Engineering record¶
Our engineering index connects eleven DBTL cycles with the associated figures and outstanding documentation.
We organised our engineering work into eleven Design–Build–Test–Learn cycles. This retrospective index links each topic to our observations and figures. It is not a dated laboratory notebook: experiment dates, operator names, plate maps, raw values and instrument files are not yet available in our public research record.
| Cycle | Engineering focus | Observations and documentation status |
|---|---|---|
| 1 | Culture conditions and preparation of Salmonella culture filtrate | We recorded growth in LB to OD600 above 1.2 and no colonies on the filtrate sterility plate after 48 h. The original plate image and count sheet remain unavailable for verification. |
| 2 | EcN bile-salt tolerance | We observed no apparent growth inhibition up to 5% sodium cholate and selected 0.2% for routine culture. The underlying data and plotted figure remain unavailable for verification. |
| 3 | EcN transformation and reporter compatibility | We compared CaCl2, RbCl and electroporation. The electroporation estimate of >10^7 CFU/µg DNA remains to be verified against clone-level data. |
| 4 | Sequence acquisition and codon optimization | Our sequence summary lists CAI >0.85, GC 48–54% and 100% Sanger identity. FASTA files and chromatograms remain unavailable for verification. |
| 5 | Culture-filtrate response associated with AI-2 | We recorded an approximately 4.8-fold response at 5–10% filtrate. The underlying curve and raw measurements remain unavailable for verification. |
| 6 | Tetrathionate tolerance and PttrB-associated reporter expression | Fig. 3; expression peaked at 0.6‰; growth decreased at 0.8–1.0‰. |
| 7 | Cross-induction matrix | Fig. 4A; methods count (21) conflicts with the plotted 7 × 4 design (28). |
| 8 | LacZ/X-Gal colorimetric output | Fig. 4A; assay timing was 12 h plus 2 h. |
| 9 | Salmonella biofilm assay | Fig. 4B and OD595 values. |
| 10 | Hok/Sok containment module | We proposed a bile-responsive containment module. The >99.99% decline claim remains unverified without a result figure or raw containment dataset. |
| 11 | L-929 cell compatibility | Fig. 5 and relative-viability values. |
Connecting observations and figures¶
Our retrospective research journal expands these entries with observations, interpretation and documentation needs. Its compilation date does not replace the actual experiment dates.
The links below connect our engineering work with the corresponding figures:
| Figure | Related record on this wiki |
|---|---|
| Fig. 3 | Tetrathionate response |
| Fig. 4A | Cross-induction assay |
| Fig. 4B | Biofilm assay |
| Fig. 5 | L-929 assay |
Our remaining documentation work is to link the original notebook pages, experiment dates, researchers, replicate-level measurements and analysis files. Missing dates and measurements remain unresolved until verified against the original records.