TraitMech

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stalk contraction

traitmech:000730 · CLASS · PROPOSED

A physiological phenotype in which a microbial cell actively reduces the end-to-end extension of its stalk.

Trait evidence (2)

  • DOI:10.2142/biophysics.8.1
    The stalk is straight at the initial stage. Then, it bends and coils into a helix near the zooid.

    Kamiguri et al. 2012, PMID:27857602, PMCID:PMC5070450, printed page 3, Results and Discussion first paragraph, left column. Direct contiguous PDF match with whitespace-only line-wrap normalization and actual typeset passage inspected; native NOT_IN_ABSTRACT retained. Junko Kamiguri is the first author; the running header says Hashimoto et al. Living source-named Vorticella sp. from activated sludge attached to glass rods was stimulated by hitting the dish; eight cells were observed at 6000 frames/s. Figures 3 and 5 show coiling and decreased end-to-end extension. The same paragraph says contour length does not change. All nine main-paper pages were inspected; raw videos were not reanalyzed. Model fits are not molecular proof. The primary PDF came from J-STAGE; an acquisition-helper failure left no original request timestamp or header receipt. Those missing fields are not reconstructed. Current taxonomic and culture identities remain unresolved.

  • DOI:10.1016/j.bpj.2012.07.038
    The stalk contraction was stalled more as the fluid viscosity and/or flow rate increased.

    Ryu et al. 2012, PMID:23009835, PMCID:PMC3433611, printed page 862, Figure 2A caption, sentence beginning The stalk contraction. Direct contiguous PDF match and actual typeset passage inspected; native NOT_IN_ABSTRACT retained. The primary PDF was retrieved from the Vanderbilt Lang Lab mirror. Source-named Vorticella convallaria contracted in microfluidic channels under varied flow and viscosity. Four to five contractions per cell per condition are not independent cells. Figure 3 uses six cells; Figure 4C uses fifteen in a separate analysis. Isometric force is extrapolated through a hydrodynamic model, not directly measured zero-shortening force. All eight main-paper pages and actual Figures 1-5 were inspected; the supplement was not. Projection and geometry assumptions remain relevant. Some extracted micrometre symbols appear as mm; no such numeric extraction is quoted. Culture/taxonomy correspondence is unresolved. No universal rate, force, calcium threshold, ATP independence or protein mechanism follows.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.2142/biophysics.8.1

Parent traits (1)

kg-microbe context

Matched 1 kg-microbe node via parent_proxy.

  • METPO:1000059 [-2.682, -2.070, -3.656, -0.652, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Discussions and Knowledge Gaps (3)

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

Review the stalk-extension endpoint and its projection-contraction parent.

CURATION TODO OPEN stalk-contraction-scope-and-parent · raised by codex · 2026-10-15

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.

The measured endpoint is reduced end-to-end stalk extension, not necessarily reduced contour length. Coiling is observed, not a universal geometric requirement. Require active cellular contraction; static stalk morphology, reduced developmental growth, passive bending, detachment and isometric force alone do not establish it. Stalk-induced body displacement is not cell-body contraction traitmech:000728, and the endpoint differs from rapid axopodial contraction traitmech:000682. The direct parent is cell body or cytoplasmic projection contraction traitmech:000729, by definition-based inference. Amos's publisher abstract places the spasmoneme within cytoplasm and a sheath. The stalk is composite; its whole sheath is not asserted to be cytoplasm. Neither locomotion nor a universal ATP-driven motor is required by this parent choice. No exact synonym or organism-level disjointness is asserted.

Evidence

  • DOI:10.1038/229127a0 NO EVIDENCE
    The coiling is produced by the contraction of an intracytoplasmic thread, the spasmoneme, within a cylindrical sheath.
    Anatomical background for interpreting the parent, not an additional inspected experimental result or counted trait support. The curated hierarchy is an inference, not an ontology assertion made by this paper.

Review the proposed stalk-contraction class without reviving obsolete morphology.

CURATION TODO OPEN stalk-contraction-metpo-assessment · raised by codex · 2026-10-15

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 and inspected current METPO release/editor/template owners contain no active exact contraction class in the bounded assessment. METPO:1000288 obsolete stalk is deprecated, under ObsoleteClass, with OMO:0001000 as its recorded reason and no replacement or consider annotation observed. It is a historical morphology label, not an active exact contraction phenotype; neither revive it nor put it in xrefs. The reason code alone does not invalidate the biology. v606 reserves METPO:1068300 in block 1068300-1068399 and repeats the unchanged v605 parent declaration METPO:1068200 so the standalone proposal emits the actual parent hierarchy. Historical v605 and the ontology pin remain unchanged. No external equivalence or SSSOM mapping is accepted; upstream adoption and human sign-off remain open.

Resolve source isolates and endpoint-specific mechanisms before adding taxa or proteins.

KNOWLEDGE GAP OPEN stalk-contraction-provenance-and-mechanism · raised by codex · 2026-10-15

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 organism names as qualified observations until culture provenance and current taxonomic identities are independently verified. Two distinct experimental papers support the endpoint; Part II of the Kamiguri study is not counted as independent replication. Preserve stimulus, load, viscosity, cell state, geometry, sampling and temporal resolution when comparing assays. Do not generalize calcium-wave models, spasmoneme chemistry, force estimates or energy claims to all microbial stalks. Protein sequence features alone cannot establish this phenotype. A protein-resolved causal graph needs authority-checked taxon-paired accessions and edge-specific experimental support. Mechanism is deferred, not asserted absent. MED/Crossref notice-field and limited publisher checks are not comprehensive correction/retraction clearance; failed retrievals and uninspected supplements remain explicit source-access limits.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added stalk contraction as active reduction of end-to-end stalk extension with two primary DOI sources and directly checked 19/14-word excerpts. Retained native NOT_IN_ABSTRACT outcomes and separate 17-word anatomy context with native UNRESOLVED. Reserved 000730, v606 and 1068300-1068399 after ignored/hidden worktree, retained-history, full proposal-range and open/draft PR checks. Linked the existing parent's future lead without closing independent questions. No canonical taxon, exact mapping or universal protein mechanism inferred. Timestamp records observed acceptance.

Recorded curation sessions

  • · codex
    • CREATE — Add stalk contraction

      Added one PROPOSED stalk-contraction phenotype, defined by active reduction of end-to-end stalk extension, supported by Kamiguri et al. 2012 and Ryu et al. 2012. Directly checked 19/14-word full-text result snippets retain native NOT_IN_ABSTRACT. Amos 1971 provides separate 17-word anatomical context with native UNRESOLVED, not an additional supporting experiment. Preserved contour-length, replication, model, source-access and culture/taxonomy limits. Reserved 000730, v606 and 1068300-1068399 after ignored/hidden, retained-history, full-range and open/draft PR checks. v606 copies the unchanged v605 parent declaration and emits the child axiom. No universal protein mechanism, exact synonym, xref or canonical taxon inferred. The record timestamp is observed acceptance, not a fabricated PDF request time.

    Read this curation session