Difference between revisions of "Team:Austin UTexas/Results/Parts"

(Created page with "{{Austin_UTexas}}")
 
 
(48 intermediate revisions by 6 users not shown)
Line 1: Line 1:
 
{{Austin_UTexas}}
 
{{Austin_UTexas}}
 +
<html>
 +
<style>
 +
 +
body{
 +
background-color:#808080;
 +
}
 +
figure {
 +
  padding: 5px;
 +
  display: table;
 +
}
 +
 +
figure img {
 +
    display: block;
 +
    width: 100%;
 +
}
 +
 +
figcaption {
 +
    display: table-caption;
 +
    caption-side: bottom;
 +
    padding: 0 5px 5px;
 +
}
 +
div.naviSection {
 +
}
 +
img.resize {
 +
  max-width:50%;
 +
  max-height:50%;
 +
    display: block;
 +
    margin-left: auto;
 +
    margin-right: auto;
 +
}
 +
 +
div.panel {
 +
    padding: 0 18px;
 +
    display: none;
 +
    background-color: #808080;
 +
}
 +
 +
.w3-button:hover{color:#ff0000!important;background-color:#fff!important}
 +
 +
 +
.w3-sidebar{height:100%;width:200px;background-color:#808080;position:fixed!important;z-index:1;overflow:auto}
 +
 +
.w3-black,.w3-hover-black:hover{color:#fff!important;background-color:#808080!important}
 +
 +
.w3-bar-block .w3-bar-item{width:100%;display:block;padding:8px 16px;text-align:left;border:none;white-space:normal;float:none;outline:0}
 +
 +
.w3-bar-block.w3-center .w3-bar-item{text-align:center}.w3-block{display:block;width:100%}
 +
 +
.w3-bar-block .w3-dropdown-hover,.w3-bar-block .w3-dropdown-click{width:100%}
 +
 +
.w3-bar-block .w3-dropdown-hover .w3-dropdown-content,.w3-bar-block .w3-dropdown-click .w3-dropdown-content{min-width:100%}
 +
 +
.w3-bar-block .w3-dropdown-hover .w3-button,.w3-bar-block .w3-dropdown-click .w3-button{width:100%;text-align:left;padding:8px 16px}
 +
 +
.w3-bar .w3-bar-item{padding:8px 16px;float:left;width:auto;border:none;display:block;outline:0;font-family:"Ailerons"}
 +
 +
.w3-bar .w3-dropdown-hover,.w3-bar .w3-dropdown-click{position:static;float:left}
 +
 +
 +
.w3-bar .w3-button{white-space:normal}
 +
 +
.w3-bar-block .w3-bar-item{width:100%;display:block;padding:8px 16px;text-align:left;border:none;white-space:normal;float:none;outline:0;font-family:'Ailerons';font-size:30px}
 +
 +
.w3-bar-block.w3-center .w3-bar-item{text-align:center}.w3-block{display:block;width:100%}
 +
 +
.w3-bar-block .w3-bar-item{width:100%;display:block;padding:8px 16px;text-align:left;border:none;white-space:normal;float:none;outline:0;color:#ffffff}
 +
 +
.w3-bar-block.w3-center .w3-bar-item{text-align:center}.w3-block{display:block;width:100%}
 +
 +
.w3-card,.w3-card-2{box-shadow:0 2px 5px 0 rgba(0,0,0,0.16),0 2px 10px 0 rgba(0,0,0,0.12)}
 +
 +
.w3-card-4,.w3-hover-shadow:hover{box-shadow:0 4px 10px 0 rgba(0,0,0,0.2),0 4px 20px 0 rgba(0,0,0,0.19)}
 +
 +
.w3-animate-fading{animation:fading 10s infinite}@keyframes fading{0%{opacity:0}50%{opacity:1}100%{opacity:0}}
 +
.w3-animate-opacity{animation:opac 0.8s}@keyframes opac{from{opacity:0} to{opacity:1}}
 +
.w3-animate-top{position:relative;animation:animatetop 0.4s}@keyframes animatetop{from{top:-300px;opacity:0} to{top:0;opacity:1}}
 +
.w3-animate-left{position:relative;animation:animateleft 0.4s}@keyframes animateleft{from{left:-300px;opacity:0} to{left:0;opacity:1}}
 +
.w3-animate-right{position:relative;animation:animateright 0.4s}@keyframes animateright{from{right:-300px;opacity:0} to{right:0;opacity:1}}
 +
.w3-animate-bottom{position:relative;animation:animatebottom 0.4s}@keyframes animatebottom{from{bottom:-300px;opacity:0} to{bottom:0;opacity:1}}
 +
.w3-animate-zoom {animation:animatezoom 0.6s}@keyframes animatezoom{from{transform:scale(0)} to{transform:scale(1)}}
 +
.w3-animate-input{transition:width 0.4s ease-in-out}.w3-animate-input:focus{width:100%!important}
 +
button,input,select,textarea{font:inherit;margin:0}optgroup{font-weight:bold}
 +
button,input{overflow:visible}button,select{text-transform:none}
 +
button,html [type=button],[type=reset],[type=submit]{-webkit-appearance:button}
 +
button::-moz-focus-inner, [type=button]::-moz-focus-inner, [type=reset]::-moz-focus-inner, [type=submit]::-moz-focus-inner{border-style:none;padding:0}
 +
button:-moz-focusring, [type=button]:-moz-focusring, [type=reset]:-moz-focusring, [type=submit]:-moz-focusring{outline:1px dotted ButtonText}
 +
fieldset{border:1px solid #c0c0c0;margin:0 2px;padding:.35em .625em .75em}
 +
legend{color:inherit;display:table;max-width:100%;padding:0;white-space:normal}textarea{overflow:auto}
 +
[type=checkbox],[type=radio]{padding:0}
 +
[type=number]::-webkit-inner-spin-button,[type=number]::-webkit-outer-spin-button{height:auto}
 +
[type=search]{-webkit-appearance:textfield;outline-offset:-2px}
 +
[type=search]::-webkit-search-cancel-button,[type=search]::-webkit-search-decoration{-webkit-appearance:none}
 +
::-webkit-input-placeholder{color:inherit;opacity:0.54}
 +
::-webkit-file-upload-button{-webkit-appearance:button;font:inherit}
 +
/* End extract */
 +
 +
 +
.w3-table,.w3-table-all{border-collapse:collapse;border-spacing:0;width:100%;display:table}.w3-table-all{border:1px solid #ccc}
 +
.w3-bordered tr,.w3-table-all tr{border-bottom:1px solid #ddd}.w3-striped tbody tr:nth-child(even){background-color:#f1f1f1}
 +
.w3-table-all tr:nth-child(odd){background-color:#fff}.w3-table-all tr:nth-child(even){background-color:#f1f1f1}
 +
.w3-hoverable tbody tr:hover,.w3-ul.w3-hoverable li:hover{background-color:#ccc}.w3-centered tr th,.w3-centered tr td{text-align:center}
 +
.w3-table td,.w3-table th,.w3-table-all td,.w3-table-all th{padding:8px 8px;display:table-cell;text-align:left;vertical-align:top}
 +
.w3-table th:first-child,.w3-table td:first-child,.w3-table-all th:first-child,.w3-table-all td:first-child{padding-left:16px}
 +
.w3-btn,.w3-button{border:none;display:inline-block;padding:8px 16px;vertical-align:middle;overflow:hidden;text-decoration:none;color:inherit;background-color:inherit;text-align:center;cursor:pointer;white-space:nowrap}
 +
.w3-btn:hover{box-shadow:0 8px 16px 0 rgba(0,0,0,0.2),0 6px 20px 0 rgba(0,0,0,0.19)}
 +
.w3-btn,.w3-button{-webkit-touch-callout:none;-webkit-user-select:none;-khtml-user-select:none;-moz-user-select:none;-ms-user-select:none;user-select:none} 
 +
.w3-disabled,.w3-btn:disabled,.w3-button:disabled{cursor:not-allowed;opacity:0.3}.w3-disabled *,:disabled *{pointer-events:none}
 +
.w3-dropdown-hover:hover > .w3-button:first-child,.w3-dropdown-click:hover > .w3-button:first-child{background-color:#ccc;color:#000}
 +
.w3-dropdown-content{cursor:auto;color:#000;background-color:#fff;display:none;position:absolute;min-width:160px;margin:0;padding:0;z-index:1}
 +
.w3-check,.w3-radio{width:24px;height:24px;position:relative;top:6px}
 +
.w3-sidebar{height:100%;width:200px;background-color:#fff;position:fixed!important;z-index:1;overflow:auto}
 +
.w3-bar-block .w3-dropdown-hover,.w3-bar-block .w3-dropdown-click{width:100%}
 +
.w3-bar-block .w3-dropdown-hover .w3-dropdown-content,.w3-bar-block .w3-dropdown-click .w3-dropdown-content{min-width:100%}
 +
.w3-bar-block .w3-dropdown-hover .w3-button,.w3-bar-block .w3-dropdown-click .w3-button{width:100%;text-align:left;padding:8px 16px}
 +
.w3-main,#main{transition:margin-left .4s}
 +
.w3-modal{z-index:3;display:none;padding-top:100px;position:fixed;left:0;top:0;width:100%;height:100%;overflow:auto;background-color:rgb(0,0,0);background-color:rgba(0,0,0,0.4)}
 +
.w3-modal-content{margin:auto;background-color:#fff;position:relative;padding:0;outline:0;width:600px}
 +
.w3-bar{width:100%;overflow:hidden}.w3-center .w3-bar{display:inline-block;width:auto}
 +
.w3-bar .w3-bar-item{padding:8px 16px;float:left;width:auto;border:none;display:block;outline:0}
 +
.w3-bar .w3-dropdown-hover,.w3-bar .w3-dropdown-click{position:static;float:left}
 +
.w3-bar .w3-button{white-space:normal}
 +
.w3-dropdown-hover.w3-mobile,.w3-dropdown-hover.w3-mobile .w3-btn,.w3-dropdown-hover.w3-mobile .w3-button,.w3-dropdown-click.w3-mobile,.w3-dropdown-click.w3-mobile .w3-btn,.w3-dropdown-click.w3-mobile .w3-button{width:100%}}
 +
.w3-button:hover{color:#000!important;background-color:#ccc!important}
 +
 +
 +
 +
</style>
 +
 +
<body>
 +
<div class = "background">
 +
<br>
 +
<h1>Part Plasmids</h1>
 +
     
 +
<br>
 +
<!-- Sidebar -->
 +
<div class="w3-sidebar w3-bar-block w3-card w3-black w3-animate-left" style="display:none" id="mySidebar">
 +
  <button class="w3-bar-item w3-button w3-large"
 +
  onclick="w3_close()">Close &times;</button>
 +
  <h2 class="w3-bar-item">Menu</h2>
 +
  <a href="https://2018.igem.org/Team:Austin_UTexas/Results/Parts" class="w3-bar-item w3-button">Part Plasmids</a>
 +
  <a href="https://2018.igem.org/Team:Austin_UTexas/Results/Assemblies" class="w3-bar-item w3-button">Assembly Plasmids</a>
 +
  <a href="https://2018.igem.org/Team:Austin_UTexas/Results/Electroporations" class="w3-bar-item w3-button">Electroporations</a>
 +
  <a href="https://2018.igem.org/Team:Austin_UTexas/Results/Conjugations" class="w3-bar-item w3-button">Conjugations</a>
 +
</div>
 +
 +
<div id="main">
 +
 +
<div class="w3-black">
 +
  <button id="openNav" class="w3-button w3-black w3-xlarge" onclick="w3_open()">&#9776;<p><b>Navigate Results</b></p></button>
 +
</div>
 +
<p> Before the plasmids could be assembled, the contributing parts must be isolated, affixed with restriction sites and customized overhangs, and inserted into a backbone so the parts could be stabilized and stored in a part plasmid. In a Golden Gate Assembly cloning reaction, the DNA sequence for the plasmid part is inserted into a plasmid containing a gene for green fluorescent protein production (GFP), on either side of which, are sites where the BsmBI enzyme cuts. The GFP gene is replaced by the plasmid part, so colonies that do not fluoresce green under UV light are sustaining the part plasmid. <b>Over the course of this project we have made a total of 48 parts.</b> For coding sequences and promoter/RBS parts, not all of the varieties of the part will be used in the assemblies. Rather, they are meant to provide a resource of alternative parts to a researcher constructing their own plasmid from the kit. For barcodes and 1-5 bridges, each must be unique to the origin in their plasmid because they are meant to identify which origin the plasmid contains. Having many varieties of antibiotic resistance and origin of replication strengthens the kit, as it allows researchers to rapidly test more origins at a time, in bacteria that may be naturally resistant to some antibiotics. </p>
 +
 +
<div class="floatleft">
 +
<figure>
 +
<img src="https://static.igem.org/mediawiki/2018/f/f9/T--Austin_UTexas--partplasmidp8.JPG" style="width:400px";>
 +
<figcaption><b>Figure 1.</b> P8 promoter part plasmid E. coli transformation, compared to control transformations with entry vector pYTK001. Under UV illumination, transformants containing the correctly assembled part plasmids were non-fluorescent while negative transformants appeared fluorescent like colonies on the control plates. Picture taken by Andrew Ly.</figcaption>
 +
</figure>
 +
</div>
 +
 +
<div class="floatright">
 +
<figure>
 +
<img src="https://static.igem.org/mediawiki/2018/c/cf/T--Austin_UTexas--improvedgrayparts.png" style="width:600px";>
 +
<figcaption><b>Figure 2.</b> A list of every part plasmid included in the kit.</figcaption>
 +
</figure>
 +
</div>
 +
 +
<script>
 +
function w3_open() {
 +
  document.getElementById("main").style.marginLeft = "25%";
 +
  document.getElementById("mySidebar").style.width = "25%";
 +
  document.getElementById("mySidebar").style.display = "block";
 +
  document.getElementById("openNav").style.display = 'none';
 +
}
 +
function w3_close() {
 +
  document.getElementById("main").style.marginLeft = "0%";
 +
  document.getElementById("mySidebar").style.display = "none";
 +
  document.getElementById("openNav").style.display = "inline-block";
 +
}
 +
</script>
 +
 +
 +
 +
</body>
 +
</html>

Latest revision as of 23:29, 17 October 2018


Part Plasmids


Before the plasmids could be assembled, the contributing parts must be isolated, affixed with restriction sites and customized overhangs, and inserted into a backbone so the parts could be stabilized and stored in a part plasmid. In a Golden Gate Assembly cloning reaction, the DNA sequence for the plasmid part is inserted into a plasmid containing a gene for green fluorescent protein production (GFP), on either side of which, are sites where the BsmBI enzyme cuts. The GFP gene is replaced by the plasmid part, so colonies that do not fluoresce green under UV light are sustaining the part plasmid. Over the course of this project we have made a total of 48 parts. For coding sequences and promoter/RBS parts, not all of the varieties of the part will be used in the assemblies. Rather, they are meant to provide a resource of alternative parts to a researcher constructing their own plasmid from the kit. For barcodes and 1-5 bridges, each must be unique to the origin in their plasmid because they are meant to identify which origin the plasmid contains. Having many varieties of antibiotic resistance and origin of replication strengthens the kit, as it allows researchers to rapidly test more origins at a time, in bacteria that may be naturally resistant to some antibiotics.

Figure 1. P8 promoter part plasmid E. coli transformation, compared to control transformations with entry vector pYTK001. Under UV illumination, transformants containing the correctly assembled part plasmids were non-fluorescent while negative transformants appeared fluorescent like colonies on the control plates. Picture taken by Andrew Ly.
Figure 2. A list of every part plasmid included in the kit.