Difference between revisions of "Taur.vil Week 11"

Revision as of 06:27, 12 November 2013

Week 11 Individual Journal

Journal Club Preparation

Terminology

1. Coccus: A bacterium of round, spheroidal, or ovoid form, less than 1 μm in diameter. [1]
2. Cariogenic: Tending to produce caries (decay of a bone or tooth, especially dental). [2] [3]
3. Otitis media: Infection of the middle ear space, behind the eardrum (tympanic membrane), characterized by pain, dizziness, and partial loss of hearing. [4]
4. Commensal: Living on or within another organism, and deriving benefit without harming or benefiting the host. [5]
5. Bacteriocins: Proteins produced by certain bacteria that exert a lethal effect on closely related bacteria; in general, bacteriocins have a narrower range of activity than antibiotics and are more potent. [6]
6. Efflux Pump: An active transport system for the removal of some antibiotics (such as tetracyclines, macrolides, and quinolones) from bacterial cells. [7]
7. Lipoprotein: Any of a class of conjugated proteins consisting of a protein combined with a lipid. [8]
8. Transpeptidase: An enzyme that catalyzes the transfer of an amino group from one peptide chain to another. [9]
9. Fastidious: In bacteriology, having precise nutritional and environmental requirements. [10]
10. ABC Transporter: Transmembrane proteins that utilize the energy of adenosine triphosphate (ATP) hydrolysis to carry out certain biological processes including translocation of various substrates across membranes and non-transport-related processes such as translation of RNA and DNA repair. [11]

Note: For many of these definitions I had a general notion of the concept, but did not have a concrete definition that I could call to mind. There were very few words in the article I had never come across before.

Outline

Importance of S. pneumoniae

S. pneumoniae is one of the leading causes of death, both world-wide and in the United States. However, efforts to treat pneumonia have stalled due to increasing antibiotic resistance. When this article was published (2001), one third of S. pneumoniae isolates within the US were resistant to penicillin and many were resistant to multiple antibiotics. One of the goals for this study was to combat this problem and identify new targets for vaccine and antibiotic development.

S. pneumoniae has many sub-strains and in this project, the R6 strain was sequenced. R6 is an unencapsulated, avirulent strain which is safe for researchers to work with. Additionally, it's lack of an outer capsule and complete complement of competence genes grants it extreme genetic malleability, making it one of the preferred models for gram-positive coccus.

Methods Used

In this study, S. pneumoniae R6 was isolated from pure colonies grown on media. The DNA was purified through phenol extractions, ethanol precipiation, and spooling, sheared, and fragments were shot-gun sequenced. Fragments were aligned in PHRED, PHRAP, and CONSED and sequence-spanning PCR and direct sequencing using custom primers were used to form a complete sequence. This sequence was confirmed by Southern Blotting, restriction digests, PCR, and electrophoresis.

Open reading frames were determined using gene prediction programs (particularly GLIMMER) to search for sequence regions matching predictive models. ORFs were labeled spr#### starting at 0001. BLAST searches were performed on all ORFs to identify functional domains, orthologous proteins, and provide possible identifications. Non-translated RNA genes were identified using a set of programs to scan for sequence similarity to known functional RNA products.

Tables and Figures

Lab Journal:

On Lab computer, downloaded updated GenMapp Builder v. 2.0b71 Opened pgAdmin III, created new data base titled tATK_20131107 Opened gmbuilder.sql in SQL window and executed Produced the predicted 159 tables Opened GenMappBuilder.bat v. 2.0b71 -Linked to our database tATK_20131107 Imported 20131107_UniProtXML_tATK_TIGR4_AJV.xml

• Took 1.62 minutes

Imported CUserskeckuserDesktop20131107_GO-OBO_tATK_KM.obo-xml

• Took 5.46 minutes
• Proceeded with additional processing: took 4.09

Imported 20131107_UniProtXML_tATK_TIG4_AJV.goa

• Took 0.03 minutes

Exported to desktop under the name of 20131107_GenMappExport_tATK_TIGR4_TPV.gdb

Duties

As team leader: timeline and milestones -deadlines: final project presentation -deadlines: final project deliverables, files and reports -weekly deadlines for each wk's wiki

Determine with team what are some of the milestones we want to hit to finish on time -Exports, QA, deliverable files --accelerate and leave down time --usually at least 2 or 3 iterations of the analysis we did for vibrio

-everybody will be writing electronic lab notebooks -want easy links to everybody narratives (in template?)

-Group action items --what and who's doing them

-Presentations next week

-When do we need drafts of the report by

Raw and edited files --need a naming convention

Main Job: need Gene IDs that will match gene database QA needs to become ID expert Coders will all work as a group, editing GenMAPP and xmlPipeDB

Personal Template

By Tauras Vilgalys

As part of Biological Databases

Please Remember the Harassing of Deities is Strictly Prohibited

Never Forget Samson