Pasteurellaceae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA824533 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bovine respiratory disease pathogens of Pasteurellaceae species Genome sequencing and assembly
| PRJNA605035 | ENA
Project description:Bovine Respiratory Disease pathogens from Pasteurellaceae family
| PRJNA720670 | ENA
Project description:Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the well-being and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. Therefore, this study utilized multi-omics data (genomics, transcriptomics, and metabolomics) analyses to study the associations between genome, transcriptome, metabolome, and BRD phenotype of feedlot crossbred cattle. The findings may be useful for the development of genomic selection strategies for BRD susceptibility, and for the development of new diagnostic and therapeutic tools.
2023-01-11 | GSE217317 | GEO
Project description:Bovine Respiratory Syncytial Virus (BRSV) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in respiratory tissues. If these changes are observed in tissues which are accessible in live animals, such as whole blood, they may be used as biomarkers of the disease. Therefore, the objective of the current study was to elucidate the whole blood transcriptomic response to an experimental challenge with BRSV, in dairy calves. Holstein-Friesian calves were either inoculated with virus (103.5 TCID50/ml x 15 ml) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). Clinical signs were scored daily and whole blood was collected in Tempus RNA tubes immediately prior to euthanasia, at day 7 post-challenge. RNA was extracted from blood and sequenced (150 bp paired-end). Sequence reads were aligned to the UMD3.1 bovine reference genome and differential gene expression analysis was performed using EdgeR. An MDS plot displayed an obvious separation between BRSV challenged and control calves based on whole blood gene expression changes, despite an observed mild clinical manifestation of the disease. There were 281 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. The top enriched KEGG pathways and gene ontology terms were associated with viral infection and included “Influenza A”, “defense response to virus”, “regulation of viral life cycle” and “innate immune response”. Highly DE genes involved in these pathways are may be beneficial for the diagnosis of subclinical BRD from blood samples.
2021-05-05 | GSE152959 | GEO
Project description:Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). The objective of this study was to elucidate the chromatin regions which were differentially open in the bronchial lymph nodes (BLN) of dairy calves experimentally challenged with BRSV, relative to unchallenged control calves. Holstein-Friesian calves were either challenged with BRSV inoculum (n=12) or mock challenged with PBS (n=6). Calves were euthanised on day 7 post-challenge. ATAC-Seq libraries were prepared from fresh BLN tissues and sequenced (75 bp paired-end). Sequence reads were aligned to the UMD3.1 reference genome and peak calling (q < 0.01) was performed with MACS2, employing the BAMPE model. Using Diffbind, 9,144 and 5,096 differentially accessible peaks were identified between BRSV challenged and control calves (P < 0.05, FDR < 0.05) using DeSeq2 and EdgeR, respectively. There were 169 and 110 genes previously found to be differentially expressed using RNA-Seq located within or up to 2kb upstream of the differentially accessible peaks identified by the DeSeq 2 and EdgeR analyses, respectively. There were 237 differentially accessible peaks positioned within 40 previously identified susceptibility loci for BRD. These open chromatin regions are likely involved in the gene transcriptional and regulatory response to infection by BRSV.
2021-01-13 | GSE148056 | GEO
Project description:Jugular whole blood samples (Tempus Blood RNA tubes) were collected and utilized from 43 cattle, specifically from all cattle diagnosed with bovine respiratory disease (BRD) during Texas backgrounding (n=32) and randomly selected cattle never treated for BRD (n=11). Total RNA was isolated from blood samples, and were library prepared and sequenced via Illumina NovaSeq 6000 S4 chemistry. Samples were bioinformatically processed in a HISAT2/StringTie2 pipeline, and stratified based on BRD diagnosis and marketing strategy (Auction versus Direct marketing and transport). Differential expression analysis was conducted in R, utilizing an additive, multifactor generalized linear model and blocking for Mississippi pasture and vaccination status. Genes were considered differentially expressed with an FDR cutoff of 0.05. The objective of this study was to identify differentially expressed genes and mechanisms within and across marketing cohorts with and without BRD.
2023-03-09 | GSE218061 | GEO
Project description:Bovine Herpesvirus 1 (BoHV-1) is a leading cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Therefore, the objective of the current study was to elucidate the whole blood mRNA transcriptomic response to an experimental challenge with BoHV-1, in dairy calves. Holstein-Friesian calves were either challenged by intranasal atomisation with BoHV1 virus (6.3 x 10^7/mL x 1.35mL) (n=12) or mock challenged with sterile phosphate buffered saline (n=6). Clinical signs were scored daily until euthanasia at day 6 post-challenge. Total RNA was extracted and sequenced from whole blood (100 bp paired-end). Sequence reads were aligned to the ARS-UCD1.2 bovine reference genome and differential gene expression analysis was performed using EdgeR. An MDS plot displayed an obvious separation between BoHV-1 challenged and control calves based on the gene expression changes in whole blood. There were 488 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BoHV-1 challenged and control calves.
2022-08-19 | GSE199108 | GEO
Project description:<p><b>Public health importance</b>: Babies born preterm, approximately 1 out of every 9 live births in the United States, have significant respiratory morbidity over the first two years of life, exacerbated by respiratory viral infections. Many (<50%) return to pediatricians, emergency rooms and pulmonologists with symptoms of respiratory dysfunction (SRD): intermittent or chronic wheezing, poor growth and an excess of upper and lower respiratory tract infections (LRTI). SRD correlate inversely with gestational age and weight at birth and is more common in those with chronic lung disease of prematurity, yet its incidence and severity varies widely among both the prematurely born and those born at term. There is evidence from clinical studies and animal models that risks of LRTI and recurrent wheezing is influenced by gut and respiratory flora and by T cell responses to infection. Information gained from this study will be used to identify characteristics, risk factors and potential mechanisms for early and persistent lung disease in children born at term and born preterm.</p> <p>This Clinical Research Study will investigate the relationships between sequential respiratory viral infections, patterns of intestinal and respiratory bacterial colonization, and adaptive cellular immune phenotypes which are associated with increased susceptibility to respiratory infections and long term respiratory morbidity in preterm and full term infants. We hypothesize that the timing and acquisition of specific viral infections and bacterial species are directly related to respiratory morbidity in the first year of life as defined by SRD and by measures of pulmonary function. We hypothesize that cellular and molecular immuno-maturity are altered due to factors presented by premature birth in such a way as to promote chronic inflammatory and cytotoxic damage to the lung, with subsequent enhanced, damaging responses to infectious agents and environmental irritants. Our preliminary studies demonstrate both feasibility and expertise in mutiparameter immunophenotyping of small volume peripheral blood samples obtained from premature infants including gene expression arrays of flow cytometry sorted cells. We will use new technologies for known viral identification, as well as high-throughput metagenome sequencing of RNA and DNA virus like particles (VLP) to be used for viral discovery in infant respiratory sample and use of high-throughput pyrosequencing (454T) of bacterial 16S rRNA to determine shifts in bacterial community structure, occurring in pre-term (PT) as compared to full term (FT) infants, over the first year of life. Finally, we present statistical approaches to stratify disease risk predictors using multivariate logistic regression modeling approaches. We propose to evaluate T cell phenotypic and functional profiles relative to viral and predominant bacterial exposures according to highly complementary, but independent, Specific Objectives.</p> <p><b>Objective 1</b>: To determine if viral respiratory infections and patterns of respiratory and gut bacterial community structure (microbiome) in prematurely born babies predict the rate and degree of immunologic maturation, and pulmonary dysfunction, measured from birth to 36 weeks corrected gestational age (CGA).</p> <p><b>Objective 2</b>: To determine the relationship between respiratory viral infections and disease severity up to one year CGA, and the lymphocyte (Lc) phenotypes documented at term gestation (birth for term infants and 36 wks/NICU discharge in preterm infants) and at one year CGA. Three secondary outcomes of this objective will be to a) relate the quantity, type and severity of viral infections with pulmonary function at one and three years of life, b) relate the viral community structure to severity of viral infections and c) to seek evidence of modulation of viral susceptibility by bacterial respiratory and gut community structure (microbiome). The relationship of colonization with known and non-identified bacterial species in both the respiratory tract and the gut will be evaluated. </p>
| phs001347 | dbGaP
Project description:Bovine Pasteurella multocida (P. multocida) serotype A is considered to be one of the major causes of bovine respiratory disease (BRD), while its secretory proteins remain poorly understood. In this study, we employed data-independent acquisition (DIA) LC-MS/MS combined with bioinformatics analysis to obtain more comprehensive and accurate information on proteins secreted by P. multocida. A total of 154 proteins were obtained from the supernatants of two isolates of bovine P. multocida serotype A (high virulent PmCQ2 and low virulent PmCQ6) cultured in Martin or BHI media，and 52 putative secretory proteins were identified.
2022-11-02 | PXD037882 |
Project description:Bovine respiratory epithelial cells have different susceptibility to bovine
respiratory syncytial virus infection. The cells derived from the lower
respiratory tract were significantly more susceptible to the virus than those
derived from the upper respiratory tract. Pre-infection with virus of lower
respiratory tract with increased adherence of P. multocida; this was not the
case for upper tract. However, the molecular mechanisms of enhanced
bacterial adherence are not completely understood. To investigate whether
virus infection regulates the cellular adherence receptor on bovine trachea-,
bronchus- and lung-epithelial cells, we performed proteomic analyses.
2020-07-28 | PXD019509 | JPOST Repository