Nicole Bournias-Vardiabasis CSU San Bernardino

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Genomics at CSU San Bernardino

Course Overview

Implementation

Lessons Learned and Future Plans

Syllabus for Biology 592

Bio 592
Winter 2010
Dr. Bournias
Genomics (aka Recombinant DNA techniques)

This is a research-based class run in collaboration with the Genomics Education Partnership at Washington Univ. in St. Louis (http://gep.wustl.edu). The research that you complete during the course will be published in a peer-reviewed scientific paper, and you will be listed as a co-author. This is an excellent opportunity to work in a student-scientist partnership and gain undergraduate research experience.

We will be studying how DNA sequence affects chromosome organization by comparing the sequences of various Drosophila species. These sequences are publicly available, but they are 'draft' sequences and not highly reliable. In the first phase of the project, you would look at the sequence data to determine if there are errors or gaps, and 'finish' the sequence to high quality. The second phase of the project, annotation, involves identifying genes and other features in your sequences. You will do this by comparison to Drosophila melanogaster, which is much better studied so that data about gene expression is available for at least some of the genes. This is a great project to look at evolutionary questions, and to see the divergence that has occurred over a rather short time frame, between very similar species.
Meeting Times: We will meet for 5-6 times so as to get everyone organized and give you the necessary background information. The rest of the time you will be working on your own project. All instructional material will be posted on Blackboard. This includes all online lecture material. We will do the final presentation/reports during week 10 and you will take a take home final during finals week.

COURSE OBJECTIVES:

  1. To understand the structure and organization of genomes
  2. To gain hands-on experience with the techniques of sequence finishing and annotation, and the use of genomic databases.
  3. To appreciate the open-ended nature of scientific research
  4. To gain experience in reading and analyzing scientific literature
  5. To develop skills in oral and written scientific communication


TEXTBOOKS:
Discovering Genomics, Proteomics and Bioinformatics by Campbell and Heyer
Second Edition, Pearson Education, 2007. (not required )

WEBSITES
Course materials will be available on Blackboard. In addition, the Genomics Education Partnership website (http://gep.wustl.edu) contains useful resources that you may be directed to during the course of the semester.
Lecture Schedule


Week Topic
2 Introduction to Genomics
3 Recombinant DNA Techniques
4 Genomic Databases
5 Environmental Genomics
6 tructures and Genomes
7 Genomics and Medicine
8 Monogenic Diseases and Genomics
9 Complex Traits and Genomics, Pharmacogenomics
10 Genomics and Ethics


KNOWLEDGE ASSESSMENT

Final exam 25%
Exercises turn in as you complete them during the first 3 weeks 15%
Washington GEP project 30%
Poster on ethics of genomics 20%
Participation 10%
Standard University Scale will be applied.