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. Brainstorming initial project ideas
3. 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
4. Should we schedule a regular meeting? Chia: Feedback from last year's advisers: regular meetings among grads are recommended. During summer, weekly lab meetings with the undergrads would be important. Perhaps let them rotate to be the team leader and lab meeting presenter so everyone gets a chance to practice their leadership skills.
5. iGEM requirements and relevant dates:
   • Team registration deadline is May 9; 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.

Recombination-based tools to alter DNA sequences

• High frequency deletion of a DNA region: Flank the region with two identical target sequences recognized by a DNA recominase (Cre or Flp) diagram

• Inversion of a DNA region (low reversion rate): Flank the region with two mutant loxP sequences, lox66 and lox71. (both are in the registry)Reference

• Reversible inversion of a DNA region: Flank with target sequences of the Hin recombinase. See 2006 Davidson team page

• Transposons:
  • Sleeping Beauty (transposon from fish) Molecular Reconstruction of Sleeping Beauty

Write-Once Memory Information Theory

• Lav R. Varshney 23:55, 17 April 2008 (EDT): A couple of basic papers on write-once memories are:

• Ronald L. Rivest and Adi Shamir, "How to Reuse a 'Write-Once' Memory," Inf. Control, vol. 55, no. 1-3, pp. 1-19, Oct.-Dec. 1982.

• Gilles Zemor and Gerard D. Cohen, "Error-correcting WOM-codes," IEEE Trans. Inf. Theory, vol. 37, no. 3, pp. 730-734, May 1991.

• Amos Fiat and Adi Shamir, "Generalized 'write-once' memories," IEEE Trans. Inf. Theory, vol. IT-30, no. 3, pp. 470-480, May 1984.

The following paper that I am working on is also rather related, so if anyone wants to take a look at the unsubmitted draft, let me know:

• Lav R. Varshney and Julius Kusuma, "Malleable Compression," in preparation.

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!  :)

(from Melbourne 07 team) - they just sink more slowly atm ;)

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? A name for this GEM suggested by Brian: E.GloLite

• Display of green fluorescent protein on Escherichia coli cell surface.
  • Jason R. Kelly 16:46, 4 April 2008 (EDT):You probably don't need to get it on the surface, they glow pretty well if you just make a bunch of GFP inside the cell (also easier to do).

• 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. Yeast cell density can be altered by mutations in secretory pathways such as sec1.

Two scientists made a microbial lava lamp. Not as fancy as what we want here but we might find their design useful. Basically, brewer's yeast cells are immobilized in a mixture of glass beads, a carbohydrate polymer from seaweed and some dye to make colored "beads". Then the beads are placed in a sucrose solution allowing yeast cells to produce CO2, which is trapped in the beads and giving them buoyancy. As the beads slowly rise to the surface, CO2 escapes and the beads drop. PDF describing details

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

Other ideas from dinner meeting on 3/31

(feel free to edit!)

1. modulation of heterocyst differentiation. See Heterocyst Differentiation and H2 Production in N2-Fixing Cyanobacteria
2. creative use of FLP recombinase for storing/removing DNA based information
3. modulation of com sensing in B. subtilis (model system in Alan Grossman's lab in the Bio Dept)
4. a bacterial diagnostic device for diabetes?

Suggestions from the meeting on 4/4

1. Various people are going to do background research on technical aspects of ideas listed above. They plan to report back on 4/11.
2. Additional idea of making bacteria responsive to electrical stimuli.

Suggestions from the meeting on 4/17

• cookb: Use of inteins (protein introns) as switches / biosensors

1. Big advantage is their modular design which allows easy creation of new functional systems
2. Could use to switch on reporter/effector using temperature change or addition of ligand
3. Huge possibilities as a biosensor (pop in ligand binding domain of choice)
   • Some ideas: glucose sensor (diabetes), pollutant detector (metal binding domains), cancer test (VEGF, other GFs), in vivo phosphotyrosine assay (SH2 domain), detection of biohazards/pesticides/organophosphate, drug testing (steroids)...

Relevant papers:

1. Skretas G and Wood DW. Regulation of protein activity with small-molecule-controlled inteins. Protein Sci. 2005 Feb;14(2):523-32. DOI:10.1110/ps.04996905 |
2. Skretas G and Wood DW. A bacterial biosensor of endocrine modulators. J Mol Biol. 2005 Jun 10;349(3):464-74. DOI:10.1016/j.jmb.2005.04.009 |
3. Gillies AR, Skretas G, and Wood DW. Engineered systems for detection and discovery of nuclear hormone-like compounds. Biotechnol Prog. 2008 Jan-Feb;24(1):8-16. DOI:10.1021/bp070144i |
4. Skretas G, Meligova AK, Villalonga-Barber C, Mitsiou DJ, Alexis MN, Micha-Screttas M, Steele BR, Screttas CG, and Wood DW. Engineered chimeric enzymes as tools for drug discovery: generating reliable bacterial screens for the detection, discovery, and assessment of estrogen receptor modulators. J Am Chem Soc. 2007 Jul 11;129(27):8443-57. DOI:10.1021/ja067754j |
5. Zeidler MP, Tan C, Bellaiche Y, Cherry S, Häder S, Gayko U, and Perrimon N. Temperature-sensitive control of protein activity by conditionally splicing inteins. Nat Biotechnol. 2004 Jul;22(7):871-6. DOI:10.1038/nbt979 |
6. Buskirk AR, Ong YC, Gartner ZJ, and Liu DR. Directed evolution of ligand dependence: small-molecule-activated protein splicing. Proc Natl Acad Sci U S A. 2004 Jul 20;101(29):10505-10. DOI:10.1073/pnas.0402762101 |
7. Ostermeier M. Engineering allosteric protein switches by domain insertion. Protein Eng Des Sel. 2005 Aug;18(8):359-64. DOI:10.1093/protein/gzi048 |

Suggestions from the meeting on 4/24

• Fundraising! Potential donors = MIT alumni (Need to create an official web site, a brochure and a standard letter/budget for continuous fundraising for MIT's iGEM team every year
• Meeting registration deadline = May 9th
• Combinatorial use of Flp and Cre target sites (see "Recombination-based tools to alter DNA sequences" above) to store info in DNA
• Couple recombinases to inteins to make novel a sensor/pathway
• Talk to Prof. Penny Chisholm to learn the basics of handling Cynanobacteria. (Growth condition and doubling time? Any potential toxicity?)