Difference between revisions of "Team:TJU China/Model"
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<div class="head">Dynamic Model of Heavy Metal Detection Biosensor</div> | <div class="head">Dynamic Model of Heavy Metal Detection Biosensor</div> | ||
| − | <div class="subhead">Minghui Yin,Sherry Dongqi Bao<br>TianJin University<br>October 15,2018</div> | + | <div class="subhead">Minghui Yin,Sherry Dongqi Bao |
| − | <div class="title">1 | + | <br>TianJin University |
| − | <div class="word">Modeling is a powerful tool in synthetic biology. It provides us with a necessary engineering approach to characterize | + | <br>October 15,2018</div> |
| − | quantitatively and predict their performance,thus help us test and modify our design.Through the dynamic model of heavy-metal detection biosensor,we hope to gain insights into the characteristics of our whole circuit's dynamics. | + | <div class="title">1 Introduction</div> |
| + | <div class="word">Modeling is a powerful tool in synthetic biology. It provides us with a necessary engineering approach to characterize | ||
| + | our pathways quantitatively and predict their performance,thus help us test and modify our design.Through the dynamic | ||
| + | model of heavy-metal detection biosensor,we hope to gain insights into the characteristics of our whole circuit's | ||
| + | dynamics. | ||
</div> | </div> | ||
| − | <div class="title">2 | + | <div class="title">2 Methods</div> |
<div class="subtitle">2.1 Analysis of metabolic pathways</div> | <div class="subtitle">2.1 Analysis of metabolic pathways</div> | ||
| − | <div class="pic"><img src="https://static.igem.org/mediawiki/2018/0/01/T--TJU_China--y1.png"></div> | + | <div class="pic"> |
| + | <img src="https://static.igem.org/mediawiki/2018/0/01/T--TJU_China--y1.png"> | ||
| + | </div> | ||
<div class="figure">Figure 1: Metabolic pathways related to plasmid#1</div> | <div class="figure">Figure 1: Metabolic pathways related to plasmid#1</div> | ||
| − | <div class="word">At the beginning, on the plasmid#1, the promoter $P_{arsR}$ isn't bound with ArsR,thus it is active.ArsR and smURFP are transcribed and translated under the control of the | + | <div class="word">At the beginning, on the plasmid#1, the promoter $P_{arsR}$ isn't bound with ArsR,thus it is active.ArsR and smURFP are |
| − | + | transcribed and translated under the control of the promoters $P_{arsR_{u}}$ and $P_{arsR_{d}}$,with subscript u | |
| − | the expression of $As^{3+}$.As ArsR is expressed gradually,it will bind with the promoter $P_{arsR}$ and make it inactive.[1]</div> | + | and d representing upstream and downstream separately.The subscript l of smURFP in the equation means leaky expression |
| − | + | without the expression of $As^{3+}$.As ArsR is expressed gradually,it will bind with the promoter $P_{arsR}$ and | |
| − | + | make it inactive.[1]</div> | |
| + | <div class="pic"> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/a/a6/T--TJU_China--m1.PNG"> | ||
</div> | </div> | ||
| − | + | <div class="word">On the plasmid#2,the fusion protein of dCas9 and RNAP(RNA polymerase) are produced after transcription and translation,and | |
| + | sgRNA is produced after transcription. | ||
| + | <div> | ||
| + | <div class="pic"> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/2/26/T--TJU_China--m2.png"> | ||
| + | </div> | ||
| + | <div class="pic"> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/2/2b/T--TJU_China--2.png"> | ||
| + | </div> | ||
| + | <div class="figure">Figure 2: Metabolic pathways related to dCas9/RNAP</div> | ||
| + | <div class="word">dCas9(*RNAP) can bind with its target DNA sequence without cutting, which is at the upstream of the promoter | ||
| + | $P_{arsR_{d}}$.Simulataneously,dCas9 can lead RNAP to bind with the promoter $P_{arsR_{d}}$ and enhance the | ||
| + | transcription of smURFP.However,because the promoter $P_{arsR_{d}}$ has already bound with ArsR,as a result,RNAP | ||
| + | can't bind with the promoter $P_{arsR_{d}}$. can’t bind with the promoter $P_{arsR_{d}}$.</div> | ||
| + | <div class="word">However,at the presence of $As^{3+}$,it can bind with ArsR,then dissociate ArsR and $P_{arsR_{d}}$,which makes the combination of RNAP and $P_{arsR_{d}}$ possible.</div> | ||
| − | + | ||
| − | + | <script src="https://2018.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> | |
| + | <script type="text/x-mathjax-config"> | ||
MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}}); | MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}}); | ||
</script> | </script> | ||
</body> | </body> | ||
<!-- <div> | <!-- <div> | ||
| + | <div class="pic"><img src=""></div> | ||
| + | |||
| + | |||
$P_{arsR_{d}}$ | $P_{arsR_{d}}$ | ||
$As^{3+}$ | $As^{3+}$ | ||
| − | + | <div class="equation"> \(P_{J23104} \xrightarrow {k_{tx1}} P_{J23104} + mRNA_{ArsR}\)</div> <div class="number">(1)</div> | |
</div> --> | </div> --> | ||
| + | |||
</html> | </html> | ||
Revision as of 18:32, 16 October 2018
<!DOCTYPE >
Dynamic Model of Heavy Metal Detection Biosensor
Minghui Yin,Sherry Dongqi Bao
TianJin University
October 15,2018
TianJin University
October 15,2018
1 Introduction
Modeling is a powerful tool in synthetic biology. It provides us with a necessary engineering approach to characterize
our pathways quantitatively and predict their performance,thus help us test and modify our design.Through the dynamic
model of heavy-metal detection biosensor,we hope to gain insights into the characteristics of our whole circuit's
dynamics.
2 Methods
2.1 Analysis of metabolic pathways
Figure 1: Metabolic pathways related to plasmid#1
At the beginning, on the plasmid#1, the promoter $P_{arsR}$ isn't bound with ArsR,thus it is active.ArsR and smURFP are
transcribed and translated under the control of the promoters $P_{arsR_{u}}$ and $P_{arsR_{d}}$,with subscript u
and d representing upstream and downstream separately.The subscript l of smURFP in the equation means leaky expression
without the expression of $As^{3+}$.As ArsR is expressed gradually,it will bind with the promoter $P_{arsR}$ and
make it inactive.[1]
On the plasmid#2,the fusion protein of dCas9 and RNAP(RNA polymerase) are produced after transcription and translation,and
sgRNA is produced after transcription.
Figure 2: Metabolic pathways related to dCas9/RNAP
dCas9(*RNAP) can bind with its target DNA sequence without cutting, which is at the upstream of the promoter
$P_{arsR_{d}}$.Simulataneously,dCas9 can lead RNAP to bind with the promoter $P_{arsR_{d}}$ and enhance the
transcription of smURFP.However,because the promoter $P_{arsR_{d}}$ has already bound with ArsR,as a result,RNAP
can't bind with the promoter $P_{arsR_{d}}$. can’t bind with the promoter $P_{arsR_{d}}$.
However,at the presence of $As^{3+}$,it can bind with ArsR,then dissociate ArsR and $P_{arsR_{d}}$,which makes the combination of RNAP and $P_{arsR_{d}}$ possible.