Team:Baskent Meds/Project

From 2013.igem.org

(Difference between revisions)
(Prototype team page)
Line 1: Line 1:
-
<!-- *** What falls between these lines is the Alert Box!  You can remove it from your pages once you have read and understood the alert *** -->
 
-
 
<html>
<html>
-
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #fe2b33;">
+
<head>
-
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;">
+
   
-
This is a template page. READ THESE INSTRUCTIONS.
+
<title>Baskent_Meds IGEMwiki</title>
-
</div>
+
<!--menu bar script-->
-
<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;">
+
    <script type="text/javascript" src="http://code.jquery.com/jquery-latest.min.js"></script>
-
You are provided with this team page template with which to start the iGEM season.  You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki.  You can find some examples <a href="https://2008.igem.org/Help:Template/Examples">HERE</a>.
+
    <script type="text/javascript">
-
</div>
+
        $(document).ready(function(){
-
<div id="warning" style="text-align: center; font-weight: bold; font-size: small; color: #f6f6f6; padding: 5px;">
+
-
You <strong>MUST</strong> have all of the pages listed in the menu below with the names specified. PLEASE keep all of your pages within your teams namespace. 
+
-
</div>
+
-
</div>
+
-
</html>
+
-
<!-- *** End of the alert box *** -->
+
$("ul.subnav").parent().append("<span></span>"); //Only shows drop down trigger when js is enabled - Adds empty span tag after ul.subnav
 +
 +
$("ul.topnav li span").click(function() { //When trigger is clicked...
 +
 +
//Following events are applied to the subnav itself (moving subnav up and down)
 +
$(this).parent().find("ul.subnav").slideDown('fast').show(); //Drop down the subnav on click
 +
$(this).parent().hover(function() {
 +
}, function(){
 +
$(this).parent().find("ul.subnav").slideUp('slow'); //When the mouse hovers out of the subnav, move it back up
 +
});
-
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
+
//Following events are applied to the trigger (Hover events for the trigger)
-
!align="center"|[[Team:Baskent_Meds|Home]]
+
}).hover(function() {
-
!align="center"|[[Team:Baskent_Meds/Team|Team]]
+
$(this).addClass("subhover"); //On hover over, add class "subhover"
-
!align="center"|[https://igem.org/Team.cgi?year=2013&team_name=Baskent_Meds Official Team Profile]
+
}, function(){ //On Hover Out
-
!align="center"|[[Team:Baskent_Meds/Project|Project]]
+
$(this).removeClass("subhover"); //On hover out, remove class "subhover"
-
!align="center"|[[Team:Baskent_Meds/Parts|Parts Submitted to the Registry]]
+
});
-
!align="center"|[[Team:Baskent_Meds/Modeling|Modeling]]
+
-
!align="center"|[[Team:Baskent_Meds/Notebook|Notebook]]
+
-
!align="center"|[[Team:Baskent_Meds/Safety|Safety]]
+
-
!align="center"|[[Team:Baskent_Meds/Attributions|Attributions]]
+
-
|}
+
 +
});
 +
/*menu bar script*/
 +
    </script>
 +
 +
<style>
 +
/*menubar css*/
 +
body
 +
{
 +
margin-left:20px;
 +
margin-right:20px;
 +
padding:0;
 +
font:10px normal Arial, Helvetica, sans-serif;
 +
background: #fff url("http://mail.baskent.edu.tr/mail/igem/scriptler/menubar/body_bg.gif") repeat-x;
 +
background-color: #FFFFFF;
 +
}
 +
ul.topnav
 +
{
 +
padding:0 20px;
 +
margin:0;
 +
float:left;
 +
width:934px;
 +
background:#222;
 +
font-size:1.2em;
 +
background:url("https://static.igem.org/mediawiki/2012/1/1b/Topnav_bg.gif") repeat-x;
 +
}
 +
ul.topnav li
 +
{
 +
float:left;
 +
list-style-type:none;
 +
margin:0;
 +
padding:0 15px 0 0;
 +
position:relative; /*--Declare X and Y axis base--*/
 +
}
 +
ul.topnav li a
 +
{
 +
padding:10px 5px;
 +
color:#fff;
 +
display:block;
 +
text-decoration:none;
 +
float:left;
 +
}
 +
ul.topnav li a:hover
 +
{
 +
background:url("https://static.igem.org/mediawiki/2012/f/f5/Topnav_hover.gif") no-repeat center top;
 +
}
 +
ul.topnav li span
 +
{
 +
/*--Drop down trigger styles--*/
 +
width:17px;
 +
height:35px;
 +
float:left;
 +
background:url("https://static.igem.org/mediawiki/2012/4/45/Subnav_btn.gif") no-repeat center top;
 +
}
 +
ul.topnav li span.subhover
 +
{
 +
/*--Hover effect for trigger--*/
 +
background-position:
 +
center bottom;
 +
cursor: pointer;
 +
}
 +
ul.topnav li ul.subnav
 +
{
 +
list-style:none;
 +
position:absolute; /*--Important - Keeps subnav from affecting main navigation flow--*/
 +
left:0;
 +
top:35px;
 +
background:#333;
 +
margin:0;
 +
padding:0;
 +
display:none;
 +
float:left;
 +
width:170px;
 +
-moz-border-radius-bottomleft:5px;
 +
-moz-border-radius-bottomright:5px;
 +
-webkit-border-bottom-left-radius:5px;
 +
-webkit-border-bottom-right-radius:5px;
 +
border:1px solid #111;
 +
}
 +
ul.topnav li ul.subnav li
 +
{
 +
margin:0;
 +
padding:0;
 +
border-top:1px solid #252525; /*--Creates bevel effect--*/
 +
border-bottom:1px solid #444; /*--Creates bevel effect--*/
 +
clear:both;
 +
width:170px;
 +
}
 +
html ul.topnav li ul.subnav li a
 +
{
 +
float:left;
 +
width:145px;
 +
background:#333 url("https://static.igem.org/mediawiki/2012/4/4b/Dropdown_linkbg.gif") no-repeat 10px center;
 +
padding-left:20px;
 +
}
 +
html ul.topnav li ul.subnav li a:hover
 +
{
 +
/*--Hover effect for subnav links--*/
 +
background:#222 url("https://static.igem.org/mediawiki/2012/4/4b/Dropdown_linkbg.gif") no-repeat 10px center;
 +
}
 +
/*menu bar css*/
 +
.style2 {
 +
font-family: "Gill Sans MT", Helvetica;
 +
font-size: 18px;
 +
}
 +
.style8 {font-size: 24px}
 +
.style9 {font-size: 20px; }
 +
.style10 {font-size: 18px; }
-
== '''Overall project''' ==
 
-
Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)
+
<!-- css ayar çekmece
 +
#mediawiki {
 +
display:none;
 +
}
 +
#global {
 +
display: none
 +
}
 +
//mediawiki altbannerını ve üstteki kullanıcı panellerini kapatıyor
 +
.noprint {
 +
display: none
 +
}
 +
#search-controls.noprint { display: none }
 +
/*.mediawiki { display: none }*/
 +
.p-logo { display: none }
 +
.globalWrapper { display: none }
 +
.top-section { display: none }
 +
#footer-box { display: none }
 +
.search-controls { display: none }
 +
#catlinks { display: none }
 +
-->
 +
</style>
 +
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"></head>
 +
<body>
 +
<div id="ana" style="position:absolute; left:-24px; top:-100px; width:1000px; height:3000px; z-index:1; background-color: #FFFFFF; layer-background-color: #FFFFFF; border: 1px none #000000;">
 +
<div id="menubar" style="position:absolute; left:25px; top:16px; width:1000px; height:200px; z-index:1">
-
== Project Details==
 
 +
<!--menu bar basladi -->
 +
<ul class="topnav">
 +
<li><a href="/Team:Baskent_Meds" title="BaskentMeds main page">Home</a></li>
 +
<li>
 +
<a href="/Team:Baskent_Meds/Project" title="Our Project Abstract">Project</a>
 +
</li>
 +
<li><a href="/Team:Baskent_Meds/Notebook" title="Our Beloved Notebook!">Notebook</a></li>
 +
<li><a href="/Team:Baskent_Meds/Results" title="Still Working on this">Results</a></li>
-
=== Part 2 ===
+
<li><a href="/Team:Baskent_Meds/Gallery" title="">Gallery</a></li>
 +
<li>
 +
<a href="/Team:Baskent_Meds/Team" title="Shall we meet?">Team</a>
 +
<ul class="subnav">
 +
<li><a href="/Team:Baskent_Meds/Instructors" title="Our ">Instructors</a></li>
 +
<li><a href="/Team:Baskent_Meds/Advisor" title="AdVisor">Advisor</a></li>
 +
<li><a href="/Team:Baskent_Meds/Students" title="Us">Student Members</a></li>
 +
</ul>
 +
</li>
-
=== The Experiments ===
+
</ul>
-
 
+
<br><br><br>
 +
<!-- menubar bitti-->
 +
</div>
-
=== Part 3 ===
 
-
== Results ==
+
<br />
 +
<br />
 +
<div id="la'book" class="style2" style="position:absolute; left:25px; top:165px; width:1000px; height:274px; z-index:1; overflow: visible;">
 +
  <div id="gecher" style="position:absolute; left:2px; top:0px; width:970px; height:468px; z-index:1">
 +
    <p align="left"><strong>Transformation of Escherichia coli In Order To Develop</strong><br>
 +
    Legionella pneumophila Sensing Bacteria</p>
 +
    <p>Our aim, as the team &ldquo;Baskent_Meds&rdquo;, is developing bacteria which can recognize Legionella pneumophila specifically at species level by legionella quorum sensing (lqs), and respond to that recognition by producing anti-Legionella peptide which is produced by someStaphylococcus strains. lqs gene locus is responsible for quorum sensing mechanism in Legionella pneumophila. On the lqs locus there are three genes; lqsA (encoding autoinducer synthase), lqsR (encoding response regulator), and lqsS (encoding a sensor kinase). LqsA is a pyridoxal-5&prime;-phosphate-dependent enzyme that catalyses the production of the signaling molecule 3-hydroxypentadecane-4-one (LAI-1; Legionella autoinduer-1), a novel member of &alpha;-hydroxyketone signalling molecules (Spirig et al., 2008). In this comprehensive and long-termed project, our initial objectives were; generating competent E. coli cells in which we are planning to clone lqs gene locus (the gene locus responsible for quorum sensing mechanism in Legionella pneumophila), and optimizing transformation procedures. pNT-1 (Tiaden et al., 2007), a pUCBM20-derivative, bearing full lqs gene cluster, and pTS-2 (Spirig et al., 2008), a pMMB207C-derivative expression vector, bearing LqsA gene were kindly provided by Prof. Dr. Hubert Hilbi.</p>
 +
    <p>Initially, E. coli competent cell groups (JM109, DH5&alpha; and XL1-Blue) were formed by exerting calcium chloride precipitation. pNT-1 and pTS-2 were transferred into competent E. coli cells using heat shock transformation method, and clones were selected with ampicillin and chloramphenicol, respectively. Plasmid isolations were performed from transformants by QIAprep Spin Miniprep Kit (Qiagen), and visualized by agarose gel electrophoresis. Our recent studies are designing our construct with BioBricks, and amplifying LqsR and LqsSby gene specific primers having restriction enzyme cut sites as small adaptors. We are going to clone these genes by digesting with these restriction enzymes followed by ligation to one of the iGEM vectors. After cloning these genes, we are planning to clone anti-Legionella peptide nucleotide sequence under lqs control. In order to check response of transformant E. coli we are planning to clone pTS-2 to BL21(DE3) E. coli for the constitutive expression and production of the LAI-1 without the handling of the pathogen strains in our laboratory.<br>
 +
      <br>
 +
    By the end of our experiments, we aim to obtain sensor E. coli cells which respond to Legionella pneumophila quorum sensing by recognizing LAI-1. Our expression construct will also enable production of the anti-Legionella peptide in response to LAI-1. Since the peptide has specific antibacterial activity on Legionella spp., the achievement of the project is the destruction of Legionella pneumophila by transformant E. coli sensor cells.    </p>

Revision as of 03:42, 1 August 2013

Baskent_Meds IGEMwiki



Transformation of Escherichia coli In Order To Develop
Legionella pneumophila Sensing Bacteria

Our aim, as the team “Baskent_Meds”, is developing bacteria which can recognize Legionella pneumophila specifically at species level by legionella quorum sensing (lqs), and respond to that recognition by producing anti-Legionella peptide which is produced by someStaphylococcus strains. lqs gene locus is responsible for quorum sensing mechanism in Legionella pneumophila. On the lqs locus there are three genes; lqsA (encoding autoinducer synthase), lqsR (encoding response regulator), and lqsS (encoding a sensor kinase). LqsA is a pyridoxal-5′-phosphate-dependent enzyme that catalyses the production of the signaling molecule 3-hydroxypentadecane-4-one (LAI-1; Legionella autoinduer-1), a novel member of α-hydroxyketone signalling molecules (Spirig et al., 2008). In this comprehensive and long-termed project, our initial objectives were; generating competent E. coli cells in which we are planning to clone lqs gene locus (the gene locus responsible for quorum sensing mechanism in Legionella pneumophila), and optimizing transformation procedures. pNT-1 (Tiaden et al., 2007), a pUCBM20-derivative, bearing full lqs gene cluster, and pTS-2 (Spirig et al., 2008), a pMMB207C-derivative expression vector, bearing LqsA gene were kindly provided by Prof. Dr. Hubert Hilbi.

Initially, E. coli competent cell groups (JM109, DH5α and XL1-Blue) were formed by exerting calcium chloride precipitation. pNT-1 and pTS-2 were transferred into competent E. coli cells using heat shock transformation method, and clones were selected with ampicillin and chloramphenicol, respectively. Plasmid isolations were performed from transformants by QIAprep Spin Miniprep Kit (Qiagen), and visualized by agarose gel electrophoresis. Our recent studies are designing our construct with BioBricks, and amplifying LqsR and LqsSby gene specific primers having restriction enzyme cut sites as small adaptors. We are going to clone these genes by digesting with these restriction enzymes followed by ligation to one of the iGEM vectors. After cloning these genes, we are planning to clone anti-Legionella peptide nucleotide sequence under lqs control. In order to check response of transformant E. coli we are planning to clone pTS-2 to BL21(DE3) E. coli for the constitutive expression and production of the LAI-1 without the handling of the pathogen strains in our laboratory.

By the end of our experiments, we aim to obtain sensor E. coli cells which respond to Legionella pneumophila quorum sensing by recognizing LAI-1. Our expression construct will also enable production of the anti-Legionella peptide in response to LAI-1. Since the peptide has specific antibacterial activity on Legionella spp., the achievement of the project is the destruction of Legionella pneumophila by transformant E. coli sensor cells.

Retrieved from "http://2013.igem.org/Team:Baskent_Meds/Project"