Difference between revisions of "Team:Edinburgh UG/Parts"

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            <h1 style="font-size: 60px; text-align: center; margin-top: 0; padding-top: 0;"> Parts </h1>
  
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            <h2 class="header-subsection"> Introduction </h2>
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            <p> The main goal of our project in the short-term was to develop and test recombinase parts in E. coli. To the best
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                of our knowledge, these parts have not been extensively tested for activity and orthogonality in bacterial
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                cells. The parts listed below have all been functionally verified, and can be used to construct the systems
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                described on our design page [link]. We report verified function in four tyrosine recombinases, none of which
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                have been correctly documented by any iGEM team before. We also report target sites for each recombinase,
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                none of which have been properly documented or entered into the registry before. We have also developed a
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                collection of orthogonal Cre-recognised Lox sites. Finally, we have developed measurement constructs for
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                each recombinase. We used these constructs to measure and confirm the activity of our basic parts. </p>
  
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            <h2 class="header-subsection"> Basic parts </h2>
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            <p> Our basic parts fall into three categories: Recombinase generators, recombinase target sites, and orthogonal target sites for Cre. We selected the recombinases Dre [1], Vika [2], VCre, and SCre [3] to form the basis of our toolkit. These recombinases were shown to not cross-react with the Cre/LoxP system [1][2][3][5], and, in the case of VCre and SCre [3], were claimed to not cross-react with one another. As part of our toolkit, we also included the associated target sites for these recombinase generators. For a snapshot of how we verified the function of these parts, scroll down to the “Demonstrate” section of this page. For a more detailed view, click on the parts registry link, which will take you to the detailed analysis of each individual part. We also included in the toolkit orthogonal target sites for Cre recombinase. Cre/LoxP is a very popular recombinase system that is frequently used in biotechnology [4]. In order to expand the potential of this system, we have developed multiple mutant Lox target sites, which have previously been identified as sites that will not react with the classic LoxP site [4]. Adding these mutant, orthogonal lox sites to the toolkits means we provide a framework whereby one Cre protein could catalyse up to ten distinct recombination events within one cell. Once again, check out the full registry pages for each part to learn more and download their individual sequences. To simplify our experimental workflows, we have also developed an inducible Cre recombinase generator, also reported below.
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            </p>
  
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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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                    <td>T7-LacO-Dre Basic</td>
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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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                    <td>Recombinase generator</td>
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                    <td>Bba_K2406081</td>
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                    <td>Shown to excise terminator inducibly</td>
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                    <td><a href="http://parts.igem.org/Part:BBa_K2406081"> http://parts.igem.org/Part:BBa_K2406081 </a> </td>
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            <figure style="text-align: center;">
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                <img src="https://static.igem.org/mediawiki/2017/0/0d/T--Edinburgh_UG--Interlab3.jpg">
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            </figure>
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<div class="highlight">
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<h5>Note</h5>
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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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<h5>Adding parts to the registry</h5>
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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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<h5>What information do I need to start putting my parts on the Registry?</h5>
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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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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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<h5>Inspiration</h5>
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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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<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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<h5>Part Table </h5>
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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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<groupparts>iGEM17 Edinburgh_UG</groupparts>
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Revision as of 22:31, 30 October 2017




Parts

Introduction

The main goal of our project in the short-term was to develop and test recombinase parts in E. coli. To the best of our knowledge, these parts have not been extensively tested for activity and orthogonality in bacterial cells. The parts listed below have all been functionally verified, and can be used to construct the systems described on our design page [link]. We report verified function in four tyrosine recombinases, none of which have been correctly documented by any iGEM team before. We also report target sites for each recombinase, none of which have been properly documented or entered into the registry before. We have also developed a collection of orthogonal Cre-recognised Lox sites. Finally, we have developed measurement constructs for each recombinase. We used these constructs to measure and confirm the activity of our basic parts.

Basic parts

Our basic parts fall into three categories: Recombinase generators, recombinase target sites, and orthogonal target sites for Cre. We selected the recombinases Dre [1], Vika [2], VCre, and SCre [3] to form the basis of our toolkit. These recombinases were shown to not cross-react with the Cre/LoxP system [1][2][3][5], and, in the case of VCre and SCre [3], were claimed to not cross-react with one another. As part of our toolkit, we also included the associated target sites for these recombinase generators. For a snapshot of how we verified the function of these parts, scroll down to the “Demonstrate” section of this page. For a more detailed view, click on the parts registry link, which will take you to the detailed analysis of each individual part. We also included in the toolkit orthogonal target sites for Cre recombinase. Cre/LoxP is a very popular recombinase system that is frequently used in biotechnology [4]. In order to expand the potential of this system, we have developed multiple mutant Lox target sites, which have previously been identified as sites that will not react with the classic LoxP site [4]. Adding these mutant, orthogonal lox sites to the toolkits means we provide a framework whereby one Cre protein could catalyse up to ten distinct recombination events within one cell. Once again, check out the full registry pages for each part to learn more and download their individual sequences. To simplify our experimental workflows, we have also developed an inducible Cre recombinase generator, also reported below.

T7-LacO-Dre Basic Recombinase generator Bba_K2406081 Shown to excise terminator inducibly http://parts.igem.org/Part:BBa_K2406081