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Item Heat Stress and Lipopolysaccharide Stimulation of Chicken Macrophage-Like Cell Line Activates Expression of Distinct Sets of Genes(Public Library Science, 10/13/16) Slawinska,Anna; Hsieh,John C.; Schmidt,Carl J.; Lamont,Susan J.; Anna Slawinska, John C. Hsieh, Carl J. Schmidt, Susan J. Lamont; Schmidt, Carl JAcute heat stress requires immediate adjustment of the stressed individual to sudden changes of ambient temperatures. Chickens are particularly sensitive to heat stress due to Developmentelopment of insufficient physiological mechanisms to mitigate its effects. One of the symptoms of heat stress is endotoxemia that results from release of the lipopolysaccharide (LPS) from the guts. Heat-related cytotoxicity is mitigated by the innate immune system, which is comprised mostly of phagocytic cells such as monocytes and macrophages. The objective of this study was to analyze the molecular responses of the chicken macrophage-like HD11 cell line to combined heat stress and lipopolysaccharide treatment in vitro. The cells were heat-stressed and then allowed a temperature-recovery period, during which the gene expression was investigated. LPS was added to the cells to mimic the heat-stress-related endotoxemia. Semi high-throughput gene expression analysis was used to study a gene panel comprised of heat shock proteins, stress-related genes, signaling molecules and immune response genes. HD11 cell line responded to heat stress with increased mRNA abundance of the HSP25, HSPA2 and HSPH1 chaperones as well as DNAJA4 and DNAJB6 co-chaperones. The anti-apoptotic gene BAG3 was also highly up-regulated, providing evidence that the cells expressed pro-survival processes. The immune response of the HD11 cell line to LPS in the heat stress environment (up-regulation of CCL4, CCL5, IL1B, IL8 and iNOS) was higher than in thermoneutral conditions. However, the peak in the transcriptional regulation of the immune genes was after two hours of temperature-recovery. Therefore, we propose the potential influence of the extracellular heat shock proteins not only in mitigating effects of abiotic stress but also in triggering the higher level of the immune responses. Finally, use of correlation networks for the data analysis aided in discovering subtle differences in the gene expression (i.e. the role of the CASP3 and CASP9 genes).Item Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences(Biomed Central Ltd, 10/19/16) Fleming,D. S.; Koltes,J. E.; Fritz-Waters,E. R.; Rothschild,M. F.; Schmidt,C. J.; Ashwell,C. M.; Persia,M. E.; Reecy,J. M.; Lamont,S. J.; D. S. Fleming, J. E. Koltes, E. R. Fritz-Waters, M. F. Rothschild, C. J. Schmidt, C. M. Ashwell, M. E. Persia, J. M. Reecy and S. J. Lamont; Schmidt, Carl JBackground: Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within-and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation. Results: Downstream fixation test (FST) analysis and subsequent gene ontology (GO) enrichment analysis elucidated major differences between the two lines. The genes with high FST values for both breeds were used to identify enriched gene ontology terms. Over-enriched GO annotations were uncovered for functions indicative of breed-related traits of pathogen resistance and reproductive ability for Fayoumi and Leghorn, respectively. Conclusions: Variant analysis elucidated GO functions indicative of breed-predominant phenotypes related to genomic variation in the lines, showing a possible link between the genetic variants and breed traits.Item Liver transcriptome response to hyperthermic stress in three distinct chicken lines(Biomed Central LTD, 11/22/16) Lan,Xi; Hsieh,John C. F.; Schmidt,Carl J.; Zhu,Qing; Lamont,Susan J.; Xi Lan, John C. F. Hsieh, Carl J. Schmidt, Qing Zhu, Susan J. Lamont; Schmidt, Carl J.Background: High ambient temperatures cause stress in poultry, especially for broiler lines, which are genetically selected for rapid muscle growth. RNA-seq technology provides powerful insights into environmental response from a highly metabolic tissue, the liver. We investigated the effects of acute (3 h, 35 degrees C) and chronic (7d of 35 degrees C for 7 h/d) heat stress on the liver transcriptome of 3-week-old chicks of a heat-susceptible broiler line, a heat-resistant Fayoumi line, and their advanced intercross line (AIL). Results: Transcriptome sequencing of 48 male chickens using Illumina HiSeq 2500 technology yielded an average of 33.9 million, 100 base-pair, single-end reads per sample. There were 8 times more differentially expressed genes (DEGs) (FDR < 0.05) in broilers (n = 627) than Fayoumis (n = 78) when comparing the acute-heat samples to the control (25 degrees C) samples. Contrasting genetic lines under similar heat treatments, the highest number of DEGs appeared between Fayoumi and broiler lines. Principal component analysis of gene expression and analysis of the number of DEGs suggested that the AIL had a transcriptomic response more similar to the Fayoumi than the broiler line during acute heat stress. The number of DEGs also suggested that acute heat stress had greater impact on the broiler liver transcriptome than chronic heat stress. The angiopoietin-like 4 (ANGPTL4) gene was identified as differentially expressed among all 6 contrasts. Ingenuity Pathway Analysis (IPA) created a novel network that combines the heat shock protein family with immune response genes. Conclusions: This study extends our understanding of the liver transcriptome response to different heat exposure treatments in distinct genetic chicken lines and provides information necessary for breeding birds to be more resilient to the negative impacts of heat. The data strongly suggest ANGPTL4 as a candidate gene for improvement of heat tolerance in chickens.Item A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes(BioMed Central, 2004) Pitel, F.; Abasht, Behnam; Morisson, M.; Crooijmans, R. P.; Vignoles, F.; Leroux, S.; Feve, K.; Bardes, S.; Milan, D.; Lagarrigue, S.; Groenen, M. A.; Douaire, M.; Vignal, A.; Pitel, F., Abasht, B., Morisson, M., Crooijmans, R. P., Vignoles, F., Leroux, S., Feve, K., Bardes, S., Milan, D., Lagarrigue, S., Groenen, M. A., Douaire, M., Vignal, A.; Abasht, BehnamThe resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5.Item Mapping quantitative trait loci affecting fatness and breast muscle weight in meat-type chicken lines divergently selected on abdominal fatness(EDP Sciences, 2006) Lagarrigue, S.; Pitel, F.; Carre, W.; Abasht, Behnam; Le Roy, P.; Neau, A.; Amigues, Y.; Sourdioux, M.; Simon, Jean; Cogburn, Larry A.; Aggrey, S. E. (Samuel E.); Leclercq, B.; Vignal, A.; Douaire, M.; Lagarrigue, S., , Pitel, F., Carre, W., Abasht, B., Le Roy, P., Neau, A., Amigues, Y., Sourdioux, M., Simon, J., Cogburn, L., Aggrey, S., Leclercq, B., Vignal, A., Douaire, M.; Carre, W.; Abasht, Behnam; Cogburn, Larry A.Quantitative trait loci (QTL) for abdominal fatness and breast muscle weight were investigated in a three-generation design performed by inter-crossing two experimental meattype chicken lines that were divergently selected on abdominal fatness. A total of 585 F2 male offspring from 5 F1 sires and 38 F1 dams were recorded at 8 weeks of age for live body, abdominal fat and breast muscle weights. One hundred-twenty nine microsatellite markers, evenly located throughout the genome and heterozygous for most of the F1 sires, were used for genotyping the F2 birds. In each sire family, those offspring exhibiting the most extreme values for each trait were genotyped. Multipoint QTL analyses using maximum likelihood methods were performed for abdominal fat and breast muscle weights, which were corrected for the effects of 8-week body weight, dam and hatching group. Isolated markers were assessed by analyses of variance. Two significant QTL were identified on chromosomes 1 and 5 with effects of about one within-family residual standard deviation. One breast muscle QTL was identified on GGA1 with an effect of 2.0 within-family residual standard deviation.Item Fatness QTL on chicken chromosome 5 and interaction with sex(EDP Sciences, 2006) Abasht, Behnam; Pitel, F.; Lagarrigue, S.; Le Bihan-Duval, Elisabeth; Le Roy, P.; Demeure, O.; Vignoles, F.; Simon, Jean; Cogburn, Larry A.; Aggrey, S. E. (Samuel E.); Vignal, A.; Douaire, M.; Abasht, B., Pitel, F., Lagarrigue, S., Le Bihan-Duval, E., Le Roy, P., Demeure, O., Vignoles, F., Simon, J., Cogburn, L., Aggrey, S., Vignal, A., Douaire, M.; Abasht, Behnam; Cogburn, Larry A.Quantitative trait loci (QTL) affecting fatness in male chickens were previously identified on chromosome 5 (GGA5) in a three-generation design derived from two experimental chicken lines divergently selected for abdominal fat weight. A new design, established from the same pure lines, produced 407 F2 progenies (males and females) from 4 F1-sire families. Body weight and abdominal fat were measured on the F2 at 9 wk of age. In each sire family, selective genotyping was carried out for 48 extreme individuals for abdominal fat using seven microsatellite markers from GGA5. QTL analyses confirmed the presence of QTL for fatness on GGA5 and identified a QTL by sex interaction. By crossing one F1 sire heterozygous at the QTL with lean line dams, three recombinant backcross 1 (BC1) males were produced and their QTL genotypes were assessed in backcross 2 (BC2) progenies. These results confirmed the QTL by sex interaction identified in the F2 generation and they allow mapping of the female QTL to less than 8 Mb at the distal part of the GGA5. They also indicate that fat QTL alleles were segregating in both fat and lean lines.Item Extent and consistency of linkage disequilibrium and identification of DNA markers for production and egg quality traits in commercial layer chicken populations(BioMed Central, 2009) Abasht, Behnam; Sandford, E.; Arango, J.; Settar, P.; Fulton, J. E.; O’Sullivan, N. P.; Hassen, A.; Habier, D.; Fernando, R. L.; Dekkers, J. C. M.; Lamont, S. J.; Abasht, B., Sandford, E., Arango, J., Settar, P., Fulton, J. E., O’Sullivan, N. P., Hassen, A.,, Habier, D., Fernando, R. L., Dekkers, J. C. M., Lamont, S. J.; Abasht, BehnamThe genome sequence and a high-density SNP map are now available for the chicken and can be used to identify genetic markers for use in marker-assisted selection (MAS). Effective MAS requires high linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), and sustained marker- QTL LD over generations. This study used data from a 3,000 SNP panel to assess the level and consistency of LD between single nucleotide polymorphisms (SNPs) over consecutive years in two egg-layer chicken lines, and analyzed one line by two methods (SNP-wise association and genome-wise Bayesian analysis) to identify markers associated with egg-quality and egg-production phenotypes.Item Using transcriptome profiling to characterize QTL regions on chicken chromosome 5(BioMed Central, 2009) Le Mignon, G.; Pitel, F.; Desert, C.; Leroux, S.; Demeure, O.; Guernec, G.; Abasht, Behnam; Douaire, M.; Le Roy, P.; Lagarrigue, S.; Le Mignon, G., Pitel, F., Desert, C., Leroux, S., Demeure, O., Guernec, G., Abasht, Behnam, Douaire, M., Le Roy, P., Lagarrigue, S.; Abasht, BehnamAlthough many QTL for various traits have been mapped in livestock, location confidence intervals remain wide that makes difficult the identification of causative mutations. The aim of this study was to test the contribution of microarray data to QTL detection in livestock species. Three different but complementary approaches are proposed to improve characterization of a chicken QTL region for abdominal fatness (AF) previously detected on chromosome 5 (GGA5).Item PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways(BioMed Central Ltd., 2015-05-19) Zhu, Yongnan; Sun, Liang; Garbarino, Alexander; Schmidt, Carl; Fang, Jinglong; Chen, Jian; Yongnan Zhu, Liang Sun, Alexander Garbarino, Carl Schmidt, Jinglong Fang and Jian Chen; Sun, Liang; Schmidt, CarlBackground High-throughput methods are generating biological data on a vast scale. In many instances, genomic, transcriptomic, and proteomic data must be interpreted in the context of signaling and metabolic pathways to yield testable hypotheses. Since humans can interpret visual information rapidly, a means for interactive visual exploration that lets biologists interpret such data in a comprehensive and exploratory manner would be invaluable. However, humans have limited memory capacity. Current visualization tools have limited viewing and manipulation capabilities to address complex data analysis problems, and visual exploratory tools are needed to reduce the high mental workload imposed on biologists. Results We present PathRings, a new interactive web-based, scalable biological pathway visualization tool for biologists to explore and interpret biological pathways. PathRings integrates metabolic and signaling pathways from Reactome in a single compound graph visualization, and uses color to highlight genes and pathways affected by input data. Pathways are available for multiple species and analysis of user-defined species or input is also possible. PathRings permits an overview of the impact of gene expression data on all pathways to facilitate visual pattern finding. Detailed pathways information can be opened in new visualizations while maintaining the overview, that form a visual exploration provenance. A dynamic multi-view bubbles interface is designed to support biologists’ analytical tasks by letting users construct incremental views that further reflect biologists’ analytical process. This approach decomposes complex tasks into simpler ones and automates multi-view management. Conclusions PathRings has been designed to accommodate interactive visual analysis of experimental data in the context of pathways defined by Reactome. Our new approach to interface design can effectively support comparative tasks over substantially larger collection than existing tools. The dynamic interaction among multi-view dataset visualization improves the data exploration. PathRings is available free at http://raven.anr.udel.edu/~sunliang/PathRings webcite and the source code is hosted on Github: https://github.com/ivcl/PathRings webcite.Item Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing(BioMed Central Ltd., 2015-05-21) Mutryn, Marie F.; Brannick, Erin M.; Fu, Weixuan; Lee, William R.; Abasht, Behnam; Marie F Mutryn, Erin M Brannick, Weixuan Fu, William R Lee and Behnam Abasht; Mutryn, Marie F.; Brannick, Erin M.; Fu, Weixuan; Abasht, BehnamBackground Improvements in poultry production within the past 50 years have led to increased muscle yield and growth rate, which may be contributing to an increased rate and development of new muscle disorders in chickens. Previously reported muscle disorders and conditions are generally associated with poor meat quality traits and have a significant negative economic impact on the poultry industry. Recently, a novel myopathy phenotype has emerged which is characterized by palpably “hard” or tough breast muscle. The objective of this study is to identify the underlying biological mechanisms that contribute to this emerging muscle disorder colloquially referred to as “Wooden Breast”, through the use of RNA-sequencing technology. Methods We constructed cDNA libraries from five affected and six unaffected breast muscle samples from a line of commercial broiler chickens. After paired-end sequencing of samples using the Illumina Hiseq platform, we used Tophat to align the resulting sequence reads to the chicken reference genome and then used Cufflinks to find significant changes in gene transcript expression between each group. By comparing our gene list to previously published histology findings on this disorder and using Ingenuity Pathways Analysis (IPA®), we aim to develop a characteristic gene expression profile for this novel disorder through analyzing genes, gene families, and predicted biological pathways. Results Over 1500 genes were differentially expressed between affected and unaffected birds. There was an average of approximately 98 million reads per sample, across all samples. Results from the IPA analysis suggested “Diseases and Disorders” such as connective tissue disorders, “Molecular and Cellular Functions” such as cellular assembly and organization, cellular function and maintenance, and cellular movement, “Physiological System Development and Function” such as tissue development, and embryonic development, and “Top Canonical Pathways” such as, coagulation system, axonal guidance signaling, and acute phase response signaling, are associated with the Wooden Breast disease. Conclusions There is convincing evidence by RNA-seq analysis to support localized hypoxia, oxidative stress, increased intracellular calcium, as well as the possible presence of muscle fiber-type switching, as key features of Wooden Breast Disease, which are supported by reported microscopic lesions of the disease.Item RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism(PLOS (Public Library of Science), 2015-10-07) Resnyk, Christopher W.; Chen, Chuming; Huang, Hongzhan; Wu, Cathy H.; Simon, Jean; Le Bihan-Duval, Elisabeth; Duclos, Michel J.; Cogburn, Larry A.; Christopher W. Resnyk, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Jean Simon, Elisabeth Le Bihan-Duval, Michel J. Duclos, Larry A. Cogburn; Resnyk, Christopher W.; Chen, Chuming; Huang, Hongzhan; Wu, Cathy H.; Cogburn, Larry A.Genetic selection for enhanced growth rate in meat-type chickens (Gallus domesticus) is usually accompanied by excessive adiposity, which has negative impacts on both feed efficiency and carcass quality. Enhanced visceral fatness and several unique features of avian metabolism (i.e., fasting hyperglycemia and insulin insensitivity) mimic overt symptoms of obesity and related metabolic disorders in humans. Elucidation of the genetic and endocrine factors that contribute to excessive visceral fatness in chickens could also advance our understanding of human metabolic diseases. Here, RNA sequencing was used to examine differential gene expression in abdominal fat of genetically fat and lean chickens, which exhibit a 2.8-fold divergence in visceral fatness at 7 wk. Ingenuity Pathway Analysis revealed that many of 1687 differentially expressed genes are associated with hemostasis, endocrine function and metabolic syndrome in mammals. Among the highest expressed genes in abdominal fat, across both genotypes, were 25 differentially expressed genes associated with de novo synthesis and metabolism of lipids. Over-expression of numerous adipogenic and lipogenic genes in the FL chickens suggests that in situ lipogenesis in chickens could make a more substantial contribution to expansion of visceral fat mass than previously recognized. Distinguishing features of the abdominal fat transcriptome in lean chickens were high abundance of multiple hemostatic and vasoactive factors, transporters, and ectopic expression of several hormones/receptors, which could control local vasomotor tone and proteolytic processing of adipokines, hemostatic factors and novel endocrine factors. Over-expression of several thrombogenic genes in abdominal fat of lean chickens is quite opposite to the pro-thrombotic state found in obese humans. Clearly, divergent genetic selection for an extreme (2.5–2.8-fold) difference in visceral fatness provokes a number of novel regulatory responses that govern growth and metabolism of visceral fat in this unique avian model of juvenile-onset obesity and glucose-insulin imbalance.Item RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism(Public Library of Science (PLOS), 2015-10-07) Resnyk, Christopher W.; Chen, Chuming; Huang, Hongzhan; Wu, Cathy H.; Simon, Jean; Le Bihan-Duval, Elisabeth; Duclos, Michel J.; Cogburn, Larry A.; Christopher W. Resnyk, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Jean Simon, Elisabeth Le Bihan-Duval, Michel J. Duclos, Larry A. Cogburn; Resnyk, Christopher W.; Chen, Chuming; Huang, Hongzhan; Wu, Cathy H.; Cogburn, Larry A.Genetic selection for enhanced growth rate in meat-type chickens (Gallus domesticus) is usually accompanied by excessive adiposity, which has negative impacts on both feed efficiency and carcass quality. Enhanced visceral fatness and several unique features of avian metabolism (i.e., fasting hyperglycemia and insulin insensitivity) mimic overt symptoms of obesity and related metabolic disorders in humans. Elucidation of the genetic and endocrine factors that contribute to excessive visceral fatness in chickens could also advance our understanding of human metabolic diseases. Here, RNA sequencing was used to examine differential gene expression in abdominal fat of genetically fat and lean chickens, which exhibit a 2.8-fold divergence in visceral fatness at 7 wk. Ingenuity Pathway Analysis revealed that many of 1687 differentially expressed genes are associated with hemostasis, endocrine function and metabolic syndrome in mammals. Among the highest expressed genes in abdominal fat, across both genotypes, were 25 differentially expressed genes associated with de novo synthesis and metabolism of lipids. Over-expression of numerous adipogenic and lipogenic genes in the FL chickens suggests that in situ lipogenesis in chickens could make a more substantial contribution to expansion of visceral fat mass than previously recognized. Distinguishing features of the abdominal fat transcriptome in lean chickens were high abundance of multiple hemostatic and vasoactive factors, transporters, and ectopic expression of several hormones/receptors, which could control local vasomotor tone and proteolytic processing of adipokines, hemostatic factors and novel endocrine factors. Over-expression of several thrombogenic genes in abdominal fat of lean chickens is quite opposite to the pro-thrombotic state found in obese humans. Clearly, divergent genetic selection for an extreme (2.5–2.8-fold) difference in visceral fatness provokes a number of novel regulatory responses that govern growth and metabolism of visceral fat in this unique avian model of juvenile-onset obesity and glucose-insulin imbalance.Item Models and Methods to Investigate Acute Stress Responses in Cattle(MDPI AG, 2015-12-03) Chen, Yi; Arsenault, Ryan; Napper, Scott; Griebel, Philip; Yi Chen, Ryan Arsenault, Scott Napper and Philip Griebel; Arsenault, RyanThere is a growing appreciation within the livestock industry and throughout society that animal stress is an important issue that must be addressed. With implications for animal health, well-being, and productivity, minimizing animal stress through improved animal management procedures and/or selective breeding is becoming a priority. Effective management of stress, however, depends on the ability to identify and quantify the effects of various stressors and determine if individual or combined stressors have distinct biological effects. Furthermore, it is critical to determine the duration of stress-induced biological effects if we are to understand how stress alters animal production and disease susceptibility. Common stress models used to evaluate both psychological and physical stressors in cattle are reviewed. We identify some of the major gaps in our knowledge regarding responses to specific stressors and propose more integrated methodologies and approaches to measuring these responses. These approaches are based on an increased knowledge of both the metabolic and immune effects of stress. Finally, we speculate on how these findings may impact animal agriculture, as well as the potential application of large animal models to understanding human stress.Item Chicken-Specific Kinome Array Reveals that Salmonella enterica Serovar Enteritidis Modulates Host Immune Signaling Pathways in the Cecum to Establish a Persistence Infection(MDPI, 2016-07-27) Kogut, Michael H.; Swaggerty, Christina L.; Byrd, James Allen; Selvaraj, Ramesh; Arsenault, Ryan J.; Michael H. Kogut, Christina L. Swaggerty, James Allen Byrd, Ramesh Selvaraj and Ryan J. Arsenault; Arsenault, Ryan JNon-typhoidal Salmonella enterica induces an early, short-lived pro-inflammatory response in chickens that is asymptomatic of clinical disease and results in a persistent colonization of the gastrointestinal (GI) tract that transmits infections to naïve hosts via fecal shedding of bacteria. The underlying mechanisms that control this persistent colonization of the ceca of chickens by Salmonella are only beginning to be elucidated. We hypothesize that alteration of host signaling pathways mediate the induction of a tolerance response. Using chicken-specific kinomic immune peptide arrays and quantitative RT-PCR of infected cecal tissue, we have previously evaluated the development of disease tolerance in chickens infected with Salmonella enterica serovar Enteritidis (S. Enteritidis) in a persistent infection model (4–14 days post infection). Here, we have further outlined the induction of an tolerance defense strategy in the cecum of chickens infected with S. Enteritidis beginning around four days post-primary infection. The response is characterized by alterations in the activation of T cell signaling mediated by the dephosphorylation of phospholipase c-!1 (PLCG1) that inhibits NF-B signaling and activates nuclear factor of activated T-cells (NFAT) signaling and blockage of interferon-! (IFN-!) production through the disruption of the JAK-STAT signaling pathway (dephosphorylation of JAK2, JAK3, and STAT4). Further, we measured a significant down-regulation reduction in IFN-! mRNA expression. These studies, combined with our previous findings, describe global phenotypic changes in the avian cecum of Salmonella Enteritidis-infected chickens that decreases the host responsiveness resulting in the establishment of persistent colonization. The identified tissue protein kinases also represent potential targets for future antimicrobial compounds for decreasing Salmonella loads in the intestines of food animals before going to market.Item Editorial: Gut Health: The New Paradigm in Food Animal Production(Frontiers Media S.A, 2016-08-31) Kogut, Michael H.; Arsenault, Ryan J.; Michael H. Kogut and Ryan J. Arsenault; Arsenault, Ryan J.Item Detection of genomic signatures of recent selection in commercial broiler chickens(Biomed Central Ltd, 2016-12) Fu,Weixuan; Lee,William R.; Abasht,Behnam; Weixuan Fu, William R Lee and Behnam Abasht; Abasht, BehnamBackground: Identification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock. In this study, we aimed at detecting signatures of recent selection in commercial broiler chickens using genotype information from single nucleotide polymorphisms (SNPs). A total of 565 chickens from five commercial purebred lines, including three broiler sire (male) lines and two broiler dam (female) lines, were genotyped using the 60K SNP Illumina iSelect chicken array. To detect genomic signatures of recent selection, we applied two methods based on population comparison, cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR), and further analyzed the results to find genomic regions under recent selection in multiple purebred lines. Results: A total of 321 candidate selection regions spanning approximately 1.45 % of the chicken genome in each line were detected by consensus of results of both XP-EHH and XP-CLR methods. To minimize false discovery due to genetic drift, only 42 of the candidate selection regions that were shared by 2 or more purebred lines were considered as high-confidence selection regions in the study. Of these 42 regions, 20 were 50 kb or less while 4 regions were larger than 0.5 Mb. In total, 91 genes could be found in the 42 regions, among which 19 regions contained only 1 or 2 genes, and 9 regions were located at gene deserts. Conclusions: Our results provide a genome-wide scan of recent selection signatures in five purebred lines of commercial broiler chickens. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta). These genes may have been under recent selection due to their essential roles in growth, Developmentelopment and reproduction in chickens. Furthermore, our results suggest that in some candidate regions, the same or opposite alleles have been under recent selection in multiple lines. Most of the candidate genes in the selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding.Item Unique genetic responses revealed in RNAseq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat(PLoS (Public Library of Science), 2017-02-06) Van Goor, Angelica; Ashwell, Chris M.; Persia, Michael E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J.; Angelica Van Goor, Chris M. Ashwell, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont; Schmidt, Carl J.Climate change and disease have large negative impacts on poultry production, but little is known about the interactions of responses to these stressors in chickens. Fayoumi (heat and disease resistant) and broiler (heat and disease susceptible) chicken lines were stimulated at 22 days of age, using a 2x2x2 factorial design including: breed (Fayoumi or broiler), inflammatory stimulus (lipopolysaccharide (LPS) or saline), and temperature (35ÊC or 25ÊC). Transcriptional changes in spleens were analyzed using RNA-sequencing on the Illumina HiSeq 2500. Thirty-two individual cDNA libraries were sequenced (four per treatment) and an average of 22 million reads were generated per library. Stimulation with LPS induced more differentially expressed genes (DEG, log2 fold change 2 and FDR 0.05) in the broiler (N = 283) than the Fayoumi (N = 85), whereas heat treatment resulted in fewer DEG in broiler (N = 22) compared to Fayoumi (N = 107). The double stimulus of LPS+heat induced the largest numbers of changes in gene expression, for which broiler had 567 DEG and Fayoumi had 1471 DEG of which 399 were shared between breeds. Further analysis of DEG revealed pathways impacted by these stressors such as Remodelling of Epithelial Adherens Junctions due to heat stress, Granulocyte Adhesion and Diapedesis due to LPS, and Hepatic Fibrosis/Hepatic Stellate Cell Activation due to LPS+heat. The genes and pathways identified provide deeper understanding of the response to the applied stressors and may serve as biomarkers for genetic selection for heat and disease tolerant chickens.Item WebGIVI: a web-based gene enrichment analysis and visualization tool(BioMed Central, 2017-05-04) Sun, Liang; Zhu, Yongnan; Mahmood, A. S. M. Ashique; Tudor, Catalina O.; Ren, Jia; Vijay-Shanker, K.; Chen, Jian; Schmidt, Carl J.; Liang Sun, Yongnan Zhu, A. S. M. Ashique Mahmood, Catalina O. Tudor, Jia Ren, K. Vijay-Shanker, Jian Chen and Carl J. Schmidt; Sun, Liang; Mahmood, A. S. M. Ashique; Tudor, Catalina O.; Ren, Jia; Vijay-Shanker, K.; Schmidt, Carl J.BACKGROUND: A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task. RESULTS: We have developed WebGIVI, an interactive web-based visualization tool (http://raven.anr.udel.edu/webgivi/) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data. CONCLUSIONS: WebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI. The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php.Item A Standard Scale to Measure Equine Keeper Status and the Effect of Metabolic Tendency on Gut Microbiome Structure(Animals (MDPI), 2021-07-01) Johnson, Alexa C. B.; Biddle, AmyThriftiness in horses has been associated with more efficient nutrient harvesting in digestion, absorption and/or utilization, but the relative contribution of the gut microbiome to host metabolic tendency is not well understood. Recognizing the unreliability of owner reported assignment of keeper status, this research describes a novel tool for calculating whether a horse is an easy (EK) or hard (HK) keeper and then characterizes microbiome differences in these groups. The Equine Keeper Status Scale (EKSS) was developed and validated based on data gathered from 240 horses. Estimates of dietary energy intakes and requirements to achieve the optimal BCS score of 5 were used in EKSS assignments. Sixty percent of owners’ characterizations disagreed with EKSS identified keeper assignments. Equine fecal 16S rRNA profiles (n = 73) revealed differences in α and β diversities and taxa abundances based on EKSS assignments. EK communities had more Planctomycetes and fewer Euryarcheaota, Spirochaetes and Proteobacteria than HK indicating functional differences in nutrient harvesting between groups. Differences in the gut microbiomes of horses based on keeper assignment point to host/microbial interactions that may underlie some differences in metabolic tendency. The EKSS enables robust, repeatable determination of keeper status which can be used by researchers and horse owners.Item The impact of differential lignin S/G ratios on mutagenicity and chicken embryonic toxicity(Journal of Applied Toxicology, 2021-08-27) Zhang, Xinwen; Levia, Delphis F.; Ebikade, Elvis Osamudiamhen; Chang, Jeffrey; Vlachos, Dionisios G.; Wu, ChangqingLignin and lignin-based materials have received considerable attention in various fields due to their promise as sustainable feedstocks. Guaiacol (G) and syringol (S) are two primary monolignols that occur in different ratios for different plant species. As methoxyphenols, G and S have been targeted as atmospheric pollutants and their acute toxicity examined. However, there is a rare understanding of the toxicological properties on other endpoints and mixture effects of these monolignols. To fill this knowledge gap, our study investigated the impact of different S/G ratios (0.5, 1, and 2) and three lignin depolymerization samples from poplar, pine, and miscanthus species on mutagenicity and developmental toxicity. A multitiered method consisted of in silico simulation, in vitro Ames test, and in vivo chicken embryonic assay was employed. In the Ames test, syringol showed a sign of mutagenicity, whereas guaiacol did not, which agreed with the T.E.S.T. simulation. For three S and G mixture and lignin monomers, mutagenic activity was related to the proportion of syringol. In addition, both S and G showed developmental toxicity in the chicken embryonic assay and T.E.S.T. simulation, and guaiacol had a severe effect on lipid peroxidation. A similar trend and comparable developmental toxicity levels were detected for S and G mixtures and the three lignin depolymerized monomers. This study provides data and insights on the differential toxicity of varying S/G ratios for some important building blocks for bio-based materials.
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