Team:ETH Zurich/project/overview/implementationsimple

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E. coli bacteria are able to communicate by producing molecules that can cross their cell membrane by simple diffusion. These molecules are called quorum sensing molecules. In our project Mosaicoli, the cells in every colony on the grid are able to sense these molecules coming from the two colonies above it, and to produce a molecule for the next colonies below it.

In order to make a pattern appear on our grid, we need to tell every cell on this grid:

to sense the signals coming from the two cells above.
if it senses only one signal, to produce a fluorescent protein and generate the signal for the cells below
to produce nothing if it senses both signals or if it does not sense any signal.

In synthetic biology, you can tell the cell to compute this algorithm by inserting a genetic circuit. Here is how we did it:

For sensing the signals coming from above, we added in every cell two genes (luxR and lasR) that produce two proteins (LuxR and LasR) that will bind respectively the blue and the red quorum sensing molecules of the figure above. The blue and red complexes created this way trigger the production of other proteins called integrases (Bxb1 and ΦC31). Integrases flip a DNA sequence between two flanking sequences called att-sites (the triangles in the animation above).
This sequence between att-sites (see the large, black T in the animation above) is placed in such a way that it blocks production of a fluorescent protein. Once an integrase is present, the DNA sequence is flipped and production becomes possible. You can see in the animation that if an integrase is present, it can remove this blocking sequence (turn the black T upside down). However if both integrases are present, this sequence is flipped twice and it blocks production of fluorescence again.
When the fluorescent protein is produced, a second protein is produced as well which triggers the production of a quorum sensing molecule sent to the cells below.

If you want to know more about quorum sensing and integrases, you can read the article Biological tools in our Background page.

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 In synthetic biology, you can tell the cell to compute this algorithm by inserting a genetic circuit. Here is how we did it:
-* For sensing the signals coming from above, we added in every cell two genes (''luxR'' and ''lasR'') that produce two proteins (LuxR and LasR) that will bind respectively the blue and the red quorum sensing molecules of the figure above. The blue and red complexes created this way trigger the production of other proteins called integrases (Bxb1 and ΦC31). Integrases flip a DNA sequence between two flanking sequences called ''att''-sites.
+* For sensing the signals coming from above, we added in every cell two genes (''luxR'' and ''lasR'') that produce two proteins (LuxR and LasR) that will bind respectively the blue and the red quorum sensing molecules of the figure above. The blue and red complexes created this way trigger the production of other proteins called integrases (Bxb1 and ΦC31). Integrases flip a DNA sequence between two flanking sequences called ''att''-sites (the triangles in the animation above).
-* A gene sequence is placed that blocks expression of the fluorescent protein (see the large, black T in the animation above). You can see in the animation that if an integrase is present, it can remove this blocking sequence (turn the black T upside down). However if both integrases are present, this sequence is flipped twice and it blocks production of fluorescence again.
+* This sequence between ''att''-sites (see the large, black T in the animation above) is placed in such a way that it blocks production of a fluorescent protein. Once an integrase is present, the DNA sequence is flipped and production becomes possible.  You can see in the animation that if an integrase is present, it can remove this blocking sequence (turn the black T upside down). However if both integrases are present, this sequence is flipped twice and it blocks production of fluorescence again.
-*When the fluorescent protein is produced, an enzyme is also produced which triggers the production of a quorum sensing molecule sent to the cells below.
+*When the fluorescent protein is produced, a second protein is produced as well which triggers the production of a quorum sensing molecule sent to the cells below.
 <br/>
 If you want to know more about quorum sensing and integrases, you can read the article [[Team:ETH_Zurich/project/background#Biotools|Biological tools]] in our Background page.