Kzebrows Week 11

Preparation for Journal Club on Your Species

First I made a list of 10 biological terms from my team's microarray paper (full PDF text here) for which I did not know the definitions. I then ran a search through Google for the biological definition of each of these terms. No one online biology dictionary had definitions for all of these so I often had to click on several links before finding an appropriate definition. I used a combination of online biological or medical dictionaries and journal articles with the definitions in their abstracts or early in the background information. I avoided using sites like Wikipedia in my search.

regulon: a group of genes regulated by the same regulatory molecule with a common binding site or promoter (definition here)
pouchitis: after a proctocolectomy an IPAA is performed (ileal pouch-anal anastomosis) in which the lower part of the small intestine is connected to the anus, creating a pouch. Pouchitis is the inflammation of the pouch that can occur following the surgery. (definition here)
chaperonin: a protein that aids in assembly and folding of protein molecules in living cells (definition here)
QRT-PCR: Real TIme Quantitative Reverse Transcription PCR, or a procedure to detect products generated during each cycle of PCR by cleaving the probe during PCR. Nuclease activity of Taq polymerase can then be used to detect amplification of a certain product. (definition here)
beta-subunit: a subdivision or distinct component of a larger protein unit (definition here)
island: a cluster of genes acquired by horizontal gene transfer that are frequently associated with bacterial adaptation (definition here)
serotype: an immunology defined variant of a micro-organism that bears a unique epitope on its surface (definition here)
type III secretion system (TTS): a syringelike apparatus used by some bacteria to penetrate the plasma membrane of a host cell and inject something, such as a toxin (definition here)
isoniazid: first-line and most commonly used anti-tuberculosis drug. Organisms are able to develop resistance very rapidly if it is used alone. Hepatic toxicity is the major side effect. (definition here)
cold shock protein: a protein expressed at low temperatures that protects cell components from changes caused by suboptimal temperatures, e.g. CspA in E. coli which binds to RNA and prevents 2-degree structure formation. (definition here)

Write an outline of the article. The length should be a minimum of the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" option in your browser to see the length). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
- What is the importance or significance of this work (i.e., your species)?
- What were the methods used in the study?
- Briefly state the result shown in each of the figures and tables.
- How do the results of this study compare to the results of previous studies (See Discussion).

- For the microarray paper (GenMAPP Users only), include the following:
  1. Describe the experimental design of the microarray data, including treatments, number of replicates (biological and/or technical), dye swaps.
  2. Determine the sample and data relationships, i.e., which files in the data correspond to which samples in the experimental design.
  3. Construct a flow chart that illustrates the above.

Guild Meeting Notes 11/10: GenMAPP Users

Experimental design (for sure do by next week)
- Treatment vs. control
- Biological vs. technical replicates: which one and how many
  - Biological replicates: independent samples
  - Technical replicates: if at any point sample is split into two and treated differently
  - NOTE: should be able to find # chips or microarrays (a combo of the above should add up to this)
- dye swaps: green and red dye behave differently in experiments
  - Figure out how many dye swaps occurred (best is even, but they could have done half and half and swapped it or used technical replicates)
- Flow chart (will go into final paper and presentation!)
Sample and data relationships: Match each chip/filename with a sample. One file should correspond to one chip. (look at by next week)
- raw.zip should have the files in it
- sdrf.txt (Sample Data Relationship File) spreadsheet
- NOTE: Double-check with Dr. Dahlquist
Create compiled raw data file with ID, sample log 2 fold, sample log size, etc.
Normalization and stats (scaling and centering data, calculating T tests and B-H/Bonferroni corrections). Can consult with Dr. Dahlquist for customized procedure.
- Goal: do a sanity check and compare to what was actually written in the paper to see if it matches (probably not identical but same magnitude and direction)
GenMAPP: format data and run through GenMAPP and MAPPFinder (converge here with Coder and QA)
- Do biological interpretation of the data, analyze, and find out something new because the paper did not have this kind of analysis previously
- Identify exceptions and feed info back to QA person (a few hundred is ok, just hopefully not more than 10% of genome)

Deliverables: responsible for describing methods, how raw data file was found, etc., data tables, GenMAPP and MAPPFinder analysis and interpretation. Compare or contrast in discussion what was found vs. what coder and QA found.