Bumgarner Lab

The focus of the Bumgarner lab’s activities in molecular virology/bacteriology is in understanding the host innate immune response and the microbial mechanisms for attenuating or evading the response. Essentially, we view the virus/bacteria as a tool for probing the host innate immune response. Our primary tool for viewing the host-response is DNA micro-array technology. The goal is to integrate over a variety of observed host-responses to better understand the mechanisms and pathways used in innate immunity. Towards this end, we have developed virology capability within the lab, have a number of external collaborations and are developing a database of microarray data related to the host response to viral infection. Our current focus in understanding the mechanism that rhinovirus uses to inhibit the host interferon response (in collaboration with Dr. Kurt Gustin at the University of Idaho).

Selected molecular virology/bacteriology publications:

Geiss GK, Carter VS, He Y, Kwieciszewski BK, Holzman T, Korth MJ, Lazaro CA, Fausto N, Bumgarner RE, Katze MG. 2003. Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein. J Virol. 77:6367-6375.
Smith MW, Yue ZN, Geiss GK, Sadovnikova NY, Carter VS, Boix L, Lazaro CA, Rosenberg GB, Bumgarner RE, Fausto N, Bruix J, Katze MG. 2003. Identification of Novel Tumor Markers in Hepatitis C Virus-associated Hepatocellular Carcinmoa. Cancer Research. 63: 859-864.
Xia M, Bumgarner RE, Lampe MF, Stamm WE. 2003. Chlamydia trachomatis Infection Alters Host Cell Transcription in Diverse Cellular Pathways. The Journal of Infectious Disease. 187:424-434.
Van’t Wout AB, Lehrman GK, Mikheeva SA, O’Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI. 2003. Cellular Gene Expression upon Immunodeficiency Virus Type 1 Infection of CD4+ -T- Cell Lines. Journal of Virology. 77:1392-1402.
Geiss GK, Salvatore M, Tumpey TM, Carter VS, Wang X, Basler CF, Taubenberger JK, Bumgarner RE, Palese P, Katze MG, Garcia-Sastre A. 2002. Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza. Proc Natl Acad Sci U S A. 99:10736-10741.
Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, Greenberg. EP. 2001. Gene expression in Pseudomonas aeruginosa biofilms. Nature. 413:860-864.
Geiss G, Jin G, Guo J, Bumgarner RE, Katze MG, Sen GC. 2001. A comprehensive view of regulation of gene expression by double-stranded RNA-mediated cell signaling. J Biol Chem. Aug 10;276(32):30178-30182.
Geiss GK, An MC, Bumgarner RE, Hammersmark E, Cunningham D, Katze MG. 2001. Global Impact of Influenza Virus on Cellular Pathways Is Mediated by both Replication-Dependent and -Independent Events. J Virol. 75:4321-4331.
Ichikawa JK, Norris A, Bangera MG, Geiss GK, van 't Wout AB, Bumgarner RE, Lory S. 2000. Interaction of pseudomonas aeruginosa with epithelial cells: identification of differentially regulated genes by expression microarray analysis of human cDNAs. Proc Natl Acad Sci U S A. 97:9659-9664.
Geiss GK, Bumgarner RE, An MC, Agy MB, van 't Wout AB, Hammersmark E, Carter VS, Upchurch D, Mullins JI, Katze MG. 2000. Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays. Virology. 266:8-16.

Links to our collaborators:

Collaborator	Location	System
Kurt Gustin	Dept. of Microbiology, Molecular Biology and Biochemistry University of Idaho	Rhino virus infection in culture
Peter Palese	Department of Microbiology, Mt. Sinai	Influenza
Kelley Hughes	Department of Microbiology, University of Washington	Salmonella
Minshen Xia & Walter E Stamm	Department of Medicine, University of Washington	Chlamydia trachomatis
James Mullins	Department of Microbiology, University of Washington	HIV
Richard Darveau	Oral Biology and Periodontics, University of Washington	Oral bacteria