Ubiquitinated protein levels remain high during ageing in <i>C. elegans</i>
Bibliographic record
Abstract
ABSTRACT A wealth of literature in different model organisms have shown that proteostasis declines with age, which results in the accumulation of aggregated proteins that generally carry polyubiquitin chains. In Koyuncu et al. (Nature, 2021), the authors use a relatively mild homogenization approach to analyze total polyubiquitinated protein levels longitudinally in C. elegans and found that the overall level of polyubiquitinated proteins decreases in wild-type nematodes. Specifically, the substantial presence of polyubiquitinated proteins in early adulthood markedly decreases at day 10 and 15 of adulthood. This finding represents the central basis of their study where they subsequently suggest that age-dependent decrease in protein polyubiquitination in wild-type animals is due to enhanced deubiquitination. Here, we find that the mild homogenization of C. elegans used in Koyuncu et al . fails to properly extract all C. elegans proteins, because it largely omits relatively insoluble proteins in the pellet. When we perform complete homogenization of wild-type nematode proteins using SDS, sonication and heat, we unequivocally observe that polyubiquitinated protein levels do not decrease with age in C. elegans . Overall, the levels of polyubiquitinated proteins remains relatively constant post-reproduction. Therefore, our findings invalidate the main conclusion of Koyuncu et al. that the ubiquitinated proteome is rewired during ageing and demonstrate that C. elegans harbor polyubiquitinated proteins throughout their lifespan.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| 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".