Team:LCG-UNAM-Mexico

From 2009.igem.org

(Difference between revisions)
 
(53 intermediate revisions not shown)
Line 1: Line 1:
 +
{{Template:LCG_top_Netscape}}<!--Do not remove the first and last lines in this page!-->
 +
 +
{|
 +
|-valign="top" border="0"
 +
|width="900px" style="padding: 0 20px 0 0;"|
 +
 +
 +
='''The Project in a nutshell'''=
 +
 +
 +
Bacteriophage infection represents an interesting process in microbiology and industry. The idea of being able to contend at a population level with such infections is the main motivation for the development of our project.<br>
 +
 +
We propose a population level approach relaying on a defense system delivered by an engineered version of the enterobacteria phage P4. The purpose of the defense construction is to modify bacteria in order to hold back the process of infection by triggering a cellular death response when a cell encounters a specific component of the infective phage. Such response will be fast enough to stop the formation process of viral particles, thus preventing the phage proliferation and population decline.<br>
 +
 +
The delivery system takes advantage of the satellite properties of P4 phage. This means that a P4 phage engineered with the defense construction will be able to infect an ''E.coli'' strain which harbors some genes from helper phage P2 that are used for complementing and completing P4 life cycle, hence creating a production line of our version of P4.<br>
 +
Besides, the defense system will consist of DNA and RNA degradation by toxins which will be transcribed by T3 or T7 RNA-Polymerases fast enough to stop phage assembly and scattering in the environment. Simultaneously, a quorum sensing signal will be diffusing to the non-infected bacteria acting as a transcriptional activator of an antisense RNA against bacteriophage's transcriptional machinery , hence "warning" the population to prepare against further T3 or T7 infection.<br>
 +
<br>
 +
We implemented a stochastic [[Team:LCG-UNAM-Mexico: | multi-scale model]]. The model will simulate the behaviour at the intracellular scale using [[Team:LCG-UNAM-Mexico:Molecular model | stochastic molecular simulations]] and at the populations scale using a [[Team:LCG-UNAM-Mexico:CA | Cellular Automata]] and a [[Team:LCG-UNAM-Mexico:odes | system of ODE's]]. <br> Simulations results are in good agreement with existing experimental data. Thanks to the structure and design of the model this can be easily modified in order to simulate infection dynamics for different bacteria and phages. Furthermore, our Molecular model can be used as a reliable tool for sampling biomolecules distributions involved in phage infection processes. <br>
 +
<html>
<html>
-
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
<header>
-
<html xmlns="http://www.w3.org/1999/xhtml">
+
<script language="JavaScript">
-
<head>
+
function mouseOver_comic(){
-
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
document.getElementById("comic").src ="https://static.igem.org/mediawiki/2009/6/60/Comic_LCG_bb.png";
-
<!-- TemplateBeginEditable name="doctitle" -->
+
-
<title>Untitled Document</title>
+
-
<!-- TemplateEndEditable -->
+
-
<!-- TemplateBeginEditable name="head" -->
+
-
<!-- TemplateEndEditable -->
+
-
<style type="text/css">
+
-
<!--
+
-
body  {
+
-
font: 100% Verdana, Arial, Helvetica, sans-serif;
+
-
background: #666666;
+
-
margin: 0; /* it's good practice to zero the margin and padding of the body element to account for differing browser defaults */
+
-
padding: 0;
+
-
text-align: center; /* this centers the container in IE 5* browsers. The text is then set to the left aligned default in the #container selector */
+
-
color: #000000;
+
}
}
-
 
+
function mouseOut_comic(){
-
.thrColHybHdr #container {
+
document.getElementById("comic").src ="https://static.igem.org/mediawiki/2009/a/a8/Comic_LCG_ba.png";
-
width: 100%;
+
-
background: #FFFFFF;
+
-
/*margin: 0 auto;  the auto margins (in conjunction with a width) center the page if needed */
+
-
text-align: left; /* this overrides the text-align: center on the body element. */
+
-
} 
+
-
.thrColHybHdr #header {
+
-
background: #629632;
+
-
padding: 0 10px;  /* this padding matches the left alignment of the elements in the divs that appear beneath it. If an image is used in the #header instead of text, you may want to remove the padding. */
+
-
}
+
-
.thrColHybHdr #header h1 {
+
-
margin: 0;
+
-
padding: 10px 0;  
+
}
}
-
.thrColHybHdr #sidebar1 {
+
 
-
float: left;  
+
</script>
-
width: 11em;  
+
</header>
-
background: #8BA870;  
+
 
-
padding: 15px 0;  
+
<style>
 +
#bodyContent { padding: 10px auto; width: 1000px; margin: auto; clear: none; }
 +
a:link { color: #659D32; text-decoration: none}
 +
a:visited { color:#659D32; text-decoration: none}
 +
a:hover { color:#f29400; text-decoration: none}
 +
a:active { color:#f29400; text-decoration: none}
 +
 
 +
</style>
 +
 
 +
<body>
 +
 
 +
<a href="https://2009.igem.org/Team:LCG-UNAM-Mexico:Comic" ><img border="0"  src="https://static.igem.org/mediawiki/2009/a/a8/Comic_LCG_ba.png" id="comic" onmouseover="mouseOver_comic()" onmouseout="mouseOut_comic()"></a>
 +
 
 +
</body>
 +
</html>
 +
 
 +
 
 +
|}
 +
 
 +
----
 +
 
 +
 
 +
<html>
 +
<header>
 +
 
 +
<script language="JavaScript">
 +
function mouseOver_parts(){
 +
document.getElementById("parts").src ="https://static.igem.org/mediawiki/2009/a/aa/Parts_b.png";
}
}
-
.thrColHybHdr #sidebar2 {
+
function mouseOut_parts(){
-
float: right;
+
document.getElementById("parts").src ="https://static.igem.org/mediawiki/2009/a/a4/Parts_a.png";
-
width: 11em;
+
-
background: #EBEBEB; padding: 15px 0;
+
-
}
+
-
.thrColHybHdr #sidebar1 h3, .thrColHybHdr #sidebar1 p, .thrColHybHdr #sidebar2 p, .thrColHybHdr #sidebar2 h3 {
+
-
margin-left: 10px;
+
-
margin-right: 10px;
+
}
}
-
.thrColHybHdr #mainContent {
+
function mouseOver_res(){
-
margin: 0 12em 0 12em;
+
document.getElementById("res").src ="https://static.igem.org/mediawiki/2009/3/35/Resources_b.png";
-
padding: 0 2em 0 2em;  
+
}
-
}  
+
function mouseOut_res(){
-
.thrColHybHdr #footer {  
+
document.getElementById("res").src ="https://static.igem.org/mediawiki/2009/9/93/Resources_a.png";
-
padding: 0 10px;
+
-
background:#DDDDDD;
+
-
}
+
-
.thrColHybHdr #footer p {
+
-
margin: 0;
+
-
padding: 10px 0;  
+
}
}
-
 
+
function mouseOver_des(){
-
.fltrt {  
+
document.getElementById("des").src ="https://static.igem.org/mediawiki/2009/2/2a/Description_b.png";
-
float: right;
+
-
margin-left: 8px;
+
}
}
-
.fltlft {  
+
function mouseOut_des(){
-
float: left;
+
document.getElementById("des").src ="https://static.igem.org/mediawiki/2009/3/3e/Description_a.png";
-
margin-right: 8px;
+
}
}
-
.clearfloat {  
+
 
-
clear:both;
+
function mouseOver_mod(){
-
    height:0;
+
document.getElementById("mod").src ="https://static.igem.org/mediawiki/2009/1/13/Modelling_b.png";
-
    font-size: 1px;
+
}
-
    line-height: 0px;
+
function mouseOut_mod(){
 +
document.getElementById("mod").src ="https://static.igem.org/mediawiki/2009/8/83/Modelling_a.png";
}
}
-
-->
 
-
</style><!--[if IE]>
 
-
<style type="text/css">
 
-
/* place css fixes for all versions of IE in this conditional comment */
 
-
.thrColHybHdr #sidebar1, .thrColHybHdr #sidebar2 { padding-top: 30px; }
 
-
.thrColHybHdr #mainContent { zoom: 1; padding-top: 15px; }
 
-
</style>
 
-
<![endif]--></head>
 
-
<body class="thrColHybHdr">
+
</script>
 +
</header>
-
<div id="container">
+
<body>
-
  <div id="header">
+
<br><br>
-
    <h1>iGem Team: UNAM</h1>
+
<table border="0" align="center" width="600" cellpadding="50"><tr><a href="https://2009.igem.org/Team:LCG-UNAM-Mexico/Description" ><img border="0" width="600" src="https://static.igem.org/mediawiki/2009/3/3e/Description_a.png" id="des" onmouseover="mouseOver_des()" onmouseout="mouseOut_des()" align="center"></a></tr>
-
  <!-- end #header --></div>
+
<br><br>
-
  <div id="sidebar1">
+
<tr><a href="https://2009.igem.org/Team:LCG-UNAM-Mexico/Parts" ><img border="0" width="600" src="https://static.igem.org/mediawiki/2009/a/a4/Parts_a.png" id="parts" onmouseover="mouseOver_parts()" onmouseout="mouseOut_parts()" align="center"></a></tr>
-
   
+
<br><br>
-
    <p>Team Members:</p>
+
<tr><a href="https://2009.igem.org/Team:LCG-UNAM-Mexico/Resources" ><img border="0" width="600" src="https://static.igem.org/mediawiki/2009/9/93/Resources_a.png" id="res" onmouseover="mouseOver_res()" onmouseout="mouseOut_res()" align="center"></a>
-
    <p>-Osbaldo Rsendis<br />
+
</tr>
-
      -Adrian Granados<br />
+
<br><br>
-
      -Laura Gomez<br />
+
<tr><a href="https://2009.igem.org/Team:LCG-UNAM-Mexico/Modelling" ><img border="0" width="600" src="https://static.igem.org/mediawiki/2009/8/83/Modelling_a.png" id="mod" onmouseover="mouseOver_mod()" onmouseout="mouseOut_mod()" align="center"></a>
-
      -Enrique Paz<br />
+
</tr>
-
      -Abraham Avelar<br />
+
-
      -Soto Gutierrez<br />
+
-
      -Enrique Quintana<br />
+
-
      -Willy Garcia<br />
+
-
      -Martin del -Castillo<br />
+
-
      -Uriel Urquiza<br />
+
-
      -Arturo Velarde<br />
+
-
      -Minerva  Trejo<br />
+
-
      -Fernando Montano<br />
+
-
    -Libertad Pantoja</p>
+
-
<p>Check out our school:</p>
+
-
    <p><a href="www.lcg.unam.mx">-LCG</a><br />
+
-
      <a href="www.ccg.unam.mx">-Center of Genomic Sciences</a><br />
+
-
      <a href="www.unam.mx">-UNAM</a></p>
+
-
<p>&nbsp;</p>
+
-
<p>&nbsp;</p>
+
-
  <!-- end #sidebar1 --></div>
+
-
  <div id="sidebar2">
+
-
   
+
-
  <!-- end #sidebar2 --></div>
+
-
  <div id="mainContent">
+
-
    <h1> Main Content </h1>
+
-
    <p>Bacteriophage infection represents an interesting process in science and industry. The idea of being able to contend at a population level with such  infections is the main motivation of the development of our project. </p>
+
-
    <p>We plan to  modify an Escherichia coli phage in order to deliver genetic material codifying  for a construction against other phages, taking advantage of some of their own properties!!! The purpose of this construction is to make a bacterial  to fight back against the spreading of some phage by triggering on  a cellular death response when a cell encounters a specific component of the  phage. Such response will be faster than the formation process of viral  particles preventing the death of the bacterial population. </p>
+
-
    <p>This population  resistance can be seen as a sort of &quot;vaccine&quot; that will hold back the process of  infection. The design of the delivery system includes the use the P4 phage and  its auxiliary genes present in the P2 helper phage. In the case of the &quot;vaccine&quot;  construct, the cellular death response will be induced by the presence of T3 or  T7 RNA polymerases which will also turn on the transcription of toxines used for  the degradation of DNA and RNA to stop the phage´s genetic material from  assembling and scattering in the environment. </p>
+
-
    <p>Furthermore, we will implement a   stochastic population model based on the basic properties of the bacterial cells  and the phages such as movement, reproduction, etc., this will allow us to  simulate the infection processes and quantify the efficiency of our system. A  possible extention of the system includes the expansion of an AHL signal through  the quorum sensing system of Vibrio fischeri in which the population will be  &quot;warned&quot; to prepare against the viral infection in the presence of T3 or T7. </p>
+
-
    <h2>About us </h2>
+
-
    <p>Hi, welcome to our site! We are students from the undergraduate program in  Genomic Sciences which is part of the National Autonomous University of Mexico.  We are working on the official version of the wiki. Here you will find advances  and general information about our project.<br />
+
-
      Here are some links:<br />
+
-
      <br />
+
-
      <a href="www.lcg.unam.mx">LCG web site</a><br />
+
-
      <a href="www.ccg.unam.mx">Center For  Genomic Sciences</a><br />
+
-
    <a href="www.unam.mx">UNAM</a></p>
+
-
    <p><br />
+
-
    </p>
+
-
    <!-- end #mainContent --></div>
+
-
<!-- This clearing element should immediately follow the #mainContent div in order to force the #container div to contain all child floats --><br class="clearfloat" />
+
-
  <div id="footer">
+
-
    <p>Footer</p>
+
-
  <!-- end #footer --></div>
+
-
<!-- end #container --></div>
+
</body>
</body>
-
 
-
 
</html>
</html>
-
|}
+
<!--Do not remove the first and last lines in this page!-->{{Template:LCG_bottom_Netscape}}
-
 
+
-
<!--- The Mission, Experiments --->
+
-
 
+
-
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
+
-
!align="center"|[[Team:LCG-UNAM-Mexico|Home]]
+
-
!align="center"|[[Team:LCG-UNAM-Mexico/Team|The Team]]
+
-
!align="center"|[[Team:LCG-UNAM-Mexico/Project|The Project]]
+
-
!align="center"|[[Team:LCG-UNAM-Mexico/Parts|Parts Submitted to the Registry]]
+
-
!align="center"|[[Team:LCG-UNAM-Mexico/Modeling|Modeling]]
+
-
!align="center"|[[Team:LCG-UNAM-Mexico/Notebook|Notebook]]
+
-
|}
+

Latest revision as of 01:15, 22 October 2009


The Project in a nutshell

Bacteriophage infection represents an interesting process in microbiology and industry. The idea of being able to contend at a population level with such infections is the main motivation for the development of our project.

We propose a population level approach relaying on a defense system delivered by an engineered version of the enterobacteria phage P4. The purpose of the defense construction is to modify bacteria in order to hold back the process of infection by triggering a cellular death response when a cell encounters a specific component of the infective phage. Such response will be fast enough to stop the formation process of viral particles, thus preventing the phage proliferation and population decline.

The delivery system takes advantage of the satellite properties of P4 phage. This means that a P4 phage engineered with the defense construction will be able to infect an E.coli strain which harbors some genes from helper phage P2 that are used for complementing and completing P4 life cycle, hence creating a production line of our version of P4.
Besides, the defense system will consist of DNA and RNA degradation by toxins which will be transcribed by T3 or T7 RNA-Polymerases fast enough to stop phage assembly and scattering in the environment. Simultaneously, a quorum sensing signal will be diffusing to the non-infected bacteria acting as a transcriptional activator of an antisense RNA against bacteriophage's transcriptional machinery , hence "warning" the population to prepare against further T3 or T7 infection.

We implemented a stochastic multi-scale model. The model will simulate the behaviour at the intracellular scale using stochastic molecular simulations and at the populations scale using a Cellular Automata and a system of ODE's.
Simulations results are in good agreement with existing experimental data. Thanks to the structure and design of the model this can be easily modified in order to simulate infection dynamics for different bacteria and phages. Furthermore, our Molecular model can be used as a reliable tool for sampling biomolecules distributions involved in phage infection processes.











Locations of visitors to this page


Retrieved from "http://2009.igem.org/Team:LCG-UNAM-Mexico"