Genome-Wide Temporal Gene Expression Reveals a Post-Reproductive Shift in the Nematode <i>Caenorhabditis briggsae</i>
Bibliographic record
Abstract
The nematodes Caenorhabditis briggsae and its well-known cousin Caenorhabditis elegans offer many features for comparative investigations of genetic pathways that affect physiological processes. Reproduction is one such process that directly impacts longevity due to its significant energetic demands. To study gene expression changes during reproductive and post-reproductive phases in both these nematodes, we conducted whole-genome transcriptome profiling at various adult stages. The results revealed that the majority of differentially expressed (DE) genes were downregulated during the reproductive period in both species. Interestingly, in C. briggsae, this trend reversed during post-reproduction, with three-quarters of the DE genes becoming upregulated. Additionally, a smaller set of DE genes showed an opposite expression trend, i.e. upregulation followed by post-reproductive downregulation. Overall, we termed this phenomenon the "post-reproductive shift". In contrast, the post-reproductive shift was much less pronounced in C. elegans. In C. briggsae, DE genes were enriched in processes related to the matrisome, muscle development and function during the reproductive period. Post-reproductive downregulated genes were enriched in DNA damage repair, stress response, and immune response. Additionally, terms related to fatty acid metabolism, catabolism, and transcriptional regulation exhibited complex patterns. Experimental manipulations in C. briggsae to affect their reproductive status predictably altered gene expression, providing in vivo support for the post-reproductive shift. Overall, our study reveals novel gene expression patterns during reproductive and post-reproductive changes in C. briggsae. The data provide a valuable resource for cross-sectional comparative studies in nematodes and other animal models to understand evolution of genetic pathways affecting reproduction and aging.
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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 | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".