2009 Annual Report 1a.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. 1b.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. 3.Progress Report 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.