Difference between revisions of "Team:HKUST-Rice/Potassium Sensor Modelling"
Stephanieyiu (Talk | contribs) |
Stephanieyiu (Talk | contribs) |
||
| Line 83: | Line 83: | ||
<div class="project_row"> | <div class="project_row"> | ||
<h1>Equations of the Model:</h1> | <h1>Equations of the Model:</h1> | ||
| − | <p><b>Phosphorylation of KdpD:<b></p> | + | <p><b>Phosphorylation of KdpD:</b></p> |
<div class="project_image"> | <div class="project_image"> | ||
<img src="https://static.igem.org/mediawiki/2015/2/22/Team_HKUST-Rice_2015_Modelling_2%3D3.PNG" alt="image caption"> | <img src="https://static.igem.org/mediawiki/2015/2/22/Team_HKUST-Rice_2015_Modelling_2%3D3.PNG" alt="image caption"> | ||
</div> | </div> | ||
| − | <p><b>Phosphyl-group Transfer:<b></p> | + | <p><b>Phosphyl-group Transfer:</b></p> |
<div class="project_image"> | <div class="project_image"> | ||
<img src="https://static.igem.org/mediawiki/2015/0/0a/Team_HKUST-Rice_2015_Modelling_4.PNG" alt="image caption"> | <img src="https://static.igem.org/mediawiki/2015/0/0a/Team_HKUST-Rice_2015_Modelling_4.PNG" alt="image caption"> | ||
</div> | </div> | ||
| − | <p><b>Binding of KdpE to promoter PkdpF:<b></p> | + | <p><b>Binding of KdpE to promoter PkdpF:</b></p> |
<div class="project_image"> | <div class="project_image"> | ||
<img src="https://static.igem.org/mediawiki/2015/8/8c/Team_HKUST-Rice_2015_Modelling_5.PNG" alt="image caption"> | <img src="https://static.igem.org/mediawiki/2015/8/8c/Team_HKUST-Rice_2015_Modelling_5.PNG" alt="image caption"> | ||
</div> | </div> | ||
| − | <p><b>Transcription:<b></p> | + | <p><b>Transcription:</b></p> |
<div class="project_image"> | <div class="project_image"> | ||
<img src="https://static.igem.org/mediawiki/2015/4/48/Team_HKUST-Rice_2015_Modelling_6.PNG" alt="image caption"> | <img src="https://static.igem.org/mediawiki/2015/4/48/Team_HKUST-Rice_2015_Modelling_6.PNG" alt="image caption"> | ||
</div> | </div> | ||
| − | <p><b>Translation:<b></p> | + | <p><b>Translation:</b></p> |
<div class="project_image"> | <div class="project_image"> | ||
<img src="https://static.igem.org/mediawiki/2015/a/af/Team_HKUST-Rice_2015_Modelling_7.PNG" alt="image caption"> | <img src="https://static.igem.org/mediawiki/2015/a/af/Team_HKUST-Rice_2015_Modelling_7.PNG" alt="image caption"> | ||
</div> | </div> | ||
| − | <p><b>Green Fluorescent Protein maturation:<b></p> | + | <p><b>Green Fluorescent Protein maturation:</b></p> |
<div class="project_image"> | <div class="project_image"> | ||
<img src="https://static.igem.org/mediawiki/2015/9/9e/Team_HKUST-Rice_2015_Modelling_8.PNG" alt="image caption"> | <img src="https://static.igem.org/mediawiki/2015/9/9e/Team_HKUST-Rice_2015_Modelling_8.PNG" alt="image caption"> | ||
</div> | </div> | ||
| − | |||
</div> | </div> | ||
| + | <div class="project_row"> | ||
| + | <h1>Data point fitting to the model:</h1> | ||
| + | <p>The experimental data from FACS were used to fit in the prediction model; then we adapt the unit conversion from [Caitlin C, Jeniffer B 13] to convert GFP per cell fluorescence intensity to concentration of GFP per cell:<p> | ||
| + | <div class="project_image"> | ||
| + | <img src="#" alt="image caption"> | ||
| + | </div> | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
Revision as of 05:32, 3 September 2015
Modelling
Model's Assumption
The effect of the endogenous Kdp system of E.coli was neglected.
In our engineered E.coli, it contains the inserted plasmid of PKdpF plus green fluorescence protein generator (BBa_E0240) in pSB3K3 backbone as well as the endogenous Kdp operon, and both operons have the same promoter, PKdpF. As a matter of fact, titration by the endogenous kdp operon of the transcription inducer, phosphorylated KdpE which binds to PKdpF was expected initially. And the titration of phosphorylated KdpE is anticipated to lower the expression of GFP. However, when the DNA copy number of both endogenous and the inserted operons were determined, it was found that the number of endogenous kdp operon is 10 times smaller than that of the inserted one:
This implied that the number of endogenous promoter PKdpF is ten times smaller than that of the inserted operon and accounts only 8.33% of the total number of promoter PKdpF in the engineered E.coli. Therefore, the titration effect of phosphorylated KdpE becomes insignificant. As a result, the effect of endogenous Kdp system was negligible.
Level of KdpD, KdpE and KdpF were assumed to be constant
In accordance to [Kremling A. 04], in the potassium ions concentration range which we were studying, from 0mM to 0.02 mM, the fluctuation of the concentration KdpF as well as KdpD and KdpE was only within 10 µM and 3 µM respectively. Due to the small fluctuation range compared to the gene expression of GFP reporter, it was reasonable to assume the concentration of KdpD, KdpE and KdpF to be constant in the model.
It was assumed that the initial concentration of mRNA for GFP, immature GFP and mature GFP equal to zero.
It was assumed that all reactions below were in steady state such that:
Equations of the Model:
Phosphorylation of KdpD:
Phosphyl-group Transfer:
Binding of KdpE to promoter PkdpF:
Transcription:
Translation:
Green Fluorescent Protein maturation:
Data point fitting to the model:
The experimental data from FACS were used to fit in the prediction model; then we adapt the unit conversion from [Caitlin C, Jeniffer B 13] to convert GFP per cell fluorescence intensity to concentration of GFP per cell: