Team:St Andrews/project/objectives

From 2010.igem.org

(Difference between revisions)
(→Know thine enemy. Cholera's Strategy: Quorum Sensing)
 
(12 intermediate revisions not shown)
Line 1: Line 1:
 +
{{:Team:St_Andrews/defaulttemplate}}
 +
<html>
<html>
-
<head>
+
<h1> Project Description </h1>
-
<head>
+
</html>
-
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.js" type="text/javascript"></script>
+
-
<script src="http://www.lycifer.co.cc/java/s3Slider.js" type="text/javascript"></script>
+
-
<script src="http://www.lycifer.co.cc/java/jquery.corner.js" type="text/javascript"></script>
+
-
<script src="http://www.lycifer.co.cc/java/liquid-canvas.js" type="text/javascript"></script>
+
-
<script src="http://www.lycifer.co.cc/java/liquid-canvas-plugins.js" type="text/javascript"></script>
+
-
<script language="JavaScript" type="text/JavaScript">
+
-
$(document).ready(function(){
+
-
$(".exphoto").corner("32px")
+
-
$(".exphoto").corner("80px tr")
+
-
$(".exmain").corner("32px bl")
+
-
$(".main").corner("80px tl")
+
-
$(".main").corner("32px bl")
+
-
$(".tag").corner("32px tl bl")
+
-
$("#navmenu-h li,#navmenu-v li").hover(
+
-
function() { $(this).addClass("iehover"); },
+
-
function() { $(this).removeClass("iehover"); }
+
-
);});
+
-
</script>
+
-
<script src="http://www.lycifer.co.cc/java/jquery.nivo.slider.pack.js" type="text/javascript"></script>
+
-
<script type="text/javascript">
+
-
$(window).load(function() {
+
-
$('#slider').nivoSlider({
+
-
effect:'fade', //Specify sets like: 'fold,fade,sliceDown'
+
-
slices:50,
+
-
animSpeed:1000,
+
-
pauseTime:5000,
+
-
startSlide:0, //Set starting Slide (0 index)
+
-
directionNav:false, //Next & Prev
+
-
directionNavHide:true, //Only show on hover
+
-
controlNav:false, //1,2,3...
+
-
controlNavThumbs:false, //Use thumbnails for Control Nav
+
-
      controlNavThumbsFromRel:true, //Use image rel for thumbs
+
-
controlNavThumbsSearch: '.jpg', //Replace this with...
+
-
controlNavThumbsReplace: '_thumb.jpg', //...this in thumb Image src
+
-
keyboardNav:false, //Use left & right arrows
+
-
pauseOnHover:true, //Stop animation while hovering
+
-
manualAdvance:false, //Force manual transitions
+
-
captionOpacity:0.8, //Universal caption opacity
+
-
beforeChange: function(){},
+
-
afterChange: function(){},
+
-
slideshowEnd: function(){} //Triggers after all slides have been shown
+
-
}
+
-
);
+
-
})
+
-
</script>
+
-
<link href='http://fonts.googleapis.com/css?family=Josefin+Sans+Std+Light' rel='stylesheet' type='text/css'>
+
-
<link rel="stylesheet" type="text/css" href="http://www.lycifer.co.cc/css/lymain6.css" />
+
-
</head>
+
-
<body>
+
-
<img class="background" border="0" src="http://farm5.static.flickr.com/4138/4850316388_ffee095f41_t_d.jpg"/>
+
-
<img class="gradient" border="0" src="http://farm5.static.flickr.com/4090/4839791534_ee9a9c2a4a_m_d.jpg"/>
+
-
<img class="gradientb" border="0" src="http://farm5.static.flickr.com/4088/4839184741_cdc2138f55_m_d.jpg"/>
+
-
<img class="lybanner" border="0" src="http://farm5.static.flickr.com/4092/4839727380_8a96bda148_b_d.jpg" width="977"/>
+
-
<ul id="navmenu-h" class="navigation2">
+
-
<li class="current"><a href="https://2010.igem.org/Team:St_Andrews">Home</a></li>
+
-
<li class="current"><a href="https://2010.igem.org/Team:St_Andrews/FAQ">About/FAQ</a>
+
-
<ul>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/FAQ#who">Who we are?</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/FAQ#competition">What is the iGEM Competition about?</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/FAQ#work">How does it work?</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/FAQ#synthetic">What is Synthetic Biology?</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/FAQ#biobrick">What are BioBricks?</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/FAQ#part">What is the Registry of Standard Biological Parts?</a></li>
+
-
</ul>  
+
-
</li>
+
=The Problem: Cholera=
-
<li><a>Team</a>
+
Cholera (V. cholerae) infects 5 million people per year, worldwide and can kill within hours if left untreated. Like all diarrheal diseases, cholera is particularly deadly in children.  
-
<ul>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members">Students</a>
+
-
<ul>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#Rachael Blackburn">Rachael Blackburn</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#Lukas Ly">Lukas Ly</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#Alasdair Morton">Alasdair Morton</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#Patrick Olden">Patrick Olden</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#David Owen">David Owen</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#Fatemeh Salimi">Fatemeh Salimi</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#Sarah Shapiro">Sarah Shapiro</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#James Taylor">James Taylor</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/members#Jonathan Ward">Jonathan Ward</a></li>
+
-
</ul>
+
-
</li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/advisors">Advisors</a>
+
-
<ul>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/advisors#Chris Hooley">Chris Hooley</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/advisors#Olivia Mendivil">Olivia Mendivil</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/advisors#John Mitchell">John Mitchell</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/advisors#Anne Smith">Anne Smith</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/advisors#Wim Verleyen">Wim Verleyen</a></li>
+
-
</ul>
+
-
</li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/official">Official Team Profile</a></li>
+
-
</ul>
+
-
</li>
+
-
<li><a>Project</a>
+
-
<ul>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/project/objectives">Objectives</a></li>
+
-
<li><a <!--href="https://2010.igem.org/Team:St_Andrews/project/laboratory"-->Laboratory</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/project/modelling">Modeling</a>
+
-
<ul>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/project/modelling#introduction">Introduction</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/project/modelling#bonnet">Under the Bonnet</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/project/modelling#overview">Basic Overview</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/project/modelling#results">Results</a></li>
+
-
</ul>
+
-
<li><a <!--href="https://2010.igem.org/Team:St_Andrews/project/notebook"-->Notebook</a></li>
+
-
<li><a <!--href="https://2010.igem.org/Team:St_Andrews/project/blog"-->Blog</a></li>
+
-
</ul>
+
-
</li>
+
-
<li><a href="#">News</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/contact">Contact</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors">Sponsors</a>
+
-
<ul>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#Wellcome Trust">Wellcome Trust</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#New England Biolabs">New England Biolabs</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#Fermentas">Fermentas</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#GENEART">GENEART</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#Mr Gene">Mr Gene</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#University of St Andrews">University of St Andrews</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#SULSA">SULSA</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#SALTIRE">SALTIRE</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#School of Biology">School of Biology</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#School of Chemistry">School of Chemistry</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#School of Physics and Astronomy">School of Physics and Astronomy</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#School of Computer Science">School of Computer Science</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#B. Jannettas">B. Jannettas</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#ijmellis">I.J.Mellis</a></li>
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/team/sponsors#flip!">flip!</a></li>
+
-
</ul>
+
-
</li>
+
-
</ul> <ul id="crumbs" class="navigation1">
+
-
<li><a href="https://2010.igem.org/Team:St_Andrews/project">Project</a></li>
+
-
<li>Objectives</li>
+
-
<li>
+
-
</ul>
+
-
</div>
+
-
<div class="ry">
+
-
<p class="right">
+
-
<script src="http://widgets.twimg.com/j/2/widget.js"></script>
+
-
<script>
+
-
new TWTR.Widget({
+
-
  version: 2,
+
-
  type: 'profile',
+
-
  rpp: 3,
+
-
  interval: 3500,
+
-
  width: 155,
+
-
  height: 390,
+
-
  theme: {
+
-
    shell: {
+
-
      background: '#ffffff',
+
-
      color: '#808080'
+
-
    },
+
-
    tweets: {
+
-
      background: '#ffffff',
+
-
      color: '#000000',
+
-
      links: '#3c07eb'
+
-
    }
+
-
  },
+
-
  features: {
+
-
    scrollbar: false,
+
-
    loop: true,
+
-
    live: true,
+
-
    hashtags: true,
+
-
    timestamp: true,
+
-
    avatars: true,
+
-
    behavior: 'default'
+
-
  }
+
-
}).render().setUser('igemsaints').start();
+
-
</script>
+
-
</p>
+
-
</div>
+
-
<div class="main">
+
-
<div class="tag">
+
-
The Problem
+
-
</div>
+
-
<div class="exmain">
+
-
The St Andrews iGEM team plan is to do something useful with quorum sensing – the method by which bacteria make decisions in a cell density dependent manner. They do this by secreting autoinducer molecules, which diffuse back into the cells and regulate their own biosynthesis. Certain concentrations of autoinducer represent to a bacterium an amount of fellow-bacteria in the environment and the response is activation or deactivation of a set of genes.
+
-
We are interested in the quorum sensing system of Vibrio cholerae, the bacterium understood to be responsible for the deadly diarrhoeal disease, <dfn>cholera</dfn>. <dfn>Cholera</dfn> is extremely rare in the developed world, but in areas with poor sanitation it affects people who drink unsafe water. Young children are the most at risk, and left untreated death can occur by dehydration. According to the WHO, cholera kills between 100,000 and 120,000 people every year. Efforts have been made towards an effective cholera vaccine suitable for young children, but they have not yet been successful. It is now suggested that synthetic probiotic bacteria could be a safe and economical way to confer resistance to cholera.
+
-
</div>
+
-
<div class="tag">
+
Whilst the standard treatment for cholera is some combination of fluids and antibiotics, there is no cure. Efforts have been made towards an effective cholera vaccine but as yet this has been unsuccessful.  
-
Quorum Sensing in <dfn>Vibrio cholerae</dfn>
+
-
</div>
+
-
<div class="exmain">
+
-
Most <dfn>cholera</dfn> cells are killed off by stomach acid, but those that remain alive attach to the gut wall and multiply. At this low cell density, autoinducer concentration is low, and virulence factors are expressed. Once high cell density is reached, enough toxin is present to cause severe diarrhoea. At this point, the autoinducer concentration is high, and virulence factors are repressed. The now avirulent V. Cholerae detach from the gut wall and are flushed out of the body to infect a new host.
+
-
Our idea is to synthesise <dfn>Escherichia coli</dfn> bacteria that will use this ingenious mechanism to communicate with <dfn>Vibrio cholerae</dfn>. Our engineered <dfn>Escherichia coli</dfn> will harmlessly colonise the gut, and in large numbers secrete the cholera autoinducer, CAI-1. This will cause an immediate high autoinducer concentration to be detected by incoming <dfn>Vibrio cholerae</dfn> cells which then become avirulent and harmlessly pass out of the body.
+
-
</div>
+
 +
It is a truth universially acknowledged that prevention is better than cure and therefore to prevent cholera from multiplying and therefore prevent causing severe illness and potential death.
-
<div class="tag">
+
Our aim is to investigate whether the basic science behind preventing cholera could work.
-
Our Plan
+
-
</div>
+
-
<div class="exmain">
+
-
The wet work will focus on two challenges. The first being to add new functionality to the signalling parts present in the registry by re-engineering the existing <dfb>LuxR</dfn> quorum sensing system to create a bistable switch. This will allow us to infer a signalling molecule concentration required to deactivate the system much lower than the concentration required to activate it. We will characterise this system by using a fluorescent protein reporter and measuring fluorescence at different cell densities. The second challenge will be adding the cholera autoinducer synthase gene CqsA to <dfn>Escherichia coli</dfn> so that CAI-1 is secreted. The eventual aim is that the bistable switching system will be used to control CqsA expression, so that the ability to compete with other bacteria in the human gut is not compromised by this metabolic burden.
+
-
The computational side of the team are focusing on generating ordinary differential equations to model quorum sensing in <dfn>Vibrio cholerae</dfn> and on modelling more complex problems such as bistability and multiple quorum loops working in tandem of our parts.
+
-
</div>
+
-
</div>
+
-
</body>
+
=Know thine enemy. Cholera's Strategy: Quorum Sensing=
-
</html>
+
 
 +
 
 +
Most cholera cells entering the gastroenteric system are killed off by stomach acid (HCl), but the few that survive, pass through the stomach and into the gut where they attach to the gut wall and multiply.
 +
 
 +
Initially, the cholera cells are at a low cell density and therefore autoinducer (a self stimulant to procreate) concentration is low, and virulence factors are expressed.
 +
 
 +
Once high cell density is reached, sufficient toxin (choleratoxin) exists to cause extreme diarrhoea. At this point the autoinducer concentration is high and virulence factors are repressed.
 +
 
 +
The now avirulent cholera cells detach from the gut wall by producing a protease and are flushed out of the body with the water leaving the intestine and once outside the body are then able to infect a new host.
 +
 
 +
Our idea is to modify E. coli which are able to communicate with cholerae. Put simply, the E.Coli will talk to the cholerae and trick the cholerae into leaving the intestine before any virulence factors are sufficient to cause illness to the host human.
 +
 
 +
Our engineered Escherichia coli will harmlessly colonise the gut and in large numbers secrete the cholera autoinducer, CAI-1. This will cause an immediate high autoinducer concentration to be detected by incoming Vibrio cholerae cells which then quickly become avirulent and leave the body naturally with the passage of products of digestion, without causing harm to the human.
 +
 
 +
=The Plan=
 +
 
 +
 
 +
 
 +
'''Biology Lab Work'''
 +
 
 +
(1) Adding new functionality to the signalling parts present in the registry by re-engineering the existing LuxR quorum sensing system to create a bistable switch. This will allow us to infer a signalling molecule concentration required to deactivate the system much lower than the concentration required to activate it. We will characterise this system by using a fluorescent protein reporter and measuring fluorescence at different cell densities.
 +
 
 +
(2) Adding the cholera autoinducer synthase gene CqsA to Escherichia coli so that CAI-1 is secreted. The eventual aim is that the bistable switching system will be used to control CqsA expression, so that the ability to compete with other bacteria in the human gut is not compromised by this metabolic burden.
 +
 
 +
 
 +
 
 +
'''Modelling''''''
 +
 
 +
Generating ordinary differential equations to model quorum sensing in V. cholerae and on modelling more complex problems such as bistability and multiple quorum loops working in tandem of our parts.

Latest revision as of 21:25, 26 October 2010


St Andrews from East Sands

University of St Andrews iGEM 2010

Welcome!

The Saints

University of St Andrews iGEM 2010

Our first year at iGEM!


Project Description

The Problem: Cholera

Cholera (V. cholerae) infects 5 million people per year, worldwide and can kill within hours if left untreated. Like all diarrheal diseases, cholera is particularly deadly in children.

Whilst the standard treatment for cholera is some combination of fluids and antibiotics, there is no cure. Efforts have been made towards an effective cholera vaccine but as yet this has been unsuccessful.

It is a truth universially acknowledged that prevention is better than cure and therefore to prevent cholera from multiplying and therefore prevent causing severe illness and potential death.

Our aim is to investigate whether the basic science behind preventing cholera could work.

Know thine enemy. Cholera's Strategy: Quorum Sensing

Most cholera cells entering the gastroenteric system are killed off by stomach acid (HCl), but the few that survive, pass through the stomach and into the gut where they attach to the gut wall and multiply.

Initially, the cholera cells are at a low cell density and therefore autoinducer (a self stimulant to procreate) concentration is low, and virulence factors are expressed.

Once high cell density is reached, sufficient toxin (choleratoxin) exists to cause extreme diarrhoea. At this point the autoinducer concentration is high and virulence factors are repressed.

The now avirulent cholera cells detach from the gut wall by producing a protease and are flushed out of the body with the water leaving the intestine and once outside the body are then able to infect a new host.

Our idea is to modify E. coli which are able to communicate with cholerae. Put simply, the E.Coli will talk to the cholerae and trick the cholerae into leaving the intestine before any virulence factors are sufficient to cause illness to the host human.

Our engineered Escherichia coli will harmlessly colonise the gut and in large numbers secrete the cholera autoinducer, CAI-1. This will cause an immediate high autoinducer concentration to be detected by incoming Vibrio cholerae cells which then quickly become avirulent and leave the body naturally with the passage of products of digestion, without causing harm to the human.

The Plan

Biology Lab Work

(1) Adding new functionality to the signalling parts present in the registry by re-engineering the existing LuxR quorum sensing system to create a bistable switch. This will allow us to infer a signalling molecule concentration required to deactivate the system much lower than the concentration required to activate it. We will characterise this system by using a fluorescent protein reporter and measuring fluorescence at different cell densities.

(2) Adding the cholera autoinducer synthase gene CqsA to Escherichia coli so that CAI-1 is secreted. The eventual aim is that the bistable switching system will be used to control CqsA expression, so that the ability to compete with other bacteria in the human gut is not compromised by this metabolic burden.


Modelling'

Generating ordinary differential equations to model quorum sensing in V. cholerae and on modelling more complex problems such as bistability and multiple quorum loops working in tandem of our parts.

Retrieved from "http://2010.igem.org/Team:St_Andrews/project/objectives"