Difference between revisions of "Team:ICT-Mumbai/Parts"

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{{ICT-Mumbai}}
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<html>
 
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<title>ICT-Mumbai 2017</title>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<link rel="stylesheet" href="https://www.w3schools.com/w3css/4/w3.css">
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<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Lato">
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
  
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<style>
  
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#sideMenu
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{display:none; /*Disable the display of the annoying side main menu*/}
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#top_title
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{display:none; /* Disable the annoying title*/}
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#content
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{padding:0px; width:100%; margin-left:0%; margin-right:0%;background-color: rgba(255,255,255);}
  
  
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body,h1,h2,h3,h4,h5,h6 {font-family: "Source Sans Pro", sans-serif;}
  
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<div class="column full_size">
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body, html {
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    height: 100%;
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    color: rgba(255,255,255);
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}
  
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<h1>Parts</h1>
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img {
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    display: block;
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    margin: auto;
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    width: 50%;
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}
  
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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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/* Create a Parallax Effect */
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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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.bgimg-1, .bgimg-2, .bgimg-3 {
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    background-attachment: fixed;
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    background-position: center;
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    background-repeat: no-repeat;
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    background-size: cover;
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}
  
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/* First image (Logo. Full height) */
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.bgimg-1 {
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    background-image: url("https://static.igem.org/mediawiki/2017/d/d5/PARTS.png");
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    min-height: 500px;
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}
  
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    <a class="w3-bar-item w3-button w3-hover-black w3-hide-medium w3-hide-large w3-right" href="javascript:void(0);" onclick="toggleFunction()" title="Toggle Navigation Menu">
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      <i class="fa fa-bars"></i>
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    </a>
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  <a href="https://2017.igem.org/Team:ICT-Mumbai" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-home" aria-hidden="true"></i>
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Home</a>
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<div class="w3-dropdown-hover">
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<button class="w3-button" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-flask" aria-hidden="true"></i>
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    Project</button></a>
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<div class="w3-dropdown-content w3-bar-block w3-animate-opacity">
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/Background" class="w3-bar-item w3-button">Background</a>
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/Description" class="w3-bar-item w3-button">Description</a>
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/Design" class="w3-bar-item w3-button">Design</a>
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/Protocols" class="w3-bar-item w3-button">Protocols</a>
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/Notebook"class="w3-bar-item w3-button">Notebook</a>
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/InterLab"class="w3-bar-item w3-button">Interlab</a>
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/Results"class="w3-bar-item w3-button">Results</a>
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</div>
 
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    <div class="w3-dropdown-hover">
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<button class="w3-button" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-users" aria-hidden="true"></i>Team</button></a>
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<div class="w3-dropdown-content w3-bar-block w3-animate-opacity">
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/Team"class="w3-bar-item w3-button">Team</a>
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        <a href="https://2017.igem.org/Team:ICT-Mumbai/Collaborations" class="w3-bar-item w3-button">Collaborations</a>
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</div>
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</div>
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    <div class="w3-dropdown-hover">
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<a href="https://2017.igem.org/Team:ICT-Mumbai/Parts" button class="w3-button" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-cogs" aria-hidden="true"></i>  Part</a>
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</div>
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<a href="https://2017.igem.org/Team:ICT-Mumbai/Safety" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-flag" aria-hidden="true"></i>
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Safety</a>
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<a href="https://2017.igem.org/Team:ICT-Mumbai/HP/Gold_Integrated" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-handshake-o" aria-hidden="true"></i>
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Human Practices</a>
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<a href="https://2017.igem.org/Team:ICT-Mumbai/Attributions" class="w3-bar-item w3-button w3-hide-small"><i class="fa fa-user-o" aria-hidden="true"></i>Attributions</a>
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  </div>
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  <!-- Navbar on small screens -->
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  <div id="navDemo" class="w3-bar-block w3-white w3-hide w3-hide-large w3-hide-medium">
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    <a href="#about" class="w3-bar-item w3-button" onclick="toggleFunction()">ABOUT</a>
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    <a href="#portfolio" class="w3-bar-item w3-button" onclick="toggleFunction()">PORTFOLIO</a>
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    <a href="#contact" class="w3-bar-item w3-button" onclick="toggleFunction()">CONTACT</a>
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    <a href="#" class="w3-bar-item w3-button">SEARCH</a>
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  </div>
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</div>
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<!-- First Parallax Image with Logo Text -->
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<div class="bgimg-1 w3-display-container" id="home">
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<div class="w3-content w3-container w3-padding-64" id="about">
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<div>
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<p style="height:70 px; font-family:'Lato'; font-size:20px; colour:lightgrey;">
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Our project involves metabolism of ammonia by <i>Escherichia coli</i> to produce a blue-coloured dye,
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indigoidine. We had to choose between using a constitutive and an inducible promoter to drive
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expression of the genes that we wish to express in <i>E. coli</i>.</p>
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<p style="height:70 px; font-family:'Lato'; font-size:20px; colour:lightgrey;">Expression from inducible promoters requires addition of an inducing molecule. However, as it would be
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cumbersome and tedious to add the inducer to the device that will house the engineered <i>E. coli</i>, and as
 +
it would also contribute to the cost, we decided to use a constitutive promoter to drive gene expression.</p>
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<p style="height:70 px; font-family:'Lato'; font-size:20px; colour:lightgrey;">We reasoned that the constitutive promoter of choice should have the following two properties: (1) it
 +
should not be a very strong promoter, so as to not lead to any toxicity to the cell, and (2) it should be
 +
active in low-nutrient conditions. Based on these two considerations, the commonly used glycolytic
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promoters were ruled out as possible choices.</p>
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<p style="height:70 px; font-family:'Lato'; font-size:20px; colour:lightgrey;">The <i>ychH</i> promoter has been described in literature to be active under low glucose conditions (Ref. 1). Crp acts as a positive transcription regulator of <i>ychH</i>, which means that this gene is expressed when glucose concentrations are low (Ref. 2; <a href="https://ecocyc.org/"><mark>EcoCyc database</mark></a>). Moreover, it is not a very strong promoter, compared to those frequently employed to express recombinant proteins in <i>E. coli</i> (Ref. 3). Therefore, the <i>ychH</i> promoter became our promoter of choice.</p>
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<br>
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<!--<div class="column full_size">
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<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;">Parts</p>
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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>
 +
<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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</div>
  
 
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
 
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
 
</ul>
 
</ul>
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<!--<div class="column full_size">
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<h5>Part Table </h5>
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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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<div class="w3-content w3-container w3-padding-64" id="about">
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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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<div class="highlight">
  
 
</html>
 
</html>
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<center>
 
<groupparts>iGEM17 ICT-Mumbai</groupparts>
 
<groupparts>iGEM17 ICT-Mumbai</groupparts>
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</center>
 
<html>
 
<html>
 
</div>
 
</div>
 
</div>
 
</div>
  
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<div class="w3-content w3-container w3-padding-64" id="about">
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<div>
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<br>
  
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<p style="height:70 px;  font-family:'Lato';  font-size:20px; colour:lightgrey;"><b>References</b></p>
 +
<ol>
 +
<li>Hollands K, Busby SJ, Lloyd GS (2007). New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome. FEMS Microbiol Lett 274:89-94. PMID: 17608696</li>
 +
<li>Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD (2013). EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 41(Database issue):D605-612. PMID: 23143106</li>
 +
<li>Deb SS, Reshamwala SMS, Lali AM (2016). A series of template plasmids for Escherichia coli genome engineering. J Microbiol Methods 125:49-57. PMID: 27071533</li>
 +
</ol>
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</p>
  
  
 
</html>
 
</html>

Latest revision as of 21:50, 1 November 2017

ICT-Mumbai 2017

Our project involves metabolism of ammonia by Escherichia coli to produce a blue-coloured dye, indigoidine. We had to choose between using a constitutive and an inducible promoter to drive expression of the genes that we wish to express in E. coli.

Expression from inducible promoters requires addition of an inducing molecule. However, as it would be cumbersome and tedious to add the inducer to the device that will house the engineered E. coli, and as it would also contribute to the cost, we decided to use a constitutive promoter to drive gene expression.

We reasoned that the constitutive promoter of choice should have the following two properties: (1) it should not be a very strong promoter, so as to not lead to any toxicity to the cell, and (2) it should be active in low-nutrient conditions. Based on these two considerations, the commonly used glycolytic promoters were ruled out as possible choices.

The ychH promoter has been described in literature to be active under low glucose conditions (Ref. 1). Crp acts as a positive transcription regulator of ychH, which means that this gene is expressed when glucose concentrations are low (Ref. 2; EcoCyc database). Moreover, it is not a very strong promoter, compared to those frequently employed to express recombinant proteins in E. coli (Ref. 3). Therefore, the ychH promoter became our promoter of choice.


Part Table

<groupparts>iGEM17 ICT-Mumbai</groupparts>


References

  1. Hollands K, Busby SJ, Lloyd GS (2007). New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome. FEMS Microbiol Lett 274:89-94. PMID: 17608696
  2. Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD (2013). EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 41(Database issue):D605-612. PMID: 23143106
  3. Deb SS, Reshamwala SMS, Lali AM (2016). A series of template plasmids for Escherichia coli genome engineering. J Microbiol Methods 125:49-57. PMID: 27071533