Difference between revisions of "Team:XJTU-China/Parts"

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{{XJTU-China}}
 
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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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<h3>Adding parts to the registry</h3>
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    #img-hairpin {
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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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    #body-container p {
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<div class="button_link">
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      font-size: 1.7rem;
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<a href="http://parts.igem.org/Add_a_Part_to_the_Registry">
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      font-family: Lato,"Helvetica Neue",Arial;
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ADD PARTS
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</a>
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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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    }
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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    #body-container {
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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</ul>
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    }
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    #groupparts {
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    }
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<h3>What information do I need to start putting my parts on the Registry?</h3>
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    #groupparts > table > thead {
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<p>The information needed to initially create a part on the Registry is:</p>
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      background-color: #2f3640;
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<ul>
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      color: white;
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<li>Part Name</li>
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    }
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<li>Part type</li>
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    pre:last-child {
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<li>Creator</li>
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      display: none;
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<li>Sequence</li>
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    }
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<li>Short Description (60 characters on what the DNA does)</li>
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  </style>
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<li>Long Description (Longer description of what the DNA does)</li>
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</head>
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<li>Design considerations</li>
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<body data-spy="scroll" data-target="#myScrollspy" data-offset="270">
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</ul>
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  <div class="universal-wrapper">
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    <div class="banner-pic">
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<p>
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      <img src="https://static.igem.org/mediawiki/2018/3/33/T--XJTU-China--Parts-banner-2.jpeg" />
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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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    </div>
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    <div class="container-fluid" id="body-container">
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</div>
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      <div class="row">
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        <nav class="navbar col-lg-3 col-sm-3" id="myScrollspy">
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          <ul class="nav nav-pills nav-stacked" id="side-nav" data-spy="affix" data-offset-top="120">
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            <li class="nav-item"><a href="#section1">Basic</a></li>
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<div class="line_divider"></div>
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            <li class="nav-item"><a href="#section2">Composite</a></li>
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<div class="clear extra_space"></div>
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            <li class="nav-item"><a href="#section3">Collection</a></li>
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          </ul>
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<div class="column full_size">
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        </nav>
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<h3>Part Table </h3>
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        <div class="col-lg-9 col-sm-9">
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          <div class="container-fluid" id="inner-container">
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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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            <h1 class="font-weight-bold text-center">Parts</h1>
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            <div id="section1">
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              <div class="page-header">
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                <h2>Basic</h2>
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              </div>
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              <h3 class="text-center">
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                <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2791008">BBa_K2791008</a>
 +
              </h3>
 +
              <p>
 +
                This part belongs to our antibiotic resistance cassette which is used to compromise the antibiotic growth pressure in directed evolution. Antibiotic resistance gene has been a convention in various genetic engineering including selecting for plasmid carrying strain or selecting for transposon mutagenesis. The thing that XJTU team focused this season is to find the quantitative nature behind this mechanism. How bacteria respond to different concentrations of antibiotic resistance against various expression levels of resistance protein? What is the suitable concentration of various antibiotics that makes <em>AB resistance</em> feasible to drive directed evolution? These are the things we try to answer in characterizing these parts.
 +
              </p>
 +
              <p>
 +
                This part is a kanamycin resistance gene flanked by Golden Gate recognition sites. To elaborate the mechanism, kanamycin interacts the 30S subunit of ribosome and causes mistranslation. This antibiotic is thought to be “harsher” to chassis thus the resistance protein has to be expressed in large amount for cells to survive. The dynamic range for kan-KanR is wider but does not match the level of cellular level of D-psicose produced by DTE. Tl-Cp hairpin is crucial for KanR to exert suitable growth pressure.
 +
              </p>
 +
              <h3 class="text-center">
 +
                <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2791009">BBa_K2791009</a>
 +
              </h3>
 +
              <p>
 +
                This part is a streptomycin resistance gene flanked by Golden Gate recognition sites. Streptomycin also interacts with bacterial ribosome and tRNA complex. This results in unstable translation complex and leads to its breakdown. This kind of disruption of translation has similar effects as indels occur in mRNA, which causes frame shift in proteins and eventually kill the cell.
 +
              </p>
 +
              <p>
 +
                The mechanism of part K2791009 is similar what we have seen in K2791008. But practically speaking, the resistance protein corresponds to streptomycin is less “strong” as KanR. We have seen pretty low growth rate even when resistance protein SmrR is efficiently expressed. This suggests K2791009 would be not a good candidate as K2791008 for our directed evolution design.
 +
              </p>
 +
              <h3 class="text-center">
 +
                <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2791010">BBa_K2791010</a>
 +
              </h3>
 +
              <p>
 +
                This part is an ampicillin resistance gene (β-lactamase) flanked by Golden Gate recognition sites. Ampicillin belongs to the family of β-lactam (penicillin) antibiotics. It enters the outer membrane of Gram-negative bacteria and mimics the D-Ala-D-Ala structure in peptidoglycan monomers. When transpeptidase binds to it, it irresistibly blocks the functionality of this enzyme and eventually breaks down bacterial cell wall.
 +
              </p>
 +
              <p>
 +
                It is expected that this antibiotic is “friendlier” to bacteria. In our characterization, it helps bacteria survival even when the inducer is in small amount. Its sensitivity region is pretty restricted thus is not ideal for directed evolution.
 +
              </p>
 +
              <h3 class="text-center">
 +
                <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2791011">BBa_K2791011</a>-
 +
                <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2791014">BBa_K2791014</a>
 +
              </h3>
 +
              <p>
 +
                The Tl-Cp cassette includes a series of 4 basic parts which are homologous but differs quantitatively. Questions this cassette tackles with are the most crucial ones underlying directed evolution and as well as synthetic biology itself: How to match the input and output of cascades of regulatory elements and how to determine the level of final yield, in this case, the antibiotic resistance proteins.
 +
              </p>
 +
              <img class="mx-auto d-block" id="img-hairpin" src="https://static.igem.org/mediawiki/2018/b/bd/T--XJTU-China--Parts-hairpin.jpg" />
 +
              <p>
 +
                The design of Tl-Cp cassette takes advantage of the helicase activity of ribosome. When ribosome approaches to the end of upstream CDS, it will unwind the hairpin structure between two CDS and make the downstream RBS approachable. The length of this hairpin structure corresponds to the optimized distance that a ribosome can unwind.
 +
              </p>
 +
              <img class="mx-auto d-block" src="https://static.igem.org/mediawiki/2018/0/05/T--XJTU-China--Parts-match.png" />
 +
              <p>
 +
                From the mechanisms above and previous researches (Mendez-Perez, 2012), we can conclude with confidence that through such hairpin structure, the downstream translational level is quantitatively associated with the upstream (which is actually driven by its own RBS).
 +
              </p>
 +
            </div>
 +
            <div id="section2">
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              <div class="page-header">
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                <h2>Composite</h2>
 +
              </div>
 +
              <p>
 +
                XJTU iGEM team has proposed a new framework for directed evolution. We have applied this framework to promote the productivity of D-psicose, a valuable rare sugar. In this case, the productivity of final product, D-psicose, undergoes a series of conversion and finally yields a distinguishable growth pressure to individual chassis cell. Four genetic devices have been constructed and unit tests been performed on each to ensure that the final device will work. The four devices are Sensing Circuit, Selecting Circuit, Coupling Circuit and Evolving Circuit.
 +
              </p>
 +
              <a href="https://2018.igem.org/Team:XJTU-China/Circuits">
 +
                <button class="btn btn-primary btn-lg">Go to Circuits</button>
 +
              </a>
 +
            </div>
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            <div id="section3">
 +
              <div class="page-header">
 +
                <h2>Collection</h2>
 +
              </div>
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              </html>
 +
                <groupparts>iGEM18 XJTU-China</groupparts>
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          </div>
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<groupparts>iGEM18 XJTU-China</groupparts>
 
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Latest revision as of 17:44, 17 October 2018

Parts

Basic

BBa_K2791008

This part belongs to our antibiotic resistance cassette which is used to compromise the antibiotic growth pressure in directed evolution. Antibiotic resistance gene has been a convention in various genetic engineering including selecting for plasmid carrying strain or selecting for transposon mutagenesis. The thing that XJTU team focused this season is to find the quantitative nature behind this mechanism. How bacteria respond to different concentrations of antibiotic resistance against various expression levels of resistance protein? What is the suitable concentration of various antibiotics that makes AB resistance feasible to drive directed evolution? These are the things we try to answer in characterizing these parts.

This part is a kanamycin resistance gene flanked by Golden Gate recognition sites. To elaborate the mechanism, kanamycin interacts the 30S subunit of ribosome and causes mistranslation. This antibiotic is thought to be “harsher” to chassis thus the resistance protein has to be expressed in large amount for cells to survive. The dynamic range for kan-KanR is wider but does not match the level of cellular level of D-psicose produced by DTE. Tl-Cp hairpin is crucial for KanR to exert suitable growth pressure.

BBa_K2791009

This part is a streptomycin resistance gene flanked by Golden Gate recognition sites. Streptomycin also interacts with bacterial ribosome and tRNA complex. This results in unstable translation complex and leads to its breakdown. This kind of disruption of translation has similar effects as indels occur in mRNA, which causes frame shift in proteins and eventually kill the cell.

The mechanism of part K2791009 is similar what we have seen in K2791008. But practically speaking, the resistance protein corresponds to streptomycin is less “strong” as KanR. We have seen pretty low growth rate even when resistance protein SmrR is efficiently expressed. This suggests K2791009 would be not a good candidate as K2791008 for our directed evolution design.

BBa_K2791010

This part is an ampicillin resistance gene (β-lactamase) flanked by Golden Gate recognition sites. Ampicillin belongs to the family of β-lactam (penicillin) antibiotics. It enters the outer membrane of Gram-negative bacteria and mimics the D-Ala-D-Ala structure in peptidoglycan monomers. When transpeptidase binds to it, it irresistibly blocks the functionality of this enzyme and eventually breaks down bacterial cell wall.

It is expected that this antibiotic is “friendlier” to bacteria. In our characterization, it helps bacteria survival even when the inducer is in small amount. Its sensitivity region is pretty restricted thus is not ideal for directed evolution.

BBa_K2791011- BBa_K2791014

The Tl-Cp cassette includes a series of 4 basic parts which are homologous but differs quantitatively. Questions this cassette tackles with are the most crucial ones underlying directed evolution and as well as synthetic biology itself: How to match the input and output of cascades of regulatory elements and how to determine the level of final yield, in this case, the antibiotic resistance proteins.

The design of Tl-Cp cassette takes advantage of the helicase activity of ribosome. When ribosome approaches to the end of upstream CDS, it will unwind the hairpin structure between two CDS and make the downstream RBS approachable. The length of this hairpin structure corresponds to the optimized distance that a ribosome can unwind.

From the mechanisms above and previous researches (Mendez-Perez, 2012), we can conclude with confidence that through such hairpin structure, the downstream translational level is quantitatively associated with the upstream (which is actually driven by its own RBS).

Composite

XJTU iGEM team has proposed a new framework for directed evolution. We have applied this framework to promote the productivity of D-psicose, a valuable rare sugar. In this case, the productivity of final product, D-psicose, undergoes a series of conversion and finally yields a distinguishable growth pressure to individual chassis cell. Four genetic devices have been constructed and unit tests been performed on each to ensure that the final device will work. The four devices are Sensing Circuit, Selecting Circuit, Coupling Circuit and Evolving Circuit.

Collection

               <groupparts>iGEM18 XJTU-China</groupparts>

Copyright © 2018 XJTU-China iGEM Team. All rights reserved.