Difference between revisions of "Team:HUST-China/Sort of three genes"

 
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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/InterLab">Interlab</a></li>
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                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Improve">Improve</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>
 
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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>
 
                               <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/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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                           <a href="#" data-toggle="dropdown" class="dropdown-toggle waves-effect waves-dark">TEAM<b class="caret"></b></a>
 
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                 <div class="about-logo">
 
                 <div class="about-logo">
 
                   <h3><strong>1. <span class="red-content">Overview</span></strong></h3>
 
                   <h3><strong>1. <span class="red-content">Overview</span></strong></h3>
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                   <p>Safe strains and safe gene products were selected to complete our project design. The products of the genes transferred into the microorganisms are all determined and do not cause any known diseases to humans, animals and plants. Any microorganisms involved in our project is encapsulate in electricity generation device. So far, the devise can recharge the phone, and in the future, electricity generation based on microbial co-culture may become a new choice of electricity production.</p>
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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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<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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                 <div class="about-logo">
 
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                   <h3><strong>2. <span class="red-content">Function</span></strong></h3>
 
                   <h3><strong>2. <span class="red-content">Function</span></strong></h3>
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                  <div class="container">
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                   <img src="https://static.igem.org/mediawiki/2018/c/cf/T--HUST-China--2018-sort-pic1.png" class="img-responsive" >
 
                   <img src="https://static.igem.org/mediawiki/2018/c/cf/T--HUST-China--2018-sort-pic1.png" class="img-responsive" >
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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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                  <h3><strong>3. <span class="red-content">Parameters</span></strong></h3>
 
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                  <p>There are not enough studies 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 see which is most important in this parameter situation.
 
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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>Ks<sub>3M</sub></td>
 
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                              <td></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></td>
 
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                              <td></td>
 
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                              <td>V<sub>max4</sub></td>
 
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                              <td></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 form 〖10〗^(-5) to 〖10〗^5，and run the simulation. At the beginning, we simply sum the concentration of Lactate outside. But it’s not fair for every parameter situations 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:</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>Result shows that in more than 10，000 parameter conditions, mles is the most important gene. So we sort three genes follow their final scores: mles, lldp, ldhA.</p>
 
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                  <h3><strong>1. <span class="red-content">Overview</span></strong></h3>
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                  <p>Safe strains and safe gene products were selected to complete our project design. The products of the genes transferred into the microorganisms are all determined and do not cause any known diseases to humans, animals and plants. Any microorganisms involved in our project is encapsulate in electricity generation device. So far, the devise can recharge the phone, and in the future, electricity generation based on microbial co-culture may become a new choice of electricity production.</p>
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                  <h3><strong>2. <span class="red-content">Function</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>
 
                   <p>(We skip some reactions in tricarboxylic acid cycle, and let Isocitrate come to Malate in one reaction.)</p>
 
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                   <h3><strong>3. <span class="red-content">Parameters</span></strong></h3>
 
                   <h3><strong>3. <span class="red-content">Parameters</span></strong></h3>
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                   <p>There are not enough studies 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 see which is most important in this parameter situation.  
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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">Result</span></strong></h3>
 
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                   <p>We generate each group ’s value form 〖10〗^(-5) to 〖10〗^5，and run the simulation. At the beginning, we simply sum the concentration of Lactate outside. But it’s not fair for every parameter situations 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:</p>
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                   <p>We generate each group ’s value from 10<sup>-5</sup> to 10<sup>5</sup>，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>
 
                       <img src="https://static.igem.org/mediawiki/2018/archive/c/cf/20181014074349%21T--HUST-China--2018-sort-pic1.png" class="img-responsive" ></div>
 
                       <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>
 
                       <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/thumb/b/b4/T--HUST-China--2018-model-new-sort1.png/1200px-T--HUST-China--2018-model-new-sort1.png" >
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                       <p>Result shows that in more than 10，000 parameter conditions, mles is the most important gene. So we sort three genes follow their final scores: mles, lldp, ldhA.</p>
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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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Sort of three genes

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