Team:Northwestern/Project

From 2014.igem.org

(Difference between revisions)
 
(44 intermediate revisions not shown)
Line 1: Line 1:
{{CSS/Main}}
{{CSS/Main}}
{{:Team:Northwestern/Templates/Reset}}
{{:Team:Northwestern/Templates/Reset}}
-
{{Team:Northwestern/Template/bootstrap}}
+
{{Team:Northwestern/Template/nav_only}}
-
{{Team:Northwestern/Template/nav}}
+
{{Team:Northwestern/Template/bootstrap/orange}}
-
 
+
-
 
+
-
 
+
<html>
<html>
-
<head>
+
<head>
-
<title>Our Project: Modelling Non-Model Organism</title>
+
<style>
-
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
+
-
<meta name="description" content="" />
+
-
<meta name="keywords" content="" />
+
-
+
-
                <style>
+
-
.jumbotron {
+
-
 
+
-
background-color: rgb(210,255,82);
+
-
background: -webkit-gradient(linear, left top, right bottom, color-stop(0%,rgba(210,255,82,1)), color-stop(100%,rgba(145,232,66,1)));
+
-
margin-top: -10px;
+
-
}
+
.btn a:visited {
.btn a:visited {
color: #fff;
color: #fff;
-
 
}
}
-
 
+
.jumbotron {
-
h4 {
+
background-image: url('https://static.igem.org/mediawiki/2014/7/71/Weird_colonies.JPG');
-
  margin-top: 25px;
+
background-repeat: no-repeat;
 +
background-attachment: fixed;
 +
backgroud-size: 100% auto;
 +
height: 400px;
}
}
-
.row {
 
-
  margin-bottom: 20px;
 
-
}
 
-
.row .row {
 
-
  margin-top: 10px;
 
-
  margin-bottom: 0;
 
-
}
 
-
[class*="col-"] {
 
-
  padding-top: 15px;
 
-
  padding-bottom: 15px;
 
-
  background-color: #fff;
 
 +
.jumbotron h1{
 +
color: #fff;
}
}
-
hr {
+
.list-group-item-text{
-
  margin-top: 40px;
+
font-size: 0.8em;
-
  margin-bottom: 40px;
+
}
}
-
navbar-wrapper {
+
.list-group {
-
  margin-top: 40px;
+
border: none;
-
}
+
-
.list-group-item-text p{
+
-
font-size: 0.8em;
+
}
}
</style>
</style>
-
</head>
 
-
 
</head>
</head>
-
<!-- NAVBAR========================================= -->
+
<body>
-
  <body>
+
<div class="animated fadeIn">
-
   
+
-
<div class="navbar-wrapper">
+
-
      <div class="container">
+
-
 
+
-
        <div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
+
-
          <div class="container">
+
-
            <div class="navbar-header">
+
-
              <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target=".navbar-collapse">
+
-
                <span class="sr-only">Toggle navigation</span>
+
-
                <span class="icon-bar"></span>
+
-
                <span class="icon-bar"></span>
+
-
                <span class="icon-bar"></span>
+
-
              </button>
+
-
              <a class="navbar-brand" href="https://2014.igem.org/Team:Northwestern/Home">Home</a>
+
-
            </div>
+
-
            <div class="navbar-collapse collapse">
+
-
              <ul class="nav navbar-nav">
+
-
              <li class="active"><a href="https://2014.igem.org/Team:Northwestern/Project">Project</a></li>
+
-
                <li><a href="https://2014.igem.org/Team:Northwestern/Team">Team</a></li>
+
-
                <li><a href="https://2014.igem.org/Team:Northwestern/Safety">Safety</a></li>
+
-
                <li><a href="https://2014.igem.org/Team:Northwestern/Notebook">Notebook</a></li>
+
-
                <li class="dropdown">
+
-
                  <a href="#"class="dropdown-toggle" data-toggle="dropdown">To be fixed soon<span class="caret"></span></a>
+
-
                  <ul class="dropdown-menu" role="menu">
+
-
                    <li><a href="#">Action</a></li>
+
-
                    <li><a href="#">Another action</a></li>
+
-
                    <li><a href="#">Something else here</a></li>
+
-
                    <li class="divider"></li>
+
-
                    <li class="dropdown-header">Nav header</li>
+
-
                    <li><a href="#">Separated link</a></li>
+
-
                    <li><a href="#">One more separated link</a></li>
+
-
                  </ul>
+
-
                </li>
+
-
              </ul>
+
-
            </div>
+
-
          </div>
+
-
        </div>
+
-
 
+
-
      </div>
+
-
    </div>
+
-
 
+
-
<!--Jumbotron-->
+
<div class="jumbotron">
<div class="jumbotron">
-
  <div class="container">
+
<div class="container">
-
    <h1>NU Models: Breaking Down Walls</h1>
+
<h1>Project Overview</h1>
-
  <p>Using the cell free system to explore non-model organisms</p>
+
</div>
-
  <p><a href="#" class="btn btn-primary btn-lg" role="button">Scroll Down to Learn more</a></p>
+
</div>
-
  </div>
+
</div>
</div>
-
 
+
 
-
<!--MAIN CONTENT--->
+
<div class="container">
-
<div class="container">
+
<div class="animated fadeInDownBig">
-
<div class="page-header">
+
   <img class="img-rounded" src="https://static.igem.org/mediawiki/2014/e/e9/Experimentaldesign.png"/>
-
   <h1>Here is a brief overview of our project<small> still a work in progress...</small></h1>
+
</div>
</div>
-
 
-
<div class="container">
 
  <div class="row">
  <div class="row">
-
        <div class="col-xs-12 col-md-8">
+
<div class="page-header">
 +
  <h4>Overview</h4>
 +
</div>     
 +
<div class="col-xs-12 col-md-8">
-
<p class="lead">The cornerstone of synthetic biology is the characterization of genetic parts for predictable action in an engineered biochemical system. Currently this characterization of parts is limited to the “Model Organisms” of synthetic biology: E. coli, yeast, and C. elegans. While this work has been very successful in pioneering research in synthetic biology, characterization in a given model organism such as the primary bacterial model, E. coli, does not necessarily hold true across all bacteria. Therefore, the majority of research overlooks the possible benefits of synthetic work in other bacteria such as Streptomyces, Pseudomonas, and Nitrosomonas.
+
<p class="lead">The cornerstone of synthetic biology is the characterization of genetic parts for predictable action in an engineered biochemical system. Currently this characterization of parts is limited to the “Model Organisms” of synthetic biology: E. coli, yeast, and C. elegans. While this work has been very successful in pioneering research in synthetic biology, characterization in a given model organism such as the primary bacterial model, E. coli, does not necessarily hold true across all bacteria. Therefore, the majority of research overlooks the possible benefits of synthetic work in other bacteria such as Streptomyces, Pseudomonas, and Nitrosomonas. </p>
-
<p>The main reason for this omission is that initiating work in these organisms is very challenging due to the present difficulty in attempting to transform these non-model strains. Standard protocols have not been developed in all bacteria for incorporation of synthetic DNA through transformation due to the difficulty in developing these protocols. The development of these protocols can be very unrewarding as the investment in time is high, the success rate is often low, and the incentive is small since very few parts are characterized for non-model strains.
+
<p>The main reason for this omission is that initiating work in these organisms is very challenging due to the present difficulty in attempting to transform these non-model strains. Standard protocols have not been developed in all bacteria for incorporation of synthetic DNA through transformation due to the difficulty in developing these protocols. The development of these protocols can be very unrewarding as the investment in time is high, the success rate is often low, and the incentive is small since very few parts are characterized for non-model strains. </p>
-
<p> NU Models seeks to crack open the field relating to non-model strains. We bypass transformation difficulties by utilizing a cell-free system to characterize a number of promoters and RBSs to incentivize future work in promising non-model strains. Past literature has indicated that characterization in cell-free systems in E. coli has a high correlation to characterization in living cell systems. This indicates that cell-free systems may also be a predictive model for living cells of non-model strains of bacteria.
+
<p> NU Models seeks to crack open the field relating to non-model strains. We bypass transformation difficulties by utilizing a cell-free system to characterize a number of promoters and RBSs to incentivize future work in promising non-model strains. Past literature has indicated that characterization in cell-free systems in E. coli has a high correlation to characterization in living cell systems. This indicates that cell-free systems may also be a predictive model for living cells of non-model strains of bacteria. </p>
-
<p> Our organisms which are non-model in the field of synthetic biology are actually model organisms in their own fields. Streptomyces species have long been a source of novel antibiotics. The impressive secondary metabolism of Streptomyces species is a unique feature to this Genus and provides potential applications impossible in E. coli. Pseudomonas has long been used in agriculture on crops to outcompete other organisms. Nitrosomonas is the model for obligate ammonia autotrophs and is used in bioremediation.
+
<p> Our organisms which are non-model in the field of synthetic biology are actually model organisms in their own fields. Streptomyces species have long been a source of novel antibiotics. The impressive secondary metabolism of Streptomyces species is a unique feature to this Genus and provides potential applications impossible in E. coli. Pseudomonas has long been used in agriculture on crops to outcompete other organisms. Nitrosomonas is the model for obligate ammonia autotrophs and is used in bioremediation.</p>
-
 
+
<p> The development of systems characterizing parts for these organisms is important for the development of new biotechnologies. The innate skill-set of these non-model organisms have potential to allow work that E. coli is ill-equipped to handle.</p>
-
<p> The development of systems characterizing parts for these organisms is important for the development of new biotechnologies. The innate skill-set of these non-model organisms have potential to allow work that E. coli is ill-equipped to handle.
+
-
 
+
-
</p>
+
</div>
</div>
-
 
          
          
<div class="col-xs-6 col-md-4">
<div class="col-xs-6 col-md-4">
     <h4>Sources</h4>
     <h4>Sources</h4>
-
         <div class="list-group">
+
          
-
                 <h4 class="list-group-item-heading">
+
                 <h5 class="list-group-item-heading">
                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseOne">Team Warsaw 2010</a>
                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseOne">Team Warsaw 2010</a>
-
                 </h4>
+
                 </h5>
-
         <div id="collapseOne" class="panel-collapse collapse in">
+
         <div id="collapseOne" class="panel-collapse collapse">
                     <p class="list-group-item-text">click<a href="https://2010.igem.org/Team:Warsaw/Project"> here</a> to view their project description. They had a similar project to ours; they characterized a library of promoters and RBS</p>
                     <p class="list-group-item-text">click<a href="https://2010.igem.org/Team:Warsaw/Project"> here</a> to view their project description. They had a similar project to ours; they characterized a library of promoters and RBS</p>
                 </div>
                 </div>
-
             </div>
+
              
          
          
          
          
-
                 <h4 class="list-group-item-heading">
+
                 <h5 class="list-group-item-heading">
                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseTwo">Freemont: Cell Free Systems</a>
                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseTwo">Freemont: Cell Free Systems</a>
-
                 </h4>
+
                 </h5>
             <div id="collapseTwo" class="panel-collapse collapse">
             <div id="collapseTwo" class="panel-collapse collapse">
-
                <div class="list-group-item-text">
+
                    <p class="list-group-item-text">The paper "Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology" can be viewed<a href="http://nar.oxfordjournals.org/content/early/2013/01/31/nar.gkt052.full.pdf#page=1&view=FitH"> here</a></p>
-
                    <p>The paper "Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology" can be viewed<a href="http://nar.oxfordjournals.org/content/early/2013/01/31/nar.gkt052.full.pdf#page=1&view=FitH">here</a></p>
+
                 </div>
                 </div>
-
             </div>
+
              
          
          
          
          
-
                 <h4 class="list-group-item-heading">
+
                 <h5 class="list-group-item-heading">
-
                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseThree">Third link</a>
+
                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseThree">Spinach Aptamer</a>
-
                 </h4>
+
                 </h5>
             <div id="collapseThree" class="panel-collapse collapse">
             <div id="collapseThree" class="panel-collapse collapse">
-
                 <div class="list-group-item-text">
+
                    <p class="list-group-item-text">The Spinach Aptamer can help with the monitoring of promoter activity via fluorescence and a paper describing such work in a cell-free system can be found <a href="http://pubs.acs.org/doi/pdf/10.1021/sb4000977"> here</a></p>
-
                     <p>third link info goes<a href="#">here</a></p>
+
                 </div>
 +
 
 +
 
 +
 
 +
                <h5 class="list-group-item-heading">
 +
                    <a data-toggle="collapse" data-parent="#accordion" href="#collapseFour">Anderson Promoter Collection</a>
 +
                </h5>
 +
            <div id="collapseFour" class="panel-collapse collapse">
 +
                     <p class="list-group-item-text">Chris Anderson and the 2006 Berkeley iGEM team categorized the relative strength of promoters; their work is detailed in the iGEM Registry of Standard Biological Parts, which can be found<a href="http://parts.igem.org/Promoters/Catalog/Anderson"> here</a></p>
                 </div>
                 </div>
 +
 +
             </div>
             </div>
         </div>
         </div>
     </div>
     </div>
 +
</div>
-
      </div>
 
-
 
-
</div>
 
-
 
-
</div>
 
-
 
-
</div>
 
</body>
</body>
</html>
</html>

Latest revision as of 00:28, 18 October 2014

Dropdown menu from bootstrap

Project Overview

Overview

The cornerstone of synthetic biology is the characterization of genetic parts for predictable action in an engineered biochemical system. Currently this characterization of parts is limited to the “Model Organisms” of synthetic biology: E. coli, yeast, and C. elegans. While this work has been very successful in pioneering research in synthetic biology, characterization in a given model organism such as the primary bacterial model, E. coli, does not necessarily hold true across all bacteria. Therefore, the majority of research overlooks the possible benefits of synthetic work in other bacteria such as Streptomyces, Pseudomonas, and Nitrosomonas.

The main reason for this omission is that initiating work in these organisms is very challenging due to the present difficulty in attempting to transform these non-model strains. Standard protocols have not been developed in all bacteria for incorporation of synthetic DNA through transformation due to the difficulty in developing these protocols. The development of these protocols can be very unrewarding as the investment in time is high, the success rate is often low, and the incentive is small since very few parts are characterized for non-model strains.

NU Models seeks to crack open the field relating to non-model strains. We bypass transformation difficulties by utilizing a cell-free system to characterize a number of promoters and RBSs to incentivize future work in promising non-model strains. Past literature has indicated that characterization in cell-free systems in E. coli has a high correlation to characterization in living cell systems. This indicates that cell-free systems may also be a predictive model for living cells of non-model strains of bacteria.

Our organisms which are non-model in the field of synthetic biology are actually model organisms in their own fields. Streptomyces species have long been a source of novel antibiotics. The impressive secondary metabolism of Streptomyces species is a unique feature to this Genus and provides potential applications impossible in E. coli. Pseudomonas has long been used in agriculture on crops to outcompete other organisms. Nitrosomonas is the model for obligate ammonia autotrophs and is used in bioremediation.

The development of systems characterizing parts for these organisms is important for the development of new biotechnologies. The innate skill-set of these non-model organisms have potential to allow work that E. coli is ill-equipped to handle.

Sources

Team Warsaw 2010

click here to view their project description. They had a similar project to ours; they characterized a library of promoters and RBS

Freemont: Cell Free Systems

The paper "Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology" can be viewed here

Spinach Aptamer

The Spinach Aptamer can help with the monitoring of promoter activity via fluorescence and a paper describing such work in a cell-free system can be found here

Anderson Promoter Collection

Chris Anderson and the 2006 Berkeley iGEM team categorized the relative strength of promoters; their work is detailed in the iGEM Registry of Standard Biological Parts, which can be found here

Retrieved from "http://2014.igem.org/Team:Northwestern/Project"