Foot and mouth disease virus (FMDV) infection in Indian cattle (Bos indicus): Profiling of serum microRNAs
Ontology highlight
ABSTRACT:
ORGANISM(S): Bos indicus
PROVIDER: GSE77489 | GEO | 2017/10/20
SECONDARY ACCESSION(S): PRJNA310627
REPOSITORIES: GEO
Similar Datasets
Project description:: Foot-and-mouth disease (FMD) is the most devastating disease of cloven-hoofed livestock, with a crippling economic burden in endemic areas and immense costs associated with outbreaks in free countries. Foot-and-mouth disease virus (FMDV), a picornavirus, will spread rapidly in naïve populations, reaching morbidity rates of up to 100% in cattle. Even after recovery, over 50% of cattle remain subclinically infected and infectious virus can be recovered from the nasopharynx. The pathogen and host factors that contribute to FMDV persistence are currently not understood. Using for the first time primary bovine soft palate multilayers in combination with proteogenomics, we analyzed the transcriptional responses during acute and persistent FMDV infection. During the acute phase viral RNA and protein was detectable in large quantities and in response hundreds of interferon-stimulated genes (ISG) were overexpressed, mediating antiviral activity and apoptosis. Although the number of pro-apoptotic ISGs and the extent of their regulation decreased during persistence, some ISGs with antiviral activity were still highly expressed at that stage. This indicates a long-lasting but ultimately ineffective stimulation of ISGs during FMDV persistence. Furthermore, downregulation of relevant genes suggests an interference with the extracellular matrix that may contribute to the skewed virus-host equilibrium in soft palate epithelial cells.
2019-01-17 | PXD012242 | Pride
Project description:The pathogen and host factors that contribute to the establishment of foot-and-mouth disease virus (FMDV) persistence are currently not understood. Using primary bovine soft palate multilayers in combination with RNA sequencing, we analyzed the transcriptional responses during acute and persistent FMDV infection.
2019-01-18 | E-MTAB-7605 | biostudies-arrayexpress
Project description:We used RNA-sequencing on the Illumina platform to analyze transcriptome profiles of BHK-21 acutely infected with FMDV. In total, we obtained more than 342.8 million raw sequencing reads. And approximately 336.5 million clean reads (98.14%) were acquired by filtering out the adapters and trimming ambiguous reads. We found that cellular response of BHK-21 is related to certain types of alterations in the host cell transcriptome profiles at 24 h post infection.
2018-12-20 | GSE124122 | GEO
Project description:India has 40 distinct zebuine cattle breeds with different adaptability and production traits. In the present study, we report the complete mitochondrial genome sequence of Indian cattle for the first time. The mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region (D-loop region). The phylogenetic analysis showed close genetic relationship among the Indian cattle breeds studied, where as, distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results will expand genomic information for further studies on evolution, domestication and conservation of indigenous cattle breeds in India.
| S-EPMC7801002 | biostudies-literature
Project description:In order to investigate the mechanisms of persistent foot-and-mouth disease virus (FMDV) infection in cattle, transcriptome alterations associated with the FMDV carrier state were characterized using a bovine whole-transcriptome microarray. Eighteen cattle (8 vaccinated with a recombinant FMDV A vaccine, 10 non-vaccinated) were challenged with FMDV A24 Cruzeiro, and the gene expression profiles of nasopharyngeal tissues collected between 21 and 35 days after challenge were compared between 11 persistently infected carriers and 7 non-carriers. Carriers and non-carriers were further compared to 2 naïve animals that had been neither vaccinated nor challenged. At a controlled false-discovery rate of 10% and a minimum difference in expression of 50%, 648 genes were differentially expressed between FMDV carriers and non-carriers, and most (467) had higher expression in carriers. Among these, genes associated with cellular proliferation and the immune response – such as chemokines, cytokines and genes regulating T and B cells – were significantly overrepresented. Differential gene expression was significantly correlated between non-vaccinated and vaccinated animals (biological correlation +0.97), indicating a similar transcriptome profile across these groups. Genes related to prostaglandin E2 production and type 2 immune polarization, as well as to the induction of regulatory T cells and T-cell exhaustion were overexpressed in carriers. In contrast, tissues from non-carrier animals expressed higher levels of complement regulators and pro-apoptotic genes that could promote virus clearance. Based on these findings, we propose that FMDV persistence in nasopharyngeal tissues of cattle is maintained by an impairment of apoptosis and the local suppression of cell-mediated antiviral immunity by inducible regulatory T cells.
2016-09-20 | GSE83514 | GEO
Project description:Foot-and-mouth disease (FMD) is a vesicular disease of cloven-hoofed animals with devastating economic implications. The current FMD vaccine, routinely used in enzootic countries, requires at least 7 days to induce protection. However, FMD vaccination is typically not recommended for use in non-enzootic areas, underscoring the need to develop new fast-acting therapies for FMD control during outbreaks. Interferons (IFNs) are among the immune system’s first line of defense against viral infections. Bovine type III IFN delivered by a replication defective adenovirus (Ad) vector has effectively blocked FMD in cattle. However, the limited duration of protection—usually only 1-3 days post-treatment (dpt)—diminishes its utility as a field therapeutic. Here we test whether polyethylene glycosylation (PEGylation) of recombinant bovine IFNλ3 (PEGboIFNλ3) can extend the duration of IFN-induced prevention of FMDV infection in both vaccinated and unvaccinated cattle. We treated groups of heifers with PEGboIFNλ3 alone or in combination with an adenovirus-based FMD O1Manisa vaccine (Adt-O1M) at either 3 or 5 days prior to challenge with homologous wild type FMDV. We found that pre-treatment with PEGboIFNλ3 was highly effective at preventing clinical FMD when administered at either time point, with or without co-administration of Adt-O1M vaccine. PEGboIFNλ3 protein was detectable systemically for >10 days and antiviral activity for 4 days following administration. Furthermore, in combination with Adt-O1M vaccine, we observed a strong induction of FMDV-specific IFNγ+ T cell response, demonstrating its adjuvanticity when co-administered with a vaccine. Our results demonstrate the promise of this modified IFN as a pre-exposure prophylactic therapy for use in emergency outbreak scenarios.
2024-03-30 | GSE262192 | GEO
Project description:Indian cattle (Bos indicus) and riverine buffalo (Bubalus bubalis) give a poor yield of milk but it has a high fat and protein percentage compared to taurine cattle. The identification of QTLs (Quantitative Trait Loci) on BTA14 and BTA6 and its subsequent fine mapping has led to identification of two non conservative mutations affecting milk production and composition. Our objective was to estimate the frequency of K232A (DGAT1--diacylglycerol-acyltransferase 1) and Y581S (ABCG2--ATP binding cassette sub family G member 2) polymorphisms in diverse cattle and buffalo breeds of India having large variation in terms of milk production.We screened the reported missense mutations in six cattle and five buffalo breeds. The DGAT1K and ABCG2Y alleles were found to be fixed in Indian cattle and buffalo breeds studied.This study provides an indirect evidence that all the Indian cattle and buffalo breeds have fixed alleles with respect to DGAT1 and ABCG2 genes reported to be responsible for higher milk fat yield, higher fat and protein percent.
| S-EPMC1636029 | biostudies-literature
Project description:BACKGROUND: Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and fertility in this breed. We present the first results of the implementation of genomic prediction in a Bos indicus (Nellore) population. METHODS: Influential bulls were genotyped with the Illumina Bovine HD chip in order to assess genomic predictive ability for weight and carcass traits, gestation length, scrotal circumference and two selection indices. 685 samples and 320 238 single nucleotide polymorphisms (SNPs) were used in the analyses. A forward-prediction scheme was adopted to predict the genomic breeding values (DGV). In the training step, the estimated breeding values (EBV) of bulls were deregressed (dEBV) and used as pseudo-phenotypes to estimate marker effects using four methods: genomic BLUP with or without a residual polygenic effect (GBLUP20 and GBLUP0, respectively), a mixture model (Bayes C) and Bayesian LASSO (BLASSO). Empirical accuracies of the resulting genomic predictions were assessed based on the correlation between DGV and dEBV for the testing group. RESULTS: Accuracies of genomic predictions ranged from 0.17 (navel at weaning) to 0.74 (finishing precocity). Across traits, Bayesian regression models (Bayes C and BLASSO) were more accurate than GBLUP. The average empirical accuracies were 0.39 (GBLUP0), 0.40 (GBLUP20) and 0.44 (Bayes C and BLASSO). Bayes C and BLASSO tended to produce deflated predictions (i.e. slope of the regression of dEBV on DGV greater than 1). Further analyses suggested that higher-than-expected accuracies were observed for traits for which EBV means differed significantly between two breeding subgroups that were identified in a principal component analysis based on genomic relationships. CONCLUSIONS: Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. Recurrent updates of the training population would be required to enable accurate prediction of the genetic merit of young animals. The technical feasibility of applying genomic prediction in a Bos indicus (Nellore) population was demonstrated. Further research is needed to permit cost-effective selection decisions using genomic information.
| S-EPMC4014866 | biostudies-other
Project description:Here we describe a custom FMDV microarray and a companion feature and template-assisted assembler software (FAT-assembler) capable of resolving virus genome sequence using a moderate number of conserved microarray features. The results demonstrate that this approach may be used to rapidly characterize naturally occurring FMDV as well as an engineered chimeric strain of FMDV. The FAT-assembler, while applied to resolving FMDV genomes, represents a new bioinformatics approach that should be broadly applicable to interpreting microarray genotyping data for other viruses or target organisms
2016-11-10 | GSE89283 | GEO
Project description:Malnad Gidda is one among the 43 registered cattle breeds of India with unique traits and spread over Western Ghats and coastal regions of Karnataka state in India. Selection of highly elite fertile bulls for the breeding purpose is a critical control point in animal breeding programmes. Therefore, to characterize the semen proteome and to understand the semen biology of this breed, a comprehensive proteomic analysis of spermatozoa and seminal plasma has been carried out by employing SCX and bRPLC fractionation strategies in a mass-spectrometry platform. The semen samples from three Malnad Gidda bulls maintained at Southern Regional Station of ICAR-NDRI under standard managemental conditions were used in the study. The proteomic characterisation of semen from Malnad Gidda breed resulted in the identification of 5, 84,520 PSMs, from 24,467 peptides from 2,815 proteins in spermatozoa and identification of 2, 77,583 PSMs from 12,047 peptides, which resulted in 1,974 proteins from seminal plasma. Out of 2,815 proteins in spermatozoa and 1,974 proteins from seminal plasma, 969 proteins were common to both seminal plasma and spermatozoa. The biological processes and cellular localization of spermatozoa proteins were studied using DAVID tool and were further enriched the identical GO terms using REVIGO online tool. The functional enrichment analysis of identified proteins indicated their roles in the biological processes like sperm motility, spermatid development, spermatogenesis, and so on. GO studies showed the commonalities and differences in the molecular functions of the proteins exclusively identified in spermatozoa, seminal plasma and common proteins. This is the first proteomic investigation conducted on the semen samples of an Indian indigenous breed; therefore, we believe that our preliminary data should significantly advance our understanding of semen proteome of Indian cattle.
2020-06-12 | PXD014172 | Pride