Washington University in St. Louis is in the spotlight for its pivotal role in the Genomics Education Partnership (GEP), a collaborative effort to provide research experience in genomics to undergraduate classrooms across the country.
Genomics, the study of an organism’s entire genome (collection of DNA), is an exciting area for students to get a taste of research.
The GEP currently consists of more than 40 faculty members from a variety of schools, including historically black and Hispanic-serving institutions, and schools with a high proportion of first generation college students.
By making it easy for undergraduate institutions to incorporate research into their regular, academic-year curricula, the GEP can reach underserved students who otherwise have limited opportunities to learn to think like scientists.
At the helm of this mission is Sarah C.R. Elgin, Ph.D., WUSTL professor of biology and professor of education in Arts & Sciences, as well as professor of biochemistry & molecular biophysics and professor of genetics in the School of Medicine.
In 2002, Elgin was one of 20 professors awarded $1 million from the Howard Hughes Medical Institute (HHMI) to bring research into the undergraduate classroom. Over the next four years, Elgin and her colleagues developed and implemented a research-based genomics course for juniors and seniors at WUSTL to polish and interpret their own portion of raw DNA sequence.
The course, Biology 4342, “Research Explorations in Genomics,” is a collaborative effort. Elgin co-teaches with Dr. Elaine Mardis of WUSTL’s Genome Sequencing Center and Dr. Jeremy Buhler of the Department of Computer Science and Engineering. Several other members of the WUSTL community provide guest lectures to illustrate how they have used genomic approaches to answer diverse questions in their own research.
Elgin’s course was so successful that she became one of eight professors to have their original HHMI grant funding renewed in 2006. With that support, she set out to make the course available to undergraduates at institutions across the country.
Researching in silico
Biology majors at WUSTL often begin their research by spending a summer in the laboratory under the guidance of a faculty, graduate student or post doctoral research mentor. However, the privilege of a summer research experience is unusual at many institutions due to inadequate facilities, limited funding, high student-to-faculty ratios, and a lack of experienced or research-active mentors.
Elgin’s course overcomes these barriers by providing students with in silico, or computer-based research opportunities.
This strategy minimizes the cost of research materials because the necessary data is freely available on the Web and most institutions already possess adequate computer facilities. Mentoring is also economized by teaching students the same electronic tools and strategies in a group setting and by relying on alumnae of the course to serve as undergraduate teaching assistants (TAs). Thus, one dedicated faculty member can provide research opportunities for a much larger number of students than would be possible in traditional, one-on-one mentoring relationships. GEP faculty and TAs learn the relevant software during summer workshops at Washington University.
“Our GEP faculty is an impressive group,” reports Elgin. “Each member has taken the basic format and adapted it to the requirements of their institution and the needs of their students. Their energy and enthusiasm are terrific!”
The GEP’s approach makes offering a research-based course a viable option for a wide variety of institutions. Students in the program are currently working on a comparative genomics problem that focuses on genes in a heterochromatic, or tightly packed, region of the DNA. In the future, students might participate in research ranging from regulation of gene expression to the evolution of a species.
The class typically begins with students claiming their own “fosmids,” or chunks of raw DNA sequence, from the GEP Web site, which acts as an organizational hub for publicly available data. A DNA sequence is a succession of letters corresponding to the primary structure of a real strand of DNA — in this case, Drosophila (fruit fly) DNA.
Drosophila is one of the most commonly studied model organisms in biology. “Understanding how its genes are organized and function will help us to understand how human genes function,” Elgin explains.
In the first part of the course, students work to improve the quality of their chunk of DNA. This process, known as “finishing,” is necessary because raw sequence data often has problem areas that can only be corrected by hand. Using specialized software, students identify gaps, potential assembly errors and low quality regions in the sequence data for their fosmid. Students then design and order additional sequencing reactions that will generate the data needed to remedy these problem areas. Weekly orders are processed simultaneously at WUSTL’s Genome Sequencing Center. Students use the resulting sequence data to polish their fosmids to high quality standards.
The second component of the course is annotation, the construction of “gene models” that distinguish coding regions of the DNA from noncoding regions. In eukaryotes such as humans and fruit flies, only a small percentage of the genome contains instructions for making proteins. Elgin explains, “It’s as though someone has given you Moby Dick, but they’ve actually given it to you in twenty volumes because they’ve interspersed gibberish into the text at random places. The students’ job is to go in there and parse out the sentences.”
Sequence data and annotation results from student work are being submitted to public databases that are used by researchers around the world. So far, one scientific paper based on student research has been published (with students as co-authors); additional papers are expected to follow.
The GEP is one of a few undergraduate programs that are taking on the challenge of working with eukaryotic genomes. These genomes are more complex and orders of magnitude larger than the more commonly studied prokaryotic (for example, bacterial) genomes. The development of a coordinated research effort that pools student contributions across institutions allows the GEP to tackle challenging, large-scale projects.
“It’s great in terms of a divide and conquer strategy,” says Elgin.
Borrowing from Confucius
To sum up the philosophy of the GEP, Elgin references an ancient Chinese proverb that states, “I hear and I forget; I see and I remember; I do and I understand.” In other words, Elgin maintains that students can’t truly understand the scientific process until they have conducted their own research.
This assertion is supported by an article recently published in Science (Oct. 31, 2008) in which Elgin and her colleagues present results from an exit survey of students who participated in either the GEP, a course without research, or a summer research experience. The evidence suggests that the GEP provides students with a more comprehensive learning experience than traditional, lecture-based courses. The results also reveal that the GEP course is comparable to a summer research experience in terms of its capacity to help students prepare for a career in science.
According to Elgin, the success of the GEP can be partially attributed to students’ sense of ownership over their research.
“It makes a huge difference to students when you tell them, ‘You’re responsible for this,'” she explains. “‘This is going to go in the databases. This is going to be used by different scientists. Do it right.'”