RIT Students Interpret Genetic Sequences to Decode Blueprint of a Fruit Fly

Rochester Institute of Technology students are getting hands-on experience interpreting raw genetic data provided by the Genomics Education Partnership at Washington University, home to one of the few high-volume genome-sequencing centers in the world.

Students in professor Gary Skuse’s Advanced Applied Genomics class are painstakingly stitching together sequences of the genetic material of a little known fruit fly.

The data is real; the work is hard and sometimes tedious. The intensity of the class requires a high teacher-to-student ratio. In this case, one professor and two teaching assistants for seven students. The upper level bioinformatics class—which applies computer science to biological applications—meets for eight hours each week in a small computer lab.

“It’s a big commitment for everyone involved,” says Skuse, director of bioinformatics in RIT’s College of Science.

What makes Advanced Applied Genomics particularly challenging is precisely what draws many students to science: the thrill of discovery. Skuse and his teaching assistants Rhea Sanchez and Ashlee Benjamin work closely with the students to unravel and interpret raw genetic data supplied by the Genomics Education Partnership, a consortium of scientists, led by geneticist Sally Elgin at Washington University. The partnership co-authored an article published in the Oct. 31 issue of Science highlighting the model curriculum that transforms undergraduate classrooms into real-world laboratories.

The partnership provides students with DNA sequences and covers the cost of regenerating poor-quality data. The rest is up to the class, which must discover what is hidden in the sequences without a lot of guidance.

Once the students have edited or “finished” the sequences—in this case, lining up 40,000 contiguous nucleotides, or molecules that make up DNA—they can begin annotating or extracting the genetic features. They note where genes begin and end, and the pattern that makes this particular fly different from its cousins. The students tap all available resources—software gene checkers that act like spell checking tools, comparisons with previously annotated flies, and, most of all, each other.

“It’s really a group effort with a lot of discussions with the students,” says Skuse. “It’s very collaborative, very interdisciplinary. I think it’s safe to say we’re past the age where a scientist works as an individual. We acknowledge that we work better as groups than as individuals.”

At the end of the quarter, Skuse will submit the results back to Washington University along with the students’ pre- and post-course surveys assessing the effectiveness of the curriculum. Their work stands a chance of getting published, but more immediately contributes to the collective knowledge of the fruit fly.

“Our primary goal is education, so effectively, we’re all learning how to teach more effectively using this real-life scenario,” Skuse says.

Note to editors: A word about fruit flies…They are cheap and efficient. They reproduce quickly and are easy to manipulate in the laboratory. They are insects, not fellow mammals and, for most scientists, do not bear the same ethical burden. Yet, as model organisms, fruit flies are giants. Scientists have studied them since the early 1900s to learn about human biology. What might seem like an impossible leap from fly to human comes down to oxygen.

“The bottom line is flies breathe air and humans breathe air,” says Gary Skuse, director of bioinformatics. “And the process of the way cells convert energy and use oxygen is the same in flies as it is humans. Life is life and there are a lot of common processes.”