Bonilla

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BigBarmB2014
Research
Oxidative stress is a fact of life for pathogenic bacteria, eukaryotic metabolically active cells and any organism in an aerobic environment. Our research focuses on studying the response to oxidative stress of the soil bacterium, Bacillus subtilis. Bacteria, pathogenic and nonpathogenic, live in complex environments and must monitor their surroundings for nutrients, noxious chemicals, predators, etc. They accomplish this by using proteins that sense the environment (sensor proteins) and proteins that enact changes in gene expression (transcription factors) to ultimately alter the physiology of the cell and accommodate the changing conditions. B. subtilis uses the stressosome, a multiprotein complex, to sense its environment and we are interested in asking the following questions: what are the roles of the individual sensors, what are the molecular protein interactions that control their activities, and what other signals does the stressosome sense besides physical environmental stress? Our preliminary results suggest the stressosome also senses oxidative stress. We approach these questions using a combination of genetics, biochemistry, molecular and microbiology techniques. 

Students in my lab will study the bacterial response to oxidative stress including reactive oxygen species, reactive nitrogen species and disulfide stress. Student projects range from classical microbial physiology assays to modern molecular techniques to understand gene expression of stressosome genes and regulation at the protein level. 

Microbial genetics projects include 1) measuring the role of individual genes in the stress response by assaying viability and recovery after exposure to chemicals that produce each of the types of oxidative stress, 2) measuring protein activation after stress in different mutant backgrounds, using reporter assays. Understanding their roles will contribute to our understanding of the bacterial stress response since many of these genes are conserved across bacterial species, including pathogens. 


Molecular projects include 1) measuring the transcriptional response in cells after each stress, specifically asking how genes are regulated at the mRNA and protein levels, 2)  directly assaying the behavior of proteins using in vivo
 assays to understand how proteins interact with each other by Co-ImmunoPrecipitation, and ask how these interactions shape the bacterial response to oxidative stress. 

Funding
Murdock College Research Program for Natural Sciences Grant 2015. P. I. 
W. M. Keck Foundation Grant 2014. Co-P. I. 

Education

Postdoctoral Research, Massachusetts Institute of Technology, 2008-2012
Ph. D. Cell Biology, University of California, San Francisco, 2008
M. A. Biology, San Francisco State University, 2002
B. A. Molecular and Cell Biology, University of California, Berkeley, 2000