Bio343: Laboratory Methods In Genomics
Spring, 2013
A. Malcolm Campbell
Davidson students will be collaborating with investigators at 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 applied 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 1:40 - 2:55 pm in Chambers 3146 (GAMCo)
Office Hours: MWF: 3 - 4 pm; or most anytime by appointment
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)
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 15 & 17 |
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 |
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 + Bakke from last week 454 and pyrosequenicng, Illumina, SOLiD, Ion Torrent, single molecule (Helicos), Nanopore Sequencer Choose Tutorial to Master Nanopore Sequencer |
Discuss Blueberry Paper + Bakke from last week Master your tutorial |
|
Week 3: |
Discuss blueberry grant proposal Master tutorial Discuss project ideas:
|
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 5 &7 |
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 12 & 14 |
Continue SSR projects 10 glossary entries for each student (graded by Dr. C.) |
| Continue SSR projects | |
| Week 6: Feb 19 & 21 |
Continue SSR projects |
Continue SSR projects |
|
| Week 7: Feb 26 & 28 |
Oral Presentation #1 with peer review
Continue SSR projects |
Continue SSR projects |
|
null Week |
Spring Break |
Spring Break |
|
Week 8: |
Respond to email feedback |
|
Meet at Summit for blueberry consumables |
|
| Week 9: Mar 19 & 21 |
Work on genes and GenSAS + SSRs |
| Work on genes and GenSAS + SSRs | |
| Week 10: Mar 26 & 28 |
Work on genes and GenSAS + SSRs |
| Work on genes and GenSAS + SSRs | |
| Week 11: Apr 2 &4 |
Easter Break |
Work on genes and GenSAS + SSRs |
|
| Week 12: Apr 9 & 11 |
Work on genes and GenSAS + SSRs |
Assess Status and Agree on Endgame Write the final paper |
|
Week 13: |
Oral Presentation #2 with peer review
|
| Finish final paper | |
| Week 14: Apr 23 & 25 |
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: Apr 30 & May 2 &7 |
Finalize paper based on comments. |
Final final due (as Word file) submitted by noon on Reading Day |
|
| No Class Optional Tuesday |
Grading
Grades will be based on: glossary
entries (10% total grade); peer reviews
(15% total grade);
final
research paper (topic TBD; 35% total grade); two oral
presentations (30% total grade) and class participation (10% 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 so it is important to keep good notes online.
Grading Scale:
| A = 100 - 94 | A- = 93 - 90 | |
| B+ = 89 - 87 | B = 86 - 83 | B- = 82 - 80 |
| C+ = 79 - 77 | C = 76 - 73 | C - = 72 - 70 |
| D+ = 69 - 66 | D = 65 - 60 | |
| F = < 59 |
© Copyright 2013 Department of Biology, Davidson College,
Davidson, NC 28035
Send comments, questions, and suggestions to: macampbell@davidson.edu