Effect of creep-feeding supplementation during the pre-weaning phase on gene co-expression in Longissimus thoracis muscle of F1 Angus x Nellore calves at weaning
Bibliographic record
Abstract
The aim of this study was to analyze gene co-expression in skeletal muscle of calves with or without creep-feeding during the pre-weaning phase. Forty-eight F1 uncastrated male Angus-Nellore calves were divided into two groups: G1 - no creep-feeding, and G2 - creep-feeding. After weaning (210 days), all animals were kept in the feedlot for 180 days under the same conditions. Weaning weight, backfat thickness, and intramuscular fat content were significantly higher in G2, with intramuscular fat and marbling score being 17.2% and 14.0% higher, respectively, compared with G1 (P < 0.05). Longissimus thoracis muscle samples were collected at weaning for transcriptome analysis (RNA-Seq) in 12 animals of each group. Gene co-expression analysis using the CEMiTool R package identified seven modules; five showed differential activity between groups (adjusted P < 0.002). Modules 1, 2, and 3 showed the greatest association with treatments. Hub genes and enrichment in biological pathways and processes were identified in these modules. The absence of supplementation was associated with increased connectivity of hub genes involved in insulin signaling, oxidative metabolism, and cell cycle regulation, including CDKN1A, FOXO1, and NAMPT. These genes were enriched in processes related to lipid oxidation and response to ketone bodies, suggesting reduced myogenic and adipogenic activity. Notably, FOXO1 has context-dependent effects on adipogenesis, acting as both an inducer and inhibitor depending on the differentiation stage. In contrast, supplementation increased the activity of hub genes involved in cell signaling, muscle development, and differentiation, such as ITGB6, REEP1, TPCN1, PPARA, PTPN11, and MAP3K20, and enriched processes associated with muscle and adipose cell development. In conclusion, creep-feeding supplementation during the pre-weaning phase altered gene co-expression in skeletal muscle, activating pathways related to myogenesis, adipogenesis, and energy metabolism. These results suggest potential lasting molecular effects consistent with increased intramuscular fat deposition during finishing.
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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 | 0.000 |
| 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".