The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Abstract

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

Implementation of a Collaborative Series of Classroom-Based Undergraduate Research Experiences Spanning Chemical Biology, Biochemistry, and Neurobiology

“…The target demographics for CUREs also vary across the undergraduate spectrum from introductory major and nonmajors courses to upper-level multisemester courses (Nadelson et al ., 2010; Brownell et al ., 2015; Rowe et al ., 2015). High-profile CUREs, including the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) and the Genomics Education Partnership (GEP), have been highly successful at linking together introductory laboratory experiments across multiple institutions with common experimental procedures and producing significant scientific and student benefit outcomes (Shaffer et al ., 2010; Jordan et al ., 2014; Lopatto et al ., 2014). …”

Enhancing Hispanic Minority Undergraduates’ Botany Laboratory Experiences: Implementation of an Inquiry-Based Plant Tissue Culture Module Exercise

“…Due to these reasons, at the Department of Biology of the University of Puerto Rico Mayagüez (UPRM), of the approximately 1500 undergraduate majors only an estimated 8% of the students are able to conduct independent research during the academic year. Recognizing these limitations and the benefits of engaging students in the scholarship of science as early as possible, faculty and departments have begun to successfully implement research-or inquiry-based laboratory exercises in small-, medium-or large-enrollment courses throughout different curricula (Shaffer et al, 2010;Siritunga, Montero-Rojas, Carrero, Toro, Vélez, & Carrero-Martínez, 2011;Wei & Woodin, 2011). nutrition, primary and secondary metabolism, and pathology); plant modification and improvement (studies in the production of interspecific and intergeneric hybrids through embryo rescues, isolation of genetic variants, and the production of genetically enhanced plants); production of pathogen-free plants (studies in abilities to stop infection of plants by viruses, bacteria and fungi); germplasm storage (studies in the conservation of genetic resources); and product formation (studies in a large number of plant-based chemicals of pharmaceutical and industrial interest).…”

CRISPR-Cas Technology In and Out of the Classroom

“…[12][13][14][15][16] CUREs often have students plan and execute a series of experiments that are directed at solving a scientific problem, sometimes in direct connection with the research interests of the faculty teaching the course. 4,14,[17][18][19][20][21] Often, these research projects are a quarter, semester, or year in length and guide students through one or more aspects of a larger research project. In some cases, these experiences can be used to generate both laboratory reagents and data as well as data pertaining to student outcomes resulting from the implementation of CUREs.…”