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United States Department of Agriculture

Agricultural Research Service

Title: Integration of Structural and Functional Genomics

Authors
item Zhao, Shu-Hong - ISU, AMES IOWA
item Kuhar, Daniel
item Recknor, Justin - ISU, AMES IOWA
item Lunney, Joan
item Nettleton, Dan - ISU, AMES IOWA
item Dawson, Harry
item Orley, Sarah - ISU, AMES IOWA
item Uthe, Jolita - NADC, AMES IOWA
item Bearson, Shawn
item Tuggle, Christopher - ISU, AMES IOWA

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: September 22, 2005
Publication Date: September 22, 2005
Citation: Zhao, S., Kuhar, D.J., Recknor, J., Lunney, J.K., Nettleton, D., Dawson, H.D., Orley, S., Uthe, J., Bearson, S.M., Tuggle, C.K. 2005. Integration of structural and functional genomies. Proceedings of Integration of Structural and Functional Genomics Sympoisium 22-25 September 2005, p. 39.

Technical Abstract: A first-generation porcine oligonucleotide set, representing 13,297 transcripts, has been designed by Qiagen-Operon. To validate this set for transcriptional profiling, microarrays were hybridized with targets from liver, lung, muscle, or small intestine. Analyses showed 11,328 oligos demonstrated expression in at least one tissue. Further, 1,810 genes showed differential expression (DE) among tissues (Bonferroni adjusted p < 0.05); expression of 9 of 11 tested genes were confirmed by quantitative real-time PCR (Q-PCR). We then used the validated array to study the systemic transcriptional response to Salmonella enterica serovar Choleraesuis infection by analyzing control, 24 hour post-infection (hpi), and 48 hpi porcine lung RNA samples. Fifty-seven genes showed DE at p<0.001 level (False Discovery Rate 12%). Q-PCR confirmed 23 of 33 DE genes. Results showed a predominant T helper 1 immune response during infection, with IFNG significantly increased at 48 hpi. Interferon-response genes (GBP1, GBP2), acute phase response genes (C1S, C1R), and antigen processing genes (MHC2TA, PSMB8, TAP1, TAP2) showed increased expression during infection. The induction of apoptotic pathways, including a novel finding that two protein-glutamine glutamyltransferase family genes (TGM1 and TGM3) showed dramatic induction at 48 hpi, was seen. This data is the first thorough investigation of gene regulation pathways that control an important porcine respiratory and foodborne bacterial infection.

Last Modified: 4/20/2014
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