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Team:IPN-UNAM-Mexico/Results
From 2009.igem.org
Preliminary results
Theoretical Results
As we could see in the first simulations in Comsol Multiphysics, with our estimated diffusion coefficients and the classical activator inhibitor dynamic equations, we recovered a spotted pattern.
Lab Results
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Modelling results
We believe the modelling part of our project is a very strong component of it. First of all, the system was designed to fulfill the requirements of a theoretical proposal by A. Turing of a reaction-diffusion model on morphogenesis, more specifically an activator-inhibitor system. These requirements were checked by calculating and using the diffusive properties of the components involved (AHLs) in our system on the Geirer and Meihnardt model of activator-inhibitor, successfully predicting the generation of patterns in our design.
Later, we wanted to recreate the generation of a pattern from its very biochemical basis to be able to predict under what conditions the pattern would form and how it would be, so we described all the biochemical steps involved in our network (form transcription to complexes formation) by constructing a kinetic model with parameters available in the literature. From this kinetic model we derived our ordinary differential equations and used it to make a spatial simulation of the behavior of a colony, predicting the formation of some kind of instability but not yet a spatiotemporal pattern.
Even when there was no explicit pattern formation on the detailed model, we did obvserve it in our simulation of the general model of activator-inhibitor; so we will explore in the future other approaches to figer out if the predictions of this model are conclusive or not, like stochastic approaches. And we will also have to compare these results with the experimental results that we will obtain with the fully implemented system.
Final Conclusions
We were able to build most of our original design (1 biobrick ligation remaining) and to experimentally test the functioning of one of our regulatory modules coupled to the autocathalytic module.
Besides having one regulatory module working as expected we also have the support from our models on the formation at least of spatiotemporal instabilities, this sustents the validity of our design on its potential to emulate an activator-inhibitor system.
The fact that our designed system is able to behave in this way under certain conditions provided by the regulatory modules shows that the original assumptions on A. Turing’s model have the potential to naturally have emerged in living organisms during evolution, and to be the underlying mechanism by which some of the naturally founded patterns are formed during morphogenesis.
We also realized during the implementation of the project that there are some details, both on the modelling and in the design, we could improve to make a better approximation of the activator-inhibitor system.
We are very excited about the reachings that our project could have if we can successfully implement it, and our results show we are going on the right direction.
Further work
The first step after the Jamboree will be finish our last biobricks ligation and test our system in different conditions and concentrations of IPTG and ATC and characterize part relative to the whole net. Then we can really see if our system was really working as we thought it should. Besides we need to find a different approach to model mathematically the interactions that take part in the project in order to predict its behavior.
As extensions of our project we are planning to work with this biobricks system in eucariotic tissues and replace de IPTG and ATC depedence with another kind of synthetic morphogens and the E. colis with GFP with melanocytes. To reproduce pigmentation patterns and fully demostrate the turing work and give great results in developmental biology.
