identifier: traitmech:000729 label: cell body or cytoplasmic projection contraction definition: A physiological phenotype in which a microbial cell actively contracts its body or a cytoplasmic projection, reducing its length or extension. definition_source: DOI:10.1242/jeb.189.1.163 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - METPO:1000059 evidence: - reference: DOI:10.1242/jeb.189.1.163 snippet: Living Vorticella showed a graded shrinkage of the cell body when Ca2+ buffer was injected into the cell body notes: Katoh and Naitoh 1994, PMID:9317557, scientific Abstract item 3, first clause. Direct namespace-qualified Europe PMC MED match; native VERIFIED. The same sentence contrasts graded cell-body shrinkage with all-or-nothing stalk coiling. This supports the curator-synthesized body/projection-shortening parent, not a universal calcium threshold. Other abstract items use Triton-extracted preparations, not the living-cell injection assay. Calcium-induced calcium release is an assumption, not direct molecular proof. Publisher requests returned 403; full Methods, figures and strain provenance were not accessed. - 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, PMID:14624035, scientific Abstract opening sentence. Direct namespace-qualified Europe PMC MED match; native VERIFIED. This supports stimulated shortening of a cytoplasmic projection rather than whole-cell locomotion. Reported calcium dependence and speed apply to this assay, not every member of the parent class. Non-detection of other filaments after fixation is not proof of their absence. Full Methods and figures were not accessed; the publisher's HTTP 200 response was an access challenge, not readable article content. Current taxonomic and culture identities remain unresolved. - reference: DOI:10.1083/jcb.118.3.585 snippet: Both recording techniques showed that the rapid contraction involves 80% of the total cell length. notes: Febvre-Chevalier and Febvre 1992, PMID:1639845, PMCID:PMC2289557, Results, Kinetics of the Contraction, printed page 588, right column. Direct extracted-PDF match with the typeset passage visually checked; native NOT_IN_ABSTRACT retained. The primary PDF was retrieved from its Semantic Scholar mirror after official PDF attempts failed. Selected Methods/Results and actual Figures 1 and 3-6 were inspected. Length was measured from head top to stalk base, not isolated cell-body length; graph axes use stalk length. The percentage is study-specific. Natural-seawater responses differ from artificially slowed responses. The specimens were collected near Villefranche and cultured at 14-18 C; current taxonomic identity is not verified. The n=20 initial-length sample is not asserted as independent contraction replication. Microtubule disassembly accompanies shortening, but this study expressly does not establish force production. Its disassembly half-time is not automatically contraction duration. The accessible JATS contains an abstract and PDF pointer, not the complete experimental text. discussions: - discussion_id: cellular-contraction-scope-and-mappings prompt: Review the shortening-defined parent without equating all contractility endpoints. kind: CURATION_TODO status: OPEN rationale: Require active reduction of cell-body length or the extension of a cytoplasmic projection. Generic force production or isometric contractility alone is insufficient. Extracellular pilus retraction, injection-system contraction, contractile-vacuole cycling and cytokinetic constriction alone do not establish this endpoint. Neither passive osmotic shrinkage, death-associated shortening nor static short-cell morphology suffices. The existing body and rapid axopodial traits are narrower children; stalk contraction traitmech:000730 is now a narrower child, defined by active reduction of stalk end-to-end extension. This does not require shortening of the stalk contour or make its sheath cytoplasm. Motility METPO:1000701 and motile METPO:1000702 concern locomotion, not necessarily shortening. Active denotes the cellular response, not demonstrated ATP-driven motor action. No universal speed, fractional shortening, trigger, calcium threshold, ATP dependence, ecological role, exact synonym for generic contractility or organism-level disjointness is asserted. posed_by: codex posed_date: '2026-10-14' - discussion_id: cellular-contraction-metpo-assessment prompt: Review the proposed shortening phenotype and its upstream hierarchy. kind: CURATION_TODO status: OPEN rationale: Pinned/current METPO releases, editor and inspected template owners yielded no active exact class in the bounded identity assessment. Deprecated Motility METPO:0000006 and METPO:000006 lead to METPO:1000701; deprecated Motile METPO:0000087 and METPO:000088 lead to METPO:1000702. These are related locomotion concepts, not exact replacements for shortening. They are not revived or put in xrefs. Keep phenotype METPO:1000059 as the direct parent. Proposal v605 reserves METPO:1068200; the ontology pin and historical child cohorts v558/v604 remain unchanged. No external equivalence or SSSOM mapping is accepted. posed_by: codex posed_date: '2026-10-14' - discussion_id: cellular-contraction-provenance-and-mechanism prompt: Resolve isolate identities and endpoint-specific mechanisms before adding exemplars or causal proteins. kind: KNOWLEDGE_GAP status: OPEN rationale: Keep source-named organisms as qualified observations, not species-wide canonical exemplars. Verify culture provenance and current taxonomic identity before adding canonical_examples. Calcium dependence, microtubule breakdown, contractile fibers and fitted calcium-wave models must not be combined into one universal mechanism. Protein sequence features alone cannot establish this phenotype. A protein-resolved graph requires authority-checked taxon-paired accessions and edge-specific perturbation evidence. No graph is asserted; mechanisms are deferred, not claimed absent. Source checks covered identified metadata fields and selected text/figures, not comprehensive correction or retraction clearance. posed_by: codex posed_date: '2026-10-14' curation_history: - timestamp: '2026-10-14T22:35:09Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added a shortening-defined cellular contraction parent with three primary DOI sources and directly checked 19/15/15-word excerpts. Retained native VERIFIED, VERIFIED and NOT_IN_ABSTRACT outcomes. Reserved 000729, v605 and 1068200-1068299 after ignored/hidden known-copy, retained-history and open/draft PR checks with full proposal-range inspection. Resolved the body and axopodial parent gaps while keeping assay and mechanism questions open. No universal molecular mechanism or canonical taxon inferred. Timestamp records observed allocation and curation acceptance. llm_assisted: true - timestamp: '2026-10-14T23:56:33Z' curator: codex action: REFINE_CONTRACTION_LABEL changes: 'Replaced the parenthetical label cellular contraction (body or cytoplasmic projection shortening) with cell body or cytoplasmic projection contraction. Preserved definition, endpoint qualifier, evidence, discussions, identifier and earlier history. The v605 template also emits the two existing child subclass axioms without modifying historical v558/v604 cohorts. Addresses external review issues #1941 and #1942; no new biology or human review promotion. Timestamp records observed acceptance of the refinements.' llm_assisted: true - timestamp: '2026-10-15T03:51:31Z' curator: codex action: LINK_STALK_CONTRACTION_CHILD changes: Linked the accepted stalk-contraction child traitmech:000730 in place of the future-lead sentence. Preserved the parent's definition, evidence, hierarchy and prior history; independent scope and mechanism questions remain OPEN. No new parent experiment or universal mechanism is asserted. llm_assisted: true