Progress 01/01/09 to 12/31/12
Outputs
Progress Report Objectives (from AD-416): 1. Profile the in vivo whole blood RNA and cytokine response to Salmonella Typhimurium infection in animals with high and low fecal shedding phenotypes. 2. Using the same animals in Aim 1, profile the in vitro whole blood RNA and cytokine response to lipopolysaccaride or Salmonella Typhimurium treatments prior to in vivo exposure to Salmonella Typhimurium of the pigs. 3. Annotate response profiles for common expression patterns and functional themes and develop regulatory network information on response to inflammatory stimuli. 4. Develop and test predictive models for identifying pigs with decreased fecal shedding post-infection. Approach (from AD-416): The assembled team has expertise and recent experience in collecting and analyzing porcine transcriptional profiling data, as well as in developing computational regulatory networks. We will propose to integrate and extend these datasets to specifically build a database containing transcriptional and regulatory factor-chromatin binding data of the inflammatory response to pathogen challenge. We will use the most comprehensive approaches possible, including the Affymetrix Porcine GeneChip' and/or pig long oligo arrays for RNA work, and chromatin immunoprecipitation methods for selected transcription factors to develop regulatory network data. These data will then be analyzed using several computational approaches to find genes and develop an understanding of regulatory networks responsible for differences in outcome after infection, and this new information will be applied to find predictors for not only which swine are more resistant to Salmonella infection and shedding but also optimal health traits. We believe this approach will be successful in both establishing molecular measures of health and disease, predicting Salmonella resistant versus susceptible pigs, and identifying the most promising targets for improving animal health and growth in challenging environments. Research progress with our colleagues at Iowa State University in transcriptionally profiling the porcine response to Salmonella shedding has proceeded to the publication stage with one manuscript submitted and another in preparation. Briefly, 120 pigs were inoculated with the same dose of Salmonella Typhimurium and a comparison was conducted between two phenotypic populations: pigs that shed low levels of Salmonella and pigs that persistently shed Salmonella. In response to Salmonella, these two extreme Salmonella shedding pig groups differed in their clinical profiles, circulating immune cytokine levels, and gene expression patterns. Thus, these data suggest that distinct, alternative immune responses to Salmonella Typhimurium infection could result in different shedding outcomes in swine. Our central goal is to identify a transcriptional profile in pigs (a �classifier�) associated with the susceptibility/resistance of pigs to Salmonella colonization, shedding and carrier status. The classifier will aid in the selection of breeder herds that have elevated resistance to Salmonella and support the development of microbial diagnostic tools to identify Salmonella-carrier pigs. The ultimate outcome will be to maximize livestock production, enhance food safety and protect human health. The results of this research have contributed substantially in the selection of porcine genes to target for the development of this classifier.
Impacts
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Publications
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report Objectives (from AD-416): 1. Profile the in vivo whole blood RNA and cytokine response to Salmonella Typhimurium infection in animals with high and low fecal shedding phenotypes. 2. Using the same animals in Aim 1, profile the in vitro whole blood RNA and cytokine response to lipopolysaccaride or Salmonella Typhimurium treatments prior to in vivo exposure to Salmonella Typhimurium of the pigs. 3. Annotate response profiles for common expression patterns and functional themes and develop regulatory network information on response to inflammatory stimuli. 4. Develop and test predictive models for identifying pigs with decreased fecal shedding post-infection. Approach (from AD-416): The assembled team has expertise and recent experience in collecting and analyzing porcine transcriptional profiling data, as well as in developing computational regulatory networks. We will propose to integrate and extend these datasets to specifically build a database containing transcriptional and regulatory factor-chromatin binding data of the inflammatory response to pathogen challenge. We will use the most comprehensive approaches possible, including the Affymetrix Porcine GeneChip' and/or pig long oligo arrays for ribonucleicacid (RNA) work, and chromatin immunoprecipitation methods for selected transcription factors to develop regulatory network data. These data will then be analyzed using several computational approaches to find genes and develop an understanding of regulatory networks responsible for differences in outcome after infection, and this new information will be applied to find predictors for not only which swine are more resistant to Salmonella infection and shedding but also optimal health traits. We believe this approach will be successful in both establishing molecular measures of health and disease, predicting Salmonella resistant versus susceptible pigs, and identifying the most promising targets for improving animal health and growth in challenging environments. Research progress with our colleagues at Iowa State University in transcriptionally profiling the porcine response to Salmonella shedding has proceeded to the bioinformatics and statistics stage of analysis. Briefly, 120 pigs were inoculated with Salmonella enterica serovar Typhimurium and monitored over a three week period to identify low shedding and highly persistent shedding pigs. Following classification of ten low and ten persistently shedding pigs based on quantitated Salmonella fecal shedding data, ribonucleicacid (RNA) from porcine blood taken throughout the study was transcriptionally profiled using Affymetrix microarray analysis. Currently the gene expression data is being analyzed for profile patterns to predict a pig�s response to Salmonella. Our goal of the project is to identify a transcriptional profile in pigs (a �classifier�) associated with the susceptibility/resistance of pigs to Salmonella colonization, shedding and carrier status. This classifier will aid in the selection of breeder herds that have elevated resistance to Salmonella and support the development of microbial diagnostic tools to identify Salmonella-carrier pigs.
Impacts
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Publications
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) 1. Profile the in vivo whole blood RNA and cytokine response to Salmonella Typhimurium infection in animals with high and low fecal shedding phenotypes. 2. Using the same animals in Aim 1, profile the in vitro whole blood RNA and cytokine response to lipopolysaccaride or Salmonella Typhimurium treatments prior to in vivo exposure to Salmonella Typhimurium of the pigs. 3. Annotate response profiles for common expression patterns and functional themes and develop regulatory network information on response to inflammatory stimuli. 4. Develop and test predictive models for identifying pigs with decreased fecal shedding post-infection. Approach (from AD-416) The assembled team has expertise and recent experience in collecting and analyzing porcine transcriptional profiling data, as well as in developing computational regulatory networks. We will propose to integrate and extend these datasets to specifically build a database containing transcriptional and regulatory factor-chromatin binding data of the inflammatory response to pathogen challenge. We will use the most comprehensive approaches possible, including the Affymetrix Porcine GeneChip' and/or pig long oligo arrays for RNA work, and chromatin immunoprecipitation methods for selected transcription factors to develop regulatory network data. These data will then be analyzed using several computational approaches to find genes and develop an understanding of regulatory networks responsible for differences in outcome after infection, and this new information will be applied to find predictors for not only which swine are more resistant to Salmonella infection and shedding but also optimal health traits. We believe this approach will be successful in both establishing molecular measures of health and disease, predicting Salmonella resistant versus susceptible pigs, and identifying the most promising targets for improving animal health and growth in challenging environments. In collaboration with investigators at Iowa State University, we have transcriptionally profiled the response of pigs that shed low levels of Salmonella compared to highly persistent Salmonella shedding pigs. Following inoculation of the pigs, Salmonella shedding status was monitored over a three week period to identify low shedding and highly persistent shedding pigs. The purpose of analyzing the gene expression of these diverse shedding populations is to find differences in the pig�s response to Salmonella that associate with the susceptibility of pigs to Salmonella colonization, shedding and carrier status. Our goal of the project is to identify traits that could be exploited to enhance the resistance of swine herds to Salmonella colonization through immunomodulation, aid in the selection of breeder herds that have elevated resistance to Salmonella, and/or support the development of microbial diagnostic tools to identify Salmonella-carrier pigs. Progress is monitored by regular e-mails, phone calls, and site visits.
Impacts
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Publications
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) 1. Profile the in vivo whole blood RNA and cytokine response to Salmonella Typhimurium infection in animals with high and low fecal shedding phenotypes. 2. Using the same animals in Aim 1, profile the in vitro whole blood RNA and cytokine response to lipopolysaccaride or Salmonella Typhimurium treatments prior to in vivo exposure to Salmonella Typhimurium of the pigs. 3. Annotate response profiles for common expression patterns and functional themes and develop regulatory network information on response to inflammatory stimuli. 4. Develop and test predictive models for identifying pigs with decreased fecal shedding post-infection. Approach (from AD-416) The assembled team has expertise and recent experience in collecting and analyzing porcine transcriptional profiling data, as well as in developing computational regulatory networks. We will propose to integrate and extend these datasets to specifically build a database containing transcriptional and regulatory factor-chromatin binding data of the inflammatory response to pathogen challenge. We will use the most comprehensive approaches possible, including the Affymetrix Porcine GeneChip' and/or pig long oligo arrays for RNA work, and chromatin immunoprecipitation methods for selected transcription factors to develop regulatory network data. These data will then be analyzed using several computational approaches to find genes and develop an understanding of regulatory networks responsible for differences in outcome after infection, and this new information will be applied to find predictors for not only which swine are more resistant to Salmonella infection and shedding but also optimal health traits. We believe this approach will be successful in both establishing molecular measures of health and disease, predicting Salmonella resistant versus susceptible pigs, and identifying the most promising targets for improving animal health and growth in challenging environments. To investigate the Salmonella-carrier state in pigs, we have completed the screening of 120 Salmonella-challenged pigs to identify low- Salmonella shedders and high-Salmonella shedders. We are currently performing gene expression analysis on the two shedding groups to identify differences in the pig�s response to Salmonella that associate with the susceptibility of pigs to Salmonella colonization, shedding and carrier status. Our goal is to develop a gene expression �predictor� for identifying pigs that are more prone to developing a carrier state with Salmonella, thereby providing targets for biotherapeutics, diagnostic testing and the identification of Salmonella-resistant lines of pigs. Progress is monitored by regular e-mails, phone calls, and site visits.
Impacts
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Publications
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) 1. Profile the in vivo whole blood RNA and cytokine response to Salmonella Typhimurium infection in animals with high and low fecal shedding phenotypes. 2. Using the same animals in Aim 1, profile the in vitro whole blood RNA and cytokine response to lipopolysaccaride or Salmonella Typhimurium treatments prior to in vivo exposure to Salmonella Typhimurium of the pigs. 3. Annotate response profiles for common expression patterns and functional themes and develop regulatory network information on response to inflammatory stimuli. 4. Develop and test predictive models for identifying pigs with decreased fecal shedding post-infection. Approach (from AD-416) The assembled team has expertise and recent experience in collecting and analyzing porcine transcriptional profiling data, as well as in developing computational regulatory networks. We will propose to integrate and extend these datasets to specifically build a database containing transcriptional and regulatory factor-chromatin binding data of the inflammatory response to pathogen challenge. We will use the most comprehensive approaches possible, including the Affymetrix Porcine GeneChip' and/or pig long oligo arrays for RNA work, and chromatin immunoprecipitation methods for selected transcription factors to develop regulatory network data. These data will then be analyzed using several computational approaches to find genes and develop an understanding of regulatory networks responsible for differences in outcome after infection, and this new information will be applied to find predictors for not only which swine are more resistant to Salmonella infection and shedding but also optimal health traits. We believe this approach will be successful in both establishing molecular measures of health and disease, predicting Salmonella resistant versus susceptible pigs, and identifying the most promising targets for improving animal health and growth in challenging environments. Significant Activities that Support Special Target Populations This project was initiated in January 2009 to investigate differences in gene transcription in low versus high Salmonella shedding pigs. The variation observed in the susceptibility of pigs to Salmonella colonization/shedding can be a result of the porcine response to infection. Since changes in gene expression during infection can vary among swine, investigating the pig�s response to Salmonella will identify genes that may be responsible for the carrier-status of the pig. We are currently collecting the data to identify low Salmonella shedders and highly persistent Salmonella shedders. Once these pigs have been identified, transcriptional analysis will be performed to search for genes that are differentially-regulated between the two groups. Our goal is to develop a gene expression �predictor� for identifying pigs that are more prone to shed Salmonella in their feces, thereby providing targets for biotherapeutics, diagnostic testing and the identification of Salmonella-resistant lines of pigs. Progress is monitored by regular e- mails, phone calls, site visits.
Impacts
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