MSU's systems biology research institute is called the Institute for Genomics, Biocomputing and Biotechnology (IGBB), and all COBRE Junior Investigators and potential Pilot Investigators currently work within the IGBB environment and with each other. Dr Nanduri is an active IGBB computational systems biology researcher and a collaborator at the Junior Investigator level with Dr. Seo. Dr Donaldson also has a productive relationship with IGBB and has published in expression proteomics done at the institute (1). Drs Wan and Seo are newer to MSU and have yet to publish work done at the IGBB, but they have preliminary data generated in the institute (see Preliminary Data in their individual project descriptions). Dr. Edelmann is also new to MSU, but she is an IGBB faculty member (home based in the College of Veterinary Medicine Department of Basic Sciences), is already collaborating with Dr. Nanduri and has planned interactions with other COBRE investigators in her project description. The IGBB is the result of merging two separate university level institutes: 1) the Life Science and Biotechnology Institute (LSBI), which acted as MSU's de facto """"""""'omics core facility"""""""" in genomics, functional genomics, and proteomics since 2002;and 2) the Institute for Digital Biology (IDB), which facilitated faculty collaborations in bioinformatics and computational biology across campus since 2004. The LSBI had predominantly technical staff and a few non-tenure track soft-funded research faculty, and the IDB was predominantly tenured faculty. The LSBI had wet-laboratories, and the IDB was virtual. Both institutes relied on each other to generate knowledge;both were jointly administered through MSU's VP for Agriculture, Forestry, and Veterinary Medicine and VP for Research and Economic Development Offices;and the same faculty were involved in both. In January 2011, it was recognized that high throughput """"""""omic"""""""" data generation and biocomputing needed to be linked more seamlessly for effective systems biology research, which enables mechanistic hypothesis driven research in a functional genomics research environment (2, 3). Therefore, the LSBI and the IDB were merged and became the IGBB. The IGBB includes MSU's de facto core DNA sequencing and proteomics facility via its OMB Circular A-21-defined, and separately budgeted, specialized service facility (4) called the Omics Biology Laboratory (OBL). Research conducted at IGBB is accomplished through one of two mechanisms: 1) by collaboration with soft-funded research assistants and research faculty employed at IGBB or 2) by fee-for-service work done in the OBL. In the current COBRE application, most of the Junior Investigators'research conducted at IGBB will be done through the fee-for-service mechanism in the Omics Biology Lab (OBL). However, some will also have formal collaborations with IGBB (through IGBB faculty or staff. All 'omic biology and biocomputing for the COBRE Junior Investigator projects and pilot projects will be done in the IGBB environment. Depending on the COBRE project, IGBB staff may be responsible for experimental steps from sample preparation to analysis and computational modeling. Alternatively, staff or students within the junior investigator projects employed in the departments may run the equipment autonomously (after formal training by an IGBB staff member). Dr. Edelmann, an IGBB faculty member and proteomics expert, is a collaborator at the Junior Investigator level with Drs. Donaldson and Nanduri, and she will also directly supervise a research associate who will work 25% for the COBRE. All techniques and technologies to be used and analysis proposed to be done have already been published by faculty and staff (see individual Junior Investigator projects) in the IGBB.

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National Institute of General Medical Sciences (NIGMS)
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Bryant, Joseph C; Dabbs, Ridge C; Oswalt, Katie L et al. (2016) Pyruvate oxidase of Streptococcus pneumoniae contributes to pneumolysin release. BMC Microbiol 16:271
Wright, Morgan L; Pendarvis, Ken; Nanduri, Bindu et al. (2016) The Effect of Oxygen on Bile Resistance in Listeria monocytogenes. J Proteomics Bioinform 9:107-119
Seo, Keun Seok (2016) Monkey Feeding Assay for Testing Emetic Activity of Staphylococcal Enterotoxin. Methods Mol Biol 1396:125-31
Park, Joo Youn; Seo, Keun Seok (2016) Quantification of a Selective Expansion of T Cell Receptor Vβ by Superantigen Using Real-Time PCR. Methods Mol Biol 1396:167-80
Alugubelly, Navatha; Hercik, Kamil; Kibler, Peter et al. (2016) Analysis of differentially expressed proteins in Yersinia enterocolitica-infected HeLa cells. Biochim Biophys Acta 1864:562-9
Brown, Lindsey R; Gunnell, Steven M; Cassella, Adam N et al. (2016) AdcAII of Streptococcus pneumoniae Affects Pneumococcal Invasiveness. PLoS One 11:e0146785
Nanduri, Bindu; Shack, Leslie A; Rai, Aswathy N et al. (2016) Use of focused ultrasonication in activity-based profiling of deubiquitinating enzymes in tissue. Anal Biochem 515:9-13
Dhital, Saphala; Stokes, John V; Park, Nogi et al. (2016) Cannabidiol (CBD) induces functional Tregs in response to low-level T cell activation. Cell Immunol :
Moon, Bo Youn; Park, Joo Youn; Robinson, D Ashley et al. (2016) Mobilization of Genomic Islands of Staphylococcus aureus by Temperate Bacteriophage. PLoS One 11:e0151409
Ferguson, Lucas; Olivier, Alicia K; Genova, Suzanne et al. (2016) Pathogenesis of Influenza D Virus in Cattle. J Virol 90:5636-42

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