Ph.D. Microbiology, University of Illinois at Urbana-Champaign, 2001

Research

I am interested in understanding the evolution of fundamental cellular systems and how microorganisms function at a systems level.  My lab focuses on two areas that allow us to explore these questions:  understanding the transcription mechanism of the protist, Giardia lamblia and comparative analyses of microbial genomes linked to wet-lab experimentation.

Students in my lab will practice bioinformatics, genetics, molecular biology and biochemistry, becoming aware of how bioinformatics is used to drive research in modern microbiology.

Unique Mechanism of Transcription in the Human Parasite, Giardia lamblia.

My wet lab uses comparative genomics to guide investigation of the basal transcription system of Giardia, using techniques of molecular biology and biochemistry.  Giardia occupies an interesting evolutionary position, being the earliest diverging eukaryote known.  Thus, the transcription system seen in Giardia will enlighten us as to how the fundamental process of transcription evolved in eukaryotic organisms, including humans.

Bioinformatics:  Comparative Analyses of Microbial Genomes.

Perhaps no other field of scientific inquiry has been more profoundly impacted by genome sequencing than microbiology.  The number of complete microbial genomes is currently over 400, and projections indicate that 1000 microbial genomes will be completed in the year 2007.  Thus, there is a wealth of data available to microbiologists that simply did not exist as little as 10 years ago.  My lab seeks to take advantage of these data to understand microbial evolution and cellular function through comparative analyses.

As part of this work, we are collaborating with Dr. Matt DeJongh (Computer Science Department, Hope College) and Dr. Nathan Tintle (Mathematics Department, Hope College) to form an interdisciplinary bioinformatics team with the goal of developing and improving software tools necessary to access and analyze genomic data.  In collaboration with Argonne National Labs, our current efforts are focused on a genome annotation suite known as the SEED (our local version). Our software enables the rapid generation of genome-scale metabolic models of microbes, allowing the prediction of organism behaviors at the whole-cell level (Systems Biology).

In addition, my lab uses techniques of comparative bioinformatics on microbial genomes to identify candidates for "missing genes" in biochemical pathways performed by microbes. These candidate genes are tested in the wet-lab, using techniques of molecular biology, genetics and biochemistry.

Investigation of the Biology of Shewanella: Bioremediation of Toxic Waste

The construction of genome-scale metabolic models and identification of "missing gene" candidates is being conducted to understand the biology of the bacterial genus, Shewanella. These organisms are able to respire (breath), using many compounds as terminal electron acceptors. Because of Shewanella's ability to use a variety of compounds for repsiration, these organisms have potential to be used in the rational cleanup of toxic waste sites. For example, Shewanella are capable of using radioactive uranium as an electron acceptor, converting soluble uranium into an insoluble form. This prevents of the spread of radioactive waste in ground water systems surrounding toxic waste sites. Modeling these organisms at a systems level, coupled with wet-lab verification of model predictions and "missing gene" candidates will lead to a better understanding of the biology Shewanella and to rational design of bioremediation strategies using these organisms.