Population Health and Reproduction

Dr. Weimer's research focuses on microbial physiology and function. This interest spans fermentation to food pathogens to host/microbe interactions to environmental survival, all of which has the underlying interest of the dichotomy between active growth and the non-culturable state. Using genomics and functional genomics - gene expression, metabolomics, proteomics, and metagenomics – Dr. Weimer’s program examines the mechanisms of gene interplay to produce a specific phenotype and the metabolism involved in the process. The interplay between the host, the microbe, and the interdependent response is a key question for his program. The primary thrust of his program is the systems biology of biological processes important for bacterial growth, survival, and persistence

Current Projects Include:

Understanding host/microbe associations using gene expression and metabolomics
Grow-independent bacterial detection methods based on genomics and phylogenomics
Biodiversity of microbes important to animal health
Defining the pathogenic microbes that inhabit the Great Salt Lake (Utah)
Establishing the parameters to induce and recover bacteria from the non-culturable state with special focus on pathogens and unique environmental bacteria.
Understanding the association of sulfur metabolism with survival in harsh living conditions, survival in the environment, and metabolism during infection



	Bart C. Weimer Professor Email: bcweimer@ucdavis.edu Department of Population Health and Reproduction School of Veterinary Medicine 2055 Haring Hall University of California Davis, CA 95616 Phone: (530) 752-5819 Fax: (530) 752-4278

	Prior to joining UC Davis Dr. Weimer was Director of the genome center, Center for Integrated BioSystems, at Utah State University where he joined the faculty in 1991. He obtained a BS (Honors) from the University of Arizona in Microbiology & Immunology and subsequently obtained a Ph.D. in Food Microbiology at Utah State University. Prior to completing a postdoctoral fellowship at the University of Melbourne (Australia) in biochemistry and genetics, he held positions with HyClone Laboratories (now ThermoFisher) and AuroTech, Inc. (now part of International Flavors and Fragrances).

Research	Dr. Weimer's research focuses on microbial physiology and function. This interest spans fermentation to food pathogens to host/microbe interactions to environmental survival, all of which has the underlying interest of the dichotomy between active growth and the non-culturable state. Using genomics and functional genomics - gene expression, metabolomics, proteomics, and metagenomics – Dr. Weimer’s program examines the mechanisms of gene interplay to produce a specific phenotype and the metabolism involved in the process. The interplay between the host, the microbe, and the interdependent response is a key question for his program. The primary thrust of his program is the systems biology of biological processes important for bacterial growth, survival, and persistence Current Projects Include: Understanding host/microbe associations using gene expression and metabolomics Grow-independent bacterial detection methods based on genomics and phylogenomics Biodiversity of microbes important to animal health Defining the pathogenic microbes that inhabit the Great Salt Lake (Utah) Establishing the parameters to induce and recover bacteria from the non-culturable state with special focus on pathogens and unique environmental bacteria. Understanding the association of sulfur metabolism with survival in harsh living conditions, survival in the environment, and metabolism during infection

Teaching	Food Safety

International Interests	Australasia – China, Thailand, Vietnam, Singapore, Hong Kong, Australia, New Zealand

	Recent Publications Genomics & Bioinformatics Lee, J-H., V.N. Karamychev, S.A. Kozyavkin, D. Mills, A.R. Pavlov, N.V. Pavlov, N.N. Polouchine, P.M. Richardson, V.V. Shakhova, A.I. Slesarev, B. Weimer, D.J. O’Sullivan. 2008. Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics 9:247-265. Parnell, J. Jacob, Todd A. Crowl, Bart C. Weimer, and Michael E. Pfrender. 2008. Biodiversity in microbial communities: system scale patterns and mechanisms. Molecular Ecology. (accepted). Desai, P., and B. C. Weimer. 2008. Gene expression in microbial systems to link growth and metabolism. In Handbook of Research on  Systems Biology Applications in Medicine, pp. 278-290, Ed. Andriani Daskalaki; IGI Global, Hershey, PA. (ISBN: 978-1-60566-076-9). Stevens, John R., Balasubramanian Ganesan, Prerak Desai, Sweta Rao, and Bart C. Weimer. 2008. Statistical issues for normalization of multi-species microarray data. Proceedings of the Nineteenth Annual Kansas State University Conference on Applied Statistics in Agriculture. Makarova, K., A. et al. B. C. Weimer, and D. A. Mills. 2006. Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. USA 103:15611-6. Co-corresponding authors. Xie, Y., A. Cutler, B. Weimer, A. Parfionovas. 2003. Statistical methods for spot detection with macroarray data. Proceedings of the 35th Symposium on the Interface. Cell Biology* Zhan, Y., X. Du, Q. Xu, G. Li, M. Zhang, J. Liu, D. Huang, B. Zhao, B. C. Weimer, D. Chen, Z. Cheng, L. Zhang, Q. Li, S. Li, Z. Zheng, S. Song, Y. Huang, Z. Ye, W. Su, S-C Lin, Y. Shen, Q. Wu. 2008. An anticancer and blood glucose-increasing endophytical fungal octaketide as ligand for nuclear orphan receptor Nur77. Nature Chemical Biology 4:548-56. Pate, B. J., K.L. White, D. Chen, K.I. Aston, B. R. Sessions, T.D. Bunch, and B. C. Weimer. 2008. A novel approach to identify bovine sperm membrane proteins that interact with receptors on the vitelline membrane of bovine oocytes. Mol. Reprod. Dev. 75:641-9. Boudina, Sihem, Heiko Bugger, Sandra Sena, Brian T. O’Neill, Vlad G. Zaha, Olesya Ilkun, Jordan J. Wright, Pradip K. Mazumder, Eric Palfreyman, Heather Theobald, Oleh Khalimonchuk, Benjamin Wayment, Kenneth J. Rodnick, Ryan Centini, Dong Chen, Sheldon E. Litwin, Bart C. Weimer, E. Dale Abel. 2008. Contribution of impaired myocardial insulin signaling to mitochondrial dysfunction and oxidative stress in the heart. Circulation. (accepted). Pate B.J., K. L. White, Q. A. Winger, L.F. Rickords, K.I. Aston, B.R. Sessons, G.P. Li, K.D. Campbell, B. Weimer, T.D. Bunch. 2007. Specific integrin subunits in bovine oocytes, including novel sequences for alpha 6 and beta 3 subunits. Mol. Reprod. Dev. 74:600-7. Champine, P., J. Michaelson, B. Weimer, D. R. Welsh, and D. B. DeWald. 2007. Microarray analysis reveals potential mechanisms of BRMS1-mediated metastasis suppression. Clinical & Experimental Metastasis. 24:551-65. Gene expression and metabolism Weimer, B., Y. Xie, L-S. Chou and A. Cutler. 2004. Gene expression arrays in food. In Microbial Products and Biotransformation, Ed. J.-L. Barredo. Humana Press, Totowa, NJ USA. Desai, P. and B. C. Weimer. 2008. Gene expression in microbial systems to link growth and metabolism. In Handbook of Research on  Systems Biology Applications in Medicine, pp. 278-290, Ed. Andriani Daskalaki; IGI Global, Hershey, PA. (ISBN: 978-1-60566-076-9). Chen, Dong, Ming-Xiang Liang, Daryll DeWald, Bart Weimer, Michael D. Peel, Bruce Bugbee, Jacob Michaelson, Elizabeth Davis, Yajun Wu. 2008. Identification of drought response genes from two alfalfa cultivars using Medicago truncatula microarrays. Acta Physiologiae Plantarum 30:183-199. Boudina, Sihem, Heiko Bugger, Sandra Sena, Brian T. O’Neill, Vlad G. Zaha, Olesya Ilkun, Jordan J. Wright, Pradip K. Mazumder, Eric Palfreyman, Heather Theobald, Oleh Khalimonchuk, Benjamin Wayment, Kenneth J. Rodnick, Ryan Centini, Dong Chen, Sheldon E. Litwin, Bart C. Weimer, E. Dale Abel. 2008. Contribution of impaired myocardial insulin signaling to mitochondrial dysfunction and oxidative stress in the heart. Circulation (accepted). Weimer, Bart C., Giovanni Rompato, Jacob Parnell, Reed Gann, Balasubramanian Ganesan, Cristian Navas, Martin Gonzalez, Mario Clavel, Steven Albee-Scott. 2009. Microbial biodiversity of Great Salt Lake, Utah. In Saline lakes around the world: unique systems with unique values. Eds. Oren, A., D. L. Naftz, and W. A. Wurtsbaugh. S. J. and Jessie E. Quinney Natural Resources Research Library, Utah State University Press, Logan. (in press). Ganesan, B., M. Stuart, and Bart C. Weimer. 2007. Carbohydrate starvation causes a metabolically active but nonculturable state in Lactococcus lactis. Appl. Environ. Microbiol. 73:2498-2512. Ganesan, B., P. Dobrowolski, and B. C. Weimer. 2006. Identification of the Leucine-to-2-Methylbutyric Acid Catabolic Pathway of Lactococcus lactis. Appl. Environ. Microbiol. 72:4264-73. Xie, Y., L-S Chou, A. Cutler, and B. Weimer. 2004. Expression profile of Lactococcus lactis ssp. lactis IL1403 during environmental stress with a DNA macroarray. Appl. Environ. Microbiol. 70:6738-6747. Desai, P., P. Champine, and B. C. Weimer. 2008. Gene expression profiles to define the mechanism of syrigopeptin 25A inhibition of Listeria monocytogenes. (submitted). Surface chemistry papers Walsh, Marie K., Xinwen Wang and Bart C. Weimer. 2001. Optimizing the immobilization of single-stranded DNA onto glass beads. J. Biochem. Biophys. Methods. 47:175-185. Weimer, B., M. Walsh, and X. Wang. 2000. Influence of a polyethylene glycol spacer on antigen capture by immobilized antibodies. J. Biochem. Biophys. Methods. 43(2):107-117. Analytical biochemistry Weimer, Bart C., Giovanni Rompato, Jacob Parnell, Reed Gann, Balasubramanian Ganesan, Cristian Navas, Martin Gonzalez, Mario Clavel, Steven Albee-Scott. Microbial biodiversity of Great Salt Lake, Utah. 2009. In Saline lakes around the world: unique systems with unique values. Eds. Oren, A., D. L. Naftz, and W. A. Wurtsbaugh. S. J. and Jessie E. Quinney Natural Resources Research Library, Utah State University Press, Logan. (in press). Weimer, B. C. 2009. (Editor). Metabolomics for food and health. In production. CRC Press, Boca Raton, FL. & Woodhead Publishing Limited, Cambridge, England. (In production). Dias, B., B. Ganesan, and B. C. Weimer. 2008. Detection of a-keto acids by capillary electrophoresis. (submitted). Weimer, B. C. 2007. Functional genomics and flavour. In Improving the flavour of cheese. Ed. Bart C. Weimer, Woodhead Publishing Limited, Cambridge, England; CRC Press, Boca Raton, FL. Liang, Y., D. R. Gardner, C. D. Miller, D. Chen, A. J. Anderson, B. C. Weimer, R. C. Sims. 2006. Biochemical pathway and enzymatic study of pyrene degradation by Mycobacterium sp. KMS. Appl. Environ. Microbiol. 72:7821-7828. Ganesan, B., P. Dobrowolski, and B. C. Weimer. 2006. Identification of the Leucine-to-2-Methylbutyric Acid Catabolic Pathway of Lactococcus lactis. Appl. Environ. Microbiol. 72:4264-73. Ganesan, B,. K. Seefeldt, R. Koka, B. Dias, and B. Weimer. 2004. Monocarboxylic acid production by lactococci and lactobacilli. Int. Dairy J. 14:2135-41. Ganesan, B., and B. Weimer. 2004. The role of the aminotransferase IlvE in production of branched chain fatty acids by Lactococcus lactis subsp. lactis. Appl. Environ. Microbiol. 70:638-641. Ganesan, B,. K. Seefeldt, and B. Weimer. 2004. Fatty acid production by Brevibacterium linens via amino acid utilization. Appl. Environ. Microbiol. 70:6385-6393. Weimer, B., and B. Dias. 2004. Volatile Sulfur detection in fermented foods. Ed. J.-L. Barredo. Microbial Products and Biotransformation. Humana Press, Totowa, NJ USA. Ummadi, M. and B. C. Weimer. 2002. Use of capillary electrophoresis-laser induced fluorescence detection to monitor bacterial growth and amino acid utilization. J. Chrom. A 964: 243-253. Ummadi, M. and B. C. Weimer. 2001. Tryptophan metabolism in Brevibacterium linens BL2. J. Dairy Sci 84:1773–1782. Seefeldt, K. and B. C. Weimer. 2000. Diversity of sulfur compounds in lactic acid bacteria J. Dairy Sci. 83: 2740-2746. Strickland, M., B. C. Weimer, and J. R. Broadbent. 1996. Capillary electrophoresis separates many compounds found in Cheddar cheese. J. Chromatography A 731:305. Real time detection Desai, P., M. K. Walsh, and B. C. Weimer. 2008. Solid phase capture of bacteria using gangliosides and detection by real time PCR. Appl. Environ. Microbiol. 74:2254-2258. Weimer, B., M. Walsh, C. Beer, X. Wang, and R. Koka. 2001. Solid-phase capture of proteins, spores, and bacteria. Appl. Environ. Microbiol. 67:1300–1307. Blake, M., and B. Weimer. 1997. Rapid and sensitive immunomagnetic detection of Bacillus stearothermophilus spores in food and environmental samples. Appl. Environ. Microbiol. 63:1643. Patents B. Weimer and Marie Walsh. 2007. Real time detection of bacterial antigens. U.S. Patent 7,220,596. B. Weimer. 2003. Real time bacterial detection. New Zealand Patent WO 99/508172. B. Weimer. 2003. Ligand-DNA composition for capture and detection of contaminants on a solid surface. U.S. Patent 6,531,278. B. Weimer. 2002. Real time bacterial detection. Australian Patent 754,077. B. Weimer. 2002. Real time bacterial detection. U.S. Patent 6,399,317. B. Weimer. 1999. Reconditioning antibiotic adulterated food products. U.S. Patent 5,998,222.

UC Davis School of Veterinary Medicine