Encapsulation is part of the setup, not the strain (#183) - #540
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Encapsulation is part of the setup, not the strain (#183)#540realmarcin wants to merge 1 commit into
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Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture: 125 mL baffled Erlenmeyer flasks holding ~10 mL of alginate-bead suspension in M3 minimal medium on a rotary shaker, with the cyanobacterium encapsulated in barium-alginate hydrogel and cells stepped from 25 to 50 mM NaCl before the final medium. The encapsulation is recorded as instrument_detail rather than left implicit because it is what makes the coculture work: it shields S. elongatus from 2,4-DNT toxicity. Read as a property of the strain it would be wrong; read as a property of the vessel it explains the result. No operating temperature and no light intensity. The paper's 32 °C and 150 rpm attach to Lysogeny broth cultures, and LB is the P. putida preculture medium — the coculture runs on M3 with light and CO2 as its inputs. Recording those numbers would be the #529 error for the fourth time in this batch, so the incubator model goes in instead of a temperature invented for it. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
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What
Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture— 125 mL baffled Erlenmeyer flasks holding ~10 mL of alginate-bead suspension in M3 minimal medium on a Multitron Pro rotary shaker, with cells stepped from 25 → 50 mM NaCl before the final medium.Why the encapsulation is in
instrument_detailThe cyanobacterium is encapsulated in barium-alginate hydrogel rather than free in suspension, and that is what makes the coculture work: it shields S. elongatus from 2,4-DNT toxicity.
Read as a property of the strain it would be wrong — the organism has no such resistance. Read as a property of the setup it explains the result. That is why it is recorded here rather than left to the description, with the snippet that states the causal link.
No temperature, no light intensity
The paper gives 32 °C and 150 rpm — for Lysogeny broth cultures. LB is the P. putida preculture medium; the coculture runs on M3 with light and CO₂ as its inputs.
Recording those numbers would be the #529 error for the fourth time in this batch. The incubator model goes in instead of a temperature invented for it.
Also checked and found clean
Before curating this record I swept the whole corpus for the superscript-type-strain rendering artefact fixed in #539 (
MPOB T→MPOBT). It is isolated — only that one record, already fixed. Worth stating as a proven negative rather than leaving as an open worry: no batch fix is needed.Checks
just validate— no issuesjust validate-references— 0 issues; both snippets verbatimjust validate-strict,just lint,just check-docs-current— exit 0uv run pytest tests/— 2375 passed, 16 skippedPart of #183.
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