Piglet immune response genes
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ABSTRACT:
PROVIDER: PRJNA1205768 | ENA |
REPOSITORIES: ENA
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Project description:The study investigated the impact of environment on the composition of the gut microbiota and mucosal immune development and function at gut surfaces in early and adult life. Piglets of similar genotype were reared in indoor and outdoor environments and in an experimental isolator facility. Mucosa-adherent microbial diversity in the pig ileum was characterized by sequence analysis of 16S rRNA gene libraries. Host-specific gene responses in gut ileal tissues to differences in microbial composition were investigated using Affymetrix microarray technology and Real-time PCR. Experiment Overall Design: Animals were reared on the sow at an outdoor or indoor facility. Additional piglets from the indoor facility were transferred to individual isolator units at 24 hours of age, and given a daily dose of antibiotic cocktail for the duration of the study. Piglets were weaned at day 28. From day 29 onwards, piglets were fed creep feed ad libitum. Ileal tissue samples were excised from N=6 piglets per group at day 5, 28 and 56.
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of the expression of genes. The goals of this study are to reveal the mechanism of side effect of excess diet tryptophan in newborn piglets through optimal high-throughput data analysis. Methods: Liver mRNA profiles of newborn piglets feeded by different tryptophan mode were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the genes level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks and Then, differential expression genes analysis between these two groups (three biological replicates per condition) was performed using Cuffdiff. The P values were adjusted using the Benjamini & Hochberg method. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, we mapped about 30 to 40 million sequence reads per sample to the pig genome (build susScr3) and identified 11,314 transcripts in the liver of newborn piglets with TopHat workflow. RNA-seq data confirmed 88 different expressed genes between the High-Low group and the 2×Trp group, and 10 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR. Conclusions: Our study represents the first detailed analysis of liver transcriptomes of newborn piglets from the groups that sow feed by High-Low and the 2×Trp methods, with biologic replicates, generated by RNA-seq technology. Functional analyses of DEGs in livers revealed that certain genes associated with cellular stress and exogenous stimulus response were strongly associated with the dysfunction of liver metabolism in newborn piglets.
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Project description:Salmonella causes inflammation in infected hosts. Inflammation is a well-characterized defensive mechanism of innate immunity. The recognition and engagement of lipopolysaccharide (LPS) endotoxins in the outer membranes of Salmonella to Toll-like receptor 4 of immune cells (macrophages and dendritic cells) trigger inflammatory responses characterized by secretion of pro-inflammatory cytokines, including TNF-beta, IL-1 and IL-6. These cytokines cause fever, anorexia, bodyweight losses, and catabolism of skeletal muscles and adipose tissues. However, molecular events underlying innate immune responses and metabolic activities during the later stage of inflammation are poorly understood. Additionally, the effects of prebiotics and antibiotics on innate immunity and nutrient metabolism are not yet reported. The objective of this study is to investigate the effects of a mannanoligosaccharide (MOS) prebiotic and virginiamycin (VIRG) sub-therapeutic antibiotic on innate immunity and glucose metabolism during late inflammation. We induced Salmonella LPS-systemic inflammation in a chicken model. Differentially regulated gene expressions were measured using 2 colour focussed oligonucleotide chicken-specific microarrays. Microarray analysis was performed on liver, intestinal and skeletal muscle tissues. We found that late inflammation was principally modulated by interleukin 3 (IL 3) and that glucose was mobilized from gluconeogenesis occurring in the intestines only. MOS and VIRG modulated innate immunity and metabolic genes differently. In contrast to VIRG, MOS terminated inflammatory responses earlier. Our results indicate IL 3 gene up-regulation in VIRG-fed chickens. To meet the higher energy requirements of VIRG chickens, genes for intestinal gluconeogenesis and liver glycolysis were respectively induced. Our study reveals the potential mechanisms by which prebiotic and antibiotic modulated innate immunity and glucose metabolism during late inflammation. 14-day old chickens were injected i.p. with saline or LPS. For each tissue and experimental conditions (saline or LPS challenge), a total of 12 microarrays (6 MOS birds + 6 VIRG birds) were used in a 2 x 2 factorial design and complete interwoven loop arrangement. We compared gene expression from prebiotic-fed birds with antibiotic-fed birds without including reference RNA. LPS challenge, antibiotic or prebiotic, innate immunity, glucose metabolism
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