Introduction of Bioinformatics in an Undergraduate Molecular Techniques Laboratory using Extreme Halophiles as Models

Northern Arizona University, Flagstaff AZ

Investigators

Abstract

Biological Sciences (61) This project is adapting research tools in bioinformatics and microarray analysis as a teaching method. The intellectual merit of this proposal addresses the problem of the technical infrastructure required for bioinformatics by introducing into an existing undergraduate molecular techniques laboratory two inquiry-based experiments: DNA sequencing and concomitant phylogenetic analysis of 16S rRNA genes recovered from novel extreme halophiles isolated from the environment; and global differential gene expression in the extremely halophilic archaeon Halobacterium sp. NRC-1 by DNA microarray analysis. The objectives for the DNA sequencing/phylogenetic study are: (i) PCR amplification of 16S rRNA genes from extremely halophilic organisms the students isolate from a nearby salt mine, (ii) sequencing these genes and submitting the sequences to GenBank, and (iii) placing the organisms phylogenetically based upon these sequences. The objectives for the microarray analysis are: (i) designing and implementing differential gene regulation experiments, (ii) extracting and labeling RNA, (iii) probing, scanning and analyzing DNA microarrays from Halobacterium NRC-1, and (iv) determining which genes are differentially expressed under the experimental conditions. The broader impacts of this proposal include: (i) advancing discovery and understanding using inquiry-based teaching and learning, (ii) integrating research and education by adapting current research on extreme halophiles into an undergraduate teaching laboratory, (iii) enhancing the technical educational infrastructure with the acquisition of instrumentation, and (iv) disseminating the results through the world wide web, GenBank, articles in peer-reviewed journals of science education, and presentations at the education divisions of professional societies.