Isolation and genomic characterization of the first phage infecting <i>Iodobacteria</i> : ϕPLPE, a myovirus having a novel set of features
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
The aquatic phage ϕPLPE infects a bacterium of the genus Iodobacter that are common inhabitants of rivers, streams and canals that produce violacein-like pigments. Our characterization of ϕPLPE reveals it to be a small, contractile-tailed phage whose 47.5 kb genome sequence is phylogenetically distant from all previously characterized phages. The genome has a generally modular organization (e.g. replication/recombination, structure/morphogenesis, lysis/lysogeny) and approximately half of its 84 open reading frames have no known homologues. It behaves as a virulent phage under the host growth conditions we have employed and, with the exception of an anti-repressor (ant) homologue, the genome lacks all the genes associated with a lysogenic lifestyle. Thus, either ϕPLPE was once a temperate phage that has lost most of its lysogeny cassette or it is a virulent phage that acquired an ant-like gene presumably for some function other than the control of lysogeny. The ϕPLPE genome has few bacterial gene homologues with the interesting exception of a putative acylhydrolase (acylase). This function has been implicated in bacterial quorum sensing since it degrades homoserine-lactone signalling molecules and can disrupt or modulate quorum signalling from either the emitter or its competitors. ϕPLPE may be an example of a phage co-opting components of the bacterial quorum-sensing apparatus to its own advantage.
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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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 it