Research journal — retrospective draft¶
We compiled this retrospective journal on 9 October 2026 to connect our engineering work with its observations and follow-up questions. This is the compilation date, not an experiment date. Entry numbers correspond to engineering cycles rather than calendar days or directed-evolution rounds.
Record status: experiment dates, experimenters and contemporaneous raw records are not yet available for verification. These retrospective entries do not replace our original dated laboratory notebook.
Entry 01 — Source material and assay context¶
Engineering cycle: 1. Experiment date / experimenter: pending verification.
We prepared the assay material and assessed its suitability for subsequent experiments. The original check images and observation sheets remain unavailable, so the checks summarised here still require verification.
Documentation pending: dated source-material record, operator attribution and original check evidence.
Entry 02 — Chassis characterisation¶
Engineering cycle: 2. Experiment date / experimenter: pending verification.
We assessed chassis tolerance to establish the culture context for later assays. The underlying measurements and plotted data remain unavailable for independent verification.
Documentation pending: original observation sheet, sample identifiers and figure or analysis-file mapping.
Entry 03 — Construct verification¶
Engineering cycle: 3. Experiment date / experimenter: pending verification.
We examined construct introduction and reporter compatibility. Clone-level verification records remain unavailable; confirmation of the individual constructs used in later assays is still pending.
Documentation pending: dated construct-verification records and identifiers linking the tested samples to subsequent figures.
Entry 04 — Sequence documentation¶
Engineering cycle: 4. Experiment date / experimenter: pending verification.
We worked on sequence design and sequencing checks. Sequence files and chromatograms remain unavailable, so sequence identity and construct junctions still require verification.
Documentation pending: versioned sequence files, sequencing evidence and source attribution.
Entry 05 — Interpreting a signal proxy¶
Engineering cycle: 5. Experiment date / experimenter: pending verification.
We examined the response to a culture-derived proxy. The original response curve and raw measurements remain unavailable. This assay does not directly quantify a single signalling molecule.
Documentation pending: original measurements, sample labels and the analysis underlying the observed response.
Entry 06 — Reporter observations¶
Engineering cycle: 6; Fig. 3. Experiment date / experimenter: pending verification.
We compared growth and reporter expression across the tetrathionate gradient. Figure 3 presents these observations. The concentration-unit discrepancy in our documentation still requires reconciliation with the original record. Reporter expression alone does not validate the complete system.
Documentation pending: raw figure inputs and our documented resolution of the unit discrepancy. Figure and interpretation.
Entry 07 — Assay matrix reconciliation¶
Engineering cycle: 7; Fig. 4A. Experiment date / experimenter: pending verification.
We assessed the combined-input response using a cross-induction matrix. The 7 × 4 design and a separate total of 21 groups in our documentation disagree. The actual analysed sample set remains to be confirmed against the original plate map.
Documentation pending: original sample layout, analysed-condition list and raw figure inputs. Evidence discussion.
Entry 08 — Readout timing¶
Engineering cycle: 8; Fig. 4A. Experiment date / experimenter: pending verification.
We evaluated the colour readout after 12 h of co-culture and 2 h of substrate development. These observations do not establish a one-hour response. This entry and Entry 07 concern the same figure and are not separate independent replications.
Documentation pending: original observation timestamps and the checked figure caption.
Entry 09 — Limits of an endpoint measurement¶
Engineering cycle: 9; Fig. 4B. Experiment date / experimenter: pending verification.
We compared crystal-violet-stained biomass between the assay groups. The endpoint reflects retained biomass; it does not independently establish viable organism counts, eradication, a particular mechanism or an in-host effect.
Documentation pending: replicate-level measurements and the original statistical output. Figure interpretation.
Entry 10 — Containment evidence review¶
Engineering cycle: 10. Experiment date / experimenter: pending verification.
We proposed a bile-responsive Hok/Sok containment module. Quantitative performance remains unverified because the corresponding raw dataset and result figure are not yet available. We cannot infer environmental safety from the design alone.
Documentation pending: original supporting records, if they exist, and the responsible research documentation. Current evidence boundary.
Entry 11 — Cell-assay interpretation¶
Engineering cycle: 11; Fig. 5. Experiment date / experimenter: pending verification.
We assessed L-929 cell compatibility and observed no statistically significant difference between the two bacterial groups. Non-significance does not establish equivalence or safety; interpretation also depends on the medium-only reference and the underlying measurements.
Documentation pending: sample-level observations, exact replicate counts, analysis output and dated operator record. Figure and limitations.
Completing the original-record links¶
For each entry, we still need to link the actual experiment date, researcher, original notebook identifier, protocol, sample identifiers, raw files and corresponding figure. Corrections will need a named reviewer and verification date. Missing observations remain unresolved until checked against the original laboratory records.
Engineering-to-figure index · Data availability · Responsible research