{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.nigericin","code":"thing-q7033077","url":"https://ver.cy/models/thing/q7033077/","name":"nigericin","alternateNames":[],"kind":"thing","status":"research-draft","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.MAT"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"Nigericin is a microbial polyether antibiotic that acts as a mobile ion carrier, exchanging potassium ions for protons across lipid membranes and thereby altering ion and pH gradients.","purpose":"Enable an AI agent to recognise nigericin, assess a sample's chemical and functional state, and judge its suitability for a specified research use.","scope":{"in":["Molecular identity, stereochemistry, identifiers, and distinction between free acid and supplied salts","Lot composition, purity, concentration, and analytical evidence","Physical state, solubility, storage history, and stability","Potassium-proton exchange under specified membrane and solution conditions","Suitability and interpretation limits for ion-gradient and cellular research","Form-specific hazard documentation and permitted handling"],"out":["Supplier products, packaging, pricing, and procurement workflows","Producing organisms and fermentation or synthesis processes","Complete inflammasome, mitochondrial, or cell-death pathway models","Experimental protocols and instrument operation","Clinical treatment decisions and therapeutic efficacy","Other ionophores as independently modelled substances"],"boundaries":[]},"distinguishingFeatures":["Require a structure and stereochemistry match rather than identification from antibiotic activity alone; nigericin is a polyether antibiotic with free-acid formula C40H68O11. [PubChem](https://pubchem.ncbi.nlm.nih.gov/compound/Nigericin)","Distinguish the free acid, PubChem CID 34230, from sodium nigericin, CID 16760591 and formula C40H67NaO11; a shared parent name does not establish identical weighing or concentration calculations. [PubChem sodium nigericin](https://pubchem.ncbi.nlm.nih.gov/compound/16760591)","Test for coupled, electroneutral potassium-proton exchange when distinguishing nigericin's transport mechanism from electrogenic potassium transport; transport behaviour supplements chemical identification. [Primary study](https://pmc.ncbi.nlm.nih.gov/articles/PMC10786283/)","Do not identify nigericin by an inflammasome readout or label it exclusively NLRP3-specific: a primary study also reports NLRP1 activation in human epithelial cells. [Primary study](https://pmc.ncbi.nlm.nih.gov/articles/PMC10786283/)"],"structure":{"bundles":[{"id":"nigericin-identity","name":"Nigericin identity","description":"Establish which chemical entity a nigericin-labelled material represents.","layers":[{"id":"molecular-recognition","name":"Molecular recognition","description":"Anchor recognition to the nigericin molecular structure.","findings":[{"id":"structure-confirmation","name":"Structure confirmation","description":"Record structural evidence sufficient to distinguish nigericin from related polyether compounds.","questions":[{"text":"Which reference structure and stereochemical specification define nigericin for this entry?","id":"structure-confirmation-q01","kind":"definition"},{"text":"Which analytical evidence establishes that the sample matches that structure rather than merely showing similar activity?","id":"structure-confirmation-q02","kind":"measurement"}]}]},{"id":"form-and-identifiers","name":"Form and identifiers","description":"Resolve the relationship between the parent substance and the supplied material.","findings":[{"id":"form-qualified-identity","name":"Form-qualified identity","description":"Keep free acid, counterion, solvation, and identifier scope explicit within the existing registry boundary.","questions":[{"text":"Is the material the free acid, a specified salt, a solvate, or an unresolved preparation?","id":"form-qualified-identity-q01","kind":"definition"},{"text":"Which CAS, PubChem, ChEBI, and EC records apply to that exact form, and which records were checked?","id":"form-qualified-identity-q02","kind":"provenance"},{"text":"Which label names denote nigericin itself and which denote a formulation containing it?","id":"form-qualified-identity-q03","kind":"boundary"}]}]}]},{"id":"lot-content-and-integrity","name":"Lot content and integrity","description":"Determine how much identified nigericin a sample contains and whether it remains usable.","layers":[{"id":"assayed-composition","name":"Assayed composition","description":"Connect declared purity to quantitative material content.","findings":[{"id":"content-basis","name":"Content basis","description":"Separate nigericin mass content from chromatographic area purity and other constituents.","questions":[{"text":"Does the reported purity measure mass fraction, chromatographic area, or another quantity?","id":"content-basis-q01","kind":"measurement"},{"text":"How do water, residual solvent, counterion, and detected impurities affect the amount of nigericin represented by a weighed sample?","id":"content-basis-q02","kind":"measurement"},{"text":"Which lot-specific certificate or analysis supports the declared content?","id":"content-basis-q03","kind":"provenance"}]}]},{"id":"integrity-over-time","name":"Integrity over time","description":"Assess whether handling history has compromised chemical or functional quality.","findings":[{"id":"stability-and-retest","name":"Stability and retest","description":"Tie continued suitability to evidence for the relevant solid or solution form.","questions":[{"text":"What storage and opening history is recorded for this nigericin lot or stock?","id":"stability-and-retest-q01","kind":"provenance"},{"text":"Which measurements detect loss of nigericin content, impurity growth, or loss of transport activity?","id":"stability-and-retest-q02","kind":"measurement"},{"text":"What evidence warrants continued use, retesting, or quarantine?","id":"stability-and-retest-q03","kind":"action"}]}]}]},{"id":"physical-state-and-preparation","name":"Physical state and preparation","description":"Represent the material state and concentration available to an experiment.","layers":[{"id":"form-dependent-properties","name":"Form-dependent properties","description":"Record physical properties with their chemical form and measurement conditions.","findings":[{"id":"solubility-and-thermal-behaviour","name":"Solubility and thermal behaviour","description":"Qualify physical constants rather than transferring values between unspecified preparations.","questions":[{"text":"What nigericin solubility is supported in the relevant solvent or medium at the stated temperature and pH?","id":"solubility-and-thermal-behaviour-q01","kind":"measurement"},{"text":"Do reported thermal values describe melting, decomposition, or boiling, and for which form and measurement conditions?","id":"solubility-and-thermal-behaviour-q02","kind":"measurement"}]}]},{"id":"available-concentration","name":"Available concentration","description":"Translate assayed material into a defensible preparation concentration.","findings":[{"id":"concentration-validity","name":"Concentration validity","description":"Track formula-mass basis, dilution, and evidence of incomplete dissolution.","questions":[{"text":"Which chemical form, formula mass, and content correction underlie the reported molar concentration?","id":"concentration-validity-q01","kind":"measurement"},{"text":"Is the working preparation fully dissolved after dilution, and how was this assessed?","id":"concentration-validity-q02","kind":"measurement"},{"text":"What preparation evidence is required before comparing this exposure with another nigericin experiment?","id":"concentration-validity-q03","kind":"action"}]}]}]},{"id":"potassium-proton-transport","name":"Potassium-proton transport","description":"Describe nigericin activity through measured ion exchange and its environmental dependencies.","layers":[{"id":"exchange-mechanism","name":"Exchange mechanism","description":"Identify the coupled transport process supported in the tested system.","findings":[{"id":"coupling-and-selectivity","name":"Coupling and selectivity","description":"Distinguish evidence for coupled exchange from ion binding or nonspecific membrane leakage.","questions":[{"text":"What measurements support coupled K+/H+ exchange and its stoichiometry in this system?","id":"coupling-and-selectivity-q01","kind":"measurement"},{"text":"Do reported selectivity values describe binding affinity, transport rate, or a downstream biological response?","id":"coupling-and-selectivity-q02","kind":"boundary"},{"text":"Which competing ions and membrane conditions were included when selectivity was measured?","id":"coupling-and-selectivity-q03","kind":"measurement"}]}]},{"id":"gradient-dependent-performance","name":"Gradient-dependent performance","description":"Connect activity to gradients, membranes, and exposure.","findings":[{"id":"transport-operating-context","name":"Transport operating context","description":"Make direction and extent of ion redistribution conditional on the actual test environment.","questions":[{"text":"What potassium concentrations and pH values occur on each membrane side before and after exposure?","id":"transport-operating-context-q01","kind":"measurement"},{"text":"How do nigericin concentration, exposure time, temperature, and membrane composition affect the observed transport?","id":"transport-operating-context-q02","kind":"measurement"},{"text":"What evidence shows that the intended gradient perturbation or pH equilibration was achieved?","id":"transport-operating-context-q03","kind":"action"}]}]}]},{"id":"research-response-interpretation","name":"Research response interpretation","description":"Connect nigericin exposure to observed responses without assigning unsupported pathway specificity.","layers":[{"id":"experimental-role","name":"Experimental role","description":"Specify the purpose and context of nigericin use.","findings":[{"id":"context-qualified-response","name":"Context-qualified response","description":"Keep ion-gradient manipulation, pH calibration, antimicrobial testing, and cellular stimulation distinguishable.","questions":[{"text":"What role is nigericin intended to serve in this experiment, and what observable result defines success?","id":"context-qualified-response-q01","kind":"definition"},{"text":"Which cell or membrane system, priming state, medium, concentration, and duration qualify the response?","id":"context-qualified-response-q02","kind":"measurement"}]}]},{"id":"causal-and-assay-limits","name":"Causal and assay limits","description":"Separate observed effects from conclusions requiring additional controls.","findings":[{"id":"response-attribution","name":"Response attribution","description":"Require controls that distinguish ion redistribution, pathway activation, and general loss of viability.","questions":[{"text":"Which controls distinguish the intended response from vehicle effects, nonspecific toxicity, and assay interference?","id":"response-attribution-q01","kind":"measurement"},{"text":"What evidence distinguishes NLRP3 involvement from NLRP1 involvement or inflammasome-independent responses in this system?","id":"response-attribution-q02","kind":"boundary"},{"text":"Which conclusions remain unsupported even if the nigericin positive control produces a signal?","id":"response-attribution-q03","kind":"boundary"}]}]}]},{"id":"handling-and-use-constraints","name":"Handling and use constraints","description":"Bind handling decisions to the identified nigericin material and applicable documentation.","layers":[{"id":"hazard-evidence","name":"Hazard evidence","description":"Establish the documented hazards and unresolved safety information.","findings":[{"id":"form-specific-classification","name":"Form-specific classification","description":"Record applicable classifications without assuming that all nigericin products have identical documentation.","questions":[{"text":"Which current SDS applies to the exact free acid, salt, or solution being handled?","id":"form-specific-classification-q01","kind":"provenance"},{"text":"What GHS classifications and exposure routes does that document identify, under which jurisdiction?","id":"form-specific-classification-q02","kind":"definition"},{"text":"Are substance-specific exposure limits documented, or is their status unresolved?","id":"form-specific-classification-q03","kind":"provenance"}]}]},{"id":"permitted-material-actions","name":"Permitted material actions","description":"Translate verified documentation into decisions for the intended research setting.","findings":[{"id":"handling-disposition","name":"Handling disposition","description":"Determine applicable storage, exposure-control, spill, and waste requirements.","questions":[{"text":"Which documented controls apply to weighing the solid versus handling a nigericin solution?","id":"handling-disposition-q01","kind":"action"},{"text":"What storage, spill-response, and disposal requirements apply to this material and its solvent?","id":"handling-disposition-q02","kind":"action"},{"text":"What evidence establishes that the proposed use is permitted in the relevant facility and jurisdiction?","id":"handling-disposition-q03","kind":"provenance"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of nigericin this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of nigericin this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of nigericin this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of nigericin this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of nigericin this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of nigericin this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of nigericin this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Identify nigericin as a potassium-proton ionophore used in research, citing sources.","Report the grade, storage and safety data of a held research stock."],"mustNot":["Assist anyone in using it to harm people or animals.","Recommend it as a treatment or supplement for a person.","Give handling information beyond its safety data sheet that lowers barriers to misuse.","Dispose of it in drains or general waste."],"requiresHuman":["Ordering, transferring or disposing of stock.","Using it in any study involving animals."]},"ethics":{"considerations":["It disrupts cellular ion balance and is toxic, so careless handling endangers workers.","Research toxins require control to prevent misuse."],"affectedParties":["Laboratory workers","Research animals","Waste handlers"]},"owners":{"steward":"The laboratory that holds the stock; institutional safety officers oversee its use.","roles":[],"masterSystems":["Laboratory chemical inventories"]},"relations":[],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.nigericin","Wikidata: Q7033077 (https://www.wikidata.org/wiki/Q7033077)"]},"properties":{"applicability":"required","items":["Chemical identity: Structure with stereochemistry; molecular formula; form-qualified CAS, PubChem, ChEBI, and EC identifiers","Supplied chemical form: Free acid, specified salt, specified solvate, or unresolved","Nigericin content and purity: Mass fraction %, chromatographic area %, and water or residual-solvent content, each with method","Preparation concentration: mg/mL or mmol/L, with chemical form and assay correction","Physical and solution state: Solid or solution; solvent; dissolved, precipitated, or unresolved; temperature in °C","Condition-qualified physical constants: Solubility in mg/mL; melting or decomposition temperature in °C; boiling data only if supported, with pressure","Ion-transport conditions: K+ and Na+ concentrations in mmol/L on both membrane sides; pH; temperature in °C; membrane composition","Functional potency: Transport rate or concentration-response endpoint with assay, exposure duration, and reference lot","Biological test context: Cell or membrane system, priming state, medium, controls, and measured endpoint","Handling eligibility: Approved for specified use, restricted, quarantined, or unresolved; linked SDS version and jurisdiction"]},"recognition":{"applicability":"required","items":["Supplied as a small quantity of white solid or solution in a labelled vial.","Not identifiable by sight; label and analysis settle identity."]},"capabilities":{"applicability":"required","items":["Resolve a labelled material to nigericin and its explicitly stated chemical form.","Compare lots using identity, content, impurity, and functional evidence.","Calculate form-corrected concentrations from verified material content.","Assess whether a preparation is suitable for a specified ion-gradient or cellular assay.","Interpret observed responses against transport conditions and pathway-specific controls.","Determine whether storage, handling, or disposal actions meet the applicable documented requirements."]},"hazards":{"applicability":"required","items":["Toxic exposure through skin contact or ingestion.","Contaminated experiments from wrong concentration or degraded stock."]},"interfaces":{"applicability":"required","items":["Globally Harmonized System of Classification and Labelling of Chemicals (GHS), United Nations."]},"context":{"applicability":"required","items":["Nigericin is used in laboratory research to study ion transport and pH gradients across biological membranes.","It is also used in cell biology research investigating inflammasome activation and associated inflammatory responses."]}},"sources":[{"title":"Wikidata item Q7033077: nigericin","url":"https://www.wikidata.org/wiki/Q7033077","note":"identity and sense of the item"},{"title":"Wikipedia: Nigericin","url":"https://en.wikipedia.org/wiki/Nigericin","note":"general description of the item"}],"openQuestions":["Which CAS and EC identifiers unambiguously map to the free acid and each supplied salt, and which historical synonyms denote exactly the same stereochemical entity?","Which measured solubility, thermal, and storage-stability values are reliable for each material form, and are any reported boiling values experimentally supported?","What minimum analytical and functional evidence is sufficient to accept a lot, particularly when its certificate reports only chromatographic area purity?","Under which membrane and ionic conditions does nigericin transport competing ions, and how do those conditions limit potassium-selective or pH-clamping interpretations?","Which current hazard classifications, exposure limits, and use restrictions apply to the exact preparation in the intended jurisdiction?"],"resources":{"spec":"/models/things/publications/thing-q7033077/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q7033077/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T11:35:47Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"missing","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{},"score":0.941}}