Difference between revisions of "Team:RDFZ-China/Model"

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               <p>Assuming that the sum of the bound and the unbound equals one, the unbound fraction Pu is thus: </p>
 
               <p>Assuming that the sum of the bound and the unbound equals one, the unbound fraction Pu is thus: </p>
 
               <div style="text-align:center;"><img src="https://static.igem.org/mediawiki/2018/f/f2/T--rdfZ-China--equation15.jpeg"/></div>
 
               <div style="text-align:center;"><img src="https://static.igem.org/mediawiki/2018/f/f2/T--rdfZ-China--equation15.jpeg"/></div>
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              <p>Bound fraction is considered for activation in gene regulation and unbound fraction for repressive regulation. </p>
 
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             <div class="topic-title" id="section2">
 
             <div class="topic-title" id="section2">
 
                 <h3>Modelling Equations</h3>
 
                 <h3>Modelling Equations</h3>
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                 <p> We provided team Tsinghua with IPTG assay with Ptac plasmid backbone in Tsinghua’s IPTG induction devices in their NEON system.Also we provided AHL for their Lux system.Tsinghua was generous to provide us some lab space and equipments to work on our projects. We worked close, both physically and intellectually, to create maximum impacts on our team projects.</p>
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             <div class="topic-title" id="section3">
 
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                 <h3>Methods</h3>
 
                 <h3>Methods</h3>
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                 <p> This year, we provided SJTU-BioX-Shanghai with plasmids expressing acoustic reporter genes arg1 and arg2. They were applied to report the location of cancer foci combining with ultrasound in their project “E.Coli for Colon Health Observation”. We also shared protocols and equipments regarding non-invasive bacteria monitoring in our section of gas vesicles.</p>
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             <div class="topic-title" id="section4">
 
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                 <h3>Results</h3>
 
                 <h3>Results</h3>
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                 <p> Zeyu Tang from the team, RDFZ-China, kindly provided help on modeling for team GBC. To be specific, Zeyu gave them one document about previous work he has done on the fermentor model, which contains deterministic ODEs for predicting the productivity of engineered bacteria in the fermentor. In addition, Zeyu wrote another document which illustrates the deduction of Hill equation, helping them create their model simulation. </p>
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                 <p> Knowing GreatBay was constructing a constitutive expressing GFP into the bacterial genome, we enquired for it and used it as a capacity monitor for characterizing the expression burden. Greatbay kindly gave it to us as a gift.
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             <div class="topic-title" id="section5">
 
             <div class="topic-title" id="section5">
 
                 <h3>Discussion</h3>
 
                 <h3>Discussion</h3>
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                 <p> Our team leader in 2017, Bowen Xiao, did a report on strategies preparing the iGEM competition; then the two teams shared resources and had a conversation on the biggest problems encounter during iGEM. Team BFSUICC-China in September met with us to discuss project updates and Jamboree preparation. </p>
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Revision as of 16:25, 16 October 2018

Modelling

Bound Fraction &Unbound Fraction

By defining a simple equation where P is the promoter region and X is the ligand that can bind with P, namely a repressor in this case:

Intuitively, the factional saturation of the promoter is denoted by Ps , which is the fraction of occupied binding sites:

At equilibrium of this reaction, the rate of forward reaction and that of backward reaction are the same:

Then we rearrange this equation and get:

Where kd is the dissociation constant of this binding event. Now we substitute equation 1.3 into equation 1.1 and hence obtain:

Assuming that the sum of the bound and the unbound equals one, the unbound fraction Pu is thus:

Bound fraction is considered for activation in gene regulation and unbound fraction for repressive regulation.

Modelling Equations

Methods

Results

Discussion

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