Difference between revisions of "Team:Alverno CA"

Line 1: Line 1:
 +
<!DOCTYPE html>
 
<html>
 
<html>
−
<head>
+
<title>W3.CSS</title>
 +
<meta name="viewport" content="width=device-width, initial-scale=1">
 +
<link rel="stylesheet" href="http://www.w3schools.com/lib/w3.css">
 +
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Lato">
 +
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Montserrat">
 +
<link rel="stylesheet" href="http://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.6.3/css/font-awesome.min.css">
 +
<style>
 +
body,h1,h2,h3,h4,h5,h6 {font-family: "Lato", sans-serif}
 +
.w3-navbar,h1,button {font-family: "Montserrat", sans-serif}
 +
.fa-anchor,.fa-coffee {font-size:200px}
 +
</style>
 +
<body>
  
−
<style type="text/css">
+
<!-- Navbar -->
 +
<ul class="w3-navbar w3-white w3-card-2 w3-top w3-left-align w3-large">
 +
  <li class="w3-hide-medium w3-hide-large w3-opennav w3-right">
 +
    <a class="w3-padding-large w3-hover w3-large w3-white" href="javascript:void(0);" onclick="myFunction()" title="Toggle Navigation Menu"><i class="fa fa-bars"></i></a>
 +
  </li>
 +
  <li><a href="#" class="https://2016.igem.org/Team:Alverno_CA">Home</a></li>
 +
  <li class="w3-hide-small"><a href="#" class="https://2016.igem.org/Team:Alverno_CA/Team">Team</a></li>
 +
  <li class="w3-hide-small"><a href="#" class="https://2016.igem.org/Team:Alverno_CA/Description">Project</a></li>
 +
  <li class="w3-hide-small"><a href="#" class="https://2016.igem.org/Team:Alverno_CA/Parts">Parts</a></li>
 +
  <li class="w3-hide-small"><a href="#" class="https://2016.igem.org/Team:Alverno_CA/Safety">Safety</a></li>
 +
  <li class="w3-hide-small"><a href="#" class="https://2016.igem.org/Team:Alverno_CA/Human_Practices">Human Practice</a></li>
 +
</ul>
  
−
#contentSub, #footer-box, #catlinks, #search-controls,
+
<!-- Navbar on small screens -->
−
#p-logo, .printfooter, .firstHeading, .visualClear {
+
<div id="navDemo" class="w3-hide w3-hide-large w3-hide-medium w3-top" style="margin-top:51px">
−
display: none;
+
  <ul class="w3-navbar w3-left-align w3-large w3-black">
−
}
+
    <li><a class="https://2016.igem.org/Team:Alverno_CA">Main</a></li>
 +
    <li><a class="https://2016.igem.org/Team:Alverno_CA/Team">Team</a></li>
 +
    <li><a class="https://2016.igem.org/Team:Alverno_CA/Description">Project</a></li>
 +
    <li><a class="https://2016.igem.org/Team:Alverno_CA/Parts">Parts</a></li>
 +
    <li><a class="https://2016.igem.org/Team:Alverno_CA/Safety">Safety</a></li>
 +
    <li><a class="https://2016.igem.org/Team:Alverno_CA/Human_Practices">Human Practice</a></li>
 +
  </ul>
 +
</div>
  
−
#top-section {
+
<!-- Header -->
−
border: 0 none;
+
<div class="w3-container w3-red w3-center w3-padding-128">
−
height: 14px;
+
  <h1 class="w3-margin w3-jumbo">How can we keep genes from interfering with each other in synthetic DNA circuits?</h1>
−
z-index: 100;
+
  <p class="w3-xlarge w3-center">Alverno_CA</p>
−
top: 0;
+
  <button class="w3-btn w3-padding-16 w3-large w3-margin-top">Click here to read more</button>
−
position: fixed;
+
</div>
−
width: 975px;
+
−
left: 50%;
+
−
margin-left: -487px;
+
−
}
+
−
+
−
#globalWrapper, #content {
+
−
width: 100%;
+
−
height: 100%;
+
−
border: 0px;
+
−
background-color: transparent;
+
−
margin: 0px;
+
−
padding: 0px;
+
−
font-size: 100%;
+
−
}
+
−
+
−
html, body, .wrapper {
+
−
width: 100%;
+
−
height: 100%;
+
−
background-color: transparent;
+
−
}
+
  
−
.navbar {
+
<!-- First Grid -->
−
margin: 0 auto;
+
<div class="w3-row-padding w3-padding-64 w3-container">
−
margin-top: 1em;
+
  <div class="w3-content">
−
padding: 1em;
+
    <div class="w3-twothird">
−
border-radius: 10px;
+
      <h1>About This Project</h1>
−
}
+
      <h5 class="w3-padding-32">Building complex biological systems with many genes requires isolating genes. Active genes can cause nearby DNA to become supercoiled, leading to unpredictable behavior of synthetic biology systems. We will test if DNA clamps (made from DNA-binding proteins) placed between genes can stop this interference. If this project succeeds, it will allow bioengineers to build more predictable genetic circuits.</h5>
 +
    </div>
  
−
</style>
+
    <div class="w3-third w3-center">
 +
      <i class="fa fa-anchor w3-padding-64 w3-text-red"></i>
 +
    </div>
 +
  </div>
 +
</div>
  
−
<link rel="stylesheet" href="https://2014.igem.org/Team:Aalto-Helsinki/bootstrap.min.css?action=raw&ctype=text/css" type="text/css">
+
<!-- Second Grid -->
−
<link rel="stylesheet" href="https://2014.igem.org/Team:Aalto-Helsinki/stylesheet.css?action=raw&ctype=text/css" type="text/css">
+
<div class="w3-row-padding w3-light-grey w3-padding-64 w3-container">
−
<meta name= "viewport" content = "initial-scale=1.0, width= device-width" />
+
  <div class="w3-content">
−
</head>
+
    <div class="w3-third w3-center">
 +
      <i class="fa fa-coffee w3-padding-64 w3-text-red w3-margin-right"></i>
 +
    </div>
  
−
<header>
+
     <div class="w3-twothird">
−
     <div class= "navbar navbar-default navbar-fixed-top">
+
      <h1>What is the context of this research?</h1>
−
        <div class="text-center col-sm-12" id="navigation">
+
      <h5 class="w3-padding-32">Programming cells often requires building "circuits" of several genes together on the same piece of DNA. Bioengineers have observed that when two genes are placed next to each other, they often unexpectedly interfere with each other’s expression in an unexpectedly orientation-dependent manner.</h5>
−
            <nav>
+
−
                <a href="https://2016.igem.org/Team:Alverno_CA">Home</a>
+
−
                <a href="https://2016.igem.org/Team:Alverno_CA/Team">Team</a>
+
−
                <a href="https://2016.igem.org/Team:Alverno_CA/Description">Project</a>
+
−
                <a href="https://2016.igem.org/Team:Alverno_CA/Parts">Parts</a>
+
−
                <a href="https://2016.igem.org/Team:Alverno_CA/Safety">Safety</a>
+
−
                <a href="https://2016.igem.org/Team:Alverno_CA/Attributions">Attributions</a>
+
−
                <a href="https://2016.igem.org/Team:Alverno_CA/Human_Practices">Human Practice</a>
+
−
            </nav>
+
−
                <a href="https://2016.igem.org/Team:Alverno_CA/Awards">Awards</a>
+
  
−
        </div>
+
      <h5 class="w3-padding-32">Nobody knows with certainty what causes this genetic crosstalk, but one promising theory involves DNA supercoiling. The transcription of DNA into RNA, the transcription process introduces supercoils, similar to kinks in a tightly-wound phone cord. Supercoils directly affect the expression of genes, turning them on or off depending on the direction of the supercoil.</p>
 
     </div>
 
     </div>
−
</header>
+
  </div>
 +
</div>
  
−
</html>
+
<!-- Third Grid -->
−
{{Alverno_CA}}
+
<div class="w3-row-padding w3-padding-64 w3-container">
−
<html>
+
  <div class="w3-content">
 +
    <div class="w3-twothird">
 +
      <h1>What is the significance of this project?</h1>
 +
      <h5 class="w3-padding-32">If successful, a DNA-binding, gene- isolating clamp could be used in any multi-gene circuit assembly, making multi-gene assemblies more predictable and their assembly much more efficient.</h5>
  
−
<head>
+
      <h5 class="w3-padding-32">This is particularly relevant when engineering metabolic pathways to produce chemicals like methanol, insulin, or antibiotics, where circuits of many genes are routinely constructed. The physical layout of these circuits can unpredictably affect production of the desired output by several orders of magnitude, so large engineered metabolic pathways must typically be hand-tuned or have many configurations screened for activity. By making gene expression more predictable, our results could greatly improve the predictability (and, therefore, designability) of large gene circuits for metabolic engineering.</p>
−
<title>Alverno iGEM 2016</title>
+
    </div>
−
<link rel="icon" href="https://pbs.twimg.com/profile_images/2199338457/alverno-logo_high_400x400.PNG">
+
  </div>
−
</head>
+
</div>
  
−
<body>
 
−
<h1><center>Alverno iGEM 2016</center></h1>
 
−
<center><img src="https://static.igem.org/mediawiki/2016/b/b9/Alverno_CA_Supercoiling_Image_1.jpeg" alt="Alverno iGEM Logo" style="width:800px;"></center>
 
  
−
<h1><center>Our Project</center></h1>
+
<!-- Forth Grid -->
−
<h2><center>How can we keep genes from interfering</center></h2>
+
<div class="w3-row-padding w3-light-grey w3-padding-64 w3-container">
−
<h2><center>with each other in synthetic DNA circuits?</h2></center>
+
  <div class="w3-content">
−
<h3>About This Project</h3>  
+
    <div class="w3-third w3-center">
−
<p>    Building complex biological systems with many genes requires isolating genes. Active genes can cause nearby DNA to become supercoiled, leading to unpredictable behavior of synthetic biology systems. We will test if DNA clamps (made from DNA-binding proteins) placed between genes can stop this interference. If this project succeeds, it will allow bioengineers to build more predictable genetic circuits. </p>  
+
      <i class="fa fa-coffee w3-padding-64 w3-text-red w3-margin-right"></i>
 +
    </div>
  
−
<p><h3>What is the context of this research?</h3></p>
+
    <div class="w3-twothird">
−
<p>    Programming cells often requires building "circuits" of several genes together on the same piece of DNA. Bioengineers have observed that when two genes are placed next to each other, they often unexpectedly interfere with each other’s expression in an unexpectedly orientation-dependent manner.</p>
+
      <h1>What are the goals of the project?</h1>
−
<p>Nobody knows with certainty what causes this genetic crosstalk, but one promising theory involves DNA supercoiling. The transcription of DNA into RNA, the transcription process introduces supercoils, similar to kinks in a tightly-wound phone cord. Supercoils directly affect the expression of genes, turning them on or off depending on the direction of the supercoil.</p>
+
      <h5 class="w3-padding-32">We will first build several plasmids (circular pieces of DNA) that demonstrate cross-talk between genes. These plasmids will consist of genes for two different fluorescent proteins (green fluorescent protein and red fluorescent protein) next to each other, in different orientations. We expect to see differences in the relative expression of the two genes depending on how they are arranged and oriented, and we will quantify this effect.</h5>
  
−
<h3>What is the significance of this project?</h3>
+
      <h5 class="w3-padding-32">Next, we will try several strategies for removing these differences, including adding extra base pairs of spacing between the two genes and adding DNA "clamps" made from DNA-binding repressor proteins between the two genes. We will again quantify the effects of cross-talk between genes, which will hopefully be ameliorated by our additions.</p>
−
<p>    If successful, a DNA-binding, gene- isolating clamp could be used in any multi-gene circuit assembly, making multi-gene assemblies more predictable and their assembly much more efficient.</p>
+
    </div>
−
<p>    This is particularly relevant when engineering metabolic pathways to produce chemicals like methanol, insulin, or antibiotics, where circuits of many genes are routinely constructed. The physical layout of these circuits can unpredictably affect production of the desired output by several orders of magnitude, so large engineered metabolic pathways must typically be hand-tuned or have many configurations screened for activity. By making gene expression more predictable, our results could greatly improve the predictability (and, therefore, designability) of large gene circuits for metabolic engineering.</p>
+
  </div>
−
​<h3>What are the goals of the project?</h3>
+
</div>
−
<p>    We will first build several plasmids (circular pieces of DNA) that demonstrate cross-talk between genes. These plasmids will consist of genes for two different fluorescent proteins (green fluorescent protein and red fluorescent protein) next to each other, in different orientations. We expect to see differences in the relative expression of the two genes depending on how they are arranged and oriented, and we will quantify this effect.</p>
+
 
−
<p>    Next, we will try several strategies for removing these differences, including adding extra base pairs of spacing between the two genes and adding DNA "clamps" made from DNA-binding repressor proteins between the two genes. We will again quantify the effects of cross-talk between genes, which will hopefully be ameliorated by our additions.</p>
+
    <div class="w3-third w3-center">
 +
      <i class="fa fa-anchor w3-padding-64 w3-text-red"></i>
 +
    </div>
 +
  </div>
 +
</div>
 +
<div class="w3-container w3-black w3-center w3-opacity w3-padding-64">
 +
    <h1 class="w3-margin w3-xlarge">Alverno Heights Academy, Sierra Madre</h1>
 +
</div>
 +
 
 +
<!-- Footer -->
 +
<footer class="w3-container w3-padding-64 w3-center w3-opacity">
 +
  <div class="w3-xlarge w3-padding-32">
 +
  <a href="#" class="w3-hover-text-indigo"><i class="fa fa-facebook-official"></i></a>
 +
  <a href="#" class="w3-hover-text-red"><i class="fa fa-pinterest-p"></i></a>
 +
  <a href="#" class="w3-hover-text-light-blue"><i class="fa fa-twitter"></i></a>
 +
  <a href="#" class="w3-hover-text-grey"><i class="fa fa-flickr"></i></a>
 +
  <a href="#" class="w3-hover-text-indigo"><i class="fa fa-linkedin"></i></a>
 +
</div>
 +
<p>Powered by <a href="http://www.w3schools.com/w3css/default.asp" target="_blank">w3.css</a></p>
 +
</footer>
 +
 
 +
<script>
 +
// Used to toggle the menu on small screens when clicking on the menu button
 +
function myFunction() {
 +
    var x = document.getElementById("navDemo");
 +
    if (x.className.indexOf("w3-show") == -1) {
 +
        x.className += " w3-show";
 +
    } else {
 +
        x.className = x.className.replace(" w3-show", "");
 +
    }
 +
}
 +
</script>
 +
 
 +
</body>
 +
</html>

Revision as of 00:40, 29 September 2016

<!DOCTYPE html> W3.CSS

How can we keep genes from interfering with each other in synthetic DNA circuits?

Alverno_CA

About This Project

Building complex biological systems with many genes requires isolating genes. Active genes can cause nearby DNA to become supercoiled, leading to unpredictable behavior of synthetic biology systems. We will test if DNA clamps (made from DNA-binding proteins) placed between genes can stop this interference. If this project succeeds, it will allow bioengineers to build more predictable genetic circuits.

What is the context of this research?

Programming cells often requires building "circuits" of several genes together on the same piece of DNA. Bioengineers have observed that when two genes are placed next to each other, they often unexpectedly interfere with each other’s expression in an unexpectedly orientation-dependent manner.
Nobody knows with certainty what causes this genetic crosstalk, but one promising theory involves DNA supercoiling. The transcription of DNA into RNA, the transcription process introduces supercoils, similar to kinks in a tightly-wound phone cord. Supercoils directly affect the expression of genes, turning them on or off depending on the direction of the supercoil.

What is the significance of this project?

If successful, a DNA-binding, gene- isolating clamp could be used in any multi-gene circuit assembly, making multi-gene assemblies more predictable and their assembly much more efficient.
This is particularly relevant when engineering metabolic pathways to produce chemicals like methanol, insulin, or antibiotics, where circuits of many genes are routinely constructed. The physical layout of these circuits can unpredictably affect production of the desired output by several orders of magnitude, so large engineered metabolic pathways must typically be hand-tuned or have many configurations screened for activity. By making gene expression more predictable, our results could greatly improve the predictability (and, therefore, designability) of large gene circuits for metabolic engineering.

What are the goals of the project?

We will first build several plasmids (circular pieces of DNA) that demonstrate cross-talk between genes. These plasmids will consist of genes for two different fluorescent proteins (green fluorescent protein and red fluorescent protein) next to each other, in different orientations. We expect to see differences in the relative expression of the two genes depending on how they are arranged and oriented, and we will quantify this effect.
Next, we will try several strategies for removing these differences, including adding extra base pairs of spacing between the two genes and adding DNA "clamps" made from DNA-binding repressor proteins between the two genes. We will again quantify the effects of cross-talk between genes, which will hopefully be ameliorated by our additions.

Alverno Heights Academy, Sierra Madre