From f46cfa4a70daa8f8ba7662d314b2db9ead35edeb Mon Sep 17 00:00:00 2001 From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com> Date: Tue, 11 Aug 2026 02:50:39 -0700 Subject: [PATCH] Encapsulation is part of the setup, not the strain (#183) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 --- ...us_Pseudomonas_PhotoPHA_DNT_Coculture.yaml | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml b/kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml index 410288a0..46877a21 100644 --- a/kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml +++ b/kb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml @@ -288,6 +288,39 @@ ecological_interactions: evidence_source: IN_VITRO snippet: exchange of further molecules beyond the unidirectional feeding with sucrose explanation: Supports additional interaction mechanisms beyond the engineered sucrose cross-feeding link. +cultivation_setup: +- cultivation_mode: BATCH + system_type: FLASK + working_volume: 10.0 + working_volume_unit: mL + instrument_detail: >- + 125 mL baffled Erlenmeyer flasks holding roughly 10 mL of alginate-bead suspension in M3 + minimal medium, on a Multitron Pro rotary shaker. The cyanobacterium is encapsulated in + barium-alginate hydrogel rather than free in suspension; that encapsulation is what + shields it from 2,4-DNT toxicity, so it is a property of the setup and not of the strain. + Cells were stepped from 25 to 50 mM NaCl over two days before the final medium. + notes: >- + No operating temperature or light intensity. The paper gives 32 °C and 150 rpm for + Lysogeny broth cultures, and LB is the P. putida preculture medium - the coculture runs + on M3 with light and CO2 as inputs, so those numbers are not the community's (#529). The + incubator model is recorded instead of a temperature invented for it. + + `cultivation_mode` is BATCH: the medium is exchanged between acclimation steps rather + than fed continuously, and no dilution rate is reported. + evidence: + - reference: PMID:32064751 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: the alginate bead suspension were portioned in ~ 10‐ml aliquots into 125‐ml baffled + Erlenmeyer flasks + explanation: The vessel and the working volume the coculture was run in. + - reference: PMID:32064751 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: By encapsulating S. elongatus within a barium-alginate hydrogel, cyanobacterial cells + were protected from the toxic effects of 2,4-DNT, enhancing the performance of the co-culture + explanation: Why the encapsulation belongs in the setup rather than being incidental. + environmental_factors: - name: Light and CO2 value: Illumination with CO2 as primary carbon input