Difference between revisions of "Team:Cadets2Vets/Experiments"

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EXPERIMENTS - CADETS2VETS</title>
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<h1>Experiments</h1>
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<p>Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.</p>
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Please remember to put all characterization and measurement data for your parts on the corresponding Registry part pages.  
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<h5>What should this page contain?</h5>
 
<ul>
 
<li> Protocols </li>
 
<li> Experiments </li>
 
<li> Documentation of the development of your project </li>
 
</ul>
 
  
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<h5>Inspiration</h5>
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<ul>
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<li><a href="https://2014.igem.org/Team:Colombia/Protocols">2014 Colombia </a></li>
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<div class="main-page "  >
<li><a href="https://2014.igem.org/Team:Imperial/Protocols">2014 Imperial </a></li>
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<div id="content">
<li><a href="https://2014.igem.org/Team:Caltech/Project/Experiments">2014 Caltech </a></li>
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18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Open Sans&quot;;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span>I.<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span><b><span style="font-size:10.0pt;font-family:
 +
&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;;color:black">Overview</span></b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black"><o:p></o:p></span></p><p class="MsoNormal" style="margin: 4.8pt 0in 6pt 0.8in; line-height: 18pt;"><span style="font-size:10.0pt;font-family:
 +
&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;;color:black">The idea of cell free expression has existed for more than 20 years. It is the notion of taking the elements required for both transcription and translation and utilizing them for an external protein expression system. This is extremely beneficial for expression of cytotoxic proteins in which high yields are difficult to produce in vivo. For our purpose within this assay, this concept is utilized in conjunction with a regulatory factor for detection. This is detection is predicated either by regulation of the RBS at the transcript level or by sequestering the binding sight of RNA polymerase.<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:38.4pt;text-indent:-38.4pt;mso-text-indent-alt:-.25in;line-height:
 +
18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Open Sans&quot;;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">        </span>II.<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span><b><span style="font-size:10.0pt;font-family:
 +
&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;;color:black">Work Flow</span></b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;
 +
mso-fareast-font-family:&quot;Times New Roman&quot;;color:black"><o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom: 1.2pt; margin-left: 0.8in; text-indent: -0.8in; line-height: 18pt;"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black">Identify trigger sequence and target plasmid or probe<o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom: 1.2pt; margin-left: 0.8in; text-indent: -0.8in; line-height: 18pt;"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black">Add target<o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom: 1.2pt; margin-left: 0.8in; text-indent: -0.8in; line-height: 18pt;"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black">Incubation<o:p></o:p></span></p><p class="MsoNormal" style="margin-bottom: 1.2pt; margin-left: 0.8in; text-indent: -0.8in; line-height: 18pt;"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black">Evaluation<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:38.4pt;text-indent:-38.4pt;mso-text-indent-alt:-.25in;line-height:
 +
18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Open Sans&quot;;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>III.<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span><b><span style="font-size:10.0pt;font-family:
 +
&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;;color:black">Reagents</span></b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black"><o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:.8in;text-indent:-.8in;mso-text-indent-alt:-.25in;line-height:18.0pt;
 +
mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black">Cell free expression kit<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:.8in;text-indent:-.8in;mso-text-indent-alt:-.25in;line-height:18.0pt;
 +
mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black">•Promega L5540<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:.8in;text-indent:-.8in;mso-text-indent-alt:-.25in;line-height:18.0pt;
 +
mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black">•Promega L1020<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:.8in;text-indent:-.8in;mso-text-indent-alt:-.25in;line-height:18.0pt;
 +
mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
 +
&quot;Times New Roman&quot;;color:black">•Promega L1110<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:.8in;text-indent:-.8in;mso-text-indent-alt:-.25in;line-height:18.0pt;
 +
mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;;color:black">•NEB E6800L<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:.8in;text-indent:-.8in;mso-text-indent-alt:-.25in;line-height:18.0pt;
 +
mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
 +
mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;;color:black">•Life Tech K990100<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;;color:black">RNASE Inhibitor (RI)<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
 +
margin-left:.8in;text-indent:-.8in;mso-text-indent-alt:-.25in;line-height:18.0pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;color:black"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;;color:black">Prepared tickets<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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&quot;Times New Roman&quot;;color:black">Trigger Plasmid<o:p></o:p></span></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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&quot;Times New Roman&quot;;color:black">Substrate if needed<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Open Sans&quot;"><span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span>I.<span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span></b><b><span style="font-size:10.0pt;font-family:
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&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;">Pre-Phase One Experiments<o:p></o:p></span></b></p><p class="MsoNormal" style="margin-top:4.8pt;margin-right:0in;margin-bottom:6.0pt;
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margin-left:.8in;line-height:18.0pt"><b><span style="font-size:10.0pt;
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font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;">Establish control experiments<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">-Constitutive GFP<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">o Switch H GFP<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Open Sans&quot;"><span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">        </span>II.<span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span></b><b><span style="font-size:10.0pt;font-family:
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&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;">Pre-Phase One Goals<o:p></o:p></span></b></p><p class="MsoNormal" style="margin-bottom: 1.2pt; margin-left: 0.8in; text-indent: -0.8in; line-height: 18pt;"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">The goal of pre-phase 1 is to establish a working positive control and negative control in lab.<o:p></o:p></span></b></p><p class="MsoNormal" style="margin-bottom: 1.2pt; margin-left: 38.4pt; text-indent: -38.4pt; line-height: 18pt;"><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Open Sans&quot;"><span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>III.<span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span></b><b><span style="font-size:10.0pt;font-family:
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&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;">Phase One Experiments<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">Clone composite circuit in e.coli<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">Test efficacy of the circuit in vivo and determine threshold limits of both arsenic and arsenite<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">Perform mini prep and quantify<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Open Sans&quot;"><span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>IV.<span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span></b><b><span style="font-size:10.0pt;font-family:
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&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;">Phase One Goals<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">The goals of this phase is to grow a large amount of the composite circuit and develop an understanding of whether or not the circuit is biologically effective. Another primary goal is to develop an understanding of how the circuit works in its entirety (upper threshold/lower threshold)<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Open Sans&quot;"><span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">        </span>V.<span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span></b><b><span style="font-size:10.0pt;font-family:
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&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;">Phase Two Experiments<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">Test the efficacy of the composite circuit instead of crude lysate<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">Test purified plasmid with Promega S30 kit<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Open Sans&quot;"><span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>VI.<span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span></b><b><span style="font-size:10.0pt;font-family:
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&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;">Phase Two Goals<o:p></o:p></span></b></p><p class="MsoNormal" style="margin-bottom: 1.2pt; margin-left: 0.8in; text-indent: -0.8in; line-height: 18pt;"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">The goal of this phase is to take the circuit out of the cell and test it in situ utilizing both a bacterial expression kit (Promega S30) and an attempt at functionalizing the circuit utilizing a formulated crude lysate for increased application space.<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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18.0pt;mso-list:l0 level1 lfo1;tab-stops:list .5in"><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Open Sans&quot;"><span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">    </span>VII.<span style="font-variant-numeric: normal; font-weight: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span></span></b><b><span style="font-size:10.0pt;font-family:
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&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:&quot;Times New Roman&quot;">Phase Three Experiments<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">Attempt at micro scaling reaction<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">Porting reactions to paper based system<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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mso-list:l0 level2 lfo1;tab-stops:list 1.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">      </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">Attempt at lyophilizing the circuit on paper both with Promega S30 kit and in the crude lysate form (if the previous phase demonstrated reasonable evidence for progressing on that front)<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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18.0pt;mso-list:l0 level3 lfo1;tab-stops:list 1.5in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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&quot;Times New Roman&quot;">Phase Three Goals<o:p></o:p></span></b></p><p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:1.2pt;
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18.0pt;mso-list:l0 level4 lfo1;tab-stops:list 2.0in"><span style="font-size:10.0pt;font-family:Wingdings;mso-fareast-font-family:Wingdings;
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mso-bidi-font-family:Wingdings;mso-bidi-font-weight:bold"><span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">          </span>§<span style="font-variant-numeric: normal; font-stretch: normal; font-size: 7pt; line-height: normal; font-family: &quot;Times New Roman&quot;;">  </span></span><b><span style="font-size:10.0pt;font-family:&quot;Open Sans&quot;,&quot;sans-serif&quot;;mso-fareast-font-family:
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&quot;Times New Roman&quot;">The goal of this phase is to successfully micro scale the reaction and port it to a lateral flow paper based system. If successful in this phase, we will have developed a biological means to detect presence of arsenic and arsenite utilizing a lateral flow paper system that is both cost effective and easy to implement.<o:p></o:p></span></b></p><p class="MsoNormal"><o:p> </o:p></p>
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<h3 id="vbid-c148c-mxkafou0" class="preview-element preview-subtitle magic-circle-holder text-element quick-text-style-menu  allow-mobile-hide" data-menu-name="PREVIEW_SUBTITLE">2304 Jefferson Ave, Tacoma, WA 98402</h3>
  
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<h1 style="margin-top:22px; font-size:50px;">Experiments</h1>
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<h1 style="margin-top:15px; margin-bottom:25px; font-size:35px;text-align:center">Ticketed Cell Free Expression System Protocol</h1>
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<p>
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<ol type="I"><li><strong>Overview</strong><ul style="list-style-type:square">  
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</p>
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<p>
+
    The idea of cell free expression has existed for more than 20 years. It is the notion of taking the elements required for both transcription and translation and utilizing them for an external protein expression system. This is extremely beneficial for expression of cytotoxic proteins in which high yields are difficult to produce in vivo. For our purpose within this assay, this concept is utilized in conjunction with a regulatory factor for detection. This is detection is predicated either by regulation of the RBS at the transcript level or by sequestering the binding sight of RNA polymerase. </p></ul>
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<p><li> <strong>Work Flow</strong>
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</p><ul>
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<li>
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  Identify trigger sequence and target plasmid or probe
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</p>
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<li>
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    Add target
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</p>
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<li>
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    Incubation
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</p>
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    Evaluation
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</p>
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  Cell free expression kit
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</p>
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<li>
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    •Promega L5540
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</p>
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<li>
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    •Promega L1020
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</p>
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    •Promega L1110
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</p>
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<li>
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    •NEB E6800L
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</p>
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<li>
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  •Life Tech K990100
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</p>
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<li>
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RNASE Inhibitor (RI)
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</p>
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<li>
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Prepared tickets
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</p>
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<li>
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Trigger Plasmid
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<p/>
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<li>
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Substrate if needed
+
</p></ul>
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<h1 style="margin-top:15px; margin-bottom:25px; font-size:35px;text-align:center">qPCR- Quantitative Polymerase Chain Reaction Protocol</h1>
 
<div class = "well">
 
<p>
 
<ol type="I"><li><strong>Overview</strong><ul style="list-style-type:square">
 
</p>
 
<p>
 
    qPCR utilizes the same basis as standard polymerase chain reaction, in which a target section of DNA can be identified and amplified via an enzymatic reaction (DNA Polymerase) and two ssDNA oligos (primers). Where qPCR differs is in the addition of either dye or probe based chemistry (this protocol will be primarily deal with the former). What this dye allows for is detection of newly formed DNA through the incorporation of a small fluorescent molecule into the new double stranded DNA (dsDNA). When the relative fluorescent units (RFU) being monitored rises above the background level (established by experimental controls) it is possible to ascertain a concentration of target gene. The relationship being the more concentrated the target the earlier in the thermocycler program signal will be generated. </p></ul>
 
<p><li> <strong>Work Flow</strong>
 
</p>
 
</p><ul>
 
<li>
 
  Initial Prepartaion
 
</p>
 
<li>
 
    Create master mix
 
</p>
 
<li>
 
    Aliquot master mix
 
</p>
 
<li>
 
    Add target DNA and standards to appropriate wells
 
</p>
 
<li>
 
Start thermocycler
 
  
</p></ul>
 
  
    <p><li> <strong>Reagents</strong>
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  ICE
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    Promega Hotstart Polyermase + Colorless Flexi buffer
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    10 mM dNTP
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    25 mM MgCl
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    Molecular Water
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  Forward and Reverse Primers in 10 uM
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  Evagreen dye 25x
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<h1 style="margin-top:15px; margin-bottom:25px; font-size:35px;text-align:center">Experimental Outline
 
<div class = "well">
 
<p>
 
<ol type="I"><li><strong>Pre-Phase One Experiments</strong><ul style="list-style-type:square">
 
</p>
 
<p>
 
  Establish control experiments
 
</p>
 
<li>
 
-Constitutive GFP
 
<p/>
 
<li>
 
o Switch H GFP
 
<p/>
 
</ul>
 
<p><li> <strong>Pre-Phase One Goals</strong>
 
</p>
 
</p><ul>
 
<li>
 
  The goal of pre-phase 1 is to establish a working positive control and negative control in lab.
 
</p></ul>
 
 
 
    <p><li> <strong>Phase One Experiments</strong>
 
 
</p><ul>
 
<li>
 
  Clone composite circuit in e.coli
 
</p>
 
<li>
 
    Test efficacy of the circuit in vivo and determine threshold limits of both arsenic and arsenite
 
</p>
 
<li>
 
    Perform mini prep and quantify
 
</p></ul>
 
   
 
 
 
<p><li> <strong>Phase One Goals</strong>
 
 
</p><ul>
 
<li>
 
  The goals of this phase is to grow a large amount of the composite circuit and develop an understanding of whether or not the circuit is biologically effective. Another primary goal is to develop an understanding of how the circuit works in its entirety (upper threshold/lower threshold)
 
</p></ul>
 
 
 
<p><li> <strong>Phase Two Experiments</strong>
 
 
</p><ul>
 
<li>
 
  Test the efficacy of the composite circuit instead of crude lysate
 
</p>
 
<li>
 
    Test purified plasmid with Promega S30 kit
 
</p></ul>
 
 
 
 
<p><li> <strong>Phase Two Goals</strong>
 
 
</p><ul>
 
<li>
 
  The goal of this phase is to take the circuit out of the cell and test it in situ utilizing both a bacterial expression kit (Promega S30) and an attempt at functionalizing the circuit utilizing a formulated crude lysate for increased application space.
 
</p></ul>
 
 
 
<p><li> <strong>Phase Three Experiments</strong>
 
 
</p><ul>
 
<li> Attempt at micro scaling reaction
 
<p/>
 
<li>
 
Porting reactions to paper based system
 
<p/>
 
<li>
 
Attempt at lyophilizing the circuit on paper both with Promega S30 kit and in the crude lysate form (if the previous phase demonstrated reasonable evidence for progressing on that front)
 
<p/><ul>
 
 
 
<p><li> <strong>Phase Three Goals</strong>
 
 
</p><ul>
 
<li>
 
  The goal of this phase is to successfully micro scale the reaction and port it to a lateral flow paper based system. If successful in this phase, we will have developed a biological means to detect presence of arsenic and arsenite utilizing a lateral flow paper system that is both cost effective and easy to implement.
 
</p></ul>
 
 
  
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Revision as of 22:39, 19 June 2017

Cadets2Vets

EXPERIMENTS - CADETS2VETS