James Bedard

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BIO 414

3 Credit Hours
Course Syllabus – Winter 2015
Dr. James Bedard 604-504-7441 ext: 4804, email: james.bedard@ufv.ca


o Lesk, A. (2012) Introduction to Genomics, 2nd ed., Oxford University Press.

Course Description

This course examines the way genetic information is encoded, ordered, and expressed on a whole organism basis. Strategies and methods for cloning DNA, obtaining sequence data, and assembling this information into continuous constructs will be explored. The course will also examine standard techniques for describing and mapping the rapidly growing body of genome information. Finally, we will look at how patterns of expression in different cells and cell types can be used to study a variety of biological processes including disease states and genetic engineering approaches. A portion of the course will involve the hands-on use of computer-based searching methods and the manipulation of data sets. Prerequisite(s): BIO 201, 202, and 220.

Student Learning Outcomes

After successfully completing this course, students will be able to:
• Fully describe methods used in the cloning and sequencing of DNA
• Discuss the challenges and strategies associated with the sequencing of whole genomes
• Construct alignment files for DNA sequences as assemble these into contiguous segments
• Understand and apply methods and strategies for searching and mapping molecular databases
• Describe the use of microarrays for examining proteomes and transcriptomes
• Discuss and critique the use of comparative methods of linking genes to disease states or biological processes
• Explain how changes in the metabolic signatures of cells can lead to a greater understanding of cell function
• Demonstrate a thorough understanding of genomics and its application in modern biological research

Evaluation and Final Grades

Grades will be determined on the basis of the percentage of total available points earned by each student individually.
Midterm Exam 20%
Assignments / Participation 15%
Presentation 10%
Final Report 20%
Final Exam 35%
Participation will be assessed through punctuality/attendance, engagement & equitable distribution of group work, & contribution to class/group discussion at appropriate times.

Tentative Course Schedule:

Date      Lecture Topic Activity / Research
Jan 6      Course Overview / The Genomics Education Partnership (GEP)* / Pre-course survey and pre-course quiz
13      Introduction to Genomics (Ch 1) / Introduction to biological databases and the GEP website**
20      Mapping, Sequencing, Annotation, and Databases (Ch 3) / Annotation Practice - Week 1
27      Mapping, Sequencing, Annotation, and Databases (continued) / Annotation Practice - Week 2

Feb 3      Comparative Genomics (Ch 4) / Annotation project - Week 1
10      No Class - Midterm Break No Class - Midterm Break
17      Comparative Genomics (continued) / Annotation project - Week 2
24      Midterm Exam / Annotation project - Week 3 (Electronic notebooks due)
Mar 3      Evolution and Genomic Change (Ch 5) / Annotation project - Week 4
10      Microarrays and Transcriptomics (Ch 9) / Annotation project - Week 5
17      Proteomics (Ch 10) / Annotation project - Week 6 (Electronic notebooks due)
24      Metabolomics (Ch 11) / Annotation project - wrap-up
31      Annotation Project Presentations / Final Papers Due
Apr 7      Annotation Project Presentations / Post-course survey and post-course quiz
* BIO 414 students have the opportunity to contribute to original research involving large scale sequencing projects from Washington University in St. Louis. Students will learn how to analyze and annotate segments of fruit fly (Drosophila) genomes.
** Including, but not limited to, NCBI BLAST, GEP UCSC Browser Mirror, Gene Record Finder, Small Exon Finder, Gene Model Checker, Fly Base, Ensembl, Clustal, ExPASy.