cell-body contraction

traitmech:000728 · CLASS · PROPOSED

A physiological phenotype in which a microbial cell actively shortens its body by contraction of intracellular structures.

Trait evidence (3)

DOI:10.1126/sciadv.add6550
Ca2+ concentrations from 10−6 to 10−2 M in the culture medium could stimulate cell contraction while maintaining the viability of the cell.

Zhang et al. 2023, PMID:36812318, PMCID:PMC9946354, Results: functional analysis of giant backbone proteins, second paragraph. Direct JATS match; native NOT_IN_ABSTRACT retained. The study identified its East Lake, Wuhan isolate as Spirostomum minus using morphology, protargol staining and SSU rDNA, then established clonal cultures at 22 C. Actual Figure 1A shows extended and contracted cell bodies. The quoted treatment maintained viability; 38-to-16 seconds describes intervals between contractions, not contraction duration. Selected Results, Methods and Discussion, actual Figures 1, 6 and 9, and relevant supplement pages were inspected. Figure 9 is a mechanistic schematic. Supplementary Figure 7 shows shortening during death, which is insufficient for this trait. Abnormal-cell counts are in Supplementary Table 2, not Table S1 as cited in the RNAi Results. Rare twisted RNAi phenotypes do not establish contraction loss in every treated cell. The source's superscript exponents mean 10^(-6) to 10^(-2) M; the normalized plain-text quotation does not preserve superscript styling.
DOI:10.1073/pnas.2217737120
Asymmetric contraction can be observed as the top end begins contracting before the bottom end

Floyd et al. 2023, PMID:37307463, PMCID:PMC10288572, Figure 4 caption, contiguous observed-asymmetry clause. Direct JATS match; native NOT_IN_ABSTRACT retained. The quoted top and bottom ends are those of the imaged Spirostomum cell body in Figure 4A-C, not Vorticella's stalk or simulated springs. The actual panel A contours and panel B solid length trajectory show body shortening; panel C shows the staggered endpoint movements. Dashed model curves are separate from observations. The 15-word caption span replaces the data-presentation excerpt rejected in #1935; historical source receipts remain in the sidecar. Actual Figures 1A and 2A-B show Spirostomum body shortening and experimental trajectories separately from fitted curves. Methods used commercially sourced cultures and high-speed imaging without compressing cells; no species identity is inferred. Supplementary Figure S3 measures length along the central backbone curve, with increasing width. Supplementary Figure S6 states that repeated contractions of the same organism were not distinguished from contractions of different organisms: five traces are not five established biological replicates. Vorticella panels measure stalk contraction, not the body endpoint. Calcium-wave and energy models are not universal molecular proof. Selected experimental sections, actual Figures 1-2 and supplementary pages 3 and 5 were inspected; raw videos and the complete model were not reanalyzed.
DOI:10.1242/jeb.189.1.163
Living Vorticella showed a graded shrinkage of the cell body when Ca2+ buffer was injected into the cell body

Katoh and Naitoh 1994, PMID:9317557, scientific Abstract item 3, first clause. Direct namespace-qualified Europe PMC MED abstract match and native VERIFIED. The same sentence contrasts graded cell-body shrinkage with all-or-nothing stalk coiling. Triton-extracted preparations in other abstract items are not the living-cell injection assay. Calcium-release causality is presented as an assumption, not direct molecular proof. Publisher HTML and PDF requests returned 403; full Methods, figures and strain provenance were not accessed. No species-wide example, quantitative threshold or universal trigger is inferred.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1126/sciadv.add6550

Parent traits (1)

phenotype METPO:1000059

kg-microbe context

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

Discussions and Knowledge Gaps (3)

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

Resolve a closer parent while distinguishing body shortening from other contractile endpoints.

CURATION TODO OPEN cell-body-contraction-scope-and-parent · raised by codex · 2026-10-14

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.

Retain phenotype METPO:1000059. Motility METPO:1000701 concerns locomotion through the environment; motile METPO:1000702 specifies independent movement using metabolic energy. Neither necessarily establishes body shortening. Body contraction is not displacement caused only by stalk coiling, rapid axopodial contraction traitmech:000682, contractile-vacuole cycling, injection-system contraction, cytokinetic constriction, passive osmotic shrinkage, death or static short-cell size. Behavioral habituation traitmech:000714 changes response probability rather than defining the contraction response. The axopodial record's broader cellular-contractility parent question is not resolved by this body-specific class; do not reparent it here. No universal speed, fractional shortening, trigger or ecological function is imposed. No organism-level disjointness or exact synonym for generic contractility is asserted.

Review the proposed phenotype without treating locomotion as an exact equivalent.

CURATION TODO OPEN cell-body-contraction-metpo-assessment · raised by codex · 2026-10-14

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.

Pinned/current METPO releases, editor and inspected template owners provided no active exact contraction class. Historical obsolete Motility identifiers METPO:0000006 and METPO:000006 point to active METPO:1000701; obsolete Motile METPO:0000087 and METPO:000088 point to active METPO:1000702. These locomotion leads are related, not exact body-contraction identities. They are not revived or placed in xrefs. The ontology pin remains unchanged; v604 proposes this phenotype below METPO:1000059. No external equivalent or SSSOM mapping has been accepted.

Resolve study-isolate and protein identities before adding canonical examples or a mechanistic graph.

KNOWLEDGE GAP OPEN cell-body-contraction-mechanism-and-provenance · raised by codex · 2026-10-14

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.

Keep study-named cultures as qualified evidence pending exact isolate/current-taxonomy correspondence. No canonical taxa, protein accessions or causal graph are asserted. Zhang's localization, RNAi and structural models support source-bounded mechanistic hypotheses, not a common protein mechanism inferred from sequence features. Category-E twisted cells were rare; other abnormal forms also occurred in controls. Figure 9's calcium-storage and energy-coupling scheme is not wholly demonstrated. A protein graph needs authority-checked taxon-paired accessions and edge-specific perturbation evidence; its omission does not claim that mechanisms are unknown. Do not generalize ATP independence or calcium concentrations to the whole class. Floyd's five traces have unresolved organism-level replication. Katoh's full Methods were not accessed. The verification sidecar retains actual sections, hashes, source-status checks and native verdicts; bounded notice checks are not comprehensive clearance.

Curation history

2026-10-14T17:32:15Z · MINTED_TRAITMECH_ID · codex
Added cell-body contraction with three primary DOI sources and directly matched 22-, 19- and 19-word excerpts. Full-text Results retain NOT_IN_ABSTRACT; the Vorticella abstract is VERIFIED. Body, stalk, axopodial, division and passive-shrinkage endpoints remain distinct. No sequence-derived mechanism or unverified canonical example imported. Reserved 000728, v604 and 1068100-1068199 after ignored/hidden, retained-history, full-content proposal and open/draft PR checks. Contig lengths, embedding components and broad editor envelopes are not METPO reservations. Other records unchanged; timestamp records observed acceptance.
2026-10-14T17:58:04Z · EVIDENCE_NOTE_CLARIFIED · codex
Clarified source superscript exponents as 10^(-6) to 10^(-2) M beside the unchanged normalized JATS excerpt (#1933). Preserved the native verdict, phenotype scope and original minting event.
2026-10-14T18:54:51Z · EXTERNAL_REVIEW_CORRECTION · codex
Addressed #1935: corrected the motility label and distinguished METPO:1000701 from the energy-dependent motile class METPO:1000702. Removed the non-claim-bearing Floyd snippet while retaining its figure-backed evidence and historical verification receipts. The two other primary excerpts, phenotype definition, parent, PROPOSED status and previous curation events remain unchanged.
2026-10-14T19:02:18Z · CLAIM_BEARING_SNIPPET_ADDED · codex
Added a directly matched 15-word Floyd Figure 4 caption excerpt reporting observed asymmetric contraction (#1935). Checked actual panels A-C and distinguished body shortening from fitted model curves. The intermediate no-snippet record failed MISSING_SNIPPET and was not published or baselined. Prior events remain intact.

Recorded curation sessions

2026-10-14T17:35:32Z · codex
- CREATE — Add cell-body contraction
  Added one PROPOSED active cell-body-shortening phenotype with Zhang 2023, Floyd 2023 and Katoh and Naitoh 1994 primary evidence. Direct 22/19/19-word snippets preserve native NOT_IN_ABSTRACT, NOT_IN_ABSTRACT and VERIFIED outcomes. Body shortening is distinct from stalk coiling, axopodial shortening, division, passive shrinkage and death. Actual selected figures and supplement pages were inspected; five contraction traces are not five identified organisms, and the Zhang abnormal-cell table is Supplementary Table 2. No universal speed, calcium/ATP mechanism, canonical taxa or sequence-derived causal proteins imported. Ignored/hidden current files, retained history and open/draft PRs were checked; contig-length and embedding numeric hits are not reservations. Reserved 000728, v604 and the full 1068100-1068199 block. The trait timestamp records observed allocation acceptance; this later CREATE records the written change. Existing records, including protected spore germination and the broader axopodial parent TODO, remain unchanged.
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2026-10-14T17:59:27Z · codex
- EDIT — Clarify source exponent notation
  Issue #1933: clarified in the first evidence notes that the primary JATS superscripts denote 10^(-6) to 10^(-2) M. The normalized quotation loses styling but remains verbatim at the text layer; its wording, native NOT_IN_ABSTRACT outcome, phenotype scope, citations and original minting event are unchanged. Appended one per-record correction event through the guarded writer; preserved the original CREATE history and notation-finding review.
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2026-10-14T18:56:54Z · codex
- EDIT — Address external contraction evidence review
  Corrected motility METPO:1000701 terminology and distinguished motile METPO:1000702 using pinned RDF definitions. Removed the Floyd data-presentation snippet because it is not a self-contained phenotype result; retained primary Figures 1A and 2A-B as explicitly qualified evidence without inventing a quotation. The two other claim-bearing primary snippets, phenotype definition and parent, PROPOSED status, existing curation/history events and immutable reviews remain unchanged. Appended a source-verification disposition distinguishing historical three-snippet receipts from current two-snippet evidence. Existing add-trait guidance already covers this failure; no rule was weakened.
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2026-10-14T19:05:21Z · codex
- EDIT — Replace Floyd pointer with observed-contraction caption
  Appended a directly matched 15-word Figure 4 caption span reporting observed asymmetric cell-body contraction. Inspected actual panels A-C: body contours, shortening trajectory and staggered endpoint movements are observations, distinct from dashed model curves. This supersedes the no-snippet intermediate described in the preceding external-review EDIT: that state failed MISSING_SNIPPET and was not published. Original 22/19/19-word and intermediate two-snippet receipts remain historical; the current record has 22/15/19-word snippets. Added a new per-record event without rewriting prior events. Clarified the add-trait skill that honest absent snippets do not bypass the frozen-baseline gate; no baseline or validation rule changed.
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