Chlamydia trachomatis

Team H(oo)KD

Project Manager/Coder: Katrina Sherbina

Quality Assurance: Hilda Delgadillo

GenMAPP User: Dillon Williams

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Final Product

Project Deliverables

Deadlines and Intermediate Milestones

Monday	Tuesday	Wednesday	Thursday	Friday
11/11	11/12	11/13	11/14 Run an export/import of gene database cycle KS/HD Create species profile KS Obtain and format raw microarray data DW	11/15
11/18	11/19 Vet the gene database exported 11/14 using XMLPipeDB, SQL, and Access KS/HD/DW Potentially start another import/export cycle KS/HD Finish formatting raw microarray data DW Begin microarray data statistical analysis DW	11/20	11/21 Finish microarray statistical analysis DW Run TallyEngine KS/HD	11/22
11/25	11/26 Perform GenMAPP and MAPPFinder Analysis DW	11/27 Thanksgiving Break	11/28 Thanksgiving Break	11/29 Thanksgiving Break
12/02	12/03 Work on the final paper outline DW Document the relational database schema HD Commit changes to GenMAPP KS	12/04	12/05 Begin writing the paper DW/KS/HD Begin working on the presentation DW/KS/HD	12/06

Annotated Bibliography of Genomics Papers for C. trachomatis

Whole genome sequencing of C. trachomatis

1. Journal article describing results of whole genome sequencing:
   • Database: PubMed
   • Search Terms: Chlamydia trachomatis [MeSH Term] AND genome [Title]
   • There were 29 results. Many of the articles that appear using the above search terms have to do with performing whole-genome analysis of C. trachomatis to look at genetic polymorphisms in the bacterium and molecular and genetic characteristics that are observed when the bacterium infects a host.
   • Stephens, R.S., Kalman, S., Lammel, C., Fan, J., Marathe, R., Aravind, L., Mitchell, W., Olinger, L., Tatusov, R., Zhao, Q., Koonin, E. V., Davis, R.W. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282: 754-759. 10.1126/science.282.5389.754.
   • The article can be viewed as an HTML.
   • The article can be viewed as a PDF.
   • This article includes Supplementary Material.
2. Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
   • How many results did you get?: 872
   • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?: Based on the titles and abstracts found in the results, it seems that research has been primarily in the direction of understanding how the disease functions and assessing the severity of the disease (and how to cure it).

Microarray articles

The EBI ArrayExpress database was used to locate each of the four following microarray articles. The search terms used were Chlamydia trachomatis under 'By organism' while the rest of the drop down menus were not altered.

The following articles appear in order of preference:

1. Omsland A, Sager J, Nair V, Sturdevant DE, Hackstadt T. , et al. Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium
   • PDF Version of Paper
   • Microarray Data
   • Chlamydiae undergo a biphasic developmental cycle characterized by an infectious cell type known as either an elementary body (EB) and an intracellular replicative form called a reticulate body (RB). Chlamydia was incubated under microaerobic conditions to test the differences in preferred energy source between EB's and RB's.
   • There weren't necessarily a "treatment" group and a "control" group. Referencing figure 4, it can be inferred that EB would be considered the "treatment" group because of the way that the ratio was set up, being EB to RB. In this way the RB would be the "control" group as they are looking at the EB population relative to the RB population.
   • 4 Biological Replicates were performed for the control and treatment; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".

Journal Club Presentation on C. trachomatis Genome Sequencing Paper

Here is the PDF version of the presentation given on November 12, 2013 on the Stephens et al. (1998) paper.

Important Files

GO OBO-XML Zip File (couldn't upload the unzipped file)

• Media: Go daily-termdb.obo-xml v1 HD 20131107.gz

Wiki Formatting

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