Bibliographic record
Abstract
Rhodobacter capsulatus is a purple non-sulfur bacterium that produces the gene \ntransfer agent RcGTA. This phage-like particle is capable of transferring ~4-kb of host \nDNA to other R. capsulatus cells in a process analogous to transduction. The genes \nknown to encode this particle are located in a ~15-kb region called the RcGTA structural \ngene cluster. As this cluster is larger than the packaging capacity of the particles, RcGTA \nis non-replicative. In addition to lacking key functions required by a phage, the RcGTA \nstructural gene cluster lacks genes likely to encode functions necessary for its gene \ntransfer activity, such as a cellular release mechanism. The costs and benefits of RcGTA \nproduction for R. capsulatus are unclear, making it difficult to explain its persistence in \nthe genome. I investigated R. capsulatus SB1003 prophages to search for other genes \ninvolved in RcGTA production and gene transfer activity. I identified two functional \nprophages, RcapNL and RcapMu, which I characterized and found to be linked to \nRcGTA production. I also compared the genome-wide transcriptional profiles in a variety \nof R. capsulatus strains and growth conditions affecting RcGTA production to identify \ngenes consistently co-regulated with the RcGTA structural gene cluster. I found nine such \ngenes at six separate loci. In characterizing several of these genes, I identified a gene \nrequired for release of RcGTA by cell lysis, a pair of putative tail fibre-encoding genes, \nand an additional gene whose product is required for binding to the recipient cell. Finally, \nI characterized features of RcGTA production by quantitatively determining the \npackaging frequency of all loci on the R. capsulatus chromosome. Remarkably, while any \ngene can be transferred, the RcGTA structural gene cluster region was under-represented \niii \nin the particles relative to the genome average. The search for a mechanistic explanation \nof this anomaly led to the discovery that RcGTA gene expression is elevated in ~3% of \nthe cells in a population, and that these cells undergo lysis to release RcGTA particles. \nThis provided us with the first quantification of the cost of RcGTA production.
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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 | 0.000 | 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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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 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".