Difference between revisions of "Team:DUT China B/Parts"

 
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<ul id="menu">
 
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         <li>
 
         <li>
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             <a ><font size="4" href="#Inspiration" >Inspiration</font></a>
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             <a href="#Basic Parts"><font size="5" >Basic Parts</font></a>
 
         <div style="text-align: center; width: 100%; height:40px"></div>
 
         <div style="text-align: center; width: 100%; height:40px"></div>
 
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       <br>
 
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             <a><font size="4" >Background</font></a>
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             <a href="#Composite Parts"><font size="5" >Composite Parts</font></a>
 
       <div style="text-align: center; width: 100%; height:40px"></div>
 
       <div style="text-align: center; width: 100%; height:40px"></div>
 
       </li>
 
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       <br>
 
       <br>
 
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         <li>
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             <a><font size="4">Chlamydomonas reinhardtii</font></a>
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             <a href="#Improve Parts"><font size="5"></font></a>
 
              
 
              
 
         </li>
 
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<div  class="cart">
 
<div  class="cart">
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               <h1  style="font-family: 'Times New Roman' !important; "><a name="Inspiration" >Inspiration </a><img src="https://static.igem.org/mediawiki/2019/9/98/T--DUT_China_B--INSPIRATION.svg" class="icon"> </h1>
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<p>This year, DUT_CHINA_B submitted a total of 14 parts, involving signal peptides located in the eye spots, mutants of rhodopsin in the Chlamydomonas reinhardtii channel, and red light-controlled protein with split renilla luciferase. Among them, the most innovative design is BBa_K3061011, BBa_K3061012 which are improved  from the old part BBa_K1159201, BBa_K1159201. After characterization, we found that the old part has low luminescence intensity. Using modeling scores, we predicted new cleavage sites and found that nanoluc splitting at new sites has higher luminescence intensity. This not only guides the design of split luciferase in the experiment, but also provides help and advice for similar work in the future.</p>
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               <h1  style="font-family: 'Times New Roman' !important; "><a name="Basic Parts" >Basic Parts</a><img src="https://static.igem.org/mediawiki/2019/a/a9/T--DUT_China_B--partsbasic.svg" class="icon"> </h1>
 
                  
 
                  
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<p style="font-family: 'Times New Roman' !important;  ">Have you ever seen the movie from MCU Antman? Imagine if the ant man's suit in the Marvel movie really exists in life，we can turn incredibly small, even to quantum scale, like the Antman who can get into Ironman’s suit and disable it in a minute, or sneak into a machine and fix it from the inside! We will have the opportunity to observe and even manipulate the world from an extremely microscopic perspective! Although the current technological development has not reached this level, it does not prevent us from exerting such bold imagination and trying to transform anything that might be used as a micro-robot. The cell is no doubt the finest complete living body and the most delicate control system we know. It is no exaggeration to compare it to a delicate life robot. But if we want natural cells to fully perform the functions we expect, the most viable way is to transform cells like machines. Cellular micro-robots have greatly attracted our attention, and we are excited to imagine such a steerable micro-robot and direct it for us. Synthetic biology is providing us with a way to build cell loops and transform cells according to our wishes, so this year, we can't wait to use synthetic biology to build such a controllable cell micro-nano robot.</p>
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<p style="font-family: 'Times New Roman' !important;  "><table class="table-fill">
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                <div style="text-align: center; width: 100%; ">
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                <img alt="" src="https://static.igem.org/mediawiki/2019/e/ed/T--DUT_China_B--mirco_robot.jpg" style="display: inline-block;width:50%;" />
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            <center> <br> <p style="left:45%;position:relative;">nanorobot</p>  </center>
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              </div>
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              <div class="cart">
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              <h1 style="font-family: 'Times New Roman' !important; ">Background <img src="https://static.igem.org/mediawiki/2019/b/b7/T--DUT_China_B--difficultities.svg" class="icon"> </h1>
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<p style="font-family: 'Times New Roman' !important; ">When synthetic materials are difficult to meet the needs of control and loading, scientists have long thought of loading and modifying biological cells or molecules, using their own characteristics to operate on a small scale. Whether it is micro-nano manufacturing, precision medicine, single cell sorting or targeted drug loading, easy to manipulate micro-nano-scale robots have irreplaceable advantages. Depending on the invasiveness of the bacteria, the ability of the virus to transduce and self-replicate, the membrane encapsulation and drug loading capacity of the cells, different cells or biomolecules have been developed for micro-nano robots for specific application scenarios for targeted drug delivery. Or gene, cell therapy. The tiny size and control system of micro-nano robots make it a powerful tool for precision medical applications.</p>
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              <p>Rigid micro-robots developed in the field of machine engineering have the best accuracy and control under programmable and automated operation, but are limited to the composition of mechanical control systems covering sensors, actuators and control circuits. The size of rigid robots is difficult to control in millimeters. Energy supply below the level and difficult to obtain wireless and reasonable output; poor biocompatibility of rigid mechanical materials also limits the development of mechanical micro-robots in the medical field. Compared with mechanical micro-nano robots, biological cells with micro-nano size and self-sufficient growth have a complete control system at the micro-nano scale, and the cell's own energy conversion system solves the micro-nano robot energy supply problem, which is also easier to carry out. Expression modification of drug proteins. </P>
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                <P> However, due to the uncertainty of the living body, the precise control of the cell micro-nano robot has become a major problem in the development of cell micro-nano robots. The control of cell mobility is one of the difficulties. One is limited to the weaker mobility of the cells themselves, and the other is limited to the sensing and motion control methods of the cells. At present, the commonly used methods are control of light, magnetism, material wrapping, etc. However, magnetic control requires more complicated external equipment and computer algorithms. The material wrapping needs to make more modifications to the cells, which may affect the activity of the cells, and may cause in vivo. Problems such as residual material modification, potential damage to the human body. Light control is a relatively convenient method of control, but still requires a more transparent application environment.</p>
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<table class="table-fill">
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     <thead>
 
     <thead>
 
     <tr>
 
     <tr>
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       <th class="text-left">Symbol</th>
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       <th class="text-left">Name</th>
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       <th class="text-left">Meaning</th>
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       <th class="text-left">Original BioBrick</th><th class="text-left">Type</th>
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       <th class="text-left">Meaning</th>
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       <th class="text-left">Description</th>
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         <th class="text-left">Meaning</th>
+
         <th class="text-left">Designer</th>
 +
         
 
       </tr>
 
       </tr>
 
     </thead>
 
     </thead>
 
     <tbody class="table-hover">
 
     <tbody class="table-hover">
 
     <tr>
 
     <tr>
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     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061001">BBa_K3061001</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">None</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">coding</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">VchR, Channel rhodopsins of Volvox carteri</td>
 +
    <td class="text-left">Kaidi Chen</td>
 
       </tr>
 
       </tr>
 
     <tr>
 
     <tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061001">BBa_K3061002</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">None</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">coding</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">signal peptide of Channelrhodopsin-2
 +
in Chlamydomonas reinhardtii</td>
 +
    <td class="text-left">Yuanzhen Zhang</td>
 
       </tr>
 
       </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061003">BBa_K3061003</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_J52008">BBa_J52008</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">reporter</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">N-rluc, N-terminal part of split Renilla luciferase</td><td class="text-left">Kaidi Chen</td>
 
       </tr>
 
       </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061004">BBa_K3061004</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_J52008">BBa_J52008</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">reporter</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">C-rluc, C-terminal part of split Renilla luciferase</td><td class="text-left">Kaidi Chen</td>
 
       </tr>
 
       </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061005 "> BBa_K3061005  </a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K2023009"> BBa_K2023009    </a> </td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">reporter</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">N-nanoluc, N-terminal part of split Guassia luciferase</td><td class="text-left">Jinwei Zhu</td>
 
       </tr>
 
       </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061006">  BBa_K3061006  </a> </td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K2023009">  BBa_K2023009  </a>  </td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">reporter</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">C-nanoluc, C-terminal part of split Guassia luciferase</td><td class="text-left">Jinwei Zhu</td>
 
       </tr>
 
       </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061007">  BBa_K3061007 </a>  </td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"> <a href="http://parts.igem.org/Part: BBa_K3061001">  BBa_K3061001  </a> </td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">coding</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">fusion VchR with green fluorescent protein Clover</td><td class="text-left">Kaidi Chen</td>
 
       </tr>
 
       </tr>
 
      
 
      
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"> <a href="http://parts.igem.org/Part:BBa_K3061008">  BBa_K3061008  </a> </td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061002">  BBa_K3061002 </a>  </td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">coding</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">fusion signal peptide ChR2 with green fluorescent protein Clover</td><td class="text-left">Kaidi Chen</td>
 
   </tr>
 
   </tr>
 +
 +
    </tbody>
 +
    </table> </p>
 +
 +
              </div>
 +
              <div class="cart">
 +
              <h1 style="font-family: 'Times New Roman' !important; "><a name="Composite Parts">Composite Parts</a><img src="https://static.igem.org/mediawiki/2019/a/af/T--DUT_China_B--partscomplex.svg" class="icon"> </h1>
 +
               
 +
<p style="font-family: 'Times New Roman' !important; "></p>
 +
              <p></p>
 +
                <p></p>
 +
<table class="table-fill">
 +
    <thead>
 +
    <tr>
 +
      <th class="text-left">Name</th>
 +
      <th class="text-left">Original BioBrick</th><th class="text-left">Type</th>
 +
      <th class="text-left">Description</th>
 +
        <th class="text-left">Designer</th>
 +
         
 +
      </tr>
 +
    </thead>
 +
    <tbody class="table-hover">
 +
   
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061009">BBa_K3061009</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K1159103">BBa_K1159103</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">composite</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">fusion N-rluc with N-terminal phytochrome interacting Factor 3 (pif3) </td><td class="text-left">Huan Liu</td>
 
   </tr>
 
   </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061010">BBa_K3061010</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K80103"> BBa_K80103</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">composite</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">fusion C-rluc with Phytochrome B(PhyB)</td><td class="text-left">Huan Liu</td>
 
   </tr>
 
   </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061011">BBa_K3061011</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K1159201">BBa_K1159201</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">composite</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">the combination of new N terminal of Guassia luciferase and Spytag</td><td class="text-left">Jinwei Zhu</td>
 
   </tr>
 
   </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061012">BBa_K3061012</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K1159200">BBa_K1159200</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">composite</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">the combination of new C terminal of Guassia luciferase and SpyCatcher</td><td class="text-left">Jinwei Zhu</td>
 
   </tr>
 
   </tr>
 
<tr>
 
<tr>
−
     <td class="text-left">A</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061013">BBa_K3061013</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K1159201"> BBa_K1159201</a></td>
−
     <td class="text-left">Concentration of PhyB</td>
+
     <td class="text-left">composite</td>
−
     <td class="text-left">Concentration of PhyB</td>
+
    <td class="text-left">the combination of N terminal of Guassia luciferase and Spytag</td><td class="text-left">Kaidi Chen</td>
 +
  </tr>
 +
<tr>
 +
     <td class="text-left"><a href="http://parts.igem.org/Part:BBa_K3061014">BBa_K3061014</a></td>
 +
    <td class="text-left"><a  href="http://parts.igem.org/Part:BBa_K1159200">BBa_K1159200</a></td>
 +
    <td class="text-left">composite</td>
 +
    <td class="text-left">the combination of C terminal of Guassia luciferase and SpyCatcher</td><td class="text-left">Kaidi Chen</td>
 
   </tr>
 
   </tr>
−
 
 
     </tbody>
 
     </tbody>
 
     </table>
 
     </table>
 
</div>
 
</div>
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−
<div class="cart" >
 
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              <h1 style="font-family: 'JosefinSans-Light' !important; ">Chlamydomonas reinhardtii<img src="https://static.igem.org/mediawiki/2019/a/a2/T--DUT_China_B--wei.svg" class="icon"> </h1>
 
−
               
 
−
<p >Chlamydomonas reinhardtii is a single-cell photoautotrophic eukaryote with the ability to accurately fold and assemble complex proteins. It can be used to express various complex proteins and high-value products. It is known as “green yeast”. It is said that the complete sequencing of the nuclear genome, chloroplast genome and mitochondrial genome and genetic transformation under three genomes are the most clear photosynthetic autotrophic eukaryotic substrates. Chlamydomonas cells have two flagellae, which are highly mobile and have a blue-light sensing system. They have the advantages of carrying protein-loading drugs and the potential for transformation using light control. They are characterized by the use of micro-nano robots. Good chassis creatures. Therefore, we hope to use Chlamydomonas as a chassis and modify it with its own strong mobility to solve the problem of mobility control of cellular nano-robots in applications.</p>
 
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                      <div style="text-align: center; width: 100%; ">
 
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                <img alt="" src="https://static.igem.org/mediawiki/2019/b/b5/T--DUT_China_B--move1.gif" style="display: inline-block;width:50%;" />              <p style="text-align: center;">Chlamydomonas reinhardtii with strong mobility</p>
 
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                </div>
 
−
                <p>The optical control system has the advantages of simple equipment, wireless control, good penetrability, etc., and Chlamydomonas itself has a blue light sensing system, so that the control of the movement of Chlamydomonas cells can be more fully utilized. Since cell micro-nano robots are mainly used in the medical field for targeted therapy, red light is more penetrating than other light tissues and is the most commonly used optical means in the medical field. Therefore, we hope to achieve red color in Chlamydomonas cells. The engineering of light control movement.</p>
 
−
                <p>To achieve the kinetic control of Chlamydomonas, how to transform its endogenous motion control and light perception system is the most effective means to achieve our transformation goals. However, because the movement of Chlamydomonas cells is controlled by two flagella, there are three different movement modes of swimming, fluctuation, and sliding under different conditions, and the movement mechanism is complicated. The specific molecular regulation network of two flagella in Chlamydomonas has not been obtained yet. Clear interpretation. Therefore, we cannot start from the molecular mechanism of the Chlamydomonasis movement. In the blue light sensing system of Chlamydomonas, we have learned that the eye spots of Chlamydomonas are used for blue light perception, and then the light signal is transmitted to the flagella to regulate the different movements of the two flagella under the action of the second messenger molecule. Therefore, we try to activate the Chlamydomonas light perception system from the light-gated ion channel at the eye spot to achieve the motion control of Chlamydomonas. But unfortunately, the mutants of the light-gated ion channels have limited redshift range, and we have not been able to find other substances that specifically activate or inhibit the rhodopsin of the Chlamydomonas channel, but only the general purpose of the cells. The second messenger molecule has a regulatory effect on it. We are unable to control the transformation of the universal messenger molecules in the cell, as this can distort the growth regulation of Chlamydomonas cells. So we have to give up on this idea.</P>
 
−
            <p>After encountering a bottleneck in the molecular mechanism transformation, we tried to find a simpler way to control the algae.We have considered that since the channel of rhodopsin is excited by blue light, in the literature search, we have learned the research method of split protein and found the work of splitting luciferase for protein interaction. It is noted that the catalytic reaction of luciferase can produce blue light. We associate it with the possibility of combining red-controlled polymerized proteins with split luciferase. This enables the generation of blue light under red light control. We call this a molecular light converter. By expressing this molecular light converter in Chlamydomonas cells, we can achieve the excitation of endogenous blue light in Chlamydomonas cells, thus realizing the activation and motion control of Chlamydomonas light perception system. Our solution is thus generated.</P>
 
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<table><tr>
 
−
        <td><img src="https://static.igem.org/mediawiki/2019/6/6c/T--DUT_China_B--molecular_light_converter_1.jpg" border=0></td>
 
−
        <td><img src=" https://static.igem.org/mediawiki/2019/8/82/T--DUT_China_B--molecular_light_converter_2.jpg" border=0></td>
 
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        <td><img src="https://static.igem.org/mediawiki/2019/f/f1/T--DUT_China_B--molecular_light_converter_3.jpg" border=0></td>
 
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          <p style="text-align: center;">Molecular light converter</p> 
 
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Latest revision as of 01:34, 22 October 2019

Document
parts

This year, DUT_CHINA_B submitted a total of 14 parts, involving signal peptides located in the eye spots, mutants of rhodopsin in the Chlamydomonas reinhardtii channel, and red light-controlled protein with split renilla luciferase. Among them, the most innovative design is BBa_K3061011, BBa_K3061012 which are improved from the old part BBa_K1159201, BBa_K1159201. After characterization, we found that the old part has low luminescence intensity. Using modeling scores, we predicted new cleavage sites and found that nanoluc splitting at new sites has higher luminescence intensity. This not only guides the design of split luciferase in the experiment, but also provides help and advice for similar work in the future.

Basic Parts

Name Original BioBrickType Description Designer
BBa_K3061001 None coding VchR, Channel rhodopsins of Volvox carteri Kaidi Chen
BBa_K3061002 None coding signal peptide of Channelrhodopsin-2 in Chlamydomonas reinhardtii Yuanzhen Zhang
BBa_K3061003 BBa_J52008 reporter N-rluc, N-terminal part of split Renilla luciferaseKaidi Chen
BBa_K3061004 BBa_J52008 reporter C-rluc, C-terminal part of split Renilla luciferaseKaidi Chen
BBa_K3061005 BBa_K2023009 reporter N-nanoluc, N-terminal part of split Guassia luciferaseJinwei Zhu
BBa_K3061006 BBa_K2023009 reporter C-nanoluc, C-terminal part of split Guassia luciferaseJinwei Zhu
BBa_K3061007 BBa_K3061001 coding fusion VchR with green fluorescent protein CloverKaidi Chen
BBa_K3061008 BBa_K3061002 coding fusion signal peptide ChR2 with green fluorescent protein CloverKaidi Chen

Composite Parts

Name Original BioBrickType Description Designer
BBa_K3061009 BBa_K1159103 composite fusion N-rluc with N-terminal phytochrome interacting Factor 3 (pif3) Huan Liu
BBa_K3061010 BBa_K80103 composite fusion C-rluc with Phytochrome B(PhyB)Huan Liu
BBa_K3061011 BBa_K1159201 composite the combination of new N terminal of Guassia luciferase and SpytagJinwei Zhu
BBa_K3061012 BBa_K1159200 composite the combination of new C terminal of Guassia luciferase and SpyCatcherJinwei Zhu
BBa_K3061013 BBa_K1159201 composite the combination of N terminal of Guassia luciferase and SpytagKaidi Chen
BBa_K3061014 BBa_K1159200 composite the combination of C terminal of Guassia luciferase and SpyCatcherKaidi Chen