Gallus gallus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA101769 | ENA |
REPOSITORIES: ENA
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Project description:Aflatoxin is a toxic secondary metabolite produced by the fungi Aspergillus flavus and A. parasiticus. Ingredients of livestock and poultry feed are often contaminated with aflatoxin. Aflatoxin affects many species including humans, dogs, cats, pigs, cattle, and poultry, with liver being the major organ affected. A chicken model was used to evaluate the effect of aflatoxin on hepatic gene expression. Seventy five day-old male broiler chicks were assigned to three dietary treatments (5 replicates of 5 chicks each) from hatch to day 21. The diets contained 0, 1 and 2 mg/kg aflatoxin/kg of feed. Feed intake, body weight gain, liver weights and serum chemistry were evaluated at the end of the study and liver samples were collected in RNase free tubes and stored at -80 ºC. Aflatoxin reduced (P ≤ 0.05) feed intake, body weight, serum total proteins, serum calcium and phosphorus but increased (P < 0.01) liver weights in a dose dependent manner. Microarray experiments were conducted using chicken long oligo arrays, to identify the changes in hepatic gene expression in chicks fed 0 (control) and 2mg/kg aflatoxin/kg of feed. A loop design was followed for microarray experiments with three technical and four biological replicates per treatment group. RNA was extracted from liver tissue and its quality was determined using gel electrophoresis. High quality RNA was purified from DNA contamination, reverse transcribed to cDNA and was used for microarray hybridizations. Microarray data was analyzed using a 2-step ANOVA model using GenePix and MAANOVA softwares, and the differentially expressed genes were identified using SAM, TIGR, and Cluster softwares. The microarray data was validated using real time PCR. It is hypothesized that genes associated with antioxidant, detoxification and immune systems were downregulated and the genes involved in cell proliferation were up-regulated in birds fed aflatoxin compared to controls Keywords: aflatoxin, chicken liver, microarrays, gene expression
2007-07-31 | GSE8603 | GEO
Project description:With the development of the poultry industry, ammonia, as a main contaminant in the air, is causing increasing problems with broiler health. To date, most studies of ammonia toxicity have focused on the nervous system and the gastrointestinal tract in mammals. However, few detailed studies have been conducted on the hepatic response to ammonia toxicity in poultry. The molecular mechanisms that underlie these effects remain unclear. In the present study, our group applied isobaric tags for relative and absolute quantitation (iTRAQ) - based quantitative proteomic analysis to investigate changes in the protein profile change in hepatic tissue of broilers exposed to high concentrations of atmospheric ammonia, with the goal of characterizing the molecular mechanisms of chronic liver injury from exposure to high ambient levels of ammonia. Overall, 30 differentially expressed proteins that are involved in nutrient metabolism (energy, lipid and amino acid), immune response, transcriptional and translational regulation, stress response and detoxification were identified. In particular, two of these proteins, beta-1 galactosidase (GLB1), and a kinase (PRKA) anchor protein 8-like (AKAP8 L), were previously suggested to be potential biomarkers of chronic liver injury. In addition to the changes in the protein profile, serum parameters and histochemical analyses of hepatic tissue also showed extensive hepatic damage in ammonia-exposed broilers. Altogether, these findings suggest that longtime exposure to high concentrations of atmospheric ammonia can trigger chronic hepatic injury in broilers via different mechanisms, providing new information that can be used for intervention using nutritional strategies in the future.
2016-06-15 | PXD001670 | Pride
Project description:Copy number variation profiles comparing control female Dehong chicken blood DNA with 3 different chicken breeds (white Leghorn, Cobb broiler, and Dou chicken) blood DNA. Each test breed had one male and one female sample, for a total of 6 test DNA samples. The goal is to determine the global copy number variation profiles between chicken breeds.
2011-04-12 | GSE28526 | GEO
Project description:We report the hepatic response of broiler chickens to an increase in stocking density. Here we compare gene expression profiles of liver cells via RNA-seq of broiler chicken raised under a high stocking density to broiler chickens raised under a lower stocking density with the objective of this study being to identify biomarkers of stress before the clinical and economic impacts are observed. We found that increasing stocking density seems to have a unique impact on hepatic gene expression prior to eliciting common clinical signs associated with stress. The cellular functions that are most affected appear to be those involved in steroidogenesis and cell movement/migration as identified by RNA-seq analysis of the liver transcriptome. These results could provide a baseline of information that future research to identify genes or molecules that could aid in the detection of negative effects of stressors such as stocking density prior to negative clinical and economic signs presenting themselves.
2021-04-12 | GSE171864 | GEO
Project description:The expression of genes were analysed in 7th 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.
2014-10-17 | GSE62443 | GEO
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.
2014-10-17 | GSE62444 | GEO
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: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.
2010-04-02 | E-GEOD-21167 | biostudies-arrayexpress
Project description:Gene expression profile of chicken lung in response to Avian influenza virus challenge in broiler chickens
| PRJNA168147 | ENA
Project description:Relative expression levels of mRNAs in chicken cecal epithelia experimentally infected with Eimeria tenella were measured at 4.5 days post-infection. Two weeks old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of Eimeria tenella. Cecal epithelia samples were collected from >12 birds in infected or uninfected group at 4.5 d following infections, in which samples from 4 birds were pooled together to form a total 3 biological replicates in each group. Parasite merozoites were also collected from four infected chickens at 5 d after infections. Uninfected control samples, merozoites and infection group samples were selected for RNA extraction and hybridization on Affymetrix microarrays. We used Affymetrix GeneChip chicken genome arrays to detail the chicken cecal epithelia gene expression in the control and E. tenella-infected birds.
2012-12-10 | GSE39602 | GEO