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
   • Deadline = 4/10. See UROP paperwork.
   • Submit application online at https://sisapp.mit.edu/uropweb/home.mit
   • UROP office: The undergrads must apply individually. No specific project proposal is needed; the sample applications from Brian are great examples.
   • We are also exploring additional UROP funding from BE, CE and Bio departments.
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?
6. iGEM requirements and relevant dates:
   • Team registration deadline is Apr 30; need to specify instructors, students, lab space, and funding. Registration fee $1000/team.
   • Jamboree: November 8-9, 2008 at MIT; $100 per undergrad and $250 for others.

Brainstorming Project Ideas

iGEM research project tracks:

1. Foundational Research - basic science and engineering research
2. Information Processing - genetically encoded control, logic, and memory
3. Energy - biological fuels, feedstocks, and other energy projects
4. Environment - sensing or remediation of environmental state
5. Health & Medicine - applied projects with the goal of directly improving the human condition
6. (new track this year) - software tools to facilitate use of standard biological parts

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!  :)

If we did this, we would want the cells to clump together so that it looks lava lamp like.

How is this combo: Flocculating E. coli + increased buoyancy + GFP or luciferase on cell surface + self-made tube-flipping device (mechanical or manual) + blue excitation light or luciferin?

• Display of green fluorescent protein on Escherichia coli cell surface.

• Chia: A microbe-based lava lamp - cute! We can make budding yeast cells clump as well. There is a family of cell surface glyco-proteins that confer cell-cell adhesion (flocculation) and/or adhesion to hydrophobic substratum [1]. Flocculation mediated by the protein Flo1p can be altered by adding certain sugar or EDTA. I'll look into methods/mutations that make yeast cells float.

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!

Bacteria with limited # of cell divisions, after flipping a switch

A neat idea initiated by Vikram. Such a GEM would have much less potential to contaminate the environment if accidentally released from the laboratory.

This might be possible if the bacterial genome shortens gradually like linear eukaryotic chromosomes. A method to linearize the E. coli genome without affecting its stability has been reported [2].

If the chromosome ends were generated differently, one might be able to implement a replication dependent shortening mechanism. (Brain power needed!)

One way to visualize chromosome shortening (besides PCR or Southern blotting) could be insertion of a reporter at various locations of the linearized chromosome. Ideally the presence/absence of the reporter would make E. coli colonies look different on a agar plate. (Say lacZ + X-gal as in blue/white screen?) If the reporter is lost right after the first division (since it's inserted very close to the initial chromosome end), the colony would be one color. If the reporter is inserted far away from chromosome ends and thus retained for many generations, the colony would be another color. - Chia