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+ | position: absolute; | ||
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+ | left:5px; | ||
+ | padding-right: 5px; | ||
+ | font-size: 128%; | ||
+ | width:150%; | ||
+ | } | ||
+ | |||
+ | .summary { | ||
+ | display:inline-block; | ||
+ | float:left; | ||
+ | } | ||
+ | |||
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+ | </style> | ||
+ | |||
+ | |||
+ | <div style="max-width:1000px; margin:0 auto; padding:0px 10px 10px 10px;"> | ||
<div class="column full_size"> | <div class="column full_size"> | ||
− | <p>Our weekly | + | <p>Our weekly activities: experiments, data analysis, and planning. For a list of our protocols, visit the <a href="https://2016.igem.org/Team:Pittsburgh/Protocols" target="_blank"> Protocols</a> page.</p> |
</div> | </div> | ||
− | <div class="table"> | + | <div class="table column full_size" style="padding-top:0;"> |
− | < | + | <h2 style="color=#1c2957; padding-top:0;">Contents</h2> |
− | <ul> | + | <ul class="table"> |
− | <li><a href="#Week1">Week 1: May 23 - May 27</a></li> | + | <li><a href="#Week1" class="table">Week 1: May 23 - May 27</a></li> |
− | <li><a href="#Week2">Week 2: May 31 - June 3</a></li> | + | <li><a href="#Week2" class="table">Week 2: May 31 - June 3</a></li> |
− | <li><a href="#Week3">Week 3: June 6 - June 12</a></li> | + | <li><a href="#Week3" class="table">Week 3: June 6 - June 12</a></li> |
+ | <li><a href="#Week4" class="table">Week 4: June 13 - June 17</a></li> | ||
+ | <li><a href="#Week5" class="table">Week 5: June 20 - June 26</a></li> | ||
+ | <li><a href="#Week6" class="table">Week 6: June 27 - July 3</a></li> | ||
+ | <li><a href="#Week7" class="table">Week 7: July 5 - July 8</a></li> | ||
+ | <li><a href="#Week8" class="table">Week 8: July 11 - July 17</a></li> | ||
+ | <li><a href="#Week9" class="table">Week 9: July 18 - July 22</a></li> | ||
+ | <li><a href="#Week10" class="table">Week 10: July 25 - July 31</a></li> | ||
+ | <li><a href="#Week11" class="table">Week 11: August 1 - August 5</a></li> | ||
+ | <li><a href="#Week12" class="table">Week 12: August 8 - August 13</a></li> | ||
+ | <li><a href="#Week13" class="table">Week 13: August 15 - August 20</a></li> | ||
+ | <li><a href="#Week14" class="table">Week 14: August 23 - August 26</a></li> | ||
+ | <li><a href="#Week15" class="table">Week 15: August 29 - September 2</a></li> | ||
+ | <li><a href="#Week16" class="table">Week 16: September 6 - September 9</a></li> | ||
+ | <li><a href="#Week17" class="table">Week 17: September 12 - September 17</a></li> | ||
+ | <li><a href="#Week18" class="table">Week 18: September 19 - September 24</a></li> | ||
+ | <li><a href="#Week19" class="table">Week 19: September 28 - September 30</a></li> | ||
+ | <li><a href="#Week20" class="table">Week 20: October 3 - October 8</a></li> | ||
+ | <li><a href="#Week21" class="table">Week 21: October 10 - October 14</a></li> | ||
+ | <li><a href="#Week22" class="table">Week 22: October 17 - October 19</a></li> | ||
+ | <li><a href="#Week23" class="table">Week 23: October 24 - October 31</a></li> | ||
+ | |||
</ul> | </ul> | ||
</div> | </div> | ||
− | <div class=" | + | <div class="notebook column full_size"> |
− | < | + | <span class="anchor" id="Week1"></span> |
− | < | + | <h1>Week 1: May 23 - May 27</h1> |
− | <ul> | + | |
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
<li>Training begins</li> | <li>Training begins</li> | ||
− | <li>Grow Top 10 competent cells.</li> | + | <li>Grow Top 10 <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#competent" target="_blank">competent cells</a>.</li> |
</ul> | </ul> | ||
− | < | + | |
− | <ul> | + | |
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
<li>Brainstorm genetic circuits for a thallium sensor</li> | <li>Brainstorm genetic circuits for a thallium sensor</li> | ||
− | <li>Lab safety training</li> | + | <li><a href="2016.igem.org/Team:Pittsburgh/Safety" target="_blank"> Lab safety training</a></li> |
</ul> | </ul> | ||
− | <a href=https://static.igem.org/mediawiki/2016/b/bc/TeamPittsburghNotebookWeek1.pdf target="_blank">Week 1 Notebook</a> | + | |
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 5px 5px 5px;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/b/bc/TeamPittsburghNotebookWeek1.pdf" target="_blank">Week 1 Notebook</a><br> | ||
<a href="#Top">Back to Top</a> | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;"class="anchor" id="Week2"></span> | ||
+ | <h1>Week 2: May 31 - June 3</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <ul> | ||
+ | <li>Test <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#competent" target="_blank">efficiency</a> of competent cells</li> | ||
+ | </ul> | ||
+ | |||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul><li>Test <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#cellfree" target="_blank">cell-free extract reaction</a> with T7-GFP plasmid</li></ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px; "> | ||
+ | <li>Contact museums and summer programs for outreach opportunities</li> | ||
+ | <li><a href="2016.igem.org/Team:Pittsburgh/Safety" target="_blank">Lab safety training</a></li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/a/a8/TeamPittsburghNotebookWeek2.pdf" target="_blank">Week 2 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week3"></span> | ||
+ | <h1>Week 3: June 6 - June 12</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
− | < | + | <div class="summary" style="padding:5px; "> |
− | < | + | <h3>Reporter</h3> |
<ul> | <ul> | ||
− | <li> | + | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#transformations" target="_blank">Transform</a> T7 promoter, amilCP, and terminator</li> |
− | <li> | + | <li>Begin assembly by <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#ligation" target="_blank">ligating</a> linearized T7 promoter and amilCP</li> |
+ | </ul></div> | ||
+ | |||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Contact museums and summer programs for outreach opportunities</li> | ||
</ul> | </ul> | ||
− | < | + | |
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/b/b3/TeamPittsburghNotebookWeek3.pdf" target="_blank">Week 3 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week4"></span> | ||
+ | <h1>Week 4: June 13 - June 17</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | |||
+ | <div class="summary" style="padding:5px; "> | ||
+ | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
− | <li> | + | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#transformations" target="_blank">Transform</a> T7-GFP plasmid, lacZ alpha fragment, and eGFP</li> |
− | <li>Lab | + | <li>Send promising T7 promoter -- amilCP ligations to be <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#sequencing" target="_blank">sequenced</a></li> |
+ | <li>Perform <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#digest" target="_blank">double digest</a> of T7 promoter and terminator from last week</li> | ||
+ | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#ligation" target="_blank">Ligate</a> double-digested T7 promoter to new reporters (lacZ and eGFP)</li> | ||
+ | </ul></div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>TECBio, DiSCoBio, and Camp BioE outreach opportunities set</li> | ||
</ul> | </ul> | ||
− | <a href=https://static.igem.org/mediawiki/2016/ | + | |
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/7/75/TeamPittsburghNotebookWeek4.pdf" target="_blank">Week 4 Notebook</a><br> | ||
<a href="#Top">Back to Top</a> | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week5"></span> | ||
+ | <h1>Week 5: June 20 - June 26</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
− | < | + | <div class="summary" style="padding:5px; "> |
− | < | + | <h3>Cell-Free Reactions</h3> |
+ | <ul> | ||
+ | <li>Reaction volume can be reduced to 5 μL with 5 ng/μL of DNA</li> | ||
+ | </ul> | ||
+ | |||
+ | <h3>Toehold Switch</h3> | ||
+ | <ul> | ||
+ | <li>Collins triggers activate the switches (both in plasmid form) to express LacZ</li> | ||
+ | </ul> | ||
+ | |||
+ | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
− | <li> | + | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#ligation" target="_blank">Ligate</a> T7 promoter -- amilCP construct to terminator</li> |
− | <li> | + | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#extraction" target="_blank">Extract</a> successful ligations of T7 promoter to eGFP</li> |
+ | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#ligation" target="_blank">Ligate</a> T7 promoter -- eGFP construct to terminator</li> | ||
+ | </ul></div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Reach out to teams to collaborate based on last year's projects</li> | ||
</ul> | </ul> | ||
− | < | + | |
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/7/7c/TeamPittsburghNotebookWeek5.pdf" target="_blank">Week 5 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week6"></span> | ||
+ | <h1>Week 6: June 27 - July 3</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | |||
+ | <div class="summary" style="padding:5px; "> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>Reaction volume can be reduced to 1 μL with 5 ng/μL of DNA</li> | ||
+ | </ul> | ||
+ | <h3>Toehold Switch</h3> | ||
+ | <ul> | ||
+ | <li>Collins plasmids express LacZ with 25 ng of switch</li> | ||
+ | <li>DNA oligos trigger Collins switches</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
− | <li> | + | <li>Identify successful ligations to terminator for amilCP and eGFP constructs using a <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#agarosegel" target="_blank">gel</a></li> |
+ | <li>Send correct plasmids for <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#sequencing" target="_blank">sequencing</a> for confirmation</li> | ||
+ | <li>Test plasmids in <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#cellfree" target="_blank">cell-free extract</a></li> | ||
+ | <li>amilCP does not produce color in cell-free reaction</li> | ||
+ | <li>eGFP produces fluorescence comparable to that from the Collins T7-GFP plasmid in cell-free reaction</li> | ||
+ | <li>Linearized plasmids containing only the promoter and insert (no terminator) do not express protein</li> | ||
+ | </ul> </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px; "> | ||
+ | <li>Work on outreach presentation for <a href="https://2016.igem.org/Team:Pittsburgh/Human_Practices" target="_blank"> Camp BioE</a></li> | ||
</ul> | </ul> | ||
− | <a href=https://static.igem.org/mediawiki/2016/ | + | |
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription"href="https://static.igem.org/mediawiki/2016/5/59/T--Pittsburgh--NotebookWeek6.pdf" target="_blank">Week 6 Notebook</a><br> | ||
<a href="#Top">Back to Top</a> | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week7"></span> | ||
+ | <h1>Week 7: July 5 - July 8</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | |||
+ | <div class="summary" style="padding:5px; "> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>384-well plate requires at least 10 μL of reaction</li> | ||
+ | </ul> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#annealing" target="_blank">Anneal</a> PO strand with catalytic strand, both with and without erbium</li> | ||
+ | <li>Test success of annealing reaction in cell-free extract and with acrylamide gels</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Sequenced amilCP construct does not contain amilCP</li> | ||
+ | <li>Unsuccessfully linearize and amplify eGFP construct using <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#pcr" target="_blank">PCR</a></li> | ||
+ | </ul></div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Practice outreach presentation for <a href="https://2016.igem.org/Team:Pittsburgh/Human_Practices" target="_blank">Camp BioE</a></li> | ||
+ | <li>Develop DNAzymes for other heavy metals</li> | ||
+ | </ul> | ||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/d/d7/T--Pittsburgh--NotebookWeek7.pdf" target="_blank">Week 7 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week8"></span> | ||
+ | <h1>Week 8: July 11 - July 17</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>Linear eGFP construct does not produce a stronger signal than its plasmid form</li> | ||
+ | </ul> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>DNAzyme duplex does not trigger toehold switch</li> | ||
+ | <li>Erbium cleaves the P substrate strand</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Restart amilCP cloning process</li> | ||
+ | </ul></div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>First presentation at <a href="https://2016.igem.org/Team:Pittsburgh/Human_Practices" target="_blank"> Camp BioE</a></li> | ||
+ | <li>Prepare for <a href="https://2016.igem.org/Team:Pittsburgh/Collaborations#UMD" target="_blank"> UMD Mid-Atlantic Meet-Up</a></li> | ||
+ | <li>Contact PLSG and NEB for sponsorship</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/c/cb/T--Pittsburgh--NotebookWeek8.pdf" target="_blank">Week 8 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week9"></span> | ||
+ | <h1>Week 9: July 18 - July 22</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>Reactions can be diluted by one-half and still produce visible results in two hours</li> | ||
+ | </ul> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>dPAGE assay of P substrate cleavage suggests that the DNAzyme works, but results are not definitive</li> | ||
+ | <li>Six-hour time course of cleavage does not yield much additional information</li> | ||
+ | <li>Reaction temperature (room temperature versus 37°C) does not produce observable effect on cleavage rates</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Continue amilCP cloning process</li></ul> | ||
+ | <h3>Amplifier</h3> | ||
+ | <ul><li>Clone RBS-T3 RNA polymerase to add into other constructs</li> | ||
+ | </ul></div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Presentation at <a href="https://2016.igem.org/Team:Pittsburgh/Human_Practices"> Camp BioEhttps://2016.igem.org/Team:Pittsburgh/Collaborations#UMD</li> | ||
+ | <li><a href="https://2016.igem.org/Team:Pittsburgh/Collaborations#UMD" target="_blank"> UMD Mid-Atlantic Meet-Up</a></li> | ||
+ | <li>Continue fundraising</li> | ||
+ | <li>Discuss systems to model</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/7/75/T--Pittsburgh--NotebookWeek9.pdf" target="_blank">Week 9 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week10"></span> | ||
+ | <h1>Week 10: July 25 - July 31</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>Reactions diluted by one-half produce significantly less protein than undiluted reactions</li> | ||
+ | </ul> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>Annealing reactions produce hybrid complexes but leave unsequestered substrate strand</li> | ||
+ | <li>DNAzyme does not cleave P substrate strand</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Continue cloning amilCP construct</li> | ||
+ | <li>Determine sequence of possible <i>lacZ</i> plasmid</li> | ||
+ | <li>Unsuccessfully grow <i>lacZ</i> from iGEM bacterial stab</li> | ||
+ | </ul> | ||
+ | <h3>Amplifier</h3> | ||
+ | <ul> | ||
+ | <li>Continue cloning T3 constructs</li></ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Presentation at <a href="https://2016.igem.org/Team:Pittsburgh/Human_Practices"> Camp BioE</a></li> | ||
+ | <li>Start modeling toehold kinetics and the economical effects of lead</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/6/64/T--Pittsburgh--NotebookWeek10.pdf" target="_blank">Week 10 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week11"></span> | ||
+ | <h1>Week 11: August 1 - August 5</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <ul> | ||
+ | <li>Obtain fluorescence readings for <a href="/Team:Pittsburgh/Collaborations#UGA" target="_blank" >UGA Archaeal InterLab</a></li></ul> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>Presence of erbium and Buffer B as part of cleavage reaction does not seem to affect reaction progress</li> | ||
+ | </ul> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>Higher catalytic-to-substrate strand ratios help increase sequestration of substrate strand, especially for G switch</li> | ||
+ | <li>Cell-free reactions suggest that cleavage of the P substrate strand does occur in the presence of erbium</li> | ||
+ | <li>dPAGE assay does not suggest cleavage</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>amilCP construct contains CFP, not amilCP</li> | ||
+ | <li>Contact Collins lab for PT3-GFP construct</li> | ||
+ | </ul> | ||
+ | <h3>Amplifier</h3> | ||
+ | <ul> | ||
+ | <li>Obtain T3 RNA polymerase gene via amplification</li> | ||
+ | <li>Ligate PT3 and PT3-RBS into plasmid backbone</li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Presentation at <a href="https://2016.igem.org/Team:Pittsburgh/Human_Practices"> Camp BioE</a></li> | ||
+ | <li>Meeting with Dr. Daniel Bain from the University of Pittsburgh Department of Geology and Environmental Science</li> | ||
+ | <li>Model population effects of lead without economic layer</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/9/9f/T--Pittsburgh--NotebookWeek11.pdf" target="_blank">Week 11 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week12"></span> | ||
+ | <h1>Week 12: August 8 - August 13</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>Begin work with lead DNAzyme</li> | ||
+ | <li>dPAGE assay does not suggest cleavage occurs under the current conditions</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Unsuccessful mutagensis of <i>lacZ</i> to remove EcoRI site for BioBricking</li> | ||
+ | </ul> | ||
+ | <h3>Amplifier</h3> | ||
+ | <ul> | ||
+ | <li>Successfully ligate PT3-RBS into plasmid backbone</li> | ||
+ | <li>Clone PT3-RBS-T3 and PT7-RBS-T3</li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li> <a href="https://2016.igem.org/Team:Pittsburgh/Human_Practices">Table at Carnegie Science Center's H<sub>2</sub>Oh! Exhibit</a></li> | ||
+ | <li>Work on Experiment.com video for crowdfunding</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/5/57/T--Pittsburgh--NotebookWeek12.pdf" target="_blank">Week 12 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week13"></span> | ||
+ | <h1>Week 13: August 15 - August 20</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <ul> | ||
+ | <li>Complete data collection for <a href="/Team:Pittsburgh/InterLab" target="_blank"> InterLab study</a></li> | ||
+ | <li>Prepare William & Mary plasmids for cell-free expression</li> | ||
+ | </ul> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>Start working with hairpin lead DNAzyme</li> | ||
+ | <li>Cell-free reactions suggest that a hairpin DNAzyme cleaves more efficiently than a DNAzyme in a duplex</li> | ||
+ | <li>Adding the DNAzyme, substrate, and metal to a cell-free reaction produces greater switch activation<br> than adding a completed cleavage reaction</li> | ||
+ | <li>Cell-free reactions suggest that cleavage efficiency is similar at 37°C and room temperature</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Unsuccessful mutagenesis of <i>lacZ</i> with DMSO </li> | ||
+ | </ul> | ||
+ | <h3>Amplifier</h3> | ||
+ | <ul> | ||
+ | <li>Unsuccessfully ligate terminator onto PT3-T3 and PT7-T3 constructs</li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Work on Experiment.com video for crowdfunding</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/8/8a/T--Pittsburgh--NotebookWeek13.pdf" target="_blank">Week 13 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week14"></span> | ||
+ | <h1>Week 14: August 23 - August 26</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <ul> | ||
+ | <li>Complete data collection for William & Mary (read our report <a href="https://static.igem.org/mediawiki/2016/4/46/T--Pittsburgh--CollaborationsWM_report.pdf" target="_blank">here</a>) </li> | ||
+ | </ul> | ||
+ | <h3>Amplifier</h3> | ||
+ | <ul> | ||
+ | <li>ligate terminator onto PT3-T3 and PT7-T3 constructs</li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Meet with Dr. Troesken from Pitt's Department of Economics to discuss lead population model</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/2/23/T--Pittsburgh--NotebookWeek14.pdf" target="_blank">Week 14 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week15"></span> | ||
+ | <h1>Week 15: August 29 - September 2</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>No reactions, including the positive control, turn purple to indicate the presence of LacZ</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Unsuccessful mutagenesis of <i>lacZ</i></li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Move lab up to campus</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/f/f7/T--Pittsburgh--NotebookWeek15.pdf" target="_blank">Week 15 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week16"></span> | ||
+ | <h1>Week 16: September 6 - September 9</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <ul> | ||
+ | <li>Obtain codon-optimized OFP, GFP, BFP, YFP, and RFP from 2015 Carnegie Mellon team</li> | ||
+ | </ul> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>Plasmids from last week's reactions did not actually contain the toehold switch</li> | ||
+ | </ul> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>Replicate results from Week 13 suggesting that hairpin lead DNAzyme sequesters and cleaves as expected</li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Experiment.com campaign approved</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/7/79/T--Pittsburgh--NotebookWeek16.pdf" target="_blank">Week 16 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week17"></span> | ||
+ | <h1>Week 17: September 12 - September 17</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>Presence of lead produces signal higher than background hairpin activation at 3.74 nM DNAzyme</li> | ||
+ | <li>Presence of lead may produce signal beyond background activation at 50 nM and 100 nM DNAzyme</li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Experiment.com campaign is live</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/4/4d/T--Pittsburgh--NotebookWeek17.pdf" target="_blank">Week 17 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week18"></span> | ||
+ | <h1>Week 18: September 19 - September 24</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>Presence of lead produces signal higher than background hairpin activation at 3.74 nM DNAzyme</li> | ||
+ | <li>Presence of lead does not produce signal beyond background activation at 50 nM and 100 nM DNAzyme</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Unsuccessful mutagenesis of <i>lacZ</i></li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Modeling</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/5/5a/T--Pittsburgh--NotebookWeek18.pdf" target="_blank">Week 18 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week19"></span> | ||
+ | <h1>Week 19: September 28 - September 30</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>PAGE analysis suggests cleavage of hairpin but is not clear</li> | ||
+ | <li>Presence of lead does not produce signal beyond background activation at 50 nM and 100 nM DNAzyme</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Unsuccessful mutagenesis of <i>lacZ</i></li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Modeling</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/4/48/T--Pittsburgh--NotebookWeek19.pdf" target="_blank">Week 19 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week20"></span> | ||
+ | <h1>Week 20: October 3 - October 8</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <h3>DNAzyme</h3> | ||
+ | <ul> | ||
+ | <li>PAGE analysis suggests cleavage of hairpin but is not clear</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Unsuccessful mutagenesis of <i>lacZ</i></li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <!--<img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Modeling</li> | ||
+ | </ul>--> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/6/62/T--Pittsburgh--NotebookWeek20.pdf" target="_blank">Week 19 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week21"></span> | ||
+ | <h1>Week 21: October 10 - October 14</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <ul> | ||
+ | <li>Characterize codon-optimized fluorescent proteins from 2015 Carnegie Mellon team</li> | ||
+ | </ul> | ||
+ | <h3>Cell-Free Reactions</h3> | ||
+ | <ul> | ||
+ | <li>Expected dosage response to lead not observed</li> | ||
+ | <li>Expected lack of activation with D switch not observed</li> | ||
+ | <li>Reaction colors do not look the same as in previous weeks</li> | ||
+ | </ul> | ||
+ | <h3>Reporter</h3> | ||
+ | <ul> | ||
+ | <li>Unsuccessful mutagenesis of <i>lacZ</i></li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Modeling</li> | ||
+ | <li>Finalize Wiki</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/c/cc/T--Pittsburgh--NotebookWeek21.pdf" target="_blank">Week 21 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week22"></span> | ||
+ | <h1>Week 22: October 17 - October 19</h1> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/b/b8/T--Pittsburgh--NotebookWetLab.jpg" alt="Wet Lab" style="padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <div class="summary" style="padding:5px;"> | ||
+ | <ul> | ||
+ | <li>Finish cloning Parts </li> | ||
+ | <li>Submit Parts</li> | ||
+ | </ul> | ||
+ | </div> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Finalize Wiki</li> | ||
+ | </ul> | ||
+ | |||
+ | <div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/f/f2/T--Pittsburgh--NotebookWeek22.pdf" target="_blank">Week 22 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | |||
+ | <span style="clear:both;" class="anchor" id="Week23"></span> | ||
+ | <h1>Week 23: October 24 - October 31</h1> | ||
+ | |||
+ | <img src="https://static.igem.org/mediawiki/2016/e/e0/T--Pittsburgh--NotebookDryLab.jpg" alt="Dry Lab" style="clear:both; padding:5px; width:100px;height:100px;float:left;"> | ||
+ | <ul class="summary" style="padding:5px;"> | ||
+ | <li>Prepare poster and presentation</li> | ||
+ | <li>Giant Jamboree!</li> | ||
+ | </ul> | ||
+ | <div style="clear:both;"> | ||
+ | <a href="#Top">Back to Top</a></div> | ||
+ | |||
+ | <!--<div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2016/9/96/T--Pittsburgh--NotebookNotebook.png" alt="notebook" style="width:125px;height:auto;padding:0 0 5px 0;"><a class="imgDescription" href="https://static.igem.org/mediawiki/2016/c/cc/T--Pittsburgh--NotebookWeek21.pdf" target="_blank">Week 21 Notebook</a><br> | ||
+ | <a href="#Top">Back to Top</a> | ||
+ | </div> --> | ||
+ | |||
+ | |||
+ | |||
+ | </div></div> | ||
− | |||
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<div class="column half_size"> | <div class="column half_size"> | ||
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<ul> | <ul> | ||
+ | <li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li> | ||
+ | <li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li> | ||
+ | <li><a href="https://2014.igem.org/Team:Kyoto/Notebook/Magnetosome_Formation#title">2014 Kyoto</a></li> | ||
+ | <li><a href="https://2014.igem.org/Team:Cornell/notebook">2014 Cornell</a></li> | ||
+ | </ul> | ||
+ | |||
+ | </div> | ||
+ | |||
+ | </html> | ||
<li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li> | <li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li> | ||
<li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li> | <li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li> |
Latest revision as of 20:34, 5 November 2016
Contact Us
Our weekly activities: experiments, data analysis, and planning. For a list of our protocols, visit the Protocols page.
Contents
- Week 1: May 23 - May 27
- Week 2: May 31 - June 3
- Week 3: June 6 - June 12
- Week 4: June 13 - June 17
- Week 5: June 20 - June 26
- Week 6: June 27 - July 3
- Week 7: July 5 - July 8
- Week 8: July 11 - July 17
- Week 9: July 18 - July 22
- Week 10: July 25 - July 31
- Week 11: August 1 - August 5
- Week 12: August 8 - August 13
- Week 13: August 15 - August 20
- Week 14: August 23 - August 26
- Week 15: August 29 - September 2
- Week 16: September 6 - September 9
- Week 17: September 12 - September 17
- Week 18: September 19 - September 24
- Week 19: September 28 - September 30
- Week 20: October 3 - October 8
- Week 21: October 10 - October 14
- Week 22: October 17 - October 19
- Week 23: October 24 - October 31
Week 1: May 23 - May 27
- Training begins
- Grow Top 10 competent cells.
- Brainstorm genetic circuits for a thallium sensor
- Lab safety training
Week 2: May 31 - June 3
- Test efficiency of competent cells
Cell-Free Reactions
- Test cell-free extract reaction with T7-GFP plasmid
- Contact museums and summer programs for outreach opportunities
- Lab safety training
Week 3: June 6 - June 12
Reporter
- Contact museums and summer programs for outreach opportunities
Week 4: June 13 - June 17
Reporter
- Transform T7-GFP plasmid, lacZ alpha fragment, and eGFP
- Send promising T7 promoter -- amilCP ligations to be sequenced
- Perform double digest of T7 promoter and terminator from last week
- Ligate double-digested T7 promoter to new reporters (lacZ and eGFP)
- TECBio, DiSCoBio, and Camp BioE outreach opportunities set
Week 5: June 20 - June 26
Cell-Free Reactions
- Reaction volume can be reduced to 5 μL with 5 ng/μL of DNA
Toehold Switch
- Collins triggers activate the switches (both in plasmid form) to express LacZ
Reporter
- Reach out to teams to collaborate based on last year's projects
Week 6: June 27 - July 3
Cell-Free Reactions
- Reaction volume can be reduced to 1 μL with 5 ng/μL of DNA
Toehold Switch
- Collins plasmids express LacZ with 25 ng of switch
- DNA oligos trigger Collins switches
Reporter
- Identify successful ligations to terminator for amilCP and eGFP constructs using a gel
- Send correct plasmids for sequencing for confirmation
- Test plasmids in cell-free extract
- amilCP does not produce color in cell-free reaction
- eGFP produces fluorescence comparable to that from the Collins T7-GFP plasmid in cell-free reaction
- Linearized plasmids containing only the promoter and insert (no terminator) do not express protein
- Work on outreach presentation for Camp BioE
Week 7: July 5 - July 8
Cell-Free Reactions
- 384-well plate requires at least 10 μL of reaction
DNAzyme
- Anneal PO strand with catalytic strand, both with and without erbium
- Test success of annealing reaction in cell-free extract and with acrylamide gels
Reporter
- Sequenced amilCP construct does not contain amilCP
- Unsuccessfully linearize and amplify eGFP construct using PCR
- Practice outreach presentation for Camp BioE
- Develop DNAzymes for other heavy metals
Week 8: July 11 - July 17
Cell-Free Reactions
- Linear eGFP construct does not produce a stronger signal than its plasmid form
DNAzyme
- DNAzyme duplex does not trigger toehold switch
- Erbium cleaves the P substrate strand
Reporter
- Restart amilCP cloning process
- First presentation at Camp BioE
- Prepare for UMD Mid-Atlantic Meet-Up
- Contact PLSG and NEB for sponsorship
Week 9: July 18 - July 22
Cell-Free Reactions
- Reactions can be diluted by one-half and still produce visible results in two hours
DNAzyme
- dPAGE assay of P substrate cleavage suggests that the DNAzyme works, but results are not definitive
- Six-hour time course of cleavage does not yield much additional information
- Reaction temperature (room temperature versus 37°C) does not produce observable effect on cleavage rates
Reporter
- Continue amilCP cloning process
Amplifier
- Clone RBS-T3 RNA polymerase to add into other constructs
- Presentation at Camp BioEhttps://2016.igem.org/Team:Pittsburgh/Collaborations#UMD
- UMD Mid-Atlantic Meet-Up
- Continue fundraising
- Discuss systems to model
Week 10: July 25 - July 31
Cell-Free Reactions
- Reactions diluted by one-half produce significantly less protein than undiluted reactions
DNAzyme
- Annealing reactions produce hybrid complexes but leave unsequestered substrate strand
- DNAzyme does not cleave P substrate strand
Reporter
- Continue cloning amilCP construct
- Determine sequence of possible lacZ plasmid
- Unsuccessfully grow lacZ from iGEM bacterial stab
Amplifier
- Continue cloning T3 constructs
- Presentation at Camp BioE
- Start modeling toehold kinetics and the economical effects of lead
Week 11: August 1 - August 5
- Obtain fluorescence readings for UGA Archaeal InterLab
Cell-Free Reactions
- Presence of erbium and Buffer B as part of cleavage reaction does not seem to affect reaction progress
DNAzyme
- Higher catalytic-to-substrate strand ratios help increase sequestration of substrate strand, especially for G switch
- Cell-free reactions suggest that cleavage of the P substrate strand does occur in the presence of erbium
- dPAGE assay does not suggest cleavage
Reporter
- amilCP construct contains CFP, not amilCP
- Contact Collins lab for PT3-GFP construct
Amplifier
- Obtain T3 RNA polymerase gene via amplification
- Ligate PT3 and PT3-RBS into plasmid backbone
- Presentation at Camp BioE
- Meeting with Dr. Daniel Bain from the University of Pittsburgh Department of Geology and Environmental Science
- Model population effects of lead without economic layer
Week 12: August 8 - August 13
DNAzyme
- Begin work with lead DNAzyme
- dPAGE assay does not suggest cleavage occurs under the current conditions
Reporter
- Unsuccessful mutagensis of lacZ to remove EcoRI site for BioBricking
Amplifier
- Successfully ligate PT3-RBS into plasmid backbone
- Clone PT3-RBS-T3 and PT7-RBS-T3
- Table at Carnegie Science Center's H2Oh! Exhibit
- Work on Experiment.com video for crowdfunding
Week 13: August 15 - August 20
- Complete data collection for InterLab study
- Prepare William & Mary plasmids for cell-free expression
DNAzyme
- Start working with hairpin lead DNAzyme
- Cell-free reactions suggest that a hairpin DNAzyme cleaves more efficiently than a DNAzyme in a duplex
- Adding the DNAzyme, substrate, and metal to a cell-free reaction produces greater switch activation
than adding a completed cleavage reaction - Cell-free reactions suggest that cleavage efficiency is similar at 37°C and room temperature
Reporter
- Unsuccessful mutagenesis of lacZ with DMSO
Amplifier
- Unsuccessfully ligate terminator onto PT3-T3 and PT7-T3 constructs
- Work on Experiment.com video for crowdfunding
Week 14: August 23 - August 26
- Complete data collection for William & Mary (read our report here)
Amplifier
- ligate terminator onto PT3-T3 and PT7-T3 constructs
- Meet with Dr. Troesken from Pitt's Department of Economics to discuss lead population model
Week 15: August 29 - September 2
Cell-Free Reactions
- No reactions, including the positive control, turn purple to indicate the presence of LacZ
Reporter
- Unsuccessful mutagenesis of lacZ
- Move lab up to campus
Week 16: September 6 - September 9
- Obtain codon-optimized OFP, GFP, BFP, YFP, and RFP from 2015 Carnegie Mellon team
Cell-Free Reactions
- Plasmids from last week's reactions did not actually contain the toehold switch
DNAzyme
- Replicate results from Week 13 suggesting that hairpin lead DNAzyme sequesters and cleaves as expected
- Experiment.com campaign approved
Week 17: September 12 - September 17
DNAzyme
- Presence of lead produces signal higher than background hairpin activation at 3.74 nM DNAzyme
- Presence of lead may produce signal beyond background activation at 50 nM and 100 nM DNAzyme
- Experiment.com campaign is live
Week 18: September 19 - September 24
DNAzyme
- Presence of lead produces signal higher than background hairpin activation at 3.74 nM DNAzyme
- Presence of lead does not produce signal beyond background activation at 50 nM and 100 nM DNAzyme
Reporter
- Unsuccessful mutagenesis of lacZ
- Modeling
Week 19: September 28 - September 30
DNAzyme
- PAGE analysis suggests cleavage of hairpin but is not clear
- Presence of lead does not produce signal beyond background activation at 50 nM and 100 nM DNAzyme
Reporter
- Unsuccessful mutagenesis of lacZ
- Modeling
Week 20: October 3 - October 8
DNAzyme
- PAGE analysis suggests cleavage of hairpin but is not clear
Reporter
- Unsuccessful mutagenesis of lacZ
Week 21: October 10 - October 14
- Characterize codon-optimized fluorescent proteins from 2015 Carnegie Mellon team
Cell-Free Reactions
- Expected dosage response to lead not observed
- Expected lack of activation with D switch not observed
- Reaction colors do not look the same as in previous weeks
Reporter
- Unsuccessful mutagenesis of lacZ
- Modeling
- Finalize Wiki
Week 22: October 17 - October 19
- Finish cloning Parts
- Submit Parts
- Finalize Wiki
Week 23: October 24 - October 31
- Prepare poster and presentation
- Giant Jamboree!