ETH 2006 Ideas

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Revision as of 13:20, 22 July 2006

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Last years brainstorming: Previous_Ideas

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

→ see [http://en.wikipedia.org/wiki/Logical_gate logical gates in wikipedia]

General 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

→ every gate on the way to the project goal is

a) of great value for the registry

b) an intermediary step (and success) for the project

Simple ALU

A kind of a simple ALU: at least two simple logic functions and a multiplexer

• [http://en.wikipedia.org/wiki/Arithmetic_logic_unit alu in wikipedia]

Half-adder or Full-adder

An implementation of a half-adder or full-adder: 1-bit adder with carry

• [http://en.wikipedia.org/wiki/Full_adder full adder in wikipedia]

An irreversible switch

An irreversible switch (lambda phage like)

A/D connverter

analog digital converter, somewhat simplified, e.g. like this:

• add some chemical be recognized by the cells, change the concentration over time (with some defined frequency) → this is our analogous signal to encode
• cell reaction, depending on chemical concentration:
  1. too low: no reaction
  2. low: reaction α, e.g. green fluorescent
  3. medium: reactions α and β, e.g. red and green fluorescent
  4. high: reaction β only: red fluorescent
• implementation notes
  • the green fluorescent protein is the reporter of a band pass filter, i.e. low and high concentrations don't pass the filter (no green)
  • the red fluorescent protein is reporter of a high pass filter, i.e. high concentrations cause the production of the protein
  • the lower boundary of the red filter is above that of of the green filter
  • to enable encoding of a signal, that is of a sequence of different concentrations, the fluorescent proteins have to be degraded quickly. this might be possible by attaching degredation recognition patterns to the proteins, but is yet another challenge. however, this could be the last "bonus" step of the project.

Sensing

What?

• acoustic
• pressure
• electric
• magnetic (exists in nature, cf. [http://magnum.mpi-bremen.de/magneto/pub/Schueler1999.pdf] and [http://www.chemcases.com/cisplat/cisplat01.htm])
• 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.

Filamentous Growth

• Make use of the Yeast Filamentous Growth to create patterns with E.Coli (a flower, a line, a fractal)
  • Under certain conditions (lack of nutrients and mating pheromon present) certain yeasts shift to filamentous growth where the cells become more elongated
  • Yeast colonies form then "tree like structures" that are quite beautiful
  • We could implement this in E.Coli (E.Coli can switch to filamentous growth in presence of magnetic fields [http://magnum.mpi-bremen.de/magneto/pub/Schueler1999.pdf] and [http://www.chemcases.com/cisplat/cisplat01.htm]) to have it reacting in this way to other chemical
  • We could use it to create patterns in the Petri plate with E. Coli.

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/(w2aabf45xs2m2n55rlyffo55)/app/home/contribution.asp?referrer=parent&backto=issue,9,14;journal,2,54;linkingpublicationresults,1:119979,1|Dictyostelium: A Prototype for Spatio-Temporal Organization and Pulsatile Intercellular Communication]
  • [http://www.nature.com/embor/journal/v7/n7/abs/7400714.html;jsessionid=86A9B2B2A6CD6EB4C7D6691BEC50CC68| 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