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

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<h1>Parts</h1>
 
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
 
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
 
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<h3>Note</h3>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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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 Parts</h3>
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<h3>Adding parts to the registry</h3>
 
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
 
  
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
 
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<a href="http://parts.igem.org/Add_a_Part_to_the_Registry">
 
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ADD PARTS
 
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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>
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<h3>Inspiration</h3>
 
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
 
  
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
 
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<ul>
 
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
 
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
 
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
 
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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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<h3>What information do I need to start putting my parts on the Registry?</h3>
 
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<p>The information needed to initially create a part on the Registry is:</p>
 
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<ul>
 
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<li>Part Name</li>
 
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<li>Part type</li>
 
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<li>Creator</li>
 
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<li>Sequence</li>
 
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<li>Short Description (60 characters on what the DNA does)</li>
 
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<li>Long Description (Longer description of what the DNA does)</li>
 
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<li>Design considerations</li>
 
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</ul>
 
  
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<p>
 
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
 
  
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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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<h3>Part Table </h3>
 
  
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<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
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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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<groupparts>iGEM18 Tokyo_Tech</groupparts>
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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_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">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_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">920</td></tr><tr>
 +
 
 +
 
 +
 
 +
 
 +
              <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>
 +
 
 +
 
 +
 
 +
 
 +
              <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>
 +
 
 +
 
 +
 
 +
 
 +
              <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>
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        <div class="container table-info-container">
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    <div class="container">
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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>
 +
                <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>
 +
                <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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<section class="cid-r6KBLFZXRg" id="image1-3j" style="background-color: #000000">
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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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                <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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            <div class="title col-12 col-md-8" style="padding-top: 30px; padding-bottom: 30px">
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                <h2 class="align-center pb-3 mbr-fonts-style display-2">
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                    Best Parts: EGFP-FMDV2a (<a href="http://parts.igem.org/Part:BBa_K2729006">BBa_K2729006</a>)
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                </h2>
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                <h3 class="mbr-section-subtitle align-center mbr-light mbr-fonts-style display-5">
 +
                    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.
 +
                </h3>
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                <h3 class="mbr-section-subtitle align-center mbr-light mbr-fonts-style display-5">
 +
                  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.
 +
                </h3>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Biosafety</h1>
 +
                <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>
 +
                <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>
 +
                <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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                <img src="https://static.igem.org/mediawiki/2018/7/76/T--Tokyo_Tech--infectious_particle_ex.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 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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Latest revision as of 03:38, 18 October 2018

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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

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