Grad Student's Quest to Clean Environment of Heavy Metals Nets High-Tech Internship

Tampa, Fla. (Sept. 5, 2008) - For the second year, USF PhD student Andrea Rocha is doing a 12-week summer internship in the Computational Biology Institute in the Computer Science and Mathematics division at the high-tech, high-prestige Oak Ridge National Laboratory (ORNL) in Oak Ridge, Tennessee. Her goal - to find the best way for a microbe, Shewanella (she-wan-ella), to immobilize or transform heavy metals found in the environment that are a toxic threat both to people and the environment. The aim is to transform the toxic metals to a non-toxic state. It’s called "bioremediation," and the potential for just the right bacteria to help eat up toxic wastes in contaminated sites is great.

"I came to USF because I was interested in bioremediation," says Rocha, who came to the College of Engineering’s Department of Civil and Environmental Engineering doctoral program armed with a master’s degree in ocean science. Her current work involves growing the most useful varieties of the Shewanella bacteria and looking for those with the best potential for reducing environmental contamination from metals such as iron, uranium, manganese and sulfur.

“Shewanella shows promise for bioremediation efforts when these toxins show up in sediments,” explains Rocha. “My goal is through computer modeling and experimental studies to find ways to enhance the activity of this bacteria.”

Rocha, who came to USF through the Bridge to the Doctorate program and whose major advisor at USF is Peter Stroot, has for the two summers been working with  Nagiza F. Samatova, a senior research scientist at ORNL. With help from Samatova, Rocha is using computer modeling programs to reconstruct the metabolic pathways of multiple strains of Shewanella and then make predictions based on the metabolic capabilities of each species.

“Shewanella is a bacterium capable of utilizing a wide variety of compounds to meet its energy and growth requirements,” explains Rocha.

During her 2007 internship, Rocha learned various computer tools and software programs in order to reconstruct the metabolic pathways of 11 different varieties of Shewanella. This year, she is using that experience to evaluate two models in predicting transcriptional gene response. Results from this study will be used to evaluate the value of these models and to make predictions about Shewanella’s response to different environmental factors. Many tools and data are available to her through the Shewanella Federation, a consortium of researchers from national laboratories and universities, she says.

To be able to do the 2007 and 2008 internships, Rocha joined the U.S. Department of Energy’s (DOE) Research Alliance in Math and Science (RAMS) program. The RAMS program is designed to provide collaborative research experiences among faculty and students at U.S. colleges and universities and DOE national laboratory researchers. Each student interns is assigned a research mentor.

For Rocha, who aspires to work at one of the national labs after getting her PhD, the experience is invaluable.

The University of South Florida is one of the nation's top 63 public research universities and one of 39 community-engaged public universities as designated by the Carnegie Foundation for the Advancement of Teaching. USF was awarded more than $300 million in research contracts and grants last year. The university offers 219 degree programs at the undergraduate, graduate, specialist and doctoral levels, including the doctor of medicine. The university has a $1.6 billion annual budget, an annual economic impact of $3.2 billion, and serves more than 45,000 students on campuses in Tampa, St. Petersburg, Sarasota-Manatee and Lakeland. USF is a member of the Big East Athletic Conference.

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News release by Randolph Fillmore