IGEM:Harvard/2006/Brainstorming

Brainstorm!

from Tiff

(From the mailing list email I sent out awhile ago)

I'd just like to suggest that we consider doing something non-cloning based, as in Willliam Shih's DNA structure stuff.

Reasons Why: - cloning is probably going to be a LOT slower (and more difficult to get working, from personal experience) than what he was talking about - he's one of the world's experts, so I'm sure that with his guidance we could do something quick and error-free - it'll be so different and so much cooler than anything else any other group could think of, because it won't be bacterial-based - it's cutting edge - drug delivery systems are hot, and necessary, and this is seriously stuff NO ONE ELSE has ever thought of or done before - if we're going to try to make something with human (ie. medical) importance, starting in bacteria is good, but the eventual transition to eukaryotes is no fun to actually do (ie. transfection)

Reasons Against: - it won't be BBa_, so it might not be so legit in the competition - none of us probably have any experience doing stuff like that, but some of us already know how to clone (if I'm wrong, please correct me :))

from Dave

Hey everyone, here are some very high-level computer science-ish ideas I came up with tonight. I have no idea how hard these would be to implement, but I'll just throw these out there to get the spherical fullerene (haha) rolling:

1. I really liked the idea of containers built using scaffolded DNA origami, and exploring these might prove useful. Once we figure out how to seal the container and get it to open in response to certain stimuli, it might be interesting to create a set of these that respond to different stimuli. I assume that the lids would have to be different in each case, which might be hard to implement in some cases.
2. I was looking at MIT's 2004 brainstorming and saw some interesting stuff concerning insulin production/regulation in the bloodstream. We could even combine this with the containers, constructing cell "factories" that produce containers of insulin. These containers could then open when the concentration of blood glucose gets too high. I'm not exactly sure what benefits (if any) this extended scheme might provide, except maybe a quicker response to rising blood sugar levels since the insulin is already produced.
3. cell instant messaging: One cell can send a message that will propagate through the network and reach a unique destination cell. The important thing would be that the intermediate cells wouldn't interact with the message; they would simply know it was a message and pass it on. Sort of like passing the salt across the table without everyone using it on the way. Difficult? Possible? No idea. Although, it would be cool if a cell realized it had certain deficiencies and was able to "query" the cellular network to find a provider for what it needed. The part could then be passed back to the cell in need. Once again, the DNA containers could be used but I'm sure there are plenty of ways to do this. We would also need to figure out how to send queries across the network and send packages back, which could be difficult.

Once again, these are very high level ideas; it's pretty late and I haven't really researched anything in detail. I'm not sure what's feasible, but hopefully this leads to something useful. Feel free to comment/edit as you like. ~Dave

from Perry

Here are some ideas that were mentioned in the mcb100 group last fall, when we were considering trying to develop our own system. some are really bad/impractical, i know, but hopefully these start some brainstorming.

- alarm clock, reporter in response to time lapse or sunlight

- stop watch, reporter expressed over time

- thermometer. different reporters or different amounts of one reporter depending on temperature.

- chemical detector. one idea was ethanol, maybe detecting different proofs; another idea was carbon monoxide.

- chip. 8 colonies = 8 bits? [i think this was mentioned in yesterday's lecture as having been attempted with failure thusfar.]

- flashlight. bioluminescent reporter gene expressed in the absence of light, or in other words, light acts as a repressor.

- litmus paper. one of two different colored reporter genes expressed in acidic or basic pH.

- color-by-numbers. there are those books that have the outlines drawn with numbers in the spaces, and a legend tells you which color you should fill into which numbered spaces. so here we would have a lawn of bacteria, separated physically into sections, and you would induce different sections to show different colors according to the stimulus: basically a multiple chemical detector system. the stimuli could diffuse to activate all bacteria in a section, or the stimuli could activate one bacterium which would send out the signal.

- wire. there was a BioWire project last year which send a coloration signal down a line of bacteria. can an electric signal be carried, maybe through ions? i guess this would require membrane ion-gates.