IGEM:Harvard/2008/Brainstorming

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We have a lot of good ideas to start working off of! Please add any ideas you have in this space, and make sure to check out the papers here

Theme

We're interested in creating an interface between living systems and electronic systems using bacteria that naturally produce electricity. This idea can go in many different directions depending on what kind of sensors we use, how we process the inputs, and how we present the output.

Bioelectricity and Nanowires

• Species
  • Shewanella
    • grows easily, is well characterized, and is similar to E. coli
  • Geobacter
  • Synechococcus
    • Photosynthetic
  • Pseudomonas
• How do we harvest/detect the electricity?
  • building an anode in a plate format

Synthetic Circuits

• Cyborg
  • Bacteria that follow a maze made by other bacteria
    • I like this idea (and no it was not mine)- I think it can incorporate a lot of the other ideas in a modular fashion that still allows us to get an end product even if not all the modules work. -MXH
      • One strain forms "walls", another strain grows between walls
        • For those people interested in chemical "painting"- we could chemical paint the walls and have the wall strain growth exclusively over the chemicals and then have the other strains be repelled by the the chemical. I don't think this is that trivial, since we can't have the walls growing until they close up the path. The could also work for people who want bacteria to detect drugs- we could paint in steroids...
        • To generate a moving blob of bacterial going thru. the maze, we could add some sort of chemoattractant to the entire plate but also make the bacteria rapidly degrade the substance. This way, a given blob will always try to move forward towards the higher source of the chemoattractant and would not be usually turn back towards the regions where it has already degraded all of the chemoattractant. In additional, it might be nice to create another layer of complexity by making one strain prone to following *magnetic field lines*. We can then place a magnet at the end of the maze and see if this helps this strain or ends up attracting it towards a place where it becomes trapped. E. coli exhibits chemotaxis (see [this paper]). The same genetic circuit could be used to trigger cell death in the absence of the chemoattractant. Additionally, the chemoattractant could also trigger increased cell growth (or can bacteria not grow any faster?) to make the leading edge of the blob move even faster. Admittedly, this might just make the blob stretch out into a long smear.
        • If we're interested in signals, stochasticity, or colors, I think we could create a really cool system whenever a blob of cells encounters a T-junction. Since the blob would then start growing in both directions and eventually split into two blobs, it would be really cool if we could have cells at the junction walls that trigger the bacteria growing in opposite directions to fluoresce in different colors.
        • The product should be extremely visually satisfying: a blob of cells that all appear one color grows and repeated splits into different colored blobs at maze branches. Each blob keeps growing, and we can track all the different blobs and see which one wins (including a subset of the initial blob that may be primed at first by magnetic fields). Additionally, this way we have lots of modules that are all nifty, but would not all need to work. At worst, we could just have walls and the bacteria grows thru. all the regions between the walls. It shouldn't be that hard to make the bacteria grow as a moving blob, so we should be able to implement that. Even this, without all the colors and magnetic sensing systems, could be pretty cool.
    • I also thought the maze idea was intriguing. -LS
  • Bacteria that play games
    • Tic-tac-toe (Neat paper about DNA tic tac toe)
      • I thought the tic-tac-toe idea was interesting. One possible approach we could take is to signal our well choice with a chemical -> those bacteria produce electricity (and maybe change color) -> send a signal to the computer -> have the computer make the bacteria's choice -> inform bacteria in chosen well w/ an electrical signal (which maybe induces a different color change). With this approach we're really more playing tic-tac-toe with the computer than with the bacteria, but it could be a cute way to, as proof of principal, make bacteria which send electrical signals to a computer in response to a chemical and then maybe make bacteria which respond to electrical signals. -LS
      • Or we could take an approach more similar to that in the paper where each human move is accompanied by the addition of a certain stimulus (or combination) which will activate only one well which could be detected with an electrical signal or color change.
        • Or it would be really cool if instead of people adding the chemicals along with their move, the bacteria did. We could create bacteria which in response to our signal, send out a signal to the bacteria in the other squares, activating only the bacteria in the desired area. I think it would be much more interesting if the bacteria are signaling with each other rather than responding to chemicals we add to induce the correct move by the bacteria -LS

• • • Programming
  • "Light-bright"
    • Pattern formation
    • Bacterial "TV"
• Water Quality tester
  • Chemicals
  • Drugs
    • Steroids
  • Acids
  • Quantitation?
  • How would this system compare to what exists already?
• Other inputs
  • Responding to electricity
  • Magnetism
  • Pressure
  • Sound
• Other outputs
  • Sound
  • Color

Other Ideas To Think about

• Bacteria that make a solid substance so you can "build" with bacteria---BioBricks!
• Bacterial "game of life"
• Bacteria that can live on Venus
• Plastic-eating bacteria
• "Autotrophic" E. coli that can survive on one-carbon sources like methane
• Bacteria that produce therapeutic antibodies
• Bacteria that express viral receptors to lure viruses away from human cells
• Bacterial drug delivery systems
• Bacteria that digest lactose for lactose intolerant people
• Logic gates
  • Either/or
• "Homesick bacteria" Spatial memory