Similar Datasets
Project description:We report the effect of binding of AliB-like ORF 1 peptide on the transcriptome and proteome of nonencapsulated pneumococci
2019-10-31 | E-MTAB-8289 | biostudies-arrayexpress
Project description:Campylobacter jejuni is a common cause of diarrheal disease worldwide. Human infection typically occurs through the ingestion of contaminated poultry products. We previously demonstrated that an attenuated Escherichia coli live vaccine strain expressing the C. jejuni N-glycan on its surface reduces the Campylobacter load in more than 50% of vaccinated leghorn and broiler birds to undetectable levels (responder birds), whereas the remainder of the animals were still colonized (non-responders). To understand the underlying mechanism, we conducted 3 larger scale vaccination and challenge studies using 135 broiler birds and found a similar responder/non responder effect. The submitted data were used for a genome-wide association study of the chicken responses to glycoconjugate vaccination against Campylobacter jejuni.
2021-11-01 | GSE181619 | GEO
Project description:Beak deformities (BD) of different forms have been documented in many wild birds. The phenomenon is termed as “the largest epizootic of gross abnormalities ever recorded among wild bird populations.” Frequencies of 1% to 3% of BD (crossed beaks) were found in several indigenous chickens including Silkies, Qingyuan Partridge, Huxu, and the Beijing-You (BJY) chickens (studied here). Birds with deformed beaks have poor production performance and induce higher mortality. Therefore, BD represents an economic as well as a welfare problem. Our lab have focused and performed studies on this complex trait/disease for 7 years. Therefore, we performed a single SNP, a pathways-based genome-wide association study (GWAS), and a genome-wide CNV detection with the genotype data of 48 BD (case) and 48 normal (control) birds from Affymetrix 600K HD genotyping arrays, using ROADTRIPS, SNP ratio test (SRT) and PennCNV, respectively. To the best of our knowledge, this is the first GWAS and CNV study to investigate the mutations and genomic structural variations in the deformed and normal beaks of chickens. The findings herein are worth of further functional characterization for better understanding the genetic mechanisms of BD in chickens and wild birds as well.
2017-07-21 | GSE101703 | GEO
Project description:Birds have a sex chromosome system in which females are heterogametic (ZW) and males are homogametic (ZZ). The differentiation of avian sex chromosomes from ancestral autosomes entailed the loss of most genes from the W chromosome during evolution. However, to what extent mechanisms evolved that counterbalance the consequences of this extensive gene dosage reduction in female birds has remained unclear. Here we report functional in vivo and evolutionary analyses of a Z-chromosome-linked microRNA (miR-2954) with strongly male-biased expression that was previously proposed to play a key role in sex chromosome dosage compensation1. We knocked out miR-2954 in chicken, which resulted in early embryonic lethality of homozygous knockout males, likely due to the highly specific upregulation of dosage-sensitive Z-linked target genes of miR-2954. Our evolutionary gene expression analyses further revealed that these dosage-sensitive target genes have become upregulated on the single Z in female birds during evolution. Altogether, our work unveils a scenario where evolutionary pressures on females following W gene loss led to the evolution of transcriptional upregulation of dosage-sensitive genes on the Z not only in female but also in male birds. The resulting overabundance of transcripts in males resulting from the combined activity of two dosage-sensitive Z gene copies was in turn offset by the emergence of a highly targeted miR-2954-mediated transcript degradation mechanism during avian evolution. Our findings demonstrate that birds have evolved a unique sex chromosome dosage compensation system in which a microRNA has become essential for male survival.
2024-04-17 | GSE257549 | GEO
Project description:The project aims at taxonomy of extinct and extant birds using proteomics.
2019-05-20 | PXD009204 | Pride
Project description:Transcriptomics analysis reveals that severity of infectious bursal disease in White Leghorn inbred chicken lines is associated with greater bursal inflammation in vivo and more rapid induction of pro-inflammatory responses following ex vivo stimulation of primary bursal cells. In order to better understand differences in the outcome of infectious bursal disease virus (IBDV) infection, we inoculated very virulent (vv) IBDV into White Leghorn chickens from inbred line W that previously had over 24% mortality, and three inbred lines (15I, C.B4 and O) that previously had 0% mortality. Within each experimental group, some individuals experienced more severe disease than others but line 15I birds experienced milder disease based on average clinical scores, percentage of birds with gross pathology, average bursal lesion scores and average peak bursal virus titre. RNA-Seq analysis revealed that more severe disease was associated with a significant up-regulation of pathways involved in inflammation, cytoskeletal regulation by Rho GTPase, nicotinic acetylcholine receptor signaling, and Wnt signaling in the bursa. Primary bursal cells cultured from line W birds and stimulated ex vivo with LPS had a more rapid up-regulation of pro-inflammatory gene expression than cells from line 15I birds, and line W birds had a significantly greater percentage of KUL01+ macrophage cells in the BF than line 15I birds. We hypothesize that a more rapid induction of pro-inflammatory cytokine responses in line W birds causes excessive inflammation and clinical disease following IBDV infection compared to line 15I, and we suggest that pro-inflammatory pathways could be targeted to engineer more disease resistant birds in the future
2021-06-02 | GSE166026 | GEO
Project description:Background: Avian infectious bronchitis (IB) is an acute and highly contagious disease of the upper-respiratory tract caused by infectious bronchitis virus (IBV). Understanding the molecular mechanisms involved in the interaction between innate and adaptive immune responses to IBV infection is a crucial element for further improvements in strategies to control IB. To this end, two chicken lines, selected for high and low serum concentration of mannose-binding lectin (MBL), a soluble pattern recognition receptor, were studied. In total, 32 birds from each line (designated L10H for high and L10L for low MBL serum concentration, respectively) were used. Sixteen birds from each line were infected with IBV at 3 weeks of age and sixteen birds were left uninfected. Eight uninfected and eight infected birds from each line were euthanized at 1 and 3 weeks post infection. RNA sequencing was performed on spleen samples from all 64 birds used in the experiment. Differential gene expression analysis was performed for four comparisons: L10L line versus L10H line for uninfected birds at weeks 1 and 3, respectively, and L10L line versus L10H line for infected birds at weeks 1 and 3, respectively. Functional analysis based on the differentially expressed genes was performed using Gene Ontology (GO) Immune System Process terms specific for Gallus gallus. Results: Comparing uninfected L10H and L10L birds, we identified 1698 and 1424 differentially expressed (DE) genes at weeks 1 and 3, respectively. For the IBV-infected birds, 1934 and 866 DE genes were identified between the two lines at weeks 1 and 3, respectively. In both cases DE genes had FDR-adjusted p-value <0.05. The two most enriched GO terms emerging from the comparison of uninfected birds between the two lines were “Lymphocyte activation involved in immune response” (GO:0002285) and “Somatic recombination of immunoglobulin genes involved in immune response” (GO:0002204) at weeks 1 and 3, respectively. When comparing IBV-infected birds between the two lines, the most enriched GO terms were “Alpha-beta T cell activation” (GO:0046631) and “Positive regulation of leukocyte activation” (GO:0002696) at weeks 1 and 3, respectively. Conclusion: Healthy birds from the two lines showed significant differences in expression profiles for subsets of both adaptive and innate immunity-related genes, whereas comparison of the IBV-infected birds from the two lines showed differences in expression of immunity-related genes involved in T cell activation and proliferation. The observed transcriptome differences between the two lines indicate that selection for MBL had a much wider effect than solely on serum MBL concentration, and in addition influenced the innate and adaptive immune responses. Future research will focus on identifying signatures of selection in order to further understand molecular pathways be responsible for differences between the two lines as well as for efficient IBV immune protection.
2016-01-25 | GSE73423 | GEO
Project description:Carbapenemase-producing Enterobacteriaceae (CPE) were almost nonexistent up to the 1990s, but are today encountered routinely in hospitals and other healthcare facilities in many countries including the United States. KPC-producing Klebsiella pneumoniae was the first to emerge and spread globally and is endemic in the United States, Israel, Greece, and Italy. Recently, NDM-producing Enterobacteriaceae and OXA-48-producing K. pneumoniae appear to be disseminating from South Asia and Northern Africa, respectively. They are almost always resistant to all ?-lactams including carbapenems and many other classes. Mortality from invasive CPE infections reaches up to 40%. To obtain the maximal benefit from the limited options available, dosing of antimicrobial agents should be optimized based on pharmacokinetic data, especially for colistin and carbapenems. In addition, multiple observational studies have associated combination antimicrobial therapy with lower mortality compared with monotherapy for these infections. The outcomes appear to be especially favorable when patients are treated with a carbapenem and a second agent such as colistin, tigecycline, and gentamicin, but the best approach is yet to be defined.
| S-EPMC4470611 | biostudies-literature
Project description:Purpose: This study would be useful to characterize the molecular mechanisms of an effective anti-bacterial response of chicken immune system. Methods: meat-type chickens were either infected with APEC O1 or given saline as a control. Thymii were collected on 1 and 5 days post-infection (dpi). The infected birds were classified based upon necropsy findings as having mild or severe pathology, representing resistant and susceptible phenotypes, respectively. Data from RNA sequencing experiments were analyzed using the R package, edgR, to identify the significantly differentially expressed (DE) genes. GO and pathway analysis using the R package GOseq identified many immune-related pathways. Results: Thousands of genes were DE at 5 dpi in susceptible vs. non-infected birds and in susceptible vs. resistant birds, as well as in susceptible birds at 1 vs. 5 dpi. In the contrast of susceptible birds with resistant or non-challenged birds, many immune response and signal transduction pathways were strongly induced, whereas the TCR signaling pathway was deeply suppressed to affect T cell development, differentiation, proliferation, and maturation. The transcriptomes of resistant and non-challenged birds were similar. Conclusions: These results provide the first comprehensive assessment of global gene networks and biological functionalities of DE genes in thymus in response to APEC infection, thus providing novel insights into key molecular genetic mechanisms that differentiate host resistance from susceptibility in this primary lymphoid tissue. These findings are foundational to the development of strategies to enhance host resistance to APEC infection.
2017-02-09 | GSE69014 | GEO