Discovering rRNA and Homeobox Genes by DNA Sequencing and Bioinformatics in an Undergraduate Molecular Biology Course

Depauw University, Greencastle IN

Investigators

Abstract

Biological Sciences (61) This project is adapting a laboratory model presented by Dr. Adele Wolfson at a PKAL workshop. In an attempt to look at questions on how sequence data is obtained, and how can it yield new knowledge and understanding about the structure, function, organization, and evolution of genes and proteins while providing a genuine research experience for students, this project will: (1) enhance a mid-level Molecular Biology course for undergraduate biology and chemistry majors by developing an inquiry-based, project-driven series of five laboratory modules in Recombinant DNA technology and Bioinformatics; and (2) create a Molecular Genetics and Bioinformatics (MGB) laboratory facility for Biology and Chemistry students engaged in collaborative research projects. Each laboratory module consists of linked experiments, and the modules constitute a semester-long project in the isolation and analysis of rRNA genes and homeobox genes from 3 sources: the nematode Caenorhabditis elegans, the closely related microscopic invertebrate Brachionus plicatilis (a rotifer), and an unknown organism for identification by rRNA gene sequence homology. The modules include specific experiments in DNA isolation, primer design and optimization, polymerase chain reaction (PCR), cloning and sequencing PCR products from rRNA and homeobox gene families, and comparative bioinformatic analysis of sequenced DNA for both molecular phylogeny (rRNA genes) and function (homeobox genes). A final module includes formal reports and presentations in multimedia formats (talks and posters). The simultaneous use of model and non-model experimental organisms gives students an experience in how new knowledge is systematically generated through controlled experimentation. The objective is to offer students the opportunity not only to explore documented concepts in a model organism, but also to apply these concepts and experimental practices to discover new knowledge about other organisms through testing of specific hypotheses. The proposed MGB facility will contribute not only to the biology departmen's curriculum, but also to a newly developed curriculum in the chemistry department and an anticipated major in Biochemistry. This plan also initiates a curricular and programmatic shift toward interdisciplinary interactions between the two departments.