The Undergraduate Genomics Research Initiative

Abstract

Modern scientific advances have transformed life sciences research but have had little influence on undergraduate training, leaving an unprecedented gap between teaching and research. Consequently, a consensus is building around the need to reform undergraduate life sciences education [1–3]. Students need to embrace scientific discovery directly, make connections across an otherwise diverse curriculum, learn to manage and interpret today's vast amounts of data, practice using computers to control instrumentation and analyze experiments, and greatly improve quantitative reasoning. Moreover, they need to appreciate that modern life sciences research is increasingly carried out by interdisciplinary teams of scientists—yet teamwork is alien to the highly competitive undergraduate life sciences culture. Indeed, a recent poll by the Science Advisory Board, an international “electronic community” of scientists and physicians, determined that “poor interpersonal skills are hampering the careers of young researchers;” they have difficulty working in teams [4]. Research experience is widely recognized as an ideal way to achieve many of these reforms simultaneously while giving students the chance to experience the emotions, challenges, and satisfactions inherent in doing research. Providing research experience to all life sciences students, however, presents a seemingly intractable scaling problem. Carefully guided by a faculty member, graduate student, or post-doc, the typical undergraduate research project is labor intensive—requiring hypotheses-driven experiments, intense data evaluation, and, often, many different techniques. Although excellent training occurs, most faculty members can productively mentor only one or few undergraduates in this kind of research. Even a major research university such as the University of California Los Angeles (UCLA) can accommodate only about 20% of qualified students in this way. The inherent blend of wet laboratory experience and in silico experimentation of genomics research makes it an ideal model to illustrate the interdisciplinary nature of life sciences research today. Clearly, a new approach to undergraduate research is required, one that reflects modern life sciences research yet enables large numbers of students to participate. We sought to address this problem by developing a microbial genome sequencing project specifically for undergraduates, The Undergraduate Genomics Research Initiative, UGRI [5]. The UGRI addresses the problems of scope and scale in two ways. First, to serve as a hub for this collaborative research network, we created a new interdisciplinary research course, LS187, “Principles and Practices of Genomics Research,” that blends topics in molecular biology, microbiology, evolution, bacterial physiology, genomics, physics, and bioinformatics in the sequencing and analysis of a microbial genome. Second, we dissolved the traditional boundary between coursework and research by enabling large numbers of students in traditional courses to directly contribute individual research effort to the LS187 hub course, in turn receiving raw data for their own analysis and report. Thousands of students annually participate in this collaborative research project. Here we describe the structure and outcomes of the first three years of the UGRI, focusing on the course, LS187. We also discuss how other institutions can adapt this collaborative research approach.