Difference between revisions of "Team:HUST-China/Comparison between PSB"

 
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Modeling overview">Modeling overview</a></li>
 
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                  <p>This page has been moved to <a href="https://2018.igem.org/Team:HUST-China/model_of_systems">"Model of Systems"</a> </p>
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                   <h3><strong>1. <span class="red-content">Abstract</span></strong></h3>
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                   <h3><strong>Part1: <span class="red-content">Abstract</span></strong></h3>
 
                   <p>Modelling is a powerful tool in synthetic biology that allows us to get a deeper understanding of our system. In order to see whether our system can work and how our system will work, we build this model to simulate our system. This model shows us the details of our system and give our intelligent device software data so that we can change the environment to increase the efficiency and stability of Optopia.</p>
 
                   <p>Modelling is a powerful tool in synthetic biology that allows us to get a deeper understanding of our system. In order to see whether our system can work and how our system will work, we build this model to simulate our system. This model shows us the details of our system and give our intelligent device software data so that we can change the environment to increase the efficiency and stability of Optopia.</p>
 
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                   <h3><strong>2. <span class="red-content">Overview</span></strong></h3>
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                   <h3><strong>Part2: <span class="red-content">Overview</span></strong></h3>
 
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             <h3 style="text-indent: 2em;"><span class="red-content">functions</span></strong></h3>
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                                 <p>These functions calculate the growth rate of <i>Synechocystis</i>. The two functions correspond to different concentrations of CO<sub>2</sub> in the solution.<img  style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/3/36/T--HUST-China--2018-model-new-c003.png">and<img  style="vertical-align:middle;height:60px" src="https://static.igem.org/mediawiki/2018/b/bf/T--HUST-China--2018-model-new-c004.png">make the growth rate decline when the concentration of CO<sub>2</sub> in the solution is too high or too low. (David et al. 2015)<sup>[1]</sup>. From the same reference we get the relationship between the light intensity and the growth rate. The function<img  style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/d/d8/T--HUST-China--2018-model-new-c005.png">is from another reference(XIONG et al. 2012) <sup>[2]</sup>. The parameter <img  style="vertical-align:middle;height:30px" src="https://static.igem.org/mediawiki/2018/0/0c/T--HUST-China--2018-model-new-c006.png"> the decline of the growth rate caused by gene editing. This parameter is introduced to make the growth model of wild <i>Synechocystis</i> fit to the growth of edited ones in the reference (Henrike et al. 2010)<sup>[3]</sup>.</p>
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                                 <p>These functions calculate the growth rate of <i>Synechocystis</i>. The two functions correspond to different concentrations of CO<sub>2</sub> in the solution.<img  style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/3/36/T--HUST-China--2018-model-new-c003.png">and<img  style="vertical-align:middle;height:60px" src="https://static.igem.org/mediawiki/2018/b/bf/T--HUST-China--2018-model-new-c004.png">make the growth rate decline when the concentration of CO<sub>2</sub> in the solution is too high or too low. (David et al. 2015)<sup>[1]</sup>. From the same reference we get the relationship between the light intensity and the growth rate. The function<img  style="vertical-align:middle;height:40px" src="https://static.igem.org/mediawiki/2018/d/d8/T--HUST-China--2018-model-new-c005.png">is from another reference(XIONG et al. 2012) <sup>[2]</sup>. The parameter <img  style="vertical-align:middle;height:30px" src="https://static.igem.org/mediawiki/2018/0/0c/T--HUST-China--2018-model-new-c006.png"> the decline of the growth rate caused by gene editing. This parameter is introduced to make the growth model of wild <i>Synechocystis</i> fit to the growth of edited ones in the reference (Henrike et al. 2010)<sup>[3]</sup>.</p>
 
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                                   <p>This function shows the inhibit of CO<sub>2</sub> to the metabolism of <i>Synechocystis</i>. The lack of carbon source will not only effect the growth rate of the bacteria, but also reduce the produce rate of lactate.</p>
 
                                   <p>This function shows the inhibit of CO<sub>2</sub> to the metabolism of <i>Synechocystis</i>. The lack of carbon source will not only effect the growth rate of the bacteria, but also reduce the produce rate of lactate.</p>
 
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                      <table class="table table-bordered table-hover" style="text-align: center;">
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                            <tr>
 +
                              <th>Parameter</th>
 +
                              <th>Description</th>
 +
                              <th>Value</th>
 +
                              <th>Unit</th>
 +
                              <th>Source</th>
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                            </tr>
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                            <tr>
 +
                              <td>q<sub>Lac,Synec</sub></td>
 +
                              <td>Lactate produced by each unit of Synechocystis.</td>
 +
                                <td>6.582×10<sup>-4</sup></td>
 +
                                <td>h<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[3]</sup></td>
 +
                            </tr>
 +
                          <tr>
 +
                              <td>Y<sub>CO<sub>2</sub>,Synec</sub></td>
 +
                              <td>Yield coefficient of Synechocystis related to CO<sub>2</sub> consuming, showing the CO<sub>2</sub> consumed for growth</td>
 +
                                <td>2.284×10<sup>2</sup></td>
 +
                                <td>1</td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>Y <sub>O<sub>2</sub>,CO<sub>2</sub></sub> </td>
 +
                              <td>O<sub>2</sub> producing coefficient related to CO<sub>2</sub> consuming.</td>
 +
                                <td>1.375</td>
 +
                                <td>1</td>
 +
                              <td>Calculated by the  stoichiometric in the chemical equation of the  photosynthesis and respiration in Synechocystis and relative molecular mass of O<sub>2</sub> and CO<sub>2</sub></td>
 +
                            </tr>
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                            <tr>
 +
                              <td>Y<sub>CO<sub>2</sub>,Lac</sub></sub></td>
 +
                              <td>O<sub>2</sub> producing coefficient related to lactate consuming.</td>
 +
                                <td>6.818×10<sup>-1</sup></td>
 +
                                <td>1</td>
 +
                              <td>Calculated by the  stoichiometric in the chemical equation of lactate producing, and relative molecular mass of CO<sub>2</sub> and lactate</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>m<sub>CO<sub>2</sub>,Synec</sub></td>
 +
                              <td>The sustain coefficient of Synechocystis. Stand for the CO<sub>2</sub> consuming by the unit dry weight of alive Synechocystis.</td>
 +
                                <td>1.164×10<sup>-1</sup></td>
 +
                                <td>h<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>μ<sub>max,Synec</sub></td>
 +
                              <td>The max growth rate of Synechocystis.</td>
 +
                                <td>5.210×10<sup>-2</sup></td>
 +
                                <td>h<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sub>CO<sub>2</sub>,Synec,1</sub></td>
 +
                              <td>The semi-saturation constant of CO<sub>2</sub> concentration when it is low.</td>
 +
                                <td>3.551×10<sup>-6</sup></td>
 +
                                <td>g⋅L<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sub>CO<sub>2</sub>,Synec,2</sub></td>
 +
                              <td>The semi-saturation constant of CO<sub>2</sub> concentration when it is high</td>
 +
                                <td>7.788×10<sup>-2</sup></td>
 +
                                <td>g⋅L<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>c<sub>l,CO<sub>2</sub></sub></td>
 +
                              <td>The critical value of CO<sub>2</sub> concentration. Different formulas are applied when CO<sub>2</sub> concentration in the solution is above or below this value. </td>
 +
                                <td>7.788×10<sup>-2</sup></td>
 +
                                <td>g⋅L<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>c<sub>max,Synec</sub></td>
 +
                              <td>The max concertation of Synechocystis in the solution.</td>
 +
                                <td>3.160×10<sup>-1</sup></td>
 +
                                <td>g⋅L<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
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 +
                              <td>I<sub>k,Synec</sub></td>
 +
                              <td>The light intensity constant of Synechocystis while the light intensity is lower than 8000Lux</td>
 +
                                <td>8.749×10<sup>2</sup></td>
 +
                                <td>Lux</td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
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 +
                              <td>k<sub>decline</sub></td>
 +
                              <td>The decline caused by the gene editing.</td>
 +
                                <td>4.209×10<sup>-1</sup></td>
 +
                                <td>1</td>
 +
                              <td>Fitting from reference <sup>[1]</sup></td>
 +
                            </tr>
 +
                         
 +
                      </table>
 +
                  </div>
 +
                </div>
 +
              </div>
 
    
 
    
 
                         </div>
 
                         </div>
Line 283: Line 392:
 
                               <h3><b>2.<i>Rhodopseudomonas palustris</i></b></h3>
 
                               <h3><b>2.<i>Rhodopseudomonas palustris</i></b></h3>
 
                               <div  class="col-md-8">  
 
                               <div  class="col-md-8">  
−
                                   <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/9/92/T--HUST-China--2018-model-new-r001.png">
+
                                   <img class="img-responsive" style="height:160px" src="https://static.igem.org/mediawiki/2018/9/92/T--HUST-China--2018-model-new-r001.png">
−
                              <div  class="col-md-8" > <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/1/11/T--HUST-China--2018-model-new-r002.png">
+
−
                              </div>
+
 
                               </div>
 
                               </div>
 
                               <div class="col-md-12">   
 
                               <div class="col-md-12">   
 
                                 <p>These are the main differential equations about the modeling  part of the <I><i>Rhodopseudomonas palustris</i></I> (abbreviated as “Rps”). Through these differential equations, we can calculate the concentrations of Rps, carbon dioxide and lactate. The parameters and variables above will be introduced below.This part is similar to that of <I><i>Synechocystis</i></I>, because in our experiment, they are both used to provide lactate to <I><i>Shewanella</i></I> and have similar genetic modification.</p>
 
                                 <p>These are the main differential equations about the modeling  part of the <I><i>Rhodopseudomonas palustris</i></I> (abbreviated as “Rps”). Through these differential equations, we can calculate the concentrations of Rps, carbon dioxide and lactate. The parameters and variables above will be introduced below.This part is similar to that of <I><i>Synechocystis</i></I>, because in our experiment, they are both used to provide lactate to <I><i>Shewanella</i></I> and have similar genetic modification.</p>
−
                               </div><div  class="col-md-8" > <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/7/7e/T--HUST-China--2018-model-new-r003.png">
+
                               </div><div  class="col-md-8" > <img class="img-responsive" style="height:70px" src="https://static.igem.org/mediawiki/2018/7/7e/T--HUST-China--2018-model-new-r003.png">
 
                               </div>
 
                               </div>
 
                           <div class="col-md-12">           
 
                           <div class="col-md-12">           
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                               <p>From the same reference we get the relationship between the light intensity and the growth rate. The function</p>
 
                               <p>From the same reference we get the relationship between the light intensity and the growth rate. The function</p>
 
                           </div>
 
                           </div>
−
                           <div  class="col-md-3" > <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/d/d4/T--HUST-China--2018-model-new-r005.png">
+
                           <div  class="col-md-3" > <img class="img-responsive" style="height:60px" src="https://static.igem.org/mediawiki/2018/d/d4/T--HUST-China--2018-model-new-r005.png">
 
                           </div>
 
                           </div>
 
                           <div class="col-md-12">           
 
                           <div class="col-md-12">           
 
                               <p>is from another reference (Xiong et al. 2012)<sup>[2]</sup>. The parameter  <img style="vertical-align:middle;height:30px" src="https://static.igem.org/mediawiki/2018/0/0c/T--HUST-China--2018-model-new-c006.png"> the decline of the growth rate caused by gene editing. This parameter is introduced to make the growth model of wild <I><i>Rhodopseudomonas palustris</i></I> fit to the growth of edited ones in the reference ( Henrike et al. 2012 )<sup>[3]</sup>.</p>
 
                               <p>is from another reference (Xiong et al. 2012)<sup>[2]</sup>. The parameter  <img style="vertical-align:middle;height:30px" src="https://static.igem.org/mediawiki/2018/0/0c/T--HUST-China--2018-model-new-c006.png"> the decline of the growth rate caused by gene editing. This parameter is introduced to make the growth model of wild <I><i>Rhodopseudomonas palustris</i></I> fit to the growth of edited ones in the reference ( Henrike et al. 2012 )<sup>[3]</sup>.</p>
 
                           </div>
 
                           </div>
−
                           <div  class="col-md-6 > <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/1/19/T--HUST-China--2018-model-new-r006.png">
+
                           <div  class="col-md-6"> <img class="img-responsive" style="height:70px" src="https://static.igem.org/mediawiki/2018/1/19/T--HUST-China--2018-model-new-r006.png">
 
                           </div>
 
                           </div>
 
                           <div class="col-md-12">           
 
                           <div class="col-md-12">           
 
                               <p>This stands for the CO<sub>2</sub> consumed by each unit of <i>Rhodopseudomonas palustris</i>. <img style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/d/d7/T--HUST-China--2018-model-new-r007.png"> is  used for growth, <img style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/6/64/T--HUST-China--2018-model-new-r008.png"> is used for lactate producing, and  <img style="vertical-align:middle;height:30px" src="https://static.igem.org/mediawiki/2018/d/d3/T--HUST-China--2018-model-new-r009.png"> used for sustaining its life.</p>
 
                               <p>This stands for the CO<sub>2</sub> consumed by each unit of <i>Rhodopseudomonas palustris</i>. <img style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/d/d7/T--HUST-China--2018-model-new-r007.png"> is  used for growth, <img style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/6/64/T--HUST-China--2018-model-new-r008.png"> is used for lactate producing, and  <img style="vertical-align:middle;height:30px" src="https://static.igem.org/mediawiki/2018/d/d3/T--HUST-China--2018-model-new-r009.png"> used for sustaining its life.</p>
 
                           </div>
 
                           </div>
−
                           <div  class="col-md-4" > <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/c/c7/T--HUST-China--2018-model-new-r010.png">
+
                           <div  class="col-md-4" > <img class="img-responsive" style="height:60px" src="https://static.igem.org/mediawiki/2018/c/c7/T--HUST-China--2018-model-new-r010.png">
 
                           </div>
 
                           </div>
 
                           <div class="col-md-12">           
 
                           <div class="col-md-12">           
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                           </div>
 
                           </div>
 
                          
 
                          
 +
 +
                          <div class="row">
 +
            <div class="col-md-12 info-blocks">
 +
              <div class="col-md-10  col-md-offset-1">
 +
                      <table class="table table-bordered table-hover" style="text-align: center;">
 +
   
 +
                            <tr>
 +
                              <th>Parameter</th>
 +
                              <th>Description</th>
 +
                              <th>Value</th>
 +
                              <th>Unit</th>
 +
                              <th>Source</th>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>q<sub>Lac,Rps</sub></td>
 +
                              <td>Lactate produced by each unit of Rps per hour</td>
 +
                                <td>6.784×10<sup>-4</sup></td>
 +
                                <td>h<sup>-1</sup></td>
 +
                              <td>In this experiment, due to genetic modification, no correlation coefficient was found,so we run the simulation in a large range of parameters for many times and use the best data.</td>
 +
                            </tr>
 +
                          <tr>
 +
                              <td>μ<sub>max,Rps</sub></td>
 +
                              <td>Maximum growth rate of Rps per hour</td>
 +
                                <td>0.332</td>
 +
                                <td>h<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[4]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sub>CO<sub>2</sub>,Rps</sub></td>
 +
                              <td>Yield coefficient of Rps</td>
 +
                                <td>4.124×10<sup>-6</sup></td>
 +
                                <td>g⋅L<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[5]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>I<sub>k,Rps</sub></td>
 +
                              <td>The light intensity constant of Rps while the light intensity is lower than 8000Lux</td>
 +
                                <td>8.892×10<sup>2</sup></td>
 +
                                <td>Lux</td>
 +
                              <td>Fitting from reference <sup>[6]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>Y<sub>CO<sub>2</sub>,Rps</sub></td>
 +
                              <td>CO<sub>2</sub> producing coefficient related to lactate consuming.</td>
 +
                                <td>2.340×10<sup>2</sup></td>
 +
                                <td>1</sup></td>
 +
                              <td>Fitting from reference <sup>[5]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>q<sub>Lac,Rps</sub></td>
 +
                              <td>Lactate produced by each unit of Rps.</td>
 +
                                <td>6.784×10<sup>-4</sup></td>
 +
                                <td>h<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[7]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>Y<sub>CO<sub>2</sub>,Lac</sub></td>
 +
                              <td>Yield coefficient of Rps related to CO<sub>2</sub> consuming, showing the CO<sub>2</sub> consumed for growth</td>
 +
                                <td>0.6921</td>
 +
                                <td>1</td>
 +
                              <td>Calculated by the  stoichiometric in the chemical equation of lactate producing, and relative molecular mass of CO<sub>2</sub> and lactate</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>m<sub>CO<sub>2</sub>,Rps</sub></td>
 +
                              <td>The sustain coefficient of Rps. Stand for the CO<sub>2</sub> consuming by the unit dry weight of alive Rps.</td>
 +
                                <td>0.1524</td>
 +
                                <td>h<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[5]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sub>decline</sub></td>
 +
                              <td>The decline caused by the gene editing.</td>
 +
                                <td>0.4209</td>
 +
                                <td>1</td>
 +
                              <td>Fitting from reference <sup>[6]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>c<sub>max,Rps</sub></td>
 +
                              <td>The max concertation of Rps in the solution.</td>
 +
                                <td>0.5211</td>
 +
                                <td>g⋅L<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[7]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sub>s,met</sub></td>
 +
                              <td>the inhibition coefficient  of CO<sub>2</sub> to the metabolism of Rhodopseudomonas palustris </td>
 +
                                <td>0.122</td>
 +
                                <td>g⋅L<sup>-1</sup></td>
 +
                              <td>Fitting from reference <sup>[5]</sup></td>
 +
                            </tr>
 +
                           
 +
                         
 +
                      </table>
 +
                  </div>
 +
                </div>
 +
              </div>
 
                   </div>
 
                   </div>
 
               </div>
 
               </div>
Line 318: Line 521:
 
           <div class="row">
 
           <div class="row">
 
             <div class="col-md-12 info-blocks">
 
             <div class="col-md-12 info-blocks">
−
                 <i class="icon-info-blocks material-icons hidden-xs"><img class="img-responsive" src="https://static.igem.org/mediawiki/2018/0/0c/T--HUST-China--2018-xiwa01.png"></i>
+
                 <i class="icon-info-blocks material-icons hidden-xs"><img class="img-responsive" style="height:60" src="https://static.igem.org/mediawiki/2018/0/0c/T--HUST-China--2018-xiwa01.png"></i>
 
                       <div class="info-blocks-in" style="background-color: #ffffff; border: 1px solid #eeeeee;border-radius:5px;">
 
                       <div class="info-blocks-in" style="background-color: #ffffff; border: 1px solid #eeeeee;border-radius:5px;">
 
                         <h3><b>3. <i>Shewanella</b></i></h3>
 
                         <h3><b>3. <i>Shewanella</b></i></h3>
Line 324: Line 527:
 
                         <p>First, we need to simulate biomass function. Our biomass function is based on monod equation:</p>
 
                         <p>First, we need to simulate biomass function. Our biomass function is based on monod equation:</p>
 
                         <div class="col-md-5" style="text-align: center;">
 
                         <div class="col-md-5" style="text-align: center;">
−
                             <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/c/c9/T--HUST-China--2018-model-new-s001.png">
+
                             <img class="img-responsive" style="height:30px" src="https://static.igem.org/mediawiki/2018/c/c9/T--HUST-China--2018-model-new-s001.png">
 
                         </div>
 
                         </div>
 
                         <div class="col-md-12">
 
                         <div class="col-md-12">
Line 331: Line 534:
 
                       </div>       
 
                       </div>       
 
                             <div class="col-md-8">
 
                             <div class="col-md-8">
−
                             <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/6/69/T--HUST-China--2018-model-new-s002.png">
+
                             <img class="img-responsive" style="height:60px" src="https://static.igem.org/mediawiki/2018/6/69/T--HUST-China--2018-model-new-s002.png">
 
                         </div>
 
                         </div>
 
                         <div class="col-md-12">
 
                         <div class="col-md-12">
Line 338: Line 541:
 
                                 <p>After this, we realized that a factor about oxygen competition is needed to add in the function. So we import a parameter to solve this problem, the function is modified to:</p>
 
                                 <p>After this, we realized that a factor about oxygen competition is needed to add in the function. So we import a parameter to solve this problem, the function is modified to:</p>
 
                                 <div class="col-md-8" style="text-align: center;">
 
                                 <div class="col-md-8" style="text-align: center;">
−
                             <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/2/2f/T--HUST-China--2018-model-new-s003.png">
+
                             <img class="img-responsive" style="height:60px" src="https://static.igem.org/mediawiki/2018/2/2f/T--HUST-China--2018-model-new-s003.png">
 
                         </div>
 
                         </div>
 
                         <div class="col-md-8">
 
                         <div class="col-md-8">
−
                             <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/8/85/T--HUST-China--2018-model-new-s004.png">
+
                             <img class="img-responsive" style="height:60px" src="https://static.igem.org/mediawiki/2018/8/85/T--HUST-China--2018-model-new-s004.png">
 
                         </div>
 
                         </div>
 
                               <div class="col-md-12">
 
                               <div class="col-md-12">
 
                                
 
                                
 
                                 <p>Taking the efficiency ratio of aerobic and anaerobic respiration (19:1) into consideration, we calculated two parameters:</p>
 
                                 <p>Taking the efficiency ratio of aerobic and anaerobic respiration (19:1) into consideration, we calculated two parameters:</p>
−
<img class="img-responsive" src="https://static.igem.org/mediawiki/2018/6/6f/T--HUST-China--2018-model-new-s015.png">
+
<img class="img-responsive" style="height:90px" src="https://static.igem.org/mediawiki/2018/6/6f/T--HUST-China--2018-model-new-s015.png">
 
                                 <p>The two parameters are used in our electricity production simulation: </p>
 
                                 <p>The two parameters are used in our electricity production simulation: </p>
 
                                 <p>The basic function is the famous Nernst equation: </p>
 
                                 <p>The basic function is the famous Nernst equation: </p>
−
<img class="img-responsive" src="https://static.igem.org/mediawiki/2018/0/0c/T--HUST-China--2018-model-new-s017.png">
+
<img class="img-responsive" style="height:70px" src="https://static.igem.org/mediawiki/2018/0/0c/T--HUST-China--2018-model-new-s017.png">
 
                                 <p>In this function Ox is oxidized type, and Red is reduced type.</p>
 
                                 <p>In this function Ox is oxidized type, and Red is reduced type.</p>
 
                                 <p>The Nernst equation is very clear and easy to use, but we have to add a <i>Shewanella</i> biomass factor to show the macroscopic electricity production. The lactic consuming value is closely related to the concentration of <i>Shewanella</i>. In addition, after the metabolic analysis of lactic in <i>Shewanella</i>, we promoted the function by modifying (or simplifying) the <img style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/7/78/T--HUST-China--2018-model-new-s005.png">  section. As a result, the electricity production function is:</p>
 
                                 <p>The Nernst equation is very clear and easy to use, but we have to add a <i>Shewanella</i> biomass factor to show the macroscopic electricity production. The lactic consuming value is closely related to the concentration of <i>Shewanella</i>. In addition, after the metabolic analysis of lactic in <i>Shewanella</i>, we promoted the function by modifying (or simplifying) the <img style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/7/78/T--HUST-China--2018-model-new-s005.png">  section. As a result, the electricity production function is:</p>
 
                         </div>
 
                         </div>
 
                                 <div class="col-md-8">
 
                                 <div class="col-md-8">
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                             <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/e/ec/T--HUST-China--2018-model-new-s006.png">
+
                             <img class="img-responsive" style="height:80px" src="https://static.igem.org/mediawiki/2018/e/ec/T--HUST-China--2018-model-new-s006.png">
 
                         </div>
 
                         </div>
 
                               <div class="col-md-12">
 
                               <div class="col-md-12">
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<p>In this function,<img style="vertical-align:middle" src="https://static.igem.org/mediawiki/2018/a/a5/T--HUST-China--2018-model-new-s007.png"></p>
+
<p>In this function,<img style="vertical-align:middle;height:50px" src="https://static.igem.org/mediawiki/2018/a/a5/T--HUST-China--2018-model-new-s007.png"></p>
 
<p>The last work in <i>Shewanella</i> modeling is the lactic consuming simulation: </p>
 
<p>The last work in <i>Shewanella</i> modeling is the lactic consuming simulation: </p>
 
<p>The concentration of lactate dominates largely on electricity production. Similarly, with the inspiration of Monod equation, we notice that the concentration of lactate acid and <i>Shewanella</i> itself is in a positive correlation to lactic consuming rate. So we have summarized the lactic consuming equation:</p>
 
<p>The concentration of lactate dominates largely on electricity production. Similarly, with the inspiration of Monod equation, we notice that the concentration of lactate acid and <i>Shewanella</i> itself is in a positive correlation to lactic consuming rate. So we have summarized the lactic consuming equation:</p>
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<img class="img-responsive" src="https://static.igem.org/mediawiki/2018/6/67/T--HUST-China--2018-model-new-s008.png">
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<img class="img-responsive" style="height:60px" src="https://static.igem.org/mediawiki/2018/6/67/T--HUST-China--2018-model-new-s008.png">
 
                             </div>       
 
                             </div>       
  
 +
              </div>
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              <div class="col-md-10  col-md-offset-1">
 +
                      <table class="table table-bordered table-hover" style="text-align: center;">
 +
   
 +
                            <tr>
 +
                              <th>Parameter</th>
 +
                              <th>Description</th>
 +
                              <th>Value</th>
 +
                              <th>Unit</th>
 +
                              <th>Source</th>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>μ<sub>Shewa,max</sub></td>
 +
                              <td>maximum specific growth rate of biomass</td>
 +
                                <td>1.192×10<sup>-1</sup></td>
 +
                                <td>g/(L·h)</td>
 +
                              <td>Fitting from reference <sup>[8]</sup></td>
 +
                            </tr>
 +
                          <tr>
 +
                              <td>c<sub>Shewa,max</sub></td>
 +
                              <td>maximum biomass (dry weight) of Shewanella <sup>[8]</sup>  ——Li F et al. 2018, 7</td>
 +
                                <td>1.531×10<sup>-3</sup></td>
 +
                                <td>g/L</td>
 +
                              <td>Fitting from reference <sup>[4]</sup></td>
 +
                            </tr>
 +
                           
 +
                            <tr>
 +
                              <td>k<sub>Shewa,O<sub>2</sub></sub> </td>
 +
                              <td>a parameter influencing the relationship between substances and biomass</td>
 +
                                <td>1.332×10<sup>-5</sup></td>
 +
                                <td>g/L</td>
 +
                              <td>Fitting from reference <sup>[9]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sub>Shewa,Lac</sub></td>
 +
                              <td>a parameter influencing the relationship between substances and biomass</td>
 +
                                <td>4.869×10<sup>-1</sup></td>
 +
                                <td>1</sup></td>
 +
                              <td>Fitting from reference <sup>[5]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sub>Shewa,1</sub></</td>
 +
                              <td>correction term regarding the rate of consumption of lactate</td>
 +
                                <td>7.325×10<sup>1</sup></td>
 +
                                <td>-</td>
 +
                              <td>Fitting from reference <sup>[9]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sup>'</sup><sub>Shewa,2</sub></td>
 +
                              <td>simplified coefficient about the Nernst equation</td>
 +
                                <td>1.235×10<sup>-1</sup></td>
 +
                                <td>-</td>
 +
                              <td>Fitting from reference <sup>[9]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>T</td>
 +
                              <td>current temperature</td>
 +
                                <td>298</td>
 +
                                <td>K</td>
 +
                              <td>Experiment data</td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>v<sub>Shewa,max</sub></td>
 +
                              <td>maximum lactate consumption rate per unit biomass</td>
 +
                                <td>7.012×10<sup>-1</sup></td>
 +
                                <td>g/(L·h)</td>
 +
                              <td>Fitting from reference <sup>[9]</sup></td>
 +
                            </tr>
 +
                            <tr>
 +
                              <td>k<sub>Shewa,3</sub></td>
 +
                              <td>constant value about lactate consuming</td>
 +
                                <td>3.056×10<sup>-1</sup></td>
 +
                                <td>g/L</td>
 +
                              <td>Fitting from reference <sup>[9]</sup></td>
 +
                            </tr>
 +
                           
 +
                      </table>
 +
                  </div>
 +
                </div>
 
               </div>
 
               </div>
 
             </div>
 
             </div>
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                     <h3><strong>Part3: <span class="red-content">Whole design</span></strong></h3>
+
                     <h3><strong>Part3: <span class="red-content">Result</span></strong></h3>
 
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                        <h3>Design of MFC</h3>
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                         <p>We have designed a bipolar chamber MFC this year. Proton exchange membrane divided it into anode chamber and cathode chamber. Anode chamber containing S.oneidensis, nutrient substance(LB、lactate ) or other electrical producing microbes were sealed to prevent the entry of external oxygen. Considering safety and oxidation-reduction potential, we put ferric chloride solution in cathode chamber so that S.oneidensis can transfer electrons outside of their membranes by electron transport chain. Then electrons will reduce ferric ion into ferrous through carbon cloth and produce electricity.We recorded open circuit voltage curve and load voltage curve of MFCs in each different systems. Also, we have measured the biomass of each system in order to ensure whether the improved electricity could be attributed to more attached <i>Shewanella</i> cells on the anodes or the higher electroactivity of single cell.[11] </p>
+
                         <p>
−
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                          The voltage output of the three systems (Rhodopseudomonas palustris- Shewanella, Synechocystis - Shewanella and Shewanella only) are shown in the following figure:
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                            <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/8/85/T--HUST-China--2018-description-picture12.png.png">
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                        <img class="img-responsive" src="https://static.igem.org/mediawiki/2018/archive/9/92/20181017203446%21T--HUST-China--2018-psb-pic10086.png">
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                        <p>
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                              <p class="red-content"><strong>Co-culture</strong></p>
+
                          The figure shows that because Rhodopseudomonas palustris  and Synechocystis can produce lactate, these two systems can produce electricity more efficiently and steadily, which demonstrates the value and feasibility of our project. In the beginning of the Synechocystis-Shewanella system, oxygen produced by Synechocystis inhibited the electricity production of Shewanella, so this system doesn’t have peak value.
−
                                <p>Obviously, the ecological relationship between microorganisms is very complex. There is not only the competition between them for the nutrient, but also the regulation of metabolites among them including induction, transgenosis and synergistic metabolism. Besides, it has been found that the co-culture of microorganisms can improve the electric efficiency of Microbial Fuel Cell under certain conditions.  </p>
+
                        </p>
−
                                <p>Metabolites exchange is a common relationship in co-culturing. Therefore, we have designed a clear microbial metabolic pathway to achieve the conversion from light to electricity as well as used more potential symbiotic relationships between the flora to help improve the electricity production efficiency of MFC.</p>
+
                        After molecular engineering, we get experiment data. It can fit our model result well. This demonstrates our model is right, so we can design a software based on model to tell us a better application experiment protocol which can get better result.
−
                                  <p>By consulting literature, we found two kinds of microorganisms——Cyanobacteria and <i>Rhodopseudomonas palustris</i>, both of which can utilize light energy and provide lactate to S.oneidensis after doing molecular construction.  </p>
+
                        <p>
−
                                    <p>In order to provide a basic growth environment, we mix the culture medium of different strains.（Please refer to our protocol section for the composition of the mediums.）</p>
+
                         
−
                               
+
                        </p>
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                                <p class="red-content"><strong><i>Synechocystis</i> PCC6803</strong></p>
+
−
                                <p>Lactate produced by <i>Synechocystis</i> PCC6803 can be used as the optimal carbon source for <i>Shewanella</i>. At the same time, acetate produced by <i>Shewanella</i> can be used as the organic carbon source of <i>Synechocystis</i> PCC6803 to increase the lactate production. And the metabolite exchange of <i>Synechocystis</i> PCC6803 and <i>Shewanella</i> is the basis for our photoautotrophic MFC.[12]. </p>
+
−
                                  <p class="red-content"><strong><i>Rhodopseudomonas palustris</i></strong></p>
+
−
                                    <p>We attempted to engineer <i>Rhodopseudomonas palustris</i> by synthetic biology to achieve the same or a better function of Synechococcus elongatus.</p>
+
−
                                    <p>In the preliminary experiment, we found that there may be more potential interactions in the co-culture of <i>Rhodopseudomonas palustris</i> and <i>Shewanella</i>, which can greatly improve the coulombic efficiency of our MFC (please refer our results section for more detials). This is an unexpected surprise for us, which improve to our confidence in the success of the project.</p>
+
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                    <h3><strong>Part4: <span class="red-content">Disscussion</span></strong></h3>
 +
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 +
                        <p>
 +
                        Based the insight we have gained from modeling, we find that concentration of carbon dioxide is the major limitation of Synechocystis-Shewanella system. Because low concentration of carbon dioxide will limit photosynthesis of Synechocystis, producing less lactate. Finally it leads to low electricity production. (Rhodopseudomonas can utilize the metabolic waste of Shewanella, so it need less carbon dioxide) Therefore, we add carbon dioxide to system and find that it can improve the electricity production. However, if we add too much carbon dioxide, the production will decrease, because excess carbon dioxide will inhibit the photosynthesis. (David et al. 2015)[1]1Finally, we find that the system has the highest voltage output when we add carbon dioxide 2.103*〖10〗^(-4)  g⁄*h.
 +
                        </p>
 +
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                 <h4><strong>Reference </strong></h4>
 
                 <h4><strong>Reference </strong></h4>
−
                <p style="font-size:12px;">[1]Henrike Niederholtmeyer, Bernd T. Wolfstädter, David F. Savage, Pamela A. Silver, Jeffrey C. Way. Engineering Cyanobacteria to Synthesize and Export Hydrophilic Products. Applied and Environmental Microbiology. 2010, 76(11): 3462-3466.</p>
+
                  <p style="font-size:12px;">[1]David Kuan, Sheldon Duff, Dusko Posarac, et al. Growth Optimization of Synechococcus elongatus PCC7942 In Lab Flasks and a 2-D Photobioreactor[J]. Can. J. Chem. Eng., 2015, 9999: 1–8</p>
−
                <p style="font-size:12px;"><span>[2] 《沼泽红假单胞菌的研究进展及其应用》王跃先、刘德海</span></p>
+
                  <p style="font-size:12px;"><span>[2]XIONG Wen, QIAN Xin, YE Rui, et al. Eco-model based analysis of Lake Taihu cyanobacteria growth factors[J]. Lake Science, 2012, 24( 5) : 698-704</span></p>
−
                <p style="font-size:12px;"><span>[3] 周茂洪 赵肖为 吴雪昌《光合细菌沼泽红假单胞菌同化磷能力的研究》 《科技通报》2002年 第2期 142-146页</span></p>
+
                  <p style="font-size:12px;"><span>[3]Henrike Niederholtmeyer, Bernd T. Wolfstädter,  David F. Savage, et al. Engineering Cyanobacteria To Synthesize and Export Hydrophilic Products[J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, June 2010, 76(11): 3462–3466</span></p>
−
                <p style="font-size:12px;"><span>[4] KEGG, https://www.genome.jp/kegg/pathway.html</span></p>
+
                  <p style="font-size:12px;"><span>[4]Song Zhiyong, Qu Yuanyuan, Zhou Jiti, et al. Identification of wild plasmids in Rhodopseudomonas palustris by reverse PCR [J]. Journal of Dalian University of Technology, 2009,01: 33-37</span></p>
−
                <p style="font-size:12px; "><span>[5] Cloning and sequence analysis of the gene encoding Lactococcus lactis malolactic enzyme: relationships with malic enzymes FEMS Microbiol Lett. 1994 Feb 1;116(1):79-86 </span></p>
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                  <p style="font-size:12px; "><span>[5] Cuihong Du.Cloning and Expression of RubisCO Gene from Rhodopseudomonas palustris and Its Characteristics of Fixed Carbon Dioxide[D].Dalian University of Technology,2003. DOI:10.7666/d.y665688.</span></p>
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                <p style="font-size:12px; "><span>[6] Fine tuning the transcription of ldhA for d-lactate production August 2012, Volume 39, Issue 8, pp 1209–1217 </span></p>
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                <p style="font-size:12px; "><span>[8] Enhancement of Hydrogen Production and Carbon Fixation in Purple Nonsulfur Bacterium Bacterium by Synthetic Biology Shou-Chen Lo</span></p>
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                <i>Shewanella</i> oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization PNAS February 24, 2009 106 (8) 2874-2879  </span></p>
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                <p style="font-size:12px;"><span>[12]Varman A. M., Yu Y., You L. & Tang Y. J. Photoautotrophic production of d-lactate in an engineered cyanobacterium. Microb. Cell Fact. 12, 117 (2013). </span></p>
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