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| | + | {{Template:LCG_top_Netscape}}<!--Do not remove the first and last lines in this page!--> |
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| | + | |width="900px" style="padding: 0 20px 0 0;"| |
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| | + | ='''The Project in a nutshell'''= |
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| | + | 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> |
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| | <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(){ |
| - | /* Tips for this Hybrid layout
| + | document.getElementById("comic").src ="https://static.igem.org/mediawiki/2009/a/a8/Comic_LCG_ba.png"; |
| - | 1. Since the side columns em-based sizing is based on the user's default font size, you will want to be sure that background graphics in the columns take that into account. Built correctly, this is more accessible for those that need larger font sizes, since the width of the columns remains proportionate. If this is undesirable with your design, simply change the width to a pixel size and be sure to change the margins on the #mainContent div accordingly.
| + | |
| - | 2. Since the sizing of side columns in this layout are based on the 100% font size in the body element, if you decrease the text size overall by using a font-size: 80% on the body element or the #container, remember that the column widths will downsize proportionately. You may want to increase their widths, and the size of the #mainContent div's side margins, to compensate for this.
| + | |
| - | 3. If font sizing is changed in differing amounts on each div instead of on the overall design (ie: #sidebar1 is given a 70% font size and #mainContent is given an 85% font size), this will proportionately change each of the divs overall size. You may want to adjust based on your final font sizing.
| + | |
| - | 4. The #container div is not necessary for this layout at the 100% width. You may want to use it to create faux columns or limit the width of the layout.
| + | |
| - | 5. It is not neccessary to have the 100% width on the #container div since, by nature, a div takes up 100% of the available space. It is here so that if you want to decrease the size of the overall container - perhaps leaving a bit of margin on each side - this will already be available for adjustment.
| + | |
| - | */
| + | |
| - | .thrColHybHdr #container {
| + | |
| - | 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; /* zeroing the margin of the last element in the #header div will avoid margin collapse - an unexplainable space between divs. If the div has a border around it, this is not necessary as that also avoids the margin collapse */
| + | |
| - | padding: 10px 0; /* using padding instead of margin will allow you to keep the element away from the edges of the div */
| + | |
| | } | | } |
| | | | |
| - | /* Tips for sidebar1: | + | |
| - | 1. Be aware that if you set a font-size value on this div, the overall width of the div will be adjusted accordingly.
| + | </script> |
| - | 2. Since we are working in ems, it's best not to use padding on the sidebar itself. It will be added to the width for standards compliant browsers creating an unknown actual width.
| + | </header> |
| - | 3. Space between the side of the div and the elements within it can be created by placing a left and right margin on those elements as seen in the ".thrColHybHdr #sidebar1 p" rule.
| + | |
| - | */
| + | <style> |
| - | .thrColHybHdr #sidebar1 {
| + | #bodyContent { padding: 10px auto; width: 1000px; margin: auto; clear: none; } |
| - | float: left;
| + | a:link { color: #659D32; text-decoration: none} |
| - | width: 11em; /* since this element is floated, a width must be given */
| + | a:visited { color:#659D32; text-decoration: none} |
| - | background: #8BA870; /* the background color will be displayed for the length of the content in the column, but no further */
| + | a:hover { color:#f29400; text-decoration: none} |
| - | padding: 15px 0; /* top and bottom padding create visual space within this div */
| + | 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; /* since this element is floated, a width must be given */
| + | |
| - | background: #EBEBEB; /* the background color will be displayed for the length of the content in the column, but no further */
| + | |
| - | padding: 15px 0; /* top and bottom padding create visual space within this div */
| + | |
| - | }
| + | |
| - | .thrColHybHdr #sidebar1 h3, .thrColHybHdr #sidebar1 p, .thrColHybHdr #sidebar2 p, .thrColHybHdr #sidebar2 h3 { | + | |
| - | margin-left: 10px; /* the left and right margin should be given to every element that will be placed in the side columns */
| + | |
| - | margin-right: 10px;
| + | |
| | } | | } |
| | | | |
| - | /* Tips for mainContent:
| + | function mouseOver_res(){ |
| - | 1. If you give this #mainContent div a font-size value different than the #sidebar1 div, the margins of the #mainContent div will be based on its font-size and the width of the #sidebar1 div will be based on its font-size. You may wish to adjust the values of these divs.
| + | document.getElementById("res").src ="https://static.igem.org/mediawiki/2009/3/35/Resources_b.png"; |
| - | 2. The space between the mainContent and sidebar1 is created with the left margin on the mainContent div. No matter how much content the sidebar1 div contains, the column space will remain. You can remove this left margin if you want the #mainContent div's text to fill the #sidebar1 space when the content in #sidebar1 ends.
| + | } |
| - | 3. To avoid float drop, you may need to test to determine the approximate maximum image/element size since this layout is based on the user's font sizing combined with the values you set. However, if the user has their browser font size set lower than normal, less space will be available in the #mainContent div than you may see on testing.
| + | function mouseOut_res(){ |
| - | 4. In the Internet Explorer Conditional Comment below, the zoom property is used to give the mainContent "hasLayout." This avoids several IE-specific bugs that may occur.
| + | document.getElementById("res").src ="https://static.igem.org/mediawiki/2009/9/93/Resources_a.png"; |
| - | */
| + | |
| - | .thrColHybHdr #mainContent {
| + | |
| - | margin: 0 12em 0 12em; /* the right margin can be given in ems or pixels. It creates the space down the right side of the page. */
| + | |
| - | padding: 0 2em 0 2em; /* padding here creates white space "inside the box." */
| + | |
| - | } | + | |
| - | .thrColHybHdr #footer {
| + | |
| - | padding: 0 10px; /* this padding matches the left alignment of the elements in the divs that appear above it. */
| + | |
| - | background:#DDDDDD;
| + | |
| - | }
| + | |
| - | .thrColHybHdr #footer p { | + | |
| - | margin: 0; /* zeroing the margins of the first element in the footer will avoid the possibility of margin collapse - a space between divs */
| + | |
| - | padding: 10px 0; /* padding on this element will create space, just as the the margin would have, without the margin collapse issue */
| + | |
| | } | | } |
| | | | |
| - | /* Miscellaneous classes for reuse */
| + | function mouseOver_des(){ |
| - | .fltrt { /* this class can be used to float an element right in your page. The floated element must precede the element it should be next to on the page. */ | + | document.getElementById("des").src ="https://static.igem.org/mediawiki/2009/2/2a/Description_b.png"; |
| - | float: right;
| + | |
| - | margin-left: 8px;
| + | |
| | } | | } |
| - | .fltlft { /* this class can be used to float an element left in your page */
| + | function mouseOut_des(){ |
| - | float: left;
| + | document.getElementById("des").src ="https://static.igem.org/mediawiki/2009/3/3e/Description_a.png"; |
| - | margin-right: 8px;
| + | |
| | } | | } |
| - | .clearfloat { /* this class should be placed on a div or break element and should be the final element before the close of a container that should fully contain a float */
| + | |
| - | 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; }
| |
| - | /* the above proprietary zoom property gives IE the hasLayout it needs to avoid several bugs */
| |
| - | </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> |
| - | <h3>Links:</h3>
| + | <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> </p> | + | |
| - | <p> </p> | + | |
| - | <!-- end #sidebar1 --></div>
| + | |
| - | <div id="sidebar2">
| + | |
| - | <h3>News!</h3>
| + | |
| - | <p>The background color on this div will only show for the length of the content. If you'd like a dividing line instead, place a border on the right side of the #mainContent div if the #mainContent div will always contain more content than the #sidebar2 div. </p>
| + | |
| - | <p>Donec eu mi sed turpis feugiat feugiat. Integer turpis arcu, pellentesque eget, cursus et, fermentum ut, sapien. </p>
| + | |
| - | <!-- end #sidebar2 --></div>
| + | |
| - | <div id="mainContent">
| + | |
| - | <h1> Main Content </h1>
| + | |
| - | <p>Bacteriophage infection represents a major problem in industry and science. 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 "vaccine" 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 "vaccine" 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 "warned" 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> |
| | | | |
| - | </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]]
| + | |
| - | |}
| + | |
"