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

Latest revision as of 23:52, 17 October 2018

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Modeling overview

1. Overview

This year, our job can be mainly divided into three parts: Comparison of Rhodopseudomonas palustris and Synechocystis, sort of three genes pathway in Rhodopseudomonas palustris, and intelligent device software.

2. Model of systems

In the past, people use Synechocystis to provide energy for electricity producing bacteria. Because it’s efficient and easier to control. But Shewanella species are heterotrophic facultative anaerobes, and produce electricity only in anaerobic environment (Justin et al.2009). So we think Rhodopseudomonas palustris may be better because its cycle photophosphorylation doesn’t produce oxygen. But Rhodopseudomonas palustris is not as efficient as Synechocystis. So we use computer simulation to find which is better.

3. Sort of three genes

In Rhodopseudomonas palustris, 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.

4. Intelligent device software

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. .

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

Rhodopseudomonas palustris

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                                <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/wetlab/protocols">Protocols</a></li>
                                <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/InterLab">Interlab</a></li>
-                              <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Improve">Improve</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">
                                <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Modeling overview">Modeling overview</a></li>
-                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Comparison between PSB">Comparison between PSB</a></li>
+                               <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/Intelligent device software">Intelligent device software</a></li>
+                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Software">Software</a></li>
                            </ul>
                        </li>
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                            <ul class="dropdown-menu">
                                <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Parts Overview">Parts Overview</a></li>
-                              <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>
                                <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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                            <ul class="dropdown-menu">
                                <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/Education&Engagement">Education&Engagement</a></li>
+                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Education_Engagement">Education&Engagement</a></li>
                            </ul>
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                            <a href="#" data-toggle="dropdown" class="dropdown-toggle waves-effect waves-dark">TEAM<b class="caret"></b></a>
                            <ul class="dropdown-menu">
-                               <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Team Members">Team Members</a></li>
+                               <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/Attributions">Attributions</a></li>
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    <div class="container">
          <div class="row">
-           <div class="col-md-9 col-md-offset-2">
+           <div class="col-md-12 ">
              <div class="col-md-12 content-text">
                  <div class="about-logo">
+<a style=" text-decoration: none; color: black;" >
                    <h3><strong>1. <span class="red-content">Overview </span></strong></h3>
-                  <p style="font-size:16px; line-height: 25px;letter-spacing:1px; text-indent:0px;">
+                 <p>
-This year, our job can mainly divided into three parts: Comparison of Rhodopseudomonas and Cyanobacteria, sort of three genes pathway in Rhodopseudomonas, and intelligent device software.
+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.
                    </p>
+ </a>
                  </div>
              </div>
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-            <div class="col-md-9 col-md-offset-2">
+            <div class="col-md-12 ">
              <div class="col-md-12 content-text">
                  <div class="about-logo">
-                   <h3><strong>2. <span class="red-content">Comparison between PSB</span></strong></h3>
+<a style=" text-decoration: none; color: black;" >
-                  <p style="font-size:16px; line-height: 25px;letter-spacing:1px; text-indent:0px;">
+                   <h3><strong>2. <span class="red-content">Model of systems</span></strong></h3>
-In the past, people use Cyanobacteria to provide energy for electricity producing bacteria. Because it’s efficient and easier to control. But Shewanella species are heterotrophic facultative anaerobes, and produce electricity only in anaerobic environment (Justin et al.2009). So we think Rhodopseudomonas may be better because it’s cycle photophosphorylation doesn’t produce oxygen. But Rhodopseudomonas is not as efficient as Cyanobacteria. So we use computer simulation to find which is better.
+                 <p>
+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.
 </p>
+</a>
                  </div>
                 </div>
             </div>
-             <div class="col-md-9 col-md-offset-2">
+             <div class="col-md-12 ">
              <div class="col-md-12 content-text">
                  <div class="about-logo">
+<a style=" text-decoration: none; color: black;" >
                    <h3><strong>3. <span class="red-content">Sort of three genes</span></strong></h3>
-                  <p style="font-size:16px; line-height: 25px;letter-spacing:1px; text-indent:0px;">
+                 <p>
-In Rhodopseudomonas, the sequence of genes in plasmid influence them expression ability. (Shou-Chen.2012) We have three gene to transfer. So we should find out which gene is most important, and we sort three genes by their importance.
+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.
+</p>
+</a>
                  </div>
              </div>
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-        <div class="col-md-9 col-md-offset-2">
+        <div class="col-md-12 ">
         <div class="col-md-12 content-text">
                  <div class="about-logo">
-                   <h3><strong>3. <span class="red-content">Intelligent device software</span></strong></h3>
+<a style=" text-decoration: none; color: black;">
-                  <p style="font-size:16px; line-height: 25px;letter-spacing:1px; text-indent:0px;">
+                   <h3><strong>4. <span class="red-content">Intelligent device software</span></strong></h3>
-Using a new multi-culture bacteria system means we should use a new fermentation strategy. So we use algorithm to know the system’s situation and decide how to control the device, letting system work more efficiently and steadily.
+                 <p>
+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.
+.
+</p>
+</a>
                  </div>
              </div>
            </div>
-            <div class="col-md-9 col-md-offset-2">
+            <div class="col-md-12 ">
              <div class="col-md-12 content-text">
              <h4><strong>Reference </strong></h4>
-           <p style="font-size:16px; line-height: 25px;letter-spacing:1px; text-indent:0px;">
+          <p>
-<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>
+<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 style="font-size:16px; line-height: 25px;letter-spacing:1px; text-indent:0px;">
+          <p>
   <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>
          </div>
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+<i>Rhodopseudomonas palustris</i>