|
|
| (47 intermediate revisions not shown) |
| Line 1: |
Line 1: |
| - | <html lang="en-US" xmlns="http://www.w3.org/1999/xhtml" dir="ltr"><head> | + | <html lang="en-US" xmlns="http://www.w3.org/1999/xhtml" dir="ltr"> |
| - | <meta http-equiv="Content-type" content="text/html; charset=utf-8">
| + | <head> |
| | + | <meta http-equiv="Content-type" content="text/html; charset=utf-8" /> |
| | | | |
| | + | |
| | + | <link rel="shortcut icon" href="http://simsekburak.com/hasan/css/images/favicon.ico" /> |
| | + | <link rel="stylesheet" href="http://simsekburak.com/hasan/css/style.css" type="text/css" media="all" /> |
| | + | <!--[if IE 6]> |
| | + | <link rel="stylesheet" href="css/ie6.css" type="text/css" media="all" /> |
| | + | <script src="http://simsekburak.com/hasan/js/png-fix.js" type="text/javascript"></script> |
| | + | <![endif]--> |
| | + | <script src="http://simsekburak.com/hasan/js/jquery-1.4.2.js" type="text/javascript"></script> |
| | + | <script src="http://simsekburak.com/hasan/js/jquery.jcarousel.js" type="text/javascript"></script> |
| | + | <script src="http://simsekburak.com/hasan/js/js-func.js" type="text/javascript"></script> |
| | | | |
| - | <link rel="shortcut icon" href="http://simsekburak.com/hasan/css/images/favicon.ico">
| + | <style> |
| - | <link rel="stylesheet" href="http://simsekburak.com/hasan/css/style.css" type="text/css" media="all">
| + | h1.firstHeading, div#p-logo, div#search-controls, div#contentSub, div#footer-box, div#catlinks{ |
| - | <!--[if IE 6]>
| + | display:none; |
| - | <link rel="stylesheet" href="css/ie6.css" type="text/css" media="all" />
| + | } |
| - | <script src="http://simsekburak.com/hasan/js/png-fix.js" type="text/javascript"></script>
| + | |
| - | <![endif]-->
| + | |
| - | <script src="http://simsekburak.com/hasan/js/jquery-1.4.2.js" type="text/javascript"></script>
| + | |
| - | <script src="http://simsekburak.com/hasan/js/jquery.jcarousel.js" type="text/javascript"></script>
| + | |
| - | <script src="http://simsekburak.com/hasan/js/js-func.js" type="text/javascript"></script>
| + | |
| | | | |
| - | <style>
| + | #top-section{ |
| - | h1.firstHeading, div#p-logo, div#search-controls, div#contentSub, div#footer-box, div#catlinks{
| + | height: 20px !important; |
| - | display:none;
| + | border: none !important; |
| - | }
| + | } |
| | | | |
| - | #top-section{
| + | div#content{ |
| - | height: 20px !important;
| + | padding: 0 !important; |
| - | border: none !important;
| + | background: transparent; |
| - | }
| + | border: none !important; |
| | + | width: auto; |
| | + | } |
| | | | |
| - | div#content{
| + | </style> |
| - | padding: 0 !important;
| + | |
| - | background: transparent;
| + | |
| - | border: none !important;
| + | |
| - | width: auto;
| + | |
| - | }
| + | |
| | | | |
| - | </style>
| |
| | | | |
| | + | </head> |
| | + | <body style="background-image: url(https://static.igem.org/mediawiki/2012/c/cb/METU-team-logo-leaves.png); background-repeat: no-repeat; background-attachment: fixed; background-position:center;"> |
| | | | |
| - | </head>
| |
| - | <body>
| |
| - | <!-- Header -->
| |
| - | <div id="header">
| |
| - | <div class="shell">
| |
| - | <h1 id="logo" class="notext"><a href="https://2012.igem.org/Team:METU/test">
| |
| - | <img width="200px" height="104px" src="/wiki/images/2/22/METU_logo.png" style="padding-top: 10px;">
| |
| - | </a>
| |
| - | </h1>
| |
| - | <h1 id="logo2" class="notext"><a href="https://2012.igem.org/Main_Page">
| |
| - | <img width="144px" height="109px" src="/wiki/images/0/08/Igem_logo.png" style="padding-top: 25px;"></a></h1>
| |
| - | <div id="navigation">
| |
| - | <ul>
| |
| - | <li><a href="https://2012.igem.org/Team:METU/test" class="active"><span>Home</span></a></li>
| |
| | | | |
| - | <li><a href="https://2012.igem.org/Team:METU/test/Team"><span>Team</span></a></li>
| + | <!-- Header --> |
| - | < li><a href="https://2012.igem.org/Team:METU /test/CODH">< span>CODH</ span></ a> | + | <div id="header"> |
| - | <div class="dd-holder">
| + | <div class="shell"> |
| - | <div class="dd-t"></div>
| + | < h1 id="logo" class="notext"><a href="https://2012.igem.org/Team:METU"> |
| - | <div class="dd">
| + | <img width="200px" height="104px" src="/wiki/images/2/22/METU_logo.png" style="padding-top: 10px;"> |
| - | <ul>
| + | </a> |
| - | <li><a href="https://2012.igem.org/ Team:METU/test/CODH#Overview" >Overview</a></li> | + | </h1> |
| - | <li><a href="https://2012.igem.org/Team:METU/test/CODH#Modelling">Modelling</a></li>
| + | < h1 id="logo2" class=" notext"><a href="https://2012.igem.org/ Main_Page"> |
| - | <li><a href="https://2012.igem.org/Team:METU/test/CODH#Results">Results</a></li>
| + | <img width="144px" height="109px" src="/wiki/images/0/08/Igem_logo.png" style="padding-top: 25px;"></a></h1> |
| - | <li><a href="https://2012.igem.org/Team:METU /test/CODH#Biobricks"> Biobricks</a></li> | + | <div id="navigation"> |
| | + | <ul> |
| | + | <li><a href="https://2012.igem.org/Team:METU" class="active"><span>Home</span></a></li> |
| | | | |
| - | </ul>
| + | <li><a href="https://2012.igem.org/Team:METU/Team"><span>Team</span></a></li> |
| - | <div class="cl"> </div>
| + | <li><a href="#"><span>Project</span></a> |
| - | </div>
| + | <div class="dd-holder"> |
| - | | + | |
| - | </div>
| + | |
| - | </li>
| + | <ul> |
| - | <li><a href="https://2012.igem.org/Team:METU/ test/KillSwitchOverview"><span> Kill-Switch</span></a> | + | <li><a href="https://2012.igem.org/Team:METU/ ProjectOverview"><span> Overview</span></a>< /li> |
| - | <div class="dd-holder">
| + | <li><a href="https://2012.igem.org/Team:METU/CODH"><span>CO Converter</span></a></li> |
| - | <div class="dd-t"></div>
| + | <li><a href="https://2012.igem.org/Team:METU/KillSwitchOverview"> <span>Kill-Switch</span></a></li> |
| - | <div class="dd">
| + | <li><a href="https://2012.igem.org/Team:METU/ CellLimiter"> <span>Cell Limiter</span></a></li> |
| - | <ul>
| + | <li><a href="https://2012.igem.org/Team:METU/ datapage"> <span>Data Page</span></a></li> |
| - | <li><a href="https://2012.igem.org/Team:METU /test/KillSwitchOverview #Overview"> Overview</a></li> | + | |
| - | <li><a href="https://2012.igem.org/Team:METU/ KillSwitch/Modelling#Modelling"> Modelling</a></li> | + | </ul> |
| - | <li><a href="https://2012.igem.org/Team:METU/ test/KillSwitchOverview#Results"> Results</a></li> | + | <div class="cl"> </div> |
| - | <li><a href="https://2012.igem.org/Team:METU/ test/ KillSwitchOverview# Biobricks"> Biobricks</a></ li> | + | </div> |
| | + | <div class="dd-b"></div> |
| | + | </div> |
| | + | </li> |
| | + | |
| | + | <li><a href="https://2012.igem.org/Team:METU/ Results"><span>Results</ span></a></li> |
| | + | |
| | + | <li><a href="#"><span>Notebook</span></a> |
| | + | <div class="dd-holder"> |
| | + | <div class="dd-t"></div> |
| | + | <div class="dd"> |
| | + | <ul> |
| | | | |
| - | </ul>
| + | <li><a href="/Team:METU/Timeline">Timeline</a></li> |
| - | <div class="cl"> </div>
| + | <li><a href="/Team:METU/Brainstorm">Brainstorming</a></li> |
| - | </div>
| + | <li><a href="https://2012.igem.org/Team:METU/Protocols">Protocols</a></li> |
| - | <div class="dd-b"></div>
| + | |
| - | </div>
| + | |
| - | </li>
| + | |
| | | | |
| - | <li><a href=" https://2012.igem.org/Team:METU/ test/ CellLimiter"><span> Cell Limiter</span></a> | + | <li class="last"><a href="/Team:METU/ Judging">Judging</ a></li> |
| - | | + | </ul> |
| - | | + | <div class="cl"> </div> |
| - | | + | </div> |
| - | | + | <div class="dd-b"></div> |
| - | <li><a href="https://2012.igem.org/Team:METU/ test/CellLimiter#Overview"> Overview</a></li> | + | </div> |
| - | <li><a href=" https://2012.igem.org/Team:METU/ test/CellLimiter#Modelling"> Modelling</a></li> | + | </li> |
| - | <li><a href=" https:// 2012.igem.org/Team:METU/ test/CellLimiter#Results"> Results</a></li> | + | <li><a href="#"><span>Human Practice</span></a> |
| - | <li><a href=" https://2012.igem.org/Team:METU/ test/CellLimiter#Biobricks"> Biobricks</a></li> | + | |
| | + | |
| | + | |
| | + | |
| | + | <li><a href="https://2012.igem.org/Team:METU/ Gallery"> Gallery</a></li> |
| | + | <li class="last"><a href="/Team:METU/ Activities"> Activities</a></li> |
| | + | </ul> |
| | + | <div class="cl"> </div> |
| | + | </div> |
| | + | <div class="dd-b"></div> |
| | + | </div> |
| | + | </li> |
| | + | <li><a href=" #"><span>Extras</ span></ a> |
| | + | <div class="dd-holder"> |
| | + | <div class="dd-t"></div> |
| | + | <div class="dd"> |
| | + | <ul> |
| | + | <li><a href="/Team:METU/Safety">Safety</a></li> |
| | + | |
| | + | <li class="last"><a href="/Team:METU/ Attributions"> Attributions</a></li > |
| | + | </ul> |
| | + | <div class="cl"> </div> |
| | + | </div> |
| | + | <div class="dd-b"></div> |
| | + | </div> |
| | + | |
| | + | </li> |
| | + | </ul> |
| | + | </div> |
| | + | <div class="cl"> </div> |
| | + | <!-- <div class="search"> |
| | + | <form action="#" method="post"> |
| | + | <span class="field"> |
| | + | <input type="text" class="blink" value="Search" title="Search" /> |
| | + | </span> |
| | + | <input type="submit" class="search-btn notext" value="Submit" /> |
| | + | </form> |
| | + | </div> |
| | + | --> |
| | | | |
| - | </ul>
| + | </div> |
| - | <div class="cl"> </div>
| + | </div> |
| - | </div>
| + | <!-- End Header --> |
| - | <div class="dd-b"></div>
| + | |
| - | </div>
| + | |
| - | </li>
| + | |
| - | | + | |
| - | <li><a href="https://2012.igem.org/Team:METU/test/Overview"><span>Notebook</span></a>
| + | |
| - | <div class="dd-holder">
| + | |
| - | <div class="dd-t"></div>
| + | |
| - | <div class="dd">
| + | |
| - | <ul>
| + | |
| - | <li><a href="https://2012.igem.org/Team:METU/test/Overview">Overview</a></li>
| + | |
| - | <li><a href="/Team:METU/Timeline">Timeline</a></li>
| + | |
| - | <li><a href="/Team:METU/Brainstorm">Brainstorm</a></li>
| + | |
| - | <li><a href="https://2012.igem.org/Team:METU/test/Protocols">Protocols</a></li>
| + | |
| - | <li><a href="/Team:METU/CloningPlan">Cloning Plan</a></li>
| + | |
| - | <li class="last"><a href="/Team:METU/Judging">Judging</a></li>
| + | |
| - | </ul>
| + | |
| - | <div class="cl"> </div>
| + | |
| - | </div>
| + | |
| - | <div class="dd-b"></div>
| + | |
| - | </div>
| + | |
| - | </li>
| + | |
| - | <li><a href="#"><span>Human Practice</span></a>
| + | |
| - | <div class="dd-holder">
| + | |
| - | <div class="dd-t"></div>
| + | |
| - | <div class="dd">
| + | |
| - | <ul>
| + | |
| - | <li><a href="https://2012.igem.org/Team:METU/Gallery">Gallery</a></li>
| + | |
| - | <li class="last"><a href="/Team:METU/Activities">Activities</a></li>
| + | |
| - | </ul>
| + | |
| - | <div class="cl"> </div>
| + | |
| - | </div>
| + | |
| - | <div class="dd-b"></div>
| + | |
| - | </div>
| + | |
| - | </li>
| + | |
| - | <li><a href="#"><span>Extras</span></a>
| + | |
| - | <div class="dd-holder">
| + | |
| - | <div class="dd-t"></div>
| + | |
| - | <div class="dd">
| + | |
| - | <ul>
| + | |
| - | <li><a href="/Team:METU/Safety">Safety</a></li>
| + | |
| - | | + | |
| - | <li class="last"><a href="/Team:METU/Attributions">Attributions</a></li>
| + | |
| - | </ul>
| + | |
| - | <div class="cl"> </div>
| + | |
| - | </div>
| + | |
| - | <div class="dd-b"></div>
| + | |
| - | </div>
| + | |
| - | | + | |
| - | </li>
| + | |
| - | </ul>
| + | |
| - | </div>
| + | |
| - | <div class="cl"> </div>
| + | |
| - | <!-- <div class="search">
| + | |
| - | <form action="#" method="post">
| + | |
| - | <span class="field">
| + | |
| - | <input type="text" class="blink" value="Search" title="Search" />
| + | |
| - | </span>
| + | |
| - | <input type="submit" class="search-btn notext" value="Submit" />
| + | |
| - | </form>
| + | |
| - | </div>
| + | |
| - | -->
| + | |
| - | | + | |
| - | </div>
| + | |
| - | </div>
| + | |
| - | <!-- End Header -->
| + | |
| | <!-- Slider --> | | <!-- Slider --> |
| | <div id="slider2"> | | <div id="slider2"> |
| | <div class="shell"> | | <div class="shell"> |
| | <div class="slider-holder2"> | | <div class="slider-holder2"> |
| - | <h1>Kill Switch</h1> | + | <h1>ACTIVITIES</h1> |
| | <div class="cl"> </div> | | <div class="cl"> </div> |
| | | | |
| Line 177: |
Line 150: |
| | <div class="col2"> | | <div class="col2"> |
| | <div id="Overview"> | | <div id="Overview"> |
| - | <h2>Overview</h2> | + | <h2> Human Practices </h2> |
| - | <span>
| + | <div class="cl"> </div> |
| | + | <p><b>1.Metu Orientation Days</b></p> |
| | + | <p>In order to promote synthetic biology and IGEM organization, as IGEM METU team we participated the event of METU Orientation Days for newly coming students. In the organization with a specific stand for our team we explained some facts about synthetic biology with the fine presentations and the posters of our professors’ works. Also, with the great effort we tried to answer every single question about both synthetic biology and IGEM competition. |
| | + | <a href="http://www.metu.edu.tr/tr/odtu-tanitim-gunleri-12"/><u>http://www.metu.edu.tr/tr/odtu-tanitim-gunleri-12</u></a> |
| | + | </p> |
| | + | <div class="cl"> </div> |
| | + | <p><img src="https://static.igem.org/mediawiki/2012/4/4b/Metu-photos-hp1.jpg" alt="" width="527px" height="371px"/> <img src="https://static.igem.org/mediawiki/2012/7/73/Metu-photos-hp2.jpg" alt="" width="300px" height="371px"/></p> |
| | + | <div class="cl"> </div> |
| | + | <p><b>2.Party time for Synthetic Biology lovers!</b></p> |
| | + | <p> |
| | + | To draw the public attention to both the synthetic biology we thought both funny and educational way, and so we said how did we integrate human practices in our synthetic biology project? The answer was in the part of parties! As IGEM members we planned a party. In the party both we had |
| | + | lots of fun and took the people attentions on IGEM competition. Actually, by that way we both gain some followers and sponsors. |
| | + | </p> |
| | + | <p><img src="https://static.igem.org/mediawiki/2012/6/6a/Metu-photos-hp3.jpg" alt="" width="371px" height="527px" /> |
| | + | <img src="https://static.igem.org/mediawiki/2012/9/9b/Metu-photos-hp4.jpg" alt="" width="371px" height="527px"/></p> |
| | + | <p><b>Our display posters from the party</b></p> |
| | + | <div class="cl"> </div> |
| | + | <table border="3" cellspacing="7" cellpadding="0"> |
| | | | |
| - | | + | <p><img src="https://static.igem.org/mediawiki/2012/d/df/Metu-photos-hp5.jpg" alt="" width="371px" height="300px" /> <img src="https://static.igem.org/mediawiki/2012/4/4b/Metu-photos-hp6.jpg" alt="" width="371px" height="300px"/></p> |
| - | Kill switch is a safety system which is necessary to control the release of genetically modified
| + | <p><b>Some photos from the party</b></p> |
| - | organisms (GMOs) into the environment. Since we aimed to construct a biofilm with GMOs which will convert CO to CO2, we needed a kill switch that can prevent our system to cause any harm to the environment. In order to achieve that aim we used the kill switch designed by Berkeley 2008 iGEM Team (Bba_K112808) and also we tried to develop it.
| + | <div class="cl"> </div> |
| - | | + | <p><b>3.iGEM Student Club</b></p> |
| - | | + | <p>Moreover, we made an effort to create and official IGEM community in METU to gain more support and member. The main aim of official iGEM community is increase the synthetic biology knowledge firstly in biological sciences department then whole university, city and country. Furthermore, this community also aims at improve practical side of the members besides the theoretical side of them. |
| - | </p>
| + | </p> |
| - | | + | <div class="cl"> </div> |
| - | </span>
| + | <p><b>4. Team Song!!!</b></p> |
| - | | + | <div class="1"> </div> |
| - | <h2>How The System Works ?</h2>
| + | |
| - | | + | <p>I wanna be the very best</p> |
| - | | + | <p>Like no one ever was</p> |
| - | | + | <p>Transformation is my real test</p> |
| - | In order to construct our kill switch system we needed a reagent that E.Coli will grow and in the absence of that reagent all the bacteria should die. For that purpose we prefered to use IPTG (Isopropyl-beta-D-thiogalactopyranoside) because it cannot be metabolised by E.Coli and that is why its concentration remains constant in the cell.<b>[1]</b>
| + | <p>Synthesizing my cause</p |
| - | | + | <div class="2"> </div> |
| - | When IPTG is present in the cell it will bind to LacI which can be produced by the promoter J23116. Basal LacI expression is already present in E.Coli but at low levels and it is hard to control the system with that much LacI. Hence, we prefered to produce it with the help of J23116.
| + | <p>I will surf across the web</p> |
| - | | + | <p>For researchs far and wide</p> |
| - | Our kill switch system includes the expression of endolysin, holin, antiholin and their production is controlled with the initial concentration of IPTG in the environment. Actually
| + | <p>Each plasmid to understand </p> |
| - | cell lysis can occur without IPTG but the lysis rate will be high. By using IPTG we aimed to keep our system under control.
| + | <p>The promoter that’s inside</p> |
| - | | + | <div class="3"> </div> |
| - | <p> < b> Endolysin-Holin System;</ b> Endolysin and holin are the proteins needed for the cell lysis. Endolysin is a lysozyme and its funtion is to hydrolyze the peptidoglycan bacterial cell wall but it needs holin to form pores on inner membrane, then it can reach periplasm and cell lysis occur. | + | <p>E.coli DH5 alpha </p> |
| | + | <p>It’s you and me</p> |
| | + | <p>I know its my destiny</p> |
| | + | <p>E.coli</p> |
| | + | <div class="4"> </div> |
| | + | <p>Oo you’re my best friend </p> |
| | + | <p>In a world we must defend</p> |
| | + | <p>E.coli (Dh5 alpha)</p> |
| | + | <p>A germ so true </p> |
| | + | <p>Our knowledge will pull us through </p> |
| | + | <p>You infect me and I will kill you</p> |
| | + | <p>E.coliiii!!!! </p> |
| | + | <p>Synthesize them all!!!</p> |
| | + | <p<Synthesize them AAAALLL!!! </p> |
| | + | <p><img src="https://static.igem.org/mediawiki/igem.org/7/76/Metu-photos-pokemon6.jpg" alt="" width="371px" height="300px" /><img src="https://static.igem.org/mediawiki/igem.org/d/d2/Metu-photos-pokemon1.jpg" alt="" width="371px" height="300px" /></p> |
| | | | |
| | + | <div class="cl"> </div> |
| | + | <p><b>5. BACK TO BASICS</b></p> |
| | + | <p>Furthermore, to gain the attention of high school students, we just “went to basics”, we went to the high school of one of our team members and presented the competition as well as synthetic biology as a field which they can choose to study. To this voluntarily presentation, 88 students chose to participate and not only the students but also the teachers and the assistant principal which was an ex-biology teacher were amazed by the opportunities synthetic biology provides. We tried to encourage the school to participate in the HS division of iGEM, hopefully next year we will see them in this competition as well. </p> |
| | + | <img src="https://static.igem.org/mediawiki/igem.org/e/e7/Metu-photos-lisesunumu-9.png" alt="" width="371px" height="300px" /><img src="https://static.igem.org/mediawiki/igem.org/f/f7/Metu-photos-lisesunumu-4.png" alt="" width="371px" height="300px" /> |
| | </p> | | </p> |
| - | </p>
| + | <p><img src="https://static.igem.org/mediawiki/igem.org/0/ 0d/Metu-photos- lisesunumu-2.png" alt="" width="371px" height=" 300px" /><img src="https://static.igem.org/mediawiki/igem.org/ 5/ 51/Metu-photos- lisesunumu- 3.png" alt="" width="371px" height=" 300px" /> |
| - | | + | </p> |
| - | <p>
| + | |
| - | <b> The fate of the Gram-negative envelope during holin-endolysin lysis:[2]</b>
| + | |
| - |
| + | |
| - | <img src="https://static.igem.org/mediawiki/ 2012/9/97/Metu-photos-model27.png.jpg" alt="From the journal Trends in Microbiology"> | + | |
| - | </p>
| + | |
| - | | + | |
| - | <p>
| + | |
| - | In this figure holins are shown as clear ovals and endolysin is shown as notched circles.
| + | |
| - | </p>
| + | |
| - | | + | |
| - | <ul>
| + | |
| - | <li><b>a-)Pre-Hole Configuration:</b> Accumulation of holin is present in the inner membrane, while endolysin accumulates in the cytosol. Holin action can be prevented with the inhibitors (shown with star and black ovals).</li>
| + | |
| - | <li> <b>b-) Hole Configuration:</b> When the holes are formed by holin in the inner membrane, endolysin can attack the murein which is important for cell lysis to occur.</li>
| + | |
| - | </ul>
| + | |
| - |
| + | |
| - |
| + | |
| - | | + | |
| - | <p><b>Antiholin;</b> It is the protein that blocks the function of holin and it is important for the regulation of cell lysis.<b>[3]</b>
| + | |
| - |
| + | |
| - | </p>
| + | |
| - | <p id="Overview">
| + | |
| - | In our system antiholin is constitutively produced by the promoter J23116 and when antiholin level is in between 1000-3000 molecules, the cell will die.<b>[4]</b> Actually,it is the number of free holin molecules that determines if the cell will die or not.
| + | |
| - | </p>
| + | |
| - | </div>
| + | |
| - | | + | |
| - | <div id="Modelling">
| + | |
| - | <h2>Modelling</h2>
| + | |
| - | <span>
| + | |
| - | <p>
| + | |
| - | | + | |
| - | <div id="main">
| + | |
| - | | + | |
| - | <h2><b> KILL-SWITCH MODEL </b></h2>
| + | |
| - | <span>
| + | |
| - |
| + | |
| - | | + | |
| - | The aim of kill-switch model is to predict the behavior of kill-switch mechanism in different IPTG concentrations. We first tried to model mechanism by the help of ODEs. Then we used SimBiology toolbox of MATLAB to simulate system.
| + | |
| - | <p>
| + | |
| - | <b>Introduction:</b>
| + | |
| - | </p>
| + | |
| - | <p>
| + | |
| - | As can be seen from the diagram our circuit involves constitutive production of LacI. LacI Promoter is negatively regulated by LacI. The control mechanism of our system is inhibition of LacI by IPTG molecule. Since LacI is inhibited by IPTG its effect on LacI promoter changes with respect to IPTG concentration.
| + | |
| - | Holin and Endolysin expression is controlled by cI promoter which is negatively regulated by cI.
| + | |
| - | Our first assumption in the model is that when the free Holin molecules, which means number of Holin molecules minus number of Antiholin molecules, reach 3000[ref] cell lysis occurs.
| + | |
| - | Because cI concentration depends on the activity of LacI promoter, we can conclude that in the presence of IPTG the concentration of cI will be high and expression of Holin and Endolysin will be lowered. Due to the constitutive production of Antiholin, we can say that free Holin molecules will be lowered and chance of cell lysis to occur will drop. However, to understand the overall behaviour of system with respect to IPTG concentration we need to model and simulate the system.
| + | |
| - | | + | |
| - | <img src="https://static.igem.org/mediawiki/2012/2/24/Metu-photos-model1.png" alt="" "
| + | |
| - | </p>
| + | |
| - | | + | |
| - | <p>
| + | |
| - | <b>Mathematical Model:</b>
| + | |
| - | </p>
| + | |
| - | | + | |
| - | In our model, we included all processes shown below.
| + | |
| - | | + | |
| - | <img src="https://static.igem.org/mediawiki/2012/8/82/Metu-photos-model2.jpg" alt="" ">
| + | |
| - | | + | |
| - | <p><b>Equations for mRNA transcription</b></p>
| + | |
| - |
| + | |
| - |
| + | |
| - |
| + | |
| - | | + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/2/29/Metu-photos-model3.png" alt="" ">
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/8/81/Metu-photos-model4.png" alt="" ">
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/c/cd/Metu-photos-model5.png" alt="" ">
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/9/9f/Metu-photos-model6.png" alt="" ">
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/8/8a/Metu-photos-model7.png" alt="" ">
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <b> Equations for Protein Translation </b>
| + | |
| - |
| + | |
| - |
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/9/9c/Metu-photos-model8.png" alt="" />
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/4/45/Metu-photos-model9.png" alt="" />
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/1/12/Metu-photos-model10.png" alt="" />
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/c/c6/Metu-photos-model11.png" alt="" />
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/5/5b/Metu-photos-model12.png" alt="" />
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/a/ab/Metu-photos-model13.png" alt="" />
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/e/e7/Metu-photos-model14.png" alt="" />
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <table class="ListTable31" border="1" cellspacing="0" cellpadding="0" style="border-collapse:
| + | |
| - | collapse;border:none;mso-border-alt:solid black .5pt;mso-border-themecolor:
| + | |
| - | text1;mso-yfti-tbllook:1184;mso-padding-alt:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <tbody><tr style="mso-yfti-irow:-1;mso-yfti-firstrow:yes">
| + | |
| - | <td valign="top" style="border-top:solid black 1.0pt;mso-border-top-themecolor:
| + | |
| - | text1;border-left:solid black 1.0pt;mso-border-left-themecolor:text1;
| + | |
| - | border-bottom:none;border-right:none;mso-border-top-alt:solid black .5pt;
| + | |
| - | mso-border-top-themecolor:text1;mso-border-left-alt:solid black .5pt;
| + | |
| - | mso-border-left-themecolor:text1;background:black;mso-background-themecolor:
| + | |
| - | text1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:517"><b><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;color:white;mso-themecolor:background1;mso-ansi-language:EN-US">Parameter<o:p></o:p></span></b></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border-top:solid black 1.0pt;mso-border-top-themecolor:
| + | |
| - | text1;border-left:none;border-bottom:none;border-right:solid black 1.0pt;
| + | |
| - | mso-border-right-themecolor:text1;mso-border-top-alt:solid black .5pt;
| + | |
| - | mso-border-top-themecolor:text1;mso-border-right-alt:solid black .5pt;
| + | |
| - | mso-border-right-themecolor:text1;background:black;mso-background-themecolor:
| + | |
| - | text1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:1"><b><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;color:white;mso-themecolor:background1;mso-ansi-language:EN-US">Description<o:p></o:p></span></b></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:0">
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-right:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:68"><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;mso-ansi-language:EN-US;mso-bidi-font-weight:bold">N<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-left:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:64"><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;mso-ansi-language:EN-US">Plasmid copy number<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:1">
| + | |
| - | <td valign="top" style="border:none;border-left:solid black 1.0pt;mso-border-left-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:4"><span class="SpellE"><span style="font-size:14.0pt;
| + | |
| - | mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;mso-bidi-font-weight:bold">P<sub>x</sub></span></span><sub><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;
| + | |
| - | mso-bidi-font-weight:bold"><o:p></o:p></span></sub></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:none;border-right:solid black 1.0pt;mso-border-right-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal"><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:
| + | |
| - | EN-US">Promoter Strength<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:2">
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-right:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:68"><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;mso-bidi-font-family:Calibri;mso-bidi-theme-font:minor-latin;
| + | |
| - | mso-ansi-language:EN-US;mso-bidi-font-weight:bold">a</span><sub><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;
| + | |
| - | mso-bidi-font-weight:bold">x<o:p></o:p></span></sub></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-left:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:64"><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;mso-ansi-language:EN-US">Degradation Rate<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:3">
| + | |
| - | <td valign="top" style="border:none;border-left:solid black 1.0pt;mso-border-left-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:4"><span class="SpellE"><span style="font-size:14.0pt;
| + | |
| - | mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;mso-bidi-font-weight:bold">K<sub>x</sub></span></span><sub><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;
| + | |
| - | mso-bidi-font-weight:bold"><o:p></o:p></span></sub></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:none;border-right:solid black 1.0pt;mso-border-right-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal"><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:
| + | |
| - | EN-US">Disassociation (Equilibrium) Constant<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:4">
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-right:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:68"><span class="SpellE"><span style="font-size:14.0pt;
| + | |
| - | mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;mso-bidi-font-weight:bold">n<sub>x</sub></span></span><sub><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;
| + | |
| - | mso-bidi-font-weight:bold"><o:p></o:p></span></sub></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-left:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:64"><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;mso-ansi-language:EN-US">Hill Coefficient<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:5">
| + | |
| - | <td valign="top" style="border:none;border-left:solid black 1.0pt;mso-border-left-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:4"><span class="SpellE"><span style="font-size:14.0pt;
| + | |
| - | mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;mso-bidi-font-weight:bold">t<sub>x</sub></span></span><sub><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;
| + | |
| - | mso-bidi-font-weight:bold"><o:p></o:p></span></sub></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:none;border-right:solid black 1.0pt;mso-border-right-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal"><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:
| + | |
| - | EN-US">Translation Rate<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:6">
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-right:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:68"><span class="SpellE"><span style="font-size:14.0pt;
| + | |
| - | mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;mso-bidi-font-weight:bold">k<sub>x</sub></span></span><sub><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;
| + | |
| - | mso-bidi-font-weight:bold"><o:p></o:p></span></sub></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-left:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:64"><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;mso-ansi-language:EN-US">Binding on rate<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:7">
| + | |
| - | <td valign="top" style="border:none;border-left:solid black 1.0pt;mso-border-left-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:4"><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;mso-ansi-language:EN-US;mso-bidi-font-weight:bold">k<sub>-x<o:p></o:p></sub></span></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:none;border-right:solid black 1.0pt;mso-border-right-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal"><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:
| + | |
| - | EN-US">Binding off rate<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | <tr style="mso-yfti-irow:8;mso-yfti-lastrow:yes">
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-right:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-left-alt:solid black .5pt;mso-border-left-themecolor:text1;
| + | |
| - | mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:text1;
| + | |
| - | background:white;mso-background-themecolor:background1;padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:68"><span class="SpellE"><span style="font-size:14.0pt;
| + | |
| - | mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;mso-bidi-font-weight:bold">D<sub>x</sub></span></span><sub><span style="font-size:14.0pt;mso-bidi-font-size:11.0pt;mso-ansi-language:EN-US;
| + | |
| - | mso-bidi-font-weight:bold"><o:p></o:p></span></sub></p>
| + | |
| - | </td>
| + | |
| - | <td valign="top" style="border:solid black 1.0pt;mso-border-themecolor:text1;
| + | |
| - | border-left:none;mso-border-top-alt:solid black .5pt;mso-border-top-themecolor:
| + | |
| - | text1;mso-border-bottom-alt:solid black .5pt;mso-border-bottom-themecolor:
| + | |
| - | text1;mso-border-right-alt:solid black .5pt;mso-border-right-themecolor:text1;
| + | |
| - | padding:1.45pt 5.4pt 1.45pt 5.4pt">
| + | |
| - | <p class="MsoNormal" style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
| + | |
| - | normal;mso-yfti-cnfc:64"><span style="font-size:14.0pt;mso-bidi-font-size:
| + | |
| - | 11.0pt;mso-ansi-language:EN-US">Diffusion rate<o:p></o:p></span></p>
| + | |
| - | </td>
| + | |
| - | </tr>
| + | |
| - | </tbody></table>
| + | |
| - | </span>
| + | |
| - | &nsbp;
| + | |
| - | &nsbp;
| + | |
| - | <p> <b> Simulation Results </b> </p>
| + | |
| - | When the IPTG concentration is 0;
| + | |
| - | | + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/c/c3/Metu-photos-model15.png.jpg" alt="" /></p>
| + | |
| - | <p>Individual graphs can be accessed here.
| + | |
| - | Because the critical point in kill-switch is “Holin-Antiholin” molecules, we ran simulation in different IPTG concentrations and to understand result easier we select the outputs as Holin and Antiholin. Since translation rate of endolysin is more than Holin and Antiholin we can assume that there will be enough endolysin to make cell lysis occur. Also from the graph above we can understand that endolysin will be in sufficient amount.
| + | |
| - | </p>
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/b/bf/Metu-photos-model16.png.jpg" alt="" height="371px" width="727px"/></p>
| + | |
| - | | + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/b/ba/Metu-photos-model17.png.jpg" alt="" height="371px" width="727px"/></p>
| + | |
| - | | + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/0/06/Metu-photos-model18.png.jpg" alt="" height="371px" width="727px" /></p>
| + | |
| - | | + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/2/2d/Metu-photos-model19.png.jpg" alt="" height="371px" width="727px"/></p>
| + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | <p>By the help of our model, we can conclude that when there is no IPTG molecule, cell lysis occur in 275 s. However when there is 100000 IPTG molecules, cell needs 2290 s to lyse. As can be seen from graphs until a very high IPTG concentration like in the Run14, the increase in Holin can eventually cause lysis. As a result of our model we concluded that after an IPTG concentration of 700000 molecule cell lysis will not occur. We are not considering the generation time of cell in this model since it can later be used for different organisms. If we consider e.coli with a generation time of 20 min, even in the medium with IPTG of 100000 molecules, it will divide before it can lyse.
| + | |
| - | </p>
| + | |
| - | | + | |
| - | <p>When IPTG concentration is 700000;</p>
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/3/34/Metu-photos-model20.png.jpg" alt="" height="371px" width="727px" /></p>
| + | |
| - | <p>Individual graphs can be accessed here.</p>
| + | |
| - | | + | |
| - | <p><b> Sensivity Analysis </b></p>
| + | |
| - | <p>Since the challenging part of modelling is choice of parameters, we conducted a sensitivity analysis to see how much result of our model depends on parameters. By the help of those, the critical values to be measured through experiments can be understood easily.
| + | |
| - | </p>
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/d/d1/Metu-photos-model21.png.jpg" alt="" height="371px" width="727px" /></p>
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/ 2012/8/85/Metu-photos-model22.png.jpg" alt="" height="371px" width="727px" /></p> | + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/8/81/Metu-photos-model23.png.jpg" alt="" height="371px" width="727px"/></p>
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/4/44/Metu-photos-model24.png.jpg" alt="" height="371px" width="727px"/></p>
| + | |
| - | <p><img src="https://static.igem.org/mediawiki/2012/4/43/Metu-photos-model25.png.jpg" alt="" height="371px" width="727px"/></p>
| + | |
| - | <p><img class="bigImg" src="https://static.igem.org/mediawiki/2012/5/5c/Metu-photos-model26.png.jpg" alt=""height="371px" width="727px" onclick="live()"/>
| + | |
| - | <img class="bigImg" style="visibility:hidden" src="https://static.igem.org/mediawiki/2012/5/5c/Metu-photos-model26.png.jpg" />
| + | |
| - | </p> | + | |
| - | | + | |
| - | | + | |
| - | </div>
| + | |
| - |
| + | |
| - | <h2><b> References </b><h2/>
| + | |
| - | <div id ="ref"/>
| + | |
| - | <p>[1]Hansen LH, Knudsen S., Sorensen SJ. (1998). The effect of the lacY gene on the induction of IPTG inducible promoters, studied in Escherichia coli and Pseudomonas fluorescens. Current Microbiology,36 (6), 341-347. doi: 10.1007/s002849900320
| + | |
| - | </p>
| + | |
| - | <p>[2]The fate of Gram-negative envelope during holin-endolysin lysis [Image]. (2000). Retrieved September 23, 2012, from: http://dx.doi.org/10.1016/S0966-842X(00)01705-4
| + | |
| - | </p>
| + | |
| - | <p>[3]Tran TA, Struck DK, Young R. (2007). The T4 RI antiholin has an N-terminal signal anchor release domain that targets it for degradation by DegP. Journal Of Bacteriology, 189 (21), 7618-7625. doi: 10.1128/JB.00854-07.
| + | |
| - | </p>
| + | |
| - |
| + | |
| - | <p> [4]Christos G. Savva, Jill S. Dewey, John Deaton, Rebecca L. White, Douglas K. Struck, Andreas Holzenburg, Ry Young. (2008). The holin of bacteriophage lambda forms rings with large diameter. Molecular Microbiology, 69 (4), 784-793. doi: 10.1111/j.1365-2958.2008.06298.x
| + | |
| - | </p>
| + | |
| | </div> | | </div> |
| | </div> | | </div> |
| Line 572: |
Line 227: |
| | | | |
| | <!-- End Main --> | | <!-- End Main --> |
| - | <!-- Footer -->
| + | <!-- Footer --> |
| - | | + | <div id="footer"> |
| - | | + | |
| - | <p class="left">Copyright © 2010 RightDirection. All rights reserved. Designed by <a href="http://chocotemplates.com" target="_blank" title="The Sweetest CSS Templates WorldWide">Chocotemplates.com</a></p> | + | <p class="left">Copyright © 2010 RightDirection. All rights reserved. Designed by <a href="http://chocotemplates.com" target="_blank" title="The Sweetest CSS Templates WorldWide">Chocotemplates.com</a></p> |
| - | | + | |
| - | | + | <a href=" https:// igem.org/Team .cgi?year= 2012&team_name= METU"> METU IGEM 2012</a> |
| - | <span>|</span>
| + | </p> |
| - | <a href="#">Team</a>
| + | <div class="cl"> </div> |
| - | <span>|</span>
| + | </div> |
| - | <a href="#">Project</a>
| + | </div> |
| - | <span>|</span>
| + | <!-- Footer --> |
| - | <a href="#">Modelling</a>
| + | |
| - | <span>|</span>
| + | |
| - | <a href="#">Notebook</a>
| + | |
| - | <span>|</span>
| + | |
| - | <a href="#">Human Practice</a>
| + | |
| - | <span>|</span>
| + | |
| - | <a href="#">???</a>
| + | |
| - | </p>
| + | |
| - | <div class="cl"> </div> | + | |
| - | </div>
| + | |
| - | </div>
| + | |
| - | <!-- Footer -->
| + | |
| | | | |
| | | | |
| | </body></html> | | </body></html> |
"
