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An Adaptable Undergraduate Molecular Biology Lab Module that Integrates Use of Genomic Resources with Bench Experiments

Daniel M. Vernon, Michelle Shafer, and Nancy R. Forsthoefel
Program in Biochemistry, Biophysics & Molecular Biology, Whitman College, Walla Walla, WA 99362

Abstract & Introduction

We have designed an undergraduate molecular biology lab module that integrates use of computer-based genomic resources with bench experiments and facilitates integration of teaching and research. Our goal was to develop a ~5 week project focused on eukaryotic gene structure and expression with the following features:

  1. involves original experiments;
  2. provides training in core molecular techniques;
  3. promotes an integrative biology perspective;
  4. exposes undergraduates to genomics and internet-accessible genomic resources
  5. incorporates plants, including the genomic model system Arabidopsis thaliana; and
  6. promotes science writing skills.

Importantly, we wanted the project framework to be flexible enough to allow students to do original experiments each year, but consistent enough to minimize lab preparation time and effort for staff. The result was the 4-6 week lab module described below (and in more detail in the following links)

Summary of Project: Provided by the instructor with a fragment of an "unknown" Arabidopsis gene sequence, student groups identified the corresponding Arabidopsis gene locus using BLAST searches, and used genome data at The Arabidopsis Information Resource (TAIR; www.arabidopsis.org) to define full gene and mRNA structures. They then searched for information on gene function, formulated a hypothesis about differential expression in developmental, environmental, or physiological contexts, and designed PCR primers to test their gene expression hypothesis. In subsequent weeks, students tested primers on Arabidopsis genomic DNA, isolated RNA from different plant organs, and performed RT-PCR to survey mRNA expression of the target gene(s). Alternatively, students used other plant genomic resourcesto identify orthologs of their Arabidopsis gene in another species, and used that species for their genomic and RT-PCR experiments. Results were formally written up in manuscript style. Course evaluations indicated that despite technical difficulties inherent in doing molecular research at the undergraduate level, students appreciated doing real experiments in a teaching laboratory. By incorporating genes related to their own research interests, faculty can use this module to integrate their research with undergraduate instruction.

Supported by NSF grant 0616166 to D.M.V. and by a Teaching Innovation Award from Whitman College

[Link to ASPB conference poster abstract]

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