Ksherbina Week 11

Katrina Sherbina

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Assignment Description

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Week 12

Week 13

Week 15

Class Journal

Week 1

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Individual Journal

Week 2

Week 3

Week 4

Week 5

Week 6

Week 7

Week 8

Week 9

Week 10

Week 11

Other

Week 5: Database Wiki

Final Project

Team H(oo)KD Project Page

Journal Club Presentation

Project Individual Journal

Paper for Journal Club:

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. doi: 10.1126/science.282.5389.754

10 Biological Terms from Paper

• Biovar - A strain differentiated from other strains by biochemical or other non-serological means.

Abedon, S. T. Supplemental Lecture (98/04/14 update). <http://www.mansfield.ohio-state.edu/~sabedon/biol3010.htm>. Accessed 10 November 2013.

• Hydrodynamic shearing - A technique that fragments DNA molecules by forcing them through a small orifice or the bore of a small-diameter tube at high velocity.

Joneja, A. & Huang, X. Supplementary Material For: A device for automated hydrodynamic shearing of genomic DNA. BioTechniques 46: 553–556.

• Serology - A type of laboratory medicine that analyzes blood serum for signs of infection by looking at antigen-antibody interactions in vivo.

Serology. (n.d.). Medical-Dictionary. <http://medical-dictionary.thefreedictionary.com/serology>. Accessed 10 November 2013.

Outline of the Article

Importance of sequencing the Chlamydia trachomatis genome

• C. trachomatis causes several diseases in human beings, including trachoma, which leads to blindness.
• C. trachomatis infections in humans may increase the risk of HIV infection.
• At the time the article was released, little was known about the two developmental stages of C. trachomatis (i.e. the elementary body and the reticulate body) as well as the bacterial pathogen's physiology and genetics.

Model Organism Database

http://efaecalis.mlst.net/ http://liferay.csb.univie.ac.at/portal/web/chlamydiaedb