identifier: traitmech:000691
label: diatom frustule production
definition: A biomineralization phenotype in which a diatom forms the siliceous valve
  and girdle-band elements of its cell wall (frustule).
definition_source: DOI:10.1007/s00709-017-1199-4
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000690
evidence:
- reference: DOI:10.1007/s00709-017-1199-4
  snippet: The basic stages of frustule morphogenesis characteristic of raphid pennate
    diatoms have been traced
  notes: Bedoshvili et al., journal issue May 2018, online 2017-12-21, PMID:29270874.
    Scientific Abstract directly read at https://pubmed.ncbi.nlm.nih.gov/29270874/
    and in Europe PMC CORE on 2026-10-10 using EXT_ID:29270874 AND SRC:MED; exact
    ID, source, title and DOI checked together. The abstract defines frustule components
    as silica valves and girdle bands and reports microscopy of morphogenesis in Encyonema
    ventricosum under the source name. This supports formation, not just an isolated
    shell's presence. Cytoskeletal proximity is not functional necessity. Full text,
    Methods, actual figures and supplements were not inspected; no canonical taxon
    or universal membrane-release mechanism is inferred.
- reference: DOI:10.1038/s41467-024-52211-x
  snippet: 'A diatom cell wall consists of two types of building blocks: two plate-shaped
    valves and several ring-shaped girdle bands.'
  notes: Aram et al. 2024, PMID:39251596, PMC11385223, Introduction. Scientific Abstract,
    Introduction, Results, Discussion and Methods directly read in official Europe
    PMC full-text XML on 2026-10-10; actual Figure 2 inspected, other actual figures
    and supplements unread. Source-qualified CORE lookup EXT_ID:39251596 AND SRC:MED
    confirmed ID, source, title and DOI. Silicon-starved CCMP1335 cultures were resupplied
    and imaged during valve formation. Figure 2 orders different cells by inferred
    maturation, not a live-cell time series. The paper retains historical Thalassiosira
    pseudonana naming while noting Cyclotella nana; this is not a current taxonomy
    assignment. Structural correlations support a membrane-mold hypothesis, not proven
    contact-site function or a universal molecular mechanism. The quote defines wall
    elements; the Results provide the production observations.
discussions:
- discussion_id: diatom-frustule-production-scope-and-mappings
  prompt: Keep frustule-element formation distinct from possession and other silica
    traits.
  kind: CURATION_TODO
  status: OPEN
  rationale: Use biomineralization traitmech:000690 as the broader phenotype because
    this endpoint entails formation of mineral cell-wall elements. It is not a material
    frustule, generic silicification, silica uptake, retention of an inherited valve
    or adsorption of preformed silica. Production of new wall elements does not require
    both valves to be synthesized anew in one cell cycle or every element to be formed
    simultaneously. Keep valve/girdle formation distinct from silica scales, auxospore
    coverings and setae; their observation alone does not establish this endpoint.
    The existing scale-production scope note distinguishes these phenotypes and is
    not an unresolved exact grounding. Do not infer organism-level disjointness or
    a universal geometry, cell-cycle schedule or fitness effect. Exact synonyms and
    external phenotype mappings remain unasserted pending authority review; process
    and material terms are not exact equivalents.
  posed_by: codex
  posed_date: '2026-10-10'
- discussion_id: diatom-frustule-production-exemplars-and-mechanisms
  prompt: Resolve assay-strain provenance and production-specific causal evidence.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: No canonical examples are assigned before reconciling study strains,
    collection provenance and current taxonomy. The two studies support wall-element
    formation but do not establish a conserved protein mechanism. The contact-site
    transport model and actin-associated expansion in Aram et al. remain proposals;
    unobserved vesicle fusion is not proof of its absence. Separate silica deposition,
    shaping, exocytosis and wall assembly when evaluating perturbation evidence. Functional
    evidence and taxon-paired accessions are required for protein edges; sequence
    features alone are insufficient. Mechanism is deferred, not claimed absent, and
    no universal intracellular route is imposed on all diatom silica structures.
  posed_by: codex
  posed_date: '2026-10-10'
curation_history:
- timestamp: '2026-10-10T20:14:43Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added diatom frustule production beneath biomineralization with two primary
    DOI citations and directly checked short snippets. Ignored-and-hidden main/worktree/open-PR
    reservation checks support 000691 and v567 block 1064400-1064499. Existing trait
    records unchanged; mappings, canonical taxa and mechanisms remain open. Timestamp
    records the observed UTC curation decision.
  llm_assisted: true