Biologists earn grants: Biology Alumni Newsletter: Summer 2011: Newsletters: News & Events: Department of Biology: Indiana University Bloomington

Biologists earn grants

Monday, June 13, 2011

Grant studies bacterial mutation

Professor Patricia Foster and Distinguished Professor Michael Lynch, along with Haixu Tang, associate professor of informatics and computing and director of bioinformatics for the Center for Genomics and Bioinformatics at IU Bloomington, and Steven Finkel, associate professor at the University of Southern California, have been awarded roughly $6.25 million from the U.S. Department of Defense to study the constraints on mutation in microorganisms. This award is one of several grants that were given by the Department of Defense to 32 universities as part of its Multidisciplinary University Research Initiative program, which is focused on multidisciplinary research efforts that intersect more than one traditional science discipline to address critical issues of concern to the nation.

Using high-throughput techniques to collect large amounts of data and bioinformatics to make sense of the data, the researchers plan to study how mutations accumulate in a species, determine whether mutations are more likely to occur in predictable areas, how the environment influences mutation rates, and evaluate the genome-wide molecular spectrum and rate of spontaneous mutations in Escherichia coli (E. coli) and at least 25 other bacterial species. The findings from this research could remarkably improve our understanding of microbial evolution. According to Foster, “The practical application of this research, as far as the Department of Defense is concerned, is forensic. They are interested in defining mutational signatures that may help to identify the source of a bacterium, be it a naturally occurring disease organism or a bioterrorism agent.”

According to the IU press release, the team’s research efforts will center on the following objectives: (1) Determine the contributions that important pathways for DNA repair make to the genomic mutation rate. (2) Determine the extent to which cellular stress responses impact mutational rate. (3) Assess the mutational response to common growth conditions. (4) Broaden the understanding of microbial mutation rates and test a recently developed model for the evolution of genomic base-composition. (5) Develop a new class of population-genetic models for understanding the evolution of mutation rate itself.

Foster added, “Our overall goal is to establish baseline parameters, achieve mechanistic understanding, and develop predictive models that will yield a comprehensive understanding of the forces that ultimately define short-term and long-term patterns of microbial molecular evolution.”

Foster, the principal investigator of the grant, is a fellow of the American Academy of Microbiology and is widely considered an expert on bacterial and microbial mutation, namely the mutagenesis of E. coli. Her lab is interested in studying the molecular mechanism of recombination-dependent mutations and the transcriptional and post-transcriptional regulation of DNA polymerases and their subunits.

Lynch, an evolutionary biologist, is a member of the U.S. National Academy of Sciences and a fellow of the American Academy of Arts and Sciences. His research is focused on mechanisms of evolution at various levels, with a focus on the roles of mutation, random genetic drift, and recombination through the use of several model systems including Daphnia and Paramecium.

Pikaard named HHMI-GBMF Investigator

Biologist Craig Pikaard is one of 15 cutting-edge scientists who will benefit from a new joint initiative sponsored by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation (HHMI-GBMF) to support fundamental plant science research. The two organizations will provide $75 million over the next five years to the new initiative that is designed to give these 15 HHMI-GBMF Investigators, who hail from 13 institutions, the flexibility to move their research in creative new directions.

“GBMF and HHMI believe the research will generate high-impact discoveries with implications for a range of intertwined concerns facing society: food production, human health, protection of the environment and identification of renewable energy resources,” said GBMF’s Chief Program Officer for Science, Vicki L. Chandler. Both groups believe such research is crucial, especially in light of the United Nations’ figures which indicate the current global population of 7 billion will grow to 10 billion by 2050. Currently 1 billion members of the world’s population suffer from lack of nutrition, and those numbers are expected to rise in the years to come. Increasing energy demands make it imperative to find alternatives to fossil fuels. Both needs mean that agriculture will face increasing demands to produce both food and fuel.

Pikaard’s research focuses on how plants control the activity of their genes, using a member of the mustard family, Arabidopsis thaliana, as his research model. His specialty is the mechanisms of gene silencing. “I anticipate that becoming an HHMI-GBMF Investigator will have a huge impact on my academic life,” he said. “It will buy a lot of creative freedom, both by allowing me to focus more time on research and by making it financially possible to move the lab in new directions that mix genetics, genomics, cell biology and protein biochemistry and that take full advantage of the amazing facilities we have here at IU.”

Pikaard, who is the Carlos O. Miller Chair of Plant Growth and Development, holds joint appointments in the Department of Biology and the Department of Molecular and Cellular Biochemistry. His new HHMI-GBMF appointment begins in September. He estimates that his new position will result in IU receiving over $1 million per year, including Pikaard’s salary and benefits, a fee paid to IU for lab space use, and over $600,000 for direct research funding per year.

Another HHMI-GBMF Investigator also has ties to the IU Department of Biology. Mark Estelle, from the University of California, San Diego, was a member of the department for nearly twenty years and like Pikaard, held the title of the Miller Chair of Plant Growth and Development.