Bio343: Laboratory Methods In Genomics
Spring, 2018
A. Malcolm Campbell (he/him/his)

Working Syllabus

Class meets T/R 9:40 - 10:55 pm in Wall B05
Office Hours: M 11-noon; T 3 - 4 pm; or most anytime by appointment

The college welcomes requests for accommodations related to disability and will grant those that are determined to be reasonable and maintain the integrity of a program or curriculum. To make such a request or to begin a conversation about a possible request, please contact the Office of Academic Access and Disability Resources, which is located in the Center for Teaching and Learning in the E.H. Little Library: Beth Bleil, Director, 704-894-2129; or Alysen Beaty, Assistant Director, 704-894-2939.  It is best to submit accommodation requests within the drop/add period; however, requests can be made at any time in the semester.  Please keep in mind that accommodations are not retroactive.

Learning Goals

• Students will experience gene expression analysis of RNAseq data.
• Students will appreciate the amount of subjectivity involved in genomics research.
• Students will understand how genomics is a suite of tools that spans the small/big biology divide.
  

Learning Objectives

1. Define terms used in RNA sequencing and assembly. (knowledge)
2. Describe what a gene is 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 transcriptomes reveal which parts of the genome are activated. (comprehension)
5. Demonstrate computer skills that are used in modern genomics. (application)
6. Examine different signaling pathways that lead to cell and tissue growth. (analysis)
7. Test whether a known pathway is activated in experimental tissue compared to control. (analysis)
8. Collect and integrate published data with RNAseq data to describe Charcot-Marie-Tooth type 2 disease. (synthesis)
9. Evaluate data quality and completeness of signaling pathway activation. (evaluation)
10. Assess the objectivity and subjectivity used in genomic research. (evaluation)
    

Bio343 is a lab-only course that is primarily data analysis by computer. I am very excited about this course for two main reasons.

1. We will be working on an inherently interesting question - Charcot-Marie-Tooth (CMT) type 2D disease. We will be looking at the transcriptome of mouse spinal chord. In particular, we will be looking at two different populations of mRNAs. One population will come from wild-type mice and the other will come from CMT mice.
   
2. We are also collaborating with Drs. Charlie Wray and Jeff Chuang Jackson Laboratory in Bar Harbor, ME. We are part of an educational pilot experiment to see if it is feasible to offer research experiences to a national network of undergraduates using RNAseq data to answer legitimate research questions. Very few students in the world get to answer an interesting biological question using RNAseq data and you are among the few who will get this experience.

The mouse strain we are working with is called Gars^P278KY and it was generated in a ENU mutagenesis project. You can read more at the MGI entry for this allele. The RNAseq was set up as 3 males and 3 females, with both wildtype and mutant animals, so 12 animals in all.  After cervical dislocation, the spinal cords were removed and flash frozen prior to RNA extraction and subsequent library construction. Emily S. is the graduate student working on this animal and CMT2D. More details here.

Because this is a research course, all of us  have to be flexible in the material we learn. 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. Each student will need to learn how to edit a wiki site used for this research project.

Student Collaborators

Required Readings

1) Online web sites

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

3) Course wiki site

Tentative Weekly Schedule

Grading
Grades will be based on:

• research summary Word File (solo author) email to Dr. C. (10% total grade)
• peer review of draft 1st half-term paper (review is 5% total grade)
• first half-term paper #1 (20% total grade)
• status report (solo author; 10% total grade)
• group oral presentation (20% total grade)
• peer review on oral presentation (5% total grade)
• peer review of draft 2nd term paper (review is 5% total grade)
• term research paper solo author (25% 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 Minor

Genomics & Bioinformatics Majors

Biology Department

© Copyright 2018 Department of Biology, Davidson College, Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu