Team:Edinburgh/Project

From 2010.igem.org

(Difference between revisions)
 
(15 intermediate revisions not shown)
Line 10: Line 10:
#body{
#body{
-
background-image:url("https://static.igem.org/mediawiki/2010/a/a8/Ed10-LargePaper.jpg");
+
background-image:url("https://static.igem.org/mediawiki/2010/9/9e/Ed10-LargePaperRipped.jpg");
background-repeat:repeat-y;
background-repeat:repeat-y;
}
}
Line 48: Line 48:
   <li><a href="https://2010.igem.org/Team:Edinburgh/BioBricks#Genomic">submitted parts</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/BioBricks#Genomic">submitted parts</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Results#Genomic">results</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Results#Genomic">results</a></li>
-
   <li><a href="https://2010.igem.org/Team:Edinburgh/Project/Future">future work</a></li>
+
   <li><a href="https://2010.igem.org/Team:Edinburgh/Project/Future">the future</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Project/References">references</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Project/References">references</a></li>
   </ul>
   </ul>
Line 55: Line 55:
  <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial" class="dir">bacterial BRIDGEs</a>
  <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial" class="dir">bacterial BRIDGEs</a>
   <ul>
   <ul>
-
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Core_repressilator">the repressilator</a></li>
+
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Core_repressilator">the project</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Red_light_producer">red light</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Red_light_producer">red light</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Red_light_sensor">red sensor</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Red_light_sensor">red sensor</a></li>
Line 64: Line 64:
   <li><a href="https://2010.igem.org/Team:Edinburgh/BioBricks#Bacterial">submitted parts</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/BioBricks#Bacterial">submitted parts</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Results#Bacterial">results</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Results#Bacterial">results</a></li>
-
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Future">future work</a></li>
+
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/Future">the future</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/References">references</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Bacterial/References">references</a></li>
   </ul>
   </ul>
Line 75: Line 75:
   <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">the bacterial model</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/Bacterial">the bacterial model</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/Signalling">the signalling model</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/Signalling">the signalling model</a></li>
 +
  <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/Tools">tools</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Results#Modelling">results</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Results#Modelling">results</a></li>
-
   <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/Future">future work</a></li>
+
   <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/Future">the future</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/References">references</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Modelling/References">references</a></li>
   </ul>
   </ul>
Line 83: Line 84:
  <li><a href="https://2010.igem.org/Team:Edinburgh/Human" class="dir">human BRIDGEs</a>
  <li><a href="https://2010.igem.org/Team:Edinburgh/Human" class="dir">human BRIDGEs</a>
   <ul>
   <ul>
-
   <li><a href="https://2010.igem.org/Team:Edinburgh/Human/Aspects">human aspects</a></li>
+
   <li><a href="https://2010.igem.org/Team:Edinburgh/Human/Communication">communication of science</a></li>
 +
  <li><a href="https://2010.igem.org/Team:Edinburgh/Human/Branding">iGEM survey</a></li>
 +
  <li><a href="https://2010.igem.org/Team:Edinburgh/Human/Conversations">conversations</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Human/Epic">the epic</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Human/Epic">the epic</a></li>
-
   <li><a href="https://2010.igem.org/Team:Edinburgh/Results#Human">results</a></li>
+
   <li><a href="https://2010.igem.org/Team:Edinburgh/Human/FutureApps">future applications</a></li>
-
   <li><a href="https://2010.igem.org/Team:Edinburgh/Human/Future">future work</a></li>
+
   <li><a href="https://2010.igem.org/Team:Edinburgh/Results#Human">further thoughts</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Human/References">references</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Human/References">references</a></li>
   </ul>
   </ul>
Line 93: Line 96:
  <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook" class="dir">lab notes&nbsp;&nbsp;&nbsp;</a>
  <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook" class="dir">lab notes&nbsp;&nbsp;&nbsp;</a>
   <ul>
   <ul>
-
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook">collaboration</a></li>
+
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Collaboration">collaboration</a></li>
 +
  <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Attribution">attribution</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/BRIDGE">BRIDGE</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/BRIDGE">BRIDGE</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Red_light_producer">red light</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Red_light_producer">red light</a></li>
Line 99: Line 103:
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Blue_light_producer">blue light</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Blue_light_producer">blue light</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Blue_light_sensor">blue sensor</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Blue_light_sensor">blue sensor</a></li>
 +
  <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Green_light_producer">green light</a></li>
 +
  <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Green_light_sensor">green sensor</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Modelling">modelling</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Modelling">modelling</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Safety">safety</a></li>
   <li><a href="https://2010.igem.org/Team:Edinburgh/Notebook/Safety">safety</a></li>
Line 114: Line 120:
<br>
<br>
-
<div id="body" style="padding: 0px 60px 10px 60px; height: 1356px">
+
<div id="body" style="padding: 0px 60px 10px 60px; height: 998px">
<br>
<br>
Line 120: Line 126:
<br>
<br>
-
<a name="Concept" id="Concept"></a><h2>BRIDGE: The concept</h2>
+
<a name="Introduction" id="Introduction"></a><h2>Genomic BRIDGEs</h2>
-
<br>
+
-
<p>BRIDGE stands for BioBrick Recombineering In Direct Genomic Editing. It is an alternative method for inserting BioBricks into the genome by using homologous recombination instead of restriction digestion, with the added bonus of not leaving a marker behind in the product.</p><br>
+
-
<br>
+
-
<center><p><img src="https://static.igem.org/mediawiki/2010/5/5c/Ed10-OriginalBridge.JPG" width="800" height="441" border="0" /></p><br>
+
-
<p>Image: Appl Environ Microbiol. 2008 July; 74(13): 4241–4245 (Fig. 1)</p><br></center>
+
-
<br>
+
-
<p>The first step of BRIDGE requires the deletion of existing DNA (probably a non-coding piece or a non-essential gene) to introduce a construct of two genes; one an antibiotic resistance gene, the other sacB, which prevents the host from growing on sucrose. After the first step we can select for cells which have taken up the construct by growing them on the relevant antibiotic.</p>
+
-
<p>The second step involves swapping the construct for another piece of DNA (e.g. a BioBrick construct). After this we can select for those with the new gene by growing the cells on sucrose.</p><br>
+
<br>
<br>
-
<a name="Advantages" id="Advantages"></a><h2>BRIDGE: The advantages</h2>
+
<p>Plasmid transformation <b>protocols</b> are the <b>backbone</b> of modern day synthetic biology, allowing for bacteria such as <i>E. coli</i> to take up foreign genetic material and express it as part of their cellular mechanisms. However, since only a relatively low number of cells are actually transformed in the process, selection markers are necessary to <b>identify</b> the cells that have acquired the plasmid; this usually takes the form of an antibiotic resistance gene built into the plasmid, which has the <b>undesired</b> effect of giving the transformed cells resistance to commonly-used antibiotics.</p>
-
<br>
+
 
-
<p>BRIDGE has a significant advantage over the current method of BioBrick insertion. For one, it is vector independent - whole PCR constructs can be inserted directly into the genome in two steps in under a week, compared to the lengthy process of vector digestion and ligation required with normal BioBricks.</p>
+
<p>What if synthetic biologists were able to <b>utilise</b> an efficient two-step recombination method for markerless gene insertion and deletion? In 2008, Wei Sun, Shifeng Wang, and Roy Curtiss III of Arizona State University <b>published</b> such a protocol, based on the lambda red recombinase system (a simple method for disrupting chromosomal genes in bacteria such as <i>E. coli</i> using PCR products). The 2010 University of Edinburgh iGEM team has <b>adapted</b> their method to take advantage of the reusability of BioBricks, such that synthetic biologists can <b>target</b> critical areas of the <i>E. coli</i> genome with even greater efficiency.</p>
-
<p>The other major advantage is that it will not leave a lasting marker in the genome. With most BioBricks we have to leave a marker (antibiotic resistance, GFP, etc) in our constructs so that we can guarantee their presence. This becomes an issue, a) when you want to use the organism in an industrial or environmental capacity, and b) when you want to insert multiple constructs (there is only a limited number of markers out there). With this system, the markers are removed every time you insert a new gene, so they can be used again and again indefinitely. You could essentially replace the entire genome with new genes.</p><br>
+
 
 +
<p><b>BRIDGE</b> stands for BioBrick Recombination In Direct Genomic Editing. It is an alternative <b>method</b> for inserting BioBricks into the genome by using homologous recombination instead of restriction digestion, with the added <b>bonus</b> of not leaving a marker behind in the product.</p><br>
<br>
<br>
<a name="Project" id="Project"></a><h2>Our Project</h2>
<a name="Project" id="Project"></a><h2>Our Project</h2>
<br>
<br>
-
<p>Our BRIDGE construct will contain chloramphenicol resistance (<i>cat</i>) and <i>sacB</i>. Both it and the desired gene will be inserted by homologous recombination using the lambda red system. For this we will need up and down-stream sequences of genes which we wish to replace.</p>
 
-
<p>To prove the principle of BRIDGE we will remove a non-essential, constitutively expressed gene from the <i>E. coli</i> genome and replace it with a well known marker, such as GFP. We also have several genes from a past project idea which we could delete to increase fatty acid synthesis, and further genes we could introduce which will result in the production of long chain alkenes from the excess fatty acids. This is not useful for our current project but it is a nice way to demonstrate the effectiveness of BRIDGE.</p>
 
-
<p>Eventually, we hoep that BRIDGE will be used to introduce whole light producer-sensor constructs, to demonstrate its ability for utilisation in further work using BioBricks.</p>
 
-
</div>
 
-
<div id="body" style="padding: 0px 60px 10px 60px; height: 1356px">
+
<p>Our BRIDGE construct contains two selection markers in order to <b>successfully</b> complete the protocol (described in greater detail <a href="https://2010.igem.org/Team:Edinburgh/Project/Protocol">here</a>): <i>cat</i>, which confers chloramphenicol resistance, and <i>sacB</i>, which is toxic when the host is grown on sucrose. Both the construct and the desired gene are inserted by homologous recombination using the lambda red recombinase system. For this we <b>require</b> up- and down-stream sequences of the genes that we wish to replace.</p>
-
<br>
+
 
 +
<p>To <b>prove</b> the principle of BRIDGE we removed a non-essential, constitutively expressed gene from the <i>E. coli</i> genome and replaced it with a well-known marker, GFP. This could have been <b>extended</b> further: we also had several genes from a past project idea which we could delete to increase fatty acid synthesis, and other genes we could introduce which would result in the production of long chain alkenes from the excess fatty acids. This is not <b>useful</b> for our current project but it would be a nice way to demonstrate the effectiveness of BRIDGE.</p>
 +
 
 +
<p>Eventually, we hoped that BRIDGE could be used to introduce whole light producer-sensor constructs, to <b>demonstrate</b> its ability for utilisation in further work using BioBricks.</p><br>
<br>
<br>
Line 158: Line 156:
  </li>
  </li>
  <li>
  <li>
-
<a href="https://2010.igem.org/Team:Edinburgh/Results#Genomic">A summary of what we achieved as part of developing the BRIDGE protocol.</a>
+
<a href="https://2010.igem.org/Team:Edinburgh/Results#Genomic">A summary of what we achieved developing the BRIDGE protocol.</a>
  </li>
  </li>
  <li>
  <li>
-
<a href="https://2010.igem.org/Team:Edinburgh/Results/Future">Our vision of the future of the BRIDGE protocol, and where we would like to go next.</a>
+
<a href="https://2010.igem.org/Team:Edinburgh/Project/Future">Our vision of the future of the BRIDGE protocol, and where we would like to go next.</a>
  </li>
  </li>
  <li>
  <li>
-
<a href="https://2010.igem.org/Team:Edinburgh/Results/References">References used throughout the section.</a><br>
+
<a href="https://2010.igem.org/Team:Edinburgh/Project/References">References used throughout the section.</a><br>
  </li>
  </li>
</ul>
</ul>
<br>
<br>
<br>
<br>
-
 
-
<a name="References" id="References"></a><h2>References</h2>
 
<br>
<br>
-
<p></p>
 
-
<br>
+
<center><a href="#top" class="dir"><img width="100" src="https://static.igem.org/mediawiki/2010/9/9f/Ed10-RTT.png"></a></center>
-
<br>
+
</div>
-
<br>
+
 
 +
<div id="windowbox" style="border: .2em solid #660000; padding: 5px; position:fixed; top:50%; right:30px; width:8%;">
 +
<span style="color:ivory;">Throughout this wiki there are words in <b>bold</b> that indicate a relevance to <b>human aspects</b>. It will become obvious that <b>human aspects</b> are a part of almost everything in <b>iGEM</b>.</span>
-
<center><a href="#top" class="dir"><img width="100" src="https://static.igem.org/mediawiki/2010/9/9f/Ed10-RTT.png"></a></center>
 
</div>
</div>

Latest revision as of 02:14, 28 October 2010







Genomic BRIDGEs


Plasmid transformation protocols are the backbone of modern day synthetic biology, allowing for bacteria such as E. coli to take up foreign genetic material and express it as part of their cellular mechanisms. However, since only a relatively low number of cells are actually transformed in the process, selection markers are necessary to identify the cells that have acquired the plasmid; this usually takes the form of an antibiotic resistance gene built into the plasmid, which has the undesired effect of giving the transformed cells resistance to commonly-used antibiotics.

What if synthetic biologists were able to utilise an efficient two-step recombination method for markerless gene insertion and deletion? In 2008, Wei Sun, Shifeng Wang, and Roy Curtiss III of Arizona State University published such a protocol, based on the lambda red recombinase system (a simple method for disrupting chromosomal genes in bacteria such as E. coli using PCR products). The 2010 University of Edinburgh iGEM team has adapted their method to take advantage of the reusability of BioBricks, such that synthetic biologists can target critical areas of the E. coli genome with even greater efficiency.

BRIDGE stands for BioBrick Recombination In Direct Genomic Editing. It is an alternative method for inserting BioBricks into the genome by using homologous recombination instead of restriction digestion, with the added bonus of not leaving a marker behind in the product.



Our Project


Our BRIDGE construct contains two selection markers in order to successfully complete the protocol (described in greater detail here): cat, which confers chloramphenicol resistance, and sacB, which is toxic when the host is grown on sucrose. Both the construct and the desired gene are inserted by homologous recombination using the lambda red recombinase system. For this we require up- and down-stream sequences of the genes that we wish to replace.

To prove the principle of BRIDGE we removed a non-essential, constitutively expressed gene from the E. coli genome and replaced it with a well-known marker, GFP. This could have been extended further: we also had several genes from a past project idea which we could delete to increase fatty acid synthesis, and other genes we could introduce which would result in the production of long chain alkenes from the excess fatty acids. This is not useful for our current project but it would be a nice way to demonstrate the effectiveness of BRIDGE.

Eventually, we hoped that BRIDGE could be used to introduce whole light producer-sensor constructs, to demonstrate its ability for utilisation in further work using BioBricks.



Table of Contents





Throughout this wiki there are words in bold that indicate a relevance to human aspects. It will become obvious that human aspects are a part of almost everything in iGEM.