Difference between revisions of "Team:Pittsburgh/Notebook"
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<div style="position:relative; padding:5px;display:block;float:left;clear:both;"> | <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: | + | <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> | </div> | ||
| Line 57: | Line 57: | ||
<span class="anchor" id="Week2"></span> | <span class="anchor" id="Week2"></span> | ||
<h1 style="clear:both;">Week 2: May 31 - June 3</h1> | <h1 style="clear:both;">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;"> |
| − | <ul> | + | <ul style="padding:5px; display:inline-block; float:left; "> |
<li>Test <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#competent" target="_blank">efficiency</a> of competent cells</li> | <li>Test <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#competent" target="_blank">efficiency</a> of competent cells</li> | ||
</ul> | </ul> | ||
| + | <div style="padding:5px; display:inline-block; float:left; "> | ||
<h3>Cell-Free Extract</h3> | <h3>Cell-Free Extract</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> | <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> |
| − | <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 style="padding:5px; display:inline-block; float:left; "> | ||
<li>Contact museums and summer programs for outreach opportunities</li> | <li>Contact museums and summer programs for outreach opportunities</li> | ||
<li>Lab safety training</li> | <li>Lab safety training</li> | ||
</ul> | </ul> | ||
| − | <a href=https://static.igem.org/mediawiki/2016/a/a8/TeamPittsburghNotebookWeek2.pdf target="_blank">Week 2 Notebook</a><br> | + | |
| + | <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> | <a href="#Top">Back to Top</a> | ||
| − | + | </div> | |
<span class="anchor" id="Week3"></span> | <span class="anchor" id="Week3"></span> | ||
| − | <h1>Week 3: June 6 - June 12</h1> | + | <h1 style="clear:both;">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 style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Reporter</h3> | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
<li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#transformations" target="_blank">Transform</a> T7 promoter, amilCP, and terminator</li> | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#transformations" target="_blank">Transform</a> T7 promoter, amilCP, and terminator</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> | <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> | + | </ul></div> |
| − | < | + | |
| − | <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 style="padding:5px; display:inline-block; float:left;"> | ||
<li>Contact museums and summer programs for outreach opportunities</li> | <li>Contact museums and summer programs for outreach opportunities</li> | ||
</ul> | </ul> | ||
| − | <a href=https://static.igem.org/mediawiki/2016/b/b3/TeamPittsburghNotebookWeek3.pdf target="_blank">Week 3 Notebook</a><br> | + | |
| + | <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> | <a href="#Top">Back to Top</a> | ||
| − | + | </div> | |
<span class="anchor" id="Week4"></span> | <span class="anchor" id="Week4"></span> | ||
| − | <h1>Week 4: June 13 - June 17</h1> | + | <h1 style="clear:both;">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 style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Reporter</h3> | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
| Line 97: | Line 110: | ||
<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>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> | <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> | + | </ul></div> |
| − | < | + | |
| − | <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 style="padding:5px; display:inline-block; float:left;"> | ||
<li>TECBio, DiSCoBio, and Tissue Engineering Camp outreach opportunities set</li> | <li>TECBio, DiSCoBio, and Tissue Engineering Camp outreach opportunities set</li> | ||
</ul> | </ul> | ||
| − | <a href=https://static.igem.org/mediawiki/2016/7/75/TeamPittsburghNotebookWeek4.pdf target="_blank">Week 4 Notebook</a><br> | + | |
| + | <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 class="anchor" id="Week5"></span> | <span class="anchor" id="Week5"></span> | ||
| − | <h1>Week 5: June 20 - June 26</h1> | + | <h1 style="clear:both;">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 style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Cell-Free Extract</h3> | <h3>Cell-Free Extract</h3> | ||
<ul> | <ul> | ||
<li>Reaction volume can be reduced to 5 μL with 5 ng/μL of DNA</li> | <li>Reaction volume can be reduced to 5 μL with 5 ng/μL of DNA</li> | ||
</ul> | </ul> | ||
| + | </div> | ||
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Toehold Switch</h3> | <h3>Toehold Switch</h3> | ||
<ul> | <ul> | ||
<li>Collins triggers activate the switches (both in plasmid form) to express LacZ</li> | <li>Collins triggers activate the switches (both in plasmid form) to express LacZ</li> | ||
</ul> | </ul> | ||
| + | </div> | ||
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Reporter</h3> | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
| Line 122: | Line 144: | ||
<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#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> | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#ligation" target="_blank">Ligate</a> T7 promoter -- eGFP construct to terminator</li> | ||
| − | </ul> | + | </ul></div> |
| − | < | + | |
| − | <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 style="padding:5px; display:inline-block; float:left;"> | ||
<li>Reach out to teams to collaborate based on last year's projects</li> | <li>Reach out to teams to collaborate based on last year's projects</li> | ||
</ul> | </ul> | ||
| − | <a href="https://static.igem.org/mediawiki/2016/7/7c/TeamPittsburghNotebookWeek5.pdf" target="_blank">Week 5 Notebook</a><br> | + | |
| + | <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> | <a href="#Top">Back to Top</a> | ||
| − | + | </div> | |
<span class="anchor" id="Week6"></span> | <span class="anchor" id="Week6"></span> | ||
| − | <h1>Week 6: June 27 - July 3</h1> | + | <h1 style="clear:both;">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 style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Cell-Free Extract</h3> | <h3>Cell-Free Extract</h3> | ||
<ul> | <ul> | ||
<li>Reaction volume can be reduced to 1 μL with 5 ng/μL of DNA</li> | <li>Reaction volume can be reduced to 1 μL with 5 ng/μL of DNA</li> | ||
| − | </ul> | + | </ul></div> |
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Toehold Switch</h3> | <h3>Toehold Switch</h3> | ||
<ul> | <ul> | ||
<li>Collins plasmids express LacZ with 25 ng of switch</li> | <li>Collins plasmids express LacZ with 25 ng of switch</li> | ||
<li>DNA oligos trigger Collins switches</li> | <li>DNA oligos trigger Collins switches</li> | ||
| − | </ul> | + | </ul></div> |
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Reporter</h3> | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
| Line 151: | Line 180: | ||
<li>eGFP produces fluorescence comparable to that from the Collins T7-GFP plasmid 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> | <li>Linearized plasmids containing only the promoter and insert (no terminator) do not express protein</li> | ||
| − | </ul> | + | </ul> </div> |
| − | < | + | |
| − | <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 style="padding:5px; display:inline-block; float:left;"> | ||
<li>Work on outreach presentation for tissue engineering camp</li> | <li>Work on outreach presentation for tissue engineering camp</li> | ||
</ul> | </ul> | ||
| − | <a href="https://static.igem.org/mediawiki/2016/5/59/T--Pittsburgh--NotebookWeek6.pdf" target="_blank">Week 6 Notebook</a><br> | + | |
| + | <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 class="anchor" id="Week7"></span> | <span class="anchor" id="Week7"></span> | ||
| − | <h1>Week 7: July 5 - July 8</h1> | + | <h1 style="clear:both;">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 style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Cell-Free Extract</h3> | <h3>Cell-Free Extract</h3> | ||
<ul> | <ul> | ||
<li>384-well plate requires at least 10 μL of reaction</li> | <li>384-well plate requires at least 10 μL of reaction</li> | ||
| − | </ul> | + | </ul></div> |
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>DNAzyme</h3> | <h3>DNAzyme</h3> | ||
<ul> | <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><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> | <li>Test success of annealing reaction in cell-free extract and with acrylamide gels</li> | ||
| − | </ul> | + | </ul></div> |
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Reporter</h3> | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
<li>Sequenced amilCP construct does not contain amilCP</li> | <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> | <li>Unsuccessfully linearize and amplify eGFP construct using <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#pcr" target="_blank">PCR</a></li> | ||
| − | </ul> | + | </ul></div> |
| − | < | + | |
| − | <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 style="padding:5px; display:inline-block; float:left;"> | ||
<li>Practice outreach presentation for tissue engineering camp</li> | <li>Practice outreach presentation for tissue engineering camp</li> | ||
<li>Develop DNAzymes for other heavy metals</li> | <li>Develop DNAzymes for other heavy metals</li> | ||
</ul> | </ul> | ||
| − | <a href="https://static.igem.org/mediawiki/2016/d/d7/T--Pittsburgh--NotebookWeek7.pdf" target="_blank">Week 7 Notebook</a><br> | + | <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> | <a href="#Top">Back to Top</a> | ||
| − | + | </div> | |
<span class="anchor" id="Week1"></span> | <span class="anchor" id="Week1"></span> | ||
| − | <h1>Week 8: July 11 - July 17</h1> | + | <h1 style="clear:both;">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 style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Cell-Free Extract</h3> | <h3>Cell-Free Extract</h3> | ||
<ul> | <ul> | ||
<li>Linear eGFP construct does not produce a stronger signal than its plasmid form</li> | <li>Linear eGFP construct does not produce a stronger signal than its plasmid form</li> | ||
| − | </ul> | + | </ul></div> |
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>DNAzyme</h3> | <h3>DNAzyme</h3> | ||
<ul> | <ul> | ||
<li>DNAzyme duplex does not trigger toehold switch</li> | <li>DNAzyme duplex does not trigger toehold switch</li> | ||
<li>Erbium cleaves the P substrate strand</li> | <li>Erbium cleaves the P substrate strand</li> | ||
| − | </ul> | + | </ul></div> |
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Reporter</h3> | <h3>Reporter</h3> | ||
<ul> | <ul> | ||
<li>Restart amilCP cloning process</li> | <li>Restart amilCP cloning process</li> | ||
| − | </ul> | + | </ul></div> |
| − | < | + | |
| − | <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 style="padding:5px; display:inline-block; float:left;"> | ||
<li>First presentation at Camp BioE</li> | <li>First presentation at Camp BioE</li> | ||
<li>Prepare for UMD Mid-Atlantic Meet-Up</li> | <li>Prepare for UMD Mid-Atlantic Meet-Up</li> | ||
<li>Contact PLSG and NEB for sponsorship</li> | <li>Contact PLSG and NEB for sponsorship</li> | ||
</ul> | </ul> | ||
| − | <a href="https://static.igem.org/mediawiki/2016/c/cb/T--Pittsburgh--NotebookWeek8.pdf" target="_blank">Week 8 Notebook</a><br> | + | |
| + | <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> | <a href="#Top">Back to Top</a> | ||
| − | + | </div> | |
<span class="anchor" id="Week9"></span> | <span class="anchor" id="Week9"></span> | ||
| − | <h1>Week 9: July 18 - July 22</h1> | + | <h1 style="clear:both;">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 style="padding:5px; display:inline-block; float:left;"> | ||
<h3>Cell-Free Extract</h3> | <h3>Cell-Free Extract</h3> | ||
<ul> | <ul> | ||
<li>Reactions can be diluted by one-half and still produce visible results in two hours</li> | <li>Reactions can be diluted by one-half and still produce visible results in two hours</li> | ||
| − | </ul> | + | </ul></div> |
| + | <div style="padding:5px; display:inline-block; float:left;"> | ||
<h3>DNAzyme</h3> | <h3>DNAzyme</h3> | ||
<ul> | <ul> | ||
| Line 226: | Line 272: | ||
<li>Six-hour time course of cleavage does not yield much additional information</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> | <li>Reaction temperature (room temperature versus 37°C) does not produce observable effect on cleavage rates</li> | ||
| − | </ul> | + | </ul></div> |
| − | <h3>Reporter</h3> | + | <div style="padding:5px; display:inline-block; float:left;"><h3>Reporter</h3> |
<ul> | <ul> | ||
<li>Continue amilCP cloning process</li> | <li>Continue amilCP cloning process</li> | ||
<li>Clone RBS-T3 RNA polymerase to add into other constructs</li> | <li>Clone RBS-T3 RNA polymerase to add into other constructs</li> | ||
| − | </ul> | + | </ul></div> |
| − | < | + | |
| − | <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 style="padding:5px; display:inline-block; float:left;"> | ||
<li>Presentation at Camp BioE</li> | <li>Presentation at Camp BioE</li> | ||
<li>UMD Mid-Atlantic Meet-Up</li> | <li>UMD Mid-Atlantic Meet-Up</li> | ||
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<li>Discuss systems to model</li> | <li>Discuss systems to model</li> | ||
</ul> | </ul> | ||
| − | <a href="https://static.igem.org/mediawiki/2016/7/75/T--Pittsburgh--NotebookWeek9.pdf" target="_blank">Week 9 Notebook</a><br> | + | |
| + | <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> | <a href="#Top">Back to Top</a> | ||
| − | + | </div> | |
</div> | </div> | ||
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Revision as of 21:58, 30 July 2016
Contact Us
Thank you to our sponsors!
Our weekly progress. For a list of our protocols, visit the Protocols page
Contents
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 Extract
- 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 Tissue Engineering Camp outreach opportunities set
Week 5: June 20 - June 26
Cell-Free Extract
- 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 Extract
- 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 consturcts 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 tissue engineering camp
Week 7: July 5 - July 8
Cell-Free Extract
- 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 tissue engineering camp
- Develop DNAzymes for other heavy metals
Week 8: July 11 - July 17
Cell-Free Extract
- 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 Extract
- 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
- Clone RBS-T3 RNA polymerase to add into other constructs
- Presentation at Camp BioE
- UMD Mid-Atlantic Meet-Up
- Continue fundraising
- Discuss systems to model
