Research in my Laboratory seeks to define the basic mechanisms by which pathogenic microbes successfully infect, colonize, and cause disease in their hosts. The research effort is organized along two thematic lines: (i) microbial pathogenomics, including host response to infection; and, (ii) molecular epidemiology, including the study of population genetics of microbes. A related research component seeks to translate the results of our laboratory-based investigations into improved diagnostic tests and methods for microbial identification, as well as to investigate opportunities for developing new generations of antimicrobial vaccines and therapeutics. A schematic representation of the research programs and activities that are and will be carried out in my group is provided below:

Peer-reviewed Publications (2003-2006):

2003

• Baechler, E. C., F. M. Batliwala, G. Karypis, P. M. Gaffney, W. A. Ortmann, K. J. Espe, K. J. Sharp, W. J. Grande, K. M. Hughes, V. Kapur , P. M. Gergersen, and T. W. Behrens. 2003. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus . Proc. Natl. Acad. Sci. USA. 100:2610-2615.

• Dar, A.M., S. Munir, S. M. Goyal and V. Kapur . 2003. Sequence analysis of the matrix (M2) protein gene of the avian pneumovirus recovered from turkey flocks in the United States. J. Clin. Microbiol. 41(6) 2748-51.

• Motiwala A.S, M. Strother, A. Amonsin, B. Byrum, S. A. Naser, J. R. Stabel, W. Shulaw, J. P. Bannantine, V. Kapur and S. Sreevatsan. 2003. Molecular Epidemiology of Mycobacterium avium subspecies paratuberculosis: Evidence for limited strain diversity, strain sharing, and identification of unique targets for diagnosis. J. Clin. Microbiol. 41:2015-2026.

• Munir, S, and V. Kapur . 2003. Transcriptional analysis of the response of poultry species to respiratory pathogens. Poultry Science. 82:885-892 .

• Rahman M.T., L. L Herron, V. Kapur , W. G. Meijer, B. A. Byrne, J. Ren, V. M. Nicholson, and J. F. Prescott. 2003. Partial genome sequencing of Rhodococcus equi ATCC 33701. Vet Microbiol. 94:143-58.

• Bannantine JP, Q. Zhang, L. L Li, and V. Kapur . 2003. Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates. BMC Microbiol. 3:10-19.

• Munir, S, and V. Kapur . 2003. Regulation of host cell transcriptional physiology by the avian pneumovirus provides key insights into host-pathogen interactions. J. Virol. 77:4899-910 .

• Herron-Olson, L, J. Freeman, Q. Zhang, E. Retzel, and V. Kapur . 2003. MGView: An alignment and visualization tool to enhance gap closure of microbial genomes. Nucleic Acids Res. 31:e106

• Dohmann, K., B. Strommenger, K. Stevenson, L. de Juan, V. Kapur , T. J. Bull, G-F Gerlach. 2003. Characterization of genetic differences between Mycobacterium avium subspecies paratuberculosis type I and type II isolates. J. Clin. Microbiol . 41:5215-23.

• Bannantine, J.P., J. K. Hansen, M. L. Paustian, A. Amonsin, L-L Li, and V. Kapur . 2003. Expression and immunogenicity of proteins encoded by sequences specific to Mycobacterium avium subsp. paratuberculosis. J. Clin. Microbiol. 42:106-14.

• Stratmann J, Strommenger B, Goethe R, Dohmann K, Gerlach GF, Stevenson K, Li LL, Zhang Q, Kapur V , and Bull TJ. 2004. A 38-kilobase pathogenicity island specific for Mycobacterium avium subsp. paratuberculosis encodes cell surface proteins expressed in the host. Infect. Immun. 72:1265-74.

2004

• Paustian ML, Amonsin A, Kapur V , Bannantine JP. 2004. Characterization of Novel Coding Sequences Specific to Mycobacterium avium subsp. paratuberculosis: Implications for Diagnosis of Johne's Disease. J.Clin.Microbiol . 42(6):2675-81

• Munir S, Singh S, Kaur K, Kapur V . 2004. Suppression subtractive hybridization coupled with microarray analysis to examine differential expression of genes in virus infected cells. Biol Proced Online 6:94-104.

• Motiwala AS, Amonsin A, Strother M, Manning EJ, Kapur V , Sreevatsan S. 2004. Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolates recovered from wild animal species. J.Clin.Microbiol . 42(4):1703-12.

• Amonsin A, Li LL, Zhang Q, Bannantine JP, Motiwala AS, Sreevatsan S, Kapur V . 2004. Multilocus short sequence repeat sequencing approach for differentiating among Mycobacterium avium subsp. paratuberculosis strains. J.Clin.Microbiol . 42(4):1694-702.

• Abrahamsen MS, Templeton TJ, Enomoto S, Abrahante JE, Zhu G, Lancto CA, Deng M, Liu C, Widmer G, Tzipori S, Buck GA, Xu P, Bankier AT, Dear PH, Konfortov BA, Spriggs HF, Iyer L, Anantharaman V, Aravind L, Kapur V . 2004. Complete genome sequence of the apicomplexan, Cryptosporidium parvum . Science . 304(5669):441-5.

• Boyce JD, Wilkie I, Harper M, Paustian ML, Kapur V , Adler B. 2004. Genomic-scale analysis of Pasteurella multocida gene expression during growth within liver tissue of chickens with fowl cholera. Microbes Infect. 6(3):290-8.

• Bannantine JP, Hansen JK, Paustian ML, Amonsin A, Li LL, Stabel JR, Kapur V . 2004. Expression and immunogenicity of proteins encoded by sequences specific to Mycobacterium avium subsp. paratuberculosis. J.Clin.Microbiol. 42(1):106-14.

• Wellehan, J. F., D. K. Nichols, L. L. Li, and V. Kapur . 2004. Three novel herpesviruses associated with stomatitis in Sudan plated lizards (Gerrhosaurus major) and a black-lined plated lizard (Gerrhosaurus nigrolineatus). J Zoo Wildl Med 35:50-4.

• Rishi, A. S., S. Munir, V. Kapur , N. D. Nelson, and A. Goyal. 2004. Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray. Planta 220:296-306.

• Xu, P., G. Widmer, Y. Wang, L. S. Ozaki, J. M. Alves, M. G. Serrano, D. Puiu, P. Manque, D. Akiyoshi, A. J. Mackey, W. R. Pearson, P. H. Dear, A. T. Bankier, D. L. Peterson, M. S. Abrahamsen, V. Kapur , S. Tzipori, and G. A. Buck. 2004. The genome of Cryptosporidium hominis. Nature 431:1107-12.

2005

• Munir, S., J. M. Sharma, and V. Kapur . 2005. Transcriptional response of avian cells to infection with Newcastle disease virus. Virus Res 107:103-8.

• Dar A., S. Munir, S. Vis hwanathan, A. Manuja, P. Griebel, S. Tikoo, H. Townsend, A. Potter, V. Kapur , L. A. Babiuk. 2005. Transcriptional analysis of avian embryonic tissues following infection with avian infectious bronchitis virus. Virus Res. 110(1-2):41-55 .

• Aakra, A., H. Vebo, L. Snipen, H. Hirt, A. Aastveit, V. Kapur , G. Dunny, B. Murray, and I. F. Nes. 2005. Transcriptional Response of Enterococcus faecalis V583 to Erythromycin. Antimicrob Agents Chemother 49:2246-59.

• Gadgil, M., V. Kapur , and W. S. Hu. 2005. Transcriptional Response of Escherichia coli to Temperature Shift. Biotechnol Prog 21:689-99.

• Gadgil, M., W. Lian, C. Gadgil, V. Kapur , and W. S. Hu. 2005. An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays. BMC Genomics 6:66.

• Halling, S. M., B. D. Peterson-Burch, B. J. Bricker, R. L. Zuerner, Z. Qing, L. L. Li, V. Kapur , D. P. Alt, and S. C. Olsen. 2005. Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis. J Bacteriol 187:2715-26.

• Hirt, H., D. A. Manias, E. M. Bryan, J. R. Klein, J. K. Marklund, J. H. Staddon, M. L. Paustian, V. Kapur , and G. M. Dunny. 2005. Characterization of the pheromone response of the Enterococcus faecalis conjugative plasmid pCF10: complete sequence and comparative analysis of the transcriptional and phenotypic responses of pCF10-containing cells to pheromone induction. J Bacteriol 187:1044-54.

• Motiwala, A. S., M. Strother, N. E. Theus, R. W. Stich, B. Byrum, W. P. Shulaw, V. Kapur , and S. Sreevatsan. 2005. Rapid detection and typing of strains of Mycobacterium avium subsp. paratuberculosis from broth cultures. J Clin Microbiol 43:2111-7.

• Paustian, M. L., V. Kapur , and J. P. Bannantine. 2005. Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates. J Bacteriol 187:2406-15.

• Li, L., J. P. Bannantine, Q. Zhang, A. Amonsin, B. J. May, D. Alt, N. Banerji, S. Kanjilal, and V. Kapur . 2005. The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc Natl Acad Sci USA. 102:12344-12349.

• Rock, R. B., S. Hu, A. Deshpande, S. Munir, B. J. May, C. A. Baker, P. K. Peterson, and V. Kapur . 2005. Transcriptional response of human microglial cells to interferon-gamma. Genes Immun 6:712-719.

• Rock, R. B., S. Hu, G. Gekker, W. S. Sheng, B. May, V. Kapur , and P. K. Peterson. 2005. Mycobacterium tuberculosis-Induced Cytokine and Chemokine Expression by Human Microglia and Astrocytes: Effects of Dexamethasone. J Infect Dis 192:2054-8.

2006

• Blazquez, J., J. M. Gomez-Gomez, A. Oliver, C. Juan, V. Kapur , and S. Martin. 2006. PBP3 inhibition elicits adaptive responses in Pseudomonas aeruginosa. Mol Microbiol 62:84-99.

• Gadgil, M., S. Mehra, V. Kapur , and W. S. Hu. 2006. TimeView: For Comparative Gene Expression Analysis. Appl Bioinformatics 5:41-4.

• Harris, N. B., J. B. Payeur, V. Kapur , and S. Sreevatsan. 2006. Short-sequence-repeat analysis of Mycobacterium avium subsp. paratuberculosis and Mycobacterium avium subsp. avium isolates collected from animals throughout the United States reveals both stability of loci and extensive diversity. J Clin Microbiol 44:2970-3.

• Janagama, H. K., K. I. Jeong, V. Kapur , P. Coussens, and S. Sreevatsan. 2006. Cytokine responses of bovine macrophages to diverse clinical Mycobacterium avium subspecies paratuberculosis strains. BMC Microbiol 6:10.

• Marsh, I. B., J. P. Bannantine, M. L. Paustian, M. L. Tizard, V. Kapur , and R. J. Whittington. 2006. Genomic comparison of Mycobacterium avium subsp. paratuberculosis sheep and cattle strains by microarray hybridization. J Bacteriol 188:2290-3.

• Motiwala, A. S., H. K. Janagama, M. L. Paustian, X. Zhu, J. P. Bannantine, V. Kapur , and S. Sreevatsan. 2006. Comparative Transcriptional Analysis of Human Macrophages Exposed to Animal and Human Isolates of Mycobacterium avium Subspecies paratuberculosis with Diverse Genotypes. Infect Immun 74:6046-56.

• Motiwala, A. S., L. Li, V. Kapur , and S. Sreevatsan. 2006. Current understanding of the genetic diversity of Mycobacterium avium subsp. paratuberculosis. Microbes Infect.

• Munir, S., K. Kaur, and V. Kapur . 2006. Avian metapneumovirus phosphoprotein targeted RNA interference silences the expression of viral proteins and inhibits virus replication. Antiviral Res 69:46-51.

• Treff, N. R., R. K. Vincent, M. L. Budde, V. L. Browning, J. F. Magliocca, V. Kapur , and J. S. Odorico. 2006. Differentiation of embryonic stem cells conditionally expressing neurogenin 3. Stem Cells 24:2529-37.

Selected Patents: US # 5,641,49 1; US # 6,030,835; US # 6,030,835, US # 6,495,334;