Bibliographic record
Abstract
Since the fi rst reports of the fascinating phenomenon of catalytically active RNAs in the 1980s, ribozyme research has become a major fi eld in the molecular and biological sciences.Following the initial, ground-breaking discoveries, in the 1990s phosphodiester-cleaving ribozymes have been studied intensively both as basic tools as well as for therapeutic applications in order to suppress target gene expression.The past decade has then seen a variety of fundamental insights into ribozymes which have profoundly changed our view on RNA catalysis: The increasing biochemical and structural knowledge of ribosomal protein synthesis revealed that the fundamental peptidyl-transfer reaction is catalyzed by rRNA.In addition, the discovery of extended motifs of the hammerhead ribozyme and its subsequent high-resolution structure solved a long-standing discrepancy in understanding hammerhead catalysis.The discovery of riboswitches as wide-spread mechanisms for the regulation of gene expression widened our view on functional roles of RNAs in modern organisms.The glmS riboswitch was discovered as the fi rst ligand-dependent, ribozyme-based genetic switch.Apart from these highlights, an increasing number of catalytically active ribozymes are discovered in a variety of organisms, although in most cases their functional role is still unknown.In addition to these fascinating discoveries in nature, in vitro selection techniques in combination with latest developments in the fi elds of RNA chemical and synthetic biology allowed for the development of a variety of engineered ribozymes utilized for various tasks.Taken together, ribozymes have been discovered in many places and show widespread functions and applications.The present Methods in Molecular Biology collection starts with an introduction by Eric Westhof, followed by protocols for investigating the catalysis of individual ribozymes.Then, a series of chapters covers specifi c methods useful for studying different aspects of ribozymes.The third part of the collection highlights techniques for specifi c applications of ribozymes.Hence the present collection covers both protocols and techniques for the characterization of ribozymes as well as introduces a variety of novel applications for catalytic RNAs.It is aimed both at the biochemist interested in the investigation of mechanistic aspects of ribozyme catalysis as well as the biomedicine researcher and life scientist interested in the application of ribozymes as tools for manipulating cellular functions.I would like to thank all authors for contributing to the present methods collection and hope that it will help fostering ribozyme research in all of the above-mentioned aspects.
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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 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.014 | 0.016 |
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".