Lau, Joann , Robinson, Dave .
A six-week laboratory project in plant molecular biology and bioinformatics with subsequent publication in the NCBI GenBank.
This project introduces molecular and bioinformatics techniques to students by having them isolate and characterize a housekeeping gene from uncharacterized plant species. The gene encodes Glyceraldehyde3-Phosphate Dehydrogenase (GAPDH), a pivotal enzyme of glycolysis. We have partnered with Bio-Rad Laboratories in the development of a complete kit for this project, called the "Cloning and Sequencing Explorer Series" (#166-5000EDU). Students start the project by extracting genomic DNA from a plant species, or cultivar, whose GAPDH has not been previously published. PCR is used to amplify a major portion of the GAPDH gene, which is then ligated to a vector for bacterial transformation. Once screened, putative clones are examined by restriction digestion and then sent off for sequencing. Once sequenced, students analyze the resulting DNA chromatograms using iFinch TM software made available by Geospiza, Inc. through purchase of this kit. This software allows students to assess the quality of their cloned-DNA sequence, distinguish between vector and GAPDH sequence, and compare it to already-published GAPDH sequences from other plants. Students can also determine gene structure, such as introns and exons. Student achievement was evaluated using pre-, mid-, and final-test assessments, as well as with a survey to assess student perceptions about the project. Student confidence about basic laboratory techniques and knowledge of bioinformatics tools was significantly increased upon completion of this exercise. This project differs from other biology lab exercises in that the final data can be published in the National Center for Biotechnology Information (NCBI) GenBank. This exercise has already resulted in the publication of at least 22 unique plant GAPDH sequences generated by students at high schools, colleges and universities throughout the country and includes species like begonia, coriander, thyme and spinach. The exercise can be repeated year after year, each time with a different plant species, or cultivar. This makes the project worthwhile for both students and instructors, and contributes significantly to the study of GAPDH biochemistry and phylogenetics.
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Full length article on this project.
1 - Bellarmine University, Biology, 2001 Newburg Road, Louisville, KY, 40205, USA
Glyceraldehyde 3-Phosphate Dehydrogenase
Presentation Type: Poster:Posters for Sections
Location: Khorassan Ballroom/Chase Park Plaza
Date: Monday, July 11th, 2011
Time: 5:30 PM