March 2, 2010

Research conducted as part of three intro biology labs last semester will become part of a national study. The research, conducted in sections of the course “Molecules, Genes and Cells,” will be contributed to the Genomics Education Partnership (GEP), a collaboration among more than 60 colleges and universities across the country and spearheaded by the Washington University in St. Louis’ biology department and Genome Sequencing Center. Other institutions involved in the GEP include California Polytechnic State University-San Luis Obiospo, Rochester Institute of Technology, Georgetown and Duke Universities and Macalester and Pomona Colleges, to name a few.

Brigit High ’12, hard at work on her lab

The goal of joining the partnership was to introduce undergraduates to original genomics research early on in their coursework, said Julie Emerson, lab coordinator with Amherst’s biology department, who organized the college’s involvement. But on a broader level, the collaboration and, by extension, the work done by Amherst undergraduates, will provide a better understanding about the relationship between the organization of DNA, the packaging of chromatin (the proteins and DNA that make up chromosomes) and how a gene is expressed as a particular trait, she noted.

“Imagine the development of any complex multicellular organism starting from a single fertilized egg,” Emerson said of the idea behind the research. “Each cell of that developing embryo contains the same DNA, but it must be read out differently at different times and locations to produce an organism with, for example, specific but basic body axes—such as a front and back—and with all of its organs in the right locations. The amount of orchestration this requires is mind-boggling.”

“Having more information about gene regulation and genome organization in general will give us all a better idea of how living organisms develop, grow and stay healthy,” she added.

Through the three GEP-structured labs, “Molecules, Genes and Cells” students learned how to annotate a specific region of newly-sequenced DNA from the fruit fly Drosophila erecta. (Drosophila erecta is a close relative of the widely-used model organism Drosophila melanogaster, whose genome sequence was published in March of 2000.) Each student in the course compared a region of DNA from the two species to locate and carefully map in Drosophila erecta all the parts of a particular gene that together code for a specific protein.

Emerson, in the lab

“Once a genome is sequenced, the next step to understanding the genetic basis of almost any trait is to find the protein-encoding regions,” Emerson said. “Although there are many good gene predictor software programs out there, what the students in our course discovered is that none of them are ideal—and they often disagree with each other—so a human brain is still required in many cases to sift through the possibilities and come up with the best gene model.”

Developing those lab skills was doubly important since it was the first biology course at Amherst for about 20 percent of the undergraduates, she said. Many of the remaining participants will declare a science major and be able to use the techniques they learned from the labs in future projects.

The labs also introduced students to the field of bioinformatics and the reality that advanced work in many areas of biology and biomedical research requires a lot of computer time going through ever-growing databases of DNA and protein sequences.

“Even though we were working with a piece of fruit fly DNA, I could easily imagine employing the same techniques we used in class for the human genome project—annotating and mapping diseases, traits and other characteristics,” said Bryce Einhorn ’11, a student in the course. “It definitely gave me valuable insight into gene research and the important advances being made in that field.”

Classmate Nathan Belkin ’12 was also cognizant of the “real-world” aspect of the labs: “The project was very insightful and useful because it was truly an application of science in action. Oftentimes labs are designed to reinforce concepts learned in lecture and not necessarily current research in the science fields. This lab, however, was the opposite. We were performing up-to-date and relevant research. This gave the lab a different and more important feel.”

Emerson said she was glad for the newfound insight that the labs and the GEP provided the students. “I think they gained a hands-on knowledge of eukaryotic gene structure—hopefully understanding it better than just by reading the textbook or listening to lectures—while contributing to ongoing, collaborative genomics research.”

“The latter, in particular, seemed important to them—they really liked knowing they were joining forces with students from dozens of colleges and universities all over the country.”