Bio343: Laboratory Methods In Genomics

Spring, 2014

A. Malcolm Campbell


Davidson students will be collaborating with investigators at NCSU and the David H. Murdock Research Institute to work on two plant genomes. For the first few weeks, you will help annotate 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. The bulk of your work will be focused on the broccoli genome.

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 two species that you probably eat with some regularity. The blueberrry is native to North American and holds many potentially beneficial compounds. Broccoli is a common vegetable served around the world. Our task will be to reconstruct some of the metabolic pathways to help plant breeders produce better food crops.

Because this is a research course, we will all have to be flexible in the material we will cover. It is impossible to know where this course will take us exactly. I have a rough plan, but nothing firm yet until we see how these projects unfold. If you need a highly structured course, this will not be a good fit for you.


Tentative Syllabus: Bio 343 Laboratory Methods in Genomics

Class meets 12:15 - 1:30 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

Just for Fun Reading

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


Tentative Weekly Schedule

Week of Semester
Subject Matter and Assignments Due
Week 1:
Jan 14 & 16

Discuss: semester-long research plans & set educational goals

Discuss: genome sequencing, DHMRI and our two species

Blueberry genome portal (development site)

BB dbEST Towson University

Wiki Online Glossary

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

Dr. Allan Brown, NCSU introduces blueberry and broccoli projects

Important terms:

  • What is the difference between contig and scaffold?
  • What are ESTs and how are they useful to us?
  • NextGen sequencing methods (basic mechanism and read length)
  • What problems arise during assembly?
  • What is our job if genomes are annotated by computers?
  • What is the difference between SSRs and QTLs?
  • What versions of BLAST might be the most helpful to us?

Amino Acids Table (memorize 1 letter code)

Genetic Code (do not memorize)

NYTimes story on Eric Lander

Week 2:
Jan 21 & 23

Dr. Charles David introduces GenSAS for use on blueberry genes.

Students are assigned gene projects.

Summarize the paper from first Bio343: Bakke et al., 2009

Work on your gene using Excel File

Useful background paper on blueberry genes.

Week 3:
Jan 28 & 30

Prepare Word File Summary on Blueberry Gene (graded by Dr. C.)

posted on class wiki

3 Minute Summary (Word) of Blueberry Gene and SSRs (graded by Dr. C.)

posted on class wiki

Week 4:
Feb 4 &6

Start on Broccoli QTL projects!

Dr. Charles David introduces IGB for use on broccoli genes.

Students are assigned QTL projects.

Start workign on your QTLs

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 11 & 13

Continue QTL projects

Continue QTL projects
Week 6:
Feb 18 & 20

Continue QTL projects

Continue QTL projects

Week 7:
Feb 25 & 27

Oral Presentation #1 with peer review (first 8 presentations)

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

Oral Presentation #1 with peer review (remaining presentations)

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


null Week
Mar 5 &7

Spring Break

Spring Break

Week 8:
Mar 11 & 13

Respond to blueberry and broccoli feedback

Continue QTL projects

Week 9:
Mar 18 & 20
Continue QTL projects
Continue QTL projects
Week 10:
Mar 25 & 27

Continue QTL projects

Continue QTL projects
Week 11:
Apr 1 & 3

Continue QTL projects

Field Trip to NCRC in Kannapolis

Week 12:
Apr 8 & 10

Continue QTL projects

Assess Status and Agree on Endgame

Write the final paper

Week 13:
Apr 15 & 17

Oral Presentation #2 with peer review (first 8 presentations)

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

Oral Presentation #2 with peer review (remaining presentations)

  • peer feedback is graded by Dr. C.
  • presentation is graded by Dr. C.
Week 14:
Apr 22 & 24

Easter Break

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 29 &
May 1 & 6
Finalize paper based on comments.

Final paper due (as Word file) submitted by noon on Reading Day
Fellowship Committee
Watson Fellowship

Course Evaluations

No Class Optional Tuesday


Grading
Grades will be based on:

The exact nature of the presentations and 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

 


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