Targeted Transcriptome Analysis of Beef Cattle Persistently Infected with Bovine Viral Diarrhea Virus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1169059 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bovine Viral Diarrhea Virus (BVDV) is an endemic virus of North American cattle populations with significant economic and animal health impacts. While BVDV infection has a myriad of clinical manifestations, a unique and problematic outcome is the establishment of a persistently infected (PI) animal following in-utero viral infection. While it is well established that PI animals serve as a constant reservoir of BVDV, the mechanism for the maintained infection remains unknown despite multiple theories. The purpose of this study was to use transcriptome analysis to further define long term immune status of adult PI cattle and offer insight into the potential mechanistic establishment of persistent BVDV infection, in utero. Peripheral blood mononuclear cells were collected from PI beef cattle (N=6) and uninfected controls (N=6) for targeted RNAseq analysis conducted using 54 genes of interest and followed by pathway enrichment analysis. Analysis revealed 29 differentially expressed genes (FDR < 0.05, fold change > 2) representing 14 significant KEGG pathways between PI and control animals (FDR < 0.05). Transcriptome changes indicate chronic upregulation of interferon gamma (IFNG) with unexpected expression of related genes, suggesting a maintained stimulation of the PI immune system resulting in virus-mediated dysregulation of immune function.
2024-12-10 | GSE278855 | GEO
Project description:This study examined tolerance to hypoxia-induced pulmonary hypertension in yearling beef cattle raised at high elevation (7120 ft/2170m).
2021-01-23 | GSE164320 | GEO
Project description:We profiled blood transcriptomics of 24 beef steers at three important stages (Entry: on arrival at the feedlot; Pulled: when sickness is identified; and Close-out: recovered, healthy cattle at shipping to slaughter) to reveal the key biological functions and regulatory factors of BRD and identify gene markers of BRD for early diagnosis and potentially use in selection.
2020-12-31 | GSE150706 | GEO
Project description:Beef cattle multi-tissue transcriptome
| PRJNA480220 | ENA
Project description:The biological mechanisms associated with the residual feed intake in ruminants have been harnessed immensely via transcriptome analysis of liver and ruminal epithelium, however, this concept has not been fully explored using whole blood. We applied whole blood transcriptome analysis and gene set enrichment analysis to identify key pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261.3 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, weekly whole blood samples were collected three times from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.
2022-04-07 | GSE198068 | GEO
Project description:Objective: Classify and further validate BRD-associated genes and mechanisms found to be differentially expressed at facility arrival in post-weaned beef cattle from multiple independent populations. Our approach was to profile and compare at-arrival whole blood transcriptomes of post-weaned beef cattle that failed to develop symptoms associated with clinical BRD and cattle that ultimately were diagnosed and treated for clinical BRD within the first 28 days of facility arrival, further stratifying diseased animals into severity cohorts. Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina Novaseq 6000. Individual samples were processed using an adaptation of the Revised Tuxedo Suite protocol (Tuxedo 2), then analyzed in R using edgeR with likelihood-ratio testing. Genes were considered differentially expressed with an FDR cutoff of 0.05. Downstream analysis involved PCA, gene ontology term enrichment, pathway analysis, protein-protein interaction networking, and IPA. Results: 132 differentially expressed genes were identified between all three cohorts. Biological processes and pathways primarily involved neutrophilic activity, antimicrobial killing, cell cornification, and inflammatory signaling/regulation. Conlusions: This study corroborated genes and pathways identified in our previous work, while providing novel genes and pathways for future analysis.
2021-12-13 | GSE161396 | GEO
Project description:Beef cattle rumen microbiota raw sequence reads
| PRJNA941091 | ENA
Project description:Creatine pyruvate (CrPyr) is a new multifunctional nutrient that can provide both pyruvate and creatine. It has been shown to relieve the heat stress of beef cattle by improving antioxidant activity and rumen microbial protein synthesis, but the mechanism of CrPyr influencing rumen fermentation remains unclear. This study aimed to use metaproteomics technologies to investigate the bacterial protein function in rumen fluid samples taken from heat-stressed beef cattle treated with or without 60 g/d CrPyr.
2021-03-31 | PXD025118 |
Project description:This study seeks to determine the construction of calves' microbiomes per time point in beef cattle. Raw sequence reads
| PRJNA948924 | ENA
Project description:miRNA profiling of bovine satellite cells (BSC) differentiated into myotubes (6th day of in vitro differentiation). BSC isolated from m. semitendinosus of beef (Hereford & Limousine) and dairy (Holstein-Friesian) cattle. Goal was to determine differences in miRNA expresion during in vitro myogenesis in beef vs dairy cattle used as a control.
2018-01-27 | GSE73778 | GEO