Additional file 4: of Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens

The common DEGs involved in two pathways (ECM-receptor interaction and Focal adhesion) in this study. (XLS 40 kb

Additional file 5: of Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens

The specific primers for q-PCR in this study. (XLS 57 kb

Additional file 4: of Decreased testosterone levels after caponization leads to abdominal fat deposition in chickens

The enriched pathways based on the 872 DEGs. (XLS 61 kb

Additional file 2: of Decreased testosterone levels after caponization leads to abdominal fat deposition in chickens

The enriched the GO-terms in the BP category based on 872 DEGs. (XLS 50 kb

Additional file 3: of Decreased testosterone levels after caponization leads to abdominal fat deposition in chickens

The 86 DEGs related to lipid metabolism using GO-terms analysis based on a total of 872 DEGs 45 up-regulated and 41 down-regulated. (XLS 75 kb

Additional file 1: of Decreased testosterone levels after caponization leads to abdominal fat deposition in chickens

872 DEGs between the capon and the control chicken groups. (XLS 311 kb

Additional file 5: of Decreased testosterone levels after caponization leads to abdominal fat deposition in chickens

Figure S1. The PPAR signaling pathway (JPG 109 kb

The structural science of functional materials

<p>Salmonella enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Controlling poultry SE infection will have great practical significance for human public health, as poultry are considered to be important sources and carriers of the disease. In this study, the splenic transcriptomes of challenged-susceptible (S), challenged-resistant (R) and non-challenged (C) chicks (3-days old, specific-pathogen-free White Leghorn) were characterized in order to identify the immune-related gene markers and pathways. A total of 934 significant differentially expressed genes (DEGs) were identified in comparisons among the C, R and S birds. First reported here, the DEGs involved in the Forkhead box O (FoxO) signaling pathway, especially FoxO3, were identified as potential markers for host resistance to SE infection. The challenged-susceptible birds exhibited strong activation of the FoxO signaling pathway, which may be a major defect causing immune cell apoptosis as part of SE-induced pathology; these S birds also showed weak activation of mitogen-activated protein kinase (MAPK)-related genes, contrasting with strong splenic activation in the R birds. Interestingly, suppression of several pathways in the immune response against Salmonella, including cytokine-cytokine receptor interaction and Jak-STAT, was only found in S birds and there was evidence of cross-talk among these pathways, perhaps contributing to susceptibility to Salmonella infection. These findings will help facilitate understanding resistance and susceptibility to SE infection in the earliest phases of the host immune response through Salmonella-induced pathways, provide new approaches to develop strategies for SE prevention and treatment, and may enhance innate resistance by genetic selection in animals.</p

Image_2_Messenger RNA Sequencing and Pathway Analysis Provide Novel Insights Into the Susceptibility to Salmonella enteritidis Infection in Chickens.TIF

<p>Salmonella enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Controlling poultry SE infection will have great practical significance for human public health, as poultry are considered to be important sources and carriers of the disease. In this study, the splenic transcriptomes of challenged-susceptible (S), challenged-resistant (R) and non-challenged (C) chicks (3-days old, specific-pathogen-free White Leghorn) were characterized in order to identify the immune-related gene markers and pathways. A total of 934 significant differentially expressed genes (DEGs) were identified in comparisons among the C, R and S birds. First reported here, the DEGs involved in the Forkhead box O (FoxO) signaling pathway, especially FoxO3, were identified as potential markers for host resistance to SE infection. The challenged-susceptible birds exhibited strong activation of the FoxO signaling pathway, which may be a major defect causing immune cell apoptosis as part of SE-induced pathology; these S birds also showed weak activation of mitogen-activated protein kinase (MAPK)-related genes, contrasting with strong splenic activation in the R birds. Interestingly, suppression of several pathways in the immune response against Salmonella, including cytokine-cytokine receptor interaction and Jak-STAT, was only found in S birds and there was evidence of cross-talk among these pathways, perhaps contributing to susceptibility to Salmonella infection. These findings will help facilitate understanding resistance and susceptibility to SE infection in the earliest phases of the host immune response through Salmonella-induced pathways, provide new approaches to develop strategies for SE prevention and treatment, and may enhance innate resistance by genetic selection in animals.</p

Biological processes of the differentially expressed proteins identified for three stages.

<p>The identified proteins were grouped into 15 categories according to their biological process for every stage (GO term with P-value < 0.05). Glucose and intermediary metabolism, muscle development, translation and protein folding were the major biological processes from day 1 to 56, day 56 to 98, and day 98 to 140.</p