Answers to life, laundry might lie in genome

1/27/2008
BY MEGHAN GILBERT
BLADE STAFF WRITER
Bowling Green State University biologists Zhaohui Xu, standing, and Paul Morris say computer comparisons will be key for students studying the bacteria in the federal research project.
Bowling Green State University biologists Zhaohui Xu, standing, and Paul Morris say computer comparisons will be key for students studying the bacteria in the federal research project.

Bowling Green State University could help the world learn more about where life began, or at least maybe get a laundry detergent that works great in hot water.

BGSU and 11 other schools are taking part in a national research project investigating a bacteria found in a volcanic hot spring in Indonesia.

"We think that life began in this kind of boiling sulfur spring, so there are a lot of teaching principles that come out of teaching about the biology of the organism," said Cheryl Kerfeld, director of the education program for the U.S. Department of Energy's Joint Genome Institute.

The federal Microbial Genome Annotation research program through the Joint Genome Institute is researching the microbe Ammonifex degensii to figure out how the organism survives in such a climate.

A genome is an organism's complete set of DNA.

"It's almost boiling water that would burn your hand instantly. That's where it's happy," said Paul Morris, an associate professor of biology at BGSU.

Zhaohui Xu, BGSU assistant professor of biological sciences, and Mr. Morris are leading the project at the university in which about 18 students are taking part during the early stages.

It's a unique project to be a part of, Ms. Xu said, because it's a national initiative with schools such as the University of California at Los Angeles, Michigan State University, and Hiram College participating. Those at the federal level are personally and physically involved.

Bacteria from this volcanic spring in Indonesia is to be studied by Bowling Green State University and 11 other schools in a U.S. Department of Energy Joint Genome Institute project.
Bacteria from this volcanic spring in Indonesia is to be studied by Bowling Green State University and 11 other schools in a U.S. Department of Energy Joint Genome Institute project.

But why look at a bacteria on the other side of the world that was just recently isolated?

One reason is because nobody has looked at it before. The students involved in this research will be the first to learn about this organism and can experience the rush of discovery, said Ms. Kerfeld, who also is a professor of plant and microbial biology at University of California-Berkeley.

"What we're going to be able to do is enlighten students and captivate their interest," she said.

"If you tell students you're not just doing a canned lab, something you already know the answer to, they are very enlightened," she said.

It's a safe bacteria with about 2,000 genes, compared to others that have about 4,000 or complex organisms with even more.

And there are practical applications because the research possibly could lead to the development of a type of laundry detergent with enzymes to get rid of proteins in hot water, since this comes from a boiling hot spring, Ms. Kerfeld said.

Studying microbes also could lead to environmental, pharmaceutical, and agricultural uses.

It's estimated that only 1 percent of the microbes on the planet have been isolated and studied.

But through such research, the energy department's Joint Genome Institute is hoping to add to the database of known genomes.

What the schools will do is take parts of the genome - BGSU has a chunk of about 100 genes - and run it through a computer program that essentially compares it to others.

Through this process, they can see what genes it has that other organisms also have. They then can look at the proteins of the known organisms and what they do (some proteins replicate cells, others export toxins) and get a feel for what this new organism does.

Those hypotheses will then be manually checked.

"Since this is a new genome we expect to find genes present that we didn't think would be in it," Mr. Morris said.

Most of the research is done in a traditional classroom at computer stations and not the traditional "wet lab" setting.

Students haven't really gotten their feet wet either since the semester just began. Right now students are getting refreshers in the microbiology they need for this type of research and are learning how the computer system works.

In the second half of the semester the students will do the actual research, Ms. Xu said.

During the pilot phase of the research program, all the participating schools are studying the same genome.

Beginning in the fall semester, the project's plans call for schools to be able to choose from a menu of genomes to research, and then complete the work individually.

There's accountability in this, too, because the results of that research will be put into a national database that other researchers will go to when they are doing similar comparisons for new bacteria, Ms. Xu said.

"This is so important to be accurate," she said. "Every step is recorded."

Ms. Xu and Mr. Morris said that they hope the project expands and more professors and students at the university become involved.

Ms. Kerfeld of the Joint Genome Institute said that is their hope as well.

Besides adding to the database of studied genomes, the goal is also to train homegrown scientists.

"We're at a very interesting time certainly in the life sciences research," Ms. Kerfeld said.

"There's a real opportunity here to have cutting-edge research and undergraduate education entwined working together," she said.

Contact Meghan Gilbert at: mgilbert@theblade.com or 419-724-6134.