Project description:Transcriptional profiling of chicken embryonic fibroblasts (DF-1 cells) comparing the effects of chicken cells transfected with duck RIG-I compared to empty-vector transfected cells following with low or highly pathogenic avian influenza. Goal was to determine the effects of duck RIG-I on influenza-induced immune gene expression.
Project description:Temporal regulation of gene expression is essential for early embryonic development. With the development of next-generation sequencing technologies, transcriptional profiling of early developmental processes in various vertebrates are already revealed. However, overall transcriptome analysis of early embryonic development in avian have never been investigated. In this study, to our knowledge, we provide comprehensive profiling of pre-oviposited embryos in chicken by whole-transcriptome RNA-seq for the first time. We demonstrated the presence of avian-specific mechanism of first- and second-wave of zygotic genome activation (ZGA). Chicken early embryo have distinct developmental programs between cleavage and area pellucida formation period. Additional speculation of epigenetic dynamics indicate that maternal-to-zygotic transition (MZT) in chicken is promoted after second-wave of ZGA, through EGK.VI to EGK.X stages. These extensive results contribute to understanding avian early embryogenesis and comparative studies with other species with many developmental aspects.
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.
Project description:Chicken brain and lung gene expression profiles following infection with two recombinant H5N3 avian influenza viruses - rH5N3 Ori (P0) and rH5N3 P6
Project description:We infected DF-1 cells with avian reovirus, and then used high-throughput sequencing to detect changes in miRNA expression profiles. This research provides a more comprehensive understanding of the interaction between viruses and host cells
Project description:Cerebrospinal fluid (CSF) proteins regulate neurogenesis, homeostasis and participate in active signalling during neuroinflammation. Components of CSF are mostly blood-derived, but partially also secreted from the brain cells. While various birds may represent suitable models for the investigation of adult constitutive neurogenesis, proteomic studies of the avian CSF examined so far solely chicken embryos. On this basis, we explored the proteomic composition of CSF and plasma in adult parrots, budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus) and chickens (Gallus gallus) using liquid chromatography–tandem mass spectrometry (nLC-MS/MS). To overcome the lack of a complete cockatiel genome information, we compared the MS/MS identification success rates after mapping all spectra from all three species against the reference proteomes of three model avian species: chicken, budgerigar and zebra finch. We show highest efficiency (8.8-4.7%) for the closest reference proteome, although part of the proteins (7.2-18%) were mapped only with other references. After filtering the selected datasets, we identified up to 746 proteins represented in the CSF and plasma of chicken, budgerigar and cockatiel. Enrichment analysis of the core proteome of these datasets revealed various metabolic and signalling pathways. Comparative analysis of CSF and plasma for each species then indicated clusters of proteins preferentially upregulated into CSF that were involved in neurogenesis, neural development and neural differentiation pathways. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel molecular evidence supporting the adult neurogenesis in birds.
