Denaturing Gradient Gel Electrophoresis Resolves Virus Sequences Amplified with Degenerate Primers
Bibliographic record
Abstract
MS primers and were absent from the yeast control.Sequence analysis of these clones indicated that 15 contained MS.Inverse PCRs corresponding to 8 of these clones provided the sequence of the entire MS and flanking region.Among the MS repeats we identified, five were simple (GA) n or (CA) n tandem repeats, while three had a more complex repeat structure (Table 1).Using specific primers for each MS (Figure 1, p1 and p3), we mapped back all 8 MS to the original YAC (Table 1).This result confirms that all the isolated MS are derived from the YAC and not from yeast genomic DNA.Finally, we tested the MS repeats for polymorphism between the BALB/cByJ and CAST/EiJ mouse strains, and determined that all were polymorphic.Data relating to these polymorphisms have been submitted to the Mouse Genome Database ( www.informatics.jax.org ; D12Lip1-7, MGI Accession IDs 1342092-1342098).The identification of these new polymorphic MS repeats in a BALBxCAST cross segregating the fld mutation was instrumental in reducing the critical genomic region and in the subsequent positional cloning of the underlying gene (5).In summary, we developed a simple PCR-based procedure for the identification of novel MS from YACs and other large-insert clones [e.g., bacterial artificial chromosome (BAC) and P1 artficial chromosome (PAC)].Although we have demonstrated the use of the technique by isolating several polymorphic markers from a mouse YAC clone, the procedure could be easily adapted to human DNA by substituting the B1/B2-specific primers with primers derived from the human Alurepeat.A major advantage of the new method over existing ones is its species specificity, which eliminates the need to gelpurify YACs and enables analysis from total yeast DNA preparations.
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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) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.006 | 0.006 |
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".