Potential origins and horizontal transfer of type III secretion systems and effectors
Bibliographic record
Abstract
A major virulence mechanism used by pathogenic Gram-negative bacteria is the delivery of effector proteins from the bacterial cytoplasm into host cells by type III secretion. Typically, genes encoding type III secretion systems (T3SS) and effectors have been horizontally acquired by the bacteria that employ them. In proteobacteria, and especially Salmonella, and attaching and effacing (A/E) pathogens, the genetic structure of these systems presents as a large locus encoding a T3SS with a small number of effectors, plus numerous small unlinked loci encoding additional individual effectors. We discuss the generation of novel effectors, and the evolution of G+C content following acquisition. We also consider the currently held view that each locus has been acquired individually, as well as propose an alternative where recombination may have redistributed and broken up clusters of effectors. It is clear that the evolution of this virulence strategy is highly complex and challenging to analyze.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.002 | 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".