Difference between revisions of "Team:UMBC-Maryland/Parts"

 
(19 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
{{Template_All_Teams}}
+
{{Team:UMBC-Maryland/TemplateTop}}
−
[[File:Team_UMBC-Maryland_banner.jpg|600px]]
+
 
<html>
 
<html>
−
 
+
<div class="divider-bar"></div>
−
<style type="text/css">
+
−
 
+
−
/* PAGE LAYOUT */
+
−
+
−
/* page background color*/
+
−
body {
+
−
background-color: #A7A9AB;
+
−
}
+
−
 
+
−
 
+
−
/* Creates a container that will wrap all of the content inside your wiki pages. */
+
−
#mainContainer { 
+
−
width: 980px;
+
−
overflow: hidden;
+
−
float:left;
+
−
margin-left: 20px;
+
−
background-color: #EEEDEA;
+
−
border-bottom: 6px solid #EE3e53;
+
−
}
+
−
 
+
−
/* Creates the container for the menu */
+
−
#menuContainer  {
+
−
float:right;
+
−
width: 150px;
+
−
background-color: #0e232f;
+
−
height: 100%;
+
−
border-top: 6px solid #EE3e53;
+
−
font-family: "Arial", Helvetica, sans-serif;
+
−
}
+
−
 
+
−
/* Creates the container for the content */
+
−
#contentContainer {
+
−
background-color: #EEEDEA;
+
−
width: 810px;
+
−
float: left;
+
−
padding: 10px;
+
−
border-top: 6px solid #EE3e53;
+
−
}
+
−
 
+
−
 
+
−
/*VISUAL STYLE (TABLES, FONTS, LINKS, IMAGES, UL) */
+
−
 
+
−
 
+
−
/*Change the styling of text for everything inside main container*/
+
−
#mainContainer p {
+
−
font-family: "Arial", Helvetica, sans-serif;
+
−
font-size: 12px;
+
−
color: #0e232f;
+
−
}
+
−
+
−
/*This changes the color and font family */
+
−
#contentContainer h1, h2, h3, h4, h5, h6 {
+
−
font-family: "Arial", Helvetica, sans-serif;
+
−
color: #0e232f;
+
−
border-bottom: none;
+
−
font-weight: bold;
+
−
text-transform: uppercase;
+
−
}
+
−
 
+
−
/*Style of the links - links are different inside the menu */
+
−
#contentContainer a {
+
−
font-weight: bold;
+
−
color: #ee3e53;
+
−
}
+
−
 
+
−
  /* Styling links on hover- links are different inside the menu */
+
−
#contentContainer a:hover{
+
−
color: #f4b248;
+
−
}
+
−
 
+
−
/*Change the styling of tables */
+
−
        #contentContainer table {
+
−
    border: 1px solid #0e232f;
+
−
    border-collapse: collapse;
+
−
    width: 90%
+
−
    margin: auto;
+
−
    margin-bottom: 15px;
+
−
    margin-top: 15px;
+
−
    margin-right: 10px;
+
−
    margin-left: 10px;
+
−
    }
+
−
 
+
−
/*Change the styling of table cells*/
+
−
    #contentContainer  td {
+
−
    padding: 10px;
+
−
    border: 1px solid #0e232f;
+
−
    border-collapse: collapse;
+
−
    vertical-align: text-top;
+
−
    background-color: #EEEDEA;
+
−
    }
+
−
 
+
−
/*Change the styling of table headers */
+
−
    #contentContainer th {
+
−
    padding: 10px;
+
−
    border: 1px solid #0e232f;
+
−
    border-collapse: collapse;
+
−
    vertical-align: text-top;
+
−
    background-color: #e8d5b7;
+
−
    }
+
−
 
+
−
 
+
−
/*MENU STYLING */
+
−
 
+
−
/*Styling for the links in the menu */
+
−
#menuContainer a {
+
−
color: #EEEDEA;
+
−
text-decoration:none;
+
−
font-weight: bold;
+
−
}
+
−
 
+
−
/* Sets the style for lists inside menuContainer  */
+
−
#menuContainer ul {
+
−
width:100%;
+
−
list-style: none;
+
−
margin: auto;
+
−
padding-top: 10px;
+
−
padding-bottom: 10px;
+
−
 
+
−
}
+
−
 
+
−
/*Styles the list items to become menu buttons */
+
−
#menuContainer ul li {
+
−
display: block;
+
−
position: relative;
+
−
padding: 10px;
+
−
margin-bottom:5px;
+
−
padding-left: -20px;
+
−
}
+
−
 
+
−
#menuContainer ul li:hover {
+
−
background: #F4B248;
+
−
color: #0e232f;
+
−
}
+
−
 
+
−
 
+
−
/*HIde the submenus and removes the padding */
+
−
#menuContainer li ul {
+
−
display: none;
+
−
padding-top:15px;
+
−
margin-left: -9px;
+
−
}
+
−
 
+
−
/*Shows the submenus once you hover*/
+
−
#menuContainer li:hover ul {
+
−
display: block;
+
−
}
+
−
 
+
−
/*style the submenu buttons*/
+
−
#menuContainer li ul li {
+
−
background: #0E232F;
+
−
width: 100%;
+
−
}
+
−
 
+
−
#menuContainer li ul li:hover {
+
−
background: #EE3E53;
+
−
color: #fff;
+
−
}
+
−
 
+
−
 
+
−
 
+
−
/*CLASSES */
+
−
/*Clear class for all the pages, adds spacing too*/
+
−
.clear{
+
−
clear:both;
+
−
height: 10px;
+
−
}
+
−
 
+
−
/* highlight box for special messages */
+
−
    .highlightBox {
+
−
    width:500px;
+
−
            margin:auto;
+
−
            background-color: #E8D5B7;
+
−
    margin-bottom: 15px;
+
−
    margin-top: 15px;
+
−
    padding: 15px;
+
−
    padding-top: 5px;
+
−
          }
+
−
 
+
−
</style>
+
−
<!-- End of CSS -->
+
−
 
+
−
 
+
−
<!-- Start of the template html elements. -->
+
−
<div id ="mainContainer"><!--This div will close on the page.-->
+
−
 
+
−
<div id="bannerContainer">
+
−
<br> <br>
+
−
+
−
</div>
+
−
 
+
−
<!-- Start of menu -->
+
−
<div id="menuContainer">
+
−
<!-- This list is your menu, every list item is a menu button and nested listed become submenu buttons -->
+
−
<ul>
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland"><li>HOME</li></a>
+
−
 
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Team"><li>TEAM</li></a>
+
−
 
+
−
 
+
−
<a href="#"><li>PROJECT
+
−
            <ul>
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Description"><li>Description</li></a>
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Experiments"><li>Experiments & Protocols</li></a> 
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Results"><li>Results</li></a> 
+
−
</ul>
+
−
</li></a>
+
−
 
+
−
<a href="#"><li>PARTS
+
−
            <ul>
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Parts"><li>Team Parts</li></a>
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Basic_Part"><li>Basic Parts</li></a> 
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Composite_Part"><li>Composite Parts</li></a>
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Part_Collection"><li>Part Collection</li></a> 
+
−
</ul>
+
−
</li></a>
+
−
 
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Notebook"><li>NOTEBOOK</li></a>
+
−
     
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Attributions"><li>ATTRIBUTIONS</li></a>
+
−
 
+
−
 
+
−
<a href="https://2015.igem.org/Team:UMBC-Maryland/Practices"><li>HUMAN PRACTICES</li></a>
+
−
 
+
−
+
−
 
+
−
</ul>
+
−
</div>
+
−
<!-- End of menu  -->
+
−
 
+
−
<!-- Start of content -->
+
−
<div id="contentContainer"><!--This div will close on the page.-->
+
−
</html>
+
−
<html>
+
−
 
+
 
<h2> Part Documentation</h2>
 
<h2> Part Documentation</h2>
  
−
We are in the process of submitting part <a href="http://parts.igem.org/Part:BBa_K1410777">BBa_K1410777</a>. This is a composite of constitutive promoter <a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a>, RBS <a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a>, and the CUP1 gene from S. cerevisiae (NCBI ID <a href="http://www.ncbi.nlm.nih.gov/gene/856450">856450</a>).
+
For our project, we ordered 3 G Blocks from IDT that we assembled into plasmids using NEB HiFi Assembly. These 3 assembled plasmids will be submitted as composite parts to the iGEM registry, each containing a promoter, RBS, and gene. For all of the parts we made, we used the strong constitutive promoter <a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a> and the RBS <a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a>.
 +
<br> <br>
 +
The first G block and composite part we made is the CUP1 gene from S. cerevisiae (NCBI ID <a href="http://www.ncbi.nlm.nih.gov/gene/856450">856450</a>) with the strong constitutive promoter <a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a> and the RBS <a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a>. The composite part for this promoter, RBS, and gene is <a href="http://parts.igem.org/Part:BBa_K1811777">BBa_K1811777</a>. The documented basic registry part for the CUP1 gene is <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_M45090">BBa_M45090</a>.
 +
<br> <br>
 +
The second G block and composite part we made is the CUP1 gene from S. cerevisiae that has been codon optimized for E. coli tRNA abundance. This codon optimized CUP1 gene is listed as a basic part with number <a href="http://parts.igem.org/Part:BBa_K1811222">BBa_K1811222</a>. The composite part with the strong constitutive promoter <a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a> and the RBS <a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a> is <a href="http://parts.igem.org/Part:BBa_K1811888">BBa_K1811888</a>.
 +
<br> <br>
 +
The third G block and composite part we made is the codon optimized CUP1 gene from S. cerevisiae fused with the LamB gene from E. coli. LamB is a gene that codes for an outer membrane transport channel that transports maltose and maltodextrins. LamB is also the receptor for phage lambda. We removed the stop codon of CUP1 and inserted its sequence into amino acid position 153 of LamB. The basic part for this gene fusion is <a href="http://parts.igem.org/Part:BBa_K1811333">BBa_K1811333</a>. The composite part with the strong constitutive promoter <a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a> and the RBS <a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a> is <a href="http://parts.igem.org/Part:BBa_K1811666">BBa_K1811666</a>.
 +
<br> <br>
 +
<br> <br>
 +
<table>
 +
<tr><td colspan="2" align="center"><b>Basic Parts</b></td></tr>
 +
<tr><td align="center"><b>Part Description</b></td><td align="center"><b>Registry Number</b></td></tr>
 +
<tr><td>Strong constitutive promoter</td><td><a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a></td></tr>
 +
<tr><td>Ribosome binding site</td><td><a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a></td></tr>
 +
<tr><td>CUP1 gene</td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_M45090">BBa_M45090</a></td></tr>
 +
<tr><td>Codon optimized CUP1 gene</td><td><a href="http://parts.igem.org/Part:BBa_K1811222">BBa_K1811222</a></td></tr>
 +
<tr><td>CUP1 LamB fusion</td><td><a href="http://parts.igem.org/Part:BBa_K1811333">BBa_K1811333</a></td></tr>
  
−
<table>
 
−
<tr><td>Strong constitutive promoter</td><td><a href="http://parts.igem.org/Part:BBa_J23100">BBa_J23100</a></td>
 
−
<tr><td>Ribosome binding site</td><td><a href="http://parts.igem.org/Part:BBa_B0034">BBa_B0034</a></td>
 
−
<tr><td>CUP1 composite part</td><td><a href="http://parts.igem.org/Part:BBa_K1410777">BBa_K1410777</a></td>
 
 
</table>
 
</table>
  
Line 250: Line 27:
 
<br>
 
<br>
  
−
<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
+
<table>
−
<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
+
<tr><td colspan="3" align="center"><b>Composite Parts</b></td></tr>
−
 
+
<tr><td>CUP1, RBS, and strong constitutive promoter</td><td><a href="http://parts.igem.org/Part:BBa_K1811777">BBa_K1811777</a></td><td></html>[[File:Umbc777.png]]<html></td></tr>
−
 
+
<tr><td>Codon optimized CUP1, RBS, and strong constitutive promoter</td><td><a href="http://parts.igem.org/Part:BBa_K1811888">BBa_K1811888</a></td><td></html>[[File:Umbc888.png]]<html></td></tr>
−
<div class="highlightBox">
+
<tr><td>CUP1 LamB fusion, RBS, and strong constitutive promoter</td><td><a href="http://parts.igem.org/Part:BBa_K1811666">BBa_K1811666</a></td><td></html>[[File:Umbc666.png]]<html></td></tr>
−
<h4>Note</h4>
+
−
<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
+
−
</div>
+
−
 
+
−
 
+
−
 
+
−
<h4>Adding parts to the registry</h4>
+
−
<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
+
−
<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
+
−
 
+
−
 
+
−
<h4>What information do I need to start putting my parts on the Registry?</h4>
+
−
<p>The information needed to initially create a part on the Registry is:</p>
+
−
<ul>
+
−
<li>Part Name</li>
+
−
<li>Part type</li>
+
−
<li>Creator</li>
+
−
<li>Sequence</li>
+
−
<li>Short Description (60 characters on what the DNA does)</li>
+
−
<li>Long Description (Longer description of what the DNA does)</li>
+
−
<li>Design considerations</li>
+
−
</ul>
+
−
 
+
−
<p>
+
−
We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
+
−
 
+
−
 
+
−
 
+
−
 
+
−
 
+
−
 
+
−
<h4>Inspiration</h4>
+
−
<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
+
−
 
+
−
<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
+
−
<ul>
+
−
<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
+
−
<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
+
−
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
+
−
</ul>
+
−
 
+
−
 
+
−
 
+
−
<h4>Part Table </h4>
+
−
</html>
+
−
<groupparts>iGEM015 Example</groupparts>
+
−
<html>
+
  
 +
</table>
  
 +
<br>
 +
<br>
  
−
</div>
 
 
</html>
 
</html>
 +
{{Team:UMBC-Maryland/TemplateBottom}}

Latest revision as of 01:13, 14 September 2015

Part Documentation

For our project, we ordered 3 G Blocks from IDT that we assembled into plasmids using NEB HiFi Assembly. These 3 assembled plasmids will be submitted as composite parts to the iGEM registry, each containing a promoter, RBS, and gene. For all of the parts we made, we used the strong constitutive promoter BBa_J23100 and the RBS BBa_B0034.

The first G block and composite part we made is the CUP1 gene from S. cerevisiae (NCBI ID 856450) with the strong constitutive promoter BBa_J23100 and the RBS BBa_B0034. The composite part for this promoter, RBS, and gene is BBa_K1811777. The documented basic registry part for the CUP1 gene is BBa_M45090.

The second G block and composite part we made is the CUP1 gene from S. cerevisiae that has been codon optimized for E. coli tRNA abundance. This codon optimized CUP1 gene is listed as a basic part with number BBa_K1811222. The composite part with the strong constitutive promoter BBa_J23100 and the RBS BBa_B0034 is BBa_K1811888.

The third G block and composite part we made is the codon optimized CUP1 gene from S. cerevisiae fused with the LamB gene from E. coli. LamB is a gene that codes for an outer membrane transport channel that transports maltose and maltodextrins. LamB is also the receptor for phage lambda. We removed the stop codon of CUP1 and inserted its sequence into amino acid position 153 of LamB. The basic part for this gene fusion is BBa_K1811333. The composite part with the strong constitutive promoter BBa_J23100 and the RBS BBa_B0034 is BBa_K1811666.



Basic Parts
Part DescriptionRegistry Number
Strong constitutive promoterBBa_J23100
Ribosome binding siteBBa_B0034
CUP1 geneBBa_M45090
Codon optimized CUP1 geneBBa_K1811222
CUP1 LamB fusionBBa_K1811333


Composite Parts
CUP1, RBS, and strong constitutive promoterBBa_K1811777Umbc777.png
Codon optimized CUP1, RBS, and strong constitutive promoterBBa_K1811888Umbc888.png
CUP1 LamB fusion, RBS, and strong constitutive promoterBBa_K1811666Umbc666.png