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080521 meeting notes

We discussed the pros and cons of the four projects that were previously discussed at the student-only meeting:

1) Self-segregating bacteria 2) Tic-tac-toe 3) Maze 4) Lava Lamp

The consensus of the group seemed to be in favor of tic-tac-toe for the following reasons: 1) There are several very interesting problems to be solved: integration of many signals, communication between wells, interface with the electrical detector, and others. 2) It allows for the integration of many interests within the group: the project combines both biological and non-biological components, addresses the significant interest within the group of using bioelectricity, and allows for integration of other interests through the “inputs” to the system (the bacteria could respond to whatever molecules are of interest to the group) 3) Mid points are also novel endpoints: even if we don’t get the whole game to work within the 10-week period, just being able to put in a stimulus and detect an electrical output will be novel. As George pointed out, electricity as an output may be more rapid than an output that depends on genetics (transcription and translation of a reporter) and that alone would be of significant interest to the synthetic biology community. 4) The project is modular: several elements can be worked on in parallel and are not necessarily interdependent for progress. We can simultaneously have groups working on the biological side (cloning) while others are working on the detector/computer side. 5) The project capitalizes on the strengths of the faculty, which is always helpful.

Those at the meeting felt that the above list didn’t apply to all of the projects, particularly item #3 – we had trouble seeing where some of the other projects might offer an interesting endpoint in the event that the full goal was not achieved. Thus, the consensus was in favor of tic-tac-toe.

If you haven’t done so already, it would probably be good for everyone to have read and be familiar with the RNA tic-tac-toe paper: Stojanovic MN and Stefanovic D. A deoxyribozyme-based molecular automaton. Nat Biotechnol 2003 Sep; 21(9) 1069-74. doi:10.1038/nbt862 pmid:12923549.

We concluded the meeting by listing a few ideas of things we will need to look into for the planning and practical execution of the project. Students – please choose one or a few items from this list to investigate on your own over your break, and be prepared to comment at the next meeting. You should communicate with each other through the Google group about who is looking into what, so we don’t have everyone looking at the same thing. Also, feel free to expand this list. Faculty and Staff – get your thinking caps on, too!

- Inputs: what could we use? How many will we need? - Are we interested in cloning into Shewanella directly, or do we want to use E coli and have the Shewanella respond to the output of the E coli? What are the pros and cons of each approach? - How are we going to communicate between wells (eg – in playing the game, how will the other wells know which move was made)? - There was some discussion of using electricity as an input to other wells, perhaps by putting electricity in, the Shewanella could not then discharge electricity, and the accumulation of electrons could change the redox potential of some molecule which could be used as a reporter – how would this work? Or, what about the use of proton gradients as reporters and/or signals? - Growth conditions for Shewanella – how much oxygen can they tolerate and still put out electricity? How anaerobic will the experiments need to be? What growth medium might this require? - The detector widget – all you engineers out there, start thinking about how this might work.

Please, keep the conversation going! Add to this list, and let people know what you find out!

iGEM will officially start on Monday, June 16th at 10 AM. We will meet in BioLabs 2062. See you there!!!