Bio343: Laboratory Methods In Genomics
Spring, 2011
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.
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
Office Hours: M & Tu: 3-4; Thurs: 2
- 3; 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 Tools (FireFox browser is best)
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 11 & 13 |
Discuss: semester-long research plans & set educational goals Discuss: domains of life, genome sequencing, DHMRI and our species Blueberry genome sequence home page Blueberry genome portal Standard Operating Procedure (SOP), Quality Control (QC), and Triage |
Amino Acids Table (memorize 1 letter code) Read the paper from first class: Bakke et al., 2009 Important background information:
|
|
Week 2: |
Discuss fieldtrip on Thursday Revise your reports in class |
Fieldtrip to DHMRI: meet in Baker parking lot near vans no later than 9:30. Bring material for notes and a camera if you have one. Read strawberry and grape genome papers (main text only for now) |
|
| Week 3: Jan 25 & 27 |
Discuss strawberry and grape genome papers Discuss blueberry grant proposal Start to explore sequences with Apollo
Establish SOP (standard operating procedures) for genes. Databases and Tools: BLAST, CDD, KEGG, BioCyc, Tcoffee, EC numbers, and phylogenetic trees, Rosaceae Genome Database, phytochemical database, and Apollo genome viewer
|
Work in groups to choose first research project - smaller scale |
|
| Week 4: Feb 1 & 3 |
Finalize plan and begin project- smaller scale 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. See results from previous years Distribute newest genome compilation. Learn very basic UNIX commands. Find orthologs in blueberry genome
|
Discuss end goals and methods for accomplishing this Update class on progress so far |
|
| Week 5: Feb 8 & 10 |
Continue projects 10 glossary entries for each student (graded by Dr. C.) |
| Continue projects - smaller scale | |
| Week 6: Feb 15 & 17 |
Continue projects - smaller scale |
Each person's portion of project due Oral
presentations with peer review |
|
| Week 7: Feb 22 & 24 |
Conclude small scale project presentations What blueberry projects shuold we do for the second half? |
First
methodology tutorial Due (graded by Dr. C.) |
|
null Week |
Spring Break |
Spring Break |
|
Week 8: |
Continue blueberry projects |
|
Artemis Visualization Tool (.jar file) PDF tutorial on Artemis (fish example) Pymol script for extracting scaffold of interest from 454 sequences.
Continue blueberry projects |
|
| Week 9: Mar 15 & 17 |
Continue blueberry projects |
| Continue blueberry projects | |
| Week 10: Mar 22 & 24 |
Continue blueberry projects Design experimental testing? |
| Continue research | |
| Week 11: Mar 29 & 31 |
Prelimonary Oral Presentations Guest visitor: Dr. Phil Meneely from Haveford College |
Continue research |
|
| Week 12: Apr 5 & 7 |
Continue research |
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 19 & 21 |
No Class - write draft |
| 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: Apr 26 & 28 May 3 |
Easter Break |
No final exam |
|
| Final final
paper due (as Word file) submitted by noon on May 3 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 2011 Department of Biology, Davidson College,
Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu