Team:ETH Zurich/Modeling

From 2012.igem.org

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=== Reaction Network ODE model ===  
=== Reaction Network ODE model ===  
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[[Image:ETH UVR8.png|right|thumb|450px|Figure 2: Overall circuit design for UVR8-TetR<sub>DBD</sub> system with feedback via pABA. See all details on  [[Team:ETH_Zurich/Modeling/Construct1|UVR8-LovTAP]] ]]
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[[Image:ETH UVR8.png|right|thumb|450px|Figure 2: Overall circuit design for the UVR8 system with feedback via PABA. See all details on  [[Team:ETH_Zurich/Modeling/UVR8|UVR8 Circuit]] ]]
To decode our light receptor input, we created a full deterministic ODE model. As systems of interacting proteins with possibly multiple homodimerisations can grow quickly in size, modelling requires a systematic approach. In order to span the ODE system, we employ rules-based models. For this methodology, we define seed species and rules on how they can interact. In practice the software Ru2ren (to be published by [http://www.csb.ethz.ch/people/cmayer Christian Mayer]) then generates the system of coupled ODEs.
To decode our light receptor input, we created a full deterministic ODE model. As systems of interacting proteins with possibly multiple homodimerisations can grow quickly in size, modelling requires a systematic approach. In order to span the ODE system, we employ rules-based models. For this methodology, we define seed species and rules on how they can interact. In practice the software Ru2ren (to be published by [http://www.csb.ethz.ch/people/cmayer Christian Mayer]) then generates the system of coupled ODEs.
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[[Team:ETH_Zurich/Modeling/UVR8|UVR8-only]]
[[Team:ETH_Zurich/Modeling/UVR8|UVR8-only]]
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Having demonstrated a realistic time frame for production of the protecting substance PABA, we continue to integrate our UVR8-TetR<sub>DBD</sub> fusion into more complex processing circuits:
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Having demonstrated a realistic time frame for production of the protecting substance PABA, we continue to model the decoder in a more complex processing circuit:
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# [[Team:ETH_Zurich/Modeling/Construct1|UVR8-LovTAP]]
 
# [[Team:ETH_Zurich/Modeling/Construct2|LovTAP-Cph8]]
# [[Team:ETH_Zurich/Modeling/Construct2|LovTAP-Cph8]]
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These are described in further detail on the individual pages.
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The circuit is described in further detail on the individual page.
{{:Team:ETH_Zurich/Templates/Footer}}
{{:Team:ETH_Zurich/Templates/Footer}}

Revision as of 21:44, 26 October 2012

Eth ecolipseeth logo.png
Eth igem logo.png


Contents

Overview

To support our colleagues in the lab, we outlined different models for different parts of our project.

Figure 1: Photoconversion cross sections calculated for various receptors. "-a/d" indicate activation and deactivation of a receptor.

Photoinduction

To calculate the activity of light receptors, we devised a model that takes emission spectra of different light sources and absorption spectra, quantum yield and extinction coefficients of the receptors from literature as an input and returns the activation and deactivation constants for the given light conditions.

This model can be used to calculate the activity of a light receptor in a light condition. Together with an mechanistical model of the receptor, it gives an estimate of the transcriptional activation due to light input.

See all the details in Photoinduction model.


Sun Protection Factor

The sun protection factor (SPF) model gives the sun protection factor we can achieve with a given amount of PABA and also what amount of PABA we need to get to a SPF.

See how much our E.colipse protects you from sun radiation in the Sun Protection Factor model!


Reaction Network ODE model

Figure 2: Overall circuit design for the UVR8 system with feedback via PABA. See all details on UVR8 Circuit

To decode our light receptor input, we created a full deterministic ODE model. As systems of interacting proteins with possibly multiple homodimerisations can grow quickly in size, modelling requires a systematic approach. In order to span the ODE system, we employ rules-based models. For this methodology, we define seed species and rules on how they can interact. In practice the software Ru2ren (to be published by Christian Mayer) then generates the system of coupled ODEs.

As an input to the decoder, we use a combination of ab initio constants from our photoconversion model and a mechanistical model of the receptor mode of action, parameters from literature and assumed respectively desired parameters. Given such models and parameters, the biological implementation can then be optimised.

We first analyse the separation (dynamic range) and timescale of UVR8 dimerisation/dissociation: UVR8-only

Having demonstrated a realistic time frame for production of the protecting substance PABA, we continue to model the decoder in a more complex processing circuit:

  1. LovTAP-Cph8

The circuit is described in further detail on the individual page.



References

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