Small nucleolar RNA dysregulation and potential roles in bovine subclinical mastitis
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Abstract Background Subclinical mastitis, caused by many pathogens including Staphylococcus aureus (S. aureus) and Staphylococcus chromogenes (S. chromogenes), presents a major challenge to the dairy industry due to its associated economic losses and poor milk quality. The molecular regulatory mechanisms, including the role of small nucleolar RNAs (snoRNAs), of the host response to mastitis pathogens remain unclear. Therefore, this study investigated snoRNA expression and potential roles during subclinical mastitis. Milk somatic cells from cows with naturally occurring S. aureus (n = 14) and S. chromogenes (n = 3) subclinical mastitis, and healthy cows (n = 4) were subjected to transcriptome sequencing and bioinformatics analyses. Results We identified 255 expressed snoRNAs including 21 differentially expressed (DE) in S. aureus-positive cows and 20 DE in S. chromogenes-positive cows. Prediction of ribosomal RNA (rRNA) modification sites found several 18S rRNA and 28S rRNA modification (pseudouridylation and 2′-O-methylation) target sites essential for ribosome function for DE snoRNAs, such as SNORA79 (18S-1319, 28S-3001), SNORA1 (18S-1496, 28S-1747), suggesting their roles in translation and immune modulation during subclinical mastitis. Correlation analysis identified DE snoRNAs-mRNAs (from the same samples) pairs with majority of the correlated mRNAs (e.g., CXCL8, IL6R, IL2, IL1R, IL18R1, STAT3, NFKB2, MYD88, VEGFA, and CD40) having immune related functions. Functional enrichment of correlated genes of snoRNAs for S. aureus-positive group (regulation of defense/immune response, leukocyte differentiation, response to cytokine, NF-κB signaling pathway, JAK-STAT signaling pathway etc.) and S. chromogenes-positive group (e.g., regulation of defense response, response to cytokine, regulation of immune response, NF-κB signaling pathway, TNF signaling pathway, and JAK-STAT signaling pathway) revealed involvement in immune and inflammatory processes. Some functional terms were common to both pathogens (e.g., NF-κB, JAK-STAT signaling, immune system processes) and suggest common regulatory mechanisms used by both pathogens to contain infection. Furthermore, snoRNA-mRNA network construction identified 7 key (hub) snoRNAs each for S. aureus-positive group (SNORA66, novelsnoRNA_26_14905 (also denoted as novelSnoRNA_86), SNORD107, SNORA1, SNORA63, SNORA79, SNORA76) and S. chromogenes-positive group (SNORD18, SNORA79, SNORA46, U2-19, SNORA66, SNORD37, SNORD49) that correlated with the most protein coding genes (|r| > 0.9; ≥ 30 mRNAs). Functional enrichment of correlated genes of hub snoRNAs reveals their involvement in immune related functions (75% of enriched terms) and metabolic processes (20% of enriched terms). Conclusion These data suggest potential regulatory roles for the DE snoRNAs and in particular, the 14 hub snoRNAs during subclinical mastitis. This study presents the first evidence linking snoRNAs to bovine subclinical mastitis and offers new insights into the molecular mechanisms underlying subclinical mastitis caused by S. aureus and S. chromogenes.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| 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) | 0.490 | 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 it