Team:Northwestern/Project

From 2014.igem.org

(Difference between revisions)
 
(112 intermediate revisions not shown)
Line 1: Line 1:
{{CSS/Main}}
{{CSS/Main}}
{{:Team:Northwestern/Templates/Reset}}
{{:Team:Northwestern/Templates/Reset}}
-
{{:Team:Northwestern/Templates/noscript}}
+
{{Team:Northwestern/Template/nav_only}}
-
{{:Team:Northwestern/Templates/Escape}}
+
{{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="" />
+
-
<link href="http://fonts.googleapis.com/css?family=Source+Sans+Pro:400,400italic,700,900" rel="stylesheet" />
+
-
<script src="js/jquery.min.js"></script>
+
-
<script src="js/jquery.dropotron.min.js"></script>
+
-
<script src="js/config.js"></script>
+
-
<script src="js/skel.min.js"></script>
+
-
<script src="js/skel-panels.min.js"></script>
+
-
<noscript>
+
-
<link rel="stylesheet" href="css/skel-noscript.css" />
+
-
<link rel="stylesheet" href="css/style.css" />
+
-
<link rel="stylesheet" href="css/style-desktop.css" />
+
-
</noscript>
+
-
<!--[if lte IE 8]><script src="js/html5shiv.js"></script><link rel="stylesheet" href="css/ie8.css" /><![endif]-->
+
-
</head>
+
-
<body class="left-sidebar">
+
-
<!-- Header Wrapper -->
+
.btn a:visited {
-
<div id="header-wrapper" class="wrapper">
+
-
<div class="container">
+
-
<div class="row">
+
-
<div class="12u">
+
-
+
-
<!-- Header -->
+
-
<div id="header">
+
-
+
-
<!-- Logo -->
+
-
<div id="logo">
+
-
<h1><a href="#">Think Outside the Cell!</a></h1>
+
-
<span class="byline">Breaking Down Walls</span>
+
-
</div>
+
-
<img src="http://www.northwestern.edu/african-studies/images/northwestern-university-seal-logo.png"/>
+
-
<!-- /Logo -->
+
-
+
-
<!-- Nav -->
+
-
<nav id="nav">
+
-
                                          <a href ="https://2014.igem.org/Main_Page"><img src="https://static.igem.org/mediawiki/2012/archive/f/f0/20120817084834!IGEM_logo.png" id="igemlogo"/></a>
+
-
<ul>
+
-
                                               
+
-
<li class="current_page_item"><a href="2014.igem.org/Team:Northwestern">Home</a></li>
+
-
<li>
+
-
                                       
+
-
<span>Project</span>
+
-
<ul>
+
-
<li><a href="#">Overview</a></li>
+
-
<li><a href="#">Parts</a></li>
+
-
<li><a href="#">Modeling</a></li>
+
-
<li>
+
-
<span>Other information</span>
+
-
<ul>
+
-
<li><a href="#">Possible list item 1</a></li>
+
-
<li><a href="#">Possible list item 2</a></li>
+
-
<li><a href="#">Possible list item 3</a></li>
+
-
<li><a href="#">Possible list item 4</a></li>
+
-
<li><a href="#">Possible list item 5</a></li>
+
-
</ul>
+
-
</li>
+
-
<li><a href="#">Even more information</a></li>
+
-
</ul>
+
-
</li>
+
-
<li><a href="https://2014.igem.org/Team:Northwestern/Team">Official team profile</a></li>
+
-
<li><a href="https://2014.igem.org/Team:Northwestern/Notebook">Notebook</a></li>
+
-
                                                <li><a href="https://2014.igem.org/Team:Northwestern/Safety">Safety</a></li>
+
-
                                                <li><a href="https://2014.igem.org/Team:Northwestern/Attributions">Attributions</a></li>
+
-
</ul>
+
-
</nav>
+
-
<!-- /Nav -->
+
-
</div>
+
color: #fff;
-
<!-- /Header -->
+
}
-
</div>
+
.jumbotron {
-
</div>
+
background-image: url('https://static.igem.org/mediawiki/2014/7/71/Weird_colonies.JPG');
-
</div>
+
background-repeat: no-repeat;
-
</div>
+
background-attachment: fixed;
-
<!-- /Header Wrapper -->
+
backgroud-size: 100% auto;
-
+
height: 400px;
-
<!-- Main Wrapper -->
+
}
-
<div class="wrapper wrapper-style2">
+
-
<div class="title">Overview</div>
+
-
<div class="container">
+
-
<div class="row">
+
-
<div class="12u">
+
-
+
-
<!-- Main -->
+
-
<div id="main">
+
-
<div>
+
-
<div class="row">
+
-
<div class="4u">
+
-
+
-
<!-- Sidebar -->
+
-
<div id="sidebar">
+
-
+
-
<section class="is">
+
-
<header>
+
-
<h2 class="title">Heading</h2>
+
-
</header>
+
-
+
-
+
-
</section>
+
-
<section class="is">
+
-
<header>
+
-
<h2 class="title">Sources</h2>
+
-
</header>
+
-
<ul class="style3">
+
-
<li><a href="#">Links</a></li>
+
-
<li><a href="#">Links</a></li>
+
-
<li><a href="#">Links</a></li>
+
-
<li><a href="#">Links</a></li>
+
-
<li><a href="#">Links</a></li>
+
-
<li><a href="#">Links</a></li>
+
-
+
.jumbotron h1{
-
</ul>
+
color: #fff;
-
</section>
+
}
-
</div>
+
-
<!-- /Sidebar -->
+
-
+
-
</div>
+
-
<div class="Main66">
+
-
+
-
<!-- Content -->
+
-
<div id="content">
+
-
<header class="style1">
+
-
<h2 class="title">We are still working on our project description...</h2>
+
-
+
-
</header>
+
-
+
-
<p>The possibilities through synthetic biology are endless, but oftentimes the foundational scientific methods are not fully optimized or explored.  Each project operates fairly autonomously, pulling on the work of others to aid research, yet sometimes plowing ahead to solve the problem at hand without the contributions from predecessors.  The most categorized and recognized promoters are the Anderson Promoters. However, the rank classification for these promoters are based on the relative strength of maximum fluorescence and nothing else
+
-
+
-
<p>We aim to categorize the function of a number of promoters based on absolute maximum fluorescence and the time it took to reach that point.  For industrial applications a quicker response time can minimize reaction time which could lead to economic benefit.  The goal of our project was to explore and compare the different transcriptional and translational rates of known model organisms such as E. coli to various non-model strains, with all processes taking place in cell free systems. Additionally, instead of testing all possible combinations of promoters, RBSs, and organisms, we tested a select number and then used predictive modeling to assess which combination yielded the strongest glow/signal/fluorescence.  This is in the hopes that by compiling a list of well-characterized parts such as promoters and RBSs, the information could be used to further the field of synthetic biology through environmental, health, and industrial applications by minimizing the need to extensively modify E. Coli to meet particular environmental factors.
+
-
</p>
+
.list-group-item-text{
 +
font-size: 0.8em;
 +
}
 +
.list-group {
 +
border: none;
 +
}
 +
</style>
 +
</head>
 +
<body>
 +
<div class="animated fadeIn">
 +
<div class="jumbotron">
 +
<div class="container">
 +
<h1>Project Overview</h1>
 +
</div>
 +
</div>
 +
</div>
 +
 
 +
 
 +
<div class="container">
 +
<div class="animated fadeInDownBig">
 +
  <img class="img-rounded" src="https://static.igem.org/mediawiki/2014/e/e9/Experimentaldesign.png"/>
 +
</div>
 +
<div class="row">
 +
<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>
-
+
<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>
 +
 
 +
<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>
 +
 
</div>
</div>
 +
       
 +
<div class="col-xs-6 col-md-4">
 +
    <h4>Sources</h4>
 +
       
 +
                <h5 class="list-group-item-heading">
 +
                    <a data-toggle="collapse" data-parent="#accordion" href="#collapseOne">Team Warsaw 2010</a>
 +
                </h5>
 +
        <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>
 +
                </div>
 +
           
 +
       
 +
       
 +
                <h5 class="list-group-item-heading">
 +
                    <a data-toggle="collapse" data-parent="#accordion" href="#collapseTwo">Freemont: Cell Free Systems</a>
 +
                </h5>
 +
            <div id="collapseTwo" class="panel-collapse collapse">
 +
                    <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>
 +
                </div>
 +
           
 +
       
 +
       
 +
                <h5 class="list-group-item-heading">
 +
                    <a data-toggle="collapse" data-parent="#accordion" href="#collapseThree">Spinach Aptamer</a>
 +
                </h5>
 +
            <div id="collapseThree" class="panel-collapse collapse">
 +
                    <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>
 +
                </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>
 +
</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"