TraitMech

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siliceous scale production

traitmech:000688 · CLASS · PROPOSED

A physiological phenotype in which a microbial cell produces siliceous scales.

Trait evidence (2)

  • DOI:10.1016/j.protis.2016.05.002
    Scales were formed one by one in silica deposition vesicles (SDVs)

    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.

  • DOI:10.1111/j.0022-3646.1996.00675.x
    The first new scales appeared within 2 h after the silica addition

    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.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1016/j.protis.2016.05.002

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve broader biomineralization placement without conflating endpoints.

CURATION TODO RESOLVED siliceous-scale-production-scope-and-parent · raised by codex · 2026-10-10

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Resolution: 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.

Verify assay-strain identity and production-specific molecular evidence.

KNOWLEDGE GAP OPEN siliceous-scale-production-exemplars-and-mechanism · raised by codex · 2026-10-10

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.

  2. · REFINE_BIOMINERALIZATION_PARENT · codex

    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.

Recorded curation sessions

  • · codex
    • CREATE — Add source-bounded siliceous scale production

      Created traitmech:000688 as a PROPOSED physiological phenotype with two independent primary DOI citations and directly read scientific-abstract snippets. Distinguished new-scale production from possession, extrusion and shell assembly; broader hierarchy, strain-level exemplars and molecular mechanism remain explicitly unresolved. Added a dry-run-first guarded writer, focused tests and METPO proposal v564 reserving the whole 1064100-1064199 block. The record timestamp is the observed 2026-10-10T05:02:23Z curation decision, not a claimed exact file-write time. Existing records were not edited.

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  • · codex
    • EDIT — Resolve siliceous scale production biomineralization parent gap

      Reparented traitmech:000688 to biomineralization traitmech:000690 by definition-based inference and resolved its parent TODO. Preserved definition, evidence, historical rationale, separate exemplar/mechanism discussion and prior history. Historical v564 template remains unchanged; v566 explicitly requests the additional upstream child axiom. No new experiment or molecular claim is asserted.

    Read this curation session