"
Team:BCCS-Bristol/Modeling-GRN
From 2008.igem.org
(→Gene Regulatory Networks (GRN) Modelling) |
(→Sender) |
||
| Line 21: | Line 21: | ||
=== Sender === | === Sender === | ||
| + | |||
| + | The sender device consists of two genes (LuxI, GFP) and a single promoter (pCpxR). We are | ||
| + | interested in the relationship between the activator protein CpxR and the production of the | ||
| + | signalling compound N-acyl-homoserine lactone (AHL). AHL is produced by the LuxI enzyme | ||
| + | which uses S-adenosylmethionine and the acylated-acyl carrier protein as substrates for the | ||
| + | reaction. | ||
| + | The concentration of the activator protein CpxR is specified as a contact profile mimicking | ||
| + | the discovery of a particle. A linear piece-wise function was selected, ranging from 0 at t = 0, | ||
| + | to a maximal CpxR protein concentration C<sub>pMax</sub> after 1 hour, taken from [15]. In the following | ||
| + | equation time t is measured in minutes, | ||
| + | |||
| + | [[Image:Sender-cpxr.PNG]] | ||
| + | |||
| + | Both LuxI and GFP are controlled by the promoter pCpxR. In reality, because both genes | ||
| + | are under the control of a single promoter, transcription would lead to the creation of a single | ||
| + | mRNA strand. This mRNA would contain both genes, however, have separate ribosome | ||
| + | binding sites (RBS) for each to allow for parallel translation. Due to the negligible effect on | ||
| + | dynamics and a lack of information regarding degradation rates of this mRNA sequence, each | ||
| + | gene transcription was treated separately. | ||
| + | The transcription phase was modelled using a Hill function for the activation of the promoter | ||
| + | with a degradation term for existing mRNA. This gives the following for mRNA concentrations | ||
| + | of LuxI I<sub>m</sub> and GFP G<sub>m</sub>: | ||
| + | |||
| + | [[Image:Sender-mRNA-system.PNG]] | ||
| + | |||
| + | Translation of the mRNAs into proteins of LuxI I<sub>p</sub> and GFP G<sub>p</sub> was modelled as proportional | ||
| + | to the current mRNA concentrations minus a degradation term, yielding the model: | ||
| + | |||
| + | [[Image:Sender-protein-system.PNG]] | ||
=== Transport === | === Transport === | ||
Revision as of 13:42, 23 October 2008
Contents |
Gene Regulatory Networks (GRN) Modelling
Introduction
Sender
The sender device consists of two genes (LuxI, GFP) and a single promoter (pCpxR). We are interested in the relationship between the activator protein CpxR and the production of the signalling compound N-acyl-homoserine lactone (AHL). AHL is produced by the LuxI enzyme which uses S-adenosylmethionine and the acylated-acyl carrier protein as substrates for the reaction. The concentration of the activator protein CpxR is specified as a contact profile mimicking the discovery of a particle. A linear piece-wise function was selected, ranging from 0 at t = 0, to a maximal CpxR protein concentration CpMax after 1 hour, taken from [15]. In the following equation time t is measured in minutes,
Both LuxI and GFP are controlled by the promoter pCpxR. In reality, because both genes are under the control of a single promoter, transcription would lead to the creation of a single mRNA strand. This mRNA would contain both genes, however, have separate ribosome binding sites (RBS) for each to allow for parallel translation. Due to the negligible effect on dynamics and a lack of information regarding degradation rates of this mRNA sequence, each gene transcription was treated separately. The transcription phase was modelled using a Hill function for the activation of the promoter with a degradation term for existing mRNA. This gives the following for mRNA concentrations of LuxI Im and GFP Gm:
Translation of the mRNAs into proteins of LuxI Ip and GFP Gp was modelled as proportional to the current mRNA concentrations minus a degradation term, yielding the model:
Transport
Reciever
