Nadia Ayoub Washington and Lee

From GEP Wiki
Jump to: navigation, search

Genomics at Washington and Lee

Course Overview

Genomics is a rapidly growing field that integrates and expands on diverse subjects such as evolution, molecular biology, and computer science. Genomics has increased our understanding of human health and evolution and directly impacted the advancement of medicine. This course provides students the opportunity to actively engage in Genomics research projects, thus increasing their understanding of the research process and the significance of Genomics tools. Students will generate and analyze original data describing the genomes of black widow spiders and fruit flies. Students will work in pairs on two projects. The first project will involve using molecular genetic tools to generate high quality sequence data for black widow (Latrodectus hesperus) genes. The second project will involve annotating segments of fruit fly (Drosophila) genomes. Students will additionally use their genes as a starting point for an independently designed comparative genomic analysis. Data generated by the first project will contribute directly to on-going research in the instructor’s lab and is intended to culminate in peer-reviewed publications. Annotation of fruit fly genomes is part of a national research project, the Genomics Education Partnership, intended to fully describe the dot chromosome of at least 12 Drosophila species. Students generating data for either project will be co-authors on publications.

Implementation

Lessons Learned and Future Plans

Syllabus for Biology 323 (Research Questions in Genomics)

Course Learning Objectives

1) Effective scientific communication. HOW: By oral presentations of data collection and analysis.
2) Understanding and use of the scientific method. HOW: Problem-solving will be a key component of completing high quality sequences and annotations. Students will additionally develop hypotheses based on the sequence data and design an analytical experiment to test these hypotheses.
3) Understanding of major concepts in biology. HOW: Annotation and comparative genomics relies on the concept of evolutionary homology. By completing these projects and delving into the related literature, students will develop a deeper understanding of molecular homology and genome evolution.
4) Use of tools and techniques of science. HOW: Design and implementation of molecular experiments coupled with intense learning of analytical tools.
5) Scientific literacy. Relevance to society. HOW: The research proposal and the final defense will require that students read and interpret multiple peer-reviewed papers in light of their course projects. Additionally, we will continually discuss how the genomics tools students are learning have been used to address fundamental questions about human health and evolution.

Readings
There is no required text. Reading assignments will be posted on Sakai’s course website.
Student assessment

25%) Reading journal and lab notebook.
o Outline of each reading assignment. Should write down at least two questions or insightful comments for every reading (keep in mind you will probably have more than two questions!). Include notes taken during discussion. After discussion, write down any new questions that arose and if you felt your original questions were addressed.
o Detailed description of any wet lab work.
o Detailed description of computer lab experiments should be recorded also, but an electronic record will often be easier and more useful. Electronic records should be noted in your journal and submitted via the course turn in folder.
o Turn in every Thursday by noon. I will return with comments on Friday.


5%) Participation in class discussions.
Hopefully, you will all feel comfortable contributing during class. However, for those of you who may feel a little shy and to help focus discussion, I’d like each of you to submit two questions or comments on each reading assignment either by email or to a Sakai forum (more details to follow).

5%) Choose 1 or 2 papers from the primary literature and lead discussion.

25%) Weekly progress reports.
o Student partners will give updates on data collection/analysis each Friday in the form of power point presentations. Progress reports should facilitate constructive feedback and group problem solving.

10%) Submission of annotated Drosophila genes to the GEP system.

10%) Submission of black widow transcript models to instructor’s internal database.

10%) 1-page written proposal of Drosophila gene analysis.
o One you have annotated all the exons, introns, etc in your segment of a fruit fly genome you will design an analysis to further your understanding of comparative genomics. This analysis could include a phylogenetic reconstruction of all published homologs of one the genes you annotated or it could include a comparison of gene location (e.g. is the orthology of your gene in the same place on the chromosome in other species). Other options are available… your interests and your genes will lead the way.

10%) Final oral presentation of data collection, annotation, and analyses.