Detection of Viral microRNA with S1 Nuclease Protection Assay
Bibliographic record
Abstract
Mammalian host cells and their viral pathogens express and make use of short noncoding RNA molecules to control the infectious cycle. In order to understand their physiological role, it is necessary to develop tools for detection and quantification of these molecules. Here, we present a simple, specific, and very sensitive protocol using short radioactive DNA oligonucleotides for hybridization to homologous RNA target in a nuclease protection assay. The S1 nuclease from Aspergillus oryzae degrades single-stranded oligonucleotides composed of either deoxynucleotides or ribonucleotides. In contrast, double-stranded DNA, double-stranded RNA, or DNA-RNA hybrids are resistant to digestion. Subsequent analysis of the protected DNA oligonucleotide with denaturing gel electrophoresis results in radioactive signals strictly proportional to the abundance of short RNA in a given sample. The protocol works equally well for in vitro cell culture assays and for tissue samples obtained from in vivo experiments.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 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 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.002 |
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".