"

From 2013hs.igem.org

Mathematical modeling

System topology

Our system is composed by two parts, the first consists of the transcription factor cI (c0051) under the regulation of a promoter with a riboswitch (J23100 and k110517) that can be activated or repressed depending on the temperature; we call this our thermosensor. The second part consist of two genes -the insecticide protein VIP and the green fluorescent protein, GFP- that are under the regulation of cI.

The thermosensor is repressed when the temperature is below 32 °C; when the temperatures reaches a range between 32 and 37 °C, the thermosensor is activated.

cI (c0051) is a gene that constitutively represses the promoter r0051. Once our promoter is activated starts the production of Vip3Ac3 and GFP. This is means that a range of 32 °C to 37 °C enables the production of the Vip and GFP.

Deterministic model

Our deterministic model represents the change in time of the concentrations of mRNAs and their corresponding proteins. It assumes that the variables behave continuously and obey kinetic rules that can be represented by constants. We are aware that, in practice, the components and variables in the model may not fall under the assumptions of a deterministic model and that there is always the chance that noise effects are being grossly underestimated; however, we propose this model as a general framework for thermoregulator modeling, upon which further work can be done.

Equations

\begin{equation} \large \frac{d[mC]}{dt} = \alpha_{1} \cdot \frac{K_{D}^h}{K_{D}^h + [cI]^h} - \mu_{1}[mC] \end{equation}

\begin{equation} \large \frac{d[C]}{dt} = \alpha_{2} \cdot f_{RBS} \cdot [mC] - \mu_{2}[C] \end{equation}

\begin{equation} \large [mC] = \frac{\alpha _{1}}{\mu _{1}} \end{equation}

\begin{equation} \large [C] = \frac{\alpha _{1} \cdot \alpha _{T}} {\mu _{1} \cdot \mu _{T}} \end{equation}

\begin{equation} \large f_{RBS} = \left\{ \begin{array}{rcl} 0 & \mbox{if} & t \geq ON \\ 1 & \mbox{if} & t < ON \end{array} \right. \end{equation}

\begin{equation} \large \frac{d[mV]}{dt} = \alpha_{3} \cdot \frac{K_{D}^h}{K_{D}^h + [C]^h} - \mu_{1}[mV] \end{equation}

\begin{equation} \large \frac{d[V]}{dt} = \alpha_{4} \cdot f_{RBS} \cdot [mV] - \mu_{4}[V] \end{equation}

\begin{equation} \large [mV] = \frac{\alpha _{3}}{\mu _{3}} \end{equation}

\begin{equation} \large [V] = \frac{\alpha _{3} \cdot \alpha _{4}} {\mu _{3} \cdot \mu _{4}} \end{equation}

\begin{equation} \large \frac{d[mG]}{dt} = \alpha_{5} \cdot \frac{K_{D}^h}{K_{D}^h + [C]^h} - \mu_{5}[mG] \end{equation}

\begin{equation} \large \frac{d[C]}{dt} = \alpha_{6} \cdot f_{RBS} \cdot [mG] - \mu_{6}[G] \end{equation}

\begin{equation} \large [mG] = \frac{\alpha _{5}}{\mu _{5}} \end{equation}

\begin{equation} \large [G] = \frac{\alpha _{5} \cdot \alpha _{6}} {\mu _{5} \cdot \mu _{6}} \end{equation}

Parameters and variables

Our gene circuit is made of six different variables: the concentrations of three proteins (cI, VIP and GFP) and their respective mRNA inside a cell. In table 1, the symbols for each variable are shown. Proteins are represented by a single letter and their mRNAs are represented by that same letter with a lowercase "m" before it.

Table 1.- Variables

Symbol	Definition	Gene size in bp
mC, C	Transcription factor cI (mRNA and protein)	----
mV, V	Insecticide protein VIP (mRNA and protein)	----
mG, G	Reporter protein GFP (mRNA and protein)	----

To parameterize our model, we chose to follow the approach of team Beijing 2009; they propose a relationship between the gene length in base pairs and the maximum transcription rate and, similarly, between the protein length in amino acid numbers and the maximum translation rate. Assuming that the number of polymerases and ribosomes are the average values determined for E. coli, the following equations are used:

Parameters

Symbol	Definition	Values	Formula	Source
α1	Transcription rate of cI	5.6	4200/Gene Length (nM/min)	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
α2	Translation rate of cI	9.6	2400RBS/Protein Length	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
α3	Transcription rate of VIP	1.74129353	4200/Gene Length (nM/min)	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
α4	Translation rate of VIP	2.985075	2400RBS/Protein Length	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
α5	Transcription rate of GFP	5.53359684	4200/Gene Length (nM/min)	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
α6	Translation rate of GFP	9.486166	2400RBS/Protein Length	https://2009.igem.org/Team:PKU_Beijing/Modeling/Parameters
Symbol	Definition	Values	Formula	Source

Simulations

The saturation values for mRNAs and proteins were calculated analytically; but since there are several variables, it becomes complicated to integrate by analytical methods, so we use methods of numerical integration in a computer program by called Simulink. The values of the parameters (rate of transcription, translation, degradation and dissociation) are the ones we have found so far, but we continue researching in order to improve and expand our model.