The Bioinformatic Enhancement of Exercises in Drosophila Genetics

Abstract

Bioinformatics is a rapidly expanding field that incorporates applications from computer science (e.g., data retrieval) with biological investigations (e.g., nucleotide and amino acid sequence analysis) (Mount, 2004). Several introductory textbooks have been written with exercises that introduce students to bioinformatics (e.g., Campbell & Heyer, 2002), and some standard genetics textbooks now include a chapter or two on bioinformatics (e.g., Hartl & Jones, 2004). Despite these advances, however, there is still a significant conceptual and technical gap between standard genetics laboratory exercises and bioinformatic experiences. Too often students are not provided with contextual experiences in bioinformatics in their standard biology laboratory exercises, or such experiences are provided to a select few who choose to enroll in specialized advanced courses, if available in the undergraduate curriculum. I have developed a set of complementary bioinformatic activities that is integrated into a genetics laboratory exercise in an introductory biology course. This approach exploits a student-driven inquiry-based mode of investigation, in that as questions arise regarding data interpretation from the genetic experiments, the students learn to explore and utilize bioinformatics tools as a means of self-learning. During this inquiry process, students begin to enter into other fields of biology (e.g., biochemistry, cell biology) and can experience the interconnections between the different life science disciplines. Finally, the bioinformatic analysis entailed herein leads the students into a discovery that provides support (at the molecular level) of the common ancestry of four divergent groups of organisms: fruit flies, humans, yeast, and roundworms. Materials The model system for the genetics laboratory exercise is the fruit fly, Drosophila melanogaster. The following required materials can be ordered from the Carolina Biological Supply Company (www.carolinabiologicalsupply.com): * One vial of Drosophila stock culture of choice (either the F1 apterous x sepia, the F1 vestigial x sepia, or the F1 vestigial x ebony cross) for each set of ten students. * One Drosophila BioKit for a class of up to 30 students. * Either a 10X hand lens or a dissecting scope for each pair of students. Notes: * Order the fruit fly stocks at least seven days prior to use to allow sufficient time for delivery. I typically order vials of the three different cultures to provide the class with some variety in this exercise. * The Drosophila BioKit contains all the necessary materials (instant Drosophila medium, culture vials, vial plugs, FlyNap anesthetic kits, labels and sorting brushes, student guides, an instructors guide, and Carolina Drosophila manuals) * The Carolina Drosophila Manual (Flagg, 1988) contains all the information regarding preparation of new Drosophila breeding vials with medium, manipulation of flies, and photographs of the phenotypes discussed in this paper. * Either dissecting microscopes or 10X hand lenses can be used to view the fruit fly phenotypes. If students work as teams of two or three, I then ask one student to serve as an observer of phenotypes and the others to serve as data gatherers. Students can then rotate these assignments throughout the lab period. Procedure Fruit Fly Lab Protocol Week 1 1. When the Drosophila stock cultures arrive, maintain them in a cool (room temperature) environment. Observe daily until approximately 20 or more adult files are visible; this typically occurs 3-5 days after receipt of the stock culture. 2. Each team of two students should set up three new vials of fresh Drosophila medium. Anesthetize the adult flies and, in each new vial, place three wild type males and three wild type females. Cap the new cultures and maintain at room temperature. …