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<section class="box features"> | <section class="box features"> | ||
<h2 class="major"><span>miniToe</span></h2> | <h2 class="major"><span>miniToe</span></h2> | ||
+ | |||
+ | <br/> | ||
+ | To achieve a better post-transcriptional regulation strategy, we designed a system which is composed of an RNA endoribonuclease (Csy4) and an RNA module named miniToe. We modeled to describe the dynamics of the miniToe system and found a way to achieve different regulation level. | ||
+ | <br/><br/> | ||
+ | |||
+ | |||
+ | |||
<p> | <p> | ||
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<div> | <div> | ||
โ | \[\rightarrow [๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{ | + | \[\rightarrow [๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] |
\[\rightarrow [๐๐
๐๐ด_{Csy4}]\] | \[\rightarrow [๐๐
๐๐ด_{Csy4}]\] | ||
\[[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]\rightarrow [๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}] + [๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}]\] | \[[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]\rightarrow [๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}] + [๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}]\] | ||
โ | \[[Protein_{๐ถ๐ ๐ฆ4}]+[crRNA-RBS-mRNA_{ | + | \[[Protein_{๐ถ๐ ๐ฆ4}]+[crRNA-RBS-mRNA_{sfGFP}]\leftrightarrow [๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{sfGFP}]\] |
โ | \[[Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{ | + | \[[Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\rightarrow [๐๐
๐๐ด_{sfGFP}] + [๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด]\] |
โ | \[[๐๐
๐๐ด_{ | + | \[[๐๐
๐๐ด_{sfGFP}]\rightarrow [๐๐
๐๐ด_{sfGFP}] + [๐๐๐๐ก๐๐๐_{sfGFP}]\] |
โ | \[[crRNA-RBS-mRNA_{ | + | \[[crRNA-RBS-mRNA_{sfGFP}]\rightarrow \emptyset\] |
\[[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]\rightarrow \emptyset\] | \[[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]\rightarrow \emptyset\] | ||
\[[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}]\rightarrow \emptyset\] | \[[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}]\rightarrow \emptyset\] | ||
โ | \[[Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{ | + | \[[Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\rightarrow \emptyset\] |
โ | \[[๐๐
๐๐ด_{ | + | \[[๐๐
๐๐ด_{sfGFP}]\rightarrow \emptyset\] |
\[[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด]\rightarrow \emptyset\] | \[[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด]\rightarrow \emptyset\] | ||
โ | \[[๐๐๐๐ก๐๐๐_{ | + | \[[๐๐๐๐ก๐๐๐_{sfGFP}]\rightarrow \emptyset\] |
</div> | </div> | ||
โ | <br />Two equations, describing the functional binding and cleavage of Csy4 protein in biology, and three parameters | + | <br />Two equations, describing the functional binding and cleavage of Csy4 protein in biology, and three parameters: |
+ | k<sub>on</sub>, k<sub>off</sub>, k<sub>obs</sub>, describing the same things in mathematics, are the core of our model. | ||
</p> | </p> | ||
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<h3>ODEs</h3> | <h3>ODEs</h3> | ||
โ | <br />To simulate the dynamics of | + | <br />To simulate the dynamics of sfGFP, we use ordinary differential equations to model the reactions above. And ODEs are given as follows: |
<div> | <div> | ||
โ | \[\frac{d[๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{ | + | \[\frac{d[๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]}{dt}=๐_{1}-๐_{d1}[๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] |
โ | \[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{ | + | \[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] |
โ | \[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{ | + | \[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] |
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\[\frac{d[Protein_{๐ถ๐ ๐ฆ4}]}{dt}=๐_{p2}[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]-๐_{dp2}[Protein_{๐ถ๐ ๐ฆ4}]\] | \[\frac{d[Protein_{๐ถ๐ ๐ฆ4}]}{dt}=๐_{p2}[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]-๐_{dp2}[Protein_{๐ถ๐ ๐ฆ4}]\] | ||
โ | \[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{ | + | \[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] |
โ | \[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{ | + | \[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] |
โ | \[\frac{d[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{ | + | \[\frac{d[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{sfGFP}]}{dt}=\] |
โ | \[-๐_{of}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{ | + | \[๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] |
โ | \[-๐_{d1}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{ | + | \[-๐_{of}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\] |
โ | \[-๐_{obs}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{ | + | \[-๐_{d1}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\] |
+ | \[-๐_{obs}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\] | ||
โ | \[\frac{d[๐๐
๐๐ด_{ | + | \[\frac{d[๐๐
๐๐ด_{sfGFP}]}{dt}=๐_{obs}[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{sfGFP}]-๐_{d3}[๐๐
๐๐ด_{sfGFP}]\] |
โ | \[\frac{d[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA]}{dt}=๐_{obs}[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{ | + | \[\frac{d[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA]}{dt}=๐_{obs}[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{sfGFP}]\] |
โ | \[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{ | + | \[-๐_{dc2}[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด]\] |
โ | \[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{ | + | \[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] |
+ | \[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\] | ||
โ | \[\frac{d[Protein_{ | + | \[\frac{d[Protein_{sfGFP}]}{dt}=๐_{p1}[๐๐
๐๐ด_{sfGFP}]-๐_{dp1}[Protein_{sfGFP}]\] |
</div> | </div> | ||
<br />For the readability, the complex symbol is simplified as: | <br />For the readability, the complex symbol is simplified as: | ||
Line 250: | Line 260: | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | <th scope="row"> | + | <th scope="row"> [๐๐๐
๐๐ดโ๐
๐ต๐โ๐๐
๐๐ด<sub>sfGFP</sub>]</th> |
<td align="center">A</td> | <td align="center">A</td> | ||
<td align="center">15</td> | <td align="center">15</td> | ||
โ | <td align="center"> | + | <td align="center">mol/L</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | <th scope="row"> | + | <th scope="row">[๐๐
๐๐ด<sub>Csy4</sub>]</th> |
<td align="center">B</td> | <td align="center">B</td> | ||
<td align="center">0</td> | <td align="center">0</td> | ||
โ | <td align="center"> | + | <td align="center">mol/L</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">[Protein<sub>๐ถ๐ ๐ฆ4</sub>]</th> | |
<td align="center">C</td> | <td align="center">C</td> | ||
<td align="center">0</td> | <td align="center">0</td> | ||
โ | <td align="center"> | + | <td align="center">mol/L</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">[Protein<sub>๐ถ๐ ๐ฆ4</sub>-crRNA-RBS-mRNA<sub>sfGFP</sub>]</th> | |
<td align="center">D</td> | <td align="center">D</td> | ||
<td align="center">0</td> | <td align="center">0</td> | ||
โ | <td align="center"> | + | <td align="center">mol/L</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">[๐๐
๐๐ด<sub>sfGFP</sub>]</th> | |
<td align="center">E</td> | <td align="center">E</td> | ||
<td align="center">0</td> | <td align="center">0</td> | ||
โ | <td align="center"> | + | <td align="center">mol/L</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">[Protein<sub>๐ถ๐ ๐ฆ4</sub>-๐๐๐
๐๐ด]</th> | |
<td align="center">F</td> | <td align="center">F</td> | ||
<td align="center">0</td> | <td align="center">0</td> | ||
โ | <td align="center"> | + | <td align="center">mol/L</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | <th scope="row"> | + | <th scope="row">[Protein<sub>sfGFP</sub>]</th> |
<td align="center">G</td> | <td align="center">G</td> | ||
<td align="center">0</td> | <td align="center">0</td> | ||
โ | <td align="center"> | + | <td align="center">mol/L</td> |
</tr> | </tr> | ||
</tbody> | </tbody> | ||
</table> | </table> | ||
โ | <br /> Because the [๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด<sub> | + | <br /> Because the [๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด<sub>sfGFP</sub>] is under controlled by a constitutive promoter, so we set the initial concentration to 15mol/L . |
โ | <br /> The | + | <br /> <br /> The parament we used in the ODEs is listed in the following table: <table width="200" border="1"> |
<tbody> | <tbody> | ||
<tr> | <tr> | ||
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</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>1</sub></th> | |
โ | <td align="center">The transcription rate of | + | <td align="center">The transcription rate of [๐๐๐
๐๐ดโ๐
๐ต๐โ๐๐
๐๐ด<sub>sfGFP</sub>]</td> |
โ | + | <td align="center">h<sup>-1</sup></td> | |
<td align="center">1.955</td> | <td align="center">1.955</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>d1</sub></th> | |
โ | <td align="center">The degradation rate of | + | <td align="center">The degradation rate of [๐๐๐
๐๐ดโ๐
๐ต๐โ๐๐
๐๐ด<sub>sfGFP</sub>]</td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">0.002</td> | <td align="center">0.002</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>2</sub></th> | |
โ | <td align="center">The transcription rate of | + | <td align="center">The transcription rate of [๐๐
๐๐ด<sub>Csy4</sub>] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">1.116</td> | <td align="center">1.116</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>d2</sub></th> | |
โ | <td align="center">The degradation rate of | + | <td align="center">The degradation rate of [๐๐
๐๐ด<sub>Csy4</sub>] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">0.241</td> | <td align="center">0.241</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>p2</sub></th> | |
โ | <td align="center">The translation rate of | + | <td align="center">The translation rate of [Protein<sub>๐ถ๐ ๐ฆ4</sub>] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">1.134</td> | <td align="center">1.134</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>dp2</sub></th> | |
โ | <td align="center">The degradation rate of | + | <td align="center">The degradation rate of [Protein<sub>๐ถ๐ ๐ฆ4</sub>] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">6.547</td> | <td align="center">6.547</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>on</sub></th> | |
โ | <td align="center">The binding constant of | + | <td align="center">The binding constant of [Protein<sub>๐ถ๐ ๐ฆ4</sub>] and [๐๐๐
๐๐ดโ๐
๐ต๐โ๐๐
๐๐ด<sub>sfGFP</sub>]</td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">23995.469</td> | <td align="center">23995.469</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>off</sub></th> | |
โ | <td align="center">The dissociation constant of | + | <td align="center">The dissociation constant of [Protein<sub>๐ถ๐ ๐ฆ4</sub>] and [๐๐๐
๐๐ดโ๐
๐ต๐โ๐๐
๐๐ด<sub>sfGFP</sub>]</td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">2.703</td> | <td align="center">2.703</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>dc1</sub></th> | |
โ | <td align="center">The degradation rate of | + | <td align="center">The degradation rate of [Protein<sub>๐ถ๐ ๐ฆ4</sub>-crRNA-RBS-mRNA<sub>sfGFP</sub>] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">0.024</td> | <td align="center">0.024</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>obs</sub></th> | |
โ | <td align="center">The cleavage rate of | + | <td align="center">The cleavage rate of [Protein<sub>๐ถ๐ ๐ฆ4</sub>] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">0.327</td> | <td align="center">0.327</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>d3</sub></th> | |
โ | <td align="center">The degradation rate of | + | <td align="center">The degradation rate of [๐๐
๐๐ด<sub>sfGFP</sub>] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">0.472</td> | <td align="center">0.472</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>dc2</sub></th> | |
โ | <td align="center">The degradation rate of | + | <td align="center">The degradation rate of [Protein<sub>๐ถ๐ ๐ฆ4</sub>-๐๐๐
๐๐ด] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">0.024</td> | <td align="center">0.024</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">๐<sub>p1</sub></th> | |
โ | <td align="center">The translation rate of | + | <td align="center">The translation rate of [Protein<sub>sfGFP</sub>]</td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">1.711</td> | <td align="center">1.711</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
โ | + | <th scope="row">k<sub>dp1</sub></th> | |
โ | <td align="center">The degradation rate of | + | <td align="center">The degradation rate of [Protein<sub>sfGFP</sub>] </td> |
โ | <td align="center"> | + | <td align="center">h<sup>-1</sup></td> |
<td align="center">0.479</td> | <td align="center">0.479</td> | ||
</tr> | </tr> | ||
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</div> | </div> | ||
<br /> | <br /> | ||
โ | <div align="center"><p >Fig.1 The dynamics of | + | <div align="center"><p >Fig.1 The dynamics of sfGFP by model prediction</p></div> |
We compare the experimental data to the simulation: | We compare the experimental data to the simulation: | ||
<div align="center"><img src="https://static.igem.org/mediawiki/2018/8/89/T--OUC-China--min2.png" width="600" > | <div align="center"><img src="https://static.igem.org/mediawiki/2018/8/89/T--OUC-China--min2.png" width="600" > | ||
Line 405: | Line 415: | ||
<h3>Discussion</h3> | <h3>Discussion</h3> | ||
โ | <br />Combining the biology and math, we now discuss why the dynamics of | + | <br />Combining the biology and math, we now discuss why the dynamics of sfGFP is like the curve in the Fig.1. In order to explain in detail, we plot the dynamics of all species in the miniToe system in Fig.3. |
<div align="center"><img src="https://static.igem.org/mediawiki/2018/2/2e/T--OUC-China--res6.png" width="600" > | <div align="center"><img src="https://static.igem.org/mediawiki/2018/2/2e/T--OUC-China--res6.png" width="600" > | ||
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โ | As we can see in the Fig.3, the red line refers to the dynamics of | + | As we can see in the Fig.3, the red line refers to the dynamics of sfGFP, which is increasing in the beginning and then drop down to a stable level. The reason for this is that the cleavage rate of Csy4 is faster than the production rate of [crRNA-RBS-mRNA<sub>sfGFP</sub>] , which cause that the [mRNA<sub>sfGFP</sub>] is decreasing after 10 hours. Before we add IPTG into our system to induce the Tac promoter, the [crRNA-RBS-mRNA<sub>sfGFP</sub>] is accumulated because it is under control by a constitutive promoter. After we add IPTG, the initial concentration of [crRNA-RBS-mRNA<sub>sfGFP</sub>] plays an important role in the production of sfGFP during the early 10 hours: even the Csy4 cleavage rate is faster than the production rate of [crRNA-RBS-mRNA<sub>sfGFP</sub>] , the [crRNA-RBS-mRNA<sub>sfGFP</sub>] which is accumulated before make the keep increasing. But after the initial amount of [crRNA-RBS-mRNA<sub>sfGFP</sub>] is used out, the [mRNA<sub>sfGFP</sub>] then drop down into a stable level with the balance of the production rate and decay rate, which result in the drop down of sfGFP curve. |
โ | + | <br /><br /> | |
โ | <h3>Sensitivities Analysis</h3> | + | <h3 id="MM">Sensitivities Analysis</h3> |
<br />After building the ODE model, we try to do something more deeply to our miniToe system by analyzing the sensitivity of parameters. Fig.4 shows the numerical integration of sensitivities of parameters in 30 hours. | <br />After building the ODE model, we try to do something more deeply to our miniToe system by analyzing the sensitivity of parameters. Fig.4 shows the numerical integration of sensitivities of parameters in 30 hours. | ||
โ | <div align="center"><img src="https://static.igem.org/mediawiki/2018/c/c4/T--OUC-China--design3-2.png" width=" | + | <div align="center"><img src="https://static.igem.org/mediawiki/2018/c/c4/T--OUC-China--design3-2.png" width="950" > |
</div> | </div> | ||
<br /> | <br /> | ||
<div align="center"><p >Fig.4 The numerical integration of sensitivities of parameters in 30h</p></div> | <div align="center"><p >Fig.4 The numerical integration of sensitivities of parameters in 30h</p></div> | ||
โ | According to the sensitivity analysis, we can find that three core parameters,k<sub>on</sub> ,k<sub>off</sub> , k<sub>obs</sub> , which is related to the protein Csy4, has different effect in the expression of | + | According to the sensitivity analysis, we can find that three core parameters, k<sub>on</sub> ,k<sub>off</sub> , k<sub>obs</sub> , which is related to the protein Csy4, has different effect in the expression of sfGFP. The two binding parameters, k<sub>on</sub> ,k<sub>off</sub> , will not influence sfGFP while the cleavage parameter, , will influence the expression in sfGFP, which indicated if we change the wild-type Csy4 to some mutation then we can achieve the different expression of sfGFP. |
โ | <br />Enlighten by the sensitivity analysis, we give a prediction curve that shows | + | <br /><br />Enlighten by the sensitivity analysis, we give a prediction curve that shows what will happen in the sfGFP expression curve if we change the Csy4, and it can be seen in the Fig.5. |
<div align="center"><img src="https://static.igem.org/mediawiki/2018/c/ca/T--OUC-China--res23.png" width="600" > | <div align="center"><img src="https://static.igem.org/mediawiki/2018/c/ca/T--OUC-China--res23.png" width="600" > | ||
</div> | </div> | ||
<br /> | <br /> | ||
โ | <div align="center"><p >Fig.5 The curve of | + | <div align="center"><p >Fig.5 The curve of sfGFP with the changing cleavage rate</p></div> |
โ | And the Fig.6 shows that the relationship between the stable expression level of | + | And the Fig.6 shows that the relationship between the stable expression level of sfGFP and the claevage rate,k<sub>obs</sub> . |
<div align="center"><img src="https://static.igem.org/mediawiki/2018/5/55/T--OUC-China--min6.png" width="600" > | <div align="center"><img src="https://static.igem.org/mediawiki/2018/5/55/T--OUC-China--min6.png" width="600" > | ||
</div> | </div> | ||
<br /> | <br /> | ||
โ | <div align="center"><p >Fig.6 The relationship between the stable expression level of | + | <div align="center"><p >Fig.6 The relationship between the stable expression level of sfGFP and the claevage rate</p></div> |
</p> | </p> | ||
<br /><br /><br /><br /> | <br /><br /><br /><br /> | ||
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โ | + | <div class="copyright1">Contact Us : oucigem@163.com | ©2018 OUC IGEM.All Rights Reserved. <br /> | |
+ | <img src="https://static.igem.org/mediawiki/2017/b/b4/T--OUC-China--foot1.jpeg"alt="banner"width="80px"> | ||
+ | <img src="https://static.igem.org/mediawiki/2017/6/62/T--OUC-China--foot2.jpeg"alt="banner"width="80px"> | ||
+ | <img src="https://static.igem.org/mediawiki/2018/f/f3/T--OUC-China--lalala.png"alt="banner"width="80px"> | ||
+ | <img src="https://static.igem.org/mediawiki/2017/5/51/T--OUC-China--NSG.png"alt="banner"height="65px"> | ||
+ | <img src="https://static.igem.org/mediawiki/2017/2/2a/T--OUC-China--ML.png"alt="banner"height="65px">  | ||
+ | </div> | ||
Latest revision as of 17:25, 5 December 2018
miniToe
To achieve a better post-transcriptional regulation strategy, we designed a system which is composed of an RNA endoribonuclease (Csy4) and an RNA module named miniToe. We modeled to describe the dynamics of the miniToe system and found a way to achieve different regulation level.
Reactions
We can describe our miniToe system to be followings:
\[\rightarrow [๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[\rightarrow [๐๐
๐๐ด_{Csy4}]\]
\[[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]\rightarrow [๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}] + [๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}]\]
\[[Protein_{๐ถ๐ ๐ฆ4}]+[crRNA-RBS-mRNA_{sfGFP}]\leftrightarrow [๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{sfGFP}]\]
\[[Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\rightarrow [๐๐
๐๐ด_{sfGFP}] + [๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด]\]
\[[๐๐
๐๐ด_{sfGFP}]\rightarrow [๐๐
๐๐ด_{sfGFP}] + [๐๐๐๐ก๐๐๐_{sfGFP}]\]
\[[crRNA-RBS-mRNA_{sfGFP}]\rightarrow \emptyset\]
\[[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]\rightarrow \emptyset\]
\[[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}]\rightarrow \emptyset\]
\[[Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\rightarrow \emptyset\]
\[[๐๐
๐๐ด_{sfGFP}]\rightarrow \emptyset\]
\[[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด]\rightarrow \emptyset\]
\[[๐๐๐๐ก๐๐๐_{sfGFP}]\rightarrow \emptyset\]
Two equations, describing the functional binding and cleavage of Csy4 protein in biology, and three parameters: kon, koff, kobs, describing the same things in mathematics, are the core of our model.
ODEs
To simulate the dynamics of sfGFP, we use ordinary differential equations to model the reactions above. And ODEs are given as follows:
\[\frac{d[๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]}{dt}=๐_{1}-๐_{d1}[๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[\frac{d[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]}{dt}=๐_{2}-๐_{d2}[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]\]
\[\frac{d[Protein_{๐ถ๐ ๐ฆ4}]}{dt}=๐_{p2}[๐๐
๐๐ด_{๐ถ๐ ๐ฆ4}]-๐_{dp2}[Protein_{๐ถ๐ ๐ฆ4}]\]
\[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[\frac{d[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{sfGFP}]}{dt}=\]
\[๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[-๐_{of}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\]
\[-๐_{d1}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\]
\[-๐_{obs}[Protein_{๐ถ๐ ๐ฆ4}][Protein_{๐ถ๐ ๐ฆ4}-crRNA-RBS-mRNA_{sfGFP}]\]
\[\frac{d[๐๐
๐๐ด_{sfGFP}]}{dt}=๐_{obs}[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{sfGFP}]-๐_{d3}[๐๐
๐๐ด_{sfGFP}]\]
\[\frac{d[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA]}{dt}=๐_{obs}[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-crRNA-RBS-๐๐
๐๐ด_{sfGFP}]\]
\[-๐_{dc2}[๐๐๐๐ก๐๐๐_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด]\]
\[-๐_{on}[Protein_{๐ถ๐ ๐ฆ4}][๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[+๐_{off}[Protein_{๐ถ๐ ๐ฆ4}-๐๐๐
๐๐ด โ ๐
๐ต๐ โ ๐๐
๐๐ด_{sfGFP}]\]
\[\frac{d[Protein_{sfGFP}]}{dt}=๐_{p1}[๐๐
๐๐ด_{sfGFP}]-๐_{dp1}[Protein_{sfGFP}]\]
For the readability, the complex symbol is simplified as:
\[\frac{d[A]}{dt}=๐_{1}-๐_{d1}[A]-๐_{on}[C][A]+๐_{off}[D]\]
\[\frac{d[B]}{dt}=๐_{2}-๐_{d2}[B]\]
\[\frac{d[C]}{dt}=๐_{p2}[B]-๐_{dp2}[C]-๐_{on}[C][A]+๐_{off}[D]\]
\[\frac{d[D]}{dt}=๐_{on}[C][A]-๐_{dp2}[C]-๐_{off}[D]-๐_{dc1}[D]-๐_{obs}[D]\]
\[\frac{d[E]}{dt}=๐_{obs}[D]-๐_{d3}[E]\]
\[\frac{d[F]}{dt}=๐_{obs}[D]-๐_{d3}[F]\]
\[\frac{d[G]}{dt}=๐_{p1}[E]-๐_{dp1}[G]\]
Data Processing
The leak in the experiment is a big problem in estimating parameters in our ODEs model, so we processing the data by following formula๏ผ \[Data(without leak)=Data(+IPTG)-Data(-IPTG)\]
By doing this, we can reduce some factor which may be influenced estimation, not just the leak, but also some background noise. So we can get more precise parameters of the Csy4.
Species, symbols and parameters
Species | Symbol | Initial value | Units |
---|---|---|---|
[๐๐๐ ๐๐ดโ๐ ๐ต๐โ๐๐ ๐๐ดsfGFP] | A | 15 | mol/L |
[๐๐ ๐๐ดCsy4] | B | 0 | mol/L |
[Protein๐ถ๐ ๐ฆ4] | C | 0 | mol/L |
[Protein๐ถ๐ ๐ฆ4-crRNA-RBS-mRNAsfGFP] | D | 0 | mol/L |
[๐๐ ๐๐ดsfGFP] | E | 0 | mol/L |
[Protein๐ถ๐ ๐ฆ4-๐๐๐ ๐๐ด] | F | 0 | mol/L |
[ProteinsfGFP] | G | 0 | mol/L |
Because the [๐๐๐ ๐๐ด โ ๐ ๐ต๐ โ ๐๐ ๐๐ดsfGFP] is under controlled by a constitutive promoter, so we set the initial concentration to 15mol/L .
The parament we used in the ODEs is listed in the following table:
Parameters | Definition | Units | Value |
---|---|---|---|
๐1 | The transcription rate of [๐๐๐ ๐๐ดโ๐ ๐ต๐โ๐๐ ๐๐ดsfGFP] | h-1 | 1.955 |
๐d1 | The degradation rate of [๐๐๐ ๐๐ดโ๐ ๐ต๐โ๐๐ ๐๐ดsfGFP] | h-1 | 0.002 |
๐2 | The transcription rate of [๐๐ ๐๐ดCsy4] | h-1 | 1.116 |
๐d2 | The degradation rate of [๐๐ ๐๐ดCsy4] | h-1 | 0.241 |
๐p2 | The translation rate of [Protein๐ถ๐ ๐ฆ4] | h-1 | 1.134 |
๐dp2 | The degradation rate of [Protein๐ถ๐ ๐ฆ4] | h-1 | 6.547 |
๐on | The binding constant of [Protein๐ถ๐ ๐ฆ4] and [๐๐๐ ๐๐ดโ๐ ๐ต๐โ๐๐ ๐๐ดsfGFP] | h-1 | 23995.469 |
๐off | The dissociation constant of [Protein๐ถ๐ ๐ฆ4] and [๐๐๐ ๐๐ดโ๐ ๐ต๐โ๐๐ ๐๐ดsfGFP] | h-1 | 2.703 |
๐dc1 | The degradation rate of [Protein๐ถ๐ ๐ฆ4-crRNA-RBS-mRNAsfGFP] | h-1 | 0.024 |
๐obs | The cleavage rate of [Protein๐ถ๐ ๐ฆ4] | h-1 | 0.327 |
๐d3 | The degradation rate of [๐๐ ๐๐ดsfGFP] | h-1 | 0.472 |
๐dc2 | The degradation rate of [Protein๐ถ๐ ๐ฆ4-๐๐๐ ๐๐ด] | h-1 | 0.024 |
๐p1 | The translation rate of [ProteinsfGFP] | h-1 | 1.711 |
kdp1 | The degradation rate of [ProteinsfGFP] | h-1 | 0.479 |
Simulation
With the help of Simbiology toolbox in Matlab๏ผwe simulate our miniToe system for 30h, the result can be seen in the Fig.1.
Fig.1 The dynamics of sfGFP by model prediction
Fig.2 The comparison between experimental data and simulation data
Discussion
Combining the biology and math, we now discuss why the dynamics of sfGFP is like the curve in the Fig.1. In order to explain in detail, we plot the dynamics of all species in the miniToe system in Fig.3.
Fig.3 The dynamics of all species in the miniToe system
Sensitivities Analysis
After building the ODE model, we try to do something more deeply to our miniToe system by analyzing the sensitivity of parameters. Fig.4 shows the numerical integration of sensitivities of parameters in 30 hours.
Fig.4 The numerical integration of sensitivities of parameters in 30h
Enlighten by the sensitivity analysis, we give a prediction curve that shows what will happen in the sfGFP expression curve if we change the Csy4, and it can be seen in the Fig.5.
Fig.5 The curve of sfGFP with the changing cleavage rate
Fig.6 The relationship between the stable expression level of sfGFP and the claevage rate
Contact Us : oucigem@163.com | ©2018 OUC IGEM.All Rights Reserved.