IGEM:MIT/2008

This page will soon host the website of the MIT team for iGEM 2008

For now it is being used for planning the following (please edit!):

1. Scheduling interviews and finalizing the undergrad team
2. Preparing the UROP application
   • The application is due on April 10. See UROP paperwork for details.
   • UROP office: The undergrads must apply individually for educational purposes even though they'll propose the same project and have very similar tasks. The office may not fund all undergrads but will work with the faculty adviser to help ensure there is enough funding.
3. Brainstorming initial project ideas
4. Creating a website for the 2008 team (probably based on 2007 page IGEM:MIT/2007)
   • For help setting up a team lab notebook, please contact User: Ricardo Vidal. He's working with OpenWetWare at MIT this year, and could help you all get familiar with some new tools that update the notebook since last year's iGEM notebooks. - Jason R. Kelly
5. Should we schedule a regular meeting?

Brainstorming Project Ideas

Information Storage Device

I was thinking a bit about information storage. There have been a whole slew of papers that suggest storing artificial messages in DNA. A few representative examples are

• C. Bancroft, T. Bowler, B. Bloom, and C. T. Clelland, "Long-Term Storage of Information in DNA," Science, vol. 293, no. 5536, pp. 1763-1765, Sept. 2001.

• P. C. Wong, K.-K. Wong, and H. Foote, "Organic data memory using the DNA approach," Commun. ACM, vol. 46, no. 1, pp. 95–98, Jan. 2003.

• J. P. L. Cox, "Long-term data storage in DNA," Trends in Biotechnology, vol. 19, no. 7, pp. 247-250, July 2001.

All of these works envision long-term storage where complicated cloning techniques with restriction enzymes, oligonucleotide synthesis or PCR, and ligation would be used for storage. I don't know much at all about this, but are there ways of making a storage device where it is moderately easy to change what is written in the memory? Basically designing some kind of encoder and decoder that makes DNA more of a rewritable medium rather than just a long-term storage medium. A related question is whether there might be a way to introduce an error-correcting circuit along the lines of

• M. G. Taylor, "Reliable information storage in memories designed from unreliable components," Bell Syst. Tech. J., vol. 47, no. 10, pp. 2299–2337, Dec. 1968.

There are probably more easily editable means of biological information storage that are more worthy of exploration.

• cookb: Hmm, that's an interesting idea and quite original for iGEM! I'm getting an image of some sort of simple physical signal (e.g., exposure to light) being converted into DNA information, sort of like a Morse code encoding words into DNA. I wonder what possible mechanisms one could use to facilitate that... But even encoding something simple like "Hello world" would be a huge deal, and have big ramifications on areas such as commercial gene synthesis.

Synthetic Taxis

Develop some sort of Kalman filter-like circuit or some other signal processing circuit to detect or track pathogens. The UCSF/UCB Center for Engineering Cellular Control Systems has started to look at some similar problems.

Bacterial lava lamp

• Reshma 10:16, 19 March 2008 (CDT): I've been wanting to make a bacterial lava lamp for a long time. The U. of Melbourne 2007 team engineered this super cool part that enables bacteria to float (used in natural systems to maintain marine bacteria at a particular depth). By combining this floatation part with a luciferase, I think you could make some nice lighting for the home!  :)

Multi-colored moss

• Jason R. Kelly 12:23, 19 March 2008 (CDT): Austin and I went out and visited Magdalena Bezanilla's lab at Umass-Amhearst that studies this moss and found out that it's not too hard to grow and genetically manipulate it. One idea was to express pigments from other plans (flowers) in the moss to make it in different colors. Magdalena thought this might be possible, could follow up with her if it was an idea that folks thought was cool. Even if it didn't work, you could make the first BioBrick parts and vectors for engineering plants!