Team:Cambridge

From 2008.igem.org

(Difference between revisions)
 
(68 intermediate revisions not shown)
Line 1: Line 1:
 +
{{Cambridge/Notitle}}
 +
<div class=bodytable>
 +
</div>
 +
__NOTOC__
 +
{{Cambridge08}}
<html>
<html>
-
<style type="text/css">
+
<table width=100% style="background:#444; padding:15px;">
-
a {
+
-
color: #6EB216;
+
-
text-decoration: none;
+
-
}
+
-
a:hover {
+
-
color: #FFFFFF;
+
-
text-decoration:none;
+
-
}
+
-
a:visited{
+
-
        color: #6EB216;
+
-
+
-
}
+
-
</style>
+
-
</html>
+
-
{|align="justify"
+
  <tr>
-
{| style="color:#FFFFFF;background-color:#166E12;" cellpadding="10" cellspacing="0" border="2" bordercolor="#FFFFFF" width="82%" align="center"
+
    <td>
-
!align="center"|[[Team:Cambridge|Home]]
+
    <a href="https://2008.igem.org/Team:Cambridge/Signalling" class="noborder"><img src="http://openwetware.org/images/9/9d/Signalling_button.gif" alt="Signalling" width="250" style="padding: 3px 0px;"></a>
-
!align="center"|[[Team:Cambridge/Team|The Team]]
+
    <a href="https://2008.igem.org/Team:Cambridge/Bacillus"><img src="http://openwetware.org/images/8/8e/Bacillus_button.gif" alt="Bacillus" width="250" style="padding: 3px 0px;"></a>
-
!align="center"|[[Team:Cambridge/Project|The Project]]
+
    </td><td>
-
!align="center"|[[Team:Cambridge/Parts|Parts Submitted to the Registry]]
+
    <a href="https://2008.igem.org/Team:Cambridge/Voltage"><img src="http://openwetware.org/images/7/74/Voltage_button.gif" alt="Voltage" width="250" style="padding: 3px;"></a>
-
!align="center"|[[Team:Cambridge/Modeling|Modeling]]
+
    <a href="https://2008.igem.org/Team:Cambridge/Modelling"><img src="http://openwetware.org/images/9/91/Modelling_button.gif" alt="Modelling" width="250" style="padding: 3px 0px;"></a>
-
!align="center"|[[Team:Cambridge/Notebook|Notebook]]
+
    </td>
-
|}
+
    <td style="height: 400; padding-left: 15px;">
 +
    <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
    <div class="contentf">
 +
    <div style="height: 400; background:#fff; line-height:170% padding: 3px 0px;">
 +
    <h1>Overview</h1>
 +
    <b>Since the emergence of Synthetic Biology</b>, bacteria have been engineered to perform a wide variety of simple tasks. They can be made to express proteins, respond to their environment and communicate primitively with each other. Presently, a key goal for the field is to create a communicating, organised and differentiated population of bacteria that can be considered a multicellular organism, capable of performing even more complex tasks. The ultimate goal for this line of research would be to mimic a brain, the most complex structure in the universe. To realize this goal requires the development of systems for rapid, robust communication and self-organised differentiation. <br /> <b> Our project sets the foundation for future research in engineered multi-cellularity by pursuing electrical and peptide signalling, and cellular self-differentiation through spontaneous spatial patterning.</b>
 +
      </div></div>
 +
      <b class="b4f"></b><b class="b3f"></b><b class="b2f"></b><b class="b1f"></b>
 +
    </td>
 +
  </tr>
 +
  <tr>
 +
    <td colspan=3>
 +
      <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
        <div class="contentf">
 +
          <div style="height: 400; padding: 5px; background:#fff;">
 +
          <h1>Voltage</h1>
 +
In order to simulate neural activity in bacteria, a mechanism resembling a synapse is necessary. At the synapse, neurotransmitter molecules are released from the presynaptic plasma membrane. The neurotransmitter diffuses through the synaptic cleft and binds to chemical receptor molecules on the membrane of the postsynaptic cell. These receptors cause ion channels to open so that ions rush out, changing the transmembrane potential. Attempting to mimic this in a prokaryotic system is particularly attractive as, in a more general sense, it provides an interface between chemical or biological and electrical systems. <br /><b> Using the amino acid glutamate as our 'neurotransmitter', we have successfully demonstrated a voltage response in bacterial cells. </b> <a href="https://2008.igem.org/Team:Cambridge/Voltage"> Read on...</a>
 +
          </div>
 +
        </div>
 +
      <b class="b4f"></b><b class="b3f"></b><b class="b2f"></b><b class="b1f"></b>
 +
    </td>
 +
  </tr>
 +
<tr>
 +
    <td colspan=3>
 +
      <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
        <div class="contentf">
 +
          <div style="height: 400; padding: 5px; background:#fff;">
 +
          <h1>Signalling</h1>
 +
Using peptide-based signalling systems from gram-positive bacteria, we have laid the foundations for a self-organising biological system, capable of expressing spatial patterns of GFP expression on a bacterial lawn. The focus of our investigation was on a simple two-component Reaction-Diffusion system, allowing for simple spatial 'patterning' of gene expression. The simplest of these patterns mimic the spots and stripes seen on animal coats. In 1952, Alan Turing famously described this Reaction-Diffusion system and suggested it as the basis for self-organization and pattern formation in biological systems. <br /><b> This is a first step in the direction of engineering multicellular behaviour. </b> <a href="https://2008.igem.org/Team:Cambridge/Signalling"> Read on...</a>
 +
          </div>
 +
        </div>
 +
      <b class="b4f"></b><b class="b3f"></b><b class="b2f"></b><b class="b1f"></b>
 +
    </td>
 +
  </tr>
 +
<tr>
 +
    <td colspan=3>
 +
      <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
        <div class="contentf">
 +
          <div style="height: 400; padding: 5px; background:#fff;">
 +
          <h1>Bacillus</h1>
 +
To build more complex cellular systems, new tools and techniques are required. We are generating standardized parts, tools, and techniques for the gram-positive chassis ''B. subtillis''. Easy to handle and transform, this bacterium offers many adantages to ''E. coli', including the ability to secrete proteins and integrate DNA into the chromosome. We have designed, built, and submitted gram-positive RBSes, promoters, and shuttle vectors.<br /> <b> As a part of this work we have confirmed single copy chromosomal insertion, demonstrated InFusion assembly, and characterized an improved GFP variant. </b>
 +
<a href="https://2008.igem.org/Team:Cambridge/Bacillus"> Read on...</a>
-
|[[Image:Cambridge_2008 Logo.gif|centre|400px]]
+
          </div>
 +
        </div>
 +
      <b class="b4f"></b><b class="b3f"></b><b class="b2f"></b><b class="b1f"></b>
 +
    </td>
 +
  </tr>
 +
<tr>
 +
    <td colspan=3>
 +
      <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
        <div class="contentf">
 +
          <div style="height: 400; padding: 5px; background:#fff;">
 +
          <h1>Modelling</h1>
 +
We have introduced a model of the AGR quorum-sensing system of S.aureus to illustrate how a typical quorum-sensing system works. The model predicts theoretical values for biological parameters (such as the threshold cell density) that can be verified and we will be also be able to predict how the system behaves if we change a number crucial parameters. This can be extremely useful in informing design decisions when building a synthetic device. We have also expanded this model into a hypothetical setup with a second parallel agr-system. <br /><b> Using this parallel signals model, we investigate how to engineer a biological patterning system.</b> <a href="https://2008.igem.org/Team:Cambridge/Modelling">Read on...</a>
 +
          </div>
 +
        </div>
 +
      <b class="b4f"></b><b class="b3f"></b><b class="b2f"></b><b class="b1f"></b>
 +
    </td>
 +
  </tr>
 +
<tr>
 +
    <td colspan=3> 
 +
    <b class="b1f"></b><b class="b2f"></b><b class="b3f"></b><b class="b4f"></b>
 +
    <div class="contentf">
 +
        <div style="height: 400; padding: 5px; background:#fff; line-height:170%" align="center">
 +
        <table>
 +
    <tr>
 +
    <td width="200"><a href="http://www.labtech.co.uk/" class="noborder"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/labtech.jpg" alt="labtech" width="131" height="17"></a></td>
 +
    <td width="200"><a href="http://www.clontech-europe.com/"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/clontech.jpg" alt="Clontech" width="112" height="34"></a></td>
 +
  <td width ="200"><a href="http://www.expressys.com/"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/expressys.jpg" alt="expressys" width="112" height="70"></a></td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://www.invitrogen.com/site/us/en/home.html"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/invirtogen.jpg" alt="invitrogen" width="160" height="25"></a></td>
 +
    <td><a href="http://www.medical-solutions.co.uk/"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/geneservice.jpg" alt="geneservice" width="140" height="26"></a></td>
 +
    <td><a href="http://www.bioscience.co.uk/"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/cambridgebioscience.jpg" alt="cambridge bioscience" width="157" height="42"></a></td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://www.zymoresearch.com/"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/zymoresearch.jpg" alt="zymo research" width="135" height="45"></a></td>
 +
    <td><a href="http://www.vwr.com/index.htm"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/vwr.jpg" alt="VWR" width="140" height="47"></a></td>
 +
    <td><a href="http://www.microzone.co.uk/"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/microzone.gif" alt="Microzone" width="131" height="44"></a></td>
 +
  </tr>
 +
  <tr>
 +
    <td><a href="http://www.finnzymes.com/"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/finnzymes.jpg" alt="Finnzymes" width="131" height="43"></a></td>
 +
    <td><a href="http://www.fisher.co.uk/"><img src="http://www.gen.cam.ac.uk/Images/logos/iGEMsponsors/fisherscientific.jpg" alt="Fisher Scientific" width="132" height="33" /></a></td>
 +
    <td><a href="http://www.dna20.com/"><img src="http://openwetware.org/images/8/88/Dna20_logo.jpg" alt="DNA 2.0" width="132" height="66" /></a></td>
 +
  </tr>
 +
    </table>
 +
    </div>
 +
    </div>
 +
    <b class="b4f"></b><b class="b3f"></b><b class="b2f"></b><b class="b1f"></b>
 +
  </td>
-
For the 2008 iGEM competition, Cambridge is working on three different projects.
+
  </tr>
-
 
+
</table>
-
== 1. Turing Patterns ==
+
</html>
-
 
+
-
We are planning to implement a simple two-component Reaction-Diffusion system in the gram-positive model organism Bacillus subtilis. In 1952, Alan Turing famously described this system and suggested it as the basis for self-organization and pattern formation in biological systems. The simplest of these patterns, which we are planning to model in bacteria, mimic the spots and stripes seen on animal coats.
+
-
 
+
-
<center>http://www.uni-muenster.de/Physik.AP/Purwins/RD/2kgl.gif</center>
+
-
http://www.uni-muenster.de/Physik.AP/Purwins/RD/struktur-e.gif
+
-
http://www.rsc.org/ej/MB/2007/b701571b/b701571b-f1.gif
+
-
 
+
-
(A) The model consists of two diffusible signals secreted by every cell. The activator, which is controlled by a stochastic bistable switch, turns on itself and its own inhibitor. (B) A field of cells can be stably patterned into two different zones, so long as the inhibitor diffuses faster than the activator. The activator and inhibitor are synthesized in the source at the center, and turned off by accumulation of the inhibitor in the periphery.
+
-
 
+
-
http://parts.mit.edu/igem07/images/3/32/Cambridge_Agr_operon_and_biochemical_pathways.png
+
-
 
+
-
We plan to use two well-characterized bacterial communication systems to generate this behavior.  The agr peptide signalling system from S. aureus will serve as our activatory signal (pictured), while the lux system from V. fischeri will serve as our inhibitor. Bacillus subtilis serves as an excellent chassis for this project because of the ease with which chromosomal integration can be performed. This project will focus on a tight integration of modeling and experiment; we will test different promoter strengths and other variables, feed these system parameters into our multi-cell models, and then use those models to tweak the regulatory machinery that will control signal production.
+
-
 
+
-
 
+
-
== 2. Voltage Output ==
+
-
 
+
-
The aim of this project is to work towards an interface between biological and electric systems. We hope to do this by measuring a voltage change due to the presence of a certain substance.
+
-
In the first instance, this substance will be glutamate, as it acts as a ligand for a prokaryotic gated potassium channel.
+
-
Our idea is to sequester K+ inside E.coli cells by using leak channel knock-out mutants, and over-expressing K+ influx pumps. Then, when glutamate is present it will open K+ channels, allowing an efflux of potassium and causing a small but measureable change in voltage in the medium.
+
-
 
+
-
 
+
-
== 3. Magnetic Bacteria ==
+
-
 
+
-
We are investigating the formation of magnetosomes (membrane bound magnetite particles) in magnetotactic bacteria. This process is believed to take place in the following steps:
+
-
i) production of invaginations along the inner membrane
+
-
ii) uptake of iron into these invaginations
+
-
iii) biomineralisation of the iron into magnetite crystals of a specific size and shape
+
-
iv) axial alignment of the magnetosomes
+
-
 
+
-
This mechanism gives the bacteria the ability to align itself like a compass needle along geomagnetic field lines.
+
-
We are attempting to engineer the uptake of soluble iron into membrane invaginations in E.coli, and stimulate formation of magnetite using genes from Magnetospirillum.
+

Latest revision as of 02:53, 30 October 2008

Signalling Bacillus Voltage Modelling

Overview

Since the emergence of Synthetic Biology, bacteria have been engineered to perform a wide variety of simple tasks. They can be made to express proteins, respond to their environment and communicate primitively with each other. Presently, a key goal for the field is to create a communicating, organised and differentiated population of bacteria that can be considered a multicellular organism, capable of performing even more complex tasks. The ultimate goal for this line of research would be to mimic a brain, the most complex structure in the universe. To realize this goal requires the development of systems for rapid, robust communication and self-organised differentiation.
Our project sets the foundation for future research in engineered multi-cellularity by pursuing electrical and peptide signalling, and cellular self-differentiation through spontaneous spatial patterning.

Voltage

In order to simulate neural activity in bacteria, a mechanism resembling a synapse is necessary. At the synapse, neurotransmitter molecules are released from the presynaptic plasma membrane. The neurotransmitter diffuses through the synaptic cleft and binds to chemical receptor molecules on the membrane of the postsynaptic cell. These receptors cause ion channels to open so that ions rush out, changing the transmembrane potential. Attempting to mimic this in a prokaryotic system is particularly attractive as, in a more general sense, it provides an interface between chemical or biological and electrical systems.
Using the amino acid glutamate as our 'neurotransmitter', we have successfully demonstrated a voltage response in bacterial cells. Read on...

Signalling

Using peptide-based signalling systems from gram-positive bacteria, we have laid the foundations for a self-organising biological system, capable of expressing spatial patterns of GFP expression on a bacterial lawn. The focus of our investigation was on a simple two-component Reaction-Diffusion system, allowing for simple spatial 'patterning' of gene expression. The simplest of these patterns mimic the spots and stripes seen on animal coats. In 1952, Alan Turing famously described this Reaction-Diffusion system and suggested it as the basis for self-organization and pattern formation in biological systems.
This is a first step in the direction of engineering multicellular behaviour. Read on...

Bacillus

To build more complex cellular systems, new tools and techniques are required. We are generating standardized parts, tools, and techniques for the gram-positive chassis ''B. subtillis''. Easy to handle and transform, this bacterium offers many adantages to ''E. coli', including the ability to secrete proteins and integrate DNA into the chromosome. We have designed, built, and submitted gram-positive RBSes, promoters, and shuttle vectors.
As a part of this work we have confirmed single copy chromosomal insertion, demonstrated InFusion assembly, and characterized an improved GFP variant. Read on...

Modelling

We have introduced a model of the AGR quorum-sensing system of S.aureus to illustrate how a typical quorum-sensing system works. The model predicts theoretical values for biological parameters (such as the threshold cell density) that can be verified and we will be also be able to predict how the system behaves if we change a number crucial parameters. This can be extremely useful in informing design decisions when building a synthetic device. We have also expanded this model into a hypothetical setup with a second parallel agr-system.
Using this parallel signals model, we investigate how to engineer a biological patterning system. Read on...
labtech Clontech expressys
invitrogen geneservice cambridge bioscience
zymo research VWR Microzone
Finnzymes Fisher Scientific DNA 2.0