Syllabus

Bio 432 – Genome Analysis - Fall 2009

Instructor: Jeffrey D. Newman Office: Heim 107 Phone: 570-321-4386 email: newman@lycoming.edu office hours: M 2:00-3:00 PM F 2:30-3:30 PM

Schedule Lecture/Discussion: MWF 11:30 - 12:20 in Heim 113 Lab: Tues 1:00 - 3:50 in Heim 109 or Computer Lab Course web site: http://moodle.lycoming.edu

Catalog Description of Course: This course examines the genome of humans, other animals, plants, and microbes to identify characteristics unique to specific groups as well as genomic features shared by multiple groups. These genomic studies include analysis of gene expression and networks of interacting proteins. The application of this information in the fields of medicine, agriculture, and evolution will be emphasized. The laboratory integrates experiments at the lab bench with a substantial bioinformatics component.

Prerequisites: Bio110 (Introduction to Biology I), Bio222 (Genetics)

Text: Discovering Genomics, Proteomics and Bioinformatics by Malcolm Campbell & Laurie Heyer, © 2007, Cold Spring Harbor Press/ Benjamin Cummings.

Research and review articles from the primary literature will be used extensively in this course. A variety of reference textbooks are available in the biology reading room (Heim 103). Genetics, Biochemistry, and Cell and Molecular Biology textbooks may prove helpful.

Learning Goals:

Content Knowledge: Students should understand:

• Approaches to large-scale high-throughput biology
• Processes by which genome sequences are determined
• Principles behind sequence analysis algorithms
• Methods to determine patterns of gene expression
• Genomic basis of innovations throughout the evolution of life
• Significance of single nucleotide polymorphisms (SNPs) for variation within a species

Skills: Students should be able to:

• Isolate genomic DNA, clone random fragments into a vector
• Assemble multiple sequencing reads into contigs
• Identify genes in assembled sequence, annotate sequence
• Isolate and work with RNA using appropriate precautions
• Synthesize fluorescent labeled cDNA, hybridize to Microarray
• Analyze & interpret microarray data
• Use software and databases at the National Center for Biotechnology Information (NCBI) and other sites

Grades will be determined based on the following assessments:

Exams 2 x 100 pts = 200 pts

Genome Papers/Presentations 2 x 50 pts = 100 pts

Laboratory Notebook Evaluation 2 x 50 pts = 100 pts

Genome Sequence Lab Report and/or Poster 100 pts

Microarray Lab Report and/or Poster 100 pts

Preparation/Participation/Problem Sets 150 pts

Total possible 750 pts

Grading Scale

	B+ = 86.7 - 89.9%	C+ = 76.7 - 79.9%	D+ = 66.7 - 69.9%
A = 93.3 – 100%	B = 83.3 – 86.7%	C = 73.3 – 76.7%	D = 63.3 – 66.7%	F= below 60%
A- = 90.0 – 93.3%	B- = 80.0 – 83.3%	C- = 70.0 – 73.3%	D- = 60.0 – 63.3%

Tentative Schedule

	Lecture Topics (reading)	Lab Activities
Week 1 8/31 – 9/4	Genetics Review (ch 1) Genetic Disease Case Study.	Genomic DNA Isolation from Chryseobacterium, Quantification GCAT Pre-Course Assessment Overview of Genome Project
Week 2 9/7 – 9/11	Methods of sequencing, assembly, annotation (ch 2).	Working with & assembling genome sequence data.
Week 3 9/14 – 9/18	Microbial genomes (ch 2)	ORF identification & annotation
Week 4 9/21 – 9/25	Comparative genomics (ch 3)	Use of databases for annotation, metabolic modeling
Week 5 9/28 – 10/2	Evolutionary genomics (ch 3)	Comparison of related genomes
Week 6 10/5 – 10/9	Environmental genomics (ch 3)	Microbial genome presentations
Week 7 10/12 – 10/16	SNP’s (ch 4) Mid-term exam (10/16)	Microarrays: Plan yeast microarray experiment, prepare media
Week 8 10/19 – 10/23	Genomics of Complex Traits (ch 5)	Microarrays: Isolate, quantify RNA
Week 9 10/26 – 10/29 (long weekend)	Microarrays (ch 6)	Microarrays: Make cDNA Probes
Week 10 11/2 – 11/6	Biomedical Applications of Microarrays (ch 7)	Microarrays: Hybridization, send for scanning
Week 11 11/9 – 11/13	Proteomics (ch 8)	Microarray Data Analysis (computer lab)
Week 12+ 11/16 – 11/23	Protein Interaction networks (ch 8)	Microarray Data Analysis (computer lab)
Week 13 11/30 – 12/4	Genomic Circuits (ch 10,11)	Microarray Data Analysis – Produce final reports (computer lab)
Week 14 12/7 – 12/11	Advanced Integrative & Systems Biology (ch 12)	Eukaryote genome presentations