Team:Bielefeld-Germany/Project/Model

From 2010.igem.org

(Difference between revisions)
(→Fitting the data)
(→Fitting the data)
Line 36: Line 36:
As seen in the fig. 1 - 3 the models for the application of the used VirA/G signaling system is quite complex. Due to the fact that there were no further details to interactions between the components of this receptor system in the literature which are helpful for modelling and a determination of these parameters would be too time-consuming we decided to fit the ''vir'' promoter activity to different concentrations of the natural inducer of the VirA/G signaling system, acetosyringone. As the promoter activity is not directly accessible we decided to measure it by using a reporter gene.  
As seen in the fig. 1 - 3 the models for the application of the used VirA/G signaling system is quite complex. Due to the fact that there were no further details to interactions between the components of this receptor system in the literature which are helpful for modelling and a determination of these parameters would be too time-consuming we decided to fit the ''vir'' promoter activity to different concentrations of the natural inducer of the VirA/G signaling system, acetosyringone. As the promoter activity is not directly accessible we decided to measure it by using a reporter gene.  
-
Promoter activity is normally measured in polymerases per second (PoPS). To correlate the concentration of a reporter gene with PoPS a synthesis rate for the reporter gene has to be measured to see how many molecules are produced by one cell in a certain time. This relation can be described as  
+
Promoter activity is normally measured in polymerases per second (PoPS). To correlate the concentration of a reporter gene with PoPS a synthesis rate for the reporter gene has to be measured to see how many molecules are produced by one cell in a certain time ([http://partsregistry.org/Part:BBa_F2620:Experience/Endy/Data_analysis | Canton and Labno, 2004]). This relation can be described as  
Line 42: Line 42:
-
with the amount of product P, the cell count X and the specific production rate of product molecules per cell and time q<sub>P</sub>.
+
with the amount of product P, the cell count X and the specific production rate of product molecules per cell and time q<sub>P</sub>. To determine the PoPS exactly from the specific production rate there is more information needed like the decay of the reporter molecule, the stability of the reporter gene mRNA, the effectivity of the reporter gene's RBS and many more. So we assumed that these parameters do not change in the time of our measurement. In addition we assumed after [http://partsregistry.org/Part:BBa_F2620:Experience/Endy/Data_analysis | Canton and Labno, 2004] that

Revision as of 19:44, 27 October 2010

{{{1}}}

Construct Maps

Model of <partinfo>K389015</partinfo>

Fig. 1: Main construct of acetosyringone inducible luciferase expression system containing constitutive expression of the two component receptor system (virA+virG).

Model of <partinfo>K389016</partinfo>

Fig. 2: Control construct of acetosyringone inducible RFP read out system.

Model of <partinfo>K389014</partinfo>

Fig. 3: Screening construct of acetosyringone inducible kanamycin resistance read out system.

Fitting the data

As seen in the fig. 1 - 3 the models for the application of the used VirA/G signaling system is quite complex. Due to the fact that there were no further details to interactions between the components of this receptor system in the literature which are helpful for modelling and a determination of these parameters would be too time-consuming we decided to fit the vir promoter activity to different concentrations of the natural inducer of the VirA/G signaling system, acetosyringone. As the promoter activity is not directly accessible we decided to measure it by using a reporter gene.

Promoter activity is normally measured in polymerases per second (PoPS). To correlate the concentration of a reporter gene with PoPS a synthesis rate for the reporter gene has to be measured to see how many molecules are produced by one cell in a certain time ([http://partsregistry.org/Part:BBa_F2620:Experience/Endy/Data_analysis | Canton and Labno, 2004]). This relation can be described as


Bielefeld Produktbildung.jpg
(1)


with the amount of product P, the cell count X and the specific production rate of product molecules per cell and time qP. To determine the PoPS exactly from the specific production rate there is more information needed like the decay of the reporter molecule, the stability of the reporter gene mRNA, the effectivity of the reporter gene's RBS and many more. So we assumed that these parameters do not change in the time of our measurement. In addition we assumed after [http://partsregistry.org/Part:BBa_F2620:Experience/Endy/Data_analysis | Canton and Labno, 2004] that

Retrieved from "http://2010.igem.org/Team:Bielefeld-Germany/Project/Model"