Team:Paris/Analysis

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Network Analysis


  • Purpose of this Section

After having designed the specific genetic networks corresponding to the different parts of our project, we have analysed them through modeling. Therefore, you will find in this page the principal results coming from the models, as well as some resulting simulations.

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This page presents the principal results of the analysis and simulation of the theoretical models of the FIFO and the oscillator circuit of our project..

Contents

FIFO behaviour

Plus factuel. Ce n'est pas intéressant de dire... nous avons dessiné un mod!èle blab bla bla. Dites directement,... voici le modèle qui correspond à ... We have designed a model corresponding to the genetic network and we have obtained the following results :

The FIFO circuit is made of a main regulator (FlhDC) that activates an intermediary regulator (FliA) and the three output genes Z1, Z2, and Z3 that are activated by the combined effect of the two regulators.

Subsystem1.jpg
Essai with fliAbis.jpg


The parameters found in the papers we have used directly lead to FIFO behaviour ! The simulation on the right, based on parameter values found in REFERENCE A DONNER directly repoduced a FIFO behaviour: the output genes are inactivated in the same order they are activated. To go further into :

Oscillations

Same comment do not tell your history, go to the facts Then, we have simulated the FIFO with a negative feedback, in order to observe oscillations. We have obtained the following results :

The first attempt for an oscillation circuit is implemented as a simple negative feedback loop connecting one output of the FIFO circuit to the input regulator.

Core system
Steady state.jpg
Core system. The core system does not oscillate.


From the simulations performed with parameters found in the literature, we conclude that the system reaches a steady state and is far from oscillating ! We evaluate the role of key interactions of the core system by successively simulating altered forms of the system. Curves below display simulations of three simple variants of the model, none of which producing sustained oscillations. Moreover, a mathematical analysis confirms that the core system cannot produce oscillations.

Simulations of three variants of the core system


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System Improvements

Our aim is to explore improvements of the core system providing both sustained oscillations and synchronization capabilities. We consider two systems based on quorum sensing thus adding at the same time a delay valuable for the oscillations and the ability to synchronize cells via HSL concentration in the environment.

The first system is inspired by [2] and is made of two coupled negative loops. The second one is a rewiring of the core system to include quorum sensing and resulting in a single negative loop. Simulation results point out that only this second system delivers sustained oscillations. Moreover we confirm that quorum sensing can indeed be used to synchronize a population of cells.

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Model and simulations || System Improvements