{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.eyespot-apparatus","code":"thing-q22329156","url":"https://ver.cy/models/thing/q22329156/","name":"eyespot apparatus","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.LIV"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"An eyespot apparatus is a subcellular light-sensing system in certain motile algae and other protists that combines photoreceptors with an associated pigmented optical structure to detect light direction and guide swimming.","purpose":"Enable an agent to recognise an eyespot apparatus, assess its structural and light-sensing state, and select observations or interventions appropriate to its host cell.","scope":{"in":["Pigment globules, their organisation, and associated photoreceptive components","Position within the host cell and alignment between optical and receptor components","Directional light modulation and stimulus-dependent receptor activity","Assembly, maintenance, and disruption of the apparatus","Evidence connecting apparatus condition to host-cell photobehaviour"],"out":["Host-organism taxonomy, geographic range, and conservation assessment","Animal eyes, ocelli, and decorative eyespot markings","Whole-chloroplast photosynthesis and general pigment metabolism","Flagellar construction and the complete locomotor system","Photoreceptor proteins considered independently of their association with the apparatus"],"boundaries":[]},"distinguishingFeatures":["It is a subcellular apparatus within a host cell, not a species, population, or individual organism.","A visible pigmented spot alone is insufficient: identification must establish or explicitly leave unresolved its association with photoreceptive components.","Its identification requires evidence of an organised light-sensing arrangement rather than carotenoid pigmentation alone.","Architecture is lineage-dependent: Chlamydomonas reinhardtii has chloroplast pigment arrays associated with plasma-membrane receptors, whereas Euglena gracilis has cytosolic eyespot globules associated with a paraflagellar photoreceptive body.","Directional light sensing must be distinguished from image formation and from a general response to changes in illumination."],"structure":{"bundles":[{"id":"identity-and-lineage","name":"Identity and lineage","description":"Establish what counts as this apparatus in the observed host.","layers":[{"id":"apparatus-boundary","name":"Apparatus boundary","description":"Separate the complete functional arrangement from its visible pigment component.","findings":[{"id":"pigment-plus-photoreception","name":"Pigment structure and photoreception","description":"Record the pigment structure and associated photoreceptive components separately before asserting the complete apparatus. Terminology can distinguish the eyespot from the larger apparatus. Source: [Kato et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7155050/).","questions":[{"text":"Does 'eyespot' in this observation mean the pigment globules or the complete photoreceptive apparatus?","id":"pigment-plus-photoreception-q01","kind":"definition"},{"text":"What evidence associates the observed pigment structure with photoreceptive components?","id":"pigment-plus-photoreception-q02","kind":"provenance"}]}]},{"id":"host-specific-architecture","name":"Host-specific architecture","description":"Qualify anatomical expectations by host identity.","findings":[{"id":"compartment-pattern","name":"Compartment pattern","description":"Chlamydomonas and Euglena demonstrate different pigment and receptor compartment arrangements; record the observed arrangement without assuming evolutionary equivalence. Source: [Kato et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7155050/).","questions":[{"text":"Which taxon, strain, and cellular stage support the proposed architectural identification?","id":"compartment-pattern-q01","kind":"provenance"},{"text":"Which components lie in the chloroplast, cytosol, plasma membrane, or paraflagellar region?","id":"compartment-pattern-q02","kind":"boundary"}]}]}]},{"id":"pigment-optics-and-geometry","name":"Pigment optics and geometry","description":"Describe the pigment structure and its spatial contribution to light sensing.","layers":[{"id":"globule-organisation","name":"Globule organisation","description":"Resolve pigment bodies, arrays, and surrounding membranes.","findings":[{"id":"array-structure","name":"Array structure","description":"Measure globule size, packing, and layer organisation where present. Ordered chloroplast globule layers are documented in Chlamydomonas reinhardtii. Source: [Schmidt et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC1533972/).","questions":[{"text":"What globule dimensions, packing pattern, and layer count are resolved by the imaging method?","id":"array-structure-q01","kind":"measurement"},{"text":"Which observations distinguish eyespot globules from neighbouring lipid bodies or other pigment deposits?","id":"array-structure-q02","kind":"boundary"}]}]},{"id":"directional-optics","name":"Directional optics","description":"Assess how geometry changes illumination reaching the receptor.","findings":[{"id":"optical-effect","name":"Optical effect","description":"Distinguish measured shielding or reflection from proposed mechanisms. Euglena eyespots should not automatically inherit the reflective role attributed to ordered algal arrays. Source: [Kato et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7155050/).","questions":[{"text":"How does illumination at the receptor vary with light direction relative to the pigment structure?","id":"optical-effect-q01","kind":"measurement"},{"text":"Is the assigned shielding or reflective role measured in this host or inferred from another system?","id":"optical-effect-q02","kind":"provenance"}]}]}]},{"id":"photoreception-and-movement-interface","name":"Photoreception and movement interface","description":"Connect local light detection to cellular responses while retaining the apparatus boundary.","layers":[{"id":"receptor-response","name":"Receptor response","description":"Identify the photoreceptive component and characterise its response.","findings":[{"id":"localised-light-detection","name":"Localised light detection","description":"Record receptor identity, localisation, and stimulus-response evidence independently. Channelrhodopsins are documented photoreceptors in Chlamydomonas reinhardtii; this identity is not a universal eyespot requirement. Source: [Kato et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7155050/).","questions":[{"text":"Which receptor is supported by molecular and localisation evidence in this host?","id":"localised-light-detection-q01","kind":"provenance"},{"text":"What wavelength, irradiance, and response latency characterise the measured receptor activity?","id":"localised-light-detection-q02","kind":"measurement"}]}]},{"id":"behavioural-coupling","name":"Behavioural coupling","description":"Separate directional navigation from other light-induced movements.","findings":[{"id":"photobehaviour-readout","name":"Photobehaviour readout","description":"Record movement toward or away from a light direction separately from transient avoidance responses, and qualify attribution to the apparatus with motility controls.","questions":[{"text":"Does the assay measure directional phototaxis, a transient light response, or a change in swimming speed?","id":"photobehaviour-readout-q01","kind":"definition"},{"text":"Which control shows that an altered response is not explained by loss of flagellar motility?","id":"photobehaviour-readout-q02","kind":"action"}]}]}]},{"id":"assembly-and-structural-state","name":"Assembly and structural state","description":"Track apparatus formation, placement, and structural disruption.","layers":[{"id":"formation-and-placement","name":"Formation and placement","description":"Relate assembly to the host cell cycle and positioning machinery.","findings":[{"id":"assembly-context","name":"Assembly context","description":"Chlamydomonas reinhardtii eyespots assemble after division and associate with a defined microtubule rootlet; apply this pattern only where supported. Source: [Boyd et al.](https://pubmed.ncbi.nlm.nih.gov/21372178/).","questions":[{"text":"At what cell-cycle stage was apparatus formation or reorganisation observed?","id":"assembly-context-q01","kind":"measurement"},{"text":"What evidence links apparatus position to a cellular landmark or assembly factor in this host?","id":"assembly-context-q02","kind":"provenance"}]}]},{"id":"component-integrity","name":"Component integrity","description":"Distinguish loss of pigment, receptor organisation, and alignment.","findings":[{"id":"structural-defect-classification","name":"Structural defect classification","description":"Classify observed defects by affected component rather than assigning a single functional state from spot visibility.","questions":[{"text":"Are pigment globules, receptor localisation, component alignment, or several of these altered?","id":"structural-defect-classification-q01","kind":"measurement"},{"text":"What additional observation is needed before a visually undetected apparatus can be classified as absent?","id":"structural-defect-classification-q02","kind":"action"}]}]}]},{"id":"observation-and-perturbation","name":"Observation and perturbation","description":"Support interpretable examinations and experiments on the apparatus.","layers":[{"id":"measurement-context","name":"Measurement context","description":"Retain conditions needed to interpret structural and functional observations.","findings":[{"id":"assay-interpretability","name":"Assay interpretability","description":"Associate each result with cell preparation, illumination history, spatial resolution, and whether the specimen was alive or fixed.","questions":[{"text":"Was the apparatus observed in a live, fixed, sectioned, or isolated preparation?","id":"assay-interpretability-q01","kind":"provenance"},{"text":"What resolution and illumination history limit conclusions about component alignment or light sensitivity?","id":"assay-interpretability-q02","kind":"measurement"}]}]},{"id":"causal-interventions","name":"Causal interventions","description":"Evaluate whether a manipulation specifically explains an apparatus-associated change.","findings":[{"id":"perturbation-attribution","name":"Perturbation attribution","description":"Record the targeted pigment, receptor, or assembly process alongside possible host-cell effects and evidence of recovery or rescue.","questions":[{"text":"Which apparatus component is targeted, and which other cellular processes could the intervention affect?","id":"perturbation-attribution-q01","kind":"boundary"},{"text":"Which matched control or rescue would support attributing the observed photobehaviour change to the apparatus?","id":"perturbation-attribution-q02","kind":"action"}]}]}]},{"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 eyespot apparatus 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 eyespot apparatus this model covers, and on what evidence?","id":"evidence-kinds-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 eyespot apparatus 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 eyespot apparatus 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 eyespot apparatus 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 eyespot apparatus this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe the eyespot apparatus and how algae use it to sense light, from reliable sources.","Record its presence and position in microscopy observations of protists."],"mustNot":["Confuse the eyespot apparatus with an animal eye in descriptions or data.","Present preliminary research on eyespots as established fact.","Release genetically modified algae from a laboratory without approval."],"requiresHuman":["Approving experiments with genetically modified algae outside contained facilities."]},"ethics":{"considerations":["Research on algal light sensing feeds into biotechnology that needs responsible oversight."],"affectedParties":["Researchers and students","Aquatic ecosystems"]},"owners":{"steward":"Nobody owns the structure; the laboratory or keeper answers for each culture.","roles":[],"masterSystems":[]},"relations":[{"target":"Q14349519","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.eyespot-apparatus","Wikidata: Q22329156 (https://www.wikidata.org/wiki/Q22329156)"]},"properties":{"applicability":"required","items":["Host and observation context: Host taxon, strain, individual cell, life stage, and culture condition","Apparatus architecture: Chloroplast-associated arrays with adjacent receptors; cytosolic globules with paraflagellar photoreception; other documented arrangement; unresolved","Pigment structure dimensions: Length and width in µm; globule diameter in nm; globule and layer counts","Pigment composition: Identified carotenoids with analytical method; unresolved","Receptor identity and localisation: Receptor or receptor complex linked to its cellular compartment and localisation evidence","Optical and receptor alignment: Component separation in nm or µm; orientation in degrees relative to defined cellular axes","Assembly condition: Assembling; structurally intact; disorganised; reduced; absent under validated observation; unresolved","Light-response profile: Response versus wavelength in nm, photon irradiance in µmol photons m−2 s−1, incidence angle in degrees, and time in ms or s"]},"recognition":{"applicability":"required","items":["A small red or orange spot inside a single-celled alga, seen under a light microscope.","Lies near the base of the flagella in swimming cells such as Chlamydomonas or Euglena."]},"capabilities":{"applicability":"required","items":["Identify a candidate apparatus using host context, microscopy, and receptor-localisation evidence.","Measure pigment organisation and its alignment with photoreceptive components.","Select illumination conditions for testing directional sensitivity.","Compare apparatus structure and photobehaviour across developmental states or controlled perturbations.","Distinguish an apparatus defect from impaired motility or compromised cell condition.","Record unresolved component identities or causal mechanisms without treating them as established."]},"hazards":{"applicability":"required","items":["Damage to the eyespot leaves the cell unable to steer towards light."]},"interfaces":{"applicability":"not-applicable","items":[]},"context":{"applicability":"required","items":["An eyespot apparatus occurs in certain motile algae and other protists, where it contributes to sensing the direction of light.","Its signals help the host cell adjust swimming in relation to illumination and conditions relevant to photosynthesis.","Researchers study the apparatus through microscopy and measurements of cellular responses to light."]}},"sources":[{"title":"Wikidata item Q22329156: eyespot apparatus","url":"https://www.wikidata.org/wiki/Q22329156","note":"identity and sense of the item"},{"title":"Wikipedia: Eyespot apparatus","url":"https://en.wikipedia.org/wiki/Eyespot_apparatus","note":"general description of the item"}],"openQuestions":["Does the registry intend to include all protist structures called eyespot apparatuses, including architectures beyond the Chlamydomonas and Euglena examples?","What minimum anatomical and functional evidence should distinguish a complete apparatus from an isolated stigma or pigment aggregate?","Which proposed optical mechanisms have been directly demonstrated in each included lineage?","What host-specific reference ranges distinguish normal assembly variation from structural defects?","Which assay combinations can reliably separate apparatus dysfunction from altered light adaptation, cell condition, or motility?"],"resources":{"spec":"/models/things/publications/thing-q22329156/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q22329156/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T09:36:53Z","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":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"not-applicable","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:28+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.interfaces":"No dedicated technical standard or regulation applies to the eyespot apparatus itself as a naturally occurring subcellular system."},"score":1.0}}