Team:ETH Zurich/labblog/20140528meet

Project selected

Wednesday, May 28th

After more than one month of endless meetings and passionate debates, we finally chose the project that will keep us occupied in the next five months. From the beautiful pattern made by the Sierpinski triangles, we will focus on cellular automata and try to implement one.

Sierpinski triangles appear when the rule 90 is followed by every cell on the grid :

Ideally we will use a microfluidic chip. We could also use a 3D printed agar plate like this one to load the colonies. On this grid we can implement the rule 90, which can be considered as a rule with 2 inputs : each cell computes a simple XOR gate of its two parents.

The logic part will be built with integrases and the colony-to-colony communication will use quorum sensing.

Every colony will receive two quorum sensing signals from the two cells above it. These two signals trigger the production of two different integrases r and s in the colony. Integrases enable to build biological XOR logic gates by switching twice a terminator. Indeed, every integrase can switch the terminator only once. Thus if the colony produces only r or only s, the terminator is switched only once, so the terminator is OFF, and the gene of interest is transcribed. If the colony produces r and s, the terminator is switched twice, so it is ON and it blocks the transcription of the gene of interest.

We need to  :

• find orthogonal quorum sensing molecules and orthogonal integrases
• discuss with microfluidics experts to check if using microfluidics is possible and presents advantages in our case
• find possible parts in the registry for integrases, and design plasmids

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