Team:Wageningen UR/Project/ModelingProj2

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[[File:Template.png|230px| A typical time series of concentrations of LuxI (cyan circles), AiiA (blue circles), internal AHL
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(green line) and external AHL (red line). LuxI and AiiA closely track each other, and are anti-phase with the concentrations of external and internal AHL. Graph and explanation taken from the article "A synchronized quorum of genetic clocks" [Tal Danino, Octavio Mondragón-Palomino, Lev Tsimring2 & Jeff Hasty, Nature, January 2010]]
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== Modeling: Fungal Track 'n Trace ==
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The Leu3p (x(2)) dimer blocks transcription from the alpha-IPM synthase (alpha IPMS) promoter. Alpha-IPM (x(1)) binding to this dimer releases it from the promoter and enhances the transcription rate. p(5) and p(6) model both constitutive expression and the transcription rate increase upon alpha-IPM binding. From alpha-IPMS mRNA (x(3)) the protein is formed, modelled by p(9). Alpha-IPMS (x(4)) enzymatically produces alpha-IPM, which is then incorporated in the beginning of this loop again. Intercellular transport of alpha-IPM creates a signal transduction through a hypha.
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Additionally, x(5) is required for modelling the enzymatic reaction. Its formation is described by p(11). Each type of molecule has also been assigned a degradation constant, such as p(8) for x(3).
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Latest revision as of 20:20, 21 September 2011

Building a Synchronized Oscillatory System

Modeling: Fungal Track 'n Trace

Spee FTnT Model-1 WUR.jpg

The Leu3p (x(2)) dimer blocks transcription from the alpha-IPM synthase (alpha IPMS) promoter. Alpha-IPM (x(1)) binding to this dimer releases it from the promoter and enhances the transcription rate. p(5) and p(6) model both constitutive expression and the transcription rate increase upon alpha-IPM binding. From alpha-IPMS mRNA (x(3)) the protein is formed, modelled by p(9). Alpha-IPMS (x(4)) enzymatically produces alpha-IPM, which is then incorporated in the beginning of this loop again. Intercellular transport of alpha-IPM creates a signal transduction through a hypha.

Additionally, x(5) is required for modelling the enzymatic reaction. Its formation is described by p(11). Each type of molecule has also been assigned a degradation constant, such as p(8) for x(3).

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