Bio343: Laboratory Methods In Genomics

Spring, 2014

A. Malcolm Campbell

Davidson students will be collaborating with investigators at NCSU and the David H. Murdock Research Institute to work on two plant genomes. For the first few weeks, you will help annotate the blueberry (Vaccinium corymbosum) genome as a way to better understand the blueberry plant. The genome sequence has not been published and we will be among the first people in the world to see what the genome has to tell us. The applied goal is to help blueberry breeders improve the crop through selective breeding using genomic markers. The bulk of your work will be focused on the broccoli genome.

Bio343 is a lab-only course that is primarily data analysis by computer. I am very excited about this course. Very few students in the world get to participate in genome annotation prior to publication. It will be a lot of fun to do real genomics research on two species that you probably eat with some regularity. The blueberrry is native to North American and holds many potentially beneficial compounds. Broccoli is a common vegetable served around the world. Our task will be to reconstruct some of the metabolic pathways to help plant breeders produce better food crops.

Because this is a research course, we will all have to be flexible in the material we will cover. It is impossible to know where this course will take us exactly. I have a rough plan, but nothing firm yet until we see how these projects unfold. If you need a highly structured course, this will not be a good fit for you.

Tentative Syllabus: Bio 343 Laboratory Methods in Genomics

Class meets 12:15 - 1:30 pm in Chambers 3146 (GAMCo)
Office Hours: MWF: 3 - 4 pm; or most anytime by appointment

Student Collaborators

Learning Outcomes

1) Define terms used in genome sequencing and assembly. (knowledge)

2) Describe a gene based on in-depth analysis of a genome. (comprehension)

3) Report your findings to the class verbally and to a wider audience in writing. (comprehension)

4) Explain how metabolic pathways are determined based on genome sequence. (comprehension)

5) Demonstrate computer skills used in modern genomics. (application)

6) Examine species-specific metabolic maps to determine if they are complete or not. (analysis)

7) Test whether a gene is present in the genome and when it is transcribed. (analysis)

8) Propose strategy to find missing genes from expected metabolic pathways. (synthesis)

9) Evaluate automated annotation quality and potential problems. (evaluation)

10) Assess real genomics research and the subjectivity that is required. (evaluation)

 

Required Readings

1) Online web sites

2) Research publications on genomes (PDFs distributed during semester)

3) Course wiki site

Just for Fun Reading

1) Genome: the autobiography of a species in 23 chromosomes. Matt Ridley. HarperCollins Publisher.

Tentative Weekly Schedule

Grading
Grades will be based on:

• blueberry Word File posted on wiki (10% total grade)
• blueberry 3 minute presentation posted on wiki (10% total grade)
• QTL presentation #1 (20% total grade)
• QTL presentation #2 (20% total grade)
• peer review on presentations (each one is 5% total grade)
• Final paper (25% total grade)
• Peer review of final paper (5% total grade)

The exact nature of the presentations and papers cannot be determined at this point. You will use the course wiki page as an online lab notebook to track your daily progress. Keep in mind that your work will be the foundation that investigators will use for subsequent research so it is important to keep good notes online.

Genomics Lecture Course

Genomics Concentration

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Send comments, questions, and suggestions to: macampbell@davidson.edu