Biology of Three ICE Families: SXT/R391, ICE<i>Bs1</i>, and ICE<i>St1</i>/ICE<i>St3</i>
Bibliographic record
Abstract
In the early 1980s, conjugative transposons were defined as large DNA segments of bacterial chromosomes capable of “intercellular transposition,” i.e., fragments able to move from the chromosome of a donor bacterium to the chromosome of a recipient bacterium during cell-to-cell contact. All these mobile genetic elements were found in pathogenic low GC Gram-positive bacteria, conferred antibiotic resistance properties, and were often capable of integrating into a large array of different sites (for review, see references 1,2,3,4). Characterization of the molecular mechanism allowing integration into and excision from the chromosome revealed that conjugative transposons such as Tn 916 do not encode a DDE transposase, but rather a site-specific tyrosine recombinase. Fundamental differences in the molecular mechanism of DNA strand exchanges catalyzed by transposases and site-specific tyrosine recombinases, and subsequent identification of conjugative mobile elements integrating into a unique site of the bacterial chromosome in both Gram-positive and Gram-negative bacteria exposed the inadequacy of the naming “conjugative transposons.” In fact, at the time the confusion in the scientific community was such that, in some instances, related elements were mislabeled as conjugative plasmids, R factors, or integrating conjugative plasmids (5). Two nomenclatures proposed to replace the obsolete term by a more adequate nomenclature: constin, an acronym that stands for conjugative, self-transmissible, integrating element, and ICE, an acronym for integrative and conjugative element (5,6). Over the years the term ICE gained a broader acceptance among many authors to describe elements found in both Gram-positive and Gram-negative bacteria, so this term is used hereafter instead of conjugative transposon.
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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) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".