Difference between revisions of "Taur.vil Week 11"

Revision as of 05:59, 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

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