Additional file 2 of A minimized symbiotic gene set from the 1.68 Mb pSymB chromid of Sinorhizobium meliloti reveals auxiliary symbiotic loci
Bibliographic record
Abstract
Additional file 2: Fig. S1. Schematic for capture of pSymB regions B108, B109, and B123 and creation of SmB1.0 via their integration into a ΔpSymB background strain. A. (1) Conjugal transfer and subsequent integration of two integrative plasmids harbouring mutant loxP sites to the right flank of B109 (purple) and the left flank of B123 (blue) into a strain of S. meliloti in which the S. fredii ETR region has been integrated into the chromosome (orange). (2) Transduction of a promoterless cre integrative plasmid into pSymB downstream of the taurine inducible promoter PtauA. (3) Resultant strain now contains loxP sites flanking the B301 region (yellow) to be deleted, that are recombined by Cre which is expressed by the addition of 10 mM taurine. (4) Conjugal transfer and subsequent integration of two integrative plasmids harbouring FRT sites to the left flank of B108 (red) and the right flank of B123 (blue) of the now adjacent B108/B109/B123 symbiotic regions. B. (1) Conjugal transfer of the PCA-inducible Flp expression plasmid pTH2505 into the S. meliloti recipient with FRT sites flanking B108/B109/B123. (2) Triparental mating and concurrent expression of Flp in the now S. meliloti donor with an E. coli recipient DH5αR. (3) Captured B108/B109/B123 regions in E. coli are re-introduced into a ΔpSymB recipient via conjugation and subsequently integrated into the chromosome at an attB landing pad via chromosomally expressed ΦC31 integrase. (4) Resultant minSymB1.0 strain with the S. fredii ETR region and B108/B109/B123 regions integrated into the chromosome.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.013 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.857 | 0.243 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".