Difference between revisions of "Team:Pittsburgh/Team"
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| − | + | <div class="column full_size"> | |
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| + | <p>Our weekly progress. For a list of our protocols, visit the <a href="https://2016.igem.org/Team:Pittsburgh/Protocols" target="_blank"> Protocols</a> page</p> | ||
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<div class="table column full_size"> | <div class="table column full_size"> | ||
| − | <h2>Contents</h2> | + | <h2 style="color:rgb(0,0,128)">Contents</h2> |
<ul class="table"> | <ul class="table"> | ||
| − | <li><a href="# | + | <li><a href="#Week1" class="table">Week 1: May 23 - May 27</a></li> |
| − | + | <li><a href="#Week2" class="table">Week 2: May 31 - June 3</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="# | + | <li><a href="#Week9" class="table">Week 9: July 18 - July 22</a></li> |
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</ul> | </ul> | ||
</div> | </div> | ||
<div class="notebook column full_size"> | <div class="notebook column full_size"> | ||
| − | <h1 class="nav"><a name=" | + | <h1 class="nav"><a name="Week1" class="nav">Week 1: May 23 - May 27</a></h1> |
| − | + | <h2>Wet Lab</h2> | |
| − | <h2 | + | <ul> |
| − | + | <li>Training begins</li> | |
| − | + | <li>Grow Top 10 <a href="https://2016.igem.org/Team:Pittsburgh/Protocols#competent" target="_blank">competent cells</a>.</li> | |
| − | + | </ul> | |
| − | + | <h2>Dry Lab</h2> | |
| − | + | <ul> | |
| − | + | <li>Brainstorm genetic circuits for a thallium sensor</li> | |
| − | <h2 | + | <li>Lab safety training</li> |
| − | + | </ul> | |
| − | + | <a 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> |
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| − | + | <h1 class="nav"><a name="Week2" class="nav">Week 2: May 31 - June 3</a></h1> | |
| − | <h1 class="nav"><a name=" | + | <h2>Wet Lab</h2> |
| − | < | + | <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 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> | |
| − | + | <h2>Dry Lab</h2> | |
| + | <ul> | ||
| + | <li>Contact museums and summer programs for outreach opportunities</li> | ||
| + | <li>Lab safety training</li> | ||
| + | </ul> | ||
| + | <a 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> | ||
| − | + | <h1 class="nav"><a name="Week3" class="nav">Week 3: June 6 - June 12</a></h1> | |
| − | + | <h2>Wet Lab</h2> | |
| − | <a href=" | + | <h3>Reporter</h3> |
| − | <a href=" | + | <ul> |
| − | + | <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> | |
| − | + | </ul> | |
| − | + | <h2>Dry Lab</h2> | |
| − | + | <ul> | |
| − | + | <li>Contact museums and summer programs for outreach opportunities</li> | |
| − | < | + | </ul> |
| − | + | <a 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> | |
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| − | < | + | <h1 class="nav"><a name="Week4" class="nav">Week 4: June 13 - June 17</a></h1> |
| − | + | <h2>Wet Lab</h2> | |
| − | + | <h3>Reporter</h3> | |
| − | + | <ul> | |
| − | + | <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>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> | ||
| + | <h2>Dry Lab</h2> | ||
| + | <ul> | ||
| + | <li>TECBio, DiSCoBio, and Tissue Engineering Camp outreach opportunities set</li> | ||
| + | </ul> | ||
| + | <a 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> | ||
| − | < | + | <h1 class="nav"><a name="Week5" class="nav">Week 5: June 20 - June 26</a></h1> |
| − | + | <h2>Wet Lab</h2> | |
| − | < | + | <h3>Reporter</h3> |
| − | < | + | <ul> |
| − | + | <li><a href="https://2016.igem.org/Team:Pittsburgh/Protocols#ligation" target="_blank">Ligate</a> T7 promoter -- amilCP construct to terminator</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> | ||
| + | <h3>Cell-Free Extract</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> | ||
| + | <h2>Dry Lab</h2> | ||
| + | <ul> | ||
| + | <li>Reach out to teams to collaborate based on last year's projects</li> | ||
| + | </ul> | ||
| + | <a 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> | ||
| − | < | + | <h1 class="nav"><a name="Week6" class="nav">Week 6: June 27 - July 3</a></h1> |
| − | <a href=" | + | <h2>Wet Lab</h2> |
| + | <h3>Reporter</h3> | ||
| + | <ul> | ||
| + | <li>Identify successful ligations to terminator for amilCP and eGFP consturcts 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> | ||
| + | <h3>Cell-Free Extract</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> | ||
| + | <h2>Dry Lab</h2> | ||
| + | <ul> | ||
| + | <li>Work on outreach presentation for tissue engineering camp</li> | ||
| + | </ul> | ||
| + | <a 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> | ||
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| − | < | + | <h1 class="nav"><a name="Week7" class="nav">Week 7: July 5 - July 8</a></h1> |
| − | < | + | <h2>Wet Lab</h2> |
| − | < | + | <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> |
| − | < | + | <h3>Cell-Free Extract</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> | ||
| + | <h2>Dry Lab</h2> | ||
| + | <ul> | ||
| + | <li>Practice outreach presentation for tissue engineering camp</li> | ||
| + | <li>Develop DNAzymes for other heavy metals</li> | ||
| + | </ul> | ||
| + | <a 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> | ||
| + | |||
| + | <h1 class="nav"><a name="Week8" class="nav">Week 8: July 11 - July 17</a></h1> | ||
| + | <h2>Wet Lab</h2> | ||
| + | <h3>Reporter</h3> | ||
| + | <ul> | ||
| + | <li>Restart amilCP cloning process</li> | ||
| + | </ul> | ||
| + | <h3>Cell-Free Extract</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> | ||
| + | <h2>Dry Lab</h2> | ||
| + | <ul> | ||
| + | <li>First presentation at Camp BioE</li> | ||
| + | <li>Prepare for UMD Mid-Atlantic Meet-Up</li> | ||
| + | <li>Contact PLSG and NEB for sponsorship</li> | ||
| + | </ul> | ||
| + | <a 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> | ||
| + | |||
| + | <h1 class="nav"><a name="Week9" class="nav">Week 9: July 18 - July 22</a></h1> | ||
| + | <h2>Wet Lab</h2> | ||
| + | <h3>Reporter</h3> | ||
| + | <ul> | ||
| + | <li>Continue amilCP cloning process</li> | ||
| + | <li>Clone RBS-T3 RNA polymerase to add into other constructs</li> | ||
| + | </ul> | ||
| + | <h3>Cell-Free Extract</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> | ||
| + | <h2>Dry Lab</h2> | ||
| + | <ul> | ||
| + | <li>Presentation at Camp BioE</li> | ||
| + | <li>UMD Mid-Atlantic Meet-Up</li> | ||
| + | <li>Continue fundraising</li> | ||
| + | <li>Discuss systems to model</li> | ||
| + | </ul> | ||
| + | <a 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> | ||
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</div> | </div> | ||
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<!-- | <!-- | ||
| − | <div class="column half_size" > | + | <div class="column half_size"> |
| − | <h5>What should this page | + | <h5>What should this page have?</h5> |
<ul> | <ul> | ||
| − | <li> | + | <li>Chronological notes of what your team is doing.</li> |
| − | <li> | + | <li> Brief descriptions of daily important events.</li> |
| − | <li> | + | <li>Pictures of your progress. </li> |
| − | <li> | + | <li>Mention who participated in what task.</li> |
</ul> | </ul> | ||
| + | |||
</div> | </div> | ||
| − | |||
| + | <div class="column half_size"> | ||
| + | <h5>Inspiration</h5> | ||
| + | <p>You can see what others teams have done to organize their notes:</p> | ||
| + | <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> | </html> | ||
Revision as of 22:12, 28 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
Wet Lab
- Training begins
- Grow Top 10 competent cells.
Dry Lab
- Brainstorm genetic circuits for a thallium sensor
- Lab safety training
Back to Top
Week 2: May 31 - June 3
Wet Lab
- Test efficiency of competent cells
Cell-Free Extract
- Test cell-free extract reaction with T7-GFP plasmid
Dry Lab
- Contact museums and summer programs for outreach opportunities
- Lab safety training
Back to Top
Week 3: June 6 - June 12
Wet Lab
Reporter
- Transform T7 promoter, amilCP, and terminator
- Begin assembly by ligating linearized T7 promoter and amilCP
Dry Lab
- Contact museums and summer programs for outreach opportunities
Back to Top
Week 4: June 13 - June 17
Wet Lab
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)
Dry Lab
- TECBio, DiSCoBio, and Tissue Engineering Camp outreach opportunities set
Back to Top
Week 5: June 20 - June 26
Wet Lab
Reporter
- Ligate T7 promoter -- amilCP construct to terminator
- Extract successful ligations of T7 promoter to eGFP
- Ligate T7 promoter -- eGFP construct to terminator
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
Dry Lab
- Reach out to teams to collaborate based on last year's projects
Back to Top
Week 6: June 27 - July 3
Wet Lab
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
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
Dry Lab
- Work on outreach presentation for tissue engineering camp
Back to Top
Week 7: July 5 - July 8
Wet Lab
Reporter
- Sequenced amilCP construct does not contain amilCP
- Unsuccessfully linearize and amplify eGFP construct using PCR
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
Dry Lab
- Practice outreach presentation for tissue engineering camp
- Develop DNAzymes for other heavy metals
Back to Top
Week 8: July 11 - July 17
Wet Lab
Reporter
- Restart amilCP cloning process
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
Dry Lab
- First presentation at Camp BioE
- Prepare for UMD Mid-Atlantic Meet-Up
- Contact PLSG and NEB for sponsorship
Back to Top
Week 9: July 18 - July 22
Wet Lab
Reporter
- Continue amilCP cloning process
- Clone RBS-T3 RNA polymerase to add into other constructs
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
Dry Lab
- Presentation at Camp BioE
- UMD Mid-Atlantic Meet-Up
- Continue fundraising
- Discuss systems to model
Back to Top
