The CRISPR-Cas Immune System and Genetic Transfers: Reaching an Equilibrium
Bibliographic record
Abstract
In 1987 Ishino et al. (1) sequenced the Escherichia coli alkaline phosphatase isozyme conversion gene (iap). Downstream of iap, they observed an array of short repeats (29 nucleotides) separated by nonrepetitive short sequences (spacers) (2). The terms “CRISPR,” for clustered regularly interspaced short palindromic repeats, and “Cas,” for CRISPR-associated genes, were first coined by Jansen et al. (3) in 2002 to describe the genetic structure of these loci. The increasing availability of genomic sequences in databases allowed Mojica et al. (4) to identify CRISPR as a specific family of repeats. Now we know that CRISPR-Cas systems are found in approximately 90% of archaeal and 40% of eubacterial sequenced genomes (5 – 7). In 2005, three groups independently reported similarities between spacer sequences and foreign mobile genetic elements (MGEs) such as phages and plasmids (8 – 10). These observations led to several hypotheses including that CRISPR-Cas systems may play a role in immunity and protect archaeal and bacterial cells from invasion by foreign DNA.
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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) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.004 |
| Scholarly communication | 0.002 | 0.005 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.003 | 0.005 |
| Insufficient payload (model declined to judge) | 0.009 | 0.005 |
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".