identifier: traitmech:000583
label: gyrotaxis
definition: A motile phenotype in which the balance of gravitational and viscous torques
  biases an organism's swimming orientation.
definition_source: DOI:10.1073/pnas.2206738119
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- METPO:1000702
evidence:
- reference: DOI:10.1073/pnas.2206738119
  snippet: The orientational response to the gravity-viscous torque balance is known
    as gyrotaxis
  notes: 'Introduction, page 1; definition checked against the publisher-formatted
    article deposited by the authors at https://api.repository.cam.ac.uk/server/api/core/bitstreams/ac9ccafe-f229-477c-9d59-b7a56cd506a0/content
    (PMID:36219692; PMC9586295). The second of the introduction''s three accumulation
    mechanisms starts ''The second is response to an external field'': it describes
    swimming in still water and gravitational restoration resisted hydrodynamically,
    then names this response gyrotaxis. This record follows Zeng''s broader usage,
    not a universal requirement or exclusion of imposed shear. Results, Figures 5-7,
    and Materials and Methods distinguish gravitational reorientation from wall-contact
    effects in Heterosigma akashiwo GY-H24. Shape asymmetry and density asymmetry
    are alternatives; bottom-heaviness is not universal. The full main article was
    read; supplementary material and movies were not inspected. No gravity-sensing
    receptor is asserted.'
- reference: DOI:10.1126/science.1167334
  snippet: The swimming direction, θ, is then set by the balance of viscous and gravitactic
    torques
  notes: Page 1068, left column beneath Figure 2; the typeset theta in the torque-balance
    sentence was visually checked because PDF extraction substitutes q. This passage
    concerns imposed shear. Live-cell experiments are on pages 1067-1069 of the full
    main article at https://stockerlab.ethz.ch/wp-content/uploads/2013/01/17.-DurhamKesslerStocker_Science2009.pdf
    (PMID:19229037). Chlamydomonas nivalis and Heterosigma akashiwo formed layers
    in a depth-varying shear chamber; dead cells did not. Gyrotactic trapping is a
    population consequence under suitable shear, not the definition of the organismal
    trait or the cause of every oceanic thin layer. Ocean-scale results are model
    predictions. The supplement and exact culture identities were not verified; no
    strain or modern C. nivalis taxon identity is inferred.
canonical_examples:
- taxon_id: NCBITaxon:2829
  taxon_label: Heterosigma akashiwo
  reference: DOI:10.1073/pnas.2206738119
  note: GY-H24 culture, examined 3-9 hours into the light phase of a 12-hour light/12-hour
    dark cycle. Figures 5-7 show gravitational reorientation and wall-modified swimming
    in a sealed, still-fluid microchannel; upward bias is not asserted for every cell
    or diurnal phase. This example follows Zeng's explicit still-water usage of gyrotaxis;
    it is not an imposed-shear experiment. The NCBI identifier is species-level, not
    a resolved GY-H24 strain accession.
discussions:
- discussion_id: gyrotaxis-physical-mechanism-representation
  prompt: Represent physical torque-mediated orientation without inventing a protein
    sensor.
  kind: CURATION_TODO
  status: OPEN
  rationale: 'The primary papers describe a physical mechanism, so the absence of
    a protein accession is not absence of mechanistic evidence. This identity/evidence
    pass omits a graph: the current MECHANISTIC coverage audit requires a protein
    node and protein example, whereas NONMECHANISTIC is reserved for measurement or
    classification contexts. Resolve a faithful representation separately instead
    of relabeling the physical mechanism or inventing a sensor. Keep gravity-viscous
    orientation distinct from wall-contact responses and high-shear trapping. Gyrotaxis
    is not an exact synonym of gravitaxis, rheotaxis, bioconvection or thin-layer
    formation. QuickGO returned no gyrotaxis term on 2026-10-04; no exact external
    xref is asserted.'
  posed_by: codex
  posed_date: '2026-10-04'
curation_history:
- timestamp: '2026-10-04T01:16:29Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added gyrotaxis with two primary DOI sources, contiguous evidence snippets
    and a light-phase-qualified GY-H24 example at verified species taxon NCBITaxon:2829.
    Ignored-and-hidden novelty searches found no exact record or METPO class. Reserved
    METPO:1053700 in proposal v460. Recorded the physical-graph representation gap
    without asserting an unsupported protein or receptor.
  llm_assisted: true
- timestamp: '2026-10-04T01:41:15Z'
  curator: codex
  action: ADDRESS_REVIEW_FINDINGS
  changes: 'Addressed PR 1646 issues 1647 and 1648: replaced the Durham population
    outcome snippet with its typeset torque-balance statement; anchored Zeng''s broader
    still-water usage to the specific introduction passage and qualified the canonical
    example. Definition and hierarchy unchanged.'
  llm_assisted: true