Team:NYMU-Taipei/modeling/m7

From 2014.igem.org

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<p>The circuit is constructed by the following parts, constitutive promoter + rbs + INPNC (k523013) + C16 + terminator (B0015). The detailed mechanism is introduced on <a href='/Team:NYMU-Taipei/project/2c1'><b>Cleanse-Attachment</b></a>.</p>
<p>The circuit is constructed by the following parts, constitutive promoter + rbs + INPNC (k523013) + C16 + terminator (B0015). The detailed mechanism is introduced on <a href='/Team:NYMU-Taipei/project/2c1'><b>Cleanse-Attachment</b></a>.</p>
</p>
</p>
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<p>In this part, we fit the parameter in the system with the experimental data from our wet lab. To test how the circuit works, GFP is added after C16 in the testing circuit. It can represent the amount of C16 protein. The amount of protein expression is transferred from the GFP florescence [1].</p>
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<p>In this part, we fit the parameter in the system with the experimental data from our wet lab. To test how the circuit works, RFP is added after C16 in the testing circuit. It can represent the amount of C16 protein. The amount of protein expression is transferred from the RFP florescence [1].</p>
       <h1>System</h1>
       <h1>System</h1>
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       <p>INPNC, C16, and GFP are the main product in the testing circuit. In the design circuit, there are only INPNC and C16. GFP can be used to test whether the circuit is functional.
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       <p>INPNC, C16, and RFP are the main product in the testing circuit. In the design circuit, there are only INPNC and C16. RFP can be used to test whether the circuit is functional.
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$$\frac{d[\text{GFP mRNA}]}{dt}=P_{const}-K_{deg_mGFP}[\text{GFP mRNA}]$$
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$$\frac{d[\text{RFP mRNA}]}{dt}=P_{const}-K_{deg_mRFP}[\text{RFP mRNA}]$$
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$$\frac{d[\text{GFP}]}{dt}=K_t[\text{GFP mRNA}]-K_{deg_GFP}[GFP]$$
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$$\frac{d[\text{RFP}]}{dt}=K_t[\text{RFP mRNA}]-K_{deg_RFP}[RFP]$$
1.&nbsp; $P_{const}$:constitutive promoter activity<br>
1.&nbsp; $P_{const}$:constitutive promoter activity<br>
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2.&nbsp; $K_{deg\_mGFP}$:GFP mRNA degradation<br>
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2.&nbsp; $K_{deg\_mRFP}$:RFP mRNA degradation<br>
3.&nbsp; $K_{t}$:Translation efficiency<br>
3.&nbsp; $K_{t}$:Translation efficiency<br>
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4.&nbsp; $K_{deg\_GFP}$:GFP degredation<br>
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4.&nbsp; $K_{deg\_RFP}$:RFP degredation<br>
</p>
</p>
       <h1>Result</h1>
       <h1>Result</h1>
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       <p>While fitting the parameter, we set range of parameter which met the range of normal promoter activity, mRNA degradation, translation rate, and protein degradation [2]. The result of fitted parameter is, $P_{const}=0.24$, $K_{deg\_mGFP}=0.15$, $K_{t}=19.45$, $K_{deg\_GFP}=0.01$. The result of simulation and experimental data is very similar.</p>
+
       <p>While fitting the parameter, we set range of parameter which met the range of normal promoter activity, mRNA degradation, translation rate, and protein degradation [2]. The result of fitted parameter is, $P_{const}=0.24$, $K_{deg\_mRFP}=0.15$, $K_{t}=19.45$, $K_{deg\_RFP}=0.01$. The result of simulation and experimental data is very similar.</p>
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<img src='/wiki/images/7/71/NYMU14_new_part_fit.png' style='display: block;margin:0 auto;'><p style=" text-align: center;">Figure 1: Result of GFP simulation and experimental data</p>
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<img src='/wiki/images/7/71/NYMU14_new_part_fit.png' style='display: block;margin:0 auto;'><p style=" text-align: center;">Figure 1: Result of RFP simulation and experimental data</p>
       <h1>Reference</h1>
       <h1>Reference</h1>
       <ol>
       <ol>
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       <li>H. A. Richards, Quantitative GFP fluorescence as an indicator of recombinant protein synthesis in transgenic plants. Plant Cell Rep (2003) 22:117–121</li>
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       <li>H. A. Richards, Quantitative RFP fluorescence as an indicator of recombinant protein synthesis in transgenic plants. Plant Cell Rep (2003) 22:117–121</li>
       </ol>
       </ol>
   </div>
   </div>

Revision as of 16:12, 16 October 2014

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New part-Attachment

Introduction

This part aims to simulate the circuit of Attachment part, which can help shorten the distance of helper E. coli and S. mutans.

The circuit is constructed by the following parts, constitutive promoter + rbs + INPNC (k523013) + C16 + terminator (B0015). The detailed mechanism is introduced on Cleanse-Attachment.

In this part, we fit the parameter in the system with the experimental data from our wet lab. To test how the circuit works, RFP is added after C16 in the testing circuit. It can represent the amount of C16 protein. The amount of protein expression is transferred from the RFP florescence [1].

System

INPNC, C16, and RFP are the main product in the testing circuit. In the design circuit, there are only INPNC and C16. RFP can be used to test whether the circuit is functional. $$\frac{d[\text{RFP mRNA}]}{dt}=P_{const}-K_{deg_mRFP}[\text{RFP mRNA}]$$ $$\frac{d[\text{RFP}]}{dt}=K_t[\text{RFP mRNA}]-K_{deg_RFP}[RFP]$$ 1.  $P_{const}$:constitutive promoter activity
2.  $K_{deg\_mRFP}$:RFP mRNA degradation
3.  $K_{t}$:Translation efficiency
4.  $K_{deg\_RFP}$:RFP degredation

Result

While fitting the parameter, we set range of parameter which met the range of normal promoter activity, mRNA degradation, translation rate, and protein degradation [2]. The result of fitted parameter is, $P_{const}=0.24$, $K_{deg\_mRFP}=0.15$, $K_{t}=19.45$, $K_{deg\_RFP}=0.01$. The result of simulation and experimental data is very similar.

Figure 1: Result of RFP simulation and experimental data

Reference

  1. H. A. Richards, Quantitative RFP fluorescence as an indicator of recombinant protein synthesis in transgenic plants. Plant Cell Rep (2003) 22:117–121

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