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

Student Collaborators

Learning Outcomes

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)

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 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)

BB dbEST Towson University

Wiki Online Glossary

Standard Operating Procedure (SOP), Quality Control (QC), and Triage

Summarize Large Scale Projects from last year
(5 min. presentations 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 22 & 24

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:
Jan 29 & 31

Discuss blueberry grant proposal

Master tutorial

Discuss project ideas:

  • Heat stress
  • Drought stress
  • Dormancy induction
  • Fruit firmness
  • Fruit size
  • Time of fruit ripening
  • Time of bloom
  • Disease resistance-focusing on resistance to fungal diseases
  • Disease resistance-focusing on resistance to viral diseases
  • Disease resistance-focusing on resistance to bacterial diseases

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
Dr. C. will be out of town

Week 7:
Feb 26 & 28

Oral Presentation #1 with peer review

  • peer feedback is graded by Dr. C.
  • presentation is graded by Dr. C.

Continue SSR projects

Continue SSR projects

null Week
Mar 5 &7

Spring Break

Spring Break

Week 8:
Mar 12 & 14

Respond to email feedback

Blueberry Genome Database

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:
Apr 16 & 18

Oral Presentation #2 with peer review
on your second blueberry project

  • peer feedback is graded by Dr. C.
  • presentation is graded by Dr. C.
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

Course Evaluations

No Class Optional Tuesday

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:

Conversion of Percentage to Letter Grade
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

Genomics Concentration

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