Category:CACAO Fall 2012/Otterbein Papers

Summary of Quorum Sensing

• One protein functions to produce the signalling molecule
• The signalling molecule can diffuse in & out of cells
• This signalling molecule is detected by a second protein, the signal receptor.
• When this receptor protein detects the signalling molecule, it binds to DNA & interacts with the RNA Polymerase to stimulate (increase) transcription.
  • CACAO students MAY NOT annotate to any function terms involving binding -- it gets abused b/c students look for "DNA binding proteins" or "zinc binding proteins".
• This signaling in turn results in the expression of lots of other genes

Papers for teams

• Team DC2 - PMID:11160083 -- look at Fig 5 for DksA.
• Team Honey Badgers - PMID:9294432 -- look at Fig 4 and Table 3 for RhlR.
• Team Roll Tide - PMID:9218766 -- look at Fig 3 for LasR.
• Team Team - PMID:9620970 -- look at Table 3 for Anr.
• Category:Team_Triple_Bond - PMID:9190808 -- look at Table 3 for Vfr.

• Don't forget to sign in - if you didn't get an email from GONUTS with a link to click on:

1. click on "Login/Create Account"
2. fill in your username (the first part of your Otterbein email address before the @)
3. click on "Email new password"
4. check your email in about 10 seconds for an email from GOwiki --- check your trash & spam folders

Steps

1. Get the paper.

2. Figure out the right UniProt accession for the protein you are going to annotate.

3. Make a page for the protein on GONUTS.

4. See if this annotation already exists (i.e. do NOT duplicate an existing annotation verbatim!)

5. Edit the Annotation table & add a row, then fill in the form with your annotation.

6. Save the form & save the table back to the page (i.e. save TWICE).

Tips and Important Info on Annotations/Challenges

• Annotate from 7pm Sunday Sept 17 until 6:59pm Sunday Sept 23
  • 5 points per complete annotation
• Challenge from 7pm Sunday Sept 23 until 6:59pm Sunday Sept 30
  • During challenge weeks, you will be unable to edit any of your annotations.

• only use the permitted 7 evidence codes
• do NOT annotate to binding terms
• try emailing the authors of the papers

• Each team will get an email from me about 1 of their annotations IF they annotate BEFORE Friday Sept 21 at noon!
  • Feedback will include changes to make to your annotation before the challenge period starts.

• You only get to keep your 5 points for the annotation if the annotation is assessed as perfect (green check mark)
  • if it has a yellow "!", there is something wrong with it, but it can be fixed or challenged to correct it.
  • if it has a red "X", it's wrong & we don't think it can be fixed.
  • if it has a purple "?", we are reviewing it again.
  • if it doesn't have any of these in the status column, we haven't assessed it yet.
• Your team or individual page will look like: