Bio343: Laboratory Methods In Genomics
Spring, 2012
A. Malcolm Campbell
Davidson students will be working NCSU and the David H. Murdock Research Institute to understand 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 bigger goal is to help blueberry breeders improve the crop through selective breeding using genomic markers.
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 a species which is poorly understood. The blueberrry is native to North American and holds many potentially beneficial compounds. Our task will be to reconstruct some of the metabolic pathways to see what metabolites we can predict would be produced in blueberries.
Tentative Syllabus: Bio 343 Laboratory Methods in Genomics
Class meets 3:05 - 4:20 pm in Chambers 3146 (GAMCo)
Office Hours: M & Tu: 9 - 10 am; Thurs: 11
- noon; or most anytime by appointment
1) Understand what a gene is through in-depth analysis of a genome.
2) Describe how a eukaryotic genome is organized.
3) Categorize species-specific metabolic maps.
4) Evaluate automated annotation quality and accuracy.
5) Organize evolutionary paths as revealed in novel genomes.
6) Assess real genomics research process and all that comes with it.
7) Demonstrate computer skills used in modern genomics.
8) Perform collaborative learning and research.
9) Employ comparative genomics of plants to understand what constitutes a new species.
Required Readings
1) Online web sites
2) Research publications on genomes (PDFs distributed during semester)
Optional Readings
1) Genome: the autobiography of a species in 23 chromosomes. Matt Ridley. HarperCollins Publisher. Available at bookstores and Amazon.com.
Tentative Weekly Schedule
Week of Semester |
Subject Matter and
Assignments Due |
| Week 1: Jan 17 & 19 |
Discuss: semester-long research plans & set educational goals Discuss: domains of life, genome sequencing, DHMRI and our species Blueberry genome portal (development site) Standard Operating Procedure (SOP), Quality Control (QC), and Triage Summarize Large Scale Projects from last year (present Thursday) |
Summarize the paper from first Bio343: Bakke et al., 2009 Important background information:
Amino Acids Table (memorize 1 letter code) Genetic Code (do not memorize) |
|
Week 2: |
Discuss strawberry and grape genome papers 454 and pyrosequenicng, Illumina, SOLiD, Ion Torrent, single molecule Choose Tutorial to Master |
|
Master your tutorial |
|
Week 3: |
Discuss blueberry grant proposal Master tutorial Discuss project ideas |
3 reports on key tutorials
Group effort to find a gene and produce SSR markers. Use this paper as starting place. Databases and Tools: BLAST, CDD, KEGG, BioCyc, Tcoffee, EC numbers, and phylogenetic trees, Rosaceae Genome Database, phytochemical database, and Apollo genome viewer |
|
| Week 4: Feb 7 & 9 |
Work as group to come up with semester projects |
Make clear the goals for each person Controlled vocabulary Problems to be addressed: Pseudogenes, transposons, horizontal gene transfer, orthologs, paralogs, homology, hypothetical genes, unknown function, quality of data for annotation. |
|
| Week 5: Feb 14 & 16 |
Continue SSR projects 10 glossary entries for each student (graded by Dr. C.) |
| Continue SSR projects | |
| Week 6: Feb 21 & 23 |
Continue SSR projects |
Continue SSR projects |
|
| Week 7: Feb 28 & Mar 1 (no class) |
Status report with peer review Continue SSR projects |
Continue SSR projects No class meeting March 1 |
|
null Week |
Spring Break |
Spring Break |
|
Week 8: |
Discuss status and goals Meet at Summit for blueberry consumables |
|
Finalize SSR Project and Read about MITEs |
|
| Week 9: Mar 20 & 22 |
Start EST experiments |
| Continue EST experiments | |
| Week 10: Mar 27 & 29 |
Continue EST experiments |
| Continue EST experiments | |
| Week 11: Apr 3 & 5 |
Continue EST experiments |
Continue EST experiments |
|
| Week 12: Apr 10 & 12 |
Easter Break |
Assess Status and Agree on Endgame Write the final paper |
|
Week 13: |
Oral Presentation #2 on your second blueberry project
|
| Finish final paper | |
| Week 14: Apr 24 & 26 |
Field Trip to NCRC in Kannapolis |
| First draft of final paper due Bring Hard Copy to collect comments form peers Peer review of draft paper (comments graded by Dr. C.) |
|
| Week 15: May 1 & 3 & 8 |
Finalize paper based on comments. |
No final exam, just final paper. |
|
| Final final
due (as Word file) submitted by noon on Reading Day Fellowships Course Evaluations |
Grading
Grades will be based on: glossary
entries (10% total grade); two online
tutorials for annotation process (20% total); peer review of tutorial
(10% total grade);
intermediate scale project and final
research paper (focus TBD; 25% total grade); two oral
presentations (30% total grade) and class participation (5% total grade). The exact
nature of the 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.
Grading Scale:
| A = 100 - 95 | A- = 94 - 92 | |
| B+ = 91 - 89 | B = 88 - 86 | B- = 85 - 83 |
| C+ = 82 - 80 | C = 79 - 77 | C - = 76 - 74 |
| D+ = 73 - 71 | D = 70 - 68 | |
| F = < 67 |
© Copyright 2012 Department of Biology, Davidson College,
Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu