Karim Sharif LaGuardia Community College

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Genomics at LaGuardia Community College

Course Overview

Genomics at LaGuardia Community College, NYC
Dr. Karim Sharif, assistant professor of biology at LaGuardia Community College, began implementation of GEP research in the summer of 2011. The nature of courses offered at LaGuardia and the school policies regarding new course offerings could not afford inclusion of GEP projects into the curricula in a fruitful manner. Therefore, Dr. Sharif opted to recruit a group of undergraduate students, interested in research, to engage in genomics research projects within the GEP. It started with two students who were taught by Dr. Sharif to annotate genes present in fosmids of Drosophila erecta. Among these students, Jason Macias was further trained during January 2012 GEP workshop, held in WU at St. Louis, to assume the responsibilities of a TA. In addition to helping and instructing other students, Jason conducts his own research in GEP projects. Since then, more students have been accepted to conduct GEP research, among them some students work as part of their internship requirement to graduate from LaGuardia.

Implementation

Goals
The GEP projects involve students in activities to understand how to identify genes in DNA sequences, find their orthologs and then identify and annotate the gene structure, including start and stop codons, splice sites, and other gene features. Additionally, they learn to use online databases of genomic information and supportive resources available for gene annotation through Washington University’s Genomics Partnership and to analyze data in comparative genomic studies. The GEP materials and exercises are designed to guide students in completing their fosmid annotations and to help them in improving the communication and analytical skills necessary for research. After initial instruction on the above topics by the TA and Dr. Sharif, students are given GEP materials, designed to guide students in fosmid annotations. They are then asked to complete gene annotation exercises available at the GEP site. These exercises prepare them in the communication and analytical skills necessary for research, so its implementation is crucial to forming a solid base of understanding. The students participate in annotation projects by engaging in research activities, within or next to Dr. Sharif’s office, for 2-4 hours a day, 4 days a week, depending on their schedule. The amount of time thus spent on the research exercises works well in the beginning to overcome the learning curve that comes with annotation. It takes several sessions of practice to utilize the web resources comfortably. Students are educated in the use of gene models, such as those predicted by Genscan and other available algorithms, but with cautions, for they can be useful in initial investigations but may also lead to wrong conclusions if adhered to resolutely. As individual students attain better understanding and skills involved in the research, they are able to work more independently and flexibly according to their schedule. Weekly meetings are held for presentations of research work, discussions and for questions that may arise concerning annotation techniques. Projects are claimed and submitted independently through TA or Dr. Sharif after a careful review.

Lessons Learned and Future Plans

Outcomes
As a group, we have claimed over 29 fosmids, identifying genes and their exon/intron boundaries in the past year. Additionally, students have attempted various difficulty levels and have also annotated genes in Drosophila mojavensis. Working together as a group and the ability to freely share information has helped greatly in gaining new understanding of gene organization. Participating in GEP projects has allowed for the research students to make inferences into the phylogenetic relationships between different species of Drosophila and has allowed for the dissemination of that information in the form of poster presentations, at national conferences across the country. Students will continue to be recruited and the model of peer tutoring by a TA will persist, for it has proven fruitful. The information gained from gene annotation will continue to be used to compare phylogenetic differences in different species of Drosophila.

Syllabus for