Team:TU Munchen/Brainstorming

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We need to come up with some ideas for our project. It might help to look at some of the [http://parts.mit.edu/igem07/index.php/Presentations presentations from last year]. Some ideas have been posted at the [http://openwetware.org/wiki/IGEM:Idea_exchange iGEM idea exchange]. Also look at a list of the [http://openwetware.org/wiki/SynBERC:MIT/Calendar/2007-8-8 most wanted Biobrick parts].

Ideas To Research

E.coli Rugby
- One group of E.coli expresses GFP if it reaches some kind of goal via chemotaxis (touchdown). Another group of E.coli uses chemotaxis to find the ones from group one and expresses CFP if it reaches them (block)
- This is an interesting idea. Can you think of any practical applications?
- With a few changes we would result in a modular E.coli: For example if you want to detect and react on some kind of substrate you could use one E.coli to find it (goal) and then the other one swimst to the first one and makes the reaction. You could expand this, for example if you want the same reaction on different substrates.You just have to build different searching E.colis (different substrates) but one reaction E.coli -> construction kit

Garbage truck rough sketch

E.Coli Filtering (like Detoxing), Codename: "Garbage Truck" :)
- Goal would be a E.Coli which can:
- 1.) detect concentration gradients of the product (I thought about Metal or bigger colloids)
- 2.) swim (flagelli movement) towards it
- 3.) incorporate these particle and thus lower the local concentration
- 4.) goto 1.) till 3.) until the threshold of internal concentration of incorporated particles is reached
- 5A.) aggregation of the "full" E.Coli to a big "clump" for easy extraction
- 5B.) a chemical agent to extract the incorporated parts without killing the bacteria for repeated usage)
- Another variant of this idea would be: After 4.) a chemical switch is activated and the E.Coli swims towards a certain "dump" area (like a garbage truck) and step 5B.) is activated. After that repeat 1.) to 5B.)

Acoustic activation
- Up to now, chemical and light-driven activation are common. Could we implement a reaction to sound in E.coli?
- probably by detecting the sound waves?

E. coli sunscreen
- Well, basically the idea behind this is: can we set the the amount of protein being expressed/RNA being transcribed via the intensity of light?

E. coli digestion: I thought about a method for easier purification of desired protein from the other proteins of E. coli --> idea: create a fusion-protein of goalprotein connected with a protease [http://www.expasy.ch/cgi-bin/lists?/peptidas.txt protease-data bank]
- aim: protease cuts other proteins like E. coli proteins or even the membrane ("way out of E.coli")--> no cell disruption necessary, purification from small proteinfragments by chromatography(size or antibody)-in any way use metalloproteases to separate
- activation of protease at a defined point of time -by coenzyme,...(so that enough protein can be produced in living Eco)
- challenges: protease shouldn`t affect your desired protein, so that the protein stays active and correct folded and isn`t cut itself by the protease

LPS detection.
- LPS is a major component of the outer membrane of Gram-negative bacteria (like E.coli), contributing greatly to the structural integrity of the bacteria, and protecting the membrane from certain kinds of chemical attack. LPS is an endotoxin, and induces a strong response from normal animal immune systems. Everything which is used for cell culture application has to be endotoxin free. So there are commercial kits available to detect LPS. To find an simple way to detect LPS would be very useful because the commercial kits a very expensive. So this would be an good application for Universities.

Random number generation in E. coli [http://www.paradise.caltech.edu/riedel/research/DAC07.pdf]

Ideas That Need More Detail

E. coli nation
- The team from Paris started last year to develop cell differentiation in E.coli. Perhaps we could further develop this concept.

E. coli hard drive
- Using a retro virus to write in E.coli: All bacteria produce inert fragments, which - after activation - are written into our plasmid.
- Each coding bit would be seperated by a defined start/stop sequence.
- To avoid bit doubling (instead of writing a 1 we write 11 or even 111), we also implement -stops-. Thus our sequence would be 1 -stop- 1 -stop- 00 -stop- etc.

Improved chemotaxis
- Chemotaxis in E. coli is essentially a random walk. Can we make it better?
- This is related to problems in computer science and dynamical systems when one needs to find a path somewhere with limited or no memory.
- Would be useful for any system where E. coli needs to get somewhere (e.g., E. coli rugby and E. coli filtering).

Rejected Ideas

E. coli as a power plant
- Use E. coli for power generation. Maybe we could find a step were we can produce energy.
- Rejection reason: This is outside of our knowledge. It is probably more efficient to burn E. Coli ;)

Measurement of E.coli density: despite the fact that you can easily measure the E.coli concentration via optical absorption, it might be useful to modify E.coli in such a way, that a certain signalling protein is expressed, once the E.coli reach a critical concentration.
- Rejection reason: E. coli does this naturally by quorum sensing [http://en.wikipedia.org/wiki/Quorum_sensing#Escherichia_coli].

Spider silk production in bacteria
- Rejection reason: We don't have the equipment.

Antibody production in E. coli
- Rejection reason: We don't have the equipment and the Warsaw team is doing this [http://openwetware.org/wiki/IGEM:UW].

Detection and removal of E. coli strains that cause illness, such as [http://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 E. coli. O157:H7]
- Rejection reason: No interest and the Nanyang team is doing this [http://openwetware.org/wiki/IGEM:NTU/2008].

Detoxification through E. coli (e.g. Mercury)
- Great idea, but the MIT team did something like this in 2007 [http://openwetware.org/wiki/IGEM:MIT/2007]. Maybe we could take it farther? Or we could focus on another contaminant (not mercury).
- The Edinburgh team designed a biosensor that detects arsenic in 2006 [http://parts.mit.edu/wiki/index.php/University_of_Edinburgh_2006]. It could be useful to read about their project.
- Rejection reason: We should look at E. coli filter instead.

Sea water filter (salt removal)
- Rejection reason: We should look at E. coli filter (for metals) instead.

Detection of blood types
- Rejection reason: We can't find a practical application.

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