Crosslinking of Proteins to mtDNA
Bibliographic record
Abstract
Mitochondrial DNA (mtDNA) nucleoids have been isolated from several organisms, including rat (liver) (), Physarum polycephalum (), Saccharomy- ces cerevisiae () and Pichia jadinii (). Most methods for nucleoid isolation have utilized detergent extraction and sucrose gradient centrifugation to separate bulk mitochondrial protein from mtDNA-associated proteins (e.g., ref. 5). The disadvantages of these methods include contamination by non-nucleoid proteins and the possibility of losing those nucleoid proteins that are not tightly bound to the complex under the conditions of the fractionation. To circumvent these problems, we have developed an in organello formaldehyde crosslinking method for isolating mtDNA nucleoids that stabilizes protein content and reduces the potential for contamination by irrelevant mitochondrial (and cellular) proteins. Additionally, it has long been suggested that mtDNA is associated with the inner membrane. To begin exploring that notion, we have used ultraviolet (UV) crosslinking as a means of detecting the binding of proteins from membrane-enriched fractions to specific sequences of mtDNA.
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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) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.005 | 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".