Difference between revisions of "Chlamydia trachomatis"

Revision as of 18:23, 5 November 2013

Team H(oo)KD:

• Project Manager/Coder: Katrina Sherbina
• Quality Assurance: Hilda Delgadillo
• GenMAPP User: Dillon Williams

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.
   • The article can be viewed as an HTML and PDF here.
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
   • 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.
   • Replicates were performed for the control and treatment in terms of technical replicates; as the article states that "Density gradient-purified EBs and RBs were incubated in quadruplicate in four-well plates...".
2. Song L, Carlson JH, Whitmire WM, Kari L et al. Chlamydia trachomatis plasmid-encoded Pgp4 is a transcriptional regulator of virulence-associated genes. Infect Immun 2013 Mar;81(3):636-44.
   • The experiment performed consisted of looking at Chlamydia's plasmid which is significantly importance towards Chlamydia's virulence. Through the experiment, the eight open reading frames within the plasmid were deleted one by one in order to better understand the function and importance of the plasmid in terms of its relationship to Chlamydia's virulence. Ultimately, it was found that the Pgp4 Open Reading Frame functions as a transcriptional regulator of the glycogen synthase gene glgA, that is likely responsible for Chlamydia's pathogenic nature.
   • The treatment was the plasmid infected with L2, L2R, L2Rp+, L2RpΔpgp4, or L2RpΔpgp5 and six replicates were made for each infected group. The control was the mock infected plasmid and six replicates were made for the control.
   • The technical replicates for each treatment and control group were six of each.
   • Microarray Data
3. Carlson JH, Whitmire WM, Crane DD, Wicke L et al. The Chlamydia trachomatis plasmid is a transcriptional regulator of chromosomal genes and a virulence factor. Infect Immun 2008 Jun;76(6):2273-83.
   • Different types of molecular and transcriptomic analyses were performed for two strains of Chlamydia trachomatis, specifically the plasmidless strain L2(25667R) and the plasmid-positive strain L2(434), to determine the function of the 7.5-kb plasmid in the bacterium.
   • There were two treatment groups: McCoy cells (4 × 107 cells) infected with L2(434) and McCoy cells L2(25667R). The control group was mock infected McCoy cells.
   • There were 6 technical replicates for the control group and each of the treatment groups.
   • Microarray data

• NOTE: Dillon looked at the Omsland et al. paper, Hilda looked at the Song et al. paper, and Katrina looked at the Carlson et al. paper.

Chosen Article for Club Journal

1. Opted for paper suggested by professor Dahlquist in post-assignment discussion:
   • Carlson, J.H. et al. (2005) Comparative Genomic Analysis of Chlamydia trachomatis Oculotropic and Genitotropic Strains Infect. Immun. 73: 6407-6418.
   • PDF Version of Microarray Paper