23 Differential microRNA expression in jejunal tissue and jejunal lymph nodes following naturally occurring Mycobacterium avium subspecies paratuberculosis infection in Holstein cows
Bibliographic record
Abstract
Abstract Mycobacterium avium subsp. Paratuberculosis (MAP) is the causal agent of Johne’s disease (JD), a chronic intestinal disease affecting ruminants worldwide. This study investigated miRNA expression in jejunal intestine (JE) and jejunal lymph nodes (JELN), and the potential regulatory roles of miRNAs during JD progression. JE and JELN tissues were collected from 5 MAP positive (JD subclinical stage) Holstein cows and 5 MAP negative cows. Following miRNA sequencing, bioinformatic processing with a standard pipeline and functional analysis with ClueGo, 272 and 333 miRNAs were identified in JE and JELN, respectively. Compared with MAP negative cows, 13 and 71 miRNAs were differently expressed (DE) (P < 0.05) in MAP infected JE and JELN, respectively. The most up-regulated and down-regulated miRNAs were bta-miR-485 (fold change = 6.18) and bta-miR-451 (fold change = -6.81), and bta-miR-331-5p (fold change = 35.56) and bta-miR-2285bk (fold change = -61.25) in JE and JELN, respectively. In JE, some DE miRNAs (miR-147 and miR-199a-5p) have been associated with glucose metabolism while several DE miRNAs in JELN have associations with immune response to disease (e.g. miR-146a and miR-146b have been associated with bovine mastitis and miR331-5p and miR-184 are important for human cancers). Target genes of JELN DE miRNAs were enriched (P < 0.05) for more gene ontology terms (n = 180) and KEGG pathways (n = 123) as compared with JE (n = 90 and 25, respectively). Furthermore, JELN DE miRNAs were uniquely enriched in several immune related pathways including immune response regulating/activating signal transduction, T-cell/B-cell receptor signaling, Toll-like receptor signaling, TNF signaling pathways, etc., suggesting potential regulatory roles for JELN DE miRNAs in the host immune response to JD. In addition, interactions between DE miRNAs and DE mRNAs (expressed in the same samples) demonstrated important functions for miR-2284/2285 family members in JELN response to MAP infection. In conclusion, these results suggest site specific regulatory roles for miRNAs during MAP infection.
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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 | 0.001 | 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".