Juan Martinez-Cruzado Univ of Puerto Rico at Mayaguez

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 Annotation Genomics in Eukaryotes (BIOL 4994)

Course Overview
This is a 2-credit research-based course for non-freshmen undergraduates or freshmen Master students who want to deepen their knowledge on genetics or genomics. Students meet once a week for four hours in a classrom with 28 PCs and projection facilities. The first four weeks consist of lectures on gene structure, molecular evolutionary theory, Drosophila genetics and evolution, and software tools for genomic analysis. Students gain experience on the use of these tools going through some of the GEP material. The fifth four-hour meeting is the most critical of the semester (see Lessons Learned).  It starts with each student being given a quiz in which s/he must annotate a small gene in one-and-a-half hour.  The quiz is discussed in the same meeting, and then a full Drosophila contig is assigned to annotate. Although it is not strictly required, most students keep coming every week to advance their projects. Students present oral and written reports on their respective contigs on the ninth week of class.  A Puerto Rican parrot (Amazona vittata) scaffold is given to each student in the tenth week, and the student must give a written and oral report on his/her scaffold in the fifteenth and last week of the semester.


Implementation
The course was first taught in the fall semester of 2009. It was devised as a one-credit course where the class would meet for 3 hours a week for the first 5 weeks. Students were then assigned a contig to analyze. The class would meet again the last week of the semester for oral presentations. Written reports were handed in a week later, during the final exams period. The class consisted of 4 students, 2 of which dropped out.

For the following semester, the course was modified to include four-hour meetings and the quiz.in the fifth week (see Course Overview).  Students had to report their first gene by the eighth week and the whole contig by the end of the semester.  However, maybe because many of them are eager to get into the parrot genome, I have found no trouble in requiring them to present the written and oral reports of the full Drosophila contigs on the ninth week meeting.

In summary, the course now stands as a stand-alone course of 25 students. I spend approximately 80 hours during the semester. They are all dedicated to annotation. We do no finishing.


Lessons Learned and Future Plans 
1. Meeting four hours a week in one period rather than in two or three periods gives far better results as students are far more able to build knowledge upon experiences they have recently gone through.

2. Many students (25) meeting in the same place and working on their respective project are far more productive than just a few (2). Having the computer classroom for those meetings where students work individually but can also consult with each other is a great advantage.

3. For some time we had we problem of procrastination. This was effectively solved by a dual strategy.  First, a quiz is given just after the fourth week of class.  In the quiz, the student is given one D. erecta gene to annotate in one-and-a-half hours and fill out a GEP Gene Annotation Report plus inform if the gene is in synteny with respect to D. melanogaster.  If the gene is not in synteny, then they must explain which rearrangements can explain the lack of synteny in the simplest fashion.  In that way, because students had to study for the quiz, they gain a better idea on how to attack the problems presented to them in the contig, and feel a weaker temptation to procrastinate.  Second, students were instructed to give a one-gene report of their contigs three weeks after contigs were distributed. The idea was that once they had accomplished something, the energy of activation needed to continue forward would be diminished. More importantly, you learn by doing, and forcing students to annotate a gene for the quiz, and giving them the opportunity to annotate the first gene of their contig in the same meeting is a critical ice-breaker.  The course later evolved to include the Puerto Rican parrot genome.  Hence, students must present the annotation of the whole contig in the form of oral and written reports by the ninth week. 

4. Having the students present Clustal W alignments and phylograms provides a quick way to detect exons out of frame.

5. Clustal W alignments are also useful for finding segments of exons that are too divergent to yield any matches in BLAST.  Two other useful strategies to find divergent exons are a) using a more permissive scoring matrix such as PAM70, b) BLAST to sequences of a species more closely related to your query than D. melanogaster.