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The Dynamic Genome Courses: Introducing Authentic Research to First-Year Undergraduates

Research Summary

Sue Wessler's research concerns the interaction between transposable elements and plant genes. Her laboratory was the first to demonstrate that elements could function as introns, that miniature inverted-repeat transposable elements (MITEs) predominate in normal genes, and that plant retrotransposons are the major cause of spontaneous insertion mutations.

The University of California, Riverside (UCR) is one of the most diverse research universities in the nation and the only Tier 1 research campus in the University of California system with a federal Hispanic-serving Institute designation. Because UCR’s large population of first-generation students is often unaware of the rigor demanded by STEM professions, they typically have a poor understanding of what constitutes academic research, or the challenges of attending a Tier 1 research university.

The Dynamic Genome (DG) course is specifically designed to address this need.  Now in its third year at UCR, the DG course is an example of a student-centered environment. This hands-on bioinformatics/wet lab course is taught in the state-of the-art Neil A Campbell Science Learning Laboratory. First articulated in Wessler’s HHMI Professor Program in 2006, the DG course is an undergraduate laboratory that replicated her successful research lab where students learn to navigate computational and experimental methodologies applied to transposable elements in plant genomes.

The focus on transposable elements (TEs) was chosen for several reasons. First, TEs represent a relatively simple genetic system with a simple purpose, to increase their copy number without killing the host. Second, TEs evolve rapidly and promote rapid genome evolution. This feature has been exploited in the design of experiments where, for example, students detect polymorphism in plant genomes due to TE insertions. This provides a memorable example of genetic variation as students experience the appearance of new polymorphisms in a population. Third, TEs are incredibly abundant—accounting for over 50 percent of the human genome and over 75 percent of some plant genomes. Their abundance makes computational analysis essential. More importantly, despite their abundance, TEs are largely ignored as researchers computationally “mask” them to reveal and study the far less abundant genes. This means that almost 50 percent of each eukaryotic genome sequence is a potential treasure trove of TEs just waiting to be discovered and analyzed by first year undergraduates participating in the DG course. This provides a virtually limitless opportunity for discovery because the sequences of eukaryotic genomes are being released for public analysis at an ever-increasing rate.

During two three-hour lab periods per week, the first five weeks of the DG course expose students to bioinformatics and experimental tools for molecular biology. In the second five weeks, students apply those tools to authentic research problems from the Wessler lab. DG course students also learn how to (i) design controlled experiments and analyze data, (ii) access DNA databases and other online tools, (iii) keep a digital notebook using iPads and software developed by the DG staff, and (iv) present their data orally and in posters. Finally, students have the opportunity to interact with professors and research scientists to learn about STEM career options, receive advice on the “workings” of a research university and college success. With the tools and knowledge from the DG course students are poised to join faculty laboratories on the UCR campus.

Taught until 2010 at the University of Georgia, the DG course came to UCR with Wessler and co-director Dr. James Burnette, attracted by the diverse student body and with an explicit goal to significantly increase both program size and impact. To insure a reliable pipeline of incoming students, the DG course was approved as an alternative to the first quarter of the traditional biology laboratory.  In practice, incoming students are randomly assigned to either lab course. This arrangement has enabled rapid enrollment growth from 66 students in three DG course sections in 2011-12, to 85 students in 5 sections in 2012-13, to a projected 200 students in 9 sections in 2013-14. Random assignment of students to either the traditional biology lab or the DG course provides an ideal control group for ongoing assessment of the effectiveness of the DG courses.

UC Riverside has proven to be fertile ground for the continued expansion of the DG course model to a projected 600 students by the year 2018. To this end, an increasing number of DG sections will be offered by other UCR faculty whose research labs address current biological problems using a diversity of model organisms such as Neurospora, C. elegans, planaria, and yeast. The community-oriented spirit of UCR has also led to the development of numerous outreach programs that often involve the participation of former DG students.

Research in the Wessler Lab

My research concerns the interaction between transposable elements and plant genes. Our laboratory was the first to demonstrate that elements could function as introns, that miniature inverted-repeat transposable elements (MITEs) predominate in normal genes, and that plant retrotransposons are the major cause of spontaneous insertion mutations. Most important to our HHMI project, we have pioneered the use of genome-wide approaches (both bioinformatic and wet bench) in transposable element discovery and analysis. This change in focus from genetic to genomic approaches led to our decision to switch from maize with its genetic strengths to its grass relative, rice, with its genomic advantages.

The decision to switch organisms was rewarded with the surprising finding that transposable elements routinely capture and rearrange gene fragments (Pack-MULEs) and the discovery of the first active MITE called mPing. Particularly exciting is our discovery of rice strains where mPing has amplified from 50 to over 700 copies within the past century and is still accumulating new insertions. With most of these insertions in or near rice genes, we have a wonderful opportunity to look at the earliest stages in transposon-mediated gene diversification. In addition, we are investigating why this transposon “burst” does not trigger host genome silencing.

Last updated June 2014

Scientist Profile

HHMI Professor
University of Georgia
Genetics, Plant Biology