Difference between revisions of "Team:HUST-China/Modeling overview"

 
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Results">Results</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Results">Results</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/wetlab/protocols">Protocols</a></li>
 
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Notebook">Notebook</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Notebook">Notebook</a></li>
 
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                           <ul class="dropdown-menu">
 
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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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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Comparison between PSB">Comparison between PSB</a></li>
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/model_of_systems">Model of systems</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Sort of three genes">Sort of three genes</a></li>
 
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Intelligent device software">Intelligent device software</a></li>  
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Software">Software</a></li>  
 
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Parts Overview">Parts Overview</a></li>
 
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Basic part">Basic part</a></li>
 
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Composite part">Composite part</a></li>
 
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Part collection">Part collection</a></li>  
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Part collection">Part collection</a></li>  
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Human Practices">Human Practices</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Human Practices">Human Practices</a></li>
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Education Engagement">Education&Engagement</a></li>  
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Education_Engagement">Education&Engagement</a></li>  
 
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                           <a href="#" data-toggle="dropdown" class="dropdown-toggle waves-effect waves-dark">TEAM<b class="caret"></b></a>
 
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Team Members">Team Members</a></li>
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                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Team">Team Members</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Collaborations">Collaborations</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Collaborations">Collaborations</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Attributions">Attributions</a></li>
 
                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Attributions">Attributions</a></li>
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         <h2 class="pageTitle">Sort of three genes</h2>
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         <h2 class="pageTitle">Modeling overview
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                   <h3><strong>1. <span class="red-content">Overview</span></strong></h3>
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                  <p>In Rhodopseudomonas, the sequence of genes in plasmid influences them expression ability. (Shou-Chen.2012) We have three genes to transfer. So we should find out which gene is the most important, and we sort three genes by their importance.</p>
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                   <h3><strong>1. <span class="red-content">Overview </span></strong></h3>
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<p>But then we meet a problem that there are not enough references about Rhodopseudomonas for us to obtain enough parameters for our simulation, so we run the simulation in a large range of parameters for many times and use the statistical result to decide how to sort the three genes
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                <p>
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This year, our job can be mainly divided into three parts: Comparison of <i>Rhodopseudomonas palustris</i> and <i>Synechocystis</i>, sort of three genes pathway in <i>Rhodopseudomonas palustris</i>, and intelligent device software.
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                   <h3><strong>2. <span class="red-content">Function</span></strong></h3>
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<a style=" text-decoration: none; color: black;" >
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                   <h3><strong>2. <span class="red-content">Model of systems</span></strong></h3>
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                  <p>(We skip some reactions in tricarboxylic acid cycle, and let Isocitrate come to Malate in one reaction.)</p>
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                <p>
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In the past, people use <i>Synechocystis</i> to provide energy for electricity producing bacteria. Because it’s efficient and easier to control. But <i>Shewanella</i> species are heterotrophic facultative anaerobes, and produce electricity only in anaerobic environment (Justin et al.2009). So we think <i>Rhodopseudomonas palustris</i> may be better because its cycle photophosphorylation doesn’t produce oxygen. But <i>Rhodopseudomonas palustris</i> is not as efficient as <i>Synechocystis</i>. So we use computer simulation to find which is better.
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                  <h3><strong>3. <span class="red-content">Sort of three genes</span></strong></h3>
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                <p>
 +
In <i>Rhodopseudomonas palustris</i>, the sequence of genes in plasmid influences their expression ability. (Shou-Chen.2012) We have three genes to transfer. So we should find out which gene is  the most important, and we sort three genes by their importance.
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</p>
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</a>
 
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                   <h3><strong>3. <span class="red-content">Parameters</span></strong></h3>
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<a style=" text-decoration: none; color: black;">
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                  <p>There are not enough references for us to get exact parameters. So we assort parameters into several groups and change one group’s value each time. At the same time, we change the expression abilities of three genes to find which is the most important in this parameter situation.
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                   <h3><strong>4. <span class="red-content">Intelligent device software</span></strong></h3>
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                  <!--表格-->
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Using a new multi-culture bacteria system means we should use a new experiment strategy. So we build a software to capture the situation of our system and learn to decide what to do to interact our system in order to get a better electricity output.
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                              <th>Income parameters</th>
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                              <th>Metabolism parameters</th>
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                              <th>Cross membrane parameters </th>
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                              <th>Ks parameters</th>
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                              <th>Gene expression</th>
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                              <td>g<sub>Pyruvate</sub></td>
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                              <td>k<sub>2LdhA</sub></td>
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                              <td>V<sub>max2</sub></td>
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                              <td>K<sub>s1</sub></td>
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                              <td>K<sub>s2</sub></td>
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                              <td>g<sub>Acetyl-CoA</sub></td>
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                              <td>k<sub>1LdhA</sub></td>
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                              <td></td>
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                              <td>Ks<sub>3A</sub></td>
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                              <td>[LdhA]</td>
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                              <td></td>
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                                <td>V<sub>max1</sub></td>
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                              <td></td>
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                              <td>Ks<sub>3M</sub></td>
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                              <td>Ks<sub>5</sub></td>
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                              <td>V<sub>max3</sub></td>
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                              <td></td>
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                              <td>K<sub>s4</sub></td>
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                              <td>V<sub>max4</sub></td>
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                              <td></td>
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                              <td>V<sub>max5</sub></td>
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                              <td></td>
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                  <h3><strong>4. <span class="red-content">Result</span></strong></h3>
 
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                  <p>We generate each group ’s value from 〖10〗^(-5) to 〖10〗^5，and run the simulation. At the beginning, we simply sum the concentration of Lactate outside. But it is not fair for each parameter situation because in some cases the value of final result is much lower than others. So we use the SOFTMAX function to turn the concentration result into scores from 0 to 1. The function is shown below:</p>
 
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                      <img src="https://static.igem.org/mediawiki/2018/archive/c/cf/20181014074349%21T--HUST-China--2018-sort-pic1.png" class="img-responsive" ></div>
 
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                      <p>If the gene expression parameter is lower than 1，we take the negative value of score. Then we sum all scores together, and get the final result.</p>
 
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                        <img src="https://static.igem.org/mediawiki/2018/archive/c/cf/20181014074548%21T--HUST-China--2018-sort-pic1.png" class="img-responsive" >
 
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                      <p>(the curve: score(x,y) means the sum of the first x parameter conditions’ scores when the model runs for y units of times)</p>
 
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                      <p>The result shows that in more than 10，000 parameter conditions, mles is the most important gene. So we sort three genes by their final scores: mles, lldp, ldhA.</p>
 
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                  <h3><strong>5. <span class="red-content">Reference</span></strong></h3>
 
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                  <p style="font-size:16px; line-height: 25px;letter-spacing:1px; text-indent:0px;">
 
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<span>[1] 1.Shou-Chen Lo. 2012. Enhancement of Hydrogen Production and Carbon Fixation in Purple Nonsulfur Bacterium by Synthetic Biology. Ph.D. Dissertation</span></p>
 
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            <h4><strong>Reference </strong></h4>
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           <p>
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<span>[1] Justin L. Burns, Thomas J. DiChristina. 2009. Anaerobic Respiration of Elemental Sulfur and Thiosulfate by Shewanella oneidensis MR-1 Requires psrA, a Homolog of the phsA Gene of Salmonella enterica Serovar Typhimurium LT2. American Society for Microbiology Journals</span></p>
 +
          <p>
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<span>[2] 2.Shou-Chen Lo. 2012. Enhancement of Hydrogen Production and Carbon Fixation in Purple Nonsulfur Bacterium by Synthetic Biology. Ph.D. Dissertation</span></p>
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<i>Rhodopseudomonas palustris</i>

Latest revision as of 23:52, 17 October 2018

HillSide Multi purpose HTML5 Template

Modeling overview

Reference

[1] Justin L. Burns, Thomas J. DiChristina. 2009. Anaerobic Respiration of Elemental Sulfur and Thiosulfate by Shewanella oneidensis MR-1 Requires psrA, a Homolog of the phsA Gene of Salmonella enterica Serovar Typhimurium LT2. American Society for Microbiology Journals

[2] 2.Shou-Chen Lo. 2012. Enhancement of Hydrogen Production and Carbon Fixation in Purple Nonsulfur Bacterium by Synthetic Biology. Ph.D. Dissertation

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Rhodopseudomonas palustris