identifier: traitmech:000635 label: pinocytosis definition: A physiological phenotype in which a microbial organism internalizes surrounding extracellular fluid and dissolved material into membrane-bound compartments formed from its plasma membrane. definition_source: DOI:10.1083/jcb.53.3.681 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000636 evidence: - reference: DOI:10.1083/jcb.53.3.681 snippet: HRP activity was found exclusively within membrane profiles within the cytoplasm, confirming the pinocytotic mode of uptake. notes: 'PMID:5028259, PMC2108769. Scientific Abstract directly read in Europe PMC XML. The full-text OCR, including Introduction, Methods, Results and Discussion, was read at https://www.ebi.ac.uk/europepmc/webservices/rest/PMC2108769/fullTextXML. Tracer uptake and author-reported intracellular HRP support vesicular fluid uptake in Neff cells. OCR is not a visual figure audit: the PDF/figures were unavailable. The authors qualify the vesicle sample as nonrandom and membrane turnover as estimated; no size distribution, numerical rate or exclusive transport route is generalized here.' - reference: DOI:10.1099/00221287-92-2-246 snippet: The reduced pinocytotic activity of stationary-phase cells remains sensitive to respiratory inhibitors. notes: PMID:1255130. Scientific Abstract directly read at the publisher and in NCBI PubMed XML. This independent study reports reduced inulin uptake in stationary-phase Acanthamoeba trophozoites while bead phagocytosis essentially ceases. It supports a condition-dependent fluid-uptake phenotype, not organismal disjointness or a specific protein mechanism. Full text and figures were unavailable; no unread methods or strain accession is inferred. canonical_examples: - taxon_id: NCBITaxon:1257118 taxon_label: Acanthamoeba castellanii str. Neff reference: DOI:10.1083/jcb.53.3.681 note: Laboratory-maintained Neff cells studied in the 1972 paper, with fluid tracers and author-reported intracellular HRP. NCBI EFetch verified this exact strain-rank name on 2026-10-06. ATCC Neff provenance at https://www.atcc.org/products/30010 gives soil from Pacific Grove, California. The paper supplies no collection accession; this does not establish vial or genome identity with ATCC 30010 or an unchanged original isolate. The legacy NCBI name is retained despite the transfer of Neff to A. terricola in DOI:10.1016/j.ejop.2024.126091; see the open taxonomy discussion. This is not a species-wide assertion. discussions: - discussion_id: pinocytosis-scope-and-hierarchy prompt: Keep vesicular fluid uptake distinct from neighboring traits. kind: CURATION_TODO status: RESOLVED rationale: Retain phenotype METPO:1000059 pending a broader endocytic capability hierarchy. This is uptake by a microbe, not induction of host-cell uptake. Macropinocytosis traitmech:000634 is a narrower ruffle-mediated mode; its existing definition supports the direct parent refinement. Do not equate pinocytosis with particle engulfment traitmech:000627, nutritional phagotrophy traitmech:000628 or prey-content aspiration traitmech:000631. These traits are not declared organismally disjoint. Solute transport across a membrane, surface adsorption, open invaginations and membrane recycling alone do not establish fluid internalization. No fixed vesicle size, ruffle, nutritional requirement or universal nonconcentrative uptake is imposed. Process-level ontology mappings and synonyms remain unasserted. posed_by: codex posed_date: '2026-10-06' resolved_date: '2026-10-06' resolution_note: Added endocytosis traitmech:000636 as the direct broader phenotype. The existing fluid-internalization definition entails this membrane-bound uptake scope. This resolves the temporary parent gap, not the separate Neff taxonomy or native-mechanism discussions; the historical scope contrasts and unasserted mappings remain applicable. Preserve the v511 phenotype axiom and add METPO:1058800 SubClassOf METPO:1058900 upstream. - discussion_id: pinocytosis-neff-taxonomy prompt: Reconcile the legacy Neff taxon name with its reassignment. kind: CURATION_TODO status: OPEN rationale: The 2024 primary taxonomy paper transfers Neff to A. terricola, whereas NCBI still labels strain 1257118 Acanthamoeba castellanii str. Neff and ATCC 30010 retains A. castellanii. Keep the issuing-authority label with explicit strain scope rather than silently generalizing to either species. The taxonomy paper's scientific abstract was directly read; its full phylogenetic data were not audited. Revisit the authority mapping when the strain identity is reconciled. evidence: - reference: DOI:10.1016/j.ejop.2024.126091 evidence_source: abstract snippet: The Neff strain is therefore transferred to A. terricola and should no longer be considered as belonging to A. castellanii. notes: PMID:38772052; exact scientific Abstract span from NCBI PubMed XML. Taxonomy evidence, not another pinocytosis experiment or independent trait replication. posed_by: codex posed_date: '2026-10-06' - discussion_id: pinocytosis-native-mechanism prompt: Resolve uptake routes before asserting molecular dependencies. kind: KNOWLEDGE_GAP status: OPEN rationale: The two experimental papers concern Acanthamoeba and do not establish independent taxon replication. The 1972 nonconcentrative uptake interpretation is study-specific. Tracer loss, metabolism and static membrane profiles limit rate and route inference; the actual figures remain unaudited. Respiratory-inhibitor sensitivity does not identify a particular uptake protein. HRP is an external tracer, not a native microbial protein exemplar. No protein accessions or causal graph are inferred. posed_by: codex posed_date: '2026-10-06' curation_history: - timestamp: '2026-10-06T05:29:34Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added pinocytosis with two primary DOI-backed scientific-abstract snippets, a strain-qualified Neff example and explicit taxonomy and source-access limits. Ignored-and-hidden searches and full pinned METPO review found no exact record. Reserved METPO:1058800 in v511 and refined macropinocytosis to this broader phenotype. llm_assisted: true - timestamp: '2026-10-06T06:47:04Z' curator: codex action: REFINE_ENDOCYTOSIS_PARENT changes: Refined the direct parent to endocytosis traitmech:000636 and resolved the temporary parent gap by definition-based inference. Preserved the historical rationale, definition, evidence, Neff example, independent taxonomy/mechanism discussions and prior history. llm_assisted: true