Bio343: Laboratory Methods In Genomics

Fall, 2008

A. Malcolm Campbell

Davidson students will be working the the Joint Genome Institute (funded by DOE) to annotate the Halorhabdus utahensis AX-2, DSM 12940 genome (See one publication). Davidson students will decode this genome that has never been analyzed before. Their work with be added to a database with the possibility of publishing their results.

This will be a stand alone lab course that is primarily data analysis by computer. DNA microarrays are fading fast but DNA sequencing will be used more each year. I want Davidson students to be skilled in an area with a long research potential.

I am very excited about this new course. Only 15 schools in the world get to participate in a pilot program run through JGI and we are the only school taking on an entire genome solo. 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

Student Collaborators

Learning Outcomes

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

2) Determine how genomes are organized.

3) Generate species-specific metabolic maps.

4) Recognize that automated annotation is imperfect and many judgment calls are necessary.

5) Evaluate evolutionary paths as revealed in novel genomes.

6) Compare the structure and function of the three domains of life.

7) Develop computer skills used in modern genomics.

8) Excel in collaborative learning and research.

 

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 to work)

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

Tentative Weekly Schedule

Week of Semester
Subject Matter and Assignments Due
Week 1:
Aug 26 & 28

Pre-Semester Assessment

Discuss Semester-Long Research Plans & Set Educational Goals

Discuss Domains of Life, Genome Sequencing, JGI and our species

Halorhabdus utahensis AX-2, DSM 12940 web site

Wiki Terminology and Online Glossary

Report Information: Word File Template (One Gene per File) (excel version)

Strategy for Coverage, Quality Control (QC), and Triage

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

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

Amino Acids Table (learn 1 letter code)

Genetic Code

Week 2:
Sep 2 & Sep 4

Examine 50 RNA gene results:

 

 

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, is the gene part of an operon?

Try these genes out to see challenges:

1) Verify start codon:
Neighborhood six frame translation with putative ORF's shown below for gene_oid=2500587809 197587..197745(-)
DNA-directed RNA polymerase, subunit N (EC 2.7.7.6) (IMGterm).
Vs
Halorubrum lacusprofundi ATCC 49239 ID 641184591

2) Verify Shine-Dalgarno sequences:

Neighborhood six frame translation with putative ORF's shown below for gene_oid=2500587812 198625..198975(-)
LSU ribosomal protein L18AE (IMGterm).

And

Neighborhood six frame translation with putative ORF's shown below for gene_oid=2500588579 976173..976517(+)
LSU ribosomal protein L12AE (IMGterm).

And

Neighborhood six frame translation with putative ORF's shown below for gene_oid=2500588578 975105..976157(+)
LSU ribosomal protein L10P (IMGterm).
** has SD but it is not called by software

And

Neighborhood six frame translation with putative ORF's shown below for gene_oid=2500588577 974467..975105(+)
LSU ribosomal protein L1P (IMGterm).

BUT, this one does not seem to have one

Neighborhood six frame translation with putative ORF's shown below for gene_oid=2500588575 971692..972180(+)
LSU ribosomal protein L11P (IMGterm).

See examples from a different species (Ammonifex)

Standard Operating Procedure - step 1.

3 Teams 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, EcoCyc, Tcoffee, EC numbers, and phylogenetic trees

Week 3:
Sep 9 &11

Peer review of first wave of genes (P/F graded critique)
Continue gene annotation
Submit lab notebook for grading
Week 4:
Sep 16 & 18

First group of glossary entries (graded by Dr. C.)
First gene web page oral presentations (peer critiqued in class)

First gene web page (graded by Dr. C.)
Read Glass et al. 2000. The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature. 407: 757 - 762.

Week 5:
Sep 23 & 25

First tutorial Due (graded by Dr. C.)
Continue gene annotation
Week 6:
Sep 30 & Oct 2

Pathways and Structures: Assembly and Annotations
Continue gene annotation and start pathways
Week 7:
Oct 7 & 9

Alternative Pathways and Missing Steps
Establish SOP for Pathways
Read Turnbaugh et al. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 444: 1027 - 1031.

Week 8:
Oct 14 & 16

Fall Break
Peer review of second wave of genes (P/F graded critique)
Continue gene and pathway annotations

Week 9:
Oct 21 & 23

Second group of glossary entries (graded by Dr. C.)
Second gene web page oral presentations (peer critiqued in class)

Second gene web page (graded by Dr. C.)
Week 10:
Oct 28 & 30

Second tutorial Due (graded by Dr. C.)
Continue gene and pathway annotations
Week 11:
Nov 4 & 6

Generate systems
Continue gene and pathway annotations
Week 12:
Nov 11 & 13

Connect Systems
Continue gene and pathway annotations
Week 13:
Nov 18 & 20

Assess Status and Agree on Endgame

Continue gene and pathway annotations

Week 14:
Nov 25
Dec 2 & 4

 Finish annotations and focus on final paper

First draft of final paper (web site) due
Peer review of draft paper (P/F graded)

Finish final paper submit lab notebook for grading
Week 15:
Dec 9

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

Grading
Grades will be based on: glossary entries (10%); online tutorials for annotation process (20%); peer review (10%); final research paper (20%); lab notebook for genes and pathways (20%); and oral presentations and class participation (20%). The exact nature of the final paper cannot be determined at this point. You will use the 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


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Send comments, questions, and suggestions to: macampbell@davidson.edu