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| | <li role="presentation" class=dropdown><a href=# class=dropdown-toggle data-toggle=dropdown role=button aria-haspopup=true aria-expanded=false>Team <span class=caret></span></a> | | <li role="presentation" class=dropdown><a href=# class=dropdown-toggle data-toggle=dropdown role=button aria-haspopup=true aria-expanded=false>Team <span class=caret></span></a> |
| | <ul class=dropdown-menu> | | <ul class=dropdown-menu> |
| − | <li><a href=https://2015.igem.org/Team:SCU_China/Atributions>Atributions</a></li> | + | <li><a href=https://2015.igem.org/Team:SCU_China/Atttributions>Attributions</a></li> |
| | <li><a href=https://2015.igem.org/Team:SCU_China/Member>Member</a></li> | | <li><a href=https://2015.igem.org/Team:SCU_China/Member>Member</a></li> |
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| − | <li role="Project" class=dropdown><a href=# class=dropdown-toggle data-toggle=dropdown role=button aria-haspopup=true aria-expanded=false>Project<span class=caret></span></a> | + | <li class="nav-current" role="Project" class=dropdown><a href=# class=dropdown-toggle data-toggle=dropdown role=button aria-haspopup=true aria-expanded=false>Project<span class=caret></span></a> |
| | <ul class=dropdown-menu> | | <ul class=dropdown-menu> |
| | <li><a href=https://2015.igem.org/Team:SCU_China/Description>Description</a></li> | | <li><a href=https://2015.igem.org/Team:SCU_China/Description>Description</a></li> |
| | <li><a href=https://2015.igem.org/Team:SCU_China/CarbonFixation>Carbon Fixation</a></li> | | <li><a href=https://2015.igem.org/Team:SCU_China/CarbonFixation>Carbon Fixation</a></li> |
| | <li><a href=https://2015.igem.org/Team:SCU_China/NitrogenFixation>Nitrogen Fixation</a></li> | | <li><a href=https://2015.igem.org/Team:SCU_China/NitrogenFixation>Nitrogen Fixation</a></li> |
| − | <li><a href=https://2015.igem.org/Team:SCU_China/Test>Test</a></li> | + | <li><a href=https://2015.igem.org/Team:SCU_China/Test>Testing</a></li> |
| − | <li><a href=https://2015.igem.org/Team:SCU_China/prom>Promoter</a></li> | + | <li><a href=https://2015.igem.org/Team:SCU_China/prom>Verification</a></li> |
| | <li><a href=https://2015.igem.org/Team:SCU_China/Modeling>Modeling</a></li> | | <li><a href=https://2015.igem.org/Team:SCU_China/Modeling>Modeling</a></li> |
| | <li><a href=https://2015.igem.org/Team:SCU_China/Notebook>Notebook</a></li> | | <li><a href=https://2015.igem.org/Team:SCU_China/Notebook>Notebook</a></li> |
| − | <li><a href=https://2015.igem.org/Team:SCU_China/Safe>Safe</a></li> | + | <li><a href=https://2015.igem.org/Team:SCU_China/Safe>Safety</a></li> |
| | <li><a href=https://2015.igem.org/Team:SCU_China/Design>Design</a></li> | | <li><a href=https://2015.igem.org/Team:SCU_China/Design>Design</a></li> |
| | | | |
| | </ul></li> | | </ul></li> |
| | + | |
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| | <li role="presentation" ><a href=https://2015.igem.org/Team:SCU_China/Parts>Parts</a></li> | | <li role="presentation" ><a href=https://2015.igem.org/Team:SCU_China/Parts>Parts</a></li> |
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| | </ul></li> | | </ul></li> |
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| − | <li class="nav-current" role="presentation" class=dropdown><a href=# class=dropdown-toggle data-toggle=dropdown role=button aria-haspopup=true aria-expanded=false>Activities<span class=caret></span></a> | + | <li role="presentation" class=dropdown><a href=# class=dropdown-toggle data-toggle=dropdown role=button aria-haspopup=true aria-expanded=false>Activities<span class=caret></span></a> |
| | <ul class=dropdown-menu> | | <ul class=dropdown-menu> |
| | <li><a href=https://2015.igem.org/Team:SCU_China/Practices>Human Practice</a></li> | | <li><a href=https://2015.igem.org/Team:SCU_China/Practices>Human Practice</a></li> |
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| | <header class="post-head"> | | <header class="post-head"> |
| | <h1 class="post-title"> | | <h1 class="post-title"> |
| − | Modeling</h1>
| + | Safety</h1> |
| | </header> | | </header> |
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| − | <h2>Energy system</h2> | + | <h2 id="1"><strong>General Safety</strong></h2> |
| − | <h3 id="1">Why </h3>
| + | <p>Before we starting our project, our team took a safety course given by Prof. Ying Tong. She taught us many basic knowledge about laboratory safety such as proper laboratory wear, common chemical reagents usage, how to discard wastes, and how to deal with specific emergencies. In addition, experienced former SCU_iGEM team members gave us some regular courses about common equipment operation. Each of our team member was required to read through Laboratory Safety Regulations of Sichuan University, and we also designed a card game to help our team members to remember the strict lab rules. </p> |
| − | <p>Aerobic repiration is the main way to provide energy to bacteria . In aerobic respiration, one Acely-CoA was consumed away and 10 ATP are produced. The electron transport chain was supposed as the main part to produce ATP. But the fact is that the system we designed to fix carbon is derived from anaerobic bacteria and the enzymes with metal active center in it may be oxidated by oxygen. Therefore a model was built to get the solution to make the two system camptible.</p>
| + | |
| − | <div style="padding:20px"class="panel panel-default"><a href="https://static.igem.org/mediawiki/2015/thumb/1/16/Scu_wmenergy.png/800px-Scu_wmenergy.png" class="thumbnail image-popup-no-margins"><img src="https://static.igem.org/mediawiki/2015/thumb/1/16/Scu_wmenergy.png/800px-Scu_wmenergy.png" /></a>
| + | |
| − | <h6 class="back"><strong>Figure 1 :CARBON FIXATION SYSTEM. In one cycle, one ATP is cost and one CoA is acetylated to Acely-CoA. </strong></h6>
| + | |
| − | </div>
| + | |
| − | | + | |
| − | <p>It is reported that all the reactions is not very fast and the enzyme damaged by oxygen is can be repaired in other way. What the oxygen effects is reversible. Therefore it is belive that some concentration of oxygen can make both two systems work at the same time. </p> | + | |
| − | <h3 id="2">What we did</h3>
| + | |
| − | <p>At first, all the reactions are assumed as elementary reaction.</p>
| + | |
| − | <h1>V=KS<SUB>1</SUB><SUP>r</SUP><SUP>1</SUP>X S<SUB>2</SUB><SUP>r</SUP><SUP>2</SUP> …S<SUB>i</SUB><SUP>r</SUP><SUP>i</SUP>…S<SUB>n</SUB><SUP>r</SUP><SUP>n</SUP></h1>
| + | |
| − | <p>V: the velocity of reaction</p>
| + | |
| − | <p>K: a constant of the reaction</p>
| + | |
| − | <p>n: the species’number of substrates and enzymes in the reaction</p>
| + | |
| − | <p>Si: the concentration of substrate or enzyme</p>
| + | |
| − | <p>ri: the cost of substrate during one reaction</p>
| + | |
| − | <div style="padding:20px"class="panel panel-default"><a href="
| + | |
| − | https://static.igem.org/mediawiki/2015/thumb/e/e8/Energysystem.jpeg/800px-Energysystem.jpeg" class="thumbnail image-popup-no-margins"><img src="
| + | |
| − | https://static.igem.org/mediawiki/2015/thumb/e/e8/Energysystem.jpeg/800px-Energysystem.jpeg" /></a>
| + | |
| − | <h6 class="back"><strong>Figure 2: Simplified pathway of energy system designed by us. </strong></h6>
| + | |
| − | </div>
| + | |
| | | | |
| − | <p>The result was assumed to be related to the degree of equation. All the unknown premeters and original moles were assumed to be 1 0.1(for enzymes). These settings make the compulation easier. Then we got all the equations in the table.</p>
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| − | <table>
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| − | <tr>
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| − | <td noWrap>
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| − | id</td>
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| − | <td noWrap>
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| − | reactants</td>
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| − | <td noWrap>
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| − | products</td>
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| − | <td noWrap>
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| − | modifiers</td>
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| − | <td noWrap>
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| − | Math</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re1</td>
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| − | <td noWrap>
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| − | s3,s18</td>
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| − | <td noWrap>
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| − | s5</td>
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| − | <td noWrap>
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| − | s6</td>
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| − | <td noWrap>
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| − | (v2*s3)/(k3+s3)</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re2</td>
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| − | <td noWrap>
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| − | s5,s9,s10</td>
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| − | <td noWrap>
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| − | s7,s11</td>
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| − | <td noWrap>
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| − | s8</td>
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| − | <td noWrap>
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| − | s5 * s9 * s10 * s8 * k1</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re3</td>
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| − | <td noWrap>
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| − | s7</td>
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| − | <td noWrap>
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| − | s13,s15</td>
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| − | <td noWrap>
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| − | s14</td>
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| − | <td noWrap>
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| − | v1 * s7 / (k2 + s7) * s14 / 0.1</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re4</td>
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| − | <td noWrap>
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| − | s13,s18</td>
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| − | <td noWrap>
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| − | s16</td>
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| − | <td noWrap>
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| − | s17</td>
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| − | <td noWrap>
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| − | (v1*s13)/(k2+s13)*s17/0.1</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re5</td>
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| − | <td noWrap>
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| − | s16,s18</td>
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| − | <td noWrap>
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| − | s19</td>
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| − | <td noWrap>
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| − | s20</td>
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| − | <td noWrap>
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| − | (v1*s16)/(k2+s16)</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re7</td>
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| − | <td noWrap>
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| − | s19</td>
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| − | <td noWrap>
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| − | s21,s9</td>
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| − | <td noWrap>
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| − | s27</td>
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| − | <td noWrap>
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| − | s19*k1*s27</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re8</td>
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| − | <td noWrap>
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| − | s3,s18</td>
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| − | <td noWrap>
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| − | s28</td>
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| − | <td noWrap>
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| − | s29</td>
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| − | <td noWrap>
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| − | s3*s18*k1*s29</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re9</td>
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| − | <td noWrap>
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| − | s21</td>
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| − | <td noWrap>
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| − | s30</td>
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| − | <td noWrap>
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| − | s29</td>
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| − | <td noWrap>
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| − | s21*k1*s29</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re10</td>
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| − | <td noWrap>
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| − | s30,s28,s32</td>
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| − | <td noWrap>
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| − | s31</td>
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| − | <td noWrap>
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| − | </td>
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| − | <td noWrap>
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| − | s30*s28*s32*k1</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re12</td>
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| − | <td noWrap>
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| − | s6</td>
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| − | <td noWrap>
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| − | s34</td>
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| − | <td noWrap>
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| − | s33</td>
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| − | <td noWrap>
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| − | s6*s33*k2*s33/9.375</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re21</td>
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| − | <td noWrap>
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| − | s29</td>
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| − | <td noWrap>
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| − | s34</td>
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| − | <td noWrap>
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| − | s33</td>
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| − | <td noWrap>
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| − | s29 * k2 * s33 / 9.375</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re24</td>
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| − | <td noWrap>
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| − | s21</td>
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| − | <td noWrap>
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| − | s34</td>
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| − | <td noWrap>
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| − | s33</td>
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| − | <td noWrap>
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| − | s21 * s33 * k2*s33/9.375</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re25</td>
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| − | <td noWrap>
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| − | s31,s33,s11</td>
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| − | <td colSpan=2 noWrap>
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| − | s32,s10,s15</td>
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| − | <td noWrap>
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| − | s31 * s33^3 * s11^10 * k1</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re26</td>
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| − | <td noWrap>
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| − | s34</td>
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| − | <td noWrap>
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| − | s6</td>
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| − | <td noWrap>
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| − | </td>
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| − | <td noWrap>
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| − | (v1*s34)/(k1+s34)</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re27</td>
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| − | <td noWrap>
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| − | s34</td>
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| − | <td noWrap>
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| − | s29</td>
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| − | <td noWrap>
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| − | </td>
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| − | <td noWrap>
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| − | (v1*s34)/(k1+s34)</td></tr>
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| − | <tr>
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| − | <td noWrap>
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| − | re28</td>
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| − | <td noWrap>
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| − | s34</td>
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| − | <td noWrap>
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| − | s21</td>
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| − | <td noWrap>
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| − | </td>
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| − | <td noWrap>
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| − | (v1*s34)/(k1+s34)</td></tr></table>
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| − | <p>table : Reaction Equations in the modeling: The concentration of oxygen in air is 9.375 mol/m3 which was assumed as the perfect condition. The efficiency of all the enzyme are 100%. All the enzymes’ working efficiences are proportional to the concentration of oxygen. the number of ATP and ADP involved in re25 is 10; all the enzyme was thought as regent.</p>
| |
| − | <p>We changed the concentration of oxygen in our assumed environment to investagate the concentration’s change of ATP and ADP.</p>
| |
| − | <h3 id="3">Results are as follows</h3>
| |
| | | | |
| − | <div style="padding:20px"class="panel panel-default"><a href=" | + | <h2 id="2"><strong>Biological components Safety</strong></h2> |
| − | https://static.igem.org/mediawiki/2015/8/85/Scu_wn0.65.png" class="thumbnail image-popup-no-margins"><img src="
| + | <p>All of the biological components we used this summer were just E.coli, which belongs to risk group 1. So there is no obvious risk of causing disease in normal human body. However, proper precaution were still taken. For example, all the E.coli we used were strictly constrained in our lab, and all the medium used to grow bacteria were boiled up in boiling water before discarding. All the items in contact with the cells (e.g. Petri dishes, conical flasks, spreader) were sterilized after using.</p> |
| − | https://static.igem.org/mediawiki/2015/8/85/Scu_wn0.65.png" /></a>
| + | |
| − | <h6 class="back"><strong>Figure 3: The best concentration of oxygen: the concentration of oxygen in our environment is 0.65*9.375mole/m3. Concentration of ATP and ADP can keep in a ratio similar to original environment. </strong></h6> | + | |
| − | </div>
| + | |
| − | <div style="padding:20px"class="panel panel-default"><a href="
| + | |
| − | https://static.igem.org/mediawiki/2015/f/f6/Scu_wn0.05.png" class="thumbnail image-popup-no-margins"><img src="
| + | |
| − | https://static.igem.org/mediawiki/2015/f/f6/Scu_wn0.05.png" /></a>
| + | |
| − | <h6 class="back"><strong>
| + | |
| − | Figure 4: Low oxygen concentration: ATP is used up and the energy system can not work. </strong></h6>
| + | |
| − | </div>
| + | |
| − | <div style="padding:20px"class="panel panel-default"><a href="
| + | |
| − | https://static.igem.org/mediawiki/2015/5/54/Scu_wn3.png" class="thumbnail image-popup-no-margins"><img src="
| + | |
| − | https://static.igem.org/mediawiki/2015/5/54/Scu_wn3.png" /></a>
| + | |
| − | <h6 class="back"><strong>
| + | |
| | | | |
| − | Figure 5: High concentration of oxygen: system can not work.</strong></h6>
| + | <h2 id="3"><strong>BioBrick Safety</strong></h2> |
| − | </div> | + | <p>None of our biobricks submitted to the registry raises obvious safety issue.</p> |
| | + | <h3><strong>1.Carbon Fixation and Nitrogen Fixation</strong></h3> |
| | + | <p>As stated, Wood-Ljungdahl pathway and nitrogen fixation system are both widespread in natural anaerobic environment. The products of biobricks in these two system cannot work in aerobic environment, that is, both ACS/CODH and nitrogenase will be inactivated when being exposed to O2. In addition, all the substrates and products of these two system (e.g. CO2, acetyl-CoA, N2) are common harmless substances in nature.</p> |
| | + | <h3><strong>2.Testing and pRhl/Las</strong></h3> |
| | + | <p>The core element used in testing is Cas9 protein. The function of Cas9 depends on certain sgRNA. Also, the inducement and repression of pRhl/Las depend on certain small molecules. Without the existence of required specific sgRNA and small molecules, both Cas9 protein and pRhl/Las cannot work.</p> |
| | | | |
| − | <p>The right concentration of oxygen can make our energy system feasible and increase the ratio of ATP/ADP. The extra ATP can be used by nitrogen fixation.</p> | + | <h2 id="4"><strong>Application Safety</strong></h2> |
| | + | <p>According to our purpose, E. <i>pangu </i> will play the role of pioneer organism in Mars immigration. Thus it raised an issue: what is the safest way of E. <i>pangu </i> application? Because the first thing we should consider is still safety. We think a device for E. <i>pangu </i> is necessary. The basic requirements for this device include temperature control, gas flow control. The temperature have to be strictly controlled or the highly variable Martian temperature will inevitably affect the function of E. <i>pangu </i>. The gas flow control is also necessary in order to ensure the inflow components contain only CO2, N2 and H2, no O2 allowed. </p> |
| | + | <p>With the device, the application safety is more easily achievable.</p> |
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| | <li><a href="#main-menu">Top</a></li> | | <li><a href="#main-menu">Top</a></li> |
| − | <li><a href="#1">Why</a></li> | + | <li><a href="#1">General Safety</a></li> |
| − | <li><a href="#2">What we did </a></li> | + | <li><a href="#2">Biological components Safety</a></li> |
| − | <li><a href="#3">Results are as follows</a></li> | + | <li><a href="#3">BioBrick Safety</a></li> |
| | + | <li><a href="#4">Application Safety</a></li> |
| | | | |
| | </ul> | | </ul> |
