Difference between revisions of "Team:SJTU-BioX-Shanghai/Signal Pathway"
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| − | <div class="my-title h5-my-responsive" id="section1"> | + | <div class="my-title h5-my-responsive" id="section1">Signal Pathway Model</div> |
| − | <p> | + | <p>Our model helps describe intracellular interactions of our multifactorial visualized detection system. We also use it to analyze and evaluate our synthetic biology system. The model was built using Simbiology, a MATLAB toolbox.</p> |
| − | <p> | + | <p>From these figures, we find several typical patterns of species variation. And the <a class="lin" target="_blank" href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Results">result</a> of our experiments also fits these patterns well.</p> |
| − | + | <div class="my-title h5-my-responsive" id="section2">Pathway Illustration</div> | |
| − | + | <div class="figure-intro"> | |
| − | + | <img src="https://static.igem.org/mediawiki/2017/6/6f/Pathw1.png" class="img-fluid"> | |
| − | <div class="my-title h5-my-responsive" id=" | + | <div class="figure-text"><strong>Figure1: Signal Pathway construct</strong>Inducers enters the cell, activates receptor and binding with repressor protein, leading to antisense producing. Then antisense binds with STAR. Finally sfGFP expression starts.</div> |
| − | < | + | <div class="my-title h5-my-responsive" id="section3">Reaction</div> |
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| − | + | ||
| − | + | ||
| + | </div> | ||
| + | <div class="my-title h5-my-responsive" id="section4">Simulation Results</div> | ||
| + | <div class="figure-intro"> | ||
| + | <img src="https://static.igem.org/mediawiki/2017/2/2b/T--SJTU-BioX-Shanghai--wcw4.png" class="img-fluid"> | ||
| + | <div class="figure-text"><strong>Figure2: sfGFP degradation over time.</strong></div> | ||
| + | </div> | ||
| + | <div class="figure-intro"> | ||
| + | <img src="https://static.igem.org/mediawiki/2017/3/3d/T--SJTU-BioX-Shanghai--wcw2.png" class="img-fluid"> | ||
| + | <div class="figure-text"><strong>Figure3: antiSTAR1 variation over time.</strong></div> | ||
| + | </div> | ||
| + | <div class="figure-intro"> | ||
| + | <img src="https://static.igem.org/mediawiki/2017/3/39/T--SJTU-BioX-Shanghai--wcw3.png" class="img-fluid"> | ||
| + | <div class="figure-text"><strong>Figure4: STAR & STAR_complex variation over time.</strong></div> | ||
| + | </div> | ||
| + | <div class="figure-intro"> | ||
| + | <img src="https://static.igem.org/mediawiki/2017/8/88/T--SJTU-BioX-Shanghai--wcw1.png" class="img-fluid"> | ||
| + | <div class="figure-text"><strong>Figure5: sfGFP& STAR_complex variation over time.</strong></div> | ||
| + | </div> | ||
| + | |||
| + | <p>From these figures, we find several typical patterns of species variation. And the <a target="_blank" href="https://2017.igem.org/Team:SJTU-BioX-Shanghai/Results">Results</a> of our experiments also fits these patterns well.</p> | ||
| + | |||
| + | <div class="my-title h5-my-responsive" id="section5">Parameters</div> | ||
| + | |||
| + | <div class="figure-intro"> | ||
| + | <table class="table table-res table-res2 table-hover" align="center"> | ||
| + | |||
| + | <thead> | ||
| + | <tr> | ||
| + | <td>Parameters</td> | ||
| + | <td>Reaction</td> | ||
| + | <td>Value</td> | ||
| + | <td>Reaction Type</td> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td>maxVproduceAsRprotein</td> | ||
| + | <td>AsrR + RNA_polymerase -> AsrR + RNA_polymerase + AsrR_protein</td> | ||
| + | <td>0.6</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>RNApolyConstant</td> | ||
| + | <td>All Reaction with Polymerase</td> | ||
| + | <td>1</td> | ||
| + | <td></td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kr_AsR_complex</td> | ||
| + | <td>As + AsrR_protein | ||
| + | <-> AsR_complex</td> | ||
| + | <td>0.8</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kf_AsR_complex</td> | ||
| + | <td>As + AsrR_protein | ||
| + | <-> AsR_complex</td> | ||
| + | <td>0.05</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>maxVproduceanti</td> | ||
| + | <td>RNA_polymerase + Promoter_STAR1 -> RNA_polymerase + Promoter_STAR1 + antiSTAR1</td> | ||
| + | <td>60</td> | ||
| + | <td>Competitive-Inhibition</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>AsrRproteinRepressConstant</td> | ||
| + | <td>RNA_polymerase + Promoter_STAR1 -> RNA_polymerase + Promoter_STAR1 + antiSTAR1</td> | ||
| + | <td>10</td> | ||
| + | <td>Competitive-Inhibition</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>kf_STAR1complex</td> | ||
| + | <td>antiSTAR1 + STAR1 | ||
| + | <-> STAR1_complex</td> | ||
| + | <td>50</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kr_STAR1complex</td> | ||
| + | <td>antiSTAR1 + STAR1 | ||
| + | <-> STAR1_complex</td> | ||
| + | <td>0.8</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>maxVproducesfGFP</td> | ||
| + | <td>Promoter_target + RNA_polymerase -> Promoter_target + RNA_polymerase + sfGFP</td> | ||
| + | <td>100</td> | ||
| + | <td>Competitive-Inhibition</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>antiRepressConstant</td> | ||
| + | <td>Promoter_target + RNA_polymerase -> Promoter_target + RNA_polymerase + sfGFP</td> | ||
| + | <td>10</td> | ||
| + | <td>Competitive-Inhibition</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kd_AsrR</td> | ||
| + | <td>AsrR -> null</td> | ||
| + | <td>0.007</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kd_RNA_polymerase</td> | ||
| + | <td>RNA_polymerase -> null</td> | ||
| + | <td>0.007</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kd_AsrR_protein</td> | ||
| + | <td>AsrR_protein -> null</td> | ||
| + | <td>0.007</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kd_antiSTAR</td> | ||
| + | <td>antiSTAR1 -> null</td> | ||
| + | <td>0.007</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kd_STAR</td> | ||
| + | <td>STAR1 -> null</td> | ||
| + | <td>0.007</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kd_STARcomplex</td> | ||
| + | <td>STAR1_complex -> null</td> | ||
| + | <td>0.007</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>kd_sfGFP</td> | ||
| + | <td>sfGFP -> null</td> | ||
| + | <td>0.007</td> | ||
| + | <td>MassAction</td> | ||
| + | </tr> | ||
| + | |||
| + | </tbody> | ||
| + | </table> | ||
| + | <div class="figure-text">Table1</div> | ||
| + | </div> | ||
| + | |||
| + | <div class="my-title h5-my-responsive" id="section6">Species</div> | ||
| + | <div class="figure-intro"> | ||
| + | <table class="table table-res table-res2 table-hover" align="center"> | ||
| + | |||
| + | <thead> | ||
| + | <tr> | ||
| + | <td>Species</td> | ||
| + | <td>Description</td> | ||
| + | <td>Initial Value </td> | ||
| + | </tr> | ||
| + | </thead> | ||
| + | <tbody> | ||
| + | <tr> | ||
| + | <td>AsrR</td> | ||
| + | <td>As repressor sequence</td> | ||
| + | <td>100</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>RNA_polymerase</td> | ||
| + | <td>RNA polymerase</td> | ||
| + | <td>2000</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>antiSTAR</td> | ||
| + | <td>antiSTAR sequence which binds with STAR to promote sfGFP</td> | ||
| + | <td>0 </td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>STAR</td> | ||
| + | <td>Small Transcription Activated RNA</td> | ||
| + | <td>200</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>STAR_complex</td> | ||
| + | <td>Complex of STAR&antiSTAR</td> | ||
| + | <td>100</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>sfGFP</td> | ||
| + | <td>Fluorescence Protein which displays green color</td> | ||
| + | <td>541.5</td> | ||
| + | </tr> | ||
| + | |||
| + | <tr> | ||
| + | <td>AsrR_protein</td> | ||
| + | <td>As repressor protein</td> | ||
| + | <td>200</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>As</td> | ||
| + | <td>As as an inducer</td> | ||
| + | <td>1000</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>AsR_complex</td> | ||
| + | <td>Complex of AsrR_protein&Promoter_STAR</td> | ||
| + | <td>0</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Promoter_STAR</td> | ||
| + | <td>Promoter which generates antiSTAR sequence</td> | ||
| + | <td>60</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>Promoter_target</td> | ||
| + | <td>Promoter which is repressed by STAR</td> | ||
| + | <td>80</td> | ||
| + | </tr> | ||
| + | </tbody> | ||
| + | </table> | ||
| + | <div class="figure-text">Table2</div> | ||
| + | </div> | ||
| + | </div> | ||
| + | |||
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| + | |||
| + | |||
| + | |||
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</div> | </div> | ||
| + | |||
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Latest revision as of 02:13, 2 November 2017
Signal PathwaySignal Pathway Model
Our model helps describe intracellular interactions of our multifactorial visualized detection system. We also use it to analyze and evaluate our synthetic biology system. The model was built using Simbiology, a MATLAB toolbox.
From these figures, we find several typical patterns of species variation. And the result of our experiments also fits these patterns well.
Pathway Illustration
Figure1: Signal Pathway constructInducers enters the cell, activates receptor and binding with repressor protein, leading to antisense producing. Then antisense binds with STAR. Finally sfGFP expression starts.
Reaction
Simulation Results
Figure2: sfGFP degradation over time.
Figure3: antiSTAR1 variation over time.
Figure4: STAR & STAR_complex variation over time.
Figure5: sfGFP& STAR_complex variation over time.
From these figures, we find several typical patterns of species variation. And the Results of our experiments also fits these patterns well.
Parameters
| Parameters | Reaction | Value | Reaction Type |
| maxVproduceAsRprotein | AsrR + RNA_polymerase -> AsrR + RNA_polymerase + AsrR_protein | 0.6 | MassAction |
| RNApolyConstant | All Reaction with Polymerase | 1 | |
| kr_AsR_complex | As + AsrR_protein <-> AsR_complex | 0.8 | MassAction |
| kf_AsR_complex | As + AsrR_protein <-> AsR_complex | 0.05 | MassAction |
| maxVproduceanti | RNA_polymerase + Promoter_STAR1 -> RNA_polymerase + Promoter_STAR1 + antiSTAR1 | 60 | Competitive-Inhibition |
| AsrRproteinRepressConstant | RNA_polymerase + Promoter_STAR1 -> RNA_polymerase + Promoter_STAR1 + antiSTAR1 | 10 | Competitive-Inhibition |
| kf_STAR1complex | antiSTAR1 + STAR1 <-> STAR1_complex | 50 | MassAction |
| kr_STAR1complex | antiSTAR1 + STAR1 <-> STAR1_complex | 0.8 | MassAction |
| maxVproducesfGFP | Promoter_target + RNA_polymerase -> Promoter_target + RNA_polymerase + sfGFP | 100 | Competitive-Inhibition |
| antiRepressConstant | Promoter_target + RNA_polymerase -> Promoter_target + RNA_polymerase + sfGFP | 10 | Competitive-Inhibition |
| kd_AsrR | AsrR -> null | 0.007 | MassAction |
| kd_RNA_polymerase | RNA_polymerase -> null | 0.007 | MassAction |
| kd_AsrR_protein | AsrR_protein -> null | 0.007 | MassAction |
| kd_antiSTAR | antiSTAR1 -> null | 0.007 | MassAction |
| kd_STAR | STAR1 -> null | 0.007 | MassAction |
| kd_STARcomplex | STAR1_complex -> null | 0.007 | MassAction |
| kd_sfGFP | sfGFP -> null | 0.007 | MassAction |
Table1
Species
| Species | Description | Initial Value |
| AsrR | As repressor sequence | 100 |
| RNA_polymerase | RNA polymerase | 2000 |
| antiSTAR | antiSTAR sequence which binds with STAR to promote sfGFP | 0 |
| STAR | Small Transcription Activated RNA | 200 |
| STAR_complex | Complex of STAR&antiSTAR | 100 |
| sfGFP | Fluorescence Protein which displays green color | 541.5 |
| AsrR_protein | As repressor protein | 200 |
| As | As as an inducer | 1000 |
| AsR_complex | Complex of AsrR_protein&Promoter_STAR | 0 |
| Promoter_STAR | Promoter which generates antiSTAR sequence | 60 |
| Promoter_target | Promoter which is repressed by STAR | 80 |
Table2
