Bio343: Laboratory Methods In Genomics

Fall, 2009

A. Malcolm Campbell

Davidson students will be working the the Joint Genome Institute's adopt a genome program (funded by the Dept. of Energy) adopt a genome program to annotate the Halomicrobium mukohataei genome (See all three publications about this species: 1994, 1997, and 2002). Davidson students will decode this genome that has never been analyzed before. Their annotation work with be added to a public database with the possibility of publishing their results.

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. It will be a lot of fun to do real genomics research on a species which is poorly understood. Our species is supposed to have an "energy component" to its metabolism which is one reason DOE is interested.

Tentative Syllabus: Bio 343 Laboratory Methods in Genomics
Office Hours: M & Tu: 3-4; Thurs: 8:30 - 9:30; or anytime by appointment

Student Collaborators

Learning Outcomes

1) Understand what a gene is through in depth analysis of a genome.

2) Describe how a 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 research 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 halophiles to understand what constitutes a new species.

 

Required Readings

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

2) Online Tools (FireFox browser is best)

3) Research publications on genomes (PDFs distributed during semester).

Tentative Weekly Schedule

Week of Semester
Subject Matter and Assignments Due
Week 1:
Aug 25 & 27

Discuss: semester-long research plans & set educational goals

Discuss: domains of life, genome sequencing, JGI and our species

Halomicrobium mukohataei genome sequence home page

Halomicrobium mukohataei genome portal

Wiki Online Glossary

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

How many do we want to compare? Eight? Sixty-four?

Read the paper from last year's course here: Bakke et al., 2009.

Read the three papers published on our species.

Start with RNA genes first and ID species specific Shine-Dalgarno sequence

Amino Acids Table (learn 1 letter code)

Genetic Code

Week 2:
Sep 1 & Sep 3

Examine RNA gene results: Sanger sequence checks

  • miscellaneous RNA genes?
  • rRNA genes
  • tRNA genes
  • 3 stop codons = no tRNAs

Identify Shine-Dalgarno sequence for our genome. Look in large ribosome subunit genes (LSU), DNA polymerase subunits, RNA polymerase subunits. Collect consensus results.

If Shine-Dalgarno is missing for a particular gene, is the gene part of an operon?

Find genes that do not have a perfect Shine-Dalgarno sequence. What can we do about these exceptions?

1) Verify start codon:
DNA-directed RNA polymerase, subunit N (EC 2.7.7.6).

2) Verify Shine-Dalgarno sequences:

See examples from a different species (Ammonifex)

Standard Operating Procedure - step 1.

Read: Armbrust et al. 2004. The Genome of the Diatom Thalassiosira pseudonana: Ecology, Evolution, and Metabolism. Science 306: 79 - 86.

RNA and Shine-Dalgarno Presentations + 1 option by Dr. C.

Controlled vocabulary

Problems to be addressed: Pseudogenes, transposons, horizontal gene transfer, orthologs, paralogs, homology, hypothetical genes, unknown function, quality of data for annotation.

Establish SOP (standard operating procedures) for genes.

Databases and Tools: BLAST, CDD, KEGG, BioCyc, Tcoffee, EC numbers, and phylogenetic trees

Week 3:
Sep 8 &10

Compare genome by 3 annotation services

The SEED for automated annotation and viewing

Manatee for automated annotation (JCVI)

Work on annotation projects - smaller scale

Work in groups to choose first research project - smaller scale
Week 4:
Sep 15 & 17

Finalize plan and begin project- smaller scale

Make clear the goals for each person

Read halophile genomics paper by Baliga et al., 2004

Discuss end goals and methods for accomplishing this
Week 5:
Sep 22 & 24

Continue projects

10 glossary entries for each student (graded by Dr. C.)
Continue projects - smaller scale
Week 6:
Sep 29 & Oct 1

Continue projects - smaller scale

Each person's portion of project due

Oral presentations with peer review
(email comments to the presenter and cc Dr. C. Your comments will be part of your class participation grade.)
Week 7:
Oct 6 &8

Conclude small scale projects
Submit final written projects based on peer feedback

What types of whole-genome projects are feasible?

First methodology tutorial Due (graded by Dr. C.)
Discuss and investigate whole-genome projects

Week 8:
Oct 13 & 15

Fall Break

Begin whole-genome projects with clear roles defined

Week 9:
Oct 20 & 22

Continue whole-genome projects

Read about cholera evolution

SOP for whole-genome projects

Continue whole-genome projects

Week 10:
Oct 27 &29

Tutorial #2 Assignments: due Nov. 12

Olivia - perl script to compare proteomes
Katie - web pages for two perl scripts (CDS and compare proteomes)
Claudia - how to find and format genome sequences
Megan - how to use web pages, what they do and how
Karen - how to deal with output from web pages
Sarah - CRISPR resources

Download Format Converter and convert all proteomes
Continue whole-genome projects
Week 11:
Nov 3 & 5

Continue whole-genome projects

Design experimental testing
Continue research
Week 12:
Nov 10 & 12

Continue research

Pathway tutorial Due (graded by Dr. C.)
Week 13:
Nov 17 &19

Continue research

Assess Status and Agree on Endgame

Write the final paper

Week 14:
Nov 24
Dec 1 & 3

Oral Presentations on your whole genome story
peer feedback - graded by Dr. C

First draft of final paper (web site) due
Bring Hard Copy to collect comments form peers
Peer review of draft paper (P/F graded)

Finish final paper
Week 15:
Dec 8

Final draft of final paper (web site) due
Fellowships
Course Evaluations
No final exam

Grading
Grades will be based on: glossary entries (10%); two online tutorials for annotation process (10% total); peer review of tutorial (10% total); final research paper (summarize the genome and its comparison to 9 others) (25%); your small scale story written report (20%); two oral presentations (20% total) and class participation (5%). The exact nature of the final paper cannot be determined at this point. You will use the 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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