10/22/2009

Blair Studies Microbial Genomics with USDA Grant

  • http-blogs-fandm-edu-wp-content-blogs-dir-29-files-2012-04-jblair-jpg Jaime Blair, assistant professor of biology  

In a field booming with new technology, Jaime Blair wants to take her students back to the "old school."

The assistant professor of biology will do so as the co-principal investigator of a grant project titled "Education in Genomics-Based Microbial Forensics," slated to begin in December. Funded by the U.S. Department of Agriculture, the project aims to create an integrated research and educational environment in which students apply microbial genomics data to solve emerging issues relating to the nation's agriculture, food and environmental systems.

Blair will recruit Franklin & Marshall students to work in collaboration with graduate students at Penn State University funded through the program. Each summer, the undergraduates will travel to State College to present their projects at symposiums.

"The hope is that it will be a good experience for our students to work in a graduate setting, and a good mentoring opportunity for the graduate students," says Blair, who will team with a group of Penn State and Lafayette College professors on the approximately $1 million grant.

Blair's students will examine the genetic diversity of Phytophthora, a group of pathogens that cause billions of dollars in crop losses around the world each year. Scientists have sequenced the entire genome of four species of Phytophthora, allowing Blair and her students to compare data between species. The students will also collect water samples at the Millport Conservancy, a 100-acre nature preserve near Lititz, to survey the natural diversity of Phytophthora.

"Part of the problem is that we have a lot of new technology, and tons of data, but we're losing people who are trained in the more traditional methods of research—out in the field," Blair says. "The goal is to integrate new technology with traditional methods. We want a new generation of scientists who will use both in their research."

Students will study the water samples from Millport using bioinformatics, the computer-based analysis of biological data sets. They will generate DNA sequence data and compare it to the populations of different species. "We want to study the level of Phytophthora diversity at Millport," Blair says. "How many species are naturally occurring there? And how diverse are they? Nothing has been done on genetic diversity at Millport."

Bioinformatics is an emerging discipline at Franklin & Marshall. Blair hopes the grant project keeps the field on an upward trajectory.

"Bioinformatics is a response to technological advances that have produced huge data sets involving genome sequences," Blair says. "How do we analyze 3 billion data points? Microsoft Excel can't handle 3 billion lines."

Jing Hu, assistant professor of computer science, and Christina Weaver, assistant professor of mathematics, have joined Blair in developing the bioinformatics program at F&M. The professors will hold a bioinformatics information session Nov. 2 in the College Houses.

The discipline is also growing at other institutions, thanks in part to Blair's research. Penn State's program will combine new technology with the study of agriculture. It will be, Blair says, "the place where bioinformatics and agriculture meet."

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