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

Student Collaborators

Learning Outcomes

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)

3) Course wiki site

Optional Readings

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

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)

BB dbEST Towson University

Wiki Online Glossary

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:

  • contigs
  • scaffolds
  • ESTs
  • NextGen sequencing
  • assembly issues
  • automated annotation
  • SSRs
  • variations of BLAST

Amino Acids Table (memorize 1 letter code)

Genetic Code (do not memorize)

NYTimes story on Eric Lander

Week 2:
Jan 24 & 26

Discuss strawberry and grape genome papers

454 and pyrosequenicng, Illumina, SOLiD, Ion Torrent, single molecule

Choose Tutorial to Master

Discuss Blueberry Paper

Master your tutorial

Week 3:
Jan 31 &
Feb 2

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
(email comments to the presenter and cc Dr. C. Your comments will be part of your class participation grade.)

Continue SSR projects

Tutorial #1 Assignments: due Mar. 3

Continue SSR projects

No class meeting March 1

null Week
Mar 6 & 8

Spring Break

Spring Break

Week 8:
Mar 13 & 15

Discuss status and goals

Meet at Summit for blueberry consumables

Blueberry Genome Database

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:
Apr 17 & 19

Oral Presentation #2 on your second blueberry project

  • peer feedback - graded by Dr. C.
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

Course Evaluations

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:

Conversion of Percentages to Letter Grades
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

Genomics Concentration

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