identifier: traitmech:000688
label: siliceous scale production
definition: A physiological phenotype in which a microbial cell produces siliceous
  scales.
definition_source: DOI:10.1016/j.protis.2016.05.002
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000690
evidence:
- reference: DOI:10.1016/j.protis.2016.05.002
  snippet: Scales were formed one by one in silica deposition vesicles (SDVs)
  notes: Nomura and Ishida 2016, PMID:27348459. Scientific abstract directly read
    on 2026-10-10 at https://rrc.nbrp.jp/references/56432?lang=en and Europe PMC CORE,
    using EXT_ID:27348459 AND SRC:MED and checking the returned source, title and
    DOI together. The study describes scale formation in Paulinella chromatophora
    under its historical name and detects silicon in vesicles with immature scales.
    Microtubule involvement in determining scale geometry is proposed, not demonstrated
    molecular necessity. Publisher access returned 403; full Methods and figures were
    not inspected. Scale production and subsequent shell assembly are distinct observations.
- reference: DOI:10.1111/j.0022-3646.1996.00675.x
  snippet: The first new scales appeared within 2 h after the silica addition
  notes: Sandgren, Hall and Barlow 1996, scientific ABSTRACT directly read on 2026-10-10
    in publisher-deposited Crossref JATS at https://api.crossref.org/works/10.1111%2Fj.0022-3646.1996.00675.x.
    Silica-limited Synura petersenii cultures suppressed scale deposition, and scale-free
    cells regenerated scales after dissolved silica addition. This supports production
    rather than possession alone. The quoted recovery timing is specific to that culture
    experiment, not a universal threshold or rate. Scale production could be uncoupled
    from cell division in this system; no obligatory growth dependence is inferred.
    Crossref print date is August 1996; its June 2008 online date is not a second
    study. Full Methods and figures were not inspected.
discussions:
- discussion_id: siliceous-scale-production-scope-and-parent
  prompt: Resolve broader biomineralization placement without conflating endpoints.
  kind: CURATION_TODO
  status: RESOLVED
  rationale: Use phenotype METPO:1000059 pending a source-backed broader biomineralization
    phenotype. This is production of scales, not mere possession, acquisition or reuse
    of preformed scales, their extrusion, or their arrangement into a shell or scale
    layer. It is not equivalent to general silicification, diatom frustule formation,
    magnetosome or ferrosome possession, substrate adhesion, or growth on a particular
    chemical. These neighboring endpoints do not alone demonstrate new-scale production.
    Do not infer a universal scale geometry, covering architecture, cell-cycle coupling
    or fitness effect. No exact synonyms, xrefs, homology or organism-level disjointness
    are asserted.
  posed_by: codex
  posed_date: '2026-10-10'
  resolved_date: '2026-10-10'
  resolution_note: Added biomineralization traitmech:000690 as the direct broader
    phenotype. Production of the mineral elements specified by this record entails
    mineral formation; this is a definition-based hierarchy inference, not a new child
    experiment. Phenotype METPO:1000059 remains an ancestor. The historical rationale
    and endpoint distinctions are preserved; the separate exemplar and mechanism gap
    remains OPEN. The v566 proposal requests the additional child axiom without rewriting
    the historical proposal cohort.
- discussion_id: siliceous-scale-production-exemplars-and-mechanism
  prompt: Verify assay-strain identity and production-specific molecular evidence.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: No canonical examples are assigned until primary assay Methods, strain
    provenance and current taxonomy are jointly reconciled. NIES-4060 is currently
    catalogued as Paulinella micropora (MYN1) at https://mcc.next.nbrp.jp/strainList.do?strainNumber=NIES-4060;
    its reference list links the 2016 historical chromatophora paper, but this collection
    association is not an independent production experiment or authority to rename
    every historical observation. The two primary abstracts support a reusable phenotype
    through different methods, not one conserved molecular pathway. Ultrastructure
    and cytoskeletal association alone cannot establish causal protein requirements.
    Separate deposition, vesicle transport, extrusion and assembly before adding causal
    edges. A protein mechanism needs functional evidence and taxon-paired accessions;
    sequence features alone cannot supply that support. Mechanism is deferred, not
    claimed absent.
  posed_by: codex
  posed_date: '2026-10-10'
curation_history:
- timestamp: '2026-10-10T05:02:23Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added siliceous scale production with two primary DOI citations, directly
    checked scientific-abstract snippets and explicit access limits. Ignored-and-hidden
    main/worktree/open-PR reservation checks support 000688 and v564 block 1064100-1064199.
    Broader hierarchy, canonical exemplars and protein mechanism remain unresolved.
    Existing records unchanged. Timestamp records the observed UTC curation decision.
  llm_assisted: true
- timestamp: '2026-10-10T08:03:12Z'
  curator: codex
  action: REFINE_BIOMINERALIZATION_PARENT
  changes: Refined the direct parent to biomineralization traitmech:000690 and resolved
    the temporary parent gap by definition-based inference. Preserved the definition,
    evidence, historical rationale, independent mechanism gap and prior curation history.
    No organism or molecular mechanism was added.
  llm_assisted: true