Alexis Nagengast and Robert Morris, Widener University
Genomics at Widener University
Syllabus for BCH 454: A Biochemistry II lab course that incorporates 8 weeks of annotation (current implementation)
BCH 454 is an inquiry-based laboratory course that combines lectures, traditional wet lab protocols and computer lab research experiences to introduce bioinformatic skills in the context of genome annotation and microarray analysis. The course is intended for upper division Biology, Chemistry and Biochemistry undergraduates who have completed BCH 451/453: Biochemistry I lecture and lab. The annotation portion lasts 7-8 weeks and is supported by the Genomics Education Partnership (GEP). Students work in groups to annotate sequence from erecta and each student is expected to prepare his or her annotated sequence information for publication in a professional journal. Lectures, assigned readings and exercises will be used to prepare students for a task of this magnitude. An expected outcome, among others listed below, will be the students’ names on a future collaborative publication involving members of the GEP nationwide. Students will apply both their annotation skills and metabolism-based knowledge from lecture to the microarray analysis and submit a manuscript style lab report.
BIO/BCH 388 is a 4 credit science elective course with 3 hours of lecture (MWF 11-11:50) and 3 hours of lab (Wed 2-4:50). The audience is primarily upper level biology or biochemistry students although it was opened to academically strong sophomore students concurrently taking Genetics for the first offering in spring 2009. The course is co-taught by Dr. Alexis Nagengast of the Chemistry Department and Dr. Robert Morris of the Biology Department; both are members of the Biochemistry Department. In spring 2009, the TA was Justin DiAngelo, a recently graduated PhD from the University of Pennsylvania interested in getting teaching experience with undergraduates. BIO/BCH 388 is planned to be offered every other spring if enrollment allows. If low enrollment prevents the course from running, the annotation project will be incorporated into the last 6 weeks of the BCH 454 Laboratory course, also co-taught by Alexis and Bob.
Lessons Learned and Future Plans
Our initial plan was to offer the course in spring 2008 but we did not have sufficient enrollment. Therefore in spring 2008, Alexis, Bob, Justin and another professor from Widener with little genomics experience met for 3-4 hours weekly to gain experience with the class materials. We originally intended to spend the first half of the semester working on Finishing and claimed a green and yellow fosmid to practice. However, our semester starts earlier than Washington University's and we had trouble submitting and getting reads back in time to be able to devote sufficient time to annotating. We were unable to complete the yellow fosmid although we found the bulletin board a very helpful resource for answering questions and finding solutions. Additionally, we don't have Apple computer labs on campus and had trouble getting ITS to set up Consed on a PC so we used our personal Mac laptops. For these reasons, it is not practical for us to do Finishing and we considered spending a lab demonstrating Finishing as a group but would not have students claim projects when the course runs.
In spring 2009, we offered the course to four students and two faculty members. We planned on spending the first half of the semester annotating green and yellow GEP fosmids from D. erecta with students working as pairs and the second half researching a cross-species analysis of a gene on the fosmid with each student working independently. However, erecta is very similar to melanogaster and we did not feel the students were being challenged. After attending the Fly Meeting and talking with other GEP faculty, we decided to spend the second half of the semester annotating fosmids from the more distant species mojavensis. Students worked individually and Wilson was able to give us mojavensis fosmids that contained the same genes that the students had on their erecta fosmids. This was much more challenging and educational for the students. They pooled their results and presented their work as an oral presentation at our Student Projects Day. We also devoted class time to how to write an abstract, read and write a scientific journal article and construct clear figures. We felt these were skills that would be important for their co-authorship on a GEP paper. The final assignment was a research journal style paper on their comparative analysis of the structure of one of their genes among melanogaster, erecta and mojavensis. This final exercise turned out to be a very nice ending to the course and reinforced the general concepts of gene structure and function and their conservation throughout evolution that we had been stressing throughout the entire semester.