identifier: traitmech:000682 label: rapid axopodial contraction definition: A physiological phenotype in which a microbial cell rapidly shortens its microtubule-supported axopodia in response to stimulation or prey uptake. definition_source: DOI:10.2108/zsj.20.1367 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000729 evidence: - reference: DOI:10.2108/zsj.20.1367 snippet: Axopodial contraction of the centrohelid heliozoon Raphidiophrys contractilis was induced by mechanical or electrical stimulation. notes: Khan et al. (2003), scientific Abstract, directly retrieved from Europe PMC for PMID:14624035 at https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A14624035%20AND%20SRC%3AMED&resultType=core&format=json. Abstract-only access; full Methods and figures were not inspected. The study reports contraction faster than 3.0 mm/sec, followed by re-elongation initially about 0.30 microm/sec, and a microtubule bundle in each axopodium. Extracellular calcium dependence is restricted to this stimulation assay, not a universal defining threshold. Failure to detect other filaments with the reported fixation method does not prove their biological absence. Source taxon spelling is retained; natural culture provenance and current taxonomic identity are not established here. - reference: DOI:10.1111/j.1550-7408.2001.tb00187.x snippet: Upon food uptake, the tubules shorten and transform into a mass of small granules when rapid axopodial contraction occurs notes: Kinoshita et al. (2001), scientific Abstract, directly read at https://pubmed.ncbi.nlm.nih.gov/11596916/ and cross-checked against Europe PMC's scientific abstract. Abstract-only access; full Methods and figures were not inspected. The study concerns Actinophrys sol. Contractile-tubule shortening and granulation accompany the food-uptake response; the authors suggest, rather than prove, a causal role. Cold and colchicine both induce microtubule disassembly, but only cold induces tubule granulation in the reported comparison. Neither intervention alone defines the natural rapid-contraction phenotype. No protein identity, effect size or strain provenance is inferred. discussions: - discussion_id: axopodial-contraction-scope-and-parent prompt: Resolve a closer cellular-contractility parent and assay boundaries. kind: CURATION_TODO status: RESOLVED rationale: Phenotype METPO:1000059 is a broad parent. Existing motile METPO:1000702 is curated around organismal locomotion; rapid shortening of a cellular projection does not alone establish whole-cell locomotion. Keep axopodial contraction separate from ordinary pseudopod extension, re-elongation, slow structural loss, stalk or whole-cell contraction, and drug-induced microtubule disassembly. The reported speed is an observation, not a universal cutoff. No exact synonyms, xrefs, SSSOM equivalences or organism-level disjointness are asserted. Closer hierarchy and comparable time-resolved assays remain open. posed_by: codex posed_date: '2026-10-08' resolved_date: '2026-10-14' resolution_note: Added cellular contraction (body or cytoplasmic projection shortening) traitmech:000729 as the direct broader phenotype. This is a definition-based subclass inference, not a new child experiment or evidence of a common molecular mechanism. Phenotype METPO:1000059 remains an ancestor. Preserved the historical rationale and endpoint boundaries; the v605 proposal requests the child axiom without rewriting the historical proposal cohort. Only the hierarchy question is resolved here. The independent time-resolved assay question is retained OPEN in axopodial-contraction-assay-comparability; provenance and mechanism remain OPEN. - discussion_id: axopodial-contraction-provenance-and-mechanism prompt: Resolve culture provenance and taxon-specific contraction mechanisms. kind: KNOWLEDGE_GAP status: OPEN rationale: The directly read abstracts do not establish natural strain provenance or accession-level identities for canonical examples. Retain the source-named organisms as qualified evidence, not universal taxon assertions; resolve their current taxonomy and original culture descriptions before adding exemplars. Calcium dependence, microtubule disassembly and contractile-tubule observations must not be combined into one universal heliozoan mechanism. A protein-resolved graph requires direct perturbation evidence and taxon-paired accessions. Mechanism is deferred, not claimed absent; tubulin sequence features alone do not establish this response. posed_by: codex posed_date: '2026-10-08' - discussion_id: axopodial-contraction-assay-comparability prompt: Establish comparable time-resolved assays for rapid axopodial contraction. kind: CURATION_TODO status: OPEN rationale: Carried forward from axopodial-contraction-scope-and-parent when only its hierarchy gap was resolved. Preserve stimulus, cell state, projection identity, length readout and temporal resolution when comparing assays. The published speed is not a universal cutoff; re-elongation, slow structural loss and drug-induced microtubule disassembly alone do not establish the rapid physiological response. No new comparative assay or biological experiment was performed by this hierarchy repair. posed_by: codex posed_date: '2026-10-14' curation_history: - timestamp: '2026-10-08T14:52:39Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added rapid axopodial contraction with two primary DOI sources and contiguous scientific-abstract snippets checked directly. Ignored-and-hidden main/worktree/open-PR checks support 000682 and v558 block 1063500-1063599. Kept natural culture provenance, closer hierarchy and protein mechanism unresolved. Distinguished rapid response from locomotion and induced structural breakdown. Existing records unchanged. Timestamp is observed UTC. llm_assisted: true - timestamp: '2026-10-14T22:35:09Z' curator: codex action: REFINE_CELLULAR_CONTRACTION_PARENT changes: Refined the direct parent to cellular contraction traitmech:000729 by definition-based inference. Preserved child definition, supporting excerpts, prior curation history and independent provenance/mechanism gaps. Resolved only the parent question. No new experiment, canonical taxon or molecular mechanism is asserted. Retained the independent assay-comparability question OPEN and qualified the Khan Europe PMC URL to SRC:MED using the verified identity. llm_assisted: true