Lisa Kadlec Wilkes University
Genomics at Wilkes University
GEP materials were implemented for the first time during the Fall 2009 semester in BIO 345 (Genetics), which is an upper-level elective. The course meets for three 50-minute lectures and one three-hour lab per week. Enrollment in this course typically ranges from around 10 to 18 students. The semester I introduced GEP materials, the enrollment was 9 students. This course already had an established lab syllabus which included both single-lab exercises and experiments that run over the course of several lab periods. I did some rearranging of the lab syllabus in order to introduce a multi-week genome annotation lab.
Although we discuss genomics in the lecture portion of the course, background specific to the genome annotation project is introduced during lab. The first year I used GEP materials we proceeded as follows: The week before starting the genome annotation lab, a portion of the lab period was devoted to a PowerPoint which covered some basics of gene finding and of BLAST. During week 2 students did a version of GEP Homework #1 during the lab period and handed in their answers to the questions. Week three started out with the "Annotation of Drosophila mojavensis" (adapted from Chris Shaffer's PowerPoint from the GEP workshop), and then the students started work on annotating a fairly straightforward D. erecta fosmid. Different sets of lab partners worked on different parts of the fosmid (so that the class as a whole covered the entire fosmid). The next two weeks in lab were largely devoted to annotation, though we spent part of the period (at the start of lab) setting up for and then starting the next experiment we were doing that semester.
Lessons Learned and Changes Made (Including Current Implementation)
Overall, my first implementation of GEP materia went pretty well, especially considering the time limitations given that GEP material consisted of just one of a number of lab exercises in the lab syllabus for the class. I had to do some retooling of the lab schedule and actually eliminate some of the previous material in order to carve out between 4 and 5 lab periods to devote to annotation. I found having a trained TA was invaluable. Time was a major challenge, but so was simply getting the students up to speed and having them gain enough confidence to start to work independently. We thought that we could get through a basic D. erecta annotation and then at least start on something from a more distant species D. mojavensis but it took almost all of the available time for the students to learn how to navigate the websites and tools and then complete their D. erecta annotation.
Student feedback indicated that while Homework 1 was helpful in some ways, the students found it largely confusing. I do believe that it teaches some important concepts. However I don't think it works well, for my students, as an introductory exercise. The next year I made changes to my implentation, as follows: We again started with a PowerPoint combining aspects of gene finding and BLAST, but then in week 2 I presented the "Annotation of D. virilis" PowerPoint and had the students work through the Simple Annotation Problem. This allowed us to start right in with actual annotation at the beginning of week 3. I assigned the "Simple Introduction to BLAST" as homework between weeks 1 and 2. I had a small class size that year, and again our time is limited, so I divided up a single D. grimshawi fosmid and different class members worked on different portions of it. Most of the next lab period was devoted to annotation work, and students also had some time in during week 5 to finish up their projects.
Overall, the revised schedule worked better. My class was able to complete annotation and submission of our selected D. grimshawi fosmid. I have continued to utilize the same overall scheme in the following years. This past fall (Fall, 2012 semester), my students worked together to annotate a D. ananassae fosmid.
Lab Schedule for Biology 345 - Genetics (Fall 2012)
August 29 Introduction/Model Organisms; Set up Drosophila di-hybrid crosses?
September 5 Mono- and di-hybrid crosses in corn and flies; Streak yeast strains for mutation experiments
September 12 Linkage and mapping in Drosophila; Streak yeast strains
September 19 Generation and characterization of mutations (yeast)
September 26 Yeast mutants, continued
October 3 Lab Quiz #1; Continue work on yeast as needed
October 10 Molecular genetics – PCR mapping of a chromosomal deficiency
October 17 Finish PCR mapping; Introduction to genome annotation
October 24 Genome annotation II
October 31 Genome annotation III
November 7 Genome annotation IV; Introduction to Drosophila development; Set up laying block
November 14 Developmental genetics—Drosophila embryogenesis; Time to finish annotation, if needed
November 21 No Lab, Thanksgiving Recess
November 28 Finish developmental genetics experiments
December 5 Lab Quiz #2; Catch up/clean up day