Classes for undergraduate research of studying genomes in bacteria will be offered fall 2010 and spring 2011, as a result of The Joint Genome Institute (JGI) approving The Center of Integrated Biosystems (CIB) at USU.

The science department began looking for an undergraduate research opportunity for its students six months ago, said Kenneth White, department head of animal, dairy and veterinary sciences. The CIB submitted an application to the JGI of Utah’s Department of Energy in hopes of taking part in its research on bacterial genomes.

The project has recently been approved and will be conducted in the form of a science elective by Jacob Parnell and Giovanni Rompato, postdoctoral scientists in metagenomics. The class will most likely be called Microbial Genome Annotation, Parnell said.

Parnell said, “We want to use these genomes as a teaching tool. It will be really hands on.”

A genome is the DNA of an organism, Parnell said, and he and Rompato will work directly with a small class of about 15 students to figure out the type of bacteria they have been given by the JGI through sequencing the genome. By the end of the class, the students will know what each genome can do after Rompato and Parnell have gone through the technicalities of the sequencing process step by step. Parnell said sequencing the genome of bacteria is the same process as sequencing the genome of humans and will, therefore, be applicable and valuable to those students studying biological science whose careers will rely heavily on genomics.

Undergraduate research plays a pertinent role in USU’s campus, said Joyce Kinkead, vice provost for undergraduate study and research. There are 1,300 students currently employed in undergraduate research and 26 percent of those who graduate say they have participated in these research opportunities.

“Whenever we have the opportunity for our students to have hands-on learning and apply what they have been learning through real situations, that is a great situation for their education and their future,” Kinkead said.

Parnell said JGI gave USU a type of bacteria it deemed to be unique, and the bacteria will ultimately produce a great deal of new information. The project is diverse and is not only applicable to one type of science, but rather meshes several studies of science together, Parnell said. He said JGI wants research teams to take these projects, because they are time intensive.

The majority of a genome’s information can be determined through computer software. However, 20 to 30 percent of the genome’s functions must be put together one piece at a time, Parnell said. Ultimately, the students who take the class will be able to figure out the evolution and ecology of the bacteria they are analyzing.

Currently, the department of animal, dairy and veterinary sciences is the only science department that has expressed interest in offering the course to their students, but the CIB will be meeting with other deparments in the future.

“At the beginning of the course we can’t say what we will have at the end, because we don’t know,” Parnell said. “So, it’s real research.”

When the class has collected most of the genome data, the students will publish a paper in a scientific journal about their experiences finding undiscovered information about the way bacteria is differentiated by genomes. Parnell said he hopes the class has a positive response from students and a similar class will be available the following year.

“It makes an excellent opportunity for undergraduate research,” said Kenneth White, the CIB’s interim director. “They will actually turn the information into identifying genes and associating functions with the particular parts. That’s where the rubber meets the road and the information becomes most informative.”

White said USU was selected among 19 other universities to participate in this type of genome research. The undergraduate research office was central in making this research possible, Parnell said. He said those in charge of undergraduate research, like Kinkead, are enthusiastic about offering cutting-edge research to students campuswide and spend a lot of time executing the application process for research approval.

“The application process involves getting a group of faculty together to talk about what they are going to do, and then they write multiple drafts,” Kinkead said.

“At some point, they have to get it submitted and then they are on tender hooks until they get news of approval.”

The course that will invest students in this genome research will bring the study of ecology and genetics together by involving topics learned in both subjects, such as pathways, promoters and operon structures, Parnell said. He said the research and publication of an essay in a scientific journal will be of merit for those students who enroll in the course.

– catherine.meidell@aggiemail.usu.edu