Topology‐dependent transcription in linear and circular plasmids of the segmented genome of <i>Borrelia burgdorferi</i>
Bibliographic record
Abstract
The segmented genome of Borrelia burgdorferi, a causative agent of Lyme disease, contains a mixture of over 20 linear and circular plasmids. Genes encoding five paralogous families of plasmid replication proteins are located on both circular and linear DNA molecules. The effect of DNA topology on the transcription of replication proteins from two B. burgdorferi plasmids, cp9 and lp17, was examined using quantitative reverse transcription polymerase chain reaction. Circular to linear conversion of a cp9-derived plasmid resulted in a 160-fold decrease in transcript levels of bbc01, believed to encode the replication initiator. A 14.9-fold reduction in plasmid copy number was also observed, resulting in a net 10.7-fold lower transcription level per gene copy on a linear versus a circular plasmid. In contrast, expression of the bbd14 replication initiator for the linear plasmid lp17 was 7.2 times higher per gene copy on a linear versus a circular plasmid. Topology-dependent transcription of these genes may help to block topological interconversions during genome evolution, offers a new avenue for global gene regulation and also has important implications for the design of genetic complementation experiments in B. burgdorferi.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".