Genetics, Molecular Biology
Washington University in St. Louis
Sarah Elgin is Viktor Hamburger Professor of Arts and Sciences, a professor of biology, a professor of genetics, and a professor of education at Washington University in St. Louis.
Sarah Elgin's Genomics Education Partnership is a collaboration of faculty from primarily undergraduate institutions nationwide with the biology and computer science departments, and The Genome Institute of Washington University in St. Louis (WUSTL). The aim is to provide students with an opportunity to participate in a large-scale genome sequencing and annotation research project, contributing to scientific discovery.
Sarah (Sally) Elgin remembers being drawn to science as a child because it offered a concrete way to understand the world around her. "I liked poking and prodding things," she says. "I wanted to figure out how they worked." It's that joy in learning new things that has pushed Elgin to create a program that provides the same opportunity for her students at Washington University in St. Louis (WUSTL).
Elgin does research on chromatin structure, how the DNA is packaged in a eukaryotic cell nucleus, and how that impacts gene expression. This includes an analysis of genomes, the DNA sequence of all of the chromosomes in an organism. In the past 20 years, high-throughput machines that can quickly determine an organism's DNA sequence have revolutionized the field, turning it from a lab-based field that looked at one gene at a time to a computationally based field focused on large-scale data collection and analysis, a field now referred to as "genomics."
As the field became increasingly complex and data oriented in recent years, Elgin realized that her students no longer had the same sort of easy access to the science that she loved as a kid. Biologists now often spend many days studying numbers and graphs on computer screens, not just working with microscope slides or fruit flies. Elgin thought she could motivate students by having them play a real role in the scientific process—not just sitting in a classroom jotting down notes—so she decided to develop curriculum to do that. "The goal is twofold: to bring more genomics into the undergraduate curriculum, and to do it in such a way that students are actually involved in the research project," she explains. The result is a research-based course; students learn to work with large data sets and interact with the university's Genome Institute in transforming a genome's raw sequence data into a more polished, finished sequence and then analyze the information in that sequence.
The task of sifting through mountains of data to find relevant information requires both computer tools and brainpower. "Think of a genome like a copy of Moby Dick—but instead of being the usual thick volume, it's 20 times longer because someone has inserted gibberish at random places," Elgin says. "Our job is to find the sentences." Computers have become good at finding the "words" within a genome, but they often fail to construct good sentences. The students analyze the computer output and learn to use several lines of evidence to construct testable models of the putative genes in an interesting region of a chromosome. As she was developing and testing the curriculum, Elgin quickly realized there was so much interesting work to do that the class could become a nationwide effort that provided a research experience for students across the country. With the help of her colleagues at Washington University, that vision became the Genomics Education Partnership (GEP), which Elgin began in 2006 with her second HHMI professor grant. The partnership now includes more than 100 colleges and universities across the country that provide students the opportunity to work on large-scale DNA sequencing projects.
The work is challenging in its own right, but it also offers students an opportunity to move the science forward. The results of the students' work serve as a foundation for papers that Elgin and others submit for publication in research journals; two journal articles based on the scientific research have been published since 2006, and one (with more than 500 student authors) is in preparation. The information also goes into a national database that scientists use for their own research. In addition, GEP faculty have published three papers in the science education literature to help others adopt this style of teaching. For students, the chance to do something that matters is an incentive to do top-notch work. Currently, the project focuses on the fruit fly's dot chromosome, which may hold important information about genome organization and gene expression. "Students are so excited to do something that doesn't end up in the wastebasket at the end of the semester," says Elgin. "They've been apprentices for so long, and they're just dying for the chance to do something real."