Transcriptome analysis of ruminal epithelia revealed potential regulatory mechanisms involved in host adaptation to gradual high fermentable dietary transition in beef cattle
Bibliographic record
Abstract
BACKGROUND: The transition from a high forage to a highly fermentable diet can induce digestive disorders in the rumen. To date, the host mechanisms that regulate the adaption to such dietary transition are largely unknown. To understand the molecular mechanisms involved in such phenomena, RNA-sequencing was performed to identify the changes in the transcriptome of ruminal epithelia during gradual transition from a diet containing 0% to 89% grain. RESULTS: In total, the expression of 11,044, 11,322 and 11,282 genes were detected in ruminal epithelia of beef heifers (n = 15) fed 0%, 72% and 89% barley grain diet, respectively. The transcriptome profiles of rumen epithelia differed between low grain diet (LGD) (0% grain) and high grain diet (HGD) (72% and 89%), and HGD tended to reduce the expression of genes involved in epithelial catalytic and binding activities. When diet was changed from 72% to 89% grain, the mean ruminal pH change was significantly different among individual heifers with five of them decreased (down group (DG); from 6.30±0.09 to 5.87±0.15, P < 0.01) and five of them increased (up group (UG); from 5.84±0.42 to 6.35±0.37, P < 0.05). The functional analysis of differentially expressed (DE) genes revealed inhibited "Immune response of leukocytes", "Attraction of phagocytes", and "Cell movement of leukocytes" (P < 0.05) functions (Z-score = -2.2, -2.2 and -2.0, respectively) in DG, and inhibited "Concentration of lipid" and "Proliferation of epithelial cells" functions in UG (Z-score = -2.0, and -1.8, respectively). In addition, the expression of genes involved in ketogenesis (HMGCL) and lipid synthesis (SREBF2, FABP4) was increased in DG, while the expression of ketogenesis (ACAT2, HMGCS) and cholesterol synthesis related genes (HMGC and FDPS) were deceased in UG. Furthermore, the upstream regulators were found to be involved in the regulation of immune response and cell cycle progress, and SNP (g.46834311A > G) in FABP4 was identified between two groups of animals (P < 0.1). CONCLUSION: The identified genes, upstream regulators, and SNP could be potential genetic markers that may account for the varied individual ruminal pH responses to the dietary transition stress.
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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".