Group
Current Research Projects
There are two fundamental aspects of our research that are embodied in all our projects: (1) Effectively utilize genomic data from different sources to discover functions for genes and proteins. (2) Enable testable models of biological systems that incorporate biochemical and genetic data. Many of our projects require the development of new computational approaches and software in order to more effectively use genomic sequence and expression data. These new methods are highlighted under Computational Tools.
Stopping Oxidative Damage
Oxygen radicals are an inherent by product of metabolism in all aerobic organisms from E. coli to humans, yet due in part to the range of biological process affected by oxidative damage we do not understand many of the ways in which organisms alleviate and repair damage. We have built an integrative model of the primary superoxide transcriptional response containing 210 protein-coding sequences from our microarray results, published microarray data, E. coli databases and the primary literature. Many of the genes regulated in E. coli have homologs in the human genome.
Making Biofuels Economical
The cost associated with degrading cellulosic and hemicellulosic components of plants cell walls is a key hurdle in developing a U.S. biomass-based industry. The primary goal of this project is to enhance the conversion of plant material to biofuels using a particularly promising microbe, Clostridium phytofermentans isolated by Dr. Leschine’s research group from a microbial community in forest soil near the Quabbin Reservoir in Massachusetts. In the recently sequenced C. phytofermentans genome we have found several putative cellulases, proteinaceous nanocompartments, a cornucopia of sugar transport systems, and other enzymes.
Evolving Smaller Genomes
Genomic and enviromental sequencing projects have provided a new portal into the genetic diversity of microorganisms. By quantifying the flux of genes into and out of genomes over evolutionary time we have demonstrated that genomes in particular lineages are shrinking. Our goal is to determine the forces reducing genomic complexity. To distinguish among competing hypotheses we are using a combination of comparative genomic studies of natural isolates and mutation accumulation experiments in the laboratory.