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Genome project fosters bioinformatics education

Student in lab

As part of the program, high school students will do microbial genome annotation and present the results of their research. Photo: Douglas Levere

By RACHEL RAIMONDI

Published October 24, 2013

“They will actually be doing a research project, and by the time they are done, they will probably be the expert on the particular gene sequence they have studied.”
Stephen Koury, research assistant professor
Department of Biotechnical and Clinical Laboratory Sciences

Next spring, students at local high schools will dive into the study of the marine bacterium Kytococcus sedentarius, thanks to a $1.1 million National Science Foundation grant to UB.

Stephen Koury and his colleagues in the School of Medicine and Biomedical Sciences, received the grant to educate regional high school teachers and recruit high school students to pursue careers in STEM (science, technology, engineering and mathematics) fields. The new program focuses on bioinformatics, an interdisciplinary field that uses software tools to store, retrieve, organize and analyze biologic information. Bioinformatics is a field of rapid growth that provides tools for better health care through improvement in prevention, detection, diagnosis and treatment of diseases.

Koury, research assistant professor in the Department of Biotechnical and Clinical Laboratory Sciences, notes that new jobs on the Buffalo Niagara Medical Campus likely will require training in biotechnology and bioinformatics; the new program will provide a pipeline for educator and student recruitment, training and mentorship in STEM fields at the high school level.

“For us to be successful, we need to create the environment where children not only want to get involved, but want to stay in Buffalo,” says Norma Nowak, professor of biochemistry, director of science and technology at UB’s New York State Center of Excellence in Bioinformatics and Life Sciences, and associate professor of oncology at Roswell Park Cancer Institute. “This needs to be the spark that lights the fire.”

Over the next three years, the grant will allow 450 high school students and 90 teachers to conduct and present scientific research in bioinformatics. The program will involve educators and students from 13 counties, including Niagara, Erie, Chautauqua, Cattaraugus, Wyoming, Genesee, Orleans, Monroe, Livingston, Allegany, Ontario, Wayne and Steuben.

The educational program will begin with a two-week workshop at UB, where high school teachers will receive training in microbial genome annotation. The teachers then will pass on their new skills to selected students in their schools, with support from UB faculty and staff.

During the first semester, students will be introduced to basic aspects of genetics and genomics. They also will receive career mentoring through a partnership with the New York State Area Health Education Center System (AHEC), a unit of UB’s Department of Family Medicine that addresses health care workforce needs.

The second semester will focus on conducting Web-based research in microbial annotation through a program called IMG-ACT, a bioinformatics tool kit available through the U.S. Department of Energy’s Joint Genome Institute. The program will end with a capstone symposium at which students will present the results of their research to university faculty, researchers and employers in the biosciences fields.

For many local students, this will be their first real-world taste of scientific experimentation. And since it’s an unscripted project, students will learn to rely on themselves, rather than the specific direction of instructors.

“We can’t say for sure what they should find,” says Koury. “They will actually be doing a research project, and by the time they are done, they will probably be the expert on the particular gene sequence they have studied. It will give them that joy of discovery.”

Koury and Rama Dey-Rao, clinical assistant professor in the Department of Biotechnical and Clinical Laboratory Sciences, initiated and implemented this innovative teaching approach in 2009 as part of a summer session teachers’ training program in bioinformatics in the Department of Biotechnical and Clinical Laboratory Sciences. The programs grew out of training Koury and Dey-Rao received at the Joint Genome Institute in Walnut Creek, Calif.

They quickly recognized that a longer program would be even more valuable.

Dey-Rao, who also holds a research position in the UB Department of Dermatology, emphasizes the ease of implementation in a classroom setting. “A computer with access to Firefox is all that is needed to teach the students how to manually annotate the genes, as well as to introduce them to basic concepts in biology, biochemistry, molecular biology and bioinformatics,” she says.

Other investigators on the project are Shannon Carlin-Menter, research assistant professor in family medicine and director of evaluation at AHEC; Mary Sienkiewicz, research instructor in family medicine and AHEC director; and Patricia A. Masso-Welch, associate professor in the Department of Biotechnical and Clinical Laboratory Sciences.