IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full System/Design

 Specifications Design Modelling Implementation Testing/Validation  

Design features imposed by our specifications:

 * The oscillatory behaviour should be based on a well known and understood dynamic (to be able to gain control over the frequency and amplitude of the oscillattions).
 * The ouput signal of the oscillator should be the variation in time of the concentration of a given chemical compound at the culture level (easier detection and easier connectivity with other systems).
 * To address noisy and instability behaviours from previous oscillators, we have decided to rely on large population of molecules in order to deal with smooth and continuous biochemical reactions.

Registry
The full system is based on 2 parts which can be found in the Registry.


 * The Prey Molecule Generator: BBa_J37015
 * The Predator Molecule Generator:: BBa_J37036

Open issues

 * We need to be able to control the prey's positive feedback loop to ensure that AHL concentration is 0 while cell cultures are growing.

__HIDER__

As of 20 August, we have updated the design of our system due to some complication we overlooked when designing our initial system. First, the prey cell must be controlled so that it does not reach a steady state before we implement it into our system. Ideally, we would like to have a method of control to induce or inhibit the expression of AHL molecules in our system. Thus, we have formulated several designs which we hope will be viable in controlling the exponential expression of AHL.

Following reserach into the riboswitch, we have decided to explore this option. We are using a theophylline induced riboswitch which will be placed between the pLuxR promoter and the LuxI protein coding region (the part which codes for the AHL). Once we inject theophylline into the system, the prey cell will then start the exponential growth.

Another idea we developed to control the exponential expression is the CRE system mentioned by Dr. Mann. Basically, the CRE system is a section of DNA which does not code for anything, but is placed in the middle of a coding region. Only until the necessary proteins to cut the sequence out of the DNA is manufactured, expression is repressed. The only drawback to this system is it requires two plasmids within the same cell, which might not be an easy task to achieve. Read more about the Cre-Lox System Design.

Into the tenth week of the iGEM project, the team has decided to scrap the riboswitch part (J37015RS) in favour of using an acylase to control the AHL levels in the prey cell. If we innoculate the culture with an acylase, it should degrade most of the AHL maintaining the concentration in an exponential growth phase. When putting the system together, we can easily remove the acylase by flushing out and adding the predator cell in it's place. Hence, the oscillator should begin with the prey cell not having reached the peak of the exponential production phase.

The acylase itself cleaves the entire lactone ring from the n-acyl homoserine lactone molecule as seen above producing homoserine lactone and a fatty acid. The products are no longer biologically active; however, the paper on the structure of AiiA has commented that HSL is a competitive inhibitor for AHL. This may lead to some problems depending upon the concentration of HSL left in the chemostat after we flush the acylase out.


 * We need some method of characterizing the half-life and activity of AiiA. We will use a Flag tag to achieve this

__HIDER__

Furthermore, we have decided to alter the design of the predator cell by adding a FLAG immunotag. The purpose of this was so that we are able to characterise the AiiA halflife and activity before producing the final system construct. When testing is done in conjunction with the modelling, this will provide us a better understanding of the way the system works. Moreover, we will be able to simulate with real values to see what we expect in our biological oscillator. The immunotag is attached to the beginning of the AiiA protein coding sequence, since we are using the AiiA sequence already containing an LVA degradation tag. We do not want the degradation tag to interfere with the immunotag, so we have decided to PCR in the immunotag to the 5' end of the sequence. The 3D design of the AiiA enzyme in one of the papers has suggested that the ends of the sequence are not close to the active site of the enzyme, so there is a small but unlikely chance that the tags will interfere with the activity of the enzyme.

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