Exploring splice variants in milk leukocytes of dairy cows with subclinical intramammary infection due to Prototheca spp. and Streptococcus agalactiae
Bibliographic record
Abstract
Alternative splicing events lead to different mRNA isoforms, potentially translated into proteins with altered structures or impaired functions, or both. This phenomenon may influence the resistance or susceptibility to diseases, such as mastitis. To explore this aspect, this study aims to analyze transcript expression, focusing on cases where multiple mRNA isoforms are present, in milk somatic cells from Holstein cattle affected by subclinical intramammary infection caused by Prototheca spp. (P+, n = 11) or Streptococcus agalactiae (Sa+, n = 11), compared with uninfected animals (Neg, n = 9). The RNA-sequencing data were analyzed using the CLC Genomics Workbench (23.0.5, Qiagen) with a large gap read mapping approach and Bos taurus ARS-UCD1.3 reference genome to identify the differentially expressed transcripts (DET) among the groups. In addition, a functional analysis of the identified DET, combined with the identification of functional variants within the expressed regions, was performed. The comparison P+ versus Neg revealed 27 annotated DET, 11 annotated DET with novel length, and 7 novel DET with no previously annotated associated gene or length. These DET mainly originated from immune-related genes involved in pathways strictly linked to the immune and inflammatory responses (i.e., antigen presentation pathway, MHC class II antigen presentation pathway, macrophage classical activation signaling pathway). In contrast, the Sa+ versus Neg comparison revealed a total of 26 DET, including 17 annotated transcripts, 8 annotated transcripts with a novel length, and 1 novel transcript from a nonannotated gene. In this case, a predominance of enriched pathways related to metabolism and detoxification processes was observed (i.e., FXR/RXR activation, xenobiotic metabolism general signaling pathway, glutathione-mediated detoxification). Functional variants were identified in regions overlapping DET encoded by KRT78, CSN1S1, and MYBPC1, which were downregulated in P+ when compared with Neg group and potentially related to mastitis resistance/susceptibility traits. The transcripts and associated functional variants identified in this study may contribute to a better understanding of bovine mastitis pathogenesis and development, providing useful insights for improving animal health and management strategies.
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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".