneugenicity using these approaches [Zijno et al., 1996]. http://purl.obolibrary.org/obo/GO_0000775 GO http://purl.obolibrary.org/obo/GO_0007059 GO Premature sister chromatid separation (PSCS) assessment Identifies the presence of single chromatids due to premature sister chromatid separation in oocytes. ex_vivo oocytes ovary rodents human premature sister chromatid separation increase http://purl.obolibrary.org/obo/GO_0007067 GO low The cytogenetic analysis of oocytes can also identify the presence of single chromatids originated because of premature sister chromatid separation (PSCS), which is one of the main mechanisms thought to result in aneuploidy in human oocytes [Angell, 1997]. http://purl.obolibrary.org/obo/GO_0000819 GO http://purl.obolibrary.org/obo/GO_0000776 GO Spectral karyotyping Identifies centromeres using spectral karyotyping to improve the accuracy of chromosome counting. ex_vivo oocytes ovary rodents human centromere identification not_specified http://purl.obolibrary.org/obo/GO_0000775 GO low identification of the centromeres can be done using ... spectral karyotyping [Márquez et al., 1998] http://purl.obolibrary.org/obo/GO_0000775 GO http://purl.obolibrary.org/obo/GO_0051276 GO standard cytogenetic methods Preparation of meiotic or mitotic metaphases to count the number of chromosomes present. in_vitro chromosome number change OECD TG 473/487 low Aneuploidy (i.e., altered chromosome number) is assessed by standard cytogenetic methods that entail the preparation of meiotic or mitotic metaphases to count the number of chromosomes present. amniocentesis Invasive diagnostic test involving sampling of amniotic fluid to detect chromosomal abnormalities in the fetus. in_vivo amniotic fluid cells amniotic fluid human chromosomal abnormalities not_specified low diagnostic tests during the first or second trimesters, such as amniocentesis http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0051301 GO amniocentesis Amniocentesis is a diagnostic test during the second trimester of pregnancy used to determine aneuploidy. in_vivo amniotic fluid cells amniotic fluid human chromosomal content of amniotic fluid cells change low amniocentesis [Crandall and Lebher, 1976; Dacu and Wilroy, 1985], http://purl.obolibrary.org/obo/CL_0000441 CL http://purl.obolibrary.org/obo/GO_0006260 GO Cell-free DNA sequencing Cell-free DNA sequencing analyzes fetal DNA fragments circulating in maternal blood to detect aneuploidy by identifying abnormal chromosome copy numbers. in_vitro blood human fetal chromosome copy number increase http://purl.obolibrary.org/obo/OBI_0001478 OBI http://purl.obolibrary.org/obo/GO_0034149 GO not specified high Recent developments in genomics approaches allow now the diagnosis of an aneuploid pregnancy by detecting fetal cell-free DNA in the blood of the mother http://purl.obolibrary.org/obo/GO_0034149 GO chorionic villus sampling Invasive diagnostic test involving sampling of chorionic villi to detect chromosomal abnormalities in the fetus. in_vivo chorionic villi cells placenta human chromosomal abnormalities not_specified low diagnostic tests during the first or second trimesters, such as chorionic villus sampling http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0051301 GO chorionic villus sampling Chorionic villus sampling obtains placental tissue to directly analyze fetal chromosomes for the presence of aneuploidy. The sampled villi are cultured and karyotyped to detect extra or missing chromosomes. in_vivo fetal chromosome number increase not_specified chorionic villus sampling [Hogge et al., 1985; Jenkins and Wapner, 1999] http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007059 GO fetal cell-free DNA analysis Detects fetal cell-free DNA in maternal blood to diagnose aneuploidy during pregnancy using genomics approaches. in_vivo blood human fetal DNA presence/abnormalities not_specified high detecting fetal cell-free DNA in the blood of the mother http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006259 GO karyotype analysis Cytogenetic analysis of peripheral blood lymphocytes to confirm the presence of chromosomal abnormalities, such as an extra chromosome. ex_vivo peripheral blood lymphocytes blood human chromosome number/structure not_specified low A karyotypical analysis of peripheral blood lymphocytes to confirm the presence of the extra chromosome http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0051301 GO physical exam A phenotypic assessment performed after birth to identify morphological features associated with aneuploidy, such as Down syndrome. in_vivo distinct facial features change http://purl.obolibrary.org/obo/HP_0000001 HP low When the diagnosis is done after birth, it may be based on the results of a physical exam. http://purl.obolibrary.org/obo/NCBITaxon_0 NCBITAXON http://purl.obolibrary.org/obo/GO_0007584 GO physical exam Postnatal assessment of physical features to identify characteristics associated with aneuploidy, such as Down syndrome. in_vivo whole organism human physical features not_specified low A physical exam children with Down syndrome have distinct facial features that include a flat face, slanting eyes and a small mouth http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0009653 GO serum marker analysis Analysis of serum markers during pregnancy is used as a diagnostic test to determine aneuploidy. in_vivo blood human levels of specific serum markers change medium and serum markers [Canick et al., 2006]. http://purl.obolibrary.org/obo/GO_0008523 GO ultrasound examination A phenotypic screening test used during pregnancy to identify potential signs of aneuploidy. in_vivo phenotypic signs of aneuploidy change http://purl.obolibrary.org/obo/OBI_0001245 OBI not_specified screening tests such as ultrasound examinations http://purl.obolibrary.org/obo/UBERON_0000052 UBERON http://purl.obolibrary.org/obo/GO_0007584 GO ultrasound examination Uses ultrasound imaging to screen for physical abnormalities indicative of aneuploidy during pregnancy. in_vivo fetus human physical abnormalities not_specified medium screening tests such as ultrasound examinations http://purl.obolibrary.org/obo/UBERON_0000929 UBERON http://purl.obolibrary.org/obo/GO_0032502 GO ultrasound examination Ultrasound examinations are used as a screening test during pregnancy to determine whether a pregnancy is aneuploid. in_vivo fetus human physical characteristics of the fetus change medium These include screening tests such as ultrasound examinations [Benacerraf, 2005; Rao and Plat, 2016]; http://purl.obolibrary.org/obo/UBERON_0004648 UBERON http://purl.obolibrary.org/obo/GO_0008523 GO E2/P4 ratio This assay measures the ratio of estradiol (E2) to progesterone (P4) levels, commonly used to assess hormonal balance. not_specified corpus luteum E2/P4 ratio not_specified http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI http://purl.obolibrary.org/obo/CHEBI_16469 CHEBI not_specified This key event is commonly measured using the E2/P4 ratio. http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO confocal microscopy Assesses altered chromosome dynamics at metaphase/anaphase using fixed or live cells. in_vitro chromosome dynamics change http://purl.obolibrary.org/obo/GO_0000226 GO http://purl.obolibrary.org/obo/GO_0000090 GO low Altered chromosome dynamics at metaphase/anaphase is generally assessed by confocal microscopy or enhanced polarizing microscopy on fixed or live cells http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007059 GO enhanced polarizing microscopy Assesses altered chromosome dynamics at metaphase/anaphase using fixed or live cells. in_vitro chromosome dynamics change http://purl.obolibrary.org/obo/GO_0000226 GO http://purl.obolibrary.org/obo/GO_0000090 GO low Altered chromosome dynamics at metaphase/anaphase is generally assessed by confocal microscopy or enhanced polarizing microscopy on fixed or live cells http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007059 GO fluorescence in situ hybridization (FISH) Uses multicolour fluorescence in situ hybridization to follow chromosome congression and measure distances between kinetochores and spindle midzone. in_vitro chromosome congression change http://purl.obolibrary.org/obo/GO_0000776 GO low Antibodies against centromeric proteins and multicolour fluorescence in situ hybridization (FISH) are useful approaches to follow chromosome congression: for example, distances between kinetochores and spindle midzone are used to evaluate the dynamics of chromosome congression http://purl.obolibrary.org/obo/GO_0005694 GO multicolour fluorescence in situ hybridization (FISH) Follows chromosome congression by using antibodies against centromeric proteins and multicolour FISH. in_vitro interkinetochore distances change not_specified Antibodies against centromeric proteins and multicolour fluorescence in situ hybridization (FISH) are useful approaches to follow chromosome congression: for example, distances between kinetochores and spindle midzone are used to evaluate the dynamics of chromosome congression; interkinetochore distances may be measured to verify a correct biorientation [Shen et al. 2005; Eichenlaub-Ritter et al., 2007; Schuh and Ellenberg, 2007; McGuinness et al., 2009; Lane et al., 2012; Mogessie and Schuh, 2017]. http://purl.obolibrary.org/obo/CL_0000240 CL http://purl.obolibrary.org/obo/GO_0051311 GO time-lapse microscopy Quantitatively describes microtubule dynamics and chromosome movement using time-lapse movies of mitotic cells expressing GFP-conjugated tubulin. in_vitro microtubule dynamics and chromosome movement change low A quantitative description of microtubule dynamics and chromosome movement has also been obtained by time-lapse movies of mitotic cells expressing green fluorescence protein (GFP)-conjugate-tubulin http://purl.obolibrary.org/obo/GO_0005874 GO http://purl.obolibrary.org/obo/GO_0007018 GO in situ hybridization In situ hybridization is used to probe individual gene transcripts, measuring their abundance within cells or tissues. in_vitro gene transcript abundance change medium More commonly, quantitative rtPCR or in situ hybridization have been used to probe individual gene transcripts (Dowling et al., 2000, Morte et al., 2010). http://purl.obolibrary.org/obo/GO_0010468 GO in situ hybridization Laboratory technique used to localize specific DNA or RNA sequences within biological samples. ex_vivo individual gene transcripts change http://purl.obolibrary.org/obo/GO_0016003 GO low More commonly, quantitative rtPCR or in situ hybridization have been used to probe individual gene transcripts http://purl.obolibrary.org/obo/GO_0006351 GO In situ hybridization Detects and localizes specific gene transcripts within tissue sections using labeled nucleic acid probes. in_vitro localization and expression of gene transcripts change http://purl.obolibrary.org/obo/OBI_0000642 OBI http://purl.obolibrary.org/obo/OBI_0000366 OBI low quantitative rtPCR or in situ hybridization have been used to probe individual gene transcripts (Dowling et al., 2000, Morte et al., 2010) http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006351 GO Microarray Measures genomic profiles and expression levels of multiple genes simultaneously in brain tissues. in_vitro cortex hippocampus human non-human primate rodent gene expression levels change http://purl.obolibrary.org/obo/OBI_0000366 OBI http://purl.obolibrary.org/obo/OBI_0000185 OBI high Microarray studies with expression profile analyses have been conducted in cortex and hippocampus of humans (Zhang et al., 2002), non-human primates, and rodent brains of various ages (Mody et al., 2001; Royland et al., 2008; Dong et al., 2015). http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006351 GO Microarray Measurement of genomic profiles using expression profile analyses to study gene expression patterns. in_vitro cortex hippocampus brain Homo sapiens non-human primates rodent genomic profiles change http://purl.obolibrary.org/obo/OBI_0000112 OBI high Microarray studies with expression profile analyses have been conducted in cortex and hippocampus of humans (Zhang et al., 2002), non-human primates, and rodent brains of various ages http://purl.obolibrary.org/obo/GO_0006351 GO Quantitative rtPCR Measures the expression levels of individual gene transcripts using reverse transcription and polymerase chain reaction. in_vitro individual gene transcript levels change http://purl.obolibrary.org/obo/OBI_0000366 OBI medium quantitative rtPCR or in situ hybridization have been used to probe individual gene transcripts (Dowling et al., 2000, Morte et al., 2010) http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006351 GO RNA-Seq Uses high-throughput sequencing to measure gene expression levels and identify differentially expressed genes. in_vitro primary mouse cortical cells mouse gene expression levels change http://purl.obolibrary.org/obo/OBI_0001271 OBI http://purl.obolibrary.org/obo/OBI_0000366 OBI high Recently RNA-Seq technology was applied to T3-treated primary mouse cortical cells and gene targets enriched in astrocytes and neurons to identify TH-responsive genes (Gil-Ibanez et al, 2015). http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006351 GO RNA-Seq High-throughput sequencing of RNA to identify TH-responsive genes in primary cells. in_vitro primary mouse cortical cells astrocytes neurons cortex mouse TH-responsive genes change high Recently RNA-Seq technology was applied to T3-treated primary mouse cortical cells and gene targets enriched in astrocytes and neurons to identify TH-responsive genes http://purl.obolibrary.org/obo/GO_0045893 GO Fluorescent microscopy with Dil staining Visualizes dendritic arborizations and spines in cell culture and tissue sections, and allows quantitative analysis of dendritic spine number. in_vitro hippocampal neurons hippocampus dendritic spine number not_specified http://purl.obolibrary.org/obo/GO_0043197 GO medium Fluorescent markers, such as Dil (1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate) permits not only the visualisation of detailed dendritic arborizations and spines in cell culture and tissue sections but is also compatible with the quantitative analysis of dendritic spine number (Cheng et al., 2014). http://purl.obolibrary.org/obo/GO_0043197 GO http://purl.obolibrary.org/obo/GO_0016358 GO Golgi-Cox impregnation Assesses neuronal and glial morphology, synapse structure, dendritic spine formation, and dendritic morphology in hippocampal cultures or in vivo studies. in_vivo hippocampal neurons hippocampus dendritic spine morphology and dendritic branching not_specified http://purl.obolibrary.org/obo/GO_0043197 GO http://purl.obolibrary.org/obo/GO_0008016 GO low Subtle cytoarchitectural features depend on more specialized birth dating procedures and staining techniques. At the micro- and ultra- structural levels, changes in neuronal and glial morphology, alterations in synapse structure, dendritic spine formation (size, shape, number, distribution of head/neck ratios in hippocampal cultures or in vivo studies) and dendritic morphology (branching points, length etc..) can be assessed in Golgi-Cox impregnated neurons (Bongmbaa et al., 2011). http://purl.obolibrary.org/obo/GO_0043197 GO http://purl.obolibrary.org/obo/GO_0050808 GO High content image analysis with RNAi screening Uses imaging algorithms to analyze synaptic punctae in vitro and in vivo. in_vitro hippocampus synaptic punctae not_specified http://purl.obolibrary.org/obo/GO_0045202 GO high Recently, a high content image analysis based on RNAi screening protocols has been suggested as a useful tool to create imaging algorithm for use in both in vitro and in vivo synaptic punctae analysis (Nieland et al., 2014). http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0050808 GO Immunocytochemistry with automated high content imaging Quantifies cell body and neurite proteins using immunocytochemistry and automated high content imaging in vitro and in vivo preparations. in_vitro hippocampus cell body and neurite protein levels not_specified http://purl.obolibrary.org/obo/UBERON_0001954 UBERON EPA and OECD developmental neurotoxicity guidelines high The quantification of cell body and neurite proteins can be carried out by performing immunocytochemistry and automated high content imaging analyses in in vitro and in vivo preparations (Harrill and Mundy, 2011, Meng et al., 2002), Pistollato et al., 2020). http://purl.obolibrary.org/obo/GO_0043005 GO http://purl.obolibrary.org/obo/GO_0048666 GO immunohistochemistry Uses antibodies to detect specific proteins in tissue sections. Can be combined with automated high content imaging. in_vivo hippocampus protein quantification change http://purl.obolibrary.org/obo/OBI_0000723 OBI OECD, 2007 medium Data in support of this key event have been collected using a wide variety of standard biochemical, molecular, cellular, histological and anatomical methods (e.g., morphometrics, protein quantification using different types of cellular staining, immunohistochemistry http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006470 GO Immunostaining for synaptic proteins Enumerates synapse number using antibodies against presynaptic and postsynaptic proteins such as vesicular glutamate transporters, vesicular GABA proteins, and PSD-95. in_vitro hippocampal primary cells hippocampus synapse number not_specified http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/PR_000001239 PR medium Immunostaining with specific antibodies that recognize presynaptic proteins of excitatory and inhibitory neurons (i.e., vesicular glutamate transporters, vesicular GABA proteins and transporters) and the postsynaptic density protein-95 kDa (PSD-95) can be applied to enumerate synapse number (Gatto and Broadie, 2010, Akashi et al., 2009). http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0050808 GO morphometrics Quantifies anatomical features using measurements. This is a routine neurohistopathology procedure. in_vivo hippocampus anatomical features change OECD, 1998 low Data in support of this key event have been collected using a wide variety of standard biochemical, molecular, cellular, histological and anatomical methods (e.g., morphometrics http://purl.obolibrary.org/obo/UBERON_0002061 UBERON http://purl.obolibrary.org/obo/GO_0048758 GO MRI/PET Non-invasive neuroimaging techniques to assess hippocampal volume using voxel-based morphometry. in_vivo hippocampus rodent hippocampal volume change low With this approach, volume of brain regions is measured by drawing ‘regions of interest’ on images from brain scans obtained from magnetic resonance imaging (MRI) or positron emission tomography (PET) scans calculating the volume enclosed http://purl.obolibrary.org/obo/UBERON_0002061 UBERON http://purl.obolibrary.org/obo/GO_0048758 GO Synaptogenesis assay kit Relies on immunostaining of cells with synaptic marker proteins such as MAP-2, PSD-95, and synaptophysin to assess synapse formation. in_vitro hippocampal primary cells hippocampus synapse formation not_specified http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/PR_000001756 PR medium There are commercially available ‘synaptogenesis assay kits’ that rely on the immunostaining of cells with common synaptic marker proteins such as MAP-2, PSD-95 and synaptophysin. http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0007416 GO Transmission electron microscopy (TEM) Assesses ultrastructural features of neurons, including synapse structure and dendritic spines. in_vivo hippocampus synapse ultrastructure not_specified http://purl.obolibrary.org/obo/OBI_0000219 OBI http://purl.obolibrary.org/obo/GO_0045202 GO low At the micro- and ultra- structural levels, changes in neuronal and glial morphology, alterations in synapse structure, dendritic spine formation (size, shape, number, distribution of head/neck ratios in hippocampal cultures or in vivo studies) and dendritic morphology (branching points, length etc..) can be assessed in Golgi-Cox impregnated neurons (Bongmbaa et al., 2011), two-photon microscopy (Ehrlich et al., 2007), transmission electron (TEM) and fluorescent microscopy (Runge et al., 2020; Pchitskaya et al., 2020). http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0007416 GO transmission electron microscopy (TEM) High-resolution microscopy used to observe ultra-structural changes in neurons, glia, and synapses. not_specified neurons glial cells hippocampus ultrastructural morphology change http://purl.obolibrary.org/obo/GO_0045224 GO low At the micro- and ultra- structural levels, changes in neuronal and glial morphology, alterations in synapse structure... can be assessed in... transmission electron (TEM) http://purl.obolibrary.org/obo/GO_0045224 GO http://purl.obolibrary.org/obo/GO_0045224 GO Two-photon microscopy Visualizes dendrites in GFP-transfected neurons and assesses dendritic spine dynamics. in_vivo GFP-transfected neurons hippocampus dendritic spine dynamics not_specified http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/OBI_0000245 OBI low Two-photon time-lapse images can be used to visualise dendrites in GFP-transfected neurons, whereas Golgi Stain is used to measure both dendrites and dendritic spines. http://purl.obolibrary.org/obo/GO_0030425 GO http://purl.obolibrary.org/obo/GO_0016358 GO Voxel-based morphometry (VBM) Measures hippocampal volume in living subjects using MRI or PET scans by drawing regions of interest. in_vivo hippocampus humans rodents hippocampal volume not_specified http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/OBI_0000211 OBI medium non-invasive, structural neuroimaging techniques in living subjects are also widely used in human studies to assess hippocampal volume using voxel-based morphometry (VBM). With this approach, volume of brain regions is measured by drawing ‘regions of interest’ on images from brain scans obtained from magnetic resonance imaging (MRI) or positron emission tomography (PET) scans calculating the volume enclosed (Mechelli et al., 2005). http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0007420 GO Electroencephalography (EEG) Measures electrical activity over many brain regions, primarily the cortex, using electrodes placed on the skull to assess brain function over time. in_vivo brain human electrical activity change high Synaptic function in the human hippocampus has been assessed using electroencephalography (EEG) and functional neuroimaging techniques EEG is a measure of electrical activity over many brain regions but primarily from the cortex using small flat metal discs (electrodes) placed over the surface of the skull. It is a readily available test that provides evidence of how the brain functions over time http://purl.obolibrary.org/obo/UBERON_0000955 UBERON Field potential recording Records electrical field potentials in hippocampal subregions (CA1 and dentate gyrus) to assess summed synaptic responses following direct stimulation of input pathways. in_vivo hippocampus field potential amplitude change http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0007268 GO low electrical field potentials recorded in two subregions of the hippocampus, area CA1 and dentate gyrus, have been assessed in vivo or in vitro Field potentials recorded in both regions of the hippocampus reflect the summed synaptic response of a population of neurons following direct stimulation of input pathways across a monosynaptic connection http://purl.obolibrary.org/obo/GO_0007268 GO Field Potential Recording Electrical field potentials are recorded in the hippocampal subregions CA1 and dentate gyrus to assess synaptic function. Changes in response amplitude due to chemical perturbations or stressors are measured in vivo, in vitro, or in hippocampal slices from treated animals. in_vivo hippocampus not_specified response amplitude change http://purl.obolibrary.org/obo/GO_0019226 GO http://purl.obolibrary.org/obo/UBERON_0001954 UBERON not_specified Field potentials recorded in both regions of the hippocampus reflect the summed synaptic response of a population of neurons following direct stimulation of input pathways across a monosynaptic connection. Changes in response amplitude due to chemical perturbations and other stressors (e.g., chemical exposures, nutritional deficits, gene knockouts) is evidence of altered synaptic function. http://purl.obolibrary.org/obo/CL_0000598 CL http://purl.obolibrary.org/obo/GO_0019226 GO Functional magnetic resonance imaging (fMRI) Uses MRI technology to measure brain activity by detecting changes in blood flow associated with neuronal activation. in_vivo brain human blood flow changes increase medium functional magnetic resonance imaging or functional MRI (fMRI) uses MRI technology to measure brain activity by detecting associated changes in blood flow. This technique relies on the fact that cerebral blood flow and neuronal activation are coupled http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0051965 GO I-O curve (input-output curve) The relationship between stimulus current strength (input) and evoked response amplitude (output) is plotted to measure excitatory synaptic transmission in the hippocampus. in_vitro hippocampus excitatory synaptic transmission change http://purl.obolibrary.org/obo/GO_0007268 GO http://purl.obolibrary.org/obo/UBERON_0001989 UBERON low Two measures, the excitatory postsynaptic potential (EPSP) and the population spike are derived from the compound field potential at increasing stimulus strengths The function described by the relationship of current strength (input, I) and evoked response (output, O), the I-O curve is the measure of excitatory synaptic transmission http://purl.obolibrary.org/obo/GO_0030282 GO http://purl.obolibrary.org/obo/GO_0007268 GO I-O curve measurement Measures excitatory synaptic transmission by deriving excitatory postsynaptic potential (EPSP) and population spike from compound field potentials at increasing stimulus strengths. in_vivo hippocampus I-O curve change http://purl.obolibrary.org/obo/GO_0035235 GO low The function described by the relationship of current strength (input, I) and evoked response (output, O), the I-O curve is the measure of excitatory synaptic transmission http://purl.obolibrary.org/obo/GO_0035235 GO Inhibitory Synaptic Transmission probe Assessment of inhibitory synaptic integrity using pairs of stimulus pulses delivered in close temporal proximity to observe suppression of the second pulse. in_vitro hippocampus degree of suppression to the 2nd pulse change http://purl.obolibrary.org/obo/GO_0048167 GO low Inhibitory Synaptic Transmission: Pairs of stimulus pulses delivered in close temporal proximity are used to probe the integrity of inhibitory synaptic transmission. An alteration in the degree of suppression to the 2nd pulse of the pair reflects altered inhibitory synaptic function http://purl.obolibrary.org/obo/GO_0044251 GO http://purl.obolibrary.org/obo/GO_0048167 GO Long-term potentiation (LTP) induction Assesses synaptic plasticity by delivering high-frequency stimulation trains to induce prolonged augmentation of synaptic response, measured by changes in EPSP and population spike amplitude. in_vivo hippocampus degree and duration of synaptic enhancement increase http://purl.obolibrary.org/obo/GO_0060073 GO low Synaptic plasticity in the form of LTP is assessed by delivering trains of high frequency stimulation to induce a prolonged augmentation of synaptic response. Probe stimuli at midrange stimulus strengths are delivered before and after application of LTP-inducing trains. The degree of increase in EPSP and PS amplitude to the probe stimulus after train application, and the duration of the induced synaptic enhancement are metrics of LTP http://purl.obolibrary.org/obo/GO_0060073 GO long-term potentiation (LTP) induction and measurement Trains of high-frequency stimulation are delivered to induce prolonged augmentation of synaptic response, and probe stimuli before and after are used to measure the degree of increase in EPSP and PS amplitude and duration of enhancement. in_vitro hippocampus synaptic plasticity (LTP) increase http://purl.obolibrary.org/obo/GO_0061313 GO http://purl.obolibrary.org/obo/GO_0042593 GO http://purl.obolibrary.org/obo/UBERON_0001989 UBERON low Synaptic plasticity in the form of LTP is assessed by delivering trains of high frequency stimulation to induce a prolonged augmentation of synaptic response Probe stimuli at midrange stimulus strengths are delivered before and after application of LTP-inducing trains The degree of increase in EPSP and PS amplitude to the probe stimulus after train application, and the duration of the induced synaptic enhancement are metrics of LTP http://purl.obolibrary.org/obo/GO_0030282 GO http://purl.obolibrary.org/obo/GO_0061313 GO LTP induction High frequency stimulation is used to induce long-term potentiation (LTP), and the degree of increase in EPSP and PS amplitude, and the duration of enhancement are measured as metrics of LTP. in_vitro hippocampus EPSP and PS amplitude increase http://purl.obolibrary.org/obo/GO_0007612 GO http://purl.obolibrary.org/obo/GO_0007611 GO low LTP represents, at the synapse and molecular level, the coincident firing of large numbers of neurons that are engaged during a learning event. The persistence of LTP emulates the duration of the memory. Synaptic plasticity in the form of LTP is assessed by delivering trains of high frequency stimulation to induce a prolonged augmentation of synaptic response. http://purl.obolibrary.org/obo/CL_0000279 CL http://purl.obolibrary.org/obo/GO_0007611 GO paired-pulse inhibition assay Pairs of stimulus pulses delivered in close temporal proximity (<30 msec) are used to probe inhibitory synaptic transmission by measuring suppression of the second pulse response. in_vitro hippocampus inhibitory synaptic transmission change http://purl.obolibrary.org/obo/GO_0007267 GO http://purl.obolibrary.org/obo/UBERON_0001989 UBERON low Pairs of stimulus pulses delivered in close temporal proximity are used to probe the integrity of inhibitory synaptic transmission The response evoked by the second pulse of the pair at brief intervals (<30 msec) arrives during the activation of feedback inhibitory loops in the hippocampus An alteration in the degree of suppression to the 2nd pulse of the pair reflects altered inhibitory synaptic function http://purl.obolibrary.org/obo/GO_0030282 GO http://purl.obolibrary.org/obo/GO_0007267 GO Patch clamp recording Measures excitatory and inhibitory synaptic currents (EPSCs and IPSCs) in single cells using intracellular and patch clamp techniques. ex_vivo hippocampal neurons hippocampus EPSCs and IPSCs change http://purl.obolibrary.org/obo/OBI_0001843 OBI low Excitatory and inhibitory synaptic currents (EPSCs and IPSCs) can also be measured in single cells, mostly ex vivo within slices of hippocampus using intracellular and patch clamp techniques as described in previous KEs http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0007268 GO Positron emission tomography (PET) Detects pairs of gamma rays emitted by a radionuclide tracer to measure blood flow and neuronal activation in the brain. in_vivo brain human blood flow increase http://purl.obolibrary.org/obo/OBI_0000275 OBI medium Positron emission tomography (PET) is a functional imaging technique that detects pairs of gamma rays emitted indirectly by a radionuclide (tracer) injected into the body Like fMRI, PET scans indirectly measure blood flow to different parts of the brain – the higher the blood flow, the greater the activation http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0051965 GO HPPD enzyme inhibition assay This assay measures the inhibition of 4-hydroxyphenyl-pyruvate dioxygenase (HPPD) enzyme activity. not_specified HPPD enzyme activity decrease http://purl.obolibrary.org/obo/GO_0050205 GO not_specified This key event commonly operates through HPPD inhibitors. http://purl.obolibrary.org/obo/GO_0050205 GO http://purl.obolibrary.org/obo/GO_0006571 GO alkaline phosphatase assay Measures cytotoxicity by detecting the release of alkaline phosphatase enzyme into the culture medium. in_vitro alkaline phosphatase release increase http://purl.obolibrary.org/obo/GO_0004036 GO http://purl.obolibrary.org/obo/GO_0008219 GO high alkaline phosphatase http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008219 GO cell count assay Measures cytotoxicity by quantifying the number of viable cells remaining in culture. in_vitro cell count decrease http://purl.obolibrary.org/obo/GO_0008219 GO high cell counts http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008219 GO dye exclusion assay Measures cytotoxicity by assessing the ability of cells to exclude certain dyes, such as trypan blue, which only enter dead or dying cells. in_vitro dye exclusion decrease http://purl.obolibrary.org/obo/GO_0008219 GO high dye exclusion assays http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008219 GO Histopathological evaluation Measures cytotoxicity in vivo by examining tissue samples under a microscope for signs of cell death and tissue damage. in_vivo not specified various organs not specified histopathological changes increase http://purl.obolibrary.org/obo/GO_0048732 GO http://purl.obolibrary.org/obo/GO_0016265 GO not_specified Cytotoxicity is measured in vivo by histopathological evaluation of tissue. The presence of dead cells and/or cellular debris is direct evidence of cytotoxicity at the time of tissue sampling. Histological evidence of previous cytotoxicity is reported as tissue degeneration and/or atrophy. http://purl.obolibrary.org/obo/UBERON_0000061 UBERON http://purl.obolibrary.org/obo/GO_0016265 GO histopathological evaluation Measures cytotoxicity in vivo by examining tissue sections for the presence of dead cells, cellular debris, tissue degeneration, or atrophy. in_vivo presence of dead cells or cellular debris increase http://purl.obolibrary.org/obo/GO_0008219 GO low Cytotoxicity is measured in vivo by histopathological evaluation of tissue. The presence of dead cells and/or cellular debris is direct evidence of cytotoxicity at the time of tissue sampling. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008219 GO histopathological evaluation Measures cytotoxicity in vivo by evaluating tissue samples for the presence of dead cells, cellular debris, degeneration, and atrophy. in_vivo tissue degeneration and atrophy increase http://purl.obolibrary.org/obo/GO_0002945 GO http://purl.obolibrary.org/obo/GO_0001904 GO low Cytotoxicity is measured in vivo by histopathological evaluation of tissue. The presence of dead cells and/or cellular debris is direct evidence of cytotoxicity at the time of tissue sampling. Histological evidence of previous cytotoxicity is reported as tissue degeneration and/or atrophy. http://purl.obolibrary.org/obo/UBERON_0000468 UBERON http://purl.obolibrary.org/obo/GO_0008219 GO LDH release assay Measures cytotoxicity by detecting the release of the intracellular enzyme lactate dehydrogenase into the culture medium. in_vitro lactate dehydrogenase release increase http://purl.obolibrary.org/obo/GO_0004457 GO http://purl.obolibrary.org/obo/GO_0008219 GO high the release of the intracellular enzyme lactate dehydrogenase http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008219 GO mitochondrial function assay Measures cytotoxicity by assessing mitochondrial activity, often using dyes like MTT or XTT. in_vitro mitochondrial function decrease http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0008219 GO high mitochondrial function http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0008219 GO cytotoxicity assay This key event measures cytotoxicity in club cells, potentially associated with Cyp2f2 bioactivation. The specific methodology is not detailed. not_specified club cells cytotoxicity increase http://purl.obolibrary.org/obo/GO_0000274 GO not_specified This key event can be associated with Cyp2f2 bioactivation. Increase, Cytotoxicity (club cells) http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0008219 GO Hematoxylin and Eosin staining Histological staining method to visualize cellular and architectural changes in tissue sections. ex_vivo endometrium rat mouse cellular and architectural changes change http://purl.obolibrary.org/obo/GO_0000278 GO medium Hematoxylin and Eosin staining to visualize the cellular and architectural changes indicative of hyperplasia. http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0008283 GO Immunohistochemistry Staining method using specific antibodies to identify and localize abnormal or increased levels of proteins in tissue sections. ex_vivo endometrium rat mouse protein levels increase http://purl.obolibrary.org/obo/GO_0010485 GO medium Immunohistochemistry staining by using specific antibodies to identify abnormal or increased levels of certain proteins. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0019521 GO Morphometry Quantitative analysis of tissue features, such as cell number, size, and distribution. ex_vivo endometrium rat mouse tissue features change http://purl.obolibrary.org/obo/OBI_0000340 OBI http://purl.obolibrary.org/obo/GO_0048856 GO medium Morphometry to conduct quantitative analysis of tissue features. http://purl.obolibrary.org/obo/UBERON_0001295 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO Uterotrophic Bioassay A short-term screening test for oestrogenic properties in rodents, assessing uterine weight and histological changes. in_vivo uterus rat mouse uterine weight and histological changes increase OECD TG 440 low OECD (2007), Test No. 440: Uterotrophic Bioassay in Rodents: A short-term screening test for oestrogenic properties http://purl.obolibrary.org/obo/UBERON_0002357 UBERON http://purl.obolibrary.org/obo/GO_0030521 GO cytotoxicity assay Measures cytotoxicity in epithelial cells, often associated with gavaged administration. in_vivo epithelial cells cytotoxicity increase not_specified This key event is often associated with gavaged administration. cytotoxicity assay This key event measures cytotoxicity in tubular epithelial cells, potentially mediated by Cyp2e1-mediated bioactivation. The specific methodology is not detailed. not_specified tubular epithelial cells kidney cytotoxicity increase http://purl.obolibrary.org/obo/GO_0000274 GO not_specified This key event can be associated with Cyp2e1-mediated bioactivation. Increase, Cytotoxicity (tubular epithelial cells) http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0008219 GO Cytotoxicity assay This assay measures cytotoxicity in hepatocytes, which is mediated by Nrf2-related genes. not_specified hepatocytes cytotoxicity increase http://purl.obolibrary.org/obo/CL_0000084 CL not_specified This key event is mediated by Nrf2-related genes. http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0008219 GO Nrf2 gene expression This key event is mediated by Nrf2-related genes. This suggests an assay measuring the expression levels of genes regulated by the Nrf2 pathway, indicating a cellular response to stress or toxicity. not_specified liver Nrf2-related gene expression increase not_specified This key event is mediated by Nrf2-related genes. http://purl.obolibrary.org/obo/GO_0003459 GO ATG_SREBF1_CIS_up assay Measures transcriptional control of HMG-CoA reductase by assessing the activity of Sterol Regulatory Element-Binding Factor 1 (SREBF1). in_vitro SREBF1 transcriptional activity increase http://purl.obolibrary.org/obo/GO_0045449 GO high The ToxCast assay ATG_SREBF1_CIS_up is one method of measuring transcriptional control of HMG-CoA reductase. http://purl.obolibrary.org/obo/PR_000008376 PR http://purl.obolibrary.org/obo/GO_0045449 GO HMG-CoA reductase activity assay This assay measures the activity of HMG-CoA reductase by quantifying the decrease in absorbance at 340 nm, which corresponds to NADPH oxidation by the HMGR catalytic subunit in the presence of HMG-CoA. in_vitro absorbance at 340 nm decrease medium The activity of HMG-CoA reductase inhibition may be measured by a commercially available kit which measures a decrease in absorbance at 340 nm, which represents the oxidation of NADPH by the catalytic subunit of HMGR in the presence of the substrate HMG-CoA. HMG-CoA reductase activity assay Measures the activity of HMG-CoA reductase by detecting the oxidation of NADPH, indicated by a decrease in absorbance at 340 nm. in_vitro HMG-CoA reductase activity decrease http://purl.obolibrary.org/obo/GO_0004420 GO medium The activity of HMG-CoA reductase inhibition may be measured by a commercially available kit which measures a decrease in absorbance at 340 nm, which represents the oxidation of NADPH by the catalytic subunit of HMGR in the presence of the substrate HMG-CoA. http://purl.obolibrary.org/obo/PR_000000840 PR http://purl.obolibrary.org/obo/GO_0006695 GO ToxCast ATG_SREBF1_CIS_up A ToxCast assay used to measure the transcriptional control of HMG-CoA reductase via Sterol Regulatory element-binding factor 1 (SREBF1). in_vitro transcriptional control of HMG-CoA reductase not_specified high The ToxCast assay ATG_SREBF1_CIS_up is one method of measuring transcriptional control of HMG-CoA reductase. Abell-Kendall technique Standard chemical method for measuring plasma cholesterol in humans. in_vitro plasma Homo sapiens plasma cholesterol level decrease http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/UBERON_0000178 UBERON medium Plasma cholesterol is a common clinical measurement in humans and the Abell-Kendall technique is the standard chemical determination method http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/GO_0042632 GO Colorimetric cholesterol assay Measures total cholesterol, including cholesteryl esters, using colorimetric detection. in_vitro total cholesterol level decrease http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI high Commerical assay kits are available for measuring cholesterol using either colorimetric or fluorometric detection. Total cholesterol assay kits often include cholesteryl esters in the measurement http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/GO_0042632 GO Lipoprotein cholesterol assay Measures cholesterol levels in different lipoprotein complexes. in_vitro lipoprotein cholesterol level decrease http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/PR_000001288 PR high Additional kits are availalbe for measuring the cholesterol in the different lipoprotein complexes http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/GO_0042158 GO Oil Red O staining Stains triglycerides and lipids in organisms such as zebrafish larvae. It is useful for clear organisms. in_vivo larva zebrafish lipid accumulation change http://purl.obolibrary.org/obo/CHEBI_3607 CHEBI http://purl.obolibrary.org/obo/GO_0008108 GO low Oil Red O staining can be used for organisms such as zebrafish larvae that are clear, however it stains triglycerides and lipids not just cholesterol (Zhou et al., 2015). http://purl.obolibrary.org/obo/CL_0000272 CL Oil Red O staining Stains triglycerides and lipids in clear organisms such as zebrafish larvae, but not specific to cholesterol. in_vivo Danio rerio lipid content not_specified http://purl.obolibrary.org/obo/CHEBI_18288 CHEBI http://purl.obolibrary.org/obo/CHEBI_16546 CHEBI medium Oil Red O staining can be used for organisms such as zebrafish larvae that are clear, however it stains triglycerides and lipids not just cholesterol Oil Red O staining A staining method used to visualize lipids, though it is not specific to cholesterol and also stains triglycerides. ex_vivo zebrafish triglycerides and lipids not_specified not_specified Oil Red O staining can be used for organisms such as zebrafish larvae that are clear, however it stains triglycerides and lipids not just cholesterol BUN/creatinine assay Measures blood urea nitrogen (BUN) and creatinine levels in serum to assess kidney dysfunction using commercial reagents. in_vivo kidney rat BUN and creatinine levels increase medium Kidney Dysfunction Assay Measuring BUN and creatinine serum blood levels (Shaki et al., 2012) Blood urea nitrogen (BUN) and creatinine, marker of kidney dysfunction, were determined by commercial reagents (obtained from Parsazmoon Co., Iran). http://purl.obolibrary.org/obo/UBERON_0000957 UBERON http://purl.obolibrary.org/obo/GO_0003027 GO Coomassie blue G250 binding method Determines total urinary protein concentration using the Coomassie blue G250 binding method. ex_vivo kidney total urinary protein not_specified not_specified Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. ELISA for beta-2-MG Quantifies urinary β2-MG using a solid phase enzyme-linked immunosorbent assay (ELISA) with monoclonal antibodies and colorimetric detection. ex_vivo kidney urinary β2-MG levels not_specified not_specified Urinary β2-MG was measured by using Enzygnost β2-MG Micro Kit (Behring Institute, Mannheim, Germany). Its method used the principle of solid phase enzyme-linked immunosorbent assay (ELISA). color intensities were measured with a wavelength of 450 nm by using a spectrophotometer Jaffé method Measures urinary creatinine using the Jaffé method. ex_vivo kidney urinary creatinine not_specified not_specified Serum and urinary creatinine (Creat-U) were measured by the methods of Heinegard and Tiderström (1973), and Jaffé, respectively (Henry, 1965). Kidney Dysfunction Assay Measures blood urea nitrogen (BUN) and creatinine serum blood levels in rats. in_vivo kidney rat blood urea nitrogen and creatinine serum levels increase http://purl.obolibrary.org/obo/CHEBI_16688 CHEBI medium Measuring BUN and creatinine serum blood levels Blood urea nitrogen (BUN) and creatinine, marker of kidney dysfunction, were determined by commercial reagents (obtained from Parsazmoon Co., Iran). http://purl.obolibrary.org/obo/UBERON_0002113 UBERON http://purl.obolibrary.org/obo/GO_0003014 GO Kidney Function Assay Quantifies multiple urinary and serum biomarkers of kidney function including total protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border antigens, NAG activity, and creatinine using immunoassays, colorimetric kits, and binding methods. in_vivo kidney urinary and serum kidney biomarkers change medium Measuring total urinary protein, albumin, transferrin, b2-microglobulin, retinolbinding protein, brush border tubular antigens, N-acetyl-b-Dglucosaminidase activity, serum and urinary creatine Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. Albumin (Alb-U), transferrin (Transf-U), β2-microglobulin (β2m-U), and retinolbinding protein (RBP-U) in urine were quantified by latex immunoassay (Bernard & Lauwerys, 1983). The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies (Mutti et al., 1985). The total activity of N-acetyl-β-Dglucosaminidase (NAG-T-U) in urine was determined colorimetrically using a kit (PPR Diagnostics Ltd.) as described elsewhere (Price et al., 1996). Serum and urinary creatinine (Creat-U) were measured by the methods of Heinegard and Tiderström (1973), and Jaffé, respectively (Henry, 1965). http://purl.obolibrary.org/obo/UBERON_0002113 UBERON Kidney Function Assay Measures total urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, and serum and urinary creatinine. in_vivo kidney human urinary protein, albumin, transferrin, β2-microglobulin, retinol-binding protein, brush border tubular antigens, N-acetyl-β-D-glucosaminidase activity, serum and urinary creatinine not_specified http://purl.obolibrary.org/obo/PR_000001417 PR http://purl.obolibrary.org/obo/PR_000000048 PR http://purl.obolibrary.org/obo/PR_000001001 PR http://purl.obolibrary.org/obo/GO_0004568 GO medium Measuring total urinary protein, albumin, transferrin, b2-microglobulin, retinolbinding protein, brush border tubular antigens, N-acetyl-b-Dglucosaminidase activity, serum and urinary creatine Total urinary protein (Prot-T-U) was determined by the Coomassie blue G250 binding method. Albumin (Alb-U), transferrin (Transf-U), β2-microglobulin (β2m-U), and retinolbinding protein (RBP-U) in urine were quantified by latex immunoassay (Bernard & Lauwerys, 1983). The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies (Mutti et al., 1985). The total activity of N-acetyl-β-Dglucosaminidase (NAG-T-U) in urine was determined colorimetrically using a kit (PPR Diagnostics Ltd.) as described elsewhere (Price et al., 1996). http://purl.obolibrary.org/obo/UBERON_0002113 UBERON http://purl.obolibrary.org/obo/GO_0003014 GO latex immunoassay Quantifies albumin, transferrin, β2-microglobulin, and retinol-binding protein in urine using latex immunoassay. ex_vivo kidney albumin, transferrin, β2-microglobulin, and retinol-binding protein levels not_specified not_specified Albumin (Alb-U), transferrin (Transf-U), β2-microglobulin (β2m-U), and retinolbinding protein (RBP-U) in urine were quantified by latex immunoassay (Bernard & Lauwerys, 1983). NAG Assay Measures N-acetyl-β-D-glucosaminidase urinary content using a colorimetric kit. in_vivo kidney human urinary N-acetyl-β-D-glucosaminidase activity not_specified http://purl.obolibrary.org/obo/GO_0004568 GO high Measuring N-acetyl-b-D-Glucosaminidase urinary content Urinary NAG activity was measured by using NAG Quantitative Kit (Shionogi, Osaka, Japan). http://purl.obolibrary.org/obo/UBERON_0002113 UBERON http://purl.obolibrary.org/obo/GO_0003014 GO sandwich enzyme-linked immunoassay Analyzes brush border tubular antigens (BBA-U) using a sandwich enzyme-linked immunoassay with monoclonal antibodies. ex_vivo kidney brush border tubular antigens not_specified not_specified The brush border tubular antigens (BBA-U) were analyzed by a sandwich enzyme-linked immunoassay using monoclonal antibodies (Mutti et al., 1985). IL-18 induction assay Measures IL-18 induction in human keratinocytes (cell line NCTC 2544) to identify allergens. in_vitro NCTC 2544 human IL-18 induction increase http://purl.obolibrary.org/obo/GO_0032609 GO medium In vitro assays based on IL-18 induction in human keratinocytes (cell line NCTC 2544) have also been developed to identify allergens http://purl.obolibrary.org/obo/PR_000001489 PR http://purl.obolibrary.org/obo/GO_0006954 GO IL-8 induction assay Measures IL-8 induction in THP-1 cells to identify allergens. in_vitro THP-1 human IL-8 induction increase http://purl.obolibrary.org/obo/GO_0001817 GO medium In vitro assays based on IL-18 induction in human keratinocytes (cell line NCTC 2544) or IL-8 induction in THP-1 cells have also been developed to identify allergens http://purl.obolibrary.org/obo/PR_000001011 PR http://purl.obolibrary.org/obo/GO_0006954 GO KeratinoSens Uses a luciferase reporter gene under control of a single copy of the ARE element of the human AKR1C2 gene stably inserted into immortalized human keratinocytes (HaCaT cells) to measure activation of the antioxidant/electrophile response element (ARE)-dependent pathway. in_vitro HaCaT cells human luciferase activity increase http://purl.obolibrary.org/obo/GO_0032018 GO http://purl.obolibrary.org/obo/GO_0004505 GO OECD TG 442D medium OECD TG 442D is the validated test guideline for measuring the activation of the antioxidant/electrophile response element (ARE) - dependant pathway The KeratinoSensTM protocol can be found in the EURL ECVAM Database Service on Alternative Methods to animal experimentation (DB-ALM): Protocol No155 for KeratinoSensTM http://purl.obolibrary.org/obo/GO_0032018 GO http://purl.obolibrary.org/obo/GO_0034599 GO KeratinoSens™ An in vitro luciferase reporter assay that measures the activation of the antioxidant/electrophile response element (ARE)-dependent pathway using immortalized human keratinocytes stably transfected with a luciferase reporter gene controlled by the ARE element of the human AKR1C2 gene. in_vitro HaCaT cells immortalized human keratinocytes human luciferase reporter activity indicating ARE pathway activation increase OECD TG 442D not_specified Currently, the only in vitro ARE-Nrf2 luciferase test method covered by this Test Guideline is the KeratinoSensTM. This assay uses a luciferase reporter gene under control of a single copy of the ARE element of the human AKR1C2 gene stably inserted into immortalized human keratinocytes (HaCaT cells) OECD TG 442D is the validated test guideline for measuring the activation of the antioxidant/electrophile response element (ARE) - dependant pathway qPCR for Keap1/Nrf2/ARE/EpRE pathway genes Quantitative real-time polymerase chain reaction measurements of the relative abundance of mRNA for genes whose expression is controlled by the Keap1/Nrf2/ARE/EpRE pathway. in_vitro mRNA abundance change http://purl.obolibrary.org/obo/GO_0006397 GO medium This work includes quantitative realtime polymerase chain reaction measurements of the relative abundance of mRNA for eleven selected genes whose expression is controlled by one of the three following pathways: Keap1/Nrf 2/ARE/EpRE, ARNT/AhR/XRE, and Nrf1/MTF/MRE http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0045449 GO qRT-PCR This assay measures the relative abundance of mRNA for eleven selected genes whose expression is controlled by the Keap1/Nrf 2/ARE/EpRE, ARNT/AhR/XRE, and Nrf1/MTF/MRE pathways using quantitative realtime polymerase chain reaction. in_vitro mRNA abundance change medium This work includes quantitative realtime polymerase chain reaction measurements of the relative abundance of mRNA for eleven selected genes whose expression is controlled by one of the three following pathways: Keap1/Nrf 2/ARE/EpRE, ARNT/AhR/XRE, and Nrf1/MTF/MRE. The Keap1/Nrf2/ARE/EpRE cell signalling assay is also the mechanistic basis for the work on skin sensitisation chemicals at CeeTox Inc. http://purl.obolibrary.org/obo/GO_0010468 GO guinea-pig occluded patch test An in vivo assay using guinea pigs to assess skin sensitisation potential of chemicals via occluded patch exposure. in_vivo skin guinea pig skin sensitisation response change low among these in vivo assays are the guinea-pig occluded patch test http://purl.obolibrary.org/obo/UBERON_0002097 UBERON http://purl.obolibrary.org/obo/GO_0006955 GO HRIPT The Human Repeat Insult Patch Test (HRIPT) is used for human sensitisation testing. in_vivo skin human sensitisation change low Human sensitisation testing is conducted with the Human Repeat Insult Patch Test (HRIPT), as described by McNamee et al. http://purl.obolibrary.org/obo/UBERON_0000175 UBERON http://purl.obolibrary.org/obo/GO_0002732 GO Human Repeat Insult Patch Test A human patch test used to assess skin sensitisation potential by repeated exposure to a substance. in_vivo skin human skin sensitisation response change low Human sensitisation testing is conducted with the Human Repeat Insult Patch Test (HRIPT) http://purl.obolibrary.org/obo/UBERON_0002097 UBERON http://purl.obolibrary.org/obo/GO_0006955 GO LLNA The murine Local Lymph Node Assay (LLNA) is an in vivo assay used to assess the sensitisation potential of chemicals and group sensitisers into potency groups. in_vivo lymph node mouse sensitisation potential and potency change medium and the murine Local Lymph Node Assay Using LLNA data, sensitisers can be grouped into potency groups (e.g. extreme, strong, moderate, weak and non-sensitisers). http://purl.obolibrary.org/obo/UBERON_0001184 UBERON http://purl.obolibrary.org/obo/GO_0002732 GO Magnusson-Kligman guinea pig maximization test An in vivo assay using guinea pigs to evaluate skin sensitisation potential through maximization exposure protocols. in_vivo skin guinea pig skin sensitisation response change low the Magnusson-Kligman guinea pig maximization test http://purl.obolibrary.org/obo/UBERON_0002097 UBERON http://purl.obolibrary.org/obo/GO_0006955 GO murine Local Lymph Node Assay An in vivo assay using mice to assess skin sensitisation potential by measuring lymph node cell proliferation. in_vivo lymph node skin mouse lymph node cell proliferation increase OECD TG 429 medium the murine Local Lymph Node Assay Using LLNA data, sensitisers can be grouped into potency groups http://purl.obolibrary.org/obo/UBERON_0000029 UBERON http://purl.obolibrary.org/obo/GO_0046649 GO murine Local Lymph Node Assay An in vivo assay measuring cell proliferation in the draining lymph nodes of mice to assess skin sensitisation potency. in_vivo lymphocytes lymph nodes skin murine sensitisation potency not_specified http://purl.obolibrary.org/obo/DOID_0051013 DOID medium the murine Local Lymph Node Assay Using LLNA data, sensitisers can be grouped into potency groups http://purl.obolibrary.org/obo/UBERON_0000651 UBERON http://purl.obolibrary.org/obo/GO_0002376 GO skin biopsy Skin biopsy is used to confirm the diagnosis of sensitisation and exclude other disorders. in_vivo skin human diagnosis of sensitisation change low Skin biopsy may help to confirm the diagnosis and exclude other disorders. http://purl.obolibrary.org/obo/UBERON_0000175 UBERON http://purl.obolibrary.org/obo/GO_0002732 GO skin biopsy A diagnostic procedure to confirm skin sensitisation and exclude other disorders by examining tissue samples. in_vivo skin human histopathological changes change low Skin biopsy may help to confirm the diagnosis and exclude other disorders http://purl.obolibrary.org/obo/UBERON_0002097 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO Spectrophotofluorimetry Measures uroporphyrin fluorescence as an indicator of uroporphyrinogen oxidation (UROX) when exposed to UV light. in_vitro avian mammalian uroporphyrin fluorescence increase medium Porphyrins fluoresce red when exposed to UV light; therefore, uroporphyrinogen oxidation (UROX) can be directly measured as uropororphyrin fluorescence in a spectrophotofluorimeter. http://purl.obolibrary.org/obo/CHEBI_58023 CHEBI http://purl.obolibrary.org/obo/GO_0055114 GO Uroporphyrinogen Oxidation (UROX) Spectrofluorimetry This assay measures the oxidation of uroporphyrinogen by quantifying the fluorescence of uroporphyrinogen in a spectrophotofluorimeter after exposure to UV light. The increase in fluorescence indicates the degree of oxidation. in_vitro liver avian mammalian uroporphyrinogen fluorescence increase low Porphyrins fluoresce red when exposed to UV light; therefore, uroporphyrinogen oxidation (UROX) can be directly measured as uropororphyrin fluorescence in a spectrophotofluorimeter. UROX has been measured spectrofluorimetrically in avian[3] and mammalian[4] species. http://purl.obolibrary.org/obo/CHEBI_17234 CHEBI http://purl.obolibrary.org/obo/GO_0055114 GO Reverse-phase HPLC assay An assay using reverse-phase HPLC with liver homogenate as the enzyme source and uroporphyrinogen III or pentacarboxyporphyrinogen I as substrates. in_vitro liver metabolite quantification decrease not_specified Another method based on reverse-phase HPLC was developed This assay system uses either uroporphyrinogen III or pentacarboxyporphyrinogen I as substrate and liver homogenate in sucrose treated with a suspension of cellulose phosphate as enzyme source. http://purl.obolibrary.org/obo/GO_0008463 GO UROD enzyme assay This assay measures the activity of UROD by co-incubating uroporphyrinogen with the enzyme under standardized conditions, stopping the reaction, esterifying products, and quantifying porphyrin esters using high performance liquid chromatography. in_vitro liver quantification of porphyrin esters not_specified medium Once uroporphyrinogen is synthesized it is co-incubated with UROD under standardized conditions. reaction products and un-metabolized substrate are esterified, and the porphyrin esters are separated and quantified using high performance liquid chromatography This enzyme assay classically utilizes milliliter quantities but has been modified to a microassay, minimizing cost and enhancing sensitivity http://purl.obolibrary.org/obo/GO_0009055 GO UROD enzyme assay with HPLC Measures UROD activity by co-incubating uroporphyrinogen with UROD, esterifying the products, and quantifying porphyrin esters using high performance liquid chromatography. in_vitro UROD activity decrease http://purl.obolibrary.org/obo/GO_0004852 GO medium Once uroporphyrinogen is synthesized it is co-incubated with UROD under standardized conditions. The reaction is then stopped, reaction products and un-metabolized substrate are esterified, and the porphyrin esters are separated and quantified using high performance liquid chromatography This enzyme assay classically utilizes milliliter quantities but has been modified to a microassay, minimizing cost and enhancing sensitivity http://purl.obolibrary.org/obo/GO_0004852 GO http://purl.obolibrary.org/obo/GO_0042168 GO HPLC with fluorescence detection Determines hepatic and urinary/fecal porphyrin patterns using high-performance liquid chromatography with fluorescence detection. not_specified liver urine feces porphyrin levels not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI not_specified The hepatic and urinary/fecal porphyrin patters can be determined using a high-performance liquid chromatograph equipped with a fluorescence detector. Kennedy et al. [3] describe the method for tissue extraction and porphyrin quantification in detail, which is rapid and highly sensitive. http://purl.obolibrary.org/obo/CHEBI_26701 CHEBI http://purl.obolibrary.org/obo/GO_0006778 GO EROD Ethoxyresorufin O-demethylation (EROD) measures CYP1A2 activity via O-demethylation of ethoxyresorufin, often used in ratio with MROD to improve specificity. in_vitro CYP1A2 enzyme activity via ethoxyresorufin O-demethylation change not_specified suggest that a ratio of MROD to ethoxyresorufin O-demethylation (EROD) is a better measure of CYP1A2 activity due to the contribution of CYP1A1 to MROD. LC/MS-MS Evaluates the identity and abundance of CYP1A2 product using HPLC coupled with mass spectrometry in human hepatic in vitro systems. in_vitro HepaRG® human primary hepatocytes liver human CYP1A2 product abundance increase medium Cryopreserved human HepaRG® or cryopreserved human primary hepatocytes are incubated in presence of a potential CYP1A2 inducer and the identity and abundance of CYP1A2 product is evaluated using analytical HPLC (High Performance Liquid Chromatography) coupled with mass spectrometry (MS) http://purl.obolibrary.org/obo/GO_0006805 GO Luciferase reporter gene (LRG) assay Measures AHR1-mediated transactivation of target genes, specifically CYP1A4/5 induction, using transfected cell lines. in_vitro AHR1-mediated transactivation increase high An LRG assay can be used to measure AHR1-mediated transactivation of a target gene. This assay is particularly useful as it can measures CYP1A4/5 induction exclusively caused by activation of the AHR This has been demonstrated to be an efficient high throughput method in various avian and mammalian studies http://purl.obolibrary.org/obo/GO_0006351 GO Methoxyresorufin O-demethylation (MROD) Measures Cyp1A2/5 activity as a function of metabolite formation using fluorometric techniques. in_vitro CYP1A2/5 enzyme activity increase medium Methoxyresorufin O-demethylation (MROD) is a classic marker of Cyp1A2/5 activity and is often used due to the ease of fluorometric techniques http://purl.obolibrary.org/obo/GO_0006805 GO MROD MROD (Methoxyresorufin O-demethylation) measures CYP1A activity as a function of metabolite formation using fluorometric techniques. It is a classic marker of Cyp1A2/5 activity. in_vitro liver metabolite formation increase http://purl.obolibrary.org/obo/GO_0009265 GO medium Methoxyresorufin O-demethylation (MROD) is a classic marker of Cyp1A2/5 activity and is often used due to the ease of fluorometric techniques http://purl.obolibrary.org/obo/GO_0009265 GO QPCR Quantitative polymerase chain reaction (QPCR) measures the levels of CYP1A2/5 messenger RNA by monitoring the amplification of a targeted gene during PCR as accumulative fluorescence. in_vitro mRNA levels increase http://purl.obolibrary.org/obo/GO_0006925 GO high Levels of CYP1A2/5 messenger RNA can be measured using QPCR. This technique monitors the amplification of a targeted gene during PCR as accumulative fluorescence QPCR has high throughput capability and a low detection limit relative to other methods. http://purl.obolibrary.org/obo/GO_0006925 GO Quantitative polymerase chain reaction (QPCR) Measures levels of CYP1A2/5 messenger RNA using fluorescent probes during PCR amplification. in_vitro CYP1A2/5 mRNA levels increase high Levels of CYP1A2/5 messenger RNA can be measured using QPCR. This technique monitors the amplification of a targeted gene during PCR as accumulative fluorescence QPCR has high throughput capability and a low detection limit relative to other methods http://purl.obolibrary.org/obo/GO_0010467 GO calcium imaging Calcium imaging uses fluorescent calcium indicators to measure transient changes in intracellular calcium concentration, reflecting neuronal depolarization and activity. not_specified neuronal tissue intracellular calcium concentration changes (fluorescent signal) in neurons not_specified not_specified Calcium imaging experiments is the most common way to detect the depolarizing action of neurons, as this is correlated with a transient increase in intracellular calcium (Voigt et al., 2001). Calcium imaging Detects depolarizing action of neurons by measuring transient increases in intracellular calcium, often using GABA agonists like muscimol. in_vitro neurons brain intracellular calcium levels increase http://purl.obolibrary.org/obo/OBI_0001851 OBI http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0051899 GO medium Calcium imaging experiments is the most common way to detect the depolarizing action of neurons, as this is correlated with a transient increase in intracellular calcium (Voigt et al., 2001). The local application of GABA agonist, muscimol, during the calcium imaging has been used the last decades in order to investigate the developmental effects of GABA in the post-synaptic neurons (Owens et al., 1996; Gangulu et al., 2001; Baltz et al., 2010; Westerholz et al., 2013). http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0051899 GO ELISA Protein levels on interneurons are measured using commercial antibody sandwich ELISA kits. in_vitro interneurons protein levels decrease medium Protein levels on interneurons can be measured by commercial available antibody sandwich ELISA kits http://purl.obolibrary.org/obo/GO_0005576 GO http://purl.obolibrary.org/obo/GO_0006454 GO ELISA Measures protein levels of GABAergic interneuron markers using antibody sandwich ELISA kits. in_vitro brain protein levels of GABAergic interneuron markers decrease http://purl.obolibrary.org/obo/PR_000001469 PR http://purl.obolibrary.org/obo/PR_000008181 PR high Protein levels on interneurons can be measured by commercial available antibody sandwich ELISA kits, Western blotting, immunohistochemistry and immunofluorescence http://purl.obolibrary.org/obo/CL_0000687 CL http://purl.obolibrary.org/obo/GO_0010457 GO immunofluorescence Immunofluorescence staining to measure protein levels of GABAergic markers on interneurons. not_specified GABAergic interneurons brain not_specified Protein expression level of GABAergic markers decrease http://www.bioassayontology.org/bao#BAO_0000050 BAO http://purl.obolibrary.org/obo/CL_0000101 CL http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI low Protein levels on interneurons can be measured by ... immunofluorescence http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0003018 GO immunofluorescence Measurement of protein levels on interneurons via fluorescence microscopy. in_vitro interneurons protein levels not_specified low Protein levels on interneurons can be measured by [...] immunofluorescence Immunohistochemistry Identifies GABAergic interneurons using antibodies against parvalbumin (PV), GABA, or GAD, followed by morphometric analysis. in_vitro brain presence and morphology of GABAergic interneurons decrease http://purl.obolibrary.org/obo/CL_0000687 CL http://purl.obolibrary.org/obo/PR_000001469 PR http://purl.obolibrary.org/obo/OBI_0000385 OBI medium Parvalbumin (PV) is a marker of GABAergic interneurons that can be identified by immunohistochemistry. GABA or GAD can be used for identification and morphometric analysis of the GABAergic neuronal population (Voigt et al., 2001; De Lima et al., 2007), with the use of anti-GABA antibodies. http://purl.obolibrary.org/obo/CL_0000687 CL http://purl.obolibrary.org/obo/GO_0007399 GO RT-PCR mRNA levels can be measured with RT-PCR. in_vitro mRNA levels decrease http://purl.obolibrary.org/obo/OBI_0000706 OBI medium mRNA levels is possible to be measured with RT-PCR. http://purl.obolibrary.org/obo/GO_0000278 GO http://purl.obolibrary.org/obo/GO_0010468 GO RT-PCR Measures mRNA levels of GABAergic interneuron markers such as parvalbumin or GAD. in_vitro brain mRNA levels of GABAergic interneuron markers decrease http://purl.obolibrary.org/obo/OBI_0000272 OBI medium mRNA levels is possible to be measured with RT-PCR. http://purl.obolibrary.org/obo/CL_0000687 CL http://purl.obolibrary.org/obo/GO_0010467 GO western blot Protein levels on interneurons can be measured by Western blotting. in_vitro interneurons protein levels decrease http://purl.obolibrary.org/obo/OBI_0000268 OBI low Protein levels on interneurons can be measured by commercial available antibody sandwich ELISA kits, Western blotting http://purl.obolibrary.org/obo/GO_0005576 GO http://purl.obolibrary.org/obo/GO_0006454 GO Western blotting Measures protein levels of GABAergic interneuron markers such as parvalbumin or GAD using antibody-based detection. in_vitro brain protein levels of GABAergic interneuron markers decrease http://purl.obolibrary.org/obo/PR_000001469 PR http://purl.obolibrary.org/obo/PR_000008181 PR medium Protein levels on interneurons can be measured by commercial available antibody sandwich ELISA kits, Western blotting, immunohistochemistry and immunofluorescence http://purl.obolibrary.org/obo/CL_0000687 CL http://purl.obolibrary.org/obo/GO_0010457 GO apoptosis inhibition assay Inhibition of apoptosis in primary rat hepatocytes is measured through phosphorylation and inactivation of p53 and modulation of Mdm2, Tfgb1/4, and AGR2, requiring protein synthesis. in_vitro primary rat hepatocytes liver rat apoptosis inhibition decrease http://purl.obolibrary.org/obo/GO_0012501 GO http://purl.obolibrary.org/obo/GO_0008219 GO medium Inhibition of apoptosis in primary rat hepatocytes was mediated through phosphorylation and inactivation of p53 and modulation of Mdm2, Tfgb1/4, and AGR2; in addition, inhibition of apoptosis required protein synthesis (Ambolet-Camoit et al., 2010; Chopra and Schrenk, 2011; Chopra et al., 2009, 2010; Davis et al., 2001; Franc et al., 2008; Paajarvi et al., 2005; Worner and Schrenk, 1996, 1998). http://purl.obolibrary.org/obo/CL_0000187 CL http://purl.obolibrary.org/obo/GO_0012501 GO initiation-promotion studies These studies provide indirect evidence of inhibition of intrafocal apoptosis and direct evidence of a threshold for the clonal expansion of altered hepatic foci. in_vivo liver rat clonal expansion of altered hepatic foci increase http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low initiation-promotion studies provide indirect evidence of inhibition of intrafocal apoptosis due to sustained AHR activation and direct evidence of a threshold for the clonal expansion of altered hepatic foci AHR activators inhibit apoptosis produced by UV light exposure of human cell lines and rat primary hepatocytes http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0006915 GO quantitative stereology A stereological method used to quantify the growth of altered hepatic foci (AHF). not_specified liver growth of AHF change http://purl.obolibrary.org/obo/GO_0051012 GO not_specified Quantitative stereology is used to quantify the growth of AHF and such studies provide a measure of this KE http://purl.obolibrary.org/obo/GO_0008283 GO quantitative stereology This method quantifies the growth of altered hepatic foci (AHF) by measuring their size and volume fraction. in_vivo liver rat growth of altered hepatic foci increase http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008284 GO low Quantitative stereology is used to quantify the growth of AHF and such studies provide a measure of this KE http://purl.obolibrary.org/obo/GO_0008284 GO UV light exposure assay This assay measures the inhibition of apoptosis in human cell lines and rat primary hepatocytes exposed to UV light. in_vitro human cell lines rat primary hepatocytes liver human rat apoptosis inhibition decrease http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/CL_0000066 CL medium AHR activators inhibit apoptosis produced by UV light exposure of human cell lines and rat primary hepatocytes http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0006915 GO histopathology Measures bile duct hyperplasia and oval cell hyperplasia using frequency of occurrence and a severity index. in_vivo bile duct liver frequency of occurrence and severity index of hyperplasia increase low Bile duct hyperplasia and oval cell hyperplasia are measured histopathological observations using frequency of occurrence and a severity index. http://purl.obolibrary.org/obo/UBERON_0002356 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO histopathological examination This assay involves the microscopic examination of tissue samples to detect tumors. in_vivo liver tumor presence not_specified http://purl.obolibrary.org/obo/UBERON_0002100 UBERON low Histopathological examination is a necessary part of lifetime cancer bioassays. This type of examination is used to detect tumors. http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0001660 GO histopathology Histopathological examination is used to detect tumors through microscopic examination of tissue samples. in_vivo liver bile duct tumor formation increase http://purl.obolibrary.org/obo/OBI_0000044 OBI low Histopathological examination is a necessary part of lifetime cancer bioassays. This type of examination is used to detect tumors. http://purl.obolibrary.org/obo/CL_0000268 CL http://purl.obolibrary.org/obo/GO_0008274 GO Affimetrix microarrays Transcriptomic expression was measured using Affimetrix microarrays. in_vitro human primary hepatocytes liver human transcriptomic expression change http://purl.obolibrary.org/obo/GO_0006955 GO high In McMullen et al (2014), transcriptomic expression was investigated in human primary hepatocytes in time and dose series exposures to the PPARα agonist GW7647 where transcriptomic expression was measured using Affimetrix microarrays... http://purl.obolibrary.org/obo/GO_0006955 GO Affymetrix microarray Measures transcriptomic expression in human primary hepatocytes exposed to PPARα agonist. in_vitro human primary hepatocytes liver human transcriptomic expression change http://purl.obolibrary.org/obo/OBI_0000615 OBI high transcriptomic expression was investigated in human primary hepatocytes in time and dose series exposures to the PPARα agonist GW7647 where transcriptomic expression was measured using Affimetrix microarrays http://purl.obolibrary.org/obo/GO_0010467 GO ChIPseq ChIPseq was conducted after completing immunoprecipitation and quantified using Illumina HiSeq 2000 sequencing to find binding to PPRE within 50K bp of differentially expressed genes. in_vitro human primary hepatocytes liver human DNA binding change http://purl.obolibrary.org/obo/GO_0005634 GO high ...and ChIPseq was conducted after completing immunoprecipitation and quantified using Illumina HiSeq 2000 sequencing to find binding to PPRE within 50K bp of differentially expressed genes. http://purl.obolibrary.org/obo/CHEBI_0001294 CHEBI http://purl.obolibrary.org/obo/GO_0005634 GO ChIPseq Identifies binding to PPRE within 50K bp of differentially expressed genes using Illumina HiSeq 2000 sequencing. in_vitro human primary hepatocytes liver human PPARα binding to PPRE not_specified http://purl.obolibrary.org/obo/GO_0003677 GO high ChIPseq was conducted after completing immunoprecipitation and quantified using Illumina HiSeq 2000 sequencing to find binding to PPRE within 50K bp of differentially expressed genes. http://purl.obolibrary.org/obo/GO_0003677 GO DNA-dependent radioligand binding assay Quantifies ligand binding in assays involving PPAR-RXR and RAR-RXR heterodimerization. in_vitro CV-1 murine ligand binding not_specified http://purl.obolibrary.org/obo/OBI_0000356 OBI http://purl.obolibrary.org/obo/GO_0005488 GO medium DNA-dependent radioligand binding assays were conducted to quantify ligand binding in the assays described in DiRenzo et al (1997). http://purl.obolibrary.org/obo/GO_0005488 GO mammalian two-hybrid assay A method used to measure the fold activation of transcriptional regulatory complexes involving PPARα, ligands, and co-repressors. in_vitro fold activation of transcriptional regulatory complex change medium Fold activation of the PPARα-GW6471-SMRT transcriptional regulatory complex was measured in mammalian two-hybrid assays (Xu et al 2001). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006351 GO mammalian two-hybrid assay Fold activation of the PPARα-GW6471-SMRT transcriptional regulatory complex was measured using mammalian two-hybrid assays. in_vitro transcriptional activation increase http://purl.obolibrary.org/obo/GO_0045927 GO medium Fold activation of the PPARα-GW6471-SMRT transcriptional regulatory complex was measured in mammalian two-hybrid assays (Xu et al 2001). http://purl.obolibrary.org/obo/GO_0006955 GO Reporter gene assay Quantifies PPAR-RXR and RAR-RXR heterodimerization and activity using expression vectors for murine PPARα, RAR and RXR transfected with reporter and expression plasmids in CV-1 cells. in_vitro CV-1 cells Heterodimerization and transcriptional activity change medium PPAR-RXR and RAR-RXR heterodimerization and activity were quantified using expression vectors for murine PPARα, RAR and RXR in CV-1 cells transfected with 1ug of reporter plasmid and 50-200ng of expression plasmid (DiRenzo et al 1997). RT-qPCR Examines the effects of PPARα transactivation on expression of downstream genes. in_vitro gene expression change http://purl.obolibrary.org/obo/OBI_0001057 OBI http://purl.obolibrary.org/obo/GO_0010467 GO medium Effects of PPARα transactivation on expression of downstream genes been examined by a variety of methods, especially RT-qPCR (Kersten et al 2014). http://purl.obolibrary.org/obo/GO_0010467 GO X-ray crystallography A structural biology technique used to determine the 3D arrangement of atoms in the PPARα ligand binding domain complexed with a ligand and co-repressor. in_vitro 3D structure of the binding complex not_specified http://purl.obolibrary.org/obo/CHMO_0000250 CHMO low X-ray crystallography was used to describe the ligand binding domain (fatty acid binding domain) of PPARα and demonstrate the binding complex of PPARα, the artificial ligand (GW6471), and the co-repressor silencing mediator for retinoid and thyroid hormone receptors (SMRT, Xu et al 2001, 2002). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005515 GO X-ray crystallography X-ray crystallography was used to describe the ligand binding domain of PPARα and demonstrate the binding complex of PPARα, GW6471, and SMRT. in_vitro ligand binding change http://purl.obolibrary.org/obo/GO_0005102 GO low X-ray crystallography was used to describe the ligand binding domain (fatty acid binding domain) of PPARα and demonstrate the binding complex of PPARα, the artificial ligand (GW6471), and the co-repressor silencing mediator for retinoid and thyroid hormone receptors (SMRT, Xu et al 2001, 2002). http://purl.obolibrary.org/obo/CHEBI_59834 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO Mitochondrial fatty acid beta oxidation assay Measures beta oxidation of fatty acids in mouse liver homogenates using a radio-labeled fatty acid substrate, with reaction products separated by centrifugation and fractional radioactivity measured. ex_vivo liver mouse fractional radioactivity of reaction products decrease http://purl.obolibrary.org/obo/GO_0006635 GO http://purl.obolibrary.org/obo/GO_0005739 GO low Beta oxidation of fatty acids in mitochondria has been measured using mouse liver homogenates where a radio-labeled fatty acid substrate was reacted for 30 minutes and then centrifuged to separate reaction products for fractional radioactivity measurements (Aoyama et al 1998). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006635 GO Promoter-reporter plasmid assay Investigates gene expression using a promoter-reporter plasmid (MCPT.Luc.1025) transfected into rat neonate cardiac myocytes to measure concentration-response effects of fatty acids on M-CPT I expression. in_vitro rat neonate cardiac myocytes heart rat M-CPT I expression change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000624 OBI http://purl.obolibrary.org/obo/OBI_0000623 OBI medium Brandt et al (1998) investigated concentration response effects of Oleate, Decanoate and Hexanoate fatty acid chains on mitochondrial carnitine palmitoyl-transferases I (M-CPT I) expression using promoter-reporter plasmid MCPT.Luc.1025 reporter transfected into rat neonate cardiac myocytes. http://purl.obolibrary.org/obo/GO_0010467 GO Promoter-reporter plasmid assay (human M-CPT I) Investigates human M-CPT I gene expression using an analogous promoter-reporter plasmid transfected into cells. in_vitro human human M-CPT I expression change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000624 OBI medium Human M-CPT I was investigate using an analogous method (Brandt et al 1998). http://purl.obolibrary.org/obo/GO_0010467 GO Promoter-reporter plasmid assay (human MCAD) Investigates human medium chain acyl-CoA dehydrogenase (MCAD) gene expression using a MCAD.luc.1054 reporter transfected into HepG2 cells in response to fatty acids. in_vitro HepG2 cells liver human MCAD expression change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000624 OBI medium Expression of human medium chain acyl-CoA dehydrogenase (MCAD) was investigated using a MCAD.luc.1054 reporter transfected into HepG2 cells in response to fatty acids with various chain lengths (Gulick et al 1994). http://purl.obolibrary.org/obo/GO_0010467 GO radio-labeled fatty acid substrate reaction Measures mitochondrial beta oxidation by reacting radio-labeled fatty acid substrates in liver homogenates and measuring fractional radioactivity of reaction products. ex_vivo liver mouse fractional radioactivity of reaction products not_specified http://purl.obolibrary.org/obo/GO_0006686 GO low Beta oxidation of fatty acids in mitochondria has been measured using mouse liver homogenates where a radio-labeled fatty acid substrate was reacted for 30 minutes and then centrifuged to separate reaction products for fractional radioactivity measurements (Aoyama et al 1998). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006686 GO western immunoblot Uses Western immunoblotting to quantify the expression of various enzymes involved in hepatic fatty acid metabolism. in_vitro liver enzyme quantification not_specified http://purl.obolibrary.org/obo/GO_0006686 GO not_specified Investigation of various enzymes involved in hepatic fatty acid metabolism described in Aoyama et al (1998) were investigated using Western immunoblot quantitiation. http://purl.obolibrary.org/obo/GO_0006686 GO Western immunoblot Quantifies various enzymes involved in hepatic fatty acid metabolism using Western immunoblot. in_vitro liver protein expression of enzymes involved in fatty acid metabolism change http://purl.obolibrary.org/obo/GO_0010457 GO low Investigation of various enzymes involved in hepatic fatty acid metabolism described in Aoyama et al (1998) were investigated using Western immunoblot quantitiation. http://purl.obolibrary.org/obo/GO_0006631 GO blood serum β-hydroxybutyrate measurement Measures β-hydroxybutyrate in blood serum, comparing wild type and PPARα knockout mice. in_vivo blood serum Mus musculus β-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/UBERON_0000178 UBERON low In Muoio et al (2002), β-hydroxybutyrate was measured in blood serum comparing wild type and PPARα knockout mice. http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/GO_0019693 GO D(-)-3-hydroxybutyric dehydrogenase assay Quantifies β-hydroxybutyrate in a cell-free system using D(-)-3-hydroxybutyric dehydrogenase, where the reaction components are measured quantitatively. in_vitro β-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/OBI_0000269 OBI low The quantification of β-hydroxybutyrate described in Cahill 2006 was measured in a cell-free system catalyzed by D(-)-p-hydroxybutyric dehydrogenase where all components of the reaction [ D(-)-fl-hydroxybutyrate + diphosphopyridine nucleotide + = acetoacetate + reduced diphosphopyridine nucleotide + H+ ] were able to be quantitatively determined (Williamson et al 1962). http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/GO_0019693 GO enzymatic assay for glucose and ketone bodies Measures glucose, L-hydroxybutyrate, and acetoacetate concentrations in neutralized perchloric filtrates using enzymatic methods. in_vitro glucose, L-hydroxybutyrate, and acetoacetate concentrations not_specified http://purl.obolibrary.org/obo/CHEBI_4167 CHEBI http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/CHEBI_15703 CHEBI http://purl.obolibrary.org/obo/OBI_0000269 OBI low In Le May et al (2000), glucose, L-hydroxybutyrate and acetoacetate concentrations were measured in the neutralized perchloric filtrates by enzymatic methods. http://purl.obolibrary.org/obo/GO_0019693 GO enzymatic method for filtrates Enzymatic methods used to measure glucose, L-hydroxybutyrate, and acetoacetate concentrations in neutralized perchloric filtrates. in_vitro glucose, L-hydroxybutyrate and acetoacetate concentrations not_specified http://purl.obolibrary.org/obo/CHEBI_35112 CHEBI http://purl.obolibrary.org/obo/CHEBI_35437 CHEBI low In Le May et al (2000), glucose, L-hydroxybutyrate and acetoacetate concentrations were measured in the neutralized perchloric filtrates by enzymatic methods. http://purl.obolibrary.org/obo/CHEBI_35112 CHEBI http://purl.obolibrary.org/obo/GO_0006096 GO SMART micro-FPLC Separates triglyceride and cholesterol fractions using gel filtration chromatography, followed by enzymatic assay. in_vitro triglyceride and cholesterol fractions not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI http://purl.obolibrary.org/obo/CHEBI_16559 CHEBI http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI low SMART micro-FPLC (Amersham Biosciences) consisting of a Superose 6 PC 3.2/30 column (Amersham Biosciences) equilibrated in PBS buffer was conducted where triglyceride and cholesterol fractions were investigated by enzymatic assay (Wako Diagnostics) as described in Badman et al (2007). Stanbio Laboratory enzymatic assay Measures serum β-hydroxybutyrate using a small-scale enzymatic assay. in_vitro serum serum β-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/OBI_0000269 OBI medium Serum β-hydroxybutyrate was measured using Stanbio Laboratory small-scale enzymatic assays in Badman et al (2007) http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/GO_0019693 GO Urine ketone test strip Quantitative measurement of ketone bodies (aceto-acetate, acetone, and 3-hydroxybutyrate) in urine using reflectometry with test strips. in_vitro ketone body concentration in urine increase not_specified Clinical observations of ketone bodies have been simplified by the development of urine test strips that can provide quantitative values for the ketone bodies aceto-acetate, acetone and 3-hydroxybutyrate using reflectometry (Penders et al 2005). http://purl.obolibrary.org/obo/CHEBI_27668 CHEBI http://purl.obolibrary.org/obo/GO_0006108 GO urine test strips Provides quantitative values for ketone bodies (acetoacetate, acetone, and 3-hydroxybutyrate) using reflectometry. in_vitro urine ketone bodies concentration not_specified http://purl.obolibrary.org/obo/CHEBI_15703 CHEBI http://purl.obolibrary.org/obo/CHEBI_17568 CHEBI http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI high Clinical observations of ketone bodies have been simplified by the development of urine test strips that can provide quantitative values for the ketone bodies aceto-acetate, acetone and 3-hydroxybutyrate using reflectometry (Penders et al 2005). http://purl.obolibrary.org/obo/GO_0019693 GO Urine test strips (reflectometry) Quantitative measurement of ketone bodies (aceto-acetate, acetone, and 3-hydroxybutyrate) using reflectometry-based urine strips. in_vitro urine aceto-acetate, acetone and 3-hydroxybutyrate not_specified http://purl.obolibrary.org/obo/CHEBI_15443 CHEBI http://purl.obolibrary.org/obo/CHEBI_15445 CHEBI http://purl.obolibrary.org/obo/CHEBI_15444 CHEBI not_specified Clinical observations of ketone bodies have been simplified by the development of urine test strips that can provide quantitative values for the ketone bodies aceto-acetate, acetone and 3-hydroxybutyrate using reflectometry (Penders et al 2005). http://purl.obolibrary.org/obo/GO_0006082 GO Wako Chemicals D-3-hydroxybutyric acid kit Measures β-hydroxybutyrate using a commercial enzymatic kit. in_vitro β-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/OBI_0000269 OBI medium by Wako Chemicals D-3-hydroxybutyric acid kit in Potthoff et al (2009). http://purl.obolibrary.org/obo/CHEBI_16003 CHEBI http://purl.obolibrary.org/obo/GO_0019693 GO D(-)-3-hydroxybutyric dehydrogenase assay Quantifies β-hydroxybutyrate in a cell-free system via enzymatic reaction catalyzed by D(-)-3-hydroxybutyric dehydrogenase. in_vitro β-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI low The quantification of β-hydroxybutyrate described in Cahill 2006 was measured in a cell-free system catalyzed by D(-)-p-hydroxybutyric dehydrogenase where all components of the reaction [ D(-)-fl-hydroxybutyrate + diphosphopyridine nucleotide + = acetoacetate + reduced diphosphopyridine nucleotide + H+ ] were able to be quantitatively determined (Williamson et al 1962). http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI http://purl.obolibrary.org/obo/GO_0042181 GO Ex vivo NMR and targeted metabolomics Measurement of the transition from fatty acids to ketone bodies as fuel for ATP production in cardiac muscle using ex vivo NMR combined with targeted quantitative myocardial metabolomic profiling by mass spectrometry. ex_vivo heart shift from fatty acid to ketone body utilization in cardiac muscle not_specified http://purl.obolibrary.org/obo/UBERON_0000944 UBERON http://purl.obolibrary.org/obo/GO_0006631 GO http://purl.obolibrary.org/obo/GO_0001664 GO not_specified The transition from using fatty acids to ketone bodies to fuel ATP production in cardiac muscle was measured in isolated heart preparation using ex vivo NMR combined with targeted quantitative myocardial metabolomic profiling using mass spectrometry (Aubert et al 2016). http://purl.obolibrary.org/obo/UBERON_0000944 UBERON http://purl.obolibrary.org/obo/GO_0008152 GO Ex vivo NMR with metabolomic profiling Measures the transition from fatty acids to ketone bodies for ATP production in cardiac muscle using NMR and mass spectrometry. ex_vivo heart myocardial metabolite levels not_specified http://purl.obolibrary.org/obo/OBI_0002723 OBI http://purl.obolibrary.org/obo/OBI_0000272 OBI low The transition from using fatty acids to ketone bodies to fuel ATP production in cardiac muscle was measured in isolated heart preparation using ex vivo NMR combined with targeted quantitative myocardial metabolomic profiling using mass spectrometry (Aubert et al 2016). http://purl.obolibrary.org/obo/UBERON_0001134 UBERON http://purl.obolibrary.org/obo/GO_0006754 GO Serum β-hydroxybutyrate measurement Measures β-hydroxybutyrate in blood serum, comparing wild type and PPARα knockout mice. in_vivo serum Mus musculus serum β-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI http://purl.obolibrary.org/obo/UBERON_0001967 UBERON medium In Muoio et al (2002), β-hydroxybutyrate was measured in blood serum where wild type and PPARα knockout mice were compared. http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI http://purl.obolibrary.org/obo/GO_0042181 GO SMART micro-FPLC with enzymatic assay Separates triglyceride and cholesterol fractions using FPLC and quantifies them via enzymatic assay. in_vitro triglyceride and cholesterol fractions not_specified http://purl.obolibrary.org/obo/CHEBI_16546 CHEBI http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI low SMART micro-FPLC (Amersham Biosciences) consisting of a Superose 6 PC 3.2/30 column (Amersham Biosciences) equilibrated in PBS buffer was conducted where triglyceride and cholesterol fractions were investigated by enzymatic assay (Wako Diagnostics) as described in Badman et al (2007). Stanbio Laboratory enzymatic assay Measures serum β-hydroxybutyrate using a small-scale enzymatic assay. in_vitro serum serum β-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI medium Serum β-hydroxybutyrate was measured using Stanbio Laboratory small-scale enzymatic assays in Badman et al (2007) http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI http://purl.obolibrary.org/obo/GO_0042181 GO Urine ketone test strip Quantitative measurement of ketone bodies (aceto-acetate, acetone, and 3-hydroxybutyrate) in urine using reflectometry with test strips. in_vitro ketone body concentration in urine not_specified not_specified Clinical observations of ketone bodies have been simplified by the development of urine test strips that can provide quantitative values for the ketone bodies aceto-acetate, acetone and 3-hydroxybutyrate using reflectometry (Penders et al 2005). urine test strips Reflectometry-based urine test strips providing quantitative values for aceto-acetate, acetone, and 3-hydroxybutyrate. ex_vivo urine aceto-acetate, acetone and 3-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16345 CHEBI http://purl.obolibrary.org/obo/CHEBI_15011 CHEBI http://purl.obolibrary.org/obo/CHEBI_35611 CHEBI not_specified Clinical observations of ketone bodies have been simplified by the development of urine test strips that can provide quantitative values for the ketone bodies aceto-acetate, acetone and 3-hydroxybutyrate using reflectometry (Penders et al 2005). http://purl.obolibrary.org/obo/GO_0006647 GO Urine test strips with reflectometry Provides quantitative values for ketone bodies (acetoacetate, acetone, 3-hydroxybutyrate) in urine using reflectometry. in_vitro urine urine ketone bodies concentration not_specified http://purl.obolibrary.org/obo/CHEBI_15703 CHEBI http://purl.obolibrary.org/obo/CHEBI_17568 CHEBI http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI high Clinical observations of ketone bodies have been simplified by the development of urine test strips that can provide quantitative values for the ketone bodies aceto-acetate, acetone and 3-hydroxybutyrate using reflectometry (Penders et al 2005). http://purl.obolibrary.org/obo/GO_0042181 GO Wako Chemicals D-3-hydroxybutyric acid kit Measures β-hydroxybutyrate using a commercial enzymatic assay kit. in_vitro β-hydroxybutyrate concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI medium by Wako Chemicals D-3-hydroxybutyric acid kit in Potthoff et al (2009). http://purl.obolibrary.org/obo/CHEBI_16534 CHEBI http://purl.obolibrary.org/obo/GO_0042181 GO Amino acid measurement assay Measures all amino acids (method unspecified). not_specified amino acid concentrations not_specified http://purl.obolibrary.org/obo/CHEBI_33709 CHEBI not_specified All amino acids were measured in Felig et al (1970A), however the analytical methods that were references were not found using Google Scholar search. http://purl.obolibrary.org/obo/CHEBI_33709 CHEBI http://purl.obolibrary.org/obo/GO_0006520 GO blood serum metabolite measurement Measures blood glucose, lactate, β-hydroxybutyrate, and nonesterified fatty acids in blood serum to assess beta oxidation capacity. in_vitro blood serum blood glucose, lactate, β-hydroxybutyrate, and nonesterified fatty acids not_specified http://purl.obolibrary.org/obo/CHEBI_4167 CHEBI http://purl.obolibrary.org/obo/CHEBI_17594 CHEBI http://purl.obolibrary.org/obo/GO_0019395 GO medium In Muoio et al (2002), blood glucose, lactate and β-hydroxybutyrate were measured in blood serum while capacity for beta oxidation of fatty acids was determined by measuring the nonesterified fatty acids in blood serum. http://purl.obolibrary.org/obo/CHEBI_15841 CHEBI http://purl.obolibrary.org/obo/GO_0019395 GO enzymatic assay Glutamate and glutamine levels are measured in fresh human plasma using enzymatic assays. in_vivo plasma Homo sapiens glutamate and glutamine concentration increase http://purl.obolibrary.org/obo/CHEBI_5913 CHEBI http://purl.obolibrary.org/obo/CHEBI_5916 CHEBI low Glutamate and glutamine were measured in fresh plasma taken from human subjects that were fasted and those in a postabsorptive state using enzymatic assays (Mariliss et al 1971). http://purl.obolibrary.org/obo/CHEBI_5913 CHEBI http://purl.obolibrary.org/obo/GO_0006520 GO enzymatic assay for glutamate and glutamine Measures glutamate and glutamine levels in fresh plasma using enzymatic methods. in_vitro plasma human glutamate and glutamine levels not_specified not_specified Glutamate and glutamine were measured in fresh plasma taken from human subjects that were fasted and those in a postabsorptive state using enzymatic assays (Mariliss et al 1971). http://purl.obolibrary.org/obo/CHEBI_16015 CHEBI http://purl.obolibrary.org/obo/GO_0009056 GO Fluorometric assay for enzyme kinetics Measures enzyme kinetics involved in glycolysis and gluconeogenesis by detecting the oxidation or reduction of pyridine nucleotides. ex_vivo heart Rattus norvegicus oxidation or reduction of pyridine nucleotides not_specified not_specified In Kashiwaya et al (1994), perfused rat hearts were prepared for metabolic flux experiments. Measurement of enzyme kinetics involved in glycoloysis and gluconeogenesis were measured using fluorometric procedures measuring the oxidation or reduction of pyridine nucleotides. fluorometric enzyme kinetics assay Measures enzyme kinetics in glycolysis and gluconeogenesis using fluorometric detection of pyridine nucleotide oxidation/reduction. in_vitro enzyme kinetics not_specified http://purl.obolibrary.org/obo/GO_0003824 GO http://purl.obolibrary.org/obo/GO_0006096 GO medium Measurement of enzyme kinetics involved in glycoloysis and gluconeogenesis were measured using fluorometric procedures measuring the oxidation or reduction of pyridine nucleotides. http://purl.obolibrary.org/obo/GO_0003824 GO http://purl.obolibrary.org/obo/GO_0006096 GO In vitro assessment of gluconeogenic capacity Assesses gluconeogenic capacity of renal cortex in rats by measuring net glucose content after adding glutamic acid and other ketogenic substrates. in_vitro renal cortex rat gluconeogenic capacity increase not_specified Goodman et al provided in vitro assessment of gluconeogenic capacity of renal cortex in rats. Glutamatic acid and other ketogenic substrates were added and measure in the system and measured as net glucose content. in vitro gluconeogenic capacity assay Assesses gluconeogenic capacity of renal cortex by measuring net glucose content after adding glutamic acid and other ketogenic substrates. in_vitro renal cortex rat net glucose content not_specified http://purl.obolibrary.org/obo/GO_0006094 GO http://purl.obolibrary.org/obo/CHEBI_4167 CHEBI low Goodman et al provided in vitro assessment of gluconeogenic capacity of renal cortex in rats. Glutamatic acid and other ketogenic substrates were added and measure in the system and measured as net glucose content. http://purl.obolibrary.org/obo/UBERON_0001285 UBERON http://purl.obolibrary.org/obo/GO_0006094 GO nonesterified fatty acids measurement Determination of beta oxidation capacity by measuring nonesterified fatty acids in blood serum. in_vivo blood serum nonesterified fatty acids concentration not_specified http://purl.obolibrary.org/obo/GO_0006343 GO not_specified capacity for beta oxidation of fatty acids was determined by measuring the nonesterified fatty acids in blood serum. http://purl.obolibrary.org/obo/CHEBI_43924 CHEBI http://purl.obolibrary.org/obo/GO_0006343 GO perfused rat heart metabolic flux Measures metabolic flux in perfused rat hearts using radio-labeled substrates to track glycolysis and gluconeogenesis. ex_vivo heart rat metabolite flux not_specified http://purl.obolibrary.org/obo/GO_0006096 GO http://purl.obolibrary.org/obo/GO_0006094 GO low In Kashiwaya et al (1994), perfused rat hearts were prepared for metabolic flux experiments. Radio-labeled substrates were used to track metabolite flux during glucolysis / gluconeogenesis. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0006094 GO Radio-labeled substrate flux assay Tracks metabolite flux during glycolysis/gluconeogenesis using radio-labeled substrates. in_vitro metabolite flux not_specified not_specified Radio-labeled substrates were used to track metabolite flux during glucolysis / gluconeogenesis. http://purl.obolibrary.org/obo/CHEBI_17234 CHEBI http://purl.obolibrary.org/obo/GO_0006096 GO Dynamic energy budget model A computational model that simulates energy allocation in organisms, validated against parameters such as food availability, animal weights, brood sizes, and survival rates. in_silico energy budget parameters not_specified not_specified Dynamic energy budget model development and validation demonstrated against various parameter values and population studies (Nisbet et al 2000). PPARalpha nuclear-receptor activation/inhibition assay An in vitro assay to determine if chemicals interfere with PPARalpha nuclear signaling by measuring receptor activation or inhibition. in_vitro human PPARalpha activation/inhibition change high In vitro human PPARalpha nuclear-receptor activation/inhibition assays have been used to determine if chemicals interfere with PPARalpha nuclear signaling (Wilbanks et al 2014, Gust et al 2015). http://purl.obolibrary.org/obo/PR_000001606 PR http://purl.obolibrary.org/obo/GO_0035556 GO Transcript expression analysis Measurement of the expression levels of PPARalpha and its target genes to assess transcriptional regulation. in_vivo transcript expression change http://purl.obolibrary.org/obo/GO_0010467 GO medium Transcript Expression of PPARalpha as well as transcript expression for genes in which PPARalpha acts as a transcriptional regulator (Wilbanks et al 2014, Deng et al 2011, Rawat et al 2010, and studies reviewed in Kersten 2014). http://purl.obolibrary.org/obo/PR_000001606 PR http://purl.obolibrary.org/obo/GO_0006351 GO Whole body weight measurement Measurement of the total body weight of animals, typically used to assess growth or toxicity effects. in_vivo mice body weight decrease http://purl.obolibrary.org/obo/VT_0001259 VT medium Whole body animal weights were measured for mice in Wilbanks et al (2014). http://purl.obolibrary.org/obo/UBERON_0000468 UBERON http://purl.obolibrary.org/obo/GO_0040007 GO pH-sensitive dye assay Measures intracellular pH using membrane-permeable pH-sensitive dyes. in_vitro intracellular pH decrease not_specified Intracellular pH can be measured in vitro using membrane permeable pH sensitive dyes http://purl.obolibrary.org/obo/GO_0005615 GO http://purl.obolibrary.org/obo/GO_0006820 GO ratiometric NIR fluorescent probe assay Measures intracellular pH in vivo using ratiometric near-infrared fluorescent probes. in_vivo intracellular pH decrease not_specified in vivo using ratiometric NIR fluorescent probes http://purl.obolibrary.org/obo/GO_0005615 GO http://purl.obolibrary.org/obo/GO_0006820 GO histological examination Measures tissue atrophy, degeneration, or necrosis in cross-sections of the nose by assessing the absence of specific cell types in the olfactory epithelium. in_vivo Bowmans Glands Sustanticular cells sensory cells nose olfactory epithelium presence or absence of specific cell types decrease http://purl.obolibrary.org/obo/UBERON_0001797 UBERON http://purl.obolibrary.org/obo/GO_0000003 GO http://purl.obolibrary.org/obo/GO_0001776 GO low Tissue atrophy/degeneration/necrosis is measured histologically is cross-sections of the nose. The absence of cell types specific to the olfactory epithelium, including Bowmans Glands, Sustanticular cells and sensory cells is commonly reported as evidence of atrophy/degeneration of olfactory epithelium after exposure http://purl.obolibrary.org/obo/UBERON_0001797 UBERON http://purl.obolibrary.org/obo/GO_0009056 GO histology Measures tissue atrophy, degeneration, or necrosis by histological examination of nasal cross-sections, assessing the presence or absence of specific olfactory epithelium cell types. in_vivo Bowman's glands sustentacular cells sensory cells nasal epithelium olfactory epithelium nose absence of olfactory epithelium-specific cell types (Bowman's glands, sustentacular cells, sensory cells) decrease http://purl.obolibrary.org/obo/UBERON_0001761 UBERON low Tissue atrophy/degeneration/necrosis is measured histologically is cross-sections of the nose. The absence of cell types specific to the olfactory epithelium, including Bowmans Glands, Sustanticular cells and sensory cells is commonly reported as evidence of atrophy/degeneration of olfactory epithelium after exposure http://purl.obolibrary.org/obo/UBERON_0001761 UBERON http://purl.obolibrary.org/obo/GO_0009887 GO immunohistochemical staining Identifies specific cell types in the olfactory epithelium, such as olfactory sensory neurons, using markers like olfactory marker protein. in_vivo olfactory sensory neurons olfactory epithelium presence or absence of olfactory sensory neurons change http://purl.obolibrary.org/obo/CL_0000054 CL low The presence or absence of specific cell types can be determined histologically (e.g. by structure and location) or through immunohistochemical staining. Olfactory sensory neurons can be identified with great specificity by staining for olfactory marker protein http://purl.obolibrary.org/obo/CL_0000054 CL AB/PAS staining Determines the presence of mucous cells by staining for AB/PAS-positive mucosubstances. in_vivo nose presence of mucous cells increase http://purl.obolibrary.org/obo/CL_0000186 CL low Staining for AB/PAS-positive mucosubstances is used to determine the presence of mucous cells, which are normally present in respiratory epithelium. http://purl.obolibrary.org/obo/CL_0000186 CL http://purl.obolibrary.org/obo/GO_0003007 GO H&E staining Measures respiratory or squamous metaplasia in cross-sections of the nose by histological examination of tissue morphology and cell types. in_vivo nose presence of respiratory or squamous epithelial cell types increase http://purl.obolibrary.org/obo/UBERON_0002108 UBERON http://purl.obolibrary.org/obo/UBERON_0000486 UBERON http://purl.obolibrary.org/obo/UBERON_0001712 UBERON low Respiratory or squamous metaplasia is measured histologically in cross-sections of the nose after H&E staining and/or use of immunohistochemical markers to show the absence of olfactory epithelial cell types and the presence of cell types of the respiratory or squamous epithelium. http://purl.obolibrary.org/obo/UBERON_0001712 UBERON http://purl.obolibrary.org/obo/GO_0003007 GO H&E staining Histological examination of tissue cross-sections using Hematoxylin and Eosin to visualize tissue morphology and cell types. ex_vivo nose olfactory epithelium presence/absence of cell types and tissue structures change low Respiratory or squamous metaplasia is measured histologically is cross-sections of the nose after H&E staining http://purl.obolibrary.org/obo/UBERON_0001030 UBERON http://purl.obolibrary.org/obo/GO_0051016 GO Immunohistochemical staining for olfactory marker protein Determines the absence of olfactory sensory neurons by staining for olfactory marker protein. in_vivo nose absence of olfactory sensory neurons decrease http://purl.obolibrary.org/obo/CL_0000174 CL low Immunohistochemical staining for olfactory marker protein is used to determine the absence of olfactory sensory neurons. http://purl.obolibrary.org/obo/CL_0000174 CL http://purl.obolibrary.org/obo/GO_0030154 GO BrdU labeling BrdU is a synthetic analogue of thymidine that is incorporated into DNA during the S phase of cell replication. Tissue sections are stained immunohistochemically with antibodies for BrdU and labeled cells are counted as dividing cells. in_vivo number of BrdU-labeled cells increase http://purl.obolibrary.org/obo/GO_0008283 GO low BrdU is a synthetic analogue of the nucleoside Thymidine. BrDu is incorporated into DNA synthesized during the S1 phase of cell replication and is stable for long periods. Labeling of dividing cells by BrdU is accomplished by infusion, bolus injection, or implantation of osmotic pumps containing BrdU for a period of time sufficient to generate measureable numbers of labeled cells. Tissue sections are stained immunhistochemically with antibodies for BrdU and labeled cells are counted as dividing cells. http://purl.obolibrary.org/obo/CHMO_0000001 CHMO http://purl.obolibrary.org/obo/GO_0008283 GO BrdU labeling BrdU is incorporated into DNA during the S1 phase of cell replication and is detected via immunohistochemical staining with antibodies for BrdU. Labeled cells are counted as dividing cells. in_vivo number of labeled cells increase http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/GO_0006260 GO low BrdU is a synthetic analogue of the nucleoside Thymidine. BrDu is incorporated into DNA synthesized during the S1 phase of cell replication and is stable for long periods. Labeling of dividing cells by BrdU is accomplished by infusion, bolus injection, or implantation of osmotic pumps containing BrdU for a period of time sufficient to generate measureable numbers of labeled cells. Tissue sections are stained immunhistochemically with antibodies for BrdU and labeled cells are counted as dividing cells. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO BrdU, Ki67, IdU Quantification - Flow Cytometry Measurement of cell proliferation biomarkers (BrdU, Ki67, or IdU) by flow cytometry, normalized to total levels of the biomarker. in_vivo cell proliferation biomarkers increase http://purl.obolibrary.org/obo/GO_0008283 GO not_specified Measurement of cell proliferation biomarkers by flow cytometry, normalized to total levels of BrdU, Ki67 or IdU. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO BrdU, Ki67, IdU Quantification - Flow Cytometry Measurement of cell proliferation biomarkers by flow cytometry, normalized to total levels of BrdU, Ki67 or IdU. in_vitro levels of BrdU, Ki67, or IdU increase http://purl.obolibrary.org/obo/GO_0008283 GO high Measurement of cell proliferation biomarkers by flow cytometry, normalized to total levels of BrdU, Ki67 or IdU. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Colourimetric Dye Assay Cells are incubated with a dye that changes colour following metabolism; Colour change can be measured and extrapolated to cell number and thus provide an indication of cellular proliferation rates in_vitro colour change change http://purl.obolibrary.org/obo/GO_0008283 GO medium Colourimetric Dye Assays Vega-Avila & Pugsley, 2011; American Type Culture Collection Cells are incubated with a dye that changes colour following metabolism; Colour change can be measured and extrapolated to cell number and thus provide an indication of cellular proliferation rates http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Colourimetric Dye Assays Cells are incubated with a dye that changes colour following metabolism. Colour change can be measured and extrapolated to cell number and thus provide an indication of cellular proliferation rates. in_vitro cell number increase http://purl.obolibrary.org/obo/GO_0008283 GO high Cells are incubated with a dye that changes colour following metabolism; Colour change can be measured and extrapolated to cell number and thus provide an indication of cellular proliferation rates http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO CyQuant Cell Proliferation Assay A DNA-binding dye is added to cell cultures, and the dye signal is measured directly to provide a cell count and thus an indication of cellular proliferation. in_vitro cell count increase http://purl.obolibrary.org/obo/GO_0008283 GO high DNA-binding dye is added to cell cultures, and the dye signal is measured directly to provide a cell count and thus an indication of cellular proliferation http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Cytoplasmic Proliferation Dye Cells are incubated with a cytoplasmic dye of a certain fluorescent intensity; Cell divisions decrease the intensity in such a way that the number of divisions can be calculated using flow cytometry measurements in_vitro fluorescent intensity decrease http://purl.obolibrary.org/obo/GO_0008283 GO high Cytoplasmic Proliferation Dye Assays Quah & Parish, 2012 Cells are incubated with a cytoplasmic dye of a certain fluorescent intensity; Cell divisions decrease the intensity in such a way that the number of divisions can be calculated using flow cytometry measurements http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Cytoplasmic Proliferation Dye Assays Cells are incubated with a cytoplasmic dye of a certain fluorescent intensity. Cell divisions decrease the intensity in such a way that the number of divisions can be calculated using flow cytometry measurements. in_vitro number of cell divisions increase http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/GO_0051301 GO medium Cells are incubated with a cytoplasmic dye of a certain fluorescent intensity; Cell divisions decrease the intensity in such a way that the number of divisions can be calculated using flow cytometry measurements http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO IdU incorporation 5-iodo-2'-deoxyuridine (IdU) is another analogue of thymidine used to measure cell proliferation as it is also incorporated into DNA during its synthesis. in_vivo DNA incorporation of IdU increase http://purl.obolibrary.org/obo/GO_0006260 GO low Similarly, 5-iodo-2'-deoxyuridine (IdU) is another analogue of thymidine used to measure cell proliferation as it is also incorporated into DNA during its synthesis (Devine & Behbehani, 2021). http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO IdU labeling Measures cell proliferation by detecting the incorporation of the thymidine analogue 5-iodo-2'-deoxyuridine (IdU) into DNA during synthesis. in_vivo DNA synthesis/cell proliferation increase http://purl.obolibrary.org/obo/GO_0008283 GO not_specified Similarly, 5-iodo-2'-deoxyuridine (IdU) is another analogue of thymidine used to measure cell proliferation as it is also incorporated into DNA during its synthesis (Devine & Behbehani, 2021). http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Ki67 immunostaining Ki67 is a cellular marker of replication detected via direct immunohistochemical staining using antibodies. Cells positive for Ki67 are counted as replicating cells. in_vivo number of Ki67-positive cells increase http://purl.obolibrary.org/obo/GO_0008283 GO low Ki67 is a cellular marker of replication not found in quiescent cells. Direct immunohistochemical staining of cells for protein Ki67 using antibodies is an alternative to the use of BrdU, with the benefit of not requiring a separate treatment (injection for pulse-labeling). Cells positive for Ki67 are counted as replicating cells. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Ki67 immunostaining Ki67 is a cellular marker of replication not found in quiescent cells. Direct immunohistochemical staining of cells for Ki67 using antibodies is used to count cells positive for Ki67 as replicating cells. in_vivo replicating cells increase http://purl.obolibrary.org/obo/GO_0008283 GO not_specified Ki67 is a cellular marker of replication not found in quiescent cells. Direct immunohistochemical staining of cells for protein Ki67 using antibodies is an alternative to the use of BrdU, with the benefit of not requiring a separate treatment (injection for pulse-labeling). Cells positive for Ki67 are counted as replicating cells. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Nucleotide Analog Incorporation Assays (e.g. BrdU, EdU) Nucleoside analogs are added to cells in culture or injected into animals and become incorporated into the DNA. Antibodies conjugated to a peroxidase or fluorescent tag are used for quantification of the incorporated nucleoside analogs using techniques such as ELISA, flow cytometry, or microscopy. in_vitro incorporation of nucleoside analogs increase http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/GO_0006260 GO Yes (No. 442B) medium Nucleoside analogs are added to cells in culture or injected into animals and become incorporated into the DNA at different rates, depending on the level of cellular proliferation; Antibodies conjugated to a peroxidase or fluorescent tag are used for quantification of the incorporated nucleoside analogs using techniques such as ELISA, flow cytometry, or microscopy http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO D-AP5 evoked electrical activity measurement An electrophysiological assay using the selective NMDA receptor antagonist D-AP5 to competitively inhibit the glutamate binding site and study NMDA receptor activity via evoked electrical activity measurements. ex_vivo NMDA receptor-containing tissue NMDA receptor-mediated evoked electrical activity decrease low D-AP5, a selective N-methyl-D-aspartate (NMDA) receptor antagonist that competitively inhibits the glutamate binding site of NMDA receptors, can be studied by evoked electrical activity measurements. AP5 has been widely used to study the activity of NMDA receptors particularly with regard to researching synaptic plasticity, learning, and memory (Evans et al.,1982; Morris, 1989). Evoked electrical activity measurements using D-AP5 This assay measures the electrical activity evoked by D-AP5, a selective NMDA receptor antagonist, to study NMDA receptor activity. ex_vivo brain electrical activity not_specified http://purl.obolibrary.org/obo/OBI_0000211 OBI http://purl.obolibrary.org/obo/PR_000001308 PR low D-AP5, a selective N-methyl-D-aspartate (NMDA) receptor antagonist that competitively inhibits the glutamate binding site of NMDA receptors, can be studied by evoked electrical activity measurements. http://purl.obolibrary.org/obo/PR_000001308 PR http://purl.obolibrary.org/obo/GO_0007268 GO NMDA receptor (MK801 site) radioligand competition binding assay A radioligand competition binding assay using the antagonist MK801 to detect and differentiate agonists and antagonists that bind to the NMDA receptor MK801 site. ex_vivo NMDA receptor-containing tissue Binding affinity of agonists/antagonists at the MK801 site of NMDA receptors change http://www.bioassayontology.org/bao#BAO_0000125 BAO http://www.bioassayontology.org/bao#BAO_0000127 BAO low The most common assay used is the NMDA receptor (MK801 site) radioligand competition binding assay (Reynolds and Palmer, 1991; Subramaniam and McGonigle, 1991; This assay is based on the use of the most potent and specific antagonist of this receptor, MK801 that is used to detect and differentiate agonists and antagonists (competitive and non-competitive) that bind to this specific site of the receptor. NMDA receptor radioligand competition binding assay (MK801 site) This assay uses the antagonist MK801 to detect and differentiate agonists and antagonists binding to the NMDA receptor. ex_vivo brain binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000377 OBI http://purl.obolibrary.org/obo/PR_000001308 PR medium The most common assay used is the NMDA receptor (MK801 site) radioligand competition binding assay (Reynolds and Palmer, 1991; Subramaniam and McGonigle, 1991; http://pdsp.med.unc.edu/UNC-CH%20Protocol%20Book.pdf; http://www.currentprotocols.com/WileyCDA/CPUnit/refId-ph0120.html). This assay is based on the use of the most potent and specific antagonist of this receptor, MK801 that is used to detect and differentiate agonists and antagonists (competitive and non-competitive) that bind to this specific site of the receptor. http://purl.obolibrary.org/obo/PR_000001308 PR http://purl.obolibrary.org/obo/GO_0015276 GO NMDA receptor targeting prediction In silico method combining database mining, molecular docking, pharmacophore searching, and chemical similarity searching to predict NMDA receptor targeting. in_silico NMDA receptor targeting not_specified high The prediction of NMDA receptor targeting is achievable by combining database mining, molecular docking, structure-based pharmacophore searching, and chemical similarity searching methods together http://purl.obolibrary.org/obo/GO_0005515 GO radioligand competition binding assay This assay uses a potent and specific antagonist (MK801) to detect and differentiate agonists and antagonists that bind to the NMDA receptor. It can also be performed using [3H]-CGP 39653, a high affinity selective antagonist at the glutamate site of NMDA receptor, which is a quantitative autoradiography technique. ex_vivo striatum cortex hippocampus binding affinity (Kd) and density (Bmax) change http://purl.obolibrary.org/obo/OBI_0000489 OBI low The most common assay used is the NMDA receptor (MK801 site) radioligand competition binding assay (Reynolds and Palmer, 1991; Subramaniam and McGonigle, 1991). Also radioligand competition binding assay can be performed using D, L-(E)-2-amino-4-[3H]-propyl-5-phosphono-3-pentenoic acid ([3H]-CGP 39653), a high affinity selective antagonist at the glutamate site of NMDA receptor, which is a quantitative autoradiography technique (Mugnaini et al., 1996). The saturation binding of radioligands are used to measure the affinity (Kd) and density (Bmax) of kainate and AMPA receptors in striatum, cortex and hippocampus (Kürschner et al., 1998). http://purl.obolibrary.org/obo/GO_0008193 GO http://purl.obolibrary.org/obo/GO_0005102 GO radioligand competition binding assay ([3H]-CGP 39653) A quantitative autoradiography technique using the high affinity selective antagonist [3H]-CGP 39653 at the glutamate site of the NMDA receptor. ex_vivo binding at the glutamate site change http://purl.obolibrary.org/obo/CHMO_0000665 CHMO not_specified Also radioligand competition binding assay can be performed using D, L-(E)-2-amino-4-[3H]-propyl-5-phosphono-3-pentenoic acid ([3H]-CGP 39653), a high affinity selective antagonist at the glutamate site of NMDA receptor, which is a quantitative autoradiography technique http://purl.obolibrary.org/obo/GO_0005515 GO Radioligand competition binding assay using [3H]-CGP 39653 This assay uses [3H]-CGP 39653, a high-affinity selective antagonist at the glutamate site of the NMDA receptor, in a quantitative autoradiography technique. ex_vivo brain binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000377 OBI http://purl.obolibrary.org/obo/PR_000001308 PR medium Also radioligand competition binding assay can be performed using D, L-(E)-2-amino-4-[3H]-propyl-5-phosphono-3-pentenoic acid ([3H]-CGP 39653), a high affinity selective antagonist at the glutamate site of NMDA receptor, which is a quantitative autoradiography technique (Mugnaini et al., 1996). http://purl.obolibrary.org/obo/PR_000001308 PR http://purl.obolibrary.org/obo/GO_0015276 GO Saturation binding of radioligands Measures the affinity (Kd) and density (Bmax) of kainate and AMPA receptors using radioligand saturation binding in brain tissue. ex_vivo striatum cortex hippocampus receptor affinity and density change not_specified The saturation binding of radioligands are used to measure the affinity (Kd) and density (Bmax) of kainate and AMPA receptors in striatum, cortex and hippocampus (Kürschner et al., 1998). AMES assay The AMES assay is an in vitro system used to assess the direct mutagenic potential of chemicals. It detects mutations in bacteria. in_vitro mutagenic potential increase http://purl.obolibrary.org/obo/GO_0000005 GO medium for example in vitro systems such as the AMES assay, are appropriate for assessing the direct mutagenic potential http://purl.obolibrary.org/obo/CHEBI_00329 CHEBI http://purl.obolibrary.org/obo/GO_0000003 GO AMES assay In vitro bacterial reverse mutation assay used to assess the direct mutagenic potential of chemicals. in_vitro Salmonella typhimurium strains not specified mutant frequency increase not_specified Traditional methods of assessing the mutagenic potential of acetate ester metabolites[4], for example in vitro systems such as the AMES assay, are appropriate for assessing the direct mutagenic potential[5] http://purl.obolibrary.org/obo/SO_0000407 SO http://purl.obolibrary.org/obo/GO_0006260 GO AMES assay An in vitro assay used to assess the direct mutagenic potential of chemicals by measuring reverse mutations in bacteria. in_vitro reverse mutations increase http://purl.obolibrary.org/obo/OBI_0000515 OBI OECD TG 471 high in vitro systems such as the AMES assay, are appropriate for assessing the direct mutagenic potential http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006468 GO Big Blue A transgenic mouse model used to measure specific types of DNA damage in vivo. in_vivo http://purl.obolibrary.org/obo/NCBITaxon_10090 DNA damage increase http://purl.obolibrary.org/obo/GO_0006302 GO low Transgenic models, for example Big Blue are capable of measuring specific types of DNA damage in vivo. http://purl.obolibrary.org/obo/CHEBI_16576 CHEBI http://purl.obolibrary.org/obo/GO_0006302 GO Big Blue assay An in vivo transgenic model used to measure specific types of DNA damage and mutations in living organisms. in_vivo mouse DNA mutations increase http://purl.obolibrary.org/obo/GO_0006468 GO low Transgenic models, for example Big Blue are capable of measuring specific types of DNA damage in vivo http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006468 GO Big Blue model Transgenic Big Blue models are capable of measuring specific types of DNA damage in vivo. in_vivo specific types of DNA damage increase http://purl.obolibrary.org/obo/GO_0000022 GO low Transgenic models, for example Big Blue [6] are capable of measuring specific types of DNA damage in vivo. http://purl.obolibrary.org/obo/CHEBI_00329 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO 6-CF accumulation assay Measures the inhibition of OAT1 and OAT3 activity by quantifying the intracellular accumulation of the fluorescent substrate 6-CF in COS-7 cells expressing the transporters. in_vitro monkey kidney COS-7 cells expressing human OAT1 and OAT3 kidney monkey human extent of accumulation of the 6-CF within the cells decrease not_specified Duan et al. (2012) measured the inhibtion of human OAT1 and OAT3 using monkey kidney COS-7 cells expressing these transporters. Inclubation with a fluorescent substrate, 6-CF, and the inhibitor at room temp for 12 min, followed by subsequent washing and lysing of the cells allowed for determination of the extent of accumulation of the 6-CF within the cells. OAT inhibition assay (renal tubule cells) Measures the inhibition of OAT activity in chicken or vulture renal tubule cells by quantifying the net transport of para-amino hippuric acid (PAH) across culture inserts. in_vitro chicken renal tubule cells vulture renal tubule cells renal tubule chicken vulture net transport of PAH decrease http://purl.obolibrary.org/obo/GO_0015845 GO http://purl.obolibrary.org/obo/CHEBI_17850 CHEBI http://purl.obolibrary.org/obo/UBERON_0000374 UBERON medium Naidoo and Swan (2009) estimated inhibition by plating chicken or vulture renal tubule cells on culture inserts, incubating with the inhibitory drug (diclofenac or meloxicam) and adding para amino hippuric acid (PAH). The net transport by the OAT was calculated as the difference between the basolateral concentration (cytoplasm) and the apical change (cytoplasm - lumen). http://purl.obolibrary.org/obo/PR_000001201 PR http://purl.obolibrary.org/obo/GO_0015845 GO OAT1/OAT3 inhibition assay This assay measures the inhibition of human OAT1 and OAT3 transporter activity by quantifying the accumulation of the fluorescent substrate 6-CF within cells. Cells are incubated with the substrate and inhibitor, washed, lysed, and the amount of accumulated substrate is determined. in_vitro COS-7 cells human monkey accumulation of 6-CF decrease medium Duan et al. (2012) measured the inhibtion of human OAT1 and OAT3 using monkey kidney COS-7 cells expressing these transporters. Inclubation with a fluorescent substrate, 6-CF, and the inhibitor at room temp for 12 min, followed by subsequent washing and lysing of the cells allowed for determination of the extent of accumulation of the 6-CF within the cells. Inhibition potency is reported as the half maximal inhibitory concentration (IC50) http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0015352 GO PAH transport assay Estimates inhibition of OAT by measuring the net transport of para amino hippuric acid (PAH) in renal tubule cells cultured on inserts. in_vitro chicken renal tubule cells vulture renal tubule cells renal tubule chicken vulture net transport by the OAT decrease not_specified Naidoo and Swan (2009) estimated inhibition by plating chicken or vulture renal tubule cells on culture inserts, incubating with the inhibitory drug (diclofenac or meloxicam) and adding para amino hippuric acid (PAH). The net transport by the OAT was calculated as the difference between the basolateral concentration (cytoplasm) and the apical change (cytoplasm - lumen). gene expression analysis Assessment of gene expression levels to detect increased transcription of known genes associated with specific cancers. not_specified gene expression levels increase not_specified Gene expression levels can also be assessed, as increased transcription of known genes have been associated with specific cancers (ex. Tumor Necrosis Factor (Pavet et al. 2014); Heat Shock Factors (Vihervaara and Sistonen 2014; Androgen Receptor (Heinlein and Chang 2004)). histopathology Cancer is detected by examining tissue samples through biopsy or histopathological examination. in_vivo tissue rodents cancer detection increase OECD 2018 low Cancer is usually detected by biopsy or histopathological examination of tissue. http://purl.obolibrary.org/obo/UBERON_0000062 UBERON http://purl.obolibrary.org/obo/GO_0045927 GO Complex I activity dipstick assay Uses CI-selective antibodies to capture Complex I from homogenates, with activity measured via NADH-dependent NBT reduction. in_vitro NBT reduction decrease http://purl.obolibrary.org/obo/GO_0003954 GO http://purl.obolibrary.org/obo/GO_0022900 GO high To assess CI activity and its inhibition in cell or tissue homogenates without interference by other components of the respiratory chain, CI-selective antibodies attached to a matrix (e.g. multiwell plates) are used (Willis et al., 2009). Homogenized tissue can directly be added for capturing of CI, the unbound supernatant is washed away and leaves a complex of the antibody and mitochondrial CI. For activity determination, NADH as electron donor and nitroblue tetrazolium (NBT) as acceptor are added. Reduced NBT forms a colored precipitate, its signal intensity is proportional to the amount of CI bound to the antibody. http://purl.obolibrary.org/obo/PR_000001541 PR http://purl.obolibrary.org/obo/GO_0006120 GO Forward Electron Transfer assay Measures the flow of electrons from NADH through Complex I to an electron acceptor, with readout via NADH consumption or acceptor reduction. in_vitro NADH consumption or electron acceptor reduction decrease http://purl.obolibrary.org/obo/GO_0003954 GO http://purl.obolibrary.org/obo/GO_0022900 GO low Submitochondrial particles or intact isolated mitochondria are incubated with NADH as electron donor and with an electron acceptor to measure the flow of electrons from NADH, through CI to the acceptor. As readout, either the consumption of NADH, or the reduction of the electron acceptor is followed photometrically or fluorometrically (Lenaz et al. 2004; Spinazzi et al. 2012; Long et al. 2009; Kirby et al. 2007). http://purl.obolibrary.org/obo/PR_000001541 PR http://purl.obolibrary.org/obo/GO_0006120 GO Intracellular ATP levels assay Measures intracellular ATP levels as an indirect readout for mitochondrial function using a luminometric luciferase/luciferin assay. in_vitro intracellular ATP levels decrease http://purl.obolibrary.org/obo/GO_0046034 GO medium ATP levels can be easily measured from lysates of in vitro cell cultures or from tissues by a luminometric luciferase/luciferin assay. The amount of light emitted is proportional to the amount of ATP in the sample (Nguyen et al. 1988, Leist et al., 1997). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0042775 GO Luminometric luciferase/luciferin assay Measures intracellular ATP levels in cell lysates or tissues by quantifying the light emitted during the luciferase-mediated oxidation of luciferin. in_vitro in vitro cell cultures tissue intracellular ATP levels decrease http://purl.obolibrary.org/obo/CHEBI_21235 CHEBI not_specified ATP levels can be easily measured from lysates of in vitro cell cultures or from tissues by a luminometric luciferase/luciferin assay. The amount of light emitted is proportional to the amount of ATP in the sample http://purl.obolibrary.org/obo/CHEBI_21235 CHEBI http://purl.obolibrary.org/obo/GO_0006611 GO NADH/NAD+ ratio imaging Measures NADH/NAD+ ratios in mitochondria using imaging methods to assess mitochondrial activity. in_vitro NADH/NAD+ ratio change http://purl.obolibrary.org/obo/GO_0006734 GO low One exemplary approach is the measurement of NADH/NAD+ ratios in mitochondria by imaging methods. This provides resolution on the level of individual mitochondria within a living cell (van Vliet et al., 2014). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006120 GO Oxygen consumption Measures the consumption of oxygen in a closed system as a parameter for mitochondrial respiratory activity, traditionally with a Clark electrode or with optical methods. Can be performed in permeabilized cells or isolated mitochondria. in_vitro cells mitochondria oxygen consumption decrease medium “Electrons, fed into the mitochondrial respiratory chain either by CI or complex II, ultimately reduce molecular oxygen to water at complex IV. In a closed system, this consumption of oxygen leads to a drop of the overall O2 concentration, and this can serve as parameter for mitochondrial respiratory activity.” http://purl.obolibrary.org/obo/CHEBI_50008 CHEBI http://purl.obolibrary.org/obo/GO_0006757 GO Oxygen consumption assay (Clark electrode) Measures oxygen consumption as a surrogate for mitochondrial respiratory activity using a Clark electrode. in_vitro oxygen consumption rate decrease http://purl.obolibrary.org/obo/GO_0006091 GO http://purl.obolibrary.org/obo/GO_0034440 GO low Measurements are traditionally done with a Clark electrode, or with more sophisticated optical methods. At the cathode of a Clark electrode, oxygen is electrolytically reduced, which initiates a current in the electrode, causing a potential difference that is ultimately recorded. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006120 GO Reverse Electron Transfer assay Measures Complex I activity by observing reverse electron flow from succinate to NAD+, forming NADH. in_vitro NADH formation increase http://purl.obolibrary.org/obo/GO_0003954 GO http://purl.obolibrary.org/obo/GO_0022900 GO low With this method, electrons enter the respiratory chain via complex II. Based on the reverse flux, this method allows the complete circumvention of complexes III and IV. As electron donor, succinate is applied, together with NAD+ as electron acceptor. Formation of NADH from NAD+ can be determined photometrically. http://purl.obolibrary.org/obo/PR_000001541 PR http://purl.obolibrary.org/obo/GO_0006120 GO Seahorse XF analysis Measures oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in live cells using a Seahorse extracellular flux analyzer. Cells are kept in a small volume and changes in oxygen levels are detected by an oxygen sensor. in_vitro cells oxygen consumption rate (OCR) decrease high “A modern convenient method to measure oxygen consumption is provided by the Seahorse technology of extracellular flux (XF) analysis, in which cells are kept in a very small volume, so that changes of oxygen levels can be detected very sensitively by an oxygen sensor.” http://purl.obolibrary.org/obo/CL_0000276 CL http://purl.obolibrary.org/obo/GO_0006757 GO Autoradiography Quantitative autoradiography measures binding of a radioactively labeled ligand ([3H]-dihydrorotenone) to the rotenone binding site of complex I in tissue sections. The assay detects competitive inhibitors that bind to the rotenone site by displacement of the labeled ligand. in_vitro substantia nigra striatum not_specified binding of inhibitor to complex I rotenone site decrease http://purl.obolibrary.org/obo/GO_0005751 GO low Binding of this rotenone-derivative is detected by autoradiography. Unselective binding is determined by measurement of [3H]-DHR binding in the presence of an excess of unlabeled rotenone. The method can be used for (a) in vitro measurements and for (b) ex vivo measurements: a) In vitro measurements. Tissues are embedded in a matrix for cutting by a cryostat. The tissue slices are then mounted onto slides. For the binding experiment, they are incubated with the test compound in the presence of labeled [3H]-DHR. Then the tissue slices are washed and prepared for autoradiographic detection (Greenamyre et al. 1992; Higgins and Greenamyre, 1996). http://purl.obolibrary.org/obo/GO_0005751 GO autoradiography This assay quantifies the displacement of a radioactively labelled ligand ([3H]-dihydrorotenone) by a toxicant in tissue samples to assess binding at the rotenone binding site of Complex I. Binding is detected by autoradiography. ex_vivo substantia nigra striatum brain displacement of radioligand decrease low To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation. Most commonly, binding of [3H]-labeled dihydrorotenone (DHR) is measured and compared in control tissue and treated tissue. Binding of this rotenone-derivative is detected by autoradiography. http://purl.obolibrary.org/obo/GO_0005102 GO colorimetric Complex I Enzyme Activity Assay Quantifies Complex I activity by measuring the oxidation of NADH to NAD+ coupled with the reduction of a dye, resulting in increased absorbance at OD=450 nm using capture antibodies. in_vitro human cell human rat mouse bovine absorbance at OD=450 nm change http://purl.obolibrary.org/obo/OBI_0000153 OBI medium After the target has been immobilized in the well, CI activity is determined by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye which leads to increased absorbance at OD=450 nm. The analysis of mitochondrial OXPHOS CI enzyme activity can be performed using human, rat, mouse and bovine cell and tissue extracts http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0016764 GO Complex I Enzyme Activity (Colorimetric) This assay measures Complex I enzyme activity using a microplate assay kit. It quantifies the oxidation of NADH to NAD+ and the simultaneous reduction of a dye, resulting in increased absorbance at OD=450 nm. in_vitro human rat mouse bovine tissue cell enzyme activity (oxidation of NADH) decrease medium The analysis of mitochondrial OXPHOS CI enzyme activity can be performed using human, rat, mouse and bovine cell and tissue extracts (abcam: http://www.abcam.com/complex-i-enzyme-activity-microplate-assay-kit-colorimetric-ab109721 ). After the target has been immobilized in the well, CI activity is determined by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye which leads to increased absorbance at OD=450 nm. http://purl.obolibrary.org/obo/GO_0006757 GO Complex I Enzyme Activity Assay (Colorimetric) Measures complex I enzyme activity by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye, leading to increased absorbance at OD=450 nm. in_vitro human rat mouse bovine complex I enzyme activity not_specified http://purl.obolibrary.org/obo/GO_0008137 GO medium The analysis of mitochondrial OXPHOS CI enzyme activity can be performed using human, rat, mouse and bovine cell and tissue extracts CI activity is determined by following the oxidation of NADH to NAD+ and the simultaneous reduction of a dye which leads to increased absorbance at OD=450 nm. http://purl.obolibrary.org/obo/GO_0008137 GO http://purl.obolibrary.org/obo/GO_0022900 GO Quantitative autoradiography Measures binding of an inhibitor at the rotenone binding site of complex I in tissues using radioactively labeled dihydrorotenone (DHR) and autoradiography. in_vitro substantia nigra striatum binding of [3H]-DHR not_specified http://purl.obolibrary.org/obo/OBI_0000697 OBI low To assess binding of an inhibitor at the rotenone binding site of CI in tissues (e.g. in the substantia nigra or in the striatum), the standard approach is to quantify the displacement of a radioactively labelled ligand of this binding site by the toxicant under evaluation. Binding of this rotenone-derivative is detected by autoradiography. http://purl.obolibrary.org/obo/GO_0008137 GO http://purl.obolibrary.org/obo/GO_0042277 GO Autophagic flux measurement via radioactive protein turnover Measurement of autophagic flux by assessing the rate of turnover of long-lived proteins labeled with [14C]-leucine or [14C]-valine, quantified by liquid scintillation counting. in_vitro protein degradation rate change http://purl.obolibrary.org/obo/GO_0006915 GO not_specified The lysosomal degradation of the autophagic cargo constitutes the autophagic flux, which can be measured by assessing the rate of turnover of long-lived proteins that are normally turned over by autophagy (Bauvy et al., 2009). This is performed by labelling intracellular proteins with either [14C]-leucine or [14C]-valine, followed by a long culture period in standard medium. The release of radioactive leucin or valin into the culture medium corresponds to the protein degradation rate in cells, and it may be measured by liquid scintillation counting. http://purl.obolibrary.org/obo/CHEBI_43924 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO confocal microscopy Visualizes mitochondrial dynamics in live cells using fluorescent dyes (e.g. DiOC6, JC-1, MitoTracker, MitoFluor probes) and measures mitochondrial speed and direction. in_vitro cells mitochondrial speed and direction change http://purl.obolibrary.org/obo/CL_0000071 CL medium A range of technologies has been used to visualize mitochondrial dynamics in live cells Most frequently, mitochondrial mobility is observed along neurites, and measurable endpoints may be mitochondrial speed and direction with regard to the cell soma http://purl.obolibrary.org/obo/CL_0000071 CL http://purl.obolibrary.org/obo/GO_0006913 GO Flow cytometry Quantitates the level of EGFP-degron fusion proteins that are selectively degraded by the proteasome. in_vitro level of EGFP-degron fusion proteins decrease http://purl.obolibrary.org/obo/OBI_0000268 OBI http://purl.obolibrary.org/obo/PR_000008136 PR high UPS activity can be continuously monitored by quantitating (by mean of flow cytometry or microscopy) the level of e.g. EGFP-degron fusion proteins (green fluorescent protein) that are selectively degraded by the proteasome http://purl.obolibrary.org/obo/GO_0043161 GO Flow cytometry/microscopy of EGFP-degron Continuous monitoring of UPS activity by quantitating the levels of EGFP-degron fusion proteins that are selectively degraded by the proteasome. in_vitro level of EGFP-degron fusion proteins change http://purl.obolibrary.org/obo/GO_0005846 GO not_specified UPS activity can be continuously monitored by quantitating (by mean of flow cytometry or microscopy) the level of e.g. EGFP-degron fusion proteins (green fluorescent protein) that are selectively degraded by the proteasome http://purl.obolibrary.org/obo/GO_0005846 GO http://purl.obolibrary.org/obo/GO_0006508 GO Fluorescence/Substrate monitoring of autophagy-related proteins Monitoring the amount and localization of autophagy-related proteins (e.g., ATG) or using GFP-LC3 fusion proteins in cell culture or transgenic mice. in_vitro mouse autophagy-related protein amount and localization change http://purl.obolibrary.org/obo/GO_0006915 GO not_specified Especially in cell culture, but also in transgenic mice, various techniques have been used to monitor autophagy by mean of fluorescence-tags or other substrates, e.g., ATG, autophagy-related protein or autophagy substrates, to monitor their fate in cells and thus provide information on disturbed ALP, or the over-expression of GFP–LC3 http://purl.obolibrary.org/obo/GO_0006508 GO http://purl.obolibrary.org/obo/GO_0006915 GO Immunocyto/histochemistry for UPS Detection of increased ubiquitin, ubiquitinated proteins, or proteasomal subunits using immunocytochemistry or immunohistochemistry. in_vitro ubiquitin or ubiquitinated proteins or proteasomal subunits levels increase http://purl.obolibrary.org/obo/GO_0005846 GO not_specified quantitative evaluation can be based on the detection of increased ubiquitin or ubiquitinated proteins, as well as proteasomal subunits, either by immunocyto/histochemistry http://purl.obolibrary.org/obo/GO_0005846 GO http://purl.obolibrary.org/obo/GO_0006508 GO Immunostaining Detects α-synuclein aggregates in cells or tissues, optionally with epitope tags or GFP. in_vitro presence of α-synuclein aggregates increase http://purl.obolibrary.org/obo/PR_000001468 PR medium The most common methods to detect AS aggregates use immunostaining for AS (in cells or in tissues). http://purl.obolibrary.org/obo/PR_000001468 PR http://purl.obolibrary.org/obo/GO_0043065 GO Immunostaining for α-synuclein (AS) aggregates Detection of AS aggregates in cells or tissues using immunostaining, potentially involving epitope-tagging or GFP coupling. in_vitro AS aggregates increase not_specified The most common methods to detect AS aggregates use immunostaining for AS (in cells or in tissues). http://purl.obolibrary.org/obo/GO_0051018 GO LC3-I to LC3-II conversion assay Measures the conversion of LC3-I to LC3-II by Western blot to study autophagic flux. in_vitro LC3-II levels increase http://purl.obolibrary.org/obo/PR_000029230 PR http://purl.obolibrary.org/obo/GO_0006914 GO medium The progression of autophagy (autophagic flux) can be studied by the conversion of LC3-I into LC3-II (i.e. a post-translational modification specific for autophagy) by mean of Western blot analysis. http://purl.obolibrary.org/obo/PR_000029230 PR http://purl.obolibrary.org/obo/GO_0006914 GO Live cell imaging with fluorescent dyes Visualizes mitochondrial dynamics in live cells using fluorescent dyes and microscopy. in_vitro mitochondrial speed and direction change http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0007006 GO medium A range of technologies has been used to visualize mitochondrial dynamics in live cells (Jakobs, 2006; Grafstein and Forman, 1980). They usually employ a combination of mitochondrial labelling with fluorescent dyes (e.g. DiOC6 (3, 3′-Dihexyloxacarbocyanine iodide), JC-1 (5,5′,6,6′-Tetrachloro-1,1′,3,3′ tetraethylbenzimida-zolylcarbo-cyanine iodide), MitoTracker, MitoFluor probes, etc.), followed by video- or confocal microscopy for live cell imaging http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0007006 GO LysoTracker Red staining Stains acidic organelles (lysosomes) in live cells to monitor autophagy. in_vitro lysosomal staining intensity change http://purl.obolibrary.org/obo/GO_0005764 GO http://purl.obolibrary.org/obo/GO_0006914 GO high the dye LysoTracker Red stains lysosomes and can be used to monitor autophagy http://purl.obolibrary.org/obo/GO_0005764 GO http://purl.obolibrary.org/obo/GO_0006914 GO MDC staining Uses monodansylcadaverine as an autophago-lysosome marker in live cells. in_vitro autophago-lysosome staining intensity change http://purl.obolibrary.org/obo/GO_0000398 GO http://purl.obolibrary.org/obo/GO_0005764 GO high The autofluorescent drug monodansylcadaverine (MDC) has also been used as autophago-lysosome marker http://purl.obolibrary.org/obo/GO_0000398 GO http://purl.obolibrary.org/obo/GO_0006914 GO Mitochondrial dynamics imaging Visualization of mitochondrial dynamics (mobility, fusion, fission) in live cells using fluorescent dyes (e.g., DiOC6, JC-1, MitoTracker) and video/confocal microscopy. in_vitro neurites mitochondrial speed, direction, fusion, and fission change http://purl.obolibrary.org/obo/GO_0005739 GO not_specified A range of technologies has been used to visualize mitochondrial dynamics in live cells (Jakobs, 2006; Grafstein and Forman, 1980). They usually employ a combination of mitochondrial labelling with fluorescent dyes (e.g. DiOC6 (3, 3′-Dihexyloxacarbocyanine iodide), JC-1 (5,5′,6,6′-Tetrachloro-1,1′,3,3′ tetraethylbenzimida-zolylcarbo-cyanine iodide), MitoTracker, MitoFluor probes, etc.), followed by video- or confocal microscopy for live cell imaging (Schwarz, 2013; Pool et al., 2006). Most frequently, mitochondrial mobility is observed along neurites, and measurable endpoints may be mitochondrial speed and direction with regard to the cell soma (Schildknecht et al. 2013). Additionally, also mitochondrial fusion and fission have been monitored by such methods (Exner et al., 2012). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0005739 GO Proteasome activity assay Uses fluorogenic substrates to determine proteasomal activity in tissue or cell homogenates. in_vitro proteasomal activity change http://purl.obolibrary.org/obo/GO_0000502 GO medium Various fluorogenic substrates (e.g., Suc-Leu-Leu-Val-Tyr-AMC for the chymotrypsin-like activity) can be used for the determination of proteasomal activity in in vivo or in vitro applications. http://purl.obolibrary.org/obo/GO_0000502 GO http://purl.obolibrary.org/obo/GO_0043161 GO Transmission electron microscopy Provides qualitative or semiquantitative estimates of lysosomes and related organelles. in_vitro lysosome morphology and count change http://purl.obolibrary.org/obo/OBI_0000223 OBI http://purl.obolibrary.org/obo/GO_0005764 GO low For qualitative or semiquantitative estimates of lysosomes and related organelles, transmission electron microscopy has been frequently used http://purl.obolibrary.org/obo/GO_0005764 GO http://purl.obolibrary.org/obo/GO_0007040 GO western blot Measures the conversion of LC3-I to LC3-II by Western blot analysis. The amount of LC3-II correlates with the number of autophagosomes. in_vitro cells tissue LC3-II protein levels increase http://purl.obolibrary.org/obo/GO_0006914 GO low The progression of autophagy (autophagic flux) can be studied by the conversion of LC3-I into LC3-II (i.e. a post-translational modification specific for autophagy) by mean of Western blot analysis. The amount of LC3-II correlates with the number of autophagosomes. http://purl.obolibrary.org/obo/CHEBI_16831 CHEBI http://purl.obolibrary.org/obo/GO_0006914 GO Western blot Detects increased ubiquitin or ubiquitinated proteins, as well as proteasomal subunits. in_vitro level of ubiquitin or ubiquitinated proteins increase http://purl.obolibrary.org/obo/OBI_0000207 OBI http://purl.obolibrary.org/obo/PR_000002279 PR http://purl.obolibrary.org/obo/GO_0000502 GO low quantitative evaluation can be based on the detection of increased ubiquitin or ubiquinated proteins, as well as proteasomal subunits, either by immunocyto/histochemistry or by western blotting http://purl.obolibrary.org/obo/GO_0000502 GO http://purl.obolibrary.org/obo/GO_0043161 GO 18-FDOPA PET Positron emission tomography using 18-fluoro-dopa to quantify dopamine presynaptic markers. in_vivo nigrostriatal pathway human dopamine presynaptic marker density decrease low 18-fluoro-dopa positron emission tomography (PET) quantification of various dopamine presynaptic markers (e.g. dopamine transporter DAT, vescicular monoamine transporter type 2 VAT2) identified by single photon emission tomography (SPECT). They permit to visualize the loss of nigrostriatal DA neurons in patients dopaminergic terminal quantification Quantification of dopaminergic terminals in the striatum by digitalization of fibers and optical density measurement or TH+ immunoreactivity. in_vivo striatum dopaminergic terminal density decrease http://purl.obolibrary.org/obo/UBERON_0005255 UBERON http://purl.obolibrary.org/obo/PR_000001742 PR medium Quantification of dopaminergic terminals in the striatum: the density of dopaminergic terminals is not homogeneous in the striatum, increasing from the rostral to the caudal part and representative regions of the striatum should be assessed. This can be done by digitalization of the fibres and quantification by optical density or quantification of the fiber density identifyied by by TH+ immunoreactivity (Tieu et al., 2011; Fernagut et al., 2007). http://purl.obolibrary.org/obo/UBERON_0005255 UBERON http://purl.obolibrary.org/obo/GO_0031175 GO Fluoro Jade stain A fluorochrome derived from fluorescein used to label degenerating neurons. in_vivo substantia nigra striatum degenerating neurons increase http://purl.obolibrary.org/obo/GO_0097103 GO medium Fluoro Jade stain is a fluorochrome derived from fluorescein used in neuroscience disciplines to label degenerating neurons. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0097103 GO haematoxylin and eosin staining Standard histological staining to identify Lewy Body-like aggregations characterized by pale eosinophilic vacuoles. in_vivo substantia nigra Lewy Body-like aggregations increase http://purl.obolibrary.org/obo/MP_0005556 MP http://purl.obolibrary.org/obo/OBI_0000378 OBI medium Indentification of LB in standard histological sections stained with haematoxylin and eosin, they are characterized by the presence of pale eosinophilic vacuoles (Betarbet et al., 2000 and 2006; Pappolla et al., 1988; Dale et al., 1992). http://purl.obolibrary.org/obo/MP_0005556 MP http://purl.obolibrary.org/obo/GO_0043065 GO HPLC Quantification of dopamine, DOPAC, and HVA content in the striatum using high performance liquid chromatography. in_vivo striatum dopamine content decrease http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI high DA, DOPAC (DA metabolite) and homovanillic acid (HVA) content in the striatum can be quantified through several methodologies such as capillary electrophoresis, spectrofluorimetry and high performance liquid chromatography (HPLC). http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0042416 GO HPLC and capillary electrophoresis for dopamine metabolites Chromatographic and electrophoretic methods used to quantify the concentration of dopamine, DOPAC, and homovanillic acid in striatal tissue. ex_vivo striatum dopamine, DOPAC, and HVA content decrease medium DA, DOPAC (DA metabolite) and homovanillic acid (HVA) content in the striatum can be quantified through several methodologies such as capillary electrophoresis, spectrofluorimetry and high performance liquid chromatography (HPLC). Immunocytochemistry and Western blot for DAT and VMAT2 Immunolabeling and protein blotting techniques used to visualize and quantify the expression levels of dopamine transporter (DAT) and vesicular monoamine transporter type 2 (VMAT2). ex_vivo dopaminergic neurons striatum DAT and VMAT2 expression levels decrease low DA transporters (DAT) and vesicular monoamine transporter type 2 (VMAT2) can be visualized and quantified using immunocytochemistry (single cell levels) or western blot followed by densitometry analysis, to quantify the changes in their expression. immunocytochemistry for TH Detection of tyrosine hydroxylase using immunocytochemistry followed by cell counting to evaluate dopaminergic neurons. ex_vivo dopaminergic neurons substantia nigra pars compacta TH+ cell count change low Detection of TH can be done either by immunocytochemistry followed by cell counting (quantitative evaluation) Immunostaining for α-synuclein and ubiquitin An immunohistochemical method used to identify and quantify Lewy bodies by detecting α-synuclein and ubiquitin aggregates in fixed neural tissue. ex_vivo neurons substantia nigra pars compacta α-synuclein and ubiquitin aggregate fluorescence intensity increase low Immuno staining for α-synuclein and ubiquitin to identify and quantify Lewy bodies presence. In vivo, α-synuclein and ubiqutin can be evaluated in the fixed tissue and quantified for fluorescence intensity PET imaging 18-fluoro-dopa positron emission tomography (PET) quantification of dopamine presynaptic markers. in_vivo substantia nigra striatum dopamine presynaptic markers decrease http://purl.obolibrary.org/obo/OBI_0000245 OBI http://purl.obolibrary.org/obo/PR_000008102 PR low Imaging techniques: 18-fluoro-dopa positron emission tomography (PET) quantification of various dopamine presynaptic markers (e.g. dopamine transporter DAT, vescicular monoamine transporter type 2 VAT2) identified by single photon emission tomography (SPECT). http://purl.obolibrary.org/obo/PR_000008102 PR http://purl.obolibrary.org/obo/GO_0015871 GO silver degeneration stain A method to trace degeneration of axons by visualizing products from disintegrated cells. in_vivo substantia nigra striatum degeneration of axons increase http://purl.obolibrary.org/obo/GO_0097102 GO http://purl.obolibrary.org/obo/OBI_0000377 OBI low The silver degeneration stain is a method to trace degeneration of axons. By this matter, products from disintegrated cells are visualized (Switzer R., 2000; Betarbet et al., 2000). http://purl.obolibrary.org/obo/GO_0030424 GO http://purl.obolibrary.org/obo/GO_0097102 GO stereological cell counting Unbiased stereological protocol for cell counting with an optical dissector system to quantify dopaminergic neurons in the substantia nigra pars compacta. in_vivo substantia nigra number of dopaminergic neurons decrease http://purl.obolibrary.org/obo/CL_0000638 CL http://purl.obolibrary.org/obo/OBI_0000740 OBI low The gold standard for counting neurons is then to use an unbiased stereological protocol for cell counting with an optical dissector system (Tieu et al., 2011). http://purl.obolibrary.org/obo/CL_0000638 CL http://purl.obolibrary.org/obo/GO_0097103 GO stereological cell counts Quantitative assessment of neurodegeneration using unbiased stereological protocols for cell counting with an optical dissector system. in_vivo http://purl.obolibrary.org/obo/CL_0000623 http://purl.obolibrary.org/obo/UBERON_0002037 neuron count decrease http://purl.obolibrary.org/obo/CL_0000540 CL low inclusion of stereological cell counts to assess neurodegeneration is representing the most sensitive method to confirm quantitatively specific morphological changes (Dauer 2008, Brooks 1992, Thiruchelvam 2000a and 2000b). http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0022008 GO TH immunocytochemistry Detection of tyrosine hydroxylase (TH) by immunocytochemistry followed by cell counting. in_vivo substantia nigra striatum tyrosine hydroxylase expression change http://purl.obolibrary.org/obo/PR_000001742 PR http://purl.obolibrary.org/obo/OBI_0000466 OBI medium Detection of TH, the enzyme responsible for catalyzing the conversion of the amino acid L-tyrosine to L-3,4-dihydroxyphenylalanine (L-DOPA), a precursor for dopamine. Detection of TH can be done either by immunocytochemistry followed by cell counting (quantitative evaluation) or by western blot followed by densitometry analysis (Betarbet et al., 2000, Lee 1987, Fetissov 1999). http://purl.obolibrary.org/obo/PR_000001742 PR http://purl.obolibrary.org/obo/GO_0006575 GO tyrosine hydroxylase (TH) detection Detection of the enzyme TH by immunocytochemistry or western blot to quantify dopaminergic neurons. in_vivo substantia nigra pars compacta (SNpc) mouse dopaminergic neuron count decrease http://purl.obolibrary.org/obo/CL_0000575 CL http://purl.obolibrary.org/obo/GO_0008152 GO medium Detection of TH, the enzyme responsible for catalyzing the conversion of the amino acid L-tyrosine to L-3,4-dihydroxyphenylalanine (L-DOPA), a precursor for dopamine. Detection of TH can be done either by immunocytochemistry followed by cell counting (quantitative evaluation) or by western blot followed by densitometry analysis (Betarbet et al., 2000, Lee 1987, Fetissov 1999). http://purl.obolibrary.org/obo/CL_0000575 CL http://purl.obolibrary.org/obo/GO_0008152 GO western blot Western blot is used to quantify the expression of tyrosine hydroxylase (TH), dopamine transporter (DAT) and vesicular monoamine transporter type 2 (VMAT2) followed by densitometry analysis. in_vitro nigrostriatal pathway protein expression levels change medium Detection of TH can be done either by immunocytochemistry followed by cell counting (quantitative evaluation) or by western blot followed by densitometry analysis http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0006454 GO western blot Detection of tyrosine hydroxylase (TH) by western blot followed by densitometry analysis. in_vivo substantia nigra striatum tyrosine hydroxylase protein levels change http://purl.obolibrary.org/obo/PR_000001742 PR http://purl.obolibrary.org/obo/OBI_0000192 OBI medium Detection of TH can be done either by immunocytochemistry followed by cell counting (quantitative evaluation) or by western blot followed by densitometry analysis (Betarbet et al., 2000, Lee 1987, Fetissov 1999). http://purl.obolibrary.org/obo/PR_000001742 PR http://purl.obolibrary.org/obo/GO_0006575 GO Akinesia test Measures the latency for an animal to move all four limbs as an indicator of motor initiation. in_vivo mice rats latency to move all limbs increase http://purl.obolibrary.org/obo/GO_0040011 GO medium the animal is placed on a flat surface and the latency until it has moved all of its four limbs is assessed. http://purl.obolibrary.org/obo/NCBITaxon_33208 NCBITAXON http://purl.obolibrary.org/obo/GO_0040011 GO DAT immunostaining Ex vivo detection of dopamine neuron terminals in the striatum using dopamine transporter immunostaining. in_vitro striatum mouse rat number of dopamine neuron terminals change low Staining of DA neuronal terminals in the striatum is therefore used as a more reliable indirect marker for striatal dopamine content. For the analysis of nigrostriatal terminals, the dopamine transporter (DAT) is visualized either by antibody-mediated staining in tissue slices or by the application of radioactively labeled DAT ligands. Dopamine transporter staining Visualizes dopamine neuron terminals in the striatum using antibody-mediated staining or radioactively labeled DAT ligands. in_vivo striatum mice rats non-human primates dopamine transporter expression not_specified http://purl.obolibrary.org/obo/PR_000001111 PR http://purl.obolibrary.org/obo/UBERON_0002435 UBERON medium the dopamine transporter (DAT) is visualized either by antibody-mediated staining in tissue slices or by the application of radioactively labeled DAT ligands. http://purl.obolibrary.org/obo/PR_000001111 PR http://purl.obolibrary.org/obo/GO_0015871 GO Forepaw Stride length Measurement of the distance between single steps of mice walking across a paper with ink applied to their forepaws. in_vivo mice distance between single steps change http://purl.obolibrary.org/obo/GO_0043464 GO low Forepaw Stride length during walking . Ink is applied to the forepaws and the mice walk across a blank sheet of paper. ... The distance between single steps on each side are measured http://purl.obolibrary.org/obo/GO_0040026 GO Forepaw stride length test Measures the distance between forepaw steps during walking to assess motor function. in_vivo mice forepaw stride length decrease http://purl.obolibrary.org/obo/GO_0040011 GO medium The distance between single steps on each side are measured. http://purl.obolibrary.org/obo/UBERON_0002101 UBERON http://purl.obolibrary.org/obo/GO_0040011 GO Grid test Measures forepaw distance and unsuccessful steps while mice hang upside down on a grid. in_vivo mice forepaw distance and step success rate not_specified http://purl.obolibrary.org/obo/GO_0040011 GO medium the average forepaw distance is measured by assessing the distance covered, divided by the number of successful forepaw steps. In the course of the analysis, the number of unsuccessful forepaw steps are detected and displayed as percentage of the total number of steps performed. http://purl.obolibrary.org/obo/UBERON_0002101 UBERON http://purl.obolibrary.org/obo/GO_0040011 GO Hang test Measures neuromuscular strength by assessing the ability of mice to hang upside down on a grid. in_vivo mice time hanging on grid decrease http://purl.obolibrary.org/obo/GO_0003012 GO medium Mice are placed on a horizontal grid. When the animals grabbed the grid with their fore- and hindpaws, the grid is inverted with the animal hanging upside down. http://purl.obolibrary.org/obo/UBERON_0000077 UBERON http://purl.obolibrary.org/obo/GO_0006936 GO HPLC or HPLC-MS for total dopamine Quantification of total dopamine and its metabolites (HVA and DOPAC) in homogenized striatal tissue using High-Performance Liquid Chromatography with electrochemical detection or mass spectrometry. ex_vivo striatum mice rats non-human primates total contents of dopamine and its two degradation metabolites HVA and DOPAC change http://purl.obolibrary.org/obo/CHEBI_17236 CHEBI http://purl.obolibrary.org/obo/OBI_0000113 OBI low the dopamine (metabolites) determined by HPLC with electrochemical detector or by HPLC-MS. The standard method used in the majority of experimental work is the determination of total contents of dopamine and its two degradation metabolites HVA and DOPAC. http://purl.obolibrary.org/obo/CHEBI_17236 CHEBI http://purl.obolibrary.org/obo/GO_0007165 GO HPLC with electrochemical detector Determines total contents of dopamine and its metabolites HVA and DOPAC in striatal tissue homogenates. ex_vivo striatum mice rats dopamine content not_specified http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/UBERON_0002435 UBERON low the striatum is quickly removed from experimental animals, homogenized in a suitable acidic buffer, and the dopamine (metabolites) determined by HPLC with electrochemical detector or by HPLC-MS. http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0042416 GO Human neurological rating scales Clinical evaluation of motor impairment and disability in Parkinson's disease patients using validated scales like UPDRS, Columbia University, or Northwestern University scales. in_vivo humans motor impairment and disability change http://purl.obolibrary.org/obo/DOID_10652 DOID low A recent systematic review and evaluation of currently used rating scales for the assessment of motor impairment and disability in PD patients identified the 1) Columbia University rating scale, 2) the Northwestern University Disability Scale, and 3) the Unified Parkinsons Disease rating scale http://purl.obolibrary.org/obo/GO_0050853 GO Microdialysis Measures extracellular dopamine levels in the striatum of live animals using a microdialysis probe. in_vivo striatum mice rats extracellular dopamine levels not_specified http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/OBI_0000218 OBI low For live in vivo detection of extracellular dopamine levels, a microdialysis probe is inserted into the striatum. http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0014045 GO Open field test Measures locomotor activity, distance traveled, and rearing behavior using infrared beams. in_vivo mice rats locomotor activity decrease http://purl.obolibrary.org/obo/GO_0040011 GO medium Infrared beams detect the animals activity for the determination of parameters such as the time spent locomoting, the distance travelled, or the number of rearings. http://purl.obolibrary.org/obo/NCBITaxon_33208 NCBITAXON http://purl.obolibrary.org/obo/GO_0040011 GO Open field test Assessment of animal activity using infrared beams to determine locomotion time, distance traveled, and rearing frequency. in_vivo time spent locomoting, distance travelled, or number of rearings change http://purl.obolibrary.org/obo/GO_0040026 GO low Open field test : Infrared beams detect the animals activity for the determination of parameters such as the time spent locomoting, the distance travelled, or the number of rearings. http://purl.obolibrary.org/obo/GO_0040026 GO PET Non-invasive imaging of dopamine neuron terminals using Positron Emission Tomography with fluorine-18 labeled L-[18F]-fluorodopa. in_vivo striatum humans non-human primates striatal uptake of L-[18F]-fluorodopa decrease http://purl.obolibrary.org/obo/CHEBI_5913 CHEBI low Based on its appropriate half life time of ca. 2 h for clinical investigations, fluorine-18 labeled L-[18F]-fluorodopa is routinely used in trace amounts for intravenous administration. Striatal uptake of L-[18F]-fluorodopa is followed by applying positron emission tomography (PET) (Leenders 1986). http://purl.obolibrary.org/obo/CL_0000772 CL http://purl.obolibrary.org/obo/GO_0006834 GO PET with L-[18F]-fluorodopa Positron emission tomography to follow striatal uptake of fluorine-18 labeled L-[18F]-fluorodopa after intravenous administration. in_vivo striatum humans non-human primates striatal uptake of L-[18F]-fluorodopa decrease low Based on its appropriate half life time of ca. 2 h for clinical investigations, fluorine-18 labeled L-[18F]-fluorodopa is routinely used in trace amounts for intravenous administration. Striatal uptake of L-[18F]-fluorodopa is followed by applying positron emission tomography (PET) Pole test Measures the time for an animal to turn and descend a pole as an indicator of motor function. in_vivo mice rats time to turn and descend increase http://purl.obolibrary.org/obo/GO_0040011 GO medium the animal is placed on a gauze-taped pole with the head upwards below the top of the pole. Two parameters are detected: 1) time until animals turn by 180°; 2) time until the animals reach the floor. http://purl.obolibrary.org/obo/NCBITaxon_33208 NCBITAXON http://purl.obolibrary.org/obo/GO_0040011 GO Pole test Assessment of motor function by measuring the time taken for an animal to turn 180 degrees and reach the floor on a gauze-taped pole. in_vivo time until 180 degree turn and time to reach floor change http://purl.obolibrary.org/obo/GO_0050853 GO low Pole test : the animal is placed on a gauze-taped pole with the head upwards below the top of the pole. Two parameters are detected: 1) time until animals turn by 180°; 2) time until the animals reach the floor. http://purl.obolibrary.org/obo/GO_0050853 GO Rotarod test Assesses motor coordination by measuring the latency for animals to fall from a rotating rod. in_vivo mice rats latency to fall decrease http://purl.obolibrary.org/obo/GO_0000002 GO medium The animals are placed on a rotating rod that is subjected to linear acceleration. The latency to fall from the rod is detected. http://purl.obolibrary.org/obo/NCBITaxon_33208 NCBITAXON http://purl.obolibrary.org/obo/GO_0000002 GO Rotation test Assessment of asymmetric motor behavior in rodents or non-human primates following unilateral lesion of the nigrostriatal system, often triggered by amphetamine. in_vivo rodents non-human primates number of left- and right turns change http://purl.obolibrary.org/obo/GO_0050853 GO low the asymmetry of remaining dopamine neurons (only on one side) triggers spontaneous asymmetric motor behaviour, i.e. rotations of the animals. http://purl.obolibrary.org/obo/GO_0050853 GO Rotation test Measures asymmetric motor behavior in animals with unilateral nigrostriatal lesions after dopamine system stimulation. in_vivo mice rats non-human primates number of rotations increase http://purl.obolibrary.org/obo/GO_0007610 GO medium the asymmetry of remaining dopamine neurons (only on one side) triggers spontaneous asymmetric motor behaviour, i.e. rotations of the animals. http://purl.obolibrary.org/obo/CL_0000604 CL http://purl.obolibrary.org/obo/GO_0040011 GO SPECT (Single Photon Emission Computed Tomography) Non-invasive monitoring of dopamine transporter (DAT) using the ligand Iodine-123-β-CIT. in_vivo monkeys humans dopamine transporter (DAT) levels change http://purl.obolibrary.org/obo/OBI_0000210 OBI low Single photon emission computed tomography (SPECT) : monitoring of dopamine transporter (DAT). Iodine-123-β-CIT is used as a sensitive ligand for dopamine and serotonin transporters http://purl.obolibrary.org/obo/GO_0005488 GO SPECT with [123I]-β-CIT Monitors dopamine transporter expression in the striatum using single photon emission computed tomography. in_vivo striatum humans non-human primates dopamine transporter binding decrease http://purl.obolibrary.org/obo/PR_000001111 PR low Iodine-123-β-CIT is used as a sensitive ligand for dopamine and serotonin transporters and was applied in monkeys and humans. http://purl.obolibrary.org/obo/PR_000001111 PR http://purl.obolibrary.org/obo/GO_0015871 GO Tyrosine hydroxylase staining Stains dopamine neurons in the substantia nigra pars compacta using tyrosine hydroxylase as a marker. ex_vivo substantia nigra pars compacta mice rats number of dopamine neurons not_specified http://purl.obolibrary.org/obo/PR_000001600 PR http://purl.obolibrary.org/obo/CL_0000604 CL medium Tyrosine hydroxylase (TH) was regularly stained as marker for DA neurons. http://purl.obolibrary.org/obo/CL_0000604 CL http://purl.obolibrary.org/obo/GO_0008219 GO Unified Parkinson's Disease Rating Scale Clinical rating scale for assessing motor impairment and disability in Parkinson's disease patients. in_vivo humans motor symptom score increase http://purl.obolibrary.org/obo/GO_0003008 GO low the Unified Parkinsons Disease rating scale ... evaluate several parameters, some of which are not motor related. Thus, only subscales are useful for readout of motor symptoms (e.g. 13 of the 42 UPDRS parameters). http://purl.obolibrary.org/obo/NCBITaxon_9606 NCBITAXON http://purl.obolibrary.org/obo/GO_0040011 GO acridine orange staining Acridine orange (AO) is a weak base that accumulates in acidic compartments like lysosomes. Red fluorescence indicates high concentration in acidic vesicles, while green fluorescence indicates lower concentration in other cell parts. in_vitro fluorescence intensity (red/green) change medium Changes in morphology can be observed by using acridine orange (AO), a weak base that accumulates in the acidic compartment of the cell mainly composed of lysosomes. Red fluorescence is exhibited when it is highly concentrated in acidic vesicles, while green fluorescence is exhibited when it's less concentrated in other parts of the cell (Li et al., 2000; Reiners et al., 2002; Kroemer and Jäättelä, 2005). http://purl.obolibrary.org/obo/CL_0000272 CL http://purl.obolibrary.org/obo/GO_0000305 GO acridine orange staining This assay uses acridine orange (AO), a weak base that accumulates in acidic compartments, to visualize lysosomal morphology and acidification via fluorescence microscopy or flow cytometry. in_vitro lysosomal acidification and morphology change http://purl.obolibrary.org/obo/GO_0005764 GO http://purl.obolibrary.org/obo/CHEBI_22438 CHEBI medium Changes in morphology can be observed by using acridine orange (AO), a weak base that accumulates in the acidic compartment of the cell mainly composed of lysosomes. This is followed by flow cytometry (Zhao et al., 2001), static cytofluometry or flow cytofluometry (Antunes et al., 2001). http://purl.obolibrary.org/obo/GO_0005764 GO antibody staining Staining with antibodies against lysosomal membrane proteins to achieve specific localization or identification. in_vitro lysosomal membrane protein localization not_specified low More specific staining can be achieved by staining with antibodies against lysosomal membrane proteins confocal microscopy High-resolution imaging used to visualize lysosomal morphology, localization, and dynamics. in_vitro lysosomal morphology, localization, and dynamics change http://purl.obolibrary.org/obo/GO_0005748 GO http://purl.obolibrary.org/obo/UBERON_0000001 UBERON low Confocal microscopy enables high-resolution imaging of cellular structures, including lysosomes. By visualizing lysosomal morphology, localization, and dynamics, confocal microscopy can directly demonstrate alterations in lysosomes caused by disruption. http://purl.obolibrary.org/obo/GO_0005748 GO flow cytometry Flow cytometry is used to quantify changes observed after acridine orange staining, providing a quantitative assessment of lysosomal content and acidity. in_vitro fluorescence intensity change high This is followed by flow cytometry (Zhao et al., 2001), static cytofluometry or flow cytofluometry (Antunes et al., 2001). http://purl.obolibrary.org/obo/CL_0000272 CL http://purl.obolibrary.org/obo/GO_0000305 GO flow cytometry Quantitative analysis of lysosomal changes using flow cytometry with dyes such as acridine orange, LysoTracker Green, or LysoSensor probes. in_vitro lysosomal acidification and permeability change http://purl.obolibrary.org/obo/GO_0005764 GO http://purl.obolibrary.org/obo/GO_0043303 GO http://purl.obolibrary.org/obo/GO_0016328 GO medium Changes in morphology can be observed by using acridine orange (AO), a weak base that accumulates in the acidic compartment of the cell mainly composed of lysosomes. This is followed by flow cytometry (Zhao et al., 2001), static cytofluometry or flow cytofluometry (Antunes et al., 2001). Lysotracker green (200 nM) is regularly used to assess lysosomal acidification; Anguissola and colleagues reported that it was excited through a 475+/240 nm band pass filter and fluorescence emission was collected through a 515+/220 nm band pass filter. Analysis is performed using microscopical methods such as High Content Analysis (Anguissola et al., 2014). More specific staining can be achieved by staining with antibodies against lysosomal membrane proteins (Kroemer and Jäättelä, 2005). http://purl.obolibrary.org/obo/GO_0005764 GO fluorescence microscopy This assay uses fluorescence microscopy to analyze lysosomal morphology, localization, and dynamics, enabling direct visualization of lysosomal alterations caused by disruption. in_vitro lysosomal morphology and localization change http://purl.obolibrary.org/obo/GO_0005764 GO low Lysosomes are typically analysed microscopically, usually with fluorescence microscopy (Kagedal et al., 2001). Confocal microscopy enables high-resolution imaging of cellular structures, including lysosomes. By visualizing lysosomal morphology, localization, and dynamics, confocal microscopy can directly demonstrate alterations in lysosomes caused by disruption. http://purl.obolibrary.org/obo/GO_0005764 GO http://purl.obolibrary.org/obo/GO_0007032 GO immunostaining of lysosomal membrane proteins This assay uses antibodies against lysosomal membrane proteins to visualize lysosomal membrane integrity and localization via fluorescence microscopy. in_vitro lysosomal membrane protein localization change http://purl.obolibrary.org/obo/GO_0005765 GO http://purl.obolibrary.org/obo/OBI_0000286 OBI low More specific staining can be achieved by staining with antibodies against lysosomal membrane proteins (Kroemer and Jäättelä, 2005). http://purl.obolibrary.org/obo/GO_0005765 GO Lysotracker green staining This assay uses Lysotracker green to assess lysosomal acidification via fluorescence microscopy or high-content analysis. in_vitro lysosomal acidification change http://purl.obolibrary.org/obo/GO_0005764 GO high Lysotracker green (200 nM) is regularly used to assess lysosomal acidification; Anguissola and colleagues reported that it was excited through a 475+/240 nm band pass filter and fluorescence emission was collected through a 515+/220 nm band pass filter. Analysis is performed using microscopical methods such as High Content Analysis (Anguissola et al., 2014). http://purl.obolibrary.org/obo/GO_0005764 GO proteomics analysis This assay uses proteomics to identify changes in protein expression or post-translational modifications associated with lysosome disruption, providing insights into molecular mechanisms. in_vitro protein expression and post-translational modifications change http://purl.obolibrary.org/obo/OBI_0000185 OBI http://purl.obolibrary.org/obo/GO_0043412 GO medium Proteomics analysis can offer a comprehensive view of the changes in protein expression, or post-translational modifications associated with lysosome disruption. By identifying alterations in protein profiles, proteomics can provide valuable insights into the molecular mechanisms involved in lysosomal dysfunction. http://purl.obolibrary.org/obo/GO_0005764 GO Chemotaxis assay Measures the migration of inflammatory cells (e.g., neutrophils) towards a chemoattractant using a chemotaxis chamber with nitrocellulose filters. in_vitro neutrophils number of migrated cells increase http://purl.obolibrary.org/obo/GO_0016477 GO http://purl.obolibrary.org/obo/GO_0006935 GO medium Chemotaxis assays can be performed in vitro/ex vivo by using Chemotaxis Chambers (for example Neuro Probe Chambers). Supernatants can be added to the bottom well of the chamber and 3–8 mm nitrocellulose filters are placed on top, while the top chamber contains the inflammatory cells (for example neutrophils). After a certain time period, the number of migrated cells towards the lower chamber can be determined by staining of the cells http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0006935 GO Haematoxylin and eosin staining Analyzes the influx of inflammatory cells (mainly neutrophils) in tissue sections through histological staining. in_vivo infiltration of inflammatory cells increase http://purl.obolibrary.org/obo/GO_0006954 GO http://purl.obolibrary.org/obo/CL_0000775 CL low Influx of inflammatory cells (mainly neutrophils) can be analysed by tissue staining by using Haematoxylin and eosin http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0006954 GO Histopathology Tissue staining with Haematoxylin and eosin is used to analyse the influx of inflammatory cells, mainly neutrophils. in_vivo neutrophils Influx of inflammatory cells increase http://purl.obolibrary.org/obo/GO_0002162 GO low Influx of inflammatory cells (mainly neutrophils) can be analysed by tissue staining by using Haematoxylin and eosin [13] http://purl.obolibrary.org/obo/UBERON_0000004 UBERON http://purl.obolibrary.org/obo/GO_0002162 GO Mouse MPO ELISA Quantifies neutrophil influx in mouse tissue lysates using a myeloperoxidase (MPO) ELISA kit. in_vivo Mus musculus myeloperoxidase activity increase http://purl.obolibrary.org/obo/PR_000011150 PR http://purl.obolibrary.org/obo/CL_0000775 CL medium In mice, neutrophil influx can be analysed using a mouse MPO ELISA kit for lysed tissue http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0006954 GO MPO ELISA Measures the influx of neutrophils in tissue lysates using a mouse MPO ELISA kit. ex_vivo http://purl.obolibrary.org/obo/CL_0000775 http://purl.obolibrary.org/obo/NCBITaxon_10090 neutrophil influx increase http://purl.obolibrary.org/obo/GO_0004601 GO medium In mice, neutrophil influx can be analysed using a mouse MPO ELISA kit for lysed tissue http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0006954 GO ELISA This assay quantifies plasma levels of pro-inflammatory cytokines using commercial kits, indicating systemic inflammatory responses. in_vivo plasma levels of pro-inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO medium Plasma levels of pro-inflammatory cytokines can be analysed by enzyme linked immunosorbent assay) ELISA using commercial kits http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO Haematoxylin and eosin staining This assay stains tissue sections to visualize histological features, including the influx of inflammatory cells such as neutrophils, confirming liver inflammation. in_vivo liver mouse infiltration of inflammatory cells increase http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0006954 GO low Liver inflammation is usually confirmed by analysis of histological features, marked by influx of inflammatory cells (mainly neutrophils) which can be stained by using Haematoxylin and eosin http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO Mouse MPO ELISA Enzyme-linked immunosorbent assay (ELISA) using a mouse myeloperoxidase (MPO) kit to quantify neutrophil infiltration in liver tissue lysates, indicating liver inflammation. in_vivo liver mice neutrophil infiltration increase low In mice, neutrophil influx can be analysed using a mouse MPO ELISA kit for lysed tissue [4]. http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0006996 GO MPO ELISA This assay quantifies myeloperoxidase (MPO) levels in lysed liver tissue, serving as a marker for neutrophil influx and inflammation. in_vivo liver mouse MPO levels increase http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0006954 GO medium In mice, neutrophil influx can be analysed using a mouse MPO ELISA kit for lysed tissue http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0006954 GO Real-time PCR This assay measures mRNA expression levels of inflammatory cytokines in tissue samples, indicating inflammatory responses. in_vivo liver mRNA expression of inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO medium mRNA expression levels of inflammatory cytokines in tissue samples can be determined by using real-time PCR as described in http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO DTNB assay Total glutathione is determined using enzyme recycling, where GSH reacts with DTNB (Ellman's reagent) in the presence of glutathione reductase, producing a yellow colored product measured at 412 nm. in_vitro total glutathione levels not_specified http://purl.obolibrary.org/obo/CHEBI_24864 CHEBI medium Enzyme recycling is a widely accepted method to determine total glutathione, in which GSH reacts with DTNB (Ellman's reagent) in the presence of glutathione reductase. Glutathione reductase reduces GSSG to GSH, which then reacts with DTNB to produce a yellow colored 5-thio-2-nitrobenzoic acid (TNB), which absorbs light at a wavelength of 412 nm (Tipple and Rogers, 2012). http://purl.obolibrary.org/obo/CHEBI_24864 CHEBI http://purl.obolibrary.org/obo/GO_0055155 GO Enzyme recycling assay Measures total glutathione by recycling GSH with glutathione reductase and DTNB, producing a yellow-colored TNB that absorbs light at 412 nm. in_vitro total glutathione levels not_specified http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0004362 GO medium Enzyme recycling is a widely accepted method to determine total glutathione, in which GSH reacts with DTNB (Ellman's reagent) in the presence of glutathione reductase. http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0006749 GO HPLC with fluorometric detection Measures glutathione levels using HPLC separation and fluorometric detection after derivatization with iodoacetic acid and dansyl chloride. in_vitro glutathione levels not_specified http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI low Another method uses HPLC separation and fluorometric detection, where iodoactetic acid is added as a thiol akylating agent followed by dansyl chloride derivatization for fluorometric detection. http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0006749 GO Monochlorobimane assay Measures glutathione levels by forming a fluorescent GSH-monochlorobimane adduct that can be measured fluorometrically. in_vitro glutathione levels not_specified http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI medium monochlorobimane can be added to culture medium in order to form a fluorescent GSH-monochlorobimane adduct that can be measured fluorometrically http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0006749 GO monochlorobimane assay Glutathione levels are measured fluorometrically by forming a fluorescent GSH-monochlorobimane adduct after adding monochlorobimane to culture medium. in_vitro GSH-monochlorobimane adduct fluorescence not_specified http://purl.obolibrary.org/obo/CHEBI_24864 CHEBI medium Similarly, monochlorobimane can be added to culture medium in order to form a fluorescent GSH-monochlorobimane adduct that can be measured fluorometrically (Kamencic et al., 2000). http://purl.obolibrary.org/obo/CHEBI_24864 CHEBI http://purl.obolibrary.org/obo/GO_0055155 GO Biotin labeling of glutathione Detects glutathione adducts on S-thiolated proteins using biotin labeling. in_vitro glutathione adducts on proteins not_specified http://purl.obolibrary.org/obo/GO_0019904 GO low Labeling of Glutathione: Use 35S-cysteine radiolabeling or biotin labeling to detect glutathione adducts on S-thiolated proteins. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019904 GO Fluorometric analysis of total S-glutathionylated proteins Quantifies total S-glutathionylated proteins by lysing samples in non-reducing buffer, precipitating proteins, reducing glutathionyl-protein adducts, and derivatizing thiols with fluorescence probes, followed by fluorometric measurement with or without HPLC separation. in_vitro total S-glutathionylated proteins not_specified http://purl.obolibrary.org/obo/GO_0019904 GO medium Quantification of Total S-Glutathionylated Proteins: Use sample lysis or homogenization in non-reducing buffer containing N-ethylmaleimide to eliminate thiols, followed by protein precipitation, reduction of gluthionyl-protein adducts, and derivatization of protein thiols or free glutathione with fluorescence probes. Fluorescence can be measured by fluorometric analysis with or without prior HPLC separation. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019904 GO Top-down proteomic approach Identifies S-glutathionylated proteins using liquid chromatography-coupled mass spectrometry on whole protein extracts from cells without labeling or anti-glutathione antibodies. in_vitro S-glutathionylated proteins not_specified http://purl.obolibrary.org/obo/GO_0019904 GO http://purl.obolibrary.org/obo/OBI_0000470 OBI medium Top-Down Proteomic Approach: Use liquid chromatography-coupled mass spectrometry to identify S-glutathionylated proteins on whole protein extract from cells without using labeling or anti-glutathione antibody. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019904 GO Western blot Use of anti-glutathione antibodies to detect glutathionylated proteins, specifically useful for individual proteins like eNOS. in_vitro glutathionylated proteins not_specified not_specified Use of Anti-Glutathione Antibodies Use commercially available anti-glutathione to detect glutathionylated proteins by Western blots, immunoprecipitation or immunocytolocalization. DAF-2 DA fluorescent indicator Measures NO production using the fluorescent indicator DAF-2 DA. in_vitro NO production increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/OBI_0000274 OBI high NO production can be measured through ... in situ fluorescent signal detection with fluorescent indicator DAF-2 DA (Itoh et al., 2000; Nagata et al., 1999; Qiu et al., 2001) http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0006809 GO EPR spin-trapping Detects superoxide or NO production using electron paramagnetic resonance spin-trapping. in_vitro superoxide or NO production increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI low Superoxides can be detected using several standard methods including ... electron paramagnetic resonance (EPR) spin-trapping (Roubaud et al., 1997) NO production can be measured through ... EPR spin-trapping (Xia et al., 2000) http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0006809 GO HPLC/fluorescence This assay uses HPLC with a fluorescence detector to measure dihydroethidium-derived fluorescence, indicating superoxide levels. in_vitro superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_30764 CHEBI medium Superoxides can be detected using several standard methods including ... HPLC/fluorescence detector-based assay using dihydroethidium (Fink et al., 2004; Zhao et al., 2003). http://purl.obolibrary.org/obo/CHEBI_30764 CHEBI http://purl.obolibrary.org/obo/GO_0003676 GO HPLC/fluorescence detector-based assay using dihydroethidium Measures superoxide production using dihydroethidium detected by HPLC with a fluorescence detector. in_vitro superoxide production increase http://purl.obolibrary.org/obo/CHEBI_26636 CHEBI http://purl.obolibrary.org/obo/OBI_0000278 OBI medium Superoxides can be detected using several standard methods including ... HPLC/fluorescence detector-based assay using dihydroethidium (Fink et al., 2004; Zhao et al., 2003) http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0042553 GO L-arginine to L-citrulline conversion This assay measures NO production through the conversion of L-arginine to L-citrulline. in_vitro L-citrulline levels increase http://purl.obolibrary.org/obo/CHEBI_6259 CHEBI http://purl.obolibrary.org/obo/CHEBI_30758 CHEBI medium NO production can be measured through the conversion of L-arginine to L-citrulline (de Bono et al., 2007) http://purl.obolibrary.org/obo/GO_0005981 GO http://purl.obolibrary.org/obo/GO_0006814 GO L-arginine to L-citrulline conversion assay Measures NO production by quantifying the conversion of L-arginine to L-citrulline. in_vitro NO production increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI medium NO production can be measured through the conversion of L-arginine to L-citrulline (de Bono et al., 2007) http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0006809 GO lucigenin-enhanced chemiluminescence Measures superoxide production using lucigenin-enhanced chemiluminescence. in_vitro superoxide production increase http://purl.obolibrary.org/obo/CHEBI_26636 CHEBI http://purl.obolibrary.org/obo/OBI_0000274 OBI medium Superoxides can be detected using several standard methods including lucigenin-enhanced chemiluminescence (Münzel et al., 2002; Tarpey et al., 1999) http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0042553 GO nitrate/nitrite determination This assay determines the total nitrate and nitrite concentration, reflecting NO production. in_vitro nitrate/nitrite concentration increase http://purl.obolibrary.org/obo/CHEBI_59888 CHEBI http://purl.obolibrary.org/obo/CHEBI_59889 CHEBI http://purl.obolibrary.org/obo/CHEBI_30758 CHEBI medium NO production can be measured through ... the determination of total nitrate and nitrite concentration (Crabtree et al., 2009; Du et al., 2013). http://purl.obolibrary.org/obo/CHEBI_30758 CHEBI http://purl.obolibrary.org/obo/GO_0006814 GO total nitrate and nitrite concentration determination Measures NO production by determining total nitrate and nitrite concentration. in_vitro NO production increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/CHEBI_17632 CHEBI medium NO production can be measured through ... the determination of total nitrate and nitrite concentration (Crabtree et al., 2009; Du et al., 2013) http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0006809 GO DAF-2 DA fluorescence This assay measures nitric oxide production using the fluorescent indicator DAF-2 DA, detecting in situ fluorescent signals. in_vitro Fluorescent signal intensity increase http://purl.obolibrary.org/obo/CHEBI_30797 CHEBI medium NO production can be measured through ... in situ fluorescent signal detection with fluorescent indicator DAF-2 DA (Itoh et al., 2000; Nagata et al., 1999; Qiu et al., 2001) http://purl.obolibrary.org/obo/CHEBI_30797 CHEBI http://purl.obolibrary.org/obo/GO_0006827 GO DAF-2 DA fluorescent signal detection Measures NO production through in situ fluorescent signal detection using the fluorescent indicator DAF-2 DA. in_vitro NO production not_specified http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI not_specified in situ fluorescent signal detection with fluorescent indicator DAF-2 DA (Itoh et al., 2000; Nagata et al., 1999; Qiu et al., 2001) http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006807 GO EPR spin-trapping Electron Paramagnetic Resonance (EPR) spectroscopy using spin-trapping agents to detect nitric oxide radicals. in_vitro EPR signal not_specified http://purl.obolibrary.org/obo/OBI_0001211 OBI low EPR spin-trapping http://purl.obolibrary.org/obo/CHEBI_16514 CHEBI EPR spin-trapping Measures NO production using electron paramagnetic resonance (EPR) spin-trapping. in_vitro NO production not_specified http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI not_specified EPR spin-trapping (Xia et al., 2000) http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006807 GO EPR spin-trapping This assay measures nitric oxide production using EPR spin-trapping. in_vitro Spin adduct formation increase http://purl.obolibrary.org/obo/CHEBI_30797 CHEBI low NO production can be measured through ... EPR spin-trapping (Xia et al., 2000) http://purl.obolibrary.org/obo/CHEBI_30797 CHEBI http://purl.obolibrary.org/obo/GO_0006827 GO L-arginine to L-citrulline conversion This assay measures nitric oxide production by quantifying the conversion of L-arginine to L-citrulline. in_vitro L-citrulline concentration increase http://purl.obolibrary.org/obo/CHEBI_5952 CHEBI http://purl.obolibrary.org/obo/GO_0006827 GO low NO production can be measured through the conversion of L-arginine to L-citrulline (de Bono et al., 2007) http://purl.obolibrary.org/obo/GO_0005981 GO http://purl.obolibrary.org/obo/GO_0006827 GO L-arginine to L-citrulline conversion Measures NO production through the conversion of L-arginine to L-citrulline. in_vitro NO production not_specified http://purl.obolibrary.org/obo/GO_0006807 GO not_specified NO production can be measured through the conversion of L-arginine to L-citrulline (de Bono et al., 2007) http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006807 GO L-arginine to L-citrulline conversion assay Measures nitric oxide (NO) production by quantifying the conversion of L-arginine to L-citrulline, a reaction catalyzed by nitric oxide synthase. in_vitro L-citrulline production from L-arginine increase http://purl.obolibrary.org/obo/GO_0034109 GO http://purl.obolibrary.org/obo/CHEBI_16581 CHEBI http://purl.obolibrary.org/obo/CHEBI_16582 CHEBI not_specified NO production can be measured through the conversion of L-arginine to L-citrulline (de Bono et al., 2007) http://purl.obolibrary.org/obo/CHEBI_16467 CHEBI http://purl.obolibrary.org/obo/GO_0034109 GO Nitrate/Nitrite determination This assay measures nitric oxide production by determining the total nitrate and nitrite concentration. in_vitro Nitrate and nitrite concentration increase http://purl.obolibrary.org/obo/CHEBI_59975 CHEBI http://purl.obolibrary.org/obo/CHEBI_59976 CHEBI low NO production can be measured through ... the determination of total nitrate and nitrite concentration (Crabtree et al., 2009; Du et al., 2013) http://purl.obolibrary.org/obo/CHEBI_30797 CHEBI http://purl.obolibrary.org/obo/GO_0006828 GO Total nitrate and nitrite concentration determination Measures NO production through the determination of total nitrate and nitrite concentration. in_vitro NO production not_specified http://purl.obolibrary.org/obo/CHEBI_17632 CHEBI http://purl.obolibrary.org/obo/CHEBI_16482 CHEBI not_specified the determination of total nitrate and nitrite concentration (Crabtree et al., 2009; Du et al., 2013) http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006807 GO ELISA Measures levels of BH4 using commercially available enzyme-linked immunosorbent assay kits. in_vitro levels of BH4 not_specified http://purl.obolibrary.org/obo/CHEBI_15715 CHEBI high ELISA kits for BH4 are also commercially available. http://purl.obolibrary.org/obo/CHEBI_15715 CHEBI http://purl.obolibrary.org/obo/GO_0006729 GO HPLC with electrochemical and fluorescence detection Measures levels of BH4, BH2, and biopterin using reverse-phase high-performance liquid chromatography with electrochemical detection for BH4 and fluorescence detection for BH2 and biopterin. in_vitro levels of BH4, BH2, and biopterin not_specified http://purl.obolibrary.org/obo/CHEBI_15715 CHEBI http://purl.obolibrary.org/obo/CHEBI_17843 CHEBI low Levels of BH4, BH2 and biopterin levels can be determined by reverse-phase high-performance liquid chromatography (HPLC) followed by electrochemical detection (for BH4) and fluorescence detection (for BH2 and biopterin) (Howells et al., 1986). http://purl.obolibrary.org/obo/CHEBI_15715 CHEBI http://purl.obolibrary.org/obo/GO_0006729 GO LC-MS/MS Measures levels of BH4, BH2, and biopterin using liquid chromatography coupled with tandem mass spectrometry, validated for detection in plasma from multiple species. in_vitro plasma human monkey dog rabbit rat mouse levels of BH4, BH2, and biopterin not_specified http://purl.obolibrary.org/obo/CHEBI_15715 CHEBI http://purl.obolibrary.org/obo/OBI_0000475 OBI medium A LC-MS/MS method has been published by Zhao et al. (2009), which was validated for detection in human, monkey, dog, rabbit, rat and mouse plasma, and used to support a successful drug approval submission. http://purl.obolibrary.org/obo/CHEBI_15715 CHEBI http://purl.obolibrary.org/obo/GO_0006729 GO HPLC Quantifies neopterin levels after conversion of enzymatically formed dihydroneopterin triphosphate into neopterin by sequential iodine oxidation and dephosphorylation. in_vitro neopterin levels decrease http://purl.obolibrary.org/obo/CHEBI_16856 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium The activity of GTPCH-1 can be detected through the quantification of neopterin by high-performance liquid chromatography (HPLC) after the conversion of enzymatically formed dihydroneopterin triphosphate into neopterin by sequential iodine oxidation and dephosphorylation. http://purl.obolibrary.org/obo/PR_000012449 PR http://purl.obolibrary.org/obo/GO_0006729 GO HPLC quantification of neopterin Quantifies neopterin levels via high-performance liquid chromatography following the enzymatic conversion of dihydroneopterin triphosphate to neopterin through iodine oxidation and dephosphorylation. in_vitro neopterin concentration decrease http://purl.obolibrary.org/obo/CHEBI_35634 CHEBI not_specified The activity of GTPCH-1 can be detected through the quantification of neopterin by high-performance liquid chromatography (HPLC) after the conversion of enzymatically formed dihydroneopterin triphosphate into neopterin by sequential iodine oxidation and dephosphorylation. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0003824 GO acetylcholine stimulation Vasodilation is measured after intra-arterial administration of acetylcholine to enhance NO release. in_vivo arteries vasodilation increase http://purl.obolibrary.org/obo/GO_0005282 GO low For the invasive approach, vasodilation is measured after intra-arterial pharmacologic stimulation with substances that enhance NO release (e.g. acetylcholine, bradykinin). http://purl.obolibrary.org/obo/UBERON_0000138 UBERON http://purl.obolibrary.org/obo/GO_0005282 GO flow-mediated vasodilation (FMD) Evaluates flow-mediated vasodilation in superficial arteries using non-invasive ultrasound-based methods. in_vivo brachial artery radial artery femoral artery flow-mediated vasodilation increase http://purl.obolibrary.org/obo/GO_0043084 GO Corretti et al. 2002 medium The non-invasive ultrasound-based method evaluates flow-mediated vasodilation (FMD) in the superficial arteries, such as brachial, radial, or femoral vessels. Guidelines for the measurement of FMD have been published (Corretti et al. 2002). http://purl.obolibrary.org/obo/UBERON_0001021 UBERON http://purl.obolibrary.org/obo/GO_0043084 GO flow-mediated vasodilation (FMD) Flow-mediated vasodilation (FMD) is evaluated in superficial arteries (brachial, radial, or femoral) using ultrasound. in_vivo brachial artery radial artery femoral artery vasodilation increase http://purl.obolibrary.org/obo/GO_0005282 GO Corretti et al. 2002 medium The non-invasive ultrasound-based method evaluates flow-mediated vasodilation (FMD) in the superficial arteries, such as brachial, radial, or femoral vessels. Guidelines for the measurement of FMD have been published (Corretti et al. 2002). http://purl.obolibrary.org/obo/UBERON_0000138 UBERON http://purl.obolibrary.org/obo/GO_0005282 GO intra-arterial pharmacologic stimulation An invasive method measuring vasodilation in response to the intra-arterial administration of substances like acetylcholine or bradykinin that enhance NO release. in_vivo vasodilation change http://purl.obolibrary.org/obo/GO_0051042 GO low For the invasive approach, vasodilation is measured after intra-arterial pharmacologic stimulation with substances that enhance NO release (e.g. acetylcholine, bradykinin). http://purl.obolibrary.org/obo/UBERON_0000634 UBERON http://purl.obolibrary.org/obo/GO_0051042 GO invasive vasodilation measurement Measures vasodilation after intra-arterial pharmacologic stimulation with substances that enhance NO release, such as acetylcholine or bradykinin. in_vivo arteries vasodilation increase http://purl.obolibrary.org/obo/GO_0043084 GO low vasodilation is measured after intra-arterial pharmacologic stimulation with substances that enhance NO release (e.g. acetylcholine, bradykinin) http://purl.obolibrary.org/obo/UBERON_0001021 UBERON http://purl.obolibrary.org/obo/GO_0043084 GO EGFR inhibition assay EGFR activity is suppressed using EGFR inhibitors (AG1478, BIBX 1522) or neutralizing antibodies to demonstrate EGFR’s involvement in signaling. in_vitro EGFR activity decrease low Suppression of EGFR activity with EGFR inhibitors such as AG1478 and BIBX 1522 or neutralizing antibodies is well suited to demonstrate EGFR’s involvement in signaling (Memon et al., 2020, Perrais et al., 2002, Val et al., 2012, Wang et al., 2019, Yu et al., 2012b). http://purl.obolibrary.org/obo/GO_0007179 GO http://purl.obolibrary.org/obo/GO_0007165 GO ELISA Detects and quantifies phosphorylated (active) EGFR using enzyme-linked immunosorbent assay. in_vitro phosphorylated EGFR levels increase medium Phosphorylated, hence active EGFR can be detected and quantified also by Enzyme-Linked Immunosorbent Assay (ELISA) http://purl.obolibrary.org/obo/PR_000001129 PR http://purl.obolibrary.org/obo/GO_0007173 GO Western blot Measures phosphorylated EGFR in cell or tissue lysates using specific antibodies to detect activated EGFR. in_vitro phosphorylated EGFR levels increase http://purl.obolibrary.org/obo/OBI_0000619 OBI low Proof of EGFR activation can be derived from protein-analytical techniques such as Western blots of e.g. untreated and treated cell or tissue lysates using specific antibodies targeting the phosphorylated EGFR epitopes http://purl.obolibrary.org/obo/PR_000001129 PR http://purl.obolibrary.org/obo/GO_0007173 GO chromatin immunoprecipitation Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo. It involves crosslinking proteins and DNA, isolating nuclear fractions, shearing DNA, immunoprecipitation with an antibody, reversing crosslinking, and sequencing associated DNA fragments. in_vivo enrichment of specific DNA sequences increase http://purl.obolibrary.org/obo/GO_0003677 GO http://purl.obolibrary.org/obo/OBI_0000073 OBI low Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo. Enrichment of specific DNA sequences represents regions on the genome that the protein of interest is associated with in vivo. http://purl.obolibrary.org/obo/CHEBI_0001367 CHEBI http://purl.obolibrary.org/obo/OBI_0000073 OBI Chromatin immunoprecipitation Measures the interaction of proteins with specific genomic regions in vivo by crosslinking, shearing DNA, and sequencing associated DNA fragments. in_vivo protein-DNA interaction not_specified http://purl.obolibrary.org/obo/OBI_0001051 OBI http://purl.obolibrary.org/obo/GO_0044877 GO low Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo. It involves the treatment of cells with formaldehyde to crosslink neighboring protein-protein and protein-DNA molecules. Nuclear fractions are isolated, the genomic DNA is sheared, and nuclear lysates are used in immunoprecipitations with an antibody against the protein of interest. After reversal of the crosslinking, the associated DNA fragments are sequenced. http://purl.obolibrary.org/obo/GO_0003677 GO electrophoretic mobility shift assay Electrophoretic mobility shift assay (EMSA) studies DNA-binding protein interactions in vitro by observing slower migration of protein-DNA complexes through a non-denaturing polyacrylamide gel compared to free DNA fragments. Components are identified with antibodies. in_vitro migration rate of protein-DNA complexes change http://purl.obolibrary.org/obo/GO_0003677 GO http://purl.obolibrary.org/obo/OBI_0000073 OBI medium Electrophoretic mobility shift assay (EMSA) provides a rapid method to study DNA-binding protein interactions in vitro. This relies on the fact that complexes of protein and DNA migrate through a non-denaturing polyacrylamide gel more slowly than free DNA fragments. http://purl.obolibrary.org/obo/CHEBI_0001367 CHEBI http://purl.obolibrary.org/obo/OBI_0000073 OBI Electrophoretic mobility shift assay Measures DNA-binding protein interactions in vitro by detecting slower migration of protein-DNA complexes in a non-denaturing polyacrylamide gel. in_vitro protein-DNA complex formation not_specified http://purl.obolibrary.org/obo/OBI_0001864 OBI http://purl.obolibrary.org/obo/GO_0003677 GO medium Electrophoretic mobility shift assay (EMSA) provides a rapid method to study DNA-binding protein interactions in vitro. This relies on the fact that complexes of protein and DNA migrate through a non-denaturing polyacrylamide gel more slowly than free DNA fragments. http://purl.obolibrary.org/obo/GO_0003677 GO Luciferase reporter gene assay Measures AhR/ARNT heterodimerization indirectly by detecting ligand binding to AhR and interaction of the heterodimer with dioxin-responsive elements on DNA, leading to luciferase expression. in_vitro COS-7 luciferase activity increase http://purl.obolibrary.org/obo/OBI_0001867 OBI http://purl.obolibrary.org/obo/GO_0045893 GO high Species-specific differences in dimerization and differences in dimerization between ARNT isoform and AhR isoform combinations have been assessed through luciferase reporter gene (LRG) assays utilizing COS-7 cells transfected with expression constructs of AhR and ARNT isoforms of mammals, birds, and fishes (Abnet et al 1999; Bak et al 2013; Doering et al 2014; 2015; Hansson & Hahn 2008; Hirose et al 1996; Karchner et al 1999; Lee et al 2007; Lee et al 2011; Prasch et al 2004; Wirgin et al 2011). However, this method is indirect as it also includes binding of a ligand to the AhR, and interaction of the AhR/ARNT heterodimer with dioxin-responsive elements on the DNA. http://purl.obolibrary.org/obo/GO_0045893 GO Chromatin immunoprecipitation Measures the interaction of proteins with specific genomic regions in vivo by crosslinking, immunoprecipitation, and sequencing of associated DNA fragments. in_vivo enrichment of specific DNA sequences increase http://purl.obolibrary.org/obo/GO_0043565 GO low Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo. It involves the treatment of cells with formaldehyde to crosslink neighboring protein-protein and protein-DNA molecules. Nuclear fractions are isolated, the genomic DNA is sheared, and nuclear lysates are used in immunoprecipitations with an antibody against the protein of interest. After reversal of the crosslinking, the associated DNA fragments are sequenced. Enrichment of specific DNA sequences represents regions on the genome that the protein of interest is associated with in vivo. http://purl.obolibrary.org/obo/GO_0045449 GO Chromatin immunoprecipitation Measures the interaction of proteins with specific genomic regions in vivo by crosslinking proteins and DNA with formaldehyde, shearing DNA, immunoprecipitating with a specific antibody, and sequencing the associated DNA fragments. in_vivo protein-DNA interaction at specific genomic regions not_specified not_specified Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo. It involves the treatment of cells with formaldehyde to crosslink neighboring protein-protein and protein-DNA molecules. Nuclear fractions are isolated, the genomic DNA is sheared, and nuclear lysates are used in immunoprecipitations with an antibody against the protein of interest. Chromatin Immunoprecipitation (ChIP) ChIP measures the interaction of proteins with specific genomic regions in vivo. Cells are treated with formaldehyde to crosslink protein-protein and protein-DNA molecules. Nuclear fractions are isolated, genomic DNA is sheared, and nuclear lysates are used in immunoprecipitations with an antibody against the protein of interest. After reversal of crosslinking, associated DNA fragments are sequenced. Enrichment of specific DNA sequences represents regions on the genome that the protein of interest is associated with in vivo. in_vitro DNA binding of HIF1-alpha/ARNT complex decrease http://purl.obolibrary.org/obo/GO_0003677 GO http://purl.obolibrary.org/obo/PR_000001123 PR http://purl.obolibrary.org/obo/PR_000001124 PR http://purl.obolibrary.org/obo/OBI_0000471 OBI http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI low Chromatin immunoprecipitation measures the interaction of proteins with specific genomic regions in vivo. It involves the treatment of cells with formaldehyde to crosslink neighboring protein-protein and protein-DNA molecules. Nuclear fractions are isolated, the genomic DNA is sheared, and nuclear lysates are used in immunoprecipitations with an antibody against the protein of interest. After reversal of the crosslinking, the associated DNA fragments are sequenced. Enrichment of specific DNA sequences represents regions on the genome that the protein of interest is associated with in vivo. http://purl.obolibrary.org/obo/GO_0003677 GO Electrophoretic mobility shift assay Measures DNA-binding protein interactions in vitro by detecting the slower migration of protein-DNA complexes through a non-denaturing polyacrylamide gel compared to free DNA fragments. in_vitro mobility shift of DNA fragments change http://purl.obolibrary.org/obo/GO_0003677 GO medium Electrophoretic mobility shift assay (EMSA) provides a rapid method to study DNA-binding protein interactions in vitro. This relies on the fact that complexes of protein and DNA migrate through a non-denaturing polyacrylamide gel more slowly than free DNA fragments. http://purl.obolibrary.org/obo/GO_0003677 GO electrophoretic mobility shift assay (EMSA) Electrophoretic mobility shift assay (EMSA) provides a rapid method to study DNA-binding protein interactions in vitro. This relies on the fact that complexes of protein and DNA migrate through a non-denaturing polyacrylamide gel more slowly than free DNA fragments. in_vitro DNA-binding protein interaction change http://purl.obolibrary.org/obo/OBI_0000070 OBI http://purl.obolibrary.org/obo/GO_0043312 GO low Electrophoretic mobility shift assay (EMSA) provides a rapid method to study DNA-binding protein interactions in vitro. This relies on the fact that complexes of protein and DNA migrate through a non-denaturing polyacrylamide gel more slowly than free DNA fragments. http://purl.obolibrary.org/obo/GO_0043312 GO candling Candling involves visually inspecting eggs to determine viability, identifying failures to hatch or lack of movement within the egg. in_vivo egg birds embryo viability decrease low In birds it may be identified as failure to hatch or lack of movement within the egg when candled http://purl.obolibrary.org/obo/CL_0002156 CL http://purl.obolibrary.org/obo/GO_0032501 GO candling Visual inspection of eggs using a light source to detect failure to hatch or lack of movement. in_vivo birds failure to hatch or lack of movement within the egg decrease http://purl.obolibrary.org/obo/GO_0042303 GO not_specified In birds it may be identified as failure to hatch or lack of movement within the egg when candled http://purl.obolibrary.org/obo/GO_0042303 GO egg candling Identifies failure to hatch or lack of movement within avian or reptilian eggs by visual inspection using a light source. in_vivo birds reptiles embryonic viability decrease http://purl.obolibrary.org/obo/GO_0009592 GO medium failure to hatch or lack of movement within the egg when candled http://purl.obolibrary.org/obo/UBERON_0000922 UBERON http://purl.obolibrary.org/obo/GO_0009592 GO heartbeat monitor Uses devices like Avitronic's Buddy monitor to detect viable avian and reptilian eggs by measuring heartbeat. in_vivo egg birds reptiles embryonic heartbeat decrease http://purl.obolibrary.org/obo/GO_0008016 GO medium heartbeat monitors are available for identifying viable avian and reptillian eggs (ex. Avitronic's Buddy monitor) http://purl.obolibrary.org/obo/UBERON_0000922 UBERON http://purl.obolibrary.org/obo/GO_0003013 GO heartbeat monitor Heartbeat monitors are used to detect viability in avian and reptilian eggs by monitoring cardiac activity. in_vivo egg avian reptilian embryonic viability increase http://purl.obolibrary.org/obo/GO_0003007 GO http://purl.obolibrary.org/obo/UBERON_0003011 UBERON low heartbeat monitors are available for identifying viable avian and reptillian eggs (ex. Avitronic's Buddy monitor) http://purl.obolibrary.org/obo/UBERON_0000082 UBERON http://purl.obolibrary.org/obo/GO_0003007 GO observation Mortality in fishes is measured by observing the absence of heartbeat, gill movement, and body movement. in_vivo heart gill body fishes heartbeat, gill movement, body movement decrease low In fishes, mortality is typically measured by observation. Lack of any heart beat, gill movement, and body movement are typical signs of death used in the evaluation of mortality. http://purl.obolibrary.org/obo/GO_0008553 GO ultrasound biomicroscopy Uses ultra-high frequency ultrasound (30-70 MHz) to detect stillborn or mummified offspring or increased resorptions in mammalian pregnancies. in_vivo uterus mammals fetal viability decrease http://purl.obolibrary.org/obo/GO_0007565 GO http://purl.obolibrary.org/obo/GO_0009592 GO low stillborn or mummified offspring, or an increased rate of resorptions early in pregnancy are all considered embryolethal, and can be detected using ultra-high frequency ultrasound (30-70 MHz; a.k.a. ultrasound biomicroscopy) http://purl.obolibrary.org/obo/UBERON_0000074 UBERON http://purl.obolibrary.org/obo/GO_0009592 GO ultrasound biomicroscopy Detection of stillborn/mummified offspring or increased rate of resorptions using ultra-high frequency ultrasound (30-70 MHz). in_vivo mammals stillborn or mummified offspring, or an increased rate of resorptions increase http://purl.obolibrary.org/obo/GO_0042303 GO not_specified In mammals, stillborn or mummified offspring, or an increased rate of resorptions early in pregnancy are all considered embryolethal, and can be detected using ultra-high frequency ultrasound (30-70 MHz; a.k.a. ultrasound biomicroscopy) Visual observation Direct observation of fish embryos/larvae to evaluate mortality based on the absence of heartbeat, gill movement, and body movement. ex_vivo fishes mortality signs decrease low In fishes, mortality is typically measured by observation. Lack of any heart beat, gill movement, and body movement are typical signs of death used in the evaluation of mortality. ELISA Measures VEGF protein levels using enzyme-linked immunosorbent assay. in_vitro VEGF protein levels decrease http://purl.obolibrary.org/obo/CHEBI_17650 CHEBI medium VEGF protein can be measured by enzyme-linked immunosorbent assay (Ivnitski-Steele et al. (2005) http://purl.obolibrary.org/obo/CHEBI_17650 CHEBI http://purl.obolibrary.org/obo/GO_0001525 GO immunohistochemistry Detects VEGF protein in tissue sections using specific antibodies. in_vivo VEGF protein levels decrease http://purl.obolibrary.org/obo/CHEBI_17650 CHEBI low VEGF protein can be measured by ... immunihistochemistry http://purl.obolibrary.org/obo/CHEBI_17650 CHEBI http://purl.obolibrary.org/obo/GO_0001525 GO QPCR Measures VEGF gene expression levels using quantitative real-time polymerase chain reaction. in_vitro VEGF gene expression decrease high VEGF gene expression, which is directly correlated with protein levels, can be measured by quantitative real-time polymerase chain reaction (QPCR) (Medford et al. 2009) http://purl.obolibrary.org/obo/GO_0010467 GO western blot Measures VEGF protein levels by separating proteins via gel electrophoresis and detecting with specific antibodies. in_vitro VEGF protein levels decrease http://purl.obolibrary.org/obo/CHEBI_17650 CHEBI http://purl.obolibrary.org/obo/OBI_0000221 OBI low VEGF protein can be measured by ... western blot (Li et al. 2016) http://purl.obolibrary.org/obo/CHEBI_17650 CHEBI http://purl.obolibrary.org/obo/GO_0001525 GO Vascular resistance calculation Vascular resistance is calculated using the formula: (mean arterial pressure minus mean right arterial pressure) divided by cardiac output. not_specified vascular resistance increase not_specified Vascular resistance cannot be measured by any direct means, but can be calculated using a formula: (mean arterial pressure minus mean right arterial pressure) divided by cardiac output (Siddiqui 2011). ambulatory blood pressure monitoring (ABPM) Measures average blood pressure over a 24-hour period, providing daytime and nighttime averages. in_vivo daytime average blood pressure increase http://purl.obolibrary.org/obo/GO_0008009 GO https://www.nice.org.uk/guidance/cg127/evidence low Stage 1 hypertension : Clinic blood pressure is 140/90 mmHg or higher and subsequent ambulatory blood pressure monitoring (ABPM) daytime average or home blood pressure monitoring (HBPM) average blood pressure is 135/85 mmHg or higher. Stage 2 hypertension : Clinic blood pressure is 160/100 mmHg or higher and subsequent ABPM daytime average or HBPM average blood pressure is 150/95 mmHg or higher. http://purl.obolibrary.org/obo/UBERON_0001040 UBERON http://purl.obolibrary.org/obo/GO_0008015 GO home blood pressure monitoring (HBPM) Measures average blood pressure in a home setting, providing an average reading over multiple measurements. in_vivo average blood pressure increase http://purl.obolibrary.org/obo/GO_0008009 GO https://www.nice.org.uk/guidance/cg127/evidence low Stage 1 hypertension : Clinic blood pressure is 140/90 mmHg or higher and subsequent ambulatory blood pressure monitoring (ABPM) daytime average or home blood pressure monitoring (HBPM) average blood pressure is 135/85 mmHg or higher. Stage 2 hypertension : Clinic blood pressure is 160/100 mmHg or higher and subsequent ABPM daytime average or HBPM average blood pressure is 150/95 mmHg or higher. http://purl.obolibrary.org/obo/UBERON_0001040 UBERON http://purl.obolibrary.org/obo/GO_0008015 GO sphygmomanometer Measures arterial blood pressure, providing systolic and diastolic blood pressure readings in millimeters of mercury (mmHg). in_vivo systolic and diastolic blood pressure increase http://purl.obolibrary.org/obo/GO_0008009 GO http://purl.obolibrary.org/obo/GO_0003090 GO http://purl.obolibrary.org/obo/GO_0003091 GO https://www.nice.org.uk/guidance/cg127/evidence medium Arterial blood pressure is commonly measured using a sphygmomanometer, which provides systolic and diastolic blood pressure measurements in millimeters of mercury (mmHg). http://purl.obolibrary.org/obo/UBERON_0001040 UBERON http://purl.obolibrary.org/obo/GO_0008015 GO fluorescence displacement assay Measures binding affinity between TTR and ligands using a fluorescent probe that is displaced by the ligand, resulting in a decrease in fluorescence intensity. in_vitro binding affinity (IC50, Ka, Kd) change http://purl.obolibrary.org/obo/GO_0005515 GO medium Cao et al (2010) used a novel fluorescence displacement method using a protein-binding probe that fluoresces when bound, and the intensity of which dips following displacement for a ligand. Ren and Guo (2012) reported use of a non-radioactive, fluorescin-T4 conjugate designed as a fluorescent probe (vs ANSA probe which is less TTR-specific) to study the binding interaction of multiple hydroxylated PBDEs with differing degrees of bromination and differing hydroxy positions and TTR. Ren et al (2016) used a fluorescence displacement assay to study 16 PFCs and found T4 to have an IC50 of 31 nM (Kd = 5 nM), as compared to PFOS (the strongest binder) TC50 of 130 nM (Kd = 20 nM). http://purl.obolibrary.org/obo/GO_0048029 GO GC/MS or LC/MS Biochemical approaches using GC/MS or LC/MS are used to measure binding affinity using recombinant TTR, with limits of detection in the low nM range. not_specified binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000269 OBI not_specified Biochemical (in chemico) approaches using GC/MS or LC/MS also exist that use recombinant (rTTR) and display limits of detection in the low nM range, including a multi-mode, ultra-high-performance LC method and anon-radioactive label, [13C6]-T4 (Aqai et al 2012). http://purl.obolibrary.org/obo/CHEBI_29864 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO GC/MS or LC/MS Measures binding affinity between TTR and ligands using mass spectrometry to quantify ligand concentrations in biochemical assays. not_specified ligand concentration (limits of detection in low nM range) change http://purl.obolibrary.org/obo/OBI_0000272 OBI http://purl.obolibrary.org/obo/OBI_0000475 OBI medium Biochemical (in chemico) approaches using GC/MS or LC/MS also exist that use recombinant (rTTR) and display limits of detection in the low nM range, including a multi-mode, ultra-high-performance LC method and a non-radioactive label, [13C6]-T4 (Aqai et al 2012). http://purl.obolibrary.org/obo/GO_0048029 GO radioligand-binding assay Measures binding affinity between TTR and ligands using radiolabeled T4 and gel-filtration to separate bound and free ligand. in_vitro binding affinity (IC50, Ka) change http://purl.obolibrary.org/obo/GO_0005515 GO http://purl.obolibrary.org/obo/GO_0048029 GO low Van den Berg et al (1991) used an in vitro competitive radioligand binding assay with gel-filtration procedure modified from Somack et al (1982) as well to screen 65 compounds from 12 chemical classes for evidence of interference with the T4 binding site of TTR using a radioligand binding assay and reported results semi-quantitatively Lans et al (1993, 1994) used purified TTR and T4 [125I] as a displaceable radioligand and gel-filtration procedure modified from Somack et al (1982) to study hydroxylated PCBs PCDDs and PCDFs and found many competitive binders in all classes Weiss et al (2009) initially determined the competitive binding of TTR with PFCs via radioligand-binding assay of Hamers et al (2006) and Lans et al (1993) http://purl.obolibrary.org/obo/GO_0048029 GO surface plasmon resonance Measures binding affinity between TTR and ligands using a surface-based biosensor to detect interactions in real-time. in_vitro binding affinity (Ka, Kd) change http://purl.obolibrary.org/obo/OBI_0000356 OBI http://purl.obolibrary.org/obo/GO_0005515 GO high Marchesini et al (2006, 2008) reported a surface plasmon resonance biosensor-based method using rTTR, a surface-based measurement which may not fully characterize the binding reaction of a homogenous solution or matrix. Optimized SPR is more sensitive, amenable to high-throughput screening and easier to perform than RLBAs. http://purl.obolibrary.org/obo/GO_0048029 GO equilibrium dialysis Directly measures free T4 and T3 concentrations by separating bound from unbound hormone. in_vitro serum human free T4/T3 concentration not_specified low Total T4 is most often measured using human serum based diagnostic kits, but free T4 (and T3) is only directly measured through equilibrium dialysis and ultrafiltration (Midgley 2001). http://purl.obolibrary.org/obo/CHEBI_50799 CHEBI http://purl.obolibrary.org/obo/GO_0001986 GO FLU-TTR assay Measures displacement of T4 from TTR using a protein-binding fluorescent probe (ANSA) that becomes highly fluorescent after binding to T4. in_vitro binding constant (K) decrease http://purl.obolibrary.org/obo/GO_0031994 GO http://purl.obolibrary.org/obo/OBI_0000215 OBI medium Cao et al 2010, Cao et al 2011 and Ren and Guo 2012 developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. This allows generation of binding constant (K) data as opposed to past efforts that generated IC50 values. http://purl.obolibrary.org/obo/PR_000001798 PR http://purl.obolibrary.org/obo/GO_0072577 GO Fluorescence displacement assay An assay using fluorescent probes (e.g., ANSA) that bind to T4; displacement of the probe by a compound of interest reduces fluorescence. in_vitro binding constant (K) change not_specified developed the FLU-TTR, based on a protein-binding fluorescent probe... that becomes highly fluorescent after binding to T4. When the compound of interest is introduced and displaces the ANSA-thyroxine probe, this fluorescence is reduced. This allows generation of binding constant (K) data http://purl.obolibrary.org/obo/GO_0008120 GO fluorescence displacement assay (FLU-TTR) Fluorescence-based assay using a protein-binding fluorescent probe (ANSA) that becomes highly fluorescent upon binding to T4; displacement by a compound of interest reduces fluorescence, allowing calculation of binding constants (K). in_vitro serum human displacement of T4 from TTR/TBG via fluorescence reduction change http://purl.obolibrary.org/obo/CHMO_0000634 CHMO http://purl.obolibrary.org/obo/CHEBI_27568 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO medium Cao et al 2010, Cao et al 2011 and Ren and Guo 2012 developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. When the compound of interest is introduced and displaces the ANSA-thyroxine probe, this fluorescence is reduced. This allows generation of binding constant (K) data as opposed to past efforts that generated IC50 values. Cao et al 2011 developed a fluorescent microtiter method for pTTR and TBG tested with bisphenol A. http://purl.obolibrary.org/obo/GO_0017144 GO immunoprecipitation-HPLC Uses polyclonal TTR antibodies covalently bound to sepharose resin to isolate TTR from plasma, followed by HPLC analysis. in_vitro plasma TTR concentration/binding not_specified low Purkey et al 2001 published a binding assay using polyclonal TTR antibodies covalently bound to sepharose resin which is then mixed with plasma pre-treated with compound of interest, washed and analyzed via HPLC. http://purl.obolibrary.org/obo/PR_0000041010 PR http://purl.obolibrary.org/obo/GO_0006636 GO immunoprecipitation-HPLC assay The immunoprecipitation-HPLC assay uses polyclonal TTR antibodies covalently bound to sepharose resin. Plasma pre-treated with compound of interest is mixed with the resin, washed, and analyzed via HPLC to measure the displacement of T4 from TTR. in_vitro plasma human displacement of T4 from TTR increase http://purl.obolibrary.org/obo/CL_0000163 CL http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0051049 GO medium Purkey et al 2001 published a binding assay using polyclonal TTR antibodies covalently bound to sepharose resin which is then mixed with plasma pre-treated with compound of interest, washed and analyzed via HPLC. http://purl.obolibrary.org/obo/CL_0000163 CL http://purl.obolibrary.org/obo/GO_0051049 GO isotope-free competitive binding assay with UPLC-MS Isotope-free competitive binding assay using 13C6-T4 to screen thyroid transport protein ligands for recombinant TTR, employing immunomagnetic beads followed by flow cytometry and UPLC-MS detection. in_vitro serum urine water human binding of T4 analogs to TTR change http://purl.obolibrary.org/obo/CHMO_0000541 CHMO http://purl.obolibrary.org/obo/CHEBI_27568 CHEBI http://www.bioassayontology.org/bao#BAO_0000189 BAO http://purl.obolibrary.org/obo/OBI_0000075 OBI high Aqai et al 2012 described a rapid and isotope-free (13C6-T4) screening of thyroid transport protein ligands, using a competitive binding assay for rTTR using fast ultrahigh performance LC-electrospray ionization triple-quadrupole MS. The method involves the use of immunomagnetic beads followed by screening with flow cytometry and UPLC-MS. The high-throughput screening mode is capable of detecting T4 in water at the part-per-trillion level and in the part-per-billion level in urine. http://purl.obolibrary.org/obo/GO_0017144 GO quantitative nuclease protection assay (qNPA) Quantitative nuclease protection assay used to screen chemicals for induction of UGT1A1 and SULT2A1 mRNA expression, measuring transcript levels of Phase II metabolizing enzymes. in_vitro human expression of UGT1A1 and SULT2A1 mRNA change http://purl.obolibrary.org/obo/GO_0004594 GO http://purl.obolibrary.org/obo/GO_0008150 GO http://purl.obolibrary.org/obo/GO_0010468 GO medium The EPA ToxCast Phase I efforts used quantitative nuclease protection assays (qNPA) to screen several hundred chemicals for UGT1A1 and SULT2A1 (Rotroff et al 2010, Sinz et al 2006). http://purl.obolibrary.org/obo/GO_0042414 GO radioligand binding assay Radioligand binding assays use [125I]-T4 as a label to demonstrate affinity for xenobiotics to human or rat transthyretin (TTR). The most commonly used method was first published by Somack et al 1982 and adapted by Hamers et al 2006, Lans et al 1993 and Ucan-Marin et al 2010. The assay involves purified TTR from human serum and is performed in a pure aqueous solution. in_vitro serum human rat affinity of xenobiotics to TTR change http://purl.obolibrary.org/obo/CL_0000163 CL http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0005488 GO low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). The most commonly used method was first published by Somack et al 1982 and adapted by Hamers et al 2006, Lans et al 1993 and Ucan-Marin et al 2010. Similar assays have been developed using [125I]-T3 as a label for affinity to chicken and bullfrog TTR (Yamauchi et al 2003). http://purl.obolibrary.org/obo/CL_0000163 CL http://purl.obolibrary.org/obo/GO_0005488 GO radioligand binding assay Measures displacement of T4 from serum transport proteins using [125I]-T4 as a label to demonstrate affinity for xenobiotics to human or rat TTR and TBG. in_vitro human rat binding affinity decrease http://purl.obolibrary.org/obo/GO_0031994 GO http://purl.obolibrary.org/obo/PR_000001798 PR low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). The most commonly used method was first published by Somack et al 1982 and adapted by Hamers et al 2006, Lans et al 1993 and Ucan-Marin et al 2010. http://purl.obolibrary.org/obo/PR_000001798 PR http://purl.obolibrary.org/obo/GO_0072577 GO radioligand binding assay In vitro assay using [125I]-T4 or [125I]-T3 as a radioligand to measure affinity of xenobiotics for human/rat TTR or TBG via a wash/separation procedure to quantify displaced free T4. in_vitro serum human rat displacement of T4 from TTR/TBG change http://purl.obolibrary.org/obo/OBI_0000986 OBI http://www.bioassayontology.org/bao#BAO_0000186 BAO http://purl.obolibrary.org/obo/CHEBI_27568 CHEBI low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). The most commonly used method was first published by Somack et al 1982 and adapted by Hamers et al 2006, Lans et al 1993 and Ucan-Marin et al 2010. Radioligand methods suffer from having to use heavily regulated isotopes and lower throughput to provide free T4 measurements (due to the extra wash/separation procedure needed). http://purl.obolibrary.org/obo/GO_0017144 GO surface plasmon resonance (SPR) biosensor assay Surface plasmon resonance (SPR) biosensor assays use recombinant TTR and TBG to measure the binding of compounds to these transport proteins. The assay was developed by Marchesini et al 2006 and validated with known thyroid disruptors and structurally related compounds. in_vitro recombinant TTR and TBG human binding affinity of compounds to TTR and TBG change http://purl.obolibrary.org/obo/CL_0000163 CL http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0005488 GO medium Marchesini et al 2006 reported on the development of two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG, validated with known thyroid disruptors and structurally related compounds including halogenated phenols, polychlorinated biphenyls, bisphenols and a hydroxylated PCB metabolite (4-OH-CB 14). TH is covalently bound to a gold-layered chip and a mixture of the compound of interest and transport protein are injected in a flow cell passing over the bound TH. http://purl.obolibrary.org/obo/CL_0000163 CL http://purl.obolibrary.org/obo/GO_0005488 GO Surface Plasmon Resonance (SPR) biosensor assay A biosensor-based assay using recombinant TTR or TBG and a gold-layered chip to measure the displacement of thyroid hormones by compounds of interest. in_vitro IC50 change high two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG the authors conclude their optimized assays are suitable for high-throughput screening http://purl.obolibrary.org/obo/GO_0008120 GO surface plasmon resonance-based biosensor assay Measures displacement of T4 from serum transport proteins using recombinant TTR and TBG, with TH covalently bound to a gold-layered chip. in_vitro binding affinity decrease http://purl.obolibrary.org/obo/GO_0031994 GO http://purl.obolibrary.org/obo/OBI_0000219 OBI high Marchesini et al 2006 reported on the development of two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG, validated with known thyroid disruptors and structurally related compounds including halogenated phenols, polychlorinated biphenyls, bisphenols and a hydroxylated PCB metabolite (4-OH-CB 14). The authors found that these biosensor methods were more sensitive (IC50 of 8.6 ± 0.7 nM for rTTR), easier to perform and more rapid that radioligand binding assays and immunoprecipitation-HPLC. http://purl.obolibrary.org/obo/PR_000001798 PR http://purl.obolibrary.org/obo/GO_0072577 GO UPLC-MS (with immunomagnetic beads) A rapid, isotope-free screening method using 13C6-T4, immunomagnetic beads, flow cytometry, and ultrahigh performance LC-electrospray ionization triple-quadrupole MS. in_vitro urine T4 concentration not_specified http://purl.obolibrary.org/obo/CHEBI_35016 CHEBI high Aqai et al 2012 described a rapid and isotope-free (13C6-T4) screening of thyroid transport protein ligands, using a competitive binding assay for rTTR using fast ultrahigh performance LC-electrospray ionization triple-quadrupole MS. The high-throughput screening mode is capable of detecting T4 in water at the part-per-trillion level and in the part-per-billion level in urine. http://purl.obolibrary.org/obo/CHEBI_35016 CHEBI competitive T4-TTR fluorescence displacement assay A competitive fluorescence displacement assay in a 96-well format used to measure compound interference with T4-TTR binding. in_vitro displacement of T4 change medium Montano et al 2012 developed a competitive T4-TTR fluorescence displacement assay in a 96-well format Equilibrium dialysis Measures free thyroxine (T4) by separating unbound hormone from protein-bound hormone using dialysis. in_vitro serum free T4 concentration not_specified http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI low free T4 is considered a more reliable measure of thyroid dysfunction and the only direct measurements for unbound thyroid hormone are equilibrium dialysis and ultrafiltration (Zoeller et al 2007). http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0072593 GO FLU-TTR (Fluorescent Probe Binding) A fluorescence-based assay using an ANSA probe that becomes highly fluorescent upon binding to T4; displacement by a compound reduces fluorescence. in_vitro binding constant (K) decrease medium developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. When the compound of interest is introduced and displaces the ANSA-thyroxine probe, this fluorescence is reduced. Fluorescence displacement assay Measures displacement of T4 from TTR using a fluorescent probe. in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI medium Cao et al 2010, Cao et al 2011 and Ren and Guo 2012 developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. http://purl.obolibrary.org/obo/GO_0072593 GO fluorescence displacement assay Measures displacement of ANSA-thyroxine probe by compounds of interest, generating binding constant data. in_vitro TTR TBG fluorescence intensity decrease http://purl.obolibrary.org/obo/CHEBI_5078 CHEBI high Cao et al 2010, Cao et al 2011 and Ren and Guo 2012 developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. When the compound of interest is introduced and displaces the ANSA-thyroxine probe, this fluorescence is reduced. http://purl.obolibrary.org/obo/CHEBI_5078 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO HPLC Quantifies extracted materials, potentially after RIA and dialysis, using High-Performance Liquid Chromatography. in_vitro TH concentration not_specified medium Extracted materials can also be quantified by HPLC. http://purl.obolibrary.org/obo/GO_0006827 GO Quantitative nuclease protection assay (qNPA) Measures expression of UGT or SULT mRNA as a surrogate for enzyme induction. in_vitro mRNA expression increase http://purl.obolibrary.org/obo/SO_0000234 SO medium The EPA ToxCast Phase I efforts used quantitative nuclease protection assays (qNPA) to screen several hundred chemicals for UGT1A1 and SULT2A1 (Rotroff et al 2010, Sinz et al 2006). http://purl.obolibrary.org/obo/PR_000017008 PR http://purl.obolibrary.org/obo/GO_0046209 GO quantitative nuclease protection assays (qNPA) In vitro cell-based assay used to screen for enzyme induction of UGT1A1 and SULT2A1 by measuring mRNA levels. in_vitro UGT or SULT mRNA expression increase high The EPA ToxCast Phase I efforts used quantitative nuclease protection assays (qNPA) to screen several hundred chemicals for UGT1A1 and SULT2A1 http://purl.obolibrary.org/obo/GO_0006981 GO Radioligand binding assay Measures displacement of T4 from serum transport proteins using radiolabeled T4. in_vitro human rat chicken bullfrog binding affinity not_specified http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). http://purl.obolibrary.org/obo/GO_0072593 GO Radioligand binding assay In vitro assay to measure displacement of radiolabeled T4 from serum transport proteins (TTR or TBG) by test compounds. in_vitro serum human rat binding affinity of test compound to TTR or TBG increase http://purl.obolibrary.org/obo/CHEBI_18185 CHEBI http://purl.obolibrary.org/obo/CL_0000163 CL low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). The most commonly used method was first published by Somack et al 1982 and adapted by Hamers et al 2006, Lans et al 1993 and Ucan-Marin et al 2010. http://purl.obolibrary.org/obo/CHEBI_18185 CHEBI Radioligand binding assay Uses radioisotope-labeled T4 or T3 ([125I]-T4/T3) to measure the competitive displacement of the hormone from transport proteins (TTR, TBG) by test compounds. in_vitro human rat chicken bullfrog Displacement of T4/T3 from transport proteins decrease low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG Radioligand methods suffer from having to use heavily regulated isotopes and lower throughput to provide free T4 measurements RIA (Radioimmunoassay) A method used to measure total thyroid hormone concentrations by combining radioimmunoassay with dialysis to estimate the free fraction. in_vitro serum total thyroid hormone change http://purl.obolibrary.org/obo/CHEBI_35056 CHEBI not_specified combining RIA to measure total TH and dialysis to estimate the free fraction http://purl.obolibrary.org/obo/CHEBI_35056 CHEBI Surface plasmon resonance (SPR) biosensor Measures binding of compounds to thyroid transport proteins using SPR technology. in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000219 OBI http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI high Marchesini et al 2006 reported on the development of two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG, validated with known thyroid disruptors and structurally related compounds including halogenated phenols, polychlorinated biphenyls, bisphenols and a hydroxylated PCB metabolite (4-OH-CB 14). http://purl.obolibrary.org/obo/GO_0072593 GO Surface plasmon resonance (SPR) biosensor assay In vitro biosensor assay to measure binding of test compounds to recombinant TTR or TBG using SPR technology. in_vitro recombinant protein human binding affinity of test compound to TTR or TBG increase http://purl.obolibrary.org/obo/CHEBI_18185 CHEBI http://purl.obolibrary.org/obo/CL_0000163 CL medium Marchesini et al 2006 reported on the development of two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG, validated with known thyroid disruptors and structurally related compounds including halogenated phenols, polychlorinated biphenyls, bisphenols and a hydroxylated PCB metabolite (4-OH-CB 14). The authors found that these biosensor methods were more sensitive (IC50 of 8.6 ± 0.7 nM for rTTR), easier to perform and more rapid that radioligand binding assays and immunoprecipitation-HPLC. http://purl.obolibrary.org/obo/CHEBI_18185 CHEBI Ultrafiltration Measures free thyroxine (T4) by filtering unbound hormone from protein-bound hormone using a membrane. in_vitro serum free T4 concentration not_specified http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI low free T4 is considered a more reliable measure of thyroid dysfunction and the only direct measurements for unbound thyroid hormone are equilibrium dialysis and ultrafiltration (Zoeller et al 2007). http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0072593 GO UPLC-MS Rapid, isotope-free screening of thyroid transport protein ligands using competitive binding assay and ultrahigh performance LC-electrospray ionization triple-quadrupole MS. in_vitro TTR T4 concentration not_specified http://purl.obolibrary.org/obo/CHEBI_5078 CHEBI high Aqai et al 2012 described a rapid and isotope-free (13C6-T4) screening of thyroid transport protein ligands, using a competitive binding assay for rTTR using fast ultrahigh performance LC-electrospray ionization triple-quadrupole MS. http://purl.obolibrary.org/obo/CHEBI_5078 CHEBI http://purl.obolibrary.org/obo/GO_0006823 GO diagnostic kits Use of human serum based diagnostic kits to measure total T4 concentrations. in_vitro serum human total T4 not_specified http://purl.obolibrary.org/obo/CHEBI_35215 CHEBI not_specified Total T4 is most often measured using human serum based diagnostic kits http://purl.obolibrary.org/obo/CHEBI_35215 CHEBI Equilibrium dialysis Measures free T4 and T3 in serum by separating free hormone from protein-bound hormone using dialysis. in_vitro free T4 concentration not_specified http://purl.obolibrary.org/obo/OBI_0000475 OBI low free T4 (and T3) is only directly measured through equilibrium dialysis and ultrafiltration (Midgley 2001). http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0009913 GO FLU-TTR Measures displacement of thyroxine from transthyretin using a fluorescent probe (ANSA). in_vitro binding constant (K) not_specified medium Cao et al 2010, Cao et al 2011 and Ren and Guo 2012 developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. http://purl.obolibrary.org/obo/PR_000001763 PR http://purl.obolibrary.org/obo/GO_0072593 GO fluorescence displacement assay Fluorescence displacement assay using a protein-binding fluorescent probe (ANSA) that becomes highly fluorescent after binding to T4; displacement by test compounds reduces fluorescence, allowing generation of binding constant data. in_vitro human displacement of fluorescent T4 probe from TTR change http://www.bioassayontology.org/bao#BAO_0000190 BAO http://purl.obolibrary.org/obo/GO_0017141 GO http://purl.obolibrary.org/obo/CHEBI_27563 CHEBI high Measuring displacement of T4 from serum transport proteins is done mainly via one of three in vitro methods: radioligand binding assay, plasmon resonance-based biosensor, or fluorescence displacement. Cao et al 2010, Cao et al 2011 and Ren and Guo 2012 developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. When the compound of interest is introduced and displaces the ANSA-thyroxine probe, this fluorescence is reduced. Cao et al 2011 developed a fluorescent microtiter method for pTTR and TBG tested with bisphenol A. Montano et al 2012 developed a competitive T4-TTR fluorescence displacement assay in a 96-well format, modified from the original method (Nilsson and Petersen 1975) and using a new selective method to extract hydroxylated metabolites while reducing fatty acid interference (modified from Hovander et al 2000). http://purl.obolibrary.org/obo/CHEBI_27563 CHEBI http://purl.obolibrary.org/obo/GO_0017141 GO HPLC High-performance liquid chromatography used to quantify extracted materials or analyze plasma pre-treated with compounds. in_vitro quantified extracted materials not_specified not_specified Extracted materials can also be quantified by HPLC. HPLC Quantifies extracted thyroid hormones using high-performance liquid chromatography. in_vitro thyroxine concentration not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI medium Extracted materials can also be quantified by HPLC. http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0009913 GO Immunoassay Measures free serum T3 using antibody-based detection methods. in_vitro free T3 concentration not_specified medium Immunoassays and MS/MS are also used. http://purl.obolibrary.org/obo/CHEBI_18267 CHEBI http://purl.obolibrary.org/obo/GO_0009913 GO MS/MS Measures free serum T3 using tandem mass spectrometry. in_vitro free T3 concentration not_specified http://purl.obolibrary.org/obo/OBI_0000473 OBI medium Immunoassays and MS/MS are also used. http://purl.obolibrary.org/obo/CHEBI_18267 CHEBI http://purl.obolibrary.org/obo/GO_0009913 GO qNPA Measures expression of UGT or SULT mRNA using quantitative nuclease protection assays. in_vitro mRNA expression not_specified high The EPA ToxCast Phase I efforts used quantitative nuclease protection assays (qNPA) to screen several hundred chemicals for UGT1A1 and SULT2A1 (Rotroff et al 2010, Sinz et al 2006). http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0042404 GO quantitative nuclease protection assay (qNPA) A method to measure the expression of phase II enzymes (UGT1A1, UGT1A6, and SULT2A1) involved in thyroid hormone metabolism. The assay is used to screen chemicals for their ability to induce these enzymes, which can contribute to systemic clearance of thyroid hormones and their conjugates from serum. in_vitro liver cells human expression of UGT1A1, UGT1A6, and SULT2A1 increase http://purl.obolibrary.org/obo/GO_0033273 GO medium Several methods measuring expression of UGT or SULT mRNA have been published; however, there have been limited efforts to develop higher-throughput methods. The EPA ToxCast Phase I efforts used quantitative nuclease protection assays (qNPA) to screen several hundred chemicals for UGT1A1 and SULT2A1 (Rotroff et al 2010, Sinz et al 2006). http://purl.obolibrary.org/obo/PR_000001947 PR http://purl.obolibrary.org/obo/GO_0033273 GO radioligand binding assay A method to measure the affinity of xenobiotics to human or rat transthyretin (TTR) and thyroxine-binding globulin (TBG) using radiolabeled T4 ([125I]-T4) as a label. The assay demonstrates the binding of compounds to TTR and TBG, indicating potential thyroid hormone disruption. in_vitro human serum rat TTR TBG human rat affinity of xenobiotics to TTR and TBG increase http://purl.obolibrary.org/obo/PR_000001945 PR http://purl.obolibrary.org/obo/PR_000001946 PR http://purl.obolibrary.org/obo/GO_0033273 GO low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). The most commonly used method was first published by Somack et al 1982 and adapted by Hamers et al 2006, Lans et al 1993 and Ucan-Marin et al 2010. Similar assays have been developed using [125I]-T3 as a label for affinity to chicken and bullfrog TTR (Yamauchi et al 2003). http://purl.obolibrary.org/obo/PR_000001945 PR http://purl.obolibrary.org/obo/GO_0033273 GO Radioligand binding assay Measures displacement of T4 from serum transport proteins using radiolabeled T4. in_vitro human rat chicken bullfrog binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). http://purl.obolibrary.org/obo/PR_000001763 PR http://purl.obolibrary.org/obo/GO_0072593 GO radioligand binding assay In vitro method using radiolabeled T4 or T3 to measure the displacement of T4 from serum transport proteins or affinity to proteins like TTR and TBG. in_vitro human rat chicken bullfrog displacement of T4 from serum transport proteins not_specified http://purl.obolibrary.org/obo/CHEBI_35215 CHEBI low Measuring displacement of T4 from serum transport proteins is done mainly via one of three in vitro methods: radioligand binding assay Radioligand binding assays, using [125 I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG Radioligand methods suffer from having to use heavily regulated isotopes and lower throughput to provide free T4 measurements RIA Radioimmunoassay used to measure total thyroid hormone (TH) levels. in_vitro total TH not_specified not_specified combining RIA to measure total TH Surface plasmon resonance (SPR)-based biosensor Measures binding of compounds to thyroid transport proteins using surface plasmon resonance technology. in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI high Marchesini et al 2006 reported on the development of two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG, validated with known thyroid disruptors and structurally related compounds including halogenated phenols, polychlorinated biphenyls, bisphenols and a hydroxylated PCB metabolite (4-OH-CB 14). http://purl.obolibrary.org/obo/PR_000001763 PR http://purl.obolibrary.org/obo/GO_0072593 GO surface plasmon resonance (SPR)-based biosensor assay A method to measure the binding affinity of compounds to recombinant TTR and thyroxine-binding globulin (TBG) using SPR technology. The assay is more sensitive, easier to perform, and more rapid than radioligand binding assays. in_vitro recombinant TTR TBG human binding affinity of compounds to TTR and TBG increase http://purl.obolibrary.org/obo/PR_000001945 PR http://purl.obolibrary.org/obo/PR_000001946 PR http://purl.obolibrary.org/obo/GO_0033273 GO medium Marchesini et al 2006 reported on the development of two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG, validated with known thyroid disruptors and structurally related compounds including halogenated phenols, polychlorinated biphenyls, bisphenols and a hydroxylated PCB metabolite (4-OH-CB 14). The authors found that these biosensor methods were more sensitive (IC50 of 8.6 ± 0.7 nM for rTTR), easier to perform and more rapid that radioligand binding assays and immunoprecipitation-HPLC. http://purl.obolibrary.org/obo/PR_000001945 PR http://purl.obolibrary.org/obo/GO_0033273 GO Ultrafiltration Measures free T4 and T3 in serum by filtering out protein-bound hormone. in_vitro free T4 concentration not_specified http://purl.obolibrary.org/obo/OBI_0000474 OBI low free T4 (and T3) is only directly measured through equilibrium dialysis and ultrafiltration (Midgley 2001). http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0009913 GO UPLC-MS A rapid, isotope-free screening method using immunomagnetic beads, flow cytometry, and ultra-high performance LC-electrospray ionization triple-quadrupole MS. in_vitro urine T4 concentration not_specified http://purl.obolibrary.org/obo/CHEBI_35215 CHEBI high Aqai et al 2012 described a rapid and isotope-free (13C6-T4) screening of thyroid transport protein ligands, using a competitive binding assay for rTTR using fast ultrahigh performance LC-electrospray ionization triple-quadrupole MS. The high-throughput screening mode is capable of detecting T4 in water at the part-per-trillion level and in the part-per-billion level in urine. http://purl.obolibrary.org/obo/CHEBI_35215 CHEBI Competitive T4-TTR fluorescence displacement assay Measures displacement of T4 from TTR using a competitive fluorescence assay in a 96-well format. in_vitro human T4 displacement from TTR increase http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/PR_000001780 PR medium Montano et al 2012 developed a competitive T4-TTR fluorescence displacement assay in a 96-well format, modified from the original method (Nilsson and Petersen 1975) and using a new selective method to extract hydroxylated metabolites while reducing fatty acid interference (modified from Hovander et al 2000). http://purl.obolibrary.org/obo/PR_000001780 PR http://purl.obolibrary.org/obo/GO_0072599 GO Equilibrium dialysis and ultrafiltration Directly measures free T4 and T3 levels in serum using equilibrium dialysis and ultrafiltration. in_vitro serum human free T4 concentration not_specified http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/UBERON_0001967 UBERON low Total T4 is most often measured using human serum based diagnostic kits, but free T4 (and T3) is only directly measured through equilibrium dialysis and ultrafiltration (Midgley 2001). http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0072599 GO Fluorescent displacement assay (FLU-TTR) Measures displacement of T4 from TTR using a fluorescent probe (ANSA). in_vitro human binding constant (K) for TTR increase http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/PR_000001780 PR medium Cao et al 2010, Cao et al 2011 and Ren and Guo 2012 developed the FLU-TTR, based on a protein-binding fluorescent probe (ANSA, or 8-anilo-1-naphthalenesulfonic acid ammonium salt) that becomes highly fluorescent after binding to T4. http://purl.obolibrary.org/obo/PR_000001780 PR http://purl.obolibrary.org/obo/GO_0072599 GO qNPA Quantitative nuclease protection assays (qNPA) were used to screen chemicals for their effects on the expression of UGT1A1 and SULT2A1 mRNA. in_vitro mRNA expression increase high The EPA ToxCast Phase I efforts used quantitative nuclease protection assays (qNPA) to screen several hundred chemicals for UGT1A1 and SULT2A1 (Rotroff et al 2010, Sinz et al 2006). http://purl.obolibrary.org/obo/GO_0010468 GO Quantitative nuclease protection assay (qNPA) Measures mRNA expression levels of Phase II enzymes UGT1A1 and SULT2A1 to assess enzyme induction as a surrogate for thyroid hormone metabolic clearance. in_vitro human UGT1A1 and SULT2A1 mRNA expression increase high The EPA ToxCast Phase I efforts used quantitative nuclease protection assays (qNPA) to screen several hundred chemicals for UGT1A1 and SULT2A1 (Rotroff et al 2010, Sinz et al 2006). radioligand binding assay This assay uses radiolabeled thyroxine ([125I]-T4) to measure the affinity of xenobiotics to human or rat transthyretin (TTR) and thyroxine-binding globulin (TBG). It involves measuring the displacement of the radioligand by the test compound. in_vitro serum human rat binding affinity decrease http://purl.obolibrary.org/obo/OBI_0000489 OBI low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). The most commonly used method was first published by Somack et al 1982 and adapted by Hamers et al 2006, Lans et al 1993 and Ucan-Marin et al 2010. http://purl.obolibrary.org/obo/GO_0005102 GO Radioligand binding assay Measures displacement of T4 from serum transport proteins using radiolabeled T4. in_vitro human rat chicken bullfrog binding affinity of xenobiotics to TTR and TBG increase http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/PR_000001780 PR http://purl.obolibrary.org/obo/PR_000001781 PR low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). http://purl.obolibrary.org/obo/PR_000001780 PR http://purl.obolibrary.org/obo/GO_0072599 GO Radioligand binding assay for thyroid hormone displacement Uses radiolabeled [125I]-T4 or [125I]-T3 to measure the affinity of xenobiotics for thyroid transport proteins (TTR and TBG) by assessing competitive displacement in vitro. in_vitro human rat chicken bullfrog displacement of radiolabeled T4/T3 from transport proteins decrease low Radioligand binding assays, using [125I]-T4 as a label, were developed to demonstrate affinity for xenobiotics to human or rat TTR and TBG (Brouwer and van den Berg 1986, Lans et al 1994). Similar assays have been developed using [125I]-T3 as a label for affinity to chicken and bullfrog TTR (Yamauchi et al 2003). Radioligand methods suffer from having to use heavily regulated isotopes and lower throughput to provide free T4 measurements (due to the extra wash/separation procedure needed). surface plasmon resonance (SPR) This assay uses recombinant TTR and TBG immobilized on a gold chip to measure the binding of thyroxine and interfering compounds. The binding is detected by changes in the refractive index of the surface. in_vitro binding affinity decrease http://purl.obolibrary.org/obo/OBI_0000489 OBI medium Marchesini et al 2006 reported on the development of two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG, validated with known thyroid disruptors and structurally related compounds including halogenated phenols, polychlorinated biphenyls, bisphenols and a hydroxylated PCB metabolite (4-OH-CB 14). The authors found that these biosensor methods were more sensitive (IC50 of 8.6 ± 0.7 nM for rTTR), easier to perform and more rapid that radioligand binding assays and immunoprecipitation-HPLC. http://purl.obolibrary.org/obo/GO_0005102 GO Surface plasmon resonance biosensor assay Measures binding of compounds to TTR and TBG using surface plasmon resonance. in_vitro human binding affinity to TTR and TBG increase http://purl.obolibrary.org/obo/PR_000001780 PR http://purl.obolibrary.org/obo/PR_000001781 PR http://purl.obolibrary.org/obo/OBI_0000274 OBI high Marchesini et al 2006 reported on the development of two surface plasmon resonance(SPR)-based biosensor assays using recombinant TTR and TBG, validated with known thyroid disruptors and structurally related compounds including halogenated phenols, polychlorinated biphenyls, bisphenols and a hydroxylated PCB metabolite (4-OH-CB 14). http://purl.obolibrary.org/obo/PR_000001780 PR http://purl.obolibrary.org/obo/GO_0072599 GO T4 glucuronidation and sulfation assay Measures the rate of T4 glucuronidation and sulfation as well as biliary excretion to inform thyroid system modulation. in_vivo mouse rat rate of T4 glucuronidation and sulfation increase http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_1901042 GO http://purl.obolibrary.org/obo/GO_0008150 GO low Measuring the rate of T4 glucuronidation and sulfation as well as biliary excretion informs the mechanism of action of thyroid system modulation. Studies involving knock/out mice and thyroidectomized rats also inform this mechanism. http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO Thyroid hormone uptake analysis Measures the rate of disappearance of radiolabeled thyroxine from plasma into tissue compartments. in_vivo tissues human rate of thyroxine disappearance from plasma decrease http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0072599 GO low Thyroid hormone uptake into human tissues has been measured by analyzing the rate of disappearance of radiolabeled TH from plasma into rapidly and slowly equilibrating tissue compartments (Visser 2010). http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0072599 GO Total T4 diagnostic kit Measures total thyroxine levels in human serum using diagnostic kits. in_vitro serum human total T4 concentration not_specified http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/UBERON_0001967 UBERON high Total T4 is most often measured using human serum based diagnostic kits, but free T4 (and T3) is only directly measured through equilibrium dialysis and ultrafiltration (Midgley 2001). http://purl.obolibrary.org/obo/CHEBI_18268 CHEBI http://purl.obolibrary.org/obo/GO_0072599 GO UPLC-MS competitive binding assay Measures competitive binding of compounds to TTR using ultrahigh performance LC-electrospray ionization triple-quadrupole MS. in_vitro human binding affinity to TTR increase http://purl.obolibrary.org/obo/PR_000001780 PR http://purl.obolibrary.org/obo/OBI_0000272 OBI high Aqai et al 2012 described a rapid and isotope-free (13C6-T4) screening of thyroid transport protein ligands, using a competitive binding assay for rTTR using fast ultrahigh performance LC-electrospray ionization triple-quadrupole MS. http://purl.obolibrary.org/obo/PR_000001780 PR http://purl.obolibrary.org/obo/GO_0072599 GO UPLC-MS/MS screening A rapid, isotope-free screening method using [13C6]-T4, immunomagnetic beads, flow cytometry, and ultra-high performance liquid chromatography-mass spectrometry to detect ligands for transport proteins. in_vitro T4 concentration/ligand binding not_specified high Aqai et al 2012 described a rapid and isotope-free (13C6-T4) screening of thyroid transport protein ligands, using a competitive binding assay for rTTR using fast ultrahigh performance LC-electrospray ionization triple-quadrupole MS. The high-throughput screening mode is capable of detecting T4 in water at the part-per-trillion level and in the part-per-billion level in urine. http://purl.obolibrary.org/obo/GO_0006826 GO droplet digital PCR Performs absolute quantification of MUC5AC and MUC5B transcript copy numbers. in_vitro mucin transcript copy numbers increase http://purl.obolibrary.org/obo/OBI_0002689 OBI medium For absolute quantification of MUC5AC and MUC5B transcript copy numbers droplet digital PCR can be performed http://purl.obolibrary.org/obo/GO_0006351 GO droplet digital PCR Droplet digital PCR is performed for absolute quantification of MUC5AC and MUC5B transcript copy numbers. in_vitro transcript copy number increase medium For absolute quantification of MUC5AC and MUC5B transcript copy numbers droplet digital PCR can be performed (Okuda et al., 2019). http://purl.obolibrary.org/obo/GO_0010468 GO ELISA Secreted mucin protein levels are detected and quantified by Enzyme-Linked Immunosorbent Assay (ELISA). in_vitro protein levels increase medium Secreted mucin protein levels can be detected and quantified by Enzyme-Linked Immunosorbent Assay (ELISA) (Yu et al., 2011, Shao et al., 2004, Wagner et al., 2003, Dohrman et al., 1998, Song et al., 2016). http://purl.obolibrary.org/obo/GO_0006460 GO ELISA Detects and quantifies secreted mucin protein levels. in_vitro secreted mucin protein levels increase high Secreted mucin protein levels can be detected and quantified by Enzyme-Linked Immunosorbent Assay (ELISA) http://purl.obolibrary.org/obo/GO_0046903 GO flow cytometry MUC5AC positive cell number is determined through flow cytometry for comparing and quantifying stressor-treated samples to control samples. in_vitro cell count increase high MUC5AC positive cell number determination through flow cytometry is another method for comparing and quantifying stressor-treated samples to control samples (Val et al., 2012). http://purl.obolibrary.org/obo/GO_0008283 GO flow cytometry Quantifies MUC5AC positive cell number by comparing stressor-treated samples to control samples. in_vitro MUC5AC positive cell number increase http://purl.obolibrary.org/obo/OBI_0000278 OBI high MUC5AC positive cell number determination through flow cytometry is another method for comparing and quantifying stressor-treated samples to control samples http://purl.obolibrary.org/obo/GO_0008283 GO histological staining Assesses the presence and severity of mucin production in histological tissue sections using hematoxylin/eosin and Alcian blue and/or periodic acid Schiff stains. in_vivo mucin production severity increase low For in vivo studies and clinical samples, an experienced pathologist may judge the presence and severity of mucin production on histological tissue sections stained with hematoxylin/eosin and Alcian blue and/or periodic acid Schiff stains http://purl.obolibrary.org/obo/GO_0045144 GO immunoassay Detects MUC5AC protein as a mucin protein detection method. in_vitro MUC5AC protein levels increase medium Immunoassay of MUC5AC protein is also used as mucin protein detection method http://purl.obolibrary.org/obo/GO_0010485 GO immunocyto/histochemistry/immunofluorescence Quantifies mucin protein levels in cytological preparations or histological tissue sections using antibodies and fluorescent dyes. in_vitro mucin protein levels increase http://purl.obolibrary.org/obo/OBI_0000281 OBI low Analytical techniques such as immunocyto/histochemistry/immunofluorescence in cytological preparations or histological tissue sections with an appropriate antibody are also common methods of mucin protein level quantification http://purl.obolibrary.org/obo/GO_0010485 GO immunocyto/histochemistry/immunofluorescence Mucin protein level quantification is performed using immunocyto/histochemistry/immunofluorescence in cytological preparations or histological tissue sections with an appropriate antibody. in_vitro tissue protein levels increase low Analytical techniques such as immunocyto/histochemistry/immunofluorescence in cytological preparations or histological tissue sections with an appropriate antibody are also common methods of mucin protein level quantification (Zhu et al., 2009, Okuda et al., 2019). http://purl.obolibrary.org/obo/GO_0006454 GO in situ hybridization In situ hybridization is used for mucin (MUC5AC, MUC5B, MUC2) mRNA quantification. in_vitro tissue mRNA levels increase low In situ hybridization is used in some studies for mucin (MUC5AC, MUC5B, MUC2) mRNA quantification (Takeyama et al., 2001, Dohrman et al., 1998, Okuda et al., 2019). http://purl.obolibrary.org/obo/GO_0010468 GO in situ hybridization Quantifies mucin (MUC5AC, MUC5B, MUC2) mRNA in tissue sections. in_vitro mucin mRNA levels increase http://purl.obolibrary.org/obo/OBI_0000559 OBI low In situ hybridization is used in some studies for mucin (MUC5AC, MUC5B, MUC2) mRNA quantification http://purl.obolibrary.org/obo/GO_0010467 GO luciferase assay Assesses mucin gene promoter activity by reporter gene expression. in_vitro mucin gene promoter activity increase medium assessment of mucin gene promoter activity by reporter gene expression (e.g. luciferase assay) allows assumptions on mucin expression levels http://purl.obolibrary.org/obo/GO_0006351 GO mass spectrometry Identifies and quantifies mucins in cell and tissue samples. in_vitro mucin levels increase http://purl.obolibrary.org/obo/OBI_0000272 OBI low Mass spectrometric approaches could be utilized for targeted identification of mucins and their quantification in cell and tissue samples http://purl.obolibrary.org/obo/GO_0045144 GO mass spectrometry Mass spectrometric approaches could be utilized for targeted identification of mucins and their quantification in cell and tissue samples. in_vitro tissue protein levels increase medium Mass spectrometric approaches could be utilized for targeted identification of mucins and their quantification in cell and tissue samples (Kesimer and Sheehan, 2012). http://purl.obolibrary.org/obo/GO_0006454 GO Northern blot Northern blot is applied for mucin gene expression measurement. in_vitro mRNA levels increase low Northern blot of mucin mRNAs can also be applied for mucin gene expression measurement (Chen et al., 2006, Zuhdi Alimam et al., 2000). http://purl.obolibrary.org/obo/GO_0010468 GO Northern blot Measures mucin gene expression by detecting mucin mRNAs. in_vitro mucin gene expression increase http://purl.obolibrary.org/obo/OBI_0000275 OBI low Northern blot of mucin mRNAs can also be applied for mucin gene expression measurement http://purl.obolibrary.org/obo/GO_0010467 GO RNase protection assay RNase protection assay (RPA) is used for mucin mRNA detection and quantification. in_vitro mRNA levels increase low For mucin mRNA detection and quantification RNase protection assay (RPA) is also used (Dohrman et al., 1998). http://purl.obolibrary.org/obo/GO_0010468 GO RNase protection assay Detects and quantifies mucin mRNA. in_vitro mucin mRNA levels increase low For mucin mRNA detection and quantification RNase protection assay (RPA) is also used http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Assesses alterations in mucin genes (MUC5AC, MUC5B) expression in cell and tissue lysates. in_vitro mucin gene expression increase http://purl.obolibrary.org/obo/OBI_0000272 OBI medium Alterations in mucin genes (MUC5AC, MUC5B) expression in cell and tissue lysates are commonly assessed by RT-PCR or RT-qPCR http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR/RT-qPCR RT-PCR or RT-qPCR are used to assess alterations in mucin gene (MUC5AC, MUC5B) expression in cell and tissue lysates. in_vitro tissue mRNA expression levels increase medium Alterations in mucin genes (MUC5AC, MUC5B) expression in cell and tissue lysates are commonly assessed by RT-PCR or RT-qPCR (Yu et al., 2011, Shao et al., 2004, Lee et al., 2011, Wagner et al., 2003, Hao et al., 2014, Zhu et al., 2009, Val et al., 2012). http://purl.obolibrary.org/obo/GO_0010468 GO Western blot Changes in mucin protein levels are detected by Western blot in cell and tissue lysates using suitable antibodies. in_vitro tissue protein levels increase low Changes in mucin protein levels can be detected by Western blot in cell and tissue lysates using suitable antibodies (Lee et al., 2011, Okuda et al., 2019, Ramsey et al., 2016). http://purl.obolibrary.org/obo/GO_0006454 GO ELISA Quantitative measurement of kisspeptin protein levels in biological samples using commercially available enzyme-linked immunosorbent assay (ELISA) kits. in_vitro kisspeptin concentration decrease http://purl.obolibrary.org/obo/GO_0072010 GO not_specified Kisspeptin can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. Studies that utilized immunoassay include (Feng et al. 2015; Cao et al. 2018; Wang et al. 2018), and include commercially available ELISA kits (e.g. Abcam ab288589 (human); Assay Genie HUDL01615 (human); LS Bio LS-F8897 (mouse)). http://purl.obolibrary.org/obo/GO_0072010 GO immunoassay Measures kisspeptin levels using commercially available ELISA kits. in_vitro human mouse kisspeptin levels decrease medium Kisspeptin can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. include commercially available ELISA kits (e.g. Abcam ab288589 (human); Assay Genie HUDL01615 (human); LS Bio LS-F8897 (mouse)) http://purl.obolibrary.org/obo/GO_0046879 GO real-time PCR Measures kisspeptin transcript abundance as an indirect indicator of kisspeptin hormone levels. in_vitro kisspeptin transcript abundance decrease medium Real time PCR can be used to measure kisspeptin transcript abundance, which is an indirect – and only semi-quantitative indicator of kisspeptin hormone levels (studies that utilized this approach include Feng et al. 2015; Cao et al. 2018; Wang et al. 2018). http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Measures kisspeptin protein levels. in_vitro kisspeptin protein levels decrease low Kisspeptin can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. http://purl.obolibrary.org/obo/GO_0046879 GO ELISA Enzyme-linked immunosorbent assay used to quantify the expression of AKT/eNOS and phospho AKT/eNOS using commercially available kits. in_vitro AKT/eNOS and phospho AKT/eNOS expression change http://purl.obolibrary.org/obo/OBI_0000115 OBI medium ELISA kits for AKT/eNOS and phospho AKT/eNOS expression are commercially available. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006447 GO ELISA ELISA kits measure the expression levels of AKT/eNOS and phospho AKT/eNOS proteins. in_vitro protein expression levels decrease high ELISA kits for AKT/eNOS and phospho AKT/eNOS expression are commercially available. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006468 GO L-arginine to L-citrulline assay This assay measures eNOS activity by quantifying the conversion of L-arginine to L-citrulline. in_vitro eNOS activity decrease medium eNOS activity can be measured using the conversion of L-arginine to L-citrulline assay. http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0001974 GO Western blot A method to determine the protein expression levels of phosphorylated eNOS, phosphorylated Akt, total Akt, and total eNOS using specific antibodies. in_vitro expression levels of phosphorylated eNOS, phosphorylated Akt, total Akt and total eNOS proteins change http://purl.obolibrary.org/obo/OBI_0000115 OBI low Western blot analysis can be performed to determine the expression levels of phosphorylated eNOS, phosphorylated Akt, total Akt and total eNOS proteins using the appropriate anti-phospho-eNOS, anti-phospho-Akt, anti-eNOS, and anti-Akt antibodies. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006468 GO Western blot Western blot analysis measures the expression levels of phosphorylated eNOS, phosphorylated Akt, total Akt, and total eNOS proteins using specific antibodies. in_vitro protein expression levels decrease http://purl.obolibrary.org/obo/OBI_0000185 OBI low Western blot analysis can be performed to determine the expression levels of phosphorylated eNOS, phosphorylated Akt, total Akt and total eNOS proteins using the appropriate anti-phospho-eNOS, anti-phospho-Akt, anti-eNOS, and anti-Akt antibodies. http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0006468 GO gel mobility shift assay Detects interference with NFAT nuclear translocation by analyzing nuclear or cytoplasmic extracts electrophoresed with end-labeled NFAT-binding site from the human IL-2 enhancer. in_vitro human NFAT DNA-binding activity decrease http://purl.obolibrary.org/obo/GO_0051643 GO low Interference with translocation of NFAT to the nucleus can be detected using gel mobility shift assays of nuclear or cytoplasmic extracts electrophoresed with end-labeled NFAT-binding site from human IL-2 enhancer (Flanagan et al. 1991). http://purl.obolibrary.org/obo/PR_000010978 PR http://purl.obolibrary.org/obo/GO_0051643 GO imaging flow cytometry Measures nuclear translocation of NFAT in lymphocytes using fluorescence-labeled anti-NFAT antibody and DAPI nuclear stain, analyzed via imaging flow cytometry. in_vitro lymphocytes nuclear translocation of NFAT change http://purl.obolibrary.org/obo/CL_0000542 CL medium Nuclear translocation of NFAT can be tested by imaging flowcytometer, in which lymphocytes are treated with fluorescence-labeled anti-NFAT antibody and DAPI (nuclear stain) and intracellular distribution of NFAT is analyzed by imaging flowcytometry with image analysis (Maguire O et al. 2013). http://purl.obolibrary.org/obo/PR_000010978 PR http://purl.obolibrary.org/obo/GO_0051643 GO ELISA Detects the binding of cyclosporin A (CsA) with cyclophilin as a surrogate measurement of calcineurin activity. in_vitro cyclophilin binding increase http://purl.obolibrary.org/obo/PR_000001237 PR high the binding of CsA with cyclophilin can be detected using an ELISA kit. Microtiter plates precoated with BSA and conjugated to cyclosporin are incubated with cyclophilin. Bound cyclophilin is then revealed by incubation with anti-cyclophilin rabbit antiserum followed by incubation with anti-rabbit globulin goat IgG coupled to alkaline phosphatase (Quesniaux et al. 1987). http://purl.obolibrary.org/obo/PR_000001237 PR http://purl.obolibrary.org/obo/GO_0005515 GO Phosphatase assay Measures the phosphatase activity of calcineurin (CN) using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP. Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted. in_vitro calcineurin phosphatase activity decrease http://purl.obolibrary.org/obo/GO_0034061 GO not_specified Phosphatase activity can be measured using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP. Kinetic analysis of FKBP12 concentration-dependent phosphatase activity and calculation of the CN inhibition constant Ki by the FKBP12-FK506 complex are conducted. Phosphatase activity of CN in the presence of cyclosporin A (CsA) , gossypol or dibefurin can also be determined in a similar manner http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0034061 GO phosphatase assay Measures phosphatase activity of calcineurin (CN) in the presence of various inhibitors such as FK506, cyclosporin A, gossypol, or dibefurin. in_vitro phosphatase activity decrease http://purl.obolibrary.org/obo/GO_0016791 GO http://purl.obolibrary.org/obo/PR_000001236 PR medium Phosphatase activity can be measured using a phosphatase assay. CN, calmodulin, FK506, and FKBP are incubated together, and the phosphatase activity is measured at various concentrations of FKBP. Phosphatase activity of CN in the presence of cyclosporin A (CsA), gossypol or dibefurin can also be determined in a similar manner (Sieber et al. 2009). http://purl.obolibrary.org/obo/PR_000001236 PR http://purl.obolibrary.org/obo/GO_0016311 GO gel shift assay Detects reductions in NFAT/AP-1 complex formation by testing nuclear extracts from stimulated or unstimulated Ar-5 T cells with a radio-labelled NFAT binding oligonucleotide. in_vitro Ar-5 T cells NFAT/AP-1 complex formation decrease low Reductions in NFAT/AP-1 complex formation can be detected using a gel shift assay to test nuclear extracts from either stimulated or unstimulated Ar-5 T cells with radio-labelled NFAT binding oligonucleotide from murine IL-2 promoter. http://purl.obolibrary.org/obo/GO_0008134 GO ELISA Measures serum antibody levels, specifically Anti-SRBC IgM and IgG levels. in_vivo serum Macaca fascicularis Anti-SRBC IgM and IgG levels decrease http://purl.obolibrary.org/obo/PR_000001453 PR http://purl.obolibrary.org/obo/PR_000001454 PR low Cynomolgus monkeys received 50 mg/kg CsA twice a day via oral gavage (10 h apart) for 23 days and were immunized with SRBC, after which the serum was examined for Anti-SRBC IgM and IgG levels using an ELISA specific for SRBC antigen (Kevin, G. et al. 2014). http://purl.obolibrary.org/obo/GO_0006959 GO ELISA Measures IgM levels in culture supernatants from SKW6.4 cells cultured with anti-CD3/CD28-stimulated PBMC supernatants in the presence of CNIs. in_vitro SKW6.4 cells peripheral blood mononuclear cells human IgM levels in culture supernatant decrease http://purl.obolibrary.org/obo/NCIT_C17843 NCIT low SKW6.4 cells (IL-6-dependent IgM-secreting human B-cell line) were cultured with anti-CD3/CD28 antibody-stimulated PBMC culture supernatant. After culturing for four days, IgM produced in the culture supernatants was measured using an ELISA kit. FK506 or CsA reduced the levels of IgM at the concentrations of 0.01 to 100 ng/mL or 0.1 to 1000 ng/mL (Sakuma et al. 2001b). http://purl.obolibrary.org/obo/GO_0003823 GO http://purl.obolibrary.org/obo/GO_0002290 GO ELISA Measures immunoglobulin IgM and IgG levels in culture supernatant after polyclonal T-cell stimulation. in_vitro T cells B cells peripheral blood mononuclear cells Homo sapiens immunoglobulin IgM and IgG levels decrease http://purl.obolibrary.org/obo/PR_000001453 PR http://purl.obolibrary.org/obo/PR_000001454 PR medium T cells and B cells isolated from human peripheral blood mononuclear cells (PBMC) were co-cultured with a CNIs for nine days in the presence of polyclonal–T-cell stimulation, after which supernatants were tested for immunoglobulin IgM and IgG levels using a Sandwich ELISA kit. Treatment with FK506 or CsA reduced the levels of IgM and IgG at the concentrations of 0.3 and 1.0 ng/mL or 50 and 100 ng/mL (Heidt et al, 2009). http://purl.obolibrary.org/obo/GO_0006959 GO ELISA Measures serum antibody levels, specifically T-cell-dependent, antigen-specific IgM and IgG levels. in_vivo serum Rattus norvegicus T-cell-dependent, antigen-specific IgM and IgG levels decrease http://purl.obolibrary.org/obo/PR_000001453 PR http://purl.obolibrary.org/obo/PR_000001454 PR low Rats were repeatedly administered FK506 orally for 4 weeks and immunized with KLH, after which the serum was examined for T-cell–dependent, antigen-specific, IgM and IgG levels using a Sandwich ELISA kit (Ulrich et al. 2004). http://purl.obolibrary.org/obo/GO_0006959 GO PFC assay Measures the number of antibody-secreting cells, specifically for SRBC antigen. in_vivo spleen cells spleen Mus musculus number of antibody-secreting cells decrease http://purl.obolibrary.org/obo/CL_0000976 CL low Mice were repeatedly administered calcineurin inhibitors (CNIs) including FK506 and CsA orally for 4 days and immunized with SRBC, after which spleen cells were examined using a PFC assay (Kino et al. 1987). http://purl.obolibrary.org/obo/CL_0000236 CL http://purl.obolibrary.org/obo/GO_0002250 GO PFC assay Plaque-forming cell (PFC) assay measures the number of antibody-secreting cells. in_vivo spleen cells spleen mouse Number of plaque-forming cells decrease low In vivo studies of antigen-specific antibodies are usually performed by measuring serum antibody levels with Enzyme-Linked ImmunoSorbent Assay (ELISA) or with a plaque-forming cell (PFC) assay. http://purl.obolibrary.org/obo/CL_0000274 CL quantitative PCR Measures cytokine mRNA levels in T cells, including Interferon-gamma, IL-2, IL-4, IL-5, IL-10, IL-13, and other B-cell-stimulatory cytokines. in_vitro T cells peripheral blood mononuclear cells Homo sapiens cytokine mRNA levels change http://purl.obolibrary.org/obo/OBI_0000663 OBI http://purl.obolibrary.org/obo/GO_0005125 GO medium In order to examine class switching, T cells derived from human PBMCs were cultured with CNIs, and cytokine mRNA levels of Interferon-gamma, IL-2, IL-4, IL-5, IL-10, IL-13, and other B-cell–stimulatory cytokines produced in T cells were measured by quantitative PCR (Dumont et al. 1998). http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0001817 GO competitive binding assay Competitive binding assays are used to assess PPARα binding, but require coupling with nuclear signaling assays to determine agonist or antagonist activity. in_vitro binding affinity not_specified medium For simple PPARα binding assessment, competitive binding assays are availables, however these must be coupled with nuclear signaling activation / inhibition assays to determine if chemicals are agonists or antagonists. http://purl.obolibrary.org/obo/CHEBI_59738 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO competitive binding assay Assesses the binding of chemicals to PPARα, typically used to determine affinity but requires additional assays to distinguish agonists from antagonists. in_vitro binding of chemicals to PPARα not_specified http://purl.obolibrary.org/obo/OBI_0000445 OBI http://purl.obolibrary.org/obo/PR_000001350 PR medium For simple PPARα binding assessment, competitive binding assays are availables, however these must be coupled with nuclear signaling activation / inhibition assays to determine if chemicals are agonists or antagonists. http://purl.obolibrary.org/obo/PR_000001350 PR http://purl.obolibrary.org/obo/GO_0008289 GO nuclear signaling activation / inhibition assay These assays are used to determine if chemicals are PPARα agonists or antagonists, when coupled with competitive binding assays. in_vitro nuclear signaling change medium For simple PPARα binding assessment, competitive binding assays are availables, however these must be coupled with nuclear signaling activation / inhibition assays to determine if chemicals are agonists or antagonists. http://purl.obolibrary.org/obo/CHEBI_59738 CHEBI http://purl.obolibrary.org/obo/GO_0005634 GO nuclear signaling activation/inhibition assay Nuclear signaling activation/inhibition assays measure downstream transcriptional activity of PPARα (e.g., reporter gene expression) to determine whether a chemical acts as an agonist or antagonist. in_vitro PPARα transcriptional activity change http://purl.obolibrary.org/obo/GO_0004879 GO medium these must be coupled with nuclear signaling activation / inhibition assays to determine if chemicals are agonists or antagonists. http://purl.obolibrary.org/obo/GO_0030261 GO X-ray crystallography X-ray crystallography was used to characterize the structure of the PPARα signaling complex, both in its suppressed state (with antagonist GW6471) and activated state (with agonist GW409544). in_vitro complex structure change low In Xu et al (2002), X-ray crystallography was used to characterize the suppressed PPARα signaling complex (PPARα / GW6471 / SMRT) and was compared against the activated PPARα complex which included binding of PPARα with the agonist GW409544 and the co-activator, steroid receptor coactivator-1 (SRC-1). http://purl.obolibrary.org/obo/CHEBI_59738 CHEBI http://purl.obolibrary.org/obo/GO_0005654 GO X-ray crystallography Characterizes the structure of the PPARα signaling complex, including suppressed (PPARα/GW6471/SMRT) and activated (PPARα/GW409544/SRC-1) states. in_vitro structure of PPARα signaling complex not_specified http://purl.obolibrary.org/obo/OBI_0000214 OBI http://purl.obolibrary.org/obo/PR_000001350 PR low X-ray crystallography was used to characterize the suppressed PPARα signaling complex (PPARα / GW6471 / SMRT) and was compared against the activated PPARα complex which included binding of PPARα with the agonist GW409544 and the co-activator, steroid receptor coactivator-1 (SRC-1). http://purl.obolibrary.org/obo/PR_000001350 PR http://purl.obolibrary.org/obo/GO_0035357 GO ChIP Evaluates DNA-protein interactions in human PPARα WT versus the V227A mutant. in_vitro human DNA-protein interaction change http://purl.obolibrary.org/obo/GO_0003677 GO medium Liu et al (2008) conducted in vitro investigations comparing human PPARα WT versus the V227A mutant in cell-based assays evaluated using chromatin immunoprecipitation (ChIP). http://purl.obolibrary.org/obo/PR_000001337 PR http://purl.obolibrary.org/obo/GO_0003677 GO competitive binding assay Evaluates binding interactions in human PPARα WT versus the V227A mutant. in_vitro human binding affinity change http://purl.obolibrary.org/obo/OBI_0000475 OBI http://purl.obolibrary.org/obo/GO_0005488 GO medium Liu et al (2008) conducted in vitro investigations comparing human PPARα WT versus the V227A mutant in cell-based assays evaluated using competitive binding assays http://purl.obolibrary.org/obo/PR_000001337 PR http://purl.obolibrary.org/obo/GO_0005515 GO GST pulldown Assesses protein-protein interactions in human PPARα WT versus the V227A mutant. in_vitro human protein-protein interaction change http://purl.obolibrary.org/obo/OBI_0000852 OBI http://purl.obolibrary.org/obo/GO_0005515 GO medium Liu et al (2008) conducted in vitro investigations comparing human PPARα WT versus the V227A mutant in cell-based assays evaluated using glutathione-S-transferase (GST) pulldown http://purl.obolibrary.org/obo/PR_000001337 PR http://purl.obolibrary.org/obo/GO_0005515 GO immunofluorescence Visualizes protein localization in human PPARα WT versus the V227A mutant. in_vitro human protein localization change http://purl.obolibrary.org/obo/OBI_0000693 OBI http://purl.obolibrary.org/obo/GO_0008104 GO medium Liu et al (2008) conducted in vitro investigations comparing human PPARα WT versus the V227A mutant in cell-based assays evaluated using immunofluorescence http://purl.obolibrary.org/obo/PR_000001337 PR http://purl.obolibrary.org/obo/GO_0008104 GO nuclear receptor reporter assay Nuclear receptor reporter assays were conducted for PPARalpha, PPARgamma, PPARsigma, and RXRalpha human cell-based assays. in_vitro human cells human reporter gene expression change medium The effects of 2,4-DNT and 2A-DNT on PPAR signaling was investigated using nuclear receptor reporter assays were conducted for (PPARalpha, PPARgamma, PPARsigma, and RXRalpha human cell-based assays, (Indigo Biosciences). http://purl.obolibrary.org/obo/GO_0007165 GO nuclear receptor reporter assays Cell-based assays using reporter genes to measure the transcriptional activity of specific nuclear receptors. in_vitro human cell-based assays human nuclear receptor transcriptional activity change high PPAR signaling was investigated using nuclear receptor reporter assays were conducted for (PPARalpha, PPARgamma, PPARsigma, and RXRalpha human cell-based assays http://purl.obolibrary.org/obo/GO_0007251 GO quantitative real-time RT-PCR Measures gene expression levels in human PPARα WT versus the V227A mutant. in_vitro human gene expression change http://purl.obolibrary.org/obo/OBI_0000662 OBI http://purl.obolibrary.org/obo/GO_0010467 GO medium Liu et al (2008) conducted in vitro investigations comparing human PPARα WT versus the V227A mutant in cell-based assays evaluated using quantitative real-time RT-PCR http://purl.obolibrary.org/obo/PR_000001337 PR http://purl.obolibrary.org/obo/GO_0010467 GO triglyceride measurement Measures triglyceride levels in human blood serum samples from populations with different PPARα genotypes. in_vivo blood serum human triglyceride levels change high In Chan et al (2006) triglycerides were measured directly from human blood serum samples from populations having the wild type PPARα gene compared to those having the V227A variant genotype. http://purl.obolibrary.org/obo/CHEBI_16258 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO X-ray crystallography X-ray crystallography was used to characterize the suppressed PPARα signaling complex (PPARα / GW6471 / SMRT) and was compared against the activated PPARα complex. in_vitro complex structure change low In Xu et al (2002), X-ray crystallography was used to characterize the suppressed PPARα signaling complex (PPARα / GW6471 / SMRT) and was compared against the activated PPARα complex which included binding of PPARα with the agonist GW409544 and the co-activator, steroid receptor coactivator-1 (SRC-1). http://purl.obolibrary.org/obo/GO_0005681 GO X-ray crystallography Characterizes the suppressed PPARα signaling complex (PPARα / GW6471 / SMRT) and compares it to the activated PPARα complex. in_vitro structure of PPARα signaling complex not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI low In Xu et al (2002), X-ray crystallography was used to characterize the suppressed PPARα signaling complex (PPARα / GW6471 / SMRT) and was compared against the activated PPARα complex which included binding of PPARα with the agonist GW409544 and the co-activator, steroid receptor coactivator-1 (SRC-1). http://purl.obolibrary.org/obo/GO_0035357 GO human epidemiological studies Observational studies in human populations used to assess the occurrence of developmental defects. in_vivo human developmental defects change low Developmental defects are typically assessed by observational studies of animal models and by human epidemiological studies. http://purl.obolibrary.org/obo/GO_0044331 GO observational study Developmental defects are assessed through observational studies of animal models and human epidemiological studies, focusing on litter-based evaluations of fetuses. in_vivo fetus developmental defects increase OECD TG 414 low Developmental defects are typically assessed by observational studies of animal models and by human epidemiological studies. A study design fit for the purpose of regulatory toxicology adheres to regulatory guidelines specified by OECD Test Guideline No. 414 (Prenatal Developmental Toxicity Study). Prenatal animal studies in mammalian species where exposure to a drug or chemical is administered to the dam describe the occurrence and severity of effects to the mother and fetuses and perform statistical evaluations on a litter basis since the dam is the exposure unit. http://purl.obolibrary.org/obo/CL_0002302 CL http://purl.obolibrary.org/obo/GO_0008523 GO Prenatal Developmental Toxicity Study Assesses developmental defects in mammalian species by evaluating the occurrence and severity of effects on the mother and fetuses following exposure to a drug or chemical. in_vivo mammalian species occurrence and severity of developmental defects increase OECD TG 414 low Developmental defects are typically assessed by observational studies of animal models and by human epidemiological studies. Prenatal animal studies in mammalian species where exposure to a drug or chemical is administered to the dam describe the occurrence and severity of effects to the mother and fetuses and perform statistical evaluations on a litter basis since the dam is the exposure unit. http://purl.obolibrary.org/obo/UBERON_0000062 UBERON http://purl.obolibrary.org/obo/GO_0032502 GO LC-MS/MS This in vivo assay measures thyroid hormone levels after incubation with substrate in whole fish microsomes. It is used to assess the rate of outer ring deiodination. in_vivo microsomes fish thyroid hormone levels decrease low Noyes et al. (2011) showed decreased rate of outer ring deiodination (mediated by DIO1 and DIO2) in whole fish microsomes after exposure to BDE-209. After incubation with the substrate, thyroid hormone levels were measured using LC-MS/MS. LC-MS/MS thyroid hormone measurement Measures thyroid hormone levels in tissue microsomes using liquid chromatography-tandem mass spectrometry. in_vivo microsomes fish thyroid hormone levels decrease http://purl.obolibrary.org/obo/CHEBI_38113 CHEBI http://purl.obolibrary.org/obo/OBI_0000473 OBI low Noyes et al. (2011) showed decreased rate of outer ring deiodination (mediated by DIO1 and DIO2) in whole fish microsomes after exposure to BDE-209. After incubation with the substrate, thyroid hormone levels were measured using LC-MS/MS. http://purl.obolibrary.org/obo/CHEBI_38113 CHEBI http://purl.obolibrary.org/obo/GO_0042401 GO radioactive iodine release assay Measures deiodinase activities by quantifying the radioactive iodine release from iodine-labelled substrates. in_vitro liver pig rat radioactive iodine release decrease http://purl.obolibrary.org/obo/GO_0004767 GO http://purl.obolibrary.org/obo/CHEBI_24868 CHEBI low A first in vitro assay measures deiodinase activities by quantifying the radioactive iodine release from iodine-labelled substrates, depending on the preferred substrates of the isoforms of deiodinases (Forhead et al., 2006; Pavelka, 2010; Houbrechts et al., 2016; Stinckens et al., 2018). Each of these assays requires a source of deiodinase which can be obtained for example using unexposed pig liver tissue (available from slaughterhouses) or rat liver tissue. http://purl.obolibrary.org/obo/GO_0004767 GO http://purl.obolibrary.org/obo/GO_0042401 GO Sandell-Kolthoff method A nonradioactive assay measuring iodide released using a photometric method based on Ce4+ reduction. in_vitro iodide release decrease http://purl.obolibrary.org/obo/CHEBI_24856 CHEBI http://purl.obolibrary.org/obo/GO_0004767 GO medium Olker et al. (2019) on the other hand used an adenovirus expression system to produce the DIO2 enzyme and developed an assay for nonradioactive measurement of iodide released using the Sandell-Kolthoff method, a photometric method based on Ce4+ reduction (Renko et al., 2012). This assay was then used to screen the ToxCast Phase 1 chemical library. http://purl.obolibrary.org/obo/GO_0004767 GO http://purl.obolibrary.org/obo/GO_0042401 GO T3 level measurement Measures T3 levels in fish species as evidence of DIO inhibition. in_vivo zebrafish fathead minnow T3 levels decrease http://purl.obolibrary.org/obo/CHEBI_18248 CHEBI low Decreased T3 levels are often used as evidence of DIO inhibition, for example after exposure to iopanoic acid, in fish species such as zebrafish (Stinckens et al., 2020) and fathead minnow (Cavallin et al., 2017). http://purl.obolibrary.org/obo/CHEBI_18248 CHEBI http://purl.obolibrary.org/obo/GO_0042401 GO ELISA Enzyme-linked immunosorbent assay used to measure total T3 and T4 concentrations in serum or tissues, commonly employed in rodent studies and human clinical tests. in_vitro serum tissues rodents humans total T3 and T4 concentrations decrease medium The ELISA method has become more routine in rodent studies. The ELISA method is commonly used as a human clinical test method. http://purl.obolibrary.org/obo/CHEBI_18287 CHEBI http://purl.obolibrary.org/obo/GO_0006590 GO HPLC-MS High-performance liquid chromatography coupled with mass spectrometry used for analytical determination of iodothyronines (T3, T4, rT3, T2) and their conjugates in serum or tissues. in_vitro serum tissues iodothyronines and their conjugates concentrations decrease low Recently, analytical determination of iodothyronines (T3, T4, rT3, T2) and their conjugates through methods employing HPLC and mass spectrometry have become more common (DeVito et al., 1999; Miller et al., 2009; Hornung et al., 2015; Nelson et al., 2016; Stinckens et al., 2016). http://purl.obolibrary.org/obo/CHEBI_18287 CHEBI http://purl.obolibrary.org/obo/GO_0006590 GO HPLC-MS High-performance liquid chromatography coupled to mass spectrometry (HPLC-MS) directly measures iodothyronines such as T3, T4, rT3 and T2 and their conjugates in biological samples. in_vivo triiodothyronine (T3) concentration decrease http://purl.obolibrary.org/obo/CHEBI_17354 CHEBI http://purl.obolibrary.org/obo/CHEBI_17351 CHEBI low Recently, analytical determination of iodothyronines (T3, T4, rT3, T2) and their conjugates through methods employing HPLC and mass spectrometry have become more common (DeVito et al., 1999; Miller et al., 2009; Hornung et al., 2015; Nelson et al., 2016; Stinckens et al., 2016). Both RIA and ELISA measure THs by a an indirect methodology, whereas analytical determination is the most direct measurement available. http://purl.obolibrary.org/obo/CHEBI_17354 CHEBI http://purl.obolibrary.org/obo/GO_0006744 GO LC-MS Liquid chromatography coupled with mass spectrometry used to measure whole-body thyroid hormone levels in fish early life stages. in_vitro whole-body fish whole-body thyroid hormone levels decrease low In fish early life stages most evidence for the ontogeny of TH synthesis comes from measurements of whole-body TH levels and using LC-MS techniques (Hornung et al., 2015) are increasingly used to accurately quantify whole-body TH levels (Nelson et al., 2016; Stinckens et al., 2016, 2020). http://purl.obolibrary.org/obo/CHEBI_18287 CHEBI http://purl.obolibrary.org/obo/GO_0006590 GO RIA Radioimmunoassay used to measure total T3 and T4 concentrations in serum or tissues, commonly employed in rodent endocrine and toxicity studies. in_vitro serum tissues rodents total T3 and T4 concentrations decrease medium The majority of T3 and T4 measurements are made using either RIA or ELISA kits. Historically, the most widely used method in toxicology is RIA. The method is routinely used in rodent endocrine and toxicity studies. http://purl.obolibrary.org/obo/CHEBI_18287 CHEBI http://purl.obolibrary.org/obo/GO_0006590 GO morphometric measurement of posterior chamber size Quantification of the posterior swim bladder chamber size using photographs and a calibrator. in_vivo swim bladder fish posterior chamber size change low Posterior chamber size can then be measured based on photographs with a calibrator. http://purl.obolibrary.org/obo/UBERON_0002033 UBERON stereomicroscopy Inflation of the posterior swim bladder chamber is observed using a stereomicroscope in transparent larvae. Chamber size is measured based on photographs with a calibrator. in_vivo swim bladder zebrafish fathead minnow posterior chamber size decrease low In several fish species, inflation of the posterior chamber can easily be observed using a stereomicroscope because the larvae are still transparent during those early developmental stages. Posterior chamber size can then be measured based on photographs with a calibrator. When observing effects on swim bladder inflation, it is important to verify that reduced swim bladder inflation occurs at concentrations significantly lower than those causing mortality http://purl.obolibrary.org/obo/UBERON_0004823 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO Stereomicroscopy for swim bladder inflation Observation of posterior chamber inflation in transparent fish larvae using a stereomicroscope, with size measurement from calibrated photographs. in_vivo swim bladder zebrafish fathead minnow posterior chamber size decrease http://purl.obolibrary.org/obo/UBERON_0002102 UBERON http://purl.obolibrary.org/obo/GO_0002164 GO medium inflation of the posterior chamber can easily be observed using a stereomicroscope because the larvae are still transparent during those early developmental stages. Posterior chamber size can then be measured based on photographs with a calibrator. http://purl.obolibrary.org/obo/UBERON_0002102 UBERON Swim bladder inflation assay Observation of posterior swim bladder inflation in transparent early-stage fish larvae (e.g., zebrafish, fathead minnow) using a stereomicroscope and measurement of posterior chamber size from photographs. in_vivo swim bladder Danio rerio Pimephales promelas posterior swim bladder size decrease http://purl.obolibrary.org/obo/GO_0048702 GO low In several fish species, inflation of the posterior chamber can easily be observed using a stereomicroscope because the larvae are still transparent during those early developmental stages. Posterior chamber size can then be measured based on photographs with a calibrator. When observing effects on swim bladder inflation, it is important to verify that reduced swim bladder inflation occurs at concentrations significantly lower than those causing mortality, since a wide variety of chemicals cause impaired posterior chamber inflation at exposure concentrations that also cause mortality (Stinckens et al., 2018). http://purl.obolibrary.org/obo/UBERON_0002086 UBERON automated observation and tracking system Measures swimming performance in fish larvae, including distance travelled, duration of movements, and swimming speed using automated observation and tracking systems. in_vivo Danio rerio swimming performance decrease http://purl.obolibrary.org/obo/GO_0008347 GO http://purl.obolibrary.org/obo/GO_0007626 GO high For fish larvae, automated observation and tracking systems are commercially available and increasingly used for measuring swimming performance including distance travelled, duration of movements, swimming speed, etc. This kind of measurements is often included in publications describing effects of chemicals in zebrafish larvae (Hagenaars et al., 2014; Stinckens et al., 2016; Vergauwen et al., 2015). http://purl.obolibrary.org/obo/GO_0007626 GO swim tunnel Measures swim performance in juvenile and adult fish using swim tunnels to collect various data. in_vivo swim performance decrease http://purl.obolibrary.org/obo/GO_0008347 GO low For juvenile and adult fish, measurements of swim performance vary. However, in some circumstances, swim tunnels have been used to measure various data (Fu et al., 2013). http://purl.obolibrary.org/obo/GO_0007626 GO stereomicroscopy Inflation of the anterior chamber is observed using a stereomicroscope in transparent larvae. Anterior chamber size is measured based on photographs with a calibrator. in_vivo swim bladder zebrafish fathead minnow anterior chamber size decrease low In several fish species, inflation of the anterior chamber can be observed using a stereomicroscope because the larvae are still transparent during the larval stage. Anterior chamber size can then be measured based on photographs with a calibrator. This is for example true for zebrafish and fathead minnow. http://purl.obolibrary.org/obo/UBERON_0004814 UBERON http://purl.obolibrary.org/obo/GO_0048750 GO Stereomicroscopy for anterior swim bladder inflation Observation and measurement of the anterior chamber size in transparent fish larvae using a stereomicroscope and calibrated photographs. in_vivo anterior swim bladder zebrafish fathead minnow anterior chamber size decrease http://purl.obolibrary.org/obo/UBERON_0002096 UBERON medium inflation of the anterior chamber can be observed using a stereomicroscope because the larvae are still transparent during the larval stage Anterior chamber size can then be measured based on photographs with a calibrator http://purl.obolibrary.org/obo/UBERON_0002096 UBERON audiometry Behavioral tests involve transmission of pure tones and measuring a behavioral response (e.g., clicking a button, startle response) to determine if the tone is perceived. in_vivo ear tone perception decrease http://purl.obolibrary.org/obo/GO_0007605 GO medium Common behavioral tests involve transmission of pure tones of defined amplitude and frequency using and audiometer or PC and using a behavioral response (e.g., clicking a button; startle response) to determine whether the tone is perceived. http://purl.obolibrary.org/obo/UBERON_0004139 UBERON http://purl.obolibrary.org/obo/GO_0007605 GO Auditory Brainstem Response (ABR) Detects auditory evoked potentials using electrodes placed on the head to measure brainstem responses to auditory stimuli. in_vivo brain auditory evoked potentials not_specified medium Auditory brainstem response (ABR): Uses electrodes placed on the head to detect auditory evoked potentials from background electrical activity in the brain. http://purl.obolibrary.org/obo/UBERON_0000956 UBERON Auditory nerve electrophysiology Invasive electrophysiological methods that involve surgical insertion of electrodes into the auditory nerves to record auditory responses. in_vivo auditory nerve not_specified auditory nerve action potential decrease http://purl.obolibrary.org/obo/OBI_0001848 OBI http://purl.obolibrary.org/obo/UBERON_0000005 UBERON http://purl.obolibrary.org/obo/OBI_0000070 OBI low Invasive electrophysiological methods involving surgical insertion of electrodes into the auditory nerves have been employed. http://purl.obolibrary.org/obo/UBERON_0000005 UBERON Behavioral audiometry Behavioral tests measure hearing by presenting pure tones of defined amplitude and frequency using an audiometer or PC, and recording a behavioral response (e.g., button press, startle response) to determine if the tone is perceived. in_vivo auditory system not_specified hearing threshold decrease http://purl.obolibrary.org/obo/GO_0017007 GO http://purl.obolibrary.org/obo/CHMO_0000001 CHMO http://purl.obolibrary.org/obo/GO_0065008 GO low Common behavioral tests involve transmission of pure tones of defined amplitude and frequency using and audiometer or PC and using a behavioral response (e.g., clicking a button; startle response) to determine whether the tone is perceived. http://purl.obolibrary.org/obo/UBERON_0000995 UBERON http://purl.obolibrary.org/obo/GO_0017007 GO Behavioral hearing test Measures hearing by transmitting pure tones and observing behavioral responses (e.g., button click, startle) to determine tone perception. in_vivo behavioral response to auditory stimuli not_specified http://purl.obolibrary.org/obo/GO_0007605 GO low Common behavioral tests involve transmission of pure tones of defined amplitude and frequency using and audiometer or PC and using a behavioral response (e.g., clicking a button; startle response) to determine whether the tone is perceived. http://purl.obolibrary.org/obo/UBERON_0001785 UBERON http://purl.obolibrary.org/obo/GO_0007605 GO Fish Auditory Evoked Potentials (AEP) Non-invasively records auditory evoked potentials via cutaneous electrodes on the fish head to measure hearing. in_vivo brain fish auditory evoked potentials not_specified http://purl.obolibrary.org/obo/GO_0007605 GO medium Non-invasive recording of Auditory Evoked Potentials (AEPs; synonymous with ABRs) are now the most common approach for measuring hearing in fish. AEPs can be recorded via electrodes attached cutaneously to the head (see review by Ladich and Fay, 2013). http://purl.obolibrary.org/obo/UBERON_0000955 UBERON fish behavioral test Conditioning and behavioral tests were employed in testing fish hearing, measuring responses to auditory stimuli. in_vivo ear fish auditory response decrease http://purl.obolibrary.org/obo/GO_0009249 GO medium Through the mid-late 1980s conditioning and behavioral tests were most commonly employed in testing fish hearing. http://purl.obolibrary.org/obo/UBERON_0004139 UBERON http://purl.obolibrary.org/obo/GO_0007605 GO invasive electrophysiological auditory nerve recording Electrophysiological method involving the surgical insertion of electrodes into the auditory nerves. in_vivo auditory nerves nerve activity change low Invasive electrophysiological methods involving surgical insertion of electrodes into the auditory nerves have been employed. Invasive fish electrophysiology Measures auditory nerve activity via surgically inserted electrodes in fish. in_vivo auditory nerve fish electrophysiological response of auditory nerve not_specified http://purl.obolibrary.org/obo/UBERON_0001876 UBERON low Invasive electrophysiological methods involving surgical insertion of electrodes into the auditory nerves have been employed. http://purl.obolibrary.org/obo/UBERON_0001876 UBERON adenovirus expression system assay Uses an adenovirus expression system to produce DIO1 enzyme and measures iodide release using the Sandell-Kolthoff method in a 96-well plate format. in_vitro iodide release decrease high Renko et al. (2015), Hornung et al. (2018) and Olker et al. (2019) on the other hand used an adenovirus expression system to produce the DIO1 enzyme and developed an assay for nonradioactive measurement of iodide released using the Sandell-Kolthoff method, a photometric method based on Ce4+ reduction (Renko et al., 2012), in a 96-well plate format chromatography-mass spectroscopy assay Uses chromatography-based method coupled to mass spectroscopy to measure products of thyroxin resulting from deiodinase type-1 activity. in_vitro liver pig rat thyroxin deiodination products decrease low Another assay uses a chromatography-based method coupled to mass spectroscopy to measure products of thyroxin resulting from deiodinase type-1 activity in vivo deiodinase activity assay Measures deiodinase activity in tissues collected from animal experiments, often using LC-MS/MS to measure thyroid hormone levels. in_vivo microsomes fish zebrafish fathead minnow mouse deiodination rate decrease low Measurements of in vivo deiodinase activity in tissues collected from animal experiments are scarce. Noyes et al. (2011) showed decreased rate of outer ring deiodination (mediated by DIO1 and DIO2) in whole fish microsomes after exposure to BDE-209. After incubation with the substrate, thyroid hormone levels were measured using LC-MS/MS. LC-MS/MS (in vivo) This assay measures thyroid hormone levels using LC-MS/MS in tissues collected from animal experiments. in_vivo microsomes fish thyroid hormone levels decrease low After incubation with the substrate, thyroid hormone levels were measured using LC-MS/MS. LC-MS/MS in vivo tissue microsome assay Measures in vivo deiodinase activity in whole fish microsomes after exposure to compounds, quantifying thyroid hormone levels using LC-MS/MS. in_vivo microsome liver zebrafish fathead minnow fish thyroid hormone levels (T3/T4) and outer ring deiodination rate decrease http://purl.obolibrary.org/obo/GO_0004399 GO http://purl.obolibrary.org/obo/CHEBI_15815 CHEBI not_specified Measurements of in vivo deiodinase activity in tissues collected from animal experiments are scarce. Noyes et al. (2011) showed decreased rate of outer ring deiodination (mediated by DIO1 and DIO2) in whole fish microsomes after exposure to BDE-209. After incubation with the substrate, thyroid hormone levels were measured using LC-MS/MS. Decreased T3 levels are often used as evidence of DIO inhibition, for example after exposure to iopanoic acid, in fish species such as zebrafish (Stinckens et al., 2020) and fathead minnow (Cavallin et al., 2017). http://purl.obolibrary.org/obo/GO_0042413 GO LC-MS/MS thyroid hormone measurement An in vivo measurement of thyroid hormone levels in fish microsomes using liquid chromatography-tandem mass spectrometry after incubation with a substrate. in_vivo microsomes fish thyroid hormone levels decrease http://purl.obolibrary.org/obo/CHEBI_36730 CHEBI low Noyes et al. (2011) showed decreased rate of outer ring deiodination (mediated by DIO1 and DIO2) in whole fish microsomes after exposure to BDE-209. After incubation with the substrate, thyroid hormone levels were measured using LC-MS/MS. http://purl.obolibrary.org/obo/CHEBI_36730 CHEBI http://purl.obolibrary.org/obo/GO_0045332 GO radioactive iodine release assay Measures deiodinase activities by quantifying the radioactive iodine release from iodine-labelled substrates. in_vitro liver pig rat radioactive iodine release decrease low A first in vitro assay measures deiodinase activities by quantifying the radioactive iodine release from iodine-labelled substrates Sandell-Kolthoff colorimetric assay Measures the release of iodine from T4 using a colorimetric method based on Ce4+ reduction. in_vitro liver pig rat iodine release decrease medium A colorimetric method (Renko et al., 2012), the Sandell-Kolthoff method, that measures the release of iodine from T4 is also available T3 level measurement Measurement of triiodothyronine (T3) levels used as evidence of deiodinase inhibition in various fish species. in_vivo zebrafish fathead minnow T3 levels decrease http://purl.obolibrary.org/obo/CHEBI_36730 CHEBI not_specified Decreased T3 levels are often used as evidence of DIO inhibition, for example after exposure to iopanoic acid, in fish species such as zebrafish (Stinckens et al., 2020) and fathead minnow (Cavallin et al., 2017). http://purl.obolibrary.org/obo/CHEBI_36730 CHEBI http://purl.obolibrary.org/obo/GO_0045332 GO body weight measurement Measures weight gain or loss over an extended period as an indicator of feeding inhibition. in_vivo body weight decrease http://purl.obolibrary.org/obo/VT_0001259 VT not_specified for extended periods by decreased weight gain or weight loss http://purl.obolibrary.org/obo/GO_0040007 GO food consumption measurement Measures the amount of food consumed by weight over a short period. in_vivo food consumption decrease http://purl.obolibrary.org/obo/GO_0007584 GO not_specified Inhibition of feeding is measured in the short-term by decreased consumption of available food by weight of food ingested http://purl.obolibrary.org/obo/GO_0007631 GO ER binding assay Radioreceptor assay using rat uterine cytosol to identify chemicals that interact with estrogen receptor (ER) subtypes (ERα and ERβ) in vitro. The assay measures the ability of a ligand/chemical to displace the endogenous hormone 17β-estradiol from the receptor. in_vitro uterine cytosol Rattus norvegicus estrogen receptor binding decrease http://purl.obolibrary.org/obo/GO_0033596 GO not_specified This assay identifies chemicals that have the potential to interact with the estrogen receptor (ER) in vitro. The radioactivity measurement provides the quantitative estimation of the bound and unbound fraction of the ligand with the receptor. Assay determines if a ligand/chemical can interact and displace the endogenous hormone 17β-estradiol http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0033596 GO Radioreceptor assay This assay identifies chemicals that can interact with the estrogen receptor (ER) in vitro using competitive protein-binding methods with a radiolabeled ligand. in_vitro Rat Uterine Cytosol Rattus norvegicus estrogen receptor binding not_specified http://purl.obolibrary.org/obo/GO_0030284 GO medium Radioreceptor assay/The estrogen receptor binding assay (using Rat Uterine Cytosol): This assay identifies chemicals that have the potential to interact with the estrogen receptor (ER) in vitro. Principle of this particular assay is based on the competitive protein-binding methods. A radiolabelled ligand and an unlabelled ligand are presented together to a specific receptor. The radioactivity measurement provides the quantitative estimation of the bound and unbound fraction of the ligand with the receptor. All cytosolic estrogen receptor subtypes that are expressed in the specific tissue, including ERα and ERβ are used for the determination of estrogen receptor binding. http://purl.obolibrary.org/obo/PR_000001049 PR http://purl.obolibrary.org/obo/GO_0030520 GO Radioreceptor assay A competitive protein-binding assay that quantifies the interaction of chemicals with the estrogen receptor (ER) by measuring the displacement of a radiolabelled ligand by an unlabelled ligand. in_vitro Uterus Rat radioactivity measurement of bound and unbound ligand fraction change http://purl.obolibrary.org/obo/OBI_0000131 OBI medium The estrogen receptor binding assay (using Rat Uterine Cytosol) Principle of this particular assay is based on the competitive protein-binding methods. The radioactivity measurement provides the quantitative estimation of the bound and unbound fraction of the ligand with the receptor. Assay determines if a ligand/chemical can interact and displace the endogenous hormone 17β-estradiol http://purl.obolibrary.org/obo/PR_000000001 PR Radioreceptor assay This assay identifies chemicals that have the potential to interact with the estrogen receptor (ER) in vitro. It measures the competitive binding of a radiolabelled ligand and an unlabelled ligand to the receptor, quantifying the bound and unbound fractions. in_vitro uterus rat receptor binding decrease http://purl.obolibrary.org/obo/OBI_0000489 OBI low This assay identifies chemicals that have the potential to interact with the estrogen receptor (ER) in vitro. Principle of this particular assay is based on the competitive protein-binding methods. The radioactivity measurement provides the quantitative estimation of the bound and unbound fraction of the ligand with the receptor. ELISA Immunoassay technique using commercially available ELISA kits to quantify GnRH protein levels in biological samples. in_vitro hypothalamus human rat GnRH protein concentration increase http://purl.obolibrary.org/obo/GO_0001508 GO http://purl.obolibrary.org/obo/GO_0022617 GO not_specified GnRH can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. Studies that utilized immunoassay include (Clarkson et al. 2008; Kriszt et al. 2015; Bo et al. 2022), and include commercially available ELISA kits (e.g. Elabscience E-EL-0071 (universal; no cross-species reactivity); Assay Genie HUFI02509 (human); Cusabio CSB-E06880h (human); Biomatik EKC39138-96T (rat)). http://purl.obolibrary.org/obo/GO_0001508 GO http://purl.obolibrary.org/obo/GO_0022617 GO immunoassay Measures GnRH secretion levels using antibody-based detection, typically via ELISA kits. in_vitro hypothalamus human rat GnRH secretion levels increase medium GnRH can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. include commercially available ELISA kits (e.g. Elabscience E-EL-0071 (universal; no cross-species reactivity); Assay Genie HUFI02509 (human); Cusabio CSB-E06880h (human); Biomatik EKC39138-96T (rat)) http://purl.obolibrary.org/obo/CHEBI_18207 CHEBI http://purl.obolibrary.org/obo/GO_0003265 GO real-time PCR Measures GnRH transcript abundance as an indirect indicator of GnRH hormone levels. in_vitro hypothalamus GnRH transcript abundance increase http://purl.obolibrary.org/obo/OBI_0000274 OBI medium Real time PCR can be used to measure GnRH transcript abundance, which is an indirect – and only semi-quantitative indicator of GnRH hormone levels http://purl.obolibrary.org/obo/GO_0003265 GO Western blot Detects GnRH protein levels using gel electrophoresis and antibody probing. in_vitro hypothalamus GnRH protein levels increase low GnRH can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. http://purl.obolibrary.org/obo/CHEBI_18207 CHEBI http://purl.obolibrary.org/obo/GO_0003265 GO gene expression analysis This assay measures changes in gene expression in specific organs to detect alterations in lipid metabolism. in_vivo stomach liver intestines gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO medium changes in gene expression http://purl.obolibrary.org/obo/GO_0003674 GO http://purl.obolibrary.org/obo/GO_0019216 GO organ breakdown product analysis This assay examines specific organs (e.g., stomach, liver, intestines) for breakdown products such as proteins to detect changes in lipid metabolism. in_vivo stomach liver intestines breakdown products in organs change http://purl.obolibrary.org/obo/GO_0030163 GO low examination of organs (ex. stomach, liver, intestines) for break-down products (ex. proteins) http://purl.obolibrary.org/obo/UBERON_0000062 UBERON http://purl.obolibrary.org/obo/GO_0016042 GO organ breakdown product examination Examination of specific organs for the presence of breakdown products, such as proteins, to assess metabolic changes. ex_vivo stomach liver intestines break-down products change not_specified examination of organs (ex. stomach, liver, intestines) for break-down products (ex. proteins) http://purl.obolibrary.org/obo/GO_0006629 GO organ examination Examination of organs (stomach, liver, intestines) for break-down products (proteins) or changes in gene expression to detect changes in lipid metabolism. in_vivo stomach liver intestines break-down products (proteins), gene expression change low Changes in lipid metabolism can be detected by examination of organs (ex. stomach, liver, intestines) for break-down products (ex. proteins) or changes in gene expression. http://purl.obolibrary.org/obo/CHEBI_3418 CHEBI http://purl.obolibrary.org/obo/GO_0006629 GO organism fat content measurement This assay measures the total fat content in an organism to detect changes in lipid metabolism. in_vivo organism fat content change http://purl.obolibrary.org/obo/GO_0019915 GO low Changes in lipid metabolism can be detected by examining organism fat content http://purl.obolibrary.org/obo/GO_0006629 GO 21-Day Fish Assay A short-term screening assay for oestrogenic and androgenic activity and aromatase inhibition in fish. in_vivo fish oestrogenic and androgenic activity change http://purl.obolibrary.org/obo/GO_0048514 GO OECD TG 230 not_specified OECD TG 230 (September 2009): 21-Day Fish Assay a Short-Term Screening for Oestrogenic and Androgenic Activity, and Aromatase Inhibition BG1luc assay Identifies estrogen receptor agonists and antagonists using the BG1luc estrogen receptor transactivation test method. in_vitro estrogen receptor transactivation not_specified http://purl.obolibrary.org/obo/GO_0004883 GO OECD TG 457 not_specified OECD TG 457 (October 2012): BG1luc estrogen receptor transactivation test method for identifying estrogen receptor agonists and antagonists. http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO EASZY assay Detects endocrine active substances acting through estrogen receptors using transgenic zebrafish embryos. in_vitro zebrafish estrogen receptor activity not_specified http://purl.obolibrary.org/obo/GO_0030331 GO OECD TG 250 not_specified OECD TG 250 (June 2021): EASZY assay - Detection of Endocrine Active Substances, acting through estrogen receptors, using transgenic tg (CYP19A1b:GFP) Zebrafish embryo http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO Estrogen Receptor Binding Assay Competitive protein-binding assay using rat uterine cytosol to identify chemicals that interact with ERα and ERβ. in_vitro uterine cytosol Rattus norvegicus bound and unbound fraction of the ligand change http://purl.obolibrary.org/obo/GO_0048484 GO not_specified US EPA (2009) Estrogen Receptor Binding Assay Using Rat Uterine Cytosol The radioactivity measurement provides the quantitative estimation of the bound and unbound fraction of the ligand with the receptor. http://purl.obolibrary.org/obo/GO_0008425 GO http://purl.obolibrary.org/obo/GO_0048484 GO Estrogen Receptor Binding Assay Identifies chemicals that interact with estrogen receptors using competitive protein-binding methods with rat uterine cytosol. in_vitro uterus rat estrogen receptor binding not_specified http://purl.obolibrary.org/obo/GO_0030331 GO US EPA (2009) Estrogen Receptor Binding Assay Using Rat Uterine Cytosol not_specified US EPA (2009) Estrogen Receptor Binding Assay Using Rat Uterine Cytosol: This assay identifies chemicals that have the potential to interact with the estrogen receptor (ER) in vitro. Principle of this particular assay is based on the competitive protein-binding methods. A radiolabelled ligand and an unlabelled ligand are presented together to a specific receptor. The radioactivity measurement provides the quantitative estimation of the bound and unbound fraction of the ligand with the receptor. All cytosolic estrogen receptor subtypes that are expressed in the specific tissue, including ERα and ERβ are used for the determination of estrogen receptor binding. http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO HRER assay Measures chemicals with ER binding affinity using human recombinant estrogen receptor in vitro. in_vitro ER binding affinity not_specified http://purl.obolibrary.org/obo/GO_0030331 GO OECD TG 493 not_specified OECD TG 493 (July 2015): Performance-Based Test Guideline for Human Recombinant Estrogen Receptor (HRER) In Vitro Assays to Detect Chemicals with ER Binding Affinity http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO OECD TG 230 21-Day Fish Assay a Short-Term Screening for Oestrogenic and Androgenic Activity, and Aromatase Inhibition. in_vivo fish tissues fish oestrogenic and androgenic activity, aromatase inhibition change OECD TG 230 not_specified OECD TG 230 (September 2009): 21-Day Fish Assay a Short-Term Screening for Oestrogenic and Androgenic Activity, and Aromatase Inhibition http://purl.obolibrary.org/obo/GO_0005160 GO OECD TG 250 EASZY assay - Detection of Endocrine Active Substances, acting through estrogen receptors, using transgenic tg (CYP19A1b:GFP) Zebrafish embryo. in_vitro Zebrafish embryo Danio rerio GFP expression change OECD TG 250 not_specified OECD TG 250 (June 2021): EASZY assay - Detection of Endocrine Active Substances, acting through estrogen receptors, using transgenic tg (CYP19A1b:GFP) Zebrafish embryo http://purl.obolibrary.org/obo/GO_0006925 GO OECD TG 493 Performance-Based Test Guideline for Human Recombinant Estrogen Receptor (HRER) In Vitro Assays to detect chemicals with ER binding affinity. in_vitro ER binding affinity change http://purl.obolibrary.org/obo/GO_0005103 GO OECD TG 493 not_specified OECD TG 493 (July 2015): Performance-Based Test Guideline for Human Recombinant Estrogen Receptor (HRER) In Vitro Assays to Detect Chemicals with ER Binding Affinity http://purl.obolibrary.org/obo/CHEBI_51533 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO QSAR models for ER interaction Predicts ER interaction using quantitative structure-activity relationship models. in_silico ER interaction potential not_specified http://purl.obolibrary.org/obo/GO_0030331 GO high QSAR models for ER interaction are available at the website of Danish (https://qsar.food.dtu.dk/) and US (https://www.epa.gov/tsca-screening-tools/epi-suitetm-estimation-program-interface) EPA and OECD (https://www.oecd.org/chemicalsafety/risk-assessment/oecdquantitativestructure-activityrelationshipsprojectqsars.htm). http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO STTA assay Identifies estrogen receptor agonists and antagonists using stably transfected cell lines expressing human ERα and/or ERβ. in_vitro hERα-HeLa-9903 VM7Luc4E2 human estrogen receptor transactivation not_specified http://purl.obolibrary.org/obo/GO_0004883 GO OECD TG 455 not_specified OECD TG 455 (June 2021): Performance-Based Test Guideline (PGBT) For Stably Transfected Transactivation In Vitro Assays to Detect Estrogen Receptor Agonists and Antagonists. It comprises several mechanistically and functionally similar test methods for the identification of estrogen receptor (i.e., ERα, and/or ERβ). The fully validated reference test methods that provide the basis for this PBTG are: 1) The Stably Transfected TA (STTA) assay using the (h) ERα-HeLa-9903 cell line; and 2) The VM7Luc ER TA assay (3) using the VM7Luc4E2 cell line1 which predominately expresses hERα with some contribution from hERβ. http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO STTA assay Stably transfected transactivation assay using hERα-HeLa-9903 cell line to detect ER agonists and antagonists. in_vitro hERα-HeLa-9903 Homo sapiens transcriptional activation change OECD TG 455 not_specified The Stably Transfected TA (STTA) assay using the (h) ERα-HeLa-9903 cell line http://purl.obolibrary.org/obo/GO_0008425 GO http://purl.obolibrary.org/obo/GO_0008425 GO T47D-Kbluc assay Measures estrogen receptor activity using the T47D-Kbluc cell line. in_vitro T47D-Kbluc human estrogen receptor activity not_specified http://purl.obolibrary.org/obo/GO_0004883 GO not_specified T47D-Kbluc assay (Wilson et al., 2004); http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO ToxCast Estrogen Receptor Agonist Pathway Model A mathematical model combining 18 high-throughput screening (HTS) assays to predict ER agonism or antagonism via AUC values. in_silico area under the curve (AUC) for ER agonism change high The ToxCast estrogen receptor (ER) pathway model is a mathematical model that combines the results of 18 high-throughput screening (HTS) assays from the ToxCast and Tox21 research programs. The output of the model provides an area under the curve (AUC) value for the potential of a chemical to cause ER agonism http://purl.obolibrary.org/obo/GO_0003677 GO ToxCast Estrogen Receptor Agonist Pathway Model Predicts ER agonism or antagonism using activity patterns from 18 high-throughput screening assays. in_silico ER agonism potential not_specified http://purl.obolibrary.org/obo/GO_0004883 GO high ToxCast Estrogen Receptor Agonist Pathway Model: The ToxCast estrogen receptor (ER) pathway model is a mathematical model that combines the results from 18 high-throughput screening (HTS) assays from the ToxCast and Tox21 research programs. The HTS assays measure ER binding, dimerization, chromatin binding, transcriptional activation and ER-dependent cell proliferation. The model uses activity patterns across the in vitro assays to predict whether a chemical is an ER agonist or antagonist or is otherwise influencing the assays through a manner dependent on the physics and chemistry of the technology platform (“assay interference”). The output of the model provides an area under the curve (AUC) value for the potential of a chemical to cause ER agonism, normalized with respect to the positive control chemical, oestradiol. http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO US EPA Estrogen Receptor Binding Assay (Rat Uterine Cytosol) In vitro competitive protein-binding assay using rat uterine cytosol and radiolabelled ligand to measure estrogen receptor binding affinity. in_vitro Uterus Rat Estrogen receptor binding change US EPA (2009) not_specified US EPA (2009) Estrogen Receptor Binding Assay Using Rat Uterine Cytosol: This assay identifies chemicals that have the potential to interact with the estrogen receptor (ER) in vitro. Principle of this particular assay is based on the competitive protein-binding methods. A radiolabelled ligand and an unlabelled ligand are presented together to a specific receptor. The radioactivity measurement provides the quantitative estimation of the bound and unbound fraction of the ligand with the receptor. Uterotrophic bioassay In vivo mammalian bioassay in rodents to assess estrogenic activity via uterine response. in_vivo uterus rodents estrogenicity change http://purl.obolibrary.org/obo/UBERON_0000453 UBERON OECD TG 440 not_specified OECD TG 440 (October 2007): Uterotrophic bioassay in rodents http://purl.obolibrary.org/obo/UBERON_0000453 UBERON Uterotrophic bioassay Measures estrogenic activity in rodents by assessing uterine growth. in_vivo uterus rodents uterine growth increase http://purl.obolibrary.org/obo/GO_0060426 GO OECD TG 440 not_specified OECD TG 440 (October 2007): Uterotrophic bioassay in rodents http://purl.obolibrary.org/obo/UBERON_0000995 UBERON http://purl.obolibrary.org/obo/GO_0060426 GO VM7Luc ER TA assay A transactivation assay using the VM7Luc4E2 cell line to detect estrogen receptor activity. in_vitro VM7Luc4E2 estrogen receptor transactivation change http://purl.obolibrary.org/obo/GO_0006351 GO OECD TG 455 not_specified The VM7Luc ER TA assay (3) using the VM7Luc4E2 cell line1 which predominately expresses hERα with some contribution from hERβ. http://purl.obolibrary.org/obo/GO_0003677 GO http://purl.obolibrary.org/obo/GO_0006351 GO VM7Luc ER TA assay Transactivation assay using VM7Luc4E2 cell line expressing hERα and hERβ to detect ER agonists and antagonists. in_vitro VM7Luc4E2 Homo sapiens transcriptional activation change OECD TG 455 not_specified The VM7Luc ER TA assay (3) using the VM7Luc4E2 cell line1 which predominately expresses hERα with some contribution from hERβ. http://purl.obolibrary.org/obo/GO_0008425 GO http://purl.obolibrary.org/obo/GO_0008425 GO Yeast estrogen screen (YES) Reporter gene assay in yeast expressing human estrogen receptor, measuring transcriptional activation (e.g., lacZ or luciferase) as an indicator of ER agonist activity. in_vitro yeast Saccharomyces cerevisiae ER transcriptional activation increase ISO 19040-1 and 19040-2 not_specified Yeast estrogen screen (YES) (ISO 19040-1 and 19040-2) Yeast estrogen screen (YES) Detects estrogenic activity using genetically modified yeast cells. in_vitro yeast estrogenic activity not_specified http://purl.obolibrary.org/obo/GO_0030331 GO ISO 19040-1 and 19040-2 not_specified Yeast estrogen screen (YES) (ISO 19040-1 and 19040-2) http://purl.obolibrary.org/obo/PR_000000187 PR http://purl.obolibrary.org/obo/GO_0030521 GO Flow cytometry Quantifies SIX1-positive cells in a suspension using fluorescently labeled antibodies. in_vitro endometrium number of SIX1-positive cells not_specified high Flow cytometry Immunofluorescence Detects the presence of the SIX1 protein in cells or tissues using fluorescently labeled antibodies. in_vitro endometrium presence of SIX1 protein not_specified medium Immunofluorescence Immunohistochemistry Detects the presence of the SIX1 protein in tissue sections using antibody-based staining. in_vivo endometrium presence of SIX1 protein not_specified low Immunohistochemistry qRT-PCR Measures the expression level of SIX1 mRNA using quantitative reverse transcription polymerase chain reaction. in_vitro endometrium expression level of SIX1 mRNA not_specified http://purl.obolibrary.org/obo/OBI_0000663 OBI medium qRT-PCR Western blotting Detects the presence and size of the SIX1 protein in a sample using gel electrophoresis and antibody-based detection. in_vitro endometrium presence and size of SIX1 protein not_specified low Western blotting Cytological analysis Collection and analysis of exfoliated cells, e.g., via smear, to assess cellular changes. ex_vivo exfoliated endometrial cells endometrium cellular morphology changes change medium Cytological analysis via collecting of exfoliated cells, e.g., smear. http://purl.obolibrary.org/obo/CL_0000543 CL http://purl.obolibrary.org/obo/GO_0030154 GO cytological analysis Cytological analysis of exfoliated cells collected via smear preparation to evaluate cellular changes associated with endometrial squamous metaplasia. in_vivo exfoliated cells endometrium uterus rodent cellular morphology of exfoliated endometrial cells change http://www.bioassayontology.org/bao#BAO_0000013 BAO http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0002062 GO http://purl.obolibrary.org/obo/GO_0003002 GO OECD TG 440 low Cytological analysis via collecting of exfoliated cells, e.g., smear. OECD (2007), Test No. 440: Uterotrophic Bioassay in Rodents http://purl.obolibrary.org/obo/CL_0002014 CL http://purl.obolibrary.org/obo/GO_0002062 GO histopathological examination Histopathological examination of tissue biopsy samples to assess endometrial squamous metaplasia. Tissue is collected, fixed, embedded, sectioned, and stained for microscopic evaluation. in_vivo endometrium uterus rodent endometrial squamous metaplasia increase http://www.bioassayontology.org/bao#BAO_0000012 BAO http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0002062 GO http://www.bioassayontology.org/bao#BAO_0000043 BAO OECD TG 440 low Histopathological examination via tissue biopsy followed by fixation, embedding, sectioning, and staining. OECD (2007), Test No. 440: Uterotrophic Bioassay in Rodents http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0002062 GO Histopathological examination Examination of tissue biopsy samples via fixation, embedding, sectioning, and staining to assess morphological changes. ex_vivo endometrium squamous metaplasia increase low Histopathological examination via tissue biopsy followed by fixation, embedding, sectioning, and staining. http://purl.obolibrary.org/obo/UBERON_0001295 UBERON http://purl.obolibrary.org/obo/GO_0030855 GO histopathology Histopathological examination is performed on tissue biopsies following fixation, embedding, sectioning, and staining to assess tissue morphology. in_vivo uterus rodent tissue morphology change http://purl.obolibrary.org/obo/OBI_0000043 OBI OECD TG 440 low Histopathological examination via tissue biopsy followed by fixation, embedding, sectioning, and staining. http://purl.obolibrary.org/obo/UBERON_0001469 UBERON Immunohistochemistry Tissue staining with antibodies specific to epithelial markers to assess protein expression and localization. ex_vivo endometrium epithelial marker expression change low Immunohistohemistry via tissue staining wiht antibodies specific to epithelial markers. http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0030154 GO Hematoxylin and Eosin staining Histopathological staining method used to visualize tissue architecture and cellular details. in_vivo endometrium rodents tissue morphology and cellular features not_specified http://purl.obolibrary.org/obo/UBERON_0001295 UBERON OECD TG 440 low Primarily measured through histopathological examination including: Hematoxylin and Eosin staining http://purl.obolibrary.org/obo/UBERON_0001295 UBERON Histopathological examination Evaluation of tissue morphology using hematoxylin and eosin staining and immunohistochemistry to detect adenosquamous carcinomas of the endometrium. ex_vivo endometrium Rodent adenososquamous carcinoma incidence increase low Primarily measured through histopathological examination including: http://purl.obolibrary.org/obo/UBERON_0001297 UBERON http://purl.obolibrary.org/obo/GO_0001649 GO Immunohistochemistry A technique used to detect specific antigens in tissue sections by exploiting the principle of antibodies binding specifically to antigens in biological tissues. ex_vivo uterus marker profiling not_specified low Immunohistochemistry to confirm the nature of each component via marker profiling. Immunohistochemistry Technique using antibodies to detect specific proteins in tissue sections to confirm cellular components. in_vivo endometrium rodents protein expression and localization not_specified http://purl.obolibrary.org/obo/OBI_0000615 OBI http://purl.obolibrary.org/obo/UBERON_0001295 UBERON OECD TG 440 low Immunohistochemistry to confirm the nature of each component via marker profiling. Uterotrophic Bioassay A short-term screening test for oestrogenic properties in rodents, assessing uterotrophic response through histopathological examination and immunohistochemistry. in_vivo uterus rodents uterine weight increase increase http://purl.obolibrary.org/obo/UBERON_0000995 UBERON http://purl.obolibrary.org/obo/GO_0032501 GO OECD TG 440 low OECD (2007), Test No. 440: Uterotrophic Bioassay in Rodents: A short-term screening test for oestrogenic properties, OECD Guidelines for the Testing of Chemicals, Section 4, OECD Publishing, Paris, https://doi.org/10.1787/9789264067417-en Primarily measured through histopathological examination including: Tissue sampling (biopsy, curettage, or hysterectomy specimen) Hematoxylin and Eosin staining Immunohistochemistry to confirm the nature of each component via marker profiling. http://purl.obolibrary.org/obo/UBERON_0000995 UBERON http://purl.obolibrary.org/obo/GO_0032501 GO anatomical examination This assay determines the phases of the estrus cycle by observing anatomical changes in the vagina and uterus. in_vivo vagina uterus anatomical changes change low The phases of the estrus cycles are determined by anatomical changes to the vagina and uterus, as well as vaginal smear/cytology (Laffan et al. 2018; Ajayi and Akhigbe 2020). http://purl.obolibrary.org/obo/UBERON_0001329 UBERON http://purl.obolibrary.org/obo/GO_0008523 GO hormone level analysis This assay measures hormone levels to determine the phase of the estrus cycle, though it is more labor-intensive and stressful to animals. in_vivo hormone levels not_specified low Analysis of hormone levels can also be performed but are more labor intensive, more stressful to animals, and less definitive than physical examination. http://purl.obolibrary.org/obo/GO_0042703 GO vaginal cytology Microscopic examination of vaginal smears to assess cellular composition and determine estrus cycle phases. in_vivo vagina vaginal cell composition change medium as well as vaginal smear/cytology (Laffan et al. 2018; Ajayi and Akhigbe 2020) vaginal smear/cytology This assay examines the cellular composition of vaginal smears to determine the phase of the estrus cycle based on anatomical changes. in_vivo vagina uterus estrus cycle phase not_specified http://purl.obolibrary.org/obo/GO_0042703 GO medium The phases of the estrus cycles are determined by anatomical changes to the vagina and uterus, as well as vaginal smear/cytology (Laffan et al. 2018; Ajayi and Akhigbe 2020). http://purl.obolibrary.org/obo/UBERON_0002356 UBERON http://purl.obolibrary.org/obo/GO_0042703 GO Amphibian Metamorphosis Assay Measures the distribution of developmental stages of treated/exposed larvae compared to control larvae using a developmental staging atlas. in_vivo Xenopus laevis distribution of developmental stages change http://purl.obolibrary.org/obo/GO_0002009 GO OECD TG 231 medium The method utilized within the 21 d Amphibian Metamorphosis Assay regulatory test guideline (OECD, 2009; US EPA 2009) relate the distribution of developmental stage of control larvae to the distributions of developmental stages of treated/exposed larvae. http://purl.obolibrary.org/obo/UBERON_0002544 UBERON http://purl.obolibrary.org/obo/GO_0002009 GO Asynchronous Development Assessment Identifies disruption of the relative timing of morphogenic milestones and/or somatic development within a single larva undergoing metamorphosis. in_vivo Xenopus laevis incidence of asynchronous development increase http://purl.obolibrary.org/obo/GO_0009653 GO http://purl.obolibrary.org/obo/GO_0032502 GO low Asynchronous development is identified as disruption of the relative timing of morphogenic milestones and/or somatic development within a single larvae undergoing metamorphosis. http://purl.obolibrary.org/obo/UBERON_0002544 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO Larval Amphibian Growth and Development Assay Measures the number of days to reach metamorphic climax (NF stage 62) in treated/exposed larvae compared to control larvae. in_vivo Xenopus laevis days to metamorphic climax change http://purl.obolibrary.org/obo/GO_0002009 GO OECD TG 241 medium The method utilized within the Larval Amphibian Growth and Development Assay regulatory test guideline (OECD, 2015; US EPA 2015) relate the number of days to reach metamorphic climax (NF stage 62) in control larvae to the number of days to NF stage 62 in treated/exposed larvae. http://purl.obolibrary.org/obo/UBERON_0002544 UBERON http://purl.obolibrary.org/obo/GO_0002009 GO Larval Amphibian Growth and Development Assay Measures time to reach metamorphic climax (NF stage 62) in Xenopus laevis larvae, comparing control and treated groups. in_vivo whole organism Xenopus laevis time to NF stage 62 change http://purl.obolibrary.org/obo/GO_0030154 GO http://purl.obolibrary.org/obo/NCBITaxon_8364 NCBITAXON OECD TG 231 low The method utilized within the Larval Amphibian Growth and Development Assay regulatory test guideline (OECD, 2015; US EPA 2015) relate the number of days to reach metamorphic climax (NF stage 62) in control larvae to the number of days to NF stage 62 in treated/exposed larvae. These data are typically analyzed for differences from control using a Cox mixed-effects proportional hazard model. http://purl.obolibrary.org/obo/NCBITaxon_8364 NCBITAXON http://purl.obolibrary.org/obo/GO_0030207 GO adult bee count Counting the number of adult bees present in a colony to assess colony size and health. in_vivo honey bee number of adult bees decrease low "Count number of adult bees, presence of sealed and open brood, assess amount of food stores by visual method or by weighing," bee health assessment Measuring dry weight, muscle development, and protein content to assess the health of individual bees. in_vivo muscle honey bee dry weight, muscle development, protein content decrease low "Assess health of bee: dry weight, muscle development, protein content" Bee health assessment Measures dry weight, muscle development, and protein content to evaluate individual bee health. in_vivo muscle Apis mellifera individual bee health metrics not_specified http://purl.obolibrary.org/obo/VT_0001259 VT medium Assess health of bee: dry weight, muscle development, protein content http://purl.obolibrary.org/obo/NCBITaxon_7460 NCBITAXON brood assessment Assessing the amount of sealed and open brood to evaluate colony reproductive success and health. in_vivo honey bee presence of sealed and open brood decrease low "Count number of adult bees, presence of sealed and open brood, assess amount of food stores by visual method or by weighing," Brood cannibalism mapping Maps eggs, larvae, and pupae on brood frames and inspects daily for missing larvae to detect cannibalism. in_vivo Apis mellifera brood cannibalism incidence increase low Cannibalism of brood can be detected by mapping eggs, larvae and pupae present on brood frames and noting developmental stages for each individual, then inspecting daily for missing larvae http://purl.obolibrary.org/obo/NCBITaxon_7460 NCBITAXON http://purl.obolibrary.org/obo/GO_0032502 GO Brood Care Behavior Evaluates brood care behavior by filming the brood nest and recording nursing frequency, total nursing period per hour, and average duration of nursing episodes for individual cells. in_vivo brood nest Apis mellifera brood care behavior metrics change http://purl.obolibrary.org/obo/NCBITaxon_7460 NCBITAXON http://purl.obolibrary.org/obo/GO_0048741 GO low Brood care behavior can be evaluated by filming the brood nest and then recording nursing frequency, total nursing period per hour, and average duration of nursing episodes for individual cells http://purl.obolibrary.org/obo/NCBITaxon_7460 NCBITAXON http://purl.obolibrary.org/obo/GO_0048741 GO Brood care behavior filming Video recording of the brood nest to measure nursing frequency, nursing duration per hour, and episode duration. ex_vivo brood nest Apis mellifera nursing frequency, total nursing period per hour, and average duration of nursing episodes change low Brood care behavior can be evaluated by filming the brood nest and then recording nursing frequency, total nursing period per hour, and average duration of nursing episodes for individual cells cannibalism detection Mapping eggs, larvae, and pupae and inspecting daily for missing larvae to detect cannibalism of brood. in_vivo honey bee presence of missing larvae increase low "Cannibalism of brood can be detected by mapping eggs, larvae and pupae present on brood frames and noting developmental stages for each individual, then inspecting daily for missing larvae" Colony strength assessment Visual or weight-based evaluation of adult bee population, sealed and open brood presence, and food stores in a honeybee colony. in_vivo colony brood honey bee Colony strength (adult bee count, brood presence, food stores) change low Count number of adult bees, presence of sealed and open brood, assess amount of food stores by visual method or by weighing Food store assessment Quantification of food stores within the colony via visual inspection or weighing. ex_vivo Apis mellifera amount of food stores change low assess amount of food stores by visual method or by weighing Pest and disease assessment Evaluates the presence or absence of pests and diseases affecting the honey bee colony via inspection. in_vivo colony Apis mellifera pest/disease presence not_specified low assess presence/absence of pests and disease Queen egg laying pattern evaluation Monitors the queen's egg laying pattern (e.g., rate, pattern) in the honey bee colony. in_vivo queen Apis mellifera queen egg laying pattern not_specified low evaluate egg laying patterns of queen Age of first forage Measures the age at which honey bees first begin foraging activities. in_vivo honey bees age of first forage not_specified not_specified Age of first forage Hypopharyngeal gland development Assesses the development of the hypopharyngeal gland in forage bees that revert to hive bees. in_vivo hypopharyngeal gland honey bees hypopharyngeal gland development not_specified not_specified Hypopharyngeal gland development in forage bees that revert to hive bees Amperometry Quantifies ROS levels using multiple-step amperometry with a stainless steel counter electrode and Ag|AgCl reference node. in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI low The levels of ROS can be quantified using multiple-step amperometry using a stainless steel counter electrode and non-leak Ag|AgCl reference node [Flaherty et al., 2017]. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Chemiluminescence analysis Detects superoxide and other ROS species using chemiluminescence probes. in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI medium Chemiluminescence analysis can detect the superoxide, where some probes have a wider range for detecting hydroxyl radical, hydrogen peroxide, and peroxynitrite [Fuloria et al., 2021]. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO colorimetric H2O2 assay Detects hydrogen peroxide (H2O2) with a colorimetric probe that produces a pink colored product, measured with a microplate reader at 540-570 nm. not_specified pink product formation increase http://purl.obolibrary.org/obo/CHEBI_29084 CHEBI medium Hydrogen peroxide (H2O2) can be detected with a colorimetric probe, which reacts with H2O2 in a 1:1 stoichiometry to produce a bright pink colored product, followed by the detection with a standard colorimetric microplate reader with a filter in the 540-570 nm range. http://purl.obolibrary.org/obo/CHEBI_29084 CHEBI Colorimetric H2O2 probe Detects hydrogen peroxide using a colorimetric probe that produces a pink product, measured spectrophotometrically. in_vitro hydrogen peroxide levels increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium Hydrogen peroxide (H2O2) can be detected with a colorimetric probe, which reacts with H2O2 in a 1:1 stoichiometry to produce a bright pink colored product, followed by the detection with a standard colorimetric microplate reader with a filter in the 540-570 nm range. http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Colorimetric H2O2 probe assay Detects hydrogen peroxide using a colorimetric probe that produces a pink colored product in a 1:1 stoichiometry. in_vitro colorimetric absorbance (540-570 nm) increase http://purl.obolibrary.org/obo/CHEBI_17433 CHEBI http://purl.obolibrary.org/obo/CHMO_0000575 CHMO not_specified Hydrogen peroxide (H2O2) can be detected with a colorimetric probe, which reacts with H2O2 in a 1:1 stoichiometry to produce a bright pink colored product, followed by the detection with a standard colorimetric microplate reader with a filter in the 540-570 nm range. http://purl.obolibrary.org/obo/CHEBI_17433 CHEBI http://purl.obolibrary.org/obo/GO_0016464 GO H2-DCF-DA fluorescent dye assay Measures ROS generation in cells using a redox-sensitive fluorescent dye, H2-DCF-DA, analyzed by flow cytometry. in_vitro ROS generation increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/OBI_0000269 OBI medium Yuan, Yan, et al., (2013) described ROS monitoring by using H2-DCF-DA, a redox-sensitive fluorescent dye. Briefly, the harvested cells were incubated with H2-DCF-DA (50 µmol/L final concentration) for 30 min in the dark at 37°C. After treatment, cells were immediately washed twice, re-suspended in PBS, and analyzed on a BD-FACS Aria flow cytometry. ROS generation was based on fluorescent intensity which was recorded by excitation at 504 nm and emission at 529 nm. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO H2DCF-DA fluorescence assay Measures ROS generation by incubating cells with the redox-sensitive fluorescent dye H2DCF-DA and analyzing the resulting fluorescent intensity via flow cytometry. in_vitro fluorescent intensity increase http://purl.obolibrary.org/obo/OBI_0001461 OBI not_specified Yuan, Yan, et al., (2013) described ROS monitoring by using H2-DCF-DA, a redox-sensitive fluorescent dye. ROS generation was based on fluorescent intensity which was recorded by excitation at 504 nm and emission at 529 nm. http://purl.obolibrary.org/obo/CHEBI_41311 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO lipid peroxidation assay Measures lipid peroxidation as an indicator of oxidative stress damage. not_specified lipid peroxidation increase http://purl.obolibrary.org/obo/GO_0032934 GO not_specified Lipid peroxidation (LPO) can be measured as an indicator of oxidative stress damage Yen, Cheng Chien, et al., (2013). http://purl.obolibrary.org/obo/CHEBI_36009 CHEBI http://purl.obolibrary.org/obo/GO_0042441 GO NBT assay Measures the generation of free radicals and their extracellular release by monitoring the conversion of NBT to a purple formazan using a plate reader at 550 nm. in_vitro cells formazan production increase http://purl.obolibrary.org/obo/CHEBI_35479 CHEBI medium Chattopadhyay, Sukumar, et al. (2002) assayed the generation of free radicals within the cells and their extracellular release in the medium by addition of yellow NBT salt solution (Park et al., 1968). Extracellular release of ROS converted NBT to a purple colored formazan. The product formed was assayed at 550 nm in an Anthos 2001 plate reader. http://purl.obolibrary.org/obo/CHEBI_35479 CHEBI NBT reduction assay Detects ROS (free radicals) by adding yellow NBT salt solution, which is converted to a purple colored formazan by extracellular ROS. in_vitro absorbance of purple formazan at 550 nm increase http://purl.obolibrary.org/obo/OBI_0000233 OBI low Chattopadhyay, Sukumar, et al. (2002) assayed the generation of free radicals within the cells and their extracellular release in the medium by addition of yellow NBT salt solution (Park et al., 1968). Extracellular release of ROS converted NBT to a purple colored formazan. http://purl.obolibrary.org/obo/CHEBI_41311 CHEBI http://purl.obolibrary.org/obo/GO_0016464 GO NBT reduction assay Measures extracellular release of ROS by reduction of NBT to formazan, quantified spectrophotometrically. in_vitro extracellular ROS release increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium Chattopadhyay, Sukumar, et al. (2002) assayed the generation of free radicals within the cells and their extracellular release in the medium by addition of yellow NBT salt solution (Park et al., 1968). Extracellular release of ROS converted NBT to a purple colored formazan. The cells were incubated with 100 ml of 1 mg/ml NBT solution for 1 h at 37 °C and the product formed was assayed at 550 nm in an Anthos 2001 plate reader. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO p-methoxy-phenol derivative fluorescent probe Detects ROS using a specific fluorescent probe, p-methoxy-phenol derivative. in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/OBI_0000218 OBI medium ROS can be detected by fluorescent probes such as p-methoxy-phenol derivative [Ashoka et al., 2020]. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Photocolorimetric ROS assay Measures ROS generation from photoirradiated chemicals to evaluate phototoxic risk, as recommended by guidelines. in_vitro ROS generation increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI ICH, 2014; PCPC, 2014 medium On the basis of the pathogenesis of drug-induced phototoxicity, a reactive oxygen species (ROS) assay was proposed to evaluate the phototoxic risk of chemicals. The ROS assay can monitor generation of ROS, such as singlet oxygen and superoxide, from photoirradiated chemicals, and the ROS data can be used to evaluate the photoreactivity of chemicals (Onoue et al. , 2014, Onoue et al. , 2013, Onoue and Tsuda, 2006). The ROS assay is a recommended approach by guidelines to evaluate the phototoxic risk of chemicals (ICH, 2014, PCPC, 2014). http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Singlet oxygen bleaching assay Measures singlet oxygen by monitoring bleaching of p-nitrosodimethylaniline at 440 nm using spectrophotometer with imidazole as acceptor. in_vitro singlet oxygen concentration (via bleaching) decrease not_specified ・Singlet oxygen can be measured by monitoring the bleaching of p -nitrosodimethylaniline at 440 nm using a spectrophotometer with imidazole as a selective acceptor of singlet oxygen [Onoue et al., 2014]. Singlet Oxygen Spectrophotometry Measurement of singlet oxygen by monitoring the bleaching of p-nitrosodimethylaniline at 440 nm. in_vitro bleaching of p-nitrosodimethylaniline change not_specified Singlet oxygen can be measured by monitoring the bleaching of p-nitrosodimethylaniline at 440 nm using a spectrophotometer http://purl.obolibrary.org/obo/GO_0006979 GO http://purl.obolibrary.org/obo/GO_0006979 GO SPION-based biosensor Detects ROS in blood using superparamagnetic iron oxide nanoparticles (SPION)-based biosensor. in_vitro blood ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI medium ROS in the blood can be detected using superparamagnetic iron oxide nanoparticles (SPION)-based biosensor [Lee et al., 2020]. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO T3 measurement This assay measures the levels of Triiodothyronine (T3) in tissues. not_specified tissues Triiodothyronine (T3) levels decrease not_specified This key event is measured the same as key event 1093: Thyroxine (T4) in tissues, decreased. ABRM contraction assay Measures the contraction force of the anterior byssus retractor muscle (ABRM) in bivalves after stimulation with acetylcholine. The assay quantifies the ability of the muscle to maintain a contracted state with minimal energy expenditure after the initial stimulus has ceased. in_vitro anterior byssus retractor muscle (ABRM) muscle bivalves muscle contraction force increase http://purl.obolibrary.org/obo/GO_0006936 GO low In bivalves, the muscle involved in valve movement is the anterior byssus retractor muscle (ABRM). This muscle and other muscles can undergo a catch state of contraction, which is characterized by a very slowly decaying force in the absence of stimulation. When contraction of the ABRM (and other catch-capable muscles) is initiated by the neurotransmitter acetylcholine, it contracts actively and remains in the contracted state with minimal energetic investment (Güth et al. 1984; Butler et al. 1998) even after the acetylcholine stimulation has ceased and internal calcium stores are returned to basal levels(Ishii et al. 1989). This unique physiology allows the muscle to maintain a closed valve without depleting energy reserves. http://purl.obolibrary.org/obo/UBERON_0001630 UBERON http://purl.obolibrary.org/obo/GO_0006936 GO force measurement This assay measures the force generated by the anterior byssus retractor muscle (ABRM) over time, specifically focusing on the slowly decaying force characteristic of the catch state contraction. The assay assesses the muscle's ability to maintain contraction with minimal energy expenditure. in_vitro anterior byssus retractor muscle bivalves mollusks muscle force increase low This muscle and other muscles can undergo a catch state of contraction, which is characterized by a very slowly decaying force in the absence of stimulation. When contraction of the ABRM (and other catch-capable muscles) is initiated by the neurotransmitter acetylcholine, it contracts actively and remains in the contracted state with minimal energetic investment (Güth et al. 1984; Butler et al. 1998) even after the acetylcholine stimulation has ceased and internal calcium stores are returned to basal levels(Ishii et al. 1989). This unique physiology allows the muscle to maintain a closed valve without depleting energy reserves. http://purl.obolibrary.org/obo/GO_0006487 GO germinal vesicle breakdown (GVBD) assessment This assay measures the initiation of germinal vesicle breakdown (GVBD), indicating progression from prophase to metaphase in oocytes. not_specified oocytes ovary germinal vesicle breakdown increase low initiation of the germinal vesicle break down (GVBD), and progression from prophase to metaphase http://purl.obolibrary.org/obo/CL_0000254 CL meiotic progression monitoring Monitoring the progression of the oocyte from prophase to metaphase. not_specified oocyte progression from prophase to metaphase change not_specified progression from prophase to metaphase oocyte electrical state measurement This assay measures changes in the electrical state of oocytes, which is associated with maturation. not_specified oocytes ovary oocyte electrical state change low change in oocyte electrical state http://purl.obolibrary.org/obo/CL_0000254 CL oocyte maturation assay Measures the progression of oocytes from prophase to metaphase, including germinal vesicle breakdown (GVBD) and changes in electrical state. in_vitro oocytes ovary oocyte maturation increase http://purl.obolibrary.org/obo/GO_0004556 GO medium change in oocyte electrical state, initiation of the germinal vesicle break down (GVBD), and progression from prophase to metaphase http://purl.obolibrary.org/obo/CL_0000023 CL http://purl.obolibrary.org/obo/GO_0004556 GO Phenotypic enzyme activity assay Measures the activity of enzymes in a phenotypic context, typically through substrate turnover or product formation. not_specified enzyme activity increase http://purl.obolibrary.org/obo/GO_0003824 GO not_specified Increase, Phenotypic enzyme activity http://purl.obolibrary.org/obo/GO_0003824 GO http://purl.obolibrary.org/obo/GO_0003824 GO histological analysis of altered hepatic foci Measures changes in the number of foci per volume of liver tissue or volume fraction of the liver to assess clonal expansion of altered hepatic foci. in_vivo liver number of foci per volume of liver tissue or volume fraction of the liver increase http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low Clonal expansion of altered hepatic foci is measure histologically as changes in the number of foci per volume of liver tissue or volume fraction of the liver histology This assay measures clonal expansion of altered hepatic foci by examining changes in the number of foci per volume of liver tissue or volume fraction of the liver. in_vivo liver number of foci per volume of liver tissue or volume fraction of the liver increase low Clonal expansion of altered hepatic foci is measure histologically as changes in the number of foci per volume of liver tissue or volume fraction of the liver (Marsman & Popp 1994; Isenberg et al. 1997; Kuwata et al. 2016) http://purl.obolibrary.org/obo/UBERON_0000868 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO Beta lactamase reporter gene assay Measures NF-kB transcriptional activity using a beta lactamase reporter gene. in_vitro NF-kB transcriptional activity increase not_specified NF-kB transcriptional activity: Beta lactamase reporter gene assay (Miller et al. 2010) ELISA This assay measures the levels of IL-6, IL-8, and Cox using ELISA. not_specified IL-6, IL-8, and Cox levels increase medium NF-κB p65 (Total/Phospho) ELISA ELISA for IL-6, IL-8, and Cox http://purl.obolibrary.org/obo/GO_0006954 GO ELISA Enzyme-linked immunosorbent assay used to quantify total and phosphorylated NF-κB p65 protein levels. in_vitro NF-κB p65 (Total/Phospho) change medium NF-κB p65 (Total/Phospho) ELISA http://purl.obolibrary.org/obo/GO_0006468 GO ELISA for IL-6, IL-8, and Cox Measures levels of IL-6, IL-8, and Cox using ELISA. in_vitro IL-6, IL-8, and Cox levels increase not_specified ELISA for IL-6, IL-8, and Cox Lentiviral NF-kB GFP reporter with flow cytometry Measures NF-kB transcription using a lentiviral GFP reporter and flow cytometry. in_vitro NF-kB transcription increase not_specified NF-kB transcription: Lentiviral NF-kB GFP reporter with flow cytometry (Moujalled et al. 2012) NF-κB p65 (Total/Phospho) ELISA Measures total and phosphorylated NF-κB p65 using ELISA. in_vitro NF-κB p65 (Total/Phospho) increase not_specified NF-κB p65 (Total/Phospho) ELISA RelA-GFP reporter assay Measures NF-κB translocation using a RelA-GFP reporter. in_vitro NF-κB translocation increase not_specified NF-κB translocation: RelA-GFP reporter assay (Wink et al 2017) Western blotting Measures IκBa phosphorylation using western blotting. in_vitro IκBa phosphorylation increase not_specified IκBa phosphorylation: Western blotting (Miller et al. 2010) BRDU incorporation Measures past cellular proliferation by incorporating BRDU into cells upon division, visualized via microscopy with a secondary label. in_vivo BRDU incorporation increase http://purl.obolibrary.org/obo/GO_0008283 GO low Past cellular proliferation can be measured directly using labels that are incorporated into cells upon cell division (BRDU or cytoplasmic proliferation dyes) BRDU must be labeled with a secondary fluorescent or other label for visualization, so it cannot be measured in living cells. http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0008283 GO BRDU incorporation BRDU incorporation measures past cellular proliferation by detecting labels incorporated into cells upon cell division using microscopy. It is stable and can be used in vivo, but requires labeling for visualization and cannot be measured in living cells. in_vitro nucleoside analog incorporation increase low Past cellular proliferation can be measured directly using labels that are incorporated into cells upon cell division (BRDU or cytoplasmic proliferation dyes) Stable, so can see proliferation from a specific time point onward. Can be used in vivo. BRDU must be labeled with a secondary fluorescent or other label for visualization, so it cannot be measured in living cells. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0008283 GO BRDU incorporation Labels incorporated into cells upon cell division to measure past cellular proliferation. BRDU must be labeled with a secondary fluorescent or other label for visualization, so it cannot be measured in living cells. in_vitro Epithelial Cells past proliferation increase http://purl.obolibrary.org/obo/GO_0008283 GO low Past cellular proliferation can be measured directly using labels that are incorporated into cells upon cell division (BRDU or cytoplasmic proliferation dyes) or indirectly by measuring a change in population size. Nucleoside analog incorporation (BRDU) Microscopy Stable, so can see proliferation from a specific time point onward. Can be used in vivo. BRDU must be labeled with a secondary fluorescent or other label for visualization, so it cannot be measured in living cells. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Cell counting Measures past cellular proliferation by quantifying an increase in cell numbers over time via microscopy. in_vitro cell count increase http://purl.obolibrary.org/obo/GO_0008283 GO medium An increase in cell numbers over time could represent proliferation or a decrease in apoptosis. http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0008283 GO CFSE assay Measures past cellular proliferation using cytoplasmic proliferation dyes like CFSE, enabling quantification of successive cell divisions via microscopy. in_vitro CFSE fluorescence intensity decrease http://purl.obolibrary.org/obo/GO_0008283 GO medium Cytoplasmic proliferation dyes: carboxyfluorescein diacetate succinimidyl ester (CFSE). Enables quantification of successive cell divisions and differentiation between slowly and rapidly cycling cells. http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0008283 GO CFSE labeling Quantifies past cellular proliferation by tracking dilution of the cytoplasmic fluorescent dye CFSE through successive cell divisions using microscopy, allowing discrimination between slowly and rapidly cycling cells. in_vitro cell division increase http://purl.obolibrary.org/obo/GO_0051301 GO http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/CHEBI_80817 CHEBI medium Cytoplasmic proliferation dyes: carboxyfluorescein diacetate succinimidyl ester (CFSE). Enables quantification of successive cell divisions and differentiation between slowly and rapidly cycling cells. The dyes are better suited to in vitro experiments. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0051301 GO CFSE staining (Microscopy) Measures past proliferation using cytoplasmic proliferation dyes like carboxyfluorescein diacetate succinimidyl ester (CFSE) to quantify successive cell divisions via microscopy. in_vitro cytoplasmic dye dilution change http://purl.obolibrary.org/obo/GO_0008283 GO not_specified Cytoplasmic proliferation dyes: carboxyfluorescein diacetate succinimidyl ester (CFSE). Microscopy Enables quantification of successive cell divisions and differentiation between slowly and rapidly cycling cells. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Cytoplasmic proliferation dye (CFSE) Labels cytoplasm to enable quantification of successive cell divisions and differentiation between slowly and rapidly cycling cells. Cells survive analysis, so these dyes can be used as part of ongoing experiments. Better suited to in vitro experiments. in_vitro Epithelial Cells past proliferation increase http://purl.obolibrary.org/obo/GO_0008283 GO low Cytoplasmic proliferation dyes: carboxyfluorescein diacetate succinimidyl ester (CFSE). Microscopy Enables quantification of successive cell divisions and differentiation between slowly and rapidly cycling cells. Cells survive analysis, so these dyes can be used as part of ongoing experiments. The dyes are better suited to in vitro experiments. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Ki67 probe Measures ongoing cellular proliferation by labeling Ki67, a protein associated with non-G0 phase proliferating cells, via microscopy. in_vitro Ki67-positive cells increase http://purl.obolibrary.org/obo/GO_0008283 GO low Ongoing current proliferation can be quantified by labeling a protein associated with the cell cycle (e.g. Ki67). Labels all non-G0 phase proliferating cells. http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0008283 GO 3D spheroid migration Assesses the migration of endothelial cells from a three-dimensional spheroid structure. in_vitro endothelial cells cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO medium 3D spheroid migration http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0016477 GO 3D spheroid migration Migration of 3D spheroids. in_vitro spheroid migration increase low 3D spheroid migration http://purl.obolibrary.org/obo/GO_0008359 GO Boyden chamber Evaluates the ability of cells to migrate through a porous membrane towards a chemoattractant. in_vitro endothelial cells cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO medium Boyden chamber: evaluates the ability of cells to migrate through a porous membrane towards a chemoattractant (substance that attracts cells) placed in the lower chamber. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0016477 GO Collagen Invasion Assay Assesses the invasive capacity of endothelial cells through a three-dimensional collagen matrix. in_vitro endothelial cells cell invasion increase http://purl.obolibrary.org/obo/CHEBI_35562 CHEBI medium Collagen Invasion Assay: Assess the invasive capacity of endothelial cells through a three-dimensional collagen matrix http://purl.obolibrary.org/obo/CL_0000115 CL Collagen Invasion Assay Assesses the invasive capacity of endothelial cells through a three-dimensional collagen matrix. in_vitro endothelial cells invasive capacity increase http://purl.obolibrary.org/obo/GO_0051163 GO not_specified Collagen Invasion Assay: Assess the invasive capacity of endothelial cells through a three-dimensional collagen matrix http://purl.obolibrary.org/obo/CL_0000038 CL http://purl.obolibrary.org/obo/GO_0051163 GO In vivo vessel density in fat pads Measures the density of blood vessels in fat pads as an indicator of angiogenesis in vivo. in_vivo fat pads vessel density increase http://purl.obolibrary.org/obo/GO_0001525 GO low In vivo: vessel density in fat pads http://purl.obolibrary.org/obo/UBERON_0001062 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO Microfluidic assay Uses microfluidic channels to create controlled environments that mimic the physiological flow conditions experienced by endothelial cells in vivo. in_vitro endothelial cells cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO medium Microfluidic assay: microfluidic channels to create controlled environments that mimic the physiological flow conditions experienced by endothelial cells in vivo (Shih) http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0016477 GO Scratch wound assay Measures the collective movement of endothelial cells to close a 'wound' created by scratching a confluent monolayer of cells. in_vitro endothelial cells cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO medium Scratch wound assay: collective movement of endothelial cells to close a 'wound' created by scratching a confluent monolayer of cells. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0016477 GO Scratch wound assay Measures the collective movement of endothelial cells to close a wound created by scratching a confluent monolayer. in_vitro endothelial cells wound closure increase http://purl.obolibrary.org/obo/GO_0030313 GO not_specified Scratch wound assay: collective movement of endothelial cells to close a "wound" created by scratching a confluent monolayer of cells. http://purl.obolibrary.org/obo/CL_0000038 CL http://purl.obolibrary.org/obo/GO_0030313 GO Time-lapse microscopy Uses live-cell imaging to observe and quantify cell migration over time. in_vitro endothelial cells cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO low Time-lapse microscopy: using live-cell imaging http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0016477 GO Tube formation assay Evaluates the ability of endothelial cells to form tube-like structures, mimicking the process of blood vessel formation (angiogenesis). in_vitro endothelial cells tube formation increase http://purl.obolibrary.org/obo/GO_0001525 GO medium Tube formation: assays evaluate the ability of endothelial cells to form tube-like structures, mimicking the process of blood vessel formation (angiogenesis) (Guo) http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0001525 GO biopsy Removal and examination of human breast tissue to diagnose tumor type and invasiveness. ex_vivo mammary gland human tumor type and invasiveness not_specified http://purl.obolibrary.org/obo/NCIT_C15189 NCIT low biopsy http://purl.obolibrary.org/obo/CL_1000577 CL http://purl.obolibrary.org/obo/GO_0016197 GO mammogram Imaging technique to detect lumps or abnormalities in human breast tissue. in_vivo mammary gland human lump or abnormality presence not_specified http://purl.obolibrary.org/obo/NCIT_C17009 NCIT medium lumps are commonly detected by palpation or mammogram http://purl.obolibrary.org/obo/UBERON_0001911 UBERON http://purl.obolibrary.org/obo/GO_0001654 GO mammogram Tumors are detected using imaging techniques in humans. in_vivo breast human tumor detection not_specified medium In humans, lumps are commonly detected by palpation or mammogram. http://purl.obolibrary.org/obo/UBERON_0004862 UBERON http://purl.obolibrary.org/obo/GO_0001553 GO microscopic examination of tissue Histopathological analysis of rodent tissue to diagnose tumor type and invasiveness. ex_vivo mammary gland rat mouse tumor type and invasiveness not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI low microscopic examination of tissue http://purl.obolibrary.org/obo/CL_1000577 CL http://purl.obolibrary.org/obo/GO_0016197 GO necropsy Post-mortem examination of rodents to detect tumors. in_vivo mammary gland rat mouse tumor presence not_specified http://purl.obolibrary.org/obo/NCIT_C3263 NCIT low necropsy of dead animals http://purl.obolibrary.org/obo/UBERON_0001911 UBERON http://purl.obolibrary.org/obo/GO_0001654 GO surgical excision Removal of affected human breast tissue for diagnostic examination. ex_vivo mammary gland human tumor type and invasiveness not_specified low surgical excision of the affected tissue http://purl.obolibrary.org/obo/CL_1000577 CL http://purl.obolibrary.org/obo/GO_0016197 GO visual observation or palpation Detection of tumors in live rodents via visual inspection or physical palpation. in_vivo mammary gland rat mouse tumor presence not_specified http://purl.obolibrary.org/obo/NCIT_C3263 NCIT http://purl.obolibrary.org/obo/UBERON_0001911 UBERON medium In rodent bioassays, tumors can be detected via visual observation or palpation of live animals http://purl.obolibrary.org/obo/UBERON_0001911 UBERON http://purl.obolibrary.org/obo/GO_0001654 GO Chromosomal Aberrations and Micronuclei Assays Detects chromosomal damage and micronuclei using microscopy, reflecting large breaks, rearrangements, or mitotic failures. in_vitro chromosomal damage increase http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0005655 GO OECD TG 473, 475, 483, 487 low OECD Test Guidelines 473, 475, 483, and 487 (OECD 2016; OECD 2016; OECD 2016; OECD 2016) Detects major DNA damage resulting from large breaks and rearrangements, or mitotic failures. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007088 GO Comet Assay with Restriction Enzymes A variant of the comet assay using restriction enzymes to identify different types of nucleotide damage. in_vitro nucleotide damage increase http://purl.obolibrary.org/obo/GO_0006974 GO high Single cell gel electrophoresis (comet assay) with restriction enzymes (Collins 2004) A variant of the comet assay in which restriction enzymes allow the identification of different types of nucleotide damage. The comet assay is more sensitive than PFGE, detecting damage from 0.1 Gy ionizing radiation (Pernot, Hall et al. 2012). A reproducible high-throughput application of the assay is available (Ge, Prasongtanakij et al. 2014; Sykora, Witt et al. 2018), and the test requires only a small (single cell) sample. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO HPLC-MS/MS Quantifies specific nucleotide lesions using high-performance liquid chromatography coupled with tandem mass spectrometry. in_vitro nucleotide lesions increase http://purl.obolibrary.org/obo/CHEBI_16773 CHEBI http://purl.obolibrary.org/obo/OBI_0000474 OBI low High performance liquid chromatography (HPLC), tandem mass spectrometry (MS/MS) Capable of quantifying low levels of specific nucleotide lesions (Madugundu, Cadet et al. 2014; Ravanat, Breton et al. 2014). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Labeled Probe pXRCC1 Uses fluorescent probes to label single strand breaks in cells. in_vitro single strand breaks increase medium Labeled probe pXRCC1 (Lorat, Brunner et al. 2015) Fluorescent probes can label single strand breaks in cells, while immunogold labeling is able to distinguish multiple single strand breaks in clusters (Lorat, Timm et al. 2016; Nikitaki, Nikolov et al. 2016). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Labeled Probes for Double Strand Breaks Uses fluorescent or immunogold-labeled probes (e.g., phosphorylated H2AX, 53BP1) to detect and quantify double strand breaks. in_vitro double strand breaks increase http://purl.obolibrary.org/obo/GO_0006302 GO medium Labeled probes including phosphorylated H2AX, 53BP1, Ku70, ATM (Lorat, Brunner et al. 2015) Fluorescent probes can label individual double breaks in cells allowing for quantification, with immunogold labeling resolving breaks in clusters (Lorat, Timm et al. 2016; Nikitaki, Nikolov et al. 2016). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006302 GO labeled probes for oxidative damage and base excision repair Uses labeled probes including Biotrin OxyDNA and anti-8-oxoguanine-DNA glycosylase (OGG1) and AP endonuclease (APE1) to detect oxidative damage and base excision repair via microscopy or FACS. in_vitro nucleotide damage (oxidative damage and base excision repair) increase http://purl.obolibrary.org/obo/GO_0006974 GO http://purl.obolibrary.org/obo/GO_0006979 GO http://purl.obolibrary.org/obo/CHMO_0000027 CHMO http://purl.obolibrary.org/obo/CHMO_0000000 CHMO medium Labeled probes including Biotrin OxyDNA and anti- 8-oxoguanine-DNA glycosylase (OGG1) for oxidative damage and AP endonuclease (APE1) for Base Excision Repair of less bulky lesions such as oxidative damage. Microscopy, FACS Most useful with FACS or other measures of average or relative intensity, as locations and numbers of damaged nucleotides can be difficult to distinguish using fluorescence microscopy. (Ogawa, Kobayashi et al. 2003; Nikitaki, Nikolov et al. 2016). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO micronuclei assay This assay detects major DNA damage resulting from large breaks and rearrangements, or mitotic failures. It requires that the damaged cell subsequently undergo replication. in_vitro Micronuclei formation increase http://purl.obolibrary.org/obo/CL_0000279 CL http://purl.obolibrary.org/obo/GO_0000271 GO OECD TG 487 medium OECD tests for chromosomal damage and micronuclei Test No. 473, 475, 483, and 487 measure longer term effects of DNA damage Detects major DNA damage resulting from large breaks and rearrangements, or mitotic failures. Damage does not appear until DNA undergoes mitosis, so slower and limited to damage in replicating cells. http://purl.obolibrary.org/obo/CL_0000071 CL http://purl.obolibrary.org/obo/GO_0006260 GO microscopy with labeled probes Fluorescent probes can label double strand breaks in cells, allowing for quantification, and immunogold labeling can resolve breaks in clusters. Probes are available for phosphorylated H2AX, 53BP1, Ku70, and ATM. in_vitro Double strand breaks increase http://purl.obolibrary.org/obo/CHEBI_59759 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO medium Fluorescent probes can label individual double breaks in cells allowing for quantification, with immunogold labeling resolving breaks in clusters (Lorat, Timm et al. 2016; Nikitaki, Nikolov et al. 2016). Labeled probes including phosphorylated H2AX, 53BP1, Ku70, ATM (Lorat, Brunner et al. 2015) Sensitive: detects damage from 0.001 Gy ionizing radiation (Rothkamm and Lobrich 2003; Ojima, Ban et al. 2008). http://purl.obolibrary.org/obo/CHEBI_50697 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Neutral Comet Assay Measures double strand breaks using gel electrophoresis under neutral conditions to minimize single strand break interference. in_vitro double strand breaks increase http://purl.obolibrary.org/obo/GO_0006302 GO medium Single cell gel electrophoresis (comet assay), neutral conditions Neutral conditions help minimize the release of single strand breaks coiled DNA and alkali lesions, allowing the measurement of double strand breaks. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006302 GO OECD TG 489 (Alkaline Comet Assay) Detects single and double strand breaks and alkali-sensitive nucleotide lesions using gel electrophoresis under alkaline conditions. in_vitro DNA strand breaks increase OECD TG 489 medium The OECD test guideline alkaline comet assay Test No. 489 (OECD 2016) detects single and double strand breaks, including those arising from repair as well as some (alkali sensitive) nucleotide lesions including some lesions from oxidative damage. Single cell gel electrophoresis (comet assay), alkali conditions When used in alkali conditions, the comet assay reveals single and double strand breaks and alkali-sensitive nucleotide lesions. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Pulsed Field Gel Electrophoresis (PFGE) Quantifies double strand breaks and can be combined with immunoblotting to detect DNA-associated proteins. in_vitro double strand breaks increase http://purl.obolibrary.org/obo/GO_0006302 GO low Pulsed field gel electrophoresis (PFGE) Permits the quantitative measurement of double strand breaks, and can be combined with immunoblotting to detect DNA-associated proteins (Lobrich, Rydberg et al. 1995; Kawashima, Yamaguchi et al. 2017). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006302 GO Unscheduled DNA synthesis test Measures DNA damage that is repaired using Nucleotide Excision Repair, specifically focusing on bulky adducts using autoradiography. in_vitro nucleotide excision repair change http://purl.obolibrary.org/obo/GO_0006284 GO OECD TG 486 not_specified The OECD test guideline for DNA synthesis Test No. 486 (OECD 1997) detects nucleotide excision repair, so it will reflect the formation of bulky DNA adducts Measures DNA damage that is repaired using Nucleotide Excision Repair - mostly bulky adducts http://purl.obolibrary.org/obo/CHEBI_4053 CHEBI http://purl.obolibrary.org/obo/GO_0006284 GO Histochemical Staining This assay uses stains to visualize specific components of the extracellular matrix in tissue sections. ex_vivo presence or distribution of extracellular matrix components not_specified http://purl.obolibrary.org/obo/GO_0031012 GO low Histochemical Staining http://purl.obolibrary.org/obo/GO_0031012 GO http://purl.obolibrary.org/obo/GO_0030198 GO Morphometric Analysis This assay quantifies morphological features of the extracellular matrix in tissue sections, often following staining. ex_vivo morphological features of extracellular matrix not_specified http://purl.obolibrary.org/obo/GO_0031012 GO medium Morphometric Analysis http://purl.obolibrary.org/obo/GO_0031012 GO http://purl.obolibrary.org/obo/GO_0030198 GO 3D Spheroid Invasion Assay Spheroids embedded in a 3D matrix, and invasion is assessed as cells migrate out from the spheroid into the surrounding matrix. in_vitro cell invasion increase http://purl.obolibrary.org/obo/GO_0016528 GO low spheroids embedded in a 3D matrix, and invasion is assessed as cells migrate out from the spheroid into the surrounding matrix http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016477 GO 3D Spheroid Invasion Assay Spheroids are embedded in a 3D matrix and invasion is assessed as cells migrate out from the spheroid into the surrounding matrix. in_vitro spheroids cells migrate out from the spheroid into the surrounding matrix not_specified not_specified 3D Spheroid Invasion Assay: spheroids embedded in a 3D matrix, and invasion is assessed as cells migrate out from the spheroid into the surrounding matrix http://purl.obolibrary.org/obo/GO_0051064 GO Electric Cell-Substrate Impedance Sensing (ECIS) Measures changes in electrical impedance as cells invade and interact with a substrate. in_vitro electrical impedance change http://purl.obolibrary.org/obo/GO_0016528 GO high Measure changes in electrical impedance as cells invade and interact with a substrate. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0007155 GO Microfluidic Invasion Assays Uses microfluidic devices to create controlled environments for studying cell invasion. in_vitro cell invasion increase http://purl.obolibrary.org/obo/GO_0016528 GO medium Use microfluidic devices to create controlled environments for studying cell invasion http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016477 GO Transwell Invasion Assay Cells migrate through a porous membrane coated with ECM proteins toward a chemoattractant. in_vitro cell invasion increase http://purl.obolibrary.org/obo/GO_0016528 GO medium Cells migrate through a porous membrane coated with ECM proteins toward a chemoattractant http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016477 GO Zymography Assesses the activity of matrix metalloproteinases (MMPs), enzymes involved in ECM degradation and cell invasion. in_vitro MMP activity increase http://purl.obolibrary.org/obo/GO_0004222 GO medium Assess the activity of matrix metalloproteinases (MMPs), enzymes involved in ECM degradation and cell invasion. http://purl.obolibrary.org/obo/CHEBI_27334 CHEBI http://purl.obolibrary.org/obo/GO_0022617 GO Electrochemiluminescent immunoassay Determination of ex vivo whole blood stimulated cytokine production using an electrochemiluminescent immunoassay from Meso Scale Discovery (MSD). ex_vivo whole blood cytokine production not_specified http://purl.obolibrary.org/obo/OBI_0000424 OBI http://purl.obolibrary.org/obo/GO_0005125 GO medium Ex vivo whole blood stimulated cytokine (IL-2, IL-4, IL-5, and IL-17) production assay in the supernatants were determined using an electrochemiluminescent immunoassay from Meso Scale Discovery (MSD; Gaithersburg, MD) (Kevin, G. et al. 2014). http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0001816 GO ELISA Quantitation of cytokine content using Sandwich Enzyme-Linked ImmunoSorbent Assay (ELISA) kits with biotin-horseradish peroxidase-streptavidin detection and 3,3',5,5'-tetramethylbenzidine substrate. in_vitro cytokine content not_specified http://purl.obolibrary.org/obo/GO_0005125 GO medium Quantitation of cytokine content was done on appropriately diluted samples, run in duplicate, using Sandwich Enzyme-Linked ImmunoSorbent Assay (ELISA) kits to test matched Antibody pairs with biotin-horseradish peroxidase-streptavidin detection and 3,3',5,5'-tetramethylbenzidine substrate. http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0001816 GO MSD electrochemiluminescent immunoassay Measures IL-2, IL-4, IL-5, and IL-17 protein levels in supernatants of ex vivo whole blood stimulated cultures using an electrochemiluminescent immunoassay from Meso Scale Discovery. ex_vivo whole blood IL-2, IL-4, IL-5, IL-17 protein concentration not_specified not_specified Ex vivo whole blood stimulated cytokine (IL-2, IL-4, IL-5, and IL-17) production assay in the supernatants were determined using an electrochemiluminescent immunoassay from Meso Scale Discovery (MSD; Gaithersburg, MD) (Kevin, G. et al. 2014). RiboQuant MultiProbe RPA system Detection of cytokine mRNAs using a RiboQuant MultiProbe RPA system with 32P-labeled riboprobes hybridized overnight with RNA samples, followed by RNase treatment, purification, electrophoresis, and quantitation using a PhosphorImager. in_vitro cytokine mRNA levels not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI http://purl.obolibrary.org/obo/SO_0000234 SO low Cytokine mRNAs were detected using a RiboQuant MultiProbe RPA system (PharMingen, San Diego, CA). Riboprobes were 32P-labeled and hybridized overnight with 10 to 30 mg of the RNA samples. The hybridized RNA was treated with RNase and purified according to the RiboQuant protocol. The samples were then electrophoresed in 6% polyacrylamide-Tris-borate-EDTA-urea gels using the Seqi -Gen GT Nucleic Acid Electrophoresis Cell (Bio-Rad, Hercules, CA), or minigels (Novex, San Diego, CA). The gels were dried, exposed and quantitated in a PhosphorImager (Molecular Dynamics, Sunnyvale, CA) using the ImageQuant software (Dumont et al. 1998). http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO vessel density measurement This assay measures the number or density of vessels in fat pads as an indicator of angiogenesis. in_vivo fat pads vessel number or density increase http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/UBERON_0002390 UBERON low it is measured in vivo through the measurment of the number or density of vessels in fat pads http://purl.obolibrary.org/obo/UBERON_0000356 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO biochemical fluorometric assay Biochemical assays used to determine changes in the activity level of enzymes. in_vitro enzyme activity change http://purl.obolibrary.org/obo/GO_0003674 GO medium changes in activity level of enzymes can be determined using biochemical fluorometric assays. http://purl.obolibrary.org/obo/GO_0003674 GO BQ assay Fluorometric assay measuring benzyloxyquinolone metabolism to determine CYP3A activity. in_vitro hepatocytes liver CYP3A enzyme activity change http://purl.obolibrary.org/obo/GO_0003824 GO medium Benzyloxyquinolone metabolism (BQ = benzyloxyquinoline-O-debenzylation) http://purl.obolibrary.org/obo/GO_0006805 GO BQ assay Benzyloxyquinolone metabolism (BQ = benzyloxyquinoline-O-debenzylation) is used to measure CYP3A activity. in_vitro hepatocytes liver enzyme activity change http://purl.obolibrary.org/obo/GO_0004372 GO low Benzyloxyquinolone metabolism (BQ = benzyloxyquinoline-O-debenzylation) and testosterone 6-β-hydroxylase activity can also be used to measure CYP3A activity. http://purl.obolibrary.org/obo/GO_0006807 GO BROD assay Fluorometric assay measuring the formation of resorufin from benzyloxyresorufin to determine CYP2B activity. in_vitro hepatocytes liver CYP2B enzyme activity change http://purl.obolibrary.org/obo/GO_0003824 GO medium the formation of resorufin from benzyloxyresorufin (benzyloxyresorufin-O-debenzylation; BROD) http://purl.obolibrary.org/obo/GO_0006805 GO BROD assay The formation of resorufin from benzyloxyresorufin (benzyloxyresorufin-O-debenzylation; BROD) is assayed to determine changes in CYP2B enzyme activity. in_vitro hepatocytes liver enzyme activity change http://purl.obolibrary.org/obo/GO_0004372 GO low For CYP2B isoforms, the formation of resorufin from pentoxyresorufin (pentoxyresorufin-O-depentylation; PROD) or from benzyloxyresorufin (benzyloxyresorufin-O-debenzylation; BROD) can be assayed, although there is some contribution from other Cyps, including those in the CYP3A family. http://purl.obolibrary.org/obo/GO_0006807 GO ELISA Enzyme-linked immunosorbent assay to quantify protein levels of CAR-dependent genes. in_vitro hepatocytes liver protein levels change http://purl.obolibrary.org/obo/PR_000000001 PR medium enzyme-linked immunosorbent assays (ELISAs) http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006412 GO microarray expression profiling Microarray technology to simultaneously quantify mRNA levels of many transcripts, including CAR-dependent genes. in_vitro hepatocytes liver mRNA levels change http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO high microarray expression profiling http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO PROD assay Fluorometric assay measuring the formation of resorufin from pentoxyresorufin to determine CYP2B activity. in_vitro hepatocytes liver CYP2B enzyme activity change http://purl.obolibrary.org/obo/GO_0003824 GO medium the formation of resorufin from pentoxyresorufin (pentoxyresorufin-O-depentylation; PROD) http://purl.obolibrary.org/obo/GO_0006805 GO PROD assay The formation of resorufin from pentoxyresorufin (pentoxyresorufin-O-depentylation; PROD) is assayed to determine changes in CYP2B enzyme activity. in_vitro hepatocytes liver enzyme activity change http://purl.obolibrary.org/obo/GO_0004372 GO low For CYP2B isoforms, the formation of resorufin from pentoxyresorufin (pentoxyresorufin-O-depentylation; PROD) or from benzyloxyresorufin (benzyloxyresorufin-O-debenzylation; BROD) can be assayed, although there is some contribution from other Cyps, including those in the CYP3A family. http://purl.obolibrary.org/obo/GO_0006807 GO qRT-PCR Quantitative real-time reverse transcription polymerase chain reaction to measure mRNA levels of CAR-dependent genes. in_vitro hepatocytes liver mRNA levels change http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO medium quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is used to measure mRNA levels of CAR-dependent genes in cultured hepatocytes or liver tissue from chemical-exposed animals. mRNA levels are statistically compared to appropriate controls to determine significant changes in CAR-dependent gene expression. in_vitro hepatocytes liver not_specified mRNA levels of CAR-dependent genes change http://purl.obolibrary.org/obo/GO_0010467 GO medium Changes in CAR-dependent gene expression is most directly determined by quantitating mRNA levels of the genes of interest isolated from chemical-exposed cultured hepatocytes or the livers of chemically-treated animals. The measurement of mRNA levels of genes of interest can be accomplished using one of several well-established methods that are widely accepted by the scientific community. Methods such as quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR), microarray expression profiling, and next generation sequencing methods (whole transcriptome RNA sequencing, e.g., RNA-seq) are highly specific, sensitive, and generate reproducible results. http://purl.obolibrary.org/obo/GO_0010467 GO RNA-seq Next generation sequencing method to quantify mRNA levels of CAR-dependent genes. in_vitro hepatocytes liver mRNA levels change http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO high next generation sequencing methods (whole transcriptome RNA sequencing, e.g., RNA-seq) http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO testosterone 6-β-hydroxylase activity assay Biochemical assay measuring testosterone 6-β-hydroxylase activity to determine CYP3A activity. in_vitro hepatocytes liver CYP3A enzyme activity change http://purl.obolibrary.org/obo/GO_0003824 GO medium testosterone 6-β-hydroxylase activity http://purl.obolibrary.org/obo/GO_0006805 GO Western blot Denaturing gel electrophoresis followed by Western blot analysis to quantify protein levels of CAR-dependent genes. in_vitro hepatocytes liver protein levels change http://purl.obolibrary.org/obo/PR_000000001 PR low denaturing gel electrophoresis followed by Western blot analysis http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006412 GO Western blot Western blot analysis is used to measure protein levels of CAR-dependent genes in cell lysates or liver tissue from chemical-exposed animals. Protein levels are statistically compared to appropriate controls to determine significant changes in CAR-dependent gene expression at the protein level. in_vitro hepatocytes liver not_specified protein levels of CAR-dependent genes change http://purl.obolibrary.org/obo/OBI_0000831 OBI medium CAR-dependent gene expression changes may also be determined at the protein level or by quantitating changes in protein (e.g., enzyme) activity. The quantitation of proteins of interest from cell lysates can be performed using immunostaining techniques such as enzyme-linked immunosorbent assays (ELISAs) or denaturing gel electrophoresis followed by Western blot analysis. http://purl.obolibrary.org/obo/OBI_0000831 OBI lipid peroxidation assay Measures lipid peroxidation in response to tissue damage, which can activate TRPA1. not_specified lipid peroxidation increase http://purl.obolibrary.org/obo/GO_0006631 GO not_specified In tesponse to tissue damage lipid peroxidation can activate TRPA1 (Bautista et al., 2013). http://purl.obolibrary.org/obo/GO_0006631 GO TRPA1 activation assay This assay measures the activation of the TRPA1 receptor in response to lipid peroxidation, which occurs following tissue damage. The methodology is not detailed beyond this. not_specified tissue TRPA1 activation increase not_specified In tesponse to tissue damage lipid peroxidation can activate TRPA1 (Bautista et al., 2013). http://purl.obolibrary.org/obo/GO_0007165 GO ChIP Measures gene-specific alterations in histone acetylation at gene regulatory sequences by immunoprecipitation of chromatin. in_vitro histone acetylation at gene regulatory sequences change http://purl.obolibrary.org/obo/GO_0016573 GO low Gene specific alterations in histone acetylation at gene regulatory seqences can be measured by chromatin immunoprecipitation (ChIPs) http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0016573 GO gene chips Measures gene expression levels using microarray technology. in_vitro gene expression change http://purl.obolibrary.org/obo/OBI_0000697 OBI http://purl.obolibrary.org/obo/GO_0010467 GO high gene chips) http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0010467 GO Gene chips Measures whole transcriptome gene expression levels by hybridizing labeled nucleic acids to complementary probes on a microarray. not_specified whole transcriptome change not_specified gene chips) RNAseq RNAseq (whole transcriptomics) measures gene expression. in_vitro gene expression change http://purl.obolibrary.org/obo/GO_0006925 GO high chromatin immunoprecipitation (ChIPs) and gene expression analysis by RT-qPCR or whole transcriptomics (RNAseq, gene chips). http://purl.obolibrary.org/obo/GO_0006925 GO RNAseq Measures whole transcriptomics by high-throughput sequencing of RNA. in_vitro whole transcriptomics change http://purl.obolibrary.org/obo/OBI_0001271 OBI http://purl.obolibrary.org/obo/GO_0005669 GO high whole transcriptomics (RNAseq http://purl.obolibrary.org/obo/GO_0005669 GO http://purl.obolibrary.org/obo/GO_0010467 GO RT-qPCR Measures gene expression levels by reverse transcription quantitative polymerase chain reaction. in_vitro gene expression change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000663 OBI medium gene expression analysis by RT-qPCR http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0010467 GO Bead-Based Motility Assay Attaches beads to cells and tracks their movement using microscopy to determine cell motility. in_vitro bead displacement increase http://purl.obolibrary.org/obo/GO_0048870 GO low Bead-Based Motility Assay: Principle: Attach beads to cells and track their movement using microscopy. Measurement: Analyze the displacement of beads to determine cell motility. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0048870 GO Collagen Invasion Assay Assesses cell invasion through a three-dimensional collagen matrix to quantify the extent of cell invasion. in_vitro extent of cell invasion increase http://purl.obolibrary.org/obo/GO_0016355 GO low Collagen Invasion Assay: Principle: Assess cell invasion through a three-dimensional collagen matrix. Measurement: Quantify the extent of cell invasion into the matrix http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016355 GO ECIS Measure changes in electrical impedance as cells migrate and interact with a substrate. Quantify impedance-based parameters to assess cell motility. in_vitro electrical impedance change medium Electric Cell-Substrate Impedance Sensing (ECIS): Principle: Measure changes in electrical impedance as cells migrate and interact with a substrate. Measurement: Quantify impedance-based parameters to assess cell motility. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0007017 GO Electric Cell-Substrate Impedance Sensing Measures changes in electrical impedance as cells migrate and interact with a substrate to quantify cell motility. in_vitro impedance-based parameters change http://purl.obolibrary.org/obo/GO_0048870 GO medium Electric Cell-Substrate Impedance Sensing (ECIS): Principle: Measure changes in electrical impedance as cells migrate and interact with a substrate. Measurement: Quantify impedance-based parameters to assess cell motility. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0048870 GO Fluorescence Recovery After Photobleaching Measures the mobility of fluorescently labeled molecules or proteins within cells by assessing fluorescence recovery in a photobleached region. in_vitro fluorescence recovery increase http://purl.obolibrary.org/obo/OBI_0000343 OBI http://purl.obolibrary.org/obo/GO_0003674 GO low Fluorescence Recovery After Photobleaching (FRAP): Principle: Measure the mobility of fluorescently labeled molecules or proteins within cells. Measurement: Assess the recovery of fluorescence in a photobleached region over time. http://purl.obolibrary.org/obo/CHEBI_25212 CHEBI FRAP Measure the mobility of fluorescently labeled molecules or proteins within cells. Assess the recovery of fluorescence in a photobleached region over time. in_vitro recovery of fluorescence increase low Fluorescence Recovery After Photobleaching (FRAP): Principle: Measure the mobility of fluorescently labeled molecules or proteins within cells. Measurement: Assess the recovery of fluorescence in a photobleached region over time. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0032287 GO Single-Cell Tracking Monitors individual cell movements using time-lapse microscopy to analyze parameters such as speed, persistence, and directionality. in_vitro cell speed, persistence, and directionality change http://purl.obolibrary.org/obo/GO_0048870 GO low Single-Cell Tracking: Principle: Monitor individual cell movements using time-lapse microscopy. Measurement: Analyze parameters such as speed, persistence, and directionality for each tracked cell. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0048870 GO Time-Lapse Microscopy Tracks the movement of individual cells over time using live-cell imaging to analyze cell trajectories, speed, and directionality. in_vitro cell trajectories, speed, and directionality change http://purl.obolibrary.org/obo/GO_0048870 GO http://purl.obolibrary.org/obo/GO_0016477 GO low Time-Lapse Microscopy: Principle: Track the movement of individual cells over time using live-cell imaging. Measurement: Analyze cell trajectories, speed, and directionality. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0048870 GO Transwell Migration Assay Measures cell migration through a porous membrane in response to a chemoattractant, with quantification of migrated cells. in_vitro number of migrated cells increase http://purl.obolibrary.org/obo/GO_0016477 GO http://purl.obolibrary.org/obo/GO_0006935 GO medium Transwell Migration Assay: Principle: Cells migrate through a porous membrane from one side to the other in response to a chemoattractant. Measurement: Count the number of cells that have migrated through the membrane or quantify fluorescence if cells are labeled. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016477 GO Wound Healing Assay Create a controlled scratch in a cell monolayer and measure the rate of closure over time to quantify cell migration. in_vitro monolayer cells not specified not specified rate of cell migration increase http://purl.obolibrary.org/obo/GO_0008360 GO http://purl.obolibrary.org/obo/GO_0008152 GO not specified low Create a controlled "wound" or scratch in a cell monolayer and monitor the closure of the gap over time. Quantify the rate of cell migration by measuring the reduction in the wound area. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008360 GO Wound Healing Assay Creates a controlled 'wound' in a cell monolayer and monitors the closure of the gap over time to quantify cell migration. in_vitro reduction in wound area decrease http://purl.obolibrary.org/obo/GO_0016477 GO http://purl.obolibrary.org/obo/GO_0042060 GO medium Wound Healing Assay (Scratch Assay): Principle: Create a controlled "wound" or scratch in a cell monolayer and monitor the closure of the gap over time. Measurement: Quantify the rate of cell migration by measuring the reduction in the wound area. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016477 GO CREB/CRE transcription activation assay Measures the activation of CREB/CRE transcription. in_vitro CREB/CRE transcription activation increase http://purl.obolibrary.org/obo/GO_0045893 GO low Activation of CREB/CRE transcription http://purl.obolibrary.org/obo/PR_000005321 PR http://purl.obolibrary.org/obo/GO_0006351 GO Fluorescent Ca2+ imaging Measures Ca2+ levels entering individual nAChR-mediated ion channels using fluorescent imaging in cells expressing nAChR. in_vitro cells expressing nAChR Ca2+ levels increase http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/PR_000001595 PR http://purl.obolibrary.org/obo/OBI_0000257 OBI medium Fluorescent Ca2+ imaging in cells expressing nAChR for evaluation of Ca2+ levels entering individual nAChR-mediated ion channels http://purl.obolibrary.org/obo/PR_000001595 PR http://purl.obolibrary.org/obo/GO_0006816 GO Fluorescent Ca2+ imaging Fluorescent imaging to measure Ca2+ levels entering individual nAChR-mediated ion channels in cells expressing nAChR. in_vitro cells expressing nAChR Ca2+ levels entering nAChR-mediated ion channels increase http://purl.obolibrary.org/obo/CHEBI_26948 CHEBI http://purl.obolibrary.org/obo/GO_0005267 GO http://purl.obolibrary.org/obo/GO_0006811 GO http://purl.obolibrary.org/obo/GO_0007165 GO not_specified Fluorescent Ca2+ imaging in cells expressing nAChR for evaluation of Ca2+ levels entering individual nAChR-mediated ion channels http://purl.obolibrary.org/obo/CHEBI_26948 CHEBI http://purl.obolibrary.org/obo/GO_0007165 GO Kinase assay Evaluates ERK1/2 activity using kinase assays. in_vitro ERK1/2 activity increase http://purl.obolibrary.org/obo/OBI_0000274 OBI medium Western blotting and kinase assays can be used to evaluate ERK1/2 phosphorylation and activity http://purl.obolibrary.org/obo/PR_000001645 PR http://purl.obolibrary.org/obo/GO_0006468 GO Pharmacological inhibition assay Uses pharmacological inhibitors to block specific pathway components and evaluate their role in signal transduction. in_vitro pathway inhibition decrease http://purl.obolibrary.org/obo/GO_0007165 GO low Pharmacological inhibition of pathway http://purl.obolibrary.org/obo/GO_0007165 GO http://purl.obolibrary.org/obo/GO_0007165 GO transcription assay Evaluation of the activation of CREB/CRE transcription. in_vitro CREB/CRE transcription increase http://purl.obolibrary.org/obo/GO_0008107 GO not_specified Activation of CREB/CRE transcription http://purl.obolibrary.org/obo/GO_0008107 GO Western blotting Evaluates ERK1/2 phosphorylation levels using western blotting techniques. in_vitro ERK1/2 phosphorylation increase http://purl.obolibrary.org/obo/OBI_0000273 OBI low Western blotting and kinase assays can be used to evaluate ERK1/2 phosphorylation and activity http://purl.obolibrary.org/obo/PR_000001645 PR http://purl.obolibrary.org/obo/GO_0006468 GO DLCO Diffusion capacity of carbon monoxide (DLCO) studies measure gas exchange across the alveolar-capillary barrier by assessing the increased affinity of hemoglobin for carbon monoxide. It provides information about the lung surface area available for gas diffusion. in_vitro lung human animal diffusion capacity of carbon monoxide decrease ATS/ERS Task Force (Graham et al., 2017) low Finally, indices of gas exchange across the alveolar-capillary barrier are tested by diffusion capacity of carbon monoxide (DLCO) studies (also referred to as transfer capacity of carbon monoxide, TLCO). The principle of the test is the increased affinity of hemoglobin to preferentially bind carbon monoxide over oxygen (Weinstock and McCannon, 2017). Complementary to spirometry and lung volume measurements, DLCO provides information about the lung surface area available for gas diffusion. http://purl.obolibrary.org/obo/GO_0002127 GO flexiVent Specialized equipment used for measuring FEV, FVC, and PEF in anesthetized and tracheotomized small laboratory animals. in_vivo lung small laboratory animals FEV, FVC and PEF change http://purl.obolibrary.org/obo/GO_0008373 GO not_specified specialized equipment such as the flexiVent system (SCIREQ®) are available for measuring FEV, FVC and PEF in anesthetized and tracheotomized small laboratory animals. http://purl.obolibrary.org/obo/UBERON_0000848 UBERON http://purl.obolibrary.org/obo/GO_0008373 GO forced oscillation An alternative technique for lung function assessment in small laboratory animals. in_vivo lung small laboratory animals lung function change http://purl.obolibrary.org/obo/GO_0008373 GO not_specified Other techniques such as plethysmography or forced oscillation are increasingly preferred for lung function assessment in small laboratory animals http://purl.obolibrary.org/obo/UBERON_0000848 UBERON http://purl.obolibrary.org/obo/GO_0008373 GO helium dilution Helium dilution measures lung volumes by inhaling a known volume and concentration of helium and measuring the final concentration. FRC is then calculated based on the dilution. in_vitro lung human lung volume (FRC) decrease low In the helium dilution method, a known volume and concentration of helium is inhaled by the subject. Helium, an inert gas that is not absorbed significantly from the lungs, is diluted in proportion to the lung volume to which it is added. The final concentration of helium is then measured and FRC calculated (Weinstock and McCannon, 2017). http://purl.obolibrary.org/obo/UBERON_0000085 UBERON http://purl.obolibrary.org/obo/GO_0002127 GO nitrogen washout Nitrogen washout measures lung volumes by administering 100% oxygen and collecting expired gas until no nitrogen is detected. The initial volume of the system (FRC) is then calculated. in_vitro lung human lung volume (FRC) decrease low The nitrogen washout method is based on the fact that nitrogen is present in the air, at a relatively constant amount. The subject is given 100% oxygen to breathe, and the expired gas, which contains nitrogen in the lung at the beginning of the test, is collected. When no more nitrogen is noted in the expirate, the volume of air expired and the entire amount of nitrogen in that volume are measured, and the initial volume of the system (FRC) can be calculated. http://purl.obolibrary.org/obo/UBERON_0000085 UBERON http://purl.obolibrary.org/obo/GO_0002127 GO plethysmography Plethysmography measures functional residual capacity (FRC), expiratory reserve volume (ERV), vital capacity (VC), inspiratory capacity (IC), total lung capacity (TLC), and residual volume (RV) in a body plethysmograph. It can be used in both conscious and anesthetized animals. in_vivo lung human animal lung volumes (FRC, ERV, VC, IC, TLC, RV) decrease OECD (2018a) low Plethysmography consists of a series of sequential measurements in a body plethysmograph, starting with the measurement of functional residual capacity (FRC) In small laboratory animals, plethysmography can be used to determine respiratory physiology parameters (minute volume, respiratory rate, time of pause and time of break), lung volume and airway resistance of conscious animals. Both whole body and head-out plethysmography can be applied, although there is a preference for the latter in the context of inhalation toxicity studies, because of its higher accuracy and reliability (OECD, 2018a; Hoymann, 2012). http://purl.obolibrary.org/obo/UBERON_0000085 UBERON spirometry Spirometry measures several different parameters during forceful exhalation, including FEV1, FVC, VC, FEV1/FVC ratio, PEF, and forced expiratory flow. It is used for diagnostic purposes and determining the degree of lung function impairment. in_vitro lung human lung function parameters (FEV1, FVC, etc.) decrease http://www.bioassayontology.org/bao#BAO_0000221 BAO ATS/ERS Task Force guidelines (Graham et al., 2019) medium The most common (“gold standard”) lung function test in human subjects is spirometry. Spirometry results are primarily used for diagnostic purposes, e.g. to discriminate between obstructive and restrictive lung diseases, and for determining the degree of lung function impairment. Specific criteria for spirometry tests have been outlined in the American Thoracic Society (ATS) and the European Respiratory Society (ERS) Task Force guidelines (Graham et al., 2019). http://purl.obolibrary.org/obo/UBERON_0000085 UBERON http://purl.obolibrary.org/obo/GO_0002127 GO cell-free decatenation assay A cell-free assay used to screen for TopoII poisons by monitoring the enzyme's ability to decatenate DNA. in_vitro decatenation activity change not_specified cell-free decatenation assay (Schroeter et al., 2015) cell-free decatenation assay This assay is used to screen TopoII 'poisons' by measuring the inhibition of TopoII enzymes in a cell-free system. in_vitro inhibition of TopoII enzymes decrease medium cell-free decatenation assay (Schroeter et al., 2015) cleavage activity assay An in vitro assay using human recombinant enzyme and double-stranded plasmid to quantify double-strand breaks. in_vitro human double-strand breaks increase not_specified The most important mode, the cleavage activity of TopoII can be studied in vitro, by using a human recombinant enzyme and an appropriate double-stranded plasmid as a target to quantitate double-strand breaks Comet assay An assay used to indirectly detect TopoII cleavage by measuring indicators of the DNA damage response, specifically DNA strand breaks. not_specified DNA damage response indicators increase not_specified A cleavage can also be indirectly detected by measuring various indicators of DNA damage response, such as ATM activity, p53 expression, γH2AX or Comet assay (Li et al 2014, Schroeter et al., 2015, Castano et al 2016). Comet assay This assay measures DNA damage by detecting DNA strand breaks in individual cells. in_vitro DNA strand breaks increase medium Comet assay (Li et al 2014, Schroeter et al., 2015, Castano et al 2016) in vivo complex enzyme assay (ICE) This assay quantifies covalent complexes of topoisomerase II bound to DNA in vivo using slot blotting and western blot techniques. in_vivo hESCs human levels of topoisomerase II covalently associated with DNA increase low hESCs were either immediately lysed in 1 % (w/v) sarkosyl (Sigma L7414). Lysates were processed according to the in vivo complex of enzyme (ICE) assay (Nitiss, Soans, Rogojina, Seth, & Mishina, 2012; Schellenberg et al., 2017). For slot blotting, ICE samples containing 1, 2 or 4 µg of DNA were transferred onto Odyssey Nitrocellulose Membranes (LI-COR Biosciences) using a Bio-Dot SF Microfiltration Apparatus (Biorad). For western blot of ICE, samples were resuspended in 12,000 units of Micrococcal Nuclease (MNase, NEB 0247S), 1 x MNase buffer (NEB, B0247S) and 100 µg / mL BSA (NEB, B9000S), then incubated at 37 °C for 6 h. in vivo complex of enzyme (ICE) assay An assay to quantify covalent enzyme-DNA complexes by isolating protein covalently bound to DNA from cell lysates. in_vivo hESCs Homo sapiens covalent enzyme-DNA complex increase low In vivo complex enzyme assay (Rodriguez et al. 2020): hESCs were either immediately lysed in 1 % (w/v) sarkosyl (Sigma L7414). Lysates were processed according to the in vivo complex of enzyme (ICE) assay Covalent complexes are quantified in two ways: by measuring the levels of protein covalently bound to DNA plasmid linearization assay This assay measures double-strand breaks induced in plasmid DNA by topoisomerase II. in_vitro double-strand breaks in plasmid DNA increase medium The plasmid linearization assay measures double strand breaks induced in plasmid DNA by topoisomerase II. slot blotting Slot blotting is used to transfer ICE samples containing DNA onto membranes for analysis. in_vitro hESCs human DNA levels increase medium For slot blotting, ICE samples containing 1, 2 or 4 µg of DNA were transferred onto Odyssey Nitrocellulose Membranes (LI-COR Biosciences) using a Bio-Dot SF Microfiltration Apparatus (Biorad). http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO western blot Western blot is used to quantify the levels of topoisomerases covalently associated with DNA in the ICE assay. in_vitro hESCs human protein levels increase low For western blot of ICE, samples were resuspended in 12,000 units of Micrococcal Nuclease (MNase, NEB 0247S), 1 x MNase buffer (NEB, B0247S) and 100 µg / mL BSA (NEB, B9000S), then incubated at 37 °C for 6 h. Samples were run in 10% SDS-PAGE and transferred to Immobilon-FL Transfer Membranes (Millipore). Comet assay Measures DNA and chromosome damage, which may indirectly indicate chromosomal aberrations such as MLL translocations. in_vitro DNA damage increase http://purl.obolibrary.org/obo/OBI_0000660 OBI http://purl.obolibrary.org/obo/GO_0006974 GO medium Assays measuring chromosomal aberrations, micronuclei or DNA and chromosome damage (Comet assay) may indirectly identify the KE through its consequences in experimental systems in vitro and in vivo. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO RT-PCR with LDI-PCR Combines reverse transcription PCR with long-distance inverse PCR to identify MLL rearrangements within the breakpoint cluster region using genomic DNA. in_vitro MLL rearrangement not_specified http://purl.obolibrary.org/obo/OBI_0000662 OBI http://purl.obolibrary.org/obo/GO_0000018 GO high RT-PCR in combination with long-distance inverse PCR (LDI-PCR) performed on isolated genomic DNA. This method allows the identification of any kind of MLL rearrangement if located within the breakpoint cluster region. http://purl.obolibrary.org/obo/GO_0006310 GO Split-signal FISH Detects MLL translocations by using two differentially labeled probes flanking the breakpoint region; a translocation splits the normally colocalized red/green signals. in_vitro presence of MLL translocation (split signal) change low Split-signal FISH: The split-signal FISH approach uses two differentially labeled probes, located in one gene at opposite sites of the breakpoint region. split-signal FISH Split-signal FISH uses two differentially labeled probes flanking a breakpoint region in a gene. A translocation results in a split of the colocalized signals, allowing detection of chromosome aberrations independent of the partner gene. in_vitro split of colocalized signals change http://purl.obolibrary.org/obo/OBI_0000044 OBI http://purl.obolibrary.org/obo/GO_0005667 GO medium Split-signal FISH: The split-signal FISH approach uses two differentially labeled probes, located in one gene at opposite sites of the breakpoint region. In normal karyotypes, two colocalized green/red signals are visible, but a translocation results in a split of one of the colocalized signals. First, the detection of a chromosome aberration is independent of the involved partner gene. http://purl.obolibrary.org/obo/CL_0000364 CL http://purl.obolibrary.org/obo/GO_0005667 GO blood cell counts Routine blood cell counts are performed to identify leukaemia cells and assess haematological parameters. in_vivo blood blood cell counts change medium Haematological methods – identification of leukaemia cells and routine blood cell counts; http://purl.obolibrary.org/obo/CL_0000756 CL http://purl.obolibrary.org/obo/GO_0001525 GO bone marrow aspirate for immunophenotypic analysis Bone marrow aspirates for immunophenotypic analyses to refine diagnosis. in_vivo bone marrow immunophenotypic profile not_specified http://purl.obolibrary.org/obo/OBI_0000268 OBI low bone marrow aspirates for immunophenotypic analyses http://purl.obolibrary.org/obo/CL_0000234 CL http://purl.obolibrary.org/obo/GO_0006955 GO Carcinogenicity assays Assays to assess the carcinogenic potential of chemicals, including endpoints that could potentially explore the AO, but with considerations on the specificity of the disease to humans. in_vivo various tissues not_specified occurrence of cancer increase OECD TG 443 not_specified The carcinogenicity assays and the extended one generation test (OECD TG 443) include endpoints that can potentially explore the AO; however, considerations should be made on the specificity of the disease to humans. clinical symptom observation Records the presence and severity of clinical symptoms observed in the organism. in_vivo clinical symptom occurrence not_specified not_specified observations of clinical symptoms. cytogenetic assay Cytogenetic assays for molecular stratification. in_vivo bone marrow chromosomal abnormalities not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/HP_0000794 HP low cytogenetic assays for molecular stratification http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007088 GO cytogenetic assays Molecular assays performed on bone marrow aspirates for molecular stratification of disease. ex_vivo bone marrow molecular stratification change not_specified cytogenetic assays for molecular stratification http://purl.obolibrary.org/obo/CHEBI_35113 CHEBI extended one generation test The extended one generation test (OECD TG 443) includes endpoints that can potentially explore the AO. in_vivo developmental and reproductive toxicity not_specified OECD TG 443 low the extended one generation test (OECD TG 443) include endpoints that can potentially explore the AO extended one-generation test Assesses reproductive toxicity endpoints across generations in rodents per OECD TG 443. in_vivo reproductive toxicity endpoints (e.g., litter size, pup survival) not_specified OECD TG 443 not_specified The carcinogenicity assays and the extended one generation test (OECD TG 443) include endpoints that can potentially explore the AO; haematological methods Identification of leukaemia cells and routine blood cell counts; observations of clinical symptoms. in_vivo blood leukaemia cell count and blood cell counts not_specified http://purl.obolibrary.org/obo/DOID_1240 DOID http://purl.obolibrary.org/obo/OBI_0000435 OBI low Haematological methods – identification of leukaemia cells and routine blood cell counts; observations of clinical symptoms. http://purl.obolibrary.org/obo/CL_0000094 CL http://purl.obolibrary.org/obo/GO_0030097 GO immunophenotypic analyses Analysis of cell surface or intracellular markers using bone marrow aspirates to identify specific cell types. ex_vivo bone marrow immunophenotype change not_specified bone marrow aspirates for immunophenotypic analyses immunophenotyping Immunophenotypic analyses are performed on bone marrow aspirates to refine diagnosis. in_vivo bone marrow cells bone marrow cell surface markers change low Following clinical diagnosis, methods for refined diagnosis include bone marrow aspirates for immunophenotypic analyses http://purl.obolibrary.org/obo/GO_0030154 GO Annexin V-FITC assay Detects apoptosis by measuring the relative percentage of Annexin V-FITC-positive/PI-negative cells using flow cytometry. in_vitro Annexin V-FITC-positive/PI-negative cells increase http://purl.obolibrary.org/obo/OBI_0000467 OBI http://purl.obolibrary.org/obo/OBI_0000268 OBI high Apoptosis is measured with Annexin V-FITC probes, and the relative percentage of Annexin V-FITC-positive/PI-negative cells is analyzed by flow cytometry [Wu et al., 2016]. http://purl.obolibrary.org/obo/GO_0005623 GO http://purl.obolibrary.org/obo/GO_0006915 GO caspase activity assay Measures caspase-3 and caspase-9 activity by quantifying the enzyme-catalyzed release of p-nitroanilide (pNA) at 405 nm. in_vitro caspase-3 and caspase-9 activity increase http://purl.obolibrary.org/obo/GO_0004197 GO http://purl.obolibrary.org/obo/PR_000001481 PR http://purl.obolibrary.org/obo/PR_000001482 PR medium Caspase-3 and caspase-9 activity is measured with the enzyme-catalyzed release of p-nitroanilide (pNA) and quantified at 405 nm [Wu et al., 2016]. http://purl.obolibrary.org/obo/PR_000001479 PR http://purl.obolibrary.org/obo/GO_0006915 GO Cell Death Detection ELISA Detects apoptotic nucleosomes by calculating absorbance subtraction at 405 nm and 490 nm. in_vitro apoptotic nucleosomes increase high Apoptotic nucleosomes are detected using Cell Death Detection ELISA kit, which was calculated as absorbance subtraction at 405 nm and 490 nm [Parajuli et al., 2014]. http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0006915 GO comet assay Quantifies DNA fragmentation by measuring tail length, head size, tail intensity, and head intensity of the comet using electrophoresis. in_vitro DNA fragmentation increase http://purl.obolibrary.org/obo/GO_0006309 GO http://purl.obolibrary.org/obo/OBI_0000889 OBI medium DNA fragmentation can be quantified with comet assay using electrophoresis, where the tail length, head size, tail intensity, and head intensity of the comet are measured [Yasuhara et al., 2003]. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006309 GO enzyme-catalyzed activity assay Measures Caspase-3 and caspase-9 activity by quantifying the release of p-nitroanilide (pNA) at 405 nm. in_vitro caspase-3 and caspase-9 activity not_specified medium Caspase-3 and caspase-9 activity is measured with the enzyme-catalyzed release of p-nitroanilide (pNA) and quantified at 405 nm [Wu et al., 2016]. http://purl.obolibrary.org/obo/GO_0006915 GO flow cytometry Analyzes the relative percentage of Annexin V-FITC-positive/PI-negative cells using Annexin V-FITC probes. in_vitro percentage of Annexin V-FITC-positive/PI-negative cells not_specified medium Apoptosis is measured with Annexin V-FITC probes, and the relative percentage of Annexin V-FITC-positive/PI-negative cells is analyzed by flow cytometry [Wu et al., 2016]. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0006915 GO gene expression analysis Measures down-regulation of anti-apoptotic gene BIRC2 (cIAP1). in_vitro expression of BIRC2 decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/PR_000001501 PR medium The apoptosis is measured with down-regulation of anti-apoptotic gene baculoviral inhibitor of apoptosis protein repeat containing 2 (BIRC2, or cIAP1) [Parajuli et al., 2014]. http://purl.obolibrary.org/obo/PR_000001501 PR http://purl.obolibrary.org/obo/GO_0043066 GO TUNEL assay Detects apoptosis by assaying endonuclease cleavage products through enzymatically end-labeling DNA strand breaks. in_vitro DNA strand breaks increase http://purl.obolibrary.org/obo/OBI_0000214 OBI http://purl.obolibrary.org/obo/GO_0000715 GO medium Apoptosis is detected with the Terminal dUTP Nick End-Labeling (TUNEL) method to assay the endonuclease cleavage products by enzymatically end-labeling the DNA strand breaks [Kressel and Groscurth, 1994]. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO TUNEL staining Visualizes germ cell death in testis sections by Terminal dUTP Nick End-Labeling (TUNEL) staining method. in_vivo testis TUNEL-positive cells increase http://purl.obolibrary.org/obo/OBI_0000214 OBI http://purl.obolibrary.org/obo/UBERON_0000473 UBERON low For the detection of apoptosis, the testes are fixed in neutral buffered formalin and embedded in paraffin. Germ cell death is visualized in testis sections by Terminal dUTP Nick End-Labeling (TUNEL) staining method [Wade et al., 2008]. The incidence of TUNEL-positive cells is expressed as the number of positive cells per tubule examined for one entire testis section per animal [Wade et al., 2008]. http://purl.obolibrary.org/obo/CL_0000034 CL http://purl.obolibrary.org/obo/GO_0006915 GO western blot Detects expression alteration of procaspases 7 and 3 using antibodies. in_vitro expression of procaspases 7 and 3 change http://purl.obolibrary.org/obo/PR_000001500 PR low The apoptosis is detected with the expression alteration of procaspases 7 and 3 by Western blotting using antibodies [Parajuli et al., 2014]. http://purl.obolibrary.org/obo/PR_000001500 PR http://purl.obolibrary.org/obo/GO_0006915 GO western blot Detects cleavage of PARP using antibodies. in_vitro PARP cleavage increase http://purl.obolibrary.org/obo/PR_000001502 PR low Cleavage of PARP is detected with Western blotting [Parajuli et al., 2014]. http://purl.obolibrary.org/obo/PR_000001502 PR http://purl.obolibrary.org/obo/GO_0006915 GO western blot Detects apoptosis by measuring the expression alteration of procaspases 7 and 3 using antibodies. not_specified protein expression change low The apoptosis is detected with the expression alteration of procaspases 7 and 3 by Western blotting using antibodies [Parajuli et al., 2014]. http://purl.obolibrary.org/obo/GO_0006985 GO ELISA Measures COX-2 protein levels using enzyme-linked immunosorbent assay, though commercial kits are not available for fishes or birds. not_specified fishes birds COX-2 protein levels increase medium COX-2 could be measured by use of ELISA or Western Blot, but commercial kits are not currently available for fishes or birds. http://purl.obolibrary.org/obo/GO_0010457 GO q-RT PCR Measures the abundance of COX-2 transcript using quantitative real-time polymerase chain reaction. in_vivo whole embryos embryonic hepatic tissue embryonic cardiac tissue fishes birds COX-2 transcript abundance increase medium COX-2 can be measured as abundance of transcript by use of quantitative real-time polymerase chain reaction (q-RT PCR). Transcript abundance of COX-2 has been measured in whole embryos of fishes (Dong et al 2010; Huang et al 2007; Teraoka et al 2008; 2014) and embryonic hepatic and cardiac tissue of birds (Fujisawa et al 2014). http://purl.obolibrary.org/obo/GO_0010467 GO q-RT PCR Quantitative real-time polymerase chain reaction (q-RT PCR) measures the abundance of COX-2 transcript. in_vivo embryo fish bird transcript abundance increase http://purl.obolibrary.org/obo/GO_0006925 GO http://purl.obolibrary.org/obo/CHEBI_50758 CHEBI medium COX-2 can be measured as abundance of transcript by use of quantitative real-time polymerase chain reaction (q-RT PCR). Transcript abundance of COX-2 has been measured in whole embryos of fishes (Dong et al 2010; Huang et al 2007; Teraoka et al 2008; 2014) and embryonic hepatic and cardiac tissue of birds (Fujisawa et al 2014). http://purl.obolibrary.org/obo/CHEBI_50758 CHEBI http://purl.obolibrary.org/obo/GO_0006925 GO Western Blot Measures COX-2 protein levels using Western Blot, though commercial kits are not available for fishes or birds. not_specified fishes birds COX-2 protein levels increase low COX-2 could be measured by use of ELISA or Western Blot, but commercial kits are not currently available for fishes or birds. http://purl.obolibrary.org/obo/GO_0010457 GO PPARγ antagonism assay This assay assesses the interaction of the stressor with PPARγ in epithelial and inflammatory cells, demonstrating its antagonistic activity. The assay is performed in the context of pulmonary exposure. in_vitro epithelial cells inflammatory cells lung PPARγ activity decrease low The stressor acts as an antagonist of PPARγ of epithelial and inflammatory cells in the lung. http://purl.obolibrary.org/obo/CHEBI_59738 CHEBI http://purl.obolibrary.org/obo/GO_0007165 GO PPARγ antagonist assay Measures the antagonistic interaction of a stressor with PPARγ in epithelial and inflammatory cells. in_vitro epithelial cells inflammatory cells lung PPARγ inactivation decrease not_specified The stressor acts as an antagonist of PPARγ of epithelial and inflammatory cells in the lung. histopathology This assay measures the accumulation of excess fibrous connective tissue in the lung, indicative of fibrosis. in_vivo lung accumulation of excess fibrous connective tissue increase http://purl.obolibrary.org/obo/GO_0001558 GO http://purl.obolibrary.org/obo/UBERON_0002048 UBERON low the accumulation of excess fibrous connective tissue (the process called fibrosis) http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0001558 GO histological staining Measures cytosolic fatty acid content using histological staining techniques. in_vitro cytosolic fatty acid content increase http://purl.obolibrary.org/obo/CHEBI_15884 CHEBI low Cytosolic fatty acid content can be measured in many ways. These include histological staining http://purl.obolibrary.org/obo/CHEBI_15884 CHEBI http://purl.obolibrary.org/obo/GO_0006631 GO lipidomics Measures the content of cytosolic fatty acids using mass spectrometry-based lipid profiling. in_vitro cytosolic fatty acid content increase http://purl.obolibrary.org/obo/CHEBI_15884 CHEBI medium Cytosolic fatty acid content can be measured in many ways. These include lipidomics approaches http://purl.obolibrary.org/obo/CHEBI_15884 CHEBI http://purl.obolibrary.org/obo/GO_0006631 GO fast-scan cyclic voltammetry Measures extracellular serotonin concentrations using fast-scan cyclic voltammetry. in_vivo brain serotonin concentration increase http://purl.obolibrary.org/obo/CHEBI_28881 CHEBI medium Serotonin concentrations can be measured via fast-scan cyclic voltammetry http://purl.obolibrary.org/obo/CHEBI_28881 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO microdialysis/high-performance liquid chromatography Measures extracellular serotonin concentrations using microdialysis coupled with high-performance liquid chromatography. in_vivo brain serotonin concentration increase http://purl.obolibrary.org/obo/CHEBI_28881 CHEBI low Serotonin concentrations can be measured via microdialysis/high-performance liquid chromatography http://purl.obolibrary.org/obo/CHEBI_28881 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO BDNF level measurement Measures altered levels of brain-derived neurotrophic factor (BDNF) associated with impaired synaptic plasticity. not_specified brain BDNF levels change http://purl.obolibrary.org/obo/CHEBI_17756 CHEBI http://purl.obolibrary.org/obo/GO_0048167 GO not_specified altered levels of brain-derived neurotrophic factor (BDNF) are associated with impaired synaptic plasticity http://purl.obolibrary.org/obo/CHEBI_17756 CHEBI http://purl.obolibrary.org/obo/GO_0048167 GO Behavioral and cognitive performance assay Measures deficits in tasks requiring cognitive effort, learning, or memory as an indirect indicator of altered neuroplasticity. in_vivo brain cognitive performance decrease http://purl.obolibrary.org/obo/GO_0060079 GO http://purl.obolibrary.org/obo/GO_0007611 GO not_specified deficits in tasks requiring cognitive effort, learning, or memory may indicate altered neuroplasticity and serve as an indirect measurement method http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0060079 GO Dopamine depletion model Uses animal models to demonstrate reduced synaptic activity following dopamine depletion. in_vivo hippocampus Mus musculus synaptic activity decrease http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0007268 GO not_specified studies have shown that dopamine depletion induces alterations in hippocampal synaptic plasticity in mice http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0007268 GO EEG Records electrical activity of the brain to detect structural and functional changes that may reflect reduced synaptic plasticity. in_vivo brain not_specified EEG patterns change http://purl.obolibrary.org/obo/GO_0030572 GO medium studies using EEG can identify structural and functional changes that may reflect reduced synaptic plasticity http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0030572 GO EEG Identifies structural and functional changes reflecting reduced synaptic plasticity using electroencephalography. in_vivo brain electrical activity change http://purl.obolibrary.org/obo/GO_0048167 GO not_specified studies using EEG or fMRI can identify structural and functional changes that may reflect reduced synaptic plasticity http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0048167 GO EEG Electroencephalography used to identify structural and functional changes reflecting reduced synaptic plasticity. not_specified structural and functional changes change http://purl.obolibrary.org/obo/OBI_0001215 OBI not_specified studies using EEG or fMRI can identify structural and functional changes that may reflect reduced synaptic plasticity. http://purl.obolibrary.org/obo/GO_0050832 GO http://purl.obolibrary.org/obo/GO_0050832 GO fMRI Identifies structural and functional changes reflecting reduced synaptic plasticity using functional magnetic resonance imaging. in_vivo brain brain activity change http://purl.obolibrary.org/obo/GO_0048167 GO not_specified studies using EEG or fMRI can identify structural and functional changes that may reflect reduced synaptic plasticity http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0048167 GO fMRI Functional magnetic resonance imaging used to identify structural and functional changes reflecting reduced synaptic plasticity. not_specified structural and functional changes change http://purl.obolibrary.org/obo/OBI_0001215 OBI not_specified studies using EEG or fMRI can identify structural and functional changes that may reflect reduced synaptic plasticity. http://purl.obolibrary.org/obo/GO_0050832 GO http://purl.obolibrary.org/obo/GO_0050832 GO Hippocampal synaptic plasticity assay Measures changes in synaptic activity in the hippocampus of animal models, such as mice, to assess the impact of dopamine depletion on neuroplasticity. in_vivo hippocampus mouse hippocampal synaptic activity decrease http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0030572 GO low studies have shown that dopamine depletion induces alterations in hippocampal synaptic plasticity in mice http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0030572 GO Peripheral biomarker measurement Measures peripheral biomarkers in blood or saliva as indicators of changes related to brain plasticity. not_specified blood saliva biomarker levels change not_specified peripheral biomarkers, such as those found in blood or saliva, can also serve as indicators of changes related to brain plasticity http://www.ebi.ac.uk/efo/EFO_0000251 EFO ELISA Measures BDNF levels in human serum using enzyme-linked immunosorbent assay technique. in_vitro serum human BDNF concentration not_specified medium BDNF can be measured in human serum using the enzyme-linked immunosorbent assay (ELISA) technique. http://purl.obolibrary.org/obo/PR_P000000001 PR http://purl.obolibrary.org/obo/GO_0038180 GO immunohistochemistry Detects BDNF in tissues using specific antibodies and staining techniques. in_vitro BDNF presence not_specified low To measure or detect BDNF, various methods can be employed, including molecular biology techniques, immunohistochemistry, and other approaches such as immunohistochemical staining http://purl.obolibrary.org/obo/PR_P000000001 PR http://purl.obolibrary.org/obo/GO_0038180 GO multiplex immunobead-based assay High-throughput screening of BDNF levels using immunobead-based multiplex assay. in_vitro BDNF concentration not_specified http://purl.obolibrary.org/obo/OBI_0002145 OBI high multiplex immunobead-based assays are employed for high-throughput and targeted screening of BDNF levels http://purl.obolibrary.org/obo/PR_P000000001 PR http://purl.obolibrary.org/obo/GO_0038180 GO qPCR Quantifies BDNF mRNA levels using quantitative real-time polymerase chain reaction. in_vitro BDNF mRNA expression not_specified medium quantitative real-time polymerase chain reaction (qPCR) http://purl.obolibrary.org/obo/GO_0010467 GO Western blot Detects BDNF protein levels using gel electrophoresis and antibody-based detection. in_vitro BDNF protein expression not_specified http://purl.obolibrary.org/obo/OBI_0001041 OBI low Western blot analysis http://purl.obolibrary.org/obo/PR_P000000001 PR http://purl.obolibrary.org/obo/GO_0038180 GO Fluo3 AM fluorescence imaging Measures intracellular calcium levels using Fluo3 AM dye and a fluorescence imaging plate reader. in_vitro human astrocytes human intracellular calcium levels increase http://purl.obolibrary.org/obo/GO_0051480 GO medium An increase in [Ca2+]i was measured using Fluo3 AM as an indicator dye after the addition of metals (single or in mixture) to the culture wells following an optimized protocol (Arey et al., 2022). The fluorescent signals were read by fluorescence imaging plate reader Synergy HT (BioTek, Winooski, VT) (Rai and others 2010). http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0006816 GO Fluo3 AM imaging An increase in intracellular calcium ([Ca2+]i) is measured using Fluo3 AM as an indicator dye after metal addition to cell culture wells. Fluorescent signals are read by a fluorescence imaging plate reader. in_vitro human astrocytes human fluorescent signal intensity increase http://purl.obolibrary.org/obo/GO_0006826 GO medium An increase in [Ca2+]i was measured using Fluo3 AM as an indicator dye after the addition of metals (single or in mixture) to the culture wells following an optimized protocol (Arey et al., 2022). The fluorescent signals were read by fluorescence imaging plate reader Synergy HT (BioTek, Winooski, VT) (Rai and others 2010). http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0007025 GO Beck Depression Inventory (BDI) A standardized questionnaire used to assess the severity of depression symptoms. not_specified severity of depression symptoms increase not_specified Depression can be detected, classified, and also measured through specific questionnaires standardized by the DSM-5, such as the Beck Depression Inventory (BDI) Brain-derived neurotrophic factor (BDNF) measurement Measurement of BDNF levels as a biomarker for depression. not_specified BDNF level change not_specified measurement of brain-derived neurotrophic factor (BDNF) clinical interview scoring Measures depression severity through standardized interviews and specific scoring. not_specified depression symptom severity not_specified not_specified assessments conducted with standardized interviews and specific scoring cortisol measurement Measurement of cortisol levels to assess HPA axis dysfunction as a biomarker for depression. not_specified adrenal gland cortisol level change http://purl.obolibrary.org/obo/CHEBI_50638 CHEBI low Molecular biomarkers are also excellent tools that may assist in detecting depression, such as alterations in serotonin, dopamine, and norepinephrine levels; dysfunction of the HPA axis (cortisol measurement) http://purl.obolibrary.org/obo/CHEBI_50638 CHEBI http://purl.obolibrary.org/obo/GO_0042893 GO Hamilton Depression Rating Scale (HAM-D) A standardized questionnaire used to measure the severity of depression symptoms. not_specified severity of depression symptoms increase not_specified Depression can be detected, classified, and also measured through specific questionnaires standardized by the DSM-5, such as the Hamilton Depression Rating Scale (HAM-D) HPA axis dysfunction (cortisol measurement) Measurement of cortisol levels to assess dysfunction of the HPA axis as a biomarker for depression. not_specified cortisol level change not_specified dysfunction of the HPA axis (cortisol measurement) norepinephrine assay Measures norepinephrine concentration as a molecular biomarker of depression. not_specified norepinephrine level not_specified not_specified alterations in serotonin, dopamine, and norepinephrine levels Patient Health Questionnaire-9 (PHQ-9) A standardized questionnaire used to measure the severity of depression symptoms. not_specified severity of depression symptoms increase not_specified Depression can be detected, classified, and also measured through specific questionnaires standardized by the DSM-5, such as the Patient Health Questionnaire-9 (PHQ-9) Serotonin, dopamine, and norepinephrine level measurement Measurement of molecular biomarkers such as alterations in serotonin, dopamine, and norepinephrine levels to assist in detecting depression. not_specified levels of serotonin, dopamine, and norepinephrine change not_specified Molecular biomarkers are also excellent tools that may assist in detecting depression, such as alterations in serotonin, dopamine, and norepinephrine levels HPLC Measures glutamate concentration with high selectivity and sensitivity when paired with microdialysis. in_vitro glutamate concentration increase http://purl.obolibrary.org/obo/CHEBI_18311 CHEBI http://purl.obolibrary.org/obo/OBI_0000268 OBI high When microdialysis is paired with other analytical methods such as High-Pressure Liquid Chromatography (HPLC), there is a higher instrumental selectivity and sensitivity (Watson et al. 2006). http://purl.obolibrary.org/obo/CHEBI_18311 CHEBI http://purl.obolibrary.org/obo/GO_0006837 GO liquid scintillation spectrometry Measures glutamate uptake by astrocytes and synaptic cleft concentration using radiolabeled glutamate (H3-glutamate). in_vitro astrocytes synaptic cleft glutamate uptake and concentration increase http://purl.obolibrary.org/obo/CHEBI_18311 CHEBI http://purl.obolibrary.org/obo/GO_0015813 GO http://purl.obolibrary.org/obo/GO_0045202 GO low Glutamate uptake by astrocytes and synaptic cleft concentration can be measured using liquid scintillation spectrometry and radiolabeled glutamate (H3 glutamate) (Lallement et al. 1991). http://purl.obolibrary.org/obo/CHEBI_18311 CHEBI http://purl.obolibrary.org/obo/GO_0015813 GO microdialysis Measures glutamate concentration in the synaptic cleft by sampling extracellular fluid. in_vivo synaptic cleft glutamate concentration increase http://purl.obolibrary.org/obo/CHEBI_18311 CHEBI http://purl.obolibrary.org/obo/GO_0045202 GO medium Another mechanism to measure the glutamate concentration in the synaptic cleft is by microdialysis sampling. http://purl.obolibrary.org/obo/CHEBI_18311 CHEBI http://purl.obolibrary.org/obo/GO_0006837 GO electrophysiology Measures the functional effects of compounds on voltage-gated sodium channels (VGSC) using electrophysiological recordings. in_vitro electrophysiological response change http://purl.obolibrary.org/obo/OBI_0000211 OBI http://purl.obolibrary.org/obo/PR_000001096 PR low the demonstration of stereo-specific effects of the pyrethroids on binding (Soderlund 1985; Brown et al., 1988) as well as electrophysiological responses (Narahashi 1982; Narahashi1996; Narahashi., 2000; Narahashi., 2002) http://purl.obolibrary.org/obo/PR_000001096 PR http://purl.obolibrary.org/obo/GO_0006811 GO immunohistochemical methods Assesses the expression and localization of voltage-gated sodium channels (VGSC) on different cell types using antibodies. in_vitro expression and localization not_specified http://purl.obolibrary.org/obo/GO_0044288 GO not_specified the expression and localization of VGSC on different cell types can be assessed using immunohistochemical methods. http://purl.obolibrary.org/obo/GO_0044288 GO immunohistochemistry Assesses the expression and localization of voltage-gated sodium channels (VGSC) on different cell types using antibodies. in_vitro VGSC expression and localization not_specified http://purl.obolibrary.org/obo/PR_000001096 PR low the expression and localization of VGSC on different cell types can be assessed using immunohistochemical methods http://purl.obolibrary.org/obo/PR_000001096 PR http://purl.obolibrary.org/obo/GO_0008104 GO mutational analysis This assay identifies point mutations in VGSC that alter channel effects and sensitivity to pyrethroid toxicity. in_vitro VGSC mutation effects change low The published literature contains hundreds of reports identifying point mutations in VGSC that alter both the effects on the channel as well as the sensitivity to pyrethroid toxicity. radioligand binding Measures the direct interaction of compounds with voltage-gated sodium channels (VGSC) using radiolabeled ligands. in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000366 OBI http://purl.obolibrary.org/obo/PR_000001096 PR medium Interaction of compounds with VGSC can be measured directly with radioligand binding (Trainer et al 1997) http://purl.obolibrary.org/obo/PR_000001096 PR http://purl.obolibrary.org/obo/GO_0015276 GO radioligand binding Measures the binding of compounds (e.g., pyrethroids) to voltage-gated sodium channels (VGSC) using radiolabeled ligands, allowing quantification of specific binding affinity (Kd) and capacity (Bmax). in_vitro ligand binding to VGSC change http://purl.obolibrary.org/obo/GO_0005102 GO http://purl.obolibrary.org/obo/GO_0005488 GO not_specified Interaction of compounds with VGSC can be measured directly with radioligand binding (Trainer et al 1997) http://purl.obolibrary.org/obo/GO_0008076 GO http://purl.obolibrary.org/obo/GO_0005244 GO Angiogenesis Imaging Visualization of blood vessel formation using microscopy techniques like confocal or intravital microscopy. not_specified blood vessel formation visualization not_specified http://purl.obolibrary.org/obo/GO_0001525 GO not_specified Angiogenesis Imaging: as confocal microscopy or intravital microscopy to visualize blood vessel formation. http://purl.obolibrary.org/obo/UBERON_0000712 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO aortic ring assay Measures angiogenesis by culturing aortic rings and observing sprouting of endothelial cells. ex_vivo aorta endothelial cell sprouting increase http://purl.obolibrary.org/obo/GO_0001525 GO low Aortic Ring Assay http://purl.obolibrary.org/obo/UBERON_0000947 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO BrdU incorporation Measures endothelial cell proliferation by quantifying the incorporation of bromodeoxyuridine into newly synthesized DNA. in_vitro endothelial cells cell proliferation increase http://purl.obolibrary.org/obo/GO_0008283 GO not_specified Assays like BrdU (bromodeoxyuridine) incorporation, MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, or EdU (5-ethynyl-2'-deoxyuridine) incorporation can be used http://purl.obolibrary.org/obo/CL_0000212 CL http://purl.obolibrary.org/obo/GO_0008283 GO BrdU incorporation Measures endothelial cell proliferation by incorporating bromodeoxyuridine into newly synthesized DNA. in_vitro endothelial cells DNA synthesis increase http://purl.obolibrary.org/obo/GO_0006260 GO http://purl.obolibrary.org/obo/GO_0008283 GO medium BrdU (bromodeoxyuridine) incorporation http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0008283 GO chorioallantoic membrane (CAM) assay In vivo assay using the chick embryo chorioallantoic membrane to observe angiogenesis. in_vivo chorioallantoic membrane Gallus gallus blood vessel formation increase http://purl.obolibrary.org/obo/GO_0001525 GO medium Chorioallantoic Membrane (CAM) Assay: In vivo assay utilizing the chick embryo CAM to observe angiogenesis http://purl.obolibrary.org/obo/UBERON_0003125 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO corneal neovascularization assay Measures angiogenesis by observing the growth of new blood vessels into the cornea. in_vivo cornea blood vessel formation increase http://purl.obolibrary.org/obo/GO_0001525 GO low Corneal Neovascularization Assay http://purl.obolibrary.org/obo/UBERON_0001764 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO Corneal neovascularization assay Measures angiogenesis by assessing new blood vessel growth into the cornea, often via micropocket assay. in_vivo cornea corneal neovascularization increase http://purl.obolibrary.org/obo/GO_0001525 GO not_specified Corneal Neovascularization Assay http://purl.obolibrary.org/obo/UBERON_0001772 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO EdU incorporation Measures endothelial cell proliferation by quantifying the incorporation of 5-ethynyl-2'-deoxyuridine into DNA. in_vitro endothelial cells cell proliferation increase http://purl.obolibrary.org/obo/GO_0008283 GO not_specified Assays like BrdU (bromodeoxyuridine) incorporation, MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, or EdU (5-ethynyl-2'-deoxyuridine) incorporation can be used http://purl.obolibrary.org/obo/CL_0000212 CL http://purl.obolibrary.org/obo/GO_0008283 GO EdU incorporation Measures endothelial cell proliferation by incorporating 5-ethynyl-2'-deoxyuridine into newly synthesized DNA. in_vitro endothelial cells DNA synthesis increase http://purl.obolibrary.org/obo/GO_0006260 GO http://purl.obolibrary.org/obo/GO_0008283 GO medium EdU (5-ethynyl-2'-deoxyuridine) incorporation http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0008283 GO ELISA Enzyme-linked immunosorbent assay used to quantify the concentration of angiogenic factors. not_specified angiogenic factor concentration change not_specified ELISA for Angiogenic Factors http://purl.obolibrary.org/obo/GO_0051237 GO ELISA for Angiogenic Factors Measures levels of angiogenic factors using enzyme-linked immunosorbent assay. not_specified angiogenic factor concentration increase not_specified ELISA for Angiogenic Factors ELISA for angiogenic factors Measures protein concentrations of angiogenic factors (e.g., VEGF, PlGF) in supernatants or tissue extracts to assess angiogenic activity. not_specified protein concentration increase http://purl.obolibrary.org/obo/GO_0009306 GO not_specified ELISA for Angiogenic Factors http://purl.obolibrary.org/obo/GO_0009306 GO Matrigel plug assay In vivo assay involving subcutaneous injection of Matrigel containing angiogenic inducers or cells to study angiogenesis. in_vivo subcutaneous tissue blood vessel formation increase http://purl.obolibrary.org/obo/GO_0001525 GO low Matrigel Plug Assay: In vivo assay involving the subcutaneous injection of Matrigel containing angiogenic inducers or cells http://purl.obolibrary.org/obo/UBERON_0010777 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO microfluidic device assay Measures directed endothelial cell migration in a controlled microfluidic environment. in_vitro endothelial cells directed cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO medium microfluidic devices to study directed migration http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0016477 GO MTT assay Measures endothelial cell viability and proliferation by reducing MTT to formazan crystals. in_vitro endothelial cells cell viability increase http://purl.obolibrary.org/obo/GO_0008283 GO high MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0008283 GO MTT assay A colorimetric assay used to measure endothelial cell proliferation via metabolic activity. in_vitro endothelial cells metabolic activity not_specified http://purl.obolibrary.org/obo/GO_0008283 GO not_specified Assays like BrdU (bromodeoxyuridine) incorporation, MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, or EdU (5-ethynyl-2'-deoxyuridine) incorporation can be used http://purl.obolibrary.org/obo/CL_0000212 CL http://purl.obolibrary.org/obo/GO_0008283 GO qPCR for angiogenic markers Quantifies mRNA expression levels of angiogenic genes (e.g., VEGF, FGF) to assess transcriptional upregulation associated with angiogenesis. not_specified gene expression increase http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Quantitative PCR (qPCR) for Angiogenic Markers http://purl.obolibrary.org/obo/GO_0010467 GO qPCR for angiogenic markers Quantifies gene expression of angiogenic markers using quantitative PCR. in_vitro gene expression of angiogenic markers increase http://purl.obolibrary.org/obo/GO_0010467 GO high Quantitative PCR (qPCR) for Angiogenic Markers http://purl.obolibrary.org/obo/GO_0001525 GO Quantitative PCR (qPCR) Quantifies the expression of angiogenic marker genes. not_specified gene expression of angiogenic markers change http://purl.obolibrary.org/obo/GO_0051176 GO not_specified Quantitative PCR (qPCR) for Angiogenic Markers http://purl.obolibrary.org/obo/GO_0051176 GO scratch/wound healing assay Measures endothelial cell migration by observing the closure of a scratch in a cell monolayer. in_vitro endothelial cells cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO medium scratch/wound healing assays http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0016477 GO Transwell migration assay Measures endothelial cell migration through a porous membrane toward a chemoattractant. in_vitro endothelial cells cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO medium Transwell migration assays http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0016477 GO tube formation assay Assesses the ability of endothelial cells to form capillary-like structures in vitro. in_vitro endothelial cells capillary-like structure formation increase http://purl.obolibrary.org/obo/GO_0048514 GO medium Tube Formation Assay: Assess the ability of endothelial cells to form capillary-like structures http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0048514 GO Tube formation assay Assesses the ability of endothelial cells to form capillary-like structures. in_vitro endothelial cells tube formation increase http://purl.obolibrary.org/obo/GO_0001545 GO medium Tube Formation Assay: Assess the ability of endothelial cells to form capillary-like structures (Stryker) http://purl.obolibrary.org/obo/UBERON_0000733 UBERON http://purl.obolibrary.org/obo/GO_0001545 GO cell transfection HPLC assay Measures the ability of transfected CYP7B protein to catalyze enzymatic reactions in a cell line incapable of synthesizing 7α-hydroxypregnenolone using HPLC analysis. in_vitro transfected cell line enzymatic reaction catalysis change http://purl.obolibrary.org/obo/GO_0003824 GO http://www.bioassayontology.org/bao#BAO_0000017 BAO http://www.bioassayontology.org/bao#BAO_0000025 BAO low CYP7B can be transfected in a cell line unable to synthesize 7α-hydroxypregnenolone in order to measure with HPLC the ability of the protein to catalyze the enzymatic reaction in presence of the appropriate substrate and cofactor (Tsutsui et al., 2008) CYP7B knockout mouse model Uses knock-out mice to confirm CYP7B deletion via RNA, protein blotting, and enzymatic activity assays, followed by measuring substrate and metabolite levels in plasma and tissues. in_vivo plasma tissues mouse substrate and metabolite levels in plasma and tissues change http://www.bioassayontology.org/bao#BAO_0000040 BAO http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0003824 GO low Experiments may include knock-out of mice (followed by RNA, protein blotting and enzymatic activity to confirm knock-out) (Li-Hawkins et al., 2000) followed by the measurement of substrate and metabolites of CYP7B in plasma and tissues (Rose., 2001). GS-MS GS-MS analysis is used to measure labeled steroid conversion in vitro with cell or tissue extract in the presence of NADPH. in_vitro labeled steroid conversion change medium Labeled steroid conversion in vitro with cell or tissue extract in presence of NADPH followed by GS-MS analysis (Rose et al., 1997; Tsutsui et al., 2008). http://purl.obolibrary.org/obo/CHEBI_16684 CHEBI http://purl.obolibrary.org/obo/GO_0019363 GO GS-MS-based steroid conversion assay Measures CYP7B activity by analyzing labeled steroid conversion using GS-MS. in_vitro steroid conversion not_specified http://purl.obolibrary.org/obo/OBI_0000473 OBI medium Labeled steroid conversion in vitro with cell or tissue extract in presence of NADPH followed by GS-MS analysis (Rose et al., 1997; Tsutsui et al., 2008). http://www.ebi.ac.uk/efo/EFO_0000727 EFO http://purl.obolibrary.org/obo/GO_0008202 GO HPLC HPLC is used to measure the enzymatic activity of CYP7B protein produced in bacteria in vitro, in the presence of precursor and cofactors. in_vitro bacteria enzymatic activity change http://purl.obolibrary.org/obo/GO_0004372 GO low CYP7B can be cloned in bacteria to produce an active protein in vitro. In presence of adequate precursor and cofactors, the enzymatic activity of the protein can be measured and analyzed using HPLC. http://purl.obolibrary.org/obo/GO_0019363 GO HPLC HPLC analysis is used to measure the metabolites produced in vitro using liver microsomes. This involves analyzing the metabolites formed after incubation with the substrate. in_vitro liver metabolite levels change medium An assay in liver microsome followed by HPLC analysis of the metabolites (Souidi et al., 2000). http://purl.obolibrary.org/obo/GO_0019363 GO HPLC analysis of liver microsome metabolites Measures CYP7B activity by performing HPLC analysis on metabolites produced in liver microsomes. in_vitro liver metabolite concentration change not_specified An assay in liver microsome followed by HPLC analysis of the metabolites (Souidi et al., 2000). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006601 GO HPLC analysis of recombinant CYP7B protein Measures the enzymatic activity of recombinant CYP7B protein produced in bacteria using HPLC in the presence of precursors and cofactors. in_vitro bacteria enzymatic activity change not_specified CYP7B can be cloned in bacteria to produce an active protein in vitro. In presence of adequate precursor and cofactors, the enzymatic activity of the protein can be measured and analyzed using HPLC. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006601 GO HPLC-based CYP7B activity assay in liver microsomes Measures CYP7B activity in liver microsomes by analyzing metabolites using HPLC. in_vitro liver CYP7B enzymatic activity not_specified http://purl.obolibrary.org/obo/OBI_0000475 OBI medium An assay in liver microsome followed by HPLC analysis of the metabolites (Souidi et al., 2000). http://www.ebi.ac.uk/efo/EFO_0000727 EFO http://purl.obolibrary.org/obo/GO_0008202 GO In vivo substrate and metabolite measurement Measures the concentration of CYP7B substrates and metabolites in the plasma and tissues of mice, often following a knock-out. in_vivo plasma tissues mice substrate and metabolite concentration change http://purl.obolibrary.org/obo/CHEBI_35116 CHEBI not_specified Experiments may include knock-out of mice (followed by RNA, protein blotting and enzymatic activity to confirm knock-out) (Li-Hawkins et al., 2000) followed by the measurement of substrate and metabolites of CYP7B in plasma and tissues (Rose., 2001). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006601 GO GC-MS Measures the concentration of 7α-hydroxypregnenolone in brain homogenates and plasma using gas chromatography-mass spectrometry. in_vivo brain plasma 7α-hydroxypregnenolone concentration decrease http://purl.obolibrary.org/obo/CHMO_0000016 CHMO medium The extracted steroids derived from brain homogenates and plasma can be measured using GC-MS analysis (Tsutsui et a;., 2008). http://purl.obolibrary.org/obo/GO_0006694 GO GC-MS Detection and quantification of steroids using gas chromatography-mass spectrometry. in_vivo brain steroid concentration decrease http://purl.obolibrary.org/obo/GO_0008204 GO low The extracted steroids derived from brain homogenates and plasma can be measured using GC-MS analysis (Tsutsui et a;., 2008). http://purl.obolibrary.org/obo/GO_0008204 GO HPLC Measures the concentration of 7α-hydroxypregnenolone in cell cultures or brain homogenates using high-performance liquid chromatography. in_vitro brain 7α-hydroxypregnenolone concentration decrease http://purl.obolibrary.org/obo/CHMO_0000015 CHMO medium Cell not expressing CYP7B can be transfected with CYP7B cDNA and incubated in presence of pregnenolone and NADPH. Concentration of 7α-hydroxypregnenolone can be measured by HPLC analysis (Haraguchi et al., 2015). Brain homogenates can be incubated in presence of pregnenolone and NADPH. Concentration of 7α-hydroxypregnenolone can be measured by HPLC analysis Haraguchi et al., 2015). http://purl.obolibrary.org/obo/GO_0006694 GO HPLC-ECD (in vitro) Measures dopamine concentration in physiological saline after incubation of brain tissue with a presumptive activator. in_vitro brain dopamine concentration increase http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium brain can be incubated in physiological saline in presence of a presumptive activator (e.g. 7α-hydroxypregnenolone, a neurosteroid) and dopamine concentration in saline is measured by HPLC-ECD http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0014059 GO line crossing assay Measures locomotor activity by counting the number of parallel lines crossed by an individual newt placed in a water‑filled aquarium over a set time period. in_vivo newt total number of lines crossed change http://purl.obolibrary.org/obo/GO_0007626 GO low To measure locomotor activity, animals can be placed individually in a water-filled aquarium (newts) marked with parallel lines to define sectors. Quantification of total number of lines crossed during a certain amount of time is then measured (Lowry et al., 2001; Moore et al., 1984). http://purl.obolibrary.org/obo/UBERON_0000468 UBERON http://purl.obolibrary.org/obo/GO_0007626 GO Locomotor activity assay (birds) Measures the total distance traveled by birds using a telemetry system implanted in a soundproof box, or by counting photobeam breaks in a box with wire-mesh floor and ceilings. in_vivo muscle birds total distance traveled decrease http://purl.obolibrary.org/obo/GO_0007626 GO http://purl.obolibrary.org/obo/CHMO_0000001 CHMO low Birds can be put in a soundproof box with a telemetry system implanted to calculate their total distance during the experiment ( or in a box with wire-mesh floor and ceilings and photobeams activated when the animal break the beam (Levens et al., 2001; Tsutsui et al., 2008). Locomotor activity is a measurement of distance per unit of time. http://purl.obolibrary.org/obo/NCBITaxon_8782 NCBITAXON http://purl.obolibrary.org/obo/GO_0007626 GO locomotor activity measurement Locomotor activity is measured as distance per unit of time. Animals are placed in an environment (aquarium or box) and the number of lines crossed or distance traveled is quantified. in_vivo distance per unit of time / number of lines crossed decrease http://purl.obolibrary.org/obo/GO_0007624 GO http://purl.obolibrary.org/obo/UO_0000067 UO low Locomotor activity is a measurement of distance per unit of time. Quantification of total number of lines crossed during a certain amount of time is then measured (Lowry et al., 2001; Moore et al., 1984). Birds can be put in a soundproof box with a telemetry system implanted to calculate their total distance during the experiment http://purl.obolibrary.org/obo/CL_0000019 CL http://purl.obolibrary.org/obo/GO_0007624 GO photobeam activity box Measures locomotor activity in birds by counting photobeam breaks in a box with wire-mesh floors and ceilings. in_vivo birds number of photobeam breaks decrease http://purl.obolibrary.org/obo/GO_0008345 GO medium in a box with wire-mesh floor and ceilings and photobeams activated when the animal break the beam (Levens et al., 2001; Tsutsui et al., 2008). http://purl.obolibrary.org/obo/NCBITaxon_8782 NCBITAXON http://purl.obolibrary.org/obo/GO_0007626 GO photobeam activity chamber Measures locomotor activity in birds by placing them in a box with wire-mesh floor and ceilings equipped with photobeams that are activated when the animal breaks the beam. in_vivo locomotor system bird beam breaks indicating movement decrease http://purl.obolibrary.org/obo/GO_0007629 GO low in a box with wire-mesh floor and ceilings and photobeams activated when the animal break the beam (Levens et al., 2001; Tsutsui et al., 2008). http://purl.obolibrary.org/obo/GO_0007629 GO http://purl.obolibrary.org/obo/GO_0007629 GO photobeam interruption Quantifies locomotor activity by measuring how many times an animal breaks photobeams in a cage with a wire-mesh floor and ceiling. in_vivo birds photobeam activations change http://purl.obolibrary.org/obo/GO_0050853 GO low in a box with wire-mesh floor and ceilings and photobeams activated when the animal break the beam http://purl.obolibrary.org/obo/GO_0050853 GO telemetry-based distance measurement Measures the total distance traveled by an animal using an implanted telemetry system within a soundproof box. in_vivo birds total distance change http://purl.obolibrary.org/obo/GO_0050853 GO low Birds can be put in a soundproof box with a telemetry system implanted to calculate their total distance during the experiment http://purl.obolibrary.org/obo/GO_0050853 GO water-filled aquarium line crossing Measures locomotor activity in newts by counting the number of lines crossed in a water-filled aquarium marked with parallel lines. in_vivo newts number of lines crossed decrease http://purl.obolibrary.org/obo/GO_0008345 GO low To measure locomotor activity, animals can be placed individually in a water-filled aquarium (newts) marked with parallel lines to define sectors. Quantification of total number of lines crossed during a certain amount of time is then measured (Lowry et al., 2001; Moore et al., 1984). http://purl.obolibrary.org/obo/NCBITaxon_8505 NCBITAXON http://purl.obolibrary.org/obo/GO_0007626 GO avian sexual behavior frequency observation Measures the frequency of specific courtship behaviors including chasing, pecking, head grabbing, and mounting in birds over a specified observation period. in_vivo bird frequency of chasing, pecking, head grabbing, and mounting change http://purl.obolibrary.org/obo/UBERON_0001211 UBERON low In bird, the frequency of chasing, pecking, head grabbing, and mounting for a X minutes observation can be measured http://purl.obolibrary.org/obo/GO_0040031 GO Male sexual behavior assay (birds) Measures the frequency of chasing, pecking, head grabbing, and mounting in male birds over a specified observation period. in_vivo birds frequency of sexual behaviors decrease low For bird, the frequency of chasing, pecking, head grabbing, and mounting for a X minutes observation can be measured (Halldin et al., 1999; Ogura et al., 2016). Male sexual behavior assay (newts) Measures the frequency and incidence of tail-vibrating behavior in male newts over a specified observation period. in_vivo newts frequency and incidence of tail-vibrating behavior decrease low For newt, sexual behavior is characterized by a tail-vibrating behavior and can be measured by counting the frequency and incidence of this behavior during X minutes. newt tail-vibrating behavior count Measures the frequency and incidence of tail-vibrating behavior in newts during a specific observation period. in_vivo newt frequency and incidence of tail-vibrating behavior change low For newt, sexual behavior is characterized by a tail-vibrating behavior and can be measured by counting the frequency and incidence of this behavior during X minutes. http://purl.obolibrary.org/obo/GO_0040031 GO Sexual behavior observation (Birds) Observation and quantification of chasing, pecking, head grabbing, and mounting behaviors in male birds in the presence of a receptive female. in_vivo birds frequency of chasing, pecking, head grabbing, and mounting decrease http://purl.obolibrary.org/obo/GO_0007049 GO low In bird, the frequency of chasing, pecking, head grabbing, and mounting for a X minutes observation can be measured http://purl.obolibrary.org/obo/NCBITaxon_23155 NCBITAXON http://purl.obolibrary.org/obo/GO_0007049 GO 2-Piperidone urine assay Detects 2-piperidone in urine as a biomarker of Cyp2E1 activity. in_vivo human 2-piperidone levels increase http://purl.obolibrary.org/obo/GO_0005615 GO high 2-Piperidone is a newly proposed biomarker of Cyp2E1 activity that is detected in urine (Cheng, et al. 2013). http://purl.obolibrary.org/obo/PR_000001119 PR http://purl.obolibrary.org/obo/GO_0006805 GO 6-hydroxychlorzoxazone/chlorzoxazone ratio Measures the ratio of 6-hydroxychlorzoxazone to chlorzoxazone to estimate CYP2E1 levels in humans using liver homogenates or cell cultures. in_vitro liver human ratio of 6-hydroxychlorzoxazone to chlorzoxazone increase http://purl.obolibrary.org/obo/GO_0004497 GO medium the ratio of 6-hydroxychlorzoxazone/chlorzoxazone can be used to estimate levels of CYP2E1 in humans (Girre, et al. 1994) http://purl.obolibrary.org/obo/PR_000001119 PR http://purl.obolibrary.org/obo/GO_0006805 GO 6-hydroxychlorzoxazone/chlorzoxazone ratio assay Measures the ratio of 6-hydroxychlorzoxazone to chlorzoxazone to estimate CYP2E1 levels in humans using liver microsomes. in_vitro liver human CYP2E1 enzyme activity not_specified http://purl.obolibrary.org/obo/UBERON_0002107 UBERON not_specified The ratio of 6-hydroxychlorzoxazone/chlorzoxazone can be used to estimate levels of CYP2E1 in humans (Girre, et al. 1994). http://purl.obolibrary.org/obo/GO_0017627 GO Chlorzoxazone metabolism Estimation of CYP2E1 levels in humans by measuring the ratio of 6-hydroxychlorzoxazone to chlorzoxazone. in_vitro 6-hydroxychlorzoxazone/chlorzoxazone ratio increase not_specified the ratio of 6-hydroxychlorzoxazone/chlorzoxazone can be used to estimate levels of CYP2E1 in humans (Girre, et al. 1994) http://purl.obolibrary.org/obo/GO_0000000 GO http://purl.obolibrary.org/obo/GO_0008150 GO Cyp2E1 knockout mouse metabolite measurement Measures metabolite production in Cyp2E1 knockout mice compared to wild-type mice to determine Cyp2E1 dependence. in_vivo mouse metabolite production decrease http://purl.obolibrary.org/obo/CHEBI_24744 CHEBI http://purl.obolibrary.org/obo/GO_0006805 GO low Chemical exposures in knockout mice are conducted and the production of the anticipated metabolites is measured. Lack of metabolite production indicates that Cyp2E1 is required for the chemical’s metabolism. http://purl.obolibrary.org/obo/PR_000001119 PR http://purl.obolibrary.org/obo/GO_0006805 GO CYP2E1-dependent chemical oxidation in liver microsomes Measures chemical oxidation by CYP2E1 in liver microsomes using specific probe substrates to confirm CYP2E1-catalyzed oxidation. in_vitro liver human chemical oxidation increase http://purl.obolibrary.org/obo/CHMO_0000000 CHMO http://purl.obolibrary.org/obo/GO_0055114 GO low Measurement of chemical oxidation by Cyp2E1 in liver microsomes; described in the methodology review by Cederbaum (Cederbaum 2014). Reactions use specific probes to confirm that the compound undergoes oxidation, and that this oxidation reaction is catalyzed by Cyp2E1. See also: (Koop 1986, Koop, et al. 1989, Reinke and Moyer 1985). http://purl.obolibrary.org/obo/CHMO_0000000 CHMO http://purl.obolibrary.org/obo/GO_0055114 GO HepG2 cytotoxicity assay Compares cytotoxicity in HepG2 versus HepG2-E47 cells to determine Cyp2E1-dependence of a compound. in_vitro HepG2 HepG2-E47 human cytotoxicity increase http://purl.obolibrary.org/obo/GO_0060548 GO http://purl.obolibrary.org/obo/GO_0008219 GO medium A compound’s Cyp2E1-dependence can be determined by comparing toxic effects in HepG2 versus HepG2-E47 cells. Chemicals that are metabolically activated by Cyp2E1 will cause cytotoxicity and oxidative stress in the E47 cells only. http://purl.obolibrary.org/obo/GO_0008219 GO HepG2/HepG2-E47 comparison This assay compares toxic effects in HepG2 (Cyp2E1 negative) versus HepG2-E47 (Cyp2E1 overexpressing) cells to determine Cyp2E1-dependence of a compound's toxicity. in_vitro HepG2 HepG2-E47 liver human cytotoxicity and oxidative stress change http://purl.obolibrary.org/obo/GO_0000303 GO medium HepG2 cells. A compound’s Cyp2E1-dependence can be determined by comparing toxic effects in HepG2 versus HepG2-E47 cells. Chemicals that are metabolically activated by Cyp2E1 will cause cytotoxicity and oxidative stress in the E47 cells only. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0043268 GO Humanized Cyp2E1 mouse metabolite measurement Measures Cyp2E1-dependent effects in humanized Cyp2E1 transgenic mice to validate human relevance. in_vivo mouse Cyp2E1-dependent toxicity increase http://purl.obolibrary.org/obo/GO_0006805 GO low Studies in these mice are conducted in order to provide evidence that the Cyp2E1-dependent effects observed in experimental animals will also occur in humans. http://purl.obolibrary.org/obo/PR_000001119 PR http://purl.obolibrary.org/obo/GO_0006805 GO Immunohistochemistry Detects Cyp2E1 protein levels in fixed liver or cultured cells using anti-Cyp2E1 antibodies. in_vitro cultured cells liver Cyp2E1 protein levels increase http://purl.obolibrary.org/obo/PR_000001119 PR medium Western blot (of protein extracted from liver or cultured cells) or immunohistochemistry (of fixed liver or cultured cells) using anti-Cyp2E1 antibodies is the most straightforward approach for directly measuring increased levels of Cyp2E1. http://purl.obolibrary.org/obo/PR_000001119 PR http://purl.obolibrary.org/obo/GO_0010457 GO mixed function oxidase assay This assay estimates levels of CYP2E1 by measuring the ratio of 6-hydroxychlorzoxazone/chlorzoxazone, or by measuring the oxidation of para-nitrophenol (PNP) to para nitrocatechol. in_vitro liver human CYP2E1 activity increase http://purl.obolibrary.org/obo/GO_0055114 GO medium Mixed function oxidase catalytic activity. Briefly, the ratio of 6-hydroxychlorzoxazone/chlorzoxazone can be used to estimate levels of CYP2E1 in humans (Girre, et al. 1994). In addition, the oxidation of para-nitrophenol (PNP) to para nitrocatechol is an efficient and relatively specific assay to determine catalytic activity dependent on CYP2E1 [e.g., (Koop 1986, Koop, et al. 1989, Reinke and Moyer 1985)]. http://purl.obolibrary.org/obo/GO_0055114 GO para-nitrophenol oxidation Measures the oxidation of para-nitrophenol to para-nitrocatechol to determine CYP2E1-dependent catalytic activity. in_vitro liver oxidation of para-nitrophenol to para-nitrocatechol increase http://purl.obolibrary.org/obo/GO_0004497 GO medium the oxidation of para-nitrophenol (PNP) to para nitrocatechol is an efficient and relatively specific assay to determine catalytic activity dependent on CYP2E1 [e.g., (Koop 1986, Koop, et al. 1989, Reinke and Moyer 1985)] http://purl.obolibrary.org/obo/PR_000001119 PR http://purl.obolibrary.org/obo/GO_0006805 GO para-nitrophenol oxidation assay Measures the oxidation of para-nitrophenol (PNP) to para nitrocatechol as a specific assay to determine catalytic activity dependent on CYP2E1. in_vitro CYP2E1 catalytic activity not_specified not_specified the oxidation of para-nitrophenol (PNP) to para nitrocatechol is an efficient and relatively specific assay to determine catalytic activity dependent on CYP2E1 http://purl.obolibrary.org/obo/GO_0017627 GO Western blot Measures Cyp2E1 protein levels in liver or cultured cells using anti-Cyp2E1 antibodies. in_vitro cultured cells liver Cyp2E1 protein levels increase http://purl.obolibrary.org/obo/PR_000001119 PR medium Western blot (of protein extracted from liver or cultured cells) or immunohistochemistry (of fixed liver or cultured cells) using anti-Cyp2E1 antibodies is the most straightforward approach for directly measuring increased levels of Cyp2E1. http://purl.obolibrary.org/obo/PR_000001119 PR http://purl.obolibrary.org/obo/GO_0010457 GO 8-oxo-dG Assay Measures oxidative damage to nucleic acids by quantifying 8-oxo-dG adducts using ELISA-based kits or HPLC. in_vitro 8-oxo-dG levels increase http://purl.obolibrary.org/obo/CHEBI_27157 CHEBI http://purl.obolibrary.org/obo/GO_0006974 GO high 8-oxo-dG. Oxidative damage to nucleic acids can be assayed by measuring 8-oxo-dG adducts (for which there are a number of ELISA based commercially available kits),or HPLC, described in Chepelev et al. (Chepelev, et al. 2015). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Amplex Red Assay Measures extracellular or extramitochondrial H2O2 levels using horseradish peroxidase to oxidize Amplex Red to resorufin. in_vitro H2O2 levels increase http://purl.obolibrary.org/obo/CHEBI_16058 CHEBI not_specified In the presence of horseradish peroxidase and H2O2, Amplex Red is oxidized to resorufin, a fluorescent molecule measurable by plate reader. http://purl.obolibrary.org/obo/CHEBI_16058 CHEBI http://purl.obolibrary.org/obo/GO_0016761 GO ARE-Nrf2 Luciferase Assay Measures Nrf2 transcriptional activity using a luciferase reporter assay under the control of antioxidant response elements (ARE). in_vitro luciferase activity increase OECD TG422D high OECD TG422D describes an ARE-Nrf2 Luciferase test method http://purl.obolibrary.org/obo/PR_P38397 PR http://purl.obolibrary.org/obo/GO_0045449 GO Chemiluminescence Measures ROS indirectly by detecting chemiluminescence emitted when ROS induce electron transitions in molecules, often amplified using reagents like luminol or lucigenin. in_vitro chemiluminescence intensity increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI OECD TG 495 not_specified Detection of ROS by chemiluminescence (https://www.sciencedirect.com/science/article/abs/pii/S0165993606001683) Detection of ROS by chemiluminescence is also described in OECD TG 495 to assess phototoxic potential. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO chemiluminescence An indirect method to detect ROS by measuring light emitted when electronically excited products return to their ground state, often using luminol or lucigenin. in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_40342 CHEBI OECD TG 495 not_specified Detection of ROS by chemiluminescence Detection of ROS by chemiluminescence is also described in OECD TG 495 to assess phototoxic potential. http://purl.obolibrary.org/obo/CHEBI_40342 CHEBI http://purl.obolibrary.org/obo/GO_0016761 GO CM-H2DCFDA Assay Measures intracellular glutathione levels using CM-H2DCFDA, which is cleaved by esterases and reacts with glutathione. in_vitro glutathione levels decrease http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/OBI_0000268 OBI medium The dye (CM-H2DCFDA) diffuses into the cell and is cleaved by esterases, the thiol reactive chlormethyl group reacts with intracellular glutathione which can be detected using flow cytometry. http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0034599 GO Cytochrome c Reduction Assay Measures superoxide levels by monitoring the oxidation of ferricytochrome c to ferrocytochrome c at 550 nm. in_vitro O2.- levels increase http://purl.obolibrary.org/obo/CHEBI_40342 CHEBI not_specified The cytochrome c reduction assay is used to measure O2.− levels. O O2.− is reduced to O2 as ferricytochrome c is oxidized to ferrocytochrome c http://purl.obolibrary.org/obo/CHEBI_40342 CHEBI http://purl.obolibrary.org/obo/GO_0019887 GO DCFH-DA assay An indirect fluorescence assay where H2O2 oxidizes DCFH to the fluorescent product DCF. in_vitro intracellular ROS production increase http://purl.obolibrary.org/obo/CHEBI_16058 CHEBI not_specified Intracellular ROS production was measured using DCFH-DA as a probe. Hydrogen peroxide oxidizes DCFH to DCF. http://purl.obolibrary.org/obo/CHEBI_16058 CHEBI http://purl.obolibrary.org/obo/GO_0016761 GO EPR spectroscopy The unpaired electrons (free radicals) found in ROS can be detected with EPR and is known as electron paramagnetic resonance. A variety of spin traps can be used. in_vitro free radicals increase http://purl.obolibrary.org/obo/CHEBI_59768 CHEBI not_specified The unpaired electrons (free radicals) found in ROS can be detected with EPR and is known as electron paramagnetic resonance. A variety of spin traps can be used. http://purl.obolibrary.org/obo/CHEBI_59768 CHEBI http://purl.obolibrary.org/obo/GO_0055114 GO flow cytometry (DCFH-DA) Measures mitochondrial ROS formation using the fluorescent probe DCFH-DA in isolated kidney mitochondria. ex_vivo kidney mean fluorescence intensity of ROS increase http://purl.obolibrary.org/obo/CHEBI_40342 CHEBI medium The mitochondrial ROS measurement was performed flow cytometry using DCFH-DA. Uranyl acetate-induced ROS generation in isolated kidney mitochondria were determined through the flow cytometry http://purl.obolibrary.org/obo/UBERON_0000380 UBERON http://purl.obolibrary.org/obo/GO_0006839 GO flow cytometry (Dih123) Detects ROS by the cleavage of nonfluorescent Dih123 into fluorescent R123, combined with propidium iodide for cell viability. in_vitro ROS and cell viability change http://purl.obolibrary.org/obo/CHEBI_40342 CHEBI medium For determination of ROS, samples taken at the indicated time points were directly transferred to FACScan tubes. Dih123 (10 mM, final concentration) was added and cells were incubated at 37°C in a humidified atmosphere (95% air/5% CO2) for 10 min. At t 5 9, propidium iodide (10 mM, final concentration) was added, and cells were analyzed by flow cytometry http://purl.obolibrary.org/obo/CL_0000000 CL Flow Cytometry with DCFH-DA Measures intracellular ROS production using DCFH-DA, which is oxidized to fluorescent DCF by ROS. in_vitro DCF fluorescence intensity increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/OBI_0000268 OBI medium Intracellular ROS production was measured using DCFH-DA as a probe. Hydrogen peroxide oxidizes DCFH to DCF. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Flow Cytometry with Dih123 Measures ROS production in cells using Dih123, which is cleaved by ROS to fluorescent R123, detected by flow cytometry. in_vitro R123 fluorescence intensity increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/OBI_0000268 OBI medium For determination of ROS, samples taken at the indicated time points were directly transferred to FACScan tubes. Dih123 (10 mM, final concentration) was added and cells were incubated at 37°C in a humidified atmosphere (95% air/5% CO2) for 10 min. At t 5 9, propidium iodide (10 mM, final concentration) was added, and cells were analyzed by flow cytometry at 60 ml/min. Nonfluorescent Dih123 is cleaved by ROS to fluorescent R123 and detected by the FL1 detector as described above for Dc (Van de Water 1995) http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO GSH depletion A downstream target of the Nrf2 pathway is involved in GSH synthesis. As an indication of oxidation status, GSH can be measured by assaying the ratio of reduced to oxidized glutathione (GSH:GSSG) using a commercially available kit. in_vitro GSH:GSSG ratio decrease http://purl.obolibrary.org/obo/CHEBI_16654 CHEBI not_specified A downstream target of the Nrf2 pathway is involved in GSH synthesis. As an indication of oxidation status, GSH can be measured by assaying the ratio of reduced to oxidized glutathione (GSH:GSSG) using a commercially available kit. http://purl.obolibrary.org/obo/CHEBI_16654 CHEBI http://purl.obolibrary.org/obo/GO_0055114 GO GSH/GSSG Ratio Detection Assay Measures the ratio of reduced to oxidized glutathione (GSH:GSSG) using a commercially available fluorometric kit to assess oxidative stress. in_vitro GSH:GSSG ratio decrease http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO high Glutathione (GSH) depletion. GSH can be measured by assaying the ratio of reduced to oxidized glutathione (GSH:GSSG) using a commercially available kit (e.g., http://www.abcam.com/gshgssg-ratio-detection-assay-kit-fluorometric-green- ab138881.html). http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0034599 GO H2O2 Production Assay with Scopoletin Measures H2O2 production in isolated mitochondria using scopoletin oxidation and spectrophotometry. ex_vivo H2O2 production increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0005739 GO low H2O2 production was measured as scopoletin oxidation. Mitochondria were incubated for 30 min in the measuring buffer (see the Materials and Methods) containing 0.5 mM succinate as an electron donor and 0.2 µM mesoxalonitrile 3‐chlorophenylhydrazone (CCCP) as an uncoupler, 10 U horseradish peroxidase and 5 µM scopoletin. http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO HyPer Probe Measures intracellular hydrogen peroxide (H2O2) levels using HyPer, a genetically encoded fluorescent sensor for in vivo and in situ imaging. in_vitro Intracellular hydrogen peroxide (H2O2) levels increase http://purl.obolibrary.org/obo/CHEBI_16145 CHEBI http://purl.obolibrary.org/obo/PR_000001475 PR not_specified Fluorescent measurement of intracellular H2O2 levels. HyPer is a genetically encoded fluorescent sensor that can be used for in vivo and in situ imaging. http://purl.obolibrary.org/obo/CHEBI_16145 CHEBI http://purl.obolibrary.org/obo/GO_0002919 GO Immunohistochemistry Immunohistochemistry for increases in Nrf2 protein levels and translocation into the nucleus in_vitro Nrf2 protein levels increase http://purl.obolibrary.org/obo/PR_000001886 PR low Immunohistochemistry for increases in Nrf2 protein levels and translocation into the nucleus http://purl.obolibrary.org/obo/PR_000001886 PR http://purl.obolibrary.org/obo/GO_0008440 GO Nitroblue Tetrazolium Assay Measures superoxide (O2.-) levels by the reduction of nitroblue tetrazolium to blue formazan. in_vitro O2.- levels increase http://purl.obolibrary.org/obo/CHEBI_40342 CHEBI not_specified The Nitroblue Tetrazolium assay is used to measure O2.− levels. O2.− reduces nitroblue tetrazolium (a yellow dye) to formazan (a blue dye) http://purl.obolibrary.org/obo/CHEBI_40342 CHEBI http://purl.obolibrary.org/obo/GO_0019887 GO qPCR qPCR of Nrf2 target genes (e.g., Nqo1, Hmox-1, Gcl, Gst, Prx, TrxR, Srxn), or by commercially available pathway-based qPCR array. in_vitro mRNA levels of Nrf2 target genes increase http://purl.obolibrary.org/obo/PR_000001887 PR medium qPCR of Nrf2 target genes (e.g., Nqo1, Hmox-1, Gcl, Gst, Prx, TrxR, Srxn), or by commercially available pathway-based qPCR array http://purl.obolibrary.org/obo/CL_0000276 CL http://purl.obolibrary.org/obo/GO_0006470 GO RNA-seq Whole transcriptome profiling by microarray or RNA-seq followed by pathway analysis (in IPA, DAVID, metacore, etc.) for enrichment of the Nrf2 oxidative stress response pathway. in_vitro gene expression levels change http://purl.obolibrary.org/obo/GO_0006979 GO high Whole transcriptome profiling by microarray or RNA-seq followed by pathway analysis (in IPA, DAVID, metacore, etc.) for enrichment of the Nrf2 oxidative stress response pathway http://purl.obolibrary.org/obo/GO_0005737 GO http://purl.obolibrary.org/obo/GO_0006979 GO Seahorse XFp Analyzer Measures mitochondrial function and oxidative stress by quantifying oxygen consumption rate (OCR) and extracellular acidification rate (ECAR). in_vitro OCR and ECAR change http://purl.obolibrary.org/obo/GO_0006091 GO http://purl.obolibrary.org/obo/GO_0006979 GO medium The Seahorse XFp Analyzer provides information on mitochondrial function, oxidative stress, and metabolic dysfunction of viable cells by measuring respiration (oxygen consumption rate; OCR) and extracellular pH (extracellular acidification rate; ECAR). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006091 GO spectrophotometry (DTNB) Determines mitochondrial GSH content by measuring the absorbance of a developed yellow color using DTNB. ex_vivo mitochondria GSH content (µg/mg protein) decrease http://purl.obolibrary.org/obo/CHEBI_15653 CHEBI low GSH content was determined using DTNB as the indicator and spectrophotometer method for the isolated mitochondria. http://purl.obolibrary.org/obo/CHEBI_15653 CHEBI http://purl.obolibrary.org/obo/GO_0006952 GO TBARS Assays for lipid peroxidation by measuring thiobarbituric acid reactive substances. in_vitro lipid peroxidation increase http://purl.obolibrary.org/obo/GO_0006644 GO not_specified Oxidative damage to lipids can be measured by assaying for lipid peroxidation using TBARS (thiobarbituric acid reactive substances) http://purl.obolibrary.org/obo/CHEBI_16233 CHEBI http://purl.obolibrary.org/obo/GO_0006644 GO TBARS Assay Measures oxidative damage to lipids by assaying for thiobarbituric acid reactive substances (TBARS) using a commercially available kit. in_vitro TBARS levels increase http://purl.obolibrary.org/obo/GO_0046490 GO high TBARS. Oxidative damage to lipids can be measured by assaying for lipid peroxidation using TBARS (thiobarbituric acid reactive substances) using a commercially available kit. http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/GO_0034440 GO western blot Western blot for increased Nrf2 protein levels in_vitro Nrf2 protein levels increase http://purl.obolibrary.org/obo/PR_000001886 PR low Western blot for increased Nrf2 protein levels http://purl.obolibrary.org/obo/PR_000001886 PR http://purl.obolibrary.org/obo/GO_0006470 GO Western Blot for Nrf2 Measures Nrf2 protein levels and translocation from cytoplasm to nucleus using western blot analysis. in_vitro Nrf2 protein levels increase http://purl.obolibrary.org/obo/GO_0043547 GO low Western blot for increased Nrf2 protein levels Western blot of cytoplasmic and nuclear fractions to observe translocation of Nrf2 protein from the cytoplasm to the nucleus http://purl.obolibrary.org/obo/PR_P38397 PR http://purl.obolibrary.org/obo/GO_0034599 GO Whole Transcriptome Profiling Measures global gene expression changes using microarray or RNA-seq, followed by pathway analysis for Nrf2 oxidative stress response. in_vitro gene expression profiles change http://purl.obolibrary.org/obo/GO_0005667 GO http://purl.obolibrary.org/obo/OBI_0002117 OBI medium Whole transcriptome profiling by microarray or RNA-seq followed by pathway analysis (in IPA, DAVID, metacore, etc.) for enrichment of the Nrf2 oxidative stress response pathway (e.g., Jackson et al. 2014) http://purl.obolibrary.org/obo/PR_P38397 PR http://purl.obolibrary.org/obo/GO_0045449 GO ALT measurement Serum levels of alanine aminotransferase (ALT) are measured using a commercial kit as an indicator of hepatotoxicity. in_vivo liver serum ALT levels increase http://purl.obolibrary.org/obo/GO_0004046 GO medium Serum levels of alanine aminotransferase (ALT) can be used as an indicator of hepatotoxicity. Serum levels of aspartate aminotransferase (AST) can also be used; however, AST is considered to be less ‘liver specific’ than ALT. Therefore, an AST/ALT ratio is often used. ALT and AST are typically measured using a commercial kit (e.g., from Sigma Aldrich or Roche); protocol: www.bio-protocol.org/e931 http://purl.obolibrary.org/obo/PR_000000021 PR caspase activation assay Caspase activation is measured using commercially available kits as an indicator of apoptosis. not_specified caspase activation increase http://purl.obolibrary.org/obo/GO_0004197 GO http://purl.obolibrary.org/obo/GO_0006915 GO medium Apoptosis can be assayed by measuring caspase activation. There are a number of commercially available caspase assay kits http://purl.obolibrary.org/obo/GO_0004197 GO http://purl.obolibrary.org/obo/GO_0006915 GO H&E staining Hematoxylin and eosin-stained liver sections are examined by a pathologist for the presence of cytotoxicity. in_vivo liver presence of cytotoxicity not_specified http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low Hematoxylin and eosin (H&E)-stained liver sections can be examined by a pathologist for the presence of cytotoxicity http://purl.obolibrary.org/obo/UBERON_0002107 UBERON LDH leakage assay Lactate dehydrogenase (LDH) leakage is measured using a colorimetric absorbance assay as an indicator of necrotic cell death. in_vivo LDH leakage increase http://purl.obolibrary.org/obo/GO_0004459 GO http://purl.obolibrary.org/obo/GO_0070265 GO medium Lactate dehydrogenase (LDH) leakage. LDH leakage is a measure of necrotic cell death, which can be detected using a colorimetric absorbance assay based on MTT reduction (Chan, et al. 2013) http://purl.obolibrary.org/obo/GO_0070265 GO MTT assay The MTT assay measures cell viability by detecting the conversion of MTT into formazan by viable cells with active metabolism. not_specified cell viability decrease http://purl.obolibrary.org/obo/GO_0008563 GO high In the MTT assay in which viable cells (with active metabolism) convert MTT into a purple compound (formazan), whereas dead cells remain colourless (Riss, et al. 2004) http://purl.obolibrary.org/obo/GO_0005623 GO http://purl.obolibrary.org/obo/GO_0008219 GO MTT assay Assessment of cell viability based on the conversion of MTT into a purple formazan compound by viable cells with active metabolism. in_vitro formazan production decrease medium This assay measures the presence of nicks in the DNA that are identified by terminal deoxynucleotidyl transferase or TdT, an enzyme that catalyzes the addition of dUTPs that are secondarily labeled with a marker; In the MTT assay in which viable cells (with active metabolism) convert MTT into a purple compound (formazan), whereas dead cells remain colourless (Riss, et al. 2004); http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0008219 GO Trypan Blue Exclusion Trypan blue dye is used to stain dead cells, while viable cells remain unstained. not_specified cell viability decrease http://purl.obolibrary.org/obo/GO_0008563 GO high Trypan Blue Exclusion. Trypan blue is a commercially available dye that only stains dead cells Trypan blue assay: non –viable cells take-up trypan blue, whereas viable cells remain colourless (Strober 2015) http://purl.obolibrary.org/obo/GO_0005623 GO http://purl.obolibrary.org/obo/GO_0008219 GO TUNEL assay The TUNEL assay measures DNA fragmentation resulting from apoptotic signaling cascades by detecting nicks in the DNA using terminal deoxynucleotidyl transferase (TdT). not_specified DNA fragmentation increase http://purl.obolibrary.org/obo/GO_0097234 GO http://purl.obolibrary.org/obo/GO_0042981 GO medium The TUNEL assay is commonly used to measure DNA fragmentation that results from apoptotic signaling cascades (Lozano, et al. 2009) This assay measures the presence of nicks in the DNA that are identified by terminal deoxynucleotidyl transferase or TdT, an enzyme that catalyzes the addition of dUTPs that are secondarily labeled with a marker http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0042981 GO BrdU incorporation assay Measures cellular proliferation by quantifying BrdU incorporation into DNA using immunohistochemistry. in_vitro BrdU incorporation increase http://purl.obolibrary.org/obo/GO_0006260 GO medium In vivo or in vitro cellular proliferation can be measured following a multiday 5-bromo-2'-deoxyuridine (BrdU) exposure and quantification of BrdU incorporation in DNA by immunohistochemistry. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0008283 GO Gene expression analysis Gene expression analysis is conducted to demonstrate increased expression of AP-1 or NF-kappaB monomers, or decreased expression of negative regulators. in_vitro liver AP-1 or NF-kappaB mRNA levels increase http://purl.obolibrary.org/obo/GO_0006925 GO medium Gene expression analysis can be conducted to demonstrate increased expression of AP-1 or NF-kappaB monomers, or decreased expression of negative regulators, which can be used as an indicator that there is increased cellular proliferation in the liver. http://purl.obolibrary.org/obo/GO_0006925 GO Gene expression analysis Measures gene expression levels of AP-1, NF-kappaB, or their negative regulators as indicators of cellular proliferation. in_vitro liver gene expression change http://purl.obolibrary.org/obo/GO_0010467 GO high Gene expression analysis can be conducted to demonstrate increased expression of AP-1 or NF-kappaB monomers, or decreased expression of negative regulators, which can be used as an indicator that there is increased cellular proliferation in the liver. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Ki-67 staining Measures cellular proliferation by staining for Ki-67, a marker of cell proliferation. in_vitro Ki-67 expression increase http://purl.obolibrary.org/obo/GO_0008283 GO medium cells or tissue sections may be stained for Ki-67 or proliferating cell nuclear antigen (PCNA) for a snapshot of cellular proliferation. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Partial hepatectomy Measures liver regeneration following surgical removal of a portion of the liver. in_vivo liver liver regeneration increase http://purl.obolibrary.org/obo/GO_0035307 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low Liver regeneration can be observed following partial hepatectomy. Method for 2/3 partial hepatectomy have been described (Mitchell and Willenbring 2008, Mitchell and Willenbring 2014) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0035307 GO PCNA staining Measures cellular proliferation by staining for proliferating cell nuclear antigen (PCNA). in_vitro PCNA expression increase http://purl.obolibrary.org/obo/PR_000001410 PR http://purl.obolibrary.org/obo/GO_0008283 GO medium cells or tissue sections may be stained for Ki-67 or proliferating cell nuclear antigen (PCNA) for a snapshot of cellular proliferation. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO abdominal CT scan Detects liver cancer in humans by imaging the abdomen to identify tumors or abnormalities in the liver. in_vivo liver human presence of liver tumors not_specified http://purl.obolibrary.org/obo/NCIT_C3264 NCIT http://purl.obolibrary.org/obo/NCIT_C3571 NCIT medium In humans, liver cancer is detected by abdominal CT scan followed by biopsy and pathological examination. http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/NCIT_C3571 NCIT abdominal CT scan with histopathological biopsy Detects liver cancer in humans by performing an abdominal CT scan, followed by biopsy and pathological examination of liver tissue. in_vivo liver human presence of liver cancer (detected via imaging and histology) increase low In humans, liver cancer is detected by abdominal CT scan followed by biopsy and pathological examination. biopsy with pathological examination Confirms liver cancer in humans by microscopic examination of tissue samples obtained via biopsy. in_vivo liver human presence of liver cancer not_specified http://purl.obolibrary.org/obo/NCIT_C15188 NCIT http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/NCIT_C3571 NCIT low liver cancer is detected by abdominal CT scan followed by biopsy and pathological examination. http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/NCIT_C3571 NCIT histological examination Measures the presence of hepatocellular adenoma (HCA) and hepatocellular carcinoma (HCC) in animal models via microscopic examination of liver tissue sections. in_vivo liver rat mouse presence of hepatocellular adenoma and hepatocellular carcinoma not_specified http://purl.obolibrary.org/obo/NCIT_C3363 NCIT http://purl.obolibrary.org/obo/NCIT_C3398 NCIT http://purl.obolibrary.org/obo/OBI_0000275 OBI OECD TG 451 low the presence of HCA and HCC are measured histologically following the standard two-year rodent bioassay, which is conducted according to OECD Test Guideline 451 (OECD 2009) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/NCIT_C3398 NCIT microarray analysis Microarray analysis evaluates the expression of several acute phase proteins (APPs) at the same time. in_vitro expression of multiple APPs change high Other techniques for evaluating the expression of several APPs at the same time are microarray analysis and total RNA sequencing (Halappanavar et al., 2011; Nelson et al., 2017). http://purl.obolibrary.org/obo/GO_0010505 GO microarray analysis Microarray analysis evaluates the expression of multiple acute phase proteins simultaneously by measuring the hybridization of labeled RNA to complementary probes on a microarray chip. in_vitro gene expression of multiple acute phase proteins increase http://purl.obolibrary.org/obo/OBI_0000695 OBI high Other techniques for evaluating the expression of several APPs at the same time are microarray analysis and total RNA sequencing (Halappanavar et al., 2011; Nelson et al., 2017). http://purl.obolibrary.org/obo/GO_0006351 GO PCR Quantitative Polymerase Chain Reaction (PCR) amplifies selected fragments of DNA or cDNA using primers and fluorescent probes to quantify gene expression. Reverse transcriptase PCR is used to quantify RNA by first synthesizing cDNA. in_vitro lung liver mouse human gene expression levels increase medium Gene expression of acute phase proteins (APPs) can be measured from tissue samples using quantitative Polymerase Chain Reaction (PCR). To evaluate this key event in mice, gene expression of Saa3 can be quantified in lung tissue and Saa1 gene in liver tissue after exposure to a stressor (Halappanavar et al., 2011; Poulsen et al., 2017; Saber et al., 2014). In humans, it is not common to measure gene expression as a tissue sample is required, however gene expression of crp, saa1, saa2 and saa4 can be measured from samples taken during surgery (Calero et al., 2014). http://purl.obolibrary.org/obo/GO_0010505 GO qPCR Quantitative Polymerase Chain Reaction (qPCR) measures gene expression by amplifying selected DNA or cDNA fragments using primers and fluorescent probes to quantify the targeted DNA. in_vitro gene expression of acute phase proteins increase http://purl.obolibrary.org/obo/GO_0010467 GO medium Gene expression of acute phase proteins (APPs) can be measured from tissue samples using quantitative Polymerase Chain Reaction (PCR). The use of fluorescent probes to quantify the expression the targeted DNA, as the binding of the probe to this DNA emits a fluorescent signal. http://purl.obolibrary.org/obo/GO_0006351 GO qPCR (human surgical samples) Quantitative PCR measures the gene expression of crp, saa1, saa2, and saa4 in human tissue samples obtained during surgery. in_vitro Homo sapiens crp, saa1, saa2, and saa4 gene expression increase http://purl.obolibrary.org/obo/GO_0010467 GO medium In humans, it is not common to measure gene expression as a tissue sample is required, however gene expression of crp, saa1, saa2 and saa4 can be measured from samples taken during surgery (Calero et al., 2014). http://purl.obolibrary.org/obo/GO_0006351 GO RNA sequencing Total RNA sequencing evaluates the expression of several acute phase proteins (APPs) at the same time. in_vitro expression of multiple APPs change high Other techniques for evaluating the expression of several APPs at the same time are microarray analysis and total RNA sequencing (Halappanavar et al., 2011; Nelson et al., 2017). http://purl.obolibrary.org/obo/GO_0010505 GO RNA sequencing Total RNA sequencing measures the expression of multiple acute phase proteins by sequencing all RNA molecules in a sample to quantify transcript levels. in_vitro gene expression of multiple acute phase proteins increase http://purl.obolibrary.org/obo/OBI_0001271 OBI high Other techniques for evaluating the expression of several APPs at the same time are microarray analysis and total RNA sequencing (Halappanavar et al., 2011; Nelson et al., 2017). http://purl.obolibrary.org/obo/GO_0006351 GO ELISA Measures serum amyloid A (SAA) isoforms in mice using enzyme-linked immunosorbent assay, where proteins are adsorbed to a surface and detected via antibody-enzyme colorimetric reaction. in_vitro blood plasma serum Mus musculus serum amyloid A (SAA) concentration not_specified http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/UBERON_0001968 UBERON medium serum amyloid A (SAA) isoforms are measured using enzyme-linked immunosorbent assay (ELISA) assays ELISA assays allows the measurement of proteins in a sample by adsorbing the desired proteins (antigens) to an inert surface. Using antibodies specific to the protein and an enzyme that catalyzes the reaction, a colorimetric signal is produced and measured http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006953 GO Immunoassay Measures C-reactive protein (CRP) and serum amyloid A (SAA) in humans using immunoassays that detect single or multiple proteins. in_vitro blood plasma serum Homo sapiens C-reactive protein (CRP) and serum amyloid A (SAA) concentration not_specified http://purl.obolibrary.org/obo/PR_000001182 PR http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/UBERON_0001968 UBERON medium In humans, most often C-reactive protein (CRP) and SAA are measured. These proteins are measured by immunoassays detecting single or multiple proteins http://purl.obolibrary.org/obo/PR_000001182 PR http://purl.obolibrary.org/obo/GO_0006953 GO Nephelometric assay Measures C-reactive protein (CRP) in humans by mixing blood samples with CRP antibody-coated latex beads, forming complexes that scatter light proportional to CRP concentration. in_vitro blood plasma serum Homo sapiens C-reactive protein (CRP) concentration not_specified http://purl.obolibrary.org/obo/PR_000001182 PR http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/UBERON_0001968 UBERON high CRP is measured by nephelometric assays a blood sample (serum or plasma) is mixed with a suspension of latex beads coated with CRP antibodies. When CRP binds to the beads, a complex is formed that produces the scattering of light. The amount of light scattered is proportional to the amount of complexes formed. While in nephelometry the amount of light scaterred is measure, in turbidimetry the amount of light that passes through the suspension is measured http://purl.obolibrary.org/obo/PR_000001182 PR http://purl.obolibrary.org/obo/GO_0006953 GO Turbidimetric assay Measures C-reactive protein (CRP) in humans by mixing blood samples with CRP antibody-coated latex beads, forming complexes that scatter light proportional to CRP concentration. in_vitro blood plasma serum Homo sapiens C-reactive protein (CRP) concentration not_specified http://purl.obolibrary.org/obo/PR_000001182 PR http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/UBERON_0001968 UBERON high CRP is measured by turbidimetric assays a blood sample (serum or plasma) is mixed with a suspension of latex beads coated with CRP antibodies. When CRP binds to the beads, a complex is formed that produces the scattering of light. The amount of light scattered is proportional to the amount of complexes formed. While in nephelometry the amount of light scaterred is measure, in turbidimetry the amount of light that passes through the suspension is measured http://purl.obolibrary.org/obo/PR_000001182 PR http://purl.obolibrary.org/obo/GO_0006953 GO Western blot Measures serum amyloid A (SAA) isoforms in mice by separating proteins via gel electrophoresis, transferring to a membrane, and detecting with antibodies to produce a colored precipitate. in_vitro blood plasma serum Mus musculus serum amyloid A (SAA) concentration not_specified http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/UBERON_0001968 UBERON low serum amyloid A (SAA) isoforms are measured using enzyme-linked immunosorbent assay (ELISA) assays or Western blot In the case of Western blot, also called immunoblot assay, proteins in a sample are first separated by gel electrophoresis. Following, the proteins are transferred to a membrane and treated with antibodies, obtaining a coloured precipitate along the band of the desired protein http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006953 GO adhesion molecule expression assay Measures the expression of adhesion molecules in vitro, which is relevant to the development of atherosclerosis. in_vitro expression of adhesion molecules not_specified not_specified expression of adhesion molecules angiography A clinical technique used to evaluate atherosclerosis without direct visualization of plaques. in_vivo arteries Homo sapiens arterial blockage or narrowing not_specified medium angiography angiography Technique to evaluate atherosclerosis without direct visualization of plaques. in_vivo arteries human atherosclerosis change low Techniques that allow the evaluation of atherosclerosis without direct visualization of plaques include angiography http://purl.obolibrary.org/obo/UBERON_0001203 UBERON ankle-arm systolic blood pressure index A clinical technique used to evaluate atherosclerosis by comparing blood pressure in the arms and ankles. in_vivo arteries Homo sapiens blood pressure ratio not_specified high ankle-arm systolic blood pressure index aortic pulse wave velocity measurement Technique for evaluation of atherosclerosis without direct visualization of plaques. in_vivo aorta pulse wave velocity increase medium Techniques that allow the evaluation of atherosclerosis without direct visualization of plaques include aortic pulse wave velocity http://purl.obolibrary.org/obo/UBERON_0000937 UBERON ApoE-/- mouse model An in vivo model using ApoE-deficient mice to study the induction and progression of atherosclerosis. in_vivo arteries Mus musculus atherosclerotic plaque development not_specified low ApoE-/- mouse models atherosclerosis assessment Assessment of atherosclerosis development in ApoE-/- and LdLr-/- mouse models and Watanabe rabbit model. in_vivo artery mouse rabbit atherosclerotic plaque development increase low the development of atherosclerotic can be assessed (Gistera, Ketelhuth, Malin, & Hansson, 2022). http://purl.obolibrary.org/obo/UBERON_0000936 UBERON http://www.ebi.ac.uk/efo/EFO_0001834 EFO C-reactive protein measurement Measures blood levels of C-reactive protein, a nonspecific inflammatory marker used to evaluate atherosclerosis. in_vivo blood Homo sapiens C-reactive protein blood levels not_specified high C-reactive protein computed tomography angiography A clinical imaging technique used to visualize atherosclerotic plaques and detect calcified components in arteries. in_vivo arteries Homo sapiens plaque visualization and calcification detection not_specified medium computed tomography angiography foam cell formation assay Evaluates the formation of foam cells in vitro, a critical step in atherosclerosis development. in_vitro foam cell formation not_specified not_specified foam cell formation IL-6 blood level measurement Measures blood levels of interleukin 6 (IL-6), a nonspecific inflammatory marker used to evaluate atherosclerosis. in_vivo blood Homo sapiens IL-6 blood levels not_specified high blood levels of interleukin 6 (IL-6) inflammatory marker quantification Measurement of nonspecific inflammatory markers in the blood, such as IL-6, CRP, and TNF-α. in_vivo blood human blood levels of IL-6, C-reactive protein and tumor necrosis factor α (TNF-α) increase http://purl.obolibrary.org/obo/CHEBI_35503 CHEBI http://purl.obolibrary.org/obo/CHEBI_35512 CHEBI not_specified Finally, nonspecific, inflammatory markers are also used to evaluate atherosclerosis. These include blood levels of interleukin 6 (IL-6), C-reactive protein and tumor necrosis factor α (TNF-α) http://purl.obolibrary.org/obo/GO_0006954 GO magnetic resonance imaging A clinical imaging technique used to visualize atherosclerotic plaques in arteries. in_vivo arteries Homo sapiens plaque visualization not_specified medium magnetic resonance imaging monocyte adhesion assay Evaluates the adhesion of monocytes to endothelial cells in vitro, a key step in atherosclerosis development. in_vitro endothelial cells monocytes monocyte adhesion to endothelial cells not_specified not_specified adhesion of monocytes to endothelial cells monocytes migration Assesses the migratory capacity of monocytes, typically using a transwell assay toward chemokine gradients. in_vitro migrated monocyte count increase not_specified monocytes migration http://purl.obolibrary.org/obo/GO_0016477 GO optical coherence tomography A clinical imaging technique used to visualize atherosclerotic plaques and measure intima thickness in arteries. in_vivo arteries Homo sapiens intima thickness and plaque visualization not_specified medium optical coherence tomography TNF-α blood level measurement Measures blood levels of tumor necrosis factor α (TNF-α), a nonspecific inflammatory marker used to evaluate atherosclerosis. in_vivo blood Homo sapiens TNF-α blood levels not_specified high tumor necrosis factor α (TNF-α) ultrasonography A clinical imaging technique used to visualize atherosclerotic plaques and measure intima thickness in arteries. in_vivo arteries Homo sapiens intima thickness and plaque visualization not_specified medium ultrasonography Vascular Imaging Direct visualization of atherosclerotic plaques using imaging techniques to measure intima thickness and calcification. in_vivo arteries Homo sapiens intima thickness of arteries, detection of calcified components increase http://purl.obolibrary.org/obo/GO_0043547 GO low Techniques that allow direct visualization of atherosclerotic plaques include ultrasonography, computed tomography angiography, magnetic resonance imaging, and optical coherence tomography These techniques can measure the intima thickness of arteries, along with detection of calcified components http://purl.obolibrary.org/obo/UBERON_0001018 UBERON http://purl.obolibrary.org/obo/DOID_10111 DOID Watanabe rabbit model An in vivo model using Watanabe heritable hyperlipidemic rabbits to study the development of atherosclerosis. in_vivo arteries Oryctolagus cuniculus atherosclerotic plaque development not_specified low Watanabe rabbit model 4-HNE assay Measures 4-hydroxy-2-nonenal and related reactive aldehydes using ELISA, immunoblotting, HPLC, or LC-MS. in_vitro 4-HNE or HNE-protein adducts increase http://purl.obolibrary.org/obo/CHEBI_27431 CHEBI medium ELISA, immunoblotting of HNE-protein adducts, HPLC or LC-MS quantification http://purl.obolibrary.org/obo/CHEBI_18423 CHEBI http://purl.obolibrary.org/obo/GO_0046491 GO BODIPY 581/591 C11 fluorescence assay Uses the oxidation-sensitive fluorescent probe BODIPY 581/591 C11 to detect lipid oxidation in cellular lipids, enabling spatial localization of peroxidation signals. not_specified oxidation-sensitive fluorescent signal increase not_specified Fluorescent probes and imaging Oxidation-sensitive fluorescent signal in cellular lipids BODIPY 581/591 C11 and related lipid oxidation probes Useful for cell-based or imaging applications and spatial localization, but probe specificity, photoxidation and calibration must be considered. Best used with complementary biochemical or analytical endpoints. http://purl.obolibrary.org/obo/GO_0016168 GO Chromatography and mass spectrometry Quantifies specific oxidized fatty acids, oxidized phospholipids, or oxidized lipid classes using HPLC, GC, or LC-MS/MS. in_vitro specific oxidized lipid species increase http://purl.obolibrary.org/obo/OBI_0001868 OBI low HPLC, GC, LC-MS/MS, lipidomics http://purl.obolibrary.org/obo/CHEBI_18423 CHEBI http://purl.obolibrary.org/obo/GO_0046491 GO Fluorescent probes and imaging Detects oxidation-sensitive fluorescent signal in cellular lipids using probes like BODIPY 581/591 C11. in_vitro oxidation-sensitive fluorescent signal increase http://purl.obolibrary.org/obo/GO_0034440 GO medium BODIPY 581/591 C11 and related lipid oxidation probes http://purl.obolibrary.org/obo/CHEBI_18423 CHEBI http://purl.obolibrary.org/obo/GO_0046491 GO LC-MS lipidomics Quantifies specific oxidized fatty acids, oxidized phospholipids, oxylipins or oxidized lipid classes using chromatography and mass spectrometry. in_vitro oxidized lipid species concentration increase http://purl.obolibrary.org/obo/GO_0042542 GO low Chromatography and mass spectrometry Specific oxidized fatty acids, oxidized phospholipids, oxylipins or oxidized lipid classes HPLC, GC, LC-MS/MS, lipidomics http://purl.obolibrary.org/obo/GO_0042542 GO Lipid hydroperoxide assay Detects primary lipid hydroperoxides using FOX assay, iodometric assays, or commercial kits. in_vitro lipid hydroperoxides increase http://purl.obolibrary.org/obo/CHEBI_25203 CHEBI medium FOX assay; iodometric assays; commercial lipid hydroperoxide kits http://purl.obolibrary.org/obo/CHEBI_18423 CHEBI http://purl.obolibrary.org/obo/GO_0046491 GO TBARS assay Measures thiobarbituric acid reactive substances, often interpreted as MDA or MDA-like products using spectrophotometric or fluorometric methods. in_vitro MDA or MDA-like products increase http://purl.obolibrary.org/obo/CHEBI_15354 CHEBI high TBARS assay; spectrophotometric or fluorometric MDA assays http://purl.obolibrary.org/obo/CHEBI_18423 CHEBI http://purl.obolibrary.org/obo/GO_0046491 GO TBARS assay This assay measures thiobarbituric acid reactive substances, often interpreted as MDA or MDA-like products, using spectrophotometric or fluorometric methods. in_vitro thiobarbituric acid reactive substances (TBARS) increase http://purl.obolibrary.org/obo/CHEBI_16644 CHEBI medium TBARS / MDA assays Thiobarbituric acid reactive substances, often interpreted as MDA or MDA-like products TBARS assay; spectrophotometric or fluorometric MDA assays http://purl.obolibrary.org/obo/GO_0032787 GO APR_HepG2_MitoMembPot High-throughput screening bioassay to determine mitochondrial membrane potential in HepG2 cells. in_vitro HepG2 mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0001836 GO high Mitochondrial membrane potential can be determined using ToxCast high-throughput screening bioassays such as “APR_HepG2_MitoMembPot” http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0001836 GO APR_Mitochondrial_membrane_potential High-throughput screening bioassay to determine mitochondrial membrane potential. in_vitro mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0001836 GO high Mitochondrial membrane potential can be determined using ToxCast high-throughput screening bioassays such as “APR_Mitochondrial_membrane_potential” http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0001836 GO high-resolution respirometry Measures proton leak and oxygen consumption rate in mitochondria. in_vitro proton leak and oxygen consumption rate increase http://purl.obolibrary.org/obo/GO_0006098 GO http://purl.obolibrary.org/obo/GO_0006850 GO medium Proton leak and oxygen consumption rate can be measured using a high-resolution respirometry (Affourtit 2018) http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006850 GO JC-1 Fluorescent probe-based assay measuring mitochondrial membrane potential using JC-1 dye. in_vitro mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0005744 GO not_specified JC-1 (Perry 2011) http://purl.obolibrary.org/obo/GO_0005744 GO http://purl.obolibrary.org/obo/GO_0006121 GO Seahorse XF analyzer Measures proton leak and oxygen consumption rate in mitochondria. in_vitro proton leak and oxygen consumption rate increase http://purl.obolibrary.org/obo/GO_0006098 GO http://purl.obolibrary.org/obo/GO_0006850 GO medium Proton leak and oxygen consumption rate can be measured using a Seahorse XF analyzer (Divakaruni 2014). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006850 GO TMRM assay A fluorescent probe-based assay that measures mitochondrial membrane potential using TMRM dye. in_vitro mitochondria Homo sapiens mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0031966 GO medium Mitochondrial membrane potential can also be measured using commercially available fluorescent probes such as TMRM (tetramethylrhodamine, methyl ester, perchlorate), TMRE (tetramethylrhodamine, ethyl ester, perchlorate) and JC-1 (Perry 2011). http://purl.obolibrary.org/obo/GO_0031966 GO http://purl.obolibrary.org/obo/GO_0006139 GO TMRM/TMRE/JC-1 fluorescent probes Fluorescent probes used to measure mitochondrial membrane potential. in_vitro mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0001836 GO http://purl.obolibrary.org/obo/CHMO_0000620 CHMO medium Mitochondrial membrane potential can also be measured using commercially available fluorescent probes such as TMRM (tetramethylrhodamine, methyl ester, perchlorate), TMRE (tetramethylrhodamine, ethyl ester, perchlorate) and JC-1 (Perry 2011). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0001836 GO tox21-mitotox-p1 High-throughput screening assay to determine mitochondrial membrane potential. in_vitro mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0001836 GO high the Tox21 high-throughput screening assay “tox21-mitotox-p1” http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0001836 GO ToxCast/Tox21 mitochondrial membrane potential HTS assay High-throughput screening bioassays that quantify mitochondrial membrane potential to detect uncoupling of oxidative phosphorylation. in_vitro HepG2 Hepatocytes mitochondrial membrane potential decrease high Mitochondrial membrane potential can be determined using ToxCast high-throughput screening bioassays such as “APR_HepG2_MitoMembPot”, “APR_Hepat_MitoFxnI”, and “APR_Mitochondrial_membrane_potential”, and the Tox21 high-throughput screening assay “tox21-mitotox-p1”. cell viability assay Assay to measure the viability of cells, often used to assess the impact of treatments or conditions on cell survival. in_vitro human cell line human cell viability change http://purl.obolibrary.org/obo/GO_0008544 GO high cell viability assay EdU incorporation assay Assay to measure cell proliferation by detecting the incorporation of EdU, a thymidine analog, into newly synthesized DNA. in_vitro human cell line human cell proliferation change http://purl.obolibrary.org/obo/GO_0008283 GO medium EdU incorporation assay EdU incorporation assay An assay used to measure cell proliferation by detecting the incorporation of EdU into DNA. in_vitro Human cell line Human DNA synthesis not_specified http://purl.obolibrary.org/obo/GO_0006262 GO not_specified EdU incorporation assay IHC Immunohistochemistry to detect the presence and localization of specific proteins, such as pro-SPC and N-cadherin, in tissue sections. in_vivo lung human protein expression and localization increase http://purl.obolibrary.org/obo/OBI_0000617 OBI http://purl.obolibrary.org/obo/PR_000000591 PR low EMT can be detected by immunostaining with pro-surfactant protein-C (pro-SPC) and N-cadherin in idiopathic pulmonary fibrosis (IPF) lung in vivo (Kim et al., 2006). http://purl.obolibrary.org/obo/PR_000000591 PR http://purl.obolibrary.org/obo/GO_0001837 GO Immunostaining Detects EMT by staining cells with antibodies against pro-SPC, N-cadherin, and vimentin to visualize protein localization and expression. in_vivo Idiopathic pulmonary fibrosis lung tissue Lung alveola Human Protein expression and localization of pro-SPC, N-cadherin, vimentin increase http://purl.obolibrary.org/obo/CL_0000451 CL http://purl.obolibrary.org/obo/CL_0000067 CL http://purl.obolibrary.org/obo/CL_0000236 CL low EMT can be detected by immunostaining with pro-surfactant protein-C (pro-SPC) and N-cadherin in idiopathic pulmonary fibrosis (IPF) lung EMT can be detected by immunostaining with vimentin in lung alveola http://purl.obolibrary.org/obo/OBI_0000331 OBI http://purl.obolibrary.org/obo/GO_0001837 GO microarray High-throughput technique to measure the expression levels of thousands of genes simultaneously. in_vitro human cell line human gene expression levels change http://purl.obolibrary.org/obo/OBI_0000366 OBI high micro array qRT-PCR Quantitative reverse transcription polymerase chain reaction to measure gene expression levels, including epithelial and mesenchymal markers. in_vitro human cell line human gene expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/PR_000001190 PR http://purl.obolibrary.org/obo/PR_000000591 PR http://purl.obolibrary.org/obo/PR_000001049 PR medium qRT-PCR http://purl.obolibrary.org/obo/PR_000001190 PR http://purl.obolibrary.org/obo/GO_0001837 GO qRT-PCR Quantitative reverse transcription PCR to measure mRNA levels of EMT markers. in_vitro Human airway epithelial cell line Airway epithelium Human mRNA expression levels of E-cadherin, N-cadherin, vimentin, ZEB, Twist, Snail change http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/CL_0000067 CL http://purl.obolibrary.org/obo/CL_0000236 CL http://purl.obolibrary.org/obo/GO_0032502 GO medium qRT-PCR,cell viability assay,Western blotting,EdU incorporation assay http://purl.obolibrary.org/obo/OBI_0100096 OBI http://purl.obolibrary.org/obo/GO_0001837 GO SNP array Technique to detect single nucleotide polymorphisms (SNPs) across the genome. in_vitro human cell line human SNP detection not_specified http://purl.obolibrary.org/obo/SO_0001483 SO high SNP array Western blotting Technique to detect and quantify specific proteins, such as epithelial and mesenchymal markers, using antibodies. in_vitro human cell line human protein expression levels change http://purl.obolibrary.org/obo/GO_0010483 GO http://purl.obolibrary.org/obo/PR_000001190 PR http://purl.obolibrary.org/obo/PR_000000591 PR http://purl.obolibrary.org/obo/PR_000001049 PR low Western blotting http://purl.obolibrary.org/obo/PR_000001190 PR http://purl.obolibrary.org/obo/GO_0001837 GO Western blotting Detects protein expression levels of EMT markers by separating proteins via SDS-PAGE and probing with specific antibodies. in_vitro Human airway epithelial cell line Airway epithelium Human Protein levels of E-cadherin, N-cadherin, vimentin, ZEB, Twist, Snail change http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/CL_0000067 CL http://purl.obolibrary.org/obo/CL_0000236 CL http://purl.obolibrary.org/obo/GO_0032502 GO medium qRT-PCR,cell viability assay,Western blotting,EdU incorporation assay http://purl.obolibrary.org/obo/OBI_0000331 OBI http://purl.obolibrary.org/obo/GO_0001837 GO ELISA Quantifies protein levels of collagen, TGF-β1, and pro-inflammatory mediators as markers of fibrogenesis. in_vitro protein concentration increase http://purl.obolibrary.org/obo/PR_000002019 PR high Real-time reverse transcription-polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assays (ELISA) measuring increased collagen, Transforming growth factor beta 1 (TGF-β1) and various pro-inflammatory mediators are used as sensitive markers of potential of substances to induce the adverse outcome of lung fibrosis. http://purl.obolibrary.org/obo/PR_000002019 PR ELISA Enzyme-linked immunosorbent assays (ELISA) are used to measure increased levels of collagen, Transforming growth factor beta 1 (TGF-β1) and various pro-inflammatory mediators. in_vitro protein levels of collagen, TGF-β1, and pro-inflammatory mediators increase http://purl.obolibrary.org/obo/CHEBI_5973 CHEBI http://purl.obolibrary.org/obo/GO_0008273 GO http://purl.obolibrary.org/obo/GO_0006954 GO medium Real-time reverse transcription-polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assays (ELISA) measuring increased collagen, Transforming growth factor beta 1 (TGF-β1) and various pro-inflammatory mediators are used as sensitive markers of potential of substances to induce the adverse outcome of lung fibrosis. http://purl.obolibrary.org/obo/CHEBI_59038 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO histopathological analysis Assesses fibrotic lung disease by morphometric analysis of diseased area versus total lung area using a numerical scale (Ashcroft score). in_vivo lung human animal fibrotic tissue area increase http://purl.obolibrary.org/obo/UBERON_0002048 UBERON low histopathological analysis is used for assessing fibrotic lung disease. Morphometric analysis of the diseased area versus total lung area is used to quantitatively stage the fibrotic disease. a numerical scale with grades from 0 to 8, originally developed by Ashcroft et al., 1988 is assigned to indicate the amount of fibrotic tissue in histological samples. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0007155 GO histopathological analysis with Ashcroft scoring Histopathological analysis of formalin-fixed, paraffin-embedded lung tissue sections is used to assess fibrotic lung disease. The amount of fibrotic tissue is staged using a numerical scale from 0 to 8 originally developed by Ashcroft et al., 1988, with modifications proposed by Hubner et al., 2008, applied to grade fibrosis in both human and animal samples. in_vivo lung human rat fibrotic tissue area in lung histological samples increase http://www.ebi.ac.uk/efo/EFO_0000413 EFO http://www.ebi.ac.uk/efo/EFO_0002765 EFO http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI low In vivo, histopathological analysis is used for assessing fibrotic lung disease. Morphometric analysis of the diseased area versus total lung area is used to quantitatively stage the fibrotic disease. a numerical scale with grades from 0 to 8, originally developed by Ashcroft et al., 1988 is assigned to indicate the amount of fibrotic tissue in histological samples. This scale is applied to diagnose lung fibrosis in both human and animal samples. Modifications to this scoring system were proposed (Hubner et al., 2008), which enables morphological distinctions thus enabling a better grading of the disease. bleomycin induced lung fibrosis in rats was scored as follows: Grade 0 – normal lung, Grade 1 – isolated alveolar septa with gentle fibrotic changes, Grade 2 – knot like formation in fibrotic areas in alveolar septa, Grade 3 – contiguous fibrotic walls of alveolar septa, Grade 4 – single fibrotic masses, Grade 5 – confluent fibrotic masses, Grade 6 – large contiguous fibrotic masses, Grade 7 – air bubbles and Grade 8 – fibrotic obliteration. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO ImageJ quantification Formalin-fixed, paraffin-embedded lung cross-sections are imaged using a wide field light microscope. ImageJ software is used to trace and quantify the total and diseased areas, calculating the diseased area as a proportion of the total area. in_vivo lung diseased area / total area increase medium Lungs are formalin fixed and paraffin embedded such that an entire cross section of lung can be presented on a slide. ImageJ software (freely available) is used to trace the total area (green line) and the diseased area (red line) imaged and quantified. The diseased area is equal to disease area/total area (Nikota et al., 2017). http://purl.obolibrary.org/obo/UBERON_0000956 UBERON http://purl.obolibrary.org/obo/GO_0001935 GO morphometric analysis Quantifies the total disease area in lung sections using ImageJ software to trace diseased and total areas. in_vivo lung diseased area ratio increase http://purl.obolibrary.org/obo/UBERON_0002048 UBERON medium ImageJ software (freely available) is used to trace the total area (green line) and the diseased area (red line) imaged and quantified. The diseased area is equal to disease area/total area (Nikota et al., 2017). http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0007155 GO qRT-PCR Measures gene expression levels of collagen, TGF-β1, and pro-inflammatory mediators as markers of fibrogenesis. in_vitro gene expression increase http://purl.obolibrary.org/obo/OBI_0000662 OBI http://purl.obolibrary.org/obo/CHEBI_35303 CHEBI http://purl.obolibrary.org/obo/PR_000002019 PR high Real-time reverse transcription-polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assays (ELISA) measuring increased collagen, Transforming growth factor beta 1 (TGF-β1) and various pro-inflammatory mediators are used as sensitive markers of potential of substances to induce the adverse outcome of lung fibrosis. http://purl.obolibrary.org/obo/CHEBI_35303 CHEBI qRT-PCR Real-time reverse transcription-polymerase chain reaction (qRT-PCR) is used to measure increased levels of collagen and Transforming growth factor beta 1 (TGF-β1). in_vitro mRNA levels of collagen and TGF-β1 increase http://purl.obolibrary.org/obo/GO_0006024 GO http://purl.obolibrary.org/obo/GO_0008273 GO medium Real-time reverse transcription-polymerase chain reaction (qRT-PCR) and enzyme-linked immunosorbent assays (ELISA) measuring increased collagen, Transforming growth factor beta 1 (TGF-β1) and various pro-inflammatory mediators are used as sensitive markers of potential of substances to induce the adverse outcome of lung fibrosis. http://purl.obolibrary.org/obo/CHEBI_5973 CHEBI http://purl.obolibrary.org/obo/GO_0007283 GO Comet assay Measures DNA damage in individual mammalian cells embedded in agarose, subjected to electrophoresis, and stained with a DNA-binding dye, allowing assessment of heterogeneity in DNA damage. in_vitro mammalian cells mammalian DNA damage increase http://purl.obolibrary.org/obo/GO_0006974 GO http://purl.obolibrary.org/obo/OBI_0000869 OBI medium Microscopic examination of individual mammalian cells embedded in agarose, subjected to electrophoresis, and stained with a DNA-binding dye provides a way of measuring DNA damage and of assessing heterogeinicity in DNA damage within a mixed cell population. (Olive P. et al. 1991). http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO DNA DSB staining (γ-H2AX foci) Detection and quantification of γ-H2AX foci, which result from the phosphorylation of histone H2AX at serine 139 at DNA double-strand break sites. in_vitro mammalian phosphorylation of histone H2AX at serine 139 increase http://purl.obolibrary.org/obo/GO_0008454 GO not_specified DNA DSB staining based on the phosphorylation of the histone H2A.X at serine 139 in response to DNA damaging agents which cause double strand breaks in cells that are cultured in microtiter plates is a rapid metod for the identification and quantification of the damage (Sealunavov et al.2002). http://purl.obolibrary.org/obo/GO_0008454 GO electrophoresis with DNA dye This assay measures DNA damage by microscopic examination of individual mammalian cells embedded in agarose, subjected to electrophoresis, and stained with a DNA-binding dye. in_vitro mammalian cells DNA damage increase http://purl.obolibrary.org/obo/GO_0000271 GO low Microscopic examination of individual mammalian cells embedded in agarose, subjected to electrophoresis, and stained with a DNA-binding dye provides a way of measuring DNA damage and of assessing heterogeinicity in DNA damage within a mixed cell population. (Olive P. et al. 1991). http://purl.obolibrary.org/obo/CHEBI_7337 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Pulsed Field Gel Electrophoresis (PFGE) Measures DNA double-strand breaks in mammalian cells by size-fractionating DNA in a pulsed-field gel and quantifying the fraction of DNA below a defined size. in_vitro mammalian cells mammalian DNA double-strand breaks increase http://purl.obolibrary.org/obo/GO_0000305 GO http://purl.obolibrary.org/obo/OBI_0000355 OBI low Pulsed field gel electrophoresis (PFGE) is the main method used for measurement of DNA DSB in mammalian cells (Blocker D et al. 1989 and 1990, Stamato T et al 1990, Ager D et al 1990). Alternatively the DNA is size fractioned in the pulsed-field gel, and the weight fraction of DNA below a certain defined size is measured (Erixo K. et al. 1990, Stenelow B. et al. 1995). http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI http://purl.obolibrary.org/obo/GO_0006303 GO Pulsed Field Gel Electrophoresis (PFGE) PFGE is used to measure DNA double-strand breaks in mammalian cells by analyzing DNA fragment size distribution. Alternatively, the weight fraction of DNA below a certain size is measured. in_vitro mammalian cells DNA fragment size decrease http://purl.obolibrary.org/obo/GO_0000271 GO medium Pulsed field gel electrophoresis (PFGE) is the main method used for measurement of DNA DSB in mammalian cells (Blocker D et al. 1989 and 1990, Stamato T et al 1990, Ager D et al 1990). Alternatively the DNA is size fractioned in the pulsed-field gel, and the weight fraction of DNA below a certain defined size is measured (Erixo K. et al. 1990, Stenelow B. et al. 1995). http://purl.obolibrary.org/obo/CHEBI_7337 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Topoisomerase II assay In vitro assays measure topoisomerase II activity based on the decantation of double-strand DNA. in_vitro double-strand DNA decantation increase http://purl.obolibrary.org/obo/GO_0000271 GO not_specified In vitro assays for topoisomerase II based on the decantation of double strand DNA are extensively reported in Nitiss et al. 2012. http://purl.obolibrary.org/obo/CHEBI_7337 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO Topoisomerase II decantation assay Measures topoisomerase II activity in vitro based on the decantation of double-strand DNA. in_vitro topoisomerase II activity change http://purl.obolibrary.org/obo/GO_0003918 GO http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI medium In vitro assays for topoisomerase II based on the decantation of double strand DNA are extensively reported in Nitiss et al. 2012. http://purl.obolibrary.org/obo/PR_000001719 PR http://purl.obolibrary.org/obo/GO_0006265 GO γ-H2AX foci assay Measures the phosphorylation of histone H2AX at serine 139, forming γ-H2AX foci, as a marker of DNA double-strand breaks (DSBs) in mammalian cells. in_vitro mammalian cells mammalian γ-H2AX foci formation increase http://purl.obolibrary.org/obo/GO_0000305 GO medium DNA DSB staining based on the phosphorylation of the histone H2A.X at serine 139 in response to DNA damaging agents which cause double strand breaks in cells that are cultured in microtiter plates is a rapid metod for the identification and quantification of the damage (Sealunavov et al.2002). http://purl.obolibrary.org/obo/PR_000007893 PR http://purl.obolibrary.org/obo/GO_0006303 GO 31P NMR spectroscopy A non-destructive nuclear magnetic resonance technique that quantifies intracellular phosphorus metabolites, including ATP, ADP, and other high-energy phosphates, to assess cellular energy status. in_vitro intracellular ATP levels decrease http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0006793 GO low ATP and other high-energy phosphates can also be quantified using ^31P nuclear magnetic resonance (NMR) spectroscopy, which allows non-destructive measurement of intracellular phosphorus metabolites and energy status (Hitchins et al., 2001). http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0006793 GO ^31P NMR spectroscopy Quantifies ATP and other high-energy phosphates non-destructively by measuring intracellular phosphorus metabolites and energy status. in_vitro intracellular phosphorus metabolites decrease low ATP and other high-energy phosphates can also be quantified using ^31P nuclear magnetic resonance (NMR) spectroscopy, which allows non-destructive measurement of intracellular phosphorus metabolites and energy status (Hitchins et al., 2001). http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI Enzymatic ATP synthase activity assay Assesses the functional capacity of the mitochondrial phosphorylation machinery by measuring ATP synthase activity. in_vitro ATP synthase activity decrease medium Enzymatic assays targeting ATP synthase activity provide complementary information on the functional capacity of the mitochondrial phosphorylation machinery and have been applied to link electron transport efficiency with ATP synthesis rates (Allakhverdiev et al., 2005; Coulson et al., 2024). http://purl.obolibrary.org/obo/GO_0045261 GO http://purl.obolibrary.org/obo/GO_0042775 GO HPLC High-performance liquid chromatography (HPLC) methods enable sensitive and accurate separation and quantification of adenosine phosphates (ATP, ADP, AMP) in cell extracts, providing detailed information on cellular energy balance. in_vitro adenosine phosphates (ATP, ADP, AMP) decrease medium In addition, high-performance liquid chromatography (HPLC) methods enable sensitive and accurate separation and quantification of adenosine phosphates (ATP, ADP, AMP) in cell extracts, providing detailed information on cellular energy balance (Juarez-Facio et al., 2021) http://purl.obolibrary.org/obo/GO_0006020 GO HPLC for adenosine phosphates Separates and quantifies adenosine phosphates (ATP, ADP, AMP) in cell extracts to provide detailed information on cellular energy balance. in_vitro adenosine phosphate levels decrease http://purl.obolibrary.org/obo/OBI_0000215 OBI medium high-performance liquid chromatography (HPLC) methods enable sensitive and accurate separation and quantification of adenosine phosphates (ATP, ADP, AMP) in cell extracts, providing detailed information on cellular energy balance (Juarez-Facio et al., 2021). http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI Luciferase-based ATP assay Measures cellular ATP levels by quantifying light emitted during the luciferase-luciferin reaction, which is proportional to ATP content. in_vitro ATP concentration decrease high Luciferase-based ATP assays are widely used to directly measure ATP concentrations, relying on the light emitted during the luciferase–luciferin reaction, which is proportional to ATP content (Lundin et al., 1976). http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0006754 GO Infrared gas analysis (IRGA) Measures net CO₂ uptake non-invasively, allowing continuous monitoring of photosynthetic performance under controlled environmental conditions. in_vivo leaf net CO₂ uptake decrease http://purl.obolibrary.org/obo/GO_0015979 GO high At the whole-organism or leaf level, infrared gas analysis (IRGA) is commonly employed to measure net CO₂ uptake. This non-invasive technique allows continuous monitoring of photosynthetic performance under controlled environmental conditions and integrates stomatal conductance, biochemical capacity, and photochemical efficiency into a single functional endpoint. http://purl.obolibrary.org/obo/UBERON_0001092 UBERON http://purl.obolibrary.org/obo/GO_0015979 GO Oxygen evolution measurement Quantifies the rate of O₂ production under illumination using Clark-type oxygen electrodes or polarographic methods, providing a measure of Photosystem II activity. in_vitro leaf discs isolated chloroplasts oxygen evolution rate decrease http://purl.obolibrary.org/obo/GO_0009523 GO medium Oxygen evolution measurements offer a direct proxy for the activity of the photosynthetic light reactions, particularly Photosystem II. Using Clark-type oxygen electrodes or polarographic methods, the rate of O₂ production under illumination can be quantified in intact tissues, leaf discs, or isolated chloroplasts, providing sensitive detection of functional impairment in the photosynthetic electron transport chain. http://purl.obolibrary.org/obo/GO_0009523 GO http://purl.obolibrary.org/obo/GO_0009767 GO Rubisco activity assay Quantifies the catalytic capacity of ribulose-1,5-bisphosphate carboxylase/oxygenase using ¹⁴C-based assays or NADH-linked spectrophotometric methods. in_vitro Rubisco activity decrease http://purl.obolibrary.org/obo/GO_0016970 GO http://purl.obolibrary.org/obo/GO_0015977 GO medium To resolve downstream biochemical constraints, Rubisco activity assays are used to quantify the catalytic capacity of ribulose-1,5-bisphosphate carboxylase/oxygenase. Both ¹⁴C-based assays and NADH-linked spectrophotometric or microtiter plate methods enable discrimination between limitations arising from carbon fixation enzymes versus upstream photochemical processes. http://purl.obolibrary.org/obo/GO_0015977 GO ¹⁴C-bicarbonate uptake assay Quantifies the incorporation of inorganic carbon into organic compounds during photosynthesis, providing an integrative measure of photosynthetic carbon assimilation. in_vitro carbon fixation rate decrease http://purl.obolibrary.org/obo/GO_0015979 GO http://purl.obolibrary.org/obo/GO_0015977 GO medium Carbon fixation rates are most directly assessed using ¹⁴C-bicarbonate uptake assays, which quantify the incorporation of inorganic carbon into organic compounds during photosynthesis. http://purl.obolibrary.org/obo/GO_0015977 GO JC-1 assay Uses the mitochondrial dye JC-1 to study mitochondrial membrane potential (MMP). in_vitro mitochondrial membrane potential change http://purl.obolibrary.org/obo/GO_0001539 GO medium The MMP can be studied with mitochondrial dyes (e.g. JC-1, rhodamine 123) (Sakamuru et al. 2012) http://purl.obolibrary.org/obo/GO_0031966 GO http://purl.obolibrary.org/obo/GO_0001539 GO lactate colorimetric assay Measures extracellular lactate levels as an indicator of increased glycolytic rate. in_vitro extracellular lactate levels increase http://purl.obolibrary.org/obo/CHEBI_16749 CHEBI http://purl.obolibrary.org/obo/GO_0006096 GO high extracellular lactate reflects an increase in glycolytic rate (colorimetric assay) which can compensate for the low ATP production in the mitochondria (Limonciel et al. 2011) http://purl.obolibrary.org/obo/CHEBI_16749 CHEBI http://purl.obolibrary.org/obo/GO_0006096 GO MMP assay Measures mitochondrial membrane potential using fluorescent dyes such as JC-1 or rhodamine 123. in_vitro mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0015986 GO not_specified The MMP can be studied with mitochondrial dyes (e.g. JC-1, rhodamine 123) (Sakamuru et al. 2012) http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006119 GO rhodamine 123 assay Uses the mitochondrial dye rhodamine 123 to study mitochondrial membrane potential (MMP). in_vitro mitochondrial membrane potential change http://purl.obolibrary.org/obo/GO_0001539 GO medium The MMP can be studied with mitochondrial dyes (e.g. JC-1, rhodamine 123) (Sakamuru et al. 2012) http://purl.obolibrary.org/obo/GO_0031966 GO http://purl.obolibrary.org/obo/GO_0001539 GO Seahorse assay Measures oxygen consumption rate (OCR) using the Seahorse device from Agilent. in_vitro oxygen consumption rate change http://purl.obolibrary.org/obo/GO_0006098 GO medium O2 consumption can now be finely measured using the Seahorse device from Agilent (Abe et al. 2010) http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006119 GO HPLC-UV Measures the binding of mercuric chloride to GSH using high performance liquid chromatography with ultraviolet detection. in_vitro binding of mercuric chloride to GSH not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI medium Binding of mercuric chloride to GSH was measured by high performance liquid chromatography (HPLC)-ultraviolet (UV) detection, HPLC-inductively coupled mass spectometry and HPLC-electrospray ionization mass spectometry (Qiao et al., 2017). http://purl.obolibrary.org/obo/CHEBI_15434 CHEBI http://purl.obolibrary.org/obo/GO_0005488 GO ICP-MS Analyzes the binding of Hg to thiol groups using multiple collector inductively coupled plasma mass spectrometry. in_vitro binding of Hg to thiol groups not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI low Binding of Hg to thiol groups was analyzed by multiple collector inductively coupled plasma mass spectometry (Wiederhold et al., 2010). http://purl.obolibrary.org/obo/CHEBI_30873 CHEBI http://purl.obolibrary.org/obo/GO_0005488 GO LC-MS/MS shotgun proteomics Liquid chromatography coupled to tandem mass spectrometry using a shotgun proteomic approach to detect acrylamide-cysteine adducts in N27 cells. in_vitro N27 cells acrylamide-cysteine adducts not_specified high The methodology to detect acrylamide-cysteine adducts has been performed by liquid chromatography coupled to tandem mass spectrometry (Martyniuk et al. 2013). In this paper the authors dected by using a shotgun proteomic approach a total of 15,243 peptides in ACR-exposed N27 cells. And from those 15,243 peptides, 103 peptides (from 100 different proteins) contained acrylamide-cysteine adducts. http://purl.obolibrary.org/obo/CHEBI_43711 CHEBI http://purl.obolibrary.org/obo/GO_0044333 GO Liquid chromatography-tandem mass spectrometry Detects acrylamide-cysteine adducts using liquid chromatography coupled to tandem mass spectrometry. in_vitro N27 acrylamide-cysteine adducts not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI http://purl.obolibrary.org/obo/OBI_0000473 OBI medium The methodology to detect acrylamide-cysteine adducts has been performed by liquid chromatography coupled to tandem mass spectrometry (Martyniuk et al. 2013). In this paper the authors detected by using a shotgun proteomic approach a total of 15,243 peptides in ACR-exposed N27 cells. And from those 15,243 peptides, 103 peptides (from 100 different proteins) contained acrylamide-cysteine adducts. http://purl.obolibrary.org/obo/CHEBI_30873 CHEBI Mass spectrometry Determines the binding of MeHg or Hg2+ with purified Thioredoxin Reductase using mass spectrometry. in_vitro binding of MeHg or Hg2+ with Thioredoxin Reductase not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI low Carvalho et al. (2011) determined the binding of MeHg or Hg2+ with purified Thioredoxin Reductase using mass spectrometry. The liquid chromatography was not applied because they have used a pure chemical system, i.e, without living cells. http://purl.obolibrary.org/obo/PR_000001509 PR http://purl.obolibrary.org/obo/GO_0005488 GO mass spectrometry analysis of thioredoxin/glutaredoxin system Uses mass spectrometry to measure the binding of mercury chloride and methylmercury to proteins of the mammalian thioredoxin and glutaredoxin systems. in_vitro mercury chloride and methylmercury binding to Trx, TrxR, GR, and Grx proteins change http://purl.obolibrary.org/obo/MS_1000073 MS http://purl.obolibrary.org/obo/GO_0046686 GO low Mass spectra analysis allowed to measure the binding of mercury chloride and methylmercury to proteins of the mamallian thioredixin system, thioredoxin reductase (Trx) and thioredoxin (Trx), and of the glutaredoxin system, glutathione reductase (GR) and glutaredoxin (Grx) (Carvahlo et al., 2008) http://purl.obolibrary.org/obo/PR_000005690 PR http://purl.obolibrary.org/obo/GO_0046686 GO Methylene blue-mediated enzyme biosensor Detects mercury-glutathione complex using a methylene blue-mediated enzyme biosensor with horseradish peroxidase. in_vitro mercury-glutathione complex not_specified medium A methylene blue-mediated enzyme biosensor was developed for the detection of mercury-glutathione complex. The biosensor was the enzyme horseradish peroxidase. The binding site of HgCl2 with the enzyme was a cysteine residue-SH (Han et al., 2001). http://purl.obolibrary.org/obo/CHEBI_15434 CHEBI http://purl.obolibrary.org/obo/GO_0005488 GO NMR Investigates the binding affinity of methylmercury by various selenium-containing ligands using proton magnetic resonance spectrometry. in_vitro Methylmercury binding affinity increase low The binding affinity of methylmercury by various selenium-containing lingands was investigated by proton magnetic resonance spectometry (Sugiura et al., 1978; Arnold et al., 1986). http://purl.obolibrary.org/obo/GO_0043167 GO photometric GSH quantification method Quantifies glutathione (GSH) loss after reaction with organic electrophiles using a photometric detection approach. in_vitro GSH loss after reaction with organic electrophiles decrease http://purl.obolibrary.org/obo/GO_0006066 GO http://purl.obolibrary.org/obo/CHMO_0000123 CHMO low A photometric method to quantify GSH loss after reactio with organic electrophiles has also been reported (Böhme et al., 2009). http://purl.obolibrary.org/obo/CHEBI_17157 CHEBI http://purl.obolibrary.org/obo/GO_0006066 GO Photometric method Quantifies GSH loss after reaction with organic electrophiles using a photometric method. in_vitro GSH loss decrease http://purl.obolibrary.org/obo/CHEBI_15434 CHEBI high A photometric method to quantify GSH loss after reaction with organic electrophiles has also been reported (Böhme et al., 2009). http://purl.obolibrary.org/obo/CHEBI_15434 CHEBI http://purl.obolibrary.org/obo/GO_0006749 GO Proton magnetic resonance spectrometry Investigates the binding affinity of methylmercury by various selenium-containing ligands using proton magnetic resonance spectrometry. in_vitro binding affinity of methylmercury not_specified low The binding affinity of methylmercury by various selenium-containing ligands was investigated by proton magnetic resonance spectometry (Sugiura et al., 1978; Arnold et al., 1986). http://purl.obolibrary.org/obo/GO_0005488 GO 3H-labeled ligand uptake assay Measures L-Glu transporter activity by quantifying the uptake of radiolabeled L-Glu or D-aspartate into cells or tissues. The amount of 3H-labeled ligand taken up reflects transporter function. not_specified Primary mixed astrocyte and neuron cultures Primary astrocyte cultures Xenopus laevis oocyte Transfected HeLa cells Hippocampal tissue Xenopus laevis Homo sapiens L-Glu transporter activity (uptake of 3H-labeled ligand) not_specified http://purl.obolibrary.org/obo/GO_0006836 GO not_specified Direct quantification, L-Glu transporter activities are determined by the amount of 3H-labeled ligand (L-Glu or D-aspartate) taken up by the cells (Primary mixed astrocyte and neuron cultures [Perez-Dominguez et al., 2014]; primary astrocyte cultures [Matos et al., 2008; Li et al., 2006; Hazell et al., 2003]; Xenopus laevis oocyte overexpressing the L-Glu transporter subtype of interest [Sogaard et al., 2013; Trotti et al., 2001]; transfected HeLa cells [Zhang and Qu, 2012]) or tissues (ex. Hippocampal tissue [Selkirk et al., 2005]) http://purl.obolibrary.org/obo/GO_0006836 GO Direct quantification of L-Glu transporter activity (Radioligand uptake) Measures L-Glu transporter activity by quantifying the uptake of 3H-labeled ligands (such as L-Glu or D-aspartate) into cells or tissues. in_vitro Primary mixed astrocyte and neuron cultures primary astrocyte cultures Xenopus laevis oocytes transfected HeLa cells Hippocampal tissue Xenopus laevis amount of 3H-labeled ligand taken up change not_specified Direct quantification, L-Glu transporter activities are determined by the amount of 3H-labeled ligand (L-Glu or D-aspartate) taken up by the cells or tissues (ex. Hippocampal tissue [Selkirk et al., 2005]) Glutamate Assay Kit (Abcam ab83389) Quantifies L-Glu concentrations in medium or incubation buffer using a colorimetric assay (OD=450 nm). in_vitro L-Glu concentration not_specified high The L-Glu concentrations in medium or in incubation buffer can be quantified by commercially-available kits quantifying the final products of the redox reaction in which L-Glu is a substrate. The kits using colorimetric final products (OD=450 nm): Glutamate Assay Kit from Abcam (ab83389) Glutamate-Glo™ Assay (Promega J7021) Quantifies L-Glu concentrations in medium or incubation buffer using a bioluminescent metabolite. in_vitro L-Glu concentration not_specified high The kit using the bioluminescent metabolite: Glutamate-Glo™ Assay from Promega (J7021) Immunocytochemistry Confirms the expression level of L-Glu transporter subtypes. in_vitro L-Glu transporter protein expression not_specified http://purl.obolibrary.org/obo/GO_0010485 GO low Expression level of L-Glu transporter subtypes should be confirmed using Western blotting or immunocytochemistry. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010485 GO Indirect quantification of L-Glu transporter activity Measures L-Glu transporter activity by determining the concentration of L-Glu remaining in the medium or buffer after incubation with cells. in_vitro cells expressing the different L-Glu transporters L-Glu residue in the medium or buffer change not_specified Indirect quantification, L-Glu transporter activities are determined by the L-Glu residue in the medium or buffer after incubation with cells expressing the different L-Glu transporters L-Glu residue quantification assay Measures the L-Glu residue in the medium or buffer after incubation with cells expressing L-Glu transporters. in_vitro L-Glu concentration in medium decrease http://purl.obolibrary.org/obo/GO_0014047 GO medium L-Glu transporter activities are determined by the L-Glu residue in the medium or buffer after incubation with cells expressing the different L-Glu transporters (Brison et al., 2014; Xin et al., 2019; Jin et al., 2015; Gu et al., 2014; Abe et alt.2000], .). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0015813 GO L-Glu transporter uptake assay Measures the uptake of 3H-labeled ligand (L-Glu or D-aspartate) by cells or tissues expressing L-Glu transporters. in_vitro Primary mixed astrocyte and neuron cultures primary astrocyte cultures Xenopus laevis oocyte transfected HeLa cells Hippocampal tissue Xenopus laevis Human Rodent L-Glu transporter activity increase http://purl.obolibrary.org/obo/GO_0015813 GO http://purl.obolibrary.org/obo/GO_0015171 GO medium L-Glu transporter activities are determined by the amount of 3H-labeled ligand (L-Glu or D-aspartate) taken up by the cells (Primary mixed astrocyte and neuron cultures [Perez-Dominguez et al., 2014]; primary astrocyte cultures [Matos et al., 2008; Li et al., 2006; Hazell et al., 2003]; Xenopus laevis oocyte overexpressing the L-Glu transporter subtype of interest [Sogaard et al., 2013; Trotti et al., 2001]; transfected HeLa cells [Zhang and Qu, 2012]) or tissues (ex. Hippocampal tissue [Selkirk et al., 2005]) http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0015813 GO radioisotope uptake Quantifies L-Glu transporter activities by measuring the amount of 3H-labeled ligand (L-Glu or D-aspartate) taken up by cells or tissues. in_vitro Primary mixed astrocyte and neuron cultures primary astrocyte cultures HeLa cells Xenopus laevis oocytes Hippocampal tissue Xenopus laevis human rodent uptake of 3H-labeled ligand increase low Direct quantification, L-Glu transporter activities are determined by the amount of 3H-labeled ligand (L-Glu or D-aspartate) taken up by the cells http://purl.obolibrary.org/obo/GO_0006827 GO Western blotting Confirms the expression level of L-Glu transporter subtypes. in_vitro L-Glu transporter protein expression not_specified http://purl.obolibrary.org/obo/GO_0010485 GO low Expression level of L-Glu transporter subtypes should be confirmed using Western blotting or immunocytochemistry. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010485 GO ALT measurement Measurement of alanine aminotransferase (ALT) levels in serum as a biomarker of liver injury. in_vivo liver ALT levels increase http://purl.obolibrary.org/obo/PR_000000001 PR high Elevated ALT (alanine aminotransferase) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON Cytokeratin-18 fragment measurement Measurement of cytokeratin-18 fragments in serum as a marker of hepatocyte injury. in_vivo liver cytokeratin-18 fragment levels increase http://purl.obolibrary.org/obo/PR_000000003 PR medium Markers of hepatocyte injury (e.g., cytokeratin-18 fragments) http://purl.obolibrary.org/obo/CL_0000024 CL http://purl.obolibrary.org/obo/GO_0008219 GO Cytokine assay Measurement of inflammatory cytokines such as TNF-α and IL-6 in serum. in_vivo liver TNF-α, IL-6 levels increase http://purl.obolibrary.org/obo/GO_0005558 GO medium Inflammatory cytokines (TNF-α, IL-6) http://purl.obolibrary.org/obo/GO_0005558 GO http://purl.obolibrary.org/obo/GO_0006954 GO Cytokine measurement Measurement of inflammatory cytokines such as TNF-α and IL-6 in serum as biomarkers of inflammation. in_vivo liver cytokine levels increase http://purl.obolibrary.org/obo/PR_000001658 PR http://purl.obolibrary.org/obo/PR_000000992 PR medium Inflammatory cytokines (TNF-α, IL-6) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO Elastography Imaging technique used to assess the presence and extent of liver fibrosis. in_vivo liver fibrosis change low Elastography (for associated fibrosis) http://purl.obolibrary.org/obo/UBERON_0000347 UBERON Elastography Elastography is used to assess liver fibrosis non-invasively by measuring tissue stiffness. in_vivo liver liver stiffness increase http://purl.obolibrary.org/obo/GO_0008544 GO medium Elastography (for associated fibrosis) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO Gene expression analysis Measurement of increased expression of inflammatory genes such as TNF-α and MCP-1 as markers of inflammation. in_vivo liver gene expression levels increase http://purl.obolibrary.org/obo/PR_000001658 PR http://purl.obolibrary.org/obo/PR_000001150 PR medium Increased expression of inflammatory genes (e.g., TNF-α, MCP-1) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO Gene expression analysis Quantification of inflammatory gene expression (e.g., TNF-α, MCP-1) as molecular markers of steatohepatitis. in_vivo liver mRNA expression of inflammatory genes increase http://purl.obolibrary.org/obo/GO_0006954 GO medium Increased expression of inflammatory genes (e.g., TNF-α, MCP-1) http://purl.obolibrary.org/obo/GO_0008465 GO H&E staining Hematoxylin and eosin staining is used to assess liver tissue morphology, including steatosis, ballooning degeneration, and lobular inflammation. in_vivo liver histological features of steatohepatitis increase http://purl.obolibrary.org/obo/UBERON_0001006 UBERON low Hematoxylin and eosin (H&E) staining Assessment of: Steatosis grade, Ballooning degeneration, Lobular inflammation http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO Hematoxylin and eosin (H&E) staining Histopathological staining used to assess morphological features of the liver including steatosis, ballooning degeneration, and lobular inflammation. ex_vivo liver steatosis grade, ballooning degeneration, lobular inflammation change http://purl.obolibrary.org/obo/OBI_0000146 OBI low Hematoxylin and eosin (H&E) staining Assessment of: Steatosis grade, Ballooning degeneration, Lobular inflammation. Histological scoring systems are considered the gold standard for detection. http://purl.obolibrary.org/obo/UBERON_0000347 UBERON Molecular Markers Quantification of inflammatory gene expression (e.g., TNF-α, MCP-1) and hepatocyte injury markers (e.g., cytokeratin-18 fragments) in liver tissue. in_vivo liver not_specified inflammatory gene expression, hepatocyte injury markers increase http://purl.obolibrary.org/obo/CHEBI_26714 CHEBI low Increased expression of inflammatory genes (e.g., TNF-α, MCP-1) Markers of hepatocyte injury (e.g., cytokeratin-18 fragments) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON MRI-PDFF Magnetic resonance imaging proton density fat fraction (MRI-PDFF) is used to quantify liver steatosis non-invasively. in_vivo liver steatosis quantification increase http://purl.obolibrary.org/obo/UBERON_0001006 UBERON medium MRI-PDFF (steatosis quantification) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON Serum Biomarkers Measurement of serum ALT, AST, and inflammatory cytokines (TNF-α, IL-6) to provide supportive evidence for steatohepatitis. in_vivo liver not_specified ALT, AST, TNF-α, IL-6 increase http://purl.obolibrary.org/obo/CHEBI_15377 CHEBI http://purl.obolibrary.org/obo/CHEBI_15378 CHEBI http://purl.obolibrary.org/obo/CHEBI_26714 CHEBI medium Elevated ALT (alanine aminotransferase) Elevated AST (aspartate aminotransferase) Inflammatory cytokines (TNF-α, IL-6) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON enzyme activity assay Measures the activity of enzymes involved in fatty acid beta oxidation. in_vitro enzyme activity decrease http://purl.obolibrary.org/obo/GO_0006635 GO http://purl.obolibrary.org/obo/OBI_0000175 OBI not_specified Activity of the enzymes that perform FABO http://purl.obolibrary.org/obo/GO_0006635 GO FABO enzyme activity Measures the activity of enzymes involved in fatty acid beta oxidation, such as acyl-CoA dehydrogenase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and thiolase. in_vitro enzyme activity decrease http://purl.obolibrary.org/obo/GO_0006635 GO not_specified Fatty acid beta oxidation (FABO) can be measured by: 1) Activity of the enzymes that perform FABO http://purl.obolibrary.org/obo/GO_0006635 GO fluorescence oxygen consumption assay Measures extracellular oxygen consumption as an indicator of fatty acid beta oxidation using fluorescence. in_vitro oxygen consumption decrease http://purl.obolibrary.org/obo/GO_0033363 GO http://purl.obolibrary.org/obo/GO_0006635 GO not_specified Flourescence assays measuring extracellular oxygen consumption http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006635 GO radiolabel assay Uses labeled palmitate to measure fatty acid beta oxidation. in_vitro palmitate oxidation decrease http://purl.obolibrary.org/obo/GO_0006635 GO http://purl.obolibrary.org/obo/CHEBI_17850 CHEBI not_specified Radiolabel assays using labeled palmitate http://purl.obolibrary.org/obo/CHEBI_17850 CHEBI http://purl.obolibrary.org/obo/GO_0006635 GO Radiolabeled palmitate assay Employs radiolabeled palmitate to trace and quantify the breakdown of fatty acids through beta oxidation pathways. in_vitro radiolabeled palmitate incorporation decrease http://purl.obolibrary.org/obo/GO_0006635 GO not_specified 3) Radiolabel assays using labeled palmitate http://purl.obolibrary.org/obo/CHEBI_15377 CHEBI http://purl.obolibrary.org/obo/GO_0006635 GO plasma membrane permeability assay Measures the permeability of the plasma membrane, which is indicative of cell damage or death. not_specified plasma membrane permeability increase not_specified Typically using plasma membrane permeability. http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0008219 GO Affymetrix Genome U34A Array Microarray assay used to measure the expression of Kupffer cell marker genes. in_vitro Kupffer cell liver marker gene expression increase high or increase in expression of Kupffer cell marker genes such as Lyz, Gzmb, and Il1b, (Genome U34A Array, Affymetrix) cytometry Measures cell surface and intracellular markers for tissue resident cell activation using flow or mass cytometry. in_vitro brain liver expression of cell surface and intracellular markers increase http://purl.obolibrary.org/obo/OBI_0000268 OBI medium Available methods include cytometry http://purl.obolibrary.org/obo/CL_0000126 CL http://purl.obolibrary.org/obo/GO_0002526 GO ELISA Measures soluble mediators (e.g., cytokines) released by activated glial or Kupffer cells in tissue or cell culture supernatants. in_vitro brain liver cytokine or mediator concentration increase http://purl.obolibrary.org/obo/PR_000001616 PR high Kupffer cell activation can be measured by means of expressed cytokines, e.g. tissue levels of TNF-a [Vajdova et al,2004], IL-6 expression, measured by immunoassays or Elisa http://purl.obolibrary.org/obo/CL_0000239 CL http://purl.obolibrary.org/obo/GO_0006954 GO gene expression analysis (qPCR / microarray) Quantification of mRNA expression levels of activation marker genes (e.g. Itgam, CD86, Arg1, MRC1, Lyz, Gzmb, Il1b) in tissue or cell culture using PCR or genome-wide arrays. in_vitro microglia Kupffer cells astrocytes brain liver mouse rat human gene expression levels of M1/M2 phenotype markers change http://purl.obolibrary.org/obo/GO_0008150 GO http://purl.obolibrary.org/obo/GO_0001783 GO http://purl.obolibrary.org/obo/CL_0000129 CL high Activation of glial cells can be assessed in tissue or cell culture models also by quantification of sets of M1/M2 phenotype markers. This can for instance be done by PCR quantification, immunocytochemistry, immunoblotting. Itgam, CD86 expression as markers of M1 microglial phenotype Arg1, MRC1, as markers of M2 microglial phenotype increase in expression of Kupffer cell marker genes such as Lyz, Gzmb, and Il1b, (Genome U34A Array, Affymetrix) http://purl.obolibrary.org/obo/CL_0000127 CL http://purl.obolibrary.org/obo/GO_0001783 GO gene expression sequencing Quantifies mRNA levels of activation markers (e.g., Itgam, Arg1) in tissue or cell cultures to assess glial or Kupffer cell polarization. in_vitro brain liver mRNA expression levels increase http://purl.obolibrary.org/obo/OBI_0002117 OBI http://purl.obolibrary.org/obo/GO_0010467 GO high Activation of glial cells can be assessed in tissue or cell culture models also by quantification of sets of M1/M2 phenotype markers. This can for instance be done by PCR quantification http://purl.obolibrary.org/obo/CL_0000126 CL Immunohistochemistry Immunohistochemistry detects protein markers in tissue sections using enzyme‑linked antibodies, allowing visualization and quantification of marker expression in situ. not_specified microglia astrocyte brain mouse rat human marker expression level (e.g., CD11b, GFAP) increase low immunohistochemistry http://purl.obolibrary.org/obo/CL_0000127 CL http://purl.obolibrary.org/obo/GO_0006954 GO immunohistochemistry Detects protein markers in tissue sections using labeled antibodies to visualize microglial and astrocyte activation. ex_vivo brain protein expression and morphological changes increase http://purl.obolibrary.org/obo/PR_000008089 PR low the most frequently used astrocyte marker is glial fibrillary acidic protein, GFAP (99% of all studies) (Eng et al., 2000). This protein is highly specific for astrocytes in the brain, and antibodies are available for immunocytochemical detection. http://purl.obolibrary.org/obo/CL_0000059 CL http://purl.obolibrary.org/obo/GO_0002526 GO PCR Quantifies the expression of specific genes, used to assess glial cell activation. in_vitro brain liver gene expression levels increase medium Activation of glial cells can be assessed in tissue or cell culture models also by quantification of sets of M1/M2 phenotype markers. This can for instance be done by PCR quantification http://purl.obolibrary.org/obo/GO_0006925 GO PET imaging Non-invasive imaging of microglial activation in patients using radiolabeled ligands (e.g., [11C]-PK 11195). in_vivo brain human microglial accumulation increase http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/CL_0000126 CL low In patients, microglial accumulation can be monitored by PET imaging, using [11C]-PK 11195 as a microglial marker (Banati et al., 2002). http://purl.obolibrary.org/obo/CL_0000126 CL http://purl.obolibrary.org/obo/GO_0002526 GO western blot Quantifies protein levels of specific markers (e.g., GFAP, CD11b) in tissue lysates to assess glial activation. ex_vivo brain protein expression levels increase http://purl.obolibrary.org/obo/PR_000008089 PR low Available methods include... western blotting http://purl.obolibrary.org/obo/CL_0000059 CL http://purl.obolibrary.org/obo/GO_0002526 GO ELISA Plate-based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of an inflammatory cytokine of interest especially when in low concentrations. in_vitro presence of inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0005515 GO medium Plate based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of an inflammatory cytokine of interest especially when in low concentrations. http://purl.obolibrary.org/obo/GO_0006954 GO Flow-cytometry Detects the intracellular cytokines with stimulation. in_vitro intracellular cytokines increase http://purl.obolibrary.org/obo/GO_0005125 GO high Detects the intracellular cytokines with stimulation. http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO Imaging tests Qualitative technique using cytokine-specific antibodies and fluorophores to visualize expression patterns, subcellular location, and protein-protein interactions. in_vitro expression patterns and subcellular location not_specified http://purl.obolibrary.org/obo/GO_0044287 GO low A qualitative technique using a cytokine specific antibodies and fluorophores can be used to visualize expression patterns, subcellular location of the target and protein-protein interactions. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0006954 GO Imaging tests A qualitative technique using cytokine-specific antibodies and fluorophores to visualize expression patterns, subcellular location of the target, and protein-protein interactions. in_vitro expression patterns and subcellular location of cytokines increase http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0008104 GO low A qualitative technique using a cytokine specific antibodies and fluorophores can be used to visualize expression patterns, subcellular location of the target and protein-protein interactions. http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO Immunoblotting (western blotting) Uses antibodies specific to proteins of interest, can be used to detect presence of pro-inflammatory mediators in samples of cell or tissue lysate. in_vitro presence of pro-inflammatory mediators increase http://purl.obolibrary.org/obo/GO_0005515 GO low Uses antibodies specific to proteins of interest, can used to detect presence of pro-inflammatory mediators in samples of cell or tissue lysate http://purl.obolibrary.org/obo/GO_0006954 GO Immunohistochemistry (IHC) Immobilized tissue or cell cultures are stained using antibodies for specificity of ligands of interest. Versions of the assays can be used to visualize localization of inflammatory cytokines. in_vitro localization of inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0051179 GO low Immobilized tissue or cell cultures are stained using antibodies for specificity of ligands of interest. Versions of the assays can be used to visualize localization of inflammatory cytokines. http://purl.obolibrary.org/obo/GO_0006954 GO Inflammatory cytokine arrays Similar to the ELISA, except using a membrane-based rather than plate-based approach. Can be used to measure multiple cytokine targets concurrently. in_vitro multiple cytokine targets increase http://purl.obolibrary.org/obo/GO_0005125 GO medium Similar to the ELISA, except using a membrane-based rather than plate-based approach. Can be used to measure multiple cytokine targets concurrently. http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO Olink Highly specific and sensitive proximity extension assay technology which uses an inflammation panel to categorize pro-inflammatory markers. in_vitro pro-inflammatory markers increase high Highly specific and sensitive proximity extension assay technology which uses an inflammation panel to categorize pro-inflammatory markers. http://purl.obolibrary.org/obo/GO_0006954 GO Radioimmunoassay Plate-based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of an inflammatory cytokine of interest especially when in low concentrations. in_vitro presence of inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0005515 GO medium Plate based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of an inflammatory cytokine of interest especially when in low concentrations. http://purl.obolibrary.org/obo/GO_0006954 GO RT-qPCR Measures mRNA expression of cytokines, chemokines and inflammatory markers. in_vitro mRNA expression increase medium Measures mRNA expression of cytokines, chemokines and inflammatory markers http://purl.obolibrary.org/obo/CHEBI_50889 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO RT-qPCR Measures mRNA expression of cytokines, chemokines and inflammatory markers. in_vitro mRNA expression of cytokines, chemokines and inflammatory markers increase http://purl.obolibrary.org/obo/GO_0010605 GO http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0008009 GO medium Measures mRNA expression of cytokines, chemokines and inflammatory markers http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0006954 GO western blot Uses antibodies specific to proteins of interest, can used to detect presence of pro-inflammatory mediators in samples of cell or tissue lysate. in_vitro tissue protein presence increase low Uses antibodies specific to proteins of interest, can used to detect presence of pro-inflammatory mediators in samples of cell or tissue lysate http://purl.obolibrary.org/obo/GO_0005576 GO http://purl.obolibrary.org/obo/GO_0006954 GO Whole blood stimulation assay Detects inflammatory cytokines in blood. in_vitro blood inflammatory cytokines increase http://purl.obolibrary.org/obo/UBERON_0000178 UBERON medium Detects inflammatory cytokines in blood http://purl.obolibrary.org/obo/GO_0006954 GO Flow cytometry Flow cytometry (FC/FACS) is used for in vivo imaging to analyze cell populations based on their physical and chemical characteristics. in_vivo cell populations change medium Flow cytometry (FC/FACS), http://purl.obolibrary.org/obo/GO_0002274 GO Flow cytometry Measures leukocyte surface markers and activation status using monoclonal antibodies. in_vitro leukocytes leukocyte surface marker expression change http://purl.obolibrary.org/obo/OBI_0000268 OBI http://purl.obolibrary.org/obo/GO_0002274 GO medium Flow cytometry (FC/FACS) Leukocyte Surface Markers (Monoclonal Antibodies to Leukocyte Surface Markers) http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0002274 GO histology Assesses leukocyte recruitment and activation by quantifying cell numbers and composition in tissue sections. in_vivo leukocytes tissue human mouse cell numbers and altered composition increase http://purl.obolibrary.org/obo/GO_0042066 GO http://purl.obolibrary.org/obo/GO_0006955 GO low Histology, increased cell numbers and altered composition http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0042066 GO Histology Assesses leukocyte infiltration and tissue composition changes via staining and microscopy. in_vivo leukocytes leukocyte cell numbers and tissue composition increase http://purl.obolibrary.org/obo/GO_0002523 GO low Histology, increased cell numbers and altered composition http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0002523 GO immunohistochemistry A technique used to visualize the distribution of specific antigens in tissue sections using antibodies. in_vivo cell numbers and composition change low immunhistochemistry Histology, increased cell numbers and altered composition http://purl.obolibrary.org/obo/CL_0000064 CL http://purl.obolibrary.org/obo/GO_0050900 GO Immunohistochemistry Detects leukocyte presence and activation markers in tissue sections using antibodies. in_vivo leukocytes leukocyte marker expression change http://purl.obolibrary.org/obo/GO_0002274 GO low immunhistochemistry http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0002274 GO Leukocyte Surface Markers Detects expression of surface markers on leukocytes using monoclonal antibodies. in_vitro leukocytes leukocyte surface marker expression change http://purl.obolibrary.org/obo/GO_0002274 GO medium Leukocyte Surface Markers (Monoclonal Antibodies to Leukocyte Surface Markers) http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0002274 GO Markers of leukocyte activation Measurement of biochemical indicators of activation such as protease release, reactive oxygen/nitrogen species (ROS/RNS), and NADPH oxidase (NOX) activity. in_vitro leukocyte protease release, ROS/RNS, NADPH oxidase (NOX) expression change http://purl.obolibrary.org/obo/CHEBI_35447 CHEBI medium Markers of leukocyte activation – protease release, ROS/RNS, NADPH oxidase (NOX), defense response - expression of anti-oxidants. http://purl.obolibrary.org/obo/CL_0000064 CL http://purl.obolibrary.org/obo/GO_0038071 GO Organs-on-a-chip Organs-on-a-chip are microfluidic devices that mimic the structure and function of human organs, used here to analyze lung inflammation and drug responses. in_vitro lung human inflammation and drug responses change medium organs-on-a-chip (Bnam et al., 2016; Ribas et al., 2017; Wufuer et al. 2016) http://purl.obolibrary.org/obo/UBERON_0000208 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO ROS/RNS Assay Measures production of reactive oxygen and nitrogen species as markers of leukocyte activation. in_vitro leukocytes ROS/RNS production increase http://purl.obolibrary.org/obo/GO_0072593 GO http://purl.obolibrary.org/obo/GO_0002274 GO medium Markers of leukocyte activation – protease release, ROS/RNS http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0002274 GO Spinning Disk Confocal Microscopy-IVM High-resolution imaging of leukocyte dynamics in live tissues. in_vivo leukocytes leukocyte recruitment and activation increase http://purl.obolibrary.org/obo/GO_0002523 GO low Spinning Disk Confocal Microscopy-IVM (Jenne et al., 2011) http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0002523 GO T-Lymphocyte & Innate Immune Cell Activation Assays Measures activation markers and functional responses of T-lymphocytes and innate immune cells. in_vitro T-lymphocytes innate immune cells immune cell activation increase http://purl.obolibrary.org/obo/GO_0002253 GO http://purl.obolibrary.org/obo/GO_0042110 GO medium T-Lymphocyte & Innate Immune Cell Activation Assays http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042110 GO Transwell Migration Assay Measures leukocyte migration across a membrane in response to chemotactic stimuli. in_vitro leukocytes leukocyte migration increase http://purl.obolibrary.org/obo/OBI_0000667 OBI http://purl.obolibrary.org/obo/GO_0002523 GO medium transwell Migration Assay (Justus et al., 2014) http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0002523 GO Two photon-intravital microscopy Two photon-intravital microscopy (TP-IVM) is an in vivo imaging technique used to visualize cellular and molecular events in living tissues. in_vivo cellular and molecular events change low two photon-intravital microscopy (TP-IVM) (van Grinsven et al., 2017) http://purl.obolibrary.org/obo/GO_0002662 GO Two-photon intravital microscopy Visualizes leukocyte recruitment and activation in live tissues using fluorescence imaging. in_vivo leukocytes leukocyte recruitment and activation increase http://purl.obolibrary.org/obo/OBI_0000415 OBI http://purl.obolibrary.org/obo/GO_0002523 GO low two photon-intravital microscopy (TP-IVM) (van Grinsven et al., 2017) http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0002523 GO ELISA Quantitative measurement of antigens such as cytokines or DAMPs in biological samples using antibody sandwich and enzymatic detection. in_vitro cytokine or DAMP concentration increase http://purl.obolibrary.org/obo/GO_0005125 GO medium Targeted enzyme-linked immunosorbent assays (ELISA) (routinely used and recommended): The amount of colour detected is directly proportional to the amount of cytokine in the sample that is bound to the capture antibody. Targeted ELISA can be used to quantify IL-1α or IL-1β that is released in the culture supernatant of the cells exposed to toxicants, in bronchoalveolar lavage fluid and serum of exposed animals. http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO immunohistochemistry Immunohistochemistry methods targeting lysosome specific proteins are used to assess nanoparticle uptake by lysosomes, often with co-localisation experiments using a LAMP1 antibody. in_vitro lung lysosome co-localisation increase http://purl.obolibrary.org/obo/OBI_0000068 OBI low In vitro, interaction of NMs with the cellular membrane is investigated by assessing their uptake by lysosomes (Chen et al., 2013; Nel et al., 2009; Varela et al., 2012). Immunohistochemistry methods targeting lysosome specific proteins are regularly employed for this purpose. A combination of Cytoviva hyperspectral microscope and immunolocalisation (Decan et al., 2016) or confocal microscopy to visualise co-localisation of fluorescence labelled nanoparticles with lysosomal markers have been used. http://purl.obolibrary.org/obo/GO_0005777 GO http://purl.obolibrary.org/obo/GO_0016372 GO Microscopic techniques Use of time-lapse, backscatter electron, or other microscopy to assess frustrated phagocytosis. in_vitro frustrated phagocytosis change http://purl.obolibrary.org/obo/GO_0002239 GO low Frustrated phagocytosis is assessed using microscopic techniques such as time-lapse microscopy, backscatter electron microscopy and others http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0002239 GO Microscopy Various microscopy techniques (time-lapse, backscatter electron, confocal, laser scanning, darkfield) used to visualize nanoparticle interaction with cells and assess frustrated phagocytosis. in_vitro epithelial cells immune cells primary human alveolar epithelial cells endothelial cells fibroblasts lung epithelium human cellular uptake and phagocytosis change http://purl.obolibrary.org/obo/GO_0004407 GO low Frustrated phagocytosis is assessed using microscopic techniques such as time-lapse microscopy, backscatter electron microscopy and others Using laser scanning, fluorescence, and enhanced darkfield microscopy, CNT interaction with the resident cells of the model was shown http://purl.obolibrary.org/obo/GO_0004407 GO Microscopy Assessment of cellular uptake, frustrated phagocytosis, and interaction of nanoparticles with lung epithelium using time-lapse microscopy, backscatter electron microscopy, confocal microscopy, and darkfield microscopy. in_vitro lung human mouse nanoparticle-cell interaction increase http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/CHEBI_23367 CHEBI low In vitro interaction of NMs with the cellular membrane is investigated by assessing their uptake by lysosomes... Immunohistochemistry methods targeting lysosome specific proteins are regularly employed for this purpose... Frustrated phagocytosis is assessed using microscopic techniques such as time-lapse microscopy, backscatter electron microscopy and others. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0006915 GO Precision cut lung slices (PCLS) Ex vivo technique that preserves native lung architecture and cell-cell communication in lung tissue slices to study nanomaterial-induced effects. ex_vivo lung nanomaterial-induced fibrosis and interaction with epithelium change low Ex vivo model of the lung – Precision cut lung slices (PCLS): Even closer to the in vivo condition than co-culture models, PCLS techniques capture the native lung architecture, cell-cell communication and cellularity of the lung. the technique has recently been assessed for its applicability to assess nanomaterial induced fibrosis ex vivo http://purl.obolibrary.org/obo/UBERON_0000853 UBERON qRT-PCR Quantification of gene expression levels using reverse transcription and real-time PCR. in_vitro gene expression level increase http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/GO_0010467 GO medium ELISA or real-time reverse transcription-polymerase chain reaction (qRT-PCR) assays can also be used to quantify the expression of genes or proteins that are regulated by the receptor binding – e.g. downstream of TLR binding. http://purl.obolibrary.org/obo/GO_0005575 GO http://purl.obolibrary.org/obo/GO_0006351 GO time-lapse microscopy Real-time observation of cellular processes using continuous imaging. in_vitro cellular behavior change http://purl.obolibrary.org/obo/GO_0006909 GO low Frustrated phagocytosis is assessed using microscopic techniques such as time-lapse microscopy, backscatter electron microscopy and others (Donaldson et al., 2010; Murphy et al., 2012; Padmore et al., 2017; Pascolo et al., 2013; Schinwald et al., 2012). http://purl.obolibrary.org/obo/GO_0000323 GO http://purl.obolibrary.org/obo/GO_0006909 GO Time-lapse microscopy Captures dynamic imaging over time to assess frustrated phagocytosis, indicating incomplete particle engulfment by phagocytic cells. in_vitro frustrated phagocytosis occurrence increase not_specified Frustrated phagocytosis is assessed using microscopic techniques such as time-lapse microscopy, backscatter electron microscopy and others (Donaldson et al., 2010; Murphy et al., 2012; Padmore et al., 2017; Pascolo et al., 2013; Schinwald et al., 2012). Western blot Detects and quantifies specific alarmin proteins released from cells using antibody-based electrophoresis and immunoblotting. in_vitro alarmin protein level increase not_specified Western blot is another method that can be used to quantify the release of various alarmins using specific antibodies. western blot Detection and quantification of specific proteins using gel electrophoresis and antibody probing. in_vitro protein expression level increase http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/GO_0005515 GO low Western blot is another method that can be used to quantify the release of various alarmins using specific antibodies. http://purl.obolibrary.org/obo/GO_0033554 GO cytokine bead array Multiplex method to detect a panel of inflammatory mediators using bead-based immunoassays. in_vitro multiple cytokine concentrations increase http://purl.obolibrary.org/obo/OBI_0000475 OBI http://purl.obolibrary.org/obo/GO_0005125 GO high In addition to assaying single protein or gene at a time, cytokine bead arrays or cytokine PCR arrays can also be used to detect a whole panel of inflammatory mediators in a multiplex method (Husain et al., 2015b). http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006954 GO cytokine bead arrays / cytokine PCR arrays Multiplex methods used to detect a whole panel of inflammatory mediators simultaneously from small sample amounts. not_specified panel of inflammatory mediators change http://purl.obolibrary.org/obo/CL_0000000 CL high cytokine bead arrays or cytokine PCR arrays can also be used to detect a whole panel of inflammatory mediators in a multiplex method ELISA Permits quantitative measurement of antigens in biological samples using the same method as described for the MIE in AOP173. Can be used with cell culture supernatants or whole cell homogenates. in_vivo antigen concentration increase medium Enzyme-linked immunosorbent assays (ELISA) – permit quantitative measurement of antigens in biological samples. Both ELISA and qRT-PCR assays are used in vivo and are readily applicable to in vitro cell culture models, where cell culture supernatants or whole cell homogenates are used for ELISA or mRNA assays. http://purl.obolibrary.org/obo/GO_0001635 GO http://purl.obolibrary.org/obo/GO_0002732 GO ELISA Quantitatively measures antigens in biological samples by detecting specific antigens using antibodies. Can be used to measure pro-inflammatory cytokines in cell culture supernatants or whole cell homogenates. in_vitro lung epithelial cells macrophages fibroblasts lung mouse rat human protein abundance of pro-inflammatory cytokines increase http://purl.obolibrary.org/obo/SO_0000414 SO http://purl.obolibrary.org/obo/GO_0001890 GO http://purl.obolibrary.org/obo/OBI_0000679 OBI medium Enzyme-linked immunosorbent assays (ELISA) - permit quantitative measurement of antigens in biological samples. Both ELISA and qRT-PCR assays are used in vivo and are readily applicable to in vitro cell culture models, where cell culture supernatants or whole cell homogenates are used for ELISA or mRNA assays. http://purl.obolibrary.org/obo/SO_0000414 SO http://purl.obolibrary.org/obo/GO_0001816 GO ELISA Quantitative measurement of antigens (e.g., pro-inflammatory cytokines) in biological samples using enzyme-linked immunosorbent assay. in_vitro protein concentration increase http://purl.obolibrary.org/obo/PR_000000001 PR medium Enzyme-linked immunosorbent assays (ELISA) – permit quantitative measurement of antigens in biological samples. Both ELISA and qRT-PCR assays are used in vivo and are readily applicable to in vitro cell culture models, where cell culture supernatants or whole cell homogenates are used for ELISA or mRNA assays. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006954 GO immunohistochemistry Detects specific immune cell types producing pro-inflammatory mediators in tissue sections using antibody staining. in_vivo presence of immune cells producing proinflammatory mediators increase http://purl.obolibrary.org/obo/OBI_0000286 OBI http://purl.obolibrary.org/obo/CL_0000451 CL low Lastly, immunohistochemistry can be used to detect specific immune cell types producing the pro-inflammatory mediators and its downstream effectors in any given tissue (Costa et al., 2017). http://purl.obolibrary.org/obo/CL_0000451 CL http://purl.obolibrary.org/obo/GO_0006955 GO immunohistochemistry A technique used to detect specific immune cell types and their downstream effectors within a tissue section. not_specified immune cell types tissue presence/location of immune cells and effectors change http://purl.obolibrary.org/obo/CL_0000000 CL low immunohistochemistry can be used to detect specific immune cell types producing the pro-inflammatory mediators and its downstream effectors in any given tissue the technique is not quantitative http://purl.obolibrary.org/obo/CL_0000000 CL qRT-PCR Measures the abundance of cytokine mRNA in a sample using reverse transcription, PCR amplification, and real-time fluorescence detection. in_vitro mouse rat human cytokine mRNA abundance increase http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/PATO_0000356 PATO medium Real-time reverse transcription-polymerase chain reaction (qRT-PCR) – will measure the abundance of cytokine mRNA in a given sample. The number of cycles required per sample to reach a certain threshold of fluorescence (set by the user – usually set in the linear phase of the amplification, and the observed difference in samples to cross the set threshold reflects the initial amount available for amplification) is used to quantify the relative amount in the samples. http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO BALF cellularity assay Measures the composition of bronchoalveolar lavage fluid (BALF) to assess lung immune response, including infiltrating cell types, cytokines, and chemokines. in_vivo lung BALF cellular composition change http://purl.obolibrary.org/obo/UBERON_0001005 UBERON http://purl.obolibrary.org/obo/GO_0006955 GO http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0008009 GO OECD inhalation test guideline for NMs low recruitment of pro-inflammatory cells is measured using BALF cellularity assay. The fluid lining the lung epithelium is lavaged (BALF) and its composition is assessed as marker of lung immune response to the toxic substances or pathogens. BALF is assessed quantitatively for types of infiltrating cells, levels and types of cytokines and chemokines. For NMs, in vivo BALF assessment is recommended as a mandatory test (discussed in ENV/JM/MONO(2012)40 and also in OECD inhalation test guideline for NMs). http://purl.obolibrary.org/obo/UBERON_0002188 UBERON http://purl.obolibrary.org/obo/GO_0006955 GO BALF cellularity assay The fluid lining the lung epithelium is lavaged (BALF) and its composition is assessed as a marker of lung immune response. BALF is assessed quantitatively for types of infiltrating cells, levels and types of cytokines and chemokines. in_vivo lung types of infiltrating cells, levels and types of cytokines and chemokines increase OECD inhalation test guideline for NMs low In vivo, recruitment of pro-inflammatory cells is measured using BALF cellularity assay. BALF is assessed quantitatively for types of infiltrating cells, levels and types of cytokines and chemokines. For NMs, in vivo BALF assessment is recommended as a mandatory test (discussed in ENV/JM/MONO(2012)40 and also in OECD inhalation test guideline for NMs). http://purl.obolibrary.org/obo/UBERON_0000208 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO ELISA Measures protein levels of pro-inflammatory mediators in cell culture models as an indicator of inflammatory cell recruitment. in_vitro protein levels of pro-inflammatory mediators increase http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI medium a suit of pro-inflammatory mediators specific to cell types are assessed using the same techniques mentioned above (real-time reverse transcription-polymerase chain reaction [qRT-PCR], enzyme-linked immunosorbent assays [ELISA], immunohistochemistry) in cell culture models, as indicative of recruitment of cells into the lungs. http://purl.obolibrary.org/obo/GO_0006954 GO immunohistochemistry Detects the presence and localization of pro-inflammatory mediators in cell culture models as an indicator of inflammatory cell recruitment. in_vitro localization of pro-inflammatory mediators increase http://purl.obolibrary.org/obo/OBI_0000466 OBI low a suit of pro-inflammatory mediators specific to cell types are assessed using the same techniques mentioned above (real-time reverse transcription-polymerase chain reaction [qRT-PCR], enzyme-linked immunosorbent assays [ELISA], immunohistochemistry) in cell culture models, as indicative of recruitment of cells into the lungs. http://purl.obolibrary.org/obo/GO_0006954 GO immunohistochemistry Immunohistochemistry is used to assess pro-inflammatory mediators specific to cell types in cell culture models. in_vitro lung pro-inflammatory mediators increase low Thus, a suit of pro-inflammatory mediators specific to cell types are assessed using the same techniques mentioned above (real-time reverse transcription-polymerase chain reaction [qRT-PCR], enzyme-linked immunosorbent assays [ELISA], immunohistochemistry) in cell culture models, as indicative of recruitment of cells into the lungs. http://purl.obolibrary.org/obo/PR_00000000001 PR http://purl.obolibrary.org/obo/GO_0006954 GO lung-on-a-chip Microfluidic lung-on-a-chip devices are used to assess the migration of select immune cells and fibroblasts toward a simulated epithelium. in_vitro immune cells fibroblasts lung migration of immune cells and fibroblasts increase low Finally, more complicated microfluidic lung-on-a-chip devices can be used to assess the migration of select immune cells and fibroblasts toward a simulated epithelium following treatment with a pro-fibrotic compound (He et al., 2017). http://purl.obolibrary.org/obo/CL_0000253 CL http://purl.obolibrary.org/obo/GO_0006956 GO microfluidic lung-on-a-chip Assesses the migration of immune cells and fibroblasts toward a simulated epithelium in a microfluidic device following treatment with pro-fibrotic compounds. in_vitro immune cells fibroblasts lung cell migration increase http://purl.obolibrary.org/obo/GO_0016477 GO low more complicated microfluidic lung-on-a-chip devices can be used to assess the migration of select immune cells and fibroblasts toward a simulated epithelium following treatment with a pro-fibrotic compound (He et al., 2017). http://purl.obolibrary.org/obo/CL_0000738 CL http://purl.obolibrary.org/obo/GO_0016477 GO precision cut lung slices Assesses the recruitment of tissue resident inflammatory cells in lung slices based on histological changes following treatment. ex_vivo lung inflammatory foci increase http://purl.obolibrary.org/obo/UBERON_0002048 UBERON low the use of precision cut lung slices can allow for limited assessment of recruitment of tissue resident inflammatory cells, based on the repertoire of cells remaining in the specific slice following harvesting. This method was used to show that there is a histological increase in inflammatory foci following treatment with bleomycin and MWCNTs (Rahman et al., 2020). http://purl.obolibrary.org/obo/GO_0006954 GO precision cut lung slices Assessment of recruitment of tissue resident inflammatory cells based on the repertoire of cells remaining in a lung tissue slice. ex_vivo tissue resident inflammatory cells lung repertoire of cells remaining in the specific slice change low the use of precision cut lung slices can allow for limited assessment of recruitment of tissue resident inflammatory cells, based on the repertoire of cells remaining in the specific slice following harvesting. This method was used to show that there is a histological increase in inflammatory foci following treatment with bleomycin and MWCNTs (Rahman et al., 2020). http://purl.obolibrary.org/obo/GO_0006954 GO qRT-PCR Measures gene expression levels of pro-inflammatory mediators in cell culture models as an indicator of inflammatory cell recruitment. in_vitro gene expression of pro-inflammatory mediators increase http://purl.obolibrary.org/obo/GO_0010467 GO medium a suit of pro-inflammatory mediators specific to cell types are assessed using the same techniques mentioned above (real-time reverse transcription-polymerase chain reaction [qRT-PCR], enzyme-linked immunosorbent assays [ELISA], immunohistochemistry) in cell culture models, as indicative of recruitment of cells into the lungs. http://purl.obolibrary.org/obo/GO_0006954 GO BALF protein content Measures total protein or albumin content in bronchoalveolar lavage fluid (BALF) to assess alveolar capillary membrane (ACM) integrity. Increased protein/albumin indicates a compromised barrier. in_vivo lung protein/albumin content increase low Compromised ACM barrier integrity in vivo can be measured by measuring total protein or total albumin content in the BALF derived from experimental animals exposed to lung toxicants or in human patients suffering from lung fibrosis. http://purl.obolibrary.org/obo/GO_0008533 GO BALF protein content Measures total protein or albumin content in bronchoalveolar lavage fluid (BALF) to assess alveolar capillary membrane integrity loss. in_vivo lung experimental animals human total protein or albumin content in BALF increase http://purl.obolibrary.org/obo/CHEBI_17405 CHEBI low Compromised ACM barrier integrity in vivo can be measured by measuring total protein or total albumin content in the BALF derived from experimental animals exposed to lung toxicants or in human patients suffering from lung fibrosis. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0008361 GO BALF urea content Measures total urea in bronchoalveolar lavage fluid (BALF) as an indicator of alveolar capillary membrane integrity loss. in_vivo lung experimental animals human total urea content in BALF increase http://purl.obolibrary.org/obo/CHEBI_16199 CHEBI low In addition to albumin, the total urea in BALF is also a good indicator of the ACM integrity loss (Schmekel et al., 1992). http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0008361 GO Calcein AM assay Measures calcein release into media following hydrolysis of calcein AM by intracellular esterases in cells with compromised membranes. in_vitro alveolar macrophages dendritic cells epithelial cells neutrophils human experimental animals calcein fluorescence in media increase http://purl.obolibrary.org/obo/GO_0016788 GO http://purl.obolibrary.org/obo/CHEBI_36986 CHEBI medium The Calcein AM assay depends on the hydrolysis of calcein AM (a non-fluorescent hydrophobic compound that permeates live cells by simple diffusion) by non-specific intracellular esterases resulting in production of calcein, a hydrophilic and strongly fluorescent compound that is readily released into the cell culture media by the damaged cells. http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0008361 GO ELISA Measures protein levels of tight junction proteins, cell adhesion molecules, and inflammatory mediators. in_vitro alveolar macrophages dendritic cells epithelial cells neutrophils human experimental animals protein concentration change http://purl.obolibrary.org/obo/GO_0050792 GO medium The other methods include targeted reverse transcription polymerase chain reaction (RT-PCR) or enzyme-linked immunosorbent assays (ELISA) for tight junction proteins, cell adhesion molecules and inflammatory mediators such as Interferon gamma (IFN-γ), IL-10, and IL-13. http://purl.obolibrary.org/obo/GO_0005911 GO http://purl.obolibrary.org/obo/GO_0008361 GO ELISA Enzyme-linked immunosorbent assay used to measure protein levels of tight junction proteins, cell adhesion molecules, and inflammatory mediators. in_vitro alveolar macrophages dendritic cells epithelial cells neutrophils human experimental animals protein levels of tight junction proteins, cell adhesion molecules, and inflammatory mediators change medium The other methods include targeted reverse transcription polymerase chain reaction (RT-PCR) or enzyme-linked immunosorbent assays (ELISA) for tight junction proteins, cell adhesion molecules and inflammatory mediators such as Interferon gamma (IFN-γ), IL-10, and IL-13. LDH release assay Measures lactate dehydrogenase released into the media following cell membrane injury, quantified via NAD reduction and tetrazolium dye conversion. in_vitro alveolar macrophages dendritic cells epithelial cells neutrophils human experimental animals LDH activity in media increase http://purl.obolibrary.org/obo/GO_0001756 GO medium Lactate dehydrogenase (LDH) release assay is a very sensitive cytotoxicity assay that measures the amount of LDH released in the media following membrane injury. The assay is based on measuring the reduction of nicotinamide adenine dinucleotide (NAD) and conversion of a tetrazolium dye that is measured at a wavelength of 490 nm. http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0008361 GO RT-PCR Measures gene expression levels of tight junction proteins, cell adhesion molecules, and inflammatory mediators. in_vitro alveolar macrophages dendritic cells epithelial cells neutrophils human experimental animals gene expression change http://purl.obolibrary.org/obo/OBI_0000664 OBI http://purl.obolibrary.org/obo/GO_0010467 GO medium The other methods include targeted reverse transcription polymerase chain reaction (RT-PCR) or enzyme-linked immunosorbent assays (ELISA) for tight junction proteins, cell adhesion molecules and inflammatory mediators such as Interferon gamma (IFN-γ), IL-10, and IL-13. http://purl.obolibrary.org/obo/GO_0005911 GO http://purl.obolibrary.org/obo/GO_0008361 GO TEER Measures transepithelial/transendothelial electrical resistance to assess tight junction integrity in cell monolayers. in_vitro epithelial cells endothelial cells human experimental animals electrical resistance decrease http://purl.obolibrary.org/obo/GO_0005911 GO medium Transepithelial/transendothelial electrical resistance (TEER) is an accepted quantitative technique that measures the integrity of tight junctions in cell culture models of endothelial and epithelial cell monolayers. Advanced in vitro co-culture models, like the EpiAlveolar model system, and other similar systems present an intact capillary membrane that can be used to assess loss in the membrane integrity (via TEER) after exposure to pro-fibrotic stressors like crystalline silica and Transforming growth factor beta (TGF-β) (Barasova et al., 2020, Kasper et al., 2011). http://purl.obolibrary.org/obo/GO_0005911 GO http://purl.obolibrary.org/obo/GO_0008361 GO trypan blue exclusion assay A dye exclusion assay where intact cells exclude trypan blue, while cells with compromised membranes take up the dye and appear blue. in_vitro alveolar macrophages dendritic cells epithelial cells neutrophils human experimental animals cell membrane integrity decrease http://purl.obolibrary.org/obo/GO_0008219 GO medium The most commonly employed method is the trypan blue exclusion assay – a dye exclusion assay where cells with intact membrane do not permit entry of the dye into cells and thus remain clear, whereas the dye diffuses into cells with damaged membrane turning them to blue colour. http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0008361 GO Trypan blue exclusion assay A dye exclusion assay where cells with intact membranes remain clear, while cells with damaged membranes take up the dye and turn blue, indicating cytotoxicity. in_vitro alveolar macrophages dendritic cells epithelial cells neutrophils lung cell viability decrease medium Cellular viability or cytotoxicity assays are the most commonly used endpoints to assess the leaky or compromised cell membrane. The most commonly employed method is the trypan blue exclusion assay – a dye exclusion assay where cells with intact membrane do not permit entry of the dye into cells and thus remain clear, whereas the dye diffuses into cells with damaged membrane turning them to blue colour. http://purl.obolibrary.org/obo/CL_0005099 CL http://purl.obolibrary.org/obo/GO_0008219 GO cytokine bead array Multiplex method using cytokine bead arrays to detect a panel of Th1 and/or Th2 cytokines in BALF supernatant, tissue homogenates, or cell pellets. in_vitro lung levels of multiple Th1 and Th2 cytokines increase http://purl.obolibrary.org/obo/OBI_0000475 OBI http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/PR_000000996 PR http://purl.obolibrary.org/obo/PR_000000997 PR http://purl.obolibrary.org/obo/PR_000001000 PR high Apart from assaying single protein or gene at a time, cytokine bead arrays or cytokine PCR arrays can be used to detect a whole panel of Th1 and/or Th2 cytokines using a multiplex method. http://purl.obolibrary.org/obo/CL_0000788 CL http://purl.obolibrary.org/obo/GO_0001817 GO cytokine bead arrays Multiplex method used to detect a whole panel of Th1 and/or Th2 cytokines simultaneously from limited sample amounts. in_vitro panel of cytokines change high Apart from assaying single protein or gene at a time, cytokine bead arrays or cytokine PCR arrays can be used to detect a whole panel of Th1 and/or Th2 cytokines using a multiplex method. This method is quantitative and especially advantageous when the sample amount available for testing is scarce. http://purl.obolibrary.org/obo/CL_0000000 CL ELISA ELISA is used to assess the levels of protein of several Th1 and Th2 cytokines including IL-4, IL-5, IL-13, IL-10, IL-12, IFN-γ, and TGF-β. BALF supernatant, tissue homogenates, or cell pellets can be used. in_vitro lung protein levels of cytokines increase http://purl.obolibrary.org/obo/GO_0008559 GO medium Targeted enzyme-linked immunosorbent assays (ELISA) or real-time quantitative polymerase chain reaction (qRT-PCR) (routinely used and recommended): The ELISA and qRT-PCR are routinely used to assess the levels of protein and mRNA of several Th1 and Th2 cytokines including IL-4, IL-5, IL- 13, IL-10, IL-12, IFN-γ . BALF supernatant collected from lungs of animals exposed to toxic substances or human patients is used. Tissue homogenates or cell pellets can also be used. http://purl.obolibrary.org/obo/GO_0008559 GO http://purl.obolibrary.org/obo/GO_0002752 GO ELISA Enzyme-linked immunosorbent assay to measure protein levels of Th1 and Th2 cytokines, including IL-4, IL-5, IL-13, IL-10, IL-12, IFN-γ, and TGF-β, in BALF supernatant, tissue homogenates, or cell pellets. in_vitro lung protein levels of Th1 and Th2 cytokines increase http://purl.obolibrary.org/obo/OBI_0000470 OBI http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/PR_000000996 PR http://purl.obolibrary.org/obo/PR_000000997 PR http://purl.obolibrary.org/obo/PR_000001000 PR medium Targeted enzyme-linked immunosorbent assays (ELISA) or real-time quantitative polymerase chain reaction (qRT-PCR) (routinely used and recommended): The ELISA and qRT-PCR are routinely used to assess the levels of protein and mRNA of several Th1 and Th2 cytokines including IL-4, IL-5, IL- 13, IL-10, IL-12, IFN-γ. BALF supernatant collected from lungs of animals exposed to toxic substances or human patients is used. http://purl.obolibrary.org/obo/CL_0000788 CL http://purl.obolibrary.org/obo/GO_0001817 GO qRT-PCR Real-time quantitative polymerase chain reaction used to assess the mRNA expression levels of Th1 and Th2 cytokines and relevant genes like Arg-1 and Arg-2. in_vitro lung mRNA levels change http://purl.obolibrary.org/obo/GO_0006360 GO http://purl.obolibrary.org/obo/GO_0010468 GO medium real-time quantitative polymerase chain reaction (qRT-PCR) The ELISA and qRT-PCR are routinely used to assess the levels of protein and mRNA of several Th1 and Th2 cytokines including IL-4, IL-5, IL- 13, IL-10, IL-12, IFN-γ. The other genes of relevance to Th2 response and eventual pro-fibrotic response include Arginine (Arg)-1 and Arg-2. http://purl.obolibrary.org/obo/GO_0006360 GO qRT-PCR Real-time quantitative polymerase chain reaction to measure mRNA levels of Th1 and Th2 cytokines, including IL-4, IL-5, IL-13, IL-10, IL-12, IFN-γ, and TGF-β, in BALF supernatant, tissue homogenates, or cell pellets. in_vitro lung mRNA levels of Th1 and Th2 cytokines increase http://purl.obolibrary.org/obo/OBI_0000663 OBI http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/PR_000000996 PR http://purl.obolibrary.org/obo/PR_000000997 PR medium Targeted enzyme-linked immunosorbent assays (ELISA) or real-time quantitative polymerase chain reaction (qRT-PCR) (routinely used and recommended): The ELISA and qRT-PCR are routinely used to assess the levels of protein and mRNA of several Th1 and Th2 cytokines including IL-4, IL-5, IL- 13, IL-10, IL-12, IFN-γ. BALF supernatant collected from lungs of animals exposed to toxic substances or human patients is used. http://purl.obolibrary.org/obo/CL_0000788 CL http://purl.obolibrary.org/obo/GO_0001817 GO Co-culture myofibroblast differentiation assay Assessment of myofibroblast differentiation using co-culture models that mimic the alveolar capillary membrane. Immunofluorescent staining for α-SMA is used to detect differentiation. in_vitro fibroblasts epithelial cells lung human mouse myofibroblast differentiation increase http://purl.obolibrary.org/obo/GO_0002094 GO http://purl.obolibrary.org/obo/GO_0030154 GO not specified low Advanced co-culture models (myofibroblast differentiation): Co-culture models that mimic the alveolar capillary membrane (such as those listed for Event 1496 & Event 1498) can be used to assess myofibroblast differentiation in response to pro-fibrotic stressors using immunofluorescent staining for α-SMA. http://purl.obolibrary.org/obo/CL_0000134 CL http://purl.obolibrary.org/obo/GO_0002094 GO Hydrogel-based fibroblast culture Uses hydrogels (e.g., collagen, fibrin) to mimic ECM and assess fibroblast proliferation, activation, and matrix synthesis. in_vitro fibroblasts cell proliferation, activation, and matrix synthesis increase http://purl.obolibrary.org/obo/GO_0031012 GO medium Hydrogels can be prepared to express inherent biological signals, mechanical properties (e.g., modulus) and biochemical properties (e.g., proteins) of the ECM. Fibroblasts are usually cultured in fibrin and type-1 collagen that represent the matrix of the wound healing. Thus, the well-constructed hydrogel can be used to assess cell proliferation, activation and matrix synthesis as reflective of fibroblast activation. http://purl.obolibrary.org/obo/CL_0000057 CL immunofluorescence Myofibroblast differentiation is assessed using immunofluorescent staining for α-SMA in co-culture models mimicking the alveolar capillary membrane or microfluidic lung-on-a-chip models. in_vitro lung α-SMA expression increase medium Co-culture models that mimic the alveolar capillary membrane (such as those listed for Event 1496 & Event 1498) can be used to assess myofibroblast differentiation in response to pro-fibrotic stressors using immunofluorescent staining for α-SMA. More complex in vitro microfluidic lung-on-a-chip models (such as the one listed for Event 1497) can be used to assess myofibroblast differentiation in the same stead. http://purl.obolibrary.org/obo/CL_0000252 CL http://purl.obolibrary.org/obo/GO_0030097 GO Immunofluorescent staining Use of α-SMA immunofluorescence in co-culture or lung-on-a-chip models to assess myofibroblast differentiation. in_vitro fibroblasts lung myofibroblast differentiation increase http://purl.obolibrary.org/obo/GO_0045628 GO medium Co-culture models... can be used to assess myofibroblast differentiation in response to pro-fibrotic stressors using immunofluorescent staining for α-SMA. http://purl.obolibrary.org/obo/GO_0045628 GO Immunofluorescent staining for α-SMA Assesses myofibroblast differentiation in co-culture models or lung-on-a-chip systems using immunofluorescent staining for α-SMA. in_vitro alveolar capillary membrane α-SMA expression increase http://purl.obolibrary.org/obo/OBI_0000566 OBI http://purl.obolibrary.org/obo/PR_000001488 PR low Co-culture models that mimic the alveolar capillary membrane (such as those listed for Event 1496 & Event 1498) can be used to assess myofibroblast differentiation in response to pro-fibrotic stressors using immunofluorescent staining for α-SMA. http://purl.obolibrary.org/obo/CL_0000192 CL Immunohistochemistry Detects proliferation of fibroblasts and activation of myofibroblasts using antibodies against vimentin, procollagen 1, and α-SMA. Semiquantitative morphometric analysis can quantify marker-expressing cells. in_vivo lung number of cells expressing fibroblast/myofibroblast markers increase http://purl.obolibrary.org/obo/GO_0048146 GO low Proliferation of fibroblasts and activation of myofibroblasts is normally detected using individual antibodies against vimentin, procollagen 1 and α-SMA, specific markers of fibroblasts and myofibroblasts (Zhang, 1994). Although only semiquantitative, morphometric analysis of the lung slices can be conducted to quantify the total number of cells expressing the markers against the control lung sections where expression of specific markers is expected to be low or nil. http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0048146 GO In vitro fibroblast proliferation assay Measurement of fibroblast proliferation using water-soluble tetrazolium salts (WST)-1 and propidium iodide staining. Dose-dependent increase in MWCNT-induced fibroblast proliferation. in_vitro primary fibroblasts immortalised fibroblasts human mouse fibroblast proliferation increase http://purl.obolibrary.org/obo/GO_0008544 GO http://purl.obolibrary.org/obo/GO_0008283 GO not specified medium Fibroblast proliferation assay: Several primary and immortalised fibroblast types can be used for the assay. Proliferation assays such as water-soluble tetrazolium salts (WST)-1 and propidium iodide staining of cells have been used to show dose-dependent increase in MWCNT-induced increase in fibroblast proliferation that is in alignment with in vivo mouse fibrogenic response (Azad et al., 2013; Vietti et al., 2013) to the same material. http://purl.obolibrary.org/obo/CL_0000134 CL http://purl.obolibrary.org/obo/GO_0008544 GO In vitro marker expression analysis Measurement of specific protein markers (type-1 collagen, Thy-1, COX2, CAV1, TGF-β, α-SMA, Smad3) to assess fibroblast proliferation and differentiation. in_vitro fibroblasts lung epithelial cells A549 cells lung expression of markers (type-1 collagen, Thy-1, COX2, CAV1, TGF-β, α-SMA, Smad3) increase http://purl.obolibrary.org/obo/GO_0034003 GO not_specified In vitro, expression of type-1 collagen, Thy-1 cell surface antigen (Thy-1), cyclooxygenase-2 (COX2) and caveolin-1 (CAV1) are used as markers of homogeneous population of fibroblasts. Increased expression of Transforming growth factor beta (TGF-β) and α-SMA is used as markers of differentiated myofibroblasts. Transcription factor SMAD family member 3 (Smad3) is the other marker measured in vitro to assess the fibroblast proliferation and differentiation. http://purl.obolibrary.org/obo/CL_0000070 CL http://purl.obolibrary.org/obo/GO_0030198 GO propidium iodide staining Fibroblast proliferation is measured using propidium iodide staining of cells, showing a dose-dependent increase in proliferation. in_vitro fibroblasts cell proliferation increase http://purl.obolibrary.org/obo/GO_0008283 GO medium Proliferation assays such as water-soluble tetrazolium salts (WST)-1 and propidium iodide staining of cells have been used to show dose-dependent increase in MWCNT-induced increase in fibroblast proliferation Several primary and immortalised fibroblast types can be used for the assay. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0008283 GO WST-1 assay Measures fibroblast proliferation using water-soluble tetrazolium salts to quantify metabolically active cells. in_vitro primary fibroblasts immortalised fibroblasts cell proliferation increase high Proliferation assays such as water-soluble tetrazolium salts (WST)-1 and propidium iodide staining of cells have been used to show dose-dependent increase in MWCNT-induced increase in fibroblast proliferation that is in alignment with in vivo mouse fibrogenic response (Azad et al., 2013; Vietti et al., 2013) to the same material. http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0008283 GO ELISA Assesses protein levels of collagen I, collagen III, elastin, and tenascin C. not_specified protein levels increase http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium The qRT-PCR, ELISA, and immunohistochemistry are routinely used to assess the levels of protein and mRNA levels. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI Hydroxyproline Assay The Hydroxyproline Assay measures the amount of hydroxyproline, a non-proteinogenic amino acid found only in collagen, to quantify collagen levels. ex_vivo collagen levels increase medium Hydroxyproline is a non-proteinogenic amino acid formed by the prolyl-4-hydroxylase. Hydroxyproline is only found in collagen and thus, it serves as a direct measure of the amount of collagen present in cells or tissues. Colorimetric methods are readily available and have been extensively used to quantify collagen using this assay (Chen & Raghunath, 2009; Nikota et al., 2017). http://purl.obolibrary.org/obo/GO_0005581 GO http://purl.obolibrary.org/obo/GO_0006955 GO Hydroxyproline assay Quantifies collagen by measuring hydroxyproline, a non-proteinogenic amino acid found only in collagen, using colorimetric methods. not_specified hydroxyproline levels increase http://purl.obolibrary.org/obo/CHEBI_17348 CHEBI http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI medium Hydroxyproline is a non-proteinogenic amino acid formed by the prolyl-4-hydroxylase. Hydroxyproline is only found in collagen and thus, it serves as a direct measure of the amount of collagen present in cells or tissues. Colorimetric methods are readily available and have been extensively used to quantify collagen using this assay (Chen & Raghunath, 2009; Nikota et al., 2017). http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI http://purl.obolibrary.org/obo/GO_0030198 GO immunohistochemistry Assesses tissue/cellular distribution of collagen, which can be quantified using morphometric analysis. not_specified collagen distribution increase http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI low The qRT-PCR, ELISA, and immunohistochemistry are routinely used to assess the levels of protein and mRNA levels. Histological staining with stains such as Masson Trichrome, Picro-sirius red are used to identify the tissue/cellular distribution of collagen, which can be quantified using morphometric analysis both in vivo and in vitro. http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI http://purl.obolibrary.org/obo/GO_0030198 GO immunohistochemistry Immunohistochemistry is used to assess protein levels and tissue/cellular distribution of collagen I, collagen III, elastin and tenacin C. in_vivo protein levels and distribution increase low The qRT-PCR, ELISA, and immunohistochemistry are routinely used to assess the levels of protein and mRNA levels. http://purl.obolibrary.org/obo/GO_0005576 GO http://purl.obolibrary.org/obo/GO_0005249 GO Masson Trichrome staining Identifies tissue/cellular distribution of collagen, which can be quantified using morphometric analysis. not_specified collagen distribution increase http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI low Histological staining with stains such as Masson Trichrome, Picro-sirius red are used to identify the tissue/cellular distribution of collagen, which can be quantified using morphometric analysis both in vivo and in vitro. http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI http://purl.obolibrary.org/obo/GO_0030198 GO Picro-sirius red staining Identifies tissue/cellular distribution of collagen, which can be quantified using morphometric analysis. not_specified collagen distribution increase http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI low Histological staining with stains such as Masson Trichrome, Picro-sirius red are used to identify the tissue/cellular distribution of collagen, which can be quantified using morphometric analysis both in vivo and in vitro. http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI http://purl.obolibrary.org/obo/GO_0030198 GO qRT-PCR Assesses mRNA levels of genes such as collagen I, collagen III, elastin, and tenascin C. not_specified mRNA levels increase http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO medium The qRT-PCR, ELISA, and immunohistochemistry are routinely used to assess the levels of protein and mRNA levels. http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO Sircol Collagen Assay Detects collagen in histology samples using Sirius Red F3BA dye, which selectively binds to collagen and is read at 540 nm. not_specified collagen quantification increase http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI medium The Serius dye has been used for many decades to detect collagen in histology samples. The Serius Red F3BA selectively binds to collagen and the signal can be read at 540 nm (Chen & Raghunath, 2009; Nikota et al., 2017). http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI http://purl.obolibrary.org/obo/GO_0030198 GO Chromatin immunoprecipitation (ChIP) Detects site-specific histone acetylation changes using chromatin immunoprecipitation. in_vitro site-specific histone acetylation increase http://purl.obolibrary.org/obo/GO_0016573 GO low detection of site-specific histone acetylation changes using chromatin immunoprecipitation (ChIP) or ChIP-on-Chip http://purl.obolibrary.org/obo/PR_000007233 PR http://purl.obolibrary.org/obo/GO_0016573 GO HDAC activity assay Measures HDAC activity using colorimetric or fluorimetric kits. in_vitro HDAC activity decrease http://purl.obolibrary.org/obo/GO_0004407 GO high HDAC inhibition can be detected directly by the measurement of HDAC activity using commercially available colorimetric or fluorimetric kits http://purl.obolibrary.org/obo/PR_000008719 PR http://purl.obolibrary.org/obo/GO_0016575 GO Immunological detection of histone acetylation Using anti-acetylated histone antibodies to detect histone acetylation. in_vitro histone acetylation change not_specified The measurement methods include the immunological detection of histone acetylation with anti-acetylated histone antibodies Mass spectrometry-based proteomics Detects global histone acetylation changes using mass spectrometry. in_vitro global histone acetylation increase http://purl.obolibrary.org/obo/GO_0016573 GO http://purl.obolibrary.org/obo/OBI_0000272 OBI medium The measurement methods include the immunological detection of histone acetylation with anti-acetylated histone antibodies The HDAC activity is measured directly with ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) by calculating the ratio of deacetylated peptide and acetylated peptide http://purl.obolibrary.org/obo/PR_000007233 PR http://purl.obolibrary.org/obo/GO_0016573 GO TGx-HDACi transcriptomic biomarker Predicts HDAC inhibition by measuring perturbations in gene expression patterns using an 81-gene transcriptomic biomarker. in_vitro TK6 human lymphoblastoid cells Homo sapiens gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO high HDAC inhibition can be predicted by perturbations in gene expression patterns as well; an 81-gene transcriptomic biomarker of HDAC inhibition, called TGx-HDACi, has shown to accurately predict HDAC inhibition after 4 hour exposures to HDI in TK6 human lymphoblastoid cells http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO UHPLC-ESI-MS/MS Measures HDAC activity directly by calculating the ratio of deacetylated peptide and acetylated peptide using ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry. in_vitro HDAC activity decrease http://purl.obolibrary.org/obo/GO_0004407 GO http://purl.obolibrary.org/obo/OBI_0000272 OBI medium The HDAC activity is measured directly with ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) by calculating the ratio of deacetylated peptide and acetylated peptide http://purl.obolibrary.org/obo/PR_000008719 PR http://purl.obolibrary.org/obo/GO_0016575 GO UHPLC-ESI-MS/MS Measures HDAC activity directly by calculating the ratio of deacetylated peptide and acetylated peptide. in_vitro ratio of deacetylated/acetylated peptide decrease medium The HDAC activity is measured directly with ultra-high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) by calculating the ratio of deacetylated peptide and acetylated peptide Western blot Detects global histone acetylation changes using immunological detection with anti-acetylated histone antibodies. in_vitro global histone acetylation increase http://purl.obolibrary.org/obo/GO_0016573 GO http://purl.obolibrary.org/obo/OBI_0000269 OBI medium The measurement methods include the immunological detection of histone acetylation with anti-acetylated histone antibodies The histones are isolated from pellets of cells treated with HDIs, followed by acid-urea-triton gel electrophoresis, western blotting, and immunohistochemistry http://purl.obolibrary.org/obo/PR_000007233 PR http://purl.obolibrary.org/obo/GO_0016573 GO Chromatin immunoprecipitation (ChIP) Measures site-specific histone acetylation changes by immunoprecipitating chromatin with acetylated histone-specific antibodies followed by DNA analysis. in_vitro site-specific histone acetylation increase http://purl.obolibrary.org/obo/GO_0016573 GO low The histone acetylation increase is detected as global histone acetylation changes by Western blot or mass spectrometry (MS)-based proteomics methods or as site-specific histone acetylation changes using chromatin immunoprecipitation (ChIP) or ChIP-on-Chip. http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0016573 GO immunodetection with anti-acetylated histone antibodies This assay detects histone acetylation levels using antibodies specific for acetylated histone epitopes, typically via immunodetection methods such as immunofluorescence or ELISA. in_vitro histone acetylation level increase http://purl.obolibrary.org/obo/GO_0016570 GO not_specified Histone acetylation is measured by the immunological detection of histone acetylation with anti-acetylated histone antibodies http://purl.obolibrary.org/obo/PR_000004562 PR http://purl.obolibrary.org/obo/GO_0016570 GO Mass spectrometry-based proteomics Measures global histone acetylation changes using mass spectrometry to detect acetylated histone peptides. in_vitro global histone acetylation increase http://purl.obolibrary.org/obo/GO_0016573 GO http://purl.obolibrary.org/obo/OBI_0000424 OBI medium The histone acetylation increase is detected as global histone acetylation changes by Western blot or mass spectrometry (MS)-based proteomics methods or as site-specific histone acetylation changes using chromatin immunoprecipitation (ChIP) or ChIP-on-Chip. http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0016573 GO Sodium [3H]acetate labeling Measures histone acetylation on chromatin by incorporating radiolabeled acetate into newly acetylated histones. in_vitro histone acetylation increase http://purl.obolibrary.org/obo/GO_0016573 GO low Histone acetylation on chromatin can be measured using the labeling method with sodium [3H]acetate [Gunjan et al., 2001]. http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0016573 GO Western blot Measures global histone acetylation changes using immunological detection with anti-acetylated histone antibodies. in_vitro global histone acetylation increase http://purl.obolibrary.org/obo/GO_0016573 GO medium Histone acetylation is measured by the immunological detection of histone acetylation with anti-acetylated histone antibodies [Richon et al., 2004]. The histone acetylation increase is detected as global histone acetylation changes by Western blot or mass spectrometry (MS)-based proteomics methods or as site-specific histone acetylation changes using chromatin immunoprecipitation (ChIP) or ChIP-on-Chip. http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0016573 GO [3H]deoxycytidine or [3H]thymidine incorporation Monitoring DNA synthesis by measuring the incorporation of tritiated deoxycytidine or thymidine into cell DNA during the S phase. in_vitro DNA synthesis change http://purl.obolibrary.org/obo/GO_0006260 GO low The incorporation of [3H]deoxycytidine or [3H]thymidine into cell DNA during the S phase can be monitored as DNA synthesis http://purl.obolibrary.org/obo/CHEBI_35163 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO [3H]thymidine incorporation Monitors DNA synthesis during S phase by measuring incorporation of radiolabeled [3H]deoxycytidine or [3H]thymidine into cellular DNA. in_vitro DNA synthesis (S-phase incorporation of radiolabeled thymidine) not_specified http://purl.obolibrary.org/obo/GO_0006260 GO not_specified The incorporation of [3H]deoxycytidine or [3H]thymidine into cell DNA during the S phase can be monitored as DNA synthesis http://purl.obolibrary.org/obo/GO_0005635 GO http://purl.obolibrary.org/obo/GO_0006260 GO DNA synthesis assay Monitors the incorporation of [3H]deoxycytidine or [3H]thymidine into cell DNA during the S phase as a measure of DNA synthesis. in_vitro DNA synthesis increase http://purl.obolibrary.org/obo/GO_0006260 GO not_specified The incorporation of [3H]deoxycytidine or [3H]thymidine into cell DNA during the S phase can be monitored as DNA synthesis [Heintz et al., 1982]. http://purl.obolibrary.org/obo/CHEBI_15712 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO flow cytometry Measures the percentage of cells in G1, G0, S, and G2/M phases using flow cytometry. in_vitro cell cycle phase distribution change http://purl.obolibrary.org/obo/GO_0044848 GO http://purl.obolibrary.org/obo/OBI_0000268 OBI medium The percentage of cells at G1, G0, S, and G2/M phases can be detected by flow cytometry http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0007049 GO flow cytometry Detection of the percentage of cells in specific cell cycle phases (G1, G0, S, and G2/M) using flow cytometry. in_vitro percentage of cells at G1, G0, S, and G2/M phases change http://purl.obolibrary.org/obo/GO_0007084 GO medium The percentage of cells at G1, G0, S, and G2/M phases can be detected by flow cytometry http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0007049 GO live-cell imaging Measures the four cell-cycle phases in living cells using four-color fluorescent proteins. in_vitro cell cycle phase distribution change http://purl.obolibrary.org/obo/GO_0044848 GO http://purl.obolibrary.org/obo/OBI_0001047 OBI low The four cell-cycle phases in living cells can be measured with four-color fluorescent proteins using live-cell imaging http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0007049 GO radiolabel incorporation Monitors DNA synthesis during the S phase by measuring the incorporation of [3H]deoxycytidine or [3H]thymidine into cell DNA. in_vitro DNA synthesis change http://purl.obolibrary.org/obo/GO_0071897 GO low The incorporation of [3H]deoxycytidine or [3H]thymidine into cell DNA during the S phase can be monitored as DNA synthesis http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO computer-assisted sperm analysis Measures changes in sperm parameters using computerized analysis. in_vivo sperm epididymis sperm parameters change http://purl.obolibrary.org/obo/CL_0000239 CL medium Changes in sperm are measured by computer-assisted sperm analysis http://purl.obolibrary.org/obo/CL_0000239 CL condensed spermatid count Measures the total number of condensed spermatids per testis by homogenizing testicular parenchyma and counting nuclei. in_vivo spermatids testis condensed spermatid count decrease http://purl.obolibrary.org/obo/CL_0000028 CL low For the measurement of the total number of condensed spermatids per testis, a weighed portion of the parenchyma from the left testis was homogenized Sperm or homogenization-resistant spermatid nuclei densities were calculated from the average number of nuclei and were expressed as total or as per gram of epididymis or testis weight http://purl.obolibrary.org/obo/CL_0000028 CL eosin-stained sperm morphology assessment Visual inspection of eosin-stained sperm from the cauda epididymis to identify morphological abnormalities in head or tail. ex_vivo sperm epididymis proportion of sperm with abnormal head or tail increase low For the assessment of sperm morphology, eosin-stained sperm collected from the cauda epididymis is observed. At least 200 sperm on each slide were examined for the proportion of sperm with abnormal head (overhooked, blunt hook, banana-shaped, amorphous, or extremely oversized) or tail (twisted, bent, corkscrew, double/multiple) [Wade et al., 2006]. http://purl.obolibrary.org/obo/CL_0000182 CL histopathologic examination Observes testicular tissue structure for normal germinal epithelial cells and Leydig cells using light microscopy or transmission electron microscopy. in_vivo germinal epithelial cells Leydig cells testis testicular tissue structure change http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/CL_0000188 CL low The testicular tissue structure is observed whether there are normal germinal epithelial cells and Leydig cells The testis is fixed for observations by light microscopy or transmission electron microscopy http://purl.obolibrary.org/obo/UBERON_0000473 UBERON histopathology Testicular tissue structure is observed by light microscopy or transmission electron microscopy to assess the presence of normal germinal epithelial cells and Leydig cells. ex_vivo germinal epithelial cells Leydig cells testis tissue structure change low The testicular tissue structure is observed whether there are normal germinal epithelial cells and Leydig cells [Mercantepe et al., 2018]. The testis is fixed for observations by light microscopy or transmission electron microscopy [McDowell and Trump, 1976; Mercantepe et al., 2018]. http://purl.obolibrary.org/obo/UBERON_0004648 UBERON http://purl.obolibrary.org/obo/GO_0009655 GO LDH and LDH-X activity Measures enzyme activity of total LDH and LDH-X in homogenized testis supernatant by monitoring NAD absorbance. in_vivo testis LDH and LDH-X activity change http://purl.obolibrary.org/obo/PR_000009089 PR low For the determination of total LDH and LDH-X in the supernatant of the homogenized testis fragment, enzyme activity was measured by monitoring the extinction of NAD absorbance http://purl.obolibrary.org/obo/PR_000009089 PR testicular volume measurement Assesses testicular atrophy using tools such as orchidometer, rulers, calipers, or ultrasonography. in_vivo testis testicular volume decrease low Testicular atrophy can be assessed by testicular volume measurement using an orchidometer, rulers, calipers, and ultrasonography http://purl.obolibrary.org/obo/UBERON_0000473 UBERON urinary zinc excretion Quantifies the amount of zinc excreted in urine to assess systemic zinc handling associated with testicular injury. not_specified urine urinary zinc excretion not_specified not_specified urinary zinc excretion urinary zinc excretion and testicular zinc content Examines zinc concentration in urine and testis, which is relevant to testicular injury. in_vivo testis zinc concentration change http://purl.obolibrary.org/obo/CHEBI_29105 CHEBI low The urinary zinc excretion and testicular zinc content are examined since zinc concentration has been shown to play an important role in the production of testicular injury http://purl.obolibrary.org/obo/UBERON_0000473 UBERON zinc measurement Urinary zinc excretion and testicular zinc content are examined to assess testicular injury. in_vivo testis urinary system zinc concentration decrease medium The urinary zinc excretion and testicular zinc content are examined since zinc concentration has been shown to play an important role in the production of testicular injury [Foster et al., 1983]. http://purl.obolibrary.org/obo/CHEBI_29083 CHEBI http://purl.obolibrary.org/obo/GO_0043066 GO immunofluorescence Visualization of CYP2E1 protein in cultured neuron cells using a rabbit polyclonal antibody for CYP2E1 and a FITC-conjugated anti-rabbit antibody, measured with a confocal laser-scanning microscope. in_vitro cultured neuron cells CYP2E1 protein levels change low Visualization of CYP2E1 can be done with immunofluorescence in cultured neuron cells. With the use of this technique, an increase or decrease of CYP2E1 can be measured. A rabbit polyclonal antibody for CYP2E1 is used in combination with a FITC-conjugated anti-rabbit antibody. With the FITC tag the CYP2E1 proteins can be made visible using fluorescence. Measurements are done with a confocal laser-scanning microscope. http://purl.obolibrary.org/obo/PR_000001110 PR http://purl.obolibrary.org/obo/GO_0019538 GO western blot Visualization of CYP2E1 protein levels using western blot analysis. in_vitro CYP2E1 protein levels change medium Another way of visualization can be done with the western blot analysis. http://purl.obolibrary.org/obo/PR_000001110 PR http://purl.obolibrary.org/obo/GO_0019538 GO 2D gel-electrophoresis and tandem mass spectrometry Proteins are purified from cells after drug incubation, separated using two-dimensional gel electrophoresis, and identified via tandem mass spectrometry. in_vitro identification of protein spots change not_specified Another possibility is the use of 2D gel-electrophoresis and tandem mass spectrometry based proteomics. Proteins are purified from cells after incubation with a drug. With 2D gel-electrophoresis the proteins are separated, afterwards the spots of interest are identified with tandem mass spectrometry. 2D gel-electrophoresis with tandem mass spectrometry Proteins are purified from cells after incubation with a drug, separated using 2D gel-electrophoresis, and spots of interest are identified with tandem mass spectrometry. in_vitro protein adduct formation increase http://purl.obolibrary.org/obo/OBI_0000368 OBI http://purl.obolibrary.org/obo/OBI_0000475 OBI low Proteins are purified from cells after incubation with a drug. With 2D gel-electrophoresis the proteins are separated, afterwards the spots of interest are identified with tandem mass spectrometry. http://purl.obolibrary.org/obo/PR_000000001 PR Biotin affinity tag-based protein adduct detection A drug labeled with a biotin affinity tag reacts with proteins and binds covalently. After incubation, drug-attached proteins are separated using the tag and identified via proteomics with LC/MS/MS. in_vitro protein adduct formation increase http://purl.obolibrary.org/obo/OBI_0000475 OBI low A drug is labelled with a biotin affinity tag, which than can react with proteins and bind covalently. After incubation with several proteins the drugs attached to the proteins are separated from the rest of the free proteins with the use of the tag. Next the proteins which are altered by the drug can be identified with proteomics. A LC/MS/MS technique is used. http://purl.obolibrary.org/obo/PR_000000001 PR LC/MS/MS This assay uses liquid chromatography coupled with tandem mass spectrometry to identify proteins altered by a biotin-labelled drug after separation of the labelled proteins from free proteins. It is used to determine protein adducts. in_vitro identification of drug-altered proteins change http://purl.obolibrary.org/obo/OBI_0000048 OBI medium A LC/MS/MS technique is used. Next the proteins which are altered by the drug can be identified with proteomics. A drug is labelled with a biotin affinity tag, which than can react with proteins and bind covalently. http://purl.obolibrary.org/obo/CHEBI_0005743 CHEBI http://purl.obolibrary.org/obo/GO_0016338 GO 2D SDS-PAGE Separates mitochondrial and cytosolic proteins based on size and pH for subsequent detection of 4-hydroxynonenal modified proteins. in_vitro protein separation not_specified low Mitochondrial and cytosolic proteins are subjected to 2D SDS-PAGE and are separated based on the size and pH. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI 2D SDS-PAGE and Immunofluorescence Proteins are separated by size and pH using 2D SDS-PAGE, followed by detection of 4-hydroxynonenal-modified proteins using a tagged polyclonal antibody. in_vitro 4-hydroxynonenal modified proteins change http://purl.obolibrary.org/obo/GO_0044004 GO low Proteomics is a tool which can be used for the detection of 4-hydroxynonenal modified proteins. Mitochondrial and cytosolic proteins are subjected to 2D SDS-PAGE and are separated based on the size and pH. With the use of a polyclonal antibody against 4-hydroxynonenal which has an immunofluorescence tag the modified proteins can be detected. http://purl.obolibrary.org/obo/PR_000000001 PR Immunofluorescence Detects 4-hydroxynonenal modified proteins using a polyclonal antibody with an immunofluorescence tag on 2D SDS-PAGE gels. in_vitro 4-hydroxynonenal modified proteins increase not_specified With the use of a polyclonal antibody against 4-hydroxynonenal which has an immunofluorescence tag the modified proteins can be detected. MALDI-TOF MS Identifies proteins of interest cut from SDS-PAGE gels using mass spectrometry analysis. in_vitro protein identification not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI medium The proteins of interest on the SDS-PAGE gel can be cut out and cleaned. Cleaning is necessary since the identification is done by a MALDI-TOF MS analysis. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI Western blot (4-hydroxynonenal) Detects 4-hydroxynonenal modified proteins using a polyclonal antibody with an immunofluorescence tag. in_vitro 4-hydroxynonenal modified proteins increase http://purl.obolibrary.org/obo/OBI_0000213 OBI http://purl.obolibrary.org/obo/CHEBI_17425 CHEBI medium With the use of a polyclonal antibody against 4-hydroxynonenal which has an immunofluorescence tag the modified proteins can be detected. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0006464 GO 2D gel electrophoresis Separates proteins based on size and pH to detect GRP78 as a biomarker for endoplasmic stress. in_vitro GRP78 protein presence not_specified low GRP78 can be used as a biomarker for endoplasmic stress and as discussed before this protein is released from the effector when the unfolded protein reaction occurs. The detection of the GRP78 protein is possible with the use of 2D gel electrophoresis in combination with proteomics. Proteins are extracted from cells, which were incubated with a toxicant, and sampled on the 2D gel. Separation is done based on the protein size and the pH value. http://purl.obolibrary.org/obo/GO_0030968 GO fluorescent reporter cell lines Measures activation of sensors, transcription factors, and targets involved in the unfolded protein response using fluorescent reporters. in_vitro activation of UPR sensors/transcription factors increase http://purl.obolibrary.org/obo/GO_0030968 GO http://purl.obolibrary.org/obo/OBI_0001861 OBI high Activation of the sensors, transcription factors and targets can be measured through several assays (Takayanagi, et al 2013) and fluorescent reporter cell lines (Wink et al., 2014) http://purl.obolibrary.org/obo/GO_0030968 GO immunohistochemistry Uses an anti-GRP78 antibody to visualize GRP78 protein in cells, indicating endoplasmic stress. in_vitro GRP78 protein presence not_specified medium Because of the low abundance the GRP78 protein can also be made visible with immunohistochemistry and imaging using an anti-GRP78 antibody. http://purl.obolibrary.org/obo/GO_0030968 GO mass spectrometry Identifies and quantifies GRP78 protein purified from 2D gels, confirming its presence as a biomarker for endoplasmic stress. in_vitro GRP78 protein presence not_specified http://purl.obolibrary.org/obo/OBI_0000473 OBI medium The protein of interest form the 2D gel can be purified and cleaned for the identification with mass spectrometry. http://purl.obolibrary.org/obo/GO_0030968 GO mass spectrometry A method used to identify purified proteins extracted from a 2D gel. in_vitro protein identification change medium The protein of interest form the 2D gel can be purified and cleaned for the identification with mass spectrometry. http://purl.obolibrary.org/obo/GO_0034611 GO Annexin V affinity assay Detects apoptosis by measuring the binding of annexin V to phosphatidylserine exposed on the outer membrane of apoptotic cells. in_vitro annexin V binding increase http://purl.obolibrary.org/obo/GO_0035004 GO medium An older but effective technique it the annexin V – affinity assay. The principle of this assay is the high affinity binding between annexin V and phosphatidylserine. In a vital cell there is a membrane lipid asymmetry where phosphatidylserine molecules are facing the cytosol. During apoptosis the membrane lipid asymmetry is lost, and the phosphatidylserine molecules are expressed in the outer membrane. When annexin-V is present in combination with Ca2+ it binds with high affinity to phosphatidylserine. http://purl.obolibrary.org/obo/CHEBI_15640 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO annexin V – affinity assay Detects phosphatidylserine exposure on the outer cell membrane, a hallmark of early apoptosis, using annexin V binding. in_vitro phosphatidylserine exposure increase medium An older but effective technique it the annexin V – affinity assay. The principle of this assay is the high affinity binding between annexin V and phosphatidylserine. In a vital cell there is a membrane lipid asymmetry where phosphatidylserine molecules are facing the cytosol. During apoptosis the membrane lipid asymmetry is lost, and the phosphatidylserine molecules are expressed in the outer membrane. http://purl.obolibrary.org/obo/CL_0000070 CL Cytochrome c detection with metal nanoclusters Detects the release of cytochrome c, an early marker of apoptosis, using metal nanoclusters with a fluorescent probe. in_vitro cytochrome c release increase medium Cytochrome c is also a protein which is released in an early stage of apoptosis. Detection of cytochrome c can be done with metal nanoclusters which have a fluorescent probe in addition to western blot assay. http://purl.obolibrary.org/obo/PR_00000006 PR http://purl.obolibrary.org/obo/GO_0006915 GO ELISA Detects cleaved caspase-3, a key executioner protein in apoptosis, using enzyme-linked immunosorbent assays. in_vitro cleaved caspase-3 levels increase medium Another technique is the detection of cleaved caspase-3, which could be done with western blot or enzyme-linked immunosorbent assays. http://purl.obolibrary.org/obo/PR_000044681 PR http://purl.obolibrary.org/obo/GO_0006985 GO LDH assay Measures the release of lactate dehydrogenase (LDH) from cells undergoing apoptosis. in_vitro LDH release increase http://purl.obolibrary.org/obo/GO_0004459 GO medium Lactate dehydrogenase (LDH) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) substances which are released from cells which undergo apoptosis. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0006915 GO MTT assay Measures the reduction of MTT by viable cells, indicating cell viability or apoptosis. in_vitro MTT reduction decrease http://purl.obolibrary.org/obo/GO_0008544 GO medium Lactate dehydrogenase (LDH) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) substances which are released from cells which undergo apoptosis. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0006915 GO western blot Detects cleaved caspase-3, a key executioner protein in apoptosis, using western blot analysis. in_vitro cleaved caspase-3 levels increase low Another technique is the detection of cleaved caspase-3, which could be done with western blot or enzyme-linked immunosorbent assays. http://purl.obolibrary.org/obo/PR_000044681 PR http://purl.obolibrary.org/obo/GO_0006985 GO Western blot for cleaved caspase-3 Detects the presence of cleaved caspase-3, a key indicator of apoptosis, using western blot. in_vitro cleaved caspase-3 levels increase http://purl.obolibrary.org/obo/GO_0004197 GO low Another technique is the detection of cleaved caspase-3, which could be done with western blot or enzyme-linked immunosorbent assays. http://purl.obolibrary.org/obo/PR_00000137 PR http://purl.obolibrary.org/obo/GO_0006915 GO Western blot for cytochrome c Detects the release of cytochrome c, an early marker of apoptosis, using western blot. in_vitro cytochrome c levels increase low Cytochrome c is also a protein which is released in an early stage of apoptosis. Detection of cytochrome c can be done with metal nanoclusters which have a fluorescent probe in addition to western blot assay. http://purl.obolibrary.org/obo/PR_00000006 PR http://purl.obolibrary.org/obo/GO_0006915 GO ELISA ELISA is used to quantify spectrin breakdown products (SBDP-145) in cerebrospinal fluid. in_vitro cerebrospinal fluid SBDP-145 concentration increase http://purl.obolibrary.org/obo/UBERON_0001359 UBERON medium First quantification can be done with an ELISA technique, from a sample taken out of the cerebrospinal fluid. http://purl.obolibrary.org/obo/GO_0006508 GO immunohistochemistry Immunohistochemistry is used to label and visualize the expression and release of SBDP-145. in_vitro SBDP-145 expression and release increase http://purl.obolibrary.org/obo/OBI_0000615 OBI low Another way is to label SBDP-145 with the use of immunohistochemistry, so that the expression and release of SBDP-145 can be made visible. http://purl.obolibrary.org/obo/GO_0010485 GO PET scan A PET scan is used to detect neurodegeneration in the brain. in_vivo brain neurodegeneration not_specified low A biomarker is needed since a common way to detect neurodegeneration is with the use of a PET scan. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0050790 GO automated image-based system Measures sperm morphology and motility using an automated image-based system. in_vitro sperm morphology and motility not_specified high Traditional spermatocytes assessment includes sperm count and concentration (haemocytometer, automated image-based system), morphology and motility (microscope, automated image-based system) flow cytometric method Assesses relative proportions of spermatogenic cell populations using flow cytometry based on DNA content and mitochondrial content. in_vitro spermatogenic cells testis relative proportions of spermatogenic cell populations not_specified high Relative proportions of spermatogenic cell populations were assessed in fixed cells using a flow cytometric method [Wade et al., 2006]. haemocytometer Measures sperm count and concentration using a haemocytometer. in_vitro sperm count and concentration not_specified medium Traditional spermatocytes assessment includes sperm count and concentration (haemocytometer, automated image-based system) The number of spermatozoa was determined by a haematocytometer [Zindy et al., 2001]. Halosperm kit Measures DNA fragmentation/integrity in sperm. in_vitro DNA fragmentation/integrity not_specified medium assays for genetic integrity (e.g. via measurement of DNA fragmentation/integrity -Halosperm kit or reactive oxygen species) microscope Sperm morphology and motility are assessed using a microscope. in_vitro spermatozoa sperm morphology, motility not_specified low Traditional spermatocytes assessment includes sperm count and concentration (haemocytometer, automated image-based system), morphology and motility (microscope, automated image-based system) http://purl.obolibrary.org/obo/CL_0002163 CL http://purl.obolibrary.org/obo/GO_0030202 GO propidium iodide staining Measures viability of spermatocytes by staining necrotic cells with propidium iodide. in_vitro cell viability not_specified medium viability (for example propidium iodide staining of necrotic cells, TUNEL assay staining apoptotic cells) propidium iodide staining Necrotic cells are identified by propidium iodide staining, which indicates membrane permeability. in_vitro cells number of necrotic cells increase medium and viability (for example propidium iodide staining of necrotic cells, TUNEL assay staining apoptotic cells). http://purl.obolibrary.org/obo/CL_0000003 CL http://purl.obolibrary.org/obo/GO_0008628 GO reactive oxygen species assay Measures reactive oxygen species in sperm. in_vitro reactive oxygen species not_specified medium assays for genetic integrity (e.g. via measurement of DNA fragmentation/integrity -Halosperm kit or reactive oxygen species) sperm morphology and motility Assesses sperm morphology and motility using microscopy or automated image-based analysis. ex_vivo spermatozoa epididymis cauda sperm morphology and motility not_specified not_specified morphology and motility (microscope, automated image-based system) http://purl.obolibrary.org/obo/CL_0000023 CL http://purl.obolibrary.org/obo/GO_0030315 GO sperm-zona pellucida interaction assay Measures sperm-zona pellucida interaction, such as ZP-receptor binding. in_vitro sperm-zona pellucida interaction not_specified medium fertilization defects (through various measures of sperm-zona pellucida (ZP) interaction, such as measurement of ZP-receptor binding) testicular sperm count Measures testicular sperm counts and daily sperm production by counting spermatids per testis. in_vivo testis spermatid count not_specified low Testicular sperm counts and daily sperm production were determined by counting the total number of spermatids per testis and divided by the testicular weight to give the results in spermatids per gram of testis [Oishi, 2001]. TUNEL assay Measures apoptosis in spermatocytes by staining apoptotic cells. in_vitro apoptosis not_specified medium viability (for example propidium iodide staining of necrotic cells, TUNEL assay staining apoptotic cells) viability assay (PI/TUNEL) Determines sperm viability by staining necrotic cells with propidium iodide and apoptotic cells with TUNEL assay. ex_vivo spermatozoa epididymis cauda sperm viability (necrotic/apoptotic) not_specified not_specified viability (for example propidium iodide staining of necrotic cells, TUNEL assay staining apoptotic cells) http://purl.obolibrary.org/obo/CL_0000023 CL http://purl.obolibrary.org/obo/GO_0006915 GO area measurement Measures the total area of a tissue, organ, or individual organism to indicate growth. in_vivo total area decrease not_specified Growth can be indicated by measuring weight, length, total volume, and/or total area of a tissue, organ or individual organism. http://purl.obolibrary.org/obo/NCBITaxon_1 NCBITAXON http://purl.obolibrary.org/obo/GO_0040007 GO length measurement Measures the length of a tissue, organ, or individual organism to indicate growth. in_vivo length decrease not_specified Growth can be indicated by measuring weight, length, total volume, and/or total area of a tissue, organ or individual organism. http://purl.obolibrary.org/obo/NCBITaxon_1 NCBITAXON http://purl.obolibrary.org/obo/GO_0040007 GO morphometric growth measurement Measures growth by quantifying weight, length, total volume, and/or total area of a tissue, organ, or organism. in_vivo tissue organ organism weight, length, total volume, and/or total area of a tissue, organ or individual organism decrease http://purl.obolibrary.org/obo/OBI_0000075 OBI http://purl.obolibrary.org/obo/GO_0040007 GO low Growth can be indicated by measuring weight, length, total volume, and/or total area of a tissue, organ or individual organism. volume measurement Measures the total volume of a tissue, organ, or individual organism to indicate growth. in_vivo total volume decrease not_specified Growth can be indicated by measuring weight, length, total volume, and/or total area of a tissue, organ or individual organism. http://purl.obolibrary.org/obo/NCBITaxon_1 NCBITAXON http://purl.obolibrary.org/obo/GO_0040007 GO weight measurement Measures the weight of a tissue, organ, or individual organism to indicate growth. in_vivo weight decrease http://purl.obolibrary.org/obo/VT_0001259 VT not_specified Growth can be indicated by measuring weight, length, total volume, and/or total area of a tissue, organ or individual organism. http://purl.obolibrary.org/obo/NCBITaxon_1 NCBITAXON http://purl.obolibrary.org/obo/GO_0040007 GO radioactive chitin synthase activity assay Measures CHS-1 activity by incubating crude enzyme preparations with radioactively labelled chitin precursors (e.g., 14C-UDP-GlcNAc) and quantifying radioactivity in formed chitin chains via scintillation counting. in_vitro Anopheles gambiae radioactivity in chitin chains increase http://purl.obolibrary.org/obo/GO_0004480 GO low One can incubate the enzyme preparation with radioactively labelled chitin precursors (e.g. 14C-UDP-GlcNAc) and measure radioactivity in the formed chitin chains by scintillation counting (Cohen 1982; Cohen and Casida 1990). http://purl.obolibrary.org/obo/GO_0006030 GO scintillation counting This assay measures chitin synthase activity by incubating the enzyme preparation with radioactively labelled chitin precursors (e.g. 14C-UDP-GlcNAc) and quantifying radioactivity in the formed chitin chains. in_vitro digestive tract Anopheles gambiae radioactivity in chitin chains increase http://purl.obolibrary.org/obo/CHEBI_50863 CHEBI low One can incubate the enzyme preparation with radioactively labelled chitin precursors (e.g. 14C-UDP-GlcNAc) and measure radioactivity in the formed chitin chains by scintillation counting (Cohen 1982; Cohen and Casida 1990). http://purl.obolibrary.org/obo/CHEBI_50863 CHEBI WGA-ELISA (sandwich-ELISA) A non-radioactive colorimetric assay where synthesized chitin is detected using wheat germ agglutinin (WGA) in a sandwich-ELISA format, utilizing HRP-conjugated WGA and a colorimetric substrate. in_vitro Anopheles gambiae amount of chitin synthesized not_specified not_specified the detection of CHS-1 activity involves the binding of chitin chains to wheat germ agglutinin (WGA) which possesses specific chitin binding properties The assay builds on the principle of a sandwich-ELISA, where chitin binds to a layer of WGA. The cleavage of the HRP substrate leads to color formation and the amount of chitin synthesized can be determined colorimetrically. http://purl.obolibrary.org/obo/GO_0006074 GO Calcofluor white staining Fluorescence-based detection of chitin in homogenates of organisms without prior sample treatment. in_vitro cuticle chitin content decrease http://purl.obolibrary.org/obo/CHEBI_15887 CHEBI not_specified Alternatively, one can also quantify glucosamine colorimetrically after deacetylation and hydrolysis of chitin (Lehmann and White 1975; Zhang and Zhu 2006). There also exists an approach based on the detection of fluorescence after staining with calcofluor white. In this assay, no treatment of the samples is necessary, the detection is carried out in homogenates of the respective organisms as calcofluor white directly binds to chitin (Henriques et al. 2020). http://purl.obolibrary.org/obo/UBERON_0002291 UBERON http://purl.obolibrary.org/obo/GO_0006033 GO Calcofluor white staining This assay detects fluorescence after staining with calcofluor white, which directly binds to chitin in homogenates. in_vitro cuticle Fluorescence intensity decrease http://purl.obolibrary.org/obo/GO_0008312 GO medium There also exists an approach based on the detection of fluorescence after staining with calcofluor white. In this assay, no treatment of the samples is necessary, the detection is carried out in homogenates of the respective organisms as calcofluor white directly binds to chitin (Henriques et al. 2020). http://purl.obolibrary.org/obo/CHEBI_59864 CHEBI http://purl.obolibrary.org/obo/GO_0005102 GO Chitin synthase activity assay Quantifies chitin content by adding homogenized chitin-containing material to a reaction measuring chitin synthase activity. not_specified chitin synthase activity not_specified http://purl.obolibrary.org/obo/GO_0004106 GO http://purl.obolibrary.org/obo/CHEBI_17029 CHEBI not_specified Another possibility is to use the non-radioactive assay developed to measure chitin synthase activity (Lucero et al. 2002; Zhang and Yan Zhu 2013). Instead of adding an enzyme extract and chitin precursors to the reaction, one could simply add homogenized chitin containing material to the reaction to quantify its chitin content. http://purl.obolibrary.org/obo/CHEBI_17029 CHEBI http://purl.obolibrary.org/obo/GO_0006030 GO Glucosamine quantification assay Quantifies glucosamine colorimetrically after deacetylation and hydrolysis of chitin. not_specified glucosamine amount not_specified http://purl.obolibrary.org/obo/CHEBI_17604 CHEBI not_specified one can also quantify glucosamine colorimetrically after deacetylation and hydrolysis of chitin (Lehmann and White 1975; Zhang and Zhu 2006) http://purl.obolibrary.org/obo/CHEBI_17029 CHEBI http://purl.obolibrary.org/obo/GO_0006032 GO Morgan-Elson assay Measures N-Acetylglucosamine (GlcNAc) colorimetrically after digestion of chitin by bacterial chitinase. not_specified N-Acetylglucosamine amount not_specified http://purl.obolibrary.org/obo/CHEBI_58265 CHEBI not_specified the N-Acetylglucosamine (GlcNAc) amount can be determined colorimetrically by a modified Morgan-Elson assay (Reissig et al. 1955; Arakane et al. 2005) http://purl.obolibrary.org/obo/CHEBI_17029 CHEBI http://purl.obolibrary.org/obo/GO_0006032 GO Radioactive precursor incorporation Quantification of chitin content by measuring incorporation of radioactively labeled UDP-GlcNAc into cuticular material. in_vitro cuticle chitin content decrease http://purl.obolibrary.org/obo/CHEBI_15887 CHEBI not_specified There also exists an approach based on the detection of fluorescence after staining with calcofluor white. In this assay, no treatment of the samples is necessary, the detection is carried out in homogenates of the respective organisms as calcofluor white directly binds to chitin (Henriques et al. 2020). Chitin can also be quantified using radioactively labelled precursors (e.g. 14C-UDP-GlcNAc) which are incorporated into in vitro cultured integument pieces or into the cuticle of whole organisms (Gijswijt et al. 1979; Turnbull and Howells 1982; Calcott and Fatig 1984; Gelman and Borkovec 1986). http://purl.obolibrary.org/obo/UBERON_0002291 UBERON http://purl.obolibrary.org/obo/GO_0030203 GO Radioactive precursor incorporation This assay quantifies chitin content by measuring the incorporation of radioactively labelled precursors (e.g. 14C-UDP-GlcNAc) into cultured integument or cuticle. in_vitro cuticle integument Radioactivity decrease http://purl.obolibrary.org/obo/GO_0008326 GO low Chitin can also be quantified using radioactively labelled precursors (e.g. 14C-UDP-GlcNAc) which are incorporated into vitro cultured integument pieces or into the cuticle of whole organisms (Gijswijt et al. 1979; Turnbull and Howells 1982; Calcott and Fatig 1984; Gelman and Borkovec 1986). http://purl.obolibrary.org/obo/CHEBI_59864 CHEBI http://purl.obolibrary.org/obo/GO_0008326 GO Radioactive precursor incorporation assay Quantifies chitin using radioactively labeled precursors (e.g., 14C-UDP-GlcNAc) incorporated into cultured integument pieces or whole organisms. in_vitro integument incorporation of radioactive precursors not_specified http://purl.obolibrary.org/obo/CHEBI_17029 CHEBI http://purl.obolibrary.org/obo/CHEBI_58104 CHEBI not_specified Chitin can also be quantified using radioactively labelled precursors (e.g. 14C-UDP-GlcNAc) which are incorporated into in vitro cultured integument pieces or into the cuticle of whole organisms (Gijswijt et al. 1979; Turnbull and Howells 1982; Calcott and Fatig 1984; Gelman and Borkovec 1986) http://purl.obolibrary.org/obo/CHEBI_17029 CHEBI http://purl.obolibrary.org/obo/GO_0006030 GO Histopathological assessment of cuticle maturity Monitors the maturity of the newly synthesized cuticle, e.g., thickness of procuticle, using histopathological methods. in_vivo cuticle Daphnia sp. procuticle thickness change http://purl.obolibrary.org/obo/UBERON_0002387 UBERON http://purl.obolibrary.org/obo/OBI_0000274 OBI low Additionally, one could apply histopathological methods to monitor the maturity of the newly synthesized cuticle (e.g. thickness of procuticle). http://purl.obolibrary.org/obo/UBERON_0002387 UBERON histopathological methods Microscopic examination to monitor the maturity and structural characteristics of the newly synthesized cuticle. ex_vivo cuticle thickness of procuticle change low one could apply histopathological methods to monitor the maturity of the newly synthesized cuticle (e.g. thickness of procuticle). http://purl.obolibrary.org/obo/UBERON_0001143 UBERON histopathology Histopathological methods are applied to monitor the maturity of the newly synthesized cuticle, specifically its thickness. ex_vivo cuticle Daphnia sp. cuticle thickness change low Additionally, one could apply histopathological methods to monitor the maturity of the newly synthesized cuticle (e.g. thickness of procuticle). observation Premature molting is determined by direct observation. No standardized tests currently exist for this endpoint. in_vivo Daphnia sp. molting increase low Premature molting can be determined by observation. No standardized tests for the endpoint of molting exist to date. http://purl.obolibrary.org/obo/GO_0042423 GO OECD 202 Daphnia sp. Acute immobilization test Assesses cumulative number of molts as an additional endpoint during a 48h acute toxicity test with Daphnia sp. in_vivo Daphnia sp. cumulative number of molts increase http://purl.obolibrary.org/obo/NCBITaxon_6654 NCBITAXON OECD TG 202 medium during an OECD 202 Daphnia sp. Acute immobilization test (OECD 2004), the cumulative number of molts can be assessed as an additional endpoint. http://purl.obolibrary.org/obo/NCBITaxon_6654 NCBITAXON OECD 211 reproduction test Molting events are counted during the OECD 211 Daphnia sp. reproduction test, optionally extended to 96 h to improve detection of premature molting. in_vivo Daphnia sp. cumulative number of molts increase http://purl.obolibrary.org/obo/GO_0007590 GO OECD TG 211 medium Molting can also be assessed during a OECD 211 Daphnia sp. Reproduction test (OECD 2012), as proposed previously (OECD 2003). One could even prolong the test to 96h to get a clearer result of this endpoint. http://purl.obolibrary.org/obo/GO_0007590 GO ex vivo quantification of 14C-labeled fatty acid oxidation to CO2 Measures the oxidation of 14C-labeled fatty acids to CO2 in an ex vivo setting. ex_vivo CO2 production not_specified http://purl.obolibrary.org/obo/GO_0006686 GO low ex vivo quantification of PPAR-induced fatty acid oxidation of 14 C-labeled fatty acids to CO 2 http://purl.obolibrary.org/obo/CHEBI_43941 CHEBI http://purl.obolibrary.org/obo/GO_0006686 GO Fatty Acid Beta Oxidation Assay Measures the beta oxidation of fatty acids in mitochondria using mouse liver homogenates with a radio-labeled fatty acid substrate. The reaction is performed for 30 minutes, followed by centrifugation to separate reaction products for fractional radioactivity measurements. Mitochondrial beta oxidation activity is normalized by adding potassium cyanide to the reaction mixture. in_vitro liver mouse beta oxidation of fatty acids decrease http://purl.obolibrary.org/obo/GO_0006635 GO http://purl.obolibrary.org/obo/GO_0005739 GO low Beta oxidation of fatty acids in mitochondria was measured using mouse liver homogenates where a radio-labeled fatty acid substrate was reacted for 30 minutes and then centrifuged to separate reaction products for fractional radioactivity measurements in Aoyama et al (1998). In Muoio et al (2002), capacity for beta oxidation of fatty acids in serum was determined by measuring the nonesterified fatty acids and transcript expression was quantified using RT-qPCR. Harrington et al (2007) administered agonists for the various PPARs and PPARpan (affecting all PPARs simultaneously) used ex vivo quantification of PPAR-induced fatty acid oxidation of 14C-labeled fatty acids to CO2. http://purl.obolibrary.org/obo/CHEBI_15377 CHEBI http://purl.obolibrary.org/obo/GO_0006635 GO NAD reduction assay Measures oxidation of acyl-CoA substrates with varying chain lengths by monitoring NAD reduction. ex_vivo liver rat NAD reduction increase http://purl.obolibrary.org/obo/CHEBI_16908 CHEBI http://purl.obolibrary.org/obo/CHEBI_57287 CHEBI low NAD reduction assays were conducted for acyl-CoA substrates with varying chain lengths where increased oxidation was observed for substrates with long chain length relative to short chain acyl-CoAs (Lazarow 1978). http://purl.obolibrary.org/obo/CHEBI_57287 CHEBI http://purl.obolibrary.org/obo/GO_0019395 GO Nonesterified fatty acids measurement Determines the capacity for beta oxidation of fatty acids in serum by measuring nonesterified fatty acids. not_specified nonesterified fatty acids not_specified http://purl.obolibrary.org/obo/CHEBI_16466 CHEBI not_specified In Muoio et al (2002), capacity for beta oxidation of fatty acids in serum was determined by measuring the nonesterified fatty acids PPAR-induced fatty acid oxidation of C14-labeled fatty acids to CO2 Agonists for various PPARs and PPARpan were administered ex vivo to quantify PPAR-induced fatty acid oxidation of C14-labeled fatty acids to CO2. ex_vivo oxidation of C14-labeled fatty acids to CO2 decrease http://purl.obolibrary.org/obo/GO_0001555 GO http://purl.obolibrary.org/obo/CHEBI_17580 CHEBI http://purl.obolibrary.org/obo/GO_0030280 GO http://www.ebi.ac.uk/efo/EFO_0002767 EFO medium Harrington et al (2007) administered agonists for the various PPARs and PPARpan (affecting all PPARs simultaneously) used ex vivo quantification of PPAR-induced fatty acid oxidation of C14-labeled fatty acids to CO2. http://purl.obolibrary.org/obo/CHEBI_15489 CHEBI http://purl.obolibrary.org/obo/GO_0001555 GO promoter-reporter assay Promoter-reporter plasmid MCPT.Luc.1025 was transfected into rat neonate cardiac myocytes to investigate concentration response effects of fatty acid chains on M-CPT I expression. in_vitro rat neonate cardiac myocytes heart rat luciferase expression change low Brandt et al (1998) investigated concentration response effects of Oleate, Decanoate and Hexanoate fatty acid chains on mitochondrial carnitine palmitoyl-transferases I (M-CPT I) expression using promoter-reporter plasmid MCPT.Luc.1025 reporter transfected into rat neonate cardiac myocytes. http://purl.obolibrary.org/obo/GO_0010468 GO promoter-reporter assay for M-CPT I Concentration response effects of Oleate, Decanoate and Hexanoate fatty acid chains on mitochondrial carnitine palmitoyl-transferase I (M-CPT I) expression were investigated using a promoter-reporter plasmid MCPT.Luc.1025 reporter transfected into rat neonate cardiac myocytes. in_vitro rat neonate cardiac myocytes heart rat M-CPT I expression via promoter-reporter change http://purl.obolibrary.org/obo/OBI_0000679 OBI http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/CL_0000746 CL http://purl.obolibrary.org/obo/NCBITaxon_10115 NCBITAXON http://purl.obolibrary.org/obo/UBERON_0000948 UBERON medium Brandt et al (1998) investigated concentration response effects of Oleate, Decanoate and Hexanoate fatty acid chains on mitochondrial carnitine palmitoyl-transferases I (M-CPT I) expression using promoter-reporter plasmid MCPT.Luc.1025 reporter transfected into rat neonate cardiac myocytes. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0001555 GO promoter-reporter plasmid assay Uses a reporter plasmid (MCPT.Luc.1025) transfected into cells to investigate the concentration response effects of fatty acids on M-CPT I expression. in_vitro rat neonate cardiac myocytes heart rat reporter expression not_specified medium investigated concentration response effects of Oleate, Decanoate and Hexanoate fatty acid chains on mitochondrial carnitine palmitoyl-transferases I (M-CPT I) expression using promoter-reporter plasmid MCPT.Luc.1025 reporter transfected into rat neonate cardiac myocytes http://purl.obolibrary.org/obo/GO_0010468 GO Radio-labeled fatty acid beta oxidation assay Measures beta oxidation of fatty acids in mouse liver homogenates using a radio-labeled fatty acid substrate, with reaction products separated by centrifugation and fractional radioactivity measured. ex_vivo liver mouse fractional radioactivity of reaction products decrease http://purl.obolibrary.org/obo/GO_0006635 GO http://purl.obolibrary.org/obo/GO_0005739 GO low Beta oxidation of fatty acids in mitochondria was measured using mouse liver homogenates where a radio-labeled fatty acid substrate was reacted for 30 minutes and then centrifuged to separate reaction products for fractional radioactivity measurements in Aoyama et al (1998). http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI http://purl.obolibrary.org/obo/GO_0006635 GO RT-qPCR Quantifies transcript expression using reverse transcription quantitative polymerase chain reaction. in_vitro transcript expression not_specified http://purl.obolibrary.org/obo/GO_0010467 GO medium transcript expression was quantified using RT-qPCR. RT-qPCR being the benchmark standard spectroscopic analysis Spectroscopic analysis was used to examine the characteristic absorption bands for fatty acid substrates and beta oxidation products in peroxisomal fractions purified from rat livers. in_vitro liver rat absorption bands change low Spectroscopic analysis of the characteristic absorption bands for fatty acid substrates and fatty acid beta oxidation products were examined for peroxisomal fractions purified from rat livers by differential and of equilibrium density centrifugation (Lazarow 1978). http://purl.obolibrary.org/obo/CHEBI_34389 CHEBI http://purl.obolibrary.org/obo/GO_0006646 GO Spectroscopic analysis of fatty acid substrates and products Examines characteristic absorption bands for fatty acid substrates and beta oxidation products in peroxisomal fractions purified from rat livers. ex_vivo liver rat absorption bands of fatty acid substrates and products not_specified http://purl.obolibrary.org/obo/CHEBI_35356 CHEBI http://purl.obolibrary.org/obo/GO_0005777 GO low Spectroscopic analysis of the characteristic absorption bands for fatty acid substrates and fatty acid beta oxidation products were examined for peroxisomal fractions purified from rat livers by differential and of equilibrium density centrifugation (Lazarow 1978). Western immunoblot quantification Quantifies expression of enzymes involved in hepatic fatty acid metabolism using Western immunoblot. ex_vivo liver protein expression not_specified http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI low Investigation of various enzymes involved in hepatic fatty acid metabolism described in Aoyama et al (1998) were investigated using Western immunoblot quantitiation. electrocardiogram Measures heart electrical activity to determine when heart rate falls to zero. in_vivo heart heart rate decrease http://purl.obolibrary.org/obo/GO_0002088 GO low Heart failure can be measured by electrocardiograms to assess heart electrical activity across a wide variety of animal taxa to determine when heart rate falls to zero (Hauser et al. 2012). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO ELISA Enzyme-linked immunosorbent assay used to quantify the depletion of Selenoproteins P, W, and S. in_vitro protein concentration (SelP, SelW, SelS) decrease http://purl.obolibrary.org/obo/GO_0008467 GO not_specified The depletion in SelP can be measured using an ELISA The depletion in SelW can be measured using an ELISA The depletion in SelS can be measured using an ELISA GPx activity assay Measures the activity of glutathione peroxidase using a colorimetric assay kit. in_vitro GPx activity decrease http://purl.obolibrary.org/obo/GO_0004602 GO medium The activity of GPx can be measured by a colorimetric assay, using a commercially available kit (e.g., Abcam ab102530) http://purl.obolibrary.org/obo/GO_0004602 GO http://purl.obolibrary.org/obo/GO_0006979 GO GSH:GSSG ratio detection assay Measures the ratio of reduced to oxidized glutathione using a fluorometric assay kit. in_vitro GSH:GSSG ratio decrease http://purl.obolibrary.org/obo/CHEBI_13458 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO medium GSH can be measured by assaying the ratio of reduced to oxidized glutathione (GSH:GSSG) using a commercially available kit (e.g., http://www.abcam.com/gshgssg-ratio-detection-assay-kit-fluorometric-green-ab138881.html) http://purl.obolibrary.org/obo/CHEBI_13458 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO HPLC High-performance liquid chromatography used to measure the methionine sulfoxide reductase activity of Selenoprotein R. in_vitro methionine sulfoxide reductase activity decrease not_specified The methionine sulfoxide reductase activity of SelR can be measured by HPLC HPLC-based SelR activity assay Measures the methionine sulfoxide reductase activity of selenoprotein R using HPLC. in_vitro SelR activity decrease http://purl.obolibrary.org/obo/GO_0008816 GO low The methionine sulfoxide reductase activity of SelR can be measured by HPLC (Chen, 2013) http://purl.obolibrary.org/obo/GO_0006979 GO TrxR activity assay Measures the activity of thioredoxin reductase using a colorimetric assay kit. in_vitro TrxR activity decrease http://purl.obolibrary.org/obo/GO_0004791 GO medium The activity of TrxR can be measured by a colorimetric assay, using a commercially available kit (e.g., Abcam ab83463) http://purl.obolibrary.org/obo/GO_0004791 GO http://purl.obolibrary.org/obo/GO_0006979 GO western blot Protein detection method used to measure the depletion of Selenoprotein H and K. in_vitro protein level decrease http://purl.obolibrary.org/obo/GO_0008467 GO low The depletion in SelH and K can be measured by western blotting Western blot Measures the depletion of selenoproteins H and K using western blotting. in_vitro SelH and SelK levels decrease low The depletion in SelH and K can be measured by western blotting (Lee, 2015, Novoselov, 2007) http://purl.obolibrary.org/obo/GO_0006979 GO Atomic Force Microscopy Demonstrates interactions of nanomaterials with the cell membrane. in_vitro nanomaterial-cell membrane interactions not_specified http://purl.obolibrary.org/obo/GO_0005886 GO low Atomic Force Microscopy (AFM) has also been used recently to demonstrate the interactions of nanomaterials with the cell membrane (Sahay et al., 2010). http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0006897 GO Co-localization pulse-chase Exposes cells to proteins with known trafficking pathways (e.g., transferrin) and nanomaterials to detect inclusion or exclusion from vesicles at different time points. in_vitro inclusion or exclusion from vesicles change http://purl.obolibrary.org/obo/GO_0005737 GO not_specified Co-localization studies of nanomaterials with specific endocytosis markers and structures “pulse-chase” design: proteins, such as transferrin or cholera toxin B (CTB), with known trafficking pathways are exposed to cells simultaneously or before the nanomaterial (“pulse”) and their inclusion or exclusion from the same vesicles is detected at different time points (“chase”) http://purl.obolibrary.org/obo/GO_0006831 GO Confocal Laser Scanning Microscopy Provides high-resolution optical imaging with depth selectivity to visualize cellular uptake of nanoparticles. in_vitro cellular uptake of nanoparticles not_specified http://purl.obolibrary.org/obo/GO_0006897 GO low Evaluation of NP cellular uptake by confocal laser scanning microscopy (CLSM). CLSM combines high-resolution optical imaging with depth selectivity which allows optical sectioning. The CLSM works by passing a laser beam through a light source aperture which is focused by an objective lens into a small area on the surface of the sample and an image is built up pixel-by-pixel by collecting the emitted photons from the fluorophores in the sample (Harush-Frenkel et al., 2006; Zhang and Monteiro-Riviere, 2009). http://purl.obolibrary.org/obo/GO_0006897 GO Confocal laser scanning microscopy (CLSM) CLSM combines high-resolution optical imaging with depth selectivity to build an image pixel-by-pixel from emitted photons. in_vitro fluorescence emission change medium Evaluation of NP cellular uptake by confocal laser scanning microscopy (CLSM). CLSM combines high-resolution optical imaging with depth selectivity which allows optical sectioning. The CLSM works by passing a laser beam through a light source aperture which is focused by an objective lens into a small area on the surface of the sample and an image is built up pixel-by-pixel by collecting the emitted photons from the fluorophores in the sample (Harush-Frenkel et al., 2006; Zhang and Monteiro-Riviere, 2009). http://purl.obolibrary.org/obo/GO_0006629 GO Confocal Microscopy Live cell imaging using fluorescent probes or GFP-fused proteins to analyze intracellular distribution and trafficking. in_vitro distribution of colour or fluorescence resonance energy transfer (FRET) change http://purl.obolibrary.org/obo/GO_0030424 GO not_specified The most widespread method for studying intracellular trafficking involves attaching different fluorescent probes to the protein and nanomaterial that allows analyzing distribution of colour or fluorescence resonance energy transfer (FRET) throughout the cell compartments. The advantage of such approach is that it allows using live cell imaging by confocal microscopy (Sahay et al., 2010). http://purl.obolibrary.org/obo/GO_0003670 GO http://purl.obolibrary.org/obo/GO_0030424 GO Density gradient subcellular fractionation Separates subcellular fractions using a density gradient and analyzes fluorescently labeled components to characterize endocytic traffic. in_vitro distribution of fluorescently labeled components in subcellular fractions change http://purl.obolibrary.org/obo/OBI_0000268 OBI http://purl.obolibrary.org/obo/GO_0006897 GO low We describe a single-step density gradient subcellular fractionation method combined with fluorescent detection analysis that provides a new tool for characterisation of endocytic traffic of polymer therapeutics for an understanding of intracellular trafficking pathways (Manunta et al., 2007). http://purl.obolibrary.org/obo/GO_0030139 GO http://purl.obolibrary.org/obo/GO_0006897 GO Density gradient subcellular fractionation A single-step method combined with fluorescent detection to characterize endocytic traffic and intracellular trafficking pathways. in_vitro endocytic traffic/intracellular trafficking not_specified http://purl.obolibrary.org/obo/GO_0051012 GO not_specified We describe a single-step density gradient subcellular fractionation method combined with fluorescent detection analysis that provides a new tool for characterisation of endocytic traffic of polymer therapeutics for an understanding of intracellular trafficking pathways http://purl.obolibrary.org/obo/GO_0051012 GO Electron microscopy Visualizes nanomaterials coupled with electron-dense labels in vesicular structures at high resolution. in_vitro presence and location of nanomaterials in vesicles not_specified http://purl.obolibrary.org/obo/OBI_0000224 OBI http://purl.obolibrary.org/obo/GO_0006897 GO low Apart from confocal microscopy, the electron microscopy is also highly useful as it allows visualizing nanomaterials coupled with electron dense labels in different vesicular structures under very high resolution. http://purl.obolibrary.org/obo/GO_0006897 GO FACS analysis Uses flow cytometry to sort and analyze cells based on light scattering and fluorescence characteristics to quantify nanoparticle cellular uptake. in_vitro cellular uptake of nanoparticles not_specified http://purl.obolibrary.org/obo/GO_0006897 GO high Fluorescence-activated cell sorter (FACS) analysis of NP cellular uptake. FACS is a specialized type of flow cytometry. It provides a method for sorting a heterogeneous mixture of biological based upon the specific light scattering and fluorescent characteristics of each cell (Harush-Frenkel et al., 2006; Zhang and Monteiro-Riviere, 2009). http://purl.obolibrary.org/obo/GO_0006897 GO Fluorescence Correlation Spectroscopy Analyzes fluctuations in fluorescence intensity to study molecular dynamics. in_vitro fluorescence intensity fluctuations change http://purl.obolibrary.org/obo/GO_0005886 GO medium Fluorescence Correlation Spectroscopy is a correlation analysis of fluctuation of the fluorescence intensity (Villamil Giraldo et al., 2016). http://purl.obolibrary.org/obo/GO_0006897 GO Fluorescent probe trafficking assay Attaches fluorescent probes to proteins and nanomaterials to analyze their distribution or FRET throughout cell compartments using live cell imaging by confocal microscopy. in_vitro intracellular distribution of fluorescence change http://purl.obolibrary.org/obo/GO_0042623 GO http://purl.obolibrary.org/obo/GO_0006897 GO low The most widespread method for studying intracellular trafficking involves attaching different fluorescent probes to the protein and nanomaterial that allows analyzing distribution of colour or fluorescence resonance energy transfer (FRET) throughout the cell compartments. The advantage of such approach is that it allows using live cell imaging by confocal microscopy (Sahay et al., 2010). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0046907 GO GFP-tagged protein trafficking assay Cells are transfected with constructs containing proteins fused with fluorescent proteins like GFP to study their localization in endocytosis vesicles or organelles. in_vitro localization of fluorescently tagged proteins change http://purl.obolibrary.org/obo/PR_000008126 PR http://purl.obolibrary.org/obo/GO_0006897 GO low Cells can be transfected with constructs containing proteins that reside in specific endocytosis vesicles or intracellular organelles, which are fused with fluorescent proteins, such as the Green Fluorescent Protein (GFP) (Sahay et al., 2010). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006897 GO Immunocytochemistry Uses specific antibodies to detect proteins present along endocytic vesicles and organelles in fixed cells. in_vitro presence of proteins in endocytic vesicles not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/GO_0006897 GO medium Another way of studying co-localization is immunocytochemistry applied to fixed cells. This method allows employing specific antibodies to different proteins present along the endocytic vesicles and organelles (Sahay et al., 2010). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006897 GO Immunocytochemistry Uses specific antibodies against proteins in endocytic vesicles and organelles on fixed cells to study co-localization. in_vitro protein localization not_specified http://purl.obolibrary.org/obo/GO_0005737 GO low Another way of studying co-localization is immunocytochemistry applied to fixed cells. This method allows employing specific antibodies to different proteins present along the endocytic vesicles and organelles http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006826 GO Inductively coupled plasma mass spectrometry (ICP-MS) Quantifies cellular uptake of metal nanoparticles (e.g., AuNPs) by ionizing the sample with plasma and separating/quantifying ions via mass spectrometry. in_vitro quantitative cellular uptake of AuNPs increase http://purl.obolibrary.org/obo/OBI_0000387 OBI medium Quantitative cellular uptake of AuNPs was performed by inductively coupled plasma mass spectrometry (ICPMS), a type of mass spectrometry capable of detecting metals and several non-metals at very low concentrations. This is achieved by ionizing the sample with inductively coupled plasma and then using a mass spectrometer to separate and quantify those ions http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0015031 GO Inductively coupled plasma mass spectrometry (ICPMS) ICPMS is a type of mass spectrometry used to detect and quantify metals and non-metals at very low concentrations. in_vitro metal concentration increase medium Quantitative cellular uptake of AuNPs was performed by inductively coupled plasma mass spectrometry (ICPMS), a type of mass spectrometry capable of detecting metals and several non-metals at very low concentrations. This is achieved by ionizing the sample with inductively coupled plasma and then using a mass spectrometer to separate and quantify those ions (Ng et al., 2015). http://purl.obolibrary.org/obo/GO_0006629 GO Lysosomal Trapping assay Uses LysoTracker Red DND-99, a fluorescent dye that accumulates in lysosomes, to detect lysosomotropism by measuring the decrease in staining with increasing concentrations of lysosomotropic compounds. in_vitro lysosomal staining intensity decrease http://purl.obolibrary.org/obo/GO_0005764 GO medium Lysosomal Trapping assay: A fluorescent dye, LysoTracker Red DND-99, which accumulates in lysosomes, is used for detecting lysosomotropism. There is a gradual decrease in the LysoTracker staining with increasing concentrations of lysosomotropic compounds. http://purl.obolibrary.org/obo/GO_0005764 GO http://purl.obolibrary.org/obo/GO_0006897 GO Pharmacologic inhibition Exclusion of specific endocytosis mechanisms is achieved using pharmacologic inhibitors of endocytosis. in_vitro endocytosis rate decrease http://purl.obolibrary.org/obo/GO_0006629 GO http://purl.obolibrary.org/obo/CHEBI_59858 CHEBI medium Exclusion of specific endocytosis mechanisms is a distinct and powerful technique to elucidate endocytosis. This can be achieved, for example, using various pharmacologic inhibitors of endocytosis that include chemical or biological agents or cell mutants (Sahay et al., 2010). http://purl.obolibrary.org/obo/GO_0006629 GO http://purl.obolibrary.org/obo/GO_0006629 GO Pharmacologic inhibitor assay Uses chemical or biological inhibitors or cell mutants to exclude specific endocytosis mechanisms. in_vitro endocytosis mechanism exclusion not_specified http://purl.obolibrary.org/obo/GO_0006897 GO medium Exclusion of specific endocytosis mechanisms is a distinct and powerful technique to elucidate endocytosis. This can be achieved, for example, using various pharmacologic inhibitors of endocytosis that include chemical or biological agents or cell mutants (Sahay et al., 2010). http://purl.obolibrary.org/obo/GO_0006897 GO Pulse-chase co-localization assay Proteins with known trafficking pathways are exposed to cells simultaneously or before nanomaterials, and their inclusion/exclusion from vesicles is detected over time. in_vitro co-localization of proteins and nanomaterials in vesicles change http://purl.obolibrary.org/obo/GO_0006897 GO low Co-localization studies of nanomaterials with specific endocytosis markers and structures “pulse-chase” design: proteins, such as transferrin or cholera toxin B (CTB), with known trafficking pathways are exposed to cells simultaneously or before the nanomaterial (“pulse”) and their inclusion or exclusion from the same vesicles is detected at different time points (“chase”) (Sahay et al., 2010). http://purl.obolibrary.org/obo/GO_0030139 GO http://purl.obolibrary.org/obo/GO_0006897 GO Subcellular Fractionation Characterizes endocytic traffic of polymer therapeutics by single-step density gradient fractionation combined with fluorescent detection analysis. in_vitro subcellular localization of polymer therapeutics change http://purl.obolibrary.org/obo/GO_0006897 GO not_specified We describe a single-step density gradient subcellular fractionation method combined with fluorescent detection analysis that provides a new tool for characterisation of endocytic traffic of polymer therapeutics for an understanding of intracellular trafficking pathways. http://purl.obolibrary.org/obo/GO_0090305 GO Transmission electron microscopy (TEM) TEM is used to visualize NPs inside cells, as light microscopy cannot resolve them at a single particle level. in_vitro nanoparticle localization change low Transmission electron microscopy (TEM) is an appropriate technique to use for visualizing NPs inside cells, since light microscopy fails to resolve them at a single particle level. TEM is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image (Brandenberger et al., 2010; Villamil Giraldo et al., 2016). http://purl.obolibrary.org/obo/GO_0006646 GO Clark electrode oxygen consumption assay Measures oxygen consumption in permeabilized cells or isolated mitochondria using an electrochemical sensor to detect oxygen reduction. in_vitro permeabilized cells isolated mitochondria oxygen consumption rate decrease http://purl.obolibrary.org/obo/GO_0033300 GO http://purl.obolibrary.org/obo/OBI_0000219 OBI low Complex III activity detection in permeabilized cells or in isolated mitochondria based on the detection of oxygen consumption. The principle of oxygen detection by a Clark electrode is based on the electrochemical reduction of oxygen at a cathode, typically composed of platinum, which is maintained at a fixed potential relative to a reference electrode. http://purl.obolibrary.org/obo/GO_0005746 GO http://purl.obolibrary.org/obo/GO_0006091 GO decylubiquinol/cytochrome c reductase assay Spectrophotometric measurement of mitochondrial complex III activity by monitoring the reduction of cytochrome c at 550 nm using decylubiquinol as an artificial electron donor. The antimycin-sensitive rate is calculated by subtracting the antimycin-insensitive rate from the total rate. in_vitro complex III enzymatic activity change http://purl.obolibrary.org/obo/GO_0000294 GO low The decylubiquinol/cytochrome c reductase assay is the standard spectrophotometric method to measure the enzymatic activity of mitochondrial complex III (ubiquinol–cytochrome c reductase) (Krähenbühl et. al, 1994). Decylubiquinol is oxidized by complex III at the Qo site of cytochrome b, and the released electrons are transferred sequentially through the Rieske iron–sulfur protein and cytochrome c₁ subunit to the terminal electron acceptor, cytochrome c. The rate of cytochrome c reduction is directly proportional to the activity of complex III in the sample (Krähenbühl et. al, 1994). http://purl.obolibrary.org/obo/GO_0005747 GO http://purl.obolibrary.org/obo/GO_0006120 GO decylubiquinol/cytochrome c reductase assay Measures the enzymatic activity of mitochondrial complex III by monitoring the reduction of cytochrome c at 550 nm using decylubiquinol as an electron donor. in_vitro isolated mitochondria submitochondrial particles rate of cytochrome c reduction increase http://purl.obolibrary.org/obo/GO_0045237 GO low The decylubiquinol/cytochrome c reductase assay is the standard spectrophotometric method to measure the enzymatic activity of mitochondrial complex III (ubiquinol–cytochrome c reductase) (Krähenbühl et. al, 1994). The reduction of cytochrome c results in a characteristic increase in absorbance at approximately 550 nm, which can be continuously monitored using a spectrophotometer. http://purl.obolibrary.org/obo/GO_0005750 GO http://purl.obolibrary.org/obo/GO_0022900 GO extracellular flux analyzer assay Measures oxygen consumption rate (OCR) in permeabilized cells using an integrated optical oxygen sensor in a microplate format, enabling high-throughput analysis of mitochondrial function. in_vitro permeabilized cells oxygen consumption rate decrease http://purl.obolibrary.org/obo/GO_0033300 GO high Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection (Plitzko et al. 2018). In the 96 well format, a cell density in the range of 30.000-80.000 cells per well (depending on the cell type) is added in a volume of 80 µl and centrifuged (200 g for 1 min) to ensure attachment on the bottom of the plate. http://purl.obolibrary.org/obo/GO_0005746 GO http://purl.obolibrary.org/obo/GO_0006091 GO optical oxygen sensor assay Measures oxygen consumption in cells using fluorescent or phosphorescent dyes that are quenched by oxygen, enabling real-time detection of mitochondrial respiration. in_vitro cells oxygen consumption rate decrease http://purl.obolibrary.org/obo/GO_0033300 GO http://purl.obolibrary.org/obo/OBI_0000219 OBI high Optical oxygen sensors operate on the principle of dynamic quenching of luminescence by molecular oxygen. Extracellular flux analyzers such as the Seahorse system emerged as the frontline technique in high content oxygen consumption detection (Plitzko et al. 2018). http://purl.obolibrary.org/obo/GO_0005746 GO http://purl.obolibrary.org/obo/GO_0006091 GO oxygen consumption measurement Oxygen consumption is detected as a readout for the activity of oxidative phosphorylation in entire mitochondria, using a Clark electrode or optical oxygen sensors. in_vitro oxygen consumption rate change http://purl.obolibrary.org/obo/GO_0009061 GO http://purl.obolibrary.org/obo/GO_0006757 GO medium Activity of complex III of the respiratory chain can be determined indirectly by the detection of oxygen consumption as a readout for the activity of oxidative phosphorylation in entire mitochondria. Complex III activity detection is conducted according to the reaction: DB (reduced) + cytochrome c (oxidized) → DB (oxidized) + cytochrome c (reduced) (550 nm) http://purl.obolibrary.org/obo/CL_0000061 CL http://purl.obolibrary.org/obo/GO_0009060 GO Complex IV Activity Assay Measures the activity of mitochondrial Complex IV by detecting the reduction of cytochrome c, which leads to a decrease in absorbance at 550 nm. in_vitro bovine heart mitochondria bovine Complex IV activity decrease http://purl.obolibrary.org/obo/GO_0006123 GO http://purl.obolibrary.org/obo/GO_0004129 GO medium The activity of complex IV is always tested in the bovine heart mitochondria provided within the kit. The kit relies on the following detection of complex IV activity: The reduction of cytochrome c, which leads to a reduction in absorbance at 550nm can be measured. Cayman MitoCheck MitoCheck® Complex IV Activity Assay Kit (Item No. 700990) Abcam MitoTox™ Complex IV OXPHOS Activity Assay Kit (ab109906) Complex IV Human Enzyme Activity Microplate Assay Kit (ab109909) BioVision Cytochrome Oxidase Activity Colorimetric Assay Kit (K287) http://purl.obolibrary.org/obo/GO_0045275 GO http://purl.obolibrary.org/obo/GO_0006123 GO Complex IV Activity Assay Measures the activity of mitochondrial complex IV by monitoring the reduction of cytochrome c and the resulting change in absorbance at 550nm. in_vitro mitochondria Bos taurus reduction of cytochrome c change http://purl.obolibrary.org/obo/GO_0005506 GO not_specified The activity of complex IV is always tested in the bovine heart mitochondria provided within the kit. The reduction of cytochrome c, which leads to a reduction in absorbance at 550nm can be measured. http://purl.obolibrary.org/obo/GO_0005506 GO cytochrome c reduction assay This assay measures complex IV activity by detecting the reduction of cytochrome c, which correlates with a reduction in absorbance at 550nm. in_vitro heart bovine absorbance at 550nm decrease medium The activity of complex IV is always tested in the bovine heart mitochondria provided within the kit. The reduction of cytochrome c, which leads to a reduction in absorbance at 550nm can be measured. mitochondrial membrane potential assay This assay uses fluorescent dyes (Rhodamine123, TMRE, TMRM, JC1) to measure mitochondrial membrane potential. Polarized mitochondria accumulate more dye, leading to a higher fluorescent signal. in_vitro fluorescent signal change medium Mitochondrial Membrane potential using fluorescent dyes More polarised mitochondria will accumulate more dye (Rhodamine123, TMRE, TMRM) - leading to a higher fluorescent signal - and the absence of membrane potential leads to an absence of fluorescent signal. http://purl.obolibrary.org/obo/CL_0000276 CL http://purl.obolibrary.org/obo/GO_0006841 GO Mitochondrial Membrane Potential Assay Measures mitochondrial membrane potential using fluorescent dyes such as Rhodamine123, TMRE, TMRM, or JC1, where dye accumulation is proportional to membrane potential. in_vitro mitochondria mitochondrial membrane potential change http://purl.obolibrary.org/obo/GO_0036350 GO http://purl.obolibrary.org/obo/GO_0031966 GO medium Mitochondrial Membrane potential using fluorescent dyes. Positive charged molecules will accumulated in the mitochondria in an inverse proportion as the membrane potential. More polarised mitochondria will accumulate more dye (Rhodamine123, TMRE, TMRM) - leading to a higher fluorescent signal - and the absence of membrane potential leads to an absence of fluorescent signal. An exception is the dye JC1, because this dye has green fluorescence when present in low concentrations (depolarisation) and red fluorescence when accumulated (hyperpolarized Perry, 2011, mitochondrial membrane potential probes and proton gradient Mitra, 2010, analysis of mitochondrial dynamics and functions using imaging approaches http://purl.obolibrary.org/obo/GO_0031966 GO http://purl.obolibrary.org/obo/GO_0036350 GO Abcam MitoTox This is a Complex V OXPHOS Activity Assay Kit (ab109907) used to measure complex V activity. in_vitro complex V activity decrease medium Abcam MitoTox™ Complex V OXPHOS Activity Assay Kit (ab109907) http://purl.obolibrary.org/obo/GO_0006463 GO Complex V activity assay Measures mitochondrial complex V (ATPase) activity by coupling ATP hydrolysis to NADH oxidation monitored at 340 nm. in_vitro heart Bos taurus ATPase activity (ATP hydrolysis) decrease http://purl.obolibrary.org/obo/GO_0016887 GO not_specified ATP is converted by ATPase to ADP. The ADP is used by pyruvate kinase to convert Phosphoenolpyruvate to pyruvate. The pyruvate is converted to lactate by lactate dehydrogenase, while oxidising NADH to NAD+. NADH oxidation is measured at 340nm. Cayman MitoCheck MitoCheck® Complex V Activity Assay Kit (Item No. 701000) Abcam MitoTox™ Complex V OXPHOS Activity Assay Kit (ab109907) http://purl.obolibrary.org/obo/GO_0005753 GO http://purl.obolibrary.org/obo/GO_0006200 GO Complex V activity assay Measures the activity of mitochondrial Complex V (ATP synthase) by detecting NADH oxidation at 340 nm through a coupled enzymatic reaction involving ATPase, pyruvate kinase, and lactate dehydrogenase. in_vitro mitochondria bovine Complex V activity decrease http://purl.obolibrary.org/obo/GO_0045333 GO http://purl.obolibrary.org/obo/GO_0042779 GO medium Complex inhibition assays specifically for complex V ATP is converted by ATPase to ADP. The ADP is used by pyruvate kinase to convert Phosphoenolpyruvate to pyruvate. The pyruvate is converted to lactate by lactate dehydrogenase, while oxidising NADH to NAD+. NADH oxidation is measured at 340nm. http://purl.obolibrary.org/obo/GO_0005753 GO http://purl.obolibrary.org/obo/GO_0042779 GO complex V activity assay This assay measures complex V activity by monitoring the conversion of ATP to ADP, which is then used by pyruvate kinase to convert Phosphoenolpyruvate to pyruvate. Pyruvate is converted to lactate, oxidizing NADH to NAD+, and NADH oxidation is measured at 340nm. in_vitro heart bovine NADH oxidation decrease medium The activity of complex IV is always tested in the bovine heart mitochondria provided within the kit or using freshly isolated mitochondria. ATP is converted by ATPase to ADP. The ADP is used by pyruvate kinase to convert Phosphoenolpyruvate to pyruvate. The pyruvate is converted to lactate by lactate dehydrogenase, while oxidising NADH to NAD+. NADH oxidation is measured at 340nm. http://purl.obolibrary.org/obo/GO_0006463 GO mitochondrial membrane potential assay This assay measures mitochondrial membrane potential using fluorescent dyes (Rhodamine123, TMRE, TMRM, JC1). Polarized mitochondria accumulate more dye, leading to a higher fluorescent signal, while depolarized mitochondria show reduced signal (except JC1, which shifts from green to red fluorescence). in_vitro fluorescent signal change medium Mitochondrial Membrane potential using fluorescent dyes Positive charged molecules will accumulated in the mitochondria in an inverse proportion as the membrane potential. More polarised mitochondria will accumulate more dye (Rhodamine123, TMRE, TMRM) - leading to a higher fluorescent signal - and the absence of membrane potential leads to an absence of fluorescent signal. http://purl.obolibrary.org/obo/CL_0000278 CL http://purl.obolibrary.org/obo/GO_0006497 GO Mitochondrial membrane potential assay Measures mitochondrial membrane potential using fluorescent dyes such as Rhodamine123, TMRE, TMRM, or JC1, where dye accumulation is proportional to membrane potential. in_vitro mitochondria mitochondrial membrane potential change http://purl.obolibrary.org/obo/GO_0042599 GO http://purl.obolibrary.org/obo/GO_0031966 GO high Mitochondrial Membrane potential using fluorescent dyes More polarised mitochondria will accumulate more dye (Rhodamine123, TMRE, TMRM) - leading to a higher fluorescent signal - and the absence of membrane potential leads to an absence of fluorescent signal. http://purl.obolibrary.org/obo/GO_0031966 GO http://purl.obolibrary.org/obo/GO_0008108 GO Blue-native polyacrylamide gel electrophoresis (BN-PAGE) Examines the structural organization, abundance, and stability of intact OXPHOS complexes and supercomplexes within the inner mitochondrial membrane. in_vitro OXPHOS complex assembly and stability change http://purl.obolibrary.org/obo/GO_0043623 GO http://purl.obolibrary.org/obo/OBI_0000367 OBI low blue-native polyacrylamide gel electrophoresis (BN-PAGE) is used to examine the structural organization, abundance, and stability of intact OXPHOS complexes and supercomplexes within the inner mitochondrial membrane. Alterations in complex assembly or loss of specific respiratory complexes detected by BN-PAGE support a mechanistic interpretation of reduced oxidative phosphorylation at the protein organization level http://purl.obolibrary.org/obo/GO_0098799 GO http://purl.obolibrary.org/obo/GO_0043623 GO enzyme activity assay Enzyme activity assays measure the catalytic activity of individual respiratory chain complexes (I–IV) using defined substrates and inhibitors to identify dysfunction of discrete components of the electron transport chain. in_vitro mitochondria catalytic activity of respiratory chain complexes decrease medium Biochemical characterization of OXPHOS impairment can be further refined through enzyme activity assays of individual respiratory chain complexes (I–IV). http://purl.obolibrary.org/obo/GO_0006754 GO High-resolution respirometry Measures oxygen consumption rates in intact or permeabilized cells, tissues, or isolated mitochondria to assess mitochondrial respiratory capacity and coupling efficiency. in_vitro oxygen consumption rate decrease http://purl.obolibrary.org/obo/GO_0009060 GO medium Functional impairment of OXPHOS is most commonly evaluated by respirometry, where oxygen consumption rates are measured in intact or permeabilized cells, tissues, or isolated mitochondria under controlled substrate and inhibitor conditions. A reduction in ADP-stimulated respiration or maximal respiratory capacity provides direct evidence for decreased mitochondrial oxidative phosphorylation http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006119 GO Luciferase-based ATP assay Quantifies ATP synthesis rates in real time or at defined endpoints to assess mitochondrial ATP output. in_vitro ATP synthesis rate decrease http://purl.obolibrary.org/obo/GO_0042777 GO http://purl.obolibrary.org/obo/OBI_0000368 OBI high Luciferase-based assays enable sensitive measurement of ATP production in real time or at defined endpoints and are widely used to assess mitochondrial ATP output. Reduced ATP synthesis, particularly when observed alongside diminished oxygen consumption, indicates impaired coupling between electron transport and phosphorylation http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0042775 GO Mitochondrial membrane potential assay Assesses mitochondrial membrane potential (ΔΨm) using potentiometric fluorescent probes to evaluate proton motive force and capacity for ATP synthesis. in_vitro mitochondrial membrane potential decrease http://purl.obolibrary.org/obo/GO_0086014 GO http://purl.obolibrary.org/obo/GO_0001539 GO high Changes in mitochondrial membrane potential (ΔΨm), assessed using potentiometric fluorescent probes, provide additional functional insight, as loss or reduction of ΔΨm reflects impaired proton motive force and compromised capacity for ATP synthesis http://purl.obolibrary.org/obo/GO_0005743 GO http://purl.obolibrary.org/obo/GO_0006817 GO potentiometric fluorescent probes Assesses changes in mitochondrial membrane potential (ΔΨm) using fluorescent probes to reflect proton motive force. in_vitro mitochondrial membrane potential (ΔΨm) decrease http://purl.obolibrary.org/obo/GO_0031648 GO medium Changes in mitochondrial membrane potential (ΔΨm), assessed using potentiometric fluorescent probes, provide additional functional insight, as loss or reduction of ΔΨm reflects impaired proton motive force and compromised capacity for ATP synthesis http://purl.obolibrary.org/obo/GO_0005741 GO http://purl.obolibrary.org/obo/GO_0006111 GO Respiratory chain complex activity assay Measures the catalytic activity of specific respiratory chain complexes (I–IV) using defined substrates and inhibitors to identify dysfunction in the electron transport chain. in_vitro respiratory chain complex activity decrease http://purl.obolibrary.org/obo/GO_0070469 GO http://purl.obolibrary.org/obo/PATO_0000033 PATO medium Biochemical characterization of OXPHOS impairment can be further refined through enzyme activity assays of individual respiratory chain complexes (I–IV). These assays measure the catalytic activity of specific complexes using defined substrates and inhibitors and can identify whether reduced oxidative phosphorylation is associated with inhibition or dysfunction of discrete components of the electron transport chain http://purl.obolibrary.org/obo/GO_0098799 GO http://purl.obolibrary.org/obo/GO_0022900 GO ³¹P nuclear magnetic resonance spectroscopy Non-invasive assessment of high-energy phosphate metabolites to evaluate cellular energetic status and mitochondrial ATP generation. in_vivo high-energy phosphate metabolites decrease http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI low in vivo ³¹P nuclear magnetic resonance (NMR) spectroscopy provides a non-invasive assessment of high-energy phosphate metabolites, allowing evaluation of cellular energetic status and supporting identification of reduced mitochondrial ATP generation http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006754 GO Hematoxylin and eosin staining Histopathology assay using hematoxylin and eosin staining to determine tissue morphology. in_vivo tissue morphology not_specified low Histopathology: performed on tissue sections Hematoxylin (nuclei) and eosin staining: determine morphology TUNEL staining Histopathology assay using TUNEL staining to detect cell death. in_vivo cell death increase low TUNEL staining: cell death ALP measurement Measures the levels of alkaline phosphatase, an enzyme released into the bloodstream when the liver is damaged. in_vivo liver ALP levels increase medium Levels of: ALT, AST, ALP, bilirubin, GGT, NTP, Ceruloplasmin, AFP http://purl.obolibrary.org/obo/CL_0000273 CL http://purl.obolibrary.org/obo/GO_0008625 GO ALT measurement Measures the levels of alanine aminotransferase, an enzyme released into the bloodstream when the liver is damaged. in_vivo liver ALT levels increase medium Levels of: ALT, AST, ALP, bilirubin, GGT, NTP, Ceruloplasmin, AFP http://purl.obolibrary.org/obo/CL_0000273 CL http://purl.obolibrary.org/obo/GO_0008625 GO Bilirubin measurement Measures the levels of bilirubin, a waste product produced by the liver, in the bloodstream. in_vivo liver bilirubin levels increase medium Levels of: ALT, AST, ALP, bilirubin, GGT, NTP, Ceruloplasmin, AFP http://purl.obolibrary.org/obo/UBERON_0004670 UBERON http://purl.obolibrary.org/obo/GO_0008317 GO Biochemistry assays Measures levels of liver enzymes and proteins such as ALT, AST, ALP, bilirubin, GGT, NTP, Ceruloplasmin, and AFP to assess liver injury. in_vivo liver human levels of liver enzymes and proteins increase http://purl.obolibrary.org/obo/PR_000000049 PR http://purl.obolibrary.org/obo/PR_000000050 PR http://purl.obolibrary.org/obo/PR_000000051 PR http://purl.obolibrary.org/obo/CHEBI_16185 CHEBI http://purl.obolibrary.org/obo/PR_000000052 PR medium Biochemistry assays Levels of: ALT, AST, ALP, bilirubin, GGT, NTP, Ceruloplasmin, AFP http://purl.obolibrary.org/obo/UBERON_0002107 UBERON Biopsy Involves the removal of liver tissue for histological examination to assess liver injury. in_vivo liver human histological changes in liver tissue change http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low Biopsy http://purl.obolibrary.org/obo/UBERON_0002107 UBERON CT Uses computed tomography imaging to visualize liver structure and detect abnormalities indicative of liver injury. in_vivo liver human liver structure and abnormalities change http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/OBI_0000274 OBI medium Imaging scans CT http://purl.obolibrary.org/obo/UBERON_0002107 UBERON GGT measurement Measures the levels of gamma-glutamyl transferase, an enzyme released into the bloodstream when the liver is damaged. in_vivo liver GGT levels increase medium Levels of: ALT, AST, ALP, bilirubin, GGT, NTP, Ceruloplasmin, AFP http://purl.obolibrary.org/obo/CL_0000273 CL http://purl.obolibrary.org/obo/GO_0008625 GO MRI Uses magnetic resonance imaging to visualize liver structure and detect abnormalities indicative of liver injury. in_vivo liver human liver structure and abnormalities change http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/OBI_0000273 OBI low Imaging scans MRI http://purl.obolibrary.org/obo/UBERON_0002107 UBERON Ultrasound Uses ultrasound imaging to visualize liver structure and detect abnormalities indicative of liver injury. in_vivo liver human liver structure and abnormalities change http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/OBI_0000275 OBI high Imaging scans Ultrasound http://purl.obolibrary.org/obo/UBERON_0002107 UBERON aCGH or SNP Microarray Copy number variations are detected using global DNA microarray technologies, but this method is unable to detect balanced chromosomal aberrations such as inversions. in_vitro copy number variations change http://purl.obolibrary.org/obo/GO_0070838 GO http://purl.obolibrary.org/obo/OBI_0001057 OBI medium CNVs are most commonly detected using global DNA microarray technologies; This method, however, is unable to detect balanced CAs, such as inversions http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO CBMN with Imaging Flow Cytometry An assay where cells are cultured with a cytokinesis blocking agent, fixed in solution, and imaged with flow cytometry to quantify micronuclei. in_vitro MN quantification increase not_specified Cells are cultured with cytokinesis blocking agent, fixed in solution, and imaged with flow cytometry to quantify MN CBMN with Microscopy Cells are cultured with cytokinesis blocking agent, fixed to slides, and undergo micronucleus quantification using microscopy. in_vitro micronucleus frequency increase http://purl.obolibrary.org/obo/GO_0005635 GO http://purl.obolibrary.org/obo/GO_0000910 GO OECD TG 487 medium Cells are cultured with cytokinesis blocking agent, fixed to slides, and undergo MN quantification using microscopy. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0000910 GO Chromosomal aberration test In vitro, the cell cycle is arrested at metaphase after 1.5 cell cycle following 3-6 hour exposure. In vivo, the test chemical is administered as a single treatment, bone marrow is collected 18-24 hrs later (TG 475), while testis is collected 24-48 hrs later (TG 483). Chromosomal aberrations are scored after staining. in_vitro bone marrow testis chromosomal aberration frequency increase http://purl.obolibrary.org/obo/GO_0000279 GO http://purl.obolibrary.org/obo/UBERON_0002371 UBERON OECD TG 473, OECD TG 475, OECD TG 483 low In vitro, the cell cycle is arrested at metaphase after 1.5 cell cycle following 3-6 hour exposure In vivo, the test chemical is administered as a single treatment, bone marrow is collected 18-24 hrs later (TG 475), while testis is collected 24-48 hrs later (TG 483). The cell cycle is arrested with a metaphase-arresting chemical (e.g., colchicine) 2-5 hours before cell collection. Once cells are fixed and stained on microscope slides, chromosomal aberrations are scored http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0000278 GO Dicentric Chromosome Assay Cells are fixed on microscope slides, chromosomes are stained, and the number of dicentric chromosomes are quantified. in_vitro dicentric chromosome frequency increase http://purl.obolibrary.org/obo/GO_0000780 GO low Cells are fixed on microscope slides, chromosomes are stained, and the number of dicentric chromosomes are quantified http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0000278 GO FISH Fluorescent assay of metaphase chromosomes that can detect chromosomal aberrations through chromosome painting and microscopic analysis. in_vitro chromosomal aberrations increase http://purl.obolibrary.org/obo/GO_0000229 GO http://purl.obolibrary.org/obo/OBI_0000458 OBI low Fluorescent assay of metaphase chromosomes that can detect CAs through chromosome painting and microscopic analysis http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0000278 GO High content imaging DNA is stained using fluorescent dyes and micronuclei are scored using high-throughput microscopy image analysis. in_vitro micronucleus frequency increase http://purl.obolibrary.org/obo/GO_0005635 GO http://purl.obolibrary.org/obo/OBI_0001047 OBI high DNA can be stained using fluorescent dyes and micronuclei can be scored high-throughput microscopy image analysis. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0000910 GO High-throughput biomarker assays Multiplexed biomarkers can be measured by flow cytometry are used to discern clastogenic and aneugenic mechanisms for MN induction. Flow cytometry-based quantification of γH2AX foci and p53 protein expression. in_vitro γH2AX foci, p53 protein expression increase http://purl.obolibrary.org/obo/GO_0006261 GO http://purl.obolibrary.org/obo/CHEBI_59748 CHEBI high High-throughput biomarker assays (indirect measures to confirm clastogenicity) Bryce et al. 2014, 2016, 2018 Khoury et al., 2013, Khoury et al., 2016) Hendriks et al., 2012, 2016; Wink et al., 2014 Multiplexed biomarkers can be measured by flow cytometry are used to discern clastogenic and aneugenic mechanisms for MN induction. Flow cytometry-based quantification of γH2AX foci and p53 protein expression (Bryce et al., 2016). http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO In-Cell Western Green fluorescent protein reporter assay to detect the activation of stress signaling pathways, including DNA damage signaling including a reporter porter that is associated with DNA double strand breaks. in_vitro γH2AX activation increase http://purl.obolibrary.org/obo/GO_0006261 GO medium Prediscreen Assay– In-Cell Western-based quantification of γH2AX Green fluorescent protein reporter assay to detect the activation of stress signaling pathways, including DNA damage signaling including a reporter porter that is associated with DNA double strand breaks. http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO Micronucleus (MN) microscopy An in vivo assay where cells are fixed on slides and micronuclei are scored using microscopy. in_vivo MN scoring increase OECD, 2016b low Cells are fixed on slides and MN are scored using microscopy. Micronucleus Assay by Microscopy in vivo Cells are fixed on slides and micronuclei are scored using microscopy. Red blood cells can also be scored for micronuclei using flow cytometry. in_vivo erythrocytes reticulocytes peripheral blood micronucleus frequency increase http://purl.obolibrary.org/obo/GO_0005635 GO http://purl.obolibrary.org/obo/CL_0000232 CL OECD TG 474 medium Cells are fixed on slides and MN are scored using microscopy. Red blood cells can also be scored for MN using flow cytometry (see below) http://purl.obolibrary.org/obo/CL_0000232 CL http://purl.obolibrary.org/obo/GO_0002320 GO Next Generation Sequencing (NGS) Copy number variations are detected by fragmenting the genome and using NGS to sequence either the entire genome (WGS) or only the exome (WES). in_vitro copy number variations change http://purl.obolibrary.org/obo/GO_0070838 GO http://purl.obolibrary.org/obo/OBI_0002145 OBI http://purl.obolibrary.org/obo/OBI_0002144 OBI high CNVs are detected by fragmenting the genome and using NGS to sequence either the entire genome (WGS), or only the exome (WES) http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO Prediscreen Assay In-Cell Western-based quantification of γH2AX. Green fluorescent protein reporter assay to detect the activation of stress signaling pathways, including DNA damage signaling associated with DNA double strand breaks. in_vitro γH2AX expression increase http://purl.obolibrary.org/obo/PR_000008150 PR http://purl.obolibrary.org/obo/GO_0006303 GO http://purl.obolibrary.org/obo/PR_000008128 PR high Green fluorescent protein reporter assay to detect the activation of stress signaling pathways, including DNA damage signaling including a reporter porter that is associated with DNA double strand breaks. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Prediscreen In-Cell Western γH2AX Green fluorescent protein reporter assay to detect activation of stress signaling pathways, including DNA damage signaling associated with DNA double-strand breaks. not_specified γH2AX levels (DNA double-strand break marker) increase http://purl.obolibrary.org/obo/GO_0043486 GO medium Green fluorescent protein reporter assay to detect the activation of stress signaling pathways, including DNA damage signaling including a reporter porter that is associated with DNA double strand breaks. http://purl.obolibrary.org/obo/GO_0006974 GO Analysis of Volatile Organic Compounds in the Breath Quantification of volatile organic compounds in the breath using mass spectrometry as lung cancer biomarkers. ex_vivo VOC concentration change medium Volatile organic compounds, which may act as lung cancer biomarkers, are collected from the breath and quantified (mostly using mass spectrometry) http://purl.obolibrary.org/obo/DOID_14371 DOID Analysis of Volatile Organic Compounds in the Breath Volatile organic compounds, which may act as lung cancer biomarkers, are collected from the breath and quantified (mostly using mass spectrometry). in_vivo lungs volatile organic compounds not_specified http://purl.obolibrary.org/obo/CHEBI_35707 CHEBI http://purl.obolibrary.org/obo/OBI_0000272 OBI medium Volatile organic compounds, which may act as lung cancer biomarkers, are collected from the breath and quantified (mostly using mass spectrometry) http://purl.obolibrary.org/obo/CHEBI_35707 CHEBI Bronchoscopy Visual inspection of the respiratory tract using white light, fluorescence, or ultrasound technologies. in_vivo respiratory tract visual presence of tumours increase low Bronchoscope (usually with a camera) is passed down through the throat to the lungs to provide a visual of the respiratory tract http://purl.obolibrary.org/obo/UBERON_0000901 UBERON http://purl.obolibrary.org/obo/DOID_14371 DOID Bronchoscopy Bronchoscope (usually with a camera) is passed down through the throat to the lungs to provide a visual of the respiratory tract; Traditionally, visualization has been performed using conventional white light, but new technologies have also allowed for visualization using fluorescence and ultrasound technologies. in_vivo lungs visualization of respiratory tract not_specified http://purl.obolibrary.org/obo/UBERON_0000082 UBERON low Bronchoscope (usually with a camera) is passed down through the throat to the lungs to provide a visual of the respiratory tract; Traditionally, visualization has been performed using conventional white light, but new technologies have also allowed for visualization using fluorescence and ultrasound technologies http://purl.obolibrary.org/obo/UBERON_0000082 UBERON Cell Transformation Assays Measurement of the tumourigenicity of a tumour/biopsy sample by analyzing changes in cell physiology and morphology in response to tumour-inducing radiation or chemicals in_vitro lung cell physiology and morphology changes change OECD TG 231 low Measurement of the tumourigenicity of a tumour/biopsy sample by analyzing changes in cell physiology and morphology in response to tumour-inducing radiation or chemicals Yes (No. 231) http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0001544 GO Cell Transformation Assays Measurement of the tumourigenicity of a tumour/biopsy sample by analyzing changes in cell physiology and morphology in response to tumour-inducing radiation or chemicals. in_vitro cell transformation increase http://purl.obolibrary.org/obo/OBI_0000668 OBI http://purl.obolibrary.org/obo/NCIT_C25554 NCIT OECD TG 231 medium Measurement of the tumourigenicity of a tumour/biopsy sample by analyzing changes in cell physiology and morphology in response to tumour-inducing radiation or chemicals http://purl.obolibrary.org/obo/GO_0005623 GO http://purl.obolibrary.org/obo/GO_0002009 GO Computed Tomography (CT) Scans CT scans are described as a 3D X-ray; They provide cross-sections of organs/tissues/bones, and can thus be used to detect tumours. in_vivo lungs tumor detection not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/NCIT_C3263 NCIT low CT scans are described as a 3D X-ray; They provide cross-sections of organs/tissues/bones, and can thus be used to detect tumours http://purl.obolibrary.org/obo/UBERON_0002048 UBERON Magnetic Resonance Imaging (MRI) This technique uses magnetic fields and radio waves (NOT ionizing radiation) to generate a picture of organs, and can thus be used to detect tumours. in_vivo lungs tumor detection not_specified http://purl.obolibrary.org/obo/OBI_0000213 OBI http://purl.obolibrary.org/obo/NCIT_C3263 NCIT low This technique uses magnetic fields and radio waves (NOT ionizing radiation) to generate a picture of organs, and can thus be used to detect tumours http://purl.obolibrary.org/obo/UBERON_0002048 UBERON Rodent Two-Year Cancer Bioassays Animals are exposed to a possible carcinogen for a long period of time (often two years), allowing for long-term cancer-related studies. in_vivo rodents carcinogenicity increase http://purl.obolibrary.org/obo/OBI_0000669 OBI http://purl.obolibrary.org/obo/NCBITaxon_10114 NCBITAXON OECD TG 451 low Animals are exposed to a possible carcinogen for a long period of time (often two years), allowing for long-term cancer-related studies http://purl.obolibrary.org/obo/NCBITaxon_10114 NCBITAXON http://purl.obolibrary.org/obo/GO_0007515 GO Sputum Analysis Sputum is collected and analyzed for a variety of markers, including mutations in KRAS and TP53, specific RNA/protein biomarkers, and chromosomal aberrations. in_vivo lungs genetic and molecular biomarkers not_specified http://purl.obolibrary.org/obo/UBERON_0001959 UBERON http://purl.obolibrary.org/obo/NCIT_C37994 NCIT http://purl.obolibrary.org/obo/NCIT_C17999 NCIT medium Sputum is collected and analyzed for a variety of markers, including mutations in KRAS and TP53, specific RNA/protein biomarkers, and chromosomal aberrations http://purl.obolibrary.org/obo/UBERON_0001959 UBERON Sputum Analysis Sputum is collected and analyzed for markers including KRAS and TP53 mutations, RNA/protein biomarkers, and chromosomal aberrations. in_vivo lung mutations in KRAS and TP53, RNA/protein biomarkers, chromosomal aberrations change low Sputum is collected and analyzed for a variety of markers, including mutations in KRAS and TP53, specific RNA/protein biomarkers, and chromosomal aberrations Transbronchial Needle Aspiration A needle is used to aspirate a tissue sample from a lesion of suspected lung cancer for analysis. in_vivo lungs tissue sample collection not_specified http://purl.obolibrary.org/obo/UBERON_0002048 UBERON low A needle is used to aspirate a tissue sample from a lesion of suspected lung cancer for analysis http://purl.obolibrary.org/obo/UBERON_0002048 UBERON Window Chamber Models Window chambers are implanted into the animal to observe tumour progression in living animals using imaging techniques such as in vivo microscopy, MRI or nuclear imaging. in_vivo tumor progression not_specified http://purl.obolibrary.org/obo/NCIT_C25153 NCIT low Window chambers are implanted into the animal to observe tumour progression in living animals using imaging techniques such as in vivo microscopy, MRI or nuclear imaging http://purl.obolibrary.org/obo/NCIT_C3263 NCIT http://purl.obolibrary.org/obo/NCIT_C25153 NCIT Xenograft Assays Tumour cells (usually human) are grown in vitro and injected into animals to induce tumour growth and/or to test the tumourigenicity of the injected cells. in_vivo tumor growth increase http://purl.obolibrary.org/obo/OBI_0000667 OBI http://purl.obolibrary.org/obo/NCIT_C25152 NCIT low Tumour cells (usually human) are grown in vitro and injected into animals to induce tumour growth and/or to test the tumourigenicity of the injected cells http://purl.obolibrary.org/obo/NCIT_C3263 NCIT http://purl.obolibrary.org/obo/NCIT_C25152 NCIT confocal microscopy Measures neural crest cell migration in vivo in developing zebrafish embryos using a sox10 fluorescent reporter fishline. in_vivo neural crest cells embryo Danio rerio cell migration decrease http://purl.obolibrary.org/obo/GO_0016477 GO http://purl.obolibrary.org/obo/NCBITaxon_7955 NCBITAXON low in vivo in developing zebrafish embryos by confocal microscopy with the sox10 fluorescent reporter fishline http://purl.obolibrary.org/obo/CL_0000097 CL http://purl.obolibrary.org/obo/GO_0016477 GO confocal microscopy In vivo imaging of zebrafish embryos using a sox10 fluorescent reporter to visualize and quantify the migration of neural crest cells. in_vivo neural crest cells zebrafish NCC migration decrease http://purl.obolibrary.org/obo/GO_0016411 GO not_specified in vivo in developing zebrafish embryos by confocal microscopy with the sox10 fluorescent reporter fishline http://purl.obolibrary.org/obo/CL_0000634 CL http://purl.obolibrary.org/obo/GO_0016411 GO confocal microscopy with sox10 fluorescent reporter An in vivo imaging technique used to visualize and quantify migratory neural crest cells in zebrafish embryos using the Sox10 fluorescent reporter line. in_vivo neural crest cells zebrafish neural crest cell migration change http://purl.obolibrary.org/obo/GO_0007157 GO low in vivo in developing zebrafish embryos by confocal microscopy with the sox10 fluorescent reporter fishline. Sox10 is a recognized marker of migratory NCCs http://purl.obolibrary.org/obo/CL_0000150 CL http://purl.obolibrary.org/obo/GO_0007157 GO scratch assay Measures neural crest cell migration in vitro by creating a scratch in a cell monolayer and observing the rate of cell movement into the scratch. in_vitro neural crest cells cell migration rate decrease http://purl.obolibrary.org/obo/GO_0016477 GO medium NCC migration can be assessed in vitro by scratch assays http://purl.obolibrary.org/obo/CL_0000097 CL http://purl.obolibrary.org/obo/GO_0016477 GO scratch assay An in vitro assay used to assess the migration of neural crest cells by monitoring the closure of a created gap in a cell monolayer. in_vitro neural crest cells NCC migration decrease http://purl.obolibrary.org/obo/GO_0016411 GO not_specified NCC migration can be assessed in vitro by scratch assays http://purl.obolibrary.org/obo/CL_0000634 CL http://purl.obolibrary.org/obo/GO_0016411 GO fluorescent microscopy Assesses collagen expression in vivo using fluorescent collagen reporter zebrafish lines. in_vivo Danio rerio collagen expression decrease http://purl.obolibrary.org/obo/GO_0005581 GO medium Collagen expression is considered a marker for NCC differentiation into chondrocytes (Bhatt et al., 2013) and can be assessed in vivo by fluorescent microscopy using fluorescent collagen reporter zebrafish lines (Hammond and Schulte-Merker, 2009). http://purl.obolibrary.org/obo/GO_0005581 GO http://purl.obolibrary.org/obo/GO_0002062 GO fluorescent microscopy using fluorescent collagen reporter zebrafish lines Assessment of collagen expression in vivo using transgenic zebrafish lines that express fluorescent proteins in response to collagen production. in_vivo zebrafish collagen expression change http://purl.obolibrary.org/obo/CHEBI_35101 CHEBI http://purl.obolibrary.org/obo/OBI_0001341 OBI not_specified can be assessed in vivo by fluorescent microscopy using fluorescent collagen reporter zebrafish lines http://purl.obolibrary.org/obo/CHEBI_35101 CHEBI http://purl.obolibrary.org/obo/GO_0030198 GO Ceratohyal angle measurement Quantitative measurement of the angle formed by the ceratohyal cartilage in zebrafish embryos to assess morphological changes. in_vivo ceratohyal cartilage Danio rerio angle formed by the ceratohyal change medium Measurements of the angle formed by the ceratohyal provide a quantitative readout. http://purl.obolibrary.org/obo/GO_0060350 GO Fluorescent collagen reporter imaging Visualization of facial cartilage structures in zebrafish embryos using fluorescent collagen reporter lines to observe structures such as the ceratohyal, Meckel’s cartilage, and the palatoquadrate. in_vivo facial cartilage Danio rerio appearance of facial cartilage structures not_specified http://purl.obolibrary.org/obo/UBERON_0005841 UBERON http://purl.obolibrary.org/obo/GO_0005581 GO medium The appearance of facial cartilage structures is readily visible in ventral views of zebrafish embryos at 5 days post fertilization. Such structures as the ceratohyal, Meckel’s cartilage, and the palatoquadrate are visible using fluorescent collagen reporter lines. http://purl.obolibrary.org/obo/UBERON_0005841 UBERON http://purl.obolibrary.org/obo/GO_0051216 GO zebrafish facial cartilage morphology Visual assessment of facial cartilage structures in zebrafish embryos at 5 days post fertilization using fluorescent collagen reporter lines, with quantitative measurement of the angle formed by the ceratohyal cartilage. in_vivo cartilage Danio rerio angle of ceratohyal cartilage change http://purl.obolibrary.org/obo/UBERON_0001725 UBERON low The appearance of facial cartilage structures is readily visible in ventral views of zebrafish embryos at 5 days post fertilization. Measurements of the angle formed by the ceratohyal provide a quantitative readout. http://purl.obolibrary.org/obo/UBERON_0001725 UBERON gene set enrichment analysis Gene set enrichment analysis (GEA) is used to analyze altered genes, comparing control and potentially disturbed differentiation. in_vitro hESC iPSC altered gene expression change medium Then it can be measured by the analysis of altered genes by gene set enrichment analysis (GEA) comparing control with potentially disturbed differentiation. http://purl.obolibrary.org/obo/GO_0030274 GO gene set enrichment analysis Analyzes altered genes by comparing control with potentially disturbed differentiation using gene set enrichment analysis. in_silico gene set enrichment change http://purl.obolibrary.org/obo/GO_0010467 GO high Then it can be measured by the analysis of altered genes by gene set enrichment analysis (GEA) comparing control with potentially disturbed differentiation. http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO hESC/iPSC differentiation system Measures altered cell differentiation by comparing control and disturbed differentiation in human embryonic stem cells or induced pluripotent stem cells. in_vitro hESC iPSC human altered gene expression change http://purl.obolibrary.org/obo/GO_0030154 GO http://purl.obolibrary.org/obo/GO_0010467 GO medium Differentiation can be measured e.g. by in vitro hESC or iPSC based differentiation systems. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0030154 GO immunofluorescence Uses immunofluorescence on brain sections with antibodies against neuronal differentiation markers to measure neuronal differentiation. in_vivo brain expression of neuronal differentiation markers change http://purl.obolibrary.org/obo/OBI_0000574 OBI http://purl.obolibrary.org/obo/GO_0030182 GO medium In the context of embryonic brain development, immunofluorescence on brain sections can be used with antibodies against neuronal differentiation markers such Tuj1, NeuN and betaIII-tubulin. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0030182 GO animal model assay An in vivo assay using animal models to study neural tube defects. in_vivo neural tube defects not_specified http://purl.obolibrary.org/obo/MP_0002422 MP not_specified In vivo animal models http://purl.obolibrary.org/obo/UBERON_0001052 UBERON http://purl.obolibrary.org/obo/GO_0021915 GO rosette formation assay An in vitro assay that measures the formation of rosettes, which are structures indicative of neural tube development. in_vitro rosette formation not_specified http://purl.obolibrary.org/obo/GO_0021915 GO not_specified In vitro assays that follow rosettes formation http://purl.obolibrary.org/obo/UBERON_0001052 UBERON http://purl.obolibrary.org/obo/GO_0021915 GO electrophysiology Historically, Na/K ATPase activity was measured via electrophysiology measurements of charge changes. in_vitro charge changes change low historically electrophysiology measurements of charge changes was more common (Moyes et al. 2021). http://purl.obolibrary.org/obo/CHEBI_62319 CHEBI http://purl.obolibrary.org/obo/GO_0006825 GO Electrophysiology Measures Na/K ATPase activity via electrophysiological recordings of charge changes. in_vitro Na/K ATPase activity decrease http://purl.obolibrary.org/obo/OBI_0000210 OBI http://purl.obolibrary.org/obo/GO_0006811 GO low historically electrophysiology measurements of charge changes was more common (Moyes et al. 2021). http://purl.obolibrary.org/obo/PR_000001042 PR http://purl.obolibrary.org/obo/GO_0006811 GO Immunoblot Measures Na/K ATPase activity via immunoblotting to detect protein levels or phosphorylation status. in_vitro Na/K ATPase protein levels or activity decrease http://purl.obolibrary.org/obo/OBI_0000619 OBI http://purl.obolibrary.org/obo/PR_000001042 PR low Generally Na/K ATPase activity is measured via immunoblots or spectrophotometry; http://purl.obolibrary.org/obo/PR_000001042 PR http://purl.obolibrary.org/obo/GO_0006811 GO Na/K ATPase activity assay Measures Na/K ATPase activity in cell lysates by detecting ATP or inorganic phosphate produced during ATP hydrolysis, coupled to colorimetric or fluorimetric dye. in_vitro Na/K ATPase activity decrease http://purl.obolibrary.org/obo/GO_0016887 GO medium Na/K ATPase activity can be measured in cell lysates preserving enzymatic activity, and corresponds to the difference between total ATPase activity and ouabain-sensitive ATPase activity. The measurement can use the leftover ATP or inorganic phosphate produced during ATP hydrolysis as its primary substrate, followed by coupling to colorimetric or fluorimetric dye (Baginski, Foa, and Zak 1967; Nowak 2002) (NovusBio kit 601-0120). http://purl.obolibrary.org/obo/PR_000001042 PR http://purl.obolibrary.org/obo/GO_0006811 GO Spectrophotometry Measures Na/K ATPase activity via spectrophotometric detection of ATP hydrolysis products. in_vitro Na/K ATPase activity decrease http://purl.obolibrary.org/obo/OBI_0000215 OBI http://purl.obolibrary.org/obo/GO_0016887 GO medium Generally Na/K ATPase activity is measured via immunoblots or spectrophotometry; http://purl.obolibrary.org/obo/PR_000001042 PR http://purl.obolibrary.org/obo/GO_0006811 GO dye transport assay This assay measures transport across a cell monolayer using fluorescent dyes, either directly (dye transport) or indirectly (competition with the dye). in_vitro transport of fluorescent dyes change medium Fluorescent dyes can also be used to measure transport across the monolayer either directly (transport of the dye itself) or indirectly (competition with the dye). http://purl.obolibrary.org/obo/GO_0006825 GO filter insert assay This assay studies the volume and composition of apical and basolateral compartments of proximal tubule cells grown on filter inserts to determine variations in vectorial transport. in_vitro proximal tubule cells proximal tubule volume and composition of apical and basolateral compartments change low When proximal tubule cells are grown on filter inserts, the volume and composition of the medium in the apical and basolateral compartments can be studied separately to determine variations in a vectorial transport. fluorescent dye transport This assay uses fluorescent dyes to measure transport across the monolayer of proximal tubule cells, either directly (transport of the dye itself) or indirectly (competition with the dye). in_vitro http://purl.obolibrary.org/obo/CL_0000057 http://purl.obolibrary.org/obo/UBERON_0001255 transport across monolayer decrease http://purl.obolibrary.org/obo/GO_0051179 GO not_specified Fluorescent dyes can also be used to measure transport across the monolayer either directly (transport of the dye itself) or indirectly (competition with the dye). http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0051179 GO vectorial transport assay Measures the volume and composition of medium in apical and basolateral compartments to determine variations in vectorial transport across proximal tubule cells grown on filter inserts. in_vitro proximal tubule cells kidney vectorial transport rate decrease http://purl.obolibrary.org/obo/CL_0000598 CL low When proximal tubule cells are grown on filter inserts, the volume and composition of the medium in the apical and basolateral compartments can be studied separately to determine variations in a vectorial transport. http://purl.obolibrary.org/obo/CL_0000598 CL water transport rate assay Measures the differential rate of water transport across a proximal tubule cell monolayer grown on filter inserts. in_vitro proximal tubule cells kidney water transport rate decrease http://purl.obolibrary.org/obo/GO_0006833 GO http://purl.obolibrary.org/obo/CL_0000598 CL low A differential measure of the rate of water transport can also be used in this format (Wilmes et al. 2014) http://purl.obolibrary.org/obo/CL_0000598 CL http://purl.obolibrary.org/obo/GO_0006833 GO blood chemistry analysis Measures serum levels of bicarbonate, potassium, and chloride to detect renal tubular acidosis, characterized by hypokalemia and hyperchloremia. in_vivo blood human serum bicarbonate, potassium, and chloride levels change http://purl.obolibrary.org/obo/CHEBI_17993 CHEBI http://purl.obolibrary.org/obo/CHEBI_24227 CHEBI http://purl.obolibrary.org/obo/CHEBI_17994 CHEBI http://purl.obolibrary.org/obo/UBERON_0000178 UBERON medium The lack in reabsorption of bicarbonate results in renal tubular acidosis, characterised by polyurea, hypokalemia and hyperchloremia. http://purl.obolibrary.org/obo/UBERON_0001285 UBERON http://purl.obolibrary.org/obo/GO_0006885 GO Blood electrolyte and acid-base analysis Measurement of serum potassium, chloride, and bicarbonate concentrations to evaluate renal tubular acidosis and associated electrolyte imbalances. in_vivo kidney Homo sapiens serum potassium, chloride, and bicarbonate levels change low The lack in reabsorption of bicarbonate results in renal tubular acidosis, characterised by polyurea, hypokalemia and hyperchloremia. bone mineralisation assessment Evaluates bone mineralisation status to detect hypophosphatemic rickets in children and bone demineralisation in adults. in_vivo bone human bone mineralisation status decrease http://purl.obolibrary.org/obo/GO_0030282 GO http://purl.obolibrary.org/obo/UBERON_0002495 UBERON low Effects on bone mineralisation (adults) and development (children) is another characteristic of FS. The lack of reabsorption of phosphate leads to bone disorders (hypophosphatemic rickets in children and bone demineralisation in adults). http://purl.obolibrary.org/obo/UBERON_0002495 UBERON http://purl.obolibrary.org/obo/GO_0030282 GO electron microscopy This assay uses electron microscopy to observe mitochondrial cytopathy, characterized by swollen and dysmorphic mitochondria without cristae, in renal tissue samples. ex_vivo http://purl.obolibrary.org/obo/UBERON_0001255 mitochondrial morphology change http://purl.obolibrary.org/obo/HP_0004947 HP low At the tissue level, a marked effect of these chemicals is the induction of mitochondrial cytopathy (swollen and dysmorphic mitochondria without cristae) (Herlitz et al. 2010). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0007007 GO mitochondrial morphology assessment Examines mitochondrial structure to detect mitochondrial cytopathy, characterized by swollen and dysmorphic mitochondria without cristae. in_vivo kidney human mitochondrial morphology not_specified http://purl.obolibrary.org/obo/GO_0005739 GO low At the tissue level, a marked effect of these chemicals is the induction of mitochondrial cytopathy (swollen and dysmorphic mitochondria without cristae) (Herlitz et al. 2010). http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0007005 GO urine analysis Measures urinary levels of phosphate, glucose, and protein to detect hyperphosphaturia, glycosuria, and proteinuria, which are clinical features of Fanconi syndrome. in_vivo kidney human urinary phosphate, glucose, and protein levels increase http://purl.obolibrary.org/obo/CHEBI_43474 CHEBI http://purl.obolibrary.org/obo/CHEBI_4167 CHEBI http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/UBERON_0001088 UBERON medium hyperphosphaturea, glycosurea and proteinurea are typical clinical features of FS, together with polyuria. http://purl.obolibrary.org/obo/UBERON_0001285 UBERON http://purl.obolibrary.org/obo/GO_0003305 GO In vitro IKK kinase assay Measures IKK activity using the CycLex IKKb inhibitor screening kit. in_vitro IKK activity decrease http://purl.obolibrary.org/obo/GO_0016301 GO medium In vitro IKK kinase assay (CycLex IKKb inhibitor screening kit) (Heyninck et al. 2014). Western blot Measures the interaction between a compound and the IKK complex using IKK antibodies in purified IKK complexes. in_vitro compound-IKK complex interaction not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI low Western blot with IKK antibodies in purified IKK complexes (Heyninck et al. 2014). http://purl.obolibrary.org/obo/GO_0005515 GO Western blot Measures specific Cys-179 interaction using mutant IKKb treatment followed by Western blotting with antiFLAG. in_vitro Cys-179 interaction not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI low Mutant IKKb treatment followed by Western blotting with antiFLAG (Heyninck et al. 2014). http://purl.obolibrary.org/obo/GO_0005515 GO Caspase 8 fluorogenic substrate assay Measures caspase 8 enzymatic activity using fluorogenic substrates that are cleaved upon activation. in_vitro caspase 8 enzymatic activity not_specified http://purl.obolibrary.org/obo/PR_000001510 PR http://purl.obolibrary.org/obo/OBI_0000378 OBI medium Caspase 8 specific fluorogenic substrates(Schattenberg et al. 2011) http://purl.obolibrary.org/obo/PR_000001510 PR http://purl.obolibrary.org/obo/GO_0097190 GO fluorogenic substrate assay This assay measures caspase 8 activity using caspase 8 specific fluorogenic substrates. in_vitro caspase 8 activity increase http://purl.obolibrary.org/obo/GO_0004372 GO http://purl.obolibrary.org/obo/CHEBI_59748 CHEBI medium Caspase 8 specific fluorogenic substrates(Schattenberg et al. 2011) http://purl.obolibrary.org/obo/CHEBI_59748 CHEBI http://purl.obolibrary.org/obo/GO_0008219 GO Western Blot Measures the presence or activation of pro-caspase 8 protein using antibody-based detection. in_vitro pro-caspase 8 protein levels not_specified http://purl.obolibrary.org/obo/PR_000001510 PR low WesternBlot (pro) caspase 8 (Fotin-Mleczek et al. 2002)(Schattenberg et al. 2011) http://purl.obolibrary.org/obo/PR_000001510 PR http://purl.obolibrary.org/obo/GO_0097190 GO direct photolabeling Direct photolabeling of tubulin with radiolabelled [3H]taxol and [3H]taxoid-derivatives to identify binding sites of taxol in tubulin. in_vitro binding sites of taxol in tubulin not_specified http://purl.obolibrary.org/obo/OBI_0000219 OBI http://purl.obolibrary.org/obo/PR_000008749 PR low Direct photolabeling of tubulin with radiolabelled [3H]taxol [13], and [3H]taxoid-derivatives to identify binding sites of taxol in tubulin [10, 11, 14, 15, 18] http://purl.obolibrary.org/obo/PR_000008749 PR electron microscopy Electron microscopy of tannin-embedded tubulin crystals stabilized with taxol to visualize the binding site of taxol in polymerized tubulin. in_vitro binding site of taxol in polymerized tubulin not_specified http://purl.obolibrary.org/obo/OBI_0000218 OBI http://purl.obolibrary.org/obo/GO_0005874 GO low Electron microscopy of tannin-embedded tubulin crystals stabilized with taxol. Projection density maps were created from the electron microscopy data and further processed to difference maps of tubulin to visualize the binding site of taxol in polymerized tubulin [12, 16] http://purl.obolibrary.org/obo/GO_0005874 GO FRET spectroscopy Fluorescence energy transfer (FRET) spectroscopy to determine the conformation of microtubule-bound taxol. in_vitro conformation of microtubule-bound taxol not_specified http://purl.obolibrary.org/obo/OBI_0000220 OBI http://purl.obolibrary.org/obo/GO_0005874 GO low Fluorescence energy transfer (FRET) spectroscopy to determine the conformation of microtubule-bound taxol [19] http://purl.obolibrary.org/obo/GO_0005874 GO HPLC sequencing Tubulin is photolabelled with [3H]taxoid-derivatives, then digested with formic acid or CNBr and clostripain or trypsin. Peptide fragments are analysed via reverse phase HPLC and sequenced to identify the photoincorporation site. in_vitro taxoid photoincorporation site identification change low To identify the photoincorporation site, the labelled complex is then digested by formic acid or CNBr in combination with either clostripain or trypsin. The obtained peptide fragments are analysed via reverse phase HPLC and the radioactive peak is sequenced. [14, 15, 18] http://purl.obolibrary.org/obo/GO_0005807 GO http://purl.obolibrary.org/obo/GO_0016338 GO Mapping studies Photolabeling of tubulin with [3H]taxoid-derivatives followed by digestion and reverse phase HPLC and sequencing to identify photoincorporation sites. in_vitro photoincorporation site not_specified http://purl.obolibrary.org/obo/GO_0005524 GO low To identify the photoincorporation site, the labelled complex is then digested by formic acid or CNBr in combination with either clostripain or trypsin. The obtained peptide fragments are analysed via reverse phase HPLC and the radioactive peak is sequenced. http://purl.obolibrary.org/obo/GO_0005524 GO http://purl.obolibrary.org/obo/GO_0005524 GO mapping studies Tubulin is photolabelled with [3H]taxoid-derivatives, digested, and the peptide fragments are analysed via reverse phase HPLC to identify the photoincorporation site. in_vitro photoincorporation site of taxol in tubulin not_specified http://purl.obolibrary.org/obo/OBI_0000219 OBI http://purl.obolibrary.org/obo/PR_000008749 PR http://purl.obolibrary.org/obo/OBI_0000215 OBI low Mapping studies: Tubulin is photolabelled with [3H]taxoid-derivatives. To identify the photoincorporation site, the labelled complex is then digested by formic acid or CNBr in combination with either clostripain or trypsin. The obtained peptide fragments are analysed via reverse phase HPLC and the radioactive peak is sequenced. [14, 15, 18] http://purl.obolibrary.org/obo/PR_000008749 PR NMR studies NMR studies and solid-state rotational echo double-resonance (REDOR) NMR to determine the orientation of microtubule-bound taxol. in_vitro orientation of microtubule-bound taxol not_specified http://purl.obolibrary.org/obo/GO_0005874 GO low NMR studies [20] and solid-state rotational echo double-resonance (REDOR) NMR [19] to determine the orientation of microtubule-bound taxol http://purl.obolibrary.org/obo/GO_0005874 GO X-ray crystallography Structural determination of the binding using X-ray crystallography. in_vitro molecular structure not_specified http://purl.obolibrary.org/obo/OBI_0001134 OBI low X-ray crystallography [17] http://purl.obolibrary.org/obo/PR_000000003 PR http://purl.obolibrary.org/obo/GO_0042512 GO X-ray crystallography X-ray crystallography to determine the structure of microtubule-bound taxol. in_vitro structure of microtubule-bound taxol not_specified http://purl.obolibrary.org/obo/GO_0005874 GO low X-ray crystallography [17] http://purl.obolibrary.org/obo/GO_0005874 GO electron microscopy Microtubule mass is quantified using electron microscopy after treatment with nocodazole, a microtubule-depolymerizing agent, to assess microtubule stability and the ratio of stable and labile fractions. in_vitro microtubule mass change low Treatment with nocodazole over different time periods and subsequent quantification of microtubule mass by electron microscopy can give an insight into microtubule stability and the ratio of stabile and labile microtubule fractions. http://purl.obolibrary.org/obo/CL_0000078 CL Fluorescence recovery after photobleaching Assesses microtubule turnover by photobleaching fluorescently-labelled tubulin (via transfection or injection) in neurons and measuring the rate of fluorescence recovery. ex_vivo neurons microtubule turnover change http://purl.obolibrary.org/obo/GO_0007201 GO http://purl.obolibrary.org/obo/CL_0000131 CL low Fluorescence recovery after photobleaching: Cultured neurons are transfected to express fluorescently-labelled tubulin or injected with x-rhodamine-tubulin (tubulin with fluorescent-label). Multiple sites along a neurite are photobleached and fluorescence recovery after photobleaching was assessed at these sites as a measure for microtubule turnover. http://purl.obolibrary.org/obo/GO_0005874 GO http://purl.obolibrary.org/obo/GO_0000221 GO immunofluorescence staining Immunofluorescence staining for acetylated tubulin (marker for stable microtubules) and tyrosinated tubulin (marker for labile microtubules) to assess the composition of microtubules in cells. in_vitro acetylated tubulin and tyrosinated tubulin levels change http://purl.obolibrary.org/obo/GO_0005874 GO medium Immunofluorescence staining for acetylated tubulin, which is a marker for stable microtubules and for tyrosinated tubulin which is a marker of labile microtubules gives insight into the composition of microtubules in cells. http://purl.obolibrary.org/obo/GO_0005874 GO http://purl.obolibrary.org/obo/GO_0007017 GO Immunofluorescence staining Staining for acetylated tubulin and tyrosinated tubulin to assess the composition of stable versus labile microtubules in cells. in_vitro composition of stable versus labile microtubules change medium Immunofluorescence staining for acetylated tubulin, which is a marker for stable microtubules and for tyrosinated tubulin which is a marker of labile microtubules gives insight into the composition of microtubules in cells. nocodazole treatment with electron microscopy Treatment with nocodazole over different time periods followed by quantification of microtubule mass using electron microscopy to assess microtubule stability and the ratio of stable and labile microtubule fractions. in_vitro microtubule mass decrease http://purl.obolibrary.org/obo/GO_0005874 GO http://purl.obolibrary.org/obo/GO_0007023 GO low Nocodazole is a microtubule-depolymerizing agent. Treatment with nocodazole over different time periods and subsequent quantification of microtubule mass by electron microscopy can give an insight into microtubule stability and the ratio of stabile and labile microtubule fractions. http://purl.obolibrary.org/obo/GO_0005874 GO http://purl.obolibrary.org/obo/GO_0007023 GO Axonal transport in mouse sciatic nerve Drug is administered to mice, the sciatic nerve is ligated, and segments are analyzed by Western blot to measure protein levels proximal and distal to the ligation. in_vivo sciatic nerve mouse protein levels change http://purl.obolibrary.org/obo/UBERON_0001444 UBERON http://purl.obolibrary.org/obo/GO_0008088 GO http://purl.obolibrary.org/obo/OBI_0000269 OBI low Axonal transport in mouse sciatic nerve: The drug is administered to mice intravenously. Mice are anesthetized and the left sciatic nerve is exposed and ligated at two points. After 24h, the ligated sciatic nerves are dissected and segments from proximal and distal sides of the ligation are collected, homogenized and analysed by Western blot. http://purl.obolibrary.org/obo/GO_0008088 GO http://purl.obolibrary.org/obo/GO_0008088 GO Axonal transport in mouse sciatic nerve Measures axonal transport of proteins in mouse sciatic nerve after systemic drug administration using Western blot analysis. in_vivo sciatic nerve mouse protein transport change http://purl.obolibrary.org/obo/UBERON_0000988 UBERON low Axonal transport in mouse sciatic nerve: The drug is administered to mice intravenously. Mice are anesthetized and the left sciatic nerve is exposed and ligated at two points. After 24h, the ligated sciatic nerves are dissected and segments from proximal and distal sides of the ligation are collected, homogenized and analysed by Western blot. http://purl.obolibrary.org/obo/UBERON_0000988 UBERON Horseradish peroxidase (HRP) microinjection HRP is injected into dorsal root ganglia neurons and visualized with 3,3’-diaminobenzidine to measure the transport length of HRP. in_vivo dorsal root ganglia neurons dorsal root ganglia transport length change http://purl.obolibrary.org/obo/UBERON_0001099 UBERON http://purl.obolibrary.org/obo/GO_0008088 GO http://purl.obolibrary.org/obo/CHEBI_9069 CHEBI low Horseradish peroxidase (HRP) microinjection: HRP is injected into dorsal root ganglia neurons and visualized by 3,3’-diaminobenzidine. Microscope recordings of the neurons showing the transport of HRP are evaluated and the transport length is measured. http://purl.obolibrary.org/obo/GO_0008088 GO http://purl.obolibrary.org/obo/GO_0008088 GO Kinesin-driven microtubule gliding assay Slide chambers coated with kinesins are used to evaluate microtubule gliding velocity, trajectory curvature, and length by visualizing rhodamine-labeled microtubules. in_vitro microtubule gliding velocity change http://purl.obolibrary.org/obo/PR_000001184 PR http://purl.obolibrary.org/obo/GO_0005874 GO medium Kinesin-driven microtubule gliding assay: Slide chambers are covered with kinesins which adhere e.g. to specific antibodies on the glass slides. Rhodamine-labelled tubulin and unlabelled tubulin are mixed and assembled to microtubule structures. Microtubules are applied to the chamber and the rhodamine fluorescence is visualized to evaluate microtubule gliding. Microtubule-bodies are located and tracked to collect data on gliding velocity, trajectory curvature and microtubule length. http://purl.obolibrary.org/obo/GO_0005874 GO http://purl.obolibrary.org/obo/GO_0007018 GO Mitochondrial trafficking assay Cells are incubated with drug or DMSO, labeled with MitoTracker Green FM, and imaged in a live cell chamber to track mitochondrial movement in neurites. in_vitro neurites mitochondrial movement change http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0043005 GO http://purl.obolibrary.org/obo/GO_0070095 GO medium Mitochondrial trafficking: Cells are incubated with drug or DMSO solution and afterwards mitochondria are labelled with MitoTracker Green FM. Cells are kept in a live cell chamber and imaged in regular intervals. The time-lapse is used to track mitochondrial movement in neurites. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0070095 GO Vesicle motility assay Isolated axoplasm from squid giant axons is analyzed using a Zeiss Axiomat to measure organelle velocities either automatically or manually by matching cursor movements to moving vesicles. ex_vivo axoplasm squid organelle velocities change http://purl.obolibrary.org/obo/UBERON_0001056 UBERON http://purl.obolibrary.org/obo/GO_0046907 GO low Vesicle motility assay: Axoplasm from squid giant axons is isolated and kept in axoplasm buffer. Preparations are analysed using a Zeiss Axiomat and organelle velocities are measured either in an automated process or by matching calibrated cursor movements to the speed of moving vesicles in agreement of two observers. http://purl.obolibrary.org/obo/GO_0043227 GO http://purl.obolibrary.org/obo/GO_0008088 GO western blot Sciatic nerves from mice are homogenized and analyzed by Western blot to assess protein levels. in_vivo sciatic nerve mouse protein levels change low Axonal transport in mouse sciatic nerve: The drug is administered to mice intravenously. Mice are anesthetized and the left sciatic nerve is exposed and ligated at two points. After 24h, the ligated sciatic nerves are dissected and segments from proximal and distal sides of the ligation are collected, homogenized and analysed by Western blot. [12] http://purl.obolibrary.org/obo/PR_000000001 PR MRC scale and dynamometer Measurement of muscle strength in toe extensors, index finger abductors, arm abductors, hip flexors, and foot dorsiflexors using the MRC scale and dynamometer. in_vivo muscle human muscle strength decrease medium Reductions in strength of toe extensors, index finger abductors, arm abductors, hip flexors, foot dorsiflexors: Measurement by using the MRC scale and dynamometer http://purl.obolibrary.org/obo/UBERON_0001134 UBERON http://purl.obolibrary.org/obo/GO_0006936 GO Nerve conduction studies Electrophysiological measurement of nerve conduction amplitudes and velocities in sensory neurons. in_vivo sensory neurons human nerve conduction amplitude and velocity change medium Nerve conduction studies: Electrophysiological measurement of nerve conduction amplitudes and velocities in sensory neurons http://purl.obolibrary.org/obo/CL_0000100 CL http://purl.obolibrary.org/obo/GO_0019228 GO Pin perception test Measurement of the distance from the tip of the great toe or index finger to a level where normal pin sensation was sensed. in_vivo sensory neurons human pin sensation distance increase medium Abnormal pin perception: Measurement of the distance in centimeters from the tip of the great toe or index finger to a level where normal pin sensation was sensed. http://purl.obolibrary.org/obo/CL_0000100 CL http://purl.obolibrary.org/obo/GO_0019233 GO Quantitative sensory testing of thermal threshold Measurement of the ability to discriminate small temperature differences at the index finger or great toe using devices like the Thermal Sensitivity Tester or NTE-2. in_vivo sensory neurons human thermal discrimination threshold change medium Quantitative sensory testing of thermal threshold: Using the Thermal Sensitivity Tester or NTE-2 (Physitemp Instruments Inc., Clifton NJ), the ability to discriminate small temperature differences at the index finger or the great toe can be quantified. http://purl.obolibrary.org/obo/CL_0000100 CL http://purl.obolibrary.org/obo/GO_0050953 GO Quantitative sensory testing of vibratory threshold Measurement of vibratory latency in seconds at the toes and fingers using automated devices like 'Vibration 2'. in_vivo sensory neurons human vibratory latency increase medium Quantitative sensory testing of vibratory threshold: Measurement of vibratory latency in seconds between the patient and the examiner in toes and fingers. Automated measurement using e.g. ‘Vibration 2’ (Physitemp Instruments Inc., Clifton NJ) which can be adjusted to different vibration amplitudes and records vibration units. http://purl.obolibrary.org/obo/CL_0000100 CL http://purl.obolibrary.org/obo/GO_0050975 GO Retrospective patient interview Patients are interviewed after chemotherapy treatment to assess symptoms of sensory axonal peripheral neuropathy. in_vivo human symptom assessment not_specified low Patients are interviewed after chemotherapy treatment and symptoms are assessed. Retrospective symptom interview Patients are interviewed after chemotherapy treatment to self-report symptoms of peripheral neuropathy, providing a clinical assessment of sensory and motor deficits. in_vivo Homo sapiens self-reported neuropathy symptom severity not_specified low - Retrospective study: Patients are interviewed after chemotherapy treatment and symptoms are assessed. [8, 9] http://purl.obolibrary.org/obo/CL_0000544 CL http://purl.obolibrary.org/obo/GO_0007608 GO strength measurement Measurement of reductions in strength of toe extensors, index finger abductors, arm abductors, hip flexors, foot dorsiflexors using the MRC scale and dynamometer. in_vivo muscle toe finger arm hip foot human muscle strength decrease low Reductions in strength of toe extensors, index finger abductors, arm abductors, hip flexors, foot dorsiflexors: Measurement by using the MRC scale and dynamometer http://purl.obolibrary.org/obo/CL_0000273 CL http://purl.obolibrary.org/obo/GO_0008274 GO Sural nerve biopsy A part of the sural nerve is removed, fixed, and investigated via light or electron microscopy. in_vivo sural nerve human nerve morphology not_specified low Sural nerve biopsy: A part of the sural nerve (some millimetres) is removed, fixed and investigated via light or electron microscopy. http://purl.obolibrary.org/obo/UBERON_0001394 UBERON http://purl.obolibrary.org/obo/GO_0061564 GO Vibration and position sensation test Measurement of vibration and position sensation at the distal phalanx of the great toe or index finger. in_vivo sensory neurons human vibration and position sensation change medium Abnormalities in vibration and position sensation: Measurement at distal phalanx of the great toe or index finger. http://purl.obolibrary.org/obo/CL_0000100 CL http://purl.obolibrary.org/obo/GO_0050975 GO 1H-NMR Measures the binding of α-diketones with proteins using proton nuclear magnetic resonance spectroscopy. in_vitro binding of α-diketones with proteins not_specified http://purl.obolibrary.org/obo/CHMO_0000630 CHMO http://purl.obolibrary.org/obo/GO_0005515 GO low The binding of α-diketones with proteins can be measured by ... 1H- ... NMR analysis http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005515 GO LC-MS Measures the binding of α-diketones with proteins using liquid chromatography-mass spectrometry. in_vitro binding of α-diketones with proteins not_specified http://purl.obolibrary.org/obo/OBI_0000475 OBI http://purl.obolibrary.org/obo/GO_0005515 GO medium The binding of α-diketones with proteins can be measured by LC-MS http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005515 GO LC-MS Liquid chromatography-mass spectrometry used to measure the binding of alpha-diketones with proteins. in_vitro protein binding not_specified http://purl.obolibrary.org/obo/CHMO_0000134 CHMO not_specified The binding of α-diketones with proteins can be measured by LC-MS http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005515 GO NMR analysis Nuclear Magnetic Resonance (1H and 13C) analysis to measure the binding of alpha-diketones with proteins. in_vitro protein binding not_specified http://purl.obolibrary.org/obo/CHMO_0000134 CHMO not_specified The binding of α-diketones with proteins can be measured by [...] 1H- and 13C NMR analysis http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005515 GO enzyme activity assay This assay demonstrates the inactivation of enzymes due to the interaction of α-diketones with arginine residues at their active sites. in_vitro enzyme inactivation decrease http://purl.obolibrary.org/obo/OBI_0000429 OBI low The inactivation of enzymes due to the interaction of α-diketones with arginine residues at their active sites has been demonstrated (Chen and Chen 2003). http://purl.obolibrary.org/obo/CHEBI_51179 CHEBI http://purl.obolibrary.org/obo/GO_0003824 GO enzyme inactivation assay Measures loss of enzymatic activity resulting from covalent modification of arginine residues by α-diketones, indicating enzyme inactivation. not_specified enzyme activity decrease http://purl.obolibrary.org/obo/GO_0003824 GO not_specified The inactivation of enzymes due to the interaction of α-diketones with arginine residues at their active sites has been demonstrated (Chen and Chen 2003). http://purl.obolibrary.org/obo/GO_0003824 GO immunohistochemistry Protein damage was measured by accumulation of ubiquitin and sequestosome-1 in the lungs of exposed mice. in_vivo lung mouse accumulation of ubiquitin and sequestosome-1 increase low Protein damage has been measured by accumulation of ubiquitin and sequestosome-1 in the lungs of exposed mice (Hubbs et al. 2016) http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0006520 GO Ubiquitin accumulation assay Measures the accumulation of ubiquitin in lung tissue of mice exposed to α-diketones, indicating protein damage. in_vivo lung mouse ubiquitin accumulation increase http://purl.obolibrary.org/obo/CHEBI_27972 CHEBI http://purl.obolibrary.org/obo/GO_0016567 GO not_specified Protein damage has been measured by accumulation of ubiquitin and sequestosome-1 in the lungs of exposed mice (Hubbs et al. 2016) http://purl.obolibrary.org/obo/CHEBI_27972 CHEBI http://purl.obolibrary.org/obo/GO_0016567 GO ubiquitin and sequestosome-1 accumulation assay Measures protein damage by detecting the accumulation of ubiquitin and sequestosome-1 in lung tissue. in_vivo lungs mice accumulation of ubiquitin and sequestosome-1 increase http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/PR_000013426 PR low Protein damage has been measured by accumulation of ubiquitin and sequestosome-1 in the lungs of exposed mice (Hubbs et al. 2016) http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010498 GO Club cell secretory protein expression Measures the expression level of club cell secretory protein (CCSP) in airway epithelium, typically via immunostaining or western blot, to detect reductions following a-diketone exposure. in_vivo airway epithelium club cell secretory protein expression decrease low Also a reduced expression of club cell secretory protein in airway epithelium has been observed after a-diketone exposure (Palmer et al. 2011). Histopathology Measures histopathological abnormalities in airway epithelium, including epithelial necrosis, flattening, loss of cilia, and gaps in the epithelial layer, via microscopic examination of tissue sections. in_vivo airway epithelium rat epithelial necrosis, flattening, loss of cilia, gaps in epithelial layer increase low Histopathological abnormalities in exposed rats, airway epithelial necrosis, flattening of the airway epithelial cells, loss of cilia (Foster et al. 2017), gaps in the epithelial layer (Hubbs et al. 2002, 2008). http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0070265 GO histopathology Assesses histopathological abnormalities in the airway epithelium, including necrosis, flattening of epithelial cells, loss of cilia, and gaps in the epithelial layer. in_vivo airway epithelium rat histopathological abnormalities increase http://purl.obolibrary.org/obo/UBERON_0002187 UBERON http://purl.obolibrary.org/obo/GO_0070265 GO low Histopathological abnormalities in exposed rats, airway epithelial necrosis, flattening of the airway epithelial cells, loss of cilia (Foster et al. 2017), gaps in the epithelial layer (Hubbs et al. 2002, 2008). http://purl.obolibrary.org/obo/UBERON_0002187 UBERON http://purl.obolibrary.org/obo/GO_0008219 GO immunohistochemistry Measures the expression of club cell secretory protein in airway epithelium. in_vivo airway epithelium club cell secretory protein expression decrease http://purl.obolibrary.org/obo/UBERON_0002187 UBERON low a reduced expression of club cell secretory protein in airway epithelium has been observed after a-diketone exposure (Palmer et al. 2011). http://purl.obolibrary.org/obo/CL_0000153 CL http://purl.obolibrary.org/obo/GO_0046903 GO protein expression analysis Measurement of the expression levels of club cell secretory protein in the airway epithelium. not_specified club cell airway epithelium club cell secretory protein expression decrease http://purl.obolibrary.org/obo/OBI_0000117 OBI not_specified reduced expression of club cell secretory protein in airway epithelium has been observed after a-diketone exposure (Palmer et al. 2011). http://purl.obolibrary.org/obo/GO_0010761 GO TEER Measures transepithelial electrical resistance as an indicator of epithelial barrier function. in_vitro airway epithelial cells transepithelial electrical resistance decrease http://purl.obolibrary.org/obo/GO_0001945 GO medium the loss of epithelial barrier function following exposure can be measured as a reduction in transepithelial electrical resistance (TEER, Fedan et al. 2006, Zaccone et al 2015) http://purl.obolibrary.org/obo/UBERON_0002187 UBERON http://purl.obolibrary.org/obo/GO_0007156 GO histological staining This assay observes fibroproliferative airway lesions in histological specimens using various tissue stainings. in_vivo airway rat fibroproliferative airway lesions increase low Fibroproliferative airway lesions can be observed in biopsies of α-diketone exposed laboratory animals in a dose dependent manner using various tissue stainings of histological specimen. http://purl.obolibrary.org/obo/UBERON_0001004 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO CT scan A medical imaging technique that uses X-rays to create detailed cross-sectional images of the lungs, revealing structural abnormalities. in_vivo lung lung structure change low CT scan http://purl.obolibrary.org/obo/UBERON_0000163 UBERON CT scan Imaging technique to visualize lung structure and detect abnormalities. in_vivo lung human lung structure abnormalities change medium CT scan http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0060485 GO FEV1 Measures the volume of air that can be forcibly exhaled in one second, assessing lung function. in_vivo lung human forced expiratory volume in 1 second decrease medium Forced expiratory volume in 1 second (FEV1) http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0007585 GO thoracoscopic lung biopsy Surgical procedure to obtain lung tissue for histological and morphological examination. in_vivo lung human histological and morphological changes change low Thoracoscopic lung biopsy showing histological and morphological changes (human, King et al. 2011) http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0030324 GO TBA assay This assay monitors lipid peroxidation using thiobarbituric acid in an in vitro system. It measures the oxidation of lipids induced by photoactivated chemicals. in_vitro lipid peroxidation increase low An in vitro system using thiobarbituric acid can monitor lipid peroxidation by photoactivated chemicals (Onoue et al., 2011, Onoue and Tsuda, 2006) http://purl.obolibrary.org/obo/GO_0042423 GO thiobarbituric acid assay An in vitro system using thiobarbituric acid to monitor lipid peroxidation by photoactivated chemicals. in_vitro lipid peroxidation increase http://purl.obolibrary.org/obo/GO_0006649 GO medium An in vitro system using thiobarbituric acid can monitor lipid peroxidation by photoactivated chemicals (Onoue et al., 2011, Onoue and Tsuda, 2006). http://purl.obolibrary.org/obo/CHEBI_25805 CHEBI http://purl.obolibrary.org/obo/GO_0034440 GO SDS-PAGE Detects denaturation of proteins using sodium dodecylsulfate polyacrylamide gel electrophoresis. in_vitro protein denaturation not_specified http://purl.obolibrary.org/obo/OBI_0000368 OBI http://purl.obolibrary.org/obo/GO_0034620 GO low sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) and other gel electrophoresis methodologies can detect denaturation of proteins http://purl.obolibrary.org/obo/GO_0016021 GO http://purl.obolibrary.org/obo/GO_0034620 GO in vivo phototoxicity testing Detects inflammatory events induced by photoreactive chemicals in vivo. in_vivo inflammatory events increase http://purl.obolibrary.org/obo/GO_0006954 GO ICH, 2014 low Inflammatory events induced by photoreactive chemicals can be detected in vivo phototoxicity testing and photopatch test in clinical (Epstein, 1964, ICH, 2014, Onoue et al., 2009). http://purl.obolibrary.org/obo/UBERON_0002416 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO photopatch test Detects inflammatory events induced by photoreactive chemicals in clinical settings. in_vivo inflammatory events increase http://purl.obolibrary.org/obo/GO_0006954 GO low Inflammatory events induced by photoreactive chemicals can be detected in vivo phototoxicity testing and photopatch test in clinical (Epstein, 1964, ICH, 2014, Onoue et al., 2009). http://purl.obolibrary.org/obo/UBERON_0002416 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO adenylyl cyclase activity assay Measures adenylyl cyclase activity as described by Salomon et al. (1974). in_vitro adenylyl cyclase activity not_specified http://purl.obolibrary.org/obo/GO_0004016 GO http://purl.obolibrary.org/obo/OBI_0000175 OBI medium Adenylyl cyclase activity can be determined through an assay as described by Salomon et al. (1974) and used by Raheja and Dip Gill (2007). http://purl.obolibrary.org/obo/PR_00000100 PR http://purl.obolibrary.org/obo/GO_0006171 GO fluorescent reporter assay Measures kinetic changes in DAG production and IP3 release using fluorescent reporters. in_vitro DAG production and IP3 release not_specified http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/CHEBI_17591 CHEBI http://purl.obolibrary.org/obo/OBI_0001861 OBI high Kinetic measurements of DAG production and IP3 release can be obtained through fluorescent reporters as in Falkenburger et al. (2013) and Dickson et al. (2013). http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/GO_0035556 GO Immunohistochemistry/Immunoblotting Determination of relative levels of specific mAChR subtypes using subtype-specific antisera. in_vitro relative levels of specific mAChR subtypes change http://purl.obolibrary.org/obo/CHEBI_15353 CHEBI not_specified Determination of the relative levels of specific mAChR subtypes in tissues has been found through the use of subtype-specific antisera http://purl.obolibrary.org/obo/CHEBI_15353 CHEBI http://purl.obolibrary.org/obo/GO_0008610 GO radioimmunoassay (RIA) Measures cAMP content as an indicator of mAChRs bound to Gi-proteins using a radioimmunoassay kit. in_vitro cAMP content not_specified http://purl.obolibrary.org/obo/CHEBI_17790 CHEBI http://purl.obolibrary.org/obo/OBI_0000274 OBI medium Changes in the activity and quantity of cAMP and the cAMP-dependent protein kinases can serve as an indicator of the activity of mAChRs bound to Gi-proteins (M2 and M4). cAMP content can be determined using a radioimmunoassay (RIA) kit (Heikkilä et al., 1991). http://purl.obolibrary.org/obo/CHEBI_17790 CHEBI http://purl.obolibrary.org/obo/GO_0019933 GO radioimmunoassay (RIA) for cAMP Quantifies the content of cyclic adenosine monophosphate (cAMP) using a radioimmunoassay kit to indicate mAChR activity bound to Gi-proteins. in_vitro cAMP content change http://purl.obolibrary.org/obo/CHEBI_42534 CHEBI not_specified Changes in the activity and quantity of cAMP and the cAMP-dependent protein kinases can serve as an indicator of the activity of mAChRs bound to Gi-proteins (M2 and M4). cAMP content can be determined using a radioimmunoassay (RIA) kit (Heikkilä et al., 1991). http://purl.obolibrary.org/obo/CHEBI_42534 CHEBI http://purl.obolibrary.org/obo/GO_0051306 GO radioligand binding The distribution and density of mAChRs can be measured using radiolabeled agonists that bind to the mAChR binding site. in_vitro binding levels increase http://purl.obolibrary.org/obo/OBI_0000048 OBI medium The distribution and density of mAChRs can be measured using radiolabeled agonists that bind to the mAChR binding site. http://purl.obolibrary.org/obo/GO_0005102 GO radioligand binding assay Measures the distribution and density of muscarinic acetylcholine receptors (mAChRs) using radiolabeled agonists that bind to the mAChR binding site. in_vitro mAChR binding levels not_specified http://purl.obolibrary.org/obo/GO_0031683 GO medium The distribution and density of mAChRs can be measured using radiolabeled agonists that bind to the mAChR binding site. Use mAChR agonist [3H] quinuclidinyl benzilate (QNB) to label mAChRs (all subtypes; see Fonnum and Sterri (2011) and measure binding levels as described by Fitzgerald and Costa (1993) and Gazit et al. (1979) http://purl.obolibrary.org/obo/PR_00000111 PR http://purl.obolibrary.org/obo/GO_0007186 GO subtype-specific antisera assay Determines the relative levels of specific mAChR subtypes in tissues using subtype-specific antisera. in_vitro relative levels of specific mAChR subtypes not_specified http://purl.obolibrary.org/obo/OBI_0000286 OBI medium Determination of the relative levels of specific mAChR subtypes in tissues has been found through the use of subtype-specific antisera as described by Dörje et al. (1991) http://purl.obolibrary.org/obo/PR_00000111 PR bioluminescent N-linked-glycosylation reporters Measures N-linked glycosylation using bioluminescent reporters. in_vitro N-linked glycosylation not_specified http://purl.obolibrary.org/obo/GO_0018279 GO high Bioluminescent N-linked-glycosylation reporters http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0018279 GO bioluminescent reporter This assay uses bioluminescent N-linked-glycosylation reporters to measure N-linked glycosylation. in_vitro bioluminescence change medium Bioluminescent N-linked-glycosylation reporters (Contessa et al., 2012) http://purl.obolibrary.org/obo/GO_0005104 GO Endo H digestion Assesses the alteration in levels of protein glycosylation by digesting radiolabeled cells with endoglycosidase H (endo H). in_vitro glycosylation mutants alteration in levels of protein glycosylation change low Alteration in levels of protein glycosylation can be measured using a lectin microarray. endo H digestion analysis Measures efficacy of inhibition of oligosaccharide processing by digesting proteins from radiolabeled cells with endo H. in_vitro efficacy of inhibition of oligosaccharide processing not_specified http://purl.obolibrary.org/obo/GO_0006486 GO low Efficacy of inhibition of the oligosaccharide processing can be measured by TCA precipitation or endo H digestion analysis of radiolabeled cells. http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0006486 GO lectin microarray Measures alteration in levels of protein glycosylation using a microarray-based assay with lectins. in_vitro levels of protein glycosylation change http://purl.obolibrary.org/obo/GO_0006486 GO http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI medium Alteration in levels of protein glycosylation can be measured using a lectin microarray. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0006486 GO TCA precipitation Measures efficacy of inhibition of oligosaccharide processing by precipitating proteins from radiolabeled cells. in_vitro efficacy of inhibition of oligosaccharide processing not_specified http://purl.obolibrary.org/obo/GO_0006486 GO low Efficacy of inhibition of the oligosaccharide processing can be measured by TCA precipitation or endo H digestion analysis of radiolabeled cells. http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0006486 GO TCA precipitation This assay measures the efficacy of inhibition of oligosaccharide processing by precipitating proteins with trichloroacetic acid (TCA). in_vitro protein levels decrease low Efficacy of inhibition of the oligosaccharide processing can be measured by TCA precipitation or endo H digestion analysis of radiolabeled cells. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005104 GO CD/FTIR Monitors secondary structure content of proteins using circular dichroism or Fourier-transform infrared spectroscopy. in_vitro secondary structure content change http://purl.obolibrary.org/obo/GO_0030246 GO medium Fibril formation, morphology and secondary structure content of proteins can be monitored in vitro by molecular probes, TEM/AFM, and CD/FTIR analyses, respectively. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0006457 GO molecular probes Monitors fibril formation and misfolded protein accumulation using molecular probes. in_vitro fibril formation increase http://purl.obolibrary.org/obo/GO_0098754 GO medium Fibril formation, morphology and secondary structure content of proteins can be monitored in vitro by molecular probes, TEM/AFM, and CD/FTIR analyses, respectively. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0006457 GO TEM/AFM Monitors fibril morphology using transmission electron microscopy or atomic force microscopy. in_vitro fibril morphology change http://purl.obolibrary.org/obo/GO_0098754 GO http://purl.obolibrary.org/obo/PATO_0000051 PATO low Fibril formation, morphology and secondary structure content of proteins can be monitored in vitro by molecular probes, TEM/AFM, and CD/FTIR analyses, respectively. http://purl.obolibrary.org/obo/GO_0098754 GO http://purl.obolibrary.org/obo/GO_0051087 GO TEM/AFM Protein morphology can be monitored in vitro by Transmission Electron Microscopy (TEM) and Atomic Force Microscopy (AFM). in_vitro protein morphology change low Fibril formation, morphology and secondary structure content of proteins can be monitored in vitro by molecular probes, TEM/AFM, and CD/FTIR analyses http://purl.obolibrary.org/obo/CHEBI_3670 CHEBI http://purl.obolibrary.org/obo/GO_0000003 GO collagen accumulation assessment This assay assesses the accumulation of collagen in the liver, indicating stellate cell activation and fibrosis. It is based on observing changes in extracellular matrix composition. not_specified liver collagen levels increase http://purl.obolibrary.org/obo/GO_0005576 GO low Activation of stellate cells results in collagen accumulation and change in extracellular matrix composition in the liver causing fibrosis. http://purl.obolibrary.org/obo/GO_0005576 GO http://www.ebi.ac.uk/efo/EFO_0004649 EFO Extracellular Matrix Composition Assay This assay measures changes in the composition of the extracellular matrix in the liver, reflecting the activation of stellate cells. in_vivo http://purl.obolibrary.org/obo/UBERON_0002107 extracellular matrix composition change change http://purl.obolibrary.org/obo/GO_0031012 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON not_specified Activation of stellate cells results in collagen accumulation and change in extracellular matrix composition in the liver causing fibrosis. http://purl.obolibrary.org/obo/GO_0031012 GO http://purl.obolibrary.org/obo/GO_0042127 GO CYP17A1 activity assay (microsomes) This assay measures CYP17A1 enzyme activity using isolated microsomes containing the enzyme system and P450-oxidoreductase. NADPH is added as an electron source, and substrate removal or product formation is measured to assess activity. in_vitro substrate removal or product formation decrease http://purl.obolibrary.org/obo/GO_0004395 GO low Inhibition of CYP17A1 can be assessed in vitro by modulating mammalian or yeast cells to express the enzyme as well as P450-oxidoreductase with/without B5. Subsequently, enzyme activity can be studied in isolated microsomes that contain the enzyme system. The reaction substrate is added and either the substrate removal or product formation is measured (Yoshimoto & Auchus, 2015). In the case of examining the ability of a chemical to inhibit the enzyme activity, the chemical is added in increasing concentrations and a constant level of substrate is added – a decreased conversion of the substrate to product, would suggest enzyme inhibition. http://purl.obolibrary.org/obo/GO_0008655 GO CYP17A1 inhibition assay Assesses inhibition of CYP17A1 activity by measuring substrate removal or product formation in isolated microsomes or purified enzyme systems with NADPH. in_vitro CYP17A1 enzyme activity decrease medium Inhibition of CYP17A1 can be assessed in vitro by modulating mammalian or yeast cells to express the enzyme as well as P450-oxidoreductase with/without B5. Subsequently, enzyme activity can be studied in isolated microsomes that contain the enzyme system. Alternatively, the isolated enzyme can be used for activity measurement in concert with purified P450-oxidoreductase with/without B5. NADPH should be added as the source of electrons for the reaction to take place. The reaction substrate is added and either the substrate removal or product formation is measured (Yoshimoto & Auchus, 2015). In the case of examining the ability of a chemical to inhibit the enzyme activity, the chemical is added in increasing concentrations and a constant level of substrate is added – a decreased conversion of the substrate to product, would suggest enzyme inhibition. HPLC with UV-detection Measures steroid substrate or product levels using high-performance liquid chromatography with UV detection. in_vitro steroid substrate or product levels not_specified medium They can be resolved by use of HPLC and the levels detected with UV-detection or scintillation counter, if for instance the substrate is radiolabeled. LC-MS Quantifies steroid substrate or product levels using liquid chromatography-mass spectrometry. in_vitro steroid substrate or product levels not_specified medium They can be quantified by use of LC-MS Scintillation counting Measurement of radiolabeled steroid substrates or products using a scintillation counter. in_vitro radiolabeled substrate or product levels change not_specified levels detected with ... scintillation counter, if for instance the substrate is radiolabeled http://purl.obolibrary.org/obo/CHEBI_28932 CHEBI http://purl.obolibrary.org/obo/GO_0006691 GO Thin-layer chromatography Measures steroid substrate or product levels using thin-layer chromatography with radiolabeled substrate. in_vitro steroid substrate or product levels not_specified low They can be quantified by use of thin-layer chromatography, which requires the use of radiolabeled substrate (Yoshimoto & Auchus, 2015). ELISA Enzyme-Linked Immunosorbent Assay is used to quantify DHEA levels after separation. in_vitro DHEA levels not_specified http://purl.obolibrary.org/obo/CHEBI_16648 CHEBI high DHEA levels can be quantified using immunoassays such as ELISA HPLC High Performance Liquid Chromatography is used to fractionate DHEA. in_vitro DHEA fractionation not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI http://purl.obolibrary.org/obo/CHEBI_16648 CHEBI medium DHEA can be fractionated using High Performance Liquid Chromatography. mass spectrometry Mass spectrometry is used to quantify DHEA levels after separation. in_vitro DHEA levels not_specified http://purl.obolibrary.org/obo/OBI_0000470 OBI http://purl.obolibrary.org/obo/CHEBI_16648 CHEBI medium DHEA levels can be quantified using mass spectrometry. RIA Radio Immuno Assay is used to quantify DHEA levels after separation. in_vitro DHEA levels not_specified http://purl.obolibrary.org/obo/CHEBI_16648 CHEBI medium DHEA levels can be quantified using immunoassays such as Radio Immuno Assay (RIA) ELISA A competitive immunoenzymatic colorimetric method for quantitative determination of androstenedione concentration in serum or plasma. in_vitro serum plasma androstenedione concentration decrease http://purl.obolibrary.org/obo/CHEBI_16822 CHEBI medium Competitive immunoenzymatic colorimetric methods (ELISA) for quantitative determination of androstenedione concentration in serum or plasma are available. http://purl.obolibrary.org/obo/CHEBI_16822 CHEBI http://purl.obolibrary.org/obo/GO_0008202 GO H295R cell-based assay A high-throughput assay using the H295R cell line to measure androstenedione levels. in_vitro H295R androstenedione concentration decrease http://purl.obolibrary.org/obo/CHEBI_16822 CHEBI high There is no OECD test guideline for the measurement of androstenedione but androstenedione can be measured using a high-throughout assay using the H295R cell line (Karmaus, 2016). http://purl.obolibrary.org/obo/CHEBI_16822 CHEBI http://purl.obolibrary.org/obo/GO_0006694 GO HPLC with radiolabeled steroid precursor Uses radiolabeled steroid precursors and HPLC for fractionation and identification of steroids, followed by liquid scintillation spectrometry for quantification of androstenedione. in_vitro androstenedione concentration decrease http://purl.obolibrary.org/obo/CHEBI_16822 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI low Androstenedione synthesis can be monitored using radiolabeled steroid precursor in association with High Performance Liquid Chromatography (HPLC). During synthesis, steroids will incorporate the radioactive label which can be afterwards, used for quantification. First of all, HPLC combined with internal standards can be used for steroids collection, fractionation and identification. Once separated from the other steroids, androstenedione can be finally quantified using liquid scintillation spectrometry. http://purl.obolibrary.org/obo/CHEBI_16822 CHEBI http://purl.obolibrary.org/obo/GO_0006694 GO HPLC-LSS Androstenedione synthesis is monitored using radiolabeled steroid precursor, followed by quantification using liquid scintillation spectrometry after HPLC fractionation and identification. in_vitro androstenedione synthesis change http://purl.obolibrary.org/obo/CHEBI_5078 CHEBI http://purl.obolibrary.org/obo/GO_0008747 GO medium Androstenedione synthesis can be monitored using radiolabeled steroid precursor in association with High Performance Liquid Chromatography (HPLC). Once separated from the other steroids, androstenedione can be finally quantified using liquid scintillation spectrometry. http://purl.obolibrary.org/obo/CHEBI_5078 CHEBI http://purl.obolibrary.org/obo/GO_0008747 GO ELISA An immunoassay method used for the identification and quantification of DHT levels, though it may overestimate levels due to lack of specificity. in_vitro DHT level decrease http://purl.obolibrary.org/obo/CHEBI_17350 CHEBI medium conventional immunoassay methods (ELISA or RIA) Conventional immunoassays have limitations in that they can overestimate the levels of DHT http://purl.obolibrary.org/obo/CHEBI_17350 CHEBI http://purl.obolibrary.org/obo/GO_0042180 GO LC-MS/MS An advanced analytical method using liquid chromatography tandem mass spectrometry for the identification and quantification of DHT levels with higher specificity. in_vitro DHT level decrease http://purl.obolibrary.org/obo/CHEBI_17350 CHEBI http://purl.obolibrary.org/obo/OBI_0000474 OBI low advanced analytical methods such as liquid chromatography tandem mass spectrometry (LC-MS/MS) levels determined by gas chromatography mass spectrometry and liquid chromatography tandem mass spectrometry http://purl.obolibrary.org/obo/CHEBI_17350 CHEBI http://purl.obolibrary.org/obo/GO_0042180 GO NCI-H295 cell assay A cell-based assay using the NCI-H295 cell line to measure DHT levels, as described in OECD Test Guideline no. 456. in_vitro NCI-H295 human DHT level decrease http://purl.obolibrary.org/obo/CHEBI_17350 CHEBI OECD TG 456 low Test guideline no. 456 (OECD 2023) uses a cell line, NCI-H295, capable of producing DHT at low levels Measurement of DHT levels in these cells require low detection and quantification limits http://purl.obolibrary.org/obo/CHEBI_17350 CHEBI http://purl.obolibrary.org/obo/GO_0042180 GO OECD TG 456 The OECD TG 456 assay uses the NCI-H295 cell line to measure DHT production, requiring low detection limits. in_vitro NCI-H295 DHT level not_specified OECD TG 456 not_specified Test guideline no. 456 (OECD 2023) uses a cell line, NCI-H295, capable of producing DHT at low levels. http://purl.obolibrary.org/obo/GO_0008202 GO RIA A radioimmunoassay method used for the identification and quantification of DHT levels, though it may overestimate levels due to cross-reactivity with testosterone. in_vitro DHT level decrease http://purl.obolibrary.org/obo/CHEBI_17350 CHEBI medium conventional immunoassay methods (ELISA or RIA) lack of specificity of the DHT antibody used in the RIA and cross-reactivity with T in samples http://purl.obolibrary.org/obo/CHEBI_17350 CHEBI http://purl.obolibrary.org/obo/GO_0042180 GO AR activation assay Measures androgen receptor (AR) activity in vitro, providing indirect information about AR activation. in_vitro AR activity decrease http://purl.obolibrary.org/obo/GO_0008207 GO http://purl.obolibrary.org/obo/PR_000001590 PR not_specified most methods that can be used to measure AR activity carried out in vitro They provide indirect information about the KE http://purl.obolibrary.org/obo/PR_000001590 PR http://purl.obolibrary.org/obo/GO_0030521 GO histological exam Detects issues during development by examining physical manifestations of abnormal development in mature individuals. in_vivo inguinoscrotal region abnormal development not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI low Issues during development can be detected by histological exam, with physical manifestation of abnormal development visible in mature individuals. http://purl.obolibrary.org/obo/UBERON_0000035 UBERON http://purl.obolibrary.org/obo/GO_0032502 GO histological exam Microscopic examination of tissue sections to identify structural or cellular abnormalities. ex_vivo inguinoscrotal morphological abnormalities change http://purl.obolibrary.org/obo/OBI_0000151 OBI low Issues during development can be detected by histological exam http://purl.obolibrary.org/obo/GO_0044427 GO physical manifestation assessment Observation of physical manifestations of abnormal development in mature individuals. in_vivo physical manifestation of abnormal development change http://purl.obolibrary.org/obo/PATO_0000001 PATO not_specified physical manifestation of abnormal development visible in mature individuals http://purl.obolibrary.org/obo/GO_0042710 GO clinical examination This assay involves palpation to locate the gonad and determine its lowest position without causing painful traction on the spermatic cord. in_vivo gonad spermatic cord gonad position not_specified http://purl.obolibrary.org/obo/UBERON_0000991 UBERON low Cryptorchidism is a birth defect that can be highlighted by a clinical examination. The aim of this palpation is to locate the gonad and determine its lowest position without causing painful traction on the spermatic cord. http://purl.obolibrary.org/obo/UBERON_0000991 UBERON http://purl.obolibrary.org/obo/GO_0003338 GO 5α-reductase inhibition assay Measures the ability of chemicals to inhibit the activity of 5α-reductase enzymes using transfected cell lines or isolated enzymes. in_vitro HEK-293 CHO COS not specified human rat dihydrotestosterone (DHT) production decrease http://purl.obolibrary.org/obo/GO_0030258 GO http://purl.obolibrary.org/obo/CHEBI_15377 CHEBI http://purl.obolibrary.org/obo/GO_0017144 GO not specified not_specified Assessing the ability of chemicals to inhibit the activity of 5α-reductase is challenging, but has been assessed using transfected cell lines. This has been demonstrated in HEK-293 cells stably transfected with human 5α-reductase type 1, 2, and 3 (Yamana et al., 2010), in CHO cells stably transfected with human 5α-reductase type 1 and 2 (Thigpens et al., 1993), and COS cells transfected with human and rat 5α-reductase with unspecified isoforms (Andersson & Russell, 1990). The output of the above methods could be decreased dihydrotestosterone (DHT) with increasing test chemical concentrations. The use of radiolabeled steroids has historic and continued use for 5α-reductase inhibition examination (Andersson & Russell, 1990; Peng et al., 2020; Thigpens et al., 1993; Yamana et al., 2010); however, alternative methods are available, such as conventional ELISA kits or advanced analytical methods such as liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). http://purl.obolibrary.org/obo/GO_0030258 GO http://purl.obolibrary.org/obo/GO_0042445 GO cell-based assay This assay assesses 5α-reductase inhibition using transfected cell lines, either as intact cells or cell homogenates. The output is typically decreased dihydrotestosterone (DHT) with increasing test chemical concentrations. in_vitro HEK-293 CHO COS human rat dihydrotestosterone (DHT) levels decrease http://purl.obolibrary.org/obo/CHEBI_59184 CHEBI http://purl.obolibrary.org/obo/OBI_0000489 OBI medium Assessing the ability of chemicals to inhibit the activity of 5α-reductase is challenging, but has been assessed using transfected cell lines. The output of the above methods could be decreased dihydrotestosterone (DHT) with increasing test chemical concentrations. This has been demonstrated in HEK-293 cells stably transfected with human 5α-reductase type 1, 2, and 3 http://purl.obolibrary.org/obo/GO_0008685 GO E. coli expressed 5α-reductase inhibition assay Measures inhibition of 5α-reductase enzyme activity using recombinant human 5α-reductase isoforms (types 1 and 2) expressed and isolated from Escherichia coli with subsequent functionality for examining enzyme inhibition. in_vitro human enzyme inhibition activity decrease http://purl.obolibrary.org/obo/GO_0004549 GO http://www.bioassayontology.org/bao#BAO_0000189 BAO low Further, 5α-reductase 1 and 2 have been successfully expressed and isolated from Escherichia coli with subsequent functionality allowing for examination of enzyme inhibition (Peng et al., 2020). http://purl.obolibrary.org/obo/GO_0004549 GO http://purl.obolibrary.org/obo/GO_0019310 GO enzyme assay This assay examines enzyme inhibition of 5α-reductase that has been expressed and isolated from Escherichia coli. It allows for examination of enzyme inhibition. in_vitro Escherichia coli enzyme inhibition decrease http://purl.obolibrary.org/obo/OBI_0000489 OBI low Further, 5α-reductase 1 and 2 have been successfully expressed and isolated from Escherichia coli with subsequent functionality allowing for examination of enzyme inhibition The output of the above methods could be decreased dihydrotestosterone (DHT) with increasing test chemical concentrations. Peng et al., 2020 http://purl.obolibrary.org/obo/GO_0008685 GO LC-MS/MS This assay uses liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) to measure 5α-reductase inhibition. in_vitro steroid levels decrease http://purl.obolibrary.org/obo/OBI_0000837 OBI http://purl.obolibrary.org/obo/CHEBI_5090 CHEBI medium or advanced analytical methods such as liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The output of the above methods could be decreased dihydrotestosterone (DHT) with increasing test chemical concentrations. Peng et al., 2020 http://purl.obolibrary.org/obo/GO_0008685 GO radiolabeled steroid assay Uses radiolabeled steroids (e.g., [3H]-testosterone) to measure 5α-reductase activity by quantifying conversion to radiolabeled DHT, enabling inhibition assessment. in_vitro radiolabeled dihydrotestosterone (DHT) formation decrease http://purl.obolibrary.org/obo/CHEBI_17368 CHEBI http://purl.obolibrary.org/obo/GO_0008483 GO http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI not_specified The use of radiolabeled steroids has historic and continued use for 5α-reductase inhibition examination (Andersson & Russell, 1990; Peng et al., 2020; Thigpens et al., 1993; Yamana et al., 2010). http://purl.obolibrary.org/obo/GO_0008202 GO EEG Brain electroencephalographic (EEG) activity is recorded to monitor the development of a seizure. in_vivo brain seizure development change http://purl.obolibrary.org/obo/OBI_0000119 OBI low Brain electroencephalographic (EEG) activity can also record the development of the seizure http://purl.obolibrary.org/obo/UBERON_0000630 UBERON electrocorticogram Measures brain activity to monitor seizure development using electrodes placed on the cortical surface. in_vivo brain brain activity change http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low An electrocorticogram record can be used to measure brain activity to monitor seizure development (Braitman and Sparenborg, 1989). http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0002360 GO whole cell patch-clamp recording Measures spontaneous inhibitory and excitatory postsynaptic currents in neurons to study seizure activity. in_vitro neurons brain spontaneous postsynaptic currents change http://purl.obolibrary.org/obo/GO_0001965 GO low Whole cell recordings of spontaneous inhibitory postsynaptic currents and excitatory postsynaptic currents have also been used to study the initial seizures occurring from exposure to organophosphates (Miller, 2015). http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0002360 GO 8-nitroguanine (DNA) content HPLC-MS/MS method used to measure 8-nitroguanine content in DNA as an indicator of peroxynitrite-mediated damage. in_vitro 8-nitroguanine content increase http://purl.obolibrary.org/obo/CHEBI_137320 CHEBI http://purl.obolibrary.org/obo/OBI_0000473 OBI low 8-nitroguanine (DNA) content HPLC-MS/MS Destruction of sample required for measurement. http://purl.obolibrary.org/obo/GO_0005623 GO http://purl.obolibrary.org/obo/GO_0006974 GO AmplexRed A small molecule fluorescent probe used to detect extracellular hydrogen peroxide in vitro. in_vitro extracellular hydrogen peroxide levels increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI medium AmplexRed Small molecule fluorescent probes Can be applied to any tissue in vitro. http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Boronate-based indicators Small molecule fluorescent probes selective for hydrogen peroxide but can interact with peroxynitrite. in_vitro hydrogen peroxide levels increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI medium Boronate-based indicators Small molecule fluorescent probe Selective for H2O2 but can interact with peroxynitrite. http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO cpYFP A protein-based fluorescent probe used to detect intracellular superoxide in vivo, reversible and targetable to specific cells and compartments. in_vivo intracellular superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_18405 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI low cpYFP Protein-based fluorescent probes Reversible. Can be targeted to specific cells and compartments. http://purl.obolibrary.org/obo/CHEBI_18405 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO DAF-FM A small molecule fluorescent probe used to detect nitric oxide in vitro. in_vitro nitric oxide levels increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI medium DAF-FM Small molecule fluorescent probe Can be applied to any tissue in vitro, but not targeted to different compartments http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006809 GO DCHF A small molecule fluorescent probe used to detect non-specific oxidation, but prone to false positives. in_vitro non-specific oxidation levels increase http://purl.obolibrary.org/obo/GO_0006979 GO http://purl.obolibrary.org/obo/OBI_0000424 OBI medium DCHF Small molecule fluorescent probe Very non selective, and can produce false positive signals. http://purl.obolibrary.org/obo/GO_0006979 GO DHE (dihydroethidium) A small molecule fluorescent probe used to detect intracellular superoxide in vitro. in_vitro intracellular superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_18405 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI medium DHE (dihydroethidium) Small molecule fluorescent probe Can be applied to any tissue in vitro, but not targeted to different compartments. http://purl.obolibrary.org/obo/CHEBI_18405 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO EMPO An EPR-based method used to detect peroxynitrite with high specificity, requiring specialized equipment. in_vitro peroxynitrite levels increase http://purl.obolibrary.org/obo/CHEBI_16937 CHEBI http://purl.obolibrary.org/obo/OBI_0000218 OBI low EMPO EPR Very specific, but requires specialized equipment, not as sensitive in tissue. http://purl.obolibrary.org/obo/CHEBI_16937 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO EPR (electron paramagnetic resonance spectroscopy) A spectroscopic method used to detect free radicals with high specificity, requiring specialized equipment. in_vitro free radical levels increase http://purl.obolibrary.org/obo/CHEBI_24990 CHEBI http://purl.obolibrary.org/obo/OBI_0000218 OBI low EPR (electron paramagnetic resonance spectroscopy) Very specific, but requires specialized equipment, not as sensitive in tissue. http://purl.obolibrary.org/obo/CHEBI_24990 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Fe[DETC]2 and Fe[MGD]2 EPR-based method used to detect nitric oxide with high specificity, requiring specialized equipment. in_vitro nitric oxide levels increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/OBI_0000218 OBI low Fe[DETC]2 and Fe[MGD]2 EPR Very specific, but requires specialized equipment, not as sensitive in tissue. http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006809 GO HPLC-MS/MS HPLC-MS/MS is used to measure 8-nitroguanine (DNA) content, requiring destruction of the sample for measurement. not_specified DNA 8-nitroguanine levels increase low Peroxynitrite 8-nitroguanine (DNA) content HPLC-MS/MS Destruction of sample required for measurement. http://purl.obolibrary.org/obo/CHEBI_0001367 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO HyPer A protein-based fluorescent probe used to detect hydrogen peroxide in vivo, targetable to specific cells and compartments. in_vivo hydrogen peroxide levels increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI low HyPer Protein-based fluorescent probes Sensitive, can be targeted to specific cells and compartments. http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO MitoPy1 A small molecule fluorescent probe used to detect mitochondrial hydrogen peroxide in vitro. in_vitro mitochondrial hydrogen peroxide levels increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI medium MitoPy1 Small molecule fluorescent probes Can be applied to any tissue in vitro. http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO MitoSox A small molecule fluorescent probe used to detect mitochondrial superoxide in vitro. in_vitro mitochondrial superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_18405 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI medium MitoSox Small molecule fluorescent probe Can be applied to any tissue in vitro. http://purl.obolibrary.org/obo/CHEBI_18405 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO mt-cpYFP A reversible protein-based fluorescent probe targeted to mitochondria for measuring superoxide. not_specified mitochondrial superoxide not_specified http://purl.obolibrary.org/obo/CHEBI_44217 CHEBI not_specified Superoxide- mitochondrial mt-cpYFP Protein-based fluorescent probes Reversible. Can be targeted to specific cells and compartments. http://purl.obolibrary.org/obo/UBERON_0000187 UBERON nitroblue tetrazolium A small molecule fluorescent probe used to detect extracellular superoxide in vitro. in_vitro extracellular superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_18405 CHEBI http://purl.obolibrary.org/obo/OBI_0000424 OBI medium nitroblue tetrazolium Small molecule fluorescent probe Can be applied to any tissue in vitro. http://purl.obolibrary.org/obo/CHEBI_18405 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO ratio of reduced to oxidized glutathione or cysteine Redox state detectors used to measure the ratio of reduced to oxidized glutathione or cysteine, suitable for steady-state activity measurements. in_vitro redox state of glutathione or cysteine change http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/CHEBI_16136 CHEBI low ratio of reduced to oxidized glutathione or cysteine Redox state detectors Slow acting. Good to look at steady state activity. Destruction of sample required for measurement. http://purl.obolibrary.org/obo/CHEBI_15428 CHEBI http://purl.obolibrary.org/obo/GO_0045454 GO roGFP or FRET Protein-based fluorescent probes used to detect non-specific oxidation, suitable for steady-state activity measurements. in_vitro non-specific oxidation levels increase http://purl.obolibrary.org/obo/GO_0006979 GO http://purl.obolibrary.org/obo/OBI_0000424 OBI low roGFP or FRET Protein-based fluorescent probes Slow acting. Good to look at steady state activity. http://purl.obolibrary.org/obo/GO_0006979 GO TBARS (thiobarbituric acid reactive substance) A method used to measure lipid peroxidation as an indicator of oxidative damage. in_vitro lipid peroxidation levels increase http://purl.obolibrary.org/obo/GO_0006691 GO http://purl.obolibrary.org/obo/OBI_0000473 OBI medium TBARS (thiobarbituric acid reactive substance) Lipid peroxidation Destruction of sample required for measurement. http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/GO_0034440 GO various trityl probes EPR spectroscopy method using trityl probes to detect intracellular or extracellular superoxide. It is very specific but requires specialized equipment and is not as sensitive in tissue. not_specified superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_30837 CHEBI not_specified Superoxide- intracellular or extracelluar various trityl probes EPR Very specific, but requires specialized equipment, not as sensitive in tissue. Comet assay with Fpg and hOGG1 The comet assay (single cell gel electrophoresis) is modified with the addition of Fpg and hOGG1 enzymes to detect oxidative DNA lesions. Treatment of DNA with either enzyme prior to electrophoresis allows detection of oxidative lesions by measuring the increase in comet tail length compared to untreated samples. in_vitro Oxidative DNA damage increase http://purl.obolibrary.org/obo/GO_0006306 GO http://purl.obolibrary.org/obo/GO_0000209 GO Comet assay protocol (not specified) not_specified Comet assay (single cell gel electrophoresis) with Fpg and hOGG1 modifications (Smith et al., 2006; Platel et al., 2011) Treatment of DNA with either enzyme prior to performing the electrophoresis step of the comet assay allows detection of oxidative lesions by measuring the increase in comet tail length when compared against untreated samples. http://purl.obolibrary.org/obo/CHEBI_18252 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Comet assay with Fpg and hOGG1 modifications The comet assay with Fpg and hOGG1 modifications measures oxidative DNA lesions by detecting increases in comet tail length after enzyme treatment. in_vitro comet tail length increase http://purl.obolibrary.org/obo/OBI_0000868 OBI http://purl.obolibrary.org/obo/GO_0006979 GO medium Comet assay (single cell gel electrophoresis) with Fpg and hOGG1 modifications (Smith et al., 2006; Platel et al., 2011) Treatment of DNA with either enzyme prior to performing the electrophoresis step of the comet assay allows detection of oxidative lesions by measuring the increase in comet tail length when compared against untreated samples. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO ELISA Enzyme-linked immunosorbant assay (ELISA) uses antibodies against 8-oxodG lesions to detect oxidative DNA damage. in_vitro 8-oxodG levels increase high Enzyme-linked immunosorbant assay (ELISA) (Dizdaroglu et al., 2002; Breton et al., 2003; Xu et al., 2008; Zhao et al. 2017) 8-oxodG can be detected using immunoassays, such as ELISA, that use antibodies against 8-oxodG lesions. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO ELISA for 8-oxodG 8-oxodG can be detected using enzyme-linked immunosorbent assay (ELISA) that uses antibodies against 8-oxodG lesions. The assay detects the increase in 8-oxodG levels as an indicator of oxidative DNA damage. in_vitro 8-oxodG levels increase http://purl.obolibrary.org/obo/CHEBI_16990 CHEBI http://purl.obolibrary.org/obo/GO_0000209 GO ELISA protocol (not specified) not_specified Oxoguanine glycosylase (hOGG1) and formamidopyrimidine-DNA glycosylase (Fpg) are base excision repair (BER) enzymes in eukaryotic and prokaryotic cells, respectively Enzyme-linked immunosorbant assay (ELISA) (Dizdaroglu et al., 2002; Breton et al., 2003; Xu et al., 2008; Zhao et al. 2017) http://purl.obolibrary.org/obo/CHEBI_16990 CHEBI http://purl.obolibrary.org/obo/GO_0000209 GO GC-MS Gas chromatography-mass spectrometry identifies modified bases or nucleosides after DNA hydrolysis and derivatization to determine oxidative DNA damage. in_vitro modified bases/nucleosides increase http://purl.obolibrary.org/obo/CHEBI_35884 CHEBI low Gas chromatography-mass spectrometry (GC-MS) The mass spectrometer results are used to determine oxidative DNA damage by identifying modified bases or nucleosides (Dizdaroglu, 1994). http://purl.obolibrary.org/obo/CHEBI_30753 CHEBI http://purl.obolibrary.org/obo/GO_0009405 GO GC-MS Gas chromatography-mass spectrometry (GC-MS) identifies modified bases or nucleosides to determine oxidative DNA damage. in_vitro oxidative DNA damage increase http://purl.obolibrary.org/obo/OBI_0000473 OBI http://purl.obolibrary.org/obo/GO_0006979 GO low Gas chromatography-mass spectrometry (GC-MS) The mass spectrometer results are used to determine oxidative DNA damage by identifying modified bases or nucleosides (Dizdaroglu, 1994). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO HPLC-EC High performance liquid chromatography with electrochemical detection (HPLC-EC) separates and quantifies 8-oxodG from digested DNA. in_vitro 8-oxodG levels increase http://purl.obolibrary.org/obo/OBI_0000215 OBI medium Quantification of 8-oxodG using HPLC-EC (Breton et al., 2003; Chepelev et al., 2015) 8-oxodG can be separated from digested DNA and precisely quantified using high performance liquid chromatography (HPLC) with electrochemical detection http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO LC-MRM/MS Liquid chromatography coupled with multiple reaction monitoring/mass spectrometry (LC-MRM/MS) detects and quantifies oxidative DNA lesions. in_vitro oxidative DNA lesions increase http://purl.obolibrary.org/obo/OBI_0000475 OBI http://purl.obolibrary.org/obo/GO_0006979 GO medium Mass spectrometry LC-MRM/MS (Mangal et al., 2009) Liquid chromatography can also be coupled with multiple reaction monitoring/ mass spectrometry to detect and quantify oxidative lesions. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Sequencing assays Various sequencing assays detect and highlight sites of DNA damage, which are then processed and sequenced. in_vitro DNA damage sites increase http://purl.obolibrary.org/obo/OBI_0000626 OBI http://purl.obolibrary.org/obo/GO_0006974 GO medium Sequencing assays Various markers are used to detect and highlight sites of DNA damage; the result is then processed and sequenced. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006974 GO Sequencing assays for oxidative DNA damage Various sequencing-based assays such as snAP-seq, OGG1-AP-seq, oxiDIP-seq, OG-seq, and click-code-seq are used to detect and highlight sites of DNA damage caused by oxidative stress. These assays sequence the DNA to identify oxidative lesions. in_vitro Oxidative DNA damage increase http://purl.obolibrary.org/obo/GO_0006306 GO http://purl.obolibrary.org/obo/GO_0000209 GO Sequencing assay protocols (not specified) not_specified Sequencing assays (Yun et al., 2017; Wu et al., 2018; Amente et al., 2019; Poetsch, 2020b) http://purl.obolibrary.org/obo/CHEBI_18252 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Alkaline elution assay Cells lysed with detergent-solution, filtered through membrane to remove all but intact DNA. in_vitro DNA strand breaks (inferred from loss of intact DNA) increase not_specified Alkaline Elution Assay Cells lysed with detergent-solution, filtered through membrane to remove all but intact DNA Alkaline Elution Assay Cells are lysed with detergent, filtered through a membrane to remove all but intact DNA, allowing detection of strand breaks. in_vitro intact DNA retention decrease http://purl.obolibrary.org/obo/OBI_0000205 OBI low Alkaline Elution Assay Cells lysed with detergent-solution, filtered through membrane to remove all but intact DNA http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Comet Assay Detects SSBs or DSBs by encapsulating single cells in agarose, lysing them, and subjecting to alkaline gel electrophoresis, forming a 'comet'-like appearance. in_vitro DNA strand breaks increase http://purl.obolibrary.org/obo/OBI_0000844 OBI OECD Approved Method medium Comet Assay (Single Cell Gel Eletrophoresis - Alkaline) To detect SSBs or DSBs, single cells are encapsulated in agarose on a slide, lysed, and subjected to gel electrophoresis at an alkaline pH (pH >13); DNA fragments are forced to move, forming a "comet"-like appearance http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO In Vitro DNA Cleavage Assay Achieves DNA cleavage using purified topoisomerase, with strand breaks separated and quantified by gel electrophoresis. in_vitro DNA strand breaks increase http://purl.obolibrary.org/obo/GO_0006310 GO http://purl.obolibrary.org/obo/OBI_0000368 OBI low In Vitro DNA Cleavage Assays using Topoisomerase Cleavage of DNA can be achieved using purified topoisomerase; DNA strand breaks can then be separated and quantified using gel electrophoresis http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006265 GO PCR Assay Assays strand breaks by observing prevention of DNA amplification, as breaks block Taq polymerase, reducing templates and preventing amplification. in_vitro DNA amplification decrease http://purl.obolibrary.org/obo/OBI_0000272 OBI high PCR assay Assay of strand breaks through the observation of DNA amplification prevention. Breaks block Taq polymerase, reducing the number of DNA templates, preventing amplification http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO PCR assay Assay of strand breaks through the observation of DNA amplification prevention. Breaks block Taq polymerase, reducing the number of DNA templates, preventing amplification. in_vitro DNA strand breaks (inferred from loss of amplification) increase not_specified PCR assay Assay of strand breaks through the observation of DNA amplification prevention. Breaks block Taq polymerase, reducing the number of DNA templates, preventing amplification Pulsed Field Gel Electrophoresis Detects DSBs by embedding cells in agarose, lysing them, and separating DNA fragments by size using gel electrophoresis with alternating voltage directions. in_vitro DNA fragment size distribution change http://purl.obolibrary.org/obo/GO_0006303 GO low Pulsed Field Gel Electrophoresis (PFGE) To detect DSBs, cells are embedded and lysed in agarose, and the released DNA undergoes gel electrophoresis in which the direction of the voltage is periodically alternated; Large DNA fragments are thus able to be separated by size http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO Pulsed Field Gel Electrophoresis (PFGE) Detects double-strand breaks by embedding cells in agarose, lysing them, and performing gel electrophoresis with periodically alternating voltage direction, allowing large DNA fragments to be separated by size. in_vitro DNA strand breaks increase low To detect DSBs, cells are embedded and lysed in agarose, and the released DNA undergoes gel electrophoresis in which the direction of the voltage is periodically alternated; Large DNA fragments are thus able to be separated by size http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO sBLISS Labels double-strand breaks in cells using double-stranded oligonucleotide adaptors, followed by selective linear amplification and next-generation sequencing. in_vitro DNA double-strand breaks increase http://purl.obolibrary.org/obo/GO_0006303 GO http://purl.obolibrary.org/obo/OBI_0002001 OBI medium sBLISS sBLISS (in-suspension breaks labeling in situ and sequencing) labels double-strand breaks (DSBs) in cells immobilized on glass coverslips, using double-stranded oligonucleotide adaptors that facilitate selective linear amplification through T7-mediated in vitro transcription (IVT), followed by next-generation sequencing (NGS) library preparation http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO sBLISS Labels double-strand breaks in cells immobilized on glass coverslips using oligonucleotide adaptors and T7-mediated IVT, followed by NGS. in_vitro DSB labeling/NGS library increase http://purl.obolibrary.org/obo/GO_0000723 GO not_specified sBLISS (in-suspension breaks labeling in situ and sequencing) labels double-strand breaks (DSBs) in cells immobilized on glass coverslips, using double-stranded oligonucleotide adaptors that facilitate selective linear amplification through T7-mediated in vitro transcription (IVT), followed by next-generation sequencing (NGS) library preparation http://purl.obolibrary.org/obo/GO_0005636 GO http://purl.obolibrary.org/obo/GO_0000723 GO STRIDE Assay Combines in situ nick translation with proximity ligation assay to detect single-strand or double-strand breaks, labeled with biotinylated nucleotides and identified by PLA signal. in_vitro DNA strand breaks increase medium STRIDE assay STRIDE (SensiTive Recognition of Individual DNA Ends) combines in situ nick translation with the proximity ligation assay (PLA) to detect single-strand breaks (sSTRIDE) or double-strand breaks (dSTRIDE). In this process, lesions labeled through nick translation with biotinylated nucleotides are identified by a PLA signal, which arises from the interaction of two anti-biotin antibodies from different species. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006281 GO STRIDE assay Combines in situ nick translation with proximity ligation assay (PLA) to detect single-strand (sSTRIDE) or double-strand (dSTRIDE) breaks via biotinylated nucleotide labeling and anti-biotin antibody signals. not_specified PLA signal (interaction of anti-biotin antibodies) not_specified http://purl.obolibrary.org/obo/GO_0006755 GO http://purl.obolibrary.org/obo/GO_0007042 GO not_specified STRIDE (SensiTive Recognition of Individual DNA Ends) combines in situ nick translation with the proximity ligation assay (PLA) to detect single-strand breaks (sSTRIDE) or double-strand breaks (dSTRIDE). In this process, lesions labeled through nick translation with biotinylated nucleotides are identified by a PLA signal, which arises from the interaction of two anti-biotin antibodies from different species. http://purl.obolibrary.org/obo/CHEBI_35163 CHEBI http://purl.obolibrary.org/obo/GO_0006755 GO Sucrose Density Gradient Centrifugation Divides DNA pieces by density using a sucrose cushion, with increased fractionation leading to lower density pieces. in_vitro DNA density distribution change http://purl.obolibrary.org/obo/OBI_0000378 OBI http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI low Sucrose density gradient centrifuge Division of DNA pieces by density, increased fractionation leads to lower density pieces, with the use of a sucrose cushion http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006259 GO Sucrose density gradient centrifugation Division of DNA pieces by density, increased fractionation leads to lower density pieces, with the use of a sucrose cushion. in_vitro DNA fragmentation (strand breaks) increase not_specified Sucrose density gradient centrifuge Division of DNA pieces by density, increased fractionation leads to lower density pieces, with the use of a sucrose cushion TUNEL Assay Detects strand breaks by labeling the 3’OH end of breaks with dUTPs using terminal deoxynucleotidyl transferase, visualized with a fluorescent dye or reporter enzyme. in_vitro DNA strand breaks increase http://purl.obolibrary.org/obo/OBI_0000215 OBI medium The TUNEL (Terminal Deoxynucleotidyl Transferase dUTP Nick End Labeling) Assay To detect strand breaks, dUTPs added to the 3’OH end of a strand break by the DNA polymerase terminal deoxynucleotidyl transferase (TdT) are tagged with a fluorescent dye or a reporter enzyme to allow visualization http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006309 GO Unwinding Assay DNA is stored in alkaline solutions with a DNA-specific dye and allowed to unwind, with increased strand damage associated with increased unwinding. in_vitro DNA unwinding increase http://purl.obolibrary.org/obo/GO_0032508 GO OECD Approved Method low Unwinding Assay DNA is stored in alkaline solutions with DNA-specific dye and allowed to unwind following removal from tissue, increased strand damage associated with increased unwinding http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0032508 GO γ-H2AX Foci Quantification - Flow Cytometry Measures γ-H2AX immunostaining in cells by flow cytometry, normalized to total levels of H2AX. in_vitro γ-H2AX levels increase http://purl.obolibrary.org/obo/PR_000029467 PR high γ-H2AX Foci Quantification - Flow Cytometry Measurement of γ-H2AX immunostaining in cells by flow cytometry, normalized to total levels of H2AX http://purl.obolibrary.org/obo/PR_000029467 PR http://purl.obolibrary.org/obo/GO_0042769 GO Array Comparative Genomic Hybridization (aCGH) or SNP Microarray Copy number variations are detected using global DNA microarray technologies, though this method cannot detect balanced chromosomal aberrations like inversions. not_specified copy number variations change medium CNVs are most commonly detected using global DNA microarray technologies; This method, however, is unable to detect balanced CAs, such as inversions http://purl.obolibrary.org/obo/CHEBI_15367 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO CBMN with Imaging Flow Cytometry Cells are cultured with a cytokinesis blocking agent, fixed in solution, and imaged with flow cytometry to quantify micronuclei. in_vitro micronuclei frequency increase high Cells are cultured with cytokinesis blocking agent, fixed in solution, and imaged with flow cytometry to quantify MN http://purl.obolibrary.org/obo/GO_0042769 GO Chromosomal aberration test In vitro, the cell cycle is arrested at metaphase after 1.5 cell cycle following 3-6 hour exposure. In vivo, the test chemical is administered and bone marrow or testis is collected, with cell cycle arrested using a metaphase-arresting chemical before scoring chromosomal aberrations. in_vitro bone marrow testis chromosomal aberration frequency increase OECD TG 473; OECD TG 475; OECD TG 483 low In vitro, the cell cycle is arrested at metaphase after 1.5 cell cycle following 3-6 hour exposure In vivo, the test chemical is administered as a single treatment and bone marrow is collected 18-24 hrs later (TG 475), while testis is collected 24-48 hrs later (TG 483). The cell cycle is arrested with a metaphase-arresting chemical (e.g., colchicine) 2-5 hours before cell collection. Once cells are fixed and stained on microscope slides, chromosomal aberrations are scored http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007059 GO Chromosomal G-banding Use of Giesma dye to stain chromosomal bands, with abnormalities determined by altered morphology. not_specified chromosomal band abnormalities change low Use of Giesma dye to stain chromosomal bands, abnormalities determined by the presence of altered morphology http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0051276 GO Dicentric Chromosome Assay (DCA) Cells are fixed on microscope slides, chromosomes are stained, and the number of dicentric chromosomes are quantified. not_specified dicentric chromosome frequency increase low Cells are fixed on microscope slides, chromosomes are stained, and the number of dicentric chromosomes are quantified http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007059 GO Fluorescent In Situ Hybridization (FISH) Fluorescent assay of metaphase chromosomes that detects chromosomal aberrations through chromosome painting and microscopic analysis. not_specified chromosomal aberrations increase low Fluorescent assay of metaphase chromosomes that can detect CAs through chromosome painting and microscopic analysis http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0007059 GO G-banding Use of Giesma dye to stain chromosomal bands, abnormalities determined by the presence of altered morphology not_specified chromosomal morphology change low Use of Giesma dye to stain chromosomal bands, abnormalities determined by the presence of altered morphology http://purl.obolibrary.org/obo/CL_0000774 CL Green fluorescent protein reporter assay Green fluorescent protein reporter assay to detect the activation of stress signaling pathways, including DNA damage signaling including a reporter porter that is associated with DNA double strand breaks. in_vitro stress signaling pathway activation increase http://purl.obolibrary.org/obo/GO_0006974 GO not_specified Green fluorescent protein reporter assay to detect the activation of stress signaling pathways, including DNA damage signaling including a reporter porter that is associated with DNA double strand breaks. http://purl.obolibrary.org/obo/GO_0006974 GO http://purl.obolibrary.org/obo/GO_0006974 GO High content imaging DNA is stained using fluorescent dyes and micronuclei are scored using high-throughput microscopy image analysis. not_specified micronuclei frequency increase high DNA can be stained using fluorescent dyes and micronuclei can be scored high-throughput microscopy image analysis. http://purl.obolibrary.org/obo/GO_0042769 GO High-throughput biomarker assays Multiplexed biomarkers are measured by flow cytometry to discern clastogenic and aneugenic mechanisms for micronuclei induction. not_specified biomarker levels change high Multiplexed biomarkers can be measured by flow cytometry are used to discern clastogenic and aneugenic mechanisms for MN induction. In-Cell Western Prediscreen assay for quantification of γH2AX. not_specified γH2AX quantification increase not_specified Prediscreen Assay– In-Cell Western -based quantification of γH2AX http://purl.obolibrary.org/obo/GO_0005525 GO Micronuclei (MN) Assay via Microscopy Micronuclei are scored in vitro using microscopy. in_vitro micronuclei frequency increase OECD TG 487 medium Micronuclei are scored in vitro using microscopy http://purl.obolibrary.org/obo/GO_0042769 GO Next Generation Sequencing (NGS): Whole Genome Sequencing (WGS) or Whole Exome Sequencing (WES) Copy number variations are detected by fragmenting the genome and using NGS to sequence either the entire genome or only the exome. not_specified copy number variations change high CNVs are detected by fragmenting the genome and using NGS to sequence either the entire genome (WGS), or only the exome (WES); Challenges with this methodology include only being able to detect CNVs in exon-rich areas if using WES, the computational investment required for the storage and analysis of these large datasets, and the lack of computational algorithms available for effectively detecting somatic CNVs http://purl.obolibrary.org/obo/CHEBI_15367 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO Prediscreen Assay In-Cell Western-based quantification of γH2AX using a green fluorescent protein reporter assay to detect the activation of stress signaling pathways, including DNA damage signaling. in_vitro γH2AX levels increase high Prediscreen Assay– In-Cell Western -based quantification of γH2AX http://purl.obolibrary.org/obo/PR_000009338 PR http://purl.obolibrary.org/obo/GO_0042769 GO Premature Chromosome Condensation (PCC) Cells are exposed to mitosis-promoting factors or protein phosphatase inhibitors, causing premature chromosome condensation. in_vitro premature chromosome condensation increase low Cells are exposed to mitosis-promoting factors (MPF) following cell fusion, causing the chromosomes to condense prematurely. In another approach, cells are exposed to protein phosphatase inhibitors, such as type 1 and 2A protein phosphatases, also causing premature chromosome condensation. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0030261 GO γH2AX foci quantification Flow cytometry-based quantification of γH2AX foci and p53 protein expression not_specified γH2AX foci increase medium Flow cytometry-based quantification of γH2AX foci and p53 protein expression http://purl.obolibrary.org/obo/CHEBI_30753 CHEBI http://purl.obolibrary.org/obo/GO_0006240 GO Fluorescent reporter assay Zebrafish transgenic lines expressing fluorescent reporters in specific photoreceptor types are used to analyze photoreceptor counts, spatial patterning, and opsin switches. in_vivo retina Danio rerio photoreceptor counts and spatial patterning change http://purl.obolibrary.org/obo/CL_0000585 CL medium Zebrafish transgenic lines expressing fluorescent reporters in specific photoreceptor types (again associated with opsin expression) have also been successfully used to analyse photoreceptor counts, spatial patterning and opsin switches (Raymond et al., 2014; Mackin et al., 2019). Examples include lines reporting rhodopsin, blue cone or UV cone expression (Raymond et al., 2014). http://purl.obolibrary.org/obo/CL_0000585 CL Immunohistochemistry Immunohistochemistry is used to label specific opsins (protein level) with antibodies, typically performed on retinal wholemounts or cryosections. ex_vivo retina opsin protein localization and quantification change http://purl.obolibrary.org/obo/OBI_0000245 OBI http://purl.obolibrary.org/obo/UBERON_0000989 UBERON low Immunohistochemistry allows for labelling specific opsins (protein level) with antibodies, mostly through the use of primary antibodies specific to the target and secondary antibodies that bind to the primary antibodies and are conjugated to e.g., a fluorescent label or alkaline phosphatase that produces a measurable product (Allison et al., 2006; DuVal et al., 2014; Houbrechts et al., 2016; DuVal and Allison, 2018). This is typically performed on retinal wholemounts or cryosections. In situ hybridization In situ hybridization is used to label opsin mRNA using complementary oligonucleotide probes on retinal sections. ex_vivo retina opsin mRNA localization change http://purl.obolibrary.org/obo/SO_0000234 SO low In situ hybridization is used to label opsin mRNA using complementary oligonucleotide probes on retinal sections (Allison et al., 2006; Gan and Flamarique, 2010; Glaschke et al., 2010; DuVal et al., 2014; Karagic et al., 2018; Mackin et al., 2019). qPCR Quantitative polymerase chain reaction (qPCR) is used to measure the relative quantification of mRNA coding for specific opsins expressed in photoreceptor subtypes. in_vitro retina relative mRNA quantification of opsins change http://purl.obolibrary.org/obo/SO_0000234 SO medium Altered opsin expression patterns indicative of altered ratios of photoreceptor subtypes are often detected by relative quantification of mRNA coding for the specific opsins expressed in the photoreceptor subtypes using qPCR (quantitative polymerase chain reaction) (Allison et al., 2006; Mackin et al., 2019). transgenic reporter assay Zebrafish transgenic lines expressing fluorescent reporters in specific photoreceptor types are used to analyse photoreceptor counts, spatial patterning and opsin switches. in_vivo photoreceptor cells retina Zebrafish fluorescent reporter expression change medium Zebrafish transgenic lines expressing fluorescent reporters in specific photoreceptor types (again associated with opsin expression) have also been successfully used to analyse photoreceptor counts, spatial patterning and opsin switches (Raymond et al., 2014; Mackin et al., 2019). http://purl.obolibrary.org/obo/GO_0010468 GO Black-white preference test Assesses preference for black or white environments, often used to evaluate visual function. in_vivo eye black-white preference change http://purl.obolibrary.org/obo/GO_0007603 GO medium Black-white preference test (Baumann et al., 2016) http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0007603 GO Diverse Mobility assay Includes tracking, touch-evoked escape-response, swirl assays, locomotion, and swimming activity assays to assess mobility and motor function. in_vivo mobility and motor function change http://purl.obolibrary.org/obo/GO_0007626 GO medium Diverse Mobility assay including Tracking, touch-evoked escape-response assays, Swirl assays, locomotion assay, swimming activity, phototactic swimming activity assay, induced locomotor response (LLR) (Baumann et al., 2016; Gao et al., 2015; Zhao et al., 2014, Dehnert et al., 2019). http://purl.obolibrary.org/obo/NCBITaxon_1 NCBITAXON http://purl.obolibrary.org/obo/GO_0007626 GO Diverse Mobility assays A collection of assays including tracking, touch-evoked escape-response, swirl, locomotion, swimming activity, phototactic swimming, and induced locomotor response (LLR). in_vivo locomotor activity and escape responses change http://purl.obolibrary.org/obo/GO_0040026 GO not_specified Diverse Mobility assay including Tracking, touch-evoked escape-response assays, Swirl assays, locomotion assay, swimming activity, phototactic swimming activity assay, induced locomotor response (LLR) http://purl.obolibrary.org/obo/NCBITaxon_0000000 NCBITAXON http://purl.obolibrary.org/obo/GO_0040026 GO Electroretinography Electroretinography measures neuronal activity in response to light stimulation. Chrispell et al., 2015 performed this measurement. in_vivo retina neuronal activity change http://purl.obolibrary.org/obo/GO_0051707 GO low Electroretinography (Chrispell et al., 2015) http://purl.obolibrary.org/obo/CL_0000706 CL http://purl.obolibrary.org/obo/GO_0007165 GO Electroretinography Measures neuronal activity in the retina in response to light stimuli. in_vivo retina retinal neuronal activity change medium Electroretinography (Chrispell et al., 2015) http://purl.obolibrary.org/obo/UBERON_0000966 UBERON http://purl.obolibrary.org/obo/GO_0007603 GO Functional calcium imaging with light sheet microscopy Visualizes neural responses in the optic tectum using calcium imaging and light sheet microscopy. in_vivo optic tectum neural response change http://purl.obolibrary.org/obo/OBI_0002140 OBI low Babkiewicz et al. (2020) used an advanced technique to display an artificial prey on a miniature OLED screen and use functional calcium imaging with light sheet microscopy to visualize a neural response in the optic tectum. http://purl.obolibrary.org/obo/UBERON_0003080 UBERON http://purl.obolibrary.org/obo/GO_0050953 GO Immunofluorescent ERK phosphorylation assay Quantifies the ratio of phosphorylated ERK to total ERK in the optic tectum using immunofluorescent antibodies. in_vivo optic tectum phosphorylated ERK to total ERK ratio change http://purl.obolibrary.org/obo/UBERON_0003080 UBERON low Analysis of neural activity in the optic tectum can be quantified as the ratio of phosphorylated extracellular signal–regulated kinase (ERK) to total ERK in the optic tectum using immunofluorescent antibodies (Randlett et al., 2015, Dehnert et al., 2019). http://purl.obolibrary.org/obo/GO_0070371 GO Light-dark transition assay Measures reaction to changes in light intensity, assessing light sensitivity. in_vivo eye light sensitivity change http://purl.obolibrary.org/obo/GO_0007603 GO medium Light-dark transition or vision startle response: reaction to change in light intensity (light sensitivity) (Brastrom et al., 2019) http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0050953 GO Opto Kinetic Response (OKR) Measures visually-mediated eye saccades in response to rotating black and white stripes. in_vivo eye rat mouse fish human eye saccades change http://purl.obolibrary.org/obo/GO_0007606 GO high Opto Kinetic response, OKR (similar protocol for Rat/mice (Segura et al., 2018), fish (Zou et al., 2010) and humans (Kang and Wildsoet, 2016)). The OKR is a visually-mediated assay in which an individual will respond to alternating black and white stripes by exhibiting eye saccades, eye movements without coordinated body movements, in the same direction as rotating stripes. http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0007603 GO Opto Motor Response (OMR) Tracks the ability of fish to swim in the direction of a perceived motion stimulus. in_vivo fish swimming direction change http://purl.obolibrary.org/obo/GO_0007626 GO medium Opto Motor Reponses, OMR. OMR tracks the ability of fish to swim in the direction of a perceived motion when presented with a whole-field stimulus (Neuhauss, 2003), (Gould et al., 2017)). http://purl.obolibrary.org/obo/NCBITaxon_7742 NCBITAXON http://purl.obolibrary.org/obo/GO_0007626 GO preference test Black-white preference test assesses visual preference. in_vivo eye preference change medium Black-white preference test (Baumann et al., 2016) http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0007606 GO immunoblotting Measures phosphorylation of GSK3 beta at residue Ser9 using anti-phospho-GSK3beta antibodies. in_vitro GSK3 beta phosphorylation at Ser9 increase http://purl.obolibrary.org/obo/GO_0006468 GO low Phosphorylation of GSK3 beta is measured by immunoblotting with anti-phospho-GSK3beta http://purl.obolibrary.org/obo/PR_000008068 PR http://purl.obolibrary.org/obo/GO_0006468 GO Immunoblotting for phospho-GSK3beta An immunoblot assay using an anti-phospho-GSK3beta antibody to detect phosphorylation of GSK3beta at Ser9, which indicates GSK3beta inactivation. in_vitro not specified not specified not specified phosphorylation of GSK3beta at Ser9 increase http://purl.obolibrary.org/obo/GO_0016310 GO not_specified Phosphorylation of GSK3 beta is measured by immunoblotting with anti-phospho-GSK3beta (Huang et al., 2019). http://purl.obolibrary.org/obo/PR_0011233 PR http://purl.obolibrary.org/obo/GO_0016310 GO Wnt/beta-catenin activity assay This assay measures GSK3 beta inactivation by assessing Wnt/beta-catenin activity using a luciferase reporter gene controlled by TCF/LEF binding sites after transfection into cells. in_vitro luciferase activity increase http://purl.obolibrary.org/obo/GO_0008553 GO medium Inactivation of GSK3 beta is measured by Wnt/beta-catenin activity assay, in which the vector containing the firefly luciferase gene controlled by TCF/LEF binding sites is transfected in the cells (Naujok et al., 2014). http://purl.obolibrary.org/obo/CHEBI_59834 CHEBI http://purl.obolibrary.org/obo/GO_0008553 GO Wnt/beta-catenin activity assay Measures GSK3 beta inactivation via firefly luciferase gene expression controlled by TCF/LEF binding sites. in_vitro Wnt/beta-catenin activity increase http://purl.obolibrary.org/obo/GO_0016055 GO http://purl.obolibrary.org/obo/GO_0003995 GO medium Inactivation of GSK3 beta is measured by Wnt/beta-catenin activity assay, in which the vector containing the firefly luciferase gene controlled by TCF/LEF binding sites is transfected in the cells http://purl.obolibrary.org/obo/PR_000008068 PR http://purl.obolibrary.org/obo/GO_0016055 GO biomarker detection Detects treatment-resistant gastric cancer and EMT using biomarkers such as transcription factors ZEB1/2, SNAI1/2, and TWIST2. not_specified gastric tissue level of transcription factors ZEB1/2, SNAI1/2, and TWIST2 increase http://purl.obolibrary.org/obo/GO_0001837 GO http://purl.obolibrary.org/obo/PR_000007118 PR http://purl.obolibrary.org/obo/PR_000007119 PR http://purl.obolibrary.org/obo/PR_000009799 PR http://purl.obolibrary.org/obo/PR_000009800 PR not_specified Treatment-resistant gastric cancer and EMT can be detected with biomarkers (Zeisberg & Neilson, 2009). Treatment-resistant gastric cancer which exhibits EMT phenotype can be detected as the increased level of the transcription factors, zinc finger E-box-binding homeobox 1/2 (ZEB1/2), SNAI1/2, and TWIST2 which are associated with the activation of EMT-related genes (Tanabe et al., 2022a and 2022b). http://purl.obolibrary.org/obo/CL_0000187 CL http://purl.obolibrary.org/obo/GO_0001837 GO biomarker detection of ZEB1/2, SNAI1/2, and TWIST2 levels Measurement of the expression levels of specific transcription factors (ZEB1/2, SNAI1/2, and TWIST2) to identify treatment-resistant gastric cancer and EMT phenotype. not_specified gastric level of the transcription factors, zinc finger E-box-binding homeobox 1/2 (ZEB1/2), SNAI1/2, and TWIST2 increase http://purl.obolibrary.org/obo/GO_0003700 GO http://purl.obolibrary.org/obo/GO_0034003 GO not_specified Treatment-resistant gastric cancer which exhibits EMT phenotype can be detected as the increased level of the transcription factors, zinc finger E-box-binding homeobox 1/2 (ZEB1/2), SNAI1/2, and TWIST2 which are associated with the activation of EMT-related genes http://purl.obolibrary.org/obo/GO_0034003 GO Transcription factor level assay Measures the increased level of the transcription factors ZEB1/2, SNAI1/2, and TWIST2, which are biomarkers of EMT activation in treatment-resistant gastric cancer. not_specified gastric cancer tissue level of transcription factors ZEB1/2, SNAI1/2, TWIST2 increase http://purl.obolibrary.org/obo/GO_0003700 GO http://purl.obolibrary.org/obo/GO_0001837 GO not_specified Treatment-resistant gastric cancer and EMT can be detected with biomarkers (Zeisberg & Neilson, 2009). Treatment-resistant gastric cancer which exhibits EMT phenotype can be detected as the increased level of the transcription factors, zinc finger E-box-binding homeobox 1/2 (ZEB1/2), SNAI1/2, and TWIST2 which are associated with the activation of EMT-related genes (Tanabe et al., 2022a and 2022b). http://purl.obolibrary.org/obo/GO_0001837 GO gene expression analysis This assay measures the regulation of gene expression by thyroid hormone receptors (TR) upon binding of thyroid hormones (T3 and T4), either increasing or decreasing target gene transcription activity. It also considers the inhibitory effect of ligand-free TR complexes with corepressors. not_specified brain gene transcription activity increase http://purl.obolibrary.org/obo/GO_0006925 GO not_specified Bound receptors, homodimerized or heterodimerized with retinoic acid, bind to thyroid response elements and regulate gene expression by either increasing or decreasing tragent gene transcription activity. There are a large number of genes regualated by TH. Both TRa and TRb are known to be expressed during neurodevelopment (ref). http://purl.obolibrary.org/obo/GO_0005737 GO http://purl.obolibrary.org/obo/GO_0006925 GO backscatter electron microscopy This assay uses backscatter electron microscopy to directly measure the interaction between high aspect ratio nanoparticles (HARN) and cells, such as macrophages or epithelial cells, to assess frustrated phagocytosis. in_vitro macrophages epithelial cells frustrated phagocytosis not_specified http://purl.obolibrary.org/obo/OBI_0000455 OBI low the analysis of interaction between HARN and cells could be performed in time-lapse microscopy [7] or backscatter electron microscopy [8] The frustrated phagocytosis could be measure by different type of microscopy analysis allowing a direct measurement. For examples, [...] backscatter electron microscopy [8] are used in the literature. http://purl.obolibrary.org/obo/CL_0000235 CL http://purl.obolibrary.org/obo/GO_0006909 GO backscatter electron microscopy This assay uses backscatter electron microscopy to analyze the interaction between HARN and cells, providing a direct measurement of frustrated phagocytosis. in_vitro macrophages epithelial cells interaction between HARN and cells change low Using in vitro cell models, such as macrophages or epithelial cells, the analysis of interaction between HARN and cells could be performed in ... backscatter electron microscopy [8]. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0006914 GO in vitro phagocytosis assay This assay measures the capacity of macrophages to complete the phagocytosis process using different macrophage cell lines (THP-1, NR8383, RAW267) and analysis by microscopy or gene expression. in_vitro THP-1 NR8383 RAW267 phagocytosis completion not_specified http://purl.obolibrary.org/obo/GO_0006909 GO medium The study of the capacity of macrophages to complete phagocytosis process could be performed in vitro using different type of macrophage cell lines (THP-1, NR8383, RAW267) and analysis by microscopy or gene expression http://purl.obolibrary.org/obo/CL_0000235 CL http://purl.obolibrary.org/obo/GO_0006909 GO In vivo rodent phagocytosis and clearance assay Evaluation of macrophage phagocytosis ability and remaining nanoparticle quantity in the body after in vivo exposure of rodents to high aspect ratio nanoparticles. in_vivo macrophages rodents Remaining quantity of material in the body / ability of macrophages to phagocyte foreign matter change http://purl.obolibrary.org/obo/GO_0006909 GO low or in vivo after exposure of rodents to different type of high aspect ratio nanoparticles and analysis of the remaining quantity of material in the body or the ability of macrophages to phagocyte foreign matter. http://purl.obolibrary.org/obo/GO_0006909 GO light microscopy This assay uses light microscopy to directly measure frustrated phagocytosis by analyzing the interaction between high aspect ratio nanoparticles (HARN) and cells. in_vitro frustrated phagocytosis not_specified low The frustrated phagocytosis could be measure by different type of microscopy analysis allowing a direct measurement. For examples, [...] light microscopy [9] http://purl.obolibrary.org/obo/CL_0000235 CL http://purl.obolibrary.org/obo/GO_0006909 GO phagocytic receptor expression analysis Indirect measurement of frustrated phagocytosis by analyzing the expression of receptors such as MARCO, MSR-1, CD36, and TLR4. in_vitro macrophages expression of MARCO, MSR-1, CD36, TLR4 change not_specified The analysis of phagocytic receptor expression such as MARCO, MSR-1, CD36, TLR4 is an indirect measurement [6]. http://purl.obolibrary.org/obo/GO_0006909 GO phagocytic receptor expression analysis This assay measures the expression of phagocytic receptors such as MARCO, MSR-1, CD36, and TLR4 as an indirect measurement of frustrated phagocytosis. in_vitro phagocytic receptor expression not_specified http://purl.obolibrary.org/obo/PR_000001409 PR http://purl.obolibrary.org/obo/PR_000001196 PR http://purl.obolibrary.org/obo/PR_000001004 PR http://purl.obolibrary.org/obo/PR_000001490 PR medium The analysis of phagocytic receptor expression such as MARCO, MSR-1, CD36, TLR4 is an indirect measurement [6]. http://purl.obolibrary.org/obo/GO_0006909 GO time-lapse microscopy This assay uses time-lapse microscopy to directly measure the interaction between high aspect ratio nanoparticles (HARN) and cells, such as macrophages or epithelial cells, to assess frustrated phagocytosis. in_vitro macrophages epithelial cells frustrated phagocytosis not_specified low Using in vitro cell models, such as macrophages or epithelial cells, the analysis of interaction between HARN and cells could be performed in time-lapse microscopy [7] The frustrated phagocytosis could be measure by different type of microscopy analysis allowing a direct measurement. For examples, time-lapse video microscopy [7] http://purl.obolibrary.org/obo/CL_0000235 CL http://purl.obolibrary.org/obo/GO_0006909 GO time-lapse microscopy This assay uses time-lapse microscopy to observe the interaction between HARN and cells over time, providing a direct measurement of frustrated phagocytosis. in_vitro macrophages epithelial cells interaction between HARN and cells change http://purl.obolibrary.org/obo/GO_0008697 GO low Using in vitro cell models, such as macrophages or epithelial cells, the analysis of interaction between HARN and cells could be performed in time-lapse microscopy [7] http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0006914 GO Ames test A biological assay to assess the mutagenic potential of chemical compounds using bacterial strains. in_vitro DNA mutation increase http://purl.obolibrary.org/obo/GO_0007092 GO not_specified DNA mutation could be analyzed with Ames test http://purl.obolibrary.org/obo/CHEBI_35221 CHEBI http://purl.obolibrary.org/obo/GO_0007092 GO Ames test Analyzes frequencies of mutations in bacteria. in_vitro mutation frequency increase OECD n°471 not_specified DNA mutation could be analyzed with Ames test or via the analysis of frequencies of mutations (OECD n°471) comet assay Detects DNA strand breaks, DNA-DNA and DNA-protein crosslinks, adducts, and oxidized nucleotides. in_vitro DNA strand breaks increase OECD n°489 not_specified comet assay with different protocols for the detection of double and single-strand breaks, DNA-DNA and DNA-protein crosslinks, adduct and oxidized nucleotides (OECD n°489) micronucleus formation Measures the formation of micronuclei as an indicator of DNA damage. in_vitro micronucleus formation increase OECD n°487 not_specified micronucleus formation (OECD n°487) mutation frequency analysis Measurement of the frequency of mutations occurring in a population of cells or organisms. not_specified frequencies of mutations increase OECD n°471 not_specified via the analysis of frequencies of mutations (OECD n°471) http://purl.obolibrary.org/obo/CHEBI_35221 CHEBI http://purl.obolibrary.org/obo/GO_0007092 GO γH2AX analysis An assay used to analyze DNA strand breaks by measuring the phosphorylation of the histone variant H2AX. in_vitro DNA strand breaks change http://purl.obolibrary.org/obo/GO_0006246 GO not_specified γH2AX for the analysis of DNA strand breaks http://purl.obolibrary.org/obo/CHEBI_35221 CHEBI http://purl.obolibrary.org/obo/GO_0006246 GO γH2AX assay Analyzes DNA strand breaks by detecting phosphorylated H2AX histone. in_vitro γH2AX levels increase not_specified γH2AX for the analysis of DNA strand breaks carcinogenesis study Assessment of cancer development in animal models following OECD guidelines. This involves monitoring for tumor formation and progression. in_vivo carcinogenesis development increase OECD TG 451 low In animal experiments, the OECD guidelines n°451 provide the procedure for the study of carcinogenesis development. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008274 GO chest X-ray Imaging technique to detect abnormalities in the lung indicative of lung cancer. in_vivo lung human presence of lung abnormalities not_specified medium the chest X-ray http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0001660 GO chest X-ray Radiographic imaging of the chest to identify pulmonary nodules or masses suggestive of lung cancer. in_vivo lung human presence of pulmonary nodules or masses increase not_specified Lung cancer can be measured in human by analysis of the sputum cytology, the chest X-ray and all the techniques usually used in this medical field. OECD TG 451 Procedure for the study of carcinogenesis development in animal experiments. in_vivo carcinogenesis development not_specified http://purl.obolibrary.org/obo/GO_0001660 GO OECD TG 451 low the OECD guidelines n°451 provide the procedure for the study of carcinogenesis development http://purl.obolibrary.org/obo/NCBITaxon_1 NCBITAXON http://purl.obolibrary.org/obo/GO_0001660 GO sputum cytology Analysis of sputum cytology to detect abnormal cells indicative of lung cancer. in_vivo lung human presence of abnormal cells not_specified low analysis of the sputum cytology http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0001660 GO sputum cytology Analysis of sputum samples to detect lung cancer cells in humans by examining cellular morphology under a microscope. in_vivo lung sputum human presence of lung cancer cells not_specified http://purl.obolibrary.org/obo/UBERON_0006610 UBERON low Lung cancer can be measured in human by analysis of the sputum cytology Sputum cytology Microscopic examination of expectorated sputum to identify malignant or pre-malignant cells indicative of lung cancer. ex_vivo lung human presence of malignant cells in sputum change http://purl.obolibrary.org/obo/UBERON_0002048 UBERON low Lung cancer can be measured in human by analysis of the sputum cytology atomic force microscopy Studies the topography of surfactant structures at air-liquid interfaces after exposure to test substances on fixed samples. in_vitro lung surface topography change http://purl.obolibrary.org/obo/CHEBI_73648 CHEBI low Atomic force microscopy The topography of surfactant structures formed at respiratory-like air-liquid interfaces upon exposure to test substances can be studied by atomic force microscopy on fixed samples. http://purl.obolibrary.org/obo/CHEBI_73648 CHEBI Atomic force microscopy Studies the topography of surfactant structures at air-liquid interfaces upon exposure to test substances. in_vitro lung topography of surfactant structures change low The topography of surfactant structures formed at respiratory-like air-liquid interfaces upon exposure to test substances can be studied by atomic force microscopy on fixed samples. Capillary surfactometer Assesses lung surfactant functionality by measuring the percent of time with an open passage in a capillary tube simulating airways. in_vitro lung percent of time with an open passage change low In the capillary surfactometer (CS), surfactant is deposited in a capillary tube of uneven diameter that simulate the cylindrical surfaces of the terminal conducting airways a constant airflow is led through the capillary. The percent of time with an open passage is used to assess the functionality of lung surfactant Captive bubble surfactometer Measures lung surfactant function by forming a film at the air-liquid interface of an air bubble and studying surface activity during cycling. in_vitro lung surface activity change low In the captive bubble surfactometer (CBS), the lung surfactant film is formed at the air-liquid interface of an air bubble suspended in liquid. The captive bubble surfactometer allows study of the rapid initial adsorption of the lung surfactant at the air-liquid interface, post-expansion adsorption, surface activity during dynamic and quasi-static cycles, and stability of the surfactant film to mechanical perturbations Constrained drop surfactometer Measures surface tension of lung surfactant films by cycling a droplet on a pedestal and analyzing drop shape in real-time. in_vitro lung surface tension change low In the constrained drop surfactometer (CDS) a droplet of lung surfactant is deposited on a sharp-edged pedestal, so that a surfactant film is formed at its air-water surface. The adsorbed lung surfactant film is cycled continuously, to mimic breathing Surface tension values are obtained by analysis of the drop shape in real-time Cryogenic transmission electron microscopy Visualizes morphological and structural changes in lung surfactant vesicles at the single membrane level. in_vitro lung morphological and structural changes in vesicles change low Cryogenic transmission electron microscopy allows visualizing morphological and structural changes at the single membrane vesicle level. Changes in the size, circularity or lamerallity of the vesicles indicate disruption of the three-dimensional surfactant structures. Cryogenic transmission electron microscopy Visualizes morphological and structural changes at the single membrane vesicle level in aqueous surfactant dispersions after vitrification. in_vitro lung vesicle size, circularity, and lamellarity change not_specified Cryogenic transmission electron microscopy allows visualizing morphological and structural changes at the single membrane vesicle level. Changes in the size, circularity or lamerallity of the vesicles indicate disruption of the three-dimensional surfactant structures. Differential scanning calorimetry Studies phase transitions in lipid membranes (lung surfactant) over temperature changes to characterize thermotropic phase behaviors. in_vitro lung enthalpy, transition temperature, and cooperativity change low Differential scanning calorimetry allows the study of phase transitions occurring in lipid membranes (such as lung surfactant) over changes in temperature Associated enthalpy, transition temperature, and cooperativity can be estimated from the thermograms. differential scanning calorimetry Studies phase transitions in lipid membranes (lung surfactant) over changes in temperature to characterize thermotropic behavior. in_vitro lung phase transition temperature change low Differential scanning calorimetry allows the study of phase transitions occurring in lipid membranes (such as lung surfactant) over changes in temperature It can be used to characterize the thermotropic phase behaviours of phospholipids in the surfactant models in the absence or presence of interacting substances. Associated enthalpy, transition temperature, and cooperativity can be estimated from the thermograms. Differential scanning calorimetry Studies phase transitions in lipid membranes of lung surfactant models by measuring thermotropic behaviors. in_vitro lung phase transitions in lipid membranes change low Differential scanning calorimetry allows the study of phase transitions occurring in lipid membranes (such as lung surfactant) over changes in temperature It can be used to characterize the thermotropic phase behaviours of phospholipids in the surfactant models in the absence or presence of interacting substances. Langmuir-Blodgett films Measures surface pressure-area isotherms of surfactant films to study interactions with test substances. in_vitro lung surface pressure-area isotherms change low Langmuir-Blodgett films are interfacial films of surfactant transferred from the air-liquid interface onto solid supports. The comparison of such isotherms in the presence or absence of the test substance gives insights in the interaction of a substance with lung surfactant at the molecular level. Surfactant adsorption test Fluorescence‑based assay that quantifies the extent and rate of lung surfactant adsorption at the air‑liquid interface by quenching fluorescence of non‑adsorbed surfactant with a light‑absorbing agent. in_vitro lung adsorption extent and rate decrease high The surfactant adsorption test is a fluorescence-based method that measures the extent and rate of adsorption of lung surfactant at the air-liquid interface. This method is high-throughput compared to the biophysical assays described above and it allows to measure the effects of physiologically relevant factors, such as temperature, surfactant concentration, or presence of inhibitors in a high number of samples http://purl.obolibrary.org/obo/GO_0006031 GO Surfactant adsorption test Measures the extent and rate of lung surfactant adsorption at the air-liquid interface using a fluorescence-based method. in_vitro lung adsorption of lung surfactant change high The surfactant adsorption test is a fluorescence-based method that measures the extent and rate of adsorption of lung surfactant at the air-liquid interface. This method is high-throughput compared to the biophysical assays described above surfactant adsorption test A fluorescence-based method that measures the extent and rate of lung surfactant adsorption at the air-liquid interface using a fluorescent probe and a light-absorbing agent. in_vitro lung fluorescence intensity decrease http://purl.obolibrary.org/obo/OBI_0000433 OBI http://purl.obolibrary.org/obo/CHEBI_73648 CHEBI high The surfactant adsorption test is a fluorescence-based method that measures the extent and rate of adsorption of lung surfactant at the air-liquid interface. Lung surfactant is labelled with a fluorescent probe, and injected into the wells of a multi-well plate containing a light-absorbing agent (typically brilliant black). The fluorescence of the lung surfactant sample in the bulk (not adsorbed at the interface) is quenched by the light-adsorbing agent. http://purl.obolibrary.org/obo/CHEBI_73648 CHEBI http://purl.obolibrary.org/obo/OBI_0000433 OBI histological staining of lung tissue This assay involves staining lung tissue from experimental animals to observe areas of atelectasis, which are indicative of alveolar collapse. in_vivo lung areas of atelectasis not_specified http://purl.obolibrary.org/obo/UBERON_0002048 UBERON low areas of atelectasis can be observed in experimental animals after staining of lung tissue from exposed animals http://purl.obolibrary.org/obo/UBERON_0002185 UBERON Immunohistochemistry for Mef2c This assay detects Mef2c-positive cells, which are specific to the anterior heart field (AHF) within the second heart field (SHF). in_vivo heart second heart field presence of Mef2c-positive cells not_specified low Mef2c positive cells are specific to the AHF (Dodou et al., 2004; Verzi et al., 2005). alanine dosimeters/NanoDots Uses the amino acid alanine to detect radiation-induced changes, and nanodots leverage nano-scale technology to provide high precision and sensitivity in radiation dose measurements. in_vitro radiation dose not_specified high Alanine dosimeters use the amino acid alanine to detect radiation-induced changes, and nanodots leverage nano-scale technology to provide high precision and sensitivity in radiation dose measurements Fluorescent Nuclear Track Detector (FNTD) Biocompatible chips with crystals of aluminum oxide doped with carbon and magnesium; used with fluorescent microscopy to visualize and quantify linear energy transfer (LET) of tracks produced by energy deposition. in_vitro linear energy transfer (LET) not_specified medium FNTDs are biocompatible chips with crystals of aluminum oxide doped with carbon and magnesium; used in conjunction with fluorescent microscopy, these FNTDs allow for the visualization and the linear energy transfer (LET) quantification of tracks produced by the deposition of energy into a material. Monte Carlo Simulations Computational algorithm that mathematically models the deposition of energy into materials. in_silico energy deposition not_specified high Monte Carlo simulations are based on a computational algorithm that mathematically models the deposition of energy into materials. Tissue equivalent proportional counter Measure the LET spectrum and calculate the equivalent dose not_specified equivalent dose not_specified not_specified Tissue equivalent proportional counter (TEPC) Straume et al, 2015 Measure the LET spectrum and calculate the equivalent dose Tissue equivalent proportional counter (TEPC) Measures the LET spectrum and calculates the equivalent dose. in_vitro LET spectrum and equivalent dose not_specified medium Measure the LET spectrum and calculate the equivalent dose UV meters or radiometers Measures UVA/UVB irradiance intensity or accumulated irradiance over time. in_vitro UVA/UVB irradiance intensity or accumulated irradiance not_specified high UVA/UVB (irradiance intensity), UV dosimeters (accumulated irradiance over time) AGD measurement Morphometric measurement of the distance between the genital papilla and the anus using a stereomicroscope with a micrometer eyepiece. in_vivo rodents anogenital distance (AGD) decrease OECD Guidance Document 151 medium The AGD is a morphometric measurement carried out by trained technicians (rodents) or medical staff (humans). In rodent studies AGD is assessed as the distance between the genital papilla and the anus, and measured using a stereomicroscope with a micrometer eyepiece. ELISA Quantifies testosterone levels in serum, cell culture medium, or tissue using traditional immunoassay techniques. in_vitro testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI medium Methods include traditional immunoassays such as ELISA and RIA http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO Fish Lifecycle Toxicity Test Measures testosterone levels in fish during a lifecycle toxicity test. in_vivo testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI US EPA OPPTS 850.1500 low Testosterone levels may also be measured by: Fish Lifecycle Toxicity Test (FLCTT) (US EPA OPPTS 850.1500) http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO H295R Steroidogenesis Assay Validated OECD assay using H295R adrenocortical carcinoma cells to measure the production of estradiol, testosterone, and other steroid hormones in the culture medium. in_vitro H295R adrenocortical carcinoma cells estradiol and testosterone production not_specified http://purl.obolibrary.org/obo/GO_0009411 GO OECD TG 456 high The H295R Steroidogenesis Assay (OECD TG 456) is (currently; anno 2025) primarily used to measure estradiol and testosterone production. This validated OECD test guideline uses adrenal H295R cells, with hormone levels measured in the cell culture medium (OECD, 2011). The U.S. EPA’s ToxCast program further advanced this method, enabling high-throughput measurement of 11 steroidogenesis-related hormones (Haggard et al., 2018). http://purl.obolibrary.org/obo/GO_0009411 GO http://purl.obolibrary.org/obo/GO_0009411 GO H295R Steroidogenesis Assay Measures testosterone and estradiol production in adrenal H295R cells using LC-MS/MS to quantify hormone levels in cell culture medium. in_vitro H295R testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006694 GO OECD TG 456 high The H295R Steroidogenesis Assay (OECD TG 456) is (currently; anno 2025) primarily used to measure estradiol and testosterone production. This validated OECD test guideline uses adrenal H295R cells, with hormone levels measured in the cell culture medium (OECD, 2011). http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO Hershberger Bioassay in Rats Measures testosterone levels in rats using the Hershberger bioassay. in_vivo testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI OECD TG 441 low Testosterone levels may also be measured by: OECD TG 441: Hershberger Bioassay in Rats (H Assay) http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO isotope-dilution gas chromatography-mass spectrometry Quantifies testosterone levels in serum using isotope-dilution gas chromatography-mass spectrometry. in_vivo testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/OBI_0000474 OBI low Testosterone can be measured by immunoassays and by isotope-dilution gas chromatography-mass spectrometry in serum http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO LC-MS/MS Quantifies testosterone levels in serum, cell culture medium, or tissue using liquid chromatography-tandem mass spectrometry. in_vitro testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/OBI_0000475 OBI medium advanced techniques like LC-MS/MS http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO liquid scintillation spectrometry Quantifies testosterone levels in serum, cell culture medium, or tissue following radiolabeling using liquid scintillation spectrometry. in_vitro testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/OBI_0000268 OBI low liquid scintillation spectrometry following radiolabeling http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO Male pubertal assay Measures testosterone levels in male pubertal rats. in_vivo testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI US EPA OPPTS 890.1500 low Testosterone levels may also be measured by: Male pubertal assay (PP Male Assay) (US EPA OPPTS 890.1500) http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO RIA Quantifies testosterone levels in serum, cell culture medium, or tissue using radioimmunoassay techniques. in_vitro testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI medium Methods include traditional immunoassays such as ELISA and RIA http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0034779 GO ELISA Immunoassay to detect progesterone levels using enzyme-linked immunosorbent assay. in_vitro progesterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI medium Classically, progesterone has been detected using immunoassays such as ELISA or RIA. http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI H295R steroidogenesis assay Uses NCI-H295R cells to measure effects on progesterone levels, though not validated for this specific purpose. in_vitro NCI-H295R progesterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI http://purl.obolibrary.org/obo/GO_0006700 GO OECD TG456 not_specified The cells used for validated H295R steroidogenesis assay (OECD TG456) (NCI-H295R) can be used to measure effects on progesterone levels, though not validated for this purpose (Haggard et al., 2018; Karmaus et al., 2016). http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI http://purl.obolibrary.org/obo/GO_0006700 GO LC-MS/MS High throughput liquid chromatography-tandem mass spectrometry to detect progesterone levels. in_vitro progesterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI http://purl.obolibrary.org/obo/OBI_0000473 OBI high Progesterone can be detected by using high throughput LC-MS/MS (Andersson et al., 2018; Evangelista et al., 2024; Stanislaus et al., 2012). http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI MA-10 assay An assay using the mouse Leydig tumor cell line MA-10 to test the effect of chemicals on progesterone levels. in_vitro MA-10 mouse Leydig tumor cell line testis mouse progesterone levels change http://purl.obolibrary.org/obo/CHEBI_35354 CHEBI not_specified These cell lines include for instance the mouse Leydig tumor cell line MA-10 or ovarian granulosa cell lines (ASCOLI, 1981; Havelock et al., 2004). can hence be used to test the effect of chemicals on progesterone levels. http://purl.obolibrary.org/obo/CHEBI_35354 CHEBI http://purl.obolibrary.org/obo/GO_0001574 GO ovarian granulosa cell assay An assay using ovarian granulosa cell lines to test the effect of chemicals on progesterone levels. in_vitro ovarian granulosa cell lines ovary progesterone levels change http://purl.obolibrary.org/obo/CHEBI_35354 CHEBI not_specified These cell lines include for instance the mouse Leydig tumor cell line MA-10 or ovarian granulosa cell lines (ASCOLI, 1981; Havelock et al., 2004). can hence be used to test the effect of chemicals on progesterone levels. http://purl.obolibrary.org/obo/CHEBI_35354 CHEBI http://purl.obolibrary.org/obo/GO_0001574 GO RIA Immunoassay to detect progesterone levels using radioimmunoassay. in_vitro progesterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI medium Classically, progesterone has been detected using immunoassays such as ELISA or RIA. http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI Corpus luteum counting Determines ovulation by counting and identifying corpus luteum in stained sections of reproductive organs after sacrifice. in_vivo ovary mouse rat number of corpus lutea not_specified http://purl.obolibrary.org/obo/UBERON_0000957 UBERON http://purl.obolibrary.org/obo/GO_0045494 GO low Another determinant of ovulation is the presence of corpus lutea. After sacrifice of the female mouse or rat, sections of the reproductive organs are stained, and histological examination is performed to count and identify corpus luteum. http://purl.obolibrary.org/obo/UBERON_0000957 UBERON http://purl.obolibrary.org/obo/GO_0045494 GO mRNA expression analysis Investigation of mRNA expression profiles of ovulation markers (e.g., AREG and EREG) in granulosa cells. in_vitro granulosa cells human rat mRNA expression of AREG and EREG increase http://purl.obolibrary.org/obo/GO_0008619 GO not_specified mRNA expression and profiles of ovulation markers can be investigated. Certain genes are overexpressed during ovulation and are considered markers of ovulation, such as AREG and EREG http://purl.obolibrary.org/obo/CL_0000124 CL http://purl.obolibrary.org/obo/GO_0007037 GO mRNA expression of ovulation markers Investigates mRNA expression profiles of ovulation markers such as AREG and EREG in granulosa cells. in_vitro granulosa cells human rat mRNA expression of ovulation markers increase http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0045494 GO medium mRNA expression and profiles of ovulation markers can be investigated. Certain genes are overexpressed during ovulation and are considered markers of ovulation, such as AREG and EREG, shown in many studies. http://purl.obolibrary.org/obo/CL_0000470 CL http://purl.obolibrary.org/obo/GO_0045494 GO Oviduct flushing Measures ovulation by flushing the oviduct and counting the number of ova (mature oocytes) after euthanasia. in_vivo oviduct mouse number of ova not_specified http://purl.obolibrary.org/obo/UBERON_0000992 UBERON http://purl.obolibrary.org/obo/GO_0045494 GO low The mice are then euthanized, and the oviducts are flushed. The number of ova (mature oocytes) are counted to determine the quality of ovulation. http://purl.obolibrary.org/obo/GO_0007276 GO http://purl.obolibrary.org/obo/GO_0045494 GO Vaginal cytology Assesses the stage in the estrous cycle by flushing the vagina or collecting a vaginal swab, followed by staining to observe cytology and determine the stage. in_vivo vagina mouse rat estrous cycle stage not_specified http://purl.obolibrary.org/obo/GO_0007545 GO medium Vaginal cytology is a method to assess the stage in the estrous cycle. This is done by flushing the vagina or collecting a vaginal swab followed by staining to observe cytology and determine the stage. http://purl.obolibrary.org/obo/UBERON_0001046 UBERON http://purl.obolibrary.org/obo/GO_0007545 GO bioactivity assay Measure the ability of the reagent to neutralize the bioactivity of human IL-1β on primary human fibroblasts in vitro. in_vitro primary human fibroblasts fibroblasts human bioactivity of human IL-1β decrease low Measure the ability of the reagent to neutralize the bioactivity of human IL-1β on primary human fibroblasts in vitro http://purl.obolibrary.org/obo/CHEBI_59137 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO Competitive inhibition binding assay Uses 125I-IL-1α to measure the binding/competition for type I IL-1R on various cell lines. in_vitro EL4 thymoma cells 3T3 fibroblasts hepatocytes Chinese hamster ovary cells mouse binding affinity/competition not_specified http://purl.obolibrary.org/obo/GO_0005125 GO not_specified Competitive inhibition binding experiments using 125 I-IL- 1 α to type I IL-1R present on EL4 thymoma cells, 3T3 fibroblasts, hepatocytes, and Chinese hamster ovary cells expressing recombinant mouse type I IL-1R http://purl.obolibrary.org/obo/GO_0005125 GO Competitive inhibition binding assay Measures the binding of 125I-IL-1α to type I IL-1R on various cell types using competitive inhibition. in_vitro EL4 thymoma cells 3T3 fibroblasts hepatocytes Chinese hamster ovary cells mouse hamster binding of 125I-IL-1α to type I IL-1R decrease http://purl.obolibrary.org/obo/GO_0005149 GO low Competitive inhibition binding experiments using 125I-IL-1α to type I IL-1R present on EL4 thymoma cells, 3T3 fibroblasts, hepatocytes, and Chinese hamster ovary cells expressing recombinant mouse type I IL-1R http://purl.obolibrary.org/obo/GO_0005102 GO ELISA Detects IL-1α or IL-1β protein levels using enzyme-linked immunosorbent assay. in_vitro IL-1α or IL-1β protein levels not_specified high Enzyme-linked immunosorbent assay (ELISA) to detect IL-1α or IL-1b protein http://purl.obolibrary.org/obo/GO_0001817 GO IL-1β neutralization assay Measures the ability of a reagent to neutralize the bioactivity of human IL-1β on primary human fibroblasts. in_vitro primary human fibroblasts human neutralization of IL-1β bioactivity decrease low Measure the ability of the reagent to neutralize the bioactivity of human IL-1β on primary human fibroblasts in vitro http://purl.obolibrary.org/obo/GO_0005125 GO Neutralization assay Cell-based assay to measure the ability of a test reagent to neutralize the bioactivity of human IL-1β on primary human fibroblasts in vitro. in_vitro primary human fibroblasts human IL-1β bioactivity decrease http://purl.obolibrary.org/obo/GO_0014070 GO http://purl.obolibrary.org/obo/CL_0000134 CL not_specified Measure the ability of the reagent to neutralize the bioactivity of human IL-1β on primary human fibroblasts in vitro http://purl.obolibrary.org/obo/GO_0014070 GO Real-time PCR Measures IL-1α or IL-1β mRNA levels using real-time polymerase chain reaction. in_vitro IL-1α or IL-1β mRNA levels not_specified medium Real time polymerase chain reaction to measure IL-1α or IL-1β mRNA http://purl.obolibrary.org/obo/GO_0010467 GO CFSE proliferation assay Measures T cell proliferation by tracking the dilution of CFSE dye in dividing cells. in_vitro T cells T cell proliferation decrease http://purl.obolibrary.org/obo/GO_0042102 GO http://purl.obolibrary.org/obo/CHEBI_51085 CHEBI medium T cell proliferation by incorporation of the analysis of CFSE labeled T cells http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042102 GO ELISA Measures IL-2 production as an indicator of T cell activation. in_vitro T cells IL-2 production decrease http://purl.obolibrary.org/obo/GO_0042110 GO medium T cell activation can be evaluated by measuring IL-2 production by ELISA http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042110 GO Thymidine incorporation T cell proliferation is measured by [3H]thymidine incorporation, a method that quantifies DNA synthesis during cell division. in_vitro T cells DNA synthesis increase http://purl.obolibrary.org/obo/GO_0006264 GO low T cell activation can be evaluated by T cell proliferation by incorporation of ... [3H]thymidine incorporation. http://purl.obolibrary.org/obo/CHEBI_50678 CHEBI http://purl.obolibrary.org/obo/GO_0007049 GO Thymidine incorporation assay Measures T cell proliferation by quantifying the incorporation of radioactive thymidine into newly synthesized DNA. in_vitro T cells T cell proliferation decrease http://purl.obolibrary.org/obo/GO_0042102 GO http://purl.obolibrary.org/obo/CHEBI_17748 CHEBI medium T cell proliferation by [...] [3H]thymidine incorporation http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042102 GO blood pressure measurement via pressure transducer Blood pressure is measured in rats using a pressure transducer connected to polyethylene tubing, with mean arterial pressure calculated from the analogue signal. in_vivo vasculature Rattus norvegicus blood pressure change low blood pressure and pulse rate measurements in rats have been collected using a pressure transducer (Utah Medical, Midvale UT) connected to polyethylene tubing. The mean arterial pressure was calculated from the analogue signal http://purl.obolibrary.org/obo/UBERON_0000468 UBERON http://purl.obolibrary.org/obo/GO_0008217 GO direct observation of embryonic heartbeats Heart rate in fish embryos is measured by direct observation of heartbeats under a dissecting microscope over a 30-second time interval. in_vivo heart fish heart rate change http://purl.obolibrary.org/obo/UBERON_0000922 UBERON medium One study measured heart beats in embryos by direct observation of heartbeats observed under a dissecting microscope over 30 second time intervals http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO ECG and blood pressure measurement in fish Heart rate and blood pressure in adult fish are measured using implanted electrodes for ECG and an indwelling dorsal aortic cannula connected to a pressure transducer. in_vivo heart vasculature fish heart rate and blood pressure change low Coated 30 gauge copper wire electrodes were implanted to collect electrocardiography (ECG) and heart rate (HR) measurements. Blood pressure was monitored with an indwelling dorsal aortic cannula that was filled with heparinized saline and attached to a pressure transducer http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO ECG recording ECG recordings are collected in human patient cohort studies in medical settings. in_vivo heart Homo sapiens electrical activity of the heart change medium In human patient cohort studies, cardiovascular status is determined from various measurements collected in medical settings: pulse rate, blood pressure and ECG recordings (Peter, Karki). http://purl.obolibrary.org/obo/CL_0000265 CL http://purl.obolibrary.org/obo/GO_0007687 GO ECG recording Electrocardiography (ECG) recordings measure electrical activity of the heart to assess cardiovascular status in human patients. in_vivo heart Homo sapiens heart rate and rhythm change low cardiovascular status is determined from various measurements collected in medical settings: pulse rate, blood pressure and ECG recordings http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO fish embryo heart rate observation Measures heart beats in fish embryos by direct observation of heartbeats under a dissecting microscope over 30 second time intervals. in_vivo heart fish heart beats change http://purl.obolibrary.org/obo/GO_0008015 GO http://purl.obolibrary.org/obo/UBERON_0000006 UBERON low One study measured heart beats in embryos by direct observation of heartbeats observed under a dissecting microscope over 30 second time intervals (Steele, 2009) http://purl.obolibrary.org/obo/UBERON_0000006 UBERON http://purl.obolibrary.org/obo/GO_0008015 GO human cardiovascular monitoring Determines cardiovascular status in human patient cohort studies by collecting pulse rate, blood pressure and ECG recordings in medical settings. in_vivo cardiovascular system heart human pulse rate, blood pressure and ECG recordings change http://purl.obolibrary.org/obo/GO_0008015 GO http://purl.obolibrary.org/obo/GO_0003012 GO low In human patient cohort studies, cardiovascular status is determined from various measurements collected in medical settings: pulse rate, blood pressure and ECG recordings (Peter, Karki). http://purl.obolibrary.org/obo/GO_0003012 GO indwelling dorsal aortic cannula Monitoring blood pressure in adult fish using an indwelling dorsal aortic cannula attached to a pressure transducer. in_vivo dorsal aorta fish blood pressure not_specified http://purl.obolibrary.org/obo/NCIT_C15417 NCIT not_specified Blood pressure was monitored with an indwelling dorsal aortic cannula that was filled with heparinized saline and attached to a pressure transducer http://purl.obolibrary.org/obo/CHEBI_16351 CHEBI http://purl.obolibrary.org/obo/GO_0007507 GO Pressure transducer blood pressure and pulse rate measurement Measures arterial blood pressure and derived pulse rate in rats using a pressure transducer connected to polyethylene tubing; pulse rate is calculated from peak systolic BP and mean arterial pressure from the analogue signal. in_vivo aorta arterial system Rattus norvegicus blood pressure (mmHg) and pulse rate (beats per minute) change http://purl.obolibrary.org/obo/GO_0002029 GO http://purl.obolibrary.org/obo/GO_0002027 GO medium In experimental settings, blood pressure and pulse rate measurements in rats have been collected using a pressure transducer (Utah Medical, Midvale UT) connected to polyethylene tubing. Pulse rate was calculated using peak systolic blood pressure of the arterial pressure tracing as the marker for a single heartbeat. The mean arterial pressure was calculated from the analogue signal (Gaspari, 2007). http://purl.obolibrary.org/obo/UBERON_0001942 UBERON http://purl.obolibrary.org/obo/GO_0002029 GO pulse rate measurement Measurement of pulse rate in human patient cohort studies collected in medical settings. in_vivo cardiovascular system Homo sapiens pulse rate change medium In human patient cohort studies, cardiovascular status is determined from various measurements collected in medical settings: pulse rate, blood pressure and ECG recordings (Peter, Karki). http://purl.obolibrary.org/obo/UBERON_0000957 UBERON http://purl.obolibrary.org/obo/GO_0008524 GO Respirometer-metabolism chamber Fish are placed in respirometer-metabolism chambers to measure cardiovascular dynamics, including heart rate and blood pressure. in_vivo heart blood vessels fish heart rate, blood pressure change http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/UBERON_0001626 UBERON http://purl.obolibrary.org/obo/GO_0007615 GO http://purl.obolibrary.org/obo/GO_0008214 GO low Collection of heart rate and vascular measurements in fish can require that the fish is hooked up to special respirometer-metabolism chambers (McKim, 1982). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0007615 GO ELISA Measures cytokine levels in cell supernatants as a marker of TLR7/8 activation. in_vitro human PBMC pDC-enriched cells mDCs human cytokine levels increase http://purl.obolibrary.org/obo/CHEBI_50830 CHEBI http://purl.obolibrary.org/obo/CHEBI_17026 CHEBI medium IFN-α in cell-free supernatants collected after stimulation of human PBMC and/or pDC-enriched cells by imidazoquinoline derivatives is detected by ELISA (Gibson et al. 2002). TNF-α and IL-6 in cell-free supernatants collected after stimulation of mDCs by RNA-LL37 are measured by ELISA (Ganguly et al. 2009). http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0050670 GO ELISA for IFN-α Quantification of IFN-α levels in cell-free supernatants using Enzyme-Linked Immunosorbent Assay. in_vitro human PBMC pDC-enriched cells human IFN-α levels not_specified medium IFN-α in cell-free supernatants collected after stimulation of human PBMC and/or pDC-enriched cells by imidazoquinoline derivatives is detected by ELISA (Gibson et al. 2002). http://purl.obolibrary.org/obo/CHEBI_40546 CHEBI http://purl.obolibrary.org/obo/GO_0051025 GO ELISA for TNF-α and IL-6 Quantification of TNF-α and IL-6 cytokine levels in cell-free supernatants using Enzyme-Linked Immunosorbent Assay. in_vitro mDCs TNF-α and IL-6 levels not_specified http://purl.obolibrary.org/obo/CHEBI_40514 CHEBI medium TNF-α and IL-6 in cell-free supernatants collected after stimulation of mDCs by RNA-LL37 are measured by ELISA (Ganguly et al. 2009). http://purl.obolibrary.org/obo/GO_0051025 GO NF-κB-luciferase reporter gene assay Measures transcriptional activation of TLR7/8 by quantifying luciferase activity in cells co-transfected with human TLR7/8 and an NF-κB-luciferase reporter. in_vitro HEK293 cells human luciferase activity increase http://purl.obolibrary.org/obo/GO_0006355 GO medium Measurement of transcriptional activation of human TLR and NF-κB-luciferase co-transfected cells HEK293 cells were transiently co-transfected with human TLR7 and a NF-κB-luciferase reporter. Luciferase activity was measured 48h post-stimulation and the results are reported as fold-increase in luciferase production relative to medium control (Gibson et al. 2002). http://purl.obolibrary.org/obo/GO_0006355 GO Reporter gene assay Measures TLR7/8 activation via luciferase activity in transfected cells. in_vitro HEK293 cells human luciferase activity increase http://purl.obolibrary.org/obo/GO_0051092 GO medium HEK293 cells were transiently co-transfected with human TLR7 and a NF-κB-luciferase reporter. The cells were incubated for 48 hours following transfection and then stimulated with various concentrations of resiquimod or imiquimod. Luciferase activity was measured 48h post-stimulation and the results are reported as fold-increase in luciferase production relative to medium control (Gibson et al. 2002). resiquimod (0.001-10 µg/mL) induced NF-κB activation in HEK293 cells transfected with human TLR7 or human TLR8 and a NF-κB-luciferase reporter is detected in the same manner (Jurk et al. 2002). http://purl.obolibrary.org/obo/PR_000001706 PR http://purl.obolibrary.org/obo/GO_0003700 GO ELISA Detects IL-23 protein levels in cell-free supernatants from R848-stimulated moDCs. in_vitro moDCs IL-23 protein levels increase http://purl.obolibrary.org/obo/PR_000000001 PR medium IL-23 in cell-free supernatants collected after R848 stimulation to moDCs is detected by ELISA (Schwarz et al. 2013). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0001817 GO qRT-PCR Measures IL-23 mRNA expression levels in R848-stimulated moDCs. in_vitro moDCs IL-23 mRNA levels increase http://purl.obolibrary.org/obo/OBI_0000665 OBI medium Expression of IL-23 mRNA in R848-stimulated moDCs is measured by qRT-PCR (Schwarz et al. 2013). http://purl.obolibrary.org/obo/GO_0010467 GO ELISA Measurement of IL-17 protein levels in skin and serum samples. in_vitro skin blood human IL-17 protein levels increase http://purl.obolibrary.org/obo/GO_0032526 GO medium Measurement of IL17 protein levels (in skin and serum) http://purl.obolibrary.org/obo/GO_0032526 GO http://purl.obolibrary.org/obo/GO_0006954 GO flow cytometry Flow cytometric analysis of psoriasis skin biopsy to measure IL-17 + and IL-22 + CD4 + T cells. ex_vivo CD4+ T cells skin frequency of IL-17 +, IL-22 +, CCR6 +, and CCR4 + T cells increase http://purl.obolibrary.org/obo/OBI_0000269 OBI http://purl.obolibrary.org/obo/CL_0000624 CL http://purl.obolibrary.org/obo/PR_000008958 PR http://purl.obolibrary.org/obo/PR_000001490 PR medium Flow cytometric analysis of psoriasis skin biopsy showed increased IL-17 + and IL-22 + CD4 + T cells http://purl.obolibrary.org/obo/CL_0000624 CL http://purl.obolibrary.org/obo/GO_0006955 GO IL17 protein measurement Measurement of IL17 protein levels in skin and serum. not_specified skin serum IL17 protein levels increase http://purl.obolibrary.org/obo/PR_000008958 PR http://purl.obolibrary.org/obo/UBERON_0002097 UBERON http://purl.obolibrary.org/obo/UBERON_0001967 UBERON not_specified Measurement of IL17 protein levels (in skin and serum) http://purl.obolibrary.org/obo/PR_000008958 PR http://purl.obolibrary.org/obo/GO_0006954 GO Protein quantification Measurement of IL-17 protein levels in skin and serum samples. not_specified skin serum IL17 protein levels increase http://purl.obolibrary.org/obo/GO_0006613 GO not_specified Measurement of IL17 protein levels (in skin and serum) http://purl.obolibrary.org/obo/GO_0006613 GO http://purl.obolibrary.org/obo/GO_0006954 GO Amyloid A deposition staining Visualization of Amyloid A deposition within skin tissue sections. ex_vivo skin human amyloid deposition increase low Amyloid A deposition was observed in the skin-stained area of the psoriasis lesion skin area http://purl.obolibrary.org/obo/CHEBI_37313 CHEBI DNA microarray analysis Analyzes gene expression patterns in skin lesions. in_vitro skin human gene expression levels change http://purl.obolibrary.org/obo/OBI_0000697 OBI http://purl.obolibrary.org/obo/OBI_0000379 OBI high DNA microarray analysis in lesions of psoriasis patients ... SAA levels are about 5 times higher than in normal skin. http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO DNA microarray analysis DNA microarray analysis to quantify SAA levels in skin lesions. ex_vivo skin human SAA levels increase http://purl.obolibrary.org/obo/CHEBI_37313 CHEBI high DNA microarray analysis in lesions of psoriasis patients ... SAA levels are about 5 times higher than in normal skin. http://purl.obolibrary.org/obo/CHEBI_37313 CHEBI ELISA Serum amyloid A (SAA) levels were measured in the serum of psoriasis patients and healthy controls using ELISA. in_vivo skin human SAA levels increase medium Serum amyloid A: SAA measurement ... measured in 35 psoriasis patients and healthy humans SAA levels are about 5 times higher than in normal skin. The average SAA of psoriasis patients was 19.1 ug / ml, and the average SAA after treatment was 6.9 ug / ml. http://purl.obolibrary.org/obo/CHEBI_59852 CHEBI http://purl.obolibrary.org/obo/GO_0006956 GO Immunohistochemistry Detects the transcription factor C/EBPβ expression in skin sections. ex_vivo skin human expression pattern of transcription factor C/EBPβ change low The transcription factor C / EBPβ, which is normally expressed only in the granular layer of the normal epidermis, was expressed in the entire epidermis in the same manner as the lesion. http://purl.obolibrary.org/obo/GO_0006351 GO Immunohistochemistry Uses primary antibodies to detect dendritic cell and lymphocyte surface markers in skin sections. ex_vivo skin human number of activated dendritic cells and T lymphocytes increase http://purl.obolibrary.org/obo/CL_0000451 CL http://purl.obolibrary.org/obo/CL_0000084 CL low The dendritic cell surface marker and lymphocyte surface marker of the section were used as the primary antibody. In the vicinity of psoriasis lesions, an increased number of activated dendritic cells was observed, with CD1a-positive Langerhans cells in the epidermis and CD83-positive CD1a-negative Langerin-negative CD11c-positive dermal dendritic cells at the epidermal border. There were significantly fewer CD3-positive T lymphocytes than lesions in normal skin. http://purl.obolibrary.org/obo/CL_0000451 CL http://purl.obolibrary.org/obo/GO_0006955 GO Immunohistochemistry Detects inflammatory keratin K6 and K16 positive keratinocytes in skin sections. ex_vivo skin human presence of inflammatory keratin K6 and K16 positive keratinocytes change http://purl.obolibrary.org/obo/CL_0000312 CL low Inflammatory keratin K6 and K16 positive keratinocytes were found in the normal part. http://purl.obolibrary.org/obo/CL_0000312 CL http://purl.obolibrary.org/obo/GO_0031424 GO immunohistochemistry (dendritic and lymphocyte markers) Immunohistochemical staining of skin biopsy sections using primary antibodies against dendritic cell and lymphocyte surface markers to identify specific cell populations. ex_vivo Langerhans cells dermal dendritic cells T lymphocytes keratinocytes skin human presence and number of specific cell types change http://purl.obolibrary.org/obo/CL_0000622 CL http://purl.obolibrary.org/obo/CL_0000170 CL http://purl.obolibrary.org/obo/CL_0000039 CL low The dendritic cell surface marker and lymphocyte surface marker of the section were used as the primary antibody. In the vicinity of psoriasis lesions, an increased number of activated dendritic cells was observed, with CD1a-positive Langerhans cells in the epidermis and CD83-positive CD1a-negative Langerin-negative CD11c-positive dermal dendritic cells at the epidermal border. There were significantly fewer CD3-positive T lymphocytes than lesions in normal skin. Inflammatory keratin K6 and K16 positive keratinocytes were found in the normal part. http://purl.obolibrary.org/obo/CL_0000622 CL http://purl.obolibrary.org/obo/GO_0006554 GO Serum amyloid A measurement Measures serum amyloid A (SAA) levels in blood serum. in_vitro human serum amyloid A levels increase medium Serum amyloid A: SAA measurement ... measured in 35 psoriasis patients and healthy humans SAA levels are about 5 times higher than in normal skin. The average SAA of psoriasis patients was 19.1 ug / ml, and the average SAA after treatment was 6.9 ug / ml. http://purl.obolibrary.org/obo/GO_0006953 GO competitive radiometric binding assay by chemiluminescence Measures the binding affinities of compounds (e.g., PPT) for estrogen receptor alpha (ERα) using chemiluminescence detection. in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/GO_0030520 GO http://purl.obolibrary.org/obo/OBI_0000275 OBI medium the binding affinities of PPT for ERα was determined by competitive radiometric binding assays by chemiluminescence http://purl.obolibrary.org/obo/PR_P20790 PR http://purl.obolibrary.org/obo/GO_0030521 GO radio receptor assay Measures the binding affinities of compounds (e.g., E2, BPA) for estrogen receptor alpha (ERα). in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/GO_0030520 GO http://purl.obolibrary.org/obo/OBI_0002671 OBI OECD TG455 medium The binding affinities of E2 and BPA for ERα can be confirmed by radio receptor assay http://purl.obolibrary.org/obo/PR_P20790 PR http://purl.obolibrary.org/obo/GO_0030521 GO size exclusion chromatography Measures dimer dissociation of ERα. in_vitro dimer dissociation not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI http://purl.obolibrary.org/obo/GO_0046983 GO medium its dimer dissociation is measured using size exclusion chromatography http://purl.obolibrary.org/obo/GO_0046983 GO Real-time PCR Detects GATA3 mRNA expression levels in CD4 T cells using reverse transcription followed by quantitative PCR. in_vitro CD4 T cells GATA3 mRNA expression increase http://purl.obolibrary.org/obo/OBI_0000662 OBI medium GATA3 mRNA in CD4 T cells can be detected by Real-time PCR (RT-PCR) http://purl.obolibrary.org/obo/PR_000007888 PR http://purl.obolibrary.org/obo/GO_0006351 GO CBA Cytometric bead array kits to determine the levels of IL-4 in cell supernatants. in_vitro IL-4 protein levels increase http://purl.obolibrary.org/obo/PR_000001120 PR medium The levels of IL-4 in the cell supernatants were determined by ... cytometric bead array (CBA) kits http://purl.obolibrary.org/obo/PR_000001120 PR http://purl.obolibrary.org/obo/GO_0001817 GO ELISA A sandwich enzyme-linked immunosorbent assay to determine the levels of IL-4 in cell supernatants. in_vitro IL-4 protein levels increase http://purl.obolibrary.org/obo/PR_000001120 PR medium The levels of IL-4 in the cell supernatants were determined by a sandwich enzyme-linked immunosorbent assay (ELISA) http://purl.obolibrary.org/obo/PR_000001120 PR http://purl.obolibrary.org/obo/GO_0001817 GO immunoblot analysis Immunoblot analysis to determine the levels of IL-4 in cell supernatants. in_vitro IL-4 protein levels increase http://purl.obolibrary.org/obo/PR_000001120 PR low The levels of IL-4 in the cell supernatants were determined by ... immunoblot analysis http://purl.obolibrary.org/obo/PR_000001120 PR http://purl.obolibrary.org/obo/GO_0001817 GO RT-PCR Reverse transcription–polymerase chain reaction to assay mRNA levels of IL-4 in cells. in_vitro IL-4 mRNA levels increase http://purl.obolibrary.org/obo/OBI_0000663 OBI medium mRNA levels of IL-4 in the cells were assayed by reverse transcription–polymerase chain reaction (RT-PCR) http://purl.obolibrary.org/obo/GO_0010467 GO [3H]-thymidine uptake Measures proliferative responses of PBMCs or B cells. in_vitro PBMCs B cells cell proliferation not_specified http://purl.obolibrary.org/obo/GO_0008283 GO medium Proliferative responses PBMCs or B cells were measured by [3H]-thymidine uptake http://purl.obolibrary.org/obo/CL_0000236 CL http://purl.obolibrary.org/obo/GO_0008283 GO ELISA Measures anti-DNA antibody levels in blood samples using dsDNA. in_vivo NZB/W F1 mice anti-DNA antibody levels increase low anti-DNA antibody was measured in ELISA using dsDNA (Yurino H. 2004). ELISA (anti-DNA) An enzyme-linked immunosorbent assay used to measure the concentration of anti-DNA antibodies in blood samples. in_vivo blood NZB/WF1 mice anti-DNA antibody levels increase not_specified blood samples were collected periodically, and anti-DNA antibody was measured in ELISA using dsDNA (Yurino H. 2004). FACS Quantifies total B cells and CD5+B cells expression in spleen and peritoneal exudates. in_vitro B cells CD5+B cells spleen peritoneal exudates B cell and CD5+B cell counts not_specified http://purl.obolibrary.org/obo/CL_0000236 CL high Fluorescence activated cell sorting (FACScan) was used for the quantitated of total B cells and CD5+B cells expression in spleen and in peritoneal exudates or B cell subset analysis (Wu WM. 2000, Peeva E. 2005). http://purl.obolibrary.org/obo/CL_0000236 CL PFC assay Examines autoantibody production by B1 cells using autologous bromelain-treated erythrocytes. in_vitro B1 cells autoantibody production not_specified low Plaque forming cell (PFC) assay using autologous bromelain-treated erythrocytes (Br-RBC) was conducted to examine the effect of EDs on autoantibody production by B1 cells (Yurino H. 2004). PFC assay Plaque forming cell (PFC) assay using autologous bromelain-treated erythrocytes (Br-RBC) is conducted to examine the effect of EDs on autoantibody production by B1 cells. in_vitro B1 cells autoantibody production by B1 cells change http://purl.obolibrary.org/obo/GO_0005104 GO http://purl.obolibrary.org/obo/CL_0000254 CL low Plaque forming cell (PFC) assay using autologous bromelain-treated erythrocytes (Br-RBC) was conducted to examine the effect of EDs on autoantibody production by B1 cells (Yurino H. 2004). http://purl.obolibrary.org/obo/GO_0005104 GO http://purl.obolibrary.org/obo/GO_0002752 GO PFC assay Measures antibody-secreting cells (plaques) formed by B1 cells using bromelain-treated erythrocytes as antigen target. in_vitro B1 cells mouse number of antibody-secreting cells (plaques) not_specified http://purl.obolibrary.org/obo/CL_0000786 CL low Plaque forming cell (PFC) assay using autologous bromelain-treated erythrocytes (Br-RBC) was conducted to examine the effect of EDs on autoantibody production by B1 cells (Yurino H. 2004). http://purl.obolibrary.org/obo/CL_0000786 CL http://purl.obolibrary.org/obo/GO_0002367 GO trypan blue exclusion test Assesses cell viability by excluding trypan blue dye. in_vitro PBMCs B cells cell viability not_specified high the cell viability was assessed by a trypan blue exclusion test (Kanda N. 1999). ACR criteria assessment Incidence of SLE was defined by American College of Rheumatology (ACR) classification criteria. not_specified human SLE incidence increase medium Incidence of SLE was defined by; 1) strict American College of Rheumatology (ACR) classification criteria (> or = 4 ACR criteria) http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0043554 GO Blood urea nitrogen measurement Measures the concentration of urea nitrogen in blood as an indicator of kidney function. in_vivo blood Mus musculus blood urea nitrogen increase medium mice can monitor by proteinuria levels, body weights, blood urea nitrogen http://purl.obolibrary.org/obo/UBERON_0002113 UBERON Body weight measurement Monitors changes in body weight as an indicator of disease progression. in_vivo Mus musculus body weight change http://purl.obolibrary.org/obo/VT_0001259 VT high mice can monitor by proteinuria levels, body weights http://purl.obolibrary.org/obo/UBERON_0000468 UBERON Hematoxylin Eosin staining Assesses histological alterations in the kidney by staining tissue sections to visualize cellular and structural details. in_vivo kidney Mus musculus histological alterations not_specified http://purl.obolibrary.org/obo/UBERON_0002113 UBERON low Histological alterations in the kidney were assessed by Hematoxylin Eosin (H&E) and Periodic acid-Schiff (PAS) staining http://purl.obolibrary.org/obo/UBERON_0002113 UBERON Immunohistochemistry for IgG and C3 Detects the expression and deposition of IgG and C3 in kidney tissue sections using antibody-based staining. in_vivo kidney Mus musculus IgG and C3 deposition increase http://purl.obolibrary.org/obo/PR_000001565 PR http://purl.obolibrary.org/obo/PR_000001010 PR http://purl.obolibrary.org/obo/UBERON_0002113 UBERON low expression of IgG and C3 was detected by immunohistochemistry http://purl.obolibrary.org/obo/PR_000001565 PR Periodic acid-Schiff staining Assesses histological alterations in the kidney by staining tissue sections to visualize carbohydrates and extracellular matrix components. in_vivo kidney Mus musculus histological alterations not_specified http://purl.obolibrary.org/obo/UBERON_0002113 UBERON low Histological alterations in the kidney were assessed by Hematoxylin Eosin (H&E) and Periodic acid-Schiff (PAS) staining http://purl.obolibrary.org/obo/UBERON_0002113 UBERON Proteinuria measurement Monitors the levels of protein in urine as an indicator of kidney dysfunction. in_vivo kidney Mus musculus proteinuria levels increase http://purl.obolibrary.org/obo/HP_0000093 HP http://purl.obolibrary.org/obo/UBERON_0002113 UBERON medium mice can monitor by proteinuria levels http://purl.obolibrary.org/obo/UBERON_0002113 UBERON Caliper Mobility Shift Assay This assay measures the enzymatic activities of JAK1, JAK2, JAK3, and TYK2 kinases. It determines the IC50 values of inhibitors against these kinases in the presence of ATP at Km concentration. in_vitro JAK kinase activity decrease http://purl.obolibrary.org/obo/GO_0016336 GO medium Enzymatic activities against JAK1, JAK2, JAK3, and TYK2 were examined using a Caliper Mobility Shift Assay. RB1 inhibited JAK3 kinase activity with an IC50 value of 40 nM without inhibiting JAK1, JAK2, or TYK2 (IC50 > 5000 nM) The PF-06651600 JAK3 inhibitor displays potent inhibitory activity with an IC50 of 33.1 nM (IC50>10 000 nM), with no activity against JAK1, JAK2, and TYK2. http://purl.obolibrary.org/obo/CHEBI_59834 CHEBI http://purl.obolibrary.org/obo/GO_0006468 GO Caliper Mobility Shift Assay This assay measures the enzymatic activities of JAK1, JAK2, JAK3, and TYK2 by examining their kinase activities in the presence of ATP. in_vitro kinase activity decrease http://purl.obolibrary.org/obo/GO_0016301 GO medium Enzymatic activities against JAK1, JAK2, JAK3, and TYK2 were examined using a Caliper Mobility Shift Assay. http://purl.obolibrary.org/obo/PR_000008952 PR http://purl.obolibrary.org/obo/GO_0006468 GO Caliper Mobility Shift Assay An enzymatic assay used to examine the kinase activities of JAK isoforms by measuring mobility shifts in the presence of ATP. in_vitro kinase activity (IC50) decrease http://purl.obolibrary.org/obo/GO_0003674 GO not_specified Enzymatic activities against JAK1, JAK2, JAK3, and TYK2 were examined using a Caliper Mobility Shift Assay. RB1 inhibited JAK3 kinase activity with an IC50 value of 40 nM without inhibiting JAK1, JAK2, or TYK2 (IC50 > 5000 nM) http://purl.obolibrary.org/obo/GO_0003674 GO Cell-based Phosphorylation Assay The PF-06651600 JAK3 inhibitor displays potent inhibitory activity with an IC50 of 33.1 nM (IC50>10 000 nM), with no activity against JAK1, JAK2, and TYK2. PF-06651600 inhibits the phosphorylation of STAT5 elicited by IL-2, IL-4, IL-7, and IL-15 with an IC50 of 244, 340, 407, and 266 nM, respectively. in_vitro STAT5 phosphorylation inhibition decrease http://purl.obolibrary.org/obo/GO_0070748 GO http://purl.obolibrary.org/obo/GO_0007165 GO http://purl.obolibrary.org/obo/GO_0008152 GO Cell-based phosphorylation assay protocol not_specified The PF-06651600 JAK3 inhibitor displays potent inhibitory activity with an IC50 of 33.1 nM (IC50>10 000 nM), with no activity against JAK1, JAK2, and TYK2. PF-06651600 inhibits the phosphorylation of STAT5 elicited by IL-2, IL-4, IL-7, and IL-15 with an IC50 of 244, 340, 407, and 266 nM, respectively (Telliez, et al. 2016) http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0007165 GO STAT5 phosphorylation inhibition assay This assay measures the inhibition of STAT5 phosphorylation induced by IL-2, IL-4, IL-7, and IL-15. in_vitro STAT5 phosphorylation decrease http://purl.obolibrary.org/obo/GO_0006468 GO medium PF-06651600 inhibits the phosphorylation of STAT5 elicited by IL-2, IL-4, IL-7, and IL-15 with an IC50 of 244, 340, 407, and 266 nM, respectively http://purl.obolibrary.org/obo/PR_000015951 PR http://purl.obolibrary.org/obo/GO_0006468 GO cell survival assay This assay measures the survival of chronic myelogenous leukemia cells after treatment with pimozide. in_vitro chronic myelogenous leukemia cells cell survival decrease http://purl.obolibrary.org/obo/GO_0008274 GO low Pimozide decreased the survival of chronic myelogenous leukemia cells resistant to kinase inhibitors http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0008274 GO flow cytometry Measures phosphorylated STAT5 expression in T lymphocytes using specific antibodies and reports mean fluorescence intensities (MFIs) for each subset. in_vitro T lymphocytes phosphorylated STAT5 expression not_specified medium Phosphorylation of STAT5 tyrosine can be detected by specific antibodies using several detection systems, including flow cytometry. In one study, phosphorylated STAT5 expression was measured in T lymphocytes, and MFIs were reported for each subset http://purl.obolibrary.org/obo/PR_000013783 PR http://purl.obolibrary.org/obo/GO_0006468 GO immunoprecipitation and immunoblotting Analyzes tyrosine phosphorylation of STAT5 induced by IL-2 using an anti-STAT5 antibody, followed by immunoblotting. in_vitro peripheral blood lymphocytes STAT5 tyrosine phosphorylation not_specified http://purl.obolibrary.org/obo/OBI_0000697 OBI low Tyrosine phosphorylation of STAT5 induced by IL-2 has been analyzed using an anti-STAT5 antibody. In the study, this antibody immunoprecipitated STAT5 (p94 kDa). Peripheral blood lymphocytes were untreated (control) or treated with IL-2, IL-4, or IL-15 for 15 min. The extracts were incubated with biotinylated oligonucleotide bound to streptavidin-coated agarose. The agarose beads were washed and the eluted protein was immunoblotted with an antibody to STAT5 http://purl.obolibrary.org/obo/PR_000013783 PR http://purl.obolibrary.org/obo/GO_0006468 GO JAK3 kinase activity assay Measures the inhibition of JAK3 kinase activity and subsequent inhibition of STAT5 phosphorylation induced by various interleukins using IC50 values. in_vitro JAK3 kinase activity decrease http://purl.obolibrary.org/obo/OBI_0000466 OBI medium Other authors described the inhibition of JAK3 kinase activity by PF-06651600, followed by inhibition of the phosphorylation of STAT5 elicited by IL-2, IL-4, IL-7, and IL-15 with IC50 values of 244, 340, 407, and 266 nM, respectively http://purl.obolibrary.org/obo/PR_000001004 PR http://purl.obolibrary.org/obo/GO_0004672 GO SH2 domain binding assay Measures the binding activity of a nicotinoyl hydrazone compound to the SH2 domain of STAT5 using IC50 values. in_vitro STAT5b SH2 domain EPO peptide binding activity decrease http://purl.obolibrary.org/obo/OBI_0000466 OBI medium A cell-permeable non-peptidic nicotinoyl hydrazone compound selectively targets the SH2 domain of STAT5 (IC50 = 47 µM against STAT5b SH2 domain EPO peptide binding activity), with markedly less recognition of the SH2 domain of STAT1, STAT3, or Lck (IC50 >500 µM). http://purl.obolibrary.org/obo/GO_0005515 GO STAT5 phosphorylation inhibition assay Measures the inhibition of STAT5 phosphorylation using specific inhibitors like pimozide and reports the decrease in phosphorylation levels. in_vitro chronic myelogenous leukemia cells PBMCs STAT5 phosphorylation decrease medium Pimozide is a specific inhibitor of STAT5 phosphorylation. Pimozide decreased the survival of chronic myelogenous leukemia cells resistant to kinase inhibitors. IL-2 markedly stimulated STAT5 phosphorylation in PBMCs from patients with chronic kidney disease (CKD). Pretreatment with pimozide (3 µM) dramatically suppressed IL-2-induced STAT5 phosphorylation, indicating that it is a potent blocker of IL-2-stimulated STAT5 phosphorylation in PBMCs from CKD patients. http://purl.obolibrary.org/obo/PR_000013783 PR http://purl.obolibrary.org/obo/GO_0006468 GO western blot Tyrosine phosphorylation of STAT5 induced by IL-2 is analyzed using an anti-STAT5 antibody and immunoblotting. in_vitro Peripheral blood lymphocytes STAT5 tyrosine phosphorylation increase low Tyrosine phosphorylation of STAT5 induced by IL-2 has been analyzed using an anti-STAT5 antibody. The extracts were incubated with biotinylated oligonucleotide bound to streptavidin-coated agarose. The agarose beads were washed and the eluted protein was immunoblotted with an antibody to STAT5 http://purl.obolibrary.org/obo/GO_0006468 GO EMSA EMSA (Electrophoresis Mobility Shift Assay) uses nuclear extracts and specific oligonucleotides to evaluate DNA binding activity, specifically of transcription factors like STAT5 to cytokine gene promoters. in_vitro YT cells Daudi cells splenocytes DNA binding activity decrease low EMSA using nuclear extracts and specific oligonucleotides, including transcription factor binding sites, such as cytokine-inducible SH2-containing protein (CIS) gene promoters, are useful to evaluate DNA binding activity Activated STAT5 binds to specific DNA-probes in splenocytes EMSA was performed using glycerol-containing 5% polyacrylamide gels (29:1) containing 0.5× Tris-borate-EDTA buffer. http://purl.obolibrary.org/obo/CHEBI_30753 CHEBI http://purl.obolibrary.org/obo/GO_0003676 GO EMSA Electrophoretic Mobility Shift Assay (EMSA) measures the DNA binding activity of transcription factors, such as STAT5, using nuclear extracts and specific oligonucleotides containing transcription factor binding sites. in_vitro splenocytes Daudi cells YT cells STAT5 DNA binding activity decrease http://purl.obolibrary.org/obo/GO_0003677 GO http://purl.obolibrary.org/obo/PR_000014163 PR low EMSA using nuclear extracts and specific oligonucleotides, including transcription factor binding sites, such as cytokine-inducible SH2-containing protein (CIS) gene promoters, are useful to evaluate DNA binding activity Nuclear extracts were prepared from untreated YT cells or cells treated with recombinant IL-2 (2 nM) for 30 min at 37°C. EMSA was performed using glycerol-containing 5% polyacrylamide gels (29:1) containing 0.5× Tris-borate-EDTA buffer. http://purl.obolibrary.org/obo/PR_000014163 PR http://purl.obolibrary.org/obo/GO_0003677 GO STAT5 tyrosine phosphorylation assay This assay measures the tyrosine phosphorylation status of STAT5 in cells, often using cell-permeable inhibitors to assess the impact on STAT5 activation. in_vitro Daudi cells STAT5 tyrosine phosphorylation decrease http://purl.obolibrary.org/obo/GO_0021774 GO http://purl.obolibrary.org/obo/PR_000014163 PR medium A cell-permeable non-peptidic nicotinoyl hydrazone compound inhibited IFN-α-stimulated STAT5 tyrosine phosphorylation in Daudi cells, but not STAT1 or STAT3 http://purl.obolibrary.org/obo/PR_000014163 PR http://purl.obolibrary.org/obo/GO_0021774 GO tyrosine phosphorylation assay Measurement of the phosphorylation state of STAT5 tyrosine residues in response to stimulation. in_vitro Daudi cells STAT5 tyrosine phosphorylation decrease http://purl.obolibrary.org/obo/GO_0006468 GO not_specified inhibited IFN-α-stimulated STAT5 tyrosine phosphorylation in Daudi cells http://purl.obolibrary.org/obo/GO_0006468 GO ELISA Measures the levels of IL-4 production in supernatants from stimulated CD4+ T cells using antibody pairs and enzymatic detection. in_vitro CD4+ T cells IL-4 protein levels decrease http://purl.obolibrary.org/obo/PR_000001020 PR medium Supernatants were collected and the levels of IL-4 production were measured by ELISA http://purl.obolibrary.org/obo/PR_000001020 PR http://purl.obolibrary.org/obo/GO_0001816 GO flow cytometry Measures cytosolic IL-4 content in stimulated cells using intracellular staining and flow cytometry analysis. in_vitro CD4+ T cells cytosolic IL-4 content decrease http://purl.obolibrary.org/obo/PR_000001020 PR http://purl.obolibrary.org/obo/OBI_0000268 OBI high flow cytometry analysis involving intracellular staining was used to measure cytosolic IL-4 content in stimulated cells http://purl.obolibrary.org/obo/PR_000001020 PR http://purl.obolibrary.org/obo/GO_0050707 GO real-time PCR Measures IL-4 mRNA expression levels in stimulated CD4+ T cells using reverse transcription and quantitative PCR. in_vitro CD4+ T cells IL-4 mRNA expression decrease medium IL-4 mRNA expression was measured by real-time PCR http://purl.obolibrary.org/obo/GO_0010467 GO 3H-thymidine incorporation assay Measures CD4+ T cell proliferation in vitro by quantifying 3H-thymidine incorporation. in_vitro CD4+ T cells PBMCs 3H-thymidine incorporation not_specified http://purl.obolibrary.org/obo/OBI_0000695 OBI http://purl.obolibrary.org/obo/GO_0042098 GO medium To assess keyhole limpet hemocyanin (KLH) antigen-specific T cell proliferation, 1 × 10^5 CD4+ T cells were co-cultured with 2 × 10^5 autologous PBMCs in 96-well plates in the presence of KLH. Cells were cultured for 5 or 7 days before being pulsed with 0.5 μCi 3[H]-thymidine (PerkinElmer) for 18 h. The cells were harvested using a 96-well cell FilterMate harvester. 3[H]-thymidine incorporation in CD4+ T cell response to biopharmaceuticals was measured by liquid scintillation counting using a TopCount NXT http://purl.obolibrary.org/obo/CL_0000788 CL http://purl.obolibrary.org/obo/GO_0042098 GO ELISA Measures anti-SRBC IgM and IgG levels in serum from cynomolgus monkeys following oral CsA administration and SRBC immunization. in_vivo serum cynomolgus monkeys anti-SRBC IgM and IgG levels change medium Serum was examined for anti-SRBC IgM and IgG levels using an ELISA specific for SRBC antigen ELISA ELISA is used to measure serum antibody levels or IgM and IgG levels in culture supernatants. It utilizes antigen-specific antibodies to quantify the amount of antibody present. in_vivo serum rat cynomolgus monkey mouse human antibody levels decrease medium TDAR can be examined in vivo and in vitro. To assess keyhole limpet hemocyanin (KLH) antigen-specific T cell proliferation, 1 × 105 CD4+ T cells were co-cultured with 2 × 105 autologous PBMCs in 96-w ell plates in the presence of KLH. http://purl.obolibrary.org/obo/GO_0005104 GO http://purl.obolibrary.org/obo/GO_0002752 GO ELISA ELISA is used to measure IgM and IgG levels in serum or culture supernatants, utilizing antigen-specific antibodies to quantify the amount of antibody present. in_vivo serum mouse IgM and IgG levels decrease medium In another study, cynomolgus monkeys received 50 mg/kg CsA twice a day via oral gavage (10 h apart) for 23 days and were immunized with SRBCs. Serum was examined for anti-SRBC IgM and IgG levels using an ELISA specific for SRBC antigen (Gaida, et al. 2015). In the final in vivo study cited here, mice were exposed to a single pharyngeal aspiration of 1,2:5,6-Dibenzanthracene, after which the supernatants of splenocytes were cultured for 24 h in the presence of lipopolysaccharide and assayed using a mouse IgM or IgG matched pairs antibody kit (Smith, et al. 2010). http://purl.obolibrary.org/obo/GO_0005104 GO http://purl.obolibrary.org/obo/GO_0002752 GO mouse IgM/IgG ELISA Measures mouse IgM or IgG levels in culture supernatants in vitro. in_vitro splenocytes spleen Mus musculus IgM or IgG levels not_specified medium the supernatants of splenocytes were cultured for 24 h in the presence of lipopolysaccharide and assayed using a mouse IgM or IgG matched pairs antibody kit http://purl.obolibrary.org/obo/PR_000000008 PR http://purl.obolibrary.org/obo/GO_0042113 GO PFC assay Measures antigen-specific plaque-forming cells in spleen cells after immunization in vivo. in_vivo spleen mouse rat antigen-specific plaque-forming splenocytes decrease http://purl.obolibrary.org/obo/CL_0000236 CL http://purl.obolibrary.org/obo/GO_0002364 GO low Other authors repeatedly administered CNIs, including FK506 and CsA, to mice orally for 4 days and immunized with sheep red blood cells (SRBCs). Spleen cells were examined using a PFC assay (Kino, et al. 1987). Antigen-specific plaque-forming splenocytes were reduced at doses of 3.2, 10, 32, and 100 mg/kg of FK506 or 32 and 100 mg/kg CsA. In another study, cynomolgus monkeys received 50 mg/kg CsA twice a day via oral gavage (10 h apart) for 23 days and were immunized with SRBCs. Serum was examined for anti-SRBC IgM and IgG levels using an ELISA specific for SRBC antigen (Gaida, et al. 2015). In the final in vivo study cited here, mice were exposed to a single pharyngeal aspiration of 1,2:5,6-Dibenzanthracene, after which the supernatants of splenocytes were cultured for 24 h in the presence of lipopolysaccharide and assayed using a mouse IgM or IgG matched pairs antibody kit (Smith, et al. 2010). http://purl.obolibrary.org/obo/CL_0000236 CL http://purl.obolibrary.org/obo/GO_0002364 GO PFC assay Measures antigen-specific plaque-forming cells in spleen cells in vivo. in_vivo spleen plaque-forming cell count decrease http://purl.obolibrary.org/obo/CL_0000988 CL low with a plaque-forming cell (PFC) assay. Spleen cells were examined using a PFC assay Antigen-specific plaque-forming splenocytes were reduced at doses of 3.2, 10, 32, and 100 mg/kg of FK506 or 32 and 100 mg/kg CsA. http://purl.obolibrary.org/obo/CL_0000235 CL http://purl.obolibrary.org/obo/GO_0002377 GO AACCI Method 22-40.01 Measures trypsin inhibitor activity in soy bean products using the standardized AACCI Method 22-40.01 protocol. not_specified Glycine max trypsin inhibitor activity change AACCI Method 22-40.01 not_specified Standard procedures for measuring TI activities in soy bean products are released as AACCI Method 22-40.01 [AACCI, 2009] http://purl.obolibrary.org/obo/GO_0006508 GO ISO 14902:2001 Measures trypsin inhibitor activity using the ISO Standard 14902:2001 protocol. not_specified Glycine max trypsin inhibitor activity change ISO 14902:2001 not_specified ISO standard for measuring TI activities is also established as Standard 14902:2001 [ISO, 2012] http://purl.obolibrary.org/obo/GO_0006508 GO trypsin inhibitor activity assay Measures the activity of trypsin inhibitors colorimetrically using a mixture of trypsin, its substrate, and sample dilutions. in_vitro trypsin inhibitor activity not_specified AACCI Method 22-40.01 medium Activity of trypsin inhibitors is measured colorimetrically using mixture of multiple dilutions of samples (TIs), trypsin and its substrate. Standard procedures for measuring TI activities in soy bean products are released as AACCI Method 22-40.01 [AACCI, 2009] and AOCS Method Ba 12-75 [AOCC, 2017]. ISO standard for measuring TI activities is also established as Standard 14902:2001 [ISO, 2012]. gel filtration chromatography Crude peptides are eluted through gel filtration chromatography and a PSTI-I-specific peak is confirmed by mass spectrometry. in_vitro pancreas rat peptide concentration increase low Synthesized crude peptides were eluted through gel filtration chromatography. PSTI-I-specific peak was confirmed by mas spectrometric measurement and analytical HPLC was performed [Graf R et al, 2003]. http://purl.obolibrary.org/obo/CHEBI_0000005 CHEBI http://purl.obolibrary.org/obo/GO_0006457 GO gel filtration chromatography Separates synthesized crude peptides based on size by eluting them through a gel filtration column, allowing fractionation and analysis of peptide populations. in_vitro peptide elution profile not_specified http://purl.obolibrary.org/obo/CHEBI_16670 CHEBI low Synthesized crude peptides were eluted through gel filtration chromatography. gel filtration chromatography This assay isolates synthesized crude peptides using gel filtration chromatography, with peaks confirmed by mass spectrometry and analytical HPLC. in_vitro PSTI-I-specific peak confirmation not_specified http://purl.obolibrary.org/obo/OBI_0000356 OBI http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/OBI_0000273 OBI low Synthesized crude peptides were eluted through gel filtration chromatography. PSTI-I-specific peak was confirmed by mas spectrometric measurement and analytical HPLC was performed [Graf R et al, 2003]. HPLC This assay measures the concentrations of MP and PSTI-II in isolated zymogen granules using HPLC. in_vivo zymogen granules Rattus norvegicus concentration of MP and PSTI-II not_specified http://purl.obolibrary.org/obo/OBI_0000273 OBI http://purl.obolibrary.org/obo/GO_0031080 GO medium In rats fed control and high protein diets, zymogen granules were isolated and concentrations of MP and PSTI-II in zymogen granules can be determined by HPLC [Tsuzuki S et al, 1991]. HPLC Concentrations of MP and PSTI-II in zymogen granules are determined by HPLC. in_vitro pancreas rat peptide concentration increase http://purl.obolibrary.org/obo/CHMO_0000083 CHMO medium In rats fed control and high protein diets, zymogen granules were isolated and concentrations of MP and PSTI-II in zymogen granules can be determined by HPLC [Tsuzuki S et al, 1991]. http://purl.obolibrary.org/obo/CHEBI_0000005 CHEBI http://purl.obolibrary.org/obo/GO_0006457 GO mass spectrometry Detects the mass-to-charge ratio of ions to confirm the presence of a specific peak corresponding to PSTI-I, thereby identifying the trypsin inhibitor protein. in_vitro mass spectrometric detection of PSTI-I not_specified http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI low PSTI-I-specific peak was confirmed by mas spectrometric measurement http://purl.obolibrary.org/obo/GO_0009306 GO reverse-phase HPLC Rat anionic trypsinogen and a pancreatic secretory trypsin inhibitor are purified from pancreatic juice by reverse-phase HPLC. in_vitro pancreas rat protein purification not_specified http://purl.obolibrary.org/obo/CHMO_0000083 CHMO low Rat anionic trypsinogen and a pancreatic secretory trypsin inhibitor were purified from the pure pancreatic juice of rats by reverse-phase HPLC [Iwai K et al, 1987]. http://purl.obolibrary.org/obo/GO_0005576 GO http://purl.obolibrary.org/obo/GO_0006457 GO reverse-phase HPLC This assay purifies rat anionic trypsinogen and pancreatic secretory trypsin inhibitor from pancreatic juice using reverse-phase HPLC. in_vivo pancreatic juice Rattus norvegicus purification of rat anionic trypsinogen and pancreatic secretory trypsin inhibitor not_specified http://purl.obolibrary.org/obo/OBI_0000273 OBI http://purl.obolibrary.org/obo/UBERON_0001900 UBERON low Rat anionic trypsinogen and a pancreatic secretory trypsin inhibitor were purified from the pure pancreatic juice of rats by reverse-phase HPLC [Iwai K et al, 1987]. amylase release assay Measures CCK concentration in plasma extracts based on their ability to stimulate amylase release from isolated rat pancreatic acini. ex_vivo pancreatic acini rat amylase release increase http://purl.obolibrary.org/obo/GO_0002674 GO low Plasma was first extracted on octadecylsilyl silica columns, and the CCK concentration was measured in the resulting extracts, based on the ability of the extracts to stimulate amylase release from isolated rat pancreatic acini [Liddle RA et al, 1984]. http://purl.obolibrary.org/obo/CL_0000198 CL http://purl.obolibrary.org/obo/GO_0002674 GO amylase release assay Measures CCK concentration by its ability to stimulate amylase release from isolated rat pancreatic acini after plasma extraction on octadecylsilyl silica columns. ex_vivo rat pancreatic acini pancreas rat CCK concentration not_specified low Plasma was first extracted on octadecylsilyl silica columns, and the CCK concentration was measured in the resulting extracts, based on the ability of the extracts to stimulate amylase release from isolated rat pancreatic acini [Liddle RA et al, 1984]. ELISA Measures CCK release from STC-1 cells after incubation with protein hydrolysates using an enzyme-linked immunosorbent assay (ELISA). in_vitro STC-1 cells mouse CCK release increase medium In order to assess the effects of protein hydrolysates on CCK release from enteroendocrine cells, each of protein hydrolysates and STC-1 cells were incubated and CCK release is measured by ELISA [Foltz M et al, 2008]. http://purl.obolibrary.org/obo/CL_0000169 CL http://purl.obolibrary.org/obo/GO_0046879 GO radioimmunoassay Measures CCK release from STC-1 cells or intestinal cell preparations using a sensitive and specific radioimmunoassay that recognizes biologically active forms of CCK. in_vitro STC-1 cells intestinal cells mouse CCK release increase medium CCK release from STC-1 cells or intestinal cell preparation were measured by sensitive and specific radioimmunoassay, which recognizes biologically active forms of CCK [Wang Y et al, 2002; Wang Y et al, 2011]. http://purl.obolibrary.org/obo/CL_0000169 CL http://purl.obolibrary.org/obo/GO_0046879 GO amylase secretion assay Measures the release of amylase from dispersed pancreatic acini as a global measure of exocrine secretion. ex_vivo pancreatic acini pancreas mice amylase release increase http://purl.obolibrary.org/obo/GO_0070488 GO low Ex vivo procedure for measuring secretion from pancreatic acini is reported [Geron E, 2014], where ex vivo culture of pancreatic acini isolated from mice is used for amylase secretion assay as a global measure http://purl.obolibrary.org/obo/CL_0000191 CL http://purl.obolibrary.org/obo/GO_0070488 GO direct imaging of pancreatic secretion Direct imaging of pancreatic secretion with subcellular resolution in ex vivo cultured pancreatic acini. ex_vivo pancreatic acini pancreas mice pancreatic secretion increase http://purl.obolibrary.org/obo/GO_0031214 GO http://purl.obolibrary.org/obo/GO_0070488 GO low ex vivo culture of pancreatic acini isolated from mice is used for amylase secretion assay as a global measure and direct imaging of pancreatic secretion with subcellular resolution http://purl.obolibrary.org/obo/CL_0000191 CL http://purl.obolibrary.org/obo/GO_0070488 GO pancreatic enzyme activity assay Measures trypsin and amylase activity in perfusate collected from the duodenum of rats after CCK injection, with trypsin activated by enterokinase and measured photometrically. in_vivo duodenum pancreas rats trypsin and amylase activity increase http://purl.obolibrary.org/obo/GO_0031214 GO low Pancreatic enzyme activities in pancreatic outlet were measured after CCA injection [Folsch UR et al, 1978]. After repeated subcutaneous injections of CCK in rats, pancreatic enzymes were collected by perfusing duodenum. trypsin in the perfusate was activated with enterokinase and its activity was measured photometrically using benzoyl arginine as substrate. Amylase activity in the perfusate was measured using Zulkovsky starch as substrate. http://purl.obolibrary.org/obo/UBERON_0001264 UBERON http://purl.obolibrary.org/obo/GO_0070488 GO pancreatic exocrine secretion measurement Measurement of pancreatic juice components (protein and enzymes) in rats with chronic pancreatitis and fistulas. in_vivo pancreas jejunum rats amounts of protein and pancreatic enzymes not_specified not_specified Pancreatic exocrine secretion was measured in rats with chronic pancreatitis and pancreatic and biliary fistulas Pancreatic juice was collected from the jejunum and the amounts of protein and pancreatic enzymes were measured. pancreatic homogenate enzyme assay Measures protein, DNA, and enzyme levels (trypsinogen, chymotrypsinogen, amylase) in pancreatic homogenates from rats, with trypsinogen and chymotrypsinogen measured after activation. in_vivo pancreas rats protein, DNA, and enzyme levels increase low In the rats fed the TI camostat, pancreatic weight and protein, DNA, and enzyme contents and trypsinogen, chymotrypsinogen, and amylase levels in the pancreatic homogenates prepared 24 hours after the last administration were measured [Goke B et al, 1986]. Levels of trypsinogen and chymotrypsinogen were measured as trypsin and chymotrypsin after activation. http://purl.obolibrary.org/obo/UBERON_0001264 UBERON http://purl.obolibrary.org/obo/GO_0070488 GO pancreatic juice collection Measures protein and pancreatic enzyme levels in pancreatic juice collected from the jejunum of rats with chronic pancreatitis and pancreatic and biliary fistulas. in_vivo pancreas jejunum rats protein and pancreatic enzyme levels increase http://purl.obolibrary.org/obo/GO_0031214 GO http://purl.obolibrary.org/obo/GO_0009306 GO low Pancreatic exocrine secretion was measured in rats with chronic pancreatitis and pancreatic and biliary fistulas [Green GM and Miyasaka K, 1983]. Pancreatic juice was collected from the jejunum and the amounts of protein and pancreatic enzymes were measured. http://purl.obolibrary.org/obo/UBERON_0001264 UBERON http://purl.obolibrary.org/obo/GO_0070488 GO photometric enzyme activity assay Photometric measurement of trypsin and amylase activity in pancreatic perfusates using benzoyl arginine and Zulkovsky starch substrates. in_vivo pancreas duodenum Rattus norvegicus trypsin and amylase activity increase http://purl.obolibrary.org/obo/GO_0008120 GO low trypsin in the perfusate was activated with enterokinase and its activity was measured photometrically using benzoyl arginine as substrate Amylase activity in the perfusate was measured using Zulkovsky starch as substrate http://purl.obolibrary.org/obo/UBERON_0001045 UBERON http://purl.obolibrary.org/obo/GO_0006638 GO trypsin activity assay This assay measures trypsin activity photometrically using benzoyl arginine as a substrate after activation with enterokinase. in_vivo duodenum rat trypsin activity increase low trypsin in the perfusate was activated with enterokinase and its activity was measured photometrically using benzoyl arginine as substrate. http://purl.obolibrary.org/obo/CHEBI_59053 CHEBI http://purl.obolibrary.org/obo/GO_0006508 GO amylase secretion assay Measures the release of amylase from dispersed pancreatic acini as a global measure of pancreatic secretion. ex_vivo pancreatic acini pancreas mouse amylase release not_specified http://purl.obolibrary.org/obo/CL_0000191 CL low Ex vivo procedure for measuring secretion from pancreatic acini is reported [Geron E, 2014], where ex vivo culture of pancreatic acini isolated from mice is used for amylase secretion assay as a global measure http://purl.obolibrary.org/obo/CL_0000191 CL http://purl.obolibrary.org/obo/GO_0046903 GO direct imaging of pancreatic secretion Direct imaging of pancreatic secretion with subcellular resolution in ex vivo cultured pancreatic acini. ex_vivo pancreatic acini pancreas mouse pancreatic secretion not_specified http://purl.obolibrary.org/obo/CL_0000191 CL low ex vivo culture of pancreatic acini isolated from mice is used for amylase secretion assay as a global measure and direct imaging of pancreatic secretion with subcellular resolution http://purl.obolibrary.org/obo/CL_0000191 CL http://purl.obolibrary.org/obo/GO_0046903 GO pancreatic content analysis Quantification of protein, DNA, amylase, and trypsin levels in pancreatic tissues or homogenates. in_vivo pancreas rats protein per weight of DNA, total level of pancreatic DNA, pancreatic levels of amylase and trypsin not_specified not_specified The concentration of protein per weight of DNA, the total level of pancreatic DNA, and the pancreatic levels of amylase and trypsin were also measured in rats after repeated CCK administration. pancreatic weight and protein, DNA, and enzyme contents and trypsinogen, chymotrypsinogen, and amylase levels in the pancreatic homogenates prepared 24 hours after the last administration were measured http://purl.obolibrary.org/obo/GO_0008283 GO Pancreatic enzyme activity assay Pancreatic enzymes (trypsin and amylase) are collected from the duodenum after perfusion and their activities are measured photometrically using specific substrates. ex_vivo pancreatic tissue pancreas rat trypsin and amylase activity increase low Pancreatic enzyme activities in pancreatic outlet were measured after CCA injection [Folsch UR et al, 1978]. pancreatic exocrine secretion assay Measures protein and pancreatic enzyme levels in pancreatic juice collected from the jejunum in rats with chronic pancreatitis and pancreatic and biliary fistulas. ex_vivo pancreatic juice rat protein and enzyme levels not_specified http://purl.obolibrary.org/obo/UBERON_0001255 UBERON http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/PR_000004748 PR not_specified Pancreatic exocrine secretion was measured in rats with chronic pancreatitis and pancreatic and biliary fistulas [Green GM and Miyasaka K, 1983]. Pancreatic juice was collected from the jejunum and the amounts of protein and pancreatic enzymes were measured. http://purl.obolibrary.org/obo/UBERON_0001255 UBERON http://purl.obolibrary.org/obo/GO_0006869 GO pancreatic exocrine secretion measurement Measures pancreatic exocrine secretion in rats with chronic pancreatitis by collecting pancreatic juice from the jejunum and analyzing protein and enzyme content. in_vivo pancreas jejunum rat pancreatic enzyme activities not_specified http://purl.obolibrary.org/obo/UBERON_0001962 UBERON low Pancreatic exocrine secretion was measured in rats with chronic pancreatitis and pancreatic and biliary fistulas [Green GM and Miyasaka K, 1983]. Pancreatic juice was collected from the jejunum and the amounts of protein and pancreatic enzymes were measured. http://purl.obolibrary.org/obo/UBERON_0001264 UBERON http://purl.obolibrary.org/obo/GO_0046903 GO trypsin activity assay Measures trypsin activity photometrically using benzoyl arginine as a substrate after activation with enterokinase. in_vivo duodenum rat trypsin activity not_specified low trypsin in the perfusate was activated with enterokinase and its activity was measured photometrically using benzoyl arginine as substrate. http://purl.obolibrary.org/obo/CHEBI_58634 CHEBI http://purl.obolibrary.org/obo/GO_0006508 GO DNA content measurement Quantifies DNA levels in the pancreas to assess acinar cell proliferation. in_vivo pancreas DNA content increase low Increased DNA content ... are indicative of acinar cell hyperplasia http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI histopathological examination Evaluates pancreatic tissue for acinar cell hyperplasia and hypertrophy through microscopic analysis. in_vivo pancreas number of mitoses per 10,000 acinar cells increase http://purl.obolibrary.org/obo/GO_0007088 GO low histopathological examination number of mitoses per 10,000 acinar cells are indicative of acinar cell hyperplasia http://purl.obolibrary.org/obo/CL_0000078 CL http://purl.obolibrary.org/obo/GO_0007088 GO mitotic index measurement Counting the number of mitoses per 10,000 acinar cells in pancreatic tissue to evaluate acinar cell proliferation and assess acinar cell hyperplasia. in_vivo pancreatic acinar cells pancreas number of mitoses per 10,000 acinar cells increase http://purl.obolibrary.org/obo/GO_0000023 GO http://purl.obolibrary.org/obo/CL_0002074 CL low Increased DNA content and number of mitoses per 10,000 acinar cells are indicative of acinar cell hyperplasia http://purl.obolibrary.org/obo/CL_0002074 CL http://purl.obolibrary.org/obo/GO_0051301 GO Pancreatic acinar cell proliferation assay Evaluation of pancreatic acinar cell proliferation using measurements of pancreatic weight, DNA and RNA levels, and histopathological examination. Parameters such as DNA content and number of mitoses per 10,000 acinar cells indicate acinar cell hyperplasia, while others suggest hypertrophy and increased protein synthesis. in_vivo pancreas not_specified DNA content, number of mitoses per 10,000 acinar cells, pancreatic weight, protein content, RNA content, protein-DNA ratio, RNA-DNA ratio, pancreatic area per nucleus increase http://purl.obolibrary.org/obo/CHEBI_16670 CHEBI http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/CL_0000158 CL http://purl.obolibrary.org/obo/UBERON_0002110 UBERON http://purl.obolibrary.org/obo/GO_0006412 GO not_specified Pancreatic acinar cell proliferation is evaluated based on measurements of pancreatic weight and DNA and RNA levels [Folsch UR et al, 1978; Povoski SP et al, 1994; Tashiro M et al, 2004], as well as histopathological examination [Povoski SP et al, 1994]. Among such parameters, Increased DNA content and number of mitoses per 10,000 acinar cells are indicative of acinar cell hyperplasia, and the others suggest pancreatic or acinar cell hypertrophy and increased pancreatic protein synthesis. http://purl.obolibrary.org/obo/CL_0000158 CL http://purl.obolibrary.org/obo/GO_0008283 GO pancreatic weight measurement Measures the weight of the pancreas as an indicator of acinar cell proliferation. in_vivo pancreas pancreatic weight increase low Pancreatic acinar cell proliferation is evaluated based on measurements of pancreatic weight http://purl.obolibrary.org/obo/UBERON_0001264 UBERON protein content Quantifies the total protein amount in pancreatic tissue, reflecting protein synthesis levels and cellular hypertrophy. in_vivo pancreas protein content increase low protein content http://purl.obolibrary.org/obo/GO_0006412 GO protein-DNA ratio Calculates the ratio of protein to DNA content, used to distinguish hypertrophy (high ratio) from hyperplasia (low ratio). in_vivo pancreas protein-DNA ratio change low protein-DNA ratio RNA content measurement Quantifies RNA levels in the pancreas to assess acinar cell proliferation and protein synthesis. in_vivo pancreas RNA content increase low measurements of ... RNA levels http://purl.obolibrary.org/obo/CHEBI_33697 CHEBI http://purl.obolibrary.org/obo/GO_0006412 GO ELISA This assay is an ELISA based NRP1-VEGF-A165 protein binding assay. in_vitro NRP1-VEGF-A165 protein binding increase medium Preparation of receptor protein and grid for virtual screening, docking of known NRP-1 targeting compounds, ELISA based NRP1-VEGF-A165 protein binding assay; more details on methodology in the referenced paper (Perez-Miller et al., 2020) http://purl.obolibrary.org/obo/GO_0005173 GO ELISA-based NRP1-VEGF-A165 protein binding assay Measures the binding of NRP1 to VEGF-A165 using an ELISA-based assay. in_vitro NRP1-VEGF-A165 binding not_specified medium ELISA based NRP1-VEGF-A165 protein binding assay immunohistochemistry Stains autopsy specimens with antibodies against SARS-CoV-2 proteins, ACE2, and NRP1 to visualize co-localization of proteins. in_vivo airway sites olfactory epithelium respiratory epithelium human co-localization of SARS-CoV-2 spike protein and NRP1 not_specified low Autopsy specimens from multiple airway sites were stained with antibodies against SARS-CoV-2 proteins, ACE2, and NRP1, to visualize co-localization of proteins Analysis of autopsy tissue from COVID-19 patients showed co-localization of the SARS-CoV-2 spike (S) protein and NRP1 in olfactory and respiratory epithelium immunohistochemistry This assay uses antibodies against SARS-CoV-2 proteins, ACE2, and NRP1 to visualize co-localization of proteins in autopsy specimens from airway sites. ex_vivo airway protein co-localization change low Autopsy specimens from multiple airway sites were stained with antibodies against SARS-CoV-2 proteins, ACE2, and NRP1, to visualize co-localization of proteins (6, 15). http://purl.obolibrary.org/obo/GO_0005243 GO microarray Measures TMPRSS2 gene expression levels. in_vitro TMPRSS2 gene expression levels change high TMPRSS2 gene expression can be measured by RNAseq and microarray pseudovirus infection assay This assay uses spike-pseudotyped viral particles expressing GFP/luciferase/bgalactosidase to assess viral entry. It compares infection rates in manipulated cells (cell lines) and determines fluorescence, bioluminescence, or luciferase activity in cell lysates. in_vitro cell lines fluorescence, bioluminescence, luciferase activity change medium using spike-pseudotyped viral particles expressing GFP/luciferase/bgalactosidase and comparing with vesicular stomatitis virus G seudotyped particles expressing the same reporter analysed in manipulated cultured with cell lines, followed by determining fluorescence, biolumincescence, luciferase activity in cell lysates [Hoffmann M, et al. (2020)]. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0046825 GO quantitative RT-PCR Measures SARS-CoV-2 entry by detecting subgenomic mRNA of the N transcript in cells manipulated with host factors. in_vitro subgenomic mRNA levels of the N transcript increase medium quantitative RT-PCR specific to the subgenomic mRNA of the N transcript, in cells manipulated with host factors that express of not TMPRSS2, cathepsinL, neuropilin-1, hACE2 RNA in situ hybridization (RNA-ISH) Measures TMPRSS2 expression levels by RNA in situ hybridization. in_vitro TMPRSS2 expression levels change low Expression levels of TMPRSS2 can be measured by RNA in situ hybridization (RNA-ISH) RNAseq Measures TMPRSS2 gene expression levels. in_vitro TMPRSS2 gene expression levels change high TMPRSS2 gene expression can be measured by RNAseq spike-pseudotyped viral particles assay Uses spike-pseudotyped viral particles expressing GFP/luciferase/β-galactosidase to measure viral entry by determining fluorescence, bioluminescence, or luciferase activity in cell lysates. in_vitro fluorescence, bioluminescence, or luciferase activity increase medium using spike-pseudotyped viral particles expressing GFP/luciferase/bgalactosidase and comparing with vesicular stomatitis virus G pseudotyped particles expressing the same reporter analysed in manipulated cultured with cell lines, followed by determining fluorescence, biolumincescence, luciferase activity in cell lysates virtual screening Screens compounds against the NRP-1 CendR site to identify potential ligands. in_silico ligand binding to NRP-1 CendR site not_specified high Virtual screen of nearly 0.5 million compounds against the NRP-1 CendR site, resulting in nearly 1,000 hits X-ray crystallography Used to show that the S1 CendR motif directly binds NRP1. in_vitro binding of S1 CendR motif to NRP1 not_specified low X-ray crystallography and biochemical approaches help to show that the S1 CendR motif directly bound NRP1 Biolayer Interferometry (BLI) Measures the interaction between recombinant ACE2 and SARS-CoV-2 spike protein by determining the dissociation constant (Kd). in_vitro dissociation constant (Kd) not_specified http://purl.obolibrary.org/obo/OBI_0000477 OBI http://purl.obolibrary.org/obo/GO_0005515 GO medium Several reports using surface plasmon resonance (SPR) or biolayer interferometry binding (BLI) approaches. to study the interaction between recombinant ACE2 and S proteins have determined a dissociation constant (Kd) for SARS-CoV S and SARS-CoV-2 S as follow, Method: BLI http://purl.obolibrary.org/obo/GO_0019062 GO ELISA Measures the expression or binding activity of ACE2 in permissive cell lines. in_vitro Calu-3 CaCo-2 Vero 293T human African grey monkey ACE2 expression or binding activity not_specified high Other assay measured alteration in the levels of permissive cell lines all express ACE2 or hACE2-expressing 293T cell (e.g. pNUO1-hACE2, pFUSE-hIgG1-Fc2), as previously demonstrated by indirect immunofluorescence (IF) or by immunoblotting are associated with ELISA(W Tai et al., nature 2020). http://purl.obolibrary.org/obo/GO_0010457 GO ELISA ELISA is used to measure alteration in the levels of permissive cell lines or hACE2-expressing 293T cells. in_vitro 293T human protein levels change medium Other assay measured alteration in the levels of permissive cell lines all express ACE2 or hACE2-expressing 293T cell (e.g. pNUO1-hACE2, pFUSE-hIgG1-Fc2), as previously demonstrated by indirect immunofluorescence (IF) or by immunoblotting are associated with ELISA(W Tai et al., nature 2020). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006470 GO Immunoblotting Detects the expression of ACE2 in permissive cell lines using antibody-based protein detection. in_vitro Calu-3 CaCo-2 Vero 293T human African grey monkey ACE2 expression not_specified http://purl.obolibrary.org/obo/OBI_0001041 OBI low Other assay measured alteration in the levels of permissive cell lines all express ACE2 or hACE2-expressing 293T cell (e.g. pNUO1-hACE2, pFUSE-hIgG1-Fc2), as previously demonstrated by indirect immunofluorescence (IF) or by immunoblotting are associated with ELISA(W Tai et al., nature 2020). http://purl.obolibrary.org/obo/GO_0010457 GO Indirect Immunofluorescence (IF) Detects the expression of ACE2 in permissive cell lines using fluorescently labeled antibodies. in_vitro Calu-3 CaCo-2 Vero 293T human African grey monkey ACE2 expression not_specified http://purl.obolibrary.org/obo/OBI_0000698 OBI low Other assay measured alteration in the levels of permissive cell lines all express ACE2 or hACE2-expressing 293T cell (e.g. pNUO1-hACE2, pFUSE-hIgG1-Fc2), as previously demonstrated by indirect immunofluorescence (IF) or by immunoblotting are associated with ELISA(W Tai et al., nature 2020). http://purl.obolibrary.org/obo/GO_0010457 GO Pseudo-typed vesicular stomatitis virus infection assay Uses VSV-SARS-S2 to measure the permissiveness of cell lines to SARS-CoV-2 spike protein-mediated infection. in_vitro Calu-3 CaCo-2 Vero human African grey monkey viral infection efficiency increase http://purl.obolibrary.org/obo/GO_0019039 GO http://purl.obolibrary.org/obo/GO_0019062 GO low Pseudo typed vesicular stomatitis virus expressing SARS-CoV-2 S (VSV-SARS-S2) expression system can be used efficiently infects cell lines, with Calu-3 human lung adenocarcinoma epithelial cell line, CaCo-2 human colorectal adenocarcinoma colon epithelial cell line and Vero African grey monkey kidney epithelial cell line being the most permissive (Hoffmann et al., 2020; Ou et al., 2020). http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0019062 GO Surface Plasmon Resonance (SPR) Measures the interaction between recombinant ACE2 and SARS-CoV-2 spike protein by determining the dissociation constant (Kd). in_vitro dissociation constant (Kd) not_specified http://purl.obolibrary.org/obo/OBI_0000477 OBI http://purl.obolibrary.org/obo/GO_0005515 GO medium Several reports using surface plasmon resonance (SPR) or biolayer interferometry binding (BLI) approaches. to study the interaction between recombinant ACE2 and S proteins have determined a dissociation constant (Kd) for SARS-CoV S and SARS-CoV-2 S as follow, Method: SPR http://purl.obolibrary.org/obo/GO_0019062 GO VSV-SARS-S2 infection assay A pseudo-typed vesicular stomatitis virus expressing SARS-CoV-2 S (VSV-SARS-S2) is used to infect cell lines and measure infection efficiency. in_vitro Calu-3 CaCo-2 Vero lung colon kidney human African green monkey infection efficiency change http://purl.obolibrary.org/obo/GO_0005667 GO medium Pseudo typed vesicular stomatitis virus expressing SARS-CoV-2 S (VSV-SARS-S2) expression system can be used efficiently infects cell lines, with Calu-3 human lung adenocarcinoma epithelial cell line, CaCo-2 human colorectal adenocarcinoma colon epithelial cell line and Vero African grey monkey kidney epithelial cell line being the most permissive http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0005667 GO flow cytometry Measures Frizzled receptor protein level on the cell surface using pan-FZD antibody. in_vitro Frizzled receptor protein level increase medium Frizzled receptor protein level on the cell surface is measured by flow cytometry with pan-FZD antibody http://purl.obolibrary.org/obo/PR_000000003 PR http://purl.obolibrary.org/obo/GO_0016055 GO Flow Cytometry Measures the level of Frizzled receptor protein on the cell surface using a pan-FZD antibody. in_vitro Homo sapiens protein level on cell surface increase not_specified Frizzled receptor protein level on the cell surface is measured by flow cytometry with pan-FZD antibody immunoblotting Measures DVL protein level using anti-DVL2 antibodies. in_vitro DVL protein level increase low DVL protein level is measured by immunoblotting with anti-DVL2 antibodies http://purl.obolibrary.org/obo/PR_000000004 PR http://purl.obolibrary.org/obo/GO_0016055 GO Immunoblotting Measures the expression of Wnt1, Wnt3a, and Wnt5a proteins using specific antibodies. in_vitro Homo sapiens Drosophila melanogaster protein expression increase not_specified Wnt1, Wnt3a, and Wnt5a protein expression are measured by immunoblotting using antibodies for Wnt1, Wnt3a, and Wnt5a, respectively WNT2, of which expression is detected by quantitative PCR, immunoblotting, and immunohistochemistry, induces EMT immunoblotting Measures Wnt1, Wnt3a, and Wnt5a protein expression using specific antibodies. in_vitro Wnt1, Wnt3a, and Wnt5a protein expression increase http://purl.obolibrary.org/obo/GO_0016055 GO http://purl.obolibrary.org/obo/GO_0010457 GO low Wnt1, Wnt3a, and Wnt5a protein expression are measured by immunoblotting using antibodies for Wnt1, Wnt3a, and Wnt5a, respectively http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0016055 GO Immunohistochemistry Detects WNT2 expression in tissue samples using immunohistochemical staining. in_vitro Homo sapiens Drosophila melanogaster protein expression increase not_specified WNT2, of which expression is detected by quantitative PCR, immunoblotting, and immunohistochemistry, induces EMT immunohistochemistry Detects WNT2 expression by immunohistochemistry. in_vivo WNT2 expression increase low WNT2, of which expression is detected by quantitative PCR, immunoblotting, and immunohistochemistry http://purl.obolibrary.org/obo/PR_000000002 PR http://purl.obolibrary.org/obo/GO_0016055 GO Quantitative PCR Measures the expression of WNT2 mRNA using reverse transcription-polymerase chain reaction. in_vitro Homo sapiens mRNA expression increase not_specified WNT2, of which expression is detected by quantitative PCR, immunoblotting, and immunohistochemistry, induces EMT quantitative PCR Detects WNT2 expression by quantitative PCR. in_vitro WNT2 expression increase medium WNT2, of which expression is detected by quantitative PCR http://purl.obolibrary.org/obo/PR_000000002 PR http://purl.obolibrary.org/obo/GO_0016055 GO quantitative reverse transcription-polymerase chain reaction (RT-PCR) Measures Fzd mRNA level. in_vitro Fzd mRNA level increase medium Fzd mRNA level is measured by quantitative reverse transcription-polymerase chain reaction (RT-PCR) http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0016055 GO immunofluorescence assay Measures beta-catenin nuclear translocation using immunofluorescence. in_vitro beta-catenin nuclear translocation not_specified http://purl.obolibrary.org/obo/PR_000000803 PR http://purl.obolibrary.org/obo/GO_0043504 GO medium The beta-catenin nuclear translocation is measured by immunofluorescence assay (Huang et al., 2019). http://purl.obolibrary.org/obo/PR_000000803 PR http://purl.obolibrary.org/obo/GO_0043504 GO western blot Measures the level of beta-catenin in the nucleus using immunoblotting with an anti-beta-catenin antibody. in_vitro beta-catenin nuclear level not_specified http://purl.obolibrary.org/obo/PR_000000803 PR http://purl.obolibrary.org/obo/GO_0005634 GO low The beta-catenin level in nucleus is measured by immunoblotting with anti-beta-catenin antibody (Huang et al., 2019). http://purl.obolibrary.org/obo/PR_000000803 PR http://purl.obolibrary.org/obo/GO_0043504 GO Wnt/beta-catenin activity assay Measures beta-catenin activity using a luciferase reporter assay where a vector containing the firefly luciferase gene controlled by TCF/LEF binding sites is transfected into cells. in_vitro beta-catenin activity not_specified http://purl.obolibrary.org/obo/PR_000000803 PR http://purl.obolibrary.org/obo/GO_0016055 GO medium Activity of beta-catenin is measured by Wnt/beta-catenin activity assay, in which the vector containing the firefly luciferase gene controlled by TCF/LEF binding sites is transfected in the cells (Naujok et al., 2014). http://purl.obolibrary.org/obo/PR_000000803 PR http://purl.obolibrary.org/obo/GO_0016055 GO ELISA Measures the concentration of 11KT using enzyme-linked immunosorbent assay. not_specified 11KT concentration decrease http://purl.obolibrary.org/obo/CHEBI_17758 CHEBI high The concentration of 11KT can be measured in a radioimmunoassay or enzyme-linked immunosorbent assay (ELISA). http://purl.obolibrary.org/obo/CHEBI_17758 CHEBI http://purl.obolibrary.org/obo/GO_0042445 GO ex vivo steroidogenesis assay Measures 11KT production using the organism's gonad after exposure to a compound. ex_vivo gonad 11KT production decrease http://purl.obolibrary.org/obo/CHEBI_17758 CHEBI http://purl.obolibrary.org/obo/GO_0006694 GO low 11KT production can be measured in an ex vivo steroidogenesis assay using the organism's gonad after it has been exposed to a compound. http://purl.obolibrary.org/obo/UBERON_0000991 UBERON http://purl.obolibrary.org/obo/GO_0006694 GO radioimmunoassay Measures the concentration of 11KT using radioactive isotopes. not_specified 11KT concentration decrease http://purl.obolibrary.org/obo/CHEBI_17758 CHEBI medium The concentration of 11KT can be measured in a radioimmunoassay or enzyme-linked immunosorbent assay (ELISA). http://purl.obolibrary.org/obo/CHEBI_17758 CHEBI http://purl.obolibrary.org/obo/GO_0042445 GO ATP content assay Measures intracellular ATP levels in sperm, reflecting metabolic activity and spermatogenesis competence. not_specified sperm ATP content not_specified not_specified sperm motility, velocity, ATP content, and lipid peroxidation(Gage et al., 2004, Xia et al., 2018, Chen et al., 2015). http://purl.obolibrary.org/obo/CL_0000553 CL http://purl.obolibrary.org/obo/GO_0007283 GO lipid peroxidation assay Measures lipid peroxidation levels in sperm, indicating oxidative stress that can impair spermatogenesis. not_specified sperm lipid peroxidation not_specified not_specified sperm motility, velocity, ATP content, and lipid peroxidation(Gage et al., 2004, Xia et al., 2018, Chen et al., 2015). http://purl.obolibrary.org/obo/CL_0000553 CL http://purl.obolibrary.org/obo/GO_0007283 GO qualitative histological assessment Examines and quantifies sperm morphology, overall quantity, and quantity within each stage through histological analysis. in_vivo testis sperm morphology and quantity change http://purl.obolibrary.org/obo/GO_0007283 GO low qualitative histological assessments (Jensen et al., 2004). Through histology, sperm morphology can be examined and quantified through the number and stage of the sperm. http://purl.obolibrary.org/obo/CL_0000239 CL http://purl.obolibrary.org/obo/GO_0007283 GO sperm density measurement Measures sperm density as an indicator of impaired spermatogenesis. in_vivo testis sperm density decrease medium Impaired spermatogenesis can also be seen by measuring sperm density http://purl.obolibrary.org/obo/CL_0000239 CL http://purl.obolibrary.org/obo/GO_0007283 GO sperm quality assessment Measures sperm motility, velocity, ATP content, and lipid peroxidation to assess sperm quality. in_vivo testis sperm motility, velocity, ATP content, and lipid peroxidation change http://purl.obolibrary.org/obo/GO_0030317 GO http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0006684 GO medium sperm quality can also be another assessment of impaired spermatogenesis such as sperm motility, velocity, ATP content, and lipid peroxidation http://purl.obolibrary.org/obo/CL_0000239 CL http://purl.obolibrary.org/obo/GO_0007283 GO Fin index calculation Calculates a fin index using the ratio of fin length to total body length to quantify fin regeneration. in_vivo fin Danio rerio fin index decrease medium Fin Index = 100 x (Fin Length/Total Length) http://purl.obolibrary.org/obo/UBERON_0002343 UBERON http://purl.obolibrary.org/obo/GO_0031102 GO Fin ray length measurement Measures the length of specific fin rays (top, bottom, middle) to assess fin regeneration. in_vivo fin Danio rerio fin ray length decrease medium measuring the length of the top fin ray, bottom fin ray, and middle fin ray http://purl.obolibrary.org/obo/UBERON_0002343 UBERON http://purl.obolibrary.org/obo/GO_0031102 GO Total fin area measurement Measures the total area of the fin to assess overall fin regeneration. in_vivo fin Danio rerio total fin area decrease medium total area of the fin http://purl.obolibrary.org/obo/UBERON_0002343 UBERON http://purl.obolibrary.org/obo/GO_0031102 GO 2D gel electrophoresis plus anti-DNP immunoblotting Identifies oxidized proteins or oxidized amino-acid residues at protein or peptide level using 2D gel electrophoresis plus anti-DNP immunoblotting. in_vitro oxidized proteins or amino-acid residues increase low 2D gel electrophoresis plus anti-DNP immunoblotting; LC-MS/MS redox proteomics; carbonyl-reactive enrichment workflows High mechanistic value because it can identify protein targets and modification sites. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006464 GO Anti-glutathione immunoblotting Measures protein S-glutathionylation as a reversible thiol redox modification using anti-glutathione immunoblotting. in_vitro protein S-glutathionylation increase http://purl.obolibrary.org/obo/GO_0006464 GO medium Anti-glutathione immunoblotting; redox proteomics; mass spectrometry Mechanistically informative for redox regulation and oxidative stress responses. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0034614 GO Anti-nitrotyrosine immunoassays Measures specific oxidized or nitrated amino-acid residues using anti-nitrotyrosine immunoassays. in_vitro nitrotyrosine residues increase medium Anti-nitrotyrosine immunoassays; LC-MS/MS; targeted proteomics Provides higher chemical specificity for particular oxidant pathways, such as peroxynitrite-associated nitration, but does not capture all protein oxidation. AOPP assays Measures bulk oxidized protein products, cross-linked proteins or protein aggregates using AOPP assays. in_vitro oxidized protein products or aggregates increase http://purl.obolibrary.org/obo/GO_0043621 GO high AOPP assays; aggregate detection; protein insolubility assays Useful for broad screening of oxidative protein burden but less specific than defined chemical or proteomic measurements. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006464 GO Biotin-switch methods Measures the oxidation state of protein thiols and disulfides using biotin-switch methods. in_vitro oxidation state of protein thiols and disulfides change http://purl.obolibrary.org/obo/GO_0018024 GO medium Biotin-switch methods; maleimide labeling; redox Western blot; differential alkylation; thiol redox proteomics Useful for reversible cysteine oxidation and redox signaling. http://purl.obolibrary.org/obo/GO_0034614 GO DNPH derivatization with spectrophotometry Measures protein carbonyl groups formed by direct oxidation or by adduction of reactive carbonyl species using DNPH derivatization with spectrophotometry. in_vitro protein carbonyl groups increase medium DNPH derivatization with spectrophotometry, ELISA, immunoblotting or OxyBlot; hydrazide-based probes Widely used, relatively stable and broadly accepted as a marker of protein oxidation. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006464 GO Nitrotyrosine and specific residue assays Detects specific oxidized or nitrated amino-acid residues, such as nitrotyrosine, using immunoassays, LC-MS/MS, or targeted proteomics. not_specified specific oxidized or nitrated amino-acid residues increase not_specified Nitrotyrosine and other specific oxidized residue assays Specific oxidized or nitrated amino-acid residues Anti-nitrotyrosine immunoassays; LC-MS/MS; targeted proteomics Protein carbonyl assays Measures protein carbonyl groups formed by direct oxidation or adduction of reactive carbonyl species using DNPH derivatization, ELISA, immunoblotting, or OxyBlot. not_specified protein carbonyl groups increase not_specified Protein carbonyl assays Protein carbonyl groups formed by direct oxidation or by adduction of reactive carbonyl species DNPH derivatization with spectrophotometry, ELISA, immunoblotting or OxyBlot; hydrazide-based probes Redox proteomics This assay identifies oxidized proteins or oxidized amino-acid residues at the protein or peptide level using techniques like 2D gel electrophoresis plus anti-DNP immunoblotting, LC-MS/MS redox proteomics, or carbonyl-reactive enrichment workflows. in_vitro oxidized proteins/peptides increase low Redox proteomics Oxidized proteins or oxidized amino-acid residues at protein or peptide level 2D gel electrophoresis plus anti-DNP immunoblotting; LC-MS/MS redox proteomics; carbonyl-reactive enrichment workflows http://purl.obolibrary.org/obo/PR_000000 PR http://purl.obolibrary.org/obo/GO_0042423 GO Thiol oxidation assays These assays measure the oxidation state of protein thiols and disulfides using methods like biotin-switch methods, maleimide labeling, redox Western blot, differential alkylation, or thiol redox proteomics. in_vitro thiol oxidation state change medium Thiol oxidation assays Oxidation state of protein thiols and disulfides Biotin-switch methods; maleimide labeling; redox Western blot; differential alkylation; thiol redox proteomics http://purl.obolibrary.org/obo/CHEBI_33265 CHEBI http://purl.obolibrary.org/obo/GO_0042423 GO enzyme assay Measures specific ion concentrations in a solution using enzymatic reactions. not_specified ion concentration increase not_specified Specific ion concentrations can be measured via enzyme assays ion chromatography Measures specific ion concentrations in a solution. not_specified ion concentration increase not_specified Specific ion concentrations can be measured via ion chromatography osmometer Measures the osmolality of a solution. not_specified osmolality increase not_specified Osmolality can be measured using an osmometer. spectrophotometry Measures specific ion concentrations in a solution using light absorption. not_specified ion concentration increase not_specified Specific ion concentrations can be measured via spectrophotometry ATP bioluminescent assay Quantifies ATP concentration by measuring luminescence emitted from the reaction of ATP with luciferase and luciferin. in_vitro ATP concentration decrease not_specified The ATP pool in cells or tissue can be quantified using a well-established ATP bioluminescent assay (Lemasters 1978; Wibom 1990). Assay principles: ATP can react with luciferase and luciferin from firefly and the luminescence emitted from the reaction is proportional to the ATP concentration http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0046034 GO NCCT_HEK293T_CellTiterGLO High-throughput screening bioassay to measure ATP levels as an indicator of cell viability or cytotoxicity. in_vitro HEK293T human ATP concentration decrease http://purl.obolibrary.org/obo/OBI_0000377 OBI high ToxCast high-throughput screening bioassays, such as “NCCT_HEK293T_CellTiterGLO” and “NIS_HEK293T_CTG_Cytotoxicity” can be used to measure this KE http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0046034 GO NIS_HEK293T_CTG_Cytotoxicity A ToxCast high-throughput screening bioassay used to measure cytotoxicity. in_vitro HEK293T cytotoxicity decrease http://purl.obolibrary.org/obo/GO_0000274 GO high ToxCast high-throughput screening bioassays, such as “NIS_HEK293T_CTG_Cytotoxicity” can be used to measure this KE. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0005829 GO Nipple retention assessment Visual assessment of nipple retention in male pups, typically conducted on postnatal day 12/13, by detecting dark spots (areolae) along the milk lines. in_vivo mammary gland Rattus norvegicus number of retained nipples increase http://purl.obolibrary.org/obo/GO_0030879 GO http://purl.obolibrary.org/obo/GO_0009791 GO OECD TG 43, OECD TG 151 medium Nipple retention (NR) is visually assessed, ideally on postnatal day (PND) 12/13 NR is occasionally observed in controls. Hence, accurate assessment of NR in controls is needed to detect substance-induced effects on masculine development It is recommended by the OECD guidance documents 43 and 151 to record NR as a quantitative number rather than a qualitative measure http://purl.obolibrary.org/obo/UBERON_0001911 UBERON http://purl.obolibrary.org/obo/GO_0030879 GO visual assessment Nipple retention (NR) is visually assessed on postnatal days 12/13 or 14 by detecting dark spots (areolae) resembling nipple precursors. The assessment is conducted when nipples are visible in female littermates. in_vivo nipple rat number of areolae/nipples increase OECD TG 43, OECD TG 151 low Nipple retention (NR) is visually assessed, ideally on postnatal day (PND) 12/13 (OECD, 2018; Schwartz et al., 2021). Nipples are detected as dark spots (or shadows) called areolae, which resemble precursors to a nipple rather than a fully developed nipple (Hass et al., 2007). It is recommended by the OECD guidance documents 43 and 151 to record NR as a quantitative number rather than a qualitative measure (OECD, 2013, 2018). http://purl.obolibrary.org/obo/CL_0002068 CL http://purl.obolibrary.org/obo/GO_0009653 GO LC/MS/MS Measures estrogen concentrations using liquid chromatography coupled with tandem mass spectrometry. in_vitro undifferentiated gonad estrogen concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/OBI_0001047 OBI medium analytical methods such as LC/MS/MS (e.g., Gravitte et al. 2021; Jalabert et al. 2021; Nouri et al. 2020) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0006704 GO radioimmunoassay Measures estrogen concentrations using radioactive isotopes and antibodies. in_vitro undifferentiated gonad estrogen concentration not_specified http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/OBI_0000474 OBI US EPA 2002 medium Estrogen concentrations can be measured via radioimmunoassay (e.g., US EPA 2002) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0006704 GO Histological examination Employs light microscopy to identify the nature of the gonad, particularly in small or early-life-stage organisms with poorly differentiated gonads. ex_vivo spermatogonia Sertoli cells Leydig cells gonads vertebrates gonad differentiation increase http://purl.obolibrary.org/obo/GO_0008585 GO http://purl.obolibrary.org/obo/UBERON_0000473 UBERON http://purl.obolibrary.org/obo/CL_0000006 CL http://purl.obolibrary.org/obo/CL_0000494 CL medium In instances where organisms are small, at early life-stages and/or have poorly differentiated gonads, it will be necessary to employ histological examination by light microscopy to identify nature of the gonad. http://purl.obolibrary.org/obo/UBERON_0000991 UBERON http://purl.obolibrary.org/obo/GO_0008585 GO visual identification of testes vs ovaries This assay determines the presence of developed testes versus ovaries by visual inspection or low-power magnification without gonad removal, fixation, or processing. in_vivo gonad presence of developed testicular tissue increase http://purl.obolibrary.org/obo/UBERON_0000473 UBERON http://purl.obolibrary.org/obo/UBERON_0000995 UBERON low Depending upon the size of the test organism and life stage it may be possible to identify the presence of developed testes versus ovaries visually or with low-power magnification without a need for gonad removal, fixation and processing. http://purl.obolibrary.org/obo/UBERON_0000062 UBERON http://purl.obolibrary.org/obo/GO_0007548 GO Visual inspection Identifies the presence of developed testes versus ovaries visually or with low-power magnification without gonad removal. in_vivo gonads presence of developed testes increase http://purl.obolibrary.org/obo/GO_0008586 GO http://purl.obolibrary.org/obo/UBERON_0000991 UBERON high Depending upon the size of the test organism and life stage it may be possible to identify the presence of developed testes versus ovaries visually or with low-power magnification without a need for gonad removal, fixation and processing. http://purl.obolibrary.org/obo/UBERON_0000991 UBERON http://purl.obolibrary.org/obo/GO_0008586 GO direct observation of phenotypic secondary sex characteristics Assessment of sex ratios in sexually dimorphic mature animals through the visual inspection of secondary sexual characteristics. in_vivo phenotypic secondary sex characteristics not_specified low For mature animals that are sexually dimorphic, direct observation of phenotypic secondary sex characteristics is a common method for assessing sex ratios. genotyping Genotyping or the use of genetic markers to determine genotypic sex ratio, particularly for animals with GSD. in_vivo genotypic sex not_specified http://purl.obolibrary.org/obo/OBI_0000722 OBI medium For animals with GSD, genotyping or the use of genetic markers can also be employed to determine genotypic sex ratio. http://purl.obolibrary.org/obo/CHEBI_0001388 CHEBI http://purl.obolibrary.org/obo/GO_0008669 GO Gonadal examination This assay determines phenotypic sex by examining the gonad via gross observation or histological examination in animals that are not sexually dimorphic or are in pubertal/juvenile stages. in_vivo gonad phenotypic sex not_specified http://purl.obolibrary.org/obo/UBERON_0000991 UBERON low examination of the gonad, either via gross observation or histological examination is required to determine phenotypic sex. http://purl.obolibrary.org/obo/UBERON_0000991 UBERON histological examination of the gonad Microscopic examination of gonadal tissue to determine phenotypic sex, especially in non-dimorphic, pubertal, or juvenile animals. ex_vivo gonad phenotypic sex not_specified low In animals that are not sexually dimorphic or those in pubertal/juvenile stages examination of the gonad, either via gross observation or histological examination is required to determine phenotypic sex. http://purl.obolibrary.org/obo/UBERON_0000115 UBERON phenotypic secondary sex characteristic observation Direct visual assessment of external sexual dimorphism (secondary sex characteristics) to classify individual animals as male or non-male for population sex ratio determination. in_vivo whole organism animals count of males and/or non-males change http://purl.obolibrary.org/obo/GO_0048104 GO low For mature animals that are sexually dimorphic, direct observation of phenotypic secondary sex characteristics is a common method for assessing sex ratios. http://purl.obolibrary.org/obo/GO_0048104 GO Phenotypic sex ratio assessment This assay measures the sex ratio in a population by direct observation of phenotypic secondary sex characteristics in mature, sexually dimorphic animals. in_vivo sex ratio change medium direct observation of phenotypic secondary sex characteristics is a common method for assessing sex ratios. sex ratio determination Determination of sex ratio is based on counts of the number of males and/or non-males in a population or a sub-sample. For sexually dimorphic animals, direct observation of phenotypic characteristics is used. in_vivo gonad number of males and females increase low Fundamentally, determination of sex ratio (and consequently male-biased sex ratio) is based on counts of the number of males and/or non males in a population, or some statistically representative sub-sample of a population. For mature animals that are sexually dimorphic, direct observation of phenotypic secondary sex characteristics is a common method for assessing sex ratios. http://purl.obolibrary.org/obo/GO_0001511 GO http://purl.obolibrary.org/obo/GO_0008544 GO ATP detection assay Measures ATP levels as an indicator of cell proliferation, as ATP is a marker of metabolically active cells. in_vitro KGN human ATP levels decrease http://purl.obolibrary.org/obo/GO_0046034 GO http://purl.obolibrary.org/obo/GO_0008283 GO high Well-established assays to detect proliferation include methods to assess ... cellular metabolism (e.g. MTT, XTT, ATP detection assays) http://purl.obolibrary.org/obo/CL_0000161 CL http://purl.obolibrary.org/obo/GO_0008283 GO BrdU assay Measures DNA synthesis as an indicator of cell proliferation by incorporating BrdU into newly synthesized DNA. in_vitro KGN human DNA synthesis decrease http://purl.obolibrary.org/obo/GO_0071897 GO http://purl.obolibrary.org/obo/GO_0008283 GO medium Well-established assays to detect proliferation include methods to assess DNA synthesis (e.g. BrdU) http://purl.obolibrary.org/obo/CL_0000161 CL http://purl.obolibrary.org/obo/GO_0008283 GO follicle counting Measures granulosa cell proliferation indirectly by counting follicles in different developmental stages (primordial, primary, secondary) in ovarian tissue. in_vivo ovary follicle count decrease http://purl.obolibrary.org/obo/GO_0001541 GO OECD 443 low Granulosa cell proliferation can therefore be measured by counting follicles in different stages (primordial, primary, secondary) http://purl.obolibrary.org/obo/CL_0000161 CL http://purl.obolibrary.org/obo/GO_0001541 GO Ki67 assay Measures the expression of Ki67, a marker of cell proliferation. in_vitro KGN human Ki67 expression decrease http://purl.obolibrary.org/obo/PR_000025849 PR http://purl.obolibrary.org/obo/GO_0008283 GO medium Well-established assays to detect proliferation include methods to assess ... proliferation proteins (e.g. PCNA, Ki67, MCM-2) http://purl.obolibrary.org/obo/CL_0000161 CL http://purl.obolibrary.org/obo/GO_0008283 GO MCM-2 assay Measures the expression of minichromosome maintenance complex component 2 (MCM-2), a marker of cell proliferation. in_vitro KGN human MCM-2 expression decrease http://purl.obolibrary.org/obo/PR_000010280 PR http://purl.obolibrary.org/obo/GO_0008283 GO medium Well-established assays to detect proliferation include methods to assess ... proliferation proteins (e.g. PCNA, Ki67, MCM-2) http://purl.obolibrary.org/obo/CL_0000161 CL http://purl.obolibrary.org/obo/GO_0008283 GO MTT assay Measures cellular metabolism as an indicator of cell proliferation by quantifying the reduction of MTT to formazan. in_vitro KGN human cellular metabolism decrease http://purl.obolibrary.org/obo/GO_0044237 GO http://purl.obolibrary.org/obo/GO_0008283 GO high Well-established assays to detect proliferation include methods to assess ... cellular metabolism (e.g. MTT, XTT, ATP detection assays) http://purl.obolibrary.org/obo/CL_0000161 CL http://purl.obolibrary.org/obo/GO_0008283 GO PCNA assay Measures the expression of proliferating cell nuclear antigen (PCNA), a marker of cell proliferation. in_vitro KGN human PCNA expression decrease http://purl.obolibrary.org/obo/PR_000012803 PR http://purl.obolibrary.org/obo/GO_0008283 GO medium Well-established assays to detect proliferation include methods to assess ... proliferation proteins (e.g. PCNA, Ki67, MCM-2) http://purl.obolibrary.org/obo/CL_0000161 CL http://purl.obolibrary.org/obo/GO_0008283 GO proliferation proteins (PCNA, Ki67, MCM-2) Assay to detect proliferation by measuring levels of specific proliferation-associated proteins. in_vitro KGN granulosa cell tumor lines ovary proliferation proteins change http://purl.obolibrary.org/obo/GO_0008283 GO not_specified proliferation proteins (e.g. PCNA, Ki67, MCM-2) http://purl.obolibrary.org/obo/CL_0000175 CL http://purl.obolibrary.org/obo/GO_0008283 GO XTT This assay measures cellular metabolism as an indicator of proliferation. in_vitro KGN ovary human cellular metabolism decrease medium methods to assess cellular metabolism (e.g. MTT, XTT) http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0009060 GO BrdU assay Measures DNA synthesis in dividing cells using 5-bromo-2’-deoxyuridine to indicate proliferation status. in_vitro DNA synthesis decrease http://purl.obolibrary.org/obo/GO_0006260 GO not_specified Commercially available methods such as the well-established 5-bromo-2’-deoxyuridine (BrdU) (Raza 1985; Muir 1990) or 5-ethynyl-2’-deoxyuridine (EdU) assay. Both assays measure DNA synthesis in dividing cells to indicate proliferation status. http://purl.obolibrary.org/obo/GO_0006260 GO BSK_3C_Proliferation A high-throughput screening bioassay used to measure cell proliferation status. in_vitro cell proliferation status decrease http://purl.obolibrary.org/obo/GO_0008283 GO high ToxCast high-throughput screening bioassays such as “BSK_3C_Proliferation”, “BSK_CASM3C_Proliferation” and “BSK_SAg_Proliferation” can be used to measure cell proliferation status. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO EdU assay Measures DNA synthesis in dividing cells using 5-ethynyl-2’-deoxyuridine to indicate proliferation status. in_vitro DNA synthesis decrease http://purl.obolibrary.org/obo/GO_0006260 GO not_specified Commercially available methods such as the well-established 5-bromo-2’-deoxyuridine (BrdU) (Raza 1985; Muir 1990) or 5-ethynyl-2’-deoxyuridine (EdU) assay. Both assays measure DNA synthesis in dividing cells to indicate proliferation status. http://purl.obolibrary.org/obo/GO_0006260 GO ToxCast proliferation assay High-throughput screening bioassays such as BSK_3C_Proliferation, BSK_CASM3C_Proliferation and BSK_SAg_Proliferation measure cell proliferation status in vitro. in_vitro cell proliferation status decrease http://purl.obolibrary.org/obo/GO_0008283 GO high ToxCast high-throughput screening bioassays such as "BSK_3C_Proliferation", "BSK_CASM3C_Proliferation" and "BSK_SAg_Proliferation" can be used to measure cell proliferation status. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO Flow cytometry Analyzes the expression of cell surface maturation markers (CD80, CD86, CD40, and CD83) on dendritic cells to assess their maturation state. in_vitro Tip-DC dendritic cells Cell surface expression of maturation markers CD80, CD86, CD40, and CD83 change http://purl.obolibrary.org/obo/CL_0000451 CL medium Maturation markers such as CD80, CD86, CD40 and CD83 can be analyzed by flowcytometry (Wilsmann-Theis et al. 2013). Analysis of maturation marker expression on cell surface http://purl.obolibrary.org/obo/CL_0000451 CL Flow cytometry Measures the expression of maturation markers such as CD80, CD86, CD40, and CD83 on the cell surface of Tip-DCs. in_vitro Tip-DCs expression of maturation markers not_specified http://purl.obolibrary.org/obo/OBI_0000268 OBI http://purl.obolibrary.org/obo/PR_000001204 PR http://purl.obolibrary.org/obo/PR_000001205 PR http://purl.obolibrary.org/obo/PR_000001199 PR http://purl.obolibrary.org/obo/PR_000001203 PR medium Maturation markers such as CD80, CD86, CD40 and CD83 can be analyzed by flowcytometry (Wilsmann-Theis et al. 2013). http://purl.obolibrary.org/obo/GO_0048468 GO RT-qPCR Real-time quantitative PCR used to quantify the mRNA expression levels of cytokines and enzymes including TNF-α, iNOS, IL-12p35, and IL-23p19. in_vitro in vitro generated Tip-DC mRNA expression change http://purl.obolibrary.org/obo/GO_0010468 GO medium Expression of TNF-α, iNOS, IL-12p35 and IL-23p19 mRNA in in vitro generated Tip-DC are quantified by RT-qPCR. http://purl.obolibrary.org/obo/CHEBI_35452 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO RT-qPCR Quantifies the mRNA expression of TNF-α, iNOS, IL-12p35, and IL-23p19 in in vitro generated Tip-DCs. in_vitro Tip-DCs mRNA expression of TNF-α, iNOS, IL-12p35, and IL-23p19 not_specified http://purl.obolibrary.org/obo/PR_000001746 PR http://purl.obolibrary.org/obo/PR_000001216 PR http://purl.obolibrary.org/obo/PR_000001473 PR http://purl.obolibrary.org/obo/PR_000001500 PR medium Expression of TNF-α, iNOS, IL-12p35 and IL-23p19 mRNA in in vitro generated Tip-DC are quantified by RT-qPCR. (Wilsmann-Theis et al. 2013). http://purl.obolibrary.org/obo/GO_0001817 GO Annexin V Binding Detects apoptotic cells by binding annexin V to exposed phosphatidylserine on the cell surface, measured by flow cytometry. in_vitro phosphatidylserine exposure increase high Apoptosis is also characterized by exposure of phosphatidylserine (PS) on the outside of apoptotic cells, which acts as a signal that triggers removal of the dying cell by phagocytosis. Annexin V, can selectively bind to PS to label apoptotic cells in which PS is exposed. http://purl.obolibrary.org/obo/CHEBI_16322 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO Apoptosis PCR Microarray Profiles gene expression of apoptotic-related genes. in_vitro gene expression change high A method to profile the gene expression of many apoptotic-related genes, for example: ligands, receptors, intracellular modulators, and transcription factors. http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0006915 GO Caspase Activity Assay Measures caspase-3 and caspase-9 activity using the enzyme-catalyzed release of p-nitroanilide (pNA). in_vitro caspase activity increase high Caspase-3 and caspase-9 activity is measured with the enzyme-catalyzed release of p-nitroanilide (pNA) and quantified at 405 nm http://purl.obolibrary.org/obo/PR_000001498 PR http://purl.obolibrary.org/obo/GO_0006915 GO Cell Death Detection ELISA Detects apoptotic nucleosomes using an ELISA-based assay. in_vitro apoptotic nucleosomes increase high Apoptotic nucleosomes are detected using the Cell Death Detection ELISA kit, which were calculated as absorbance subtraction at 405 nm and 490 nm. http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0006915 GO Cleaved Caspase-3 Immunocytochemistry Detects caspase activity in apoptotic cells using antibodies against cleaved caspase-3, measured by flow cytometry. in_vitro caspase activity increase medium antibodies that specifically recognize the cleaved fragments of caspases and their substrates can be used to specifically detect caspase activity in apoptotic cells by immunocytochemistry. http://purl.obolibrary.org/obo/PR_000001010 PR http://purl.obolibrary.org/obo/GO_0006915 GO Colony-Forming Assay Measures cell survival by counting the number of colonies formed by proliferating cells. in_vitro cell survival decrease http://purl.obolibrary.org/obo/GO_0008283 GO low Colony-forming assay can be used to define the number of cells in a population that are capable of proliferating and forming large groups of cells. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO DAPI Fluorescent staining of DNA in live and fixed cells to measure nuclear changes. in_vitro DNA binding change http://purl.obolibrary.org/obo/GO_0005739 GO not_specified Binds strongly to adenine–thymine-rich regions in the DNA. DAPI can stain live and fixed cells. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0008219 GO DAPI Staining Stains DNA to visualize nuclei in live and fixed cells. in_vitro DNA staining increase Yes high Binds strongly to adenine–thymine-rich regions in the DNA. DAPI can stain live and fixed cells. http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI http://purl.obolibrary.org/obo/GO_0007000 GO Fluorescence Correlation Spectroscopy (FCS) Measures protease activity using fluorescence correlation spectroscopy. in_vitro protease activity increase medium Used to measure protease activity. http://purl.obolibrary.org/obo/GO_0008233 GO http://purl.obolibrary.org/obo/GO_0006915 GO hematoxylin and eosin staining Hematoxylin and eosin staining is used to visualize nuclear and cytoplasmic features indicative of cell death, such as nuclear fragmentation and plasma membrane blebbing. in_vitro morphological changes change low Dyes such as Giemsa or hematoxylin, which are purple in colour and therefore easily viewed using light microscopy, are commonly used to stain the nucleus. Other features of apoptosis and necrosis, such as plasma membrane blebbing or rupture, can be identified by staining the cytoplasm with eosin. http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0008219 GO Hematoxylin and Eosin Staining Stains nuclei blue and cytoplasm pink to visualize cytomorphological alterations in cells. in_vitro nuclear condensation increase medium Hematoxylin stains nuclei blue and eosin stains the cytoplasm/extracellular matrix pink, allowing for the visualization of the cytomorphological alterations of cells. http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0006915 GO Hoechst 33342 Staining Stains DNA to measure DNA condensation in live and fixed cells. in_vitro DNA condensation increase Yes high Analyzing Cell Death by Nuclear Staining with Hoechst 33342 (Crowley, Marfell, & Waterhouse, 2015a). http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO Mitochondrial Dye Staining Indicates mitochondrial membrane potential using fluorescent dyes such as JC-1, Rhodamine, DiOC6, or Mitotracker red. in_vitro mitochondrial membrane potential decrease high These mitochondrial dyes can indicate disintegration of the mitochondrial outer membrane’s electrochemical gradient, as different fluorescence is observed between healthy and apoptotic cells. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006915 GO mitochondrial transmembrane potential measurement Measures the mitochondrial transmembrane potential using TMRE staining and flow cytometry, indicative of cytochrome c release during apoptosis. in_vitro mitochondrial transmembrane potential decrease http://purl.obolibrary.org/obo/GO_0001974 GO high flow cytometry can be used to quantitate the number of cells that have reduced mitochondrial transmembrane potential, which is commonly associated with cytochrome c release during apoptosis. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006915 GO Nicoletti Assay Measures DNA content in apoptotic nuclei at the pre-G1 phase of the cell cycle. in_vitro DNA content decrease medium Measures DNA content in nuclei at the pre-G1 phase of the cell cycle (apoptotic nuclei have less DNA than nuclei in healthy cells). http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO PhiPhiLux Assay Detects caspase-3 activity using a fluorescent molecule that becomes fluorescent upon cleavage by caspase-3. in_vitro caspase-3 activity increase high The PhiPhiLux molecule becomes fluorescent once it is cleaved by caspase-3, indicating caspase activity. http://purl.obolibrary.org/obo/PR_000001010 PR http://purl.obolibrary.org/obo/GO_0006915 GO Propidium Iodide Uptake Measures cell death by staining dead cells with propidium iodide (PI), which binds to DNA and is detected by flow cytometry. in_vitro cell death increase http://purl.obolibrary.org/obo/GO_0008219 GO high Measuring Cell Death by Propidium Iodide (PI) Uptake and Flow Cytometry (Crowley & Waterhouse, 2015a) http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008219 GO SAMDI-MS Assay Detects caspase activity using self-assembled monolayers for matrix-assisted laser desorption ionization time-of-flight mass spectrometry. in_vitro caspase activity increase medium This assay detects caspase activity. http://purl.obolibrary.org/obo/PR_000001498 PR http://purl.obolibrary.org/obo/GO_0006915 GO TMRE Staining Measures mitochondrial transmembrane potential by staining with TMRE, detected by flow cytometry. in_vitro mitochondrial transmembrane potential decrease high flow cytometry can be used to quantitate the number of cells that have reduced mitochondrial transmembrane potential, which is commonly associated with cytochrome c release during apoptosis. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006915 GO Trypan Blue Uptake Measures cell death by staining dead cells with trypan blue, which is taken up by cells with compromised membranes. in_vitro cell death increase http://purl.obolibrary.org/obo/GO_0008219 GO medium Measuring Cell Death by Trypan Blue Uptake and Light Microscopy (Crowley, Marfell, Christensen, et al., 2015d) http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008219 GO TUNEL In situ terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labelling used to detect apoptotic cells by labeling DNA strand breaks. in_vitro apoptotic cells increase http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/GO_0006773 GO OECD TG low in situ terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labelling can be used to detect apoptotic cells (Bever & Fekete, 1999; Uribe et al., 2013). Apoptosis is detected with the TUNEL method to assay the endonuclease cleavage products by enzymatically end-labelling the DNA strand breaks. http://purl.obolibrary.org/obo/CHEBI_30157 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO TUNEL assay Detects apoptotic cells by labeling DNA strand breaks using terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labeling. in_vitro DNA fragmentation increase http://purl.obolibrary.org/obo/GO_0006915 GO Yes medium in situ terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick-end labelling can be used to detect apoptotic cells (Bever & Fekete, 1999; Uribe et al., 2013). http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO Western blot Uses antibodies to detect the expression of various apoptotic markers such as caspases, cytochrome-c, and Bcl-2. in_vitro expression of apoptotic markers change http://purl.obolibrary.org/obo/GO_0010847 GO low Apoptosis can be detected with the expression of various apoptotic markers by western blotting using antibodies. Markers can include: cytosolic cytochrome-c; caspases 2, 3, 6, 7, 8, 9, 10; Bax; Bcl-2 (apoptosis inhibitor); BIRC2; BIRC3; GAPDH; PARP; CDK2; CDK4; cyclin D1; p53; p63; p73; cytokeratin-18 http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006915 GO Western Blot Detects apoptotic markers using antibodies against specific proteins. in_vitro protein expression change low Apoptosis can be detected with the expression of various apoptotic markers by western blotting using antibodies. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006915 GO commercial enzyme assay Measures inhibition of cytochrome oxidase using commercially available enzyme assay kits. in_vitro cytochrome oxidase activity decrease http://purl.obolibrary.org/obo/GO_0004129 GO http://purl.obolibrary.org/obo/OBI_0000272 OBI high Inhibition of cytochrome oxidase is measured by [...] commercially available enzyme assays (e.g., Sigma-Aldrich CYTOCOX1; Abcam ab239711; Abnova KA6690) http://purl.obolibrary.org/obo/PR_000000167 PR http://purl.obolibrary.org/obo/GO_0022900 GO histochemistry Measures inhibition of cytochrome oxidase using histochemical staining methods. in_vivo cytochrome oxidase activity decrease http://purl.obolibrary.org/obo/GO_0004129 GO http://purl.obolibrary.org/obo/OBI_0000223 OBI low Inhibition of cytochrome oxidase is measured by [...] histochemistry (Melendez-Ferro et al. 2013) http://purl.obolibrary.org/obo/PR_000000167 PR http://purl.obolibrary.org/obo/GO_0022900 GO spectrophotometry Measures inhibition of cytochrome oxidase using spectrophotometric methods. in_vitro cytochrome oxidase activity decrease http://purl.obolibrary.org/obo/GO_0004129 GO medium Inhibition of cytochrome oxidase is measured by spectrophotometry (Miro et al. 1998) http://purl.obolibrary.org/obo/PR_000000167 PR http://purl.obolibrary.org/obo/GO_0022900 GO blood tests Blood tests analyze blood samples for signs of infection, inflammation, or immune system activity, which can indicate encephalitis. in_vivo immune cells blood inflammatory markers increase http://purl.obolibrary.org/obo/GO_0006952 GO medium Blood tests http://purl.obolibrary.org/obo/GO_0006952 GO Blood tests Blood tests are used to detect signs of infection or immune response. in_vivo blood human signs of infection or immune response not_specified http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0006955 GO high Blood tests http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0006955 GO Brain biopsy Brain biopsy involves the removal of a small piece of brain tissue for examination under a microscope. in_vivo brain human brain tissue abnormalities not_specified http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/OBI_0000215 OBI low Brain biopsy http://purl.obolibrary.org/obo/UBERON_0000955 UBERON Brain biopsy A surgical procedure to remove a small piece of brain tissue for examination. in_vivo brain tissue morphology and pathology change low Brain biopsy http://purl.obolibrary.org/obo/UBERON_0001038 UBERON CT scan Computed tomography scan is used to detect structural abnormalities in the brain. in_vivo brain human brain structural abnormalities not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/UBERON_0000955 UBERON medium Computed tomography scan (CT or CAT scan) http://purl.obolibrary.org/obo/UBERON_0000955 UBERON EEG Electroencephalogram measures electrical activity in the brain to detect abnormalities. in_vivo brain human brain electrical activity abnormalities not_specified http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Electroencephalogram (EEG) http://purl.obolibrary.org/obo/UBERON_0000955 UBERON Electroencephalogram (EEG) A test that detects electrical activity in your brain using small, metal discs (electrodes) attached to your scalp. in_vivo neurons brain electrical activity change http://purl.obolibrary.org/obo/OBI_0001482 OBI low Electroencephalogram (EEG) http://purl.obolibrary.org/obo/UBERON_0001038 UBERON Intracranial pressure monitoring Intracranial pressure monitoring measures the pressure inside the skull to detect swelling or other issues. in_vivo brain human intracranial pressure increase http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Intracranial pressure monitoring (ICP), measuring the pressure inside the skull http://purl.obolibrary.org/obo/UBERON_0000955 UBERON MRI Magnetic resonance imaging is used to detect structural abnormalities or inflammation in the brain. in_vivo brain human brain structural abnormalities or inflammation not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Magnetic resonance imaging (MRI) http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO MRI Magnetic resonance imaging (MRI) is a medical imaging technique used to visualize the internal structures of the brain, detecting signs of inflammation or damage associated with encephalitis. in_vivo brain brain structure and function change low Magnetic resonance imaging (MRI) http://purl.obolibrary.org/obo/UBERON_0000015 UBERON http://purl.obolibrary.org/obo/GO_0005694 GO Spinal tap Spinal tap (lumbar puncture) is used to collect cerebrospinal fluid for analysis of infection or inflammation. in_vivo cerebrospinal fluid human cerebrospinal fluid abnormalities not_specified http://purl.obolibrary.org/obo/UBERON_0001377 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO low Spinal tap (lumbar puncture) http://purl.obolibrary.org/obo/UBERON_0001377 UBERON http://purl.obolibrary.org/obo/GO_0006954 GO spinal tap Spinal tap (lumbar puncture) involves collecting cerebrospinal fluid (CSF) to analyze for signs of infection, inflammation, or immune system abnormalities. in_vivo immune cells spinal cord CSF composition change low Spinal tap (lumbar puncture) http://purl.obolibrary.org/obo/GO_0006952 GO Urine and stool tests Laboratory analysis of urine or stool samples to detect pathogens or metabolic markers. in_vitro urinary tract gastrointestinal tract pathogens or metabolic markers change not_specified Urine and stool tests Urine and stool tests Urine and stool tests are used to detect signs of infection or other abnormalities. in_vivo urine stool human signs of infection or other abnormalities not_specified http://purl.obolibrary.org/obo/UBERON_0001088 UBERON http://purl.obolibrary.org/obo/UBERON_0001956 UBERON medium Urine and stool tests http://purl.obolibrary.org/obo/UBERON_0001088 UBERON activated partial thromboplastin time Assessment of the intrinsic and common pathways of coagulation by measuring clotting time. not_specified blood human activated partial thromboplastin time not_specified not_specified Coagulation parameters include ... activated partial thromboplastin time http://purl.obolibrary.org/obo/UBERON_0000042 UBERON http://purl.obolibrary.org/obo/GO_0007569 GO antithrombin III Measurement of antithrombin III levels in the blood. not_specified blood human antithrombin III not_specified not_specified Coagulation parameters include ... antithrombin III coagulation parameter measurement Measures coagulation parameters such as platelet count, prothrombin time, activated partial thromboplastin time, D-dimer, fibrinogen, and antithrombin III in blood. in_vivo blood human coagulation parameters not_specified not_specified Coagulation and inflammatory parameters are measured in COVID-19 patients [Di Nisio et al. 2021]. Coagulation parameters include platelet count, prothrombin time, activated partial thromboplastin time, D-dimer, fibrinogen, antithrombin III [Di Nisio et al. 2021]. These parameters are measured in the blood. http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0050817 GO Coagulation parameters measurement Measures coagulation and inflammatory parameters including platelet count, prothrombin time, activated partial thromboplastin time, D-dimer, fibrinogen, and antithrombin III in the blood of COVID-19 patients. in_vivo blood human platelet count, prothrombin time, activated partial thromboplastin time, D-dimer, fibrinogen, antithrombin III change http://purl.obolibrary.org/obo/UBERON_0000908 UBERON http://purl.obolibrary.org/obo/CHEBI_16520 CHEBI low Coagulation and inflammatory parameters are measured in COVID-19 patients [Di Nisio et al. 2021]. Coagulation parameters include platelet count, prothrombin time, activated partial thromboplastin time, D-dimer, fibrinogen, antithrombin III [Di Nisio et al. 2021]. These parameters are measured in the blood. http://purl.obolibrary.org/obo/UBERON_0000908 UBERON http://purl.obolibrary.org/obo/GO_0007596 GO D-dimer Measures the level of D-dimer in blood, a fibrin degradation product indicating clot breakdown. in_vivo blood human D-dimer concentration change medium Coagulation parameters include platelet count, prothrombin time, activated partial thromboplastin time, D-dimer, fibrinogen, antithrombin III [Di Nisio et al. 2021]. http://purl.obolibrary.org/obo/CHEBI_58789 CHEBI http://purl.obolibrary.org/obo/GO_0008065 GO fibrinogen Measurement of fibrinogen concentration in the blood. not_specified blood human fibrinogen not_specified not_specified Coagulation parameters include ... fibrinogen http://purl.obolibrary.org/obo/CHEBI_16831 CHEBI http://purl.obolibrary.org/obo/GO_0007569 GO platelet count Measures the number of platelets in a blood sample, indicating coagulation status. in_vivo blood human platelet number change medium Coagulation parameters include platelet count, prothrombin time, activated partial thromboplastin time, D-dimer, fibrinogen, antithrombin III [Di Nisio et al. 2021]. http://purl.obolibrary.org/obo/CL_0000765 CL http://purl.obolibrary.org/obo/GO_0008065 GO prothrombin time Measures the time it takes for blood to clot, assessing the extrinsic pathway of coagulation. in_vivo blood human clotting time change medium Coagulation parameters include platelet count, prothrombin time, activated partial thromboplastin time, D-dimer, fibrinogen, antithrombin III [Di Nisio et al. 2021]. http://purl.obolibrary.org/obo/UBERON_0000901 UBERON http://purl.obolibrary.org/obo/GO_0008065 GO Whole blood coagulation and complement activation assay In vitro whole human blood model to test activation of coagulation and complement systems, as well as clot formation. in_vitro blood human coagulation and complement activation increase low In vitro systems Whole human blood model for testing the activation of coagulation and complement system, as well as clot formation [Ekstrand-Hammarström, B. et al. Biomaterials 2015, 51, 58-68, Ekdahl, K.N., et al. Nanomedicine: Nanotechnology, Biology and Medicine 2018, 14, 735-744, Ekdahl, K.N., et al. Science and Technology of Advanced Materials, 20:1, 688-698,] http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0007596 GO whole human blood model Tests the activation of coagulation and complement system, as well as clot formation in whole human blood. in_vitro blood human activation of coagulation and complement system, clot formation not_specified http://purl.obolibrary.org/obo/GO_0050817 GO not_specified Whole human blood model for testing the activation of coagulation and complement system, as well as clot formation [Ekstrand-Hammarström, B. et al. Biomaterials 2015, 51, 58-68, Ekdahl, K.N., et al. Nanomedicine: Nanotechnology, Biology and Medicine 2018, 14, 735-744, Ekdahl, K.N., et al. Science and Technology of Advanced Materials, 20:1, 688-698,] http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0050817 GO APTT Activated partial thromboplastin time (APTT) measures the time taken for fibrin clot formation after the addition of calcium to phospholipid and contact activator-treated plasma, reflecting the intrinsic and common coagulation pathways. in_vitro time taken for fibrin clot formation not_specified not_specified Activated partial prothrombin time (APTT). Platelet poor plasma [PPP] is incubated at 37°C then phospholipid (cephalin) and a contact activator (e.g. Kaolin, micronized silica, or ellagic acid) are added. This leads to the conversion of Factor XI [FXI] to FXIa. The remainder of the pathway is not activated as no calcium is present. The addition of calcium (pre-warmed to 37°C) initiates clotting. The APTT is the time taken from the addition of calcium to the formation of a fibrin clot. D-dimer concentration assay Measures cross-linked fibrin degradation products containing D-dimer in EDTA anticoagulated whole blood or plasma using a fluorescence immunoassay. in_vitro blood D-dimer concentration increase medium D-Dimer can be measured by a fluorescence immunoassay. To determine cross-linked fibrin degradation products containing D-dimer in EDTA anticoagulated whole blood and plasma specimens. The test is used as an aid in the assessment and evaluation of patients suspected of having disseminated intravascular coagulation or thromboembolic events including pulmonary embolism http://purl.obolibrary.org/obo/PR_000001490 PR http://purl.obolibrary.org/obo/GO_0042730 GO Fibrinogen concentration assay Measures fibrinogen concentration by clotting diluted plasma with a high concentration of thrombin and comparing the clotting time to a calibration curve. in_vitro blood fibrinogen concentration decrease medium Decreased fibrinogen concentrations. Diluted plasma is clotted with a high concentration of Thrombin. The tested plasma is diluted (usually 1:10 but this may vary if the Fibrinogen concentration is very low or very high) to minimize the effect of 'inhibitory substances' within the plasma e.g. heparin, elevated levels of FDPs. The use of a high concentration of Thrombin (typically 100 U/ml) ensures that the clotting times are independent of Thrombin concentration over a wide range of Fibrinogen levels. http://purl.obolibrary.org/obo/PR_000009337 PR http://purl.obolibrary.org/obo/GO_0007596 GO Platelet count Measures the number of platelets per microliter in blood. in_vitro blood platelet count not_specified high Platelet Measurements- A platelet count is the number of platelets a person has per microliter. The ideal platelet range is 150,000 – 400,000 per microliter in most healthy people. http://purl.obolibrary.org/obo/CL_0000056 CL http://purl.obolibrary.org/obo/GO_0007599 GO Prothrombin time (PT) Measures the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium to blood. in_vitro blood clotting time not_specified medium Prothrombin time (PT) is a blood test that measures how long it takes blood to clot. PT measures the time required for fibrin clot formation after the addition of tissue thromboplastin and calcium. http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0007596 GO 5EU RNA labeling Labels newly synthesized RNA with 5-ethynyl uridine (5EU) to measure RNA synthesis. in_vitro newly synthesized RNA not_specified http://purl.obolibrary.org/obo/GO_0009304 GO medium 5EU RNA labeling, capture of biotinylated 5EU labeled RNA http://purl.obolibrary.org/obo/SO_0000655 SO http://purl.obolibrary.org/obo/GO_0009304 GO Electron microscopy Visualizes viral particles to confirm viral production. in_vitro viral particle presence not_specified low electron microscopy In vitro reconstitution system Assesses the formation of liquid organelles in vitro. in_vitro liquid organelle formation not_specified low formation of liquid organelles is assessed in vitro reconstitution systems http://purl.obolibrary.org/obo/GO_0006996 GO Infectivity assay Measures the ability of released virions to infect cells. in_vitro viral infectivity increase low infectivity assays http://purl.obolibrary.org/obo/NCBITaxon_2697049 NCBITAXON IRF7-GFP splicing reporter Assesses splicing activity using a GFP reporter system. in_vitro splicing activity not_specified http://purl.obolibrary.org/obo/GO_0000375 GO medium IRF7-GFP splicing reporter http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0000375 GO Membrane SUnSET assay Measures the transport of plasma membrane proteins to the cell surface. in_vitro plasma membrane protein transport not_specified http://purl.obolibrary.org/obo/GO_0015031 GO low Membrane SUnSET assay for transport of plasma membrane proteins to the cell surface http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0015031 GO Plaque assay Measures viral infectivity by counting plaque-forming units. in_vitro plaque-forming units increase low Plaque assays http://purl.obolibrary.org/obo/NCBITaxon_2697049 NCBITAXON Plaque assay A microbiological assay used to quantify infectious viral particles by counting plaques formed in a cell monolayer. in_vitro viral production/infectivity not_specified low Plaque assays, infectivity assays, RT-qPCR to detect viral RNA in released virions puromycin incorporation This assay measures translation by assessing the incorporation of puromycin into newly synthesized proteins in HeLa cells. in_vitro HeLa puromycin incorporation change medium Transient expression of FLAG-Nsp1 in HeLa cells and puromycin incorporation assay http://purl.obolibrary.org/obo/PR_0000003 PR http://purl.obolibrary.org/obo/GO_0006412 GO puromycin incorporation assay Measures protein translation by quantifying the incorporation of puromycin into nascent polypeptide chains. in_vitro HeLa cells translation rate not_specified http://purl.obolibrary.org/obo/GO_0006412 GO not_specified Transient expression of FLAG-Nsp1 in HeLa cells and puromycin incorporation assay http://purl.obolibrary.org/obo/GO_0006412 GO Radioactive nucleoside labeling Labels newly synthesized viral RNA with radioactive nucleosides to measure viral replication. in_vitro newly synthesized viral RNA increase low Labelling by radioactive nucleosides http://purl.obolibrary.org/obo/GO_0019062 GO RT-PCR This assay detects mRNA transcripts of SARS-CoV-2, targeting genes like RdRp/helicase (Hel), spike (S), and nucleocapsid (N). in_vitro mRNA transcript levels increase medium The mRNA transcripts are detected by the real-time reverse transcription-PCR (RT-PCR) assay. RT-PCR assays targeting RdRp/helicase (Hel), spike (S), and nucleocapsid (N) genes of SARS-CoV-2 [Chan et al.]. http://purl.obolibrary.org/obo/CHEBI_5973 CHEBI http://purl.obolibrary.org/obo/GO_0006468 GO RT-PCR Detects SARS-CoV-2 mRNA transcripts using reverse transcription followed by PCR amplification. in_vitro SARS-CoV-2 mRNA transcripts increase medium The mRNA transcripts are detected by the real-time reverse transcription-PCR (RT-PCR) assay http://purl.obolibrary.org/obo/GO_0019083 GO RT-qPCR (viral replication) Quantifies viral RNA to measure viral replication in infected cells. in_vitro infected cells viral RNA quantity increase http://purl.obolibrary.org/obo/GO_0019062 GO high viral replication is measured by RT-qPCR in infected cells http://purl.obolibrary.org/obo/NCBITaxon_2697049 NCBITAXON http://purl.obolibrary.org/obo/GO_0019062 GO Sucrose pelleting binding assay Verifies the formation of the Nsp1–40S ribosomal complex. in_vitro Nsp1–40S complex formation not_specified low Sucrose pelleting binding assay to verify Nsp1–40S complex formation http://purl.obolibrary.org/obo/GO_0043233 GO http://purl.obolibrary.org/obo/GO_0006412 GO cytokine analysis TLR function is measurable by analysing components of downstream cascades and read outs of inflammatory mediators (IL6, IL8, IL10, Il17, INF, TNFalpha, etc). ex_vivo PBMCs human inflammatory mediator levels change http://purl.obolibrary.org/obo/GO_0002162 GO medium TLR function in response to stressors is measurable by analysing components of downstream cascades and read outs of inflammatory mediators (IL6, IL8, IL10, Il17, INF, TNFalpha, etc). http://purl.obolibrary.org/obo/GO_0002162 GO Ex vivo analysis of TLR stressors Measures levels of TLR-specific stressors such as cell-free DNA/RNA and mtDNA in biological samples like serum or plasma. ex_vivo serum plasma levels of TLR-specific stressors not_specified not_specified Levels of TLR specific stressors (for instance for TLR9, cell free DNA/RNA, mtDNA) are measurable in biological samples (serum, plasma) ex vivo stimulation Analysis of inflammatory mediators and downstream cascades following the stimulation of patient-isolated cells (e.g., PBMCs). ex_vivo PBMCs inflammatory mediators (IL6, IL8, IL10, Il17, INF, TNFalpha) change http://purl.obolibrary.org/obo/GO_0001501 GO not_specified TLR function in response to stressors is measurable by analysing components of downstream cascades and read outs of inflammatory mediators (IL6, IL8, IL10, Il17, INF, TNFalpha, etc). This can be done by ex vivo stimulations of cells isolated from patients for instance PBMCs. http://purl.obolibrary.org/obo/GO_0006954 GO ex vivo stimulation of PBMCs Analysis of TLR function by stimulating isolated patient PBMCs and measuring downstream cascade components and inflammatory mediators like IL6, IL8, etc. ex_vivo PBMCs inflammatory mediators and downstream cascade components change not_specified TLR function in response to stressors is measurable by analysing components of downstream cascades and read outs of inflammatory mediators (IL6, IL8, IL10, Il17, INF, TNFalpha, etc). This can be done by ex vivo stimulations of cells isolated from patients for instance PBMCs. Ex vivo TLR function assay Measures TLR function in response to stressors by analyzing downstream inflammatory mediators (e.g., IL6, IL8, IL10, IL17, IFN, TNFalpha) in ex vivo stimulated cells such as PBMCs. ex_vivo PBMCs levels of inflammatory mediators not_specified not_specified TLR function in response to stressors is measurable by analysing components of downstream cascades and read outs of inflammatory mediators (IL6, IL8, IL10, Il17, INF, TNFalpha, etc). This can be done by ex vivo stimulations of cells isolated from patients for instance PBMCs. mRNA analysis TLR expression levels are measurable by mRNA analysis. ex_vivo PBMCs human TLR expression levels change http://purl.obolibrary.org/obo/GO_0006925 GO medium TLR expression levels on different cell types and different tissues are measurable by mRNA analysis http://purl.obolibrary.org/obo/GO_0006925 GO protein analysis TLR expression levels are measurable by protein analysis. ex_vivo PBMCs human TLR expression levels change http://purl.obolibrary.org/obo/GO_0005576 GO medium TLR expression levels on different cell types and different tissues are measurable by mRNA analysis and by protein analysis http://purl.obolibrary.org/obo/GO_0005576 GO TLR knock-out mice Uses genetically modified mice lacking specific TLRs to study TLR function in vivo. in_vivo Mus musculus TLR function not_specified low TLR knock-out mice TLR polymorphism analysis Measures TLR gain-of-function and loss-of-function polymorphisms. ex_vivo TLR polymorphisms not_specified not_specified TLR gain of function and loss of function polymorphisms are measurable TLR Reporter assay TLR Reporter assays are used to measure TLR activation. in_vitro reporter gene expression increase high TLR Reporter assays http://purl.obolibrary.org/obo/GO_0007165 GO TLR Reporter assay Measures TLR activity using reporter gene assays to detect downstream signaling events. in_vitro TLR activity not_specified not_specified TLR Reporter assays ACE2 activity assay Measures ACE2 activity using fluorescently labeled peptide substrates, quantifying catalytic products directly or markers of activation of receptors for the products indirectly. in_vitro ACE2 catalytic activity change http://purl.obolibrary.org/obo/GO_0004393 GO not_specified ACE2 activity using fluorescently labeled peptide substrates measuring catalytic products (direct) or markers of activation of receptors for the products (indirect) of ACE2 activity (Rice, 2004; Sodhi, 2008; Roca-Ho, 2017 1; Lu and Sun, 2020; Xiao 2017) http://purl.obolibrary.org/obo/GO_0004553 GO ACE2 activity assay Measurement of ACE2 catalytic activity using fluorescently labeled peptide substrates to quantify catalytic products or downstream receptor activation. in_vitro catalytic products change not_specified ACE2 activity using fluorescently labeled peptide substrates measuring catalytic products (direct) or markers of activation of receptors for the products (indirect) of ACE2 activity fluorescent peptide substrate assay Measures ACE2 activity using fluorescently labeled peptide substrates to detect catalytic products. in_vitro ACE2 activity not_specified http://purl.obolibrary.org/obo/GO_0003824 GO medium ACE2 activity using fluorescently labeled peptide substrates measuring catalytic products (direct) http://purl.obolibrary.org/obo/GO_0004180 GO immunoprecipitation Measures ACE2 protein levels in tissue extracts or preparations using immunoprecipitation. in_vitro ACE2 protein levels not_specified low protein in tissue extracts/preparations by immunoprecipitation http://purl.obolibrary.org/obo/GO_0019538 GO immunostaining Measures ACE2 protein levels in live tissues or cultured cells using immunostaining. in_vitro ACE2 protein levels not_specified medium protein in live tissues or cultured cells by immunostaining (Humming 2007; Fraga-Silva et al., 2011; Ren 2006; Warner 2005) http://purl.obolibrary.org/obo/GO_0019538 GO Immunostaining Detection of ACE2 protein in live tissues or cultured cells via immunostaining. in_vitro protein presence/localization change not_specified protein in live tissues or cultured cells by immunostaining quantitative proteomic analysis High-throughput and quantitative measurement of ACE2 protein levels using proteomic analysis. in_vitro ACE2 protein levels not_specified http://purl.obolibrary.org/obo/OBI_0000175 OBI high high throughput and quantitative measurement of protein by quantitative proteomic analysis (Park 2020; Stegbauer 2020) http://purl.obolibrary.org/obo/GO_0019538 GO Quantitative proteomic analysis High-throughput quantitative measurement of ACE2 protein levels. in_vitro protein levels change high high throughput and quantitative measurement of protein by quantitative proteomic analysis RT-PCR Measures ACE2 mRNA levels using reverse transcription polymerase chain reaction. in_vitro ACE2 mRNA levels not_specified http://purl.obolibrary.org/obo/GO_0010467 GO medium ACE2 levels mRNA by RT-PCR (Sodhi 2018; Roca-Ho, 2017) http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Measurement of ACE2 mRNA levels using reverse transcription polymerase chain reaction. in_vitro mRNA levels change not_specified ACE2 levels mRNA by RT-PCR scRNA-seq Measures ACE2 mRNA levels at single-cell resolution using single-cell RNA sequencing. in_vitro ACE2 mRNA levels not_specified http://purl.obolibrary.org/obo/OBI_0002181 OBI http://purl.obolibrary.org/obo/GO_0010467 GO high ACE2 levels mRNA by [...] scRNA seq (e.g. Qi. et al 2020) http://purl.obolibrary.org/obo/GO_0010467 GO scRNA-seq Single-cell RNA sequencing to measure ACE2 mRNA levels. in_vitro mRNA levels change high ACE2 levels mRNA by ... scRNA seq Western blotting Measures ACE2 protein levels in tissue extracts or preparations using Western blotting. in_vitro ACE2 protein levels not_specified low protein in tissue extracts/preparations by [...] Western blotting (Koka 2008) http://purl.obolibrary.org/obo/GO_0019538 GO Western blotting Measurement of ACE2 protein levels in tissue extracts using immunoprecipitation or Western blotting. in_vitro protein levels change not_specified protein in tissue extracts/preparations by immunoprecipitation or Western blotting flow cytometry Flow cytometry measures circulating neutrophil-platelet complexes in whole blood based on fluorescence-labelling of platelets and leukocytes. The endpoint is quantified as the percentage of total leukocytes (neutrophils) that stain for a platelet-specific marker. in_vivo neutrophils platelets leukocytes humans animals neutrophil-platelet complexes increase http://purl.obolibrary.org/obo/GO_0007018 GO high Flow cytometry is the method of choice to measure circulating neutrophil-platelet complexes in both humans and animals. http://purl.obolibrary.org/obo/CL_0000755 CL http://purl.obolibrary.org/obo/GO_0007018 GO Flow cytometry Measures circulating neutrophil-platelet complexes in whole blood using fluorescence-labelling of platelets and leukocytes, quantified as the percentage of leukocytes staining for a platelet-specific marker. in_vivo neutrophils platelets human animal percentage of leukocytes with platelet markers increase http://purl.obolibrary.org/obo/OBI_0000796 OBI medium Flow cytometry is the method of choice to measure circulating neutrophil-platelet complexes in both humans and animals. This technique is based on fluorescence-labelling of platelets and leukocytes in whole blood. Characteristic side scatter properties of leukocyte subtypes already permit basic discrimination of platelets binding to neutrophils, monocytes and lymphocytes. However, leukocyte subtype-specific antibodies generate more accurate data. The endpoint is quantified as the percentage of total leukocytes (i.e. neutrophils) that also stain for a platelet-specific marker. http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0098609 GO Histochemical and immunofluorescent imaging Visualizes platelet recruitment and neutrophil-platelet complexes in tissue sections using frozen or paraffin-embedded samples, optionally coupled with confocal or electron microscopy. in_vivo neutrophils platelets most organs location of platelet recruitment and neutrophil-platelet complexes increase http://purl.obolibrary.org/obo/OBI_0000558 OBI low Histochemical and immunofluorescent imaging of frozen or paraffin-embedded tissue sections. This approach can provide valuable information about the location of platelet recruitment and neutrophil-platelet complexes within tissue microenvironments of most organs. These techniques can be coupled with confocal or electron microscopy to provide higher resolution visualization of platelet-neutrophil interactions. http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0098609 GO Imaging flow cytometry Combines flow cytometry with fluorescence microscopy to assess the number of bound platelets and involved interaction molecules. in_vivo neutrophils platelets human animal number of bound platelets and interaction molecules increase medium Flow cytometry coupled with fluorescence microscopy (imaging flow cytometry). This approach enables direct assessment of both number of bound platelets as well as involved interaction molecules and coincidental events. http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0098609 GO Intravital microscopy Tracks labeled cells in live animals over time to analyze dynamic interactions between platelets and neutrophils in organs such as liver, lung, and brain. in_vivo neutrophils platelets liver lung brain animal dynamic interactions between platelets and neutrophils increase low Live cell imaging coupled with intravital microscopy (IVM) allows to track labeled cells in live animals over longer time periods in organs including liver, lung, and brain. This approach can be used to analyze the dynamic interactions between platelets and neutrophils (e.g., duration of interactions and behavioural changes in neutrophils and/or platelets upon contact). http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0098609 GO Microfluidic assay Visualizes neutrophil-platelet interactions in real time using isolated cells or whole blood perfused through a chamber coated with immobilized proteins or cells, with specific antibodies for visualization. in_vitro neutrophils platelets human neutrophil-platelet interactions increase low Microfluidic assays can allow to visualize neutrophil-platelet interactions in real time in vitro. This approach involves the use of isolated cells or whole blood that are perfused through a chamber coated with immobilized proteins or cells. Specific cells are visualized thanks to the use of specific antibodies. http://purl.obolibrary.org/obo/CL_0000775 CL http://purl.obolibrary.org/obo/GO_0098609 GO Chlorophyll fluorescence analysis Measures the maximum quantum yield of PSII (Fv/Fm) as a non-invasive indicator of PSII photochemical efficiency and photoinhibitory damage using pulse-amplitude-modulated (PAM) fluorometry. in_vivo leaf maximum quantum yield of PSII (Fv/Fm) decrease http://purl.obolibrary.org/obo/GO_0010208 GO http://purl.obolibrary.org/obo/GO_0009523 GO high chlorophyll fluorescence analysis, particularly the measurement of the maximum quantum yield of PSII (Fv/Fm), which provides a sensitive, non-invasive indicator of PSII photochemical efficiency and photoinhibitory damage Pulse-amplitude-modulated (PAM) fluorometry and related modulated fluorescence techniques allow both dark-adapted and light-adapted measurements, enabling assessment of effective PSII quantum yield and dynamic responses to stressors http://purl.obolibrary.org/obo/GO_0009523 GO http://purl.obolibrary.org/obo/GO_0019684 GO D1 protein degradation assay Assesses degradation or modification of the D1 protein of PSII, a primary target of photodamage and herbicide interaction, to support evidence of PSII damage. in_vivo D1 protein degradation increase http://purl.obolibrary.org/obo/GO_0009523 GO low degradation or modification of the D1 protein of PSII can be assessed to support evidence of PSII damage. The D1 protein is a primary target of photodamage and herbicide interaction, and increased D1 turnover or instability is closely linked to declines in PSII efficiency http://purl.obolibrary.org/obo/GO_0019684 GO Photosynthetic oxygen evolution Measures oxygen evolution rates using polarographic oxygen electrodes to assess the functional integrity of the PSII water-splitting complex and downstream electron transport capacity. in_vivo leaf photosynthetic oxygen evolution rate decrease http://purl.obolibrary.org/obo/GO_0018661 GO http://purl.obolibrary.org/obo/GO_0009523 GO medium PSII efficiency can also be evaluated through measurements of photosynthetic oxygen evolution rates, typically using polarographic oxygen electrodes with leaf discs, algal cultures, or isolated chloroplasts. These measurements directly reflect the functional integrity of the PSII water-splitting complex and downstream electron transport capacity http://purl.obolibrary.org/obo/GO_0009523 GO http://purl.obolibrary.org/obo/GO_0019684 GO transcription profiling Measures transcription profiles of human bronchial alveolar lavage samples, focusing on downregulation of fibrinolytic cascade genes. in_vitro bronchial alveolar lavage human gene expression of fibrinolytic cascade proteins decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0042730 GO medium transcription profiles of e.g. human bronchial alveolar lavage (BAL) samples can be measured, with targeted analyses focused on downregulation of genes transcribing for proteins involved in the fibrinolytic cascade, e.g. uPA (PLAU), uPAR (PLAUR) http://purl.obolibrary.org/obo/CHEBI_33697 CHEBI http://purl.obolibrary.org/obo/GO_0042730 GO Transcription profiling of BAL samples This assay measures gene expression levels in human bronchial alveolar lavage (BAL) specimens, focusing on downregulation of fibrinolytic genes such as uPA (PLAU) and uPAR (PLAUR). ex_vivo lung human mRNA expression levels of PLAU and PLAUR decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0042730 GO low transcription profiles of e.g. human bronchial alveolar lavage (BAL) samples can be measured, with targeted analyses focused on downregulation of genes transcribing for proteins involved in the fibrinolytic cascade, e.g. uPA (PLAU), uPAR (PLAUR) http://purl.obolibrary.org/obo/GO_0042730 GO transcriptional profiling Transcriptional profiling of human bronchial alveolar lavage (BAL) samples measures the expression of genes involved in the fibrinolytic cascade, such as uPA (PLAU) and uPAR (PLAUR). in_vitro bronchial alveolar lavage human gene expression decrease high In addition, transcription profiles of e.g. human bronchial alveolar lavage (BAL) samples can be measured, with targeted analyses focused on downregulation of genes transcribing for proteins involved in the fibrinolytic cascade, e.g. uPA (PLAU), uPAR (PLAUR). http://purl.obolibrary.org/obo/CHEBI_59834 CHEBI http://purl.obolibrary.org/obo/GO_0008270 GO viscoelastic haemostatic assay Evaluates thrombus formation under low shear stress and differentiates causes of coagulopathy. in_vitro human thrombus formation and coagulopathy causes change http://purl.obolibrary.org/obo/GO_0072378 GO http://purl.obolibrary.org/obo/GO_0050817 GO medium Devices for performing viscoelastic haemostatic assays (VHA) are available in most intensive care units as a near-patient method for evaluating thrombus formation under low shear stress. Outputs of such assays are primarily used in the setting of major haemorrhage to rapidly determine the need for replacement of specific blood products. Importantly, VHA can differentiate causes of coagulopathy, for example, coagulation factor deficiency vs thrombocytopenia vs excessive fibrinolysis. http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0007596 GO Whole blood fibrinolysis assay An in vitro whole human blood model that assesses dysregulation of the fibrinolytic cascade, including cross-talk between blood cells and plasma proteins, using parameters such as complement, contact, coagulation, and fibrinolysis system activation, as well as cell phenotypes measured by flow cytometry and cytokine/chemokine generation. in_vitro Homo sapiens fibrinolytic cascade dysregulation change http://purl.obolibrary.org/obo/GO_0007596 GO http://purl.obolibrary.org/obo/GO_0006955 GO low In vitro systems Whole human blood model for testing the dysregulation of fibrinolysis. The same model system allows for analysis of any kind of cross talk between blood cells and plasma proteins as reflected in the cascade system (complement, contact, coagulation, fibrinolysis systems activation etc) parameters, other plasma protein alterations and cell phenotypes (flow cytometry, cyto/chemokine generation, protein release etc) http://purl.obolibrary.org/obo/GO_006094 GO http://purl.obolibrary.org/obo/GO_0007596 GO whole human blood model Tests dysregulation of fibrinolysis and cross-talk between blood cells and plasma proteins in cascade systems. in_vitro human fibrinolysis dysregulation and cascade system parameters change http://purl.obolibrary.org/obo/GO_0042730 GO http://purl.obolibrary.org/obo/GO_0007596 GO low Whole human blood model for testing the dysregulation of fibrinolysis. The same model system allows for analysis of any kind of cross talk between blood cells and plasma proteins as reflected in the cascade system (complement, contact, coagulation, fibrinolysis systems activation etc) parameters http://purl.obolibrary.org/obo/PR_000009358 PR http://purl.obolibrary.org/obo/GO_0042730 GO Transcriptional profiling Measures transcriptional activation of genes involved in the bradykinin system (KLKB1, KNG1, KLK1, CPN1, BDKRB1, BDKRB2, SERPING1) and RAAS system (AGT, AGTR1, AGTR2, ACE2, ACE) in human samples. in_vivo BAL human gene expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0004952 GO http://purl.obolibrary.org/obo/GO_0001992 GO medium In human samples (e.g. BAL) the activation of the bradykinin system could potentially be measured on transcriptional level, with focus on activation of KLKB1, KNG1, KLK1, CPN1, and the BK receptors BDKRB1 and BDKRB2, as well as potential down-regulation of SERPING1. Activation of the RAAS system should also be monitored, specifically on AGT, AGTR1, and AGTR2. Additional indications may be obtained from transcriptional up-regulation of ACE2 (potential result as a compensatory mechanism due to the “high-jacking” by the virus) and down-regulation of ACE. http://purl.obolibrary.org/obo/GO_0002031 GO Whole blood assay Testing the activation of the kallikrein system using a whole human blood model. in_vitro human blood cells blood human kallikrein system activation increase low Whole human blood model for testing the activation of the kallikrein system (10.1016/j.biomaterials.2015.01.031, 10.1016/j.nano.2017.12.008, 10.1080/14686996.2019.1625721). http://purl.obolibrary.org/obo/GO_0043067 GO Whole human blood model Tests the activation of the kallikrein system in vitro using whole human blood. in_vitro blood human kallikrein system activation increase http://purl.obolibrary.org/obo/UBERON_0000178 UBERON medium Whole human blood model for testing the activation of the kallikrein system (10.1016/j.biomaterials.2015.01.031, 10.1016/j.nano.2017.12.008, 10.1080/14686996.2019.1625721). The system has initially been applied only to nanomaterials. http://purl.obolibrary.org/obo/GO_0008009 GO CRP measurement Measures excessive serum levels of C-reactive protein (CRP), a pro-inflammatory mediator. in_vivo serum human CRP serum levels increase http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium excessive serum levels of pro-inflammatory mediator C-reactive protein (CRP) http://purl.obolibrary.org/obo/GO_0006954 GO D-dimer measurement Measures increased levels of D-dimer in serum, a marker of hyperinflammation. in_vivo serum human D-dimer serum levels increase http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium high levels of D-dimer http://purl.obolibrary.org/obo/GO_0050817 GO Ferritin measurement Measures high levels of ferritin in serum, a marker of hyperinflammation. in_vivo serum human ferritin serum levels increase http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium high levels of ferritin http://purl.obolibrary.org/obo/GO_0006954 GO IL1β measurement Measures serum levels of IL1β, a molecular marker associated with hyperinflammation. in_vivo serum human IL1β serum levels increase http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium Other molecular markers associated with hyperinflammation include IL1β http://purl.obolibrary.org/obo/GO_0006954 GO IL6 measurement Measures high serum levels of IL6 protein, a causal and indicative marker of hyperinflammation. in_vivo serum human IL6 serum levels increase http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium high serum levels of IL6 protein and accumulation of neutrophils to be causal and indicative of hyperinflammation http://purl.obolibrary.org/obo/GO_0006954 GO Lactate dehydrogenase measurement Measures increased lactate dehydrogenase levels in serum, a marker of tissue damage. in_vivo serum human lactate dehydrogenase serum levels increase http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium increased lactate dehydrogenase http://purl.obolibrary.org/obo/GO_0044237 GO Lymphocyte count Measures the reduction or absence of lymphocytes (lymphopenia) in serum. in_vivo lymphocytes serum human lymphocyte count decrease http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium reduced or absence of lymphocytes (lymphopenia) http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0006955 GO Neutrophil accumulation measurement Assessment of neutrophil accumulation. The assay quantifies accumulation of neutrophils. in_vivo neutrophils Neutrophil accumulation increase http://purl.obolibrary.org/obo/CL_0000733 CL http://purl.obolibrary.org/obo/GO_0008367 GO medium accumulation of neutrophils http://purl.obolibrary.org/obo/CL_0000733 CL http://purl.obolibrary.org/obo/GO_0008367 GO Neutrophil to lymphocyte ratio Measures the ratio of neutrophils to lymphocytes in serum, a clinical marker of hyperinflammation. in_vivo neutrophils lymphocytes serum human neutrophil to lymphocyte ratio increase http://purl.obolibrary.org/obo/CL_0000094 CL http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium Higher neutrophil to lymphocyte ratio is another clinical marker http://purl.obolibrary.org/obo/CL_0000094 CL http://purl.obolibrary.org/obo/GO_0006955 GO TNFα measurement Measures serum levels of TNFα, a molecular marker associated with hyperinflammation. in_vivo serum human TNFα serum levels increase http://purl.obolibrary.org/obo/UBERON_0000177 UBERON medium Other molecular markers associated with hyperinflammation include TNFɑ http://purl.obolibrary.org/obo/GO_0006954 GO 3-nitrotyrosine assay Measures 3-nitrotyrosine as a marker of protein oxidation. in_vitro 3-nitrotyrosine levels increase http://purl.obolibrary.org/obo/CHEBI_17996 CHEBI medium Oxidation of protein can be measured by the detection of protein carbonyl content (PCC), 3-nitrotyrosine, advanced oxidation protein products, or BPDE protein adduct. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI 8-oxo-dG ELISA Measures 8-oxo-dG (8-hydroxy-2'-deoxyguanosine) as a marker of DNA oxidation using ELISA. in_vitro 8-oxo-dG levels increase http://purl.obolibrary.org/obo/CHEBI_17588 CHEBI high DNA oxidation can be detected with 8-oxo-dG / 8-hydroxy-2'-deoxyguanosine (8-OHdG) by ELISA or HPLC http://purl.obolibrary.org/obo/CHEBI_15975 CHEBI advanced oxidation protein products assay Measures advanced oxidation protein products as a marker of protein oxidation. in_vitro advanced oxidation protein products increase medium Oxidation of protein can be measured by the detection of protein carbonyl content (PCC), 3-nitrotyrosine, advanced oxidation protein products, or BPDE protein adduct. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI BPDE protein adduct assay Measures BPDE protein adducts as a marker of protein oxidation. in_vitro BPDE protein adduct levels increase medium Oxidation of protein can be measured by the detection of protein carbonyl content (PCC), 3-nitrotyrosine, advanced oxidation protein products, or BPDE protein adduct. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI catalase activity assay Measures catalase enzyme activity, which resolves hydrogen peroxide into water and oxygen. in_vitro catalase activity increase http://purl.obolibrary.org/obo/GO_0004096 GO medium The level of catalase, glutathione, or superoxide dismutase can be measured as anti-oxidants. Catalase is an anti-oxidative enzyme that catalyses the resolution of hydrogen peroxide (H2O2) into H2O and O2. http://purl.obolibrary.org/obo/PR_000001239 PR http://purl.obolibrary.org/obo/GO_0006979 GO cell-based exogenous antioxidant assay Measures antioxidant capacity in cells exposed to exogenous antioxidants. in_vitro antioxidant capacity increase medium Oxygen radical antioxidant capacity (ORAC), hydroxyl radical antioxidant capacity (HORAC), total antioxidant capacity (TAC), the cell-based exogenous antioxidant assay can be used for measuring the antioxidant capacity. http://purl.obolibrary.org/obo/CHEBI_22574 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO colorimetric H2O2 assay Detects hydrogen peroxide (H2O2) using a colorimetric probe that produces a pink product measured at 540-570 nm. in_vitro H2O2 levels increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI high Hydrogen peroxide (H2O2) can be detected with a colorimetric probe, which reacts with H2O2 in a 1:1 stoichiometry to produce a bright pink colored product, followed by the detection with a standard colorimetric microplate reader with a filter in the 540-570 nm range. http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO DCFH-DA assay Measures hydroxyl, peroxyl, or other ROS using the fluorescence probe DCFH-DA at 480 nm/530 nm. in_vitro ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI high Hydroxyl, peroxyl, or other ROS can be measured using a fluorescence probe, 2', 7'-Dichlorodihydrofluorescin diacetate (DCFH-DA), at fluorescence detection at 480 nm/530 nm. http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO EMSA Measures the binding of Nrf2 to ARE sequences using radioactively labeled ARE sequences and visualizing DNA-protein complexes on a gel. in_vitro Nrf2-ARE complex formation increase low EMSA is a technique that measures the binding of Nrf2 to ARE sequences. The intensity of the complex can indicate Nrf2 binding activity. http://purl.obolibrary.org/obo/GO_0003677 GO glutathione assay Measures glutathione levels as an antioxidant marker. in_vitro glutathione levels increase http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI medium The level of catalase, glutathione, or superoxide dismutase can be measured as anti-oxidants. http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Immunofluorescence Assesses the cellular localization of Nrf2 using antibodies and fluorescently labeled secondary antibodies. in_vitro Nrf2 cellular localization change low Immunofluorescence can be used to assess the cellular localization of Nrf2. Nrf2 localization within the cell (e.g., cytoplasm or nucleus) can indicate its activation status. http://purl.obolibrary.org/obo/CHEBI_16263 CHEBI http://purl.obolibrary.org/obo/GO_0006955 GO intracellular nitric oxide assay Detects nitric oxide levels within cells. in_vitro intracellular nitric oxide levels increase http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI medium Nitric oxide can be detected in intracellular nitric oxide assay http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/GO_0006806 GO intracellular ROS assay Detects reactive oxygen species (ROS) within cells using fluorescence probes. in_vitro intracellular ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI medium ROS can be detected by intracellular ROS assay http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO Luciferase Reporter Assay Measures Nrf2 activity by transfecting cells with a reporter plasmid containing Nrf2-responsive antioxidant response element (ARE) sequences and a luciferase gene, and measuring luciferase activity. in_vitro luciferase activity change medium This widely used method involves creating a reporter plasmid containing Nrf2-responsive antioxidant response element (ARE) sequences and a luciferase gene. Increased luciferase activity indicates Nrf2 activation, while decreased activity suggests diminished Nrf2 activity. http://purl.obolibrary.org/obo/CHEBI_16263 CHEBI http://purl.obolibrary.org/obo/GO_0006955 GO MDA-TBA assay Measures malondialdehyde (MDA) as a marker of lipid peroxidation using thiobarbituric acid (TBA) reactive substances. in_vitro MDA levels increase http://purl.obolibrary.org/obo/CHEBI_15355 CHEBI http://purl.obolibrary.org/obo/GO_0046470 GO medium Lipid peroxidation can be monitored by thiobarbituric acid (TBA) reactive substances in biological samples. MDA and TBA form MDA-TBA adduct in a 1:2 stoichiometry and detected by colorimetric or fluorometric measurement. http://purl.obolibrary.org/obo/CHEBI_18059 CHEBI http://purl.obolibrary.org/obo/GO_0034440 GO Nrf2 qPCR assay Assesses Nrf2 activity at the transcriptional level by quantifying mRNA levels of Nrf2 target genes (e.g., NQO1, HO-1) using quantitative PCR. in_vitro mRNA expression of Nrf2 target genes change http://purl.obolibrary.org/obo/GO_0032730 GO not_specified b. Quantitative PCR (qPCR): - Assessing Nrf2 activity at the transcriptional level can be achieved through qPCR. - Specific Nrf2 target genes (e.g., NQO1, HO-1) are selected and their mRNA levels are quantified. - Increased expression of these genes is indicative of Nrf2 activation, while reduced expression suggests diminished Nrf2 activity. http://purl.obolibrary.org/obo/CHEBI_15886 CHEBI http://purl.obolibrary.org/obo/GO_0010467 GO Nrf2-ARE luciferase reporter assay Measures Nrf2 transcriptional activity using a luciferase reporter construct containing antioxidant response element (ARE) sequences. in_vitro Nrf2 transcriptional activity increase http://purl.obolibrary.org/obo/OBI_0000466 OBI medium This widely used method involves creating a reporter plasmid containing Nrf2-responsive antioxidant response element (ARE) sequences and a luciferase gene. Cells of interest are transfected with the Nrf2-ARE luciferase reporter construct. After exposure to the stressor of interest, cells are lysed, and luciferase activity is measured. Increased luciferase activity indicates Nrf2 activation, while decreased activity suggests diminished Nrf2 activity. http://purl.obolibrary.org/obo/PR_000000064 PR http://purl.obolibrary.org/obo/GO_0034599 GO ORAC assay Measures oxygen radical antioxidant capacity as an oxidative stress marker. in_vitro oxygen radical antioxidant capacity increase medium Oxygen radical antioxidant capacity (ORAC), hydroxyl radical antioxidant capacity (HORAC), total antioxidant capacity (TAC), the cell-based exogenous antioxidant assay can be used for measuring the antioxidant capacity. http://purl.obolibrary.org/obo/CHEBI_22574 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO PEGylated bilirubin-coated iron oxide nanoparticles assay Detects ROS in whole blood using PEGylated bilirubin-coated iron oxide nanoparticles. in_vivo whole blood ROS levels increase http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/UBERON_0000178 UBERON medium ROS can be detected by PEGylated bilirubin-coated iron oxide nanoparticles in whole blood http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO protein carbonyl content (PCC) assay Detects protein oxidation by measuring protein carbonyl content (PCC) using specific reagents that react with carbonyl groups on oxidized proteins. in_vitro not specified not specified not specified protein oxidation increase http://purl.obolibrary.org/obo/CHEBI_25234 CHEBI http://purl.obolibrary.org/obo/PR_000000001 PR not_specified Oxidation of protein can be measured by the detection of protein carbonyl content (PCC), 3-nitrotyrosine, advanced oxidation protein products, or BPDE protein adduct. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006801 GO protein carbonyl content assay Measures protein carbonyl content as a marker of protein oxidation. in_vitro protein carbonyl content increase medium Oxidation of protein can be measured by the detection of protein carbonyl content (PCC), 3-nitrotyrosine, advanced oxidation protein products, or BPDE protein adduct. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI qPCR Assesses Nrf2 activity at the transcriptional level by quantifying mRNA levels of specific Nrf2 target genes (e.g., NQO1, HO-1). in_vitro mRNA levels of Nrf2 target genes change http://purl.obolibrary.org/obo/GO_0006955 GO medium Assessing Nrf2 activity at the transcriptional level can be achieved through qPCR. Increased expression of these genes is indicative of Nrf2 activation, while reduced expression suggests diminished Nrf2 activity. http://purl.obolibrary.org/obo/GO_0006955 GO superoxide dismutase assay Measures superoxide dismutase enzyme activity as an antioxidant marker. in_vitro superoxide dismutase activity increase http://purl.obolibrary.org/obo/GO_0004784 GO medium The level of catalase, glutathione, or superoxide dismutase can be measured as anti-oxidants. http://purl.obolibrary.org/obo/PR_000025083 PR http://purl.obolibrary.org/obo/GO_0006979 GO TAC assay Measures total antioxidant capacity as an oxidative stress marker. in_vitro total antioxidant capacity increase medium Oxygen radical antioxidant capacity (ORAC), hydroxyl radical antioxidant capacity (HORAC), total antioxidant capacity (TAC), the cell-based exogenous antioxidant assay can be used for measuring the antioxidant capacity. http://purl.obolibrary.org/obo/CHEBI_22574 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO TBA reactive substances assay An assay measuring lipid peroxidation by detecting thiobarbituric acid (TBA) reactive substances, including malondialdehyde (MDA) and 4-hydroxynonenal (4-HNE), in biological samples via colorimetric or fluorometric measurement. in_vitro lipid peroxidation products (MDA, 4-HNE) level change http://purl.obolibrary.org/obo/CHEBI_16461 CHEBI http://purl.obolibrary.org/obo/GO_0006512 GO not_specified Lipid peroxides decompose to form malondialdehyde (MDA) and 4, hydroxynonenal (4-HNE), natural bi-products of lipid peroxidation. Lipid peroxidation can be monitored by thiobarbituric acid (TBA) reactive substances in biological samples. MDA and TBA form MDA-TBA adduct in a 1:2 stoichiometry and detected by colorimetric or fluorometric measurement. http://purl.obolibrary.org/obo/CHEBI_16333 CHEBI http://purl.obolibrary.org/obo/GO_0006512 GO Western Blotting Detects Nrf2 protein levels in cell or tissue samples using specific antibodies. in_vitro Nrf2 protein levels change low This method allows the detection of Nrf2 protein levels in cell or tissue samples. Increased Nrf2 protein levels suggest Nrf2 activation, while reduced levels indicate diminished activity. http://purl.obolibrary.org/obo/CHEBI_16263 CHEBI http://purl.obolibrary.org/obo/GO_0006955 GO histology This methodology describes the sustentacular cells as a major non-neuronal component of the olfactory epithelium and details their biological roles, including mechanical support, nutrient provision, and maintenance of ion balance. The methodology does not describe a specific assay, but rather a characterization of the cells. not_specified olfactory epithelium sustentacular cell characteristics not_specified http://purl.obolibrary.org/obo/UBERON_0002633 UBERON http://purl.obolibrary.org/obo/CL_0000000 CL low The sustentacular cells are one of the major non neuronal cellular constituents of the olfactory epithelium (OE). The sustentacular cells provide mechanical strength to the olfactory epithelium, generate the olfactory binding protein, and support the other cells with nutrients (Choi and Goldstein, 2018). Sustentacular cells are responsible for the maintenance of the ion and water balance within the olfactory epithelium (Suzuki et al., 2000). http://purl.obolibrary.org/obo/GO_0005674 GO Sustentacular cell count Measures the number of sustentacular cells in the olfactory epithelium. not_specified sustentacular cells olfactory epithelium sustentacular cell count decrease http://purl.obolibrary.org/obo/CL_0000177 CL http://purl.obolibrary.org/obo/UBERON_0001754 UBERON not_specified The sustentacular cells are one of the major non neuronal cellular constituents of the olfactory epithelium (OE). Sustentacular cells provide mechanical strength to the olfactory epithelium, generate the olfactory binding protein, and support the other cells with nutrients (Choi and Goldstein, 2018). http://purl.obolibrary.org/obo/CL_0000177 CL olfactory sensory neuron characterization Characterization of olfactory sensory neurons (OSNs) in the olfactory epithelium, including their structure, location, and role in olfactory reception and transduction. not_specified olfactory sensory neurons olfactory epithelium olfactory sensory neuron characteristics not_specified http://purl.obolibrary.org/obo/CL_0000100 CL http://purl.obolibrary.org/obo/UBERON_0001753 UBERON http://purl.obolibrary.org/obo/GO_0007606 GO not_specified The olfactory sensory neurons (OSNs) together with a number nonneuronal cells form the olfactory epithelium (OE). OSNs in the OE could be differentiated into hundreds of subsets, depending on the phenotype of odorant receptor proteins. The OSNs are undoubtedly the OE’s parenchymal cells responsible for olfactory reception and transduction. http://purl.obolibrary.org/obo/CL_0000100 CL http://purl.obolibrary.org/obo/GO_0007606 GO clinical examination Detection of stroke through physical and neurological assessment. in_vivo human stroke diagnosis not_specified http://purl.obolibrary.org/obo/MONDO_0005130 MONDO low It is detected by clinical examination http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0050878 GO CT Angiography Performs contrast-enhanced CT imaging of cerebral blood vessels to identify vascular occlusion or abnormalities associated with stroke. in_vivo brain Homo sapiens stroke presence change low CT Angiography http://purl.obolibrary.org/obo/UBERON_0000955 UBERON CT Angiography Imaging technique to visualize blood vessels in the brain to detect vascular abnormalities. in_vivo brain blood vessels human vascular abnormality detection not_specified http://purl.obolibrary.org/obo/NCIT_C16959 NCIT medium CT Angiography http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0008015 GO non-contrasted head computed tomogram (CT) A diagnostic imaging technique used to visualize the internal structures of the head without contrast agents to detect signs of stroke. in_vivo brain stroke detection change http://purl.obolibrary.org/obo/CHMO_0000147 CHMO low detected by clinical examination stat non-contrasted head computed tomogram (CT) http://purl.obolibrary.org/obo/UBERON_0000847 UBERON non-contrasted head CT Non-contrasted head computed tomography (CT) is used to detect stroke by imaging the brain without the use of contrast agents. in_vivo http://purl.obolibrary.org/obo/UBERON_0000955 brain abnormalities change http://purl.obolibrary.org/obo/OBI_0000370 OBI low It is detected by clinical examination stat non-contrasted head computed tomogram (CT) http://purl.obolibrary.org/obo/UBERON_0000955 UBERON perfusion imaging Imaging technique to assess blood flow in the brain to identify areas of hypoperfusion. in_vivo brain human cerebral blood flow not_specified medium perfusion imaging http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0019725 GO Antibody staining Specific antibody-based staining used to identify and differentiate retinal layers and specific photoreceptor cell types. not_specified retina eye retinal layers and photoreceptor types change low Specific antibody staining might help to identify the different retinal layers and photoreceptor types cell layer diameter measurement Measurement of cell layer diameter is used to assess changes in eye structure and layers. in_vivo retina cell layer diameter change low Measurement of cell layer diameter is the most popular and simple method to assess changes in eye structure and layers. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008533 GO electron microscopy Uses electron microscopy on histological sections to visualize and assess subcellular changes in the eye structure. ex_vivo eye subcellular changes change http://purl.obolibrary.org/obo/GO_0044325 GO low This can either be electron microscopy for subcellular changes http://purl.obolibrary.org/obo/GO_0044325 GO http://purl.obolibrary.org/obo/GO_0040031 GO electron microscopy Assessment of retinal layer structure using electron microscopy to detect subcellular changes in ocular tissue. in_vivo retina eye subcellular changes in retinal layers change http://purl.obolibrary.org/obo/FAO_0000017 FAO http://purl.obolibrary.org/obo/GO_0005575 GO low This can either be electron microscopy for subcellular changes For assessment of eye structure and layers, mostly simple morphometric analyses based on histological sections are sufficient. http://purl.obolibrary.org/obo/UBERON_0007123 UBERON http://purl.obolibrary.org/obo/GO_006138 GO HE staining Normal histological staining (e.g., HE staining) to distinguish retinal layers. in_vivo eye retina retinal layer structure not_specified http://purl.obolibrary.org/obo/OBI_0000375 OBI http://purl.obolibrary.org/obo/GO_0060041 GO low usually, they are easily distinguishable by normal histological staining (e.g. HE staining). http://purl.obolibrary.org/obo/UBERON_0000966 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO histological section analysis Morphometric analysis of histological sections to assess eye structure and layers using light microscopy. in_vivo eye retina cell layer diameter change http://purl.obolibrary.org/obo/GO_0060041 GO http://purl.obolibrary.org/obo/UBERON_0000966 UBERON low For assessment of eye structure and layers, mostly simple morphometric analyses based on histological sections are sufficient. Measurement of cell layer diameter is the most popular and simple method to assess changes in eye structure and layers. http://purl.obolibrary.org/obo/UBERON_0000966 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO histology Morphometric analyses of histological sections are used to assess eye structure and layers, identifying retinal layers and photoreceptor types with or without antibody staining. in_vivo retina retinal layer structure change http://purl.obolibrary.org/obo/OBI_0000044 OBI low For assessment of eye structure and layers, mostly simple morphometric analyses based on histological sections are sufficient. Specific antibody staining might help to identify the different retinal layers and photoreceptor types usually, they are easily distinguishable by normal histological staining (e.g. HE staining). http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008533 GO immunohistochemistry Specific antibody staining to identify different retinal layers and photoreceptor types. in_vivo eye retina retinal layer identification not_specified http://purl.obolibrary.org/obo/OBI_0000619 OBI http://purl.obolibrary.org/obo/GO_0060041 GO low Specific antibody staining might help to identify the different retinal layers and photoreceptor types. http://purl.obolibrary.org/obo/UBERON_0000966 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO light microscopy morphometry Measures cell layer diameter in retinal tissue using light microscopy of histological sections to assess structural changes. ex_vivo retina retinal pigment epithelium eye cell layer diameter change not_specified For assessment of eye structure and layers, mostly simple morphometric analyses based on histological sections are sufficient. Measurement of cell layer diameter is the most popular and simple method to assess changes in eye structure and layers. http://purl.obolibrary.org/obo/UBERON_00001017 UBERON http://purl.obolibrary.org/obo/GO_0071555 GO pigmentation grade assessment Measurement of the pigmentation grade of the retinal pigment epithelium to assess structural changes. in_vivo eye retinal pigment epithelium pigmentation grade change http://purl.obolibrary.org/obo/CL_0000068 CL http://purl.obolibrary.org/obo/GO_0043473 GO low measurement of the pigmentation grade of the retinal pigment epithelium can be used to assess structural changes. http://purl.obolibrary.org/obo/CL_0000068 CL http://purl.obolibrary.org/obo/GO_0043473 GO semi-quantitative severity grading Semi-quantitative assessment of severity grades of morphological changes in the retina. in_vivo eye retina severity grade of morphological changes change http://purl.obolibrary.org/obo/GO_0060041 GO low semi-quantitative assessment of severity grades of morphological changes can be assessed. http://purl.obolibrary.org/obo/UBERON_0000966 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO morphological analysis Relative eye size is determined by morphological analysis with electromicroscopy or analysis of digital images. This involves measuring larger corneal diameters relative to the axial length or larger eye diameter relative to body length. not_specified eye relative eye size increase low Relative eye size: larger corneal diameters relative to the axial length or larger eye diameter relative to body length (Baumann et al., 2016; Hall, 2008) determined by morphological analysis with electromicroscopy or analysis of digital images http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0008533 GO morphological analysis with electromicroscopy Determination of relative eye size using morphological analysis with electromicroscopy. in_vivo eye relative eye size decrease low Relative eye size: larger corneal diameters relative to the axial length or larger eye diameter relative to body length (Baumann et al., 2016; Hall, 2008) determined by morphological analysis with electromicroscopy or analysis of digital images http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0001654 GO morphological live imaging Visualization of the aqueous outflow tract using morphological live imaging. in_vivo eye aqueous outflow tract visualization not_specified low Morphological live imaging + Aqueous outflow tract visualization (Chawla et al., 2018) http://purl.obolibrary.org/obo/UBERON_0001828 UBERON http://purl.obolibrary.org/obo/GO_0070286 GO morphological live imaging Live imaging of the eye to assess morphological changes, including visualization of the aqueous outflow tract. in_vivo http://purl.obolibrary.org/obo/UBERON_0000970 eye morphology change http://purl.obolibrary.org/obo/PATO_0000906 PATO http://purl.obolibrary.org/obo/OBI_0000070 OBI medium Morphological live imaging + Aqueous outflow tract visualization (Chawla et al., 2018) http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0048703 GO Morphological live imaging + Aqueous outflow tract visualization Real-time imaging technique to visualize the aqueous outflow tract and morphological changes in the eye. not_specified eye aqueous outflow tract aqueous outflow tract visualization change not_specified Morphological live imaging + Aqueous outflow tract visualization (Chawla et al., 2018) http://purl.obolibrary.org/obo/GO_0040039 GO ocular biometry Measurement of eye size using ocular biometry techniques. in_vivo eye eye size decrease medium Ocular biometry (Kang and Wildsoet, 2016) http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0001654 GO plasticine spherical ball Measurement of eye size using a plasticine spherical ball. in_vivo eye eye size decrease low Use of plasticine spherical ball (Brooke et al., 1999) http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0001654 GO relative eye size analysis Determines relative eye size by comparing corneal diameters to axial length or eye diameter to body length using morphological analysis with electron microscopy or digital image analysis. ex_vivo eye relative eye size decrease http://purl.obolibrary.org/obo/UBERON_0000971 UBERON http://purl.obolibrary.org/obo/GO_0003002 GO medium Relative eye size: larger corneal diameters relative to the axial length or larger eye diameter relative to body length (Baumann et al., 2016; Hall, 2008) determined by morphological analysis with electromicroscopy or analysis of digital images http://purl.obolibrary.org/obo/UBERON_0000971 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO 32P Post labelling This assay detects bulky DNA adducts by isolating DNA, digesting it into 3'-deoxynucleoside monophosphates, radiolabeling the adducts with 32P-orthophosphate, and separating and quantifying them using thin-layer chromatography and scintillation counting. in_vitro bulky DNA adducts increase low 32P Post labelling is used for the detection of DNA adducts (for PAHs and also Aristolochic Acid) The DNA is isolated using the standard methods and digested into 3'-deoxynucleoside monophosphates. A 32P-orthophosphate from [gamma-32P] ATP is used to radiolabel the adducts in a reaction catalyzed by T4 polynucleotide kinase. The radiolabelled nucleotides are separated and detected by thin-layer chromatography. They are quantified by scintillation counting. CE-MS Quantifies bulky DNA adducts using capillary electrophoresis coupled to mass spectrometry. in_vitro bulky DNA adducts level increase not_specified capillary electrophoresis mass spectrometry (CE–MS) CometChip assay DNA synthesis inhibitors (hydroxyurea and 1-β-d-arabinofuranosyl cytosine) are used to convert bulky lesions into detectable single-strand breaks (SSBs) in HepaRG™ cells. The percentage of DNA in the comet tail is proportional to the level of strand breaks. in_vitro HepaRG™ cells Homo sapiens bulky DNA adducts increase http://purl.obolibrary.org/obo/CHMO_0000000 CHMO http://purl.obolibrary.org/obo/SO_0000704 SO medium This variation of the assay uses DNA synthesis inhibitors to convert bulky lesions into detectable SSBs. HepaCometChip uses Hydroxyurea (HU) and 1-β-d-arabinofuranosyl cytosine (AraC) to detect SSBs formed from bulky adducts in the presence of the high metabolism of HepaRG™ cells. HU inhibits the enzyme ribonucleotide reductase. This enzyme mediates the synthesis of deoxyribonucleotides (dNTPs). When it is inhibited dNTPs are depleted which inhibits NER. AraC’s structure allows it to be incorporated into DNA and interrupts DNA elongation. HU and AraC delay the removal of NER and SSB intermediates. The prolonged presence of NER intermediates are indicators of bulky lesions and can be observed as comet detectable SSBs. The number of bulky lesions is then measured by detecting the % of DNA found in the tail of the comet compared to untreated samples. Percentage DNA in the comet tail is proportional to the level of strand breaks. http://purl.obolibrary.org/obo/GO_0005654 GO http://purl.obolibrary.org/obo/GO_0006281 GO CometChip assay This assay detects bulky DNA lesions by converting them into detectable single-strand breaks (SSBs) using DNA synthesis inhibitors, and measuring the percentage of DNA in the comet tail as an indicator of strand breaks. in_vitro HepaRG™ cells percentage of DNA in comet tail increase medium CometChip assay (modified by adding DNA synthesis inhibitors (Ngo et al.,2020) The number of bulky lesions is then measured by detecting the % of DNA found in the tail of the comet compared to untreated samples. Isotope dilution mass spectrometry This method measures bulky DNA adducts using mass spectrometry techniques, including isotope dilution mass spectrometry (MS), liquid chromatography mass spectrometry (LC–MS), gas chromatography mass spectrometry (GC–MS), and capillary electrophoresis mass spectrometry (CE–MS). in_vitro bulky DNA adducts increase medium A variety of other methods are available to measure bulky DNA adducts including Isotope dilution mass spectrometry (MS) liquid chromatography mass spectrometry (LC–MS), gas chromatography mass spectrometry (GC–MS), capillary electrophoresis mass spectrometry (CE–MS). liquid chromatography mass spectrometry (LC–MS) This method measures bulky DNA adducts using liquid chromatography mass spectrometry. not_specified DNA DNA adducts increase not_specified A variety of other methods are available to measure bulky DNA adducts including liquid chromatography mass spectrometry (LC–MS) http://purl.obolibrary.org/obo/CL_0000724 CL http://purl.obolibrary.org/obo/GO_0006305 GO Aldeflour kit ALDH activity can be assessed using AldeflourTM kit using different approaches. in_vitro ALDH activity decrease medium several ALDH activity assay kits using different approaches are commercially available; e.g. AldeflourTM kit (Flahaut et al, 2016). http://purl.obolibrary.org/obo/GO_0055153 GO Aldefluor assay Measures ALDH activity using a fluorescent substrate that is converted to a fluorescent product by ALDH enzymes. in_vitro ALDH activity decrease not_specified several ALDH activity assay kits using different approaches are commercially available; e.g. AldeflourTM kit (Flahaut et al, 2016) ALDH1A2 mRNA measurement Measures ALDH1A2 mRNA levels using various probes. in_vitro ALDH1A2 mRNA levels not_specified not_specified ALDH1A2 mRNA and protein levels can be measured using various probes, antibodies as well as ELISA kits that are commercially available. atRA formation assay Assesses ALDH1A2 enzyme activity by measuring the formation of all-trans retinoic acid (atRA). in_vitro atRA formation decrease not_specified Enzyme activity can be assessed in assays including measurement of atRA formation (Arnold et al, 2015) ELISA Measures ALDH1A2 protein levels using commercially available enzyme-linked immunosorbent assay kits. not_specified ALDH1A2 protein levels change http://purl.obolibrary.org/obo/OBI_0000430 OBI not_specified ALDH1A2 mRNA and protein levels can be measured using various probes, antibodies as well as ELISA kits that are commercially available. mRNA and protein level measurement Measurement of ALDH1A2 mRNA and protein levels using probes, antibodies, or ELISA kits. in_vitro ALDH1A2 mRNA and protein levels change not_specified ALDH1A2 mRNA and protein levels can be measured using various probes, antibodies as well as ELISA kits that are commercially available. http://purl.obolibrary.org/obo/GO_0006447 GO NADH formation assay Assesses ALDH1A2 enzyme activity by measuring the formation of NADH. in_vitro NADH formation decrease not_specified Enzyme activity can be assessed in assays including measurement of ... NADH formation (Harper et al, 2018; Schindler et al, 1998) qPCR Quantitative PCR measures the mRNA levels of ALDH1A2 using specific probes. in_vitro ALDH1A2 mRNA levels decrease http://purl.obolibrary.org/obo/OBI_0000716 OBI http://purl.obolibrary.org/obo/SO_0000234 SO medium ALDH1A2 mRNA and protein levels can be measured using various probes, antibodies as well as ELISA kits that are commercially available. http://purl.obolibrary.org/obo/PR_000016107 PR http://purl.obolibrary.org/obo/GO_0010467 GO HPLC High performance liquid chromatography is used to directly measure atRA concentration in serum. in_vivo serum humans animals atRA concentration decrease http://purl.obolibrary.org/obo/CHEBI_25360 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium Direct measurements of atRA in serum (humans, animals) can be performed by various chromatographic methods including high performance liquid chromatography (HPLC) http://purl.obolibrary.org/obo/CHEBI_25360 CHEBI LC-MS Liquid chromatography-tandem mass spectrometry is used to directly measure atRA concentration in serum. in_vivo serum humans animals atRA concentration decrease http://purl.obolibrary.org/obo/CHEBI_25360 CHEBI http://purl.obolibrary.org/obo/OBI_0000473 OBI medium Direct measurements of atRA in serum (humans, animals) can be performed by various chromatographic methods including liquid chromatography-tandem mass spectrometry (LC-MS) http://purl.obolibrary.org/obo/CHEBI_25360 CHEBI RAR-RXR-RARE reporter assay Reporter assays utilizing RAR-RXR-RARE promoter elements detect the presence of atRA in tissues in a semi-quantitative manner. in_vitro tissues atRA presence decrease http://purl.obolibrary.org/obo/CHEBI_25360 CHEBI medium Indirect measurements in cells and animal models can be performed with reporter assays utilizing RAR-RXR-RARE or RXR-RXR-RARE promoter elements, which are activated by atRA, driving expression of reporter proteins. http://purl.obolibrary.org/obo/CHEBI_25360 CHEBI http://purl.obolibrary.org/obo/GO_0048384 GO RAR-RXR-RARE/RXR-RXR-RARE reporter assay An indirect measurement technique where atRA activates specific promoter elements (RAR-RXR-RARE or RXR-RXR-RARE) to drive the expression of reporter proteins. in_vitro reporter cell lines tissues mouse reporter protein expression change http://purl.obolibrary.org/obo/OBI_0000119 OBI not_specified Indirect measurements in cells and animal models can be performed with reporter assays utilizing RAR-RXR-RARE or RXR-RXR-RARE promoter elements, which are activated by atRA, driving expression of reporter proteins. These reporter assays can detect the presence of atRA in tissues in a semi-quantitative manner. Examples include reporter mouse lines (Carlsen et al, 2021; Rossant et al, 1991; Solomin et al, 1998), reporter cell lines (Wagner et al, 1992) and transient transfection of constructs for in vitro cell-based assays (Chassot et al, 2020) http://purl.obolibrary.org/obo/CHEBI_35418 CHEBI http://purl.obolibrary.org/obo/GO_0009951 GO Reporter assay Reporter assays using RAR-RXR-RARE or RXR-RXR-RARE promoter elements detect the presence of atRA in cells and animal models by driving expression of reporter proteins in a semi-quantitative manner. in_vitro reporter mouse lines reporter cell lines in vitro cell-based assays mouse cell line atRA presence decrease http://purl.obolibrary.org/obo/GO_0033273 GO http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Indirect measurements in cells and animal models can be performed with reporter assays utilizing RAR-RXR-RARE or RXR-RXR-RARE promoter elements, which are activated by atRA, driving expression of reporter proteins. These reporter assays can detect the presence of atRA in tissues in a semi-quantitative manner. Examples include reporter mouse lines (Carlsen et al, 2021; Rossant et al, 1991; Solomin et al, 1998), reporter cell lines (Wagner et al, 1992) and transient transfection of constructs for in vitro cell-based assays (Chassot et al, 2020). http://purl.obolibrary.org/obo/CHEBI_15377 CHEBI http://purl.obolibrary.org/obo/GO_0033273 GO GFP Reporter Assay This assay uses a transgenic animal model where the Stra8 promoter drives the expression of GFP, allowing semi-quantitative detection of Stra8 promoter activation. in_vivo oocyte presence or absence of Stra8 promoter activation change http://purl.obolibrary.org/obo/OBI_0000675 OBI medium Indirect measurements in animal models can be performed using the Stra8 promoter element driving expression of reporter protein GFP. This reporter assay can detect the presence (GFP) or absence (GFP negative) of Stra8 promoter activation in a semi-quantitative manner. http://purl.obolibrary.org/obo/SO_0000167 SO http://purl.obolibrary.org/obo/GO_0007126 GO Meiotic factor expression analysis Measures mRNA and/or protein levels of meiotic initiation factors such as STRA8, SYCP3, and γH2AX using primers/probes for mRNA detection and antibodies for protein detection. not_specified mRNA and/or protein levels of meiotic factors (STRA8, SYCP3, γH2AX) not_specified not_specified The expression of meiotic factors, such as STRA8, SYCP3, γH2AX, can be assessed at mRNA and/or protein levels and levels measured using primers/probes and antibodies that are commercially available. mRNA/protein expression assay Assessment of meiotic factor expression (e.g., STRA8, SYCP3, γH2AX) at the mRNA or protein level using commercial primers, probes, or antibodies. not_specified expression levels of meiotic factors change http://purl.obolibrary.org/obo/OBI_0000064 OBI not_specified The expression of meiotic factors, such as STRA8, SYCP3, γH2AX, can be assessed at mRNA and/or protein levels and levels measured using primers/probes and antibodies that are commercially available. http://purl.obolibrary.org/obo/GO_0007299 GO RT-qPCR Meiotic factor expression (STRA8, SYCP3, γH2AX) is assessed at the mRNA level using commercially available primers and probes. in_vitro oocyte mRNA levels of meiotic factors change http://purl.obolibrary.org/obo/GO_0006925 GO medium The expression of meiotic factors, such as STRA8, SYCP3, γH2AX, can be assessed at mRNA and/or protein levels and levels measured using primers/probes and antibodies that are commercially available. http://purl.obolibrary.org/obo/GO_0006925 GO Stra8 promoter-GFP reporter assay Detects the presence or absence of Stra8 promoter activation in a semi-quantitative manner using GFP expression driven by the Stra8 promoter element. in_vivo GFP expression change http://purl.obolibrary.org/obo/GO_0006355 GO http://purl.obolibrary.org/obo/GO_0042221 GO medium Indirect measurements in animal models can be performed using the Stra8 promoter element driving expression of reporter protein GFP (Feng et al, 2021). This reporter assay can detect the presence (GFP) or absence (GFP negative) of Stra8 promoter activation in a semi-quantitative manner. http://purl.obolibrary.org/obo/GO_0007126 GO Stra8 promoter-GFP reporter assay Detects the presence or absence of Stra8 promoter activation in a semi-quantitative manner using GFP expression. in_vitro oocyte ovary not_specified Stra8 promoter activation decrease http://purl.obolibrary.org/obo/CL_0000533 CL http://purl.obolibrary.org/obo/CHMO_0000331 CHMO low Indirect measurements in animal models can be performed using the Stra8 promoter element driving expression of reporter protein GFP (Feng et al, 2021). This reporter assay can detect the presence (GFP) or absence (GFP negative) of Stra8 promoter activation in a semi-quantitative manner. http://purl.obolibrary.org/obo/CL_0000533 CL http://purl.obolibrary.org/obo/GO_0007126 GO western blot Meiotic factor expression (STRA8, SYCP3, γH2AX) is assessed at the protein level using commercially available antibodies. in_vitro oocyte protein levels of meiotic factors change http://purl.obolibrary.org/obo/GO_0005576 GO low The expression of meiotic factors, such as STRA8, SYCP3, γH2AX, can be assessed at mRNA and/or protein levels and levels measured using primers/probes and antibodies that are commercially available. http://purl.obolibrary.org/obo/GO_0006457 GO Anti-Müllerian hormone (AMH) measurement Measurement of AMH levels in blood samples as a surrogate marker for estimating the follicle pool in humans. in_vivo blood human AMH levels decrease http://purl.obolibrary.org/obo/CHEBI_16780 CHEBI http://purl.obolibrary.org/obo/UBERON_0000178 UBERON high The most established biomarker for estimation of the follicle pool is anti-Müllerian hormone (AMH). It is readily measured in a blood sample and the levels are rather stable throughout the menstrual cycle. http://purl.obolibrary.org/obo/CHEBI_16780 CHEBI http://purl.obolibrary.org/obo/GO_0001541 GO Follicle counting Counting of follicles of different sizes in animal studies to assess ovarian reserve. in_vivo ovary animal follicle count decrease http://purl.obolibrary.org/obo/UBERON_0001056 UBERON http://purl.obolibrary.org/obo/UBERON_0000992 UBERON OECD TG 416, OECD TG 443 low In animal studies, counting of follicles of different sizes is included in OECD guidelines: TG 416 (Two-Generation Reproductive Toxicity Study) and TG 443 (Extended One-Generation Reproductive Toxicity Study). http://purl.obolibrary.org/obo/UBERON_0001056 UBERON http://purl.obolibrary.org/obo/GO_0001541 GO histological assessment Assessing overall ovary histology to indirectly measure the size of the follicle pool. in_vivo ovary ovary histology change low The size of the pool can also be measured indirectly by assessing overall ovary histology by histological assessments http://purl.obolibrary.org/obo/UBERON_0004658 UBERON http://purl.obolibrary.org/obo/GO_0007262 GO Meiotic markers expression Measurement of mRNA and protein expression of meiotic markers as an indirect method to estimate the follicle pool. in_vivo ovary meiotic markers expression change http://purl.obolibrary.org/obo/GO_0007126 GO http://purl.obolibrary.org/obo/UBERON_0000992 UBERON medium The size of the pool can also be measured indirectly by mRNA and protein expression of meiotic markers. http://purl.obolibrary.org/obo/GO_0007126 GO Ovary histology assessment Histological assessment of overall ovary tissue to estimate the follicle pool. in_vivo ovary ovary histology change http://purl.obolibrary.org/obo/UBERON_0000992 UBERON http://purl.obolibrary.org/obo/OBI_0000274 OBI low The size of the pool can also be measured indirectly by assessing overall ovary histology by histological assessments. http://purl.obolibrary.org/obo/UBERON_0000992 UBERON http://purl.obolibrary.org/obo/GO_0001541 GO ADP-Glo Kinase Assay Measures Fyna kinase activity by quantifying ADP production, suitable for screening and kinase selectivity profiling. in_vitro ADP production change http://purl.obolibrary.org/obo/GO_0004672 GO http://purl.obolibrary.org/obo/OBI_0000429 OBI high Adp-GloTM Kinase Assay can be used to measure Fyna kinase activity. The assay is well suited for measuring the effects chemical compounds have on the activity of a broad range of purified kinases, making it ideal for both primary screening as well as kinase selectivity profiling (Zegzouti et al., 2009). http://purl.obolibrary.org/obo/PR_000001218 PR http://purl.obolibrary.org/obo/GO_0006468 GO Adp-Glo Kinase Assay The Adp-Glo Kinase Assay measures Fyna kinase activity and is suitable for measuring the effects of chemical compounds on a broad range of purified kinases. in_vitro Fyna kinase activity change high Adp-GloTM Kinase Assay can be used to measure Fyna kinase activity. The assay is well suited for measuring the effects chemical compounds have on the activity of a broad range of purified kinases, making it ideal for both primary screening as well as kinase selectivity profiling (Zegzouti et al., 2009). ELISA An enzyme-linked immunosorbent assay (ELISA) that measures changes in Fyna kinase activity by detecting phosphorylation of an immobilized substrate using an anti-tyrosine phosphate antibody. The extent of substrate phosphorylation is quantified by absorbance, fluorescence, or fluorescence polarization. in_vitro Fyna kinase activity decrease http://purl.obolibrary.org/obo/GO_0016301 GO http://purl.obolibrary.org/obo/PR_000001897 PR not_specified Changes in activity of Fyna kinase can be evaluated with enzyme-linked immunosorbent assay (ELISA). This type of ELISA method is based on kinase phosphorylation of an immobilized substrate, which is detected using anti-tyrosine phosphate antibody. The extent of the substrate phosphorylation can be measured by absorbance, fluorescence, or fluorescence polarization (Jelić et al., 2007). http://purl.obolibrary.org/obo/PR_000001897 PR http://purl.obolibrary.org/obo/GO_0016301 GO ELISA Measures Fyna kinase activity by detecting phosphorylation of an immobilized substrate using anti-tyrosine phosphate antibody, quantified by absorbance, fluorescence, or fluorescence polarization. in_vitro substrate phosphorylation change http://purl.obolibrary.org/obo/GO_0004672 GO http://purl.obolibrary.org/obo/OBI_0000429 OBI medium Changes in activity of Fyna kinase can be evaluated with enzyme-linked immunosorbent assay (ELISA). This type of ELISA method is based on kinase phosphorylation of an immobilized substrate, which is detected using anti-tyrosine phosphate antibody. The extent of the substrate phosphorylation can be measured by absorbance, fluorescence, or fluorescence polarization (Jelić et al., 2007). http://purl.obolibrary.org/obo/PR_000001218 PR http://purl.obolibrary.org/obo/GO_0006468 GO ELISA Measures Plxna2 activity indirectly as an indicator of phosphorylation changes. in_vitro Plxna2 activity change http://purl.obolibrary.org/obo/GO_0004672 GO medium Phosphorylation changes of Plxna2 tyrosine can be detected indirectly by using ELISA method to measure Plxna2 activity http://purl.obolibrary.org/obo/PR_000001234 PR http://purl.obolibrary.org/obo/GO_0006468 GO western blot Detects phosphorylation changes of Plxna2 tyrosine using specific antibodies. in_vitro Plxna2 tyrosine phosphorylation change http://purl.obolibrary.org/obo/GO_0006468 GO low Phosphorylation changes of Plxna2 tyrosine can be detected directly using western blot Fyn kinase dependent phosphorylation of plxna2 was measured with western blotting using α-Fyn (rabbit mAb), α-Flag M2 (mouse mAb), α-phosphotyrosine 4G10 (mouse mAb), and α-Src pY416 (rabbit mAb) http://purl.obolibrary.org/obo/PR_000001234 PR http://purl.obolibrary.org/obo/GO_0006468 GO qPCR Quantitative PCR (qPCR) measures the amount of specific RNA by monitoring the amplification reaction using fluorescence. in_vitro RNA expression level increase http://purl.obolibrary.org/obo/OBI_0000662 OBI http://purl.obolibrary.org/obo/CHEBI_33695 CHEBI medium This technique is primarily used to measure the amount of specific RNA which is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR) (Wong & Medrano, 2005). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Reverse transcription polymerase chain reaction is used to measure the amount of specific RNA by converting RNA to cDNA and amplifying it. in_vitro RNA expression level increase http://purl.obolibrary.org/obo/OBI_0000663 OBI http://purl.obolibrary.org/obo/CHEBI_33695 CHEBI medium Overexpression can be measured with reverse transcription polymerase chain reaction (RT-PCR). This technique is primarily used to measure the amount of specific RNA which is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR) (Wong & Medrano, 2005). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR / qPCR Measurement of specific RNA levels through real-time monitoring of the amplification reaction using fluorescence to quantify gene expression. in_vitro amount of specific RNA change http://purl.obolibrary.org/obo/GO_0010468 GO not_specified Overexpression can be measured with reverse transcription polymerase chain reaction (RT-PCR). This technique is primarily used to measure the amount of specific RNA which is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR) Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010468 GO CYP26B1 mRNA measurement Measures CYP26B1 mRNA levels using various probes. not_specified CYP26B1 mRNA levels not_specified not_specified CYP26b1 mRNA and protein levels can be measured using various probes, antibodies as well as ELISA kits that are commercially available. ELISA CYP26B1 protein levels can be measured using commercially available ELISA kits. in_vitro CYP26B1 protein levels not_specified medium CYP26b1 mRNA and protein levels can be measured using various probes, antibodies as well as ELISA kits that are commercially available. http://purl.obolibrary.org/obo/GO_0006925 GO microsomal enzyme activity assay Measurement of CYP26B1 enzyme activity by measuring the conversion of retinoic acid (RA) to its metabolites in microsomes. in_vitro conversion of RA to metabolites change not_specified Enzyme activity can be measured in different types of assays including using microsomes measuring conversion of RA to metabolites http://purl.obolibrary.org/obo/GO_0008153 GO microsome assay Enzyme activity is measured in microsomes by measuring conversion of RA to metabolites. in_vitro liver conversion of RA to metabolites not_specified low Enzyme activity can be measured in different types of assays including using microsomes measuring conversion of RA to metabolites (Van Wauwe et al, 1988). http://purl.obolibrary.org/obo/GO_0009265 GO mRNA measurement Measurement of CYP26B1 mRNA levels using various probes. in_vitro CYP26b1 mRNA levels change not_specified CYP26b1 mRNA and protein levels can be measured using various probes http://purl.obolibrary.org/obo/GO_0000003 GO qPCR Measures CYP26B1 mRNA levels using commercially available probes to assess transcript abundance. in_vitro CYP26B1 mRNA levels not_specified http://purl.obolibrary.org/obo/GO_0003183 GO not_specified CYP26b1 mRNA and protein levels can be measured using various probes, antibodies as well as ELISA kits that are commercially available. http://purl.obolibrary.org/obo/GO_0050794 GO western blot CYP26B1 protein levels can be measured using various antibodies. in_vitro CYP26B1 protein levels not_specified low CYP26b1 mRNA and protein levels can be measured using various probes, antibodies as well as ELISA kits that are commercially available. http://purl.obolibrary.org/obo/GO_0006925 GO HPLC Direct measurement of atRA in serum using high performance liquid chromatography. in_vivo serum humans animals atRA concentration not_specified not_specified Direct measurements of atRA in serum (humans, animals) can be performed by various chromatographic methods for instance by high performance liquid chromatography (HPLC) LC-MS Direct measurement of atRA in serum using liquid chromatography-tandem mass spectrometry. in_vivo serum humans animals atRA concentration not_specified not_specified Direct measurements of atRA in serum (humans, animals) can be performed by various chromatographic methods liquid chromatography-tandem mass spectrometry (LC-MS) luciferase assay Indirect measurement of activity and potency of RXRs and RARs via luciferase assays in cell lines. in_vitro activity and potency of RXRs and RARs not_specified not_specified Indirect measurement of activity and potency of RXRs and RARs is possible via luciferase assays in cell lines luciferase assay Luciferase assays in cell lines are used for indirect measurement of activity and potency of RXRs and RARs. in_vitro luciferase expression increase medium Indirect measurement of activity and potency of RXRs and RARs is possible via luciferase assays in cell lines, for example http://purl.obolibrary.org/obo/GO_0003677 GO reporter assay Indirect measurement of atRA in tissues using reporter assays with RAR-RXR-RARE or RXR-RXR-RARE promoter elements driving expression of reporter proteins. in_vivo tissues animals presence of atRA not_specified not_specified Indirect measurements in animal models can be performed with various reporter assays with RAR-RXR-RARE or RXR-RXR-RARE promoter elements driving expression of reporter proteins reporter assay Reporter assays with RAR-RXR-RARE or RXR-RXR-RARE promoter elements driving expression of reporter proteins detect the presence of ATRA in tissues in a semi-quantitative manner. in_vivo tissues animals reporter protein expression increase medium Indirect measurements in animal models can be performed with various reporter assays with RAR-RXR-RARE or RXR-RXR-RARE promoter elements driving expression of reporter proteins. http://purl.obolibrary.org/obo/GO_0003677 GO mRNA and protein measurement Measures mRNA and protein levels of meiotic factors such as Stra8, Sycp3, and gH2AX using commercially available probes and antibodies. in_vivo testis mRNA and protein levels of meiotic factors not_specified low Meiotic factors, such as Stra8, Sycp3, gH2AX mRNA and protein levels can be measured using various probes and antibodies that are commercially available http://purl.obolibrary.org/obo/GO_0007126 GO mRNA and protein quantification using probes and antibodies Quantifies mRNA and protein levels of meiotic factors (Stra8, Sycp3, gH2AX) using commercially available probes and antibodies. not_specified mRNA and protein levels of Stra8, Sycp3, and gH2AX change not_specified Meiotic factors, such as Stra8 , Sycp3 , g H2AX mRNA and protein levels can be measured using various probes and antibodies that are commercially available eg. ( Bowles et al, 2006 ). reporter assay The Stra8 promoter element drives expression of GFP, allowing detection of Stra8 induction in a semi-quantitative manner (presence or absence of GFP). in_vivo male germ cells GFP expression increase medium Indirect measurements in animal models can be performed using the Stra8 promoter element driving expression of reporter protein GFP (Feng et al, 2021). This reporter assay can detect the presence (GFP) or absence (GFP negative) of Stra8 induction in a semi-quantitative manner. http://purl.obolibrary.org/obo/GO_0010468 GO Stra8 mRNA quantification Measures the mRNA levels of the Stra8 gene, a key regulator of meiotic initiation in male germ cells, using commercially available probes. in_vitro male germ cells testis not_specified Stra8 mRNA levels increase http://purl.obolibrary.org/obo/GO_0006351 GO not_specified Meiotic factors, such as Stra8, Sycp3, gH2AX mRNA and protein levels can be measured using various probes and antibodies that are commercially available Indirect measurements in animal models can be performed using the Stra8 promoter element driving expression of reporter protein GFP http://purl.obolibrary.org/obo/PR_XXXXXXX PR http://purl.obolibrary.org/obo/GO_0007124 GO Stra8 promoter reporter assay Detects the presence or absence of Stra8 induction using a Stra8 promoter element driving expression of reporter protein GFP in a semi-quantitative manner. in_vivo testis GFP expression not_specified http://purl.obolibrary.org/obo/GO_0003924 GO http://purl.obolibrary.org/obo/OBI_0001861 OBI low Indirect measurements in animal models can be performed using the Stra8 promoter element driving expression of reporter protein GFP This reporter assay can detect the presence (GFP) or absence (GFP negative) of Stra8 induction in a semi-quantitative manner http://purl.obolibrary.org/obo/GO_0007126 GO western blot Meiotic factor protein levels (Stra8, Sycp3, gH2AX) are measured using commercially available antibodies. not_specified male germ cells protein levels of meiotic factors change low Meiotic factors, such as Stra8, Sycp3, gH2AX mRNA and protein levels can be measured using various probes and antibodies that are commercially available Meiotic factors, such as Stra8, Sycp3, gH2AX mRNA and protein levels can be measured using various probes and antibodies that are commercially available eg. (Bowles et al, 2006). http://purl.obolibrary.org/obo/GO_0007027 GO Comet assay Detects DNA damage at single-cell resolution using single cell gel electrophoresis. not_specified DNA damage not_specified http://purl.obolibrary.org/obo/GO_0006974 GO http://purl.obolibrary.org/obo/OBI_0000663 OBI OECD TG 489 not_specified Comet assay, or single cell gel electrophoresis assay, can detect DNA damage at single-cell resolution The alkaline Comet Assay is part of OECD Test Guideline 489 http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0042769 GO DNA ladder assay Measures apoptosis by separating DNA fragments via agarose gel electrophoresis, detecting apoptosis in many cells at later stages. not_specified DNA fragmentation not_specified http://purl.obolibrary.org/obo/GO_0006915 GO not_specified DNA laddering can be used to measure apoptosis at later stages only and is used to detect apoptosis of many cells, as it involves separation of DNA by agarose gel electrophoresis http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO germ cell marker probe/antibody assay Direct measurement of total germ cell number using specific probes and antibodies directed against germ cell markers. in_vivo germ cells total germ cell number change http://purl.obolibrary.org/obo/CL_0000021 CL not_specified Direct measurements of total germ cell number in animal models can be performed with using various probes and antibodies to germ cell markers that are commercially available http://purl.obolibrary.org/obo/CL_0000021 CL reporter assay Uses germ cell-specific promoter elements driving expression of reporter proteins to quantitatively detect germ cells. in_vivo testis Mus musculus germ cell number decrease http://purl.obolibrary.org/obo/CL_0000025 CL http://purl.obolibrary.org/obo/OBI_0000477 OBI not_specified Direct measurements of total germ cell number in animal models can be performed with using various probes and antibodies to germ cell markers that are commercially available and reporter assays using germ cell specific promoter elements driving expression of reporter proteins. These reporter assays can detect the presence of germ cells in a quantitative manner. Examples include reporter mouse line OG2 http://purl.obolibrary.org/obo/CL_0000025 CL http://purl.obolibrary.org/obo/GO_0007281 GO TUNEL assay Detects apoptotic DNA fragmentations using terminal deoxynucleotidyl transferase dUTP nick end labeling. not_specified apoptotic DNA fragmentation not_specified http://purl.obolibrary.org/obo/OBI_0000269 OBI not_specified Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, which detects apoptotic DNA fragmentations http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO ASC oligomer detection Detects ASC oligomers or ASC specks as a marker of NLRP3 inflammasome activation. in_vitro ASC oligomer or ASC speck formation increase http://purl.obolibrary.org/obo/GO_0061700 GO medium Formation of ASC oligomers reflects inflammasome activation thus ASC oligomers are often used to assess NLRP3 activation. http://purl.obolibrary.org/obo/PR_P25509 PR http://purl.obolibrary.org/obo/GO_0061700 GO Caspase 1 FLICA Assay Measures active CASP1 enzyme by fluorescent labeling, analyzed via fluorescence microscopy, plate reader, or flow cytometry. in_vitro active CASP1 enzyme activity increase http://purl.obolibrary.org/obo/PR_P29466 PR high For measuring CASP1 activity as a result of inflammasome assembly and activation, Caspase 1 Fluorescein (FLICA) Assay can be used FLICA allows active CASP1 enzyme fluorescent labelling that can be analyzed using fluorescence microscopy, fluorescence plate reader or flow cytometry. http://purl.obolibrary.org/obo/PR_P29466 PR http://purl.obolibrary.org/obo/GO_0002755 GO co-immunoprecipitation Co-immunoprecipitation assays are used for specific protein interaction detection (e.g. NLRP3 and ASC/PYCARD) as a result of NLRP3 inflammasome assembly. in_vitro Protein-protein interaction increase http://purl.obolibrary.org/obo/OBI_0000073 OBI low Furthermore, co-immunoprecipitation assays can be used for specific protein interaction detection (e.g. NLRP3 and ASC/PYCARD) as a result of NLRP3 inflammasome assembly co-immunoprecipitation Detects specific protein interactions, such as NLRP3 and ASC/PYCARD, as a result of NLRP3 inflammasome assembly. in_vitro protein-protein interaction (e.g., NLRP3 and ASC/PYCARD) increase http://purl.obolibrary.org/obo/OBI_0000836 OBI low co-immunoprecipitation assays can be used for specific protein interaction detection (e.g. NLRP3 and ASC/PYCARD) as a result of NLRP3 inflammasome assembly http://purl.obolibrary.org/obo/GO_0061700 GO http://purl.obolibrary.org/obo/GO_0061700 GO ELISA Measures secreted IL1B and/or IL18 levels using specific antibodies to detect activated inflammasome. in_vitro secreted IL1B and/or IL18 levels increase http://purl.obolibrary.org/obo/PR_P00724 PR medium A common method of detection of activated inflammasome is the measurement of secreted IL1B and/or IL18 levels with the enzyme-linked immunosorbent assay (ELISA) using specific antibodies http://purl.obolibrary.org/obo/GO_0061700 GO http://purl.obolibrary.org/obo/GO_0002755 GO BHAS 42 Cell Transformation Assay An in vitro assay using Bhas 42 cells to identify potential carcinogenicity of chemicals with initiating and/or promoting activity. in_vitro Bhas 42 cell transformation increase http://purl.obolibrary.org/obo/GO_0002573 GO OECD GD 231 low OECD (2016e) Organisation for economic co-operation and development. Guidance document 231 on the in vitro BHAS 42 Cell Transformation Assay. This GD provides an in vitro procedure using the Bhas 42 CTA, which can be used for hazard identification of potential carcinogenicity of chemicals with initiating and/or promoting activity. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0001656 GO Flow cytometry Measures DNA content and cell cycle stage in suspended cells to estimate cell ploidy and genomic instability. in_vitro cell ploidy and DNA content not_specified http://purl.obolibrary.org/obo/GO_0006260 GO http://purl.obolibrary.org/obo/GO_0007049 GO high Flow cytometry is another multicellular approach that, through the measurement of cells in suspension while they are passing through a laser beam, scatter light and emit fluorescence, estimates cell ploidy measuring DNA content (that is proportional to the intensity of the fluorescence) and the stage of the cells in cell cycle. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0007049 GO Fluorescence in situ hybridization (FISH) Stains each chromosome with different colored fluorophores to detect chromosomal rearrangements or modifications. in_vivo chromosomal rearrangements or modifications not_specified http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0019380 GO medium Fluorescence in situ hybridization (FISH), referred to as spectral karyotyping (SKY), is a method that has facilitated the assessment of chromosomal instability: this technique stains each chromosome with different colored fluorophore readily enabling the presence of rearrangements or modifications in chromosomes http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0051276 GO HPRT/XPRT gene mutation test Detects gene mutations in the hprt and xprt genes in mammalian cells in vitro. in_vitro mammalian gene mutations increase OECD TG 476 medium OECD (2016a) Organisation for economic co-operation and development. Test guideline 476: in vitro mammalian cell gene mutation tests using the hprt and xprt gene. http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0006281 GO Karyotype analysis Analyzes the karyotype of a single cell to identify chromosome number abnormalities (aneuploidy) and genomic rearrangements such as inversions and translocations. in_vivo chromosome number abnormalities and rearrangements not_specified http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0019380 GO low The analysis of the karyotype of a single cell permits the identification of chromosome number abnormalities, called aneuploidy, and the identification of rearrangements in the entire genome, such as inversions and translocations http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0051276 GO PCR for microsatellite instability (MSI) Amplifies known microsatellite regions to compare the lengths of short tandem repeats in tumoral and normal DNA, detecting microsatellite instability. in_vitro microsatellite instability not_specified http://purl.obolibrary.org/obo/SO_0000289 SO http://purl.obolibrary.org/obo/SO_0001057 SO high PCR (polymerase chain reaction) is a multicellular approach, used to detect MSI: it amplifies known microsatellite regions, and the lengths of the PCR products (short tandem repeats) are compared in the tumoral and normal DNA to determine the state of MSI http://purl.obolibrary.org/obo/SO_0000289 SO http://purl.obolibrary.org/obo/GO_0006281 GO thymidine kinase gene mutation assay In vitro mammalian cell gene mutation tests using the thymidine kinase gene to assess gene mutation. in_vitro mammalian cells gene mutation frequency increase OECD TG 490 medium OECD (2016b) Organisation for economic co-operation and development. Test guideline 490: in vitro mammalian cell gene mutation tests using the thymidine kinase gene. http://purl.obolibrary.org/obo/GO_0006281 GO Thymidine kinase gene mutation test Detects gene mutations in the thymidine kinase gene in mammalian cells in vitro. in_vitro mammalian gene mutations increase OECD TG 490 medium OECD (2016b) Organisation for economic co-operation and development. Test guideline 490: in vitro mammalian cell gene mutation tests using the thymidine kinase gene. http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0006281 GO affinity purification-mass spectrometry Identifies host-viral protein interactions by purifying protein complexes and analyzing them via mass spectrometry. in_vitro HEK293T protein-protein interaction not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI http://purl.obolibrary.org/obo/GO_0005515 GO medium Global analysis of SARS-CoV-2 host interacting proteins using affinity purification-mass spectrometry http://purl.obolibrary.org/obo/GO_0005515 GO co-immunoprecipitation Detects protein-protein interactions by immunoprecipitating a target protein and identifying binding partners. in_vitro protein-protein interaction not_specified http://purl.obolibrary.org/obo/GO_0005515 GO low Co-immunoprecipitation and western blot http://purl.obolibrary.org/obo/GO_0005515 GO immunoblotting Used to detect specific proteins in a sample, often following immunoprecipitation. in_vitro protein-protein interaction not_specified not_specified protein-protein interaction (immunoprecipitation, immunoblotting) http://purl.obolibrary.org/obo/GO_0043284 GO immunofluorescent microscopy Visualizes in-situ co-location of viral and host proteins using fluorescently labeled antibodies. in_vitro protein co-localization not_specified http://purl.obolibrary.org/obo/OBI_0000453 OBI http://purl.obolibrary.org/obo/GO_0008104 GO low in-situ co-location of viral and host proteins (immunofluorescent or confocal microscopy) Immunofluorescent microscopy http://purl.obolibrary.org/obo/GO_0008104 GO immunoprecipitation Measures protein-protein interaction using immunoprecipitation, often followed by immunoblotting. in_vitro protein complex formation change low Detection of IFN-I suppression involves measuring protein-protein interaction (immunoprecipitation, immunoblotting) Co-immunoprecipitation and western blot Immunoprecipitation http://purl.obolibrary.org/obo/GO_0043031 GO luciferase reporter assay Measures gene promoter/transcription activation by detecting luciferase activity as a reporter for IFN-I production and signaling. in_vitro luciferase activity decrease http://purl.obolibrary.org/obo/OBI_0000466 OBI http://purl.obolibrary.org/obo/GO_0010467 GO medium IFN-I production and signaling luciferase reporter assays http://purl.obolibrary.org/obo/GO_0034340 GO quantitative PCR Measures gene up/down regulation by quantifying mRNA levels of IFN-I or related genes. in_vitro mRNA expression level change http://purl.obolibrary.org/obo/OBI_0000662 OBI http://purl.obolibrary.org/obo/GO_0010467 GO high gene up/down regulation (quantitative PCR) http://purl.obolibrary.org/obo/GO_0006351 GO western blot Detects and quantifies specific proteins in cell lysates using gel electrophoresis and antibody probing. in_vitro protein expression level not_specified http://purl.obolibrary.org/obo/OBI_0001051 OBI http://purl.obolibrary.org/obo/GO_0005886 GO low Co-immunoprecipitation and western blot Fluorescence quantification immunoblotting http://purl.obolibrary.org/obo/GO_0010457 GO qPCR Measures the amount of specific RNA by monitoring the amplification reaction using fluorescence in real-time. in_vitro RNA expression level decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/CHEBI_33697 CHEBI medium a technique called real-time PCR or quantitative PCR (qPCR) (Wong & Medrano, 2005). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR RT-PCR measures the amount of specific RNA by monitoring the amplification reaction using fluorescence, also known as real-time PCR or quantitative PCR (qPCR). in_vitro amount of specific RNA decrease medium Repression of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). This technique is primarily used to measure the amount of specific RNA which is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR) (Wong & Medrano, 2005). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/CHEBI_50889 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO RT-PCR Measures the amount of specific RNA by reverse transcribing RNA to cDNA and amplifying it using polymerase chain reaction. in_vitro RNA expression level decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/CHEBI_33697 CHEBI medium Repression of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-qPCR Reverse transcription polymerase chain reaction (RT-PCR) followed by quantitative PCR (qPCR) to measure the amount of specific RNA transcripts, indicating repression of Gbx2 expression. in_vitro Gbx2 RNA expression level decrease http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Repression of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. Measuring changes in Gbx2 expression are described in detail in (Rhinn et al., 2003; Nakayama et al., 2017; Wang et al., 2018). http://purl.obolibrary.org/obo/GO_0010467 GO qPCR Quantitative PCR (qPCR) measures the amount of specific RNA by monitoring the amplification reaction using fluorescence in real-time. in_vitro RNA expression level not_specified http://purl.obolibrary.org/obo/OBI_0000663 OBI medium a technique called real-time PCR or quantitative PCR (qPCR) (Wong & Medrano, 2005). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Reverse transcription polymerase chain reaction (RT-PCR) measures the amount of specific RNA by monitoring the amplification reaction using fluorescence. Real-time PCR or quantitative PCR (qPCR) is used for quantification. in_vitro amount of specific RNA increase medium Inhibition of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). This technique is primarily used to measure the amount of specific RNA which is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR) (Wong & Medrano, 2005). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/CHEBI_36784 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO RT-PCR Reverse transcription polymerase chain reaction is used to measure the amount of specific RNA by converting RNA to cDNA and amplifying it. in_vitro RNA expression level not_specified http://purl.obolibrary.org/obo/OBI_0000662 OBI medium Inhibition of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). http://purl.obolibrary.org/obo/GO_0010467 GO qPCR Measures the amount of specific RNA by monitoring the amplification reaction using fluorescence in real-time. in_vitro RNA expression level not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000664 OBI medium a technique called real-time PCR or quantitative PCR (qPCR) (Wong & Medrano, 2005). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Reverse transcription polymerase chain reaction (RT-PCR) measures the amount of specific RNA by monitoring the amplification reaction using fluorescence. Real-time PCR or quantitative PCR (qPCR) is used for quantification. in_vitro amount of specific RNA increase medium Inhibition of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). This technique is primarily used to measure the amount of specific RNA which is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR) (Wong & Medrano, 2005). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/CHEBI_36789 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO RT-PCR Measures the amount of specific RNA by reverse transcribing RNA to cDNA and amplifying it using polymerase chain reaction. in_vitro RNA expression level not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000668 OBI medium Inhibition of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Reverse transcription polymerase chain reaction (RT-PCR) is used to measure the amount of specific RNA by monitoring the amplification reaction using fluorescence, known as real-time PCR or quantitative PCR (qPCR). This technique is routinely used for analysis of gene expression. in_vitro six1b RNA expression level increase http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Inhibition of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO qPCR Measures the amount of specific RNA by monitoring the amplification reaction using fluorescence in real-time. in_vitro RNA expression level decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000663 OBI medium a technique called real-time PCR or quantitative PCR (qPCR) Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Reverse transcription polymerase chain reaction (RT-PCR) measures the amount of specific RNA by monitoring the amplification reaction using fluorescence. Real-time PCR or quantitative PCR (qPCR) is a related technique. in_vitro amount of specific RNA decrease medium Inhibition of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). This technique is primarily used to measure the amount of specific RNA which is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR) Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/CHEBI_36784 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO RT-PCR Reverse transcription polymerase chain reaction (RT-PCR) is used to measure the amount of specific RNA by monitoring the amplification reaction using fluorescence, known as real-time PCR or quantitative PCR (qPCR). This technique is routinely used for analysis of gene expression. in_vitro eya1 RNA expression level decrease http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Inhibition of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). Combined RT-PCR and qPCR are routinely used for analysis of gene expression. http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Measures the amount of specific RNA by reverse transcribing RNA into cDNA and amplifying it using polymerase chain reaction. in_vitro RNA expression level decrease http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000662 OBI medium Inhibition of expression can be measured with reverse transcription polymerase chain reaction (RT-PCR). http://purl.obolibrary.org/obo/GO_0010467 GO cell surface biotinylation Distinguishes between intracellular and cell surface forms of CFTR protein. in_vitro cell surface CFTR protein decrease http://purl.obolibrary.org/obo/GO_0008104 GO low cell surface biotinylation, enabling a distinction between intracellular and cell surface forms of the protein if one wishes to study plasma membrane-expressed CFTR http://purl.obolibrary.org/obo/GO_0008104 GO chloride sweat test Measures chloride concentration in sweat to diagnose CFTR dysfunction in vivo. in_vivo sweat gland human sweat chloride concentration increase http://purl.obolibrary.org/obo/GO_0006821 GO Gibson and Cooke technique (quantitative pilocarpine iontophoresis sweat test) low In vivo, CFTR dysfunction is demonstrated by the chloride sweat test, the gold standard diagnostic tool for cystic fibrosis. The sweat test should be performed according to clinical guidelines using the Gibson and Cooke technique http://purl.obolibrary.org/obo/GO_0006821 GO immunocytochemistry Detects CFTR protein expression and localization in cells. in_vitro CFTR protein expression decrease http://purl.obolibrary.org/obo/GO_0008104 GO medium decreased expression of CFTR mRNA and protein in cells and tissues can be directly assessed using ... immunocyto-/histochemical methods http://purl.obolibrary.org/obo/GO_0008104 GO nasal potential difference Assesses net transepithelial active ion transport and epithelial ion conductance in vivo. in_vivo nasal epithelium human nasal potential difference change http://purl.obolibrary.org/obo/GO_0006811 GO low As a complementary diagnostic measure, nasal potential difference (NPD) can be assessed to gauge net transepithelial active ion transport and epithelial ion conductance http://purl.obolibrary.org/obo/UBERON_0001722 UBERON http://purl.obolibrary.org/obo/GO_0006811 GO nasal potential difference (NPD) A diagnostic measure used to gauge net transepithelial active ion transport and epithelial ion conductance in the nasal epithelium. in_vivo nasal epithelium transepithelial active ion transport and epithelial ion conductance decrease http://purl.obolibrary.org/obo/GO_0006811 GO low nasal potential difference (NPD) can be assessed to gauge net transepithelial active ion transport and epithelial ion conductance http://purl.obolibrary.org/obo/UBERON_0001304 UBERON http://purl.obolibrary.org/obo/GO_0006811 GO Northern blot Measures CFTR mRNA expression levels in cells and tissues. in_vitro CFTR mRNA expression decrease http://purl.obolibrary.org/obo/GO_0010467 GO low decreased expression of CFTR mRNA and protein in cells and tissues can be directly assessed using ... Northern blot http://purl.obolibrary.org/obo/GO_0010467 GO patch-clamping Assesses CFTR channel function in real-time by measuring current flow through CFTR. in_vitro CFTR channel current decrease http://purl.obolibrary.org/obo/GO_0006811 GO low CFTR channel function can be assessed in real-time using patch-clamping of whole (single) cells or cell patches http://purl.obolibrary.org/obo/GO_0006811 GO radiolabeled tracer efflux Measures CFTR channel function by studying the efflux of radiolabeled tracers. in_vitro tracer efflux decrease http://purl.obolibrary.org/obo/GO_0006811 GO medium Measuring the efflux of radiolabeled tracers is another means of studying CFTR channel function http://purl.obolibrary.org/obo/GO_0006811 GO RT-PCR Measures CFTR mRNA expression levels in cells and tissues. in_vitro CFTR mRNA expression decrease http://purl.obolibrary.org/obo/GO_0010467 GO medium decreased expression of CFTR mRNA and protein in cells and tissues can be directly assessed using RT-PCR http://purl.obolibrary.org/obo/GO_0010467 GO Ussing chamber Measures transepithelial voltage and short-circuit current to assess CFTR ion transport. ex_vivo epithelium short-circuit current decrease http://purl.obolibrary.org/obo/GO_0006811 GO medium The most commonly used method to study CFTR ion transport, however, utilizes the Ussing chamber to measure transepithelial voltage or 'active transport potential' and short-circuit current http://purl.obolibrary.org/obo/GO_0006811 GO confocal fluorescence microscopy Uses confocal fluorescence microscopy in XZ mode to measure ASL height in 3D organotypic airway epithelial models, calibrated with a fluorophore-dextran conjugate. in_vitro human airway epithelial cells mouse airway epithelial cells human mouse ASL height decrease low confocal fluorescence microscopy scanning in the vertical plane (i.e., in XZ mode) was used to measure ASL height in human and mouse 3D organotypic airway epithelial models, and changes in ASL height could be calibrated using a fluorophore-dextran conjugate low-temperature scanning electron microscopy Uses low-temperature scanning electron microscopy to measure ASL height in excised, rapidly frozen specimens of bovine tracheal epithelium and guinea pig lungs. ex_vivo tracheal epithelium lungs bovine guinea pig ASL height decrease low low-temperature scanning electron microscopy in excised, rapidly frozen specimens of bovine tracheal epithelium and guinea pig lungs micro-optical coherence tomography Uses micro-optical coherence tomography to measure ASL height in differentiated human bronchial epithelial cells. in_vitro human bronchial epithelial cells human ASL height decrease medium ASL height was measured using micro-optical coherence tomography in differentiated human bronchial epithelial cells microelectrode technique Uses a microelectrode technique to measure ASL height in live guinea pigs. in_vivo guinea pig ASL height decrease low a microelectrode technique was employed to determine ASL height in live guinea pigs synchrotron phase contrast x-ray imaging Uses synchrotron phase contrast x-ray imaging to measure ASL height in excised mouse tracheas and live mice. in_vivo trachea mouse ASL height decrease http://purl.obolibrary.org/obo/OBI_0000275 OBI low synchrotron phase contrast x-ray imaging in excised mouse tracheas and live mice videomicroscopy Uses videomicroscopy under a cold light source or strobe lights to measure ASL height in excised guinea pig and sheep tracheas. ex_vivo trachea guinea pig sheep ASL height decrease low a specifically designed chamber allowed for evaluation of ASL height in excised guinea pig and sheep tracheas using videomicroscopy under a cold light source or strobe lights Digital high-speed video imaging Measures ciliary beat frequency (CBF) by capturing high-speed video and manually counting beats in slow motion. in_vitro ciliated bovine bronchial epithelial cells normal human bronchial epithelial cells human nasal epithelial cells bovine human ciliary beat frequency decrease low Digital high-speed video imaging with a manual count of CBF in slow motion video play is the most commonly used method for CBF measurement CBF measurement in vitro generally involves mounting the tissue at the air-liquid interface on a stage followed by microscopic analysis and acquisition of images and/or video recordings of beating cilia http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0003341 GO Doppler optical coherence tomography (D-OCT) Measures ciliary beat frequency (CBF) using non-contact imaging to detect micromotion in cilia. ex_vivo rabbit tracheal cultures rabbit ciliary beat frequency decrease medium Doppler optical coherence tomography (D-OCT) can also be applied, a mesoscopic non-contact imaging modality that provides high-resolution tomographic images and detects micromotion simultaneously D-OCT has been used to quantitatively measure CBF in ex vivo rabbit tracheal cultures http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0003341 GO Photometry Measures ciliary beat frequency (CBF) using light-based detection methods. in_vitro ciliated bovine bronchial epithelial cells normal human bronchial epithelial cells human nasal epithelial cells bovine human ciliary beat frequency decrease medium Photometry and video-microscopy have been used to measure CBF in vitro and ex vivo http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0003341 GO 3D-SPECT Evaluates mucociliary clearance in experimental animals using three-dimensional single-photon emission computed tomography. in_vivo lung experimental animals clearance rate of radio-labeled particles decrease low 3D-SPECT (Ortiz Belda et al., 2016). 3D-SPECT Three-dimensional SPECT imaging to evaluate mucociliary clearance in experimental animals. in_vivo animal MCC not_specified low or by 3D-SPECT air-liquid interface (ALI) epithelial model tracing In vitro assessment of mucus transport by tracing the movement of inert particles in murine or human airway epithelial models grown at the air-liquid interface. in_vitro murine nasal epithelial cells human nasal epithelial cells murine bronchial epithelial cells human bronchial epithelial cells murine small airway epithelial cells human small airway epithelial cells nasal bronchial small airway murine human mucus transport not_specified medium Murine and human nasal, bronchial and small airway epithelial models grown at the air-liquid interface are also suitable in vitro test systems for determining mucus transport by tracing inert particle movement dye transit test MCC is assessed by observing the transit of dyes such as indigo carmine or methylene blue. in_vivo nasopharynx human dye transit time change low Using the same principle, the test can also be performed or complemented with dyes such as indigo carmine or methylene blue (Deborah and Prathibha, 2014). http://purl.obolibrary.org/obo/GO_0006334 GO Fiberoptic bronchoscope Directly observes particle movement across airway epithelia to determine mucus velocity or transport rates in larger animals. in_vivo airway epithelia dog mucus velocity or transport rate decrease low Direct observation of particle movement across airway epithelia to determine mucus velocity or transport rates by using a fiberoptic bronchoscope may be helpful when working in larger animals such as dogs (King, 1998). fluorescence videography/fluoroscopy Visual assessment of mucociliary clearance in explanted tissues using fluorescence techniques. ex_vivo trachea animal MCC not_specified low fluorescence videography/fluoroscopy (in explanted tracheas etc.) Fluorescence videography/fluoroscopy Assesses mucociliary transport in explanted tracheas using fluorescence imaging to visualize particle movement. ex_vivo trachea experimental animals mucus velocity or transport rate decrease low fluorescence videography/fluoroscopy (in explanted tracheas etc.) (Grubb et al., 2016; Rogers et al., 2018). Gamma-scintigraphy Assesses mucociliary clearance (MCC) by tracking radio-labeled particles via gamma camera imaging to calculate clearance rates. in_vivo lung trachea bronchi human clearance rate of radio-labeled particles decrease low MCC has been assessed traditionally following inhalation of radio-labeled particles such as 99Tcm-labeled polystyrene particles, resin particles or serum albumin and following their clearance at regular intervals by radioimaging using gamma cameras (Agnew et al., 1986; Kärjä et al., 1982). gamma-scintigraphy Imaging technique used in experimental animals to evaluate mucociliary clearance. in_vivo animal MCC not_specified low In experimental animals, MCC has been evaluated by gamma-scintigraphy Saccharin transit test (STT) Measures nasal mucociliary clearance by timing the transport of saccharin from the nasal cavity to the nasopharynx, where its taste is perceived. in_vivo nasal cavity human saccharin transit time increase medium Probably one of the simplest methods is the saccharin transit test (STT). For this test, a small particle of saccharin is placed behind the anterior end of the inferior turbinate. The saccharin will be transported by mucociliary action toward the nasopharynx, where its sweet taste is perceived. When MCC is impaired, saccharin transit times will increase, with a 10- to 20-minute delay being considered a clinical sign of decreased MCC. Videomicroscopy Assesses cilia function and mucociliary transport in freshly excised frog palate preparations using video microscopy. ex_vivo frog palate frog cilia function and mucociliary transport decrease low In vitro, freshly excised frog palate preparations have been used to assess cilia function and mucociliary transport by videomicroscopy (Macchione et al., 1995; Macchione et al., 1999; Trindade et al., 2007). videomicroscopy of frog palate Use of videomicroscopy on freshly excised frog palate preparations to assess cilia function and mucociliary transport. ex_vivo palate frog cilia function and mucociliary transport not_specified low In vitro, freshly excised frog palate preparations have been used to assess cilia function and mucociliary transport by videomicroscopy Immunofluorescence Detects FOXJ1 protein levels by using fluorescent antibodies to visualize the protein in cells or tissues under a microscope. in_vitro FOXJ1 protein levels decrease http://purl.obolibrary.org/obo/GO_0043062 GO medium immunofluorescence http://purl.obolibrary.org/obo/GO_0010485 GO immunofluorescence FOXJ1 protein levels are measured using immunofluorescence, a technique that uses antibodies to detect specific proteins within cells or tissues. in_vitro protein levels decrease http://purl.obolibrary.org/obo/OBI_0000233 OBI medium FOXJ1 protein levels can be measured by immunofluorescence (Arbi et al., 2016; Gomperts et al., 2007; Valencia-Gattas et al., 2016) http://purl.obolibrary.org/obo/GO_0006925 GO Immunohistochemistry Detects FOXJ1 protein levels in tissue sections using specific antibodies and enzymatic detection methods. in_vivo FOXJ1 protein levels decrease http://purl.obolibrary.org/obo/GO_0043062 GO medium immunohistochemistry http://purl.obolibrary.org/obo/GO_0010485 GO immunohistochemistry FOXJ1 protein levels are measured using immunohistochemistry, a technique that uses antibodies to detect specific proteins in tissue sections. in_vivo protein levels decrease http://purl.obolibrary.org/obo/OBI_0000233 OBI low FOXJ1 protein levels can be measured by immunohistochemistry (Abedalthagafi et al., 2016; Danielian et al., 2007; Gao et al., 2015) http://purl.obolibrary.org/obo/GO_0006925 GO In situ hybridization Detects FOXJ1 mRNA levels in tissue sections using labeled RNA probes that hybridize to complementary mRNA sequences. in_vivo FOXJ1 mRNA levels decrease http://purl.obolibrary.org/obo/GO_0032770 GO low in situ hybridization http://purl.obolibrary.org/obo/GO_0010467 GO in situ hybridization FOXJ1 mRNA levels are measured using in situ hybridization, a technique that detects specific mRNA molecules within cells or tissues. in_vivo mRNA levels decrease http://purl.obolibrary.org/obo/OBI_0000703 OBI low FOXJ1 mRNA levels that can be measured by in situ hybridization (Hackett et al., 1995; Stubbs et al., 2012) http://purl.obolibrary.org/obo/GO_0006925 GO Luciferase assay Measures FOXJ1 transcriptional activity by quantifying luciferase expression driven by FOXJ1 transcription factor binding sites. in_vitro FOXJ1 transcriptional activity decrease http://purl.obolibrary.org/obo/GO_0003700 GO high reporter gene expression levels (e.g. luciferase assay) of genes harboring FOXJ1 transcription factor binding sites http://purl.obolibrary.org/obo/GO_0006351 GO luciferase assay FOXJ1 protein activity is inferred from reporter gene expression levels (e.g. luciferase assay) of genes harboring FOXJ1 transcription factor binding sites. in_vitro reporter gene expression change medium In addition, FOXJ1 protein activity can be inferred from reporter gene expression levels or from reporter gene expression levels (e.g. luciferase assay) of genes harboring FOXJ1 transcription factor binding sites (Brekman et al., 2014; Lim et al., 1997) http://purl.obolibrary.org/obo/GO_0006925 GO Northern blot FOXJ1 mRNA levels are measured using Northern blot analysis, a technique that detects specific RNA molecules. in_vitro mRNA levels decrease http://purl.obolibrary.org/obo/OBI_0000703 OBI low FOXJ1 mRNA levels can be measured by Northern blot analysis (Hackett et al., 1995) http://purl.obolibrary.org/obo/GO_0006925 GO qRT-PCR Measures FOXJ1 mRNA levels by reverse transcribing RNA to cDNA and amplifying it using quantitative PCR. in_vitro FOXJ1 mRNA levels decrease http://purl.obolibrary.org/obo/GO_0032770 GO high FOXJ1 mRNA levels that can be measured by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR FOXJ1 mRNA levels are measured using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR), a technique that quantifies the amount of specific mRNA molecules. in_vitro mRNA levels decrease http://purl.obolibrary.org/obo/OBI_0000703 OBI medium FOXJ1 mRNA levels that can be measured by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) (Arbi et al., 2016; Brekman et al., 2014; Didon et al., 2013a; Jacquet et al., 2009; Milara et al., 2012; Stubbs et al., 2012) http://purl.obolibrary.org/obo/GO_0006925 GO Western blot Measures FOXJ1 protein levels by separating proteins via gel electrophoresis and detecting them with specific antibodies. in_vitro FOXJ1 protein levels decrease http://purl.obolibrary.org/obo/GO_0043062 GO low FOXJ1 protein levels can be measured by Western blot analysis http://purl.obolibrary.org/obo/GO_0010485 GO western blot FOXJ1 protein levels are measured using Western blot analysis, a technique that separates proteins by size and detects specific proteins using antibodies. in_vitro protein levels decrease http://purl.obolibrary.org/obo/OBI_0000233 OBI low FOXJ1 protein levels can be measured by Western blot analysis (Brekman et al., 2014; Didon et al., 2013a; Gomperts et al., 2007; Jacquet et al., 2009; Milara et al., 2012) http://purl.obolibrary.org/obo/GO_0006925 GO 3D-SIM immunofluorescence Quantifies ciliary precursors using three-dimensional superresolution structured illumination microscopy and spot detection tools. in_vitro number of ciliary precursors decrease http://purl.obolibrary.org/obo/GO_0005929 GO low Mature cilia numbers could be deduced from ciliary precursors in immunofluorescence assays: ciliary precursors can be calculated from three-dimensional superresolution structured illumination microscopy (3D-SIM) images using e.g. a spot detection tool (Nikon Elements AR 4 Software) (Nanjundappa et al., 2019). http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0044782 GO acetylated tubulin immunofluorescence staining Detects and enumerates cilia by staining acetylated tubulin, a ciliary marker, followed by microscope image scoring. in_vitro number of cilia decrease http://purl.obolibrary.org/obo/GO_0005929 GO medium Acetylated tubulin is a common ciliary marker (Kim et al., 2013; Piperno and Fuller, 1985), and apical acetylated tubulin staining with subsequent microscope image scoring is a frequently used method of cilia detection and enumeration (Johnson et al., 2018; Mao et al., 2018; Stubbs et al., 2008). http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0044782 GO cilia length measurement Measures cilia length by staining ciliated cells/tissue with dyes or antibodies, visualizing via microscopy, and quantifying length using image analysis software. in_vitro cilia length decrease http://purl.obolibrary.org/obo/GO_0005929 GO medium For cilia length measurement, the ciliated cells/tissue needs to be stained (Diff-Quik: Dade Behring stain, hematoxylin and eosin staining, labelling with antibodies for ciliary markers such as alpha-tubulin), visualized by microscopy and cilia length quantified (using e.g. ImageJ software or MetaMorph Microscopy Automation & Image Analysis Software) (Brekman et al., 2014; Leopold et al., 2009b; Li et al., 2014). http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0044782 GO scanning electron microscopy Scanning electron microscopy is used to identify ciliated cells by the presence of axonemal structures on the cell surface. ex_vivo axonemal structures decrease low Ciliated cells can also be identified by the presence of axonemal structures on the cell surface using scanning electron microscopy (Gomperts et al., 2007). http://purl.obolibrary.org/obo/CL_0000122 CL http://purl.obolibrary.org/obo/GO_0001543 GO scanning electron microscopy Identifies ciliated cells by visualizing axonemal structures on the cell surface. in_vitro presence of cilia decrease http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0005930 GO low Ciliated cells can also be identified by the presence of axonemal structures on the cell surface using scanning electron microscopy (Gomperts et al., 2007). http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0044782 GO Behavioral screening for auditory response defects High-throughput assay that monitors the rapid escape reflex of zebrafish in response to a loud sound to detect auditory response defects. in_vivo inner ear vestibular system Danio rerio auditory response defects increase http://purl.obolibrary.org/obo/GO_0007605 GO http://purl.obolibrary.org/obo/GO_0050911 GO high High-throughput behavioral screening method for detecting auditory response defects in zebrafish. Assay monitors a rapid escape reflex in response to a loud sound (Bang et al., 2002). http://purl.obolibrary.org/obo/UBERON_0000409 UBERON http://purl.obolibrary.org/obo/GO_0007605 GO Direct observation of internal anatomic structures Direct observation of internal anatomic structures of zebrafish embryos to detect defects visible under a dissecting microscope. in_vivo inner ear Danio rerio anatomic defects not_specified http://purl.obolibrary.org/obo/GO_0042472 GO http://purl.obolibrary.org/obo/NCBITaxon_7955 NCBITAXON low Direct observation of internal anatomic structures of zebrafish embryos. Defects visible under the dissecting microscope (Whitfield, 2002) http://purl.obolibrary.org/obo/UBERON_0001845 UBERON http://purl.obolibrary.org/obo/GO_0042472 GO escape reflex assay High-throughput screening method to detect auditory response defects in zebrafish by monitoring a rapid escape reflex in response to a loud sound. in_vivo inner ear zebrafish escape reflex decrease high High-throughput behavioral screening method for detecting auditory response defects in zebrafish. Assay monitors a rapid escape reflex in response to a loud sound (Bang et al., 2002). http://purl.obolibrary.org/obo/UBERON_0000025 UBERON http://purl.obolibrary.org/obo/GO_0007604 GO microscopy Direct observation of internal anatomic structures of zebrafish embryos to identify defects using a dissecting microscope. in_vivo inner ear zebrafish anatomical defects change low Direct observation of internal anatomic structures of zebrafish embryos. Defects visible under the dissecting microscope (Whitfield, 2002) http://purl.obolibrary.org/obo/UBERON_0004824 UBERON http://purl.obolibrary.org/obo/GO_0032501 GO Swimming pattern comparison Comparison of swimming patterns with wild-type fish to identify vestibular defects. in_vivo inner ear Danio rerio swimming behavior defects decrease http://purl.obolibrary.org/obo/GO_0007606 GO http://purl.obolibrary.org/obo/NCBITaxon_7955 NCBITAXON low Dog-eared embryos are less responsive to vibrational stimuli, fail to maintain balance when swimming, and may circle when disturbed, a behavior characteristic of fish with vestibular defects (Nicolson et al., 1998) http://purl.obolibrary.org/obo/UBERON_0001046 UBERON http://purl.obolibrary.org/obo/GO_0007606 GO Swimming pattern comparison Comparison of swimming behaviors, including response to vibrational stimuli and balance maintenance, against wild-type fish to identify vestibular defects. in_vivo vestibular system Zebrafish swimming patterns and vestibular response change http://purl.obolibrary.org/obo/UBERON_0001146 UBERON low Comparison of swimming patterns with wild-type fish. Dog-eared embryos are less responsive to vibrational stimuli, fail to maintain balance when swimming, and may circle when disturbed, a behavior characteristic of fish with vestibular defects http://purl.obolibrary.org/obo/GO_0050828 GO FITC-dextran assay In vivo measurement of fluorescein isothiocyanate-dextran crossing from the intestinal lumen into the blood to assess paracellular permeability. in_vivo intestine mouse FITC-dextran concentration in serum increase medium In mice, one way to study intestinal paracellular permeability is by measuring the ability of fluorescein isothiocyanate (FITC)-dextran to cross from the lumen into the blood. After gavaging mice with FITC-dextran, the concentrations are measured in collected serum samples http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0015700 GO FITC-dextran serum assay In vivo method that measures intestinal paracellular permeability by assessing the ability of FITC-dextran to cross from the intestinal lumen into the blood. in_vivo intestine mouse paracellular permeability increase low In mice, one way to study intestinal paracellular permeability is by measuring the ability of fluorescein isothiocyanate (FITC-dextran) to cross from the lumen into the blood. After gavaging mice with FITC-dextran, the concentrations are measured in collected serum samples (doi:10.3791/57032). IPA Intestinal Permeability Assessment (IPA) measures the ability of lactulose and mannitol to permeate the small intestinal barrier, reflecting paracellular and transcellular passage, respectively, by measuring their levels in urine. in_vivo small intestine human lactulose/mannitol ratio in urine increase medium Intestinal Permeability Assessment (IPA) directly measures the ability of two non-metabolized sugar molecules (lactulose and mannitol) to permeate the small intestinal barrier... http://purl.obolibrary.org/obo/UBERON_0002623 UBERON http://purl.obolibrary.org/obo/GO_0008508 GO Lucifer Yellow (LY) leakage assay An in vitro assay used to measure the permeability and integrity of a cell monolayer using the fluorescent dye Lucifer Yellow. in_vitro Caco-2 intestinal epithelial cells (IEC) primary epithelial cells enterocyte-like cells intestinal epithelium human barrier integrity and permeability change http://purl.obolibrary.org/obo/GO_0051030 GO medium Transepithelial electrical resistance ( TEER ) or the Lucifer Yellow ( LY ) leakage assay are techniques to measure barrier integrity and permeability of a cell layer Epi-Intestinal TM is an example of 3D human primary cell-based organotypic small intestinal model which allows evaluation of TEER and LY leakage assay http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0051030 GO Lucifer Yellow leakage assay In vitro assay using Lucifer Yellow dye to measure permeability of a cell layer. in_vitro Caco-2 intestinal epithelial cells primary epithelial cells intestine human Lucifer Yellow leakage increase medium Transepithelial electrical resistance (TEER) or the Lucifer Yellow (LY) leakage assay are techniques to measure barrier integrity and permeability of a cell layer http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0015700 GO TEER In vitro measurement of transepithelial electrical resistance to assess barrier integrity of a cell layer. in_vitro Caco-2 intestinal epithelial cells primary epithelial cells intestine human transepithelial electrical resistance decrease medium Transepithelial electrical resistance (TEER) or the Lucifer Yellow (LY) leakage assay are techniques to measure barrier integrity and permeability of a cell layer http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0030855 GO Transepithelial electrical resistance (TEER) Measures the electrical resistance across a cell layer to assess barrier integrity and permeability. in_vitro Caco-2 intestinal epithelial cells (IEC) primary epithelial cells enterocyte-like cells intestinal epithelium human barrier integrity and permeability change medium Transepithelial electrical resistance ( TEER ) or the Lucifer Yellow ( LY ) leakage assay are techniques to measure barrier integrity and permeability of a cell layer Epi-Intestinal TM is an example of 3D human primary cell-based organotypic small intestinal model which allows evaluation of TEER http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0098951 GO Ussing chamber Ex vivo technique combining electrophysiology and probes of different molecular sizes to assess paracellular intestinal permeability. ex_vivo intestine epithelial barrier function change low ex vivo in Ussing chambers combining electrophysiology and probes of different molecular sizes. The latter is still the gold standard technique for assessing the epithelial barrier function http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0015700 GO Ussing chamber An ex vivo technique that combines electrophysiology and probes of different molecular sizes to assess epithelial barrier function and paracellular intestinal permeability. ex_vivo intestine paracellular intestinal permeability change low ex vivo in Ussing chambers combining electrophysiology and probes of different molecular sizes. The latter is still the gold standard technique for assessing the epithelial barrier function ELISA Detects antibodies in blood using enzyme-linked immunosorbent assay. in_vitro blood presence of antibodies not_specified medium ELISA, Indirect immunofluorescence assay (IIFA) for antibodies http://purl.obolibrary.org/obo/CHEBI_50849 CHEBI http://purl.obolibrary.org/obo/GO_0006955 GO Histopathology Examines tissue lesions through microscopic analysis of autopsy samples. ex_vivo tissue tissue lesions not_specified low Serum sample, autopsy, histopathology for tissue lesions http://purl.obolibrary.org/obo/UBERON_0000483 UBERON Indirect immunofluorescence assay (IIFA) Detects antibodies in blood using fluorescence-labeled secondary antibodies. in_vitro blood presence of antibodies not_specified medium Indirect immunofluorescence assay (IIFA) for antibodies http://purl.obolibrary.org/obo/CHEBI_50849 CHEBI http://purl.obolibrary.org/obo/GO_0006955 GO Quantitative reverse transcription PCR (qRT-PCR) Measures viral load in samples by quantifying genome copies. in_vitro nasal swab oropharyngeal swab rectal swab saliva viral load (log10 genome copies) increase high Quantitative reverse transcription PCR (qRT-PCR) for viral load (log10 genome copies) http://purl.obolibrary.org/obo/GO_0039694 GO SARS-CoV-2 spike protein neutralizing antibodies in saliva Detects neutralizing antibodies against SARS-CoV-2 spike protein in saliva. in_vitro saliva neutralizing antibodies not_specified medium SARS-CoV-2 spike protein neutralizing antibodies in saliva from animals that developed serum antibodies http://purl.obolibrary.org/obo/CHEBI_50849 CHEBI http://purl.obolibrary.org/obo/GO_0019064 GO TCID50 assay Measures infectious virus levels by determining the tissue culture infectious dose where 50% of cells show cytopathic effect. in_vitro levels of infectious virus not_specified low Titration (Tissue culture infectious dose where 50% of infected cells display cytopathic effect [TCID50 assay]: levels of infectious virus, or viral titre) http://purl.obolibrary.org/obo/NCBITaxon_10239 NCBITAXON Viral whole genome sequencing Sequences the entire viral genome to identify viral strains and mutations. in_vitro viral genome sequence not_specified medium Viral whole genome sequencing http://purl.obolibrary.org/obo/GO_0039694 GO Virus neutralization test (VNT) An assay used to measure the ability of antibodies to neutralize a virus. in_vitro antibodies not_specified http://purl.obolibrary.org/obo/CHEBI_15370 CHEBI not_specified Virus neutralization test (VNT) for antibodies http://purl.obolibrary.org/obo/CHEBI_15370 CHEBI http://purl.obolibrary.org/obo/GO_0006955 GO Virus neutralization test (VNT) Measures the ability of antibodies to neutralize viral infectivity. in_vitro blood virus neutralization not_specified low Virus neutralization test (VNT) for antibodies http://purl.obolibrary.org/obo/NCBITaxon_10239 NCBITAXON Virus-specific immunoglobulin characterization Characterizes virus-specific immunoglobulins in samples. in_vitro blood virus-specific immunoglobulins not_specified medium Virus-specific immunoglobulin characterization http://purl.obolibrary.org/obo/CHEBI_50849 CHEBI http://purl.obolibrary.org/obo/GO_0006955 GO Behavioral Tests Tests such as Morris Water Maze and Novel Object Recognition used to evaluate cognitive functions related to synaptic plasticity. in_vivo cognitive functions change low Evaluate cognitive functions related to synaptic plasticity. Confocal Microscopy Observes dendritic spine morphology and density changes. in_vitro brain dendritic spine morphology and density not_specified http://purl.obolibrary.org/obo/GO_0043195 GO low Observe dendritic spine morphology and density changes. http://purl.obolibrary.org/obo/GO_0043195 GO http://purl.obolibrary.org/obo/GO_0061005 GO EEG Measures electrical activity in the brain. in_vivo brain brain electrical activity change low EEG http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0050877 GO Electron Microscopy Visualizes synaptic ultrastructure. in_vitro brain synaptic ultrastructure not_specified http://purl.obolibrary.org/obo/GO_0045202 GO low Visualize synaptic ultrastructure. http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0050808 GO ELISA Evaluates protein expression. in_vitro protein expression change http://purl.obolibrary.org/obo/GO_0010483 GO high Evaluate proteins expression. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010467 GO Field Potential Recording Measures neurotransmission efficiency and receptor function by recording currents. Evaluates synaptic plasticity, such as LTP and LTD. in_vitro neurotransmission efficiency and receptor function change http://purl.obolibrary.org/obo/GO_0007268 GO http://purl.obolibrary.org/obo/GO_0048167 GO low Measures neurotransmition efficiency and receptor function by currents recordings. Evaluate synaptic plasticity, such as LTP and LTD http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0007268 GO Golgi Staining Analyzes dendritic spine density and morphology. in_vitro brain dendritic spine density and morphology not_specified http://purl.obolibrary.org/obo/GO_0043195 GO low Analyze dendritic spine density and morphology. http://purl.obolibrary.org/obo/GO_0043195 GO http://purl.obolibrary.org/obo/GO_0061005 GO HPLC Quantifies neurotransmitter levels directly. in_vitro neurotransmitter levels change medium Quantifies neurotransmitter levels directly. http://purl.obolibrary.org/obo/CHEBI_25512 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO Immunohistochemistry Evaluates expression and localization of pre- and post-synaptic proteins, mitochondrial imaging, inflammation, and immune responses using microscopies. in_vitro brain protein expression and localization change http://purl.obolibrary.org/obo/GO_0008104 GO http://purl.obolibrary.org/obo/GO_0006954 GO low Evaluate expression and locarization for pre- and post synaptic proteins, mitochondrial imaging, infkammation and immune responses using microscopies. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0008104 GO Microdialysis Quantifies neurotransmitter levels directly. in_vivo brain neurotransmitter levels change low Quantifies neurotransmitter levels directly. http://purl.obolibrary.org/obo/CHEBI_25512 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO Morris Water Maze Evaluates cognitive functions related to synaptic plasticity. in_vivo brain cognitive function change http://purl.obolibrary.org/obo/GO_0050890 GO http://purl.obolibrary.org/obo/GO_0048167 GO low Evaluate cognitive functions related to synaptic plasticity. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0050890 GO MRI Evaluates brain structure and function. in_vivo brain brain structure and function change http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low MRI http://purl.obolibrary.org/obo/UBERON_0000955 UBERON patch clamp Measures neurotransmission efficiency and receptor function by currents recordings. Evaluate synaptic plasticity, such as LTP and LTD in_vitro synapse current recordings change http://purl.obolibrary.org/obo/OBI_0000639 OBI low Electrophysiology (Patch Clamp, Field Potential Recording) : Measures neurotransmition efficiency and receptor function by currents recordings. http://purl.obolibrary.org/obo/CL_0000538 CL http://purl.obolibrary.org/obo/GO_0006508 GO Patch Clamp Measures neurotransmission efficiency and receptor function by recording currents. Evaluates synaptic plasticity, such as LTP and LTD. in_vitro neurotransmission efficiency and receptor function change http://purl.obolibrary.org/obo/GO_0007268 GO http://purl.obolibrary.org/obo/GO_0048167 GO low Measures neurotransmition efficiency and receptor function by currents recordings. Evaluate synaptic plasticity, such as LTP and LTD http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0007268 GO PET Evaluates brain metabolic activity and function. in_vivo brain brain metabolic activity change low PET http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0008152 GO Two-photon Microscopy Observes dendritic spine morphology and density changes. in_vitro brain dendritic spine morphology and density not_specified http://purl.obolibrary.org/obo/GO_0043195 GO low Observe dendritic spine morphology and density changes. http://purl.obolibrary.org/obo/GO_0043195 GO http://purl.obolibrary.org/obo/GO_0061005 GO Western Blot Evaluates protein expression. in_vitro protein expression change http://purl.obolibrary.org/obo/GO_0010483 GO medium Evaluate proteins expression. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010467 GO alpha diversity measurement This assay measures the diversity within a single microbial community using indices such as Shannon, Chao1, OTU richness, Simpson, Faith’s Phylogenetic diversity, and ACE. in_vitro gut alpha diversity not_specified high Gut microbiome diversity measurements include alpha diversity (among the commonly used estimators there are: Shannon index, Chao1 index, Operational Taxonomic Unit (OTU) richness, Simpson index, Faith’s Phylogenetic diversity, and Abundance-based Coverage Estimators (ACE) index) amplicon sequencing This assay sequences specific nucleic acid regions to profile the taxonomical composition of the gut microbiome. in_vitro gut taxonomical profile not_specified high nucleic acids (amplicon sequencing, WGS, metatranscriptomics), proteins (metaproteomics) and metabolites (metabolomics) based methodologies are used to obtain the taxonomical and/or the functional profiles of the gut microbiome COG encoding proteins analysis This assay analyzes the proportions of Clusters of Orthologous Groups (COG) encoding proteins in the gut microbiome. in_vitro gut COG proportions not_specified high proportions of Clusters of Orthologous Groups (COG) encoding proteins Firmicutes/Bacteroidetes ratio measurement This assay measures the ratio of Firmicutes to Bacteroidetes in the gut microbiome as an indicator of dysbiosis. in_vitro gut Firmicutes/Bacteroidetes ratio not_specified high The Firmicutes/Bacteroidetes (F/B) ratio is widely accepted to have an important influence in maintaining normal intestinal homeostasis. Increased or decreased F/B ratio is used as an indicator of dysbiosis functional state analysis by MS This assay identifies peptides and proteins using mass spectrometry to assess the functional state of the gut microbiome. in_vitro gut functional state not_specified medium functional states based on peptides and/or proteins identified by MS metabolomics This assay profiles metabolites from microbial communities to assess the functional activity of the gut microbiome. in_vitro gut metabolomic profile not_specified high nucleic acids (amplicon sequencing, WGS, metatranscriptomics), proteins (metaproteomics) and metabolites (metabolomics) based methodologies are used to obtain the taxonomical and/or the functional profiles of the gut microbiome metagenomic functional composition prediction This assay predicts the functional composition of the gut microbiome using databases such as KEGG. in_silico gut functional composition not_specified high evidence of functional dysbiosis are obtained by comparing e.g. metagenomic functional compositions predicted from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database metaproteomics Metaproteomics is used to obtain the functional profiles of the gut microbiome. It involves identifying and quantifying proteins in a sample to assess microbial activity. not_specified gut protein abundance change medium Among the culture independent methods, nucleic acids (amplicon sequencing, WGS, metatranscriptomics), proteins (metaproteomics) and metabolites (metabolomics) based methodologies are used to obtain the taxonomical and/or the functional profiles of the gut microbiome http://purl.obolibrary.org/obo/GO_0006457 GO metatranscriptomics This assay sequences RNA from microbial communities to profile the functional activity of the gut microbiome. in_vitro gut functional profile not_specified high nucleic acids (amplicon sequencing, WGS, metatranscriptomics), proteins (metaproteomics) and metabolites (metabolomics) based methodologies are used to obtain the taxonomical and/or the functional profiles of the gut microbiome Metatranscriptomics A culture-independent nucleic acid-based methodology used to obtain functional profiles of the gut microbiome by sequencing the total RNA transcripts of microbial communities. not_specified gut functional profile of gut microbiome change not_specified Among the culture independent methods, nucleic acids (amplicon sequencing, WGS, metatranscriptomics), proteins (metaproteomics) and metabolites (metabolomics) based methodologies are used to obtain the taxonomical and/or the functional profiles of the gut microbiome whole genome sequencing (WGS) This assay sequences the entire genome of microbial samples to profile the taxonomical and functional composition of the gut microbiome. in_vitro gut taxonomical and functional profile not_specified high nucleic acids (amplicon sequencing, WGS, metatranscriptomics), proteins (metaproteomics) and metabolites (metabolomics) based methodologies are used to obtain the taxonomical and/or the functional profiles of the gut microbiome CASP1 Fluorescein Assay (FLICA) Detects activation of caspase-1 (CASP1) as an indicator of pyroptosis initiation. in_vitro CASP1 activation increase http://purl.obolibrary.org/obo/GO_0004197 GO http://purl.obolibrary.org/obo/GO_0070269 GO medium Pyroptosis initiation can be inferred from CASP1 activation hence the CASP1 Fluorescein Assay (FLICA) is also used by researchers as detection method http://purl.obolibrary.org/obo/PR_000001461 PR http://purl.obolibrary.org/obo/GO_0070269 GO fluorescent microscopy Visualizes loss of membrane integrity during pyroptosis using fluorescent microscopy. in_vitro loss of membrane integrity increase http://purl.obolibrary.org/obo/GO_0070269 GO low Den Hartigh and Fink also describe LDH release assay as well as fluorescent microscopy method for visualization of loss of membrane integrity during pyroptosis http://purl.obolibrary.org/obo/GO_0005886 GO http://purl.obolibrary.org/obo/GO_0070269 GO Hoechst 33342 and propidium iodide double staining Detects chromatin condensation (Hoechst 33342) and membrane damage (propidium iodide) to identify pyroptotic cells, though it may also detect other cell death types. in_vitro chromatin condensation and membrane damage increase http://purl.obolibrary.org/obo/GO_0006325 GO http://purl.obolibrary.org/obo/GO_0070269 GO medium Hoechst 33342 (chromatin condensation detection) and propidium iodide (probe for membrane damage) double staining can be used for pyroptotic cell detection although this method also detects other cell death types (e.g. apoptotis) http://purl.obolibrary.org/obo/GO_0000785 GO http://purl.obolibrary.org/obo/GO_0070269 GO LDH release assay Measures the release of lactate dehydrogenase (LDH) as an indicator of plasma membrane damage and cytotoxicity. in_vitro LDH release increase http://purl.obolibrary.org/obo/GO_0004459 GO high LDH is released when plasma membrane is damaged and is a common measure of cytotoxicity. LDH release assays using commercially available kit and a quick, cost-effective method adapted from Decker et al [8] are described by Rayamajhi and colleagues [9]. Den Hartigh and Fink also describe LDH release assay http://purl.obolibrary.org/obo/GO_0005886 GO Embryonic heart and great artery morphological assessment Examination of embryonic cardiovascular structures to identify developmental defects such as septal defects, outflow tract abnormalities, and aortic arch malformations following nutritional or chemical stress. in_vivo heart pharyngeal arches great vessels aortic arch pulmonary arteries subclavian artery carotid artery ductus arteriosus quail rat heart developmental defects and great artery morphological abnormalities change low Vitamin A deficiency in embryos results in heart developmental defects such as septal defects, abnormalities to the inflow and outflow tract, aortic arch abnormalities and coronary malformations in quail and rat (Dersch & Zile, 1993; Heine et al., 1985; Wilson & Warkany, 1949, 1950). Heart developmental defect assessment Assessment of heart developmental defects in embryos, including septal defects, inflow and outflow tract abnormalities, aortic arch abnormalities, and coronary malformations. in_vivo heart quail rat heart developmental defects increase http://purl.obolibrary.org/obo/GO_0007507 GO low Vitamin A deficiency in embryos results in heart developmental defects such as septal defects, abnormalities to the inflow and outflow tract, aortic arch abnormalities and coronary malformations in quail and rat (Dersch & Zile, 1993; Heine et al., 1985; Wilson & Warkany, 1949, 1950). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0007507 GO Pharyngeal arch analysis Analysis of pharyngeal arches and their arteries to assess correct vascular development and formation of the great vessels. in_vivo pharyngeal arches pharyngeal arteries quail rat vascular development and formation of the great vessels change http://purl.obolibrary.org/obo/UBERON_0003104 UBERON http://purl.obolibrary.org/obo/GO_0001944 GO low The pharyngeal arches include the pharyngeal arteries, which are responsible for correct vascular development. There are six pharyngeal arteries from which the third, fourth and sixth artery will become part of the great vessels. http://purl.obolibrary.org/obo/UBERON_0003105 UBERON http://purl.obolibrary.org/obo/GO_0001944 GO Bioluminescence Imaging (BLI) Measurement of light emitted by luciferase-expressing tumor cells to assess tumor growth. in_vivo tumor bioluminescent signal increase http://purl.obolibrary.org/obo/OBI_0000275 OBI medium Bioluminescence Imaging (BLI): Measurement of light emitted by luciferase-expressing tumor cells. http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0008283 GO Bioluminescence Imaging (BLI) Bioluminescence Imaging (BLI) measures light emitted by luciferase-expressing tumor cells. in_vivo luciferase-expressing tumor cells tumor light emission increase medium Measurement of light emitted by luciferase-expressing tumor cells. BrdU Assay using bromodeoxyuridine incorporation to measure cell proliferation. in_vitro DNA synthesis increase http://purl.obolibrary.org/obo/OBI_0000275 OBI medium Cell Proliferation Assays (MTT/MTS, BrdU) http://purl.obolibrary.org/obo/CL_0000003 CL http://purl.obolibrary.org/obo/GO_0006260 GO Caliper measurement Use of calipers to measure tumor dimensions for volume calculation. in_vivo tumor tumor volume increase medium Imagery using caliper measurement on http://purl.obolibrary.org/obo/UBERON_0001032 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO Clinical measurement and palpation Direct physical measurement and palpation to assess tumor size and growth. in_vivo tumor tumor size increase low Clinical measurement and palpation http://purl.obolibrary.org/obo/UBERON_0001032 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO Colony formation Assay to measure the ability of cells to form colonies, indicating cell proliferation and viability. in_vitro colony count increase http://purl.obolibrary.org/obo/OBI_0000275 OBI medium Colony formation http://purl.obolibrary.org/obo/CL_0000003 CL http://purl.obolibrary.org/obo/GO_0008283 GO CT Computed Tomography to provide detailed images of tumors for volume calculation. in_vivo tumor tumor volume increase http://purl.obolibrary.org/obo/OBI_0000275 OBI medium Computed Tomography (CT) http://purl.obolibrary.org/obo/UBERON_0001032 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO Flow Cytometry Quantification of tumor cells based on DNA content using flow cytometry. in_vitro tumor cell count increase http://purl.obolibrary.org/obo/OBI_0000275 OBI high Flow Cytometry: Quantification of tumor cells based on DNA content. http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0008283 GO Flow Cytometry Quantification of tumor cells based on their DNA content. in_vitro tumor cells DNA content change medium Flow Cytometry: Quantification of tumor cells based on DNA content. histopathology Histopathology with fluorescence imaging, dyes or weight is used to directly measure tumor growth. ex_vivo tumor tumor size/mass increase low Histopathology with fluorescence imaging, dyes or weight MRI Magnetic Resonance Imaging to provide detailed images of tumors for volume calculation. in_vivo tumor tumor volume increase http://purl.obolibrary.org/obo/OBI_0000275 OBI low Magnetic Resonance Imaging (MRI) http://purl.obolibrary.org/obo/UBERON_0001032 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO MTT/MTS/BrdU Cell Proliferation Assays (MTT/MTS, BrdU) measure cell proliferation. in_vitro tumor cells cell proliferation increase http://purl.obolibrary.org/obo/GO_0008283 GO medium Cell Proliferation Assay s (MTT/MTS, BrdU) http://purl.obolibrary.org/obo/GO_0008283 GO PET Positron Emission Tomography using radioactive tracers to measure metabolic activity and tumor growth. in_vivo tumor metabolic activity increase http://purl.obolibrary.org/obo/OBI_0000275 OBI low Positron Emission Tomography (PET) Imaging: measurement of metabolic activity using radioactive tracers. http://purl.obolibrary.org/obo/UBERON_0001032 UBERON http://purl.obolibrary.org/obo/GO_0008152 GO Serum Biomarkers Measurement of specific biomarkers in serum that indicate tumor growth or presence. in_vivo blood biomarker levels increase high Serum Biomarkers Ultrasound Use of ultrasound imaging to provide detailed images of tumors for volume calculation. in_vivo tumor tumor volume increase http://purl.obolibrary.org/obo/OBI_0000275 OBI medium ultrasound can provide detailed images for volume calculation http://purl.obolibrary.org/obo/UBERON_0001032 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO Indirect immunohistochemistry Immunohistochemical staining of tissue sections to visualize and quantify StAR protein expression using mean optical density and area percentage. in_vitro ovarian tissue peritoneal tissue Human expression index (EI) change http://purl.obolibrary.org/obo/GO_0000055 GO low Indirect immunohistochemistry for the detection of Steroidogenic Acute Regulatory Protein (StAR) A pathological image analysis system is used to measure mean optical density (MOD) analysis The MOD and area % are used to calculate the expression index, EI (%) = MOD × area % http://purl.obolibrary.org/obo/GO_0000055 GO indirect immunohistochemistry Detection of StAR protein in ovarian or peritoneal tissues using polyclonal antibodies and pathological image analysis to measure staining intensity and area. in_vivo ovarian tissue peritoneal tissue human StAR protein expression index increase http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/GO_0008104 GO low Indirect immunohistochemistry for the detection of Steroidogenic Acute Regulatory Protein (StAR): A pathological image analysis system is used to measure mean optical density (MOD) analysis under high-magnification (×400) microscopy. The MOD and area % are used to calculate the expression index, EI (%) = MOD × area % http://purl.obolibrary.org/obo/GO_0006694 GO qRT-PCR Quantitative real-time PCR to measure mRNA levels of StAR and H19 genes using fluorescein detection. in_vitro KGN cells mouse Leydig cells human mouse mRNA levels increase http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/SO_0000234 SO medium StAR protein is measure by quantitative real time PCR (qRT-PCR): qPCR is performed in a 25-μl reaction containing 0.5 to 1.5 μl of cDNA using fluorescein in real-time PCR detection systems. The threshold cycle values of each sample are used to calculate mRNA levels. http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR Quantitative real-time PCR (qRT-PCR) is used to measure mRNA levels of Steroidogenic Acute Regulatory Protein (StAR) in human ovarian granulosa tumor cell line (KGN cells) and mouse Leydig cells. cDNA is synthesized from total RNA and amplified using specific primers for human and mouse StAR genes. The threshold cycle values are used to calculate mRNA levels. in_vitro KGN cells mouse Leydig cells ovarian granulosa cells Leydig cells human mouse mRNA levels of StAR increase http://purl.obolibrary.org/obo/SO_0000673 SO low For qRT-PCR analyses, cDNA is synthesized using reagent kit in a 20-μl reaction containing 0.5 μg of total RNA collected from human ovarian granulosa tumor cell line ( KGN cells ), mouse Leydig cells. Human StAR forward: 5′-GGCATCCTTAGCAACCAAGA Human StAR reverse: 5′-TCTCCTTGACATTGGGGTTC Mouse StAR forward: 5′-TTGGGCATACTCAACAACCA Mouse StAR reverse: 5′-GAAACACCTTGCCCACATCT http://purl.obolibrary.org/obo/GO_0010467 GO Mass spectrometry An analytical method to measure estrogen levels in serum based on mass spectroscopic techniques. in_vitro serum estrogen levels increase medium Radioimmunoassay (RIA) and analytical method based on mass spectroscopic are used for estrogen measurement present in serum http://purl.obolibrary.org/obo/CHEBI_17586 CHEBI http://purl.obolibrary.org/obo/GO_0030521 GO Radioimmunoassay A method to measure estrogen levels in serum using radioactive isotopes and antibodies. in_vitro serum estrogen levels increase medium Radioimmunoassay (RIA) and analytical method based on mass spectroscopic are used for estrogen measurement present in serum http://purl.obolibrary.org/obo/CHEBI_17586 CHEBI http://purl.obolibrary.org/obo/GO_0030521 GO immunocytochemistry Detects the activated form of TP53 using antibodies against phosphorylated TP53 in tissue sections. in_vivo phosphorylated TP53 levels increase http://purl.obolibrary.org/obo/OBI_0000274 OBI medium by immunocytochemistry on tissue sections http://purl.obolibrary.org/obo/PR_000008068 PR http://purl.obolibrary.org/obo/GO_0006468 GO Western Blot Detects the activated form of TP53 using antibodies against phosphorylated TP53 in protein extracts. in_vitro phosphorylated TP53 levels increase http://purl.obolibrary.org/obo/OBI_0000275 OBI medium Antibody against phosphorylated TP53 are used to detect the activated form of TP53. This is made by immunocytochemistry techniques through Western Blot analysis on protein extract http://purl.obolibrary.org/obo/PR_000008068 PR http://purl.obolibrary.org/obo/GO_0006468 GO Calcium imaging Indirectly measures VGSC function by monitoring changes in intracellular calcium levels using fluorescent calcium indicators. not_specified intracellular calcium concentration not_specified http://purl.obolibrary.org/obo/GO_0006816 GO medium Other approaches can be used to indirectly measure VGSC function, including radiotracer flux, fluorescent approaches, and calcium imaging. http://purl.obolibrary.org/obo/PR_000001016 PR http://purl.obolibrary.org/obo/GO_0006811 GO Fluorescent approaches Indirectly measures VGSC function using fluorescent indicators to monitor ion movements or membrane potential changes. not_specified fluorescence intensity not_specified http://purl.obolibrary.org/obo/GO_0006811 GO medium Other approaches can be used to indirectly measure VGSC function, including radiotracer flux, fluorescent approaches, and calcium imaging. http://purl.obolibrary.org/obo/PR_000001016 PR http://purl.obolibrary.org/obo/GO_0006811 GO Radiotracer flux Indirectly measures VGSC function by tracking the flux of radiolabeled ions. not_specified ion flux not_specified http://purl.obolibrary.org/obo/GO_0006811 GO medium Other approaches can be used to indirectly measure VGSC function, including radiotracer flux, fluorescent approaches, and calcium imaging. http://purl.obolibrary.org/obo/PR_000001016 PR http://purl.obolibrary.org/obo/GO_0006811 GO radiotracer flux This approach indirectly measures VGSC function by measuring the flux of radiotracers. not_specified radiotracer flux change not_specified Other approaches can be used to indirectly measure VGSC function, including radiotracer flux, fluorescent approaches, and calcium imaging. http://purl.obolibrary.org/obo/GO_0006825 GO Voltage-clamp Measures transmembrane currents resulting from ion channel opening and closing using two microelectrodes to control membrane potential and record currents. in_vitro neuron transmembrane currents not_specified http://purl.obolibrary.org/obo/GO_0005216 GO low Voltage-clamp techniques typically use two microelectrodes, allowing control of the membrane potential (‘clamping’) and recording of transmembrane currents that result from ion channel opening and closing (Guan et al., 2013). http://purl.obolibrary.org/obo/PR_000001016 PR http://purl.obolibrary.org/obo/GO_0006811 GO clonal survival assay Measures cell survival and proliferation capacity. in_vitro human cell line human cell survival not_specified low clonal survival assay COMET assay Measures DNA damage by detecting DNA strand breaks in individual cells. in_vitro DNA strand breaks not_specified OECD TG 489 medium COMET assay CyQuant cell Proliferation assay Measures cell proliferation using fluorescent DNA binding dye. in_vitro mice cell proliferation not_specified high CyQuant cell Proliferation assay FACS Measures cell characteristics using fluorescence-activated cell sorting. in_vitro human cell line human cell characteristics not_specified high FACs Flowcytometry Technology used to analyze the physical and chemical characteristics of particles in a fluid as they pass through a laser beam. in_vitro cellular characteristics not_specified http://purl.obolibrary.org/obo/OBI_0000034 OBI medium Flowcytometry Immuno staining Detects protein expression and localization using antibody-based staining. in_vitro protein expression and localization not_specified medium Immuno staining Immunogold EM Detects protein localization using electron microscopy with gold-labeled antibodies. in_vitro canine protein localization not_specified low Immunogold EM Microarray Measures gene expression levels using hybridization to probe arrays. in_vitro gene expression levels not_specified high Microarray qRT PCR Measures gene expression levels using reverse transcription and quantitative PCR. in_vitro gene expression levels not_specified high qRT PCR qRT PCR qRT PCR is used to quantify RNA levels. in_vitro RNA levels increase http://purl.obolibrary.org/obo/OBI_0000703 OBI medium qRT PCR,RIP assay,Immunogold EM(Wan G et al 2013) http://purl.obolibrary.org/obo/CHEBI_50835 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO RIP assay Measures RNA-protein interactions by immunoprecipitating RNA-binding proteins. in_vitro canine RNA-protein interactions not_specified low RIP assay RNA sequence analysis Measures gene expression levels through sequencing of RNA. in_vitro gene expression levels not_specified high RNA sequence analysis RNA sequencing RNA sequence analysis is used to quantify RNA levels. in_vitro RNA levels increase http://purl.obolibrary.org/obo/OBI_0000703 OBI high RNA sequence analysis,Immuno staining,immunoblotting,Flowcytometry,COMET assay,qRT PCR(Liu Z et al 2017) http://purl.obolibrary.org/obo/CHEBI_50835 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO Western blotting Measures protein levels using antibody-based detection. in_vitro human cell line human protein levels not_specified low Western blotting ELISA ELISA measures the levels of SIRT1 protein. in_vitro mouse SIRT1 protein levels decrease medium qRT-PCR,Western blotting,Luciferase reporter assay,ELISA,cell culture http://purl.obolibrary.org/obo/GO_0010457 GO Luciferase reporter assay Luciferase reporter assay measures the transcriptional activity of SIRT1. in_vitro human SIRT1 transcriptional activity decrease medium qRT-PCR,Western blotting,Luciferase reporter assay H2,H4,H7,H8,H9 Micro-array, qRT-PCR,Western blotting,Luciferase reporter assay http://purl.obolibrary.org/obo/GO_0006351 GO micro-array Microarrays are used to measure the expression levels of thousands of genes simultaneously. in_vitro Human Mouse Gene expression levels decrease high Micro-array (Shen ZL et al 2016) Micro-array, qRT-PCR,Western blotting,Luciferase reporter assay http://purl.obolibrary.org/obo/GO_0010468 GO Micro-array Micro-array measures the levels of SIRT1 mRNA. in_vitro human SIRT1 mRNA levels decrease high Micro-array (Shen ZL et al 2016) Micro-array, qRT-PCR,Western blotting,Luciferase reporter assay http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR Quantitative reverse transcription PCR measures the levels of SIRT1 mRNA. in_vitro human SIRT1 mRNA levels decrease medium qRT-PCR,Western blotting,Luciferase reporter assay H2,H4,H7,H8,H9 Micro-array, qRT-PCR,Western blotting,Luciferase reporter assay http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Western blotting measures the levels of SIRT1 protein. in_vitro human SIRT1 protein levels decrease low qRT-PCR,Western blotting,Luciferase reporter assay H2,H4,H7,H8,H9 Micro-array, qRT-PCR,Western blotting,Luciferase reporter assay http://purl.obolibrary.org/obo/GO_0010457 GO bioluminescence imaging Bioluminescence imaging detects light produced by bioluminescent cells or reporters, used for tracking cells in vivo or in vitro. in_vivo Human cell line humans bioluminescence signal change medium bioluminescence imaging http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0044237 GO bioluminesence imaging Bioluminesence imaging visualizes and quantifies metastatic spread of breast cancer cells in vivo. in_vivo Human cell line Breast Human metastatic tumor burden increase low bioluminesence imaging http://purl.obolibrary.org/obo/GO_0000000 GO http://purl.obolibrary.org/obo/GO_0000000 GO cell invasion assay Measures the ability of cells to invade through a matrix, indicating metastatic potential. in_vitro Human cell line Humans cell invasion not_specified http://purl.obolibrary.org/obo/GO_0016525 GO http://purl.obolibrary.org/obo/OBI_0000556 OBI medium cell invasion assay http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016479 GO cell invasion assay Quantifies the ability of cells to invade through an extracellular matrix barrier, modeling metastatic spread. in_vitro Human cell line Breast Homo sapiens Number of invading cells increase low cell invasion assay Cell line,humans,Human cell line studies Direct measure Cell migration assay Assesses cell motility, typically measuring movement across a surface or through a porous membrane. in_vitro Human cell line human migratory capacity increase http://purl.obolibrary.org/obo/GO_0016477 GO not_specified cell migration assay Cell line,humans,Human cell line studies http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016477 GO immunoblotting Detects specific proteins using antibodies and measures their expression levels. in_vitro Human cell line Humans protein expression not_specified http://purl.obolibrary.org/obo/OBI_0000268 OBI http://purl.obolibrary.org/obo/GO_0010485 GO low immunoblotting http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0019538 GO Immunofluorescence Uses fluorescent antibodies to visualize specific proteins or structures within cells. in_vitro Human cell line Humans protein localization not_specified http://purl.obolibrary.org/obo/OBI_0000564 OBI http://purl.obolibrary.org/obo/GO_0008104 GO low Immunofluorescence http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0008104 GO Immunohistochemistry Uses antibodies to detect specific proteins in tissue sections, often used to study protein expression and localization. in_vivo Humans protein expression and localization not_specified http://purl.obolibrary.org/obo/OBI_0000563 OBI http://purl.obolibrary.org/obo/GO_0008104 GO low Immunohistochemistry http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0008104 GO immunoprecipitation Immunoprecipitation isolates specific proteins from a sample using antibodies, allowing for further analysis of protein interactions or modifications. in_vitro Human cell line humans protein-protein interaction change low immunoprecipitation http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0043031 GO Luciferase reporter assay Luciferase reporter assays measure gene expression by quantifying the amount of luciferase enzyme produced from a reporter construct. This indicates transcriptional activity. in_vitro Human cell line humans luciferase activity change medium Luciferase reporter assay http://purl.obolibrary.org/obo/GO_0010468 GO Luciferase reporter assay Uses luciferase enzyme to measure gene expression or promoter activity. in_vitro Human cell line Humans promoter activity not_specified http://purl.obolibrary.org/obo/OBI_0000555 OBI http://purl.obolibrary.org/obo/GO_0010467 GO high Luciferase reporter assay http://purl.obolibrary.org/obo/SO_0000167 SO http://purl.obolibrary.org/obo/GO_0006351 GO Luciferase reporter assay A method to measure gene transcription or promoter activity by measuring the light produced by a luciferase enzyme. in_vitro Human cell line human reporter gene activity not_specified http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Luciferase reporter assay Microarray Measures the expression levels of thousands of genes simultaneously. in_vitro Human cell line Humans gene expression not_specified http://purl.obolibrary.org/obo/GO_0010467 GO high Microarray http://purl.obolibrary.org/obo/SO_0000316 SO http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR Quantitative reverse transcription polymerase chain reaction to measure gene expression levels. in_vitro Human cell line Humans gene expression not_specified http://purl.obolibrary.org/obo/GO_0010467 GO medium Cell line,humans,Human cell line studies qRT-PCR http://purl.obolibrary.org/obo/SO_0000316 SO http://purl.obolibrary.org/obo/GO_0010467 GO wound healing assay Measures the ability of cells to migrate into a scratch or wound area, indicating migratory potential. in_vitro Human cell line Humans cell migration not_specified http://purl.obolibrary.org/obo/OBI_0000686 OBI http://purl.obolibrary.org/obo/GO_0016479 GO medium Wound scratch & Transwell assay http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0016479 GO wound healing assay Wound healing assays measure the rate at which cells migrate to close a gap in a cell monolayer. in_vitro Human cell line humans wound closure rate increase medium wound healing assay http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0008359 GO extracellular recording Extracellular recordings show changes in the activity of several cells surrounding a microelectrode. Unit recordings characterize APs by high frequency activity on a millisecond timescale. in_vitro electrical activity change http://www.bioassayontology.org/bao#BAO_0000136 BAO low Rather than on or in the cell, extracellular recordings show changes in the activity of several cells surrounding a microelectrode. http://purl.obolibrary.org/obo/CL_0000755 CL http://purl.obolibrary.org/obo/GO_0005284 GO Extracellular recording (unit recording) Measures changes in the activity of multiple cells surrounding a microelectrode, with action potentials characterized by high-frequency activity on a millisecond timescale. in_vitro electrical activity of multiple cells reflecting action potentials change http://purl.obolibrary.org/obo/GO_0001508 GO low Rather than on or in the cell, extracellular recordings show changes in the activity of several cells surrounding a microelectrode. These are referred to as unit recordings where APs are characterized by high frequency of activity on msec timescale. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0001508 GO extracellular recording (unit recording) Measurement of electrical activity changes in several cells surrounding a microelectrode, often using spike sorting to distinguish individual units. in_vivo high frequency of electrical activity change low extracellular recordings show changes in the activity of several cells surrounding a microelectrode. These are referred to as unit recordings where APs are characterized by high frequency of activity on msec timescale. http://purl.obolibrary.org/obo/CL_0000000 CL FRET assay Utilizes fluorescence resonance energy transfer (FRET) between specialized fluorophores to detect membrane potential shifts associated with action potentials. not_specified FRET fluorescence efficiency (membrane potential) change http://purl.obolibrary.org/obo/GO_0009055 GO http://purl.obolibrary.org/obo/GO_0042391 GO high Another optical technique uses dyes that are sensitive to changes in voltage or fluorescence resonance energy transfer (FRET) using specialized fluorophores that respond based on changes in membrane potential. Large changes in FRET fluorescence are indicative of changes in electrical activity. Under the correct conditions, FRET fluorescence can reflect changes in action potential generation. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0060079 GO Intracellular recording (sharp electrode) Measures membrane voltage changes by inserting sharp glass microelectrodes directly into the intracellular space of the neuron, capturing action potentials as steep increases in voltage. in_vitro membrane voltage changes reflecting action potentials change http://purl.obolibrary.org/obo/GO_0001508 GO http://purl.obolibrary.org/obo/GO_0051899 GO http://purl.obolibrary.org/obo/OBI_0000278 OBI low In the intracellular recording, sharp glass microelectrodes are inserted directly into the intracellular space of the neuron and membrane voltage is measured. Membrane voltage increases dramatically once a threshold depolarization is reached and an action potential is reflected in a short duration steep increase in voltage followed by a rapid fall. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0001508 GO Local field potential recording Measures the synchronized electrical potential of a group of cells, often used in laminated structures with known anatomical inputs to assess neurotransmission. in_vivo synchronized electrical potential reflecting group activity change http://purl.obolibrary.org/obo/GO_0007268 GO low Local field potentials are also extracellular recordings, but measure the synchronized electrical potential of a group of cells whose source may be difficult to determine. Commonly used in laminated structures with known anatomical inputs, stimulating electrodes are placed on the input presynaptic axonal field and electrical responses induced after a short synaptic delay represent neurotransmission from pre to postsynaptic neurons. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0007268 GO Microelectrode array (MEA) Records action potential signals from multiple electrodes simultaneously, providing parameters such as firing rate and bursting rates to characterize electrical activity. in_vitro firing rate and bursting rates reflecting action potentials change http://purl.obolibrary.org/obo/GO_0001508 GO http://purl.obolibrary.org/obo/OBI_0001857 OBI medium Microelectrode arrays (MEAs) are a form of extracellular recording, consisting of chips that contain multiple electrodes, typically arranged in a small grid. MEA recordings provide multiple parameters of electrical activity, with firing rate and bursting rates as the most common to characterize APs. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0001508 GO Optical measurement (ion-sensitive dyes) Uses Na+ or Ca++ sensitive dyes that fluoresce in response to ion binding, providing an indirect measure of action potential generation by detecting changes in bulk ion concentration. in_vitro fluorescence changes reflecting bulk ion concentration change http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/CHEBI_26708 CHEBI http://purl.obolibrary.org/obo/OBI_0000221 OBI high These include the use of Na+ or Ca++ sensitive dyes that fluoresce in response to the binding of one of these ions. Single APs are not detected, but changes in bulk ion concentration over a finite period of time primarily reflect the firing rate of the cells. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0001508 GO Patch clamp recording (current clamp configuration) Measures action potentials by recording changes in membrane voltage using electrodes placed on the cell, allowing all channel types to contribute to the AP response. in_vitro membrane voltage changes reflecting action potentials change http://purl.obolibrary.org/obo/GO_0001508 GO http://purl.obolibrary.org/obo/GO_0051899 GO low In patch recording, in contrast to evaluating specific channel activity as described in KE1 for VGSC activation, to evaluate AP, the current clamp configuration is commonly employed. The action potential is reflected in a rapid fluctuation in voltage. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0001508 GO voltage-sensitive dye assay Employs voltage-sensitive fluorescent dyes whose fluorescence intensity varies with membrane potential, allowing optical tracking of action potential-related voltage changes. not_specified membrane potential changes change http://purl.obolibrary.org/obo/GO_0042391 GO http://purl.obolibrary.org/obo/GO_0060079 GO high Another optical technique uses dyes that are sensitive to changes in voltage or fluorescence resonance energy transfer (FRET) using specialized fluorophores that respond based on changes in membrane potential. Large changes in FRET fluorescence are indicative of changes in electrical activity. Under the correct conditions, FRET fluorescence can reflect changes in action potential generation. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0060079 GO voltage-sensitive dyes / FRET Optical techniques using voltage-sensitive dyes or FRET-based specialized fluorophores to respond to changes in membrane potential. in_vitro FRET fluorescence change high Another optical technique uses dyes that are sensitive to changes in voltage or fluorescence resonance energy transfer (FRET) using specialized fluorophores that respond based on changes in membrane potential. Large changes in FRET fluorescence are indicative of changes in electrical activity. ELISA Quantifies kisspeptin protein levels in biological samples using commercially available enzyme-linked immunosorbent assay kits. in_vitro kisspeptin concentration increase not_specified Kisspeptin can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. Studies that utilized immunoassay include (Adachi et al. 2007; Clarkson et al. 2008; Wang et al. 2014), and include commercially available ELISA kits (e.g. Abcam ab288589 (human); Assay Genie HUDL01615 (human); LS Bio LS-F8897 (mouse)). immunoassay Measures kisspeptin levels using commercially available ELISA kits. in_vitro human mouse kisspeptin levels increase medium Kisspeptin can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. include commercially available ELISA kits (e.g. Abcam ab288589 (human); Assay Genie HUDL01615 (human); LS Bio LS-F8897 (mouse)) http://purl.obolibrary.org/obo/GO_0046879 GO real time PCR Measures kisspeptin transcript abundance as an indirect indicator of kisspeptin hormone levels. in_vitro kisspeptin transcript abundance increase http://purl.obolibrary.org/obo/OBI_0000662 OBI medium Real time PCR can be used to measure kisspeptin transcript abundance, which is an indirect – and only semi-quantitative indicator of kisspeptin hormone levels http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Measures kisspeptin protein levels. in_vitro kisspeptin protein levels increase low Kisspeptin can be measured via immunoassay or Western blotting, with immunoassay the preferred technique. http://purl.obolibrary.org/obo/GO_0046879 GO ELISA Commercially available ELISA kits are used to measure Luteinizing hormone and Follicle-stimulating hormone levels. These kits utilize antibodies to quantify the hormone concentration in a sample. in_vitro human mouse hormone concentration decrease medium Commercially ELISA kits are available for Luteinizing hormone (e.g. Abcam AB303746 (human); Aviva OKCA00156 (mouse); ThermoFisher EHLH (human)) and Follicle-stimulating hormone (e.g. ThermoFisher EH202RB (human); ALPCO 11-FSHHU-E01 (human); ENZO ENZ-KIT108 (human)). Immunoassay Measures gonadotropin levels from blood or urine samples using immunoassay techniques. in_vitro blood urine human mouse gonadotropin levels decrease medium Gonadotropin levels are generally measured from blood or urine samples by immunoassay or Western blotting, with immunoassay the preferred technique. Commercially ELISA kits are available for Luteinizing hormone (e.g. Abcam AB303746 (human); Aviva OKCA00156 (mouse); ThermoFisher EHLH (human)) and Follicle-stimulating hormone (e.g. ThermoFisher EH202RB (human); ALPCO 11-FSHHU-E01 (human); ENZO ENZ-KIT108 (human)). Real-time PCR Measures gonadotropin transcript abundance as an indirect indicator of gonadotropin hormone levels. in_vitro gonadotropin transcript abundance decrease medium Real time PCR can be used to measure gonadotropin transcript abundance, which is an indirect – and only semi-quantitative indicator of gonadotropin hormone levels. Western blotting Measures gonadotropin levels from blood or urine samples using Western blotting techniques. in_vitro blood urine gonadotropin levels decrease low Gonadotropin levels are generally measured from blood or urine samples by immunoassay or Western blotting, with immunoassay the preferred technique. extracellular field potential recordings Measures neurotransmission by recording postsynaptic responses induced by stimulation of presynaptic axonal fields. in_vitro neurons postsynaptic responses change http://purl.obolibrary.org/obo/GO_0007268 GO low In extracellular field potential recordings stimulating electrodes placed on the input presynaptic axonal field induce after a short synaptic delay a response in the postsynaptic cells reflecting neurotransmission. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0007268 GO Extracellular recordings Measures neurotransmission by recording field potentials outside neurons, reflecting postsynaptic responses after presynaptic stimulation. in_vitro extracellular field potentials change low In extracellular field potential recordings stimulating electrodes placed on the input presynaptic axonal field induce after a short synaptic delay a response in the postsynaptic cells reflecting neurotransmission. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0007268 GO in vitro neurotransmitter release assay Measures neurotransmitters released into the media in vitro. in_vitro neurons neurotransmitter release change http://purl.obolibrary.org/obo/GO_0007269 GO medium Biochemical assessment of neurotransmission (i.e. in vivo microdialysis or in vitro measurement of neurotransmitters released into the media) are also common and well described in the literature. http://purl.obolibrary.org/obo/CHEBI_25512 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO In vivo microdialysis Measures neurotransmission by sampling extracellular fluid in vivo to quantify neurotransmitters released into the media. in_vivo brain neurotransmitter concentration in extracellular fluid change http://purl.obolibrary.org/obo/GO_0005615 GO low Biochemical assessment of neurotransmission (i.e. in vivo microdialysis or in vitro measurement of neurotransmitters released into the media) are also common and well described in the literature. http://purl.obolibrary.org/obo/GO_0007268 GO in vivo microdialysis Measures neurotransmitters released in vivo. in_vivo brain neurotransmitter release change http://purl.obolibrary.org/obo/GO_0007269 GO low Biochemical assessment of neurotransmission (i.e. in vivo microdialysis or in vitro measurement of neurotransmitters released into the media) are also common and well described in the literature. http://purl.obolibrary.org/obo/CHEBI_25512 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO intracellular recordings Measures neurotransmission by recording excitatory and inhibitory currents in postsynaptic neurons using electrodes positioned inside the cell. in_vitro neurons excitatory and inhibitory currents change http://purl.obolibrary.org/obo/GO_0007268 GO low Intracellular recordings measure neurotransmission following stimulation of presynaptic neurons via excitatory and inhibitory currents by electrodes positioned inside the postsynaptic neuron. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0007268 GO microelectrode array (MEA) recordings Measures neurotransmission by recording synchronized network activity and correlation of neuronal activity across multiple electrodes. in_vitro neurons synchronized network activity change http://purl.obolibrary.org/obo/GO_0007268 GO medium In microelectrode arrays, neurotransmission is reflected by parameters including synchronized network activity, correlation of neuronal activity across multiple electrodes, and activity evoked by direct stimulation. http://purl.obolibrary.org/obo/GO_0044446 GO http://purl.obolibrary.org/obo/GO_0007268 GO NNF assay Assesses the impact of chemical exposure on neural network formation and function using rodent cortical neurons. in_vitro cortical neurons cortex rodent neural network formation and function change http://purl.obolibrary.org/obo/GO_0044446 GO http://purl.obolibrary.org/obo/GO_0007268 GO medium A standardized NNF test system to assess the potential impact of chemical exposure on neural network formation and function has been developed using rodent cortical neurons (Frank et al., 2017). http://purl.obolibrary.org/obo/GO_0044446 GO http://purl.obolibrary.org/obo/GO_0007268 GO patch clamp Measures neurotransmission by recording excitatory and inhibitory currents in postsynaptic neurons using electrodes positioned inside the cell. in_vitro neurons excitatory and inhibitory currents change http://purl.obolibrary.org/obo/GO_0007268 GO low patch clamp intracellular and extracellular recordings patch clamp techniques http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0007268 GO Patch Clamp Patch clamp technique measures neurotransmission by recording postsynaptic currents following stimulation of presynaptic neurons. It can capture excitatory and inhibitory currents in the postsynaptic neuron. in_vitro neurons brain rodent postsynaptic currents change http://purl.obolibrary.org/obo/GO_0065008 GO http://purl.obolibrary.org/obo/GO_0007268 GO low Intracellular recordings measure neurotransmission following stimulation of presynaptic neurons via excitatory and inhibitory currents by electrodes positioned inside the postsynaptic neuron. Similar currents can be assessed using patch clamp techniques. Patch Clamp http://purl.obolibrary.org/obo/CL_0000548 CL http://purl.obolibrary.org/obo/GO_0007268 GO pH sensitive dye assay Optical approaches using pH sensitive dyes incorporated into pre-synaptic vesicles measure neurotransmission by detecting fluorescent changes upon release into the synaptic cleft. in_vitro synapse fluorescent signal change change medium As described above for KE2, Action Potential Generation, optical approaches can also be used to measure neurotransmission, such as the use of pH sensitive dyes that are incorporated into the pre-synaptic vesicles, dyes that change fluorescent properties once released into the synaptic cleft due to a difference in pH between the vesicle compartment and the synaptic cleft. http://purl.obolibrary.org/obo/CL_0000279 CL pH-sensitive dye assay Measures neurotransmission using pH-sensitive dyes that change fluorescent properties upon release into the synaptic cleft. in_vitro neurons neurotransmitter release change http://purl.obolibrary.org/obo/GO_0007269 GO http://purl.obolibrary.org/obo/CHMO_0000745 CHMO medium optical approaches can also be used to measure neurotransmission, such as the use of pH sensitive dyes that are incorporated into the pre-synaptic vesicles, dyes that change fluorescent properties once released into the synaptic cleft due to a difference in pH between the vesicle compartment and the synaptic cleft. http://purl.obolibrary.org/obo/CHEBI_25512 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO RT-qPCR Measures sox9 expression levels using reverse transcription quantitative polymerase chain reaction. in_vitro sox9 expression decrease http://purl.obolibrary.org/obo/GO_0010467 GO medium RT-qPCR, to measure sox9 expression http://purl.obolibrary.org/obo/GO_0010467 GO CHART Measures slincR molecular localization using capture hybridization analysis of RNA targets (CHART). in_vivo Danio rerio slincR molecular localization not_specified http://purl.obolibrary.org/obo/GO_0006403 GO low slincR molecular localization can be measured by capture hybridization analysis of RNA targets (CHART) and was measured in 48 hpf zebrafish embryos (Garcia et al., 2018). http://purl.obolibrary.org/obo/GO_0006403 GO in situ hybridization Measures slincR tissue localization of expression using in situ hybridization. in_vivo Danio rerio slincR tissue localization of expression not_specified low slincR tissue localization of expression can be measured by in situ hybridization and has been measured in embryonic zebrafish at 24, 36, 48, 60, and 72 hpf (Garcia et al., 2017). RT-qPCR Measures slincR gene expression using quantitative reverse transcriptase polymerase chain reaction. in_vivo Danio rerio slincR gene expression increase http://purl.obolibrary.org/obo/GO_0010467 GO medium slincR gene expression can be measured by quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and has been measured in embryonic zebrafish at 48 and 96 hours post fertilization (hpf) (Garcia et al., 2017). http://purl.obolibrary.org/obo/GO_0010467 GO Ceramide synthase activity assay Measures the activity of ceramide synthases (CerS) by quantifying the acylation of Sphiganine (Sa) to form (dihydro-)ceramide or the reacylation of Sphingosine (So). in_vitro Ceramide synthase activity decrease http://purl.obolibrary.org/obo/GO_0016271 GO not_specified Ceramide synthases (CerS) are enzymes that catalyze the acylation of Sphiganine (Sa) to form (dihydro-)ceramide (a precursor for ceramide and complex sphingolipds) and also the reacylation of Sphingosine (So) that is derived from the turnover of complex sphingolipids http://purl.obolibrary.org/obo/GO_0016271 GO http://purl.obolibrary.org/obo/GO_0006665 GO Sphinganine (Sa) quantification assay Measures the levels of Sphinganine (Sa) in biological samples, which increases upon inhibition of CerS. in_vitro Sphinganine levels increase http://purl.obolibrary.org/obo/CHEBI_17885 CHEBI not_specified The inhibition of CerS results in an increase of Sa, So, and, often, Sa/So ratio http://purl.obolibrary.org/obo/CHEBI_17885 CHEBI http://purl.obolibrary.org/obo/GO_0006665 GO Complex sphingolipid measurement This assay measures the levels of complex sphingolipids, such as sphingomyelin and gangliosides, which are essential components of eukaryotic membranes. not_specified complex sphingolipid levels decrease http://purl.obolibrary.org/obo/CHEBI_26781 CHEBI http://purl.obolibrary.org/obo/CHEBI_26732 CHEBI http://purl.obolibrary.org/obo/CHEBI_17760 CHEBI not_specified Complex sphingolipids are derived from ceramide and have a rather large structural diversity. They inlude, for example, sphingomyelin (SM) and glycosphingolipids such as gangliosides (GM), and are essential constituents or eukaryotic membranes a decrease in sphingolipids may result in a variety of adverse effecfts http://purl.obolibrary.org/obo/CHEBI_26781 CHEBI http://purl.obolibrary.org/obo/GO_0061025 GO fluorescence binding assay Measures the binding and affinity of compounds for the Smoothened (SMO) receptor using fluorescence. in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000356 OBI medium Verification of binding and affinity for SMO can be measured using fluorescence binding assays http://purl.obolibrary.org/obo/PR_000001491 PR http://purl.obolibrary.org/obo/GO_0001659 GO fluorescence binding assays An assay used to measure the binding and affinity of molecules to the Smoothened (SMO) receptor using fluorescent probes. in_vitro binding and affinity for SMO not_specified http://purl.obolibrary.org/obo/GO_0005125 GO not_specified Verification of binding and affinity for SMO can be measured using fluorescence binding assays http://purl.obolibrary.org/obo/GO_0005125 GO photoaffinity labeling Measures the binding and affinity of compounds for the Smoothened (SMO) receptor using photoaffinity labeling. in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000356 OBI low affinity for SMO can be measured using [...] photoaffinity labeling respectively http://purl.obolibrary.org/obo/PR_000001491 PR http://purl.obolibrary.org/obo/GO_0001659 GO photoaffinity labeling A method used to study the binding and affinity of ligands to the SMO receptor by using light-activated chemical probes to form covalent bonds. in_vitro binding and affinity for SMO not_specified http://purl.obolibrary.org/obo/GO_0005125 GO not_specified Verification of binding and affinity for SMO can be measured using [...] photoaffinity labeling http://purl.obolibrary.org/obo/GO_0005125 GO Immunofluorescence and microscopy Uses primary antibodies to tag GLI in combination with a secondary stain for the nucleus to determine protein translocation. in_vitro GLI translocation to the nucleus decrease http://purl.obolibrary.org/obo/OBI_0000665 OBI http://purl.obolibrary.org/obo/OBI_0000245 OBI http://purl.obolibrary.org/obo/GO_0046907 GO http://purl.obolibrary.org/obo/GO_0005634 GO low Immunofluorescence and microscopy can be used to determine how much of a protein has translocated to the nucleus. Primary antibodies can be used to tag GLI in combination with a secondary stain for the nucleus (Blotta, Jakubikova et al. 2012). http://purl.obolibrary.org/obo/GO_0046907 GO immunofluorescence and microscopy Using primary antibodies against a target protein and secondary stains for the nucleus to visualize and quantify protein localization via microscopy. in_vitro protein translocation to the nucleus not_specified http://purl.obolibrary.org/obo/OBI_0000102 OBI not_specified Immunofluorescence and microscopy can be used to determine how much of a protein has translocated to the nucleus. Primary antibodies can be used to tag GLI in combination with a secondary stain for the nucleus http://purl.obolibrary.org/obo/GO_0006826 GO Nuclear protein extracts analysis Analyzes nuclear protein extracts to determine if the protein of interest (GLI1/2) translocated to the nucleus. in_vitro GLI1/2 translocation to the nucleus decrease http://purl.obolibrary.org/obo/GO_0046907 GO http://purl.obolibrary.org/obo/GO_0005634 GO medium Nuclear protein extracts can be analysed to determine if the protein of interest (GLI1/2) translocated to the nucleus (Kim, Kato et al. 2009). http://purl.obolibrary.org/obo/GO_0046907 GO Nuclear Translocation Assay (NTA) Determines the amount of protein that translocates into the nucleus. in_vitro protein translocation to the nucleus decrease http://purl.obolibrary.org/obo/GO_0046907 GO http://purl.obolibrary.org/obo/GO_0005634 GO medium A nuclear translocation assay (NTA) can be applied to determine the amount of protein that translocate into the nucleus (Dixon and Lim 2010). http://purl.obolibrary.org/obo/GO_0046907 GO ATP modulation assay This assay measures the activation of IP3R by assessing its modulation by ATP. The methodology is not further specified. not_specified IP3R activation change http://purl.obolibrary.org/obo/GO_0007025 GO not_specified The activation of IP3R can be modulated by various factors: ATP http://purl.obolibrary.org/obo/CHEBI_59738 CHEBI http://purl.obolibrary.org/obo/GO_0007025 GO IP3R activation assay Measures the activation of IP3R modulated by factors such as Ca²⁺ and ATP. not_specified IP3R activation not_specified not_specified The activation of IP3R can be modulated by various factors: Sensitization by Ca²⁺, ATP differential display Differential display compares gene expression profiles between different samples to identify differentially expressed genes. in_vitro differential gene expression change http://purl.obolibrary.org/obo/GO_0010467 GO medium Changes in gene expression can be measured using differential display http://purl.obolibrary.org/obo/GO_0010467 GO DNA microarray assay DNA microarray assay measures the expression levels of thousands of genes simultaneously. in_vitro gene expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO high Changes in gene expression can be measured using DNA microarray assay http://purl.obolibrary.org/obo/GO_0010467 GO Northern blot Northern blotting is used to measure changes in gene expression. in_vitro gene expression levels decrease low Changes in gene expression can be measured using Northern/Southern blotting http://purl.obolibrary.org/obo/GO_0010468 GO RAGE Rapid analysis of gene expression (RAGE) measures gene expression levels using PCR-based methods. in_vitro gene expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO medium Changes in gene expression can be measured using rapid analysis of gene expression (RAGE) http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Reverse transcription PCR (RT-PCR) measures gene expression levels by amplifying cDNA generated from RNA. in_vitro gene expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO medium Changes in gene expression can be measured using RT-PCR http://purl.obolibrary.org/obo/GO_0010467 GO SAGE Serial analysis of gene expression (SAGE) measures gene expression levels by sequencing short gene-specific tags. in_vitro gene expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO medium Changes in gene expression can be measured using serial analysis of gene expression (SAGE) http://purl.obolibrary.org/obo/GO_0010467 GO 3D CT scan Quantifies palatal shelf outgrowth during development using imaging techniques. in_vivo palatal shelves distance between palatal shelves decrease http://purl.obolibrary.org/obo/UBERON_0003608 UBERON low Palatal shelf outgrowth can be quantified using imaging techniques such as 3D CT scans during development. http://purl.obolibrary.org/obo/UBERON_0003608 UBERON dissection and measurement Embryos are dissected and the facial prominences are measured. ex_vivo facial prominences size of facial prominences decrease low Embryos can be dissected and the facial prominences measured (Rice, Connor et al. 2006). http://purl.obolibrary.org/obo/GO_0048756 GO facial prominence measurement Measures the size of facial prominences in dissected embryos. ex_vivo facial prominences facial prominence size decrease http://purl.obolibrary.org/obo/UBERON_0004085 UBERON low Embryos can be dissected and the facial prominences measured (Rice, Connor et al. 2006). http://purl.obolibrary.org/obo/UBERON_0004085 UBERON morphometric measurement Dissection of embryos followed by direct measurement of facial prominences. ex_vivo facial prominences facial prominence size decrease low Embryos can be dissected and the facial prominences measured (Rice, Connor et al. 2006). revised Smith-modified Kernahan ‘Y’ classification A morphological classification system used to describe the type, location, and extent of orofacial cleft deformities. not_specified lip palate type, location, and extent of OFC deformities not_specified low Techniques such as the revised Smith-modified Kernahan ‘Y’ classification can be used describe the type, location, and extent of OFC deformities http://purl.obolibrary.org/obo/GO_0044974 GO Smith-modified Kernahan 'Y' classification A classification system used to describe the type, location, and extent of orofacial cleft deformities. in_vivo lip palate human animal classification of orofacial cleft deformities not_specified http://purl.obolibrary.org/obo/HP_0000202 HP http://purl.obolibrary.org/obo/UBERON_0002177 UBERON http://purl.obolibrary.org/obo/UBERON_0001655 UBERON low Techniques such as the revised Smith-modified Kernahan ‘Y’ classification can be used describe the type, location, and extent of OFC deformities (Khan, Ullah et al. 2013). http://purl.obolibrary.org/obo/UBERON_0001655 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO visual observation Orofacial clefts (OFC) are visually observed and classified based on affected tissues and severity. in_vivo lip palate human animal presence and classification of orofacial clefts not_specified http://purl.obolibrary.org/obo/HP_0000202 HP http://purl.obolibrary.org/obo/UBERON_0002177 UBERON http://purl.obolibrary.org/obo/UBERON_0001655 UBERON low OFC can be visually observed both in humans and in animals. It can be classified by which tissues (e.g.cleft lip and palate) are effected and its’ severity (complete/incomplete, unilateral/bilateral). http://purl.obolibrary.org/obo/UBERON_0001655 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO antibody staining Antibody staining of tissue sections determines location and amounts of BMP4, BMP2, FGF10. in_vivo protein localization and quantity not_specified http://purl.obolibrary.org/obo/GO_0008104 GO medium Antibody staining of tissue sections can be used to determine location and amounts of BMP4, BMP2, FGF10 http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0008104 GO Antibody staining of tissue sections Determines location and amounts of specific proteins (BMP4, BMP2, FGF10) in tissue sections using labeled antibodies. not_specified location and amounts of BMP4, BMP2, FGF10 change not_specified Antibody staining of tissue sections can be used to determine location and amounts of BMP4, BMP2, FGF10 differential display Differential display measures changes in gene expression. in_vitro gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO medium Changes in gene expression can be measured using differential display http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO DNA microarray assay DNA microarray assay measures changes in gene expression. in_vitro gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO high Changes in gene expression can be measured using DNA microarray assay http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO Northern/Southern blotting Northern and Southern blotting measure changes in gene expression. in_vitro gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO low Changes in gene expression can be measured using Northern/Southern blotting http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO RAGE Rapid analysis of gene expression measures changes in gene expression. in_vitro gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO high Changes in gene expression can be measured using rapid analysis of gene expression (RAGE) http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO RNA in situ hybridization RNA in situ hybridization determines sites of gene expression. in_vivo gene expression localization not_specified http://purl.obolibrary.org/obo/GO_0010467 GO low RNA in situ hybridization can be used to determine sites of gene expression http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Reverse transcription polymerase chain reaction measures changes in gene expression. in_vitro gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO medium Changes in gene expression can be measured using RT-PCR http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO SAGE Serial analysis of gene expression measures changes in gene expression. in_vitro gene expression changes change http://purl.obolibrary.org/obo/GO_0010467 GO high Changes in gene expression can be measured using serial analysis of gene expression (SAGE) http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO Fluorescence microscopy Fluorescent proteins are used to tag SMO, cilia, and the plasma membrane to determine if SMO has relocated to the cilia. in_vitro cilia SMO localization change low Fluorescent proteins can be used tag SMO, cilia and the plasma membrane to determine if SMO has relocated to the cilia (Filipova, Diaz Garcia et al. 2020). http://purl.obolibrary.org/obo/CHEBI_62889 CHEBI http://purl.obolibrary.org/obo/GO_0006646 GO Fluorescent binding assay Measures the binding of a compound to SMO using fluorescence. in_vitro compound binding to SMO increase http://purl.obolibrary.org/obo/GO_0005515 GO medium Fluorescent binding assay can be used to verify if a compound binds to SMO (Chen, Taipale et al. 2002). http://purl.obolibrary.org/obo/GO_0005515 GO Fluorescent protein tagging Uses fluorescent proteins to tag SMO, cilia, and the plasma membrane to determine SMO relocation to the cilia. in_vitro SMO relocation to cilia increase http://purl.obolibrary.org/obo/GO_0005929 GO http://purl.obolibrary.org/obo/GO_0008104 GO medium Fluorescent proteins can be used tag SMO, cilia and the plasma membrane to determine if SMO has relocated to the cilia (Filipova, Diaz Garcia et al. 2020). http://purl.obolibrary.org/obo/GO_0008104 GO Myc-tagged SMO activation assay Uses engineered cell lines expressing Myc-tagged SMO to measure SMO activation. in_vitro engineered cell lines SMO activation increase http://purl.obolibrary.org/obo/GO_0043065 GO medium Cell lines can be engineered to express Myc-tagged SMO. This gives a user friendly readout of SMO activation. (Corbit, Aanstad et al. 2005). http://purl.obolibrary.org/obo/GO_0043065 GO Cell behaviour assays Signal transduction events of cells are monitored. Cells are exposed to varying levels of signaling proteins and the resulting actions of a cell are observed (changes in structure, cell shape, matrix binding etc.). in_vitro cell actions (structure, shape, matrix binding) change low Cell behaviour assays (Svoboda & Reenstra, 2002) Signal transduction events of cells are monitored. Cells are exposed to varying levels of signaling proteins and the resulting actions of a cell are observed (changes in structure, cell shape, matrix binding etc.). http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0007165 GO Cell behaviour assays Monitors signal transduction events in cells exposed to signaling proteins by observing changes in structure, cell shape, and matrix binding. in_vitro cell morphological changes change http://purl.obolibrary.org/obo/GO_0008360 GO http://purl.obolibrary.org/obo/GO_0007165 GO medium Signal transduction events of cells are monitored. Cells are exposed to varying levels of signaling proteins and the resulting actions of a cell are observed (changes in structure, cell shape, matrix binding etc.). http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0000902 GO ELISA Uses antibodies to detect the presence of a protein in a liquid sample, particularly useful for low concentrations. in_vitro protein concentration change http://purl.obolibrary.org/obo/PR_000000001 PR high Plate-based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of a protein of interest especially when in low concentrations http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019538 GO Enzyme-linked immunosorbent assay (ELISA) Plate-based assay technique using antibodies to detect presence of a protein in a liquid sample, especially when in low concentrations. not_specified presence/concentration of a protein change not_specified Plate-based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of a protein of interest especially when in low concentrations Fluorescence microscopy/spectroscopy Measures cell localization, protein interactions, signal propagation, amplification, and integration in real-time or upon stimulation. in_vitro protein localization and interactions change http://purl.obolibrary.org/obo/GO_0008104 GO Yes medium Measures cell localization, protein interactions, signal propagation, amplification, and integration in the cell in real-time, or upon stimulation. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0007165 GO FRAP Determines mobility and diffusion of small molecules by measuring fluorescence recovery after photobleaching. in_vitro molecular mobility change http://purl.obolibrary.org/obo/GO_0035556 GO medium Determines mobility and diffusion of small molecules. http://purl.obolibrary.org/obo/CHEBI_59999 CHEBI http://purl.obolibrary.org/obo/GO_0032496 GO FRET Illuminates interactions between biological molecules using fluorescence resonance energy transfer. in_vitro molecular interactions change http://purl.obolibrary.org/obo/OBI_0000343 OBI http://purl.obolibrary.org/obo/GO_0005515 GO medium Assay helps illuminate the interactions between biological molecules http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0005515 GO GFP Acts as a fluorescent reporter for intracellular signaling events such as second messengers (Ca2+, cAMP) or pH in cell compartments. in_vitro intracellular signaling events change http://purl.obolibrary.org/obo/PR_000008451 PR http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI high GFP assays act as fluorescent reporters but also as a marker of intracellular signalling events i.e. second messengers Ca2+ and cAMP, or for pH in different various cell compartments http://purl.obolibrary.org/obo/GO_0035591 GO http://purl.obolibrary.org/obo/GO_0035556 GO GFP assays GFP assays act as fluorescent reporters but also as a marker of intracellular signalling events i.e. second messengers Ca2+ and cAMP, or for pH in different various cell compartments in_vitro fluorescence intensity (Ca2+, cAMP, pH) change medium Green Fluorescent Protein (GFP) (Zaccolo and Pozzan, 2000) GFP assays act as fluorescent reporters but also as a marker of intracellular signalling events i.e. second messengers Ca2+ and cAMP, or for pH in different various cell compartments http://purl.obolibrary.org/obo/GO_0007165 GO Immunohistochemistry Using antibodies with recognition epitopes to locate active configurations or phosphorylated proteins within a cell or cell lysate via blotting techniques. in_vitro location of active configurations or phosphorylated proteins change http://purl.obolibrary.org/obo/GO_0006473 GO not_specified For example, antibodies with recognition epitopes can be used to locate active configurations or phosphorylated proteins within a cell or cell lysate. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006473 GO Immunohistochemistry Uses antibodies to locate active configurations or phosphorylated proteins within cells or cell lysates. in_vitro protein phosphorylation change http://purl.obolibrary.org/obo/GO_0006468 GO low antibodies with recognition epitopes can be used to locate active configurations or phosphorylated proteins within a cell or cell lysate. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006468 GO Immunoprecipitation Isolates and concentrates a specific protein from mixed samples to detect changes in signaling molecule activity. in_vitro protein activity change http://purl.obolibrary.org/obo/PR_000000001 PR Chromatin immunoprecipitation approved for analyzing histone modifications low Involves isolating and concentrating a particular protein from mixed samples to detect changes in signalling molecule activity. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0007165 GO Immunoprecipitation Involves isolating and concentrating a particular protein from mixed samples to detect changes in signalling molecule activity. in_vitro signalling molecule activity change low Immunoprecipitation (Svoboda & Reenstra, 2002) Involves isolating and concentrating a particular protein from mixed samples to detect changes in signalling molecule activity. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0007165 GO Kinase assays Monitors the activity of a kinase of interest by blocking it with inhibitors. in_vitro kinase activity change http://purl.obolibrary.org/obo/GO_0016301 GO medium Block kinase with inhibitors to monitor the activity of a kinase of interest. http://purl.obolibrary.org/obo/GO_0004672 GO http://purl.obolibrary.org/obo/GO_0035556 GO Ratiometric or single-wavelength dyes Detects alterations in signal-transduction activities via monitoring changes in detectable wavelengths. in_vitro changes in detectable wavelengths change medium Ratiometric or single-wavelength dyes (Svoboda & Reenstra, 2002) Detects alterations in signal-transduction activities via monitoring changes in detectable wavelengths. http://purl.obolibrary.org/obo/GO_0007165 GO Ratiometric or single-wavelength dyes Detects alterations in signal-transduction activities by monitoring changes in detectable wavelengths. in_vitro signal-transduction activity change http://purl.obolibrary.org/obo/GO_0007165 GO high Detects alterations in signal-transduction activities via monitoring changes in detectable wavelengths. http://purl.obolibrary.org/obo/GO_0007165 GO http://purl.obolibrary.org/obo/GO_0007267 GO RT-qPCR Measures mRNA expression of the gene of interest using reverse transcription and quantitative polymerase chain reaction. in_vitro mRNA expression change http://purl.obolibrary.org/obo/OBI_0000663 OBI http://purl.obolibrary.org/obo/SO_0000234 SO high Measures mRNA expression of the gene of interest. http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO DAF-FM fluorescent probe Used to detect low concentrations of NO by reacting with it to become a fluorescent benzotriazole that can then be visualized and measured. in_vitro NO levels change http://purl.obolibrary.org/obo/CHEBI_16136 CHEBI medium Used to detect low concentrations of NO by reacting with it to become a fluorescent benzotriazole that can then be visualized and measured. http://purl.obolibrary.org/obo/CHEBI_16136 CHEBI http://purl.obolibrary.org/obo/GO_0046210 GO ELISA kit Used to determine levels of NO and iNOS in serum by immobilizing the target antigen and binding it to associated antibodies linked to reporter enzymes. The activity of the reporter enzymes is then measured to determine levels of NO and iNOS. in_vitro NO and iNOS levels change http://purl.obolibrary.org/obo/CHEBI_16136 CHEBI http://purl.obolibrary.org/obo/PR_000001218 PR medium Used to determine levels of NO and iNOS in serum by immobilizing the target antigen and binding it to associated antibodies linked to reporter enzymes. The activity of the reporter enzymes is then measured to determine levels of NO and iNOS. http://purl.obolibrary.org/obo/CHEBI_16136 CHEBI http://purl.obolibrary.org/obo/GO_0006809 GO Griess assay Levels of nitrite/nitrate (NOx) are determined using the NO assay kit. Nitrate reductase is used to convert nitrate into nitrite and the Griess reagent is then used to quantify levels of nitrite. in_vitro nitrite/nitrate levels (NOx) change medium Levels of nitrite/nitrate (NOx) are determined using the NO assay kit. Nitrate reductase is used to convert nitrate into nitrite and the Griess reagent is then used to quantify levels of nitrite. http://purl.obolibrary.org/obo/CHEBI_59678 CHEBI http://purl.obolibrary.org/obo/GO_0042053 GO Immunofluorescence Uses fluorescent dye-labeled eNOS antibodies to visualize and determine eNOS levels. in_vitro eNOS levels change http://purl.obolibrary.org/obo/PR_000001217 PR low Uses fluorescent dye-labeled eNOS antibodies to visualize and determine eNOS levels. http://purl.obolibrary.org/obo/PR_000001217 PR http://purl.obolibrary.org/obo/GO_0006809 GO Immunohistochemical staining Uses an antibody to detect and measure levels of eNOS. in_vivo eNOS levels change http://purl.obolibrary.org/obo/PR_000001217 PR low Uses an antibody to detect and measure levels of eNOS. http://purl.obolibrary.org/obo/PR_000001217 PR http://purl.obolibrary.org/obo/GO_0006809 GO Nitric oxide/nitrate/nitrite (NOx) assay kit (Griess assay) Levels of nitrite/nitrate (NOx) are determined using the NO assay kit. Nitrate reductase is used to convert nitrate into nitrite and the Griess reagent is then used to quantify levels of nitrite. in_vitro nitrite/nitrate levels change http://purl.obolibrary.org/obo/CHEBI_16680 CHEBI http://purl.obolibrary.org/obo/CHEBI_17632 CHEBI medium Levels of nitrite/nitrate (NOx) are determined using the NO assay kit. Nitrate reductase is used to convert nitrate into nitrite and the Griess reagent is then used to quantify levels of nitrite. http://purl.obolibrary.org/obo/CHEBI_16136 CHEBI http://purl.obolibrary.org/obo/GO_0046210 GO Western blotting/immunoblotting Western blotting/immunoblotting is used to determine levels of inducible and endothelial NOS (NO synthesizing enzyme) in its phosphorylated and unphosphorylated forms, as well as nitrotyrosine (an indicator of NO). NOS and nitrotyrosine are detected by antibodies of each protein, visualized using chemiluminescence, and quantified using densitometry. in_vitro NOS and nitrotyrosine protein levels change http://purl.obolibrary.org/obo/GO_0006809 GO low Western blotting/immunoblotting is used to determine levels of inducible and endothelial NOS (NO synthesizing enzyme) in its phosphorylated and unphosphorylated forms, as well as nitrotyrosine (an indicator of NO). NOS and nitrotyrosine are detected by antibodies of each protein, visualized using chemiluminescence, and quantified using densitometry. http://purl.obolibrary.org/obo/PR_000001216 PR http://purl.obolibrary.org/obo/GO_0006809 GO BrdU incorporation staining Measures bromodeoxyuridine (BrdU) incorporation via staining to assess DNA synthesis. in_vitro endothelial cells vasculature DNA synthesis decrease http://purl.obolibrary.org/obo/GO_0006260 GO low Bromodeoxyuridine (BrdU) detected with staining incorporation Reduced BrdU incorporation can indicate a lack of DNA synthesis. http://purl.obolibrary.org/obo/CL_0001266 CL http://purl.obolibrary.org/obo/GO_0006260 GO BrdU staining Measures BrdU incorporation to assess DNA synthesis, where reduced incorporation indicates lack of DNA synthesis. in_vitro BrdU incorporation decrease http://purl.obolibrary.org/obo/GO_0071897 GO medium Bromodeoxyuridine (BrdU) detected with staining incorporation Reduced BrdU incorporation can indicate a lack of DNA synthesis. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0006260 GO Cell morphology and size Cell morphology and size are measured using light microscopy or flow cytometry to identify enlarged and flattened senescent endothelial cells. in_vitro endothelial cells blood vessels human cell morphology and size change low Cell morphology and size measured with light microscopy or flow cytometry. Senescent cells exhibit an enlarged and flattened morphology. http://purl.obolibrary.org/obo/CL_0000315 CL http://purl.obolibrary.org/obo/GO_0003006 GO Concentration-response curves to vasodilators/vasoconstrictors Measures endothelial relaxation/contraction of blood vessels to assess endothelial dysfunction, where decreased response indicates endothelial dysfunction. in_vivo blood vessels endothelial relaxation/contraction decrease http://purl.obolibrary.org/obo/GO_0042311 GO http://purl.obolibrary.org/obo/GO_0042310 GO low Concentration-response curves to vasodilators/vasoconstrictors Measurement of endothelial relaxation/contraction of blood vessels can give insight into endothelial dysfunction. This can be induced by endothelium-independent stimuli to stimulate vasodilation or vasoconstriction. A decreased stimuli response can be indicative of endothelial dysfunction. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_1901607 GO ECIS Measures endothelial barrier changes and monolayer resistance using a range of frequencies. in_vitro endothelial barrier resistance change medium Electric Cell Substrate Impedance Sensing (ECIS) Measurement of endothelial barrier changes and monolayer resistance using a range of frequencies. ELISA Endothelin is an endothelium-derived vasoconstrictor. in_vitro endothelin concentration increase medium Detection of contractile factors (eg. endothelin) using enzyme-linked immunosorbent assay (ELISA). Endothelin is an endothelium-derived vasoconstrictor. http://purl.obolibrary.org/obo/CHEBI_59754 CHEBI http://purl.obolibrary.org/obo/GO_0007525 GO ELISA for endothelin Detects endothelin, an endothelium-derived vasoconstrictor, to assess endothelial dysfunction. in_vitro endothelin concentration increase medium Detection of contractile factors (eg. endothelin) using enzyme-linked immunosorbent assay (ELISA). Endothelin is an endothelium-derived vasoconstrictor. http://purl.obolibrary.org/obo/GO_0042310 GO Immunohistochemistry Detects senescence markers such as Ki67 and Lamin B1, where reduced Ki67 indicates reduced proliferation and reduced Lamin B1 indicates impaired nuclear integrity. in_vitro expression of senescence markers (Ki67, Lamin B1) decrease medium Immunohistochemistry to detect senescence markers. Markers include Ki67 and Lamin B1. Reduced Ki67 can indicate reduced proliferation. Reduced Lamin B1 indicates impaired structural integrity of the nucleus. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0008283 GO Immunohistochemistry detection of senescence markers (Ki67, Lamin B1) Uses immunohistochemistry to detect senescence-associated markers Ki67 and Lamin B1; reduced Ki67 indicates reduced proliferation and reduced Lamin B1 indicates impaired nuclear structural integrity. in_vitro endothelium immunohistochemical detection of senescence markers (Ki67, Lamin B1) decrease not_specified Markers include Ki67 and Lamin B1. Reduced Ki67 can indicate reduced proliferation. Reduced Lamin B1 indicates impaired structural integrity of the nucleus. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0008283 GO Light microscopy or flow cytometry Measures cell morphology and size, where senescent cells exhibit an enlarged and flattened morphology. in_vitro cell morphology and size change http://purl.obolibrary.org/obo/GO_0000902 GO high Cell morphology and size measured with light microscopy or flow cytometry. Senescent cells exhibit an enlarged and flattened morphology. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0090398 GO Permeability assay Measures endothelial permeability using fluorescent dyes or stains to detect macromolecules crossing the barrier. in_vitro endothelial permeability increase medium Permeability assays Measurement of endothelial permeability using fluorescent dyes or stains to detect the various sized macromolecules that cross the barrier. SA-beta-gal staining Measures senescence-associated β-galactosidase activity, a marker for senescent cells. in_vitro senescence-associated β-galactosidase activity increase medium Senescence-associated beta-galactosidase staining (SA-beta-gal) Can be used to measure senescence-associated β-galactosidase activity, a marker for senescent cells. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0090398 GO Hematoxylin-eosin (HE) staining Measures aortic wall thickness, intima-media wall thickness (IMT), wall shear stress, outer media perimeter, and media cross section area (CSA). in_vivo aorta aortic wall thickness, IMT, wall shear stress, outer media perimeter, media CSA not_specified http://purl.obolibrary.org/obo/MP_0004975 MP medium Used to measure aortic wall thickness, intima-media wall thickness (IMT), wall shear stress, outer media perimeter, and media cross section area (CSA). http://purl.obolibrary.org/obo/UBERON_0000947 UBERON http://purl.obolibrary.org/obo/GO_0001974 GO Matrigel assay Measures the ability to form vascular networks using a gelatinous protein mixture on culture plates. in_vitro vascular network formation not_specified medium Uses a gelatinous protein mixture that is added onto culture plates, and measures the ability to form vascular networks http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0001525 GO NIS-Elements image analysis Measures intraluminal perimeter and vessel wall thickness using image analysis software. in_vivo blood vessels intraluminal perimeter and vessel wall thickness not_specified medium Used to measure intraluminal perimeter (which in turn is used to calculate circular luminal diameter) and vessel wall thickness. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0001974 GO Permeability Assays Uses dyes or stains to detect macromolecules crossing the barrier, measuring vascular permeability. in_vitro blood vessels vascular permeability not_specified http://purl.obolibrary.org/obo/GO_0090280 GO medium Uses dyes or stains to detect the various sized macromolecules that cross the barrier, measures vascular permeability. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0001974 GO Pulse wave velocity (PWV) Measures blood vessel stiffness using Doppler probe and electrocardiogram (ECG). in_vivo blood vessels blood vessel stiffness not_specified low Used to measure blood vessel stiffness. Calculated using measurements from a Doppler probe and electrocardiogram (ECG). http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0001974 GO Sonography Uses ultrasound waves to measure IMT and intima-media area, markers of vascular structure and stiffness. in_vivo blood vessels IMT and intima-media area not_specified http://purl.obolibrary.org/obo/MP_0004975 MP high Uses ultrasound waves to measure IMT and intima-media area, both of which are markers of vascular structure and are used to calculate vascular stiffness. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0001974 GO Verhoeff-van Gieson staining Measures elastin-collagen content in blood vessels, with Verhoeff stain highlighting elastin and van Gieson highlighting collagen. in_vivo blood vessels elastin-collagen content not_specified http://purl.obolibrary.org/obo/PR_000009403 PR http://purl.obolibrary.org/obo/PR_000005016 PR medium Measures elastin-collagen content in blood vessels, with Verhoeff stain highlighting elastin and van Gieson highlighting collagen. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0001974 GO Wire myography Measures relaxed inner diameter of blood vessels using passive length-tension relationship. ex_vivo blood vessels relaxed inner diameter not_specified low Blood vessels are mounted in wire myograph systems and the relaxed inner diameter is estimated from the passive length-tension relationship between each artery. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0001974 GO ELISA Quantifies drebrin levels in neuronal extracts using an enzyme-linked immunoassay kit. in_vitro primary hippocampal neurons hippocampus human rodent drebrin protein levels decrease medium For enzyme-linked immunoassay, after the incubation of chemicals the extracts of neurons were quantified using ELISA kit for drebrin (ALzMEd, Inc.) http://purl.obolibrary.org/obo/GO_0008104 GO immunocytochemistry Detects drebrin localization in cultured neurons via immunostaining and high-content imaging. in_vitro primary hippocampal neurons hippocampus human rodent drebrin cluster density along dendrites decrease http://purl.obolibrary.org/obo/OBI_0000570 OBI http://purl.obolibrary.org/obo/GO_0043197 GO high For immunocytochemistry, the cultured neurons were incubated with chemicals for 1 hour. After fixation, cultured neurons were immunostained with anti-drebrin and anti-MAP2 antibodies. The cluster density of drebrin along the dendrites was automatically quantified using high content analysis instruments (Hanamura et al, 2019, Mitsuoka et al, 2019). http://purl.obolibrary.org/obo/GO_0060077 GO western blot Detects drebrin protein levels in neuronal or tissue extracts via gel electrophoresis and immunoblotting. in_vitro primary hippocampal neurons brain hippocampus human rodent drebrin protein levels decrease low Loss of drebrin from dendritic spines can be detected by immunocytochemistry, ELISA or Western blotting in cultured human and rodent neurons and brain tissues (Counts et al., 2006; Ishizuka et al., 2014). http://purl.obolibrary.org/obo/GO_0008104 GO A280 Spectroscopy Direct assay for protein concentration determination in solution by measuring absorbance at 280 nm. not_specified protein concentration not_specified not_specified Direct assay method for protein concentration determination in solution through measuring absorbance at 280 nm. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019538 GO A280(Spectroscopy) A direct assay method for determining protein concentration in solution by measuring absorbance at 280 nm. not_specified absorbance at 280 nm change not_specified Direct assay method for protein concentration determination in solution through measuring absorbance at 280 nm. http://purl.obolibrary.org/obo/PR_000000001 PR Bicinchoninic Acid Assay (BCA) Quantifies total protein in a sample through colorimetric changes mediated by protein reduction of Cu+2 to Cu+1. not_specified total protein concentration not_specified not_specified Can assist in quantification of total protein in a sample with colorimetric changes propagated through proteins mediated reduction of Cu+2 to Cu+1. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019538 GO ELISA Detects carbonyl content on proteins using a plate reader following a chromogenic reaction. not_specified carbonyl content on proteins not_specified http://purl.obolibrary.org/obo/GO_0006465 GO not_specified Carbonyl content on proteins detected using a plate reader following chromogenic reaction http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0036211 GO Lowry Assay Quantifies protein levels by measuring the spectral shift to the blue form of the dye caused by protein binding. not_specified protein levels not_specified not_specified Binding of administered agents to proteins causes measurable spectral shift to the blue form of the dye which can be used to quantify protein-levels. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019538 GO Mass Spectrometry Measures the mass-to-charge ratio of ions to identify and quantify molecules and architectural changes such as the post-translational modifications of proteins. not_specified post-translational modifications of proteins not_specified http://purl.obolibrary.org/obo/GO_0036211 GO http://purl.obolibrary.org/obo/OBI_0000274 OBI not_specified Technique involves measuring the mass-to-charge ratio of ions to identify and quantify molecules and architectural changes such as the post-translational modifications of proteins http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0036211 GO Protein Mass Spectrometry Proteins are digested with proteases (e.g., trypsin) and observed as peaks with different mass-to-charge ratios in tandem mass spectrometry. not_specified protein mass-to-charge ratios not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/GO_0006508 GO not_specified Proteins initially digested various recombinant proteases, most often trypsin and are then subsequently observed at the tandem mass spectrometer (MS1) as a series of peaks, each with a different mass-to-charge ratio. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019538 GO Proximity Ligation Assay An immunohistochemical tool for in situ detection of endogenous proteins, protein modifications, and protein interactions with high specificity and sensitivity. not_specified protein modifications and interactions not_specified http://purl.obolibrary.org/obo/GO_0036211 GO not_specified An immunohistochemical tool that can help perform in situ detection of endogenous proteins, protein modifications, and protein interactions with high specificity and sensitivity http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0036211 GO Western Blot Immunoblotting technique using antibody to detect its antigen and measure protein levels. not_specified protein levels not_specified not_specified Immunoblotting technique using antibody to detect its antigen and can be used for measuring protein levels. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0019538 GO clinical physical examination Diagnosis of hypospadias in humans by physical examination, recognizing the absence of ventral prepuce and excess dorsal prepuce. in_vivo penis Homo sapiens presence of hypospadias not_specified http://purl.obolibrary.org/obo/MONDO_0007653 MONDO http://purl.obolibrary.org/obo/OBI_0000070 OBI low In humans, hypospadias is diagnosed clinically by physical examination of the infant and is at first recognized by the absence of ventral prepuce and concurrent excess dorsal prepuce http://purl.obolibrary.org/obo/UBERON_0000988 UBERON http://purl.obolibrary.org/obo/GO_0072073 GO histological assessment Microscopic examination of transverse sections of the penis to identify hypospadias based on the urethral opening location relative to the os penis or corpus cavernosum. ex_vivo penis urethral opening location in transverse sections change low Fetal and neonatal identification of hypospadias may require microscopic examination for proper evaluation of the pathology...or by histological assessment in which the presence of the urethral opening in proximal, transverse sections (for example co-occuring with the os penis or corpus cavernosum) indicates hypospadias (Mahawong et al., 2014; Sinclair et al., 2017; Vilela et al., 2007). http://purl.obolibrary.org/obo/UBERON_0002824 UBERON http://purl.obolibrary.org/obo/GO_0009791 GO macroscopic assessment Postnatal assessment of hypospadias in mice and rats by visual inspection for genital abnormalities. in_vivo genitalia Mus musculus Rattus norvegicus genital abnormalities not_specified OECD TG 414, 416, 421/422, 443 low In mice and rats, macroscopic assessment of hypospadias may be performed postnatally, and several OECD test guidelines (TG) require macroscopic examination of genital abnormalities in in vivo toxicity studies (TG 414, 416, 421/422, 443). http://purl.obolibrary.org/obo/UBERON_0004738 UBERON http://purl.obolibrary.org/obo/GO_0009791 GO macroscopic assessment Postnatal macroscopic examination of mice and rats for genital abnormalities, including hypospadias. in_vivo genitalia Mus musculus Rattus norvegicus presence of hypospadias not_specified http://purl.obolibrary.org/obo/MONDO_0007653 MONDO http://purl.obolibrary.org/obo/OBI_0000070 OBI OECD TG 414, 416, 421/422, 443 medium In mice and rats, macroscopic assessment of hypospadias may be performed postnatally, and several OECD test guidelines (TG) require macroscopic examination of genital abnormalities in in vivo toxicity studies (TG 414, 416, 421/422, 443). http://purl.obolibrary.org/obo/UBERON_0000988 UBERON http://purl.obolibrary.org/obo/GO_0072073 GO physical examination Clinical diagnosis of hypospadias in humans based on visual inspection, recognizing the absence of ventral prepuce and excess dorsal prepuce. in_vivo genitalia Homo sapiens presence/absence of ventral prepuce and excess dorsal prepuce change low In humans, hypospadias is diagnosed clinically by physical examination of the infant and is at first recognized by the absence of ventral prepuce and concurrent excess dorsal prepuce (Baskin, 2000). http://purl.obolibrary.org/obo/UBERON_0004738 UBERON http://purl.obolibrary.org/obo/GO_0009791 GO scanning electron microscopy Microscopic examination of fetal and neonatal tissue to evaluate hypospadias pathology using scanning electron microscopy. ex_vivo penis Mus musculus Rattus norvegicus presence of hypospadias not_specified http://purl.obolibrary.org/obo/MONDO_0007653 MONDO low Fetal and neonatal identification of hypospadias may require microscopic examination for proper evaluation of the pathology. This can be done by scanning electron microscopy http://purl.obolibrary.org/obo/UBERON_0000988 UBERON http://purl.obolibrary.org/obo/GO_0072073 GO scanning electron microscopy Microscopic examination of fetal/neonatal tissues using scanning electron microscopy to identify hypospadias. ex_vivo genitalia urethral opening location change http://purl.obolibrary.org/obo/OBI_0000288 OBI low Fetal and neonatal identification of hypospadias may require microscopic examination for proper evaluation of the pathology. This can be done by scanning electron microscopy (Uda et al., 2004). http://purl.obolibrary.org/obo/UBERON_0002824 UBERON http://purl.obolibrary.org/obo/GO_0009791 GO semiquantitative histological assessment Semiquantitative histological approach measuring the percentage of urethral internalization in transverse sections of the penis to classify hypospadias severity. ex_vivo penis Mus musculus Rattus norvegicus percentage of urethral internalization decrease http://purl.obolibrary.org/obo/MONDO_0007653 MONDO low In a semiquantitative, histological approach, the number of transverse sections of the penis with internalization of the urethra was related to the total length of the penis, achieving a percentage of urethral internalization. In this study, ≤89% of urethral internalization was defined as indicative of mild hypospadias http://purl.obolibrary.org/obo/UBERON_0000057 UBERON http://purl.obolibrary.org/obo/GO_0072073 GO urethral internalization quantification A semiquantitative histological approach where the percentage of urethral internalization is calculated based on the number of transverse sections with internalized urethra relative to the total penis length. ex_vivo penis percentage of urethral internalization decrease low In a semiquantitative, histological approach, the number of transverse sections of the penis with internalization of the urethra was related to the total length of the penis, achieving a percentage of urethral internalization. In this study, ≤89% of urethral internalization was defined as indicative of mild hypospadias (Stewart et al., 2018). http://purl.obolibrary.org/obo/UBERON_0002824 UBERON http://purl.obolibrary.org/obo/GO_0009791 GO Histological staining Uses dyes such as trypan blue to differentiate different parts of the lens. ex_vivo lens differentiation of lens parts not_specified http://purl.obolibrary.org/obo/UBERON_0001762 UBERON low Uses dyes such as trypan blue to differentiate different parts of the lens. http://purl.obolibrary.org/obo/UBERON_0001762 UBERON http://purl.obolibrary.org/obo/GO_0002088 GO Lens opacification grading systems Systems used to classify the severity of cataracts using various scoring systems such as the Modified Merriam-Focht Cataract Scoring System, Lens Opacities Classification System III (LOC III), and others. in_vivo lens severity of lens opacification increase http://purl.obolibrary.org/obo/UBERON_0000082 UBERON medium Systems used to classify the severity of cataracts. There are multiple types including: the Modified Merriam-Focht Cataract Scoring System, Lens Opacities Classification System III (LOC III), Word Health Organization Cataract Grading System, Lens Opacities Classification System I (LOCI), Lens Opacities Classification System II (LOC II), Wisconsin Clinical and Photographic Cataract Grading System, Wilmer Clinical and Photographic Grading System, Oxford Clinical Cataract Grading System, Age-Related Eye Disease Study, National Eye Institute Clinical Cataract Grading System, Japanese Cooperative Cataract Research Group Cataract Grading System http://purl.obolibrary.org/obo/UBERON_0001762 UBERON Microscopy Examination Tests can help to examine interlocking processes and membrane architecture of lens. ex_vivo lens interlocking processes and membrane architecture change low Tests can help to examine interlocking processes and membrane architecture of lens. http://purl.obolibrary.org/obo/UBERON_0000973 UBERON http://purl.obolibrary.org/obo/GO_0003674 GO Microscopy Examination Examines interlocking processes and membrane architecture of the lens. ex_vivo lens membrane architecture of lens change http://purl.obolibrary.org/obo/UBERON_0001762 UBERON low Tests can help to examine interlocking processes and membrane architecture of lens. http://purl.obolibrary.org/obo/UBERON_0001762 UBERON http://purl.obolibrary.org/obo/GO_0061024 GO Optical coherence tomography (OCT) Optical signals are sent towards a tissue, where they either pass through or are reflected. These signals are then interpreted to build a spatial image of the tissue. in_vivo lens spatial image of lens tissue not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/UBERON_0001762 UBERON medium Optical signals are sent towards a tissue, where they either pass through or are reflected. These signals are then interpreted to build a spatial image of the tissue. http://purl.obolibrary.org/obo/UBERON_0001762 UBERON Optical coherence tomography (OCT) Optical signals are sent towards a tissue, where they either pass through or are reflected. These signals are then interpreted to build a spatial image of the tissue. in_vivo lens spatial image of tissue change medium Optical signals are sent towards a tissue, where they either pass through or are reflected. http://purl.obolibrary.org/obo/UBERON_0000973 UBERON Scheimpflug imaging Allows for the photography of obliquely tilted specimens without losing focus, used for cataract grading. in_vivo http://purl.obolibrary.org/obo/UBERON_0001964 cataract severity increase http://purl.obolibrary.org/obo/DOID_1402 DOID medium This technique allows for the photography of obliquely tilted specimens without losing focus. Cataract grading systems that utilize this principle include the Oxford Scheimpflug System, the Nidek EAS-1000, and the Zeiss Schfeimpflug video camera. http://purl.obolibrary.org/obo/UBERON_0001964 UBERON http://purl.obolibrary.org/obo/DOID_1402 DOID Scheimpflug imaging This technique allows for the photography of obliquely tilted specimens without losing focus. Cataract grading systems that utilize this principle include the Oxford Scheimpflug System, the Nidek EAS-1000, and the Zeiss Schfeimpflug video camera. in_vivo lens image of obliquely tilted specimens change medium This technique allows for the photography of obliquely tilted specimens without losing focus. http://purl.obolibrary.org/obo/UBERON_0000973 UBERON Slit Lamp Grading System Measures the light intensity reflected from opacities in nuclear cataracts. This also includes various techniques such as retroillumination. in_vivo lens light intensity reflected from opacities change low Measures the light intensity reflected from opacities in nuclear cataracts. http://purl.obolibrary.org/obo/UBERON_0000973 UBERON Alizarin red stain for calcium deposition This assay visualizes calcified elements of the bone, indicating the final step of osteoblastic bone formation and mineralization activity. in_vitro bone calcium deposition not_specified http://purl.obolibrary.org/obo/GO_0005509 GO low Alizarin red staining can be used to visualize calcified elements of the bone, the final step of osteoblastic bone formation and mineralization activity. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0030282 GO ALP assay These assays measure a mineralization protein produced by osteoblasts, Alkaline phosphatase (ALP). in_vitro bone Alkaline phosphatase levels change http://purl.obolibrary.org/obo/GO_0004253 GO not_specified These assays measure a mineralization protein produced by osteoblasts, Alkaline phosphatase (ALP). http://purl.obolibrary.org/obo/CHEBI_5974 CHEBI http://purl.obolibrary.org/obo/GO_0040020 GO BAP immunoassay Measures bone-specific alkaline phosphatase (BAP), a mineralization protein produced by osteoblasts. in_vitro osteoblasts bone bone-specific alkaline phosphatase (BAP) change http://purl.obolibrary.org/obo/GO_0008463 GO not_specified This assay measures a mineralization protein produced by osteoblasts, bone-specific alkaline phosphatase (BAP) http://purl.obolibrary.org/obo/CL_0000204 CL http://purl.obolibrary.org/obo/GO_0044214 GO BoneTRAP assay Measures tartrate-resistant acid phosphatase (TRAP), an osteoclast specific bone-resorbing molecule. in_vitro bone Tartrate-resistant acid phosphatase levels increase not_specified Measures tartrate-resistant acid phosphatase (TRAP), an osteoclast specific bone-resorbing molecule. http://purl.obolibrary.org/obo/GO_0043058 GO BoneTRAP assay This assay measures tartrate-resistant acid phosphatase (TRAP), an osteoclast-specific bone-resorbing molecule. in_vitro TRAP activity not_specified http://purl.obolibrary.org/obo/GO_0004771 GO medium Measures tartrate-resistant acid phosphatase (TRAP), an osteoclast specific bone-resorbing molecule. http://purl.obolibrary.org/obo/PR_000001584 PR http://purl.obolibrary.org/obo/GO_0030316 GO Bromodeoxyuridine (BrdU) labelling This assay measures cell proliferation. in_vitro cell proliferation not_specified http://purl.obolibrary.org/obo/GO_0008283 GO medium Measures cell proliferation. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO CTX assays This assay measures C-terminal type I collagen telopeptide (ICTP or CTX), a product of bone collagen degradation. in_vitro CTX levels not_specified medium Measures C-terminal type I collagen telopeptide (ICTP or CTX), a product of bone collagen degradation. http://purl.obolibrary.org/obo/GO_0030574 GO HPLC This assay measures hydroxylysine glycosides, products of bone collagen degradation. in_vitro hydroxylysine glycosides levels not_specified http://purl.obolibrary.org/obo/CHEBI_17276 CHEBI medium Measures hydroxylysine glycosides, products of bone collagen degradation. http://purl.obolibrary.org/obo/GO_0030574 GO Hydroxylysine glycosides assay HPLC or ELISA assay measuring hydroxylysine glycosides (including GHYL or GHL and GGHL), which are products of bone collagen degradation. not_specified bone hydroxylysine glycosides levels not_specified http://purl.obolibrary.org/obo/GO_0006425 GO not_specified Measures hydroxylysine glycosides, products of bone collagen degradation. http://purl.obolibrary.org/obo/GO_0006425 GO Hydroxyproline assay Measures hydroxyproline, a product of bone collagen degradation. in_vitro bone Hydroxyproline levels increase http://purl.obolibrary.org/obo/GO_0006338 GO not_specified Measures hydroxyproline, a product of bone collagen degradation. http://purl.obolibrary.org/obo/CHEBI_24804 CHEBI http://purl.obolibrary.org/obo/GO_0006338 GO Hypronosticon assay This assay measures hydroxyproline, a product of bone collagen degradation. in_vitro hydroxyproline levels not_specified http://purl.obolibrary.org/obo/CHEBI_17275 CHEBI medium Measures hydroxyproline, a product of bone collagen degradation. http://purl.obolibrary.org/obo/CHEBI_17275 CHEBI http://purl.obolibrary.org/obo/GO_0030574 GO ICTP assay This assay measures C-terminal type I collagen telopeptide (ICTP or CTX), a product of bone collagen degradation. in_vitro ICTP levels not_specified medium Measures C-terminal type I collagen telopeptide (ICTP or CTX), a product of bone collagen degradation. http://purl.obolibrary.org/obo/GO_0030574 GO Immunoassays for non-collagenous matrix proteins This assay measures non-collagenous matrix proteins such as bone sialoprotein (BSP), osteonectin, osteopontin, and matrix gla protein (MGP). in_vitro non-collagenous matrix protein levels not_specified http://purl.obolibrary.org/obo/PR_000000099 PR medium Non-collagenous matrix proteins, such as bone sialoprotein (BSP), osteonectin, osteopontin, and matrix gla protein (MGP) can be measured via immunoassays. Changes in the amount of non-collagenous matrix proteins before and after a stressor indicate alterations in bone formation. http://purl.obolibrary.org/obo/GO_0060348 GO Immunocytochemical assays for cathepsin K This assay measures cathepsin K, a collagen cleaving molecule. in_vitro cathepsin K levels not_specified http://purl.obolibrary.org/obo/PR_000001496 PR low Measures cathepsin K, a collagen cleaving molecule. http://purl.obolibrary.org/obo/PR_000001496 PR http://purl.obolibrary.org/obo/GO_0030574 GO L-type Wako ALP J2 assay This assay measures alkaline phosphatase (ALP), a mineralization protein produced by osteoblasts. in_vitro alkaline phosphatase activity not_specified http://purl.obolibrary.org/obo/GO_0004036 GO medium These assays measure a mineralization protein produced by osteoblasts, Alkaline phosphatase (ALP). http://purl.obolibrary.org/obo/PR_000004008 PR http://purl.obolibrary.org/obo/GO_0001649 GO NTX assays This assay measures N-terminal type I collagen telopeptide (NTX), a product of bone collagen degradation. in_vitro NTX levels not_specified medium Measures N-terminal type I collagen telopeptide (NTX), a product of bone collagen degradation. http://purl.obolibrary.org/obo/GO_0030574 GO OSCAtest osteocalcin assay This assay measures osteocalcin (OCN), a mineralization protein produced by osteoblasts. in_vitro human osteocalcin levels not_specified http://purl.obolibrary.org/obo/PR_000001300 PR medium These assays measure a mineralization protein produced by osteoblasts, osteocalcin (OCN). http://purl.obolibrary.org/obo/PR_000001300 PR http://purl.obolibrary.org/obo/GO_0001649 GO Osteoblast numbers and surface This assay determines osteoblast formation by comparing the number of osteoblasts before and after a stressor in cell culture and histological bone samples. in_vitro bone osteoblast numbers not_specified http://purl.obolibrary.org/obo/CL_0000189 CL low Osteoblast formation can be determined by comparing the number of osteoblasts before and after a stressor in cell culture and histological bone samples. http://purl.obolibrary.org/obo/CL_0000189 CL http://purl.obolibrary.org/obo/GO_0001649 GO Osteomark Ntx urine or serum ELISA assay This assay measures N-terminal type I collagen telopeptide (NTX), a product of bone collagen degradation. in_vitro NTX levels not_specified medium Measures N-terminal type I collagen telopeptide (NTX), a product of bone collagen degradation. http://purl.obolibrary.org/obo/GO_0030574 GO Ostk-PR assay This assay measures osteocalcin (OCN), a mineralization protein produced by osteoblasts. in_vitro bovine osteocalcin levels not_specified http://purl.obolibrary.org/obo/PR_000001300 PR medium These assays measure a mineralization protein produced by osteoblasts, osteocalcin (OCN). http://purl.obolibrary.org/obo/PR_000001300 PR http://purl.obolibrary.org/obo/GO_0001649 GO Pirijinorin ICTP via RIA2 antibody assay This assay measures C-terminal type I collagen telopeptide (ICTP or CTX), a product of bone collagen degradation. in_vitro ICTP levels not_specified medium Measures C-terminal type I collagen telopeptide (ICTP or CTX), a product of bone collagen degradation. http://purl.obolibrary.org/obo/GO_0030574 GO Procollagen PICP assay This assay measures procollagen type I C-terminal peptide (PICP), a product of osteoblastic collagen production. in_vitro PICP levels not_specified medium Type I collagen (COL1A1 gene) is the most common form of collagen found in bone. During osteoblastic collagen production and processing, procollagen type I N-terminal peptide (PINP) and procollagen I C-terminal (PICP) are generated and released into the bloodstream. http://purl.obolibrary.org/obo/GO_0032964 GO Pyrilinks assay This assay measures deoxypyridinoline (dpy), a product of bone collagen degradation. in_vitro deoxypyridinoline levels not_specified http://purl.obolibrary.org/obo/CHEBI_27991 CHEBI medium Measures deoxypyridinoline (dpy), a product of bone collagen degradation. http://purl.obolibrary.org/obo/CHEBI_27991 CHEBI http://purl.obolibrary.org/obo/GO_0030574 GO Tandem-R Ostase assay This assay measures alkaline phosphatase (ALP), a mineralization protein produced by osteoblasts. in_vitro alkaline phosphatase activity not_specified http://purl.obolibrary.org/obo/GO_0004036 GO medium These assays measure a mineralization protein produced by osteoblasts, Alkaline phosphatase (ALP). http://purl.obolibrary.org/obo/PR_000004008 PR http://purl.obolibrary.org/obo/GO_0001649 GO Total Dpy assay This assay measures deoxypyridinoline (dpy), a product of bone collagen degradation. in_vitro deoxypyridinoline levels not_specified http://purl.obolibrary.org/obo/CHEBI_27991 CHEBI medium Measures deoxypyridinoline (dpy), a product of bone collagen degradation. http://purl.obolibrary.org/obo/CHEBI_27991 CHEBI http://purl.obolibrary.org/obo/GO_0030574 GO TRAP Measures tartrate-resistant acid phosphatase (TRAP), an osteoclast-specific bone-resorbing molecule, using the BoneTRAP assay. in_vitro bone TRAP activity increase not_specified BoneTRAP assay Measures tartrate-resistant acid phosphatase (TRAP), an osteoclast specific bone-resorbing molecule. http://purl.obolibrary.org/obo/CL_0001020 CL http://purl.obolibrary.org/obo/GO_0001508 GO Calcium stable isotope tracers Measurement of inorganic skeletal matrix markers such as calcium, phosphorus which, above all, reflect calcium-phosphorus homeostasis and are indicators for the status of bone mineralization. in_vivo calcium-phosphorus homeostasis and bone mineralization status not_specified http://purl.obolibrary.org/obo/GO_0055074 GO http://purl.obolibrary.org/obo/GO_0030282 GO medium Measurement of inorganic skeletal matrix markers such as calcium, phosphorus which, above all, reflect calcium-phosphorus homeostasis and are indicators for the status of bone mineralization. http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0055074 GO DXA Dual-energy x-ray absorptiometry (DEXA) is an imaging technique used to measure bone mineral density and detect changes in bone remodeling over time by comparing serial images of the same bone region. in_vivo bone not_specified bone mineral density change not_specified Dual-energy x-ray absorptiometry (DE)XA Recurrent imaging of the same bone region in a specific time interval and subsequent overlay of these images, allows for the identification of bone remodeling units and state of bone remodeling. Dynamic bone histomorphometry Quantitative evaluation of bone mineralization from fluorochrome labeled samples to measure bone remodeling and structure over time. ex_vivo trabecular bone cortical bone bone formation rate and bone resorption rate change low Dynamic histomorphometry comprised the evaluation of bone mineralization from fluorochrome labeled samples. Thus, it is a quantitative measure of bone remodeling in addition to evaluation of bone structure over time. http://purl.obolibrary.org/obo/UBERON_0001156 UBERON http://purl.obolibrary.org/obo/GO_0045110 GO Dynamic bone histomorphometry Dynamic histomorphometry comprised the evaluation of bone mineralization from fluorochrome labeled samples. Thus, it is a quantitative measure of bone remodeling in addition to evaluation of bone structure over time. in_vivo bone bone mineralization and bone remodeling not_specified http://purl.obolibrary.org/obo/GO_0046825 GO http://purl.obolibrary.org/obo/GO_0030282 GO http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Dynamic histomorphometry comprised the evaluation of bone mineralization from fluorochrome labeled samples. Thus, it is a quantitative measure of bone remodeling in addition to evaluation of bone structure over time. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0046825 GO Single-energy x-ray absorptiometry Recurrent imaging of the same bone region in a specific time interval and subsequent overlay of these images allows for the identification of bone remodeling units and state of bone remodeling. in_vivo bone bone remodeling units and state of bone remodeling not_specified http://purl.obolibrary.org/obo/GO_0046825 GO http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Recurrent imaging of the same bone region in a specific time interval and subsequent overlay of these images, allows for the identification of bone remodeling units and state of bone remodeling. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0046825 GO Spectrophotometry Quantifies calcium concentration in serum using spectrophotometric assay. in_vivo blood serum calcium concentration not_specified http://purl.obolibrary.org/obo/CHEBI_18345 CHEBI not_specified Spectrophotometry Measurements of bone minerals in bodily fluids: http://purl.obolibrary.org/obo/CHEBI_18345 CHEBI http://purl.obolibrary.org/obo/GO_0030282 GO Spectrophotometry Measurement of inorganic skeletal matrix markers such as calcium, phosphorus which, above all, reflect calcium-phosphorus homeostasis and are indicators for the status of bone mineralization. in_vivo calcium-phosphorus homeostasis and bone mineralization status not_specified http://purl.obolibrary.org/obo/GO_0055074 GO http://purl.obolibrary.org/obo/GO_0030282 GO medium Measurement of inorganic skeletal matrix markers such as calcium, phosphorus which, above all, reflect calcium-phosphorus homeostasis and are indicators for the status of bone mineralization. http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0055074 GO Trabeculae measurements Rods and plates forming the trabecular can indicate bone remodeling by altering the bone turnover states (bone formation and resorption) and microarchitecture. in_vivo bone bone turnover states and microarchitecture not_specified http://purl.obolibrary.org/obo/GO_0046825 GO http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Rods and plates forming the trabecular can indicate bone remodeling by altering the bone turnover states (bone formation and resorption) and microarchitecture. http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0046825 GO Trabeculae measurements Rods and plates forming the trabecular can indicate bone remodeling by altering the bone turnover states (bone formation and resorption) and microarchitecture. not_specified bone trabecular bone volume density change low Rods and plates forming the trabecular can indicate bone remodeling by altering the bone turnover states (bone formation and resorption) and microarchitecture. Trabeculae measurements Quantifies structural parameters of rods and plates in trabecular bone such as volume density, thickness, and orientation. ex_vivo trabecular bone trabecular microarchitecture (rods and plates) change http://purl.obolibrary.org/obo/GO_0001545 GO http://purl.obolibrary.org/obo/GO_0051016 GO low Rods and plates forming the trabecular can indicate bone remodeling by altering the bone turnover states (bone formation and resorption) and microarchitecture http://purl.obolibrary.org/obo/GO_0051016 GO Trabecular microarchitecture analysis Quantitative assessment of rod and plate volume density, thickness, orientation, and curvature to indicate bone turnover states and microarchitecture changes. ex_vivo trabecular bone rod and plate volume density, thickness, orientation, and curvature change http://purl.obolibrary.org/obo/UBERON_0002410 UBERON low Trabeculae measurements: Rod volume density (Ro.BV/TV) Plate volume density (Pl.BV/TV) Rods and plates forming the trabecular can indicate bone remodeling by altering the bone turnover states (bone formation and resorption) and microarchitecture http://purl.obolibrary.org/obo/UBERON_0002410 UBERON http://purl.obolibrary.org/obo/GO_0001503 GO X-ray and imaging options Uses techniques such as DXA, QCT, and SPA to perform recurrent imaging of the same bone region to identify bone remodeling units and state. in_vivo bone bone remodeling units and state of bone remodeling change http://purl.obolibrary.org/obo/GO_0051016 GO not_specified Recurrent imaging of the same bone region in a specific time interval and subsequent overlay of these images, allows for the identification of bone remodeling units and state of bone remodeling. http://purl.obolibrary.org/obo/UBERON_0000555 UBERON http://purl.obolibrary.org/obo/GO_0051016 GO Alizarin red staining Stains calcium cations in bone using alizarin red. in_vivo bone calcium cation deposition decrease low Alizarin red reacts with calcium cation to form a chelate. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0030282 GO Bone connectivity modeling Mathematical models (Euler’s characteristic, Betti numbers) used to reconstruct and quantify the 3D connectivity of cancellous bone. in_silico cancellous bone connectivity density decrease medium These mathematical models allow for the 3D reconstruction of connectivity in cancellous bone. Bone loss, as seen as a decrease in strength and bone stiffness, can result from a decrease in connective bone tissue. Bone mechanical resistance testing Mechanical tests such as three-point bending or stress-strain analysis to evaluate energy absorption and bone integrity. ex_vivo bone mechanical resistance (e.g., Young’s modulus, energy-absorbing capacity) decrease low Measurements of bone mechanical resistance indicates changes in bone integrity possibly due to bone loss, as weaker bones are unable to withstand to as much mechanical force as healthy bones. Three-point bending test. Is a structural mechanical test where the entire bone is hold in a fixture attached to a material testing machine and the mid-diaphysis is loaded until broken. Calcein green staining Stains calcium in bone to label new bone deposition using calcein green. in_vivo bone bone formation decrease http://purl.obolibrary.org/obo/GO_0060348 GO low Less bone deposition and/or reduced mineral dense bones indicate bone loss. xylenol orange, calcein green, and tetracycline are calcium binding fluorescent dyes that are used to label new bone deposition. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0060348 GO Calcium staining (Xylenol orange, Calcein green, Tetracycline, Von Kossa, Alizarin red) Staining methods using fluorescent dyes or chemical reagents to visualize bone formation markers or calcium deposits. in_vitro bone bone deposition and calcium content decrease http://purl.obolibrary.org/obo/CHEBI_26833 CHEBI not_specified Less bone deposition and/or reduced mineral dense bones indicate bone loss. xylenol orange, calcein green, and tetracycline are calcium binding fluorescent dyes that are used to label new bone deposition. Von Kossa method is based on the binding of silver ions to anions (phosphates, sulphates, or carbonates) of calcium salts alizarin red reacts with calcium cation to form a chelate. http://purl.obolibrary.org/obo/GO_0001500 GO Connectivity density Mathematical model for 3D reconstruction of connectivity in cancellous bone. in_silico bone bone connectivity decrease high These mathematical models allow for the 3D reconstruction of connectivity in cancellous bone. Bone loss, as seen as a decrease in strength and bone stiffness, can result from a decrease in connective bone tissue. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON DEXA Bone mineral density (BMD) is a direct measurement of bone matrix composition. Less mineral dense bones indicate bone loss. in_vivo bone bone mineral density decrease medium Bone mineral density (BMD) is a direct measurement of bone matrix composition. Less mineral dense bones indicate bone loss. http://purl.obolibrary.org/obo/UBERON_0000901 UBERON http://purl.obolibrary.org/obo/GO_0008553 GO Energy-absorbing bone capacity Measures the energy-absorbing capacity of bone, indicating bone integrity. in_vivo bone energy-absorbing bone capacity decrease low Measurements of bone mechanical resistance indicates changes in bone integrity possibly due to bone loss, as weaker bones are unable to withstand to as much mechanical force as healthy bones. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON Euler’s characteristic Mathematical model for 3D reconstruction of connectivity in cancellous bone. in_silico bone bone connectivity decrease high These mathematical models allow for the 3D reconstruction of connectivity in cancellous bone. Bone loss, as seen as a decrease in strength and bone stiffness, can result from a decrease in connective bone tissue. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON Histomorphometry Static bone histomorphometry with structural measurements is the quantitative measure of bone structure at a fixed time point. in_vivo bone bone structure parameters change low Static bone histomorphometry with structural measurements is the quantitative measure of bone structure at a fixed time point. http://purl.obolibrary.org/obo/UBERON_0000901 UBERON http://purl.obolibrary.org/obo/GO_0008553 GO Magnetic resonance imaging Measures bone mineral density (BMD) using magnetic resonance imaging. in_vivo bone bone mineral density decrease medium Bone mineral density (BMD) is a direct measurement of bone matrix composition. Less mineral dense bones indicate bone loss. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0046849 GO Quantitative computed tomography Measures bone mineral density (BMD) using quantitative computed tomography. in_vivo bone bone mineral density decrease medium Bone mineral density (BMD) is a direct measurement of bone matrix composition. Less mineral dense bones indicate bone loss. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0046849 GO Single energy x-ray absorptiometry Measures bone mineral density (BMD) using single energy x-ray absorptiometry. in_vivo bone bone mineral density decrease medium Bone mineral density (BMD) is a direct measurement of bone matrix composition. Less mineral dense bones indicate bone loss. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0046849 GO Static bone histomorphometry Quantitative measurement of bone structure (2D and 3D) via biopsy of the iliac crest to assess bone volume and thickness. ex_vivo iliac crest Bone volume fraction (BV/TV) decrease low Static bone histomorphometry of an intact iliac crest bone biopsy Bone volume fraction (BV/TV) Static bone histomorphometry with structural measurements is the quantitative measure of bone structure at a fixed time point. http://purl.obolibrary.org/obo/UBERON_0000922 UBERON Stress-strain curve Measures the strain exhibited on a bone according to increasing applied stress until fracture. in_vivo bone stress-strain curve change low Stress-strain curve. Measures the strain exhibited on a bone according to increasing applied stress until fracture. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON Tetracycline staining Stains calcium in bone to label new bone deposition using tetracycline. in_vivo bone bone formation decrease http://purl.obolibrary.org/obo/GO_0060348 GO low Less bone deposition and/or reduced mineral dense bones indicate bone loss. xylenol orange, calcein green, and tetracycline are calcium binding fluorescent dyes that are used to label new bone deposition. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0060348 GO Three-point bending test Measures bone mechanical properties by applying load to the mid-diaphysis until fracture. in_vivo bone bone mechanical properties decrease low Three-point bending test. Is a structural mechanical test where the entire bone is hold in a fixture attached to a material testing machine and the mid-diaphysis is loaded until broken. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON Ultrasound (quantitative bone ultrasonography) Measures bone mineral density (BMD) using quantitative bone ultrasonography. in_vivo bone bone mineral density decrease medium Bone mineral density (BMD) is a direct measurement of bone matrix composition. Less mineral dense bones indicate bone loss. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0046849 GO Von Kossa staining Von Kossa method based on binding of silver ions to anions of calcium salts and reduction to form dark staining; used to detect calcium salts; reduced staining indicates bone loss. not_specified bone calcium salt staining intensity decrease not_specified Von Kossa (calcium salt stain, non-specific) Von Kossa method is based on the binding of silver ions to anions (phosphates, sulphates, or carbonates) of calcium salts and the reduction of silver salts to form dark brown or black metallic silver staining. Xylenol orange staining Stains calcium in bone to label new bone deposition using xylenol orange. in_vivo bone bone formation decrease http://purl.obolibrary.org/obo/GO_0060348 GO low Less bone deposition and/or reduced mineral dense bones indicate bone loss. xylenol orange, calcein green, and tetracycline are calcium binding fluorescent dyes that are used to label new bone deposition. http://purl.obolibrary.org/obo/UBERON_0002474 UBERON http://purl.obolibrary.org/obo/GO_0060348 GO Flow Cytometry Technique used to detect expression and binding properties of the cell surface protein CDCP1 in ovarian cancer cells in vitro. in_vitro ovarian cancer cell ovary Homo sapiens CDCP1 expression and binding properties increase medium Expression and binding properties of the cell surface protein was detected in ovarian cancer cell (in vitro) using flow cytometry and western blot technique flow cytometry Flow cytometry technique used to detect expression and binding properties of the cell surface protein (CDCP1) in ovarian cancer cells in vitro. in_vitro ovarian cancer cells Homo sapiens cell surface protein expression change http://purl.obolibrary.org/obo/OBI_0000278 OBI medium Expression and binding properties of the cell surface protein was detected in ovarian cancer cell (in vitro) using flow cytometry and western blot technique http://purl.obolibrary.org/obo/GO_0010457 GO gamma-ray detection probe Gamma-ray detection probe used for overcoming the conventional radio-immunoscintigraphy problems for the detection of ovarian cancer in female patients. in_vivo ovary Homo sapiens ovarian cancer detection not_specified low Gitsch et al., had developed gamma-ray detection probe for overcoming the conventional radio-immunoscintigraphy problems for the detection of ovarian cancer in female patients MRI Magnetic resonance imaging (MRI) technique used to monitor tumor microvascular permeability in a rat model of human ovarian cancer. in_vivo ovary Rattus norvegicus tumor microvascular permeability change http://purl.obolibrary.org/obo/OBI_0000275 OBI low Gossmann et al., had shown the effects of angiogenesis inhibition on tumor microvascular permeability was monitored with the help of magnetic resonance imaging (MRI) technique in a rat model of human ovarian cancer http://purl.obolibrary.org/obo/GO_0001525 GO PET/CT Positron emission tomography/computed tomography (PET/CT) used for the detection of ovarian tumor in human patients, with reported sensitivity and accuracy of 73% and 91%, respectively. in_vivo ovary Homo sapiens ovarian tumor detection not_specified low Kim et al., had used the detection of magnetic resonance imaging (MRI) and positron emission tomography/computed tomography (PET/CT) for the detection of ovarian tumor in human patient. Sensitivity and accuracy of the PET/CT technique for detecting the ovarian tumor was reported 73% and 91%. Western Blot Technique used to detect expression and binding properties of the cell surface protein CDCP1 in ovarian cancer cells in vitro. in_vitro ovarian cancer cell ovary Homo sapiens CDCP1 expression increase low Expression and binding properties of the cell surface protein was detected in ovarian cancer cell (in vitro) using flow cytometry and western blot technique western blot Western blot technique used to detect expression and binding properties of the cell surface protein (CDCP1) in ovarian cancer cells in vitro. in_vitro ovarian cancer cells Homo sapiens cell surface protein expression change low Expression and binding properties of the cell surface protein was detected in ovarian cancer cell (in vitro) using flow cytometry and western blot technique http://purl.obolibrary.org/obo/GO_0010457 GO contractile factor detection assay Detection of contractile factors (e.g., endothelin, thromboxane A2). not_specified levels of contractile factors not_specified http://purl.obolibrary.org/obo/CHEBI_39175 CHEBI http://purl.obolibrary.org/obo/CHEBI_18213 CHEBI not_specified Detection of contractile factors, including endothelin (ET), thromboxane A2 (TXA2) ECIS Evaluation of the functional integrity of the microvascular barrier using Electric Cell-Substrate Impedance Sensing (ECIS). in_vitro barrier integrity not_specified not_specified Evaluation of the functional integrity of the barrier: Electric Cell-Substrate Impedance Sensing (ECIS) enzymatic activity assay Assays designed to measure the specific enzymatic activity of coagulation and/or fibrinolytic factors. in_vitro enzymatic activity change low Differential expression of coagulation and/or fibrinolytic factors ... by ... various assays for their specific enzymatic activity. http://purl.obolibrary.org/obo/GO_0004273 GO http://purl.obolibrary.org/obo/GO_0016861 GO enzymatic activity assays Measurement of the enzymatic activity of coagulation and/or fibrinolytic factors (e.g., PAI-1, tPA, uPA). not_specified enzymatic activity of coagulation/fibrinolytic factors not_specified http://purl.obolibrary.org/obo/GO_0003824 GO not_specified Differential expression of coagulation and/or fibrinolytic factors (e.g. plasminogen activator inhibitor 1(PAI-1), plasminogen activator (tPA), urokinase (uPA)) by various RNA measurement assays, various immune based assays using specific antibodies, or various assays for their specific enzymatic activity exosomal marker analysis Analysis and quantification of exosomal markers. not_specified levels of exosomal markers not_specified http://purl.obolibrary.org/obo/GO_0070062 GO not_specified Analysis and quantification of exosomal markers http://purl.obolibrary.org/obo/GO_0070062 GO FACS-SCAN assay Differential expression of surface adhesion molecules (e.g., ICAM-1, VCAM-1) measured by FACS-SCAN assay. in_vitro expression of surface adhesion molecules not_specified http://purl.obolibrary.org/obo/PR_000000981 PR http://purl.obolibrary.org/obo/PR_000001030 PR not_specified Differential expression of surface adhesion molecules (eg. ICAM-1, VCAM-1) by FACS-SCAN assay FITC-dextran permeability assay Evaluation of the functional integrity of the microvascular barrier using FITC-dextran permeability assays. in_vitro barrier permeability not_specified not_specified Evaluation of the functional integrity of the barrier: Electric Cell-Substrate Impedance Sensing (ECIS), trans-endothelial electrical resistance (TEER), FITC-dextran permeability assays histochemical staining Assesses the structural integrity of microvasculature by basic histochemical staining of tissue sections. in_vivo microvasculature not_specified structural integrity change low Macroscopic and microscopic observations of the structural integrity of the structure of the MV (basic histochemical staining or immunostaining for specific cellular markers) histochemical staining Macroscopic and microscopic observations of the structural integrity of the microvasculature using basic histochemical staining. not_specified structural integrity of microvasculature not_specified http://purl.obolibrary.org/obo/UBERON_0001986 UBERON not_specified Macroscopic and microscopic observations of the structural integrity of the structure of the MV (basic histochemical staining or immunostaining for specific cellular markers) http://purl.obolibrary.org/obo/UBERON_0001986 UBERON immune based assays Assays using specific antibodies to detect cytokines, matrix metalloproteinases, or coagulation factors. in_vitro protein concentration change medium Differential expression of pro-inflammatory and or anti-inflammatory cytokines by ... various immune based assays using specific antibodies Differential expression of matrix metalloproteinases ... by ... various immune based assays using specific antibodies or fluorescent tags Differential expression of coagulation and/or fibrinolytic factors ... by ... various immune based assays using specific antibodies http://purl.obolibrary.org/obo/GO_0006955 GO immune-based assays Differential expression of coagulation and/or fibrinolytic factors (e.g., PAI-1, tPA, uPA) measured by various immune-based assays using specific antibodies. not_specified expression of coagulation/fibrinolytic factors not_specified not_specified Differential expression of coagulation and/or fibrinolytic factors (e.g. plasminogen activator inhibitor 1(PAI-1), plasminogen activator (tPA), urokinase (uPA)) by various RNA measurement assays, various immune based assays using specific antibodies immune-based assays Differential expression of pro-inflammatory and/or anti-inflammatory cytokines measured by various immune-based assays using specific antibodies. not_specified expression of cytokines not_specified http://purl.obolibrary.org/obo/GO_0005125 GO not_specified Differential expression of pro-inflammatory and or anti-inflammatory cytokines by various RNA measurement assays, various immune based assays using specific antibodies http://purl.obolibrary.org/obo/GO_0005125 GO immune-based assays Differential expression of matrix metalloproteinases (e.g., MMP2, MMP3, MMP9, MMP12) measured by various immune-based assays using specific antibodies or fluorescent tags. not_specified expression of matrix metalloproteinases not_specified http://purl.obolibrary.org/obo/GO_0004222 GO not_specified Differential expression of matrix metalloproteinases (e.g. MMP2, MMP3, MMP9, MMP12) by various RNA measurement assays or various immune based assays using specific antibodies or fluorescent tags http://purl.obolibrary.org/obo/GO_0004222 GO immunostaining Measures expression of specific cellular markers to assess structural integrity of the microvasculature via histochemical staining or immunostaining. not_specified cellular marker expression not_specified http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI not_specified basic histochemical staining or immunostaining for specific cellular markers http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0048514 GO prostaglandin detection assay Detection of prostaglandins (PG) as a marker of tissue/cell stress. not_specified levels of prostaglandins not_specified http://purl.obolibrary.org/obo/CHEBI_15843 CHEBI not_specified Detection of tissue/cell stress markers: (e.g. reactive oxygen species (ROS); prostaglandins (PG) http://purl.obolibrary.org/obo/CHEBI_15843 CHEBI proteomic approaches Differential expression of coagulation and/or fibrinolytic factors (e.g., PAI-1, tPA, uPA) measured by proteomic approaches. not_specified expression of coagulation/fibrinolytic factors not_specified not_specified including proteomic approaches [10.1172/JCI148635] proteomic approaches Differential expression of pro-inflammatory and/or anti-inflammatory cytokines measured by proteomic approaches. not_specified expression of cytokines not_specified http://purl.obolibrary.org/obo/GO_0005125 GO not_specified including proteomic approaches [10.1172/JCI148635] http://purl.obolibrary.org/obo/GO_0005125 GO proteomic approaches Large-scale protein analysis to identify differential expression of cytokines or coagulation factors. in_vitro proteome profile change medium including proteomic approaches [10.1172/JCI148635] RNA measurement assays Differential expression of coagulation and/or fibrinolytic factors (e.g., PAI-1, tPA, uPA) measured by various RNA measurement assays. not_specified expression of coagulation/fibrinolytic factors not_specified not_specified Differential expression of coagulation and/or fibrinolytic factors (e.g. plasminogen activator inhibitor 1(PAI-1), plasminogen activator (tPA), urokinase (uPA)) by various RNA measurement assays RNA measurement assays Differential expression of pro-inflammatory and/or anti-inflammatory cytokines measured by various RNA measurement assays. not_specified expression of cytokines not_specified http://purl.obolibrary.org/obo/GO_0005125 GO not_specified Differential expression of pro-inflammatory and or anti-inflammatory cytokines by various RNA measurement assays http://purl.obolibrary.org/obo/GO_0005125 GO RNA measurement assays Differential expression of matrix metalloproteinases (e.g., MMP2, MMP3, MMP9, MMP12) measured by various RNA measurement assays. not_specified expression of matrix metalloproteinases not_specified http://purl.obolibrary.org/obo/GO_0004222 GO not_specified Differential expression of matrix metalloproteinases (e.g. MMP2, MMP3, MMP9, MMP12) by various RNA measurement assays http://purl.obolibrary.org/obo/GO_0004222 GO RNA measurement assays Various assays (such as qPCR) to measure the differential expression of RNA for cytokines, matrix metalloproteinases, or coagulation factors. in_vitro RNA expression levels change high Differential expression of pro-inflammatory and or anti-inflammatory cytokines by various RNA measurement assays Differential expression of matrix metalloproteinases (e.g. MMP2, MMP3, MMP9, MMP12) by various RNA measurement assays Differential expression of coagulation and/or fibrinolytic factors ... by various RNA measurement assays http://purl.obolibrary.org/obo/GO_0010467 GO ROS detection assay Detection of reactive oxygen species (ROS) as a marker of tissue/cell stress. not_specified levels of reactive oxygen species not_specified http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO not_specified Detection of tissue/cell stress markers: (e.g. reactive oxygen species (ROS) http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI http://purl.obolibrary.org/obo/GO_0006979 GO stress marker detection assay Measures levels of cellular stress markers such as ROS, prostaglandins, vasoactive peptides, and receptor activity. not_specified stress marker concentration/activity not_specified http://purl.obolibrary.org/obo/CHEBI_26523 CHEBI not_specified Detection of tissue/cell stress markers: (e.g. reactive oxygen species (ROS); prostaglandins (PG); vasoactive peptides, such as angiotensin II (Ang II), angiotensin (1-7) (Ang 1-7) or activity of their receptors http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0033554 GO TEER Evaluation of the functional integrity of the microvascular barrier using trans-endothelial electrical resistance (TEER). in_vitro barrier integrity not_specified not_specified Evaluation of the functional integrity of the barrier: Electric Cell-Substrate Impedance Sensing (ECIS), trans-endothelial electrical resistance (TEER) TEER Trans-endothelial electrical resistance (TEER) is used to evaluate the functional integrity of the barrier. in_vitro trans-endothelial electrical resistance change medium Evaluation of the functional integrity of the barrier: Electric Cell-Substrate Impedance Sensing (ECIS), trans-endothelial electrical resistance (TEER), FITC-dextran permeability assays http://purl.obolibrary.org/obo/CL_0002025 CL vasoactive peptide detection assay Detection of vasoactive peptides (e.g., angiotensin II, angiotensin 1-7) or activity of their receptors as a marker of tissue/cell stress. not_specified levels of vasoactive peptides or receptor activity not_specified http://purl.obolibrary.org/obo/CHEBI_18355 CHEBI http://purl.obolibrary.org/obo/CHEBI_64689 CHEBI not_specified Detection of tissue/cell stress markers: (e.g. reactive oxygen species (ROS); prostaglandins (PG); vasoactive peptides, such as angiotensin II (Ang II), angiotensin (1-7) (Ang 1-7) or activity of their receptors western blot Differential expression of surface adhesion molecules is measured by Western blotting. in_vitro protein expression change low Differential expression of surface adhesion molecules (eg. ICAM-1, VCAM-1) by FACS-SCAN assay [e.g. 10.1186/s13054-021-03631-4] or Western blotting http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0006470 GO Western blotting Differential expression of surface adhesion molecules (e.g., ICAM-1, VCAM-1) measured by Western blotting. in_vitro expression of surface adhesion molecules not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI http://purl.obolibrary.org/obo/PR_000000981 PR http://purl.obolibrary.org/obo/PR_000001030 PR not_specified Differential expression of surface adhesion molecules (eg. ICAM-1, VCAM-1) by FACS-SCAN assay [e.g. 10.1186/s13054-021-03631-4] or Western blotting [e.g. 110.3389/fcvm.2021.687783] cytokine arrays Similar to the ELISA, except using a membrane-based rather than plate-based approach. Can be used to measure multiple cytokine targets concurrently. in_vitro cytokine levels increase high Can be used to measure multiple cytokine targets concurrently. http://purl.obolibrary.org/obo/CHEBI_51533 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO ELISA Plate-based assay technique using antibodies to detect presence of a protein in a liquid sample, particularly inflammatory cytokines in low concentrations. in_vitro presence of inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0005575 GO medium Plate based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of an inflammatory cytokine of interest especially when in low concentrations. http://purl.obolibrary.org/obo/GO_0006954 GO ELISA Plate based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of an inflammatory cytokine of interest especially when in low concentrations. in_vitro protein presence increase medium Plate based assay technique using antibodies to detect presence of a protein in a liquid sample. http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006954 GO Flow-cytometry Detects intracellular cytokines with stimulation. in_vitro intracellular cytokines increase http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0005622 GO high Detects the intracellular cytokines with stimulation. http://purl.obolibrary.org/obo/GO_0006954 GO Imaging tests Qualitative technique using cytokine specific antibodies and fluorophores to visualize expression patterns, subcellular location, and protein-protein interactions. in_vitro expression patterns and subcellular location not_specified http://purl.obolibrary.org/obo/GO_0044334 GO low A qualitative technique using a cytokine specific antibodies and fluorophores can be used to visualize expression patterns, subcellular location of the target and protein-protein interactions. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0006954 GO Imaging tests A qualitative technique using cytokine-specific antibodies and fluorophores to visualize expression patterns, subcellular location of the target, and protein-protein interactions. in_vitro expression patterns and subcellular location of inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0008104 GO low A qualitative technique using a cytokine specific antibodies and fluorophores can be used to visualize expression patterns, subcellular location of the target and protein-protein interactions. http://purl.obolibrary.org/obo/GO_0006954 GO Immunoblotting (western blotting) Uses antibodies specific to proteins of interest, can be used to detect presence of pro-inflammatory mediators in samples of cell or tissue lysate. in_vitro presence of pro-inflammatory mediators increase http://purl.obolibrary.org/obo/GO_0005575 GO low Uses antibodies specific to proteins of interest, can used to detect presence of pro-inflammatory mediators in samples of cell or tissue lysate http://purl.obolibrary.org/obo/GO_0006954 GO Immunohistochemistry (IHC) Immobilized tissue or cell cultures are stained using antibodies for specificity of ligands of interest, particularly to visualize localization of inflammatory cytokines. in_vitro localization of inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0051179 GO low Immobilized tissue or cell cultures are stained using antibodies for specificity of ligands of interest. Versions of the assays can be used to visualize localization of inflammatory cytokines. http://purl.obolibrary.org/obo/GO_0006954 GO Inflammatory cytokine arrays Membrane-based assay similar to ELISA, used to measure multiple cytokine targets concurrently. in_vitro multiple cytokine targets increase http://purl.obolibrary.org/obo/GO_0005125 GO medium Similar to the ELISA, except using a membrane-based rather than plate-based approach. Can be used to measure multiple cytokine targets concurrently. http://purl.obolibrary.org/obo/GO_0006954 GO Radioimmunoassay Plate-based assay technique using antibodies to detect presence of a protein in a liquid sample, particularly inflammatory cytokines in low concentrations. in_vitro presence of inflammatory cytokines increase http://purl.obolibrary.org/obo/GO_0005575 GO medium Plate based assay technique using antibodies to detect presence of a protein in a liquid sample. Can be used to identify presence of an inflammatory cytokine of interest especially when in low concentrations. http://purl.obolibrary.org/obo/GO_0006954 GO RT-qPCR Measures mRNA expression of cytokines, chemokines and inflammatory markers. in_vitro mRNA expression increase medium Measures mRNA expression of cytokines, chemokines and inflammatory markers http://purl.obolibrary.org/obo/CHEBI_50889 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO RT-qPCR Measures mRNA expression of cytokines, chemokines and inflammatory markers. in_vitro mRNA expression of cytokines, chemokines and inflammatory markers increase http://purl.obolibrary.org/obo/GO_0010605 GO http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0008009 GO medium Measures mRNA expression of cytokines, chemokines and inflammatory markers http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0006954 GO western blot Uses antibodies specific to proteins of interest, can used to detect presence of pro-inflammatory mediators in samples of cell or tissue lysate. in_vitro tissue protein presence increase low Uses antibodies specific to proteins of interest, can used to detect presence of pro-inflammatory mediators in samples of cell or tissue lysate http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006954 GO Whole blood stimulation assay Detects inflammatory cytokines in blood. ex_vivo blood inflammatory cytokines in blood increase http://purl.obolibrary.org/obo/UBERON_0000178 UBERON medium Detects inflammatory cytokines in blood http://purl.obolibrary.org/obo/GO_0006954 GO BrdU labeling Staining method used to identify proliferating cells and measures neurogenesis. not_specified cells proliferating cells not_specified not_specified Staining method used to identify proliferating cells and measures neurogenesis. http://purl.obolibrary.org/obo/CL_0000321 CL http://purl.obolibrary.org/obo/GO_0022008 GO Bromodeoxyuridine (BrdU) labeling Bromodeoxyuridine (BrdU) labeling is a staining method used to identify proliferating cells and measure neurogenesis. in_vivo brain neurogenesis increase http://purl.obolibrary.org/obo/GO_0022008 GO medium Staining method used to identify proliferating cells and measures neurogenesis. http://purl.obolibrary.org/obo/CL_0000068 CL http://purl.obolibrary.org/obo/GO_0022008 GO ELISA The enzyme-linked immunosorbent assay (ELISA) detects and quantifies levels of macromolecules such as peptides, proteins, antibodies, and hormones. in_vitro protein levels change high The enzyme-linked immunosorbent assay (ELISA) is a technique that detects and quantifies levels of macromolecules such as peptides, proteins, antibodies, and hormones. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0019538 GO ELISA The enzyme-linked immunosorbent assay (ELISA) is a technique that detects and quantifies levels of macromolecules such as peptides, proteins, antibodies, and hormones. It can be used to detect specific molecules in neurons that represent loss in integrity such as PSD-95, synapsin 1 or drebrin. not_specified neurons brain protein levels (PSD-95, synapsin 1, drebrin) decrease medium The enzyme-linked immunosorbent assay (ELISA) is a technique that detects and quantifies levels of macromolecules such as peptides, proteins, antibodies, and hormones. It can be used to detect specific molecules in neurons that represent loss in integrity such as PSD-95, synapsin 1 or drebrin. http://purl.obolibrary.org/obo/GO_0051607 GO Fluoro-Jade stain Fluoro-Jade stain detects and labels degenerating neurons. ex_vivo brain degenerating neurons increase http://purl.obolibrary.org/obo/GO_0097150 GO medium Detects and labels degenerating neurons. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0097150 GO Golgi-Cox Method The Golgi-Cox Method visualizes neuronal morphology in vivo. in_vivo brain neuronal morphology change http://purl.obolibrary.org/obo/GO_0007420 GO low Visualizes neuronal morphology in vivo. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0048666 GO Immunoassay/microscopy Various methods that use the specificity of antigen-antibody binding for detection and quantification of target molecules such as PSD-95, synpasin 1, Ki-67 and drebrin. not_specified neurons brain protein levels (PSD-95, synpasin 1, Ki-67, drebrin) decrease low Various methods that use the specificity of antigen-antibody binding for detection and quantification of target molecules such as PSD-95, synpasin 1, Ki-67 and drebrin. http://purl.obolibrary.org/obo/GO_0051607 GO Immunoassay/microscopy Various methods that use the specificity of antigen-antibody binding for detection and quantification of target molecules. in_vitro target molecule levels change http://purl.obolibrary.org/obo/OBI_0000278 OBI medium Various methods that use the specificity of antigen-antibody binding for detection and quantification of target molecules such as PSD-95, synpasin 1, Ki-67 and drebrin. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0019538 GO MRI Scan Magnetic resonance imaging (MRI) is an imaging technique used to visualize organs and tissues in the body, including demyelination. in_vivo brain demyelination not_specified http://purl.obolibrary.org/obo/OBI_0000214 OBI http://purl.obolibrary.org/obo/GO_0022005 GO low Magnetic resonance imaging (MRI) is an imaging technique used to visualize organs and tissues in the body. MRI can be used to view demyelination. http://purl.obolibrary.org/obo/GO_0043209 GO http://purl.obolibrary.org/obo/GO_0022005 GO MTT Assay The MTT assay is a colorimetric assay used to assess cell metabolic activity based on the reduction of MTT. in_vitro cell metabolic activity change http://purl.obolibrary.org/obo/GO_0008565 GO http://purl.obolibrary.org/obo/OBI_0001851 OBI high 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) Assay – colorimetric assay used to assess cell metabolic activity based on the reduction of (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0044237 GO MTT Assay MTT assay measures cell metabolic activity to assess neurodegeneration or neurogenesis levels. in_vitro brain not_specified cell viability decrease http://purl.obolibrary.org/obo/OBI_0001873 OBI OECD TG 442D high Cell viability and proliferation assays can be used to measure increased levels of neurodegeneration or decreased levels of neurogenesis. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/OBI_0001873 OBI SYNPLA Synaptic proximity ligation assay (SYNPLA) is a technique that detects learning-induced synaptic plasticity. in_vitro brain synaptic plasticity increase http://purl.obolibrary.org/obo/GO_0048167 GO medium Synaptic proximity ligation assay (SYNPLA) is a technique that detects learning-induced synaptic plasticity. http://purl.obolibrary.org/obo/GO_0045202 GO http://purl.obolibrary.org/obo/GO_0048167 GO TUNEL Assay TUNEL assay detects apoptosis by labeling DNA strand breaks. in_vitro brain not_specified apoptosis increase http://purl.obolibrary.org/obo/GO_0012501 GO OECD TG 456 low Apoptosis is detected with the TUNEL method to assay the endonuclease cleavage products by enzymatically end-labeling the DNA strand breaks. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0012501 GO TUNEL assay The TUNEL assay detects apoptosis by assaying endonuclease cleavage products through enzymatically end-labeling DNA strand breaks. ex_vivo DNA strand breaks increase http://purl.obolibrary.org/obo/OBI_0000213 OBI http://purl.obolibrary.org/obo/GO_0006915 GO medium Apoptosis is detected with the TUNEL method to assay the endonuclease cleavage products by enzymatically end-labeling the DNA strand breaks. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO Western Blot Western Blot is a technique for protein identification from a complex mixture after size separation, transfer to solid support, and marking target protein. in_vitro protein levels change http://purl.obolibrary.org/obo/OBI_0000221 OBI medium Protein identification from a complex mixture after size separation, transfer to solid support and marking target protein. http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0019538 GO Western Blot Protein identification from a complex mixture after size separation, transfer to solid support and marking target protein. Specific markers include PSD-95, synpasin 1, Ki-67 and drebrin. not_specified neurons brain protein levels (PSD-95, synpasin 1, Ki-67, drebrin) decrease low Protein identification from a complex mixture after size separation, transfer to solid support and marking target protein. Specific markers include PSD-95, synpasin 1, Ki-67 and drebrin. http://purl.obolibrary.org/obo/GO_0051607 GO Whole-cell electrophysiology Whole-cell electrophysiology measures intracellular electrical properties by visualizing ionic currents. in_vitro brain ionic currents change http://purl.obolibrary.org/obo/OBI_0001270 OBI http://purl.obolibrary.org/obo/GO_0034765 GO low Measures intracellular electrical properties by visualizing ionic currents. http://purl.obolibrary.org/obo/CL_0000540 CL http://purl.obolibrary.org/obo/GO_0034765 GO Alcian blue staining with Clca3 Combines Alcian blue staining with goblet cell marker Clca3 to measure goblet cell area relative to bronchial basement membrane. in_vivo bronchial epithelium goblet cell area increase http://purl.obolibrary.org/obo/CL_0000183 CL medium AB staining can be combined with goblet cell marker, Clca3, expressed as the goblet cell area / bronchial basement membrane (Leverkoehne et al, 2006; Song et al, 2016). http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0030154 GO BrDU incorporation Identifies proliferating goblet cells in tissue specimens using Bromo-deoxyuridine incorporation. in_vivo epithelium number of proliferating goblet cells increase http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0008283 GO medium Bromo-deoxyuridine (BrDU) incorporation can be used to identify the proliferating goblet cells in tissue specimens (GRANT & Specian, 1998; Hino et al., 2012). http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0008283 GO hematoxylin and eosin and Alcian blue-PAS staining Stains the entire epithelial area with hematoxylin and eosin and goblet cells with Alcian blue-PAS to measure the proportion of AB-PAS-stained surface. in_vivo epithelium proportion of AB-PAS-stained surface increase http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/UBERON_0000483 UBERON medium Alternatively, many researchers use hematoxylin and eosin to stain the entire epithelial area (total number of nuclei) and Alcian blue (AB)-periodic acid-Schiff (PAS) to stain the intracellular mucous glycoconjugates, marking goblet cells. The change in goblet cell numbers is defined by the change in the proportion of AB-PAS-stained surface of the entire epithelial cell area over a length of 2 mm of the basal lamina (Takeyama et al, 2008). http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0030154 GO Ki-67 immunofluorescent staining Ki-67 immunofluorescent staining to measure increase in goblet cells via proliferation in pure goblet cell cultures. in_vitro goblet cells conjunctiva increase in goblet cells via proliferation increase http://purl.obolibrary.org/obo/GO_0008283 GO medium In a culture that consist solely of goblet cells (e.g., from conjunctiva), increase in goblet cells via proliferation was measured by Ki-67 immunofluorescent staining http://purl.obolibrary.org/obo/CL_0000221 CL http://purl.obolibrary.org/obo/GO_0008283 GO Ki-67 immunofluorescent staining Measures increase in goblet cells via proliferation in a culture consisting solely of goblet cells using Ki-67 immunofluorescent staining. in_vitro goblet cells number of Ki-67-positive cells increase http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0008283 GO medium In a culture that consist solely of goblet cells (e.g., from conjunctiva), increase in goblet cells via proliferation was measured by Ki-67 immunofluorescent staining (Gu et al., 2008). http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0008283 GO light or electron microscopy Identifies mucin-producing secretory granules of goblet cells using light or electron microscopy. in_vivo epithelium number of goblet cells increase http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/UBERON_0000483 UBERON low The mucin-producing secretory granules of goblet cells can be identified easily by light or electron microscopy (Rogers, 1994). http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0030154 GO light or electron microscopy Identification of mucin-producing secretory granules in goblet cells using light or electron microscopy. ex_vivo presence of mucin-producing secretory granules not_specified http://purl.obolibrary.org/obo/CHEBI_35312 CHEBI http://purl.obolibrary.org/obo/GO_0005523 GO low The mucin-producing secretory granules of goblet cells can be identified easily by light or electron microscopy (Rogers, 1994). http://purl.obolibrary.org/obo/CL_0000221 CL http://purl.obolibrary.org/obo/GO_0051011 GO MUC5 antibody staining Staining tissue or ALI culture with antibody recognizing MUC5 to count labeled cells or calculate percentage of positive cells. in_vitro number of labeled cells/mm of epithelium or percentage of positive cells increase medium The increased number of goblet cells can be measured by staining the tissue or ALI culture with antibody recognizing MUC5 and counting the number of labeled cells/mm of epithelium or percentage of positive cells in the epithelium http://purl.obolibrary.org/obo/CL_0000221 CL http://purl.obolibrary.org/obo/GO_0008283 GO MUC5 antibody staining Measures the number of goblet cells by staining tissue or ALI culture with antibody recognizing MUC5 and counting labeled cells. in_vitro epithelium number of MUC5-positive cells increase http://purl.obolibrary.org/obo/CL_0000183 CL medium The increased number of goblet cells can be measured by staining the tissue or ALI culture with antibody recognizing MUC5 and counting the number of labeled cells/mm of epithelium or percentage of positive cells in the epithelium (Casalino-Matsuda et al, 2006; Jia et al, 2021; Lou et al, 1998; Tyner et al., 2006). http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0030154 GO PCNA staining Identifies proliferating goblet cells in the crypt of the intestinal wall using Proliferating Cell Nuclear Antigen 19A2 staining. in_vivo intestinal crypt rabbit number of proliferating goblet cells increase http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0008283 GO medium Proliferating Cell Nuclear Antigen 19A2 (PCNA) staining was used to identify proliferating goblet cells in the crypt of the intestinal wall in rabbits (GRANT & Specian, 1998). http://purl.obolibrary.org/obo/CL_0000183 CL http://purl.obolibrary.org/obo/GO_0008283 GO transmission electron microscopy Stages of metaplastic transformation are identified using transmission electron microscopy. in_vivo epithelium metaplastic transformation stages change low The stages of metaplastic transformation can be identified as early cilia-goblet cells, late cilia-goblet, and mature goblet cells using transmission electron micrographs (Tyner et al, 2006). http://purl.obolibrary.org/obo/CL_0000044 CL http://purl.obolibrary.org/obo/GO_0030154 GO DCPIP reduction Measures succinate quinone reductase (SQR) activity by the reduction of DCPIP in the presence of 2,3-dimethoxy-6-methyl-1,4-benzoquinone (UQ2) as an electron acceptor. in_vitro SQR activity not_specified http://purl.obolibrary.org/obo/GO_0004096 GO not_specified SQR activity can be measured by reduction of 2,6-dichlorophenolindophenol (DCPIP) in the presence of the 2,3-dimethoxy-6-methyl-1,4-benzoquinone (UQ2), which accepts electrons from the ubiquinone reduction site and transfers them to DCPIP, thus being a measure of the rate of the entire reaction catalysed by complex II. http://purl.obolibrary.org/obo/PR_000016595 PR http://purl.obolibrary.org/obo/GO_0004096 GO DCPIP reduction assay SQR activity can be measured by reduction of DCPIP in the presence of UQ2, which accepts electrons from the ubiquinone reduction site and transfers them to DCPIP, thus being a measure of the rate of the entire reaction catalysed by complex II. in_vitro reduction of DCPIP decrease http://purl.obolibrary.org/obo/GO_0055114 GO low It can be measured by reduction of 2,6-dichlorophenolindophenol (DCPIP) in the presence of the 2,3-dimethoxy-6-methyl-1,4-benzoquinone (UQ2), which accepts electrons from the ubiquinone reduction site and transfers them to DCPIP, thus being a measure of the rate of the entire reaction catalysed by complex II. http://purl.obolibrary.org/obo/GO_0055114 GO MTT assay SDH activity can be measured by use of the water-soluble dye MTT in the presence of the intermediate electron carrier PMS, to intercept electrons before their transport to ubiquinone, and convey them to MTT, which changes colour following its reduction. in_vitro colour change of MTT change http://www.bioassayontology.org/bao#BAO_0000077 BAO http://purl.obolibrary.org/obo/GO_0055114 GO medium It can be measured by use of the water-soluble dye 2-(4,5-dimethyl-2-thiazolyl)-3,5-diphenyl-2H-tetrazolium bromide (MTT) in the presence of the intermediate electron carrier phenazine methosulfate (PMS), to intercept electrons before their transport to ubiquinone, and convey them to MTT, which changes colour following its reduction. http://purl.obolibrary.org/obo/CHEBI_6884 CHEBI http://purl.obolibrary.org/obo/GO_0055114 GO MTT assay for SDH activity Measures succinate dehydrogenase (SDH) activity by using MTT as a water-soluble dye and PMS as an intermediate electron carrier to intercept electrons and observe color change upon reduction. in_vitro rate of color change (reduction of MTT) change http://purl.obolibrary.org/obo/CHMO_0000155 CHMO not_specified Succinate dehydrogenase (SDH) activity ... Can be measured by use of the water-soluble dye 2-(4,5-dimethyl-2-thiazolyl)-3,5-diphenyl-2H-tetrazolium bromide (MTT) in the presence of the intermediate electron carrier phenazine methosulfate (PMS), to intercept electrons before their transport to ubiquinone, and convey them to MTT, which changes colour following its reduction. http://purl.obolibrary.org/obo/PR_000000002 PR http://purl.obolibrary.org/obo/GO_0004528 GO MTT reduction Measures succinate dehydrogenase (SDH) activity by the reduction of MTT in the presence of phenazine methosulfate (PMS) as an intermediate electron carrier. in_vitro SDH activity not_specified http://purl.obolibrary.org/obo/GO_0003954 GO http://purl.obolibrary.org/obo/CHMO_0001078 CHMO not_specified SDH activity can be measured by use of the water-soluble dye 2-(4,5-dimethyl-2-thiazolyl)-3,5-diphenyl-2H-tetrazolium bromide (MTT) in the presence of the intermediate electron carrier phenazine methosulfate (PMS), to intercept electrons before their transport to ubiquinone, and convey them to MTT, which changes colour following its reduction. http://purl.obolibrary.org/obo/PR_000016595 PR http://purl.obolibrary.org/obo/GO_0003954 GO SDH activity assay (MTT/PMS) Measures succinate dehydrogenase activity by spectrophotometric detection of color change using MTT and PMS as electron acceptors in the presence of succinate. in_vitro mitochondria succinate dehydrogenase activity decrease http://purl.obolibrary.org/obo/GO_0000060 GO http://purl.obolibrary.org/obo/GO_0022900 GO medium Succinate dehydrogenase (SDH) activity corresponds to reaction (1), above. It can be measured by use of the water-soluble dye 2-(4,5-dimethyl-2-thiazolyl)-3,5-diphenyl-2H-tetrazolium bromide (MTT) in the presence of the intermediate electron carrier phenazine methosulfate (PMS), to intercept electrons before their transport to ubiquinone, and convey them to MTT, which changes colour following its reduction. http://purl.obolibrary.org/obo/PR_000001738 PR http://purl.obolibrary.org/obo/GO_0022900 GO SQR activity assay (DCPIP/UQ2) Measures succinate quinone reductase activity by spectrophotometric detection of color change using DCPIP and UQ2 as electron acceptors in the presence of succinate. in_vitro mitochondria succinate quinone reductase activity decrease http://purl.obolibrary.org/obo/GO_0022900 GO medium Succinate quinone reductase (SQR) activity corresponds to the overall reaction (i.e. 1 and 2), above. It can be measured by reduction of 2,6-dichlorophenolindophenol (DCPIP) in the presence of the 2,3-dimethoxy-6-methyl-1,4-benzoquinone (UQ2), which accepts electrons from the ubiquinone reduction site and transfers them to DCPIP, thus being a measure of the rate of the entire reaction catalysed by complex II. http://purl.obolibrary.org/obo/GO_0022900 GO HOMA-IR A single-sample method to estimate insulin resistance using fasting plasma insulin and glucose levels, suitable for epidemiological studies. in_vivo insulin resistance increase http://purl.obolibrary.org/obo/GO_0042592 GO high the homeostatic model for insulin resistance (HOMA-IR), a single sample method, are simpler and less invasive, but show greater interindividual variability and only moderate agreement with the HEC. They are more suitable as epidemiological tools for population assessments http://purl.obolibrary.org/obo/GO_0008286 GO http://purl.obolibrary.org/obo/GO_0042592 GO Homeostatic Model for Insulin Resistance (HOMA-IR) The homeostatic model for insulin resistance (HOMA-IR) is a simpler, less invasive method for measuring insulin resistance that uses a single blood sample to calculate insulin resistance based on fasting glucose and insulin levels. It shows greater interindividual variability and only moderate agreement with the gold standard HEC, but is more suitable as an epidemiological tool for population assessments. in_vivo whole body human fasting glucose and insulin levels not_specified http://purl.obolibrary.org/obo/GO_0033559 GO http://purl.obolibrary.org/obo/GO_0042593 GO not specified high Other methods, such as the homeostatic model for insulin resistance (HOMA-IR), a single sample method, are simpler and less invasive, but show greater interindividual variability and only moderate agreement with the HEC. They are more suitable as epidemiological tools for population assessments. http://purl.obolibrary.org/obo/GO_0042593 GO hyperinsulineamic euglycaemic clamp Measures insulin resistance by infusing insulin intravenously to achieve steady-state glycemia, considered the gold standard. in_vivo insulin resistance increase http://purl.obolibrary.org/obo/GO_0006006 GO http://purl.obolibrary.org/obo/GO_0008286 GO low The hyperinsulineamic euglycaemic clamp (HEC), involving intravenous infusion of insulin to reach steady state glycemic is considered the gold standard http://purl.obolibrary.org/obo/GO_0008286 GO http://purl.obolibrary.org/obo/GO_0006006 GO hyperinsulineamic euglycaemic clamp The hyperinsulineamic euglycaemic clamp (HEC) involves intravenous infusion of insulin to reach steady state glycemic. in_vivo plasma insulin and glucose levels increase low The hyperinsulineamic euglycaemic clamp (HEC), involving intravenous infusion of insulin to reach steady state glycemic is considered the gold standard http://purl.obolibrary.org/obo/GO_0042485 GO hyperinsulineamic euglycaemic clamp (HEC) A gold standard method involving the intravenous infusion of insulin to reach a steady-state glycemic level to assess insulin sensitivity. in_vivo insulin sensitivity/resistance via steady state glycemic control change low The hyperinsulineamic euglycaemic clamp (HEC), involving intravenous infusion of insulin to reach steady state glycemic is considered the gold standard, but is challenging, expensive and invasive. H2O2 generation assay Measures hydrogen peroxide generation by isolated mitochondria as an indicator of mitochondrial superoxide generation. ex_vivo mitochondria hydrogen peroxide generation increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0005739 GO low the H2O2 generated by dismutation within the mitochondrial matrix diffuses rapidly to the exterior, meaning that H2O2 generation by isolated mitochondria can be used to measure superoxide generation (Murphy, 2009) http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006801 GO WISC The Wechsler Intelligence Scale for Children (WISC) is a standardized test used to measure intelligence and cognitive abilities in children. not_specified human intelligence quotient (IQ) decrease low WISC (Wechsler Intelligence Scale for Children) Direct Costs Measures measurable expenses directly related to the issue, such as healthcare expenditures, social service costs, compensatory education, and monitoring. not_specified direct costs increase not_specified Direct Costs: These are measurable expenses directly related to the issue, such as healthcare expenditures, social service costs, compensary education and monitoring. Direct Costs assessment A method to quantify measurable expenses such as healthcare expenditures, social service costs, and compensatory education. not_specified healthcare expenditures, social service costs, compensary education and monitoring increase not_specified Direct Costs: These are measurable expenses directly related to the issue, such as healthcare expenditures, social service costs, compensary education and monitoring. disability-adjusted life year (DALY) assessment This assay assesses intangible costs, including reduced quality of life, using tools like disability-adjusted life years (DALYs). not_specified disability-adjusted life years increase low Intangible Costs: These include reduced quality of life, psychological distress, and social stigma. Tools such as quality-adjusted life years (QALYs) and disability-adjusted life years (DALYs) are used to assess the burden on individuals' well-being. human capital approach An economic method used to estimate indirect costs, including productivity losses due to morbidity, premature mortality, absenteeism, or lower IQ. not_specified productivity losses increase not_specified Indirect Costs: These refer to productivity losses due to morbidity, premature mortality, absenteeism or lower IQ. Method such as the human capital approach is commonly used to estimate these costs. quality-adjusted life year (QALY) assessment This assay assesses intangible costs, including reduced quality of life, using tools like quality-adjusted life years (QALYs). not_specified quality-adjusted life years decrease low Intangible Costs: These include reduced quality of life, psychological distress, and social stigma. Tools such as quality-adjusted life years (QALYs) and disability-adjusted life years (DALYs) are used to assess the burden on individuals' well-being. Western blot A technique used to detect and quantify specific proteins in a sample by using gel electrophoresis and antibodies. in_vitro Bcl-2 protein levels decrease http://purl.obolibrary.org/obo/OBI_0000613 OBI http://purl.obolibrary.org/obo/PR_000008886 PR low measured by Western Blot http://purl.obolibrary.org/obo/PR_000008886 PR http://purl.obolibrary.org/obo/GO_0006915 GO Immunofluorescence (IF) Localizes Bax protein in cells or tissues using fluorescently labeled antibodies and confocal or fluorescence microscopy for high-resolution imaging. in_vitro cells tissues Bax protein localization increase http://purl.obolibrary.org/obo/GO_0008104 GO medium This technique is used for localizing Bax protein in cells or tissues. Fluorescently labeled primary or secondary antibodies bind to Bax, and confocal or fluorescence microscopy is used for imaging. IF provides high-resolution spatial distribution of Bax expression(6). http://purl.obolibrary.org/obo/GO_0006915 GO Immunohistochemistry (IHC) Detects Bax protein expression in tissue sections using Bax-specific antibodies, an enzyme-conjugated secondary antibody, and a chromogenic substrate for visualization under a microscope. in_vivo tissue sections Bax protein expression increase http://purl.obolibrary.org/obo/GO_0010485 GO low IHC detects Bax protein expression in tissue sections. After tissue fixation and antigen retrieval, Bax-specific antibodies are applied, followed by an enzyme-conjugated secondary antibody. A chromogenic substrate (e.g., DAB) generates a color reaction, allowing visualization under a microscope, which is useful for studying tissue-specific expression (4,8). http://purl.obolibrary.org/obo/GO_0006915 GO Northern blotting Detects Bax mRNA expression by isolating RNA, separating it by gel electrophoresis, transferring to a membrane, and hybridizing with a labeled Bax-specific probe. in_vitro tissues cells Bax mRNA expression increase http://purl.obolibrary.org/obo/GO_0010467 GO low This is a standard approach for detecting Bax mRNA expression. RNA is isolated from tissues or cells, separated by size using gel electrophoresis, transferred to a membrane, and hybridised with a labelled Bax-specific probe. The signal indicates both the existence and size of the Bax transcripts (9). http://purl.obolibrary.org/obo/GO_0006915 GO Quantitative Real-Time PCR (qRT-PCR) Measures Bax mRNA expression levels by RNA extraction, reverse transcription to cDNA, and amplification using gene-specific primers with fluorescent dyes or probes for real-time quantification. in_vitro Bax mRNA expression increase http://purl.obolibrary.org/obo/GO_0010467 GO high Used to measure Bax mRNA expression levels, this method involves RNA extraction, reverse transcription to cDNA, and amplification using gene-specific primers. Fluorescent dyes or probes (e.g., SYBR Green, TaqMan) help quantify Bax mRNA in real-time, making it a sensitive method for gene expression analysis (6,7). http://purl.obolibrary.org/obo/GO_0006915 GO TUNEL Assay Detects apoptotic DNA fragmentation, often correlated with Bax activation, using labeled nucleotides to identify DNA strand breaks in situ. in_vivo ovarian tissue apoptotic DNA fragmentation increase http://purl.obolibrary.org/obo/GO_0043066 GO http://purl.obolibrary.org/obo/GO_0006915 GO medium While not directly measuring Bax, the TUNEL assay detects apoptotic DNA fragmentation, often correlated with Bax activation. It is used in ovarian apoptosis studies alongside Bax expression analysis(4,10). http://purl.obolibrary.org/obo/CHEBI_15977 CHEBI http://purl.obolibrary.org/obo/GO_0006915 GO Liquid chromatography–mass spectrometry This assay measures glutathione conjugation products using liquid chromatography coupled with mass spectrometry. in_vitro glutathione conjugation products not_specified http://purl.obolibrary.org/obo/OBI_0000475 OBI medium Liquid chromatography–mass spectrometry (Pallante et al. 1986; Plakunov et al. 1987; Pflugmacher et al. 1998; Wiegand et al. 2001a; Dai et al. 2008; Dionisio, Gautam, and Fomsgaard 2019). http://purl.obolibrary.org/obo/CHEBI_15434 CHEBI http://purl.obolibrary.org/obo/GO_0006749 GO ELISA Immunoassay technique used to measure the concentration of gonadotropins (Luteinizing hormone and Follicle-stimulating hormone) in blood or urine samples. in_vitro gonadotropin concentration increase not_specified Commercial ELISA kits are available for Luteinizing hormone (e.g. Abcam AB303746 (human); Aviva OKCA00156 (mouse); ThermoFisher EHLH (human)) and Follicle-stimulating hormone (e.g. ThermoFisher EH202RB (human); ALPCO 11-FSHHU-E01 (human); ENZO ENZ-KIT108 (human). Gonadotropin levels are generally measured from blood or urine samples by immunoassay or Western blotting, with immunoassay the preferred technique. immunoassay Measures gonadotropin levels in blood or urine samples using antibody-based detection. in_vitro blood urine human mouse gonadotropin concentration increase http://purl.obolibrary.org/obo/CHEBI_35337 CHEBI http://purl.obolibrary.org/obo/OBI_0000466 OBI medium Gonadotropin levels are generally measured from blood or urine samples by immunoassay or Western blotting, with immunoassay the preferred technique. Commercial ELISA kits are available for Luteinizing hormone (e.g. Abcam AB303746 (human); Aviva OKCA00156 (mouse); ThermoFisher EHLH (human)) and Follicle-stimulating hormone (e.g. ThermoFisher EH202RB (human); ALPCO 11-FSHHU-E01 (human); ENZO ENZ-KIT108 (human). http://purl.obolibrary.org/obo/CHEBI_35337 CHEBI http://purl.obolibrary.org/obo/GO_0046887 GO real-time PCR Measures gonadotropin transcript abundance as an indirect indicator of hormone levels, focusing on the beta subunit. in_vitro gonadotropin transcript abundance increase medium Real time PCR can be used to measure gonadotropin transcript abundance, which is an indirect – and only semi-quantitative indicator of gonadotropin hormone levels. Since gonadotropins share a common alpha subunit, focus is generally on the beta subunit (studies that utilized this approach include Schirman-Hildesheim et al. 2008; Bo et al. 2022; Oride et al. 2023). http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Detects gonadotropin proteins in blood or urine samples using gel electrophoresis and antibody probing. in_vitro blood urine gonadotropin protein levels increase http://purl.obolibrary.org/obo/CHEBI_35337 CHEBI low Gonadotropin levels are generally measured from blood or urine samples by immunoassay or Western blotting, with immunoassay the preferred technique. http://purl.obolibrary.org/obo/CHEBI_35337 CHEBI http://purl.obolibrary.org/obo/GO_0046887 GO Western blot Detects specific proteins such as phosphorylated MEK and ERK1/2 by separating proteins via gel electrophoresis, transferring to a membrane, and probing with antibodies. in_vitro phosphorylation level of MEK and ERK1/2 proteins change http://purl.obolibrary.org/obo/OBI_0000747 OBI http://purl.obolibrary.org/obo/GO_0006468 GO low Western blotting http://purl.obolibrary.org/obo/GO_0000165 GO Western blot Western blotting and immunoblotting are used to detect and quantify the activation of MEK and ERK1/2 proteins. in_vitro protein activation increase not_specified Western blotting and immunoblotting. western blot Western blotting and immunoblotting are used to detect specific proteins and assess their levels. This is achieved by separating proteins by size using gel electrophoresis, transferring them to a membrane, and using antibodies to identify and quantify the target proteins. in_vitro protein levels increase http://purl.obolibrary.org/obo/OBI_0000233 OBI low Western blotting and immunoblotting. http://purl.obolibrary.org/obo/GO_0007165 GO western blot Western blotting is used to detect and quantify specific proteins, such as MEK and ERK1/2, by using antibodies to bind to the proteins of interest. in_vitro protein phosphorylation increase http://purl.obolibrary.org/obo/GO_0006468 GO low Western blotting and immunoblotting. http://purl.obolibrary.org/obo/GO_0000165 GO embryo viability assessment Quantifies the percentage of embryos that are successfully fertilized and remain viable. in_vivo percent of fertilized, viable embryos decrease not_specified percent of fertilized, viable embryos http://purl.obolibrary.org/obo/GO_0007565 GO offspring production assessment Measures the reproductive capacity of mature organisms by counting the total number of offspring produced per pair, individual, or population. in_vivo number of offspring produced decrease http://purl.obolibrary.org/obo/UBERON_0000001 UBERON not_specified number of offspring produced (per pair, individual, or population) http://purl.obolibrary.org/obo/GO_0044475 GO viable offspring production Measures the ability of reproductively mature organisms to produce viable offspring, including the number of offspring produced and the percentage of fertilized, viable embryos. in_vivo number of viable offspring decrease http://purl.obolibrary.org/obo/GO_0000003 GO low Effects on the production of viable offspring is measured or detected through the ability (or inability) of reproductively mature organisms to produce offspring, number of offspring produced (per pair, individual, or population), and/or percent of fertilized, viable embryos. http://purl.obolibrary.org/obo/GO_0000003 GO BDNF quantitative real-time PCR Quantifies BDNF exon-specific mRNA expression in hippocampal neuronal cultures using TaqMan-based qRT-PCR, normalized to actin. in_vitro hippocampal neuronal cultures hippocampus Rattus norvegicus BDNF mRNA expression change http://purl.obolibrary.org/obo/CHEBI_75592 CHEBI http://purl.obolibrary.org/obo/UBERON_0001954 UBERON http://purl.obolibrary.org/obo/GO_0010467 GO medium BDNF quantitative real-time PCR. Hippocampal neuronal cultures were exposed to normal bath solution or 1.0 or 2.0μM Pb2+ for 5 days, and subsequently RNA was harvested according to manufacturer’s instructions (RNeasy; Qiagen), quantified by reading the absorbance at 260 nm, and converted to complementary DNA (cDNA) using 1 μg RNA according to manufacturer’s instructions (High Capacity Reverse Transcription Kit 4368814; Applied Biosystems). Quantitative real-time PCR (q-rtPCR) was performed in triplicate using TaqMan Gene Expression Assays (Applied Biosystems) with 50 ng cDNA using the following probes: Actin (Rat, Rn00667869_m1; Applied Biosystems) and BDNF exon I, exon II, exon IV, and exon IX (Applied Biosystems). http://purl.obolibrary.org/obo/GO_0010467 GO ELISA BDNF protein levels are quantified in cell culture media using a sandwich ELISA. BDNF content is normalized to total protein content. in_vitro DIV12 cells BDNF protein levels change http://purl.obolibrary.org/obo/CHEBI_6236 CHEBI http://purl.obolibrary.org/obo/GO_0005829 GO medium BDNF release via ELISA. Sandwich ELISAs were performed on DIV12 cell culture media using the BDNF Emax ImmunoAssay System kit (Promega, Madison, WI) according to the manufacturer’s instructions. BDNF protein content was divided by total protein for each sample to determine the number of picograms of peptide per microgram of total protein (Stansfield and others 2012). http://purl.obolibrary.org/obo/CHEBI_6236 CHEBI http://purl.obolibrary.org/obo/GO_0022613 GO In vivo microdialysis Monitors extracellular neurotransmitter levels in the CNS of living animals via a microdialysis probe, allowing real-time measurement during pharmacological manipulations. in_vivo brain extracellular neurotransmitter levels change http://purl.obolibrary.org/obo/OBI_0000219 OBI http://purl.obolibrary.org/obo/UBERON_0000955 UBERON http://purl.obolibrary.org/obo/GO_0007269 GO low In vivo microdialysis is a well-established method for monitoring the extracellular levels of neurotransmitters in the CNS. Microdialysis allows online estimates of neurotransmitters in living animals and is a suitable method for monitoring the extracellular levels of neurotransmitters during local administration of pharmacological agents (Hammarlund-Udenaes 2000). http://purl.obolibrary.org/obo/CHEBI_25512 CHEBI http://purl.obolibrary.org/obo/GO_0007269 GO q-rtPCR BDNF mRNA levels are quantified in hippocampal neuronal cultures exposed to lead using quantitative real-time PCR with TaqMan probes. Results are expressed as fold change relative to control. in_vitro hippocampal neurons hippocampus BDNF mRNA expression change http://purl.obolibrary.org/obo/GO_0006925 GO medium BDNF quantitative real-time PCR. Hippocampal neuronal cultures were exposed to normal bath solution or 1.0 or 2.0μM Pb2+ for 5 days, and subsequently RNA was harvested... Data were analyzed as previously described (Livak and Schmittgen, 2001), and results were expressed as fold change in gene expression relative to control http://purl.obolibrary.org/obo/GO_0006925 GO quantitative real-time PCR Measurement of BDNF gene expression levels (exons I, II, IV, and IX) using TaqMan probes and cDNA derived from hippocampal neuronal cultures. in_vitro hippocampal neuronal cultures Rat gene expression (fold change) change http://purl.obolibrary.org/obo/GO_0010468 GO not_specified BDNF quantitative real-time PCR. Hippocampal neuronal cultures were exposed to normal bath solution or 1.0 or 2.0μM Pb2+ for 5 days, and subsequently RNA was harvested Quantitative real-time PCR (q-rtPCR) was performed in triplicate using TaqMan Gene Expression Assays http://purl.obolibrary.org/obo/GO_0006351 GO Sadavongvivad (1970) biogenic amine estimation Extraction and estimation of biogenic amines (DA, NE, 5-HT) from homogenized brain tissue using fluorescence measurement. ex_vivo brain biogenic amine levels change http://purl.obolibrary.org/obo/CHEBI_16237 CHEBI http://purl.obolibrary.org/obo/CHEBI_16226 CHEBI http://purl.obolibrary.org/obo/CHEBI_16235 CHEBI not_specified Weighed brain tissues were homogenized in a Potter-Elvehjem type A homogenizer with a teflon pestle using cold acidified n-butanol. The biogenic amines were extracted and estimated according to the procedure of Sadavongvivad (1970). Fluorescence was measured in a Aminco SPF-500 spectrofluorometer http://purl.obolibrary.org/obo/GO_0050853 GO Spectrofluorometric biogenic amine assay Measures fluorescence of extracted biogenic amines (dopamine, norepinephrine, 5-hydroxytryptamine) from homogenized brain tissue using acidified n-butanol extraction and spectrofluorometry. ex_vivo brain biogenic amine levels not_specified http://purl.obolibrary.org/obo/CHEBI_18243 CHEBI http://purl.obolibrary.org/obo/CHEBI_18248 CHEBI http://purl.obolibrary.org/obo/CHEBI_28754 CHEBI http://purl.obolibrary.org/obo/UBERON_0000955 UBERON low Weighed brain tissues were homogenized in a Potter-Elvehjem type A homogenizer with a teflon pestle using cold acidified n-butanol. The biogenic amines were extracted and estimated according to the procedure of Sadavongvivad (1970). Fluorescence was measured in a Aminco SPF-500 spectrofluorometer (Chandra et al., 1981). http://purl.obolibrary.org/obo/GO_0042136 GO bisulfite genomic sequencing A DNA-methylation assay that involves sodium bisulphite treatment of DNA, converting unmethylated cytosines to uracil, followed by genomic sequencing. in_vitro site-specific DNA methylation change http://purl.obolibrary.org/obo/GO_0006306 GO http://purl.obolibrary.org/obo/OBI_0002143 OBI low Bisulfite genomic sequencing of multiple clones is a DNA-methylation assay that entails initial modification of DNA by sodium bisulphite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent genomic sequencing. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO DNA-methylation array Involves hybridization of bisulfite-treated DNA to arrays, with methylation data represented by fluorescent signals from methylated and unmethylated alleles. in_vitro genome-wide DNA methylation change http://purl.obolibrary.org/obo/GO_0006306 GO http://purl.obolibrary.org/obo/OBI_0000185 OBI high DNA-methylation arrays involve the modified DNA being hybridisied after bisulfite treatment to previously designed arrays and each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles printed in the platform. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO high performance liquid chromatography (HPLC) Provides a reliable measure of total 5-methylcytosine DNA content but requires large sample amounts and specialized machinery. in_vitro global DNA methylation change http://purl.obolibrary.org/obo/GO_0006306 GO http://purl.obolibrary.org/obo/OBI_0001048 OBI medium High performance liquid chromatography (HPLC) provides a reliable measure of the total 5-methylcytosine DNA content but requires important amounts of sample and specialised machinery. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO high-performance capillary electrophoresis (HPCE) Provides a reliable measure of total 5-methylcytosine DNA content using small sample amounts but requires specialized machinery. in_vitro global DNA methylation change http://purl.obolibrary.org/obo/GO_0006306 GO http://purl.obolibrary.org/obo/OBI_0001049 OBI medium High-performance capillary electrophoresis (HPCE) provides reliable measure of the total 5-methylcytosine DNA content starting with small amounts of sample, but requires specialised machinery. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO histone methyltransferase activity assay Measures histone methyltransferase activity or inhibition on specific histones using commercially available kits. in_vitro histone methyltransferase activity change http://purl.obolibrary.org/obo/GO_0042054 GO http://purl.obolibrary.org/obo/GO_0016571 GO not_specified Histone methylation can be detected directly by measuring histone methyltransferase activity/inhibition on specific histones using commercially available kits http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0016571 GO HPCE High-performance capillary electrophoresis measures total 5-methylcytosine DNA content. in_vitro 5-methylcytosine DNA content change low High-performance capillary electrophoresis (HPCE) provides reliable measure of the total 5- methylcytosine DNA content starting with small amounts of sample. http://purl.obolibrary.org/obo/CHEBI_00329 CHEBI HPLC High performance liquid chromatography measures total 5-methylcytosine DNA content. in_vitro 5-methylcytosine DNA content change low High performance liquid chromatography (HPLC) provides a reliable measure of the total 5- methylcytosine DNA content but requires important amounts of sample. http://purl.obolibrary.org/obo/CHEBI_00329 CHEBI Immunostaining In situ DNA-methylation imaging using anti-5-methylcytosine antibodies. ex_vivo 5-methylcytosine localization change http://purl.obolibrary.org/obo/GO_0006306 GO low Immunostaining with anti-5-methylcytosine antibodies requires the use of other markers to map the stained regions http://purl.obolibrary.org/obo/CHEBI_35332 CHEBI http://purl.obolibrary.org/obo/GO_0006306 GO immunostaining with anti-5-methylcytosine antibodies Detects DNA methylation in situ using antibodies, requiring other markers to map stained regions, with variability depending on the antibody used. in_vitro DNA methylation localization change http://purl.obolibrary.org/obo/GO_0006306 GO low Immunostaining with anti-5-methylcytosine antibodies requires the use of other markers to map the stained regions and has variability depending on the antibody badge. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO methyl-DIP Immunoprecipitation with anti-5-methylcytosine antibodies followed by microarray hybridization or ultrasequencing. in_vitro DNA methylation change medium Methylated DNA immunoprecipitation (methyl-DIP) involves immunoprecipitation with anti-5- methylcytosine antibodies followed by hybridisation to genomic microarrays or ultrasequencing, allowing the identification of methyl-CpG rich sequences. http://purl.obolibrary.org/obo/CHEBI_00329 CHEBI methylated DNA immunoprecipitation (methyl-DIP) Involves immunoprecipitation with anti-5-methylcytosine antibodies followed by hybridization to genomic microarrays or sequencing to identify methyl-CpG rich sequences. in_vitro methyl-CpG rich sequences change http://purl.obolibrary.org/obo/GO_0006306 GO http://purl.obolibrary.org/obo/OBI_0000286 OBI medium Methylated DNA immunoprecipitation (methyl-DIP) involves immunoprecipitation with anti-5-methylcytosine antibodies followed by hybridisation to genomic microarrays or ultrasequencing, allowing the identification of methyl-CpG rich sequences. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO methylation-specific PCR Uses bisulfite-modified DNA and primers specific for methylated versus unmethylated DNA to detect DNA methylation patterns. in_vitro DNA methylation pattern change http://purl.obolibrary.org/obo/GO_0006306 GO medium Methylation-specific PCR uses bisulfite modified DNA and subsequent amplification with primers that are specific for methylated versus unmethylated DNA. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO MethyLight A high-throughput quantitative methylation assay using fluorescence-based real-time PCR technology on bisulfite-modified DNA. in_vitro DNA methylation levels change http://purl.obolibrary.org/obo/GO_0006306 GO http://purl.obolibrary.org/obo/OBI_0000662 OBI high MethyLight is a high-throughput quantitative methylation assay that uses fluorescence-based real-time PCR technology. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO pyrosequencing A DNA-sequencing method that emits light during nucleotide incorporation, used to detect methylation-dependent DNA sequence variation after bisulfite treatment. in_vitro DNA methylation sequence change http://purl.obolibrary.org/obo/OBI_0000627 OBI medium Pyrosequencing is a DNA-sequencing method in which light is emitted as a result of an enzymatic reaction each time a nucleotide is incorporated into the growing DNA chain. http://purl.obolibrary.org/obo/GO_0005694 GO http://purl.obolibrary.org/obo/GO_0006306 GO western blot Detects specific histone methylation levels using antibodies raised against specific histone modifications. in_vitro histone methylation levels change http://purl.obolibrary.org/obo/GO_0016571 GO low indirectly as detection of specific histone methylation levels by western blotting with antibodies raised against specific histone modifications http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0016571 GO Zebrafish epigenetic biomarker assessment Assessment of DNA global methylation, gene expression of DNA/histone epigenetic modifications, and morphological abnormalities in zebrafish embryos. in_vivo Danio rerio DNA global methylation and gene expression change http://purl.obolibrary.org/obo/GO_0006306 GO low Zebrafish has been proposed as a model for gene expression assessment of epigenetic biomarkers (Torres et al. 2021). In this model, morphological abnormalities and epigenetic changes were assessed at 80 hours-post fertilization, including DNA global methylation and gene expression of both DNA and histone epigenetic modifications http://purl.obolibrary.org/obo/CHEBI_35332 CHEBI http://purl.obolibrary.org/obo/GO_0043066 GO zebrafish epigenetic biomarker assessment In vivo model using zebrafish to assess morphological abnormalities and epigenetic changes, including DNA global methylation and gene expression of epigenetic modifications. in_vivo Danio rerio epigenetic biomarkers change http://purl.obolibrary.org/obo/GO_0040029 GO http://purl.obolibrary.org/obo/NCBITaxon_7955 NCBITAXON low Zebrafish has been proposed as a model for gene expression assessment of epigenetic biomarkers (Torres et al. 2021). In this model, morphological abnormalities and epigenetic changes were assessed at 80 hours-post fertilization, including DNA global methylation and gene expression of both DNA and histone epigenetic modifications http://purl.obolibrary.org/obo/NCBITaxon_7955 NCBITAXON http://purl.obolibrary.org/obo/GO_0040029 GO ELISA Measures protein expression using enzyme-linked immunosorbent assay. in_vitro protein expression not_specified http://purl.obolibrary.org/obo/GO_0010485 GO high Protein expression can be measured in cells/tissue lysate as well as in situ. Most common methods are immunohistochemistry (in situ), western blot analysis and enzyme-linked immunosorbent assays (ELISA) http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0010485 GO immunohistochemistry Detects protein expression in situ using labeled antibodies. in_vitro protein expression not_specified http://purl.obolibrary.org/obo/GO_0010485 GO low Protein expression can be measured in cells/tissue lysate as well as in situ. Most common methods are immunohistochemistry (in situ) http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0010485 GO in situ hybridization Localizes specific RNA sequences in cells or tissues using complementary binding of a labeled nucleotide probe. in_vitro RNA sequence localization not_specified http://purl.obolibrary.org/obo/CHEBI_33697 CHEBI low In situ hybridization localize specific RNA sequences in cells/tissues by means of complementary binding of a nucleotide probe to a specific sequence of RNA. http://purl.obolibrary.org/obo/CHEBI_33697 CHEBI http://purl.obolibrary.org/obo/GO_0010467 GO luciferase reporter gene assay Measures gene expression using the chemiluminescent reaction catalyzed by luciferase. in_vitro luciferase activity not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/CHEBI_25000 CHEBI medium The chemiluminescent reaction catalysed by luciferase is one of the most sensitive analytical tools for measuring gene expression identified. http://purl.obolibrary.org/obo/CHEBI_25000 CHEBI http://purl.obolibrary.org/obo/GO_0010467 GO microarray expression profiling Simultaneously quantitates many different transcripts using microarray technology. in_vitro transcript levels not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/SO_0000673 SO high microarray expression profiling http://purl.obolibrary.org/obo/SO_0000673 SO http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR Quantitates mRNA levels of specific genes using reverse transcription and polymerase chain reaction. in_vitro mRNA levels not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/CHEBI_33699 CHEBI medium Gene expression is directly determined by quantitating mRNA levels of the genes of interest through several established methods such as: (quantitative) real time reverse transcription polymerase chain reaction (q)RT-PCR) http://purl.obolibrary.org/obo/CHEBI_33699 CHEBI http://purl.obolibrary.org/obo/GO_0010467 GO RNA sequencing Quantitates many different transcripts simultaneously using whole transcriptome sequencing. in_vitro transcript levels not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/SO_0000673 SO high whole transcriptome RNA sequencing http://purl.obolibrary.org/obo/SO_0000673 SO http://purl.obolibrary.org/obo/GO_0010467 GO western blot Measures protein expression in cell or tissue lysates using gel electrophoresis and antibody detection. in_vitro protein expression not_specified http://purl.obolibrary.org/obo/GO_0010485 GO medium Protein expression can be measured in cells/tissue lysate as well as in situ. Most common methods are immunohistochemistry (in situ), western blot analysis http://purl.obolibrary.org/obo/CHEBI_36080 CHEBI http://purl.obolibrary.org/obo/GO_0010485 GO Color Doppler sonography Ultrasound technique using Doppler effect to assess blood flow in endometrial tissues. in_vivo endometrium uterus human blood flow in endometrial tissue not_specified http://purl.obolibrary.org/obo/GO_0008015 GO medium Saline infusion sonography and Color Doppler sonography were used to differentiate between endometrial cancer, endometrial hyperplasia, endometriosis, myoma or tamoxifen induced endometrial thickness (Achiron et al., 1995; Widrich et al., 1996). http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0008015 GO FIGO 3-Grade Assessment Histological classification of endometrial cancer into three grades based on glandular differentiation and solid growth patterns. ex_vivo endometrium human histological grade of endometrial cancer not_specified http://purl.obolibrary.org/obo/OBI_0000388 OBI FIGO 3-Grade Assessment medium The International federation of Gynecology and Obstetrics (FIGO) 3-Grade Assessment of the Glandular Component, identifies three grades of endometrial cancer: Grade 1 is well differentiated, composed almost entirely of well-formed glands, and presents less than or equal to 5% solid non-squamous growth pattern; Grade 2 is moderately differentiated and characterized by 6%-50% solid non-squamous growth pattern; Grade 3 which is poorly differentiated and has more than 50% solid non-squamous growth pattern (Creasman et al., 2006; Ellenson et al., 2015); http://purl.obolibrary.org/obo/UBERON_0002074 UBERON http://purl.obolibrary.org/obo/GO_0030154 GO FIGO 3-Grade Assessment Classification of endometrial cancer grades based on the percentage of solid non-squamous growth pattern in the glandular component. ex_vivo endometrium human solid non-squamous growth pattern percentage change low The International federation of Gynecology and Obstetrics (FIGO) 3-Grade Assessment of the Glandular Component, identifies three grades of endometrial cancer: Grade 1 is well differentiated, composed almost entirely of well-formed glands, and presents less than or equal to 5% solid non-squamous growth pattern; Grade 2 is moderately differentiated and characterized by 6%-50% solid non-squamous growth pattern; Grade 3 which is poorly differentiated and has more than 50% solid non-squamous growth pattern http://purl.obolibrary.org/obo/GO_0030198 GO intraoperative ultrasound Intraoperative ultrasound is used during surgery to evaluate myometrial invasion and lymphatic spread of endometrial carcinoma. in_vivo uterus myometrial invasion depth or lymphatic metastasis presence not_specified http://purl.obolibrary.org/obo/UBERON_0001284 UBERON low Other methods like magnetic resonance imaging, positron emission tomography or intraoperative ultrasound or three-dimensional sonography are not indicated for diagnosis but may be useful to gain information about the invasion depth of the myometrium or lymphatic metastases (Brosens et al., 1995; Teefey et al., 1996; Bonilla et al., 1997). http://purl.obolibrary.org/obo/UBERON_0001284 UBERON Magnetic resonance imaging Non-invasive imaging technique to assess myometrial invasion and lymphatic metastases in endometrial cancer. in_vivo uterus myometrium lymph nodes human myometrial invasion depth not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI low Other methods like magnetic resonance imaging, positron emission tomography or intraoperative ultrasound or three-dimensional sonography are not indicated for diagnosis but may be useful to gain information about the invasion depth of the myometrium or lymphatic metastases (Brosens et al., 1995; Teefey et al., 1996; Bonilla et al., 1997). http://purl.obolibrary.org/obo/UBERON_0000058 UBERON http://purl.obolibrary.org/obo/GO_0016197 GO OECD TG 451 Carcinogenicity Study A long-term in vivo study to assess carcinogenic potential, including morphometric examination of uterine gland profiles in histological sections. in_vivo uterus rat mouse number of uterine gland profiles not_specified http://purl.obolibrary.org/obo/OBI_0000469 OBI http://purl.obolibrary.org/obo/UBERON_0002074 UBERON OECD TG 451 low OECD (2018), Test No. 451: Carcinogenicity Studies, OECD Guidelines for the Testing of Chemicals Morphometric examination of the number of uterine gland profiles in representative transverse histological sections stained with the periodic acid-Schiff (PAS) procedure. http://purl.obolibrary.org/obo/UBERON_0002074 UBERON http://purl.obolibrary.org/obo/GO_0048732 GO PAS staining Morphometric examination of the number of uterine gland profiles in representative transverse histological sections using the periodic acid-Schiff (PAS) procedure. in_vivo uterus number of uterine gland profiles change http://purl.obolibrary.org/obo/GO_0008283 GO OECD TG 451 low Morphometric examination of the number of uterine gland profiles in representative transverse histological sections stained with the periodic acid-Schiff (PAS) procedure. http://purl.obolibrary.org/obo/GO_0008283 GO Positron emission tomography Imaging technique to detect metabolic activity and potential metastases in endometrial cancer. in_vivo uterus lymph nodes human metabolic activity of tumors not_specified http://purl.obolibrary.org/obo/GO_0007399 GO low Other methods like magnetic resonance imaging, positron emission tomography or intraoperative ultrasound or three-dimensional sonography are not indicated for diagnosis but may be useful to gain information about the invasion depth of the myometrium or lymphatic metastases (Brosens et al., 1995; Teefey et al., 1996; Bonilla et al., 1997). http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0007399 GO Saline infusion sonography Ultrasound procedure using saline infusion to enhance visualization of endometrial abnormalities. in_vivo endometrium uterus human endometrial abnormalities not_specified http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/DOID_3307 DOID medium Saline infusion sonography and Color Doppler sonography were used to differentiate between endometrial cancer, endometrial hyperplasia, endometriosis, myoma or tamoxifen induced endometrial thickness (Achiron et al., 1995; Widrich et al., 1996). http://purl.obolibrary.org/obo/UBERON_0002372 UBERON http://purl.obolibrary.org/obo/GO_0048626 GO Saline infusion sonography and Color Doppler sonography Sonographic techniques used to differentiate between various endometrial pathologies including cancer, hyperplasia, and endometriosis. in_vivo endometrium human endometrial pathology differentiation change not_specified Saline infusion sonography and Color Doppler sonography were used to differentiate between endometrial cancer, endometrial hyperplasia, endometriosis, myoma or tamoxifen induced endometrial thickness http://purl.obolibrary.org/obo/UBERON_0001045 UBERON http://purl.obolibrary.org/obo/GO_0042258 GO Three-dimensional sonography An advanced ultrasound imaging technique that provides three-dimensional visualization of the endometrium to evaluate the depth of myometrial invasion and detect lymphatic metastases in endometrial cancer. in_vivo endometrium uterus lymph nodes human depth of myometrial invasion and presence of lymphatic metastases change http://purl.obolibrary.org/obo/UBERON_0001249 UBERON low Other methods like magnetic resonance imaging, positron emission tomography or intraoperative ultrasound or three-dimensional sonography are not indicated for diagnosis but may be useful to gain information about the invasion depth of the myometrium or lymphatic metastases (Brosens et al., 1995; Teefey et al., 1996; Bonilla et al., 1997). http://purl.obolibrary.org/obo/UBERON_0001246 UBERON http://purl.obolibrary.org/obo/GO_0001199 GO Transvaginal ultrasound Ultrasonography performed via the vagina for the potential early detection of endometrial carcinomas. in_vivo endometrium human endometrial pathology change not_specified Transvaginal ultrasound may be a potential mean of early detection of endometrial carcinomas http://purl.obolibrary.org/obo/UBERON_0001045 UBERON http://purl.obolibrary.org/obo/GO_0009617 GO Transvaginal ultrasound Imaging technique to assess endometrial thickness and detect potential abnormalities. in_vivo endometrium uterus human endometrial thickness increase http://purl.obolibrary.org/obo/OBI_0000275 OBI high Transvaginal ultrasound may be a potential mean of early detection of endometrial carcinomas, but this measurement alone is not sufficient to define endometrial pathology. http://purl.obolibrary.org/obo/UBERON_0002372 UBERON Immunohistochemistry Method used to visualize and quantify protein levels in tissue sections. ex_vivo protein levels change http://purl.obolibrary.org/obo/GO_0012501 GO low Immunohistochemistry: protein levels (Konings et al., 2018) http://purl.obolibrary.org/obo/GO_0012501 GO Immunohistochemistry Measures SULT1E1 protein levels in tissues using immunohistochemical staining. in_vitro SULT1E1 protein levels not_specified http://purl.obolibrary.org/obo/GO_0032549 GO low Immunohistochemistry: protein levels (Konings et al., 2018) http://purl.obolibrary.org/obo/GO_0010485 GO LC/MS Measures levels of sulphated estrogens and the ratio of conjugated E2 to non-conjugated E2 in tissues or plasma. in_vitro tissue plasma sulphated estrogens levels not_specified http://purl.obolibrary.org/obo/OBI_0000473 OBI medium liquid chromatography/mass spectrometry (LC/MS); LC-MS/MS after chemical or enzymatic hydrolysis and extraction (Borghoff et al., 2016, Wudy et al., 2018). http://purl.obolibrary.org/obo/GO_0008146 GO Northern blotting Measures SULT1E1 mRNA expression levels using Northern blot analysis. in_vitro SULT1E1 mRNA expression not_specified http://purl.obolibrary.org/obo/GO_0010468 GO low qRT-PCRn, Northern blotting: SULT1E1 expression (Konings et al., 2018) http://purl.obolibrary.org/obo/GO_0010468 GO qRT-PCR Measures SULT1E1 gene expression levels using quantitative reverse transcription polymerase chain reaction. in_vitro SULT1E1 gene expression not_specified http://purl.obolibrary.org/obo/GO_0010467 GO medium qRT-PCRn, Northern blotting: SULT1E1 expression (Konings et al., 2018) http://purl.obolibrary.org/obo/GO_0010467 GO QSAR model Computational model to predict potent inhibition of estrogen sulfotransferase. in_silico SULT1E1 inhibition potential not_specified high Computational models for SULTE1 activation and such as QSAR model for E2-SULT inhibition are also used to demonstrate the criteria for potent inhibition of estrogen sulfotransferase (Harju et al., 2007; Gosavi et al., 2013). http://purl.obolibrary.org/obo/GO_0004307 GO Radioimmuno Assay Measures levels of sulphated estrogens or the ratio of conjugated E2 to non-conjugated E2 using radioactive labeled antibodies. in_vitro tissue plasma sulphated estrogens levels not_specified low Radioimmuno Assay (RIA) http://purl.obolibrary.org/obo/GO_0008146 GO Sulfotransferase kinetic assay Measures SULT activity (formation of E2 sulfate) using radiometric assays. in_vitro V79-1E1 Chinese hamster cells HepG2 E2 sulfate formation rate decrease medium Sulfotransferase kinetic assay: radiometric assays (Hempel et al., 2000; Falany et al., 1995) http://purl.obolibrary.org/obo/GO_0006898 GO Sulfotransferase kinetic assay Measures SULT1E1 activity by quantifying the formation of E2 sulfate using radiometric methods. in_vitro V79-1E1 Chinese hamster cells HepG2 cells Salmonella typhimurium Escherichia coli SULT1E1 activity decrease http://purl.obolibrary.org/obo/GO_0004307 GO medium Sulfotransferase kinetic assay: radiometric assays (Hempel et al., 2000; Falany et al., 1995) http://purl.obolibrary.org/obo/GO_0004307 GO 500-MHz proton nuclear magnetic resonance Measures the dissociation constant (Kd) between IAV and sialic acid glycan receptors using NMR spectroscopy. in_vitro dissociation constant (Kd) not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI low 500-MHz proton nuclear magnetic resonance (NMR) http://purl.obolibrary.org/obo/GO_0019062 GO BLI Biolayer interferometry (BLI) was used to measure the dissociation constant (Kd) between purified viruses and human/avian receptors. in_vitro dissociation constant (Kd) not_specified medium Xiong, X., Coombs, P., Martin, S. et al. Receptor binding by a ferret-transmissible H5 avian influenza virus. Nature 497, 392–396 (2013). http://purl.obolibrary.org/obo/GO_0005102 GO carbohydrate microarray Measures the binding of IAV to immobilized sialyl glycans to determine receptor specificity. in_vitro binding specificity not_specified http://purl.obolibrary.org/obo/OBI_0001862 OBI high Carbohydrate microarray http://purl.obolibrary.org/obo/GO_0019062 GO carbohydrate microarray Profiles binding specificity of pandemic and seasonal influenza virus hemagglutinins to 2,6- and 2,3-linked sialyl glycans using a carbohydrate microarray. in_vitro binding to 2,6- and 2,3-linked sialyl glycans change http://www.ebi.ac.uk/efo/EFO_0007988 EFO http://purl.obolibrary.org/obo/GO_0005515 GO high Carbohydrate microarray Pandemic viruses were able to bind both 2,6 and 2,3 linked sialyl glycans while seasonal viruses only bound 2,6 http://www.bioassayontology.org/bao#BAO_0000370 BAO http://purl.obolibrary.org/obo/GO_0005515 GO crystallography Determines the three-dimensional structure of IAV hemagglutinin bound to sialic acid receptors. in_vitro structural features of receptor binding not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI low crystallography http://purl.obolibrary.org/obo/PR_000008858 PR http://purl.obolibrary.org/obo/GO_0019062 GO glycan microarray with scanning ellipsometry sensor Measures the binding of IAV to synthetic glycans using a glycan microarray platform with ellipsometry detection. in_vitro binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0001862 OBI high Glycan microarray with a scanning ellipsometry sensor http://purl.obolibrary.org/obo/GO_0019062 GO HAI Hemagglutination assay (HAI) was used to determine the impact of specific mutations at site 226 in HA on sialic acid linkage binding preference. in_vitro hemagglutination change low Rogers, G., Paulson, J., Daniels, R. et al. Single amino acid substitutions in influenza haemagglutinin change receptor binding specificity. http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0005102 GO hemagglutination assay Measures the ability of IAV to agglutinate red blood cells, indicating binding to sialic acid receptors. in_vitro hemagglutination activity not_specified medium Hemagglutination assay, HAI http://purl.obolibrary.org/obo/GO_0019062 GO Hemagglutination assay (HAI) Assesses the ability of influenza viruses to agglutinate red blood cells, indicating binding to sialic acid receptors and linkage specificity. in_vitro red blood cells Human Avian Equine Receptor binding specificity and linkage preference change low Hemagglutination assay, HAI Specific mutations at site 226 in HA impact sialic acid linkage binding preference Human, avian, and equine H3 Influenza A viruses have different abilities to bind sialic acid (human prefer 2,6, animals prefer 2,3). hemagglutination assay, receptor binding assay using sialylglycopolymers, biolayer interferometry analysis, carbohydrate microarray analysis, crystallography Combines multiple techniques including hemagglutination, sialylglycopolymer binding, BLI, carbohydrate microarray, and crystallography to characterize changes in H5N1 hemagglutinin receptor binding during human infection. in_vitro receptor binding to 2,3-linked sialic acid decrease http://www.bioassayontology.org/bao#BAO_0000371 BAO http://purl.obolibrary.org/obo/GO_0005515 GO http://www.bioassayontology.org/bao#BAO_0000047 BAO low Hemagglutination assay, receptor binding assay using sialylglycopolymers, biolayer interferometry analysis, carbohydrate microarray analysis, crystallography H5N1 infection of human leads to decreased ability to bind 2,3 linked sialic acid http://www.bioassayontology.org/bao#BAO_0000370 BAO http://purl.obolibrary.org/obo/GO_0005515 GO hemagglutination inhibition (HAI) assay Assesses the impact of specific mutations in influenza hemagglutinin on sialic acid linkage binding preference using the hemagglutination inhibition assay. in_vitro sialic acid linkage binding preference change http://www.bioassayontology.org/bao#BAO_0000371 BAO http://purl.obolibrary.org/obo/GO_0005515 GO low Hemagglutination assay, HAI Specific mutations at site 226 in HA impact sialic acid linkage binding preference http://www.bioassayontology.org/bao#BAO_0000370 BAO http://purl.obolibrary.org/obo/GO_0005515 GO microscale thermophoresis Measures the dissociation constant (Kd) between IAV and sialic acid glycan receptors using MST with recombinant HA trimers. in_vitro dissociation constant (Kd) not_specified medium microscale thermophoresis (MST) using recombinant HA trimers http://purl.obolibrary.org/obo/GO_0019062 GO MST Microscale thermophoresis (MST) was used to measure the dissociation constant (Kd) between recombinant HA trimers and human/avian receptors. in_vitro dissociation constant (Kd) not_specified medium Xiong, X., Coombs, P., Martin, S. et al. Receptor binding by a ferret-transmissible H5 avian influenza virus. Nature 497, 392–396 (2013). http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0005102 GO NMR Dissociation constant (Kd) measurement using 500-MHz proton nuclear magnetic resonance (NMR) to assess binding affinity between X-31BHA virus (H3N2) and a(2,3)-Sialyl-lactose. in_vitro dissociation constant (Kd) not_specified low Sauter, N. K. et al. Hemagglutinins from two influenza virus variants bind to sialic acid derivatives with millimolar dissociation constants: a 500-MHz proton nuclear magnetic resonance study. http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0005102 GO solid-phase receptor binding assay Measures the binding of IAV to immobilized receptors to assess receptor binding efficiency. in_vitro receptor binding efficiency not_specified medium Solid-phase receptor binding assay http://purl.obolibrary.org/obo/GO_0019062 GO surface biolayer interferometry Measures the dissociation constant (Kd) between IAV and sialic acid glycan receptors using BLI with purified viruses. in_vitro dissociation constant (Kd) not_specified http://purl.obolibrary.org/obo/OBI_0001939 OBI medium surface biolayer interferometry (BLI) with purified viruses http://purl.obolibrary.org/obo/GO_0019062 GO Colocalization of immunofluorescence Detects colocalization of influenza virus with clathrin-mediated endocytic markers. in_vitro colocalization not_specified http://purl.obolibrary.org/obo/OBI_0000600 OBI http://purl.obolibrary.org/obo/GO_0006898 GO medium Colocalization of immunofluorescence influenza entry via clathrin-mediated pathway http://purl.obolibrary.org/obo/NCBITaxon_11320 NCBITAXON http://purl.obolibrary.org/obo/GO_0006898 GO colocalization of immunofluorescence Uses colocalization of immunofluorescence to show influenza entry via the clathrin-mediated pathway. in_vitro colocalization of viral components with clathrin increase low Colocalization of immunofluorescence influenza entry via clathrin- mediated pathway http://purl.obolibrary.org/obo/GO_0006628 GO Electron microscopy Visualizes virus binding and entry into cells using electron microscopy. Shows virus bound to microvilli, in coated pits, coated vesicles, and large smooth-surfaced vacuoles, indicating endocytosis. in_vitro virus entry pathway not_specified http://purl.obolibrary.org/obo/GO_0006915 GO low Virus was seen bound to microvilli, in coated pits, coated vesicles, and large smooth-surfaced vacuoles, low pH was required for fusion, suggesting entry by endocytosis http://purl.obolibrary.org/obo/GO_0006915 GO Electron microscopy Visualizes virus binding to microvilli, coated pits, coated vesicles, and large smooth-surfaced vacuoles, indicating endocytic entry. in_vitro canine kidney cells virus localization not_specified http://purl.obolibrary.org/obo/OBI_0000218 OBI http://purl.obolibrary.org/obo/GO_0019062 GO low Virus was seen bound to microvilli, in coated pits, coated vesicles, and large smooth-surfaced vacuoles, low pH was required for fusion, suggesting entry by endocytosis http://purl.obolibrary.org/obo/NCBITaxon_11320 NCBITAXON http://purl.obolibrary.org/obo/GO_0006897 GO Flow cytometry Measures IAV cell entry via non-clathrin-dependent routes. in_vitro cell entry efficiency not_specified http://purl.obolibrary.org/obo/GO_0019062 GO high IAV cell entry via non-clathrin dependent route http://purl.obolibrary.org/obo/NCBITaxon_11320 NCBITAXON http://purl.obolibrary.org/obo/GO_0019062 GO flow cytommetry Utilizes flow cytommetry to demonstrate IAV cell entry via a non-clathrin dependent route. in_vitro virus entry change medium Flow cytommetry IAV cell entry via non-clathrin dependent route http://purl.obolibrary.org/obo/GO_0006629 GO Luciferase reporter assay A biochemical assay used to quantify viral entry or infection levels by measuring luciferase enzymatic activity. in_vitro luciferase activity not_specified high Luciferase reporter assay Macropinocytosis is an alternative entry pathway http://purl.obolibrary.org/obo/NCBITaxon_6631 NCBITAXON http://purl.obolibrary.org/obo/GO_0018176 GO luciferase reporter assay Employs a luciferase reporter assay to demonstrate macropinocytosis as an alternative entry pathway for the virus. in_vitro macropinocytosis activity increase medium Luciferase reporter assay Macropinocytosis is an alternative entry pathway http://purl.obolibrary.org/obo/GO_0006627 GO Luciferase reporter assay Measures viral entry via macropinocytosis as an alternative pathway. in_vitro viral entry efficiency not_specified http://purl.obolibrary.org/obo/OBI_0001868 OBI http://purl.obolibrary.org/obo/GO_0044351 GO medium Macropinocytosis is an alternative entry pathway http://purl.obolibrary.org/obo/NCBITaxon_11320 NCBITAXON http://purl.obolibrary.org/obo/GO_0044351 GO Real-time fluorescent microscopy Tracks the assembly of endocytic machinery around individual influenza viruses during entry. in_vitro endocytic machinery assembly not_specified http://purl.obolibrary.org/obo/GO_0006897 GO medium Clathrin-mediated and clathrin- and caveolin-independent endocytic pathways used in parallel with similar efficiency http://purl.obolibrary.org/obo/NCBITaxon_11320 NCBITAXON http://purl.obolibrary.org/obo/GO_0006897 GO real-time fluorescent microscopy Uses real-time fluorescent microscopy to observe clathrin-mediated and clathrin- and caveolin-independent endocytic pathways used in parallel during viral entry. in_vitro endocytic pathway usage change medium Real- time fluorescent microscopy Clathrin-mediated and clathrin- and caveolin-independent endocytic pathways used in parallel with similar efficiency http://purl.obolibrary.org/obo/GO_0006629 GO Real-time fluorescent microscopy Tracks virus entry in real-time using fluorescent microscopy. Determines that clathrin-mediated and clathrin- and caveolin-independent endocytic pathways are used in parallel. in_vitro virus entry pathway not_specified http://purl.obolibrary.org/obo/GO_0006886 GO http://purl.obolibrary.org/obo/GO_0006899 GO low Clathrin-mediated and clathrin- and caveolin-independent endocytic pathways used in parallel with similar efficiency http://purl.obolibrary.org/obo/GO_0006915 GO co-precipitation Identifies protein-protein interactions by precipitating a target protein and its binding partners using specific antibodies. in_vitro protein-protein interaction change http://purl.obolibrary.org/obo/GO_0005515 GO low Expression of reporter gene construct and co-precipitation, fluorescent microscopy, western blot http://purl.obolibrary.org/obo/GO_0005515 GO Co-precipitation and gel shift assay Measures interaction between labeled IAV NS1 protein and CPSF 30kDa protein via co-precipitation and assesses CPSF binding to pre-mRNA using gel shift assay. in_vitro NS1-CPSF 30kDa interaction and CPSF binding to pre-mRNA decrease http://purl.obolibrary.org/obo/GO_0005515 GO http://purl.obolibrary.org/obo/GO_0003723 GO http://www.bioassayontology.org/bao#BAO_0000226 BAO low Co-precipitation and gel shift assay labeled IAV NS1 protein co-precipitated with CPSF 30kDa protein and incubation with NS1 prevented CPSF binding to pre-mRNA for processing http://purl.obolibrary.org/obo/GO_0000387 GO fluorescent microscopy Visualizes the location and distribution of proteins or other molecules in cells using fluorescent labels. in_vitro protein localization change http://purl.obolibrary.org/obo/GO_0008104 GO low Expression of reporter gene construct and co-precipitation, fluorescent microscopy, western blot http://purl.obolibrary.org/obo/GO_0008104 GO gel shift assay Detects protein-DNA or protein-RNA interactions by observing shifts in the electrophoretic mobility of nucleic acids. in_vitro protein-RNA binding change low Co-precipitation and gel shift assay http://purl.obolibrary.org/obo/GO_0006396 GO immunohistochemistry Detection of specific antigens in tissue sections using antibodies. ex_vivo nasal epithelial cells human protein expression change http://purl.obolibrary.org/obo/GO_0010468 GO not_specified RNA (RT-PCR) and protein (Western and immunohistochemistry) expression http://purl.obolibrary.org/obo/GO_0005515 GO immunohistochemistry Detects the presence and location of specific proteins in tissue sections using antibody-based staining. in_vitro human nasal epithelial cells nasal epithelium human protein localization change http://purl.obolibrary.org/obo/GO_0008104 GO low RNA (RT-PCR) and protein (Western and immunohistochemistry) expression http://purl.obolibrary.org/obo/GO_0008104 GO reporter gene assay Measures the activity of a promoter or regulatory sequence by expressing a reporter gene such as luciferase or GFP. in_vitro reporter gene expression change high Expression of reporter gene construct and co-precipitation, fluorescent microscopy, western blot http://purl.obolibrary.org/obo/GO_0045087 GO RT-PCR Measures RNA expression levels of specific genes using reverse transcription and polymerase chain reaction. in_vitro human nasal epithelial cells nasal epithelium human RNA expression change http://purl.obolibrary.org/obo/GO_0010467 GO medium RNA (RT-PCR) and protein (Western and immunohistochemistry) expression http://purl.obolibrary.org/obo/GO_0010467 GO Transfection of reporter genes with RT-qPCR Measures expression of reporter genes driven by different RNA polymerase promoters via transfection followed by RT-qPCR to assess selective degradation of Pol-II transcripts by PA-X. in_vitro Pol-II transcript levels decrease http://www.bioassayontology.org/bao#BAO_0000011 BAO http://purl.obolibrary.org/obo/GO_0034280 GO medium Transfection of reporter genes with different Pol-driven promoters and evaluation of expression by RT-qPCR Selective degradation of Pol-II transcripts by PA-X http://purl.obolibrary.org/obo/GO_0034280 GO Western blot Detects and quantifies specific proteins in a sample using gel electrophoresis and antibody-based detection. in_vitro human nasal epithelial cells nasal epithelium human protein expression change http://purl.obolibrary.org/obo/GO_0010457 GO medium RNA (RT-PCR) and protein (Western and immunohistochemistry) expression http://purl.obolibrary.org/obo/GO_0010457 GO FRET Measures calcium release via Förster Resonance Energy Transfer (FRET) to assess RyR activation. in_vitro calcium release increase http://purl.obolibrary.org/obo/GO_0051209 GO http://purl.obolibrary.org/obo/GO_0022849 GO medium assessment of calcium release (FRET) http://purl.obolibrary.org/obo/PR_00000112 PR http://purl.obolibrary.org/obo/GO_0006816 GO immunofluorescence microscopy Visualization of infected cells, can target specific proteins or processes. in_vitro infected cells increase http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0005607 GO low Immunofluorescence microscopy Visualization of infected cells, can target specific proteins or processes http://purl.obolibrary.org/obo/CL_0000004 CL http://purl.obolibrary.org/obo/GO_0005607 GO Immunofluorescence microscopy Visualization of infected cells, targeting specific proteins or processes related to influenza virus. in_vitro presence of viral proteins increase low Immunofluorescence microscopy: Visualization of infected cells, can target specific proteins or processes In situ hybridization Track localization of RNA viral genomes in cells. in_vitro localization of viral RNA increase low In situ hybridization: Track localization of RNA viral genomes in cells In vitro polyadenylation assay Identify sequences important for polyadenylation in influenza virus RNA. in_vitro polyadenylation activity increase low In vitro polyadenylation assay: Identify sequences important for polyadenylation Northern Blot Analyze differences in splicing efficiencies of influenza virus mRNAs. in_vitro splicing efficiency change low Plasmid expression measured by Northern Blot: Analyze differences in splicing efficiencies Single molecule FRET Detects molecular interactions and conformational changes of influenza virus promoter RNA at the single-molecule level using Förster resonance energy transfer. in_vitro conformational states of influenza virus promoter RNA not_specified http://purl.obolibrary.org/obo/GO_0006351 GO http://purl.obolibrary.org/obo/GO_0019083 GO low Single molecule FRET Molecule- molecule interactions http://purl.obolibrary.org/obo/GO_0019083 GO Single molecule FRET Measure molecule-molecule interactions in influenza virus promoter RNA. in_vitro molecular interactions change low Single molecule FRET: Molecule- molecule interactions Electron microscopy An imaging technique used to visualize the morphological process of viral budding. not_specified budding morphology not_specified http://purl.obolibrary.org/obo/OBI_0000249 OBI low Electron microscopy Visualize budding http://purl.obolibrary.org/obo/GO_0006323 GO Electron microscopy Visualizes the budding of influenza A virus by capturing high-resolution images of viral particles. in_vitro visualization of viral budding not_specified http://purl.obolibrary.org/obo/GO_0019076 GO low Visualize budding Structural analysis of the roles of influenza A virus membrane-associated proteins in assembly and morphology. http://purl.obolibrary.org/obo/GO_0019076 GO Virus-like particles Measures specific contributions of proteins to the viral life cycle by assessing the assembly and budding of plasmid-derived virus-like particles. in_vitro assembly and budding of virus-like particles not_specified http://purl.obolibrary.org/obo/GO_0019064 GO low Measure specific contributions of proteins to the viral life cycle Influenza virus hemagglutinin and neuraminidase, but not the matrix protein, are required for assembly and budding of plasmid-derived virus-like particles. http://purl.obolibrary.org/obo/GO_0019064 GO Virus-like particles formation assay Measures the assembly and budding of plasmid-derived virus-like particles to determine the contributions of specific viral proteins to the viral life cycle. in_vitro human cell lines formation of virus-like particles not_specified http://purl.obolibrary.org/obo/CL_0000000 CL not_specified Measure specific contributions of proteins to the viral life cycle Formation of virus-like particles from human cell lines exclusively expressing influenza neuraminidase. http://purl.obolibrary.org/obo/GO_0006323 GO metabolomics Measures changes in metabolite levels to investigate downstream effects of gene expression. in_vitro metabolite levels change http://purl.obolibrary.org/obo/OBI_0000366 OBI http://purl.obolibrary.org/obo/CHMO_0000009 CHMO high Effects on expression of downstream genes can be investigating using metabolomics and RT-qPCR approaches. http://purl.obolibrary.org/obo/CHEBI_25834 CHEBI http://purl.obolibrary.org/obo/GO_0008152 GO RT-qPCR Measures changes in gene expression levels using reverse transcription quantitative polymerase chain reaction. in_vitro gene expression increase http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000274 OBI medium Effects on expression of downstream genes can be investigating using metabolomics and RT-qPCR approaches. http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO luciferase reporter gene assay A cell-based reporter gene assay that measures RAR receptor transactivation by quantifying the expression of luciferase driven by RARE-containing promoters. in_vitro luciferase expression change http://purl.obolibrary.org/obo/OBI_0000144 OBI not_specified RAR receptor transactivation can be measured indirectly by using cell-based reporter gene assays. Expression of luciferase and β-galactosidase reporters driven by RARE-containing promoters have been employed RAR reporter gene assay Measures RAR receptor transactivation using luciferase or β-galactosidase reporters driven by RARE-containing promoters. in_vitro RAR receptor transactivation increase http://purl.obolibrary.org/obo/OBI_0000424 OBI medium RAR receptor transactivation can be measured indirectly by using cell-based reporter gene assays. Expression of luciferase and β-galactosidase reporters driven by RARE-containing promoters have been employed RAR reporter assays are commercially available (e.g. INDIGO Biosciences) http://purl.obolibrary.org/obo/PR_000001319 PR http://purl.obolibrary.org/obo/GO_0006351 GO reporter gene assay RAR receptor transactivation is measured indirectly using cell-based reporter gene assays. These assays use luciferase and β-galactosidase reporters driven by RARE-containing promoters. in_vitro reporter gene expression increase http://purl.obolibrary.org/obo/GO_0006950 GO medium RAR receptor transactivation can be measured indirectly by using cell-based reporter gene assays. Expression of luciferase and β-galactosidase reporters driven by RARE-containing promoters have been employed RAR reporter assays are commercially available (e.g. INDIGO Biosciences). http://purl.obolibrary.org/obo/GO_0005102 GO β-galactosidase reporter gene assay A cell-based reporter gene assay that measures RAR receptor transactivation by quantifying the expression of β-galactosidase driven by RARE-containing promoters. in_vitro β-galactosidase expression change http://purl.obolibrary.org/obo/OBI_0000144 OBI not_specified Expression of luciferase and β-galactosidase reporters driven by RARE-containing promoters have been employed ELISA The protein amount of individual Cdks, cyclins, as well as their phosphorylated forms can be detected using enzyme-linked immunosorbent assays (ELISAs). in_vitro protein amount of Cdks and cyclins change medium as well as through enzyme-linked immunosorbent assays (ELISAs) http://purl.obolibrary.org/obo/GO_0006457 GO ELISA Detects the protein amount of individual Cdks, cyclins, and their phosphorylated forms using enzyme-linked immunosorbent assay. in_vitro protein expression level not_specified http://purl.obolibrary.org/obo/GO_0010457 GO http://purl.obolibrary.org/obo/GO_0004323 GO http://purl.obolibrary.org/obo/GO_0004693 GO medium using immunodetection methods such as western blotting or enzyme-linked immunosorbent assays (ELISAs) http://purl.obolibrary.org/obo/GO_0007049 GO mass spectrometry The protein amount of individual Cdks, cyclins, as well as their phosphorylated forms can be detected using mass spectrometric approaches. in_vitro protein amount of Cdks and cyclins change medium as well as through mass spectrometric approaches http://purl.obolibrary.org/obo/GO_0006457 GO mass spectrometry Detects the protein amount of individual Cdks, cyclins, and their phosphorylated forms using mass spectrometric approaches. in_vitro protein expression level not_specified http://purl.obolibrary.org/obo/GO_0010457 GO http://purl.obolibrary.org/obo/GO_0004323 GO http://purl.obolibrary.org/obo/GO_0004693 GO medium through mass spectrometric approaches http://purl.obolibrary.org/obo/GO_0007049 GO microarray Microarray provides a global analysis of the transcript levels of cyclins and Cdks across the cell cycle. in_vitro global transcript levels of cyclins and Cdks change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/CHEBI_33697 CHEBI high in the context of a more global analysis using microarray or RNAseq methods http://purl.obolibrary.org/obo/GO_0010467 GO microarray Measures the mRNA content of cyclins and Cdks in a global analysis using microarray technology. in_vitro mRNA expression level not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0004323 GO http://purl.obolibrary.org/obo/GO_0004693 GO high in the context of a more global analysis using microarray http://purl.obolibrary.org/obo/GO_0007049 GO qPCR The mRNA content of specific cyclins and Cdks can be measured using qPCR. in_vitro mRNA content of cyclins and Cdks change medium The mRNA content of specific cyclins and Cdks can be measured using qPCR http://purl.obolibrary.org/obo/GO_0010468 GO qPCR Measures the mRNA content of specific cyclins and Cdks using quantitative polymerase chain reaction. in_vitro mRNA expression level not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0004323 GO http://purl.obolibrary.org/obo/GO_0004693 GO medium The mRNA content of specific cyclins and Cdks can be measured using qPCR http://purl.obolibrary.org/obo/GO_0007049 GO RNAseq Measures the mRNA content of cyclins and Cdks in a global analysis using RNA sequencing. in_vitro mRNA expression level not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0004323 GO http://purl.obolibrary.org/obo/GO_0004693 GO high using microarray or RNAseq methods http://purl.obolibrary.org/obo/GO_0007049 GO RNAseq RNA sequencing provides a global analysis of the mRNA content of specific cyclins and Cdks at various phases of the cell cycle. in_vitro mRNA expression levels of cyclins and Cdks change not_specified The mRNA content of specific cyclins and Cdks can be measured using ... RNAseq methods http://purl.obolibrary.org/obo/OBI_0100096 OBI http://purl.obolibrary.org/obo/GO_0010467 GO western blot The protein amount of individual Cdks, cyclins, as well as their phosphorylated forms can be detected using immunodetection methods such as western blotting. in_vitro protein amount of Cdks and cyclins change low The protein amount of individual Cdks, cyclins, as well as their phosphorylated forms can be detected using immunodetection methods such as western blotting http://purl.obolibrary.org/obo/GO_0006457 GO western blot Detects the protein amount of individual Cdks, cyclins, and their phosphorylated forms using immunodetection. in_vitro protein expression level not_specified http://purl.obolibrary.org/obo/GO_0010457 GO http://purl.obolibrary.org/obo/GO_0004323 GO http://purl.obolibrary.org/obo/GO_0004693 GO low The protein amount of individual Cdks, cyclins, as well as their phosphorylated forms can be detected using immunodetection methods such as western blotting http://purl.obolibrary.org/obo/GO_0007049 GO 3H-thymidine incorporation Measures cell proliferation by quantifying the incorporation of tritiated thymidine into newly synthesized DNA, detected via autoradiography or scintillation techniques. in_vitro neural progenitor cells cortex DNA synthesis decrease http://purl.obolibrary.org/obo/GO_0071897 GO http://purl.obolibrary.org/obo/GO_0008283 GO medium Incorporation of thymidine analogues tritiated thymidine (3H-thymidine) These thymidine analogues can be detected by autoradiography or scintillation techniques (3H-thymidine) http://purl.obolibrary.org/obo/CL_0000081 CL http://purl.obolibrary.org/obo/GO_0006260 GO BrdU immunostaining This assay measures cell proliferation by detecting bromodeoxyuridine (BrdU) incorporated into newly synthesised DNA via immunofluorescence. in_vitro neural progenitor cells cortex amount of BrdU detected increase http://purl.obolibrary.org/obo/GO_0006260 GO http://purl.obolibrary.org/obo/GO_0008283 GO medium These thymidine analogues can be detected by ... immunofluorescence (BrdU) http://purl.obolibrary.org/obo/CHEBI_0001347 CHEBI http://purl.obolibrary.org/obo/GO_0006260 GO immunostaining/flow cytometry of cell cycle proteins Detects expression of cell cycle regulators such as Ki-67, PCNA, MCM2, and PH3 using immunostaining or flow cytometry to assess proliferating neural progenitor cells. not_specified neural progenitor cells expression of cell cycle proteins change not_specified 2. Immunostaining or flow cytometric analysis of proteins associated with the cell cycle, such as cell cycle regulators or proteins with important functions during mitosis. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0007049 GO in-situ hybridization Measures cell proliferation by quantifying mRNA transcripts of cycling neural progenitor cell markers via in-situ hybridization techniques. in_vitro neural progenitor cells cortex mRNA expression of cycling markers decrease http://purl.obolibrary.org/obo/GO_0008283 GO low In-situ hybridization (ISH) techniques can be applied to quantify mRNA transcripts of various markers of cycling NPCs http://purl.obolibrary.org/obo/CL_0000081 CL http://purl.obolibrary.org/obo/GO_0007049 GO In-situ hybridization (ISH) This assay measures cell proliferation by quantifying mRNA transcripts of various markers of cycling NPCs. in_vitro neural progenitor cells cortex mRNA transcript levels increase http://purl.obolibrary.org/obo/GO_0008283 GO medium In-situ hybridization (ISH) techniques can be applied to quantify mRNA transcripts of various markers of cycling NPCs http://purl.obolibrary.org/obo/CHEBI_0001322 CHEBI http://purl.obolibrary.org/obo/GO_0008283 GO Ki-67 immunostaining Measures cell proliferation by detecting the nuclear protein Ki-67, expressed in all active phases of the cell cycle except G0, via immunofluorescence. in_vitro neural progenitor cells cortex Ki-67 expression decrease http://purl.obolibrary.org/obo/PR_000031250 PR http://purl.obolibrary.org/obo/GO_0008283 GO medium Ki-67 is a nuclear protein expressed in actively dividing cells during all phases of the cell cycle, except for the resting phase (G0) Immunofluorescent imaging of Ki-67 can be used to identify and quantify proliferating NPCs http://purl.obolibrary.org/obo/CL_0000081 CL http://purl.obolibrary.org/obo/GO_0007049 GO MCM2 immunostaining Measures cell proliferation by detecting minichromosome maintenance protein 2 (MCM2), part of the DNA replication initiation complex, via immunofluorescence. in_vitro neural progenitor cells cortex MCM2 expression decrease http://purl.obolibrary.org/obo/PR_000010381 PR http://purl.obolibrary.org/obo/GO_0008283 GO medium Minichromosome maintenance protein 2 (MCM2) is part of the DNA replication initiation complex and is expressed throughout the cell cycle MCM2 can be detected in developing and adult NPCs http://purl.obolibrary.org/obo/CL_0000081 CL http://purl.obolibrary.org/obo/GO_0006270 GO PCNA immunostaining Measures cell proliferation by detecting proliferating cell nuclear antigen (PCNA), a component of DNA replication and repair, via immunofluorescence. in_vitro neural progenitor cells cortex PCNA expression decrease http://purl.obolibrary.org/obo/PR_000012802 PR http://purl.obolibrary.org/obo/GO_0008283 GO medium Proliferating cell nuclear antigen (PCNA) is an important component for DNA replication and repair, and is present throughout the cell cycle PCNA immunofluorescence can be used to assess proliferating NPCs http://purl.obolibrary.org/obo/CL_0000081 CL http://purl.obolibrary.org/obo/GO_0006260 GO PH3 immunostaining Measures cell proliferation by detecting phosphohistone H3 (PH3), present during G2 and M phases of the cell cycle, via immunofluorescence. in_vitro neural progenitor cells cortex PH3 expression decrease http://purl.obolibrary.org/obo/PR_000002084 PR http://purl.obolibrary.org/obo/GO_0008283 GO medium Phosphohistone H3 (PH3) is present during the G2 and M phases of cell division has been employed to measure NPC proliferation http://purl.obolibrary.org/obo/CL_0000081 CL http://purl.obolibrary.org/obo/GO_0007088 GO thymidine analogue incorporation Measures cell proliferation by quantifying the incorporation of nucleoside analogues (3H-thymidine, BrdU, or EdU) into newly synthesized DNA during the S phase. in_vitro neural progenitor cells nucleoside analogue incorporation not_specified http://purl.obolibrary.org/obo/GO_0008283 GO http://purl.obolibrary.org/obo/GO_0006260 GO not_specified During this process, the nucleoside subunits inserted into the newly synthesised DNA can be labelled and quantified, thus providing a means to measure cell proliferation. This is typically done by using various analogues of the nucleoside thymidine, such as tritiated thymidine (3H-thymidine), bromodeoxyuridine (BrdU) or 5-ethynyl-2'-deoxyuridine (EdU) http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO time-lapse imaging Measures cell proliferation by tracking neural progenitor cells over time using live-cell imaging techniques to assess proliferation rates and patterns. in_vitro neural progenitor cells cortex cell division rate decrease http://purl.obolibrary.org/obo/GO_0008283 GO low Time-lapse Imaging: Live-cell imaging techniques allow tracking of neural progenitor cells over time and assessment of their proliferation rates and patterns http://purl.obolibrary.org/obo/CL_0000081 CL http://purl.obolibrary.org/obo/GO_0051301 GO time-lapse imaging Live-cell imaging technique used to track neural progenitor cells over time to assess proliferation rates and patterns. in_vitro neural progenitor cells proliferation rates and patterns not_specified http://purl.obolibrary.org/obo/GO_0008283 GO low Live-cell imaging techniques allow tracking of neural progenitor cells over time and assessment of their proliferation rates and patterns http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008283 GO electron energy loss analysis Electron Energy Loss Analysis allows the study of very small volumes, less than 500 A in diameter. not_specified elemental composition not_specified not_specified electron energy loss analysis Electron Energy Loss Analysis makes possible the study of very small volumes, less than 500 A in diameter secondary ion emission Secondary Ion Mass Analysis permits the study of elements at low and even trace element concentration, including light elements such as hydrogen and beryllium. not_specified elemental composition not_specified not_specified secondary ion emission Analysis by secondary ion emission permits the study of elements at low and even trace element concentration, and even the lightest elements such as hydrogen and beryllium are detected secondary ion emission Also known as Secondary Ion Mass Analysis (SIMS), this method permits the study of elements at low and even trace concentrations, including light elements. not_specified trace element concentration not_specified http://purl.obolibrary.org/obo/CHMO_0000025 CHMO not_specified secondary ion emission Analysis by secondary ion emission permits the study of elements at low and even trace element concentration, and even the lightest elements such as hydrogen and beryllium are detected. X-ray emission X-ray microanalysis is used to analyze elements, though it has relatively low sensitivity and cannot analyze light elements. not_specified elemental composition not_specified not_specified X-ray emission X-ray microanalysis is the most used method, many biological problems cannot be solved because of its relatively low sensitivity and inability to analyze light elements X-ray microanalysis A method for elemental analysis in biological samples, providing information on the distribution and concentration of elements within cells or tissues. in_vitro elemental concentration change not_specified Methods include X-ray emission, secondary ion emission and electron energy loss analysis. Although X-ray microanalysis is the most used method, many biological problems cannot be solved because of its relatively low sensitivity and inability to analyze light elements. Annexin-V PI staining Measures apoptosis in cells by detecting phosphatidylserine exposure and membrane integrity using fluorescent dyes. in_vitro germinal epithelium cells Leydig cells testis apoptotic cells increase http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/GO_0005623 GO medium Annexin-V PI staining http://purl.obolibrary.org/obo/GO_0005623 GO http://purl.obolibrary.org/obo/GO_0006915 GO Spectrophotometric hemoglobin assay Quantifies hemoglobin concentration in blood or tissue samples using spectrophotometry. in_vitro testis blood vessels hemoglobin concentration not_specified http://purl.obolibrary.org/obo/PR_000008940 PR http://purl.obolibrary.org/obo/OBI_0000218 OBI high Spectrophotometric hemoglobin assay http://purl.obolibrary.org/obo/PR_000008940 PR http://purl.obolibrary.org/obo/GO_0006709 GO TGF-β gene expression This assay measures the expression levels of TGF-β-dependent genes, typically using techniques like RT-PCR or qPCR. It assesses the activation of the TGF-β signaling pathway. in_vitro testis TGF-β gene expression increase medium TGF-β-dependent gene expression http://purl.obolibrary.org/obo/GO_0008273 GO TGF-β-dependent gene expression Measures the expression of genes regulated by TGF-β signaling, often using techniques like qPCR or RNA-seq. in_vitro Leydig cells germinal epithelium cells testis gene expression levels not_specified http://purl.obolibrary.org/obo/GO_0007179 GO http://purl.obolibrary.org/obo/GO_0010467 GO medium TGF-β-dependent gene expression http://purl.obolibrary.org/obo/GO_0000786 GO http://purl.obolibrary.org/obo/GO_0007179 GO histological examination Detects failure of the epididymis to develop and other abnormalities in the epididymis and surrounding reproductive tissue through microscopic tissue analysis. in_vivo epididymis reproductive tissue presence or absence of epididymal agenesis and other abnormalities not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI http://purl.obolibrary.org/obo/UBERON_0000957 UBERON http://purl.obolibrary.org/obo/UBERON_0000474 UBERON low Histological observations are required to detect failure for the epididymis to develop, as well as other abnormalities with the epididymis and surrounding reproductive tissue. http://purl.obolibrary.org/obo/UBERON_0000957 UBERON http://purl.obolibrary.org/obo/GO_0032502 GO histology Histological examination is used to detect the failure of the epididymis to develop and other abnormalities in the epididymis and surrounding reproductive tissue. in_vivo epididymis reproductive tissue epididymal development and morphology change low Histological observations are required to detect failure for the epididymis to develop, as well as other abnormalities with the epididymis and surrounding reproductive tissue. http://purl.obolibrary.org/obo/UBERON_0004834 UBERON http://purl.obolibrary.org/obo/GO_0008533 GO organ weight measurement Measures the weight of the epididymis, with lower weight suggesting potential developmental issues. in_vivo epididymis organ weight decrease http://purl.obolibrary.org/obo/UBERON_0000957 UBERON medium Lower organ weight is suggestive that problems may be present but not a substitute for histological examination. http://purl.obolibrary.org/obo/UBERON_0000957 UBERON http://purl.obolibrary.org/obo/GO_0032502 GO histological observation Detects failure of urethral development and other abnormalities in the urethra and surrounding reproductive tissue. in_vivo urethra reproductive tissue urethral tube closure not_specified http://purl.obolibrary.org/obo/UBERON_0000057 UBERON low Histological observations are required to detect failure for the urethra to develop, as well as other abnormalities with the urethra and surrounding reproductive tissue. http://purl.obolibrary.org/obo/UBERON_0000057 UBERON histology Histological observations are used to detect failure of the urethra to develop and other abnormalities in the urethra and surrounding reproductive tissue. in_vivo urethra reproductive tissue urethral development and abnormalities change low Histological observations are required to detect failure for the urethra to develop, as well as other abnormalities with the urethra and surrounding reproductive tissue. http://purl.obolibrary.org/obo/UBERON_0004739 UBERON http://purl.obolibrary.org/obo/GO_0048766 GO enzyme immunoassay Measures changes in INSL3 protein levels. in_vitro INSL3 protein levels decrease http://purl.obolibrary.org/obo/GO_0032553 GO medium protein (via Western blotting or enzyme immunoassays) http://purl.obolibrary.org/obo/GO_0032553 GO enzyme immunoassay This assay measures INSL3 levels by quantifying protein levels using enzyme immunoassays. in_vitro protein levels decrease medium INSL3 is measured by … protein (via enzyme immunoassays) real time PCR This assay measures INSL3 levels by quantifying changes in gene expression using real time PCR. in_vitro gene expression decrease medium INSL3 is measured by changes in gene expression (via real time PCR) http://purl.obolibrary.org/obo/GO_0010468 GO real time PCR Measures changes in INSL3 gene expression levels. in_vitro INSL3 gene expression decrease http://purl.obolibrary.org/obo/GO_0010467 GO medium INSL3 is measured by changes in gene expression (via real time PCR) http://purl.obolibrary.org/obo/GO_0010467 GO western blot This assay measures INSL3 levels by quantifying protein levels using Western blotting. in_vitro protein levels decrease low INSL3 is measured by … protein (via Western blotting) Western blotting Measures changes in INSL3 protein levels. in_vitro INSL3 protein levels decrease http://purl.obolibrary.org/obo/GO_0032553 GO low protein (via Western blotting) http://purl.obolibrary.org/obo/GO_0032553 GO proteomics Measures the proteome-wide abundance of proteins, enabling detection of ligand-induced alterations in protein expression within the PPAR signaling network. not_specified protein abundance levels (proteome) change http://purl.obolibrary.org/obo/GO_0019538 GO not_specified Targeted gene expression assays along with “omic” tools such as transcriptomics or proteomics can be used to determine if known or suspected ligands of the PPAR isoforms disrupt gene expression in the PPAR pathway. http://purl.obolibrary.org/obo/GO_0010467 GO proteomics Large-scale study of proteins to detect changes in protein expression or function within the PPAR signaling network. not_specified protein expression or function change http://purl.obolibrary.org/obo/GO_0016591 GO http://purl.obolibrary.org/obo/GO_0010457 GO high Targeted gene expression assays along with “omic” tools such as transcriptomics or proteomics can be used to determine if known or suspected ligands of the PPAR isoforms disrupt gene expression in the PPAR pathway. http://purl.obolibrary.org/obo/GO_0032369 GO targeted gene expression assay Measures the expression levels of specific genes within the PPAR signaling pathway, typically using quantitative PCR or similar methods, to detect ligand-induced alterations. not_specified expression levels of specific PPAR pathway genes change http://purl.obolibrary.org/obo/GO_0010467 GO not_specified Targeted gene expression assays along with “omic” tools such as transcriptomics or proteomics can be used to determine if known or suspected ligands of the PPAR isoforms disrupt gene expression in the PPAR pathway. http://purl.obolibrary.org/obo/GO_0010467 GO targeted gene expression assay Measures the expression levels of specific genes within the PPAR signaling network to detect disruptions. not_specified gene expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0032369 GO not_specified Targeted gene expression assays along with “omic” tools such as transcriptomics or proteomics can be used to determine if known or suspected ligands of the PPAR isoforms disrupt gene expression in the PPAR pathway. http://purl.obolibrary.org/obo/GO_0032369 GO Gene expression analysis Reveals disruptions in key genes responsible for proper lipid storage and transport using targeted or global gene expression analyses. in_vitro liver gene expression levels change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0006869 GO medium targeted or global gene expression analyses can reveal disruptions in key genes responsible for proper lipid storage and transport http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0019915 GO gene expression analysis Measures mRNA levels of genes involved in lipid storage and transport, either targeted panels or genome-wide, to detect transcriptional disruptions associated with lipid homeostasis. not_specified liver gene expression levels (mRNA) of lipid metabolism genes not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0006629 GO not_specified targeted or global gene expression analyses can reveal disruptions in key genes responsible for proper lipid storage and transport http://purl.obolibrary.org/obo/GO_0006629 GO Histopathology Confirms lipid deposits in liver sections through microscopic examination. in_vivo liver lipid deposits increase http://purl.obolibrary.org/obo/GO_0005811 GO http://purl.obolibrary.org/obo/UBERON_0002107 UBERON low histopathology can confirm lipid deposits in liver sections http://purl.obolibrary.org/obo/GO_0005811 GO http://purl.obolibrary.org/obo/GO_0019915 GO lipidomics Direct or global measurement of fatty acids and lipid species to quantify lipid storage. in_vitro liver cells liver fatty acids and other lipid species change http://purl.obolibrary.org/obo/CHEBI_24430 CHEBI not_specified Fatty acids and other lipid species can be measure directly or measured globally using lipidomic methodologies http://purl.obolibrary.org/obo/CHEBI_24430 CHEBI http://purl.obolibrary.org/obo/GO_0005523 GO Lipidomics Measures fatty acids and other lipid species directly or globally using lipidomic methodologies. in_vitro liver lipid species levels change http://purl.obolibrary.org/obo/GO_0019915 GO http://purl.obolibrary.org/obo/CHEBI_15841 CHEBI high Fatty acids and other lipid species can be measure directly or measured globally using lipidomic methodologies http://purl.obolibrary.org/obo/GO_0005811 GO http://purl.obolibrary.org/obo/GO_0019915 GO affinity assay Biochemical assay to assess the affinity of ligands for PPAR isoforms. in_vitro binding affinity of ligands to PPAR isoforms change http://purl.obolibrary.org/obo/GO_0005488 GO medium affinity assays assess the affinity and location of binding by known or potential ligands to the PPAR isoforms http://purl.obolibrary.org/obo/GO_0005488 GO affinity assay Assesses the affinity of known or potential ligands to PPAR isoforms. in_vitro ligand binding affinity not_specified http://purl.obolibrary.org/obo/OBI_0000471 OBI http://purl.obolibrary.org/obo/GO_0035370 GO medium affinity assays [...] can all be used to assess the affinity and location of binding by known or potential ligands to the PPAR isoforms http://purl.obolibrary.org/obo/PR_000001274 PR http://purl.obolibrary.org/obo/GO_0008034 GO in silico analysis In silico analyses are used as a screening tool to determine if a molecule can bind to PPAR isoforms. in_silico binding affinity change http://purl.obolibrary.org/obo/GO_0005694 GO high In silico analyses are a powerful screening tool to determine if a molecule of interest may be able to bind to one or more of the PPAR isoforms http://purl.obolibrary.org/obo/GO_0005694 GO in silico analysis Screens molecules for potential binding to PPAR isoforms. in_silico predicted ligand binding not_specified http://purl.obolibrary.org/obo/OBI_0001823 OBI high In silico analyses are a powerful screening tool to determine if a molecule of interest may be able to bind to one or more of the PPAR isoforms in silico primary analyses coupled with confirmation steps using cell-based report assays and x-ray crystallography for PPAR isoforms http://purl.obolibrary.org/obo/PR_000001274 PR http://purl.obolibrary.org/obo/GO_0008034 GO nuclear signaling assay Determines if a potential ligand acts as an agonist or antagonist for PPAR isoforms. in_vitro ligand activity (agonist/antagonist) not_specified http://purl.obolibrary.org/obo/GO_0035370 GO medium Nuclear signaling assays can be used to determine if a potential ligand of interest acts as an agonists or antagonists. http://purl.obolibrary.org/obo/PR_000001274 PR http://purl.obolibrary.org/obo/GO_0090597 GO Nuclear signaling assay Nuclear signaling assays measure the transcriptional activity of PPAR isoforms to determine whether a ligand acts as an agonist or antagonist. in_vitro PPAR isoform transcriptional activity change http://purl.obolibrary.org/obo/GO_0001071 GO not_specified Nuclear signaling assays can be used to determine if a potential ligand of interest acts as an agonists or antagonists. Nuclear signaling assays, affinity assays, x-ray crystallography, and in silico analyses can all be used to assess the affinity and location of binding by known or potential ligands to the PPAR isoforms http://purl.obolibrary.org/obo/GO_0006355 GO x-ray crystallography Confirms the binding location of ligands to PPAR isoforms. in_vitro ligand binding site not_specified http://purl.obolibrary.org/obo/OBI_0000378 OBI http://purl.obolibrary.org/obo/GO_0030234 GO low confirmation of binding location should be done via x-ray crystallography x-ray crystallography for PPAR isoforms http://purl.obolibrary.org/obo/PR_000001274 PR http://purl.obolibrary.org/obo/GO_0008034 GO activity assay These assays measure PPAR isoform signaling activity, determining if a ligand acts as an agonist or antagonist. in_vitro PPAR isoform signaling activity change not_specified Activity assays, nuclear signaling assays, and transcriptomic or proteomic analyses can identify disrupted nuclear signaling as the result of ligand binding to PPAR isoforms (Kojo et al. 2003; Li et al. 2017; Gao et al. 2020; Murase et al. 2023; Ardenkjær-Skinnerup et al. 2024). Activity assays These assays determine if a potential ligand acts as an agonist or antagonist via direct measurement of ligand binding activity to PPAR isoforms. in_vitro ligand binding activity not_specified http://purl.obolibrary.org/obo/GO_0005488 GO http://purl.obolibrary.org/obo/GO_0032369 GO not_specified Activity assays, nuclear signaling assays, and transcriptomic or proteomic analyses can identify disrupted nuclear signaling as the result of ligand binding to PPAR isoforms http://purl.obolibrary.org/obo/GO_0007219 GO nuclear signaling assay Assesses the translocation or transcriptional activity of PPAR isoforms within the nucleus, often using immunofluorescence or subcellular fractionation followed by activity read‑outs. not_specified PPAR isoform nuclear signaling change not_specified nuclear signaling assays Nuclear signaling assays These assays measure the disruption of nuclear signaling pathways downstream of PPAR isoform activation or inhibition. in_vitro nuclear signaling pathway activity not_specified http://purl.obolibrary.org/obo/GO_0007219 GO http://purl.obolibrary.org/obo/GO_0032369 GO not_specified Activity assays, nuclear signaling assays, and transcriptomic or proteomic analyses can identify disrupted nuclear signaling as the result of ligand binding to PPAR isoforms http://purl.obolibrary.org/obo/GO_0007219 GO proteomic analysis Measures global protein abundance or post‑translational modifications to identify changes in PPAR‑associated proteins after ligand treatment. not_specified protein abundance of PPAR‑related proteins change not_specified transcriptomic or proteomic analyses proteomic analysis These analyses can identify disrupted nuclear signaling as the result of ligand binding to PPAR isoforms. in_vitro protein levels change medium Activity assays, nuclear signaling assays, and transcriptomic or proteomic analyses can identify disrupted nuclear signaling as the result of ligand binding to PPAR isoforms (Kojo et al. 2003; Li et al. 2017; Gao et al. 2020; Murase et al. 2023; Ardenkjær-Skinnerup et al. 2024). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006457 GO Transcriptomic analyses These assays analyze gene expression changes in PPAR isoform pathways to infer disrupted nuclear signaling. in_vitro gene expression changes not_specified http://purl.obolibrary.org/obo/GO_0005667 GO http://purl.obolibrary.org/obo/GO_0010467 GO high analysis of gene targets in the PPAR isoform pathways http://purl.obolibrary.org/obo/GO_0006351 GO transcriptomic analysis These analyses can identify disrupted nuclear signaling as the result of ligand binding to PPAR isoforms by analyzing gene targets in the PPAR isoform pathways. in_vitro gene expression levels of PPAR isoform targets change medium Activity assays, nuclear signaling assays, and transcriptomic or proteomic analyses can identify disrupted nuclear signaling as the result of ligand binding to PPAR isoforms (Kojo et al. 2003; Li et al. 2017; Gao et al. 2020; Murase et al. 2023; Ardenkjær-Skinnerup et al. 2024). http://purl.obolibrary.org/obo/GO_0006925 GO enzyme assay Measures sodium concentrations using enzyme assays. in_vitro sodium concentration not_specified http://purl.obolibrary.org/obo/CHEBI_29105 CHEBI http://purl.obolibrary.org/obo/OBI_0000269 OBI medium Sodium concentrations can be measured via ... enzyme assays flux chamber assay Measures the rate of sodium uptake into gills based on the change in measured concentrations in the experimental chamber. ex_vivo gills sodium uptake rate decrease http://purl.obolibrary.org/obo/CHEBI_29105 CHEBI http://purl.obolibrary.org/obo/UBERON_0002535 UBERON low Flux chambers can be used to measure the rate of sodium uptake into gills based on the change in measured concentrations in the experimental chamber http://purl.obolibrary.org/obo/UBERON_0002535 UBERON http://purl.obolibrary.org/obo/GO_0006814 GO ion chromatography Measures sodium concentrations using ion chromatography. in_vitro sodium concentration not_specified http://purl.obolibrary.org/obo/CHEBI_29105 CHEBI http://purl.obolibrary.org/obo/OBI_0000215 OBI medium Sodium concentrations can be measured via ion chromatography spectrophotometry Measures sodium concentrations using spectrophotometry. in_vitro sodium concentration not_specified http://purl.obolibrary.org/obo/CHEBI_29105 CHEBI medium Sodium concentrations can be measured via ... spectrophotometry enzyme assay Measures sodium concentrations in plasma using enzyme assays. in_vitro plasma sodium concentration decrease http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/UBERON_0001969 UBERON medium Sodium concentrations in plasma can be measured via enzyme assays http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0050801 GO ion chromatography Measures sodium concentrations in plasma using ion chromatography. in_vitro plasma sodium concentration decrease http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/CHMO_0000015 CHMO medium Sodium concentrations in plasma can be measured via ion chromatography http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0050801 GO spectrophotometry Measures sodium concentrations in plasma using spectrophotometry. in_vitro plasma sodium concentration decrease http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/OBI_0001047 OBI medium Sodium concentrations in plasma can be measured via spectrophotometry http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0050801 GO Hematocrit test A hematocrit test measures the proportion of red blood cells in whole blood, which contributes to blood viscosity. in_vitro hematocrit increase not_specified A hematocrit test can measure the proportion of red blood cells in blood. hematocrit test Measures the proportion of red blood cells in blood. in_vitro blood proportion of red blood cells not_specified not_specified A hematocrit test can measure the proportion of red blood cells in blood. http://purl.obolibrary.org/obo/CL_0000232 CL http://purl.obolibrary.org/obo/GO_0034455 GO viscometer Measures blood viscosity using a viscometer, reported in centipoise (CP) or millipascal-second (mPA•s) units. in_vitro blood blood viscosity increase not_specified Viscosity can be measured using a viscometer (Lee et al. 2012) and is often reported in centipoise (CP) units, which is equivalent to millipascal-second (mPA•s; mPa•sec). http://purl.obolibrary.org/obo/UBERON_0000178 UBERON http://purl.obolibrary.org/obo/GO_0008015 GO blood pressure measurement Measures the force of blood against the walls of the arteries. in_vivo heart blood vessels blood pressure increase http://purl.obolibrary.org/obo/GO_0008015 GO http://www.ebi.ac.uk/efo/EFO_0004445 EFO medium increased blood pressure http://purl.obolibrary.org/obo/UBERON_0001087 UBERON http://purl.obolibrary.org/obo/GO_0003013 GO heart rate measurement Measures the number of heartbeats per unit of time. in_vivo heart heart rate increase http://purl.obolibrary.org/obo/GO_0002151 GO http://www.ebi.ac.uk/efo/EFO_0004368 EFO medium increased heart rate http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO stroke volume measurement Measures the volume of blood pumped per heartbeat. in_vivo heart stroke volume decrease http://purl.obolibrary.org/obo/GO_0002026 GO http://www.ebi.ac.uk/efo/EFO_0004446 EFO medium decreased stroke volume http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0003013 GO Drebrin immunocytochemistry Measures the number of drebrin clusters in cells. in_vitro number of drebrin clusters not_specified not_specified Drebrin immunocytochemistry can be used to measure the number of drebrin clusters. http://purl.obolibrary.org/obo/GO_0061024 GO cAMP-Glo™ Assay Monitors the level of intracellular cAMP in the cell with receptors that are modulated by lipid and free fatty acid agonists. in_vitro intracellular cAMP levels increase http://purl.obolibrary.org/obo/CHEBI_17761 CHEBI high Monitors the level of intracellular cAMP in the cell with receptors that are modulated by lipid and free fatty acid agonists. http://purl.obolibrary.org/obo/CHEBI_17761 CHEBI http://purl.obolibrary.org/obo/GO_0019933 GO Chromatin immunoprecipitation (ChIP) Detects p53 binding to DNA at target gene promoters. in_vitro p53 binding to DNA increase http://purl.obolibrary.org/obo/PR_000000011 PR low Detects p53 binding to DNA at target gene promoters. http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0003677 GO Electrophoretic Mobility Shift Assay (EMSA) Measures DNA-binding activity of NF-κB to specific response elements. in_vitro DNA-binding activity of NF-κB increase http://purl.obolibrary.org/obo/OBI_0000207 OBI http://purl.obolibrary.org/obo/PR_000000014 PR low Measures DNA-binding activity of NF-κB to specific response elements. http://purl.obolibrary.org/obo/PR_000000014 PR http://purl.obolibrary.org/obo/GO_0003677 GO Electrophoretic Mobility Shift Assay (EMSA) Measures DNA-binding activity of STAT proteins to specific response elements. in_vitro DNA-binding activity of STAT proteins increase http://purl.obolibrary.org/obo/OBI_0000207 OBI http://purl.obolibrary.org/obo/PR_000000016 PR low Measures DNA-binding activity of STAT proteins to specific response elements. http://purl.obolibrary.org/obo/PR_000000016 PR http://purl.obolibrary.org/obo/GO_0003677 GO ELISA Measures intracellular cAMP concentrations to assess activation of the cAMP-PKA pathway. in_vitro intracellular cAMP concentrations increase http://purl.obolibrary.org/obo/CHEBI_17761 CHEBI medium Measures intracellular cAMP concentrations to assess activation of the cAMP-PKA pathway. http://purl.obolibrary.org/obo/CHEBI_17761 CHEBI http://purl.obolibrary.org/obo/GO_0019933 GO ELISA Quantifies levels of specific heat shock proteins in cell extracts. in_vitro levels of heat shock proteins increase medium Quantifies levels of specific heat shock proteins in cell extracts. http://purl.obolibrary.org/obo/GO_0009408 GO ELISA Quantifies NF-κB DNA-binding activity in nuclear extracts. in_vitro NF-κB DNA-binding activity increase http://purl.obolibrary.org/obo/PR_000000014 PR medium Quantifies NF-κB DNA-binding activity in nuclear extracts. http://purl.obolibrary.org/obo/PR_000000014 PR http://purl.obolibrary.org/obo/GO_0003677 GO Immunofluorescence Visualizes localization and expression of heat shock proteins in cells. in_vitro localization and expression of heat shock proteins increase low Visualizes localization and expression of heat shock proteins in cells. http://purl.obolibrary.org/obo/GO_0008104 GO Immunofluorescence Visualizes localization and expression of p53. in_vitro localization and expression of p53 increase http://purl.obolibrary.org/obo/PR_000000011 PR low Visualizes localization and expression of p53. http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0008104 GO Immunofluorescence Visualizes localization and expression of UPR markers in cells. in_vitro localization and expression of UPR markers increase low Visualizes localization and expression of UPR markers in cells. http://purl.obolibrary.org/obo/GO_0008104 GO Immunohistochemistry Visualizes the activation of MAPKs (JNK and p38) in tissue sections using specific antibodies. in_vivo activation of MAPKs in tissue sections increase http://purl.obolibrary.org/obo/PR_000000124 PR low Visualizes the activation of MAPKs (JNK and p38) in tissue sections using specific antibodies. http://purl.obolibrary.org/obo/PR_000000124 PR http://purl.obolibrary.org/obo/GO_0000165 GO Immunohistochemistry Visualizes the activation of MAPKs (JNK and p38) in tissue sections using specific antibodies. in_vivo MAPK activation increase low Visualizes the activation of MAPKs (JNK and p38) in tissue sections using specific antibodies. http://purl.obolibrary.org/obo/GO_0007165 GO qPCR Quantifies mRNA levels of p53-regulated genes such as p21, Bax, and H3K27me3. in_vitro mRNA levels of p53-regulated genes increase http://purl.obolibrary.org/obo/PR_000000012 PR medium Quantifies mRNA levels of p53-regulated genes such as p21, Bax, and H3K27me3. http://purl.obolibrary.org/obo/GO_0010467 GO qPCR and RT-PCR Quantifies mRNA levels of UPR-regulated genes such as ATF4 and CHOP. not_specified mRNA levels of UPR-regulated genes such as ATF4 and CHOP change http://purl.obolibrary.org/obo/GO_0010467 GO not_specified qPCR and RT-PCR Quantifies mRNA levels of UPR-regulated genes such as ATF4 and CHOP. http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR Quantifies mRNA levels of AKT1 and PI3K. in_vitro mRNA levels of AKT1 and PI3K increase http://purl.obolibrary.org/obo/PR_000000092 PR medium Quantifies mRNA levels of AKT1 and PI3K. http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR Quantifies mRNA levels of JNK, MAPK1(ERK), and MAPK14(p38). in_vitro mRNA levels of JNK, MAPK1(ERK), and MAPK14(p38) increase http://purl.obolibrary.org/obo/PR_000001267 PR medium Quantifies mRNA levels of JNK, MAPK1(ERK), and MAPK14(p38). http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Quantifies mRNA levels of PKA-RII and PKA-C. in_vitro mRNA levels of PKA-RII and PKA-C increase http://purl.obolibrary.org/obo/OBI_0000663 OBI medium Quantifies mRNA levels of PKA-RII and PKA-C. http://purl.obolibrary.org/obo/GO_0010467 GO Western Blot Measures levels of heat shock proteins such as HSP70 and HSP83. in_vitro levels of heat shock proteins increase http://purl.obolibrary.org/obo/PR_000000017 PR low Measures levels of heat shock proteins such as HSP70 and HSP83. http://purl.obolibrary.org/obo/GO_0009408 GO Western Blot Measures levels of JAK2 and STAT3. in_vitro levels of JAK2 and STAT3 increase http://purl.obolibrary.org/obo/PR_000000015 PR low Measures levels of JAK2 and STAT3. http://purl.obolibrary.org/obo/GO_0046493 GO Western Blot Measures levels of p53 and its downstream target proteins to assess activation. in_vitro levels of p53 and its downstream target proteins increase http://purl.obolibrary.org/obo/PR_000000011 PR low Measures levels of p53 and its downstream target proteins to assess activation. http://purl.obolibrary.org/obo/PR_000000011 PR http://purl.obolibrary.org/obo/GO_0072331 GO Western Blot Measures levels of UPR markers such as PERK, IRE1α, ATF-6. in_vitro levels of UPR markers increase low Measures levels of UPR markers such as PERK, IRE1α, ATF-6. http://purl.obolibrary.org/obo/GO_0030968 GO Western Blot Detects phosphorylation and degradation of IκBα, indicating activation of the NF-κB pathway. in_vitro phosphorylation and degradation of IκBα increase http://purl.obolibrary.org/obo/PR_000000013 PR low Detects phosphorylation and degradation of IκBα, indicating activation of the NF-κB pathway. http://purl.obolibrary.org/obo/PR_000000013 PR http://purl.obolibrary.org/obo/GO_0007249 GO Western Blot Detects the phosphorylation state of MAPK family members (ERK, JNK, p38), indicating activation. in_vitro phosphorylation of MAPK family members increase http://purl.obolibrary.org/obo/PR_000000124 PR low Detects the phosphorylation state of MAPK family members (ERK, JNK, p38), indicating activation. http://purl.obolibrary.org/obo/PR_000000124 PR http://purl.obolibrary.org/obo/GO_0000165 GO Western Blot Detects phosphorylation of proteins such as PI3K and AKT. in_vitro phosphorylation of PI3K and AKT increase http://purl.obolibrary.org/obo/PR_000001505 PR low Detects phosphorylation of proteins such as PI3K and AKT. http://purl.obolibrary.org/obo/GO_0014065 GO Western Blot Detects phosphorylation of PKA substrates, indicating pathway activation. in_vitro phosphorylation of PKA substrates increase http://purl.obolibrary.org/obo/PR_000001509 PR low Detects phosphorylation of PKA substrates, indicating pathway activation. http://purl.obolibrary.org/obo/GO_0019933 GO Chromatin immunoprecipitation (ChIP) Measures expression of genes regulated by the Hippo pathway. in_vitro expression of genes regulated by the Hippo pathway not_specified http://purl.obolibrary.org/obo/GO_0035329 GO low Measures expression of genes regulated by the Hippo pathway. http://purl.obolibrary.org/obo/GO_0035329 GO Electrophoretic Mobility Shift Assay (EMSA) Measures DNA-binding activity of STAT proteins to specific response elements. in_vitro DNA-binding activity of STAT proteins not_specified http://purl.obolibrary.org/obo/PR_000017752 PR low Measures DNA-binding activity of STAT proteins to specific response elements. http://purl.obolibrary.org/obo/PR_000017752 PR http://purl.obolibrary.org/obo/GO_0046300 GO ELISA Quantifies TGF-β ligand concentration in samples. in_vitro TGF-β ligand concentration not_specified http://purl.obolibrary.org/obo/PR_000002005 PR high Quantifies TGF-β ligand concentration in samples. http://purl.obolibrary.org/obo/PR_000002005 PR http://purl.obolibrary.org/obo/GO_0007179 GO Immunofluorescence Evaluated notch fluorescence levels using anti-Notch1 primary antibody. in_vitro Notch1 fluorescence levels not_specified http://purl.obolibrary.org/obo/PR_000001116 PR medium Evaluated notch fluorescence levels using anti-Notch1 primary antibody http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0007219 GO Immunofluorescence Visualizes nuclear vs. cytoplasmic localization of Hippo pathway expression. in_vitro nuclear vs. cytoplasmic localization of Hippo pathway expression not_specified http://purl.obolibrary.org/obo/GO_0035329 GO medium Visualizes nuclear vs. cytoplasmic localization of Hippo pathway expression. http://purl.obolibrary.org/obo/GO_0035329 GO Immunofluorescence Visualizes nuclear vs. cytoplasmic localization of SMAD2/3. in_vitro nuclear vs. cytoplasmic localization of SMAD2/3 not_specified http://purl.obolibrary.org/obo/PR_000012608 PR medium Visualizes nuclear vs. cytoplasmic localization of SMAD2/3. http://purl.obolibrary.org/obo/PR_000012608 PR http://purl.obolibrary.org/obo/GO_0007179 GO Immunofluorescence Evaluated β-catenin expression in the nucleus and cytoplasm. in_vitro β-catenin expression localization not_specified http://purl.obolibrary.org/obo/PR_000001299 PR medium Evaluated β-catenin expression in the nucleus and cytoplasm http://purl.obolibrary.org/obo/PR_000001299 PR http://purl.obolibrary.org/obo/GO_0016055 GO Immunohistochemistry Measures expression of levels of SHH pathway members. in_vitro expression levels of SHH pathway members not_specified http://purl.obolibrary.org/obo/OBI_0000424 OBI http://purl.obolibrary.org/obo/GO_0007224 GO medium Measures expression of levels of SHH pathway members. http://purl.obolibrary.org/obo/GO_0007224 GO luciferase reporter assay Evaluates WNT/β-catenin pathway activity by performing reporter gene assays with luciferase expression vectors containing wild-type and mutant TCF/LEF binding sites, comparing luciferase activities in_vitro luciferase activity change http://purl.obolibrary.org/obo/GO_0008523 GO medium Evaluates WNT/β-catenin pathway activity by performing reporter gene assays with luciferase expression vectors containing wild-type and mutant TCF/LEF binding sites, comparing luciferase activities http://purl.obolibrary.org/obo/GO_0008523 GO Luciferase reporter assay Evaluates WNT/β-catenin pathway activity by performing reporter gene assays with luciferase expression vectors containing wild-type and mutant TCF/LEF binding sites, comparing luciferase activities. in_vitro WNT/β-catenin pathway activity not_specified http://purl.obolibrary.org/obo/OBI_0000470 OBI http://purl.obolibrary.org/obo/GO_0016055 GO medium Evaluates WNT/β-catenin pathway activity by performing reporter gene assays with luciferase expression vectors containing wild-type and mutant TCF/LEF binding sites, comparing luciferase activities http://purl.obolibrary.org/obo/GO_0016055 GO http://purl.obolibrary.org/obo/GO_0016055 GO qPCR Quantifies mRNA levels of Notch1,3 and 4 as well as notch signalling downstream targets. in_vitro mRNA levels of Notch1,3 and 4 and downstream targets not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/PR_000001116 PR high Quantifies mRNA levels of Notch1,3 and 4 as well as notch signalling downstream targets. http://purl.obolibrary.org/obo/GO_0007219 GO http://purl.obolibrary.org/obo/GO_0007219 GO qPCR Measures expression of Wnt/β-catenin signaling pathway-related genes and mRNA levels. in_vitro mRNA levels of Wnt/β-catenin signaling pathway-related genes not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/SO_0000234 SO high Measures expression of Wnt/β-catenin signaling pathway-related genes and mRNA levels. http://purl.obolibrary.org/obo/GO_0016055 GO qRT-PCR Quantifies mRNA levels of AKT1 and PI3K. in_vitro mRNA levels of AKT1 and PI3K not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/PR_000000010 PR high Quantifies mRNA levels of AKT1 and PI3K. http://purl.obolibrary.org/obo/GO_0014065 GO qRT-PCR Quantifies mRNA levels of JNK, MAPK1(ERK), and MAPK14(p38). in_vitro mRNA levels of JNK, MAPK1(ERK), and MAPK14(p38) not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/PR_000000085 PR high Quantifies mRNA levels of JNK, MAPK1(ERK), and MAPK14(p38). http://purl.obolibrary.org/obo/GO_0000165 GO Western Blot Detects expression levels of Hippo pathway proteins. in_vitro expression levels of Hippo pathway proteins not_specified http://purl.obolibrary.org/obo/GO_0035329 GO low Detects expression levels of Hippo pathway proteins. http://purl.obolibrary.org/obo/GO_0035329 GO Western Blot Detects GLI protein levels and their activation state. in_vitro GLI protein levels and activation state not_specified http://purl.obolibrary.org/obo/PR_000008084 PR low Detects GLI protein levels and their activation state. http://purl.obolibrary.org/obo/PR_000008084 PR http://purl.obolibrary.org/obo/GO_0007224 GO Western Blot Measures levels of JAK2 and STAT3. in_vitro levels of JAK2 and STAT3 not_specified http://purl.obolibrary.org/obo/PR_000001236 PR low Measures levels of JAK2 and STAT3. http://purl.obolibrary.org/obo/GO_0046300 GO Western Blot Measures protein expression of Notch1 using bicinchoninc acid protein assay kit. in_vitro Notch1 protein expression not_specified http://purl.obolibrary.org/obo/PR_000001116 PR low Measures protein expression of Notch1 using bicinchoninc acid protein assay kit. http://purl.obolibrary.org/obo/PR_000001116 PR http://purl.obolibrary.org/obo/GO_0007219 GO Western Blot Detects the phosphorylation state of MAPK family members (ERK, JNK, p38), indicating activation. in_vitro phosphorylation state of MAPK family members not_specified http://purl.obolibrary.org/obo/PR_000000084 PR low Detects the phosphorylation state of MAPK family members (ERK, JNK, p38), indicating activation. http://purl.obolibrary.org/obo/PR_000000084 PR http://purl.obolibrary.org/obo/GO_0000165 GO Western Blot Detects phosphorylation status of SMAD2/3 proteins. in_vitro phosphorylation status of SMAD2/3 proteins not_specified http://purl.obolibrary.org/obo/PR_000012608 PR low Detects phosphorylation status of SMAD2/3 proteins. http://purl.obolibrary.org/obo/PR_000012608 PR http://purl.obolibrary.org/obo/GO_0007179 GO Western Blot Detects β-catenin protein levels by using specific primary antibodies. in_vitro β-catenin protein levels not_specified http://purl.obolibrary.org/obo/PR_000001299 PR low Detects β-catenin protein levels by using specific primary antibodies. http://purl.obolibrary.org/obo/PR_000001299 PR http://purl.obolibrary.org/obo/GO_0016055 GO FRET-based assay Measures HSD17B2 activity using fluorescence resonance energy transfer for high throughput in vitro screening. in_vitro HSD17B2 activity not_specified http://purl.obolibrary.org/obo/GO_0003824 GO high Homogeneous proximity (Kokko et al.,2006) and fluorescence resonance energy transfer (FRET)-based assays (Kokko et al., 2007) (high throughput in vitro screening) http://purl.obolibrary.org/obo/GO_0008202 GO Homogeneous proximity assay Measures HSD17B2 activity using a homogeneous proximity-based assay for high throughput in vitro screening. in_vitro HSD17B2 activity not_specified http://purl.obolibrary.org/obo/GO_0003824 GO high Homogeneous proximity (Kokko et al.,2006) and fluorescence resonance energy transfer (FRET)-based assays (Kokko et al., 2007) (high throughput in vitro screening) http://purl.obolibrary.org/obo/GO_0008202 GO HPLC-based assay Measures HSD17B2 activity in tissue samples using high-performance liquid chromatography. in_vitro HSD17B2 activity not_specified http://purl.obolibrary.org/obo/GO_0003824 GO medium Sensitive HPLC-based methods can be used for tissue sample analysis (Delvoux et al., 2007). http://purl.obolibrary.org/obo/GO_0008202 GO Immunohistochemistry Detects HSD17B2 protein in tissue sections using immunohistochemistry. in_vivo HSD17B2 protein not_specified http://purl.obolibrary.org/obo/GO_0008104 GO low Immunohistochemistry: HSD17B2 protein (Miyashita et al., 2015, 2004, Hashimoto et al., 2018). http://purl.obolibrary.org/obo/GO_0008104 GO Northern blot Measures HSD17B2 mRNA expression levels using Northern blotting. in_vitro HSD17B2 mRNA expression not_specified http://purl.obolibrary.org/obo/GO_0010467 GO low qRT-PCR, Northern blot: HSD17B2 mRNA expression http://purl.obolibrary.org/obo/GO_0010467 GO qRT-PCR Measures HSD17B2 mRNA expression levels using quantitative reverse transcription polymerase chain reaction. in_vitro HSD17B2 mRNA expression not_specified http://purl.obolibrary.org/obo/GO_0010467 GO medium qRT-PCR, Northern blot: HSD17B2 mRNA expression http://purl.obolibrary.org/obo/GO_0010467 GO Radiometric assay Measures HSD17B2 enzyme activity using radiometric methods after extraction and separation by thin layer chromatography or HPLC. in_vitro HSD17B2 enzyme activity not_specified http://purl.obolibrary.org/obo/GO_0003824 GO low Radiometric assays (Singh and Reed 1991) after extraction and separation by thin layer chromatography (Kitawaki et al., 2000) or HPLC in whole cells and lysates http://purl.obolibrary.org/obo/GO_0008202 GO C3 measurement Measurement of Complement 3 (C3) levels in rat uterus. in_vivo uterus rat C3 levels increase http://purl.obolibrary.org/obo/CHEBI_29896 CHEBI low Complement 3 (C3). It has been demonstrated that C3 could be regarded as an estrogen sensitive marker in rat uterus http://purl.obolibrary.org/obo/CHEBI_29896 CHEBI http://purl.obolibrary.org/obo/GO_0006954 GO Calbindin-D9k (CaBP-9k) gene and protein expression An assay measuring the expression of Calbindin-D9k gene and protein, which is regulated by E2 in the uterus. not_specified uterus mammals Calbindin-D9k expression increase http://purl.obolibrary.org/obo/GO_0010467 GO low Expression of Calbindin-D9k (CaBP-9k) gene and protein. The 9 kilodalton vitamin D-dependent calcium binding protein (CaBP9k), calbindin-D9k, is expressed in the intestine and uterus of mammals (bgee.org; L’ Horset et al., 1990) Different studies demonstrated that in the mammals uterus, the expression of CaBP-9k is regulated by hormones such as E2 and P4. http://purl.obolibrary.org/obo/GO_0010467 GO Complement 3 (C3) expression An assay measuring the expression of Complement 3, which is regulated by E2 in the rat uterus. not_specified uterus rat Complement 3 expression increase http://purl.obolibrary.org/obo/PR_000001000 PR http://purl.obolibrary.org/obo/GO_0010467 GO low Complement 3 (C3). It has been demonstrated that C3 could be regarded as an estrogen sensitive marker in rat uterus (Diel et al., 2000; Sundstrom et al., 1989) http://purl.obolibrary.org/obo/PR_000001000 PR http://purl.obolibrary.org/obo/GO_0010467 GO enzyme-linked immunosorbent assay (ELISA) An in vitro assay used to measure circulating levels of estrogens, such as E2, in serum. in_vitro serum estrogen levels not_specified http://purl.obolibrary.org/obo/OBI_0000476 OBI medium enzyme-linked immunosorbent assay (ELISA) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI glutamate assay Measures blood glutamate concentration, which is inversely related to plasma estrogen and progesterone levels. not_specified blood plasma glutamate concentration decrease http://purl.obolibrary.org/obo/CHEBI_16236 CHEBI not_specified blood glutamate levels are inversely related to plasma estrogen and progesterone level in plasma (Zlotnik et al., 2011) http://purl.obolibrary.org/obo/CHEBI_16236 CHEBI http://purl.obolibrary.org/obo/GO_0006536 GO LC/MS-based methods An in vitro assay using liquid chromatography/mass spectrometry to measure estrogens and estrogen metabolites in serum. in_vitro estrogen and estrogen metabolite levels not_specified http://purl.obolibrary.org/obo/OBI_0001047 OBI medium Liquid chromatography/mass spectrometry (LC/MS)-based methods are also becoming more widely used (as cost and sample size requirements decrease), particularly for measurement of estrogens and estrogen metabolites. http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI multiplex immunoassay An in vitro assay used to measure circulating levels of estrogens, such as E2, in serum. in_vitro serum estrogen levels not_specified high multiplex immunoassay http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI OECD TG 440 Uterotrophic bioassay An in vivo bioassay that measures the uterine response to estrogens in rodents, assessing estrogenic activity. in_vivo uterus rodents uterine response to estrogens increase OECD TG 440 low OECD TG 440 Uterotrophic bioassay in rodents http://purl.obolibrary.org/obo/UBERON_0001295 UBERON radioimmunoassay (RIA) An in vitro assay used to measure circulating levels of estrogens, such as E2, in serum. in_vitro serum estrogen levels not_specified http://purl.obolibrary.org/obo/OBI_0000475 OBI medium standard methods are available for serum estrogen analysis include radioimmunoassay (RIA) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI Serum estrogen analysis Quantification of circulating E2 levels using RIA, ELISA, multiplex immunoassay, or LC/MS. in_vitro humans animals circulating E2 levels not_specified http://purl.obolibrary.org/obo/CHEBI_16510 CHEBI medium In the regulatory area standard methods are available for serum estrogen analysis include radioimmunoassay (RIA), enzyme-linked immunosorbent assay (ELISA), and multiplex immunoassay. Liquid chromatography/mass spectrometry (LC/MS)-based methods are also becoming more widely used http://purl.obolibrary.org/obo/CHEBI_16510 CHEBI Uterotrophic bioassay Uterotrophic bioassay in rodents to assess estrogenic activity. in_vivo uterus rodents uterine response increase OECD TG 440 low OECD TG 440 Uterotrophic bioassay in rodents http://purl.obolibrary.org/obo/UBERON_0004639 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO Uterotrophic bioassay In vivo uterotrophic bioassay in rodents (OECD TG 440) to assess estrogenic activity and E2 availability in the uterus. in_vivo uterus rodents uterine weight increase http://purl.obolibrary.org/obo/UBERON_0000995 UBERON http://purl.obolibrary.org/obo/GO_0003700 GO http://purl.obolibrary.org/obo/GO_0033598 GO OECD TG 440 low OECD TG 440 Uterotrophic bioassay in rodents In vivo http://purl.obolibrary.org/obo/UBERON_0000995 UBERON http://purl.obolibrary.org/obo/GO_0033598 GO ELISA Detects IgA anti-tTG antibodies as a marker for gluten interaction. in_vitro IgA anti-tTG antibody levels increase high ELISA: To detect IgA anti-tTG antibodies as a marker for gluten interaction (Dieterich, 1998; Di Niro, 2012). http://purl.obolibrary.org/obo/GO_0006955 GO Flow cytometry Analyzes cell surface markers for gluten peptide presentation. in_vitro cell surface marker expression not_specified http://purl.obolibrary.org/obo/OBI_0000269 OBI high Flow cytometry: To analyze cell surface markers for gluten peptide presentation (Meresse, 2004; Di Niro, 2012; Steinsbo, 2014). http://purl.obolibrary.org/obo/GO_0002478 GO Flow cytometry Analysis of cell surface markers for gluten peptide presentation. in_vitro cell surface markers for gluten peptide presentation not_specified not_specified Flow cytometry: To analyze cell surface markers for gluten peptide presentation HLA-binding assay Assesses the stability and affinity of peptide-HLA complexes. in_vitro stability and affinity of peptide-HLA complexes not_specified medium HLA-binding assays: To assess the stability and affinity of peptide-HLA complexes (Molberg, 1998; Vader, 2002; Sollid, 2012). http://purl.obolibrary.org/obo/GO_0005515 GO HPLC Purifies gluten peptides for further analysis. in_vitro purification of gluten peptides not_specified medium HPLC: To purify gluten peptides for further analysis (Van de Wal, 1998b; Van de Wal, 1999; Vader, 2002). Immunohistochemistry Visualizes tTG-gluten complexes in tissues. in_vitro presence of tTG-gluten complexes not_specified low Immunohistochemistry & Immunofluorescence: To visualize tTG-gluten complexes (Dieterich, 1997; Di Niro, 2012). http://purl.obolibrary.org/obo/GO_0006461 GO mass spectrometry Mass spectrometry is used to analyze deamidated gluten peptides and their interaction with HLA-DQ. in_vitro peptide-HLA interaction change medium Mass spectrometry: To analyze deamidated gluten peptides and their interaction with HLA-DQ (Van de Wal, 1998b; Vader, 2002; Fallang, 2009). http://purl.obolibrary.org/obo/GO_0005173 GO Mass spectrometry Analyzes deamidated gluten peptides and their interaction with HLA-DQ. in_vitro presence and structure of deamidated gluten peptides not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI medium Mass spectrometry: To analyze deamidated gluten peptides and their interaction with HLA-DQ (Van de Wal, 1998b; Vader, 2002; Fallang, 2009). peptide binding assay These assays measure the direct binding of gluten peptides to HLA-DQ molecules. in_vitro binding affinity increase http://purl.obolibrary.org/obo/GO_0005103 GO medium Peptide binding assays: To measure the direct binding of gluten peptides to HLA-DQ molecules (Sollid, 1989; Arentz-Hansen, 2000; Sollid, 2012). http://purl.obolibrary.org/obo/GO_0005173 GO Peptide binding assay Measures the direct binding of gluten peptides to HLA-DQ molecules. in_vitro binding affinity of gluten peptides to HLA-DQ not_specified http://purl.obolibrary.org/obo/GO_0042287 GO medium Peptide binding assays: To measure the direct binding of gluten peptides to HLA-DQ molecules (Sollid, 1989; Arentz-Hansen, 2000; Sollid, 2012). http://purl.obolibrary.org/obo/GO_0042287 GO Serological typing & ASO probes Identification of HLA-DQ alleles in patients. in_vitro HLA-DQ alleles not_specified medium Serological typing & ASO probes: To identify HLA-DQ alleles in patients Surface plasmon resonance Measures TCR affinity for HLA-DQ-gluten complexes. in_vitro TCR affinity for HLA-DQ-gluten complexes not_specified http://purl.obolibrary.org/obo/OBI_0000219 OBI medium Surface plasmon resonance (SPR): To measure TCR affinity for HLA-DQ-gluten complexes (Vader, 2002b; Broughton, 2012; Petersen, 2014). http://purl.obolibrary.org/obo/GO_0002474 GO http://purl.obolibrary.org/obo/GO_0005515 GO T cell proliferation assay Measures T cell response to gluten peptides. in_vitro T cells T cell proliferation increase http://purl.obolibrary.org/obo/GO_0042102 GO medium T cell proliferation assays: To measure T cell response to gluten peptides (Lundin, 1993; Meresse, 2004; Tollefsen, 2006). http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042102 GO T cell proliferation assays Assays used to measure the T cell response to gluten peptides. in_vitro T cell T cell response to gluten peptides not_specified not_specified T cell proliferation assays: To measure T cell response to gluten peptides Tetramer staining Detects gluten-specific T cells bound to HLA-DQ. in_vitro T cells frequency of gluten-specific T cells not_specified medium Tetramer staining: To detect gluten-specific T cells bound to HLA-DQ (Qiao, 2011; Broughton, 2012). http://purl.obolibrary.org/obo/CL_0000084 CL Chromium release assay Measures the cytotoxicity of gluten-specific CD8+ T cells. in_vitro CD8+ T cells human cytotoxicity increase low Chromium release assays: To measure the cytotoxicity of gluten-specific CD8+ T cells http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0019835 GO Cytokine production assay Measures cytokine release (e.g., IFN-γ) to assess T cell activation. in_vitro T cells human cytokine release increase medium Cytokine production assays: To measure cytokine release (e.g., IFN-γ) to assess T cell activation http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0001817 GO Flow cytometry Detects TCR expression and cell surface markers on gluten-reactive T cells. in_vitro T cells human TCR expression and cell surface markers not_specified http://purl.obolibrary.org/obo/OBI_0000268 OBI high Flow cytometry: To detect TCR expression and cell surface markers on gluten-reactive T cells http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042110 GO Mass spectrometry Analyzes deamidated gluten peptides and their interactions with TCRs. in_vitro deamidated gluten peptides and TCR interactions not_specified http://purl.obolibrary.org/obo/OBI_0000475 OBI low Mass spectrometry: To analyze deamidated gluten peptides and their interactions with TCRs http://purl.obolibrary.org/obo/GO_0042277 GO Mass spectrometry This assay analyzes deamidated gluten peptides and their interactions with TCRs. in_vitro Peptide-TCR interactions change low To analyze deamidated gluten peptides and their interactions with TCRs (van de Wal et al., 1998; Vader et al., 2003). http://purl.obolibrary.org/obo/GO_0008529 GO http://purl.obolibrary.org/obo/GO_0005488 GO T cell proliferation assay Measures the activation and proliferation of gluten-reactive T cells in response to gluten peptides. in_vitro T cells human T cell proliferation increase medium T cell proliferation assays: To measure the activation and proliferation of gluten-reactive T cells in response to gluten peptides http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042098 GO TCR sequencing Identifies the specific gene sequences of gluten-reactive T cell receptors. in_vitro T cells human TCR gene sequences not_specified medium TCR sequencing: To identify the specific gene sequences of gluten-reactive T cell receptors http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042110 GO Tetramer staining A method to identify gluten-reactive T cells by utilizing HLA-peptide complexes that bind to the T cells. in_vitro gluten-reactive T cells binding of HLA-peptide complexes to T cells not_specified http://purl.obolibrary.org/obo/GO_0051281 GO not_specified Tetramer staining: To identify gluten-reactive T cells by binding HLA-peptide complexes to T cells http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0051281 GO Tetramer staining Identifies gluten-reactive T cells by binding HLA-peptide complexes to T cells. in_vitro T cells human gluten-reactive T cells not_specified medium Tetramer staining: To identify gluten-reactive T cells by binding HLA-peptide complexes to T cells http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042110 GO ELISA ELISA is used to detect antibodies specific for TG2 and deamidated gluten. in_vitro antibody levels increase http://purl.obolibrary.org/obo/GO_0005104 GO medium detect antibodies specific for TG2 and deamidated gluten with enzyme-linked immunosorbent assay (ELISA) http://purl.obolibrary.org/obo/GO_0002252 GO ELISA Detects antibodies specific for TG2 and deamidated gluten using enzyme-linked immunosorbent assay. in_vitro presence of antibodies specific for TG2 and deamidated gluten not_specified medium enzyme-linked immunosorbent assay (ELISA) molecular biological techniques This assay detects gene rearrangement events (e.g., V(D)J recombination) using molecular biology methods such as PCR or sequencing. in_vitro gene rearrangement change http://purl.obolibrary.org/obo/GO_0002504 GO low Gene rearrangement itself can be detected through molecular biological techniques. http://purl.obolibrary.org/obo/CHEBI_16996 CHEBI http://purl.obolibrary.org/obo/GO_0002504 GO rapid test kits Rapid test kits are used to detect antibodies specific for TG2 and deamidated gluten. in_vitro antibody levels increase http://purl.obolibrary.org/obo/GO_0005104 GO high detect antibodies specific for TG2 and deamidated gluten with rapid test kits. http://purl.obolibrary.org/obo/GO_0002252 GO rapid test kits Detects antibodies specific for TG2 and deamidated gluten using rapid test kits. in_vitro presence of antibodies specific for TG2 and deamidated gluten not_specified high rapid test kits ELISA Quantifies cytokine production in biological samples using enzyme-linked immunosorbent assay. in_vitro cytokine production not_specified http://purl.obolibrary.org/obo/GO_0001817 GO high ELISA http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0001817 GO flow cytometry Measures immune cell activation and cytokine production at the single-cell level using fluorescently labeled antibodies. in_vitro immune cell activation and cytokine production not_specified http://purl.obolibrary.org/obo/OBI_0000268 OBI http://purl.obolibrary.org/obo/GO_0002253 GO http://purl.obolibrary.org/obo/GO_0001817 GO medium flow cytometry http://purl.obolibrary.org/obo/CL_0000451 CL http://purl.obolibrary.org/obo/GO_0006955 GO microscopy and staining This assay uses microscopy and staining to assess immune cell activation. in_vitro immune cells immune cell activation increase low Methods could include, flow cytometry, microscopy and staining, ELISA, RT-PC, oxidative burst assays, Toll-like receptor simuation assays. http://purl.obolibrary.org/obo/CL_0000251 CL http://purl.obolibrary.org/obo/GO_0002752 GO microscopy and staining Visualizes immune cell morphology and protein expression using dyes or fluorescent probes. in_vitro immune cell morphology and protein expression not_specified low microscopy and staining http://purl.obolibrary.org/obo/CL_0000451 CL http://purl.obolibrary.org/obo/GO_0006955 GO oxidative burst assay This assay measures the production of reactive oxygen species (ROS) during an oxidative burst. in_vitro immune cells reactive oxygen species production increase medium Methods could include, flow cytometry, microscopy and staining, ELISA, RT-PC, oxidative burst assays, Toll-like receptor simuation assays. http://purl.obolibrary.org/obo/CHEBI_29048 CHEBI http://purl.obolibrary.org/obo/GO_0045469 GO oxidative burst assay Measures the respiratory burst activity of immune cells, indicating their activation status. in_vitro respiratory burst activity not_specified http://purl.obolibrary.org/obo/GO_0045088 GO medium oxidative burst assays http://purl.obolibrary.org/obo/CL_0000451 CL http://purl.obolibrary.org/obo/GO_0045088 GO RT-PCR RT-PCR is used to measure cytokine production at the mRNA level. in_vitro immune cells cytokine mRNA levels increase medium Methods could include, flow cytometry, microscopy and staining, ELISA, RT-PC, oxidative burst assays, Toll-like receptor simuation assays. http://purl.obolibrary.org/obo/CHEBI_50835 CHEBI http://purl.obolibrary.org/obo/GO_0010468 GO Toll-like receptor simulation assays Assays designed to simulate or measure the response triggered by Toll-like receptor activation. in_vitro pathogen recognition change http://purl.obolibrary.org/obo/GO_0004843 GO low Toll-like receptor simuation assays http://purl.obolibrary.org/obo/GO_0004843 GO http://purl.obolibrary.org/obo/GO_0050830 GO Toll-like receptor stimulation assay Assesses the activation of Toll-like receptors and downstream signaling pathways in immune cells. in_vitro Toll-like receptor activation not_specified http://purl.obolibrary.org/obo/GO_0004888 GO http://purl.obolibrary.org/obo/GO_0002224 GO medium Toll-like receptor simuation assays http://purl.obolibrary.org/obo/GO_0004888 GO http://purl.obolibrary.org/obo/GO_0002224 GO AlphaLISA Measures the reactivity of monoclonal antibodies to gluten and TG2 antigens. in_vitro plasma cells intestinal biopsies human antibody reactivity not_specified high The resulting monoclonal antibodies can be analyzed for their reactivity to gluten and TG2 antigens, by ELISA or AlphaLISA http://purl.obolibrary.org/obo/CL_0000232 CL http://purl.obolibrary.org/obo/GO_0042113 GO AlphaLISA Measures the reactivity of monoclonal antibodies to gluten and TG2 antigens using an AlphaLISA bead-based immunoassay. in_vitro Single plasma cells intestinal biopsies reactivity to gluten and TG2 antigens change medium The resulting monoclonal antibodies can be analyzed for their reactivity to gluten and TG2 antigens, by ... AlphaLISA http://purl.obolibrary.org/obo/CL_0000142 CL http://purl.obolibrary.org/obo/GO_0030234 GO ELISA Measures the reactivity of monoclonal antibodies to gluten and TG2 antigens. in_vitro plasma cells intestinal biopsies human antibody reactivity not_specified medium The resulting monoclonal antibodies can be analyzed for their reactivity to gluten and TG2 antigens, by ELISA or AlphaLISA http://purl.obolibrary.org/obo/CL_0000232 CL http://purl.obolibrary.org/obo/GO_0042113 GO ELISA Measures the reactivity of monoclonal antibodies to gluten and TG2 antigens using an enzyme-linked immunosorbent assay. in_vitro Single plasma cells intestinal biopsies reactivity to gluten and TG2 antigens change medium The resulting monoclonal antibodies can be analyzed for their reactivity to gluten and TG2 antigens, by ELISA http://purl.obolibrary.org/obo/CL_0000142 CL http://purl.obolibrary.org/obo/GO_0030234 GO flow cytometry Detects and characterizes gluten-specific IgA+ plasma cells using fluorescently labeled peptides. in_vitro IgA+ plasma cells intestinal biopsies human gluten-specific IgA+ plasma cells not_specified http://purl.obolibrary.org/obo/OBI_0000791 OBI http://purl.obolibrary.org/obo/CL_0000786 CL high fluorescently labeled peptides (e.g., biotinylated gliadin peptides) can be used in flow cytometry to sort and analyze gluten-specific IgA+ plasma cells, allowing for the detection and characterization of B cell activation in celiac lesions http://purl.obolibrary.org/obo/CL_0000232 CL http://purl.obolibrary.org/obo/GO_0042113 GO ELISPOT An ELISPOT assay is used to detect the mobilization of memory T cells reactive against gliadin following a 3-day gluten challenge. in_vitro T cells number of IFNγ-secreting T cells increase http://purl.obolibrary.org/obo/CL_0000255 CL http://purl.obolibrary.org/obo/GO_0006139 GO medium A 3-day gluten challenge induces the mobilization of memory T cells reactive against gliadin, which can be detected by IFNγ enzyme-linked immunospot (ELISPOT) assay. http://purl.obolibrary.org/obo/CL_0000255 CL http://purl.obolibrary.org/obo/GO_0042493 GO EmA Detects IgA antibodies against tissue transglutaminase 2 (TG2) in the endomysium, indicating celiac disease. in_vitro IgA anti-TG2 antibody titer increase http://purl.obolibrary.org/obo/GO_0003823 GO http://purl.obolibrary.org/obo/GO_0002456 GO not_specified The most common serological tests various serological tests are EmAs (antibodies specific for TG2 in the endomysium, which is a form of perivascular connective tissue) and TG2-Ab assays (ELISA), reaching a sensitivity of 98.1% and a specificity of 94.7% in patients with biopsy-confirmed cases (Dieterich et al., 1997; Dieterich et al., 1998). For patients IgA deficient, EMAs and TG2 assay with IgG, considering that IgG may be elevated due to other autoimmune diseases, and the predictive value is lower (Dieterich et al., 1998). http://purl.obolibrary.org/obo/GO_0002456 GO EmA assay Detects antibodies specific for TG2 in the endomysium, a form of perivascular connective tissue, used for serological testing in celiac disease diagnosis. in_vitro human presence of endomysial antibodies not_specified medium The most common serological tests various serological tests are EmAs (antibodies specific for TG2 in the endomysium, which is a form of perivascular connective tissue) and TG2-Ab assays (ELISA) flow cytometry T cells can be detected using HLA-DQ–gluten tetramers by flow cytometry. in_vitro T cells T cell population change http://purl.obolibrary.org/obo/CL_0000255 CL medium Otherwise, T cells can be detected with HLA-DQ–gluten tetramers by flow cytometry. http://purl.obolibrary.org/obo/CL_0000255 CL http://purl.obolibrary.org/obo/GO_0002422 GO Flow cytometry with HLA-DQ–gluten tetramers Flow cytometry using HLA-DQ–gluten tetramers to detect specific T cells. in_vitro T cells T cell count not_specified http://purl.obolibrary.org/obo/OBI_0001485 OBI http://purl.obolibrary.org/obo/CL_0000182 CL not_specified T cells can be detected with HLA-DQ–gluten tetramers by flow cytometry http://purl.obolibrary.org/obo/CL_0000182 CL http://purl.obolibrary.org/obo/GO_0002376 GO HLA typing Genetic testing to identify HLA-DQ2 or HLA-DQ8 alleles. in_vitro HLA allele presence not_specified http://purl.obolibrary.org/obo/GO_0050886 GO not_specified HLA typing is useful as the disease is unlikely when individuals do not carry HLA-DQ2 or HLA-DQ8 HLA typing Determines the presence of HLA-DQ2 or HLA-DQ8 alleles, which are associated with celiac disease susceptibility. in_vitro human presence of HLA-DQ2 or HLA-DQ8 alleles not_specified medium HLA typing is useful as the disease is unlikely when individuals do not carry HLA-DQ2 or HLA-DQ8 HLA-DQ–gluten tetramer flow cytometry Detects T cells specific for gluten using HLA-DQ–gluten tetramers and flow cytometry. in_vitro T cells human presence of gluten-specific T cells not_specified http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/OBI_0000268 OBI medium T cells can be detected with HLA-DQ–gluten tetramers by flow cytometry. http://purl.obolibrary.org/obo/CL_0000084 CL IFNγ ELISPOT assay Detects memory T cells reactive against gliadin by measuring interferon-gamma (IFNγ) secretion using enzyme-linked immunospot assay. in_vitro memory T cells human IFNγ secretion by gliadin-reactive T cells increase http://purl.obolibrary.org/obo/PR_000001559 PR medium A 3-day gluten challenge induces the mobilization of memory T cells reactive against gliadin, which can be detected by IFNγ enzyme-linked immunospot (ELISPOT) assay. http://purl.obolibrary.org/obo/CL_0000084 CL TG2-Ab ELISA Detects antibodies against tissue transglutaminase 2 (TG2) using enzyme-linked immunosorbent assay, used for serological testing in celiac disease diagnosis. in_vitro human presence of TG2 antibodies not_specified medium The most common serological tests various serological tests are EmAs (antibodies specific for TG2 in the endomysium, which is a form of perivascular connective tissue) and TG2-Ab assays (ELISA) LC-MS/MS Detection of TH distribution via Liquid Chromatography-Mass Spectrometry/Mass Spectrometry for quantitative and qualitative assessment of multiple THs. in_vivo TH distribution change medium While detection of TH distribution via LC-MS/MS is probably the best and most advanced approach for quantitative and qualitative assessment of multiple THs, it requires a high level of hands-on skills and costly equipment (De Angelis et al., 2022; Kinne et al., 2010). LC-MS/MS TH distribution analysis An advanced liquid chromatography-tandem mass spectrometry approach used for quantitative and qualitative assessment of multiple thyroid hormone distributions. in_vivo brain TH distribution change low While detection of TH distribution via LC-MS/MS is probably the best and most advanced approach for quantitative and qualitative assessment of multiple THs LC-MS/MS thyroid hormone distribution assay Quantitative and qualitative assessment of multiple thyroid hormones in biological samples using liquid chromatography-tandem mass spectrometry. in_vivo thyroid hormone levels change http://purl.obolibrary.org/obo/GO_0042402 GO http://purl.obolibrary.org/obo/OBI_0000474 OBI low While detection of TH distribution via LC-MS/MS is probably the best and most advanced approach for quantitative and qualitative assessment of multiple THs, it requires a high level of hands-on skills and costly equipment http://purl.obolibrary.org/obo/CHEBI_26975 CHEBI http://purl.obolibrary.org/obo/GO_0042402 GO MCT8-transfected cell uptake Measures uptake of radiolabeled T3 or T4 into cells transfected with MCT8, using either MDCK-1, JEG3, or COS1 cells. This allows for specific assessment of MCT8-mediated transport. in_vitro MDCK-1 JEG3 COS1 canine human African green monkey uptake of radiolabeled T3/T4 decrease medium More recently, the use of cell lines expressing solely MCT8 as TH transporter has become a standard method to measure uptake of radiolabeled T3 or T4 into cells in culture. These assays typically employ either MCT8-transfected Madin-Darby canine kidney (MDCK-1) cells (Braun et al., 2012; Braun & Schweizer, 2015; Johannes et al., 2016; Kinne et al., 2010; Kinne et al., 2009; Roth et al., 2010; Wirth et al., 2009) or MCT8-transfected Human Placenta Choriocarcinoma (JEG3) and African green monkey kidney fibroblast-like cells (COS1) cells (Chen et al., 2022; Groeneweg et al., 2013; Ianculescu et al., 2010). radiolabeled T3/T4 uptake assay Measures the uptake of radiolabeled T3 or T4 into cultured cells to assess MCT8-mediated thyroid hormone transport. in_vitro MDCK-1 JEG3 COS1 canine human African green monkey uptake of radiolabeled T3/T4 decrease http://purl.obolibrary.org/obo/GO_0072562 GO http://purl.obolibrary.org/obo/GO_0015301 GO low Early studies have examined the inhibition of T3 or T4 uptake into cells by measuring the uptake of radiolabeled T3/T4 into cultured cells More recently, the use of cell lines expressing solely MCT8 as TH transporter has become a standard method to measure uptake of radiolabeled T3 or T4 into cells in culture. These assays typically employ either MCT8-transfected Madin-Darby canine kidney (MDCK-1) cells MCT8-transfected Human Placenta Choriocarcinoma (JEG3) and African green monkey kidney fibroblast-like cells (COS1) cells http://purl.obolibrary.org/obo/GO_0072562 GO Sandell-Kolthoff spectrophotometry A non-radioactive, high-throughput screening assay that measures T3 uptake by MDCK cells overexpressing human MCT8 using the Sandell-Kolthoff reaction. in_vitro MDCK canine T3 uptake decrease high This spectrophotometric assay, based on the Sandell-Kolthoff reaction (Sandell & Kolthoff, 1937), measures T3 uptake by MDCK cells overexpressing human MCT8. TH level/enzyme activity measurement In vivo assessment of MCT8 inhibition by measuring the impact of toxicants on TH levels, TH-related enzyme activities, and/or downstream effects. in_vivo TH levels, enzyme activities, downstream effects change low In vivo observations of MCT8 inhibition are typically indirect, relying on the impact of toxicants on TH levels, TH-related enzyme activities, and/or downstream effects. CD25 Phenotyping Identification of activated CD4+ T cells by measuring the expression of the IL-2 receptor α-chain (CD25) following gluten challenge. ex_vivo CD4+ T cells small intestinal biopsies lamina propria CD25 expression increase http://purl.obolibrary.org/obo/CL_0000668 CL http://purl.obolibrary.org/obo/GO_0042110 GO low Activated T cells, specifically CD25+ (expressing the IL-2 receptor α-chain), can be identified through phenotyping. When small intestinal biopsies from celiac disease patients on a gluten-free diet are challenged ex vivo with gluten, CD4+ T cells in the lamina propria become activated and express CD25 http://purl.obolibrary.org/obo/CL_0000712 CL http://purl.obolibrary.org/obo/GO_0042110 GO Competitive PCR for cytokine mRNA quantification Quantification of cytokine mRNA expression using competitive PCR, where mRNA is reverse-transcribed, amplified, and visualized on agarose gels. in_vitro intestinal biopsies Homo sapiens cytokine mRNA expression not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI low Quantification of Cytokine mRNA Expression: Competitive PCR is employed to compare cytokine production at the mRNA level. mRNA is reverse-transcribed, amplified by PCR, and visualized on agarose gels. Band intensities are analyzed to determine the ratios of cytokine expression (Nilsen et al., 1998). http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO ELISA T/B-cell cooperation is assessed by measuring murine IL-2 secretion, a marker of T cell activation, using ELISA. ELISA is also used to quantify cytokines in biopsies. in_vitro T cells B cells biopsies murine IL-2 secretion increase medium In Vitro T/B-Cell Cooperation Assay: T/B-cell cooperation is assessed by culturing A20 B-cells with TCR transfectants in the presence of various complexes and conditions. Murine IL-2 secretion, a marker of T cell activation, is measured by ELISA as the readout (Di Niro et al., 2012). Additional Applications of ELISA: ELISA is also used to quantify cytokines in biopsies, providing insights into immune responses (Nilsen et al., 1998). http://purl.obolibrary.org/obo/CL_0000255 CL http://purl.obolibrary.org/obo/GO_0002487 GO ELISA for cytokine quantification Quantification of cytokines in biopsies using ELISA to assess immune responses. in_vitro intestinal biopsies Homo sapiens cytokine levels not_specified high ELISA is also used to quantify cytokines in biopsies, providing insights into immune responses (Nilsen et al., 1998). http://purl.obolibrary.org/obo/GO_0005125 GO http://purl.obolibrary.org/obo/GO_0006955 GO ELISA for IL-2 An in vitro assay measuring murine IL-2 secretion as a proxy for T cell activation during T/B-cell cooperation studies. in_vitro A20 B-cells TCR transfectants Murine IL-2 secretion change http://purl.obolibrary.org/obo/CHEBI_35443 CHEBI http://purl.obolibrary.org/obo/GO_0042110 GO medium T/B-cell cooperation is assessed by culturing A20 B-cells with TCR transfectants in the presence of various complexes and conditions. Murine IL-2 secretion, a marker of T cell activation, is measured by ELISA as the readout http://purl.obolibrary.org/obo/CL_0000712 CL http://purl.obolibrary.org/obo/GO_0042110 GO Phenotyping Identifies activated CD4+ T cells by detecting CD25 expression using flow cytometry or immunofluorescence. ex_vivo http://purl.obolibrary.org/obo/CL_0000842 http://purl.obolibrary.org/obo/UBERON_0002108 http://purl.obolibrary.org/obo/NCBITaxon_9606 CD25 expression increase http://purl.obolibrary.org/obo/GO_0002253 GO medium Activated T cells, specifically CD25+ (expressing the IL-2 receptor α-chain), can be identified through phenotyping. http://purl.obolibrary.org/obo/CL_0000842 CL http://purl.obolibrary.org/obo/GO_0002253 GO Proliferation assay Measurement of T cell proliferation using tritiated thymidine incorporation after incubation with antigen-presenting cells and gliadin peptides. in_vitro CD4+ T cells antigen-presenting cells Homo sapiens T cell proliferation increase http://purl.obolibrary.org/obo/GO_0042098 GO http://purl.obolibrary.org/obo/OBI_0000427 OBI medium Proliferation assays are performed using antigen-presenting cells (APCs), specific peptides or digested gliadin, and T cells labeled with a marker such as tritiated thymidine (³H). After incubation, plates are harvested, and the incorporation of ³H is measured to assess T cell proliferation (Arentz-Hansen et al., 2000, Broughton et al., 2012, Fallang et al., 2009). http://purl.obolibrary.org/obo/CL_0000788 CL http://purl.obolibrary.org/obo/GO_0042098 GO proliferation assay T cell proliferation is measured using ³H-labeled T cells, antigen-presenting cells (APCs), and peptides or gliadin. Incorporation of ³H into harvested plates is quantified to assess proliferation. in_vitro T cells antigen-presenting cells ³H incorporation increase medium Proliferation assays are performed using antigen-presenting cells (APCs), specific peptides or digested gliadin, and T cells labeled with a marker such as tritiated thymidine (³H). After incubation, plates are harvested, and the incorporation of ³H is measured to assess T cell proliferation (Arentz-Hansen et al., 2000, Broughton et al., 2012, Fallang et al., 2009). http://purl.obolibrary.org/obo/CL_0000255 CL http://purl.obolibrary.org/obo/GO_0008283 GO T cell isolation from intestinal biopsies Isolation of gluten-reactive T cells from intestinal biopsies of celiac disease patients. ex_vivo CD4+ T cells small intestinal biopsies lamina propria Homo sapiens presence of gluten-reactive T cells not_specified http://purl.obolibrary.org/obo/UBERON_0000059 UBERON low Gluten-reactive T cells can be isolated from patients with celiac disease but not from healthy controls. http://purl.obolibrary.org/obo/CL_0000788 CL http://purl.obolibrary.org/obo/GO_0006955 GO T cell phenotyping Identification of activated T cells expressing CD25 through phenotyping after ex vivo gluten challenge. ex_vivo CD4+ T cells small intestinal biopsies lamina propria Homo sapiens expression of CD25 increase http://purl.obolibrary.org/obo/GO_0042110 GO medium Activated T cells, specifically CD25+ (expressing the IL-2 receptor α-chain), can be identified through phenotyping. When small intestinal biopsies from celiac disease patients on a gluten-free diet are challenged ex vivo with gluten, CD4+ T cells in the lamina propria become activated and express CD25 (Lundin et al., 1993). http://purl.obolibrary.org/obo/CL_0000788 CL http://purl.obolibrary.org/obo/GO_0042110 GO T/B-cell cooperation assay Assessment of T/B-cell cooperation by measuring murine IL-2 secretion via ELISA after culturing A20 B-cells with TCR transfectants. in_vitro A20 B-cells TCR transfectants Mus musculus IL-2 secretion increase http://purl.obolibrary.org/obo/GO_0032611 GO medium T/B-cell cooperation is assessed by culturing A20 B-cells with TCR transfectants in the presence of various complexes and conditions. Murine IL-2 secretion, a marker of T cell activation, is measured by ELISA as the readout (Di Niro et al., 2012). http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0050900 GO Tritiated thymidine (³H) incorporation assay Measurement of T cell proliferation by quantifying the incorporation of tritiated thymidine into DNA. in_vitro antigen-presenting cells (APCs) T cells tritiated thymidine incorporation increase http://purl.obolibrary.org/obo/GO_0008283 GO medium Proliferation assays are performed using antigen-presenting cells (APCs), specific peptides or digested gliadin, and T cells labeled with a marker such as tritiated thymidine (³H). After incubation, plates are harvested, and the incorporation of ³H is measured to assess T cell proliferation http://purl.obolibrary.org/obo/CL_0000712 CL http://purl.obolibrary.org/obo/GO_0008283 GO automated cell counters An indirect method to measure blood plasma volume via hematocrit values using automated cell counters. in_vivo blood cells blood hematocrit values change not_specified Hematocrit values are often used as an indirect measure of blood plasma volume (Gordon et al. 2003) via automated cell counters enzyme assays Measures specific ion concentrations in blood plasma using enzyme assays. in_vitro blood plasma ion concentration not_specified medium Specific ion concentrations can be measured via ion chromatography, spectrophotometry, or enzyme assays Evans blue dye Measures blood plasma volume directly using Evans blue dye. in_vivo blood plasma blood plasma volume decrease low Blood plasma volume can be measured directly by Evans blue dye http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/GO_0003013 GO hematocrit Indirectly measures blood plasma volume via hematocrit values using automated cell counters. in_vivo blood hematocrit change medium Hematocrit values are often used as an indirect measure of blood plasma volume (Gordon et al. 2003) via automated cell counters and subsequent calculation http://purl.obolibrary.org/obo/UBERON_0000178 UBERON ion chromatography Measures specific ion concentrations in blood plasma. in_vitro blood plasma ion concentration not_specified medium Specific ion concentrations can be measured via ion chromatography radio isotopes Measures blood plasma volume directly using radio isotopes. in_vivo blood plasma blood plasma volume decrease low Blood plasma volume can be measured directly by Evans blue dye or radio isotopes http://purl.obolibrary.org/obo/UBERON_0001969 UBERON http://purl.obolibrary.org/obo/GO_0003013 GO spectrophotometry Measures specific ion concentrations in blood plasma using spectrophotometry. in_vitro blood plasma ion concentration not_specified medium Specific ion concentrations can be measured via ion chromatography, spectrophotometry, or enzyme assays NTE inhibition assay Measures the inhibition of NTE enzyme activity through phosphorylation and aging reactions. in_vitro nervous tissue NTE enzyme activity decrease not_specified Two-step reaction of NTE inhibition and aging. In the upper reaction, binding of the chemical inhibits the enzyme via phosphorylation followed by an irreversible aging reaction that displaces an R group attached to oxygen (pathway of the “neurotoxic” organophosphates). NTE inhibition assay Measures the inhibition of the NTE serine hydrolase enzyme, specifically looking at the slowing down of its rate of hydrolysis due to interaction with organophosphates via phosphorylation. not_specified rate of hydrolysis decrease http://purl.obolibrary.org/obo/GO_0004637 GO http://purl.obolibrary.org/obo/CHEBI_35244 CHEBI not_specified organophosphates and structurally similar chemicals are able to interact with the serine esterase domain of NTE via phosphorylation, greatly slowing down its rate of hydrolysis and making it essentially inhibited. http://purl.obolibrary.org/obo/GO_0006585 GO LPC measurement Measures levels of lysophosphatidylcholine (LPC), a mixture of fatty acid hydrolysis products of phospholipids, distributed along cell membranes and involved in various physiological functions. not_specified LPC levels not_specified http://purl.obolibrary.org/obo/CHEBI_25823 CHEBI not_specified LPC is a mixture of various fatty acid tails that are the hydrolysis products of phospholipids LPC has been noted to be distributed along cell membranes of many cell types LPC levels are regulated by the activity of numerous enzymes in the body http://purl.obolibrary.org/obo/CHEBI_25823 CHEBI http://purl.obolibrary.org/obo/GO_0006644 GO LPC membrane integration assay Measures the integration of lysophosphatidylcholine (LPC) into cell membranes, particularly in glial cells, to assess membrane integrity and permeability changes. in_vitro glial cells central nervous system LPC integration into cell membranes increase http://purl.obolibrary.org/obo/CHEBI_17839 CHEBI http://purl.obolibrary.org/obo/GO_0016020 GO http://purl.obolibrary.org/obo/CL_0000125 CL not_specified LPC specifically has been shown to integrate into cell membranes of glial cells in the CNS when present at elevated levels, and that this accumulation can further lead to increased membrane permeability which is harmful to the cells http://purl.obolibrary.org/obo/GO_0016020 GO http://purl.obolibrary.org/obo/GO_0008366 GO membrane permeability assay This assay measures the integrity of cell membranes by assessing permeability. Increased membrane permeability indicates disruption of membrane function due to lysophospholipid integration. in_vitro glial cells CNS membrane permeability increase low and that this accumulation can further lead to increased membrane permeability which is harmful to the cells (Elamrani & Blume, 1982; Plemel, et al., 2018). http://purl.obolibrary.org/obo/CL_0000070 CL Oligodendrocyte death assay Measures the death of oligodendrocytes, the myelinating cells in the CNS, which can occur due to various mechanisms such as pro-inflammatory cytokine death pathways, oxidative damage, elevation of the sphingomyelinase-ceramide pathway, and genetic alterations. not_specified oligodendrocytes CNS brain spinal cord oligodendrocyte death increase http://purl.obolibrary.org/obo/GO_0042552 GO http://purl.obolibrary.org/obo/UBERON_0000955 UBERON not_specified Oligodendrocytes are the myelinating cells in the CNS (Arnett, et al., 2004). In cases of disease or toxic insult, oligodendrocyte death can occur from a number of mechanisms. http://purl.obolibrary.org/obo/CL_0000129 CL http://purl.obolibrary.org/obo/GO_0008219 GO Histological staining for myelin This assay measures the loss of myelin sheaths in nervous tissue by visualizing myelin lamellae and their fragmentation. in_vivo central nervous system myelin sheath integrity decrease http://purl.obolibrary.org/obo/GO_0043209 GO http://purl.obolibrary.org/obo/GO_0002526 GO low Demyelination is defined by the loss of myelin sheaths in nervous tissue, typically following insult from injury or disease. Demyelinating lesions can occur anywhere within the CNS including on myelin surrounding axons of both sensory and motor neurons http://purl.obolibrary.org/obo/GO_0043209 GO http://purl.obolibrary.org/obo/GO_0002526 GO histopathology Histopathology is used to identify the loss of myelin sheaths in nervous tissue, indicating demyelination. This is typically observed following injury or disease. in_vivo nervous tissue CNS loss of myelin sheaths decrease low Demyelination is defined by the loss of myelin sheaths in nervous tissue, typically following insult from injury or disease. http://purl.obolibrary.org/obo/CL_0000564 CL http://purl.obolibrary.org/obo/GO_0007468 GO proteolytic enzyme assay This assay measures the activity of proteolytic enzymes involved in the removal of myelin fragments after initial myelin breakdown. not_specified nervous tissue proteolytic enzyme activity increase not_specified removal of the fragments by proteolytic and lipolytic enzymes that can digest the myelin pieces http://purl.obolibrary.org/obo/GO_0006508 GO Enzyme immunoassay Measures INSIG1 protein abundance directly. in_vitro INSIG1 protein abundance not_specified medium INSIG1 protein can be measured via Western blotting or enzyme immunoassay. http://purl.obolibrary.org/obo/GO_0010483 GO Real-time PCR Measures INSIG1 transcript abundance as an indirect indicator of INSIG1 protein abundance. in_vitro INSIG1 transcript abundance not_specified medium Real time PCR can be used to measure INSIG1 transcript abundance, which is an indirect – and only semi-quantitative indicator of INSIG1 protein abundance. http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Measures INSIG1 protein abundance directly. in_vitro INSIG1 protein abundance not_specified low INSIG1 protein can be measured via Western blotting or enzyme immunoassay. http://purl.obolibrary.org/obo/GO_0010483 GO Enzyme immunoassay Measures SREBP2 protein abundance directly. in_vitro SREBP2 protein abundance increase medium SREBP2 protein can be measured via Western blotting or enzyme immunoassay. http://purl.obolibrary.org/obo/GO_0010457 GO Real-time PCR Measures SREBP2 transcript abundance as an indirect indicator of SREBP2 protein abundance. in_vitro SREBP2 transcript abundance increase medium Real time PCR can be used to measure SREBP2 transcript abundance, which is an indirect – and only semi-quantitative indicator of SREBP2 protein abundance. http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Measures SREBP2 protein abundance directly. in_vitro SREBP2 protein abundance increase http://purl.obolibrary.org/obo/OBI_0000275 OBI low SREBP2 protein can be measured via Western blotting or enzyme immunoassay. http://purl.obolibrary.org/obo/GO_0010457 GO Enzyme immunoassay Measures protein levels for cholesterol synthesis enzymes. in_vitro protein abundance of cholesterol synthesis enzymes increase http://purl.obolibrary.org/obo/GO_0006694 GO http://purl.obolibrary.org/obo/GO_0016126 GO not_specified Protein levels for cholesterol synthesis enzymes can be measured via Western blotting or enzyme immunoassay. http://purl.obolibrary.org/obo/GO_0006694 GO Enzyme immunoassay Measures protein levels of cholesterol synthesis enzymes. in_vitro protein levels increase http://purl.obolibrary.org/obo/PATO_0000470 PATO http://purl.obolibrary.org/obo/GO_0006695 GO medium Protein levels for cholesterol synthesis enzymes can be measured via Western blotting or enzyme immunoassay http://purl.obolibrary.org/obo/GO_0006695 GO Real time PCR Measures transcript abundance of genes for cholesterol synthesis enzymes, providing an indirect and semi-quantitative indicator of protein abundance. in_vitro transcript abundance of cholesterol synthesis genes increase http://purl.obolibrary.org/obo/GO_0006694 GO http://purl.obolibrary.org/obo/GO_0016126 GO not_specified Real time PCR can be used to measure transcript abundance of genes for cholesterol synthesis enzymes, which is an indirect – and only semi-quantitative indicator of protein abundance. http://purl.obolibrary.org/obo/GO_0006694 GO Real-time PCR Measures transcript abundance of genes for cholesterol synthesis enzymes as an indirect indicator of protein abundance. in_vitro transcript abundance increase http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0006695 GO medium Real time PCR can be used to measure transcript abundance of genes for cholesterol synthesis enzymes http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0006695 GO stable isotope labeling Stable isotope labeling techniques (deuterium oxide preferred) measure the incorporation of deuterium into new cholesterol to assess the rate of cholesterol synthesis. in_vivo deuterium incorporation increase http://purl.obolibrary.org/obo/GO_0008729 GO low Overall assessment for the rate of cholesterol synthesis can be done by stable isotope labeling techniques (deuterium oxide (2H2O) preferred) and measuring the incorporation of deuterium into new cholesterol (Previs et al. 2011). http://purl.obolibrary.org/obo/CHEBI_6048 CHEBI http://purl.obolibrary.org/obo/GO_0008729 GO Stable isotope labeling Measures the rate of cholesterol synthesis by incorporating deuterium into new cholesterol. in_vivo rate of cholesterol synthesis increase http://purl.obolibrary.org/obo/GO_0006695 GO http://purl.obolibrary.org/obo/CHEBI_15422 CHEBI low Overall assessment for the rate of cholesterol synthesis can be done by stable isotope labeling techniques (deuterium oxide (2H2O) preferred) and measuring the incorporation of deuterium into new cholesterol http://purl.obolibrary.org/obo/CHEBI_16113 CHEBI http://purl.obolibrary.org/obo/GO_0006695 GO Western blotting Measures protein levels for cholesterol synthesis enzymes. in_vitro protein abundance of cholesterol synthesis enzymes increase http://purl.obolibrary.org/obo/GO_0006694 GO http://purl.obolibrary.org/obo/GO_0016126 GO not_specified Protein levels for cholesterol synthesis enzymes can be measured via Western blotting or enzyme immunoassay. http://purl.obolibrary.org/obo/GO_0006694 GO Western blotting Measures protein levels of cholesterol synthesis enzymes. in_vitro protein levels increase http://purl.obolibrary.org/obo/PATO_0000470 PATO http://purl.obolibrary.org/obo/GO_0006695 GO low Protein levels for cholesterol synthesis enzymes can be measured via Western blotting http://purl.obolibrary.org/obo/GO_0006695 GO calculation based on triglyceride and cholesterol levels An estimation method for LDL cholesterol levels derived from measured triglyceride and total cholesterol levels using a formula. in_vitro LDL cholesterol levels increase high estimation from calculations based on triglyceride and cholesterol levels http://purl.obolibrary.org/obo/PR_00000105 PR http://purl.obolibrary.org/obo/GO_0006869 GO enzyme immunoassay An immunoassay technique that uses enzymes to detect and quantify LDL cholesterol levels. in_vitro LDL cholesterol levels increase high enzyme immunoassays http://purl.obolibrary.org/obo/PR_00000105 PR http://purl.obolibrary.org/obo/GO_0006869 GO gradient gel electrophoresis A method to separate and quantify LDL particles based on their size using a gel matrix under an electric field. in_vitro LDL cholesterol levels increase http://purl.obolibrary.org/obo/OBI_0000368 OBI medium gradient gel electrophoresis http://purl.obolibrary.org/obo/PR_00000105 PR http://purl.obolibrary.org/obo/GO_0006869 GO high-performance liquid chromatography A chromatographic technique to separate and quantify LDL cholesterol based on its chemical properties. in_vitro LDL cholesterol levels increase high high-performance liquid chromatography http://purl.obolibrary.org/obo/PR_00000105 PR http://purl.obolibrary.org/obo/GO_0006869 GO LDL cholesterol assay Various laboratory methods are used to measure plasma LDL cholesterol levels, such as gradient gel electrophoresis, high-performance liquid chromatography, enzyme immunoassays, and calculations based on triglyceride and cholesterol levels. in_vitro plasma LDL cholesterol levels increase http://purl.obolibrary.org/obo/CHMO_0000000 CHMO not_specified A variety of methods are available to assess low-density lipoprotein (LDL) cholesterol levels, including gradient gel electrophoresis, high-performance liquid chromatography, enzyme immunoassays, and estimation from calculations based on triglyceride and cholesterol levels (Islam et al. 2022). http://purl.obolibrary.org/obo/CHMO_0000000 CHMO http://purl.obolibrary.org/obo/GO_0006869 GO RADAR assay The RADAR assay measures genomic androgen receptor activity in medaka fish embryos using a spg1-gfp construct under control of the AR-binding promoter spiggin1. in_vivo medaka fish genomic AR activity increase http://purl.obolibrary.org/obo/GO_0008270 GO OECD TG 251 medium The Rapid Androgen Disruption Activity Reporter (RADAR) assay included in OECD test guideline no. 251 can be used to measure genomic AR activity (OECD, 2022). Employing a spg1-gfp construct under control of the AR-binding promoter spiggin1 in medaka fish embryos, any stressor activating or inhibiting the androgen axis will be detected. http://purl.obolibrary.org/obo/PR_000001590 PR http://purl.obolibrary.org/obo/GO_0030521 GO RADAR assay The Rapid Androgen Disruption Activity Reporter (RADAR) assay measures genomic AR activity using a spg1-gfp construct under control of the AR-binding promoter spiggin1 in medaka fish embryos. Any stressor activating or inhibiting the androgen axis will be detected. in_vitro medaka fish embryos medaka GFP expression increase OECD TG 251 medium The Rapid Androgen Disruption Activity Reporter (RADAR) assay included in OECD test guideline no. 251 can be used to measure genomic AR activity (OECD, 2022). Employing a spg1-gfp construct under control of the AR-binding promoter spiggin1 in medaka fish embryos, any stressor activating or inhibiting the androgen axis will be detected. This includes for instance stressors that agonize or antagonize AR, as well as stressors that modulate androgen synthesis or metabolism. http://purl.obolibrary.org/obo/PR_000000044 PR http://purl.obolibrary.org/obo/GO_0000165 GO Cytokine secretion assay Measures T-cell activation by quantifying the amount of cytokines secreted by stimulated T-cells. not_specified gluten reactive adaptive T-cells cytokine secretion increase not_specified measureing of T-cell activation by T cell stimulation assays (e.g. cytokine secretion assays cytotoxicity assay This assay measures the ability of T cells to kill target cells, indicating cytotoxic activity. in_vitro T cells cytotoxicity increase medium Detection methods could include the measureing of T-cell activation by T cell stimulation assays (e.g. cytokine secretion assays, cytotoxicity assay) http://purl.obolibrary.org/obo/CL_0000311 CL http://purl.obolibrary.org/obo/GO_0001906 GO ELISA Quantifies peptide-HLA-DQ complexes using enzyme-linked immunosorbent assay. in_vitro peptide-HLA-DQ complex concentration increase high quantification of peptide-HLA-DQ complexes by ELISA (e.g. against HLA-peptide complex) http://purl.obolibrary.org/obo/GO_0002495 GO mass spectrometry This assay identifies and quantifies peptides using mass spectrometry, specifically peptide mass fingerprinting. in_vitro peptide mass fingerprint change low or mass spectrometry (e.g. peptide mass fingerprinting). http://purl.obolibrary.org/obo/CHEBI_33834 CHEBI http://purl.obolibrary.org/obo/GO_0006508 GO mass spectrometry Mass spectrometry used for the quantification of peptide-HLA-DQ complexes via peptide mass fingerprinting. in_vitro peptide mass fingerprinting / peptide-HLA-DQ complex concentration change not_specified quantification of peptide-HLA-DQ complexes by ... mass spectrometry (e.g. peptide mass fingerprinting). mass spectrometry Identifies and quantifies peptides using peptide mass fingerprinting. in_vitro peptide presence/abundance increase http://purl.obolibrary.org/obo/OBI_0000272 OBI medium quantification of peptide-HLA-DQ complexes by ... mass spectrometry (e.g. peptide mass fingerprinting) http://purl.obolibrary.org/obo/CHEBI_16612 CHEBI http://purl.obolibrary.org/obo/GO_0006518 GO T cell stimulation assay This assay measures T-cell activation through stimulation, assessing responses like cytokine secretion. in_vitro T cells cytokine secretion increase medium Detection methods could include the measureing of T-cell activation by T cell stimulation assays (e.g. cytokine secretion assays http://purl.obolibrary.org/obo/CL_0000311 CL http://purl.obolibrary.org/obo/GO_0042452 GO T cell stimulation assay Measures T-cell activation through cytokine secretion or cytotoxicity. in_vitro T-cells T-cell activation increase http://purl.obolibrary.org/obo/GO_0042110 GO http://purl.obolibrary.org/obo/GO_0070683 GO medium T-cell activation by T cell stimulation assays (e.g. cytokine secretion assays, cytotoxicity assay) http://purl.obolibrary.org/obo/CL_0000084 CL http://purl.obolibrary.org/obo/GO_0042110 GO Enzyme immunoassay Measures PCSK9 protein abundance directly using antibody-based detection. in_vitro PCSK9 protein abundance increase high PCSK9 protein can be measured via ... enzyme immunoassay http://purl.obolibrary.org/obo/GO_0010457 GO Real-time PCR Measures PCSK9 transcript abundance as an indirect indicator of PCSK9 protein abundance. in_vitro PCSK9 transcript abundance increase medium Real time PCR can be used to measure PCSK9 transcript abundance http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Measures PCSK9 protein abundance directly. in_vitro PCSK9 protein abundance increase http://purl.obolibrary.org/obo/OBI_0000272 OBI low PCSK9 protein can be measured via Western blotting http://purl.obolibrary.org/obo/GO_0010457 GO Antibody-Based Assay Detects specific DNA adducts (e.g., 8-oxo-dG) using ELISA or immunoblotting with adduct-specific antibodies. not_specified DNA adduct levels increase http://purl.obolibrary.org/obo/OBI_0000707 OBI not_specified Antibody-Based Assays ChIP Assesses functional and structural changes at the molecular level, including interactions with the LMNA locus. in_vitro protein-DNA interactions not_specified http://purl.obolibrary.org/obo/GO_0003677 GO low Functional and structural assessments (e.g., microscopy, ChIP, RNA-Seq). http://purl.obolibrary.org/obo/GO_0006325 GO Comet assay Measures DNA strand breaks in individual cells exposed to chemicals, with additional locus-specific analysis to infer damage to the LMNA locus. in_vitro DNA strand breaks increase http://purl.obolibrary.org/obo/OBI_0000356 OBI http://purl.obolibrary.org/obo/GO_0000305 GO OECD TG 489 medium Comet Assay (Single-Cell Gel Electrophoresis): Measures DNA strand breaks in individual cells exposed to chemicals. Damage to the LMNA locus can be inferred through additional locus-specific analysis. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0042769 GO ELISA Quantifies DNA adducts using antibodies specific to common DNA adducts, such as 8-oxo-dG. in_vitro DNA adducts increase http://purl.obolibrary.org/obo/OBI_0000617 OBI http://purl.obolibrary.org/obo/CHEBI_23888 CHEBI high Antibody-Based Assays: ELISA or immunoblotting with antibodies specific to common DNA adducts (e.g., 8-oxo-dG). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006974 GO Immunoblotting Quantifies DNA adducts using antibodies specific to common DNA adducts, such as 8-oxo-dG. in_vitro DNA adducts increase http://purl.obolibrary.org/obo/OBI_0000616 OBI http://purl.obolibrary.org/obo/CHEBI_23888 CHEBI medium Antibody-Based Assays: ELISA or immunoblotting with antibodies specific to common DNA adducts (e.g., 8-oxo-dG). http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006974 GO Immunofluorescence Microscopy Visualizes nuclear shape abnormalities (e.g., blebbing, lobulation) caused by LMNA mutations using antibodies against lamin A/C. in_vitro nuclear morphology not_specified http://purl.obolibrary.org/obo/OBI_0000458 OBI http://purl.obolibrary.org/obo/GO_0005635 GO low Nuclear Morphology Assessment: Immunofluorescence Microscopy: Antibodies against lamin A/C are used to visualize nuclear shape abnormalities (e.g., blebbing, lobulation) caused by LMNA mutations. http://purl.obolibrary.org/obo/GO_0005635 GO http://purl.obolibrary.org/obo/GO_0007000 GO Live-Cell Imaging Tracks real-time changes in nuclear envelope integrity in response to chemical exposure. in_vitro nuclear envelope integrity not_specified http://purl.obolibrary.org/obo/OBI_0000515 OBI http://purl.obolibrary.org/obo/GO_0005635 GO low Live-Cell Imaging: Tracks real-time changes in nuclear envelope integrity in response to chemical exposure. http://purl.obolibrary.org/obo/GO_0005635 GO http://purl.obolibrary.org/obo/GO_0007007 GO Mass Spectrometry Identifies and quantifies chemical adducts bound to DNA, including those at the LMNA locus. in_vitro DNA adducts increase http://purl.obolibrary.org/obo/OBI_0000272 OBI http://purl.obolibrary.org/obo/CHEBI_23888 CHEBI medium Mass Spectrometry (MS): Identifies and quantifies chemical adducts bound to DNA, including those at the LMNA locus. http://purl.obolibrary.org/obo/CHEBI_16991 CHEBI http://purl.obolibrary.org/obo/GO_0006974 GO NGS Detects chemical-induced LMNA mutations at the molecular level. in_vitro LMNA mutations not_specified http://purl.obolibrary.org/obo/OBI_0000626 OBI http://purl.obolibrary.org/obo/GO_0006468 GO high Direct mutation detection (e.g., NGS, PCR). http://purl.obolibrary.org/obo/GO_0006281 GO PCR Detects chemical-induced LMNA mutations at the molecular level. in_vitro LMNA mutations not_specified http://purl.obolibrary.org/obo/GO_0006468 GO medium Direct mutation detection (e.g., NGS, PCR). http://purl.obolibrary.org/obo/GO_0006281 GO Reporter Assay Uses cell lines engineered with LMNA reporters (e.g., fluorescent markers) to detect mutations or disruptions in nuclear envelope stability. in_vitro LMNA reporter activity not_specified http://purl.obolibrary.org/obo/GO_0005635 GO medium Reporter Assays: Cell lines engineered with LMNA reporters (e.g., fluorescent markers) to detect mutations or disruptions in nuclear envelope stability. http://purl.obolibrary.org/obo/PR_000001217 PR http://purl.obolibrary.org/obo/GO_0007007 GO Reporter Assays Uses engineered cell lines with LMNA reporters (e.g., fluorescent markers) to detect mutations or disruptions in nuclear envelope stability. in_vitro engineered cell lines mutations or disruptions in nuclear envelope stability change not_specified Reporter Assays : Cell lines engineered with LMNA reporters (e.g., fluorescent markers) to detect mutations or disruptions in nuclear envelope stability. http://purl.obolibrary.org/obo/GO_0005740 GO RNA-Seq Assesses functional changes at the molecular level, including gene expression changes related to LMNA mutations. in_vitro gene expression not_specified http://purl.obolibrary.org/obo/OBI_0001271 OBI http://purl.obolibrary.org/obo/GO_0010467 GO high Functional and structural assessments (e.g., microscopy, ChIP, RNA-Seq). http://purl.obolibrary.org/obo/GO_0010467 GO γ-H2AX foci formation Quantifies phosphorylation of histone H2AX at sites of DNA double-strand breaks using immunofluorescence microscopy or flow cytometry. in_vitro γ-H2AX levels increase http://purl.obolibrary.org/obo/PR_000008064 PR http://purl.obolibrary.org/obo/GO_0006303 GO medium γ-H2AX Foci Formation: Phosphorylation of histone H2AX at sites of DNA double-strand breaks is a marker for DNA damage. Immunofluorescence microscopy or flow cytometry can quantify γ-H2AX levels. http://purl.obolibrary.org/obo/PR_000008064 PR http://purl.obolibrary.org/obo/GO_0042769 GO AV Node Tissue Slices Isolated tissue preparations for measurement of conduction delays using extracellular electrodes or optical mapping. ex_vivo AV node conduction delay increase http://purl.obolibrary.org/obo/GO_0060048 GO low AV Node Tissue Slices Isolated tissue preparations allow for measurement of conduction delays using extracellular electrodes or optical mapping. http://purl.obolibrary.org/obo/UBERON_0002184 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Blood Tests Laboratory analysis of blood electrolytes and thyroid function to identify reversible causes of AV conduction delay. in_vivo blood human electrolyte levels, thyroid hormone levels change low Blood Tests Evaluate potential reversible causes (e.g., electrolyte levels, thyroid function). Calcium Imaging Uses calcium-sensitive fluorescent dyes (e.g., Fluo-4, Fura-2) to measure intracellular calcium transients critical for AV nodal depolarization and conduction. in_vitro AV nodal cells atrioventricular node intracellular calcium transients decrease http://purl.obolibrary.org/obo/OBI_0001512 OBI http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI medium Cellular Calcium Handling Purpose: Measures intracellular calcium transients critical for AV nodal conduction. Key Method: Use calcium-sensitive fluorescent dyes (e.g., Fluo-4, Fura-2). http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0006874 GO Calcium-sensitive fluorescent dyes Measures intracellular calcium transients critical for AV nodal conduction using dyes like Fluo-4 or Fura-2. in_vitro AV nodal cells heart intracellular calcium transients decrease http://purl.obolibrary.org/obo/GO_0006816 GO medium Cellular Calcium Handling Use calcium-sensitive fluorescent dyes (e.g., Fluo-4, Fura-2). http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0006816 GO Computational Model Simulates ionic currents, action potential propagation, and AV node conduction at the cellular level to predict effects of molecular changes. in_silico AV node simulated conduction velocity, action potential duration change medium Computational Modeling Purpose: Simulates ionic currents, action potential propagation, and AV node conduction at the cellular level. Relevance: Predicts how molecular or cellular changes contribute to prolonged conduction. http://purl.obolibrary.org/obo/CL_0000746 CL http://purl.obolibrary.org/obo/GO_0007040 GO Computational Modeling Simulates ionic currents, action potential propagation, and AV node conduction at the cellular level. in_silico simulated conduction delay increase http://purl.obolibrary.org/obo/GO_0006811 GO high Computational Modeling Simulates ionic currents, action potential propagation, and AV node conduction at the cellular level. http://purl.obolibrary.org/obo/UBERON_0002184 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Connexin Analysis (Immunohistochemistry/Confocal Microscopy) Evaluates the expression and distribution of gap junction proteins like Connexin 43 and 45 using microscopy. in_vitro cardiac tissue gap junction protein expression and connectivity decrease http://purl.obolibrary.org/obo/GO_0044253 GO low Connexin Analysis... Techniques: Immunohistochemistry or confocal microscopy. Decreased gap junction connectivity slows conduction velocity. http://purl.obolibrary.org/obo/GO_0044253 GO Drug Study Pharmacological modulation using agents like verapamil (Ca2+ channel blocker) or isoproterenol (beta-agonist) to alter AV nodal conduction. in_vivo heart AV nodal conduction effect (e.g., PR interval prolongation) change low Drug Studies Calcium Channel Blockers (e.g., Verapamil): Induce AV conduction delay to study mechanisms. Beta-adrenergic Agonists (e.g., Isoproterenol): Test enhancement of AV conduction. http://purl.obolibrary.org/obo/UBERON_0002083 UBERON http://purl.obolibrary.org/obo/GO_0007040 GO Electrocardiogram (ECG) Measures the electrical activity of the heart, specifically the PR interval to assess AV node conduction delay. in_vivo heart human PR interval duration increase high Electrocardiogram (ECG) Findings Prolonged PR Interval: >200 ms (in adults), reflecting delayed conduction through the AV node. http://purl.obolibrary.org/obo/UBERON_0002184 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Electrophysiology Study (EPS) Provides detailed mapping of conduction pathways in the heart for diagnostic clarification. in_vivo heart human conduction pathway mapping not_specified http://purl.obolibrary.org/obo/GO_0061363 GO low Electrophysiology Study (EPS) Provides detailed mapping of conduction pathways for diagnostic clarification in complex cases. http://purl.obolibrary.org/obo/UBERON_0005296 UBERON http://purl.obolibrary.org/obo/GO_0061363 GO Genetic Models (Knockout or Transgenic Mice) Models with specific ion channel or connexin mutations to study the cellular basis of AV conduction delay. in_vivo heart Mus musculus AV conduction delay increase http://purl.obolibrary.org/obo/GO_0060048 GO low Genetic Models Knockout or Transgenic Mice: Models with specific ion channel or connexin mutations (e.g., HCN4, Cav1.3) help study the cellular basis of AV conduction delay. http://purl.obolibrary.org/obo/UBERON_0002184 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Holter Monitoring Continuous ECG recording to evaluate intermittent or progressive AV conduction abnormalities. in_vivo heart human AV conduction abnormalities change http://purl.obolibrary.org/obo/GO_0060048 GO medium Holter Monitoring Used to evaluate intermittent or progressive AV conduction abnormalities. http://purl.obolibrary.org/obo/UBERON_0002184 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Immunostaining Localizes ion channels in AV nodal cells using immunohistochemical techniques. in_vitro AV nodal cells heart ion channel localization not_specified http://purl.obolibrary.org/obo/GO_0008104 GO medium Immunostaining Localizes ion channels in AV nodal cells. http://purl.obolibrary.org/obo/GO_0005216 GO http://purl.obolibrary.org/obo/GO_0008104 GO Immunostaining Immunostaining localizes ion channels in AV nodal cells to assess their expression and distribution. in_vitro AV nodal cells heart protein localization change http://purl.obolibrary.org/obo/GO_0005243 GO low Immunostaining: Localizes ion channels in AV nodal cells. http://purl.obolibrary.org/obo/GO_0006469 GO Ion Channel Expression Studies Ion channel expression studies assess the expression and function of ion channels critical for AV node conduction using techniques like qPCR, Western blot, and immunostaining. in_vitro AV nodal cells heart rodent human expression levels of ion channels (Cav1.2, HCN channels, Kv, Kir) decrease http://purl.obolibrary.org/obo/GO_0005267 GO medium qPCR and Western Blot: Quantify the expression of ion channels like L-type Ca²⁺ channels (Cav1.2): Key for depolarization in AV node cells. Immunostaining: Localizes ion channels in AV nodal cells. Reduced expression or dysfunction of these channels correlates with conduction delays. http://purl.obolibrary.org/obo/GO_0005265 GO http://purl.obolibrary.org/obo/OBI_0100096 OBI Langendorff-Perfused Hearts Enables study of the whole heart, including AV node function, under controlled conditions. ex_vivo heart AV node function not_specified http://purl.obolibrary.org/obo/GO_0008016 GO low Langendorff-Perfused Hearts Enables study of the whole heart, including AV node function, under controlled conditions. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0003008 GO Microelectrode Studies Measures transmembrane potentials in tissue slices or isolated nodal regions to detect conduction delays. ex_vivo AV node transmembrane potential and conduction delay increase http://purl.obolibrary.org/obo/GO_0001603 GO low Microelectrode Studies Detects conduction delay between atrial and ventricular regions. http://purl.obolibrary.org/obo/UBERON_0002184 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Optical Mapping Visualizes electrical activity across cardiac tissue using voltage-sensitive dyes to track conduction velocity. ex_vivo heart conduction velocity decrease http://purl.obolibrary.org/obo/GO_0001603 GO medium Optical Mapping Tracks conduction velocity across the AV node and surrounding regions. http://purl.obolibrary.org/obo/UBERON_0002184 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Patch-Clamp Recording Measures ionic currents and action potentials in single AV nodal cells to assess ion channel function. in_vitro AV nodal cells heart ionic currents and action potential duration change http://purl.obolibrary.org/obo/OBI_0000218 OBI http://purl.obolibrary.org/obo/GO_0001508 GO low Patch-Clamp Recording Measures ionic currents and action potentials in single AV nodal cells. http://purl.obolibrary.org/obo/CL_0000308 CL http://purl.obolibrary.org/obo/GO_0006811 GO qPCR Quantifies the expression of ion channels critical for AV node conduction. in_vitro AV nodal cells heart ion channel mRNA expression decrease http://purl.obolibrary.org/obo/OBI_0000269 OBI http://purl.obolibrary.org/obo/GO_0010467 GO high qPCR and Western Blot Quantify the expression of ion channels like: L-type Ca²⁺ channels (Cav1.2). http://purl.obolibrary.org/obo/PR_000001196 PR http://purl.obolibrary.org/obo/GO_0006811 GO Western Blot Quantifies the protein expression of ion channels critical for AV node conduction. in_vitro AV nodal cells heart ion channel protein expression decrease http://purl.obolibrary.org/obo/OBI_0000272 OBI http://purl.obolibrary.org/obo/GO_0010457 GO medium qPCR and Western Blot Quantify the expression of ion channels like: L-type Ca²⁺ channels (Cav1.2). http://purl.obolibrary.org/obo/PR_000001196 PR http://purl.obolibrary.org/obo/GO_0006811 GO Blood Tests Detects systemic or metabolic causes of bradycardia by measuring electrolyte levels, thyroid function, and drug toxicity. in_vitro blood human electrolyte levels change http://purl.obolibrary.org/obo/CHEBI_24926 CHEBI high Detects systemic or metabolic causes of bradycardia. Electrolyte levels (e.g., hyperkalemia or hypokalemia). http://purl.obolibrary.org/obo/CHEBI_24926 CHEBI http://purl.obolibrary.org/obo/GO_0050801 GO Calcium Imaging Detects intracellular calcium cycling abnormalities in pacemaker cells using calcium-sensitive dyes. in_vitro pacemaker cells heart intracellular calcium cycling change http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/GO_0006816 GO medium Detects intracellular calcium cycling abnormalities in pacemaker cells. Use of calcium-sensitive dyes (e.g., Fluo-4, Fura-2) to track calcium transients. http://purl.obolibrary.org/obo/CHEBI_29108 CHEBI http://purl.obolibrary.org/obo/GO_0006816 GO Carotid Sinus Massage Evaluates baroreceptor sensitivity by observing bradycardia response to carotid sinus massage. in_vivo carotid sinus heart human heart rate response decrease high Evaluates baroreceptor sensitivity in suspected reflex bradycardia. Gentle massage of the carotid sinus to observe bradycardia response. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0042391 GO Connexin Studies Evaluates gap junction proteins for conduction abnormalities in cardiac tissue. in_vitro cardiac tissue heart gap junction protein expression change http://purl.obolibrary.org/obo/GO_0005921 GO http://purl.obolibrary.org/obo/PR_000000896 PR medium Evaluates gap junction proteins (e.g., Connexin 43, 45) for conduction abnormalities. http://purl.obolibrary.org/obo/GO_0005921 GO http://purl.obolibrary.org/obo/GO_0010646 GO ECG Electrocardiogram records the electrical activity of the heart to detect bradycardia, evaluate heart rhythm, and identify conduction abnormalities such as prolonged PR interval, sinus bradycardia, and bradyarrhythmias. in_vivo heart human heart rate (bpm), PR interval duration decrease not_specified Heart rate < 60 bpm (measured from R-R intervals). Prolonged PR interval (indicating slowed atrioventricular conduction). Sinus bradycardia: Normal P wave followed by a QRS complex. http://purl.obolibrary.org/obo/UBERON_0000945 UBERON http://purl.obolibrary.org/obo/GO_0002025 GO Echocardiography Echocardiography uses ultrasound to visualize cardiac structure and function, assessing chamber size and contractility to detect structural causes of bradycardia. in_vivo heart human cardiac chamber dimension or stroke volume change http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0003007 GO low Echocardiography Non-invasive visualization of cardiac structure and function. Evaluates structural causes (e.g., fibrosis, chamber enlargement) contributing to bradycardia. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0003007 GO Echocardiography Non-invasive visualization of cardiac structure and function to evaluate structural causes of bradycardia. in_vivo heart human cardiac structure and function change http://purl.obolibrary.org/obo/OBI_0000278 OBI http://purl.obolibrary.org/obo/UBERON_0010000 UBERON high Non-invasive visualization of cardiac structure and function. Evaluates structural causes (e.g., fibrosis, chamber enlargement) contributing to bradycardia. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0007507 GO Electrocardiogram (ECG) The gold standard for detecting bradycardia and evaluating heart rhythm by measuring heart rate and conduction intervals. in_vivo heart human heart rate decrease http://purl.obolibrary.org/obo/OBI_0000269 OBI high The gold standard for detecting bradycardia and evaluating heart rhythm. Heart rate < 60 bpm (measured from R-R intervals). http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Electrophysiology Study (EPS) Invasive procedure using catheter placement to map the heart’s electrical conduction system and identify areas of delayed or blocked conduction. in_vivo heart human conduction times change http://purl.obolibrary.org/obo/GO_0060048 GO low Detailed mapping of the heart’s electrical conduction system. Identifies the site of dysfunction (e.g., SA node, AV node, His-Purkinje system). http://purl.obolibrary.org/obo/UBERON_0005206 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Genetic Testing Identifies hereditary conditions predisposing to bradycardia through whole-genome or targeted sequencing. in_vitro human genetic mutations change http://purl.obolibrary.org/obo/SO_0000704 SO medium Identifies hereditary conditions predisposing to bradycardia. Whole-genome or targeted sequencing for mutations in HCN4, SCN5A, or other related genes. http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO Heart Rate Monitoring Simplified method to detect bradycardia by measuring beats per minute using manual pulse checks or wearable devices. in_vivo heart human beats per minute decrease high Simplified method to detect bradycardia. Beats per minute (bpm) measured over 30–60 seconds. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0002026 GO Holter Monitor Continuous 24-48 hour ambulatory ECG monitoring to detect intermittent bradycardia episodes and assess heart rate variability over extended periods. in_vivo heart human heart rate (bpm) over time decrease not_specified Continuous 24–48-hour monitoring to detect intermittent bradycardia. http://purl.obolibrary.org/obo/UBERON_0000945 UBERON http://purl.obolibrary.org/obo/GO_0002025 GO Immunostaining Detects and localizes ion channels and related proteins in cardiac tissue. in_vitro cardiac tissue heart protein localization change http://purl.obolibrary.org/obo/GO_0008104 GO medium Measures expression of ion channels (e.g., HCN4, Cav1.3, Kv channels). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0008104 GO Molecular Profiling Detects genetic or molecular abnormalities linked to bradycardia using qPCR, Western Blot, and Immunostaining. in_vitro http://purl.obolibrary.org/obo/CL_0000066 http://purl.obolibrary.org/obo/CL_0000067 http://purl.obolibrary.org/obo/UBERON_0000948 gene expression, protein levels change http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/GO_0005576 GO medium Measures expression of ion channels (e.g., HCN4, Cav1.3, Kv channels). http://purl.obolibrary.org/obo/GO_0010467 GO Molecular Profiling (qPCR, Western Blot, Immunostaining) Techniques used to measure the expression levels of specific ion channel proteins. in_vitro expression of ion channels change medium Measures expression of ion channels (e.g., HCN4, Cav1.3, Kv channels). http://purl.obolibrary.org/obo/GO_0006351 GO MRI or CT Scans Advanced imaging for structural abnormalities in the conduction system of the heart. in_vivo heart human structural abnormalities change http://purl.obolibrary.org/obo/UBERON_0010000 UBERON medium Advanced imaging for structural abnormalities in the conduction system. Detects fibrosis or infiltrative diseases affecting the SA or AV node. http://purl.obolibrary.org/obo/UBERON_0005206 UBERON http://purl.obolibrary.org/obo/GO_0007507 GO Optical Mapping Visualizes electrical activity in cardiac tissues using voltage-sensitive dyes to detect localized slowing in conduction velocity or pacemaker activity. in_vitro cardiac tissue heart conduction velocity decrease http://purl.obolibrary.org/obo/OBI_0000272 OBI http://purl.obolibrary.org/obo/GO_0060048 GO medium Visualizes electrical activity in cardiac tissues using voltage-sensitive dyes. Detects localized slowing in conduction velocity or pacemaker activity. http://purl.obolibrary.org/obo/UBERON_0002090 UBERON http://purl.obolibrary.org/obo/GO_0060048 GO Patch-Clamp Recording Directly measures ion channel activity in isolated pacemaker cells or conduction tissue to assess channel function. in_vitro pacemaker cells conduction tissue cells heart ion channel activity change http://purl.obolibrary.org/obo/OBI_0000273 OBI http://purl.obolibrary.org/obo/GO_0005216 GO low Directly measures ion channel activity in isolated pacemaker cells or conduction tissue. Reduced activity of HCN channels (funny current, If). http://purl.obolibrary.org/obo/GO_0005216 GO http://purl.obolibrary.org/obo/GO_0006811 GO qPCR Measures expression of ion channels and related genes in cardiac tissue. in_vitro cardiac tissue heart gene expression change http://purl.obolibrary.org/obo/OBI_0000275 OBI http://purl.obolibrary.org/obo/GO_0010467 GO high Measures expression of ion channels (e.g., HCN4, Cav1.3, Kv channels). http://purl.obolibrary.org/obo/SO_0000704 SO http://purl.obolibrary.org/obo/GO_0010467 GO Stress Testing Observes heart rate response to exercise to identify underlying pathology in bradycardia. in_vivo heart human heart rate response to exercise decrease medium To observe heart rate response to exercise. Bradycardia persisting during exercise indicates underlying pathology. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0002026 GO Valsalva Maneuver Tests autonomic control over heart rate by observing bradycardia triggered by exaggerated vagal response. in_vivo heart human heart rate response decrease http://purl.obolibrary.org/obo/OBI_0000281 OBI high Tests autonomic control over heart rate. Bradycardia triggered by exaggerated vagal response. http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/GO_0002116 GO Western Blot Measures protein expression of ion channels and related proteins in cardiac tissue. in_vitro cardiac tissue heart protein expression change http://purl.obolibrary.org/obo/GO_0010463 GO medium Measures expression of ion channels (e.g., HCN4, Cav1.3, Kv channels). http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0010463 GO estrogen serum levels Indirectly measures aromatase induction by quantifying estrogen levels in serum. in_vivo estrogen levels increase http://purl.obolibrary.org/obo/UBERON_0001967 UBERON medium Levels of estrogens in serum can offer an indirect measurement of aromatase induction. http://purl.obolibrary.org/obo/GO_0006706 GO immunohistochemistry Measures aromatase protein levels in tissue sections using immunohistochemistry. in_vivo aromatase protein levels increase http://purl.obolibrary.org/obo/OBI_0000691 OBI low Aromatase protein levels can be measured by Western blot from cell cultures and liver microsomal samples (You et al., 2001) and by immunohistochemistry on tissue sections (You et al., 2001, Segawa et al., 2005) http://purl.obolibrary.org/obo/GO_0010457 GO in situ hybridization Measures aromatase mRNA expression levels in tissue samples using in situ hybridization. in_vivo endometrial carcinoma tissue aromatase mRNA expression increase http://purl.obolibrary.org/obo/OBI_0000671 OBI low Aromatase mRNA expression can be measured by RT-PCR [in JEG-3 choriocarcinoma cells cultures (Laville et al., 2006); in H295R Human Adrenocortical Carcinoma Cells (Sanderson et al., 2002); in KGN Human Ovarian Granulose-Like Tumor Cell Line (Morinaga et al., 2004)] and in situ hybridization [endometrial carcinoma tissue samples (Segawa et al., 2005)] http://purl.obolibrary.org/obo/GO_0010467 GO RT-PCR Measures aromatase mRNA expression levels using reverse transcription polymerase chain reaction. in_vitro JEG-3 choriocarcinoma cells H295R Human Adrenocortical Carcinoma Cells KGN Human Ovarian Granulose-Like Tumor Cell Line aromatase mRNA expression increase medium Aromatase mRNA expression can be measured by RT-PCR [in JEG-3 choriocarcinoma cells cultures (Laville et al., 2006); in H295R Human Adrenocortical Carcinoma Cells (Sanderson et al., 2002); in KGN Human Ovarian Granulose-Like Tumor Cell Line (Morinaga et al., 2004)] http://purl.obolibrary.org/obo/GO_0010467 GO tritium release assay Measures catalytic aromatase activity by quantifying tritium released after the conversion of tritium-labelled androstenedione into estrone. in_vitro JEG-3 choriocarcinoma cells H295R Human Adrenocortical Carcinoma Cells KGN Human Ovarian Granulose-Like Tumor Cell Line liver aromatase activity increase low The catalytic aromatase activity was determined by using the tritium release assay (measurement of tritium released after the conversion of tritium-labelled androstenedione into estrone by cells or hepatic microsomes as described previously (Drenth et al., 1998; Lephart and Simpson, 1991) with minor modifications [in JEG-3 choriocarcinoma cells cultures (Laville, 2006); in H295R Human Adrenocortical Carcinoma Cells (Sanderson et al., 2002); in hepatic microsomal samples (You et al., 2001); in KGN Human Ovarian Granulose-Like Tumor Cell Line (Morinaga et al., 2004)]. http://purl.obolibrary.org/obo/GO_0003999 GO Western blot Measures aromatase protein levels using Western blot from cell cultures and liver microsomal samples. in_vitro liver aromatase protein levels increase http://purl.obolibrary.org/obo/OBI_0000690 OBI medium Aromatase protein levels can be measured by Western blot from cell cultures and liver microsomal samples (You et al., 2001) http://purl.obolibrary.org/obo/GO_0010457 GO immunoassay Measures estradiol levels using antibody-based detection methods, often in plasma or serum samples. in_vitro estradiol concentration increase http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI medium Estradiol can be measured via immunoassay, mass spectrometry or Western blotting, with immunoassay the preferred technique Studies that utilized immunoassay include (Sashida and Johnson 1976; Spears et al. 1998; Li et al. 2008; Murray et al. 2008; Gan et al. 2024), and include commercially available ELISA kits (e.g. Neogen 402110 (non-species specific); ALPCO 11-ESTHU-E01 (human); Cayman Chemical 501890 (non-species specific)) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO mass spectrometry Quantifies estradiol levels using mass spectrometry-based techniques, providing high specificity and sensitivity. in_vitro estradiol concentration increase http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/OBI_0000274 OBI low Estradiol can be measured via immunoassay, mass spectrometry or Western blotting, with immunoassay the preferred technique http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO Western blotting Detects estradiol or related proteins using antibody-based detection on a membrane, though less common for hormone quantification. in_vitro estradiol or related protein levels increase http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI low Estradiol can be measured via immunoassay, mass spectrometry or Western blotting, with immunoassay the preferred technique http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0046879 GO Calcium Imaging Tracks intracellular calcium transients using fluorescent calcium-sensitive dyes to measure real-time changes in intracellular calcium. in_vitro SA node cells intracellular calcium transients change http://purl.obolibrary.org/obo/OBI_0001851 OBI http://purl.obolibrary.org/obo/GO_0006816 GO medium Tracks intracellular calcium transients that occur during pacemaker activity. Fluorescent calcium-sensitive dyes (e.g., Fluo-4 or Fura-2) are used to measure real-time changes in intracellular calcium. http://purl.obolibrary.org/obo/CL_0000746 CL http://purl.obolibrary.org/obo/GO_0006816 GO Computational Modeling Simulates pacemaker activity based on measured parameters like ionic currents and channel expression to predict responses to interventions or mutations. in_silico simulated pacemaker activity change http://purl.obolibrary.org/obo/OBI_0000218 OBI http://purl.obolibrary.org/obo/GO_0006811 GO high Simulates pacemaker activity based on measured parameters like ionic currents and channel expression. Predicts responses to interventions or mutations in SA node cells. http://purl.obolibrary.org/obo/CL_0000746 CL http://purl.obolibrary.org/obo/GO_0006811 GO Confocal Microscopy Visualizes ion channel localization and structural features of SA node cells. in_vitro SA node cells ion channel localization change http://purl.obolibrary.org/obo/OBI_0001047 OBI http://purl.obolibrary.org/obo/GO_0005216 GO low Visualizes ion channel localization and structural features of SA node cells. http://purl.obolibrary.org/obo/GO_0005216 GO ECG (Electrocardiogram) Detects overall heart rhythm and indirectly assesses SA node function, identifying issues like sinus bradycardia or sinus arrest. in_vivo heart heart rhythm change http://purl.obolibrary.org/obo/OBI_0000269 OBI http://purl.obolibrary.org/obo/GO_0002162 GO high Detects overall heart rhythm and indirectly assesses SA node function. Identifies issues like sinus bradycardia or sinus arrest. http://purl.obolibrary.org/obo/UBERON_0005157 UBERON http://purl.obolibrary.org/obo/GO_0002027 GO Gene Expression Analysis Measures the expression of key ion channel genes using techniques such as qPCR, RNA sequencing, or in situ hybridization. in_vitro SA node cells SA node expression of key ion channel genes change high Measures the expression of key ion channel genes (e.g., HCN4, T-type, and L-type Ca²⁺ channels). Techniques: qPCR, RNA sequencing, or in situ hybridization. Gene Expression Analysis Quantifies the expression levels of key ion channel genes using techniques such as qPCR, RNA sequencing, or in situ hybridization. in_vitro gene expression change http://purl.obolibrary.org/obo/GO_0010367 GO high Measures the expression of key ion channel genes (e.g., HCN4, T-type, and L-type Ca²⁺ channels). Techniques: qPCR, RNA sequencing, or in situ hybridization. http://purl.obolibrary.org/obo/GO_0010367 GO Isolated Tissue Studies Measures spontaneous contractions and electrical activity in isolated SA node tissue using organ baths or Langendorff-perfused heart models. ex_vivo SA node spontaneous contractions change http://purl.obolibrary.org/obo/GO_0006936 GO low Measures spontaneous contractions and electrical activity in isolated SA node tissue. Techniques: Use of organ baths or Langendorff-perfused heart models. http://purl.obolibrary.org/obo/UBERON_0005157 UBERON http://purl.obolibrary.org/obo/GO_0006936 GO Microelectrode Array (MEA) Measures electrical signals from a population of cells in culture, detecting spontaneous action potentials generated by pacemaker cells. in_vitro SA node cells spontaneous action potentials change http://purl.obolibrary.org/obo/OBI_0001471 OBI http://purl.obolibrary.org/obo/GO_0001508 GO medium Measures electrical signals from a population of cells in culture. Detects spontaneous action potentials generated by pacemaker cells. http://purl.obolibrary.org/obo/CL_0000746 CL http://purl.obolibrary.org/obo/GO_0001508 GO MRI/CT Scans Provides anatomical imaging of the SA node in large-scale studies, though resolution is limited. in_vivo SA node anatomical imaging not_specified http://purl.obolibrary.org/obo/OBI_0000215 OBI http://purl.obolibrary.org/obo/OBI_0000214 OBI high Provides anatomical imaging of the SA node in large-scale studies, though resolution is limited. http://purl.obolibrary.org/obo/UBERON_0005157 UBERON Optical Mapping Monitors voltage changes across a tissue using voltage-sensitive dyes to track electrical activity visually. ex_vivo SA node voltage changes change http://purl.obolibrary.org/obo/GO_0001538 GO medium Monitors voltage changes across a tissue. Useful for observing SA node function in situ or in isolated tissue. Voltage-sensitive dyes are used to track electrical activity visually. http://purl.obolibrary.org/obo/UBERON_0005157 UBERON http://purl.obolibrary.org/obo/GO_0042391 GO Patch-Clamp Technique Records ionic currents across the cell membrane and characterizes action potentials in single pacemaker cells using a glass micropipette electrode. in_vitro SA node cells ionic currents change http://purl.obolibrary.org/obo/GO_0005249 GO low Records ionic currents across the cell membrane. Measures specific currents (e.g., If current through HCN channels, Ca²⁺, and K⁺ currents). Characterizes action potentials in single pacemaker cells. http://purl.obolibrary.org/obo/CL_0000746 CL http://purl.obolibrary.org/obo/GO_0034765 GO Pharmacological Testing Evaluates the response of SA node cells to drugs targeting ion channels, such as If inhibitors or calcium/potassium channel blockers. in_vitro SA node cells response to drugs change http://purl.obolibrary.org/obo/GO_0005216 GO low Evaluates the response of SA node cells to drugs targeting ion channels. If inhibitors (e.g., Ivabradine) to study funny current activity. Calcium or potassium channel blockers to assess their contribution to pacemaker function. http://purl.obolibrary.org/obo/GO_0005216 GO http://purl.obolibrary.org/obo/GO_0006811 GO Protein Detection Identifies ion channel proteins using Western blotting, immunocytochemistry, or flow cytometry. in_vitro ion channel protein presence/abundance change medium Identifies ion channel proteins involved in pacemaker activity. Techniques: Western blotting, immunocytochemistry, or flow cytometry. qPCR Measures the expression of key ion channel genes such as HCN4, T-type, and L-type Ca²⁺ channels. in_vitro SA node cells gene expression change http://purl.obolibrary.org/obo/OBI_0000662 OBI http://purl.obolibrary.org/obo/GO_0010467 GO medium Measures the expression of key ion channel genes (e.g., HCN4, T-type, and L-type Ca²⁺ channels). Techniques: qPCR, RNA sequencing, or in situ hybridization. http://purl.obolibrary.org/obo/PR_000001150 PR http://purl.obolibrary.org/obo/GO_0010467 GO Western blotting Identifies ion channel proteins involved in pacemaker activity. in_vitro SA node cells protein expression change http://purl.obolibrary.org/obo/GO_0010457 GO low Identifies ion channel proteins involved in pacemaker activity. Techniques: Western blotting, immunocytochemistry, or flow cytometry. http://purl.obolibrary.org/obo/GO_0005216 GO http://purl.obolibrary.org/obo/GO_0010457 GO ELISA An immunoassay technique used to quantify testosterone levels in testis tissue or homogenate. in_vitro testis testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI medium traditional immunoassays such as ELISA http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006724 GO LC-MS/MS A liquid chromatography-tandem mass spectrometry technique used to quantify testosterone levels in testis tissue or homogenate. in_vitro testis testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/OBI_0001047 OBI medium advanced techniques like LC-MS/MS http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006724 GO liquid scintillation spectrometry A technique used to quantify radiolabeled testosterone levels in testis tissue or homogenate. in_vitro testis testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/OBI_0000275 OBI medium liquid scintillation spectrometry following radiolabeling http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006724 GO RIA A radioimmunoassay technique used to quantify testosterone levels in testis tissue or homogenate. in_vitro testis testosterone levels decrease http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI medium traditional immunoassays such as RIA http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/GO_0006724 GO NAD+/NADH ratio measurement Measures the ratio of NAD+ to NADH, which is an indicator of redox homeostasis. not_specified NAD+/NADH ratio change http://purl.obolibrary.org/obo/CHEBI_15846 CHEBI http://purl.obolibrary.org/obo/CHEBI_16908 CHEBI http://purl.obolibrary.org/obo/GO_0045454 GO not_specified Measure the NAD+/NADH ratio and other oxidative biomarkers. http://purl.obolibrary.org/obo/CHEBI_15846 CHEBI http://purl.obolibrary.org/obo/GO_0045454 GO oxidative biomarkers measurement Measures other oxidative biomarkers to assess redox homeostasis. not_specified oxidative biomarkers change http://purl.obolibrary.org/obo/GO_0006979 GO not_specified Measure the NAD+/NADH ratio and other oxidative biomarkers. http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0006979 GO metabolomics analysis Measures metabolic profiles and related biomarkers to assess disruptions in glucolipid metabolism. not_specified metabolic profiles and biomarkers not_specified not_specified Metabolomics analysis and related biomarkers. Behavior test A test to measure abnormal behavior in subjects. not_specified abnormal behavior not_specified http://purl.obolibrary.org/obo/GO_0007610 GO not_specified Behavior test. http://purl.obolibrary.org/obo/GO_0007610 GO Zebrafish Larvae Morphological Examination This assay examines the morphological features of zebrafish larvae to detect malformations. in_vivo Danio rerio malformations increase not_specified Zebrafish Larvae Morphological Examination enzyme-linked immunosorbent assay A method for measuring serum estrogen and progesterone levels using enzyme-linked antibodies. in_vitro blood serum estrogen and progesterone levels not_specified medium Standard methods for serum estrogen and progesterone analysis include enzyme-linked immunosorbent assay (ELISA) LC/MS Liquid chromatography/mass spectrometry (LC/MS) is used to measure serum estrogen and progesterone levels in rodents. in_vitro serum rodents serum estrogen and progesterone levels increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/CHEBI_16236 CHEBI OECD TG 408 not_specified Liquid chromatography/mass spectrometry (LC/MS)-based methods are also becoming more widely used (as cost and sample size requirements decrease), particularly for measurement of estrogens and estrogen metabolites. http://purl.obolibrary.org/obo/CHEBI_24431 CHEBI liquid chromatography/mass spectrometry A method for measuring estrogens and estrogen metabolites using liquid chromatography coupled with mass spectrometry. in_vitro blood estrogens and estrogen metabolites not_specified medium Liquid chromatography/mass spectrometry (LC/MS)-based methods are also becoming more widely used (as cost and sample size requirements decrease), particularly for measurement of estrogens and estrogen metabolites. multiplex immunoassay A method for simultaneously measuring multiple analytes, including serum estrogen and progesterone levels, using multiple antibodies. in_vitro blood serum estrogen and progesterone levels not_specified high Standard methods for serum estrogen and progesterone analysis include multiplex immunoassay radioimmunoassay A method for measuring serum estrogen and progesterone levels using radioactive isotopes. in_vitro blood serum estrogen and progesterone levels not_specified medium Standard methods for serum estrogen and progesterone analysis include radioimmunoassay (RIA) Anti-Müllerian hormone (AMH) measurement This assay measures the levels of Anti-Müllerian hormone (AMH) as a biomarker for estimating the follicular pool in humans. in_vivo human levels of Anti-Müllerian hormone (AMH) change http://purl.obolibrary.org/obo/CHEBI_60474 CHEBI medium The follicular pool in humans cannot be directly counted in vivo. Surrogate markers are employed instead. Anti-Müllerian hormone (AMH) is the most well-established biomarker for estimating the follicular pool. http://purl.obolibrary.org/obo/GO_0001541 GO Follicle counting (histological) Quantitative and qualitative histological examination of ovarian tissue sections to count primordial and developing follicles. in_vivo ovary follicle count change http://purl.obolibrary.org/obo/CL_0000440 CL http://purl.obolibrary.org/obo/GO_0007532 GO OECD 416, OECD 443, U.S. FDA Redbook 2000 low qualitative analysis of the F0 generation's ovaries to identify the depletion of primordial follicles. Counting how many F1 primordial follicles are there in ovaries using quantitative evaluation Examining the ovaries histologically is highlighted in the guideline for determining follicle numbers. Primordial, primary, secondary, and antral follicles are among the several follicle stages that can be examined under a microscope by sectioning and staining ovarian tissue. Follicle counts are done to identify any possible harmful effects on folliculogenesis Quantitative analysis is used to ascertain how many primordial follicles are present http://purl.obolibrary.org/obo/CL_0000440 CL http://purl.obolibrary.org/obo/GO_0007532 GO OECD 416 two generation reproductive toxicity study This assay involves weighing ovaries and qualitative analysis to identify depletion of primordial follicles, followed by quantitative evaluation of primordial follicles in F1 generation ovaries. in_vivo ovary number of primordial follicles decrease http://purl.obolibrary.org/obo/GO_0001544 GO http://purl.obolibrary.org/obo/UBERON_0000992 UBERON OECD TG 416 low OECD 416 two generation reproductive toxicity study (2001): Weigh each ovary separately. qualitative analysis of the F0 generation's ovaries to identify the depletion of primordial follicles. Counting how many F1 primordial follicles are there in ovaries using quantitative evaluation (may be paired with small developing follicles). http://purl.obolibrary.org/obo/GO_0001544 GO http://purl.obolibrary.org/obo/GO_0001541 GO Ovarian follicle count (OECD 416) This assay measures the number of primordial follicles in ovaries through histological sectioning and qualitative/quantitative analysis to detect depletion. in_vivo ovary primordial follicle count decrease http://purl.obolibrary.org/obo/UBERON_0000035 UBERON OECD 416 low OECD 416 two generation reproductive toxicity study (2001): Weigh each ovary separately. qualitative analysis of the F0 generation's ovaries to identify the depletion of primordial follicles. Counting how many F1 primordial follicles are there in ovaries using quantitative evaluation (may be paired with small developing follicles). Although not required, the selection of ovarian portions, quantity of animals, and section process must all be statistically reliable http://purl.obolibrary.org/obo/UBERON_0000035 UBERON http://purl.obolibrary.org/obo/GO_0001558 GO qualitative ovarian analysis Qualitative analysis of ovaries to identify the depletion of primordial follicles. in_vivo ovary primordial follicle depletion decrease OECD 416 low qualitative analysis of the F0 generation's ovaries to identify the depletion of primordial follicles. Ovarian qualitative analysis to identify degradation of primordial follicles. http://purl.obolibrary.org/obo/GO_0008752 GO histological examination Histological examination of reproductive organs (vagina, cervix, uterine horns, ovaries) assesses estrous stage and identifies features like follicular cysts and changes in uterine epithelium. It is invasive. in_vivo vagina cervix uterus ovary rat mouse presence of follicular cysts, uterine epithelium height, vaginal cornification change low This technique is invasive and does not allow individual estrous cyclicity assessment. Persistent estrous is characterized in ovary by the presence of numbers of ovarian follicular cysts vagina may show cornification (Westwood, 2008, Dixon, 2014, Shirai 2017, see also Fig. 16). http://purl.obolibrary.org/obo/UBERON_0004635 UBERON http://purl.obolibrary.org/obo/GO_0008737 GO Histological examination Microscopic examination of longitudinal and transverse tissue sections of the vagina, cervix, uterine horns, and ovaries to assess estrous staging and reproductive organ pathology. ex_vivo vagina cervix uterine horns ovaries tissue morphology and presence of follicular cysts/corpora lutea change OECD TG 443 low Histological examination of the reproductive organs The minimal requirement for estrous staging evaluation by histology is the complete longitudinal sections of the vagina and cervix, transverse sections of the mid-portion of both uterine horns, and middle sections of both ovaries Persistent estrous is characterized in ovary by the presence of numbers of ovarian follicular cysts (due to pre-ovulatory follicles losing the capacity to ovulate) absence of basophilic corpora lutea and decreased corpora lutea while uterine epithelium becomes tall columnar and vagina may show cornification http://purl.obolibrary.org/obo/UBERON_0001135 UBERON http://purl.obolibrary.org/obo/GO_0016581 GO Histological examination of reproductive organs Microscopic examination of longitudinal sections of the vagina, cervix, uterine horns, and ovaries to assess estrous staging and reproductive health. ex_vivo vagina cervix uterine horns ovaries rat mouse histological changes in reproductive organs change http://purl.obolibrary.org/obo/UBERON_0000992 UBERON http://purl.obolibrary.org/obo/UBERON_0000995 UBERON http://purl.obolibrary.org/obo/UBERON_0000996 UBERON http://purl.obolibrary.org/obo/UBERON_0003351 UBERON OECD TG 443 low The minimal requirement for estrous staging evaluation by histology is the complete longitudinal sections of the vagina and cervix, transverse sections of the mid-portion of both uterine horns, and middle sections of both ovaries (Goldman 2007; Byers, 2012). Persistent estrous is characterized in ovary by the presence of numbers of ovarian follicular cysts (due to pre-ovulatory follicles losing the capacity to ovulate) absence of basophilic corpora lutea and decreased corpora lutea while uterine epithelium becomes tall columnar and vagina may show cornification (Westwood, 2008, Dixon, 2014, Shirai 2017, see also Fig. 16). http://purl.obolibrary.org/obo/UBERON_0000992 UBERON http://purl.obolibrary.org/obo/GO_0019953 GO Urine biochemistry Analysis of urine composition to determine estrous cycle stage. in_vivo urine biochemical markers change http://purl.obolibrary.org/obo/UBERON_0001088 UBERON medium Vaginal wall impedance and urine biochemistry are alternative methods. http://purl.obolibrary.org/obo/UBERON_0001088 UBERON http://purl.obolibrary.org/obo/GO_0042698 GO vaginal smear Estrous cycle is monitored by observing changes in vaginal smear cytology, looking for cornified epithelial cells. It is non-invasive and inexpensive. in_vivo epithelial cells vagina rat mouse number of cornified epithelial cells increase www.oecd.org medium Estrous cycle can be monitored in the rat and mouse by observing the changes in the vaginal smear cytology. It seems to be the most common technique used to determine the phases of the estrous cycle. The estrous phase shows abundant non-nucleate cornified epithelial cells. http://purl.obolibrary.org/obo/CL_0002149 CL http://purl.obolibrary.org/obo/GO_0008283 GO Vaginal smear cytology Observation of changes in vaginal smear cytology to determine the phases of the estrous cycle in rodents. The estrous phase shows abundant non-nucleate cornified epithelial cells with granular cytoplasm and irregular cell shape. Persistent estrous is characterized by cornified vaginal smears for 10 or more days. in_vivo vagina cervix uterine horns ovaries rat mouse Estrous cycle phase not_specified http://purl.obolibrary.org/obo/UBERON_0001705 UBERON http://purl.obolibrary.org/obo/GO_0001525 GO http://purl.obolibrary.org/obo/CL_0000000 CL OECD TG 421, OECD TG 422, OECD TG 416, OECD TG 443, USA EPA OCSPP 890.1450 low The estrous phase shows abundant non-nucleate cornified epithelial cells. The cytoplasm is granular, and the cells are irregular in shape. Persistent estrous is characterized by cornified vaginal smears for 10 or more days. Monitoring of estrous cyclicity is included in OECD test guidelines (TG 421: Reproduction/Developmental Toxicity Screening Test, 2016; TG 422 Combined Repeated Dose Toxicity Study with the Reproduction/Developmental Toxicity Screening Test, 2016; TG 416: Two-Generation Reproduction Toxicity, 2001; TG 443: Extended One-Generation Reproductive Toxicity Study, 2018; and in USA EPA OCSPP 890.1450. Pubertal Development and Thyroid Function in Intact Juvenile/Peripubertal Female Rats Assay, 2011. Vaginal smear at necropsy is also required in OECD TG 408, OECD TG 421, OECD TG 422 while it is optional in OECD TG 407. http://purl.obolibrary.org/obo/CL_0000010 CL http://purl.obolibrary.org/obo/UBERON_0001705 UBERON Vaginal smear cytology Collection and microscopic examination of vaginal cells to determine the stage of the estrous cycle based on cellular morphology. in_vivo vagina rat mouse vaginal cytology change http://purl.obolibrary.org/obo/GO_0042698 GO OECD TG 421, OECD TG 422, OECD TG 416, OECD TG 443, USA EPA OCSPP 890.1450 medium Estrous cycle can be monitored in the rat and mouse by observing the changes in the vaginal smear cytology. The estrous phase shows abundant non-nucleate cornified epithelial cells. Persistent estrous is characterized by cornified vaginal smears for 10 or more days. http://purl.obolibrary.org/obo/GO_0042698 GO Vaginal wall impedance Measurement of electrical impedance of the vaginal wall to determine estrous cycle stage. in_vivo vagina vaginal wall impedance change http://purl.obolibrary.org/obo/UBERON_0000996 UBERON medium Vaginal wall impedance and urine biochemistry are alternative methods. http://purl.obolibrary.org/obo/UBERON_0000996 UBERON http://purl.obolibrary.org/obo/GO_0042698 GO Visual assessment of estrous cycle Visual observation of the vaginal opening to identify proestrous or estrous stages based on physical characteristics such as swelling, moisture, and color. in_vivo vagina mouse rat estrous cycle stage change http://purl.obolibrary.org/obo/GO_0042698 GO http://purl.obolibrary.org/obo/UBERON_0000996 UBERON high Visual observation of the vagina is the fastest method. It requires no special equipment and is best used when only proestrous or estrous stages need to be identified. In the proestrous phase, the vaginal opening appears full, swollen and moist (Ajayi, 2020). The vaginal opening of mice in proestrous is characterized by swollen, moist, pink tissue. http://purl.obolibrary.org/obo/UBERON_0000996 UBERON http://purl.obolibrary.org/obo/GO_0042698 GO Visual assessment of vaginal opening Visual observation of the vagina to identify proestrous or estrous stages. In proestrous the vaginal opening appears full, swollen and moist; as the mouse enters estrous the opening becomes less pink, less moist, and less swollen. in_vivo vagina mouse vaginal opening morphology and swelling change http://purl.obolibrary.org/obo/UBERON_0001029 UBERON low Visual observation of the vagina is the fastest method. In the proestrous phase, the vaginal opening appears full, swollen and moist (Ajayi, 2020). As the mouse enters estrous, the vaginal opening becomes less pink, less moist, and less swollen (Byers, 2012). http://purl.obolibrary.org/obo/UBERON_0001029 UBERON http://purl.obolibrary.org/obo/GO_0065007 GO visual observation Visual observation of the vagina assesses estrous stage by observing the appearance of the vaginal opening (fullness, swelling, moisture, color). It is non-invasive but subjective. in_vivo vagina mouse rat vaginal opening appearance change low Visual observation of the vagina is the fastest method. It requires no special equipment and is best used when only proestrous or estrous stages need to be identified. In the proestrous phase, the vaginal opening appears full, swollen and moist (Ajayi, 2020). http://purl.obolibrary.org/obo/UBERON_0004735 UBERON http://purl.obolibrary.org/obo/GO_0008283 GO chlorophyll a fluorescence Fluorescence measurements are used as indirect indicators of QB-site occupation, detecting changes in fluorescence yield and PSII photochemical efficiency due to disrupted electron transfer. in_vitro fluorescence yield and PSII photochemical efficiency change high Fluorescence-based techniques, including chlorophyll a fluorescence measurements, are frequently applied as indirect but sensitive indicators of QB-site occupation. Inhibitor binding disrupts electron transfer from QA to QB, leading to characteristic changes in fluorescence yield and PSII photochemical efficiency (Sundby, Chow and Anderson, 1993; Maxwell and Johnson, 2000). isothermal titration calorimetry ITC provides label-free, real-time measurements of binding kinetics and thermodynamics between PSII inhibitors and PSII protein complexes or isolated D1 fragments. in_vitro binding affinity, stoichiometry, and energetics not_specified medium Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) provide label-free, real-time measurements of binding kinetics and thermodynamics between PSII inhibitors and PSII protein complexes or isolated D1 fragments. molecular docking Molecular docking is used to predict the binding orientation of PSII inhibitors within the QB niche of the D1 protein. in_silico predicted binding orientation not_specified high In silico approaches, including quantitative structure–activity relationship (QSAR) modelling and molecular docking, are widely used to predict the affinity and binding orientation of PSII inhibitors within the QB niche of the D1 protein. QSAR modelling Quantitative structure–activity relationship modelling is used to predict the affinity and binding orientation of PSII inhibitors within the QB niche of the D1 protein. in_silico predicted binding affinity and orientation not_specified high In silico approaches, including quantitative structure–activity relationship (QSAR) modelling and molecular docking, are widely used to predict the affinity and binding orientation of PSII inhibitors within the QB niche of the D1 protein. radioligand binding assay Radiolabelled herbicides are used to quantify competitive displacement of plastoquinone or reference inhibitors from isolated thylakoid membranes or PSII preparations. in_vitro thylakoid membranes binding constants and competitive inhibition profiles not_specified medium Radioligand binding assays represent a classical and highly specific experimental approach, in which radiolabelled herbicides are used to directly quantify competitive displacement of plastoquinone or reference inhibitors from isolated thylakoid membranes or PSII preparations (Tischer and Strotmann, 1977; Vermaas, Renger and Arntzen, 1984). Radioligand binding assay Uses radiolabelled herbicides to directly quantify competitive displacement of plastoquinone or reference inhibitors from isolated thylakoid membranes or PSII preparations. in_vitro thylakoid membranes competitive displacement of plastoquinone or reference inhibitors change not_specified Radioligand binding assays represent a classical and highly specific experimental approach, in which radiolabelled herbicides are used to directly quantify competitive displacement of plastoquinone or reference inhibitors from isolated thylakoid membranes or PSII preparations These assays provide quantitative binding constants and competitive inhibition profiles. resistance mutant analysis Analyses of naturally occurring or experimentally induced mutations in the psbA gene encoding the D1 protein are used to link chemical binding to functional inhibition and photosynthetic impairment. in_vitro sensitivity to inhibitors change low Resistance mutant analyses, based on naturally occurring or experimentally induced mutations in the psbA gene encoding the D1 protein, offer strong mechanistic evidence for Q B -site binding. http://purl.obolibrary.org/obo/GO_0015979 GO resistance mutant analysis Analyses of naturally occurring or experimentally induced mutations in the psbA gene encoding the D1 protein to assess altered sensitivity to PSII inhibitors. in_vivo sensitivity to PSII inhibitors change low Resistance mutant analyses, based on naturally occurring or experimentally induced mutations in the psbA gene encoding the D1 protein, offer strong mechanistic evidence for QB-site binding. Altered sensitivity to PSII inhibitors in mutants affecting key QB-site residues (e.g. Ser-264/268) directly links chemical binding to functional inhibition and photosynthetic impairment (Sundby, Chow and Anderson, 1993; Alfonso et al., 1996; Oettmeier, 1999). surface plasmon resonance SPR provides label-free, real-time measurements of binding kinetics and thermodynamics between PSII inhibitors and PSII protein complexes or isolated D1 fragments. in_vitro binding affinity, stoichiometry, and energetics not_specified medium Surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) provide label-free, real-time measurements of binding kinetics and thermodynamics between PSII inhibitors and PSII protein complexes or isolated D1 fragments. X-ray crystallography X-ray crystallography of PSII complexes is used to visualize herbicide occupancy within the QB site, confirming binding modes and key amino-acid interactions at atomic resolution. in_vitro atomic resolution structure of herbicide binding not_specified low Finally, structural biology approaches, including X-ray crystallography of PSII complexes, have provided direct visualization of herbicide occupancy within the QB site, confirming binding modes and key amino-acid interactions at atomic resolution (Broser et al., 2011; Zimmermann et al., 2006). X-ray crystallography X-ray crystallography of PSII complexes provides direct visualization of herbicide occupancy within the QB site, confirming binding modes and key amino-acid interactions. in_vitro herbicide occupancy not_specified http://purl.obolibrary.org/obo/OBI_0000489 OBI low Finally, structural biology approaches, including X-ray crystallography of PSII complexes, have provided direct visualization of herbicide occupancy within the QB site, confirming binding modes and key amino-acid interactions at atomic resolution (Broser et al., 2011; Zimmermann et al., 2006). http://purl.obolibrary.org/obo/GO_0005102 GO antagonist compound assay Measures receptor stimulation indirectly by blocking activation using specific antagonists (e.g., methysergide, 8-OH-DPAT, MK212, WAY 161503). not_specified brain receptor activation decrease not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors by serotonin (5-HT) is often measured indirectly by use of antagonist compounds to block activation of receptors (methysergide for 5-HT1/5-HT2 in Ortega et al. 2013, 8-OH-DPAT for 5-HT1a in Perez-Maceira et al. 2014 and Perez-Maceria et al. 2016; MK212 for 5-HT2c in Perez-Maceira et al. 2014 and Perez-Maceria et al. 2016; WAY 161503 for 5-HT2c in Perez-Maceria et al. 2016; overview of compounds in Barnes et al. 2021). immunohistochemistry Localizes and detects protein expression of 5-HT1a and 5-HT2c receptors in brain tissue. not_specified brain protein expression increase not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including radiolabeled compounds, receptor binding, real time PCR, in situ hybridization, Western and Northern blotting, and immunohistochemistry immunohistochemistry Technique used to visualize the distribution of specific proteins in tissue sections using antibodies. ex_vivo brain protein localization not_specified http://purl.obolibrary.org/obo/GO_0030236 GO not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including [...] immunohistochemistry http://purl.obolibrary.org/obo/GO_0030236 GO in situ hybridization Detects and localizes mRNA expression of 5-HT1a and 5-HT2c receptors in brain tissue. not_specified brain mRNA expression increase not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including radiolabeled compounds, receptor binding, real time PCR, in situ hybridization in situ hybridization Laboratory technique used to localize specific nucleic acid sequences within biological tissue. ex_vivo brain mRNA localization not_specified http://purl.obolibrary.org/obo/GO_0030236 GO not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including [...] in situ hybridization http://purl.obolibrary.org/obo/GO_0010467 GO northern blot This assay measures the stimulation of brain 5-HT1a and 5-HT2c receptors by quantifying RNA levels using Northern blotting. in_vitro brain RNA levels increase low Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including radiolabeled compounds, receptor binding, real time PCR, in situ hybridization, Western and Northern blotting, and immunohistochemistry (Barnes et al. 2021). http://purl.obolibrary.org/obo/CHEBI_50887 CHEBI http://purl.obolibrary.org/obo/GO_0006261 GO radiolabeled compounds Uses radiolabeled compounds to study the stimulation of brain 5-HT1a and 5-HT2c receptors. not_specified brain receptor stimulation increase not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including radiolabeled compounds real time PCR Quantifies gene expression levels of 5-HT1a and 5-HT2c receptors. not_specified brain gene expression increase not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including radiolabeled compounds, receptor binding, real time PCR receptor binding Measures the binding of ligands to brain 5-HT1a and 5-HT2c receptors. not_specified brain receptor binding increase not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including radiolabeled compounds, receptor binding Western blotting Detects and quantifies protein levels of 5-HT1a and 5-HT2c receptors. not_specified brain protein expression increase not_specified Stimulation of brain 5-HT1a, 5-HT2c receptors have been studied by a variety of techniques including radiolabeled compounds, receptor binding, real time PCR, in situ hybridization, Western and Northern blotting histological examination Detects increased nasal lesions through microscopic examination of nasal tissue sections. in_vivo nasal tissue nasal lesions increase low Increased nasal lesions are detected from histological examination of nasal tissue. http://purl.obolibrary.org/obo/UBERON_0001704 UBERON http://purl.obolibrary.org/obo/GO_0009605 GO chest x-ray Detects increased pulmonary edema through radiographic imaging of the chest. in_vivo lung pulmonary edema increase http://purl.obolibrary.org/obo/MP_0002115 MP http://purl.obolibrary.org/obo/OBI_0000275 OBI medium Clinically, chest x-rays, ultrasound, and other imaging techniques can be used. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0043209 GO histological examination Detects increased pulmonary edema through microscopic examination of tissue sections. in_vivo lung pulmonary edema increase http://purl.obolibrary.org/obo/MP_0002115 MP http://purl.obolibrary.org/obo/UBERON_0002048 UBERON low Increased pulmonary edema is detected from histological examination. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0043209 GO imaging techniques Other imaging techniques are used clinically to detect increased pulmonary edema by visualizing lung tissue abnormalities. in_vivo lung pulmonary edema increase http://purl.obolibrary.org/obo/UBERON_0002048 UBERON low Clinically, chest x-rays, ultrasound, and other imaging techniques can be used. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON ultrasound Detects increased pulmonary edema through ultrasonic imaging of the chest. in_vivo lung pulmonary edema increase http://purl.obolibrary.org/obo/MP_0002115 MP medium Clinically, chest x-rays, ultrasound, and other imaging techniques can be used. http://purl.obolibrary.org/obo/UBERON_0002048 UBERON http://purl.obolibrary.org/obo/GO_0043209 GO behavioral studies Assessment of olfactory function in laboratory mammals by measuring their ability to avoid odors or detect food. This assesses the behavioral response to olfactory stimuli. in_vivo olfactory bulb olfactory epithelium laboratory mammals ability to avoid odors or detect food decrease http://purl.obolibrary.org/obo/GO_0008318 GO medium In laboratory mammals, loss of olfactory function is often detected in behavioral studies in which laboratory mammals lose the ability to avoid odors or detect food. http://purl.obolibrary.org/obo/UBERON_0002038 UBERON http://purl.obolibrary.org/obo/GO_0009249 GO behavioral studies Detects loss of olfactory function in laboratory mammals by assessing their ability to avoid odors or detect food. in_vivo olfactory system mammals olfactory function decrease low In laboratory mammals, loss of olfactory function is often detected in behavioral studies in which laboratory mammals lose the ability to avoid odors or detect food. http://purl.obolibrary.org/obo/UBERON_0001823 UBERON http://purl.obolibrary.org/obo/GO_0007608 GO odor testing Detects loss of olfactory function in humans via clinical odor testing. in_vivo olfactory system human olfactory function decrease low Loss of olfactory function can be detected clinically in humans via odor testing. http://purl.obolibrary.org/obo/UBERON_0001823 UBERON http://purl.obolibrary.org/obo/GO_0007608 GO flow cytometry Measures the level of PD-L1 protein expression on the cell surface of cancer cells using fluorescently labeled antibodies, allowing quantification of membrane-bound PD-L1. in_vitro cancer cells tumor human membrane-bound PD-L1 expression level increase http://purl.obolibrary.org/obo/OBI_0000471 OBI http://purl.obolibrary.org/obo/GO_0009897 GO medium PD-L1 ... can be expressed in several forms: cytoplasmic, membrane-bound, soluble, or in extracellular vesicles. the membrane form is the most well-documented, particularly for inhibiting T cell activity (Lin et al., 2024). tumor cells overexpress this ligand http://purl.obolibrary.org/obo/PR_000007059 PR http://purl.obolibrary.org/obo/GO_0006955 GO PD-L1 expression analysis Measures the overexpression of PD-L1 in cancer cells, which is associated with immune escape and tumor microenvironment establishment. not_specified cancer cells PD-L1 expression level increase http://purl.obolibrary.org/obo/GO_0002757 GO not_specified PD-L1 (Programmed Death-Ligand 1, or B7-H1/CD274) is known to be a promising therapeutic target in the development of anti-tumor treatments. In the context of cancer, tumor cells overexpress this ligand, which contributes to immune escape and the establishment of the Tumor MicroEnvironment (TME) (Riella et al., 2012). http://purl.obolibrary.org/obo/PR_P20844 PR http://purl.obolibrary.org/obo/GO_0006955 GO western blot Western blot is used to detect the expression levels of PD-L1, a membrane protein, by identifying its IgV and IgC domains. This allows for the assessment of PD-L1 overexpression in cancer cells. not_specified cancer cells T lymphocytes B lymphocytes tumor microenvironment PD-L1 protein expression levels increase low PD-L1 is a membrane protein belonging to the immunoglobulin family (IgSF). It has two main domains: an N-terminal variable immunoglobulin (IgV) domain and a C-terminal constant immunoglobulin (IgC) domain (Lin et al., 2008) (Jiang et al., 2019). In the context of cancer, tumor cells overexpress this ligand, which contributes to immune escape and the establishment of the Tumor MicroEnvironment (TME) (Riella et al., 2012). http://purl.obolibrary.org/obo/GO_0006470 GO CD25 expression assay Measures the expression of CD25 (Interleukin 2 receptor ɑ-chain), a marker of Treg cells. not_specified CD4+ lymphocytes CD25 expression not_specified not_specified they are also characterized by a high expression of CD25 (Interleukin 2 receptor ɑ-chain) flow cytometry Flow cytometry is used to identify and quantify CD4+ lymphocytes, differentiating between Th17 and Treg cells based on surface markers and intracellular proteins. not_specified CD4+ lymphocytes Treg cells Th17 cells ratio of Th17 to Treg cells change medium The ratio between Th17 and T regulatory (Treg) cells is essential for maintaining a balanced immune environment Both cells are derived from CD4+ lymphocytes, a subset of T lymphocytes. In cancer or in autoimmune diseases, this balance between the two phenotypes is disturbed with a higher presence of Treg and leads to adverse outcomes http://purl.obolibrary.org/obo/CL_0002163 CL http://purl.obolibrary.org/obo/GO_0030097 GO FoxP3 expression assay Measures the expression of FoxP3, a transcription factor that reflects Treg activity. not_specified CD4+ lymphocytes FoxP3 expression not_specified not_specified the expression of FoxP3 well reflects the Treg activity (Fontenot et al., 2003) Pro-inflammatory cytokine measurement Quantification of IL-17, IL-22, or IL-23 production to identify Th17 cell activity. not_specified Th17 cells CD4+ lymphocytes IL-17, IL-22, or IL-23 levels increase not_specified the role of Th17 cells is to enhance the immune response by producing pro-inflammatory signals like IL-17, IL-22, or IL-23 http://purl.obolibrary.org/obo/GO_0019864 GO Treg/Th17 cell ratio assessment Evaluation of the balance between T regulatory (Treg) and Th17 cell populations, inferred through the expression of lineage-specific markers such as FoxP3, CD25, and pro-inflammatory cytokines (IL-17, IL-22, IL-23). Specific laboratory methodology is not separately recorded in the provided text. not_specified CD4+ lymphocytes T regulatory cells Th17 cells Treg/Th17 cell ratio change not_specified The ratio between Th17 and T regulatory (Treg) cells is essential for maintaining a balanced immune environment Consequently, the expression of FoxP3 well reflects the Treg activity they are also characterized by a high expression of CD25 the role of Th17 cells is to enhance the immune response by producing pro-inflammatory signals like IL-17, IL-22, or IL-23 this balance between the two phenotypes is disturbed with a higher presence of Treg CTL cytotoxicity assay Measures the ability of cytotoxic T lymphocytes (CTLs) or CD8+ T cells to kill target cells, typically tumor cells, through mechanisms such as granule exocytosis, death receptor pathways, or cytokine release. in_vitro CTLs CD8+ T cells tumor cells target cell death increase http://purl.obolibrary.org/obo/CL_0000624 CL http://purl.obolibrary.org/obo/GO_0006915 GO http://purl.obolibrary.org/obo/GO_0031982 GO medium CTLs or CD8+ T cells are key components of the adaptive immune system, playing a crucial role in protecting against viral infections, bacteria, and tumor development. CTLs kill tumor cells after recognizing tumor-derived peptides presented on MHC class I molecules through their T-cell receptor. CTLs form an immunological synapse with the target cell (including cancer cells) and deploy three main killing pathways http://purl.obolibrary.org/obo/CL_0000057 CL http://purl.obolibrary.org/obo/GO_0006915 GO cytokine release assay Measures the indirect killing capability of CTLs by quantifying the release of cytokine factors such as TNFα or IFN-γ. in_vitro CTLs CD8+ T cells tumor cells cytokine release (TNFα or IFN-γ) increase http://purl.obolibrary.org/obo/CHEBI_34432 CHEBI http://purl.obolibrary.org/obo/CHEBI_35011 CHEBI not_specified these cells can kill target cells indirectly through the release of cytokine factors like TNFα or IFN-γ http://purl.obolibrary.org/obo/GO_0051030 GO FasL/Fas binding assay This assay measures the binding of Fas ligand (FasL) expressed by CTLs to Fas (CD95) on the surface of tumor cells, activating the extrinsic apoptotic cascade. not_specified CTLs cancer cells FasL/Fas binding increase http://purl.obolibrary.org/obo/CHEBI_5980 CHEBI http://purl.obolibrary.org/obo/CHEBI_5981 CHEBI http://purl.obolibrary.org/obo/GO_0006983 GO not_specified Finally, in the death receptor pathway, CTLs express Fas ligand (FasL) that binds Fas (CD95) on the cell surface of tumor cells, activating their extrinsic apoptotic cascade (Preglej and Ellmeier, 2022). http://purl.obolibrary.org/obo/GO_0006983 GO perforin/granzyme assay This assay assesses the granule exocytosis pathway, where CTLs release perforin to form pores in the tumor cell membrane, allowing granzymes to enter and trigger caspase-dependent apoptosis. not_specified CTLs cancer cells perforin pore formation and granzyme entry increase http://purl.obolibrary.org/obo/CHEBI_26868 CHEBI http://purl.obolibrary.org/obo/GO_0006983 GO not_specified Second, in the granule exocytosis pathway, CTLs release perforin, which forms pores in the tumor cell membrane, allowing granzymes to enter and trigger caspase-dependent apoptosis. http://purl.obolibrary.org/obo/GO_0006983 GO In situ hybridization Measures the localization of SIX1 mRNA in tissue using in situ hybridization. in_vivo tissue localization of SIX1 mRNA not_specified http://purl.obolibrary.org/obo/GO_0006417 GO low In situ hybridization to measure localiztion of SIX1 mRNA in tissue. http://purl.obolibrary.org/obo/GO_0006417 GO Quantitative PCR Measures the expression level of SIX1 gene using quantitative polymerase chain reaction. in_vitro SIX1 gene expression increase http://purl.obolibrary.org/obo/GO_0010467 GO medium Quantitative PCR and RNA sequencing for general expression. http://purl.obolibrary.org/obo/GO_0010467 GO RNA sequencing RNA sequencing was used to measure SIX1 gene expression levels. This is a general expression assay. in_vitro gene expression level increase high Quantitative PCR and RNA sequencing for general expression. http://purl.obolibrary.org/obo/GO_0010505 GO RNA sequencing Measures the expression level of SIX1 gene using high-throughput RNA sequencing. in_vitro SIX1 gene expression increase http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0001271 OBI high Quantitative PCR and RNA sequencing for general expression. http://purl.obolibrary.org/obo/GO_0010467 GO ELISA ELISA (Enzyme-Linked Immunosorbent Assay) is a plate-based assay used to detect and quantify SIX1 protein levels in a sample. in_vitro protein concentration increase http://purl.obolibrary.org/obo/OBI_0000233 OBI medium ELISA http://purl.obolibrary.org/obo/GO_0006457 GO ELISA Detection and quantification of SIX1 protein expression using enzyme-linked immunosorbent assay. in_vitro SIX1 protein expression increase http://purl.obolibrary.org/obo/GO_0010485 GO medium ELISA http://purl.obolibrary.org/obo/GO_0010485 GO flow cytometry Flow cytometry is used to quantify SIX1 protein expression in individual cells based on antibody binding and fluorescence. in_vitro protein expression level increase medium Flow cytometry http://purl.obolibrary.org/obo/GO_0006457 GO Flow cytometry Detection and quantification of SIX1 protein expression in cells using fluorescently labeled antibodies and flow cytometry. in_vitro SIX1 protein expression increase http://purl.obolibrary.org/obo/GO_0010485 GO high Flow cytometry http://purl.obolibrary.org/obo/GO_0010485 GO immunofluorescence Immunofluorescence uses fluorescently labeled antibodies to detect and visualize SIX1 protein expression in cells or tissues. in_vitro protein expression increase http://purl.obolibrary.org/obo/GO_0005243 GO http://www.bioassayontology.org/bao#BAO_0002357 BAO low Immunofluorescence http://purl.obolibrary.org/obo/GO_0006457 GO Immunofluorescence Detection and quantification of SIX1 protein expression in cells or tissues using fluorescently labeled antibodies. in_vitro SIX1 protein expression increase http://purl.obolibrary.org/obo/GO_0010485 GO medium Immunofluorescence http://purl.obolibrary.org/obo/GO_0010485 GO immunohistochemistry Immunohistochemistry uses antibodies to detect and visualize SIX1 protein expression in tissue sections. in_vivo protein expression increase http://purl.obolibrary.org/obo/GO_0005243 GO http://www.bioassayontology.org/bao#BAO_0002358 BAO low Immunohistochemistry http://purl.obolibrary.org/obo/GO_0006457 GO Immunohistochemistry Detection and quantification of SIX1 protein expression in tissue sections using labeled antibodies. in_vivo SIX1 protein expression increase http://purl.obolibrary.org/obo/GO_0010485 GO low Immunohistochemistry http://purl.obolibrary.org/obo/GO_0010485 GO western blot Western blotting is used for the detection and quantification of SIX1 protein levels. It involves separating proteins by size and detecting the target protein using antibodies. in_vitro protein expression level increase http://purl.obolibrary.org/obo/OBI_0000233 OBI http://purl.obolibrary.org/obo/GO_0005103 GO low Western blotting http://purl.obolibrary.org/obo/GO_0006457 GO Western blotting Detection and quantification of SIX1 protein expression using antibody-based protein detection on a membrane. in_vitro SIX1 protein expression increase http://purl.obolibrary.org/obo/GO_0010485 GO low Western blotting http://purl.obolibrary.org/obo/GO_0010485 GO EPR spectroscopy Electron paramagnetic resonance (EPR) spectroscopy detects paramagnetic intermediates like semiquinone radicals, providing a direct probe into redox cycling events at the mitochondrial level. It monitors the formation and stability of these intermediates under controlled conditions. in_vitro mitochondria formation and stability of paramagnetic intermediates increase low Electron paramagnetic resonance (EPR) spectroscopy provides a highly sensitive and specific method for detecting paramagnetic intermediates such as semiquinone radicals, thereby offering a direct probe into redox cycling events at the mitochondrial level. EPR spectroscopy Electron paramagnetic resonance (EPR) spectroscopy detects paramagnetic intermediates such as semiquinone radicals, providing a direct probe into redox cycling events at the mitochondrial level. in_vitro mitochondria formation and stability of semiquinone radicals increase low Electron paramagnetic resonance (EPR) spectroscopy provides a highly sensitive and specific method for detecting paramagnetic intermediates such as semiquinone radicals, thereby offering a direct probe into redox cycling events at the mitochondrial level. Through the application of EPR spectroscopy under controlled oxygen and substrate conditions, it is possible to monitor the formation and stability of these intermediates in situ. spectrophotometry Spectrophotometry monitors changes in absorbance associated with the generation and stabilization of semiquinone radicals, allowing detection and quantification of radical intermediates. in_vitro mitochondria absorbance changes indicative of semiquinone radical formation increase medium The detection of radical formation within redox cyclers by spectrophotometry relies on the ability to monitor changes in absorbance associated with the generation and stabilization of specific radical intermediates, most commonly semiquinone radicals. By recording the absorption spectrum during redox cycling under anaerobic or low-oxygen conditions (to prevent rapid reoxidation), the formation of the radical intermediate can be detected in real time. Amplex Red Ultra assay The Amplex Red Ultra assay quantitatively measures hydrogen peroxide (H₂O₂) using a horseradish peroxidase (HRP)-catalyzed reaction that produces the fluorescent compound resorufin, allowing real-time monitoring of mitochondrial ROS production. in_vitro mitochondria hydrogen peroxide concentration increase http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0005747 GO http://purl.obolibrary.org/obo/GO_0005750 GO http://purl.obolibrary.org/obo/GO_0004788 GO high The Amplex® Red Ultra assay has emerged as a sensitive and specific technique for the quantitative measurement of hydrogen peroxide (H₂O₂), a primary and relatively stable ROS generated by mitochondria (Grivennikova et al. 2018). The fluorescence intensity of resorufin is directly proportional to the amount of H₂O₂ present, allowing real-time monitoring of mitochondrial ROS production. To perform the assay, isolated mitochondria or permeabilized cells are incubated in a reaction buffer containing Amplex Red Ultra, HRP, and appropriate mitochondrial substrates and inhibitors. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0042773 GO Coelenterazine chemiluminescence A non-invasive method using coelenterazine derivatives that undergo oxidative decarboxylation in the presence of ROS to emit blue light. in_vitro intact cells mitochondria light emission intensity increase http://purl.obolibrary.org/obo/OBI_0000248 OBI http://purl.obolibrary.org/obo/CHEBI_15374 CHEBI high Coelenterazine chemiluminescence is a sensitive and non-invasive analytical method for detecting elevated mitochondrial reactive oxygen species (ROS), particularly superoxide (O₂•⁻) and hydrogen peroxide (H₂O₂), in intact cells and isolated mitochondria The intensity of this light emission is directly proportional to the amount of ROS present, enabling real-time quantification of oxidative stress under physiological and pathophysiological conditions. Coelenterazine chemiluminescence is particularly suited for high-throughput screening and longitudinal studies http://purl.obolibrary.org/obo/UBERON_0000199 UBERON http://purl.obolibrary.org/obo/GO_0002235 GO Coelenterazine chemiluminescence This assay detects elevated mitochondrial ROS (superoxide and hydrogen peroxide) using coelenterazine, a luminescent substrate that emits photons upon reaction with ROS. The intensity of light emission is proportional to ROS amount. in_vitro intact cells mitochondria ROS levels (superoxide and hydrogen peroxide) increase http://purl.obolibrary.org/obo/CHEBI_30764 CHEBI http://purl.obolibrary.org/obo/CHEBI_29084 CHEBI http://purl.obolibrary.org/obo/GO_0045969 GO high Coelenterazine chemiluminescence is a sensitive and non-invasive analytical method for detecting elevated mitochondrial reactive oxygen species (ROS), particularly superoxide (O₂•⁻) and hydrogen peroxide (H₂O₂), in intact cells and isolated mitochondria (Lucas et al. 1992; Teranishi et al. 1997). The intensity of this light emission is directly proportional to the amount of ROS present, enabling real-time quantification of oxidative stress under physiological and pathophysiological conditions. Unlike fluorescence-based ROS probes, which often require excitation light that may introduce phototoxicity or interfere with mitochondrial function, chemiluminescence avoids exogenous illumination and thereby minimizes assay artifacts. http://purl.obolibrary.org/obo/GO_0045969 GO http://purl.obolibrary.org/obo/GO_0045969 GO Coelenterazine chemiluminescence Coelenterazine chemiluminescence detects mitochondrial ROS, particularly superoxide and hydrogen peroxide, by emitting light upon oxidative decarboxylation, enabling real-time quantification of oxidative stress. in_vitro mitochondria ROS-induced luminescence increase http://purl.obolibrary.org/obo/CHEBI_26635 CHEBI http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0005746 GO http://purl.obolibrary.org/obo/GO_0005759 GO high Coelenterazine chemiluminescence is a sensitive and non-invasive analytical method for detecting elevated mitochondrial reactive oxygen species (ROS), particularly superoxide (O₂•⁻) and hydrogen peroxide (H₂O₂), in intact cells and isolated mitochondria (Lucas et al. 1992; Teranishi et al. 1997). The intensity of this light emission is directly proportional to the amount of ROS present, enabling real-time quantification of oxidative stress under physiological and pathophysiological conditions. In experimental applications, cells or mitochondria are incubated with coelenterazine under controlled metabolic conditions. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0042773 GO Electron Paramagnetic Resonance (EPR) Electron Paramagnetic Resonance (EPR) spectroscopy directly detects unpaired electrons in paramagnetic species, such as mitochondrial ROS, using spin-trapping agents to stabilize and identify specific radical species. in_vitro mitochondria ROS radical concentration increase http://purl.obolibrary.org/obo/CHEBI_26635 CHEBI http://purl.obolibrary.org/obo/CHEBI_25516 CHEBI http://purl.obolibrary.org/obo/CHEBI_16480 CHEBI http://purl.obolibrary.org/obo/OBI_0000218 OBI http://purl.obolibrary.org/obo/OBI_0000219 OBI low Electron paramagnetic resonance (EPR) spectroscopy, also known as electron spin resonance (ESR), is a powerful and direct analytical technique for the detection of unpaired electrons in paramagnetic species, including free radicals such as reactive oxygen species (ROS). Native ROS such as superoxide (O₂•⁻), hydroxyl radicals (•OH), and nitric oxide (NO•) are typically too reactive and short-lived to be measured directly by EPR. Therefore, EPR detection of mitochondrial ROS relies primarily on the use of spin-trapping agents (Griendling et al. 2016). To measure mitochondrial ROS formation using EPR, isolated mitochondria or permeabilized cells are incubated with suitable substrates and respiratory chain inhibitors in the presence of the spin trap. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0042773 GO MitoSOX MitoSOX is a fluorogenic probe that selectively detects mitochondrial superoxide in live cells by oxidizing to a fluorescent product that binds to mitochondrial DNA. in_vitro mitochondria mitochondrial superoxide levels increase http://purl.obolibrary.org/obo/CHEBI_26635 CHEBI http://purl.obolibrary.org/obo/GO_0005759 GO http://purl.obolibrary.org/obo/GO_0042775 GO http://purl.obolibrary.org/obo/GO_0005739 GO medium MitoSOX™ dyes are a family of fluorogenic probes specifically designed for the selective detection of mitochondrial superoxide in live cells. Upon entry into the mitochondria, MitoSOX Red is oxidized specifically by superoxide to form a highly fluorescent ethidium-like product that binds to mitochondrial DNA, emitting red fluorescence upon excitation. In practical applications, live cells or isolated mitochondria are incubated with MitoSOX Red under controlled conditions, typically at concentrations of 2–5 μM for 10–30 minutes at 37°C. http://purl.obolibrary.org/obo/GO_0005739 GO http://purl.obolibrary.org/obo/GO_0006122 GO ELISA Measures protein expression levels of α1-ARs in homogenized tissues or cultured cells using subtype-specific antibodies. in_vitro protein expression levels not_specified http://purl.obolibrary.org/obo/OBI_0000278 OBI http://purl.obolibrary.org/obo/PR_000001234 PR high Western Blot and ELISA. Protein expression levels of α1-ARs can be measured in homogenized tissues or cultured cells using subtype-specific antibodies. http://purl.obolibrary.org/obo/PR_000001234 PR http://purl.obolibrary.org/obo/GO_0010457 GO Fluorescence confocal microscopy Directly visualizes the cellular and subcellular distribution of the alpha-1a adrenergic receptor in intact cells using fluorescent probes or α1a-GFP fusion constructs. in_vitro cellular and subcellular location of the alpha-1a adrenergic receptor change low The cellular and subcellular location of the alpha-1a adrenergic receptor can be measured using fluorescence confocal microscopy . This technique allows for the direct visualization of the receptor's distribution in intact cells, through the use of fluorescent probes that bind specifically to the receptor or protein fusion constructs (such as α1a-GFP). fluorescence confocal microscopy Measures the cellular and subcellular location of the alpha-1a adrenergic receptor using fluorescent probes or protein fusion constructs. in_vitro receptor distribution not_specified http://purl.obolibrary.org/obo/PR_000001234 PR low The cellular and subcellular location of the alpha-1a adrenergic receptor can be measured using fluorescence confocal microscopy. This technique allows for the direct visualization of the receptor's distribution in intact cells, through the use of fluorescent probes that bind specifically to the receptor or protein fusion constructs (such as α1a-GFP). http://purl.obolibrary.org/obo/PR_000001234 PR http://purl.obolibrary.org/obo/GO_0006886 GO immunofluorescence Specific antibodies against α1-AR subtypes enable localization of receptor proteins at the cellular level. These methods provide qualitative and semi-quantitative data regarding receptor expression patterns and cellular localization. in_vitro receptor expression and localization change low Immunohistochemistry and Immunofluorescence Specific antibodies against α1-AR subtypes (α1A, α1B, α1D) enable localization of receptor proteins at the cellular level. These methods provide qualitative and semi-quantitative data regarding receptor expression patterns and cellular localization. http://purl.obolibrary.org/obo/GO_0008424 GO immunohistochemistry Uses specific antibodies against α1-AR subtypes to localize receptor proteins at the cellular level, providing qualitative and semi-quantitative data. in_vitro receptor expression patterns not_specified http://purl.obolibrary.org/obo/OBI_0000286 OBI http://purl.obolibrary.org/obo/PR_000001234 PR medium Immunohistochemistry and Immunofluorescence. Specific antibodies against α1-AR subtypes (α1A, α1B, α1D) enable localization of receptor proteins at the cellular level. These methods provide qualitative and semi-quantitative data regarding receptor expression patterns and cellular localization. http://purl.obolibrary.org/obo/PR_000001234 PR http://purl.obolibrary.org/obo/GO_0006886 GO qPCR Assesses mRNA expression of α1-AR subtypes (ADRA1A, ADRA1B, ADRA1D) to reflect transcriptional regulation. in_vitro mRNA expression not_specified http://purl.obolibrary.org/obo/OBI_0000274 OBI http://purl.obolibrary.org/obo/SO_0000234 SO high Molecular Quantification (qPCR). Quantitative PCR can be employed to assess mRNA expression of α1-AR subtypes (ADRA1A, ADRA1B, ADRA1D), reflecting transcriptional regulation that may accompany receptor activation or downregulation. http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0045449 GO qPCR Assesses mRNA expression levels of α1-AR subtypes (ADRA1A, ADRA1B, ADRA1D) to evaluate transcriptional regulation associated with receptor activation or downregulation. in_vitro mRNA expression of α1-AR subtypes change high Molecular Quantification (qPCR) Quantitative PCR can be employed to assess mRNA expression of α1-AR subtypes (ADRA1A, ADRA1B, ADRA1D), reflecting transcriptional regulation that may accompany receptor activation or downregulation. western blot Measures protein expression levels of α1-ARs in homogenized tissues or cultured cells using subtype-specific antibodies. in_vitro protein expression levels not_specified http://purl.obolibrary.org/obo/OBI_0000272 OBI http://purl.obolibrary.org/obo/PR_000001234 PR medium Western Blot and ELISA. Protein expression levels of α1-ARs can be measured in homogenized tissues or cultured cells using subtype-specific antibodies. http://purl.obolibrary.org/obo/PR_000001234 PR http://purl.obolibrary.org/obo/GO_0010457 GO Western Blot and ELISA Quantifies protein expression levels of α1-ARs in homogenized tissues or cultured cells using subtype-specific antibodies to compare expression across experimental conditions. in_vitro protein expression levels of α1-ARs change medium Western Blot and ELISA Protein expression levels of α1-ARs can be measured in homogenized tissues or cultured cells using subtype-specific antibodies. These techniques are useful for comparing expression between experimental conditions or treatment groups. 24-hour urinary free cortisol Measurement of free cortisol in urine over 24 hours, used for monitoring conditions like Cushing's syndrome. in_vitro urine urinary free cortisol levels not_specified low Twenty-four-hour urinary free cortisol is a reliable indicator of serum free cortisol and is useful for monitoring Cushing's syndrome. http://purl.obolibrary.org/obo/CHEBI_17286 CHEBI http://purl.obolibrary.org/obo/GO_0006707 GO automated immunoassay Widely used method for measuring total cortisol in serum, though with limitations in specificity and inter-assay variability. in_vitro serum total cortisol levels not_specified high Automated immunoassays are widely used, although they have limitations in specificity and show significant inter-assay variability. http://purl.obolibrary.org/obo/CHEBI_17286 CHEBI http://purl.obolibrary.org/obo/GO_0006707 GO fluorimetric analysis Early technique for measuring cortisol using fluorescence properties. in_vitro cortisol levels not_specified not_specified The earliest techniques for measuring cortisol involved fluorimetric analysis experiments. http://purl.obolibrary.org/obo/CHEBI_17286 CHEBI http://purl.obolibrary.org/obo/GO_0006707 GO LC-MS/MS Highly specific and sensitive method for measuring cortisol in saliva and urine using liquid chromatography-tandem mass spectrometry. in_vitro saliva urine cortisol levels not_specified http://purl.obolibrary.org/obo/OBI_0000475 OBI medium Liquid chromatography-tandem mass spectrometry (LC-MS/MS) provides greater specificity and sensitivity and is recommended for salivary and urinary cortisol measurements. http://purl.obolibrary.org/obo/CHEBI_17286 CHEBI http://purl.obolibrary.org/obo/GO_0006707 GO mass spectrometry The gold standard technique for molecular characterization and quantification of free serum cortisol. in_vitro free serum cortisol change http://purl.obolibrary.org/obo/CHEBI_17265 CHEBI not_specified The gold standard for detecting free serum cortisol is mass spectrometry, a technique employed for molecular characterization and also used to quantify free cortisol levels. http://purl.obolibrary.org/obo/CHEBI_17265 CHEBI salivary cortisol assay Non-invasive method for measuring cortisol in saliva, reflecting changes in serum free cortisol. in_vitro saliva salivary cortisol levels not_specified medium Salivary cortisol reflects changes in serum free cortisol and offers a non-invasive alternative, although reference ranges have not yet been standardized. http://purl.obolibrary.org/obo/CHEBI_17286 CHEBI http://purl.obolibrary.org/obo/GO_0006707 GO Evans Blue / sulforhodamine B uptake Quantitative dye extraction or imaging measures plasma leakage in zebrafish embryos, reflecting loss of vascular integrity. in_vivo whole embryo Danio rerio Evans Blue or sulforhodamine B uptake increase http://purl.obolibrary.org/obo/GO_0061570 GO http://purl.obolibrary.org/obo/GO_0097708 GO low Quantitative dye extraction or imaging to measure plasma leakage. http://purl.obolibrary.org/obo/UBERON_0001044 UBERON http://purl.obolibrary.org/obo/GO_0097708 GO Evans Blue / sulforhodamine B uptake Quantitative dye extraction or imaging to measure plasma leakage. in_vivo vasculature fish plasma leakage increase http://purl.obolibrary.org/obo/GO_0090280 GO medium Evans Blue / sulforhodamine B uptake: Quantitative dye extraction or imaging to measure plasma leakage. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0090280 GO Fluorescent tracer leakage assay Injection of high-molecular-weight FITC- or TexasRed-dextran into circulation followed by time-lapse imaging to quantify extravasation. in_vivo vasculature fish extravasation index increase http://purl.obolibrary.org/obo/GO_0090280 GO medium Fluorescent tracer leakage assay (microangiography): Injection of high-molecular-weight FITC- or TexasRed-dextran into circulation followed by time-lapse imaging to quantify extravasation. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/GO_0090280 GO Hemorrhage frequency or severity index Assessment of the percentage of embryos showing localized bleeding, especially near the heart or brain. in_vivo heart brain fish embryos % embryos showing localized bleeding increase not_specified Hemorrhage frequency or severity index: % embryos showing localized bleeding, particularly near the heart or brain. http://purl.obolibrary.org/obo/UBERON_0000634 UBERON Hemorrhage frequency or severity index Measurement of the percentage of embryos showing localized bleeding, particularly near the heart or brain. in_vivo heart brain fish hemorrhage frequency increase http://purl.obolibrary.org/obo/UBERON_0000948 UBERON http://purl.obolibrary.org/obo/UBERON_0000955 UBERON medium Hemorrhage frequency or severity index: % embryos showing localized bleeding, particularly near the heart or brain. http://purl.obolibrary.org/obo/UBERON_0001981 UBERON http://purl.obolibrary.org/obo/MP_0001266 MP Immunostaining of junctional markers Quantification of VE-cadherin or ZO-1 continuity index (proportion of intact junction length). in_vitro endothelial cells junctional marker continuity index decrease http://purl.obolibrary.org/obo/PR_000001168 PR http://purl.obolibrary.org/obo/PR_000008940 PR http://purl.obolibrary.org/obo/GO_0030054 GO medium Immunostaining of junctional markers: Quantification of VE-cadherin or ZO-1 continuity index (proportion of intact junction length). http://purl.obolibrary.org/obo/GO_0005912 GO http://purl.obolibrary.org/obo/GO_0034329 GO Immunostaining of junctional markers Quantification of VE-cadherin or ZO-1 continuity index (proportion of intact junction length). in_vitro endothelial cells VE-cadherin/ZO-1 continuity index decrease http://purl.obolibrary.org/obo/CL_0000535 CL low Immunostaining of junctional markers: Quantification of VE-cadherin or ZO-1 continuity index (proportion of intact junction length). http://purl.obolibrary.org/obo/CL_0000535 CL http://purl.obolibrary.org/obo/GO_0007017 GO Macromolecular permeability (Papp) Apparent permeability coefficient using fluorescent dextrans in Transwell systems. in_vitro endothelial cells apparent permeability coefficient increase http://purl.obolibrary.org/obo/CL_0000115 CL medium Macromolecular permeability (Papp): Apparent permeability coefficient using fluorescent dextrans in Transwell systems. http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0090280 GO Pericardial or tissue edema scoring Morphometric assessment of pericardial area or edema volume using image analysis. in_vivo pericardium tissue fish edema volume increase http://purl.obolibrary.org/obo/MP_0001265 MP http://purl.obolibrary.org/obo/UBERON_0002407 UBERON medium Pericardial or tissue edema scoring: Morphometric assessment of pericardial area or edema volume using image analysis. http://purl.obolibrary.org/obo/UBERON_0002407 UBERON http://purl.obolibrary.org/obo/MP_0001265 MP Pericardial or tissue edema scoring Morphometric assessment of pericardial area or edema volume using image analysis. in_vivo pericardium tissue fish embryos pericardial area or edema volume increase not_specified Pericardial or tissue edema scoring: Morphometric assessment of pericardial area or edema volume using image analysis. TEER Measures ionic conductance across endothelial monolayers; expressed as % decrease from baseline. in_vitro endothelial cells Ionic conductance decrease medium Trans-Endothelial Electrical Resistance (TEER): Measures ionic conductance across endothelial monolayers; expressed as % decrease from baseline (Ω·cm²). http://purl.obolibrary.org/obo/CL_0000188 CL Trans-Endothelial Electrical Resistance (TEER) Measures ionic conductance across endothelial monolayers; expressed as % decrease from baseline (Ω·cm²). in_vitro endothelial cells TEER decrease http://purl.obolibrary.org/obo/CL_0000115 CL medium Trans-Endothelial Electrical Resistance (TEER): Measures ionic conductance across endothelial monolayers; expressed as % decrease from baseline (Ω·cm²). http://purl.obolibrary.org/obo/CL_0000115 CL http://purl.obolibrary.org/obo/GO_0005125 GO Chromatin Immunoprecipitation followed by qPCR or seq Measures AR binding to androgen response elements on chromatin via antibody-mediated DNA pull-down and quantification. in_vitro GT tissues AR DNA binding decrease http://purl.obolibrary.org/obo/GO_0003677 GO http://purl.obolibrary.org/obo/GO_0000785 GO low AR DNA binding, which measures androgen response elements on chromatin, can be measured via: Chromatin Immunoprecipitation followed by qPCR or seq. http://purl.obolibrary.org/obo/PR_P20343 PR http://purl.obolibrary.org/obo/GO_0003677 GO Immunofluorescence Measures the amount of AR protein in the cell nucleus via antibody-based fluorescent staining and microscopy. in_vitro GT tissues nuclear AR localization decrease http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0008104 GO medium Nuclear AR localization, which is the amount of AR protein in the cell nucleus, can be measured via: Immunofluorescence http://purl.obolibrary.org/obo/PR_P20343 PR http://purl.obolibrary.org/obo/GO_0008104 GO Immunohistochemistry Measures the amount of AR protein in the cell nucleus via antibody-based staining of tissue sections. in_vivo GT tissues nuclear AR localization decrease http://purl.obolibrary.org/obo/GO_0005634 GO http://purl.obolibrary.org/obo/GO_0008104 GO low Nuclear AR localization, which is the amount of AR protein in the cell nucleus, can be measured via: Immunohistochemistry http://purl.obolibrary.org/obo/PR_P20343 PR http://purl.obolibrary.org/obo/GO_0008104 GO In situ hybridization Measures mRNA levels of AR-regulated genes via labeled probe hybridization in tissue sections. in_vivo GT tissues AR target gene mRNA levels decrease http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO low Expression of AR target genes, which measure either mRNA or protein levels of AR-regulated genes, can be measured via: In situ hybridization http://purl.obolibrary.org/obo/GO_0010467 GO Proteomics Measures protein levels of AR-regulated genes via mass spectrometry or antibody-based methods. in_vitro GT tissues AR target gene protein levels decrease http://purl.obolibrary.org/obo/SO_0000104 SO http://purl.obolibrary.org/obo/GO_0032549 GO medium Expression of AR target genes, which measure either mRNA or protein levels of AR-regulated genes, can be measured via: Proteomics http://purl.obolibrary.org/obo/GO_0019538 GO RNA-seq Measures mRNA levels of AR-regulated genes via high-throughput sequencing. in_vitro GT tissues AR target gene mRNA levels decrease http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO high Expression of AR target genes, which measure either mRNA or protein levels of AR-regulated genes, can be measured via: RNA-seq http://purl.obolibrary.org/obo/GO_0010467 GO RT-qPCR Measures mRNA levels of AR-regulated genes via reverse transcription and quantitative PCR. in_vitro GT tissues AR target gene mRNA levels decrease http://purl.obolibrary.org/obo/SO_0000234 SO http://purl.obolibrary.org/obo/GO_0010467 GO high Expression of AR target genes, which measure either mRNA or protein levels of AR-regulated genes, can be measured via: RT-qPCR http://purl.obolibrary.org/obo/GO_0010467 GO Western blot Measures the amount of AR protein in nuclear fractions via gel electrophoresis and antibody detection. in_vitro GT tissues nuclear AR protein levels decrease http://purl.obolibrary.org/obo/GO_0032549 GO medium Nuclear AR localization, which is the amount of AR protein in the cell nucleus, can be measured via: Western blot http://purl.obolibrary.org/obo/PR_P20343 PR http://purl.obolibrary.org/obo/GO_0008104 GO ICH or Western blot Measures the phosphorylation state of FGFR2-IIIb as an indicator of receptor activation. in_vitro genital tissue phosphorylation state of FGFR2-IIIb not_specified http://purl.obolibrary.org/obo/GO_0006468 GO http://purl.obolibrary.org/obo/OBI_0000278 OBI medium ICH or Western blot http://purl.obolibrary.org/obo/GO_0006468 GO IHC/IF Immunohistochemistry and immunofluorescence measuring protein expression of FGF10 and FGFR2-IIIb in tissue sections. ex_vivo genital tissue FGF10 and FGFR2-IIIb protein expression decrease http://purl.obolibrary.org/obo/GO_0006814 GO low Expression of FGF10 and FGFR2-IIIb: IHC/IF http://purl.obolibrary.org/obo/GO_0006814 GO IHC/IF Immunohistochemistry and immunofluorescence techniques to detect protein expression and localization of FGF10 and FGFR2-IIIb in genital tissue. in_vivo genital tissue protein expression and localization not_specified http://purl.obolibrary.org/obo/GO_0008104 GO low IHC/IF http://purl.obolibrary.org/obo/GO_0008104 GO Immunoprecipitation Immunoprecipitation followed by phospho-Western blotting to measure the activation/phosphorylation state of FGFR2-IIIb. in_vitro genital tissue phosphorylation of FGFR2-IIIb decrease http://purl.obolibrary.org/obo/GO_0004220 GO not_specified Immunoprecipation followed by phospho-Western blotting http://purl.obolibrary.org/obo/GO_0004220 GO In situ hybridization Detects the spatial distribution of FGF10 and FGFR2-IIIb mRNA in genital tissue sections. in_vivo genital tissue mRNA spatial distribution not_specified http://purl.obolibrary.org/obo/OBI_0000505 OBI http://purl.obolibrary.org/obo/GO_0010467 GO low In situ hybridation http://purl.obolibrary.org/obo/GO_0010467 GO In situ hybridization Detects the spatial distribution of mRNA of genes induced by FGF signaling in genital tissue sections. in_vivo genital tissue mRNA spatial distribution of FGF-induced genes not_specified http://purl.obolibrary.org/obo/OBI_0000505 OBI http://purl.obolibrary.org/obo/GO_0010467 GO low Expression of genes induced by FGF signaling can be measured via: In situ hybridization http://purl.obolibrary.org/obo/GO_0010467 GO RNA-seq RNA-seq is a sequencing-based approach to measure the abundance of RNA transcripts. It is used to assess the expression of genes induced by FGF signaling. in_vitro genital tissue gene expression change high RNA-seq Expression of genes induced by FGF signaling can be measured via: RNA-seq http://purl.obolibrary.org/obo/GO_0010505 GO RNA-seq Measures the expression levels of genes induced by FGF signaling using high-throughput sequencing. in_vitro genital tissue mRNA expression levels of FGF-induced genes not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0001271 OBI high Expression of genes induced by FGF signaling can be measured via: RNA-seq http://purl.obolibrary.org/obo/GO_0010467 GO RT-qPCR Measures the expression levels of FGF10 and FGFR2-IIIb mRNA using reverse transcription quantitative polymerase chain reaction. in_vitro genital tissue mRNA expression levels not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000664 OBI medium RT-qPCR http://purl.obolibrary.org/obo/GO_0010467 GO RT-qPCR Measures the expression levels of genes induced by FGF signaling using reverse transcription quantitative polymerase chain reaction. in_vitro genital tissue mRNA expression levels of FGF-induced genes not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/OBI_0000664 OBI medium Expression of genes induced by FGF signaling can be measured via: RT-qPCR http://purl.obolibrary.org/obo/GO_0010467 GO Western blot Western blot measuring total protein expression levels of FGF10 and FGFR2-IIIb. in_vitro genital tissue FGF10 and FGFR2-IIIb protein expression decrease http://purl.obolibrary.org/obo/GO_0006814 GO low Expression of FGF10 and FGFR2-IIIb: Western blotting http://purl.obolibrary.org/obo/GO_0006814 GO Western blotting Measures protein levels of FGF10 and FGFR2-IIIb in genital tissue lysates. in_vitro genital tissue protein levels not_specified http://purl.obolibrary.org/obo/OBI_0000278 OBI http://purl.obolibrary.org/obo/GO_0043085 GO medium Western blotting http://purl.obolibrary.org/obo/GO_0019538 GO BrdU or EdU incorporation assay An assay measuring DNA synthesis by incorporating BrdU or EdU into newly synthesized DNA, indicating cell proliferation. in_vivo preputial epithelium DNA synthesis change http://purl.obolibrary.org/obo/GO_0006260 GO medium Ki-67 immunostaining and BrdU or EdU incorporation assays for proliferation http://purl.obolibrary.org/obo/GO_0008283 GO Cleaved caspase-3 assay An assay detecting the activated form of caspase-3, a key executor of apoptosis. in_vivo preputial epithelium cleaved caspase-3 levels increase http://purl.obolibrary.org/obo/GO_0006915 GO medium TUNEL and cleaved caspase-3 for apoptosis http://purl.obolibrary.org/obo/GO_0006915 GO Hematoxylin and eosin staining Quantitative and qualitative histological assessment of preputial epithelial morphology using hematoxylin and eosin staining. in_vivo preputial epithelium not_specified epithelial morphology not_specified low Direct evidence with well validated and widely used techniques based on quantitative and qualitative histological measurements. Hematoxylin and eosin staining http://purl.obolibrary.org/obo/UBERON_0001810 UBERON http://purl.obolibrary.org/obo/GO_0048735 GO Hematoxylin and eosin staining A histological staining technique used to visualize tissue structure and morphology. in_vivo preputial epithelium tissue morphology change low Hematoxylin and eosin staining http://purl.obolibrary.org/obo/GO_0009653 GO Ki-67 immunostaining An immunostaining assay using Ki-67 antibody to measure cell proliferation. in_vivo preputial epithelium cell proliferation change http://purl.obolibrary.org/obo/GO_0008283 GO medium Ki-67 immunostaining and BrdU or EdU incorporation assays for proliferation http://purl.obolibrary.org/obo/GO_0008283 GO Serial sectioning with stereo microscopy A technique involving serial sectioning of tissue followed by stereo microscopy and morphometric analysis to assess tissue structure. in_vivo preputial epithelium tissue structure change http://purl.obolibrary.org/obo/OBI_0000388 OBI low Serial sectioning with stereo microscopy, imaging, morphometric analysis http://purl.obolibrary.org/obo/GO_0009653 GO Serial sectioning with stereo microscopy, imaging, morphometric analysis A methodology involving the creation of sequential tissue slices for microscopic imaging and quantitative morphometric measurement. ex_vivo preputial epithelium morphometric parameters change low Serial sectioning with stereo microscopy, imaging, morphometric analysis TUNEL and cleaved caspase-3 for apoptosis Detection of apoptosis in preputial epithelial cells using TUNEL assay and cleaved caspase-3 immunostaining. in_vivo preputial epithelium not_specified apoptosis increase http://purl.obolibrary.org/obo/GO_0012501 GO medium TUNEL and cleaved caspase-3 for apoptosis http://purl.obolibrary.org/obo/CL_0000066 CL http://purl.obolibrary.org/obo/GO_0012501 GO TUNEL assay A method to detect DNA fragmentation by labeling the terminal ends of nucleic acids, indicating apoptosis. in_vivo preputial epithelium DNA fragmentation increase http://purl.obolibrary.org/obo/GO_0043066 GO medium TUNEL and cleaved caspase-3 for apoptosis http://purl.obolibrary.org/obo/GO_0006915 GO gross anatomical observation Direct observation of anatomical features to assess the degree of separation and timing of preputial separation. in_vivo prepuce rat degree of preputial separation change http://purl.obolibrary.org/obo/UBERON_0001378 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO medium Gross anatomical observations are a direct, standardized, and reproducible strategy and can be conducted periodically. Binary scoring and ordinal scales can be employed to describe degree of separation and timing. http://purl.obolibrary.org/obo/UBERON_0001378 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO gross anatomical observation This assay involves direct, standardized, and reproducible observations of anatomical features. Binary scoring and ordinal scales are used to assess the degree of separation and timing of events. in_vivo degree of separation and timing change low Gross anatomical observations are a direct, standardized, and reproducible strategy and can be conducted periodically. Binary scoring and ordinal scales can be employed to describe degree of separation and timing. http://purl.obolibrary.org/obo/UBERON_0000001 UBERON http://purl.obolibrary.org/obo/GO_0009653 GO Estradiol immunoassay Quantifies estradiol levels in ovarian tissue using antibody-based detection methods, typically ELISA, which is the preferred technique for measuring hormone concentrations. in_vitro ovaries not_specified estradiol concentration increase Rosner et al. 2013 medium Estradiol can be measured via immunoassay, mass spectrometry or Western blotting, with immunoassay the preferred technique (for review of techniques see Rosner et al. 2013). Studies that utilized immunoassay include (Sashida and Johnson 1976; Spears et al. 1998; Li et al. 2008; Murray et al. 2008; Gan et al. 2024), and include commercially available ELISA kits (e.g. Neogen 402110; ALPCO 11-ESTHU-E01; Cayman Chemical 501890). http://purl.obolibrary.org/obo/CHEBI_16240 CHEBI http://purl.obolibrary.org/obo/GO_0006694 GO immunoassay Measures estradiol levels using antibody-based detection methods, often in the form of ELISA kits. in_vitro ovaries estradiol concentration increase http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/OBI_0000470 OBI medium Estradiol can be measured via immunoassay, mass spectrometry or Western blotting, with immunoassay the preferred technique Studies that utilized immunoassay include (Sashida and Johnson 1976; Spears et al. 1998; Li et al. 2008; Murray et al. 2008; Gan et al. 2024), and include commercially available ELISA kits (e.g. Neogen 402110; ALPCO 11-ESTHU-E01; Cayman Chemical 501890) http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0006700 GO mass spectrometry Quantifies estradiol levels using mass spectrometry-based techniques. in_vitro ovaries estradiol concentration increase http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/OBI_0000274 OBI low Estradiol can be measured via immunoassay, mass spectrometry or Western blotting, with immunoassay the preferred technique http://purl.obolibrary.org/obo/CHEBI_16422 CHEBI http://purl.obolibrary.org/obo/GO_0006700 GO real time PCR Measures transcription levels of key steroid biosynthesis genes, such as cyp19 (aromatase), as an indirect indicator of potential changes in estradiol levels. in_vitro ovaries gene expression change http://purl.obolibrary.org/obo/OBI_0000662 OBI http://purl.obolibrary.org/obo/GO_0010467 GO medium transcription of key steroid biosynthesis genes, particularly cyp19 (aromatase) would be an indirect – and only semi-quantitative indicator of potential changes in estradiol hormone levels Enzymes involved in steroid biosynthesis in the ovaries can also be studied via immunoassay, Western blotting, or real time PCR (studies that utilized this approach include Li et al. 2008; Gan et al. 2024) http://purl.obolibrary.org/obo/PR_000001168 PR http://purl.obolibrary.org/obo/GO_0006700 GO real-time PCR Quantifies transcription of the aromatase gene (cyp19) via quantitative real-time PCR, providing a semi-quantitative indicator of potential estradiol synthesis. not_specified ovary cyp19 mRNA expression increase http://purl.obolibrary.org/obo/OBI_0000274 OBI not_specified Since estradiol is generally synthesized from other steroids, real time PCR is generally not used, but transcription of key steroid biosynthesis genes, particularly cyp19 (aromatase) would be an indirect – and only semi-quantitative indicator of potential changes in estradiol hormone levels. Enzymes involved in steroid biosynthesis in the ovaries can also be studied via immunoassay, Western blotting, or real time PCR (studies that utilized this approach include Li et al. 2008; Gan et al. 2024). http://purl.obolibrary.org/obo/UBERON_0000099 UBERON http://purl.obolibrary.org/obo/GO_0006694 GO western blot A technique used to measure estradiol levels (per the text context, though typically used for proteins). in_vitro estradiol levels change http://purl.obolibrary.org/obo/CHEBI_13555 CHEBI http://purl.obolibrary.org/obo/OBI_0000145 OBI not_specified Estradiol can be measured via immunoassay, mass spectrometry or Western blotting http://purl.obolibrary.org/obo/CHEBI_13555 CHEBI http://purl.obolibrary.org/obo/GO_0009410 GO Western blotting Detects and quantifies proteins involved in estradiol biosynthesis, such as enzymes. in_vitro ovaries protein expression change http://purl.obolibrary.org/obo/PR_000000001 PR low Estradiol can be measured via immunoassay, mass spectrometry or Western blotting, with immunoassay the preferred technique Enzymes involved in steroid biosynthesis in the ovaries can also be studied via immunoassay, Western blotting, or real time PCR (studies that utilized this approach include Li et al. 2008; Gan et al. 2024) http://purl.obolibrary.org/obo/PR_000000001 PR http://purl.obolibrary.org/obo/GO_0006694 GO Albumin measurement Measurement of serum albumin levels, which decrease in liver cirrhosis due to impaired synthetic function. in_vitro albumin level decrease http://purl.obolibrary.org/obo/PR_000001402 PR high Decreased albumin http://purl.obolibrary.org/obo/PR_000001402 PR http://purl.obolibrary.org/obo/GO_0043043 GO Bilirubin measurement Measurement of serum bilirubin levels, which increase in liver cirrhosis due to impaired excretion. in_vitro bilirubin level increase http://purl.obolibrary.org/obo/CHEBI_16947 CHEBI high Elevated bilirubin http://purl.obolibrary.org/obo/CHEBI_16947 CHEBI http://purl.obolibrary.org/obo/GO_0042181 GO Fibrosis biomarker measurement Measurement of serum biomarkers such as hyaluronic acid and procollagen peptides, which increase in liver fibrosis. in_vitro fibrosis biomarker level increase http://purl.obolibrary.org/obo/CHEBI_16656 CHEBI http://purl.obolibrary.org/obo/PR_000000001 PR high Fibrosis biomarkers (e.g., hyaluronic acid, procollagen peptides) http://purl.obolibrary.org/obo/GO_0031012 GO http://purl.obolibrary.org/obo/GO_0008544 GO Masson's trichrome staining Histopathological staining method to visualize collagen fibers and assess fibrosis in liver tissue. ex_vivo liver collagen deposition increase http://purl.obolibrary.org/obo/CHEBI_35282 CHEBI http://purl.obolibrary.org/obo/GO_0008544 GO low Masson's trichrome staining http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO Prothrombin time measurement Measurement of prothrombin time, which is prolonged in liver cirrhosis due to impaired synthesis of clotting factors. in_vitro prothrombin time increase high Prolonged prothrombin time http://purl.obolibrary.org/obo/PR_000001603 PR http://purl.obolibrary.org/obo/GO_0007596 GO Serum Biomarker Analysis Measurement of various blood components including albumin, bilirubin, prothrombin time, and specific fibrosis markers to assess liver function. in_vivo blood liver albumin, bilirubin, prothrombin time, and fibrosis biomarkers change http://purl.obolibrary.org/obo/CHEBI_35371 CHEBI high Decreased albumin Elevated bilirubin Prolonged prothrombin time Fibrosis biomarkers (e.g., hyaluronic acid, procollagen peptides) http://purl.obolibrary.org/obo/UBERON_0000348 UBERON http://purl.obolibrary.org/obo/GO_0051055 GO Sirius Red staining Histopathological staining method to specifically visualize collagen deposition in liver tissue. ex_vivo liver collagen deposition increase http://purl.obolibrary.org/obo/CHEBI_35282 CHEBI http://purl.obolibrary.org/obo/GO_0008544 GO low Sirius Red staining for collagen deposition http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO Transient elastography (FibroScan) Non-invasive imaging method to assess liver stiffness, which correlates with fibrosis stage. in_vivo liver liver stiffness increase high Transient elastography (FibroScan) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0008544 GO Ultrasound imaging Non-invasive imaging method to assess liver morphology, including nodular surface and splenomegaly. in_vivo liver spleen liver morphology change high Ultrasound imaging (nodular surface, splenomegaly) http://purl.obolibrary.org/obo/UBERON_0002107 UBERON http://purl.obolibrary.org/obo/GO_0000902 GO ultrasound imaging Imaging of the liver to assess for nodular surface and splenomegaly. in_vivo liver spleen nodular surface and splenomegaly change medium Ultrasound imaging (nodular surface, splenomegaly) http://purl.obolibrary.org/obo/UBERON_0000182 UBERON http://www.ebi.ac.uk/efo/EFO_0001721 EFO MRI scan Uterine weight can be estimated non-destructively by MRI scan. in_vivo uterus estimated uterine weight increase http://purl.obolibrary.org/obo/GO_0005737 GO http://purl.obolibrary.org/obo/UBERON_0001334 UBERON medium Uterine weight can be estimated non-destructively by ultrasound or MRI scan (Harb and Adam 2005). http://purl.obolibrary.org/obo/UBERON_0001334 UBERON http://purl.obolibrary.org/obo/GO_0008327 GO ultrasound Uterine weight can be estimated non-destructively by ultrasound. in_vivo uterus estimated uterine weight increase http://purl.obolibrary.org/obo/GO_0005737 GO http://purl.obolibrary.org/obo/UBERON_0001334 UBERON medium Uterine weight can be estimated non-destructively by ultrasound or MRI scan (Harb and Adam 2005). http://purl.obolibrary.org/obo/UBERON_0001334 UBERON http://purl.obolibrary.org/obo/GO_0008327 GO uterine weight measurement Uterine weight is measured directly after surgical removal, generally during necropsy. in_vivo uterus uterine weight increase low Uterine weight is measured directly after surgical removal, generally during necropsy. http://purl.obolibrary.org/obo/UBERON_0002358 UBERON http://purl.obolibrary.org/obo/GO_0040007 GO Microarray High-throughput sequencing detects the global enrichment of the COL3A1 pathway and related extracellular matrix (ECM)-receptor interaction gene sets. in_vitro gene set enrichment increase high Transcriptomics (RNA-Seq / Microarray): High-throughput sequencing can detect the global enrichment of the COL3A1 pathway and related extracellular matrix (ECM)-receptor interaction gene sets via Gene Set Enrichment Analysis (GSEA) or KEGG pathway analysis. http://purl.obolibrary.org/obo/GO_0007165 GO RNA-Seq High-throughput sequencing to detect global enrichment of the COL3A1 pathway and related extracellular matrix (ECM)-receptor interaction gene sets. in_vitro enrichment of COL3A1 pathway and ECM-receptor interaction gene sets not_specified http://purl.obolibrary.org/obo/OBI_0001271 OBI http://purl.obolibrary.org/obo/GO_0007160 GO high Transcriptomics (RNA-Seq / Microarray): High-throughput sequencing can detect the global enrichment of the COL3A1 pathway and related extracellular matrix (ECM)-receptor interaction gene sets via Gene Set Enrichment Analysis (GSEA) or KEGG pathway analysis. http://purl.obolibrary.org/obo/GO_0007160 GO RNA-Seq High-throughput sequencing detects the global enrichment of the COL3A1 pathway and related extracellular matrix (ECM)-receptor interaction gene sets. in_vitro gene set enrichment increase high Transcriptomics (RNA-Seq / Microarray): High-throughput sequencing can detect the global enrichment of the COL3A1 pathway and related extracellular matrix (ECM)-receptor interaction gene sets via Gene Set Enrichment Analysis (GSEA) or KEGG pathway analysis. http://purl.obolibrary.org/obo/GO_0007165 GO RT-qPCR RT-qPCR is used to quantify the relative mRNA expression levels of the Col3a1 gene in tissue samples or cultured cells. in_vitro tissue samples mRNA expression levels increase medium RT-qPCR (Reverse Transcription-Quantitative Polymerase Chain Reaction): Widely used to quantify the relative mRNA expression levels of the Col3a1 gene in tissue samples or cultured cells. http://purl.obolibrary.org/obo/GO_0010468 GO RT-qPCR Quantifies the relative mRNA expression levels of the Col3a1 gene in tissue samples or cultured cells. in_vitro mRNA expression levels of Col3a1 not_specified http://purl.obolibrary.org/obo/GO_0010467 GO http://purl.obolibrary.org/obo/SO_0000234 SO medium RT-qPCR (Reverse Transcription-Quantitative Polymerase Chain Reaction): Widely used to quantify the relative mRNA expression levels of the Col3a1 gene in tissue samples or cultured cells. http://purl.obolibrary.org/obo/GO_0006351 GO avian morphological assessment Observation of species-specific morphological changes such as feather plumage, eye color, skull ossification, and feather wear in birds. in_vivo skin eye skeleton birds morphological changes change low In birds there can be species-specific changes such as feather plumage, eye color, skull ossification, feather wear, and eye color balanopreputial separation assessment Assesses the onset of puberty in male rodents by visual inspection of balanopreputial separation. in_vivo penis rodents balanopreputial separation not_specified high balanopreputial separation (separation of the foreskin from penis) in males are often used as visual indicators of onset of puberty http://purl.obolibrary.org/obo/UBERON_0000988 UBERON http://purl.obolibrary.org/obo/GO_0040008 GO body size measurement Assesses the onset of puberty in reptiles, amphibians, and fish by measuring body weight or length. in_vivo reptiles amphibians fish body size increase high Size (body weight or length) is generally a better predictor of maturity than age in reptiles ... amphibians ... and fish http://purl.obolibrary.org/obo/NCBITaxon_1 NCBITAXON http://purl.obolibrary.org/obo/GO_0040008 GO eye color assessment Assesses the onset of puberty in birds by visual inspection of species-specific changes in eye color. in_vivo eye birds eye color changes not_specified high In birds there can be species-specific changes such as ... eye color ... are often used as visual indicators of onset of puberty http://purl.obolibrary.org/obo/UBERON_0000970 UBERON http://purl.obolibrary.org/obo/GO_0040008 GO feather plumage assessment Assesses the onset of puberty in birds by visual inspection of species-specific changes in feather plumage. in_vivo feathers birds feather plumage changes not_specified high In birds there can be species-specific changes such as feather plumage ... are often used as visual indicators of onset of puberty http://purl.obolibrary.org/obo/UBERON_0000025 UBERON http://purl.obolibrary.org/obo/GO_0040008 GO hormone level measurement Assesses the onset of puberty by measuring changes in hormone levels from baseline, such as gonadotropins, testosterone, and estradiol. in_vivo hormone levels change http://purl.obolibrary.org/obo/CHEBI_17347 CHEBI http://purl.obolibrary.org/obo/CHEBI_16469 CHEBI medium changes in hormone levels from baseline (i.e. gonadotropins, testosterone, estradiol) are more invasive but alternative assessment methods http://purl.obolibrary.org/obo/CHEBI_24628 CHEBI http://purl.obolibrary.org/obo/GO_0040008 GO mature ova assessment Assesses the onset of puberty by determining the presence of mature ova. in_vivo ovary mature ova not_specified low Determining an individual has mature ova or sperm ... are more invasive but alternative assessment methods, with development of mature ova or sperm ultimately a more direct assessment of the onset of puberty http://purl.obolibrary.org/obo/GO_0007276 GO http://purl.obolibrary.org/obo/GO_0040008 GO size assessment Size (body weight or length) is measured as a predictor of maturity in reptiles, amphibians, and fish. in_vivo whole organism reptiles amphibians fish body weight/length increase http://purl.obolibrary.org/obo/GO_0008366 GO low Size (body weight or length) is generally a better predictor of maturity than age in reptiles (Ball and Wade 2013; Marn and Kooijman 2022), amphibians (Ryser 1996; Morrison and Hero 2003), and fish (Ryu et al. 2013; Espigares et al. 2015). http://purl.obolibrary.org/obo/CL_0000000 CL http://purl.obolibrary.org/obo/GO_0008366 GO skull ossification assessment Assesses the onset of puberty in birds by visual inspection of skull ossification. in_vivo skull birds skull ossification not_specified high In birds there can be species-specific changes such as ... skull ossification ... are often used as visual indicators of onset of puberty http://purl.obolibrary.org/obo/UBERON_0003129 UBERON http://purl.obolibrary.org/obo/GO_0040008 GO vaginal opening assessment Assesses the onset of puberty in female rodents by visual inspection of vaginal opening. in_vivo vagina rodents vaginal opening not_specified high vaginal opening in females ... are often used as visual indicators of onset of puberty http://purl.obolibrary.org/obo/UBERON_0000995 UBERON http://purl.obolibrary.org/obo/GO_0040008 GO histological examination Microscopic study of tissue structure to identify and verify the presence and development of reproductive organs. ex_vivo reproductive organs ovaries sex and organ morphology change http://purl.obolibrary.org/obo/OBI_0000115 OBI http://purl.obolibrary.org/obo/UBERON_0001064 UBERON low Verification of sex is done by histological examination of reproductive organs. http://purl.obolibrary.org/obo/UBERON_0001064 UBERON http://purl.obolibrary.org/obo/GO_0051311 GO histological examination This assay involves the microscopic examination of tissue sections to verify the sex by analyzing the structure of reproductive organs. in_vivo reproductive organs sex verification not_specified http://purl.obolibrary.org/obo/UBERON_0000990 UBERON low Verification of sex is done by histological examination of reproductive organs. http://purl.obolibrary.org/obo/UBERON_0000990 UBERON http://purl.obolibrary.org/obo/GO_0007548 GO histological examination This assay verifies phenotypic sex by examining reproductive organs histologically. in_vivo reproductive organs phenotypic sex not_specified low Verification of phenotypic sex can be done by histological examination of reproductive organs. http://purl.obolibrary.org/obo/UBERON_0000087 UBERON http://purl.obolibrary.org/obo/GO_0007548 GO Histological examination of reproductive organs Histological examination of reproductive organs is used to verify the phenotypic sex of individuals in a population, allowing for the determination of sex ratio. in_vivo reproductive organs not_specified proportion of females to males change low Sex ratio is determined by the proportion of females to males in a population. Verification of phenotypic sex can be done by histological examination of reproductive organs. sex ratio determination Sex ratio is determined by calculating the proportion of females to males within a population. not_specified reproductive organs proportion of females to males increase not_specified Sex ratio is determined by the proportion of females to males in a population. http://purl.obolibrary.org/obo/GO_0008441 GO RAR transactivation assay This assay measures the transcriptional activation of RAR in response to retinoids, providing an indirect measure of RAR activation levels. in_vitro RAR transcriptional activation decrease http://purl.obolibrary.org/obo/GO_0048390 GO http://purl.obolibrary.org/obo/GO_0006351 GO OECD Detailed review paper on the Retinoid System, 2021, OECD Validation report on a RAR transactivation method, 2025 medium in vitro RAR and RAR-RXR transactivation assays (OECD Detailed review paper on the Retinoid System, 2021, OECD Validation report on a RAR transactivation method, 2025), as measured in upstream KEs. http://purl.obolibrary.org/obo/PR_000001700 PR http://purl.obolibrary.org/obo/GO_0006351 GO RAR transactivation assay This assay measures the transactivation activity of RAR and RAR-RXR in vitro, serving as an indirect assessment of RAR activation. in_vitro RAR transactivation activity increase OECD Detailed Paper Review on Retinoids, Validation report on a RAR transactivation method not_specified in vitro RAR and RAR-RXR transactivation assays (OECD Detailed Paper Review on Retinoids, Validation report on a RAR transactivation method).