Team:ETH Zurich/Biology

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= Biology - Overview =
'''A brief overview of our SmoColi system can be found here, click on the experiments or subparts to jump to the corresponding sections.'''
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[[File:ETH SmoColi.png|200px|left|thumb|'''Overview of the SmoColi system.''' Depending on the concentration of smoke respectively sensor molecule, a GFP band appears at a certain distance from the entry of the tube. Beyond a certain concentration cells turn red.]]

== General idea==

SmoColi is a bacterial system which is able to sense and quantify smoke in the air. The quantification of smoke works in the same way as a thermometer: A band of GFP gets shifted along an axis depending on the concentration of smoke sensed by the bacteria. If the amount of smoke gets too high, an alarm system is switched on (system turns red) and thus warns people when the smoke could cause health damage.

Experiments are performed in ''Escherichia coli'' strains JM101 and DH5&alpha;. We established SmoColi as a compatible three plasmid system with different antibiotic resistances. Thus we are able to include the whole network into the same cells. See [[Team:ETH Zurich/Biology/MolecularMechanism|Technical implementation]] for details about the biological implementation.
 
SmoColi can be used in channels and tubes of different sizes depending on the application field. Because of the simple setup of the system it is a convenient mean to define concentrations of sensor molecules from air probes. It could be used for example as a rapid test to quantify specific molecules in probes.


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== BioBricks and experimental results ==

Our BioBricks added to the registry can be found in the [[Team:ETH Zurich/Achievements/BioBricks|BioBrick]] chapter. We characterized the parts BBa_K625000 and BBa_K625001 and added the results to the [[Team:ETH Zurich/Achievements/Results|experimental results]]. For other experiments performed and background information of experiments swith to the [[Team:ETH Zurich/Biology/Validation|Validation]] chapter.
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[[File:SmoColi.JPG|350px|right|thumb|'''SmoColi pixels'''
:)As a side project we sorted and spotted ''E. coli'' expressing either RFP, GFP or &beta;-galactosidase with a FACS machine.]]

== Network elements ==

The SmoColi circuit design can be divided into three different subsystems: 

1.	a sensor

2.	bandpass filter

3.	alarm system

Both a repressor (coupled to an inverter) or an activator can be used as sensor parts of the system. In our case we used AlcR (from ''Aspergillus nidulans''), respectively XylR (from ''Pseudomonas putida'') regulatory proteins in order to sense compounds present in smoke and thereby to induce the different parts of our network.

Upon sensing the specific molecule the circuit gets activated and our SmoColi bacteria start notifying us about the presence of toxic substances in air. For a detailed description of the circuit design please [https://2011.igem.org/Team:ETH_Zurich/Biology/Detector click here].
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