identifier: traitmech:000734 label: eukaryotic flagellar axoneme internalization definition: A physiological phenotype in which a microbial eukaryote internalizes the intact axoneme of its own cilium or flagellum into its cell body. definition_source: DOI:10.1002/cm.21637 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - METPO:1000059 evidence: - reference: DOI:10.1002/cm.21637 snippet: axonemes remain intact during internalization notes: Venard et al. 2020, PMID:33103844, PMCID:PMC7944584, Results 2.2, TEM interpretation paragraph following Figure 2. Contiguous span checked in direct PMC HTML; native NOT_IN_ABSTRACT retained. Live phase microscopy, fixed immunofluorescence and TEM concern Rhizoclosmatium globosum JEL800 and Spizellomyces punctatus DAOM BR117. Internalized cross-sections retain 9+2 architecture without a surrounding ciliary membrane; fixed TEM is not continuous same-cell tracking. Figure 1's 23 and 32 cells are selected retraction events, not biological-culture counts. Methods time zero is plating, whereas Figure 2's TEM caption says post-retraction; retain that timing discrepancy. Table 1 labels length/diameter with rate units unlike Table 2; no numerical conversion or rate is asserted here. Main text and all five actual main figures were inspected. The main PDF and actual supplemental PDFs/videos remain unread. Subsequent degradation is a separate phase, not a requirement for this internalization phenotype. - reference: DOI:10.1083/jcb.201701074 snippet: Bd zoospores retracting their flagella by coiling the entire axoneme into the cell body notes: Fritz-Laylin et al. 2017, PMID:28473602, PMCID:PMC5461030.1, Discussion JATS s11, printed page 1681, PDF page 9. Direct normalized JATS and typeset passage checked; native NOT_IN_ABSTRACT retained. Bd denotes Batrachochytrium dendrobatidis, source strain JEL423, with synchronized zoospores observed under the described confinement preparation. Results s10, Discussion s11 and Methods s20 were read, along with selected PDF pages. Video 5 was inspected through 16 sampled frames and one enlarged frame, not continuous playback or every-frame analysis. File metadata reports 10.1 seconds at nominal 10 fps, burned-in labels span 0-20 seconds, and the caption states 0.1-second acquisition with 20-fps playback. These are not silently reconciled; no retraction rate or replicate count is inferred. The paper's WASP/SCAR pseudopod experiments do not establish an axoneme-internalization mechanism. discussions: - discussion_id: eukaryotic-axoneme-internalization-scope prompt: Review intact withdrawal separately from later axonemal disassembly. kind: CURATION_TODO status: OPEN rationale: The defining endpoint is internalization of the cell's own intact eukaryotic axoneme. Static internal localization, uptake of another cell's material, external coiling, failed assembly, motor arrest, passive breakage or shedding alone do not establish it. Venard et al. 2020 place internalization within a broader cilium-disassembly program while distinguishing subsequent degradation. The operational resorption record traitmech:000733 requires shortening through axonemal disassembly, not intact withdrawal alone. Later degradation can occur after internalization; no organism-level disjointness or permanently intact internal axoneme is asserted. Autotomy traitmech:000731 and bacterial polar flagellar ejection traitmech:000732 have different endpoints; bacterial periplasmic flagella and type IV pili are different structures. Phenotype METPO:1000059 is a definition-based parent inference, without a locomotion requirement. evidence: - reference: DOI:10.1091/mbc.E24-12-0577 reference_title: Dynamic remodeling of centrioles and the microtubule cytoskeleton in the lifecycle of chytrid fungi. supports: SUPPORT evidence_source: full_text snippet: Centrioles separated from the degrading axoneme and remained parallel explanation: Supports the later-degradation and centriole-remodeling distinction, not an additional definition citation, a universal centriole fate or a same-cell kinetic measurement. notes: Long et al. 2025, PMID:40833813, PMCID:PMC12659703.2, Results S7, Centrioles shorten but are not degraded during ciliary disassembly, sentence following the coiled-complex observation; Figure 4C. Direct JATS match; native NOT_IN_ABSTRACT retained. R. globosum JEL800 fixed U-ExM stages are not longitudinal trajectories. Actual Figure 4, all supplement text and visual supplement pages 4, 7 and 8 were inspected. The main-text S2 pointer concerns a transcriptomic figure; the relevant centriole panels are S3F-H. Figure 4's caption gives about 4.5-fold expansion, versus 5.5 +/- 0.2 in Results S6 (Supplemental Figure S3A-B); no absolute-size conversion is inferred. Figure 4F counts 16, 3, 26 and 41 sporangia across categories from three to five independent experiments, not retraction events. The two-hour timeline is attributed to 2020, not a new measurement. Other actual main figures, the main PDF and other supplement pages were not visually inspected. The preprint is another version, not another study. posed_by: codex posed_date: '2026-10-15' - discussion_id: eukaryotic-axoneme-internalization-metpo prompt: Review microbial-eukaryote scope and the proposed phenotype parent. kind: CURATION_TODO status: OPEN rationale: No active exact term was identified in the inspected pinned/current METPO release, editor and templates. Deprecated METPO:0000089 and METPO:000090 carry OMO:0001000; METPO:1000381 carries IAO:0000226. Their active replacement METPO:1000704 denotes locomotory flagellar possession, not internalization. Deprecated ciliated METPO:0000093 and METPO:000094 carry OMO:0001000, while METPO:1000385 carries IAO:0000226; no replacement or consider annotation was observed for those or deprecated flagellum METPO:1000123 with OMO:0001000. Historical identifiers are not exact xrefs and are not reactivated. https://github.com/berkeleybop/metpo/issues/521 leaves reason-code interpretation unresolved. Upstream's bacterial/archaeal focus requires maintainer review of microbial-eukaryote inclusion. Proposal v610 reserves METPO:1068700 in 1068700-1068799, not a released identifier or human-approved mapping. The ontology pin is unchanged. posed_by: codex posed_date: '2026-10-15' - discussion_id: eukaryotic-axoneme-internalization-mechanism prompt: Keep observable internalization separate from universal molecular mechanisms. kind: KNOWLEDGE_GAP status: OPEN rationale: Do not require a universal reeling, lash-around, membrane-loss, cortical tethering, actin-dependent, dynein-dependent or proteolytic mechanism. The 2020 latrunculin live-movie analysis selected complete retractions and excluded cells retaining cilia; its conditional results cannot establish all-cell retraction probabilities. Do not transfer 2017 pseudopod perturbations or 2025 transcript/orthology patterns to this phenotype. A gene, domain, motif or profile alone does not establish intact axoneme internalization. A protein-resolved graph requires taxon-paired, authority-checked accessions and edge-specific evidence. No universal rate, cell-cycle stage, complete degradation, protein recycling, exact synonym or equivalent external mapping is asserted. posed_by: codex posed_date: '2026-10-15' - discussion_id: eukaryotic-axoneme-internalization-provenance prompt: Resolve canonical strain provenance while preserving source-access limits. kind: KNOWLEDGE_GAP status: OPEN rationale: The named laboratory strains remain qualified life-stage observations, not authority-verified canonical taxa or proof of natural provenance. Two distinct supporting publications are not a claim of independent-lab replication. The 2025 follow-up shares authors with earlier work and is scope context, not a third definition citation. Qualified MED/Crossref identities and available notice fields were checked, not comprehensive correction/retraction clearance. The linked 2017 Comment/Editorial, DOI:10.1080/15384101.2017.1360655, PMID:28820330, PMC5628642, has no returned abstract and its content remains unread; it is not counted evidence. Publisher/PMC access failures remain failures. The 2020 supplement endpoint returned an API error with HTTP 200, not a ZIP; no actual supplement contents are inferred. No raw-data reanalysis, paid research or human scientific sign-off is implied. posed_by: codex posed_date: '2026-10-15' curation_history: - timestamp: '2026-10-15T20:08:47.827435+00:00' curator: codex action: MINTED_TRAITMECH_ID changes: Added the microbial-eukaryote intact-axoneme internalization phenotype with two primary DOI sources and checked 5/14-word full-text snippets. Kept a nine-word 2025 later-degradation excerpt in a scope discussion, not definition evidence. All three retain native NOT_IN_ABSTRACT. Reserved 000734, v610 and 1068700-1068799 after ignored/hidden current-file, retained-history, complete-range and open/draft PR checks. Preserved source-access and assay limitations; no obsolete identifier, canonical taxon, exact mapping or universal protein mechanism is inferred. The timestamp is the observed allocation decision, not source acquisition. llm_assisted: true - timestamp: '2026-10-15T21:05:50Z' curator: codex action: CORRECT_EVIDENCE_LOCATOR changes: 'Corrected the 2025 expansion-factor locator from Methods/S3B to Results S6, MTOC remodeling from mitosis to ciliogenesis, first paragraph, citing Supplemental Figure S3A-B. Cached JATS S6/S15 and actual Figure S3 were reread for issue #1950. Preserved values, discrepancy, definition, source roles, snippets and previous history.' llm_assisted: true