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Hello, and welcome to the OpenWetWare discussion page! We will be using this page to post discussion ideas and meeting minutes.

Below this introductory section is a section entitled "Discussion". This is where you may post your ideas on the project and where meeting minutes will be posted as well. To keep this page as neat and organized as possible, please try to adhere to the following format:

Date and time (mm/dd hh:ss) Name
Your discussion text will go here. Type as much as you want in this box; we want to be able to discuss issues and post resources on this talk page, so please don't be shy! Don't worry about hitting enter; the box will automatically wrap your text around.

However, you are always free to hit the enter button whenever you wish to start a new line.

When editing this page, you will find the coding for the table above. Simply copy the template and replace the date and time, name, subject, and text fields with the appropriate information. Hopefully, this will be an excellent way to view submissions to the talk page in an organized manner.

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As a final note, please feel free to edit any information that you feel may be incorrect or poorly worded. It might also be a good idea to notify the person of changes you may have made to his or her submissions.

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Project Models

Listed here are the various models being considered for use in our project. One of our biggest concerns with most of these models is if we can use operators outside of promoter regions rather than as part of a promoter.

5/30 8:35 pm Meagan Musselman
Proposed Mechanism Option 1 (2x4)
This is one of the final options for a 2:4 decoder that we discussed on Friday. It would use 1 sRNA and three promoters that would be easy enough to make using PCR.

The following link leads to a Powerpoint about this model: File:2-4.ppt 2-4.png

Proposed Mechanism Option 2 (2x4)
This is one of the final options for a 2x4 decoder that we discussed on Friday. It would use 1 repressor protein (TetR), two activator proteins (T7 RNAP, ExsA, or sigma-32?), two negatively-regulating sRNAs (Spot42 and Sgrs), and one positively-regulating sRNA (possibly DsrA or RprA, or a synthetic one we would choose to make).


6/04 11:29 am Meagan Musselman
Proposed Mechanism Option 3 (2x4)
The other day we found more information about two small RNAs that both negatively regulate the same gene. So, this is another model for a 2x4 decoder that would use 2 small RNAs and three repressors


Rejected Mechanism Option 1 (3x8)
This is a potential 3x8 schematic that uses three autoinducer systems used in quorum-sensing bacteria, three 2-hybrid systems and one 3-hybrid system, and two microRNAs (previously Hin recombinase, but we believe that will not work). Each autoinducer is tied to one output, and any combination of two of the three outputs will use a 2-hybrid system where transcription will be activated when a protein-<html>&alpha;</html> subunit hybrid and a protein-zinc fingers hybrid dimerize. When all three inputs are positive, the 3-hybrid system activates the final gene and microRNAs are produced to shut off all other promoters. This design was rejected due to the amount of time it would take to build, even though the autoinducers were to be cut out.

The following link leads to a Powerpoint presentation of this model: File:3x8 Take 3.ppt 3x8-2.jpg

Rejected Mechanism Option 2 (2x4)
This is the first 2x4 schematic brought up. We have decided against this model because we believe that the dual subunit system will not be able to terminate transcription by knocking off RNA polymerase. There are also slight concerns with how well a dual subunit activation/repression system will work, but these can be avoided by replacing the system with two repression systems P and Q.


Rejected Mechanism Option 3 (3x8)
This is a potential 3x8 schematic that uses mRNAs coding for activator proteins/RNA polymerases and tRNAs that bind to stop codons. For more information on how this model works, please click here to link to a PDF file explaining the concept. One prominent issue concerns the interference of stop codon-binding tRNAs with regular cell growth and metabolism.

TRNA Model.jpg

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General Discussion

Date and time (05/06 2:30) Graham Heimberg
incomplete list of reading suggestions
1. Intro to Systems Biology by Uri Alo in Molecular cell 2008

2.Mark Ptashne's Getentic Switch

3. MCB 250 textbook (electronic copy will be made available)

4. MCB 252 textbook (electronic copy will be made available)

4/29 6:00 PM Dave Korenchan
Discussion Section

Hey guys, I figured I'd write the first text box. Let me know anytime if you have any ideas for improving discussion on this page.

Your friendly neighborhood Webmaster,

Dave K.

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