Difference between revisions of "Team:Tokyo Tech/Parts"

 
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                <h2 class="align-center mbr-bold mbr-white pb-3 mbr-fonts-style display-1">Basic Parts</h2>
 
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       <h2 class="mbr-section-title mbr-fonts-style align-center pb-3 display-2">Basic Parts</h2>
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       <h2 class="mbr-section-title mbr-fonts-style align-center pb-3 display-2">Parts</h2>
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       <h3 class="mbr-section-subtitle mbr-fonts-style align-center pb-5 mbr-light display-5">TokyoTech 2018 iGEM Team Basic Parts</h3>
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       <h3 class="mbr-section-subtitle mbr-fonts-style align-center pb-5 mbr-light display-5">TokyoTech 2018 iGEM Team Parts</h3>
 
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               <th class="head-item mbr-fonts-style display-7">Name</th><th class="head-item mbr-fonts-style display-7">Type</th><th class="head-item mbr-fonts-style display-7">Description</th><th class="head-item mbr-fonts-style display-7">Design</th><th class="head-item mbr-fonts-style display-7">Length(bp)</th></tr>
 
               <th class="head-item mbr-fonts-style display-7">Name</th><th class="head-item mbr-fonts-style display-7">Type</th><th class="head-item mbr-fonts-style display-7">Description</th><th class="head-item mbr-fonts-style display-7">Design</th><th class="head-item mbr-fonts-style display-7">Length(bp)</th></tr>
 
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729000">BBa_K2729000</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV1 C</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">300</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729000">BBa_K2729000</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV1 C</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">300</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><p><a href="http://parts.igem.org/Part:BBa_K2729001">BBa_K2729001</a></p></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV2 C</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">300</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729001">BBa_K2729001</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV2 C</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">300</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729002">BBa_K2729002</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV3 C</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">300</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729002">BBa_K2729002</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV3 C</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">300</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729003">BBa_K2729003</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV4 C</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">300</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729003">BBa_K2729003</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV4 C</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">300</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729004">BBa_K2729004</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV3 E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">1479</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729004">BBa_K2729004</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV3 E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">1479</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729005">BBa_K2729005</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV4 E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">1485</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729005">BBa_K2729005</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV4 E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">1485</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729006">BBa_K2729006</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">EGFP_FMDV2a</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">948</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729006">BBa_K2729006</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">EGFP_FMDV2a</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">950</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729007">BBa_K2729007</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DsRed_FMDV2a</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">908</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729007">BBa_K2729007</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DsRed_FMDV2a</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">908</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729008">BBa_K2729008</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">YFP_FMDV2a</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">945</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729008">BBa_K2729008</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">ZsYellow_FMDV2a</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">920</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729009">BBa_K2729009</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">AmCyan_FMDV2a</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">918</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729009">BBa_K2729009</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">AmCyan_FMDV2a</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">920</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729010">BBa_K2729010</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV1 AncC_prM_E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">2028</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729010">BBa_K2729010</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV1 AncC_prM_E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">2028</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729011">BBa_K2729011</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV2 AncC_prM_E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">2028</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729011">BBa_K2729011</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV2 AncC_prM_E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">2028</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729012">BBa_K2729012</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV3 AncC_prM_E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">2022</td></tr><tr>  
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729012">BBa_K2729012</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV3 AncC_prM_E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">2022</td></tr><tr>
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               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729013">BBa_K2729013</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV4 AncC_prM_E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">2028</td></tr></tbody>
 
               <td class="body-item mbr-fonts-style display-7"><a href="http://parts.igem.org/Part:BBa_K2729013">BBa_K2729013</a></td><td class="body-item mbr-fonts-style display-7">Coding</td><td class="body-item mbr-fonts-style display-7">DENV4 AncC_prM_E</td><td class="body-item mbr-fonts-style display-7">Hayato Ito, Kotaro Miyamoto, Hajime Fujita</td><td class="body-item mbr-fonts-style display-7">2028</td></tr></tbody>
 
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         <div class="container table-info-container">
 
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</section>
 
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<section class="header5 cid-r6KyNixgMR" id="header5-36" style="background-color: #000000">
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    <div class="container">
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        <div class="row justify-content-center">
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            <div class="mbr-white col-md-10">
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-5">Note: Validated Parts (Silver Medal Criteria)</h1>
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                <span class="mbr-text align-center mbr-fonts-style" style="font-size: 1.2rem">DENV2 C, EGFP-FMDV2a and DsRed-Express-FMDV2a are essential for pseudo-virus production. As one of the structural genes, DENV2 C plays an important role in virus structural formation. EGFP-FMDV2a and DsRed-Express-FMDV2a are enclosed in pseudo-virus and programmed to code functional fluorescence proteins after infecting the host cells.</span>
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                <span class="mbr-text align-center mbr-fonts-style" style="font-size: 1.2rem">To get specific sequence and charanterization information, please see the following Parts Pages.</span>
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            </div>
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<br></section>
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<section class="cid-r6KBLFZXRg" id="image1-3j" style="background-color: #000000">
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    <figure class="mbr-figure container">
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            <div class="image-block" style="width: 84%; background-color: #ffffff">
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                <img src="https://static.igem.org/mediawiki/2018/9/9c/T--Tokyo_Tech--silver_val_parts.png" width="1400" alt="Mobirise" title="">
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            </div>
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    </figure>
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<br></section>
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<section class="header5 cid-r6KBNEvhfa" id="header5-3k" style="background-color: #000000">
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    <div class="container">
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        <div class="row justify-content-center">
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            <div class="mbr-white col-md-10">
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                <span class="mbr-text align-center mbr-fonts-style" style="font-size: 1.2rem">Figure: List of validated parts and the features<br></span>
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                     Our team made new pseudovirus that can infect Vero cells and introduce the gene including this EGFP-FMDV2a. With the assistance of "self-cleaving" 2A peptides, fluorescence protein is produced inside of the cell and folded so that it can emit fluorescence at the end. Since EGFP contains chromophore mutations that make the protein 35 times brighter than wild-type GFP
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                     Our team made new pseudovirus that can infect Vero cells and introduce the gene including this EGFP-FMDV2a. With the assistance of "self-cleaving" 2A peptides, EGFP is produced inside of the cell and folded so that it can emit fluorescence at the end.
 
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Biosafety</h1>
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                <span class="mbr-text align-center mbr-fonts-style" style="font-size: 1.2rem">As you can see in Fig. 1, on native virus genome, structural genes and non-structural genes are integrated on the same sequence. Thus, the whole genome are replicated and that make viruses possible to replicate themselves in host cells.</span>
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                <span class="mbr-text align-center mbr-fonts-style" style="font-size: 1.2rem">However, as you can see our construct design in Fig. 2, structural and non-structural regions are splitted so that the pseudo-virus cannot replicate themselves in host cells because RNA polymerase from non-structural V gene cannot replicate structural genes.</span>
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                <span class="mbr-text align-center mbr-fonts-style" style="font-size: 1.2rem">To sum up, our system starts and ends in one place and doesn't harm environment.</span>
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                <span class="mbr-text align-center mbr-fonts-style" style="font-size: 1.2rem">Figure 1: Infection process of native virus and production of infectious pseudo-virus<br></span>
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                <img src="https://static.igem.org/mediawiki/2018/9/91/T--Tokyo_Tech--presentation9.png" width="1400" alt="Mobirise" title="">
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                <span class="mbr-text align-center mbr-fonts-style" style="font-size: 1.2rem">Figure 2: Infection process of our pseudo-virus for validating biosafety<br></span>
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Parts

Parts

TokyoTech 2018 iGEM Team Parts

NameTypeDescriptionDesignLength(bp)
BBa_K2729000CodingDENV1 CHayato Ito, Kotaro Miyamoto, Hajime Fujita300
BBa_K2729001CodingDENV2 CHayato Ito, Kotaro Miyamoto, Hajime Fujita300
BBa_K2729002CodingDENV3 CHayato Ito, Kotaro Miyamoto, Hajime Fujita300
BBa_K2729003CodingDENV4 CHayato Ito, Kotaro Miyamoto, Hajime Fujita300
BBa_K2729004CodingDENV3 EHayato Ito, Kotaro Miyamoto, Hajime Fujita1479
BBa_K2729005CodingDENV4 EHayato Ito, Kotaro Miyamoto, Hajime Fujita1485
BBa_K2729006CodingEGFP_FMDV2aHayato Ito, Kotaro Miyamoto, Hajime Fujita950
BBa_K2729007CodingDsRed_FMDV2aHayato Ito, Kotaro Miyamoto, Hajime Fujita908
BBa_K2729008CodingZsYellow_FMDV2aHayato Ito, Kotaro Miyamoto, Hajime Fujita920
BBa_K2729009CodingAmCyan_FMDV2aHayato Ito, Kotaro Miyamoto, Hajime Fujita920
BBa_K2729010CodingDENV1 AncC_prM_EHayato Ito, Kotaro Miyamoto, Hajime Fujita2028
BBa_K2729011CodingDENV2 AncC_prM_EHayato Ito, Kotaro Miyamoto, Hajime Fujita2028
BBa_K2729012CodingDENV3 AncC_prM_EHayato Ito, Kotaro Miyamoto, Hajime Fujita2022
BBa_K2729013CodingDENV4 AncC_prM_EHayato Ito, Kotaro Miyamoto, Hajime Fujita2028

Note: Validated Parts (Silver Medal Criteria)

DENV2 C, EGFP-FMDV2a and DsRed-Express-FMDV2a are essential for pseudo-virus production. As one of the structural genes, DENV2 C plays an important role in virus structural formation. EGFP-FMDV2a and DsRed-Express-FMDV2a are enclosed in pseudo-virus and programmed to code functional fluorescence proteins after infecting the host cells. To get specific sequence and charanterization information, please see the following Parts Pages.

Mobirise

Figure: List of validated parts and the features

Best Parts: EGFP-FMDV2a (BBa_K2729006)

Our team made new pseudovirus that can infect Vero cells and introduce the gene including this EGFP-FMDV2a. With the assistance of "self-cleaving" 2A peptides, EGFP is produced inside of the cell and folded so that it can emit fluorescence at the end.

Since EGFP is 35 times brighter than wild-type GFP and FMDV2a precisely works in our assumption, you can easily check the degree of infection by measuring fluorescence intensity.


Biosafety

As you can see in Fig. 1, on native virus genome, structural genes and non-structural genes are integrated on the same sequence. Thus, the whole genome are replicated and that make viruses possible to replicate themselves in host cells. However, as you can see our construct design in Fig. 2, structural and non-structural regions are splitted so that the pseudo-virus cannot replicate themselves in host cells because RNA polymerase from non-structural V gene cannot replicate structural genes. To sum up, our system starts and ends in one place and doesn't harm environment.

Mobirise

Figure 1: Infection process of native virus and production of infectious pseudo-virus

Mobirise

Figure 2: Infection process of our pseudo-virus for validating biosafety

Address

2 Chome-12-1
Ookayama, Meguro, Tokyo

Contacts

Email: igem2018tokyotech@gmail.com

Links

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