Fiona S. L. Brinkman, Professor
B.Sc., University of Waterloo
Genomics and bioinformatics provide powerful new methods for the study of microbes and microbial pathogenicity, hence the development of a new field, Pathogenomics. I am forming an interdisciplinary "wet-lab" and computer lab to investigate the following fundamental pathogenomics questions:
How does a given pathogen and the property of pathogenicity evolve?
What components of a bacterial genome sequence can be utilized to predict the subcellular localization of proteins, particularly cell surface-exposed proteins of relevance for pathogenicity?
What components of a genome sequence can be used to identify virulence factors?
To investigate these questions, the laboratory will be performing and developing computational analyses of genomes, individual proteins and other laboratory data to facilitate the generation of new hypotheses relevant to bacterial pathogenesis. These hypotheses will then be tested in the laboratory using molecular genetic tools and model host systems. Analyses include:
- Improved computational detection of horizontal gene transfer through both codon usage bias and sequence similarity approaches, as horizontal gene transfer appears to be an important mechanism in the evolution of new pathogens. Laboratory confirmation of true cases of horizontal gene transfer, leading to a more accurate evaluation of the role horizontal gene transfer has played in the evolution of a new pathogen (or the evolution of new pathogenic properties in an existing pathogen).
- Analysis of a database of bacterial proteins of known subcellular localization and development of an improved version of the program PSORT to predict subcellular localization of bacterial proteins. The focus is toward eventual prediction of surface-exposed regions of proteins. Structural modeling and analysis of key surface-exposed bacterial membrane proteins complements this work.
- Analysis of currently known and sequenced virulence factors in all bacterial pathogens to identify sequence and structure commonalties (particularly features of pathogenicity/genomic islands), functional subgroupings, and their distributions within and between species.
Software development for these projects will focus primarily on development of web-based applications and viewing tools. Some projects are in collaboration with the Pathogenomics Project that I coordinate (see link below). This laboratory endeavors to provide a stimulating interdisciplinary research environment for students to learn about bioinformatics, genomics, bacterial pathogenicity, molecular biology, and microbiology.