BGSU biology undergraduates will soon be contributing to the body of knowledge in genomics while they learn. BGSU has been selected as one of 12 institutions nationwide to pilot the new Microbial Genome Annotation research program through the U.S. Department of Energy Joint Genome Institute (DOE JGI).
Analysis of the genomes of microorganisms is an important new tool in understanding the biology of organisms, and with new technologies available, complete bacterial genomes can be sequenced in a matter of hours. Undergraduates will have the opportunity to computationally map the DNA of a microbe, conduct experiments to test their findings, publish their work in the worldwide online genome database—and gain valuable skills in genomics and bioinformatics.
Bowling Green will collaborate with the Department of Energy and the other 11 pilot schools, which include Michigan State University, UCLA, the University of Nebraska at Lincoln, the University of South Florida and Hiram College. “The scope of the project is to work in teams,” an important skill for young scientists to learn, said BGSU project director Dr. Zhaohui Xu, biological sciences.
Xu became aware of the JGI program at a bioinformatics workshop where she met Dr. Cheryl Kerfeld, director of the JGI Education Department and leader of the nationwide initiative. Xu and her biology colleagues Drs. George Bullerjahn, Paul Morris and department chair Scott Rogers wrote the application to be part of it. Bowling Green’s reputation in microbiology and genomics, along with the support of the biological sciences department, helped secure its place as one of the first universities in the country to collaborate on the project, Xu said.
An Indonesian hot spring is the home of the bacterium whose genome is the first to be annotated by the Undergraduate Microbial Genome Annotation Program. Photo courtesy of Karl Stetter.
The first genome to be analyzed is a microbe found in Indonesian volcanic hot springs. “What we hope to gain from this is some insights into how bacteria survive in extreme environments,” Morris said. “If we can learn how life can survive in these environments, it can help us address some of our environmental and energy challenges today,” Xu added.
Assembling DNA sequences into complete genomes may also allow scientists to identify enzymes for potential commercial applications, they pointed out. Though invisible to the naked eye, microbes are powerful organisms that play a critical role in the atmosphere and the environment, and can have many practical applications, such as cleaning up oil spills and conversion of plant products to ethanol.
The project is also in line with National Science Foundation initiatives to improve the training of students in the science, mathematics, engineering and technology disciplines, Xu and Morris said.
Changing science education, building knowledge
The project represents an important step for science in general and for BGSU in particular, according to Xu and Morris. “This is certainly the most exciting change in our undergraduate program since we developed the marine biology program a quarter century ago,” Morris said. “It’s an opportunity in several directions.”
In the initial phase, beginning in January, Xu, Morris and their students will use the Collaborative Genomics Annotation Tool, a bioinformatic platform being developed by Kerfeld and colleagues at the Argonne National Laboratory in Chicago to begin decoding the first genome, which will also be worked on by the other participating schools. Then, each school will choose a microbe to “adopt,” Xu said, and the project will expand to other biology faculty, who can incorporate the organism into their courses across the curriculum. Xu has already been working on a special microbial genomics course dedicated to the genome analysis program.
The bioinformatic analysis of genomes “could raise interesting questions and hypotheses,” Xu said. “The next step, in two to three years, we will be looking at functional genomic research and ‘wet lab’ experiments to test and verify what we find with our computers.” She and Morris also foresee spin-off research projects for those who want to look more deeply at a gene sequence. “Student research in this project could evolve into honors theses and projects and real publications,” she said. “Students will be making meaningful contributions. Their results will be deposited to online databases and be accessible to research communities around the globe.”
The excitement of discovery is powerful, Morris said. “They’ll be looking at stuff no one has seen before.”
Because the students’ data will be credited with their names attached, there is considerable accountability involved, the two biologists said. Responsibility for quality control will rest with participating faculty, who will conduct backup checking of data. In addition, “redundancy is good,” observed Xu, and if more than one institution works the same sequence, it will actually be helpful in ensuring accuracy.
A vast undertaking
The originator of the groundbreaking Human Genome Project, which was later taken over by the National Institutes of Health in the late 1980s, the Department of Energy is the world leader of genomic research of microbes that contribute to environmental stewardship and clean energy, Xu said.
The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories: Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge and Pacific Northwest, along with the Stanford Human Genome Center, to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and cleanup.
“They have an ambitious plan,” Xu explained, noting that the JGI hopes to sequence the genome of all cultured bacteria and archaea in the next few years, and “the amount of sequence is huge.” With more than 5,000 genomes, averaging 4 to 5 million base pairs each, “they need the input of a big community, including our BGSU undergraduates, to annotate all that,” Xu said. There are about 100 genomes “in the pipeline now,” she added.
Hence, the education component drawing in undergraduate researchers—a move predicted to revolutionize undergraduate biology research, according to Xu and Morris. As one of the first participants, BGSU will help develop new models to be disseminated nationally that will help transform life sciences education.