Team:VCU/Project

From 2011.igem.org

(Difference between revisions)
(Prototype team page)
 
(2 intermediate revisions not shown)
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 *** -->
+
[[File:VCU iGEM banner.png|960px|center]]
-
 
+
<br />
-
<html>
+
<center>
-
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #fe2b33;">
+
===THE 2011 VCU iGEM PROJECT===
-
<div id="template" style="text-align: center; font-weight: bold; font-size: large; color: #f6f6f6; padding: 5px;">
+
</center>
-
This is a template page. READ THESE INSTRUCTIONS.
+
-
</div>
+
-
<div id="instructions" style="text-align: center; font-weight: normal; font-size: small; color: #f6f6f6; padding: 5px;">
+
-
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>.
+
-
</div>
+
-
<div id="warning" style="text-align: center; font-weight: bold; font-size: small; color: #f6f6f6; padding: 5px;">
+
-
You <strong>MUST</strong> have a team description page, a project abstract, a complete project description, a lab notebook, and a safety page.  PLEASE keep all of your pages within your teams namespace. 
+
-
</div>
+
-
</div>
+
-
</html>
+
-
 
+
-
<!-- *** End of the alert box *** -->
+
-
 
+
{|align="justify"
{|align="justify"
-
|You can write a background of your team here.  Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
 
-
|[[Image:VCU_logo.png|200px|right|frame]]
 
-
|-
 
|
|
-
''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''
+
|
-
|[[Image:VCU_team.png|right|frame|Your team picture]]
+
|-
|-
-
|
 
-
|align="center"|[[Team:VCU | Team Example]]
 
|}
|}
 +
<br />
-
<!--- The Mission, Experiments --->
+
<html>
 +
<head>
-
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
+
<title>wiki_prototype</title>
-
!align="center"|[[Team:VCU|Home]]
+
-
!align="center"|[[Team:VCU/Team|Team]]
+
<style type="text/css">
-
!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=VCU Official Team Profile]
+
-
!align="center"|[[Team:VCU/Project|Project]]
+
-
!align="center"|[[Team:VCU/Parts|Parts Submitted to the Registry]]
+
-
!align="center"|[[Team:VCU/Modeling|Modeling]]
+
-
!align="center"|[[Team:VCU/Notebook|Notebook]]
+
-
!align="center"|[[Team:VCU/Safety|Safety]]
+
-
!align="center"|[[Team:VCU/Attributions|Attributions]]
+
-
|}
+
 +
#centeredmenu {
 +
  float:left;
 +
  width:100%;
 +
  background:#fff;
 +
  border-bottom:4px solid #000;
 +
  overflow:hidden;
 +
  position:relative;
 +
}
 +
#centeredmenu ul {
 +
  clear:left;
 +
  float:left;
 +
  list-style:none;
 +
  margin:0;
 +
  padding:0;
 +
  position:relative;
 +
  left:50%;
 +
  text-align:center;
 +
}
 +
#centeredmenu ul li {
 +
  display:block;
 +
  float:left;
 +
  list-style:none;
 +
  margin:0;
 +
  padding:0;
 +
  position:relative;
 +
  right:50%;
 +
}
 +
#centeredmenu ul li a {
 +
  display:block;
 +
  margin:0 0 0 1px;
 +
  padding:3px 10px;
 +
  background:#FDD017;
 +
  color:black;
 +
  text-decoration:none;
 +
  line-height:1.3em;
 +
  font: bold 12px Verdana;
 +
}
 +
#centeredmenu ul li a:hover {
 +
  background:#414141;
 +
  color:white;
 +
}
 +
#centeredmenu ul li a:hover {
 +
  color:#fff;
 +
  background:#000;
 +
  font-weight:bold;
 +
}
-
== '''Overall project''' ==
+
</style>
 +
</head>
 +
<body>
-
Your abstract
+
<div id="centeredmenu">
 +
  <ul>
 +
      <li><a href="https://2011.igem.org/Team:VCU">Home</a></li>
 +
      <li><a href="https://2011.igem.org/Team:VCU/Abstract">Abstract</a></li>
 +
      <li><a href="https://2011.igem.org/Team:VCU/Project">Project</a></li>
 +
      <li><a href="https://2011.igem.org/Team:VCU/Team">Team</a></li>
 +
  <li><a href="https://2011.igem.org/Team:VCU/Safety">Safety</a></li>
 +
  <li><a href="">Synthetic Biology at VCU</a></li>
 +
  </ul>
 +
</div>
 +
<br>
 +
<br>
 +
<p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<b>Isoprenoids</b> are a class of extremely diverse naturally occurring compounds that are commonly found in plants.  These compounds serve a variety of functions in their host, and have been found to have a number of aromatic, flavor, and pharmaceutical properties.  Many increasingly important drugs, such as artemisinin and Taxol are isoprenoids.  Isoprenoids are produced in their natural host by a class of enzymes known as terpene synthases.  Isoprenoids are classified based on the number of carbons, and fall into three main groups: monoterpenoids (10), sesquiterpenoids (15), and diterpenoids (20).  Extracting isoprenoids from their natural source is generally expensive, inefficient, and environmentally burdensome.  For this reason, the development of a synthetic biology solution to commercial isoprenoid biosynthesis is a fast-growing area of research.  Our project has focused on the synthesis of nerolidol, a sesquiterpenoid found in strawberries, in prokaryotic hosts.  Nerolidol is thought to aid in trans-dermal delivery of patch medications.
 +
</p>
 +
<p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<b><i>Synechococcus elongatus</i></b> is a model cyanobacterium that we are developing as a platform for metabolic engineering.  As a heterotrophic organism, <i>Synechococcus</i> would be an opportune means to minimize input costs and thus maximize output efficiency if developed as a viable biomachine.  Because it lacks the extensive genetic characterization such as that of E. coli, it presents a unique set of challenges for synthetic biology.  Our work with <i>Synechococcus</i> involves characterizing and modeling promoter strength, developing a viable nerolidol-producing strain, and modeling its circadian rhythm.
 +
</p>
 +
<p>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Modeling <i>Synechococcus</i> promoters.  Understanding the promoters of the host is imperative for any synthetic biology experiment.  A significant part of our research has been to characterize and predict <i>Synechococcus</i> promoter strength through a model based on a position-weighted matrix (PWM).  A PWM is a matrix representation of the occurrence of a specific character at a given position.  This type of representation can give us insight into the relative frequencies of each of the 4 bases throughout the various motifs of a promoter.  A promoter is made of several motifs.  At each position in the motifs, trends can be seen in the relative occurrence of each of the 4 bases, as seen in the figure below, adapted from Rhodius and Mutalik 2009, in which they used a PWM to model <i>E. coli</i> promoters.
 +
</p>
 +
INSERT FIGURE HERE.
 +
<p>
 +
To generate our PWM, we used a computational tool called Motif Occurrence Detection Suite (MOODS).  We are currently determining the fit of our model to known promoter strengths using a Pearson’s correlation.  Because of their simplicity to build and interpret, PWMs are popular in determining transcriptional factor binding sites.  PWMs assume and equal additive contribution for each position in the motif.  Whether or not this assumption is true for promoters is not yet known.  We hope to elucidate this matter as we investigate <i>Synechococcus</i> promoter strengths.
 +
</p>
-
 
+
</body>
-
 
+
<html>
-
 
+
-
 
+
-
 
+
-
== Project Details==
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
=== Part 2 ===
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
=== The Experiments ===
+
-
 
+
-
 
+
-
 
+
-
 
+
-
=== Part 3 ===
+
-
 
+
-
 
+
-
 
+
-
 
+
-
== Results ==
+

Latest revision as of 02:42, 26 September 2011

VCU iGEM banner.png


THE 2011 VCU iGEM PROJECT


wiki_prototype



        Isoprenoids are a class of extremely diverse naturally occurring compounds that are commonly found in plants. These compounds serve a variety of functions in their host, and have been found to have a number of aromatic, flavor, and pharmaceutical properties. Many increasingly important drugs, such as artemisinin and Taxol are isoprenoids. Isoprenoids are produced in their natural host by a class of enzymes known as terpene synthases. Isoprenoids are classified based on the number of carbons, and fall into three main groups: monoterpenoids (10), sesquiterpenoids (15), and diterpenoids (20). Extracting isoprenoids from their natural source is generally expensive, inefficient, and environmentally burdensome. For this reason, the development of a synthetic biology solution to commercial isoprenoid biosynthesis is a fast-growing area of research. Our project has focused on the synthesis of nerolidol, a sesquiterpenoid found in strawberries, in prokaryotic hosts. Nerolidol is thought to aid in trans-dermal delivery of patch medications.

        Synechococcus elongatus is a model cyanobacterium that we are developing as a platform for metabolic engineering. As a heterotrophic organism, Synechococcus would be an opportune means to minimize input costs and thus maximize output efficiency if developed as a viable biomachine. Because it lacks the extensive genetic characterization such as that of E. coli, it presents a unique set of challenges for synthetic biology. Our work with Synechococcus involves characterizing and modeling promoter strength, developing a viable nerolidol-producing strain, and modeling its circadian rhythm.

        Modeling Synechococcus promoters. Understanding the promoters of the host is imperative for any synthetic biology experiment. A significant part of our research has been to characterize and predict Synechococcus promoter strength through a model based on a position-weighted matrix (PWM). A PWM is a matrix representation of the occurrence of a specific character at a given position. This type of representation can give us insight into the relative frequencies of each of the 4 bases throughout the various motifs of a promoter. A promoter is made of several motifs. At each position in the motifs, trends can be seen in the relative occurrence of each of the 4 bases, as seen in the figure below, adapted from Rhodius and Mutalik 2009, in which they used a PWM to model E. coli promoters.

INSERT FIGURE HERE.

To generate our PWM, we used a computational tool called Motif Occurrence Detection Suite (MOODS). We are currently determining the fit of our model to known promoter strengths using a Pearson’s correlation. Because of their simplicity to build and interpret, PWMs are popular in determining transcriptional factor binding sites. PWMs assume and equal additive contribution for each position in the motif. Whether or not this assumption is true for promoters is not yet known. We hope to elucidate this matter as we investigate Synechococcus promoter strengths.

Retrieved from "http://2011.igem.org/Team:VCU/Project"