Team:ETH Zurich/labblog/20140528meet

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== Project selected ==  
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== Week 1 : Project selected ==  
==== Wednesday, May 28th ====
==== Wednesday, May 28th ====
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Sierpinski triangles appear when the rule 90 is followed by every cell on the grid :
Sierpinski triangles appear when the rule 90 is followed by every cell on the grid :
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[[File:ETH Zurich Rule 90.PNG|600px]]
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[[File:ETH Zurich Rule 90.PNG|center|500px|thumb|Pattern given by rule 90 if only one cell is switched on in the first row at the beginning. The pattern appears row by row.]]
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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.
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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 6, which is the simplification of rule 90 considered as a rule with 2 inputs : each cell computes a simple XOR gate of its two parents.
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[[File:ETH Zurich 3Dprint agar plate.png|600px]]
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[[File:ETH Zurich 3Dprint agar plate.png|center|600px|thumb|Arrangement of p and q cells on the chip]]
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[[File:ETH Zurich Rule 6.PNG|center|300px|thumb|Pattern given by rule 6 if only one cell is switched on in the first row at the beginning. The pattern appears row by row.]]
The logic part will be built with integrases and the colony-to-colony communication will use quorum sensing.
The logic part will be built with integrases and the colony-to-colony communication will use quorum sensing.
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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.  
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Every colony will receive two quorum sensing signals (QSp and QSq) 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 GFP and QS1 or QS2 are produced (depending on the colony). If the colony produces r and s, the terminator is switched twice, so it is ON and it blocks expression of GFP and of the quorum sensing molecule.  
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[[File:ETH Zurich xor integrase.PNG|800px]]
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[[File:ETH Zurich xor gate.PNG|center|800px|thumb|Rule that will be computed by all cells : an XOR gate between the signals from the 2 cells above. Biologically, integrases p and q are able to bind sites around a terminator and switch this terminator, thereby turning off the effect of the terminator and enabling gfp transcription. If p and q integrases are both present, the terminator is switched twice and comes back to its initial state, gfp is not transcribed.]]
We need to  :
We need to  :
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*find possible parts in the registry for integrases, and design plasmids
*find possible parts in the registry for integrases, and design plasmids
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Latest revision as of 14:33, 11 October 2014