Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1104621 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28815607_1.fastq.gz | Fastqsanger.gz | |||
| SRR28815608_1.fastq.gz | Fastqsanger.gz | |||
| SRR28815609_1.fastq.gz | Fastqsanger.gz | |||
| SRR28815610_1.fastq.gz | Fastqsanger.gz | |||
| SRR28815611_1.fastq.gz | Fastqsanger.gz |
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Project description:The purpose of this study was to investigate the effects of high levels of Tenebrio molitor dietary inclusion (15%) on molecular mechanisms that influence poultry health in a broiler chicken diet.
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Project description:Optimization of broiler chicken breast muscle protein accretion is key for the efficient production of poultry meat, whose demand is steadily increasing. In a context where antimicrobial growth promoters use is being restricted, it is important to find alternatives as well as to characterize the effect of immunological stress on broiler chicken growth. Despite of its importance, research on broiler chicken muscle protein dynamics has been mostly limited to the study of mixed protein turnover. The present study aims to characterize the effect of a bacterial challenge and the feed supplementation of a citrus and a cucumber extract on broiler chicken individual breast muscle proteins fractional synthesis rates (FSR) using a recently developed dynamic proteomics pipeline. 21 day-old broiler chickens were administered a single 2H2O dose before being culled at different timepoints. A total of 60 breast muscle protein extracts from five experimental groups (Unchallenged, Challenged, Control Diet, Diet 1 and Diet 2) were analyzed using a DDA proteomics approach. Proteomics data was filtered in order to reliably calculate multiple proteins FSR making use of a newly developed bioinformatics pipeline. Broiler breast muscle proteins FSR uniformly decreased following a bacterial challenge, this change was judged significant for 15 individual proteins, the two major functional clusters identified as well as for mixed breast muscle protein. Citrus or cucumber extract feed supplementation did not show any effect on the breast muscle protein FSR of immunologically challenged broilers. The present study has identified potential predictive markers of breast muscle growth and provided new information on broiler chicken breast muscle protein turnover which could be essential for improving the efficiency of broiler chicken meat production.
2024-04-04 | PXD044325 | Pride
Project description:Understanding and manipulating the avian gastrointestinal tract, where nutrient absorption and vital host-pathogen interactions occur, is critical for improving poultry health and productivity. To advance research in this area, chicken three-dimensional intestinal enteroid models have been developed and characterised. In this study, we report a comprehensive transcriptome atlas for 43,587 intestinal enteroid cells derived from broiler and layer chickens. Our analyses reveal clusters representing mesenchymal, epithelial, endothelial, immune and neuronal cell lineages. We classified the mesenchymal lineage into nine populations, including fibroblasts, telocytes, myofibroblasts, smooth myocytes, pericytes, and interstitial cells of Cajal, reflecting anatomically distinct intestinal layers. We identified significant heterogeneity within the epithelial lineage, including enterocytes, goblet cells, Paneth cells, tuft cells, and various enteroendocrine cell subtypes. Additionally, we provide evidence for populations of macrophages, monocytes, γδT cell, NK cells, heterophils and dendritic cells. Differential gene expression tests between layer and broiler enteroids revealed extensive cell type-specific variation, pointing at differences in immune function and appetite regulation, with the most pronounced changes in epithelial cell types. Overall, this study offers a cell-resolved perspective of chicken three-dimensional intestinal enteroids, uncovering extensive heterogeneity masked by bulk transcriptomics. Additionally, we provide a catalogue of cell-specific marker genes to explore the function and organization of the chicken gastrointestinal tract.
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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.
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Project description:Bacterial infections remain an important cause of morbidity in poultry production. The molecular characteristics and dynamic changes in immune cell populations after bacterial infection have yet to be fully understood. Beijing-You chicken and Cobb broiler, two broiler breeds with different disease resistance, were infected with Salmonella typhimurium, and inflammation models were constructed. We characterized chicken spleen CD45+ immune cells by single-cell RNA sequencing.
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Project description:The expression of genes were analysed in muscle of 18th day of embryonic stage between Aseel, an indigenous slow-growing chicken, and control broiler, a fast-growing broiler chicken line. The whole embryo was collected in TRIZOL and total RNA was isolated. The expression profile of gene was determined in 64k Agilent chicken microarray chip. The Cy3 dye was used for detection. The fold change of expression was analysed in Aseel as compared to broiler chicken line.
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Project description:An experiment was conducted to investigate the effects of dietary inclusion of rye, a model ingredient to increase gut viscosity, between 14 and 28 days of age on immune competence related parameters and performance of broiler. A total number of 960 one-day-old male Ross 308 chicks were weighed and randomly allocated to 24 pens (40 birds per pen), and the birds in every 8 replicate pens were assigned to one of three experimental diets including graded levels, 0%, 5%, and 10% of rye. Tested immune competence related parameters were composition of the intestinal microbiota, genes expression in gut tissue, and gut morphology. The inclusion of 5% or 10% rye in the diet (d14-28) resulted in decreased performance and litter quality, but in increased villus height and crypt depth in the small intestine (jejunum) of the broilers. Relative bursa and spleen weights were not affected by dietary inclusion of rye. In the jejunum, no effects on number and size of goblet cells, and only trends on microbiota composition in the digesta were observed. Dietary inclusion of rye affected expression of genes involved in cell cycle processes of the jejunal enterocyte cells, thereby influencing cell growth, cell differentiation and cell survival, which in turn were consistent with the observed differences in the morphology of the gut wall. In addition, providing rye-rich diets to broilers affected the complement and coagulation pathways, which are parts of the innate immune system. These pathways are involved in eradicating invasive pathogens. Overall, it can be concluded that inclusion of 5% or 10% rye to the grower diet of broilers had limited effects on performance. Ileal gut morphology, microbiota composition of jejunal digesta, and gene expression profiles of jejunal tissue, however, were affected by dietary rye inclusion level, indicating that rye supplementation to broiler diets might affect immune competence of the birds.
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