Differentially Expressed Genes in Blood from Young Pigs between Two Swine Lines Divergently Selected for Feed Efficiency: Potential Biomarkers for Improving Feed Efficiency

The goal of this study was to find potential gene expression biomarkers in blood of piglets that can be used to predict pigs’ future feed efficiency. Using RNA-seq technology, we found 453 genes were differentially expressed (false discovery rate (FDR) ≤ 0.05) in the blood of two Yorkshire lines of pigs divergently selected for feed efficiency (FE) based on residual feed intake (RFI). Genes involved in several biosynthetic processes were overrepresented among genes more highly expressed in the low RFI line compared to the high RFI line. Weighted gene co-expression network analysis (WGCNA) also revealed genes involved in some of these biosynthesis processes and having similar patterns of expression formed clusters. The average expression in the clusters was highly associated with lines (p \u3c 3.9E-07, R2 \u3e 0.59). Current findings implied these biosynthesis pathways might be more active in the high RFI line. After further stringent validation, some of the differentially expressed genes (DEGs) will be selected for validation as biomarkers for feed efficiency

Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae

BACKGROUND: Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution. RESULTS: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution was distinctly non-uniform. Although both Pseudoviridae and Metaviridae tend to cluster within pericentromeric heterochromatin, this association is significantly more pronounced for all three Metaviridae sublineages (Metavirus, Tat and Athila). Among these, Tat and Athila are strictly associated with pericentromeric heterochromatin. CONCLUSIONS: The non-uniform genomic distribution of the Pseudoviridae and the Metaviridae can be explained by a variety of factors including target-site bias, selection against integration into euchromatin and pericentromeric accumulation of elements as a result of suppression of recombination. However, comparisons based on the age of elements and their chromosomal location indicate that integration-site specificity is likely to be the primary factor determining distribution of the Athila and Tat sublineages of the Metaviridae. We predict that, like retroelements in yeast, the Athila and Tat elements target integration to pericentromeric regions by recognizing a specific feature of pericentromeric heterochromatin

Feeding Behavior of Yorkshire Pigs Selected for Residual Feed Intake

Feeding behavior traits were evaluated in Yorkshire gilts from the fourth generation of the ISU residual feed intake (RFI) selection experiment. Gilts were fed using FIRE feeders. Compared to the randomly selected control line, pigs from the line selected for lower RFI, had lower residual feed intake, ate less per day, spent less time eating per day, and ate faster per visit, regardless of whether analysis was over the whole test period, the first half of test period, or the second half of test period. In conclusion, selection for lower RFI has significantly changed feeding behavior, which could be part of the reason why they are more efficient

Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium

To elucidate the host transcriptional response to Salmonella enterica serovar Typhimurium, Affymetrix porcine GeneChip analysis of pig mesenteric lymph nodes was used to identify 848 genes showing differential expression across different times after inoculation or when compared to non-inoculated controls. Annotation analyses showed that a high proportion of these differentially expressed (DE) genes are involved in immune and inflammatory responses. T helper 1, innate/inflammatory, and antigen-processing pathways were induced at 24 h post-inoculation (hpi) and/or 48 hpi, while apoptosis and antigen presentation/dendritic cell function pathways were downregulated at 8 hpi. Cluster analyses revealed that most DE genes annotated as NFκB targets were grouped into a specific induced subcluster, while many translation-related DE genes were found in a repressed subcluster. Quantitative polymerase chain reaction analyses confirmed the Affymetrix results, revealing transcriptional induction of NFκB target genes at 24 hpi and suppression of the NFκB pathway from 24 to 48 hpi. We propose that such NFκB suppression in antigen-presenting cells may be the mechanism by which S. Typhimurium eludes a strong inflammatory response to establish a carrier status in pigs

Analysis of Porcine Transcriptional Response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the Mesenteric Lymph Node

<p>Abstract</p> <p>Background</p> <p>Specific knowledge of the molecular pathways controlling host-pathogen interactions can increase our understanding of immune response biology as well as provide targets for drug development and genetic improvement of disease resistance. Toward this end, we have characterized the porcine transcriptional response to <it>Salmonella enterica </it>serovar Choleraesuis (<it>S</it>. Choleraesuis), a <it>Salmonella </it>serovar that predominately colonizes swine, yet can cause serious infections in human patients. Affymetrix technology was used to screen for differentially expressed genes in pig mesenteric lymph nodes (MLN) responding to infection with <it>S</it>. Choleraesuis at acute (8 hours (h), 24 h and 48 h post-inoculation (pi)) and chronic stages (21 days (d) pi).</p> <p>Results</p> <p>Analysis of variance with false discovery rate control identified 1,853 genes with significant changes in expression level (<it>p</it>-value < 0.01, <it>q</it>-value < 0.26, and fold change (FC) > 2) during infection as compared to un-inoculated control pigs. Down-regulation of translation-related genes at 8 hpi and 24 hpi implied that <it>S</it>. Choleraesuis repressed host protein translation. Genes involved in the Th1, innate immune/inflammation response and apoptosis pathways were induced significantly. However, antigen presentation/dendritic cell (DC) function pathways were not affected significantly during infection. A strong NF<it>κ</it>B-dependent response was observed, as 58 known NF<it>κ</it>B target genes were induced at 8, 24 and/or 48 hpi. Quantitative-PCR analyses confirmed the microarray data for 21 of 22 genes tested. Based on expression patterns, these target genes can be classified as an "Early" group (induced at either 8 or 24 hpi) and a "Late" group (induced only at 48 hpi). Cytokine activity or chemokine activity were enriched within the Early group genes GO annotations, while the Late group was predominantly composed of signal transduction and cell metabolism annotated genes. Regulatory motif analysis of the human orthologous promoters for both Early and Late genes revealed that 241 gene promoters were predicted to contain NF<it>κ</it>B binding sites, and that of these, 51 Early and 145 Late genes were previously not known to be NF<it>κ</it>B targets.</p> <p>Conclusion</p> <p>Our study provides novel genome-wide transcriptional profiling data on the porcine response to <it>S</it>. Choleraesuis and expands the understanding of NF<it>κ</it>B signaling in response to <it>Salmonella </it>infection. Comparison of the magnitude and timing of porcine MLN transcriptional response to different <it>Salmonella </it>serovars, <it>S</it>. Choleraesuis and <it>S</it>. Typhimurium, clearly showed a larger but later transcriptional response to <it>S</it>. Choleraesuis. Both microarray and QPCR data provided evidence of a strong NF<it>κ</it>B-dependent host transcriptional response during <it>S</it>. Choleraesuis infection. Our data indicate that a lack of strong DC-mediated antigen presentation in the MLN may cause <it>S</it>. Choleraesuis infected pigs to develop a systemic infection, and our analysis predicts nearly 200 novel NF<it>κ</it>B target genes which may be applicable across mammalian species.</p

Kinetic Profile of Chicken Macrophage Immune Response upon exposure to Salmonella-derived Endotoxin

Large scale gene expression studies expedite the discovery process and provide a comprehensive view of host immune response. We used the Affymetrix GeneChip chicken genome array to determine the nature and breadth of the gene activation elicited by endotoxin from Salmonella typhimirium (ST) 798. The data obtained from this type of research are important to improve vaccine development efficacy and to enhance animal health and food safety. Our findings may contribute to elucidation of disease response pathways

Prevention of Mycobacterium avium Subspecies paratuberculosis (MAP) Infection in Balb/c mice by Feeding Lactobacillus acidophilus Strain NP-51®

The immune responses of 390 BALB/c mice fed the probiotic Lactobacillus acidophilus strain NP51 ® and infected with Mycobacterium avium subspecies paratuberculosis (MAP) were evaluated in a 6-month trial. Mice were randomized to nine treatment groups that fed either viable- or heat-killed NP51 and inoculated with either viable- or heatkilled MAP or sterile phosphate-buffered saline. Feeding the NP51 resulted in higher numbers of T lymphocytes in the spleen including the CD8 + cytotoxic T lymphocytes. In addition, feeding the NP51 lowered the number of immune suppressive T regulatory cells CD4 + CD25 + and CD8 + CD25 + cells in the spleen. Additionally, feeding the NP51 resulted in higher concentration of interferon-gamma in the supernatant of splenocytes cultured in vitro. These results suggest that feeding the NP51 to BALB/c mice might prevent the progression of MAP infection in mice