ETH 2006 Ideas

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(Sensing)
(Oscillation related)
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* frequency divider / multiplier
* frequency divider / multiplier
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* use the mechanism developped in [[Wikipedia:Dictyostelid|''Dictyostelium discoideum'' (D.D.)]] (an Amoebae: a unicellular organism).
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** when the food supply is exhausted, D.D. aggregates to form a multicellular assembly: a fruting body (to spread farther in the environment)
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** this aggregation is controlled by cyclic cAMP release (cyclic cellular automata)
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**[http://www.springerlink.com/media/4nc6a0rrrq3rqm678rwy/contributions/w/8/4/4/w844857013725232.pdf|''Dictyostelium'': A Prototype for Spatio-Temporal Organization and Pulsatile Intercellular Communication]
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**[http://www.nature.com/embor/journal/v7/n7/pdf/7400714.pdf| Transcriptional regulation of Dictyostelium pattern formation]
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**we could for example make E. Coli grow in a certain fashion (a line, a flower or a fractal) using this system
== Limitations to lift ==
== Limitations to lift ==

Revision as of 08:55, 18 July 2006

back to ETH 2006

Last years brainstorming: Previous_Ideas

Contents

Cellular automata / Quorum controlled behaviour

  • Game of Life or other semitotalistic automata
    • [http://en.wikipedia.org/wiki/Conway%27s_Game_of_Life wikipedia]
    • [http://csb.inf.ethz.ch/igem-2006 life demo]
    • [http://www.ics.uci.edu/~eppstein/ca/lifelike.html others]
  • propagate a pulse in culture
  • Predator-prey-veggies (or just predator-prey)

State representation:

  • switches and reporters
  • cell life (self destruct and regenerate)

Stepping could be done by

  • an exogenious signal, so each step is a process converging to a steady state (avoid problem of developing a dynamic system)
  • generations
  • oscillating system in cells

(Normally cellular automata are stepped synchronously, but it's often not really necessary)

The matrix would not be as regular as in the mathematical models of corse ...

Logic

  • A kind of a simple ALU: at least two simple logic functions and a multiplexer
  • An implementation of a full-adder: 1-bit adder with carry
    • [http://en.wikipedia.org/wiki/Full_adder full adder in wikipedia]
    • [http://en.wikipedia.org/wiki/Logical_gate logical gate in wikipedia]
  • An irreversible switch (lambda phage like)

Notes

Can't find any logic gates except inverters in the registry, looks interesting.

→ because of that, even simplier gates (AND, OR, XOR, ...) are required

Sensing

What?

  • acoustic
  • pressure
  • electric
  • magnetic (exists in nature, cf. [http://magnum.mpi-bremen.de/magneto/pub/Schueler1999.pdf])
  • light (BB exists[http://partsregistry.org/Featured_Parts:Light_Sensor])
  • temperature (first BBs by 2005 Toronto team [http://parts2.mit.edu/r/parts/partsdb/pgroup.cgi?pgroup=iGEM&group=iGEM_Toronto])
  • chemicals, metals
  • number of neighbor cells (related to «Game of Life» idea): it seems that another team tried similar in 2004 [http://2006.igem.org/wiki/index.php/IAP2004:Polkadorks]

Agents (sense & act)

  • fire squad: get bacteria to find a reaction on the plate and extinguish it
  • bacteria sensing high atmoshpere and switching to produce ozon (to refill ozon holes)
  • extract sun milk when needed (depending on sun intensity & skin properties :-) )

Multi-level sensing

  • a system which has more than on/off levels, e.g.
    • does nothing if ligand is not present
    • turns green on low concentrations
    • starts stinking (e.g. by producing ammonium) on high concentrations

System that potentially could sense any chemical substance

  • leucine zippers that could only build dimer with a bridge
  • chemical substance that should be detected is bridge
  • the bridge dimerization could be realised by fusionate an original part of a leucine zipper monomer with the antibody that is generated for the chemical substance
    • If we can get two different recognition side for antibody and antigen this could work
    • mice could generate the searched antibody, but for test we could use already described antibodies.

Oscillation related

  • frequency discrimination
  • synchronize oscillations among cells (or have emergent synchronous oscillations in the culture)
  • frequency divider / multiplier
  • use the mechanism developped in Dictyostelium discoideum (D.D.) (an Amoebae: a unicellular organism).
    • when the food supply is exhausted, D.D. aggregates to form a multicellular assembly: a fruting body (to spread farther in the environment)
    • this aggregation is controlled by cyclic cAMP release (cyclic cellular automata)
    • [http://www.springerlink.com/media/4nc6a0rrrq3rqm678rwy/contributions/w/8/4/4/w844857013725232.pdf|Dictyostelium: A Prototype for Spatio-Temporal Organization and Pulsatile Intercellular Communication]
    • [http://www.nature.com/embor/journal/v7/n7/pdf/7400714.pdf| Transcriptional regulation of Dictyostelium pattern formation]
    • we could for example make E. Coli grow in a certain fashion (a line, a flower or a fractal) using this system

Limitations to lift

  • E. coli can't move (Seems Penn state had moving E. Coli last year: Penn_StateProjectDes)
  • need to control growth to stabilize cell culture structures if they are desired

Misc

  • optical lenses: program different (light) refraction angles
  • fractals: let the bacteria culture grow such that fractal patterns appear
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