Shifted Reverse PAGE: a novel approach based on structure switching for the discovery of riboswitches and aptamers
Bibliographic record
Abstract
Abstract Riboswitches are regulatory sequences composed of an aptamer domain capable of binding a ligand and an expression platform that allows the control of the downstream gene expression based on a conformational change. Current bioinformatic methods for their discovery have various limitations. To circumvent this, we developed an experimental technique to discover new riboswitches called SR-PAGE (Shifted Reverse Polyacrylamide Gel Electrophoresis). A ligand-based regulatory molecule is recognized by exploiting the conformational change of the sequence following binding with the ligand within a native polyacrylamide gel. Known riboswitches were tested with their corresponding ligands to validate our method. SR-PAGE was imbricated within an SELEX to enrich switching RNAs from a TPP riboswitch-based degenerate library to change its binding preference from TPP to thiamine. The SR-PAGE technique allows performing a large screening for riboswitches, search in several organisms and test more than one ligand simultaneously.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".