Team:KAIST Korea/Notebook Labnote/2012 8

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<section id="1">
<section id="1">
<div class="date">August 1<sup>st</sup> 2012</div></br>
<div class="date">August 1<sup>st</sup> 2012</div></br>
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<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
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<div class="note-title">PCR amplification of <i>Moth_1191</i>, <i>1199</i> gene : decreasing annealing temperature down to 45℃</div>
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<div id="content_note" >
 +
 +
<span id="little">To make sure there’s no problem with unspecific binding or annealing temperature, we decreased annealing condition down to 45℃.</span>
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</br></br>
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<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0801Fig1" src="https://static.igem.org/mediawiki/2012/e/e1/KAIST_08012012_Fig1.png"></img></div>
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<div style="clear:both;"></div>
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 +
</br>
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<span id="little">There was no band and it became certain that there are no problems with annealing procedure.</span>
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</br>
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</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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<div class="note-title">Induction of <i>Moth_0109</i> gene (sampling) and running SDS-PAGE gel. </div>
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<div id="content_note" >
 +
 +
<span id="little">We induced <i>Moth_0109</i> gene in pBAD/myc vector with different Arabinose conditions and temperature: 10mM, 30mM and 37℃, 30℃. And then, we run the sample into SDS-PAGE gel. The gel is stained with coomassie blue for 1 hour and de-stained for overnight.</span>
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</br></br>
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</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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<div class="note-title">PCR amplification of <i>Moth_1191</i>, <i>1199</i> gene with Gibson and TOPO primer</div>
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<div id="content_note" >
 +
 +
<span id="little">To see whether there are any problem with Gibson primers that we’ve designed, we did one more pcr amplification. Primers for Gibson assembly and TOPO cloning are mixed, and we could see any problems with forward or reverse primers. </span>
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</br></br>
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<b>Results</b></br></br>
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<div align="center"><img id="figure" alt="0801Fig2" src="https://static.igem.org/mediawiki/2012/6/62/KAIST_08012012_Fig2.png"></img></div>
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<div style="clear:both;"></div>
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</br>
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<span id="little">Each lane indicates:</br></br>
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<ul style="list-style-type:square">
 +
<li><i>Moth_1191_1</i> : TOPO forward primer and Gibson reverse primer</li>
 +
<li><i>Moth_1191_2</i> : Gibson forward primer and TOPO reverse primer</li>
 +
<li><i>Moth_1199_1</i> : Gibson forward primer and TOPO reverse primer</li>
 +
<li><i>Moth_1199_2</i> : TOPO forward primer and Gibson reverse primer</li>
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</ul>
 +
</br>
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Correct size of band appeared when topo forward primer and Gibson reverse primer was used in amplification of both genes. Therefore, we can conclude that there is some unknown problem with forward primers.</span>
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</br>
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</div>
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</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">pPoC and pPoCpi OE PCR with changed primers</div>
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<div id="content_note" >
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<b>Results</b></br></br>
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<div align="center"><img id="figure" alt="2_0801Fig1" src="https://static.igem.org/mediawiki/2012/8/81/KAIST_2nd_08012012_Fig1.png"></img></div>
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<div style="clear:both;"></div>
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</br>
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<span id="little">→ Gel extracted</span>
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</br>
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</div>
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<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
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</section>
</section>
<section id="2">
<section id="2">
<div class="date">August 2<sup>nd</sup> 2012</div></br>
<div class="date">August 2<sup>nd</sup> 2012</div></br>
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<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
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<div class="note-title">Primer design for FDH derived from <i>Candida boidinii</i> mutant</div>
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<div id="content_note" >
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<b>Results</b></br></br>
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<div align="center"><img id="figure" alt="0802Fig1" src="https://static.igem.org/mediawiki/2012/b/b8/KAIST_08022012_Fig1.png"></img></div>
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<div style="clear:both;"></div>
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</br>
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<b>Discussion</b></br></br>
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<span id="little">These primers are universial primer that can be used for insertion of this gene into both pTrcHis2A vector and pBAD/mycHisC vector. </span>
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</br>
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</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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<div class="note-title">Expression check of <i>Moth_0109</i> gene on pBAD/mycHisC vector (Result)</div>
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<div id="content_note" >
 +
 +
<span id="little">For each samples of different induction conditions, we run SDS-PAGE gel and checked the presence of 59.94 kDa protein, formate tetrahydrofolate ligase. </span>
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</br></br>
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<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0802Fig2" src="https://static.igem.org/mediawiki/2012/7/7c/KAIST_08022012_Fig2.png"></img></div>
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<div style="clear:both;"></div>
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 +
</br>
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<b>Discussion</b></br></br>
 +
 +
<span id="little">The band of PAGE gel was not certain, so we </span>
 +
<!--이것도 쓰다가 말았음;; -->
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</br>
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</div>
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</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
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<div class="note-title">pPoC and pPoCpi cloning - Digestion</div>
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<div id="content_note" >
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<span id="little">Restriction enzyme digestion</span>
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</br></br>
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<span>
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<ul style="padding:0px 0px 0px 40px;">
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<li>Enzyme pre-mix / each reaction – 37℃ 1hr, 80℃ 20min</li></br>
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<div align="center"><img id="figure" alt="2_0802Fig1" src="https://static.igem.org/mediawiki/2012/1/1e/KAIST_2nd_08022012_Fig1.png"></img></div>
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<div style="clear:both;"></div>
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</br>
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<li>Digestion mixture – 37℃ 1hr, 80℃ 20min</li></br>
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<div align="center"><img id="figure" alt="2_0802Fig2" src="https://static.igem.org/mediawiki/2012/7/79/KAIST_2nd_08022012_Fig2.png"></img></div>
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<div style="clear:both;"></div>
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 +
</br>
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</ul>
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</span>
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</br>
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</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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<div class="note-title">Bxb1 integrase transformation</div>
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<div id="content_note" >
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<span id="little">Synthesized gene arrived.</br></span>
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<span id="little">Transformed into DH5α </span>
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</br>
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</div>
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<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
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</section>
</section>
 +
<section id="3">
<section id="3">
<div class="date">August 3<sup>rd</sup> 2012</div></br>
<div class="date">August 3<sup>rd</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
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<div class="note-title">Bxb1 integrase-DH5α streaking</div>
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<div id="content_note" >
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<b>Discussions</b></br></br>
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<span id="little">Synthesized gene was cloned into pGEM-B1 vector. It seems the vector concentration is too high so that too much colonies may appeared.</span>
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</br>
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</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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<div class="note-title">pPoC and pPoCpi cloning - Ligation</div>
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<div id="content_note" >
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<span id="little">Ligation - 16℃ overnight</span>
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</br></br>
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<div align="center"><img id="figure" alt="2_0803Fig3" src="https://static.igem.org/mediawiki/2012/8/81/KAIST_2nd_08032012_Fig1.png"></img></div>
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<div style="clear:both;"></div>
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</br>
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<span id="little">Transformed into DH5α chemically competent cell.</span>
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</br>
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</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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<div class="note-title">BBa_J04450 transformation into DH5α</div>
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<div id="content_note" >
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<span id="little">For pSB1C3 vector amplification</span>
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</br>
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</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
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</section>
</section>
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<section id="4">
<section id="4">
<div class="date">August 4<sup>th</sup> 2012</div></br>
<div class="date">August 4<sup>th</sup> 2012</div></br>
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<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
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<div class="note-title"><i>1191</i> and <i>1199</i> forward primer design</div>
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<div id="content_note" >
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<span id="little">We designed new forward primers for both <i>1191</i> and <i>1199</i> gene that are thought to solve problems appeared during PCR amplification.</span>
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</br></br>
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<b>Results</b></br></br>
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<div align="center"><img id="figure" alt="0804Fig1" src="https://static.igem.org/mediawiki/2012/5/59/KAIST_08042012_Fig1.png"></img></div>
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<div style="clear:both;"></div>
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</br>
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</div>
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</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
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<div class="note-title">BBa_J04450 and Bxb1-pGEM colony picking and inoculation.</div>
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<div id="content_note" >
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<span id="little">Made master plates and inoculated in 3mL of LB.</span>
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</br>
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</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="5">
<section id="5">
<div class="date">August 5<sup>th</sup> 2012</div></br>
<div class="date">August 5<sup>th</sup> 2012</div></br>
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<div id="content_note" >
 +
<span id="little">No Special Event!</span>
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</br>
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</div>
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<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="6">
<section id="6">
<div class="date">August 6<sup>th</sup> 2012</div></br>
<div class="date">August 6<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
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<div class="note-title">BBa_J04450 Plasmid miniprep</div>
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 +
<div id="content_note" >
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<span id="little">BBa_J04450(pSB1C3): 285.8ng/uL</span></br>
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<span id="little">purity:2.10</span>
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</br>
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</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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<div class="note-title">Requested part arrived</div>
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 +
<div id="content_note" >
 +
 +
<span id="little">Each parts were streaked on appropriate plates.</br></br>
 +
<ul>
 +
<li>BBa_I11020</li>
 +
<li>BBa_I11022</li>
 +
<li>BBa_I11023</li>
 +
<li>BBa_I11030</li>
 +
<li>BBa_K137007</li>
 +
<li>BBa_K137008</li>
 +
<li>BBa_K137010</li>
 +
<li>BBa_K112001</li>
 +
<li>BBa_K112141</li>
 +
<li>BBa_K112142</li>
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</ul>
 +
</span>
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</br></br>
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</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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 +
<div class="note-title">BBa_K381001(GFP) and BBa_K398005(pSB1C3) transformation</div>
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 +
<div id="content_note" >
 +
 +
<span id="little">BBa_K381001(GFP): for GFP control</span></br>
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<span id='little'>BBa_K398005(pSB1C3): for pSB1C3 template</span></br>
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</br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="7">
<section id="7">
<div class="date">August 7<sup>th</sup> 2012</div></br>
<div class="date">August 7<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">FDH gene PCR amplification</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0807Fig1" src="https://static.igem.org/mediawiki/2012/7/7b/KAIST_08072012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">We amplified 2 samples of formate dehydrogenase gene with the primers we designed. From gel electrophoresis picture, we can say that oligonucleotides with the proper size 1100bp are present in the sample.</span>
 +
<div align="center"><img id="figure" alt="0807Fig2" src="https://static.igem.org/mediawiki/2012/e/eb/KAIST_08072012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">BBa_J04450(pSB1C3) enzyme cut check(single cut with EcoRI)</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0807Fig1" src="https://static.igem.org/mediawiki/2012/9/93/KAIST_2nd_08072012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">Vector was double digested. The insert and vector sizes were correct</span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">pPoC and pPoCpi OE PCR product nested PCR</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0807Fig2" src="https://static.igem.org/mediawiki/2012/9/91/KAIST_2nd_08072012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">→ Gel extracted</span>
 +
 +
</br>
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">BBa_K398005 Plasmid miniprep & single cut check with EcoRI</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0807Fig3" src="https://static.igem.org/mediawiki/2012/c/c9/KAIST_2nd_08072012_Fig3.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Overlapping PCR</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">pPoC insert</span>
 +
</br></br>
 +
<div align="center"><img id="figure" alt="2_0807Fig4" src="https://static.igem.org/mediawiki/2012/d/d5/KAIST_2nd_08072012_Fig4.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">
 +
<ul style="list-style-type:square; padding:0px 0px 0px 40px;">
 +
<li>HSTaq Pol MM : 25uL</li>
 +
<li>DW : 1uL</li>
 +
<li>templates : 22uL</li>
 +
<li>primers : 2uL</li>
 +
 +
</ul>
 +
</span></br></br>
 +
 +
<span id="little">pPoCpi insert</span>
 +
</br></br>
 +
<div align="center"><img id="figure" alt="2_0807Fig4" src="https://static.igem.org/mediawiki/2012/d/d5/KAIST_2nd_08072012_Fig4.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">
 +
<ul style="list-style-type:square; padding:0px 0px 0px 40px;">
 +
<li>HSTaq Pol MM : 25uL</li>
 +
<li>templates : 23.2uL</li>
 +
<li>primers : 2uL</li>
 +
</ul>
 +
</span>
 +
</br>
 +
</br>
 +
<b>Results</b></br></br>
 +
<div align="center"><img id="figure" alt="2_0807Fig5" src="https://static.igem.org/mediawiki/2012/e/ea/KAIST_2nd_08072012_Fig5.png"></img></div>
 +
<div style="clear:both;"></div>
 +
</br>
 +
<span id ="little">→ Concentration after gel extraction was not sufficient for cloning</span></br></br>
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Overlapping PCR template preparation</div>
 +
 +
<div id="content_note" >
 +
 +
<div align="center"><img id="figure" alt="2_0807Fig6" src="https://static.igem.org/mediawiki/2012/9/99/KAIST_2nd_08072012_Fig6.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<div align="center"><img id="figure" alt="2_0807Fig7" src="https://static.igem.org/mediawiki/2012/3/3a/KAIST_2nd_08072012_Fig7.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
 +
</section>
</section>
 +
 +
<section id="8">
<section id="8">
<div class="date">August 8<sup>th</sup> 2012</div></br>
<div class="date">August 8<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">FDH gene and pTrcHis2A, pBAD/mycHisC vector enzyme digestion</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Procedure</b></br></br>
 +
 +
<span id="little">We mixed restriction enzymes and buffers with DNA samples as shown below.</span></br></br>
 +
 +
<div align="center"><img id="figure" alt="0808Fig1" src="https://static.igem.org/mediawiki/2012/3/31/KAIST_08082012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<span id="little">After mixing the enzymes and buffer with the sample, we incubated the sample on 37℃ for 1 hour and then on 65℃ for 20minutes. </span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">pTrcHis2A, pBAD/myc vector dephosphorylation</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Procedure</b></br></br>
 +
<span id="little">We mixed phosphatidase and buffer with DNA sample as shown below.</span></br></br>
 +
<div align="center"><img id="figure" alt="0808Fig2" src="https://static.igem.org/mediawiki/2012/4/49/KAIST_08082012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">After mixing the enzyme and buffer with the sample, we incubated the sample on 37℃ for 1 hour 20minutes and then on 70℃ for 5minutes. </span>
 +
 +
</br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">ligation of FDH gene with pTrcHis2A and pBAD/mycHisC vectors</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Procedure</b></br></br>
 +
<span id="little">We mixed ligase and buffer with DNA sample as shown below.</span>
 +
</br></br>
 +
<div align="center"><img id="figure" alt="0808Fig3" src="https://static.igem.org/mediawiki/2012/4/4e/KAIST_08082012_Fig3.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">After mixing the enzyme and buffer with the sample, we incubated the sample on 16℃ for 16 hours.</span>
 +
 +
</br>
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Primer amplification of <i>1191</i> and <i>1199</i></div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0808Fig4" src="https://static.igem.org/mediawiki/2012/5/5d/KAIST_08082012_Fig4.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussion</b></br></br>
 +
 +
</br>
 +
</div>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">Overlapping PCR</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">pPoC insert</span></br></br>
 +
<div align="center"><img id="figure" alt="2_0808Fig2" src="https://static.igem.org/mediawiki/2012/9/9b/KAIST_2nd_08082012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">pPoCpi insert</span></br></br>
 +
<div align="center"><img id="figure" alt="2_0808Fig3" src="https://static.igem.org/mediawiki/2012/5/53/KAIST_2nd_08082012_Fig3.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<span>
 +
<ul style="list-style-type:square">
 +
 +
<li>HSTaq Pol MM : 25uL</li>
 +
<li>DW : 5.2uL</li>
 +
<li>templates : 19.8uL</li>
 +
<li>primers : 2uL</li>
 +
<li>pfu-x : 0.1uL</li>
 +
 +
</ul>
 +
</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0808Fig1" src="https://static.igem.org/mediawiki/2012/3/31/KAIST_2nd_08082012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">→ Gel extraction</span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Overlapping PCR template preparation</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0808Fig4" src="https://static.igem.org/mediawiki/2012/5/5d/KAIST_2nd_08082012_Fig4.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
 +
</section>
</section>
 +
<section id="9">
<section id="9">
<div class="date">August 9<sup>th</sup> 2012</div></br>
<div class="date">August 9<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">vector transformation into TOP10 cell</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Transformation of pTrcHis2A vector into TOP10 cell was successful. So we did vector mini-preparation after the transformation. However, transformation of pBAD vector has failed, so we ligated the samples again. </span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0809Fig1" src="https://static.igem.org/mediawiki/2012/e/e9/KAIST_08092012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">This is gel picture to confirm that FDH is well inserted into TOP10 cells. 3 wells on the left are PCR product of <!--??/--></span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">Bxb1 integrase cloning into pTrcHis2a and pBADmycHisC</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Bxb1 integrase: 1515bp</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0809Fig1" src="https://static.igem.org/mediawiki/2012/3/33/KAIST_2nd_08092012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">→ Gel extracted</span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Extracted OE PCR product cloning into pSB1C3</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">pSB1C3 was originated from BBa_K398005.</br></br>Transformed into TOP10</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<span id="little">Transformed colony was grown in LB media. No colony shows fluorescence. </span>
 +
 +
</br></br>
 +
<b>Discussions</b></br></br>
 +
 +
<span id="little">We think cloning failed.</span>
 +
 +
</br></br>
 +
 +
</div>
 +
 +
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="10">
<section id="10">
<div class="date">August 10<sup>th</sup> 2012</div></br>
<div class="date">August 10<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title"> Bxb1-pTrc, pBAD colony inoculation</div>
 +
 +
<div id="content_note" >
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Overlapping PCR</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">In this time, PCR was done first 18 cycles without any primer.</br>
 +
After that, we add 1uL of primers. And then PCR was done 20 cycles more.
 +
</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0810Fig1" src="https://static.igem.org/mediawiki/2012/7/79/KAIST_2nd_08102012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussions</b></br></br>
 +
<span id="little">With this OE PCR conditions, yield was better than previous conditions.</span>
 +
 +
</br>
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">pPoC, pPoCpi insert cloning into pSB1C3</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">pSB1C3 was derived from BBa_K398005
 +
</span>
 +
</br></br>
 +
 +
<span>
 +
<ol style="padding:0px 0px 0px 40px;">
 +
<li>Digestion – 37℃ 1hr, 80℃ 20min</li>
 +
<div align="center"><img id="figure" alt="2_0810Fig5" src="https://static.igem.org/mediawiki/2012/5/5d/KAIST_2nd_08102012_Fig5.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<li>Dephosphorylation – 37℃ 30min, 80℃ 10min</li>
 +
<div align="center"><img id="figure" alt="2_0810Fig6" src="https://static.igem.org/mediawiki/2012/8/87/KAIST_2nd_08102012_Fig6.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<li>Ligation – 37℃ 2hr</li>
 +
<div align="center"><img id="figure" alt="2_0810Fig7" src="https://static.igem.org/mediawiki/2012/f/fb/KAIST_2nd_08102012_Fig7.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
</ol>
 +
</span>
 +
</br></br>
 +
<span id="little">Ligated products were transformed into DH5α.</span>
 +
 +
 +
</br>
 +
</div>
 +
</br>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Transformed cell inoculation and colony PCR</div>
 +
 +
<div id="content_note" >
 +
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0810Fig8" src="https://static.igem.org/mediawiki/2012/3/3c/KAIST_2nd_08102012_Fig8.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussions</b></br></br>
 +
<span id="little">only pPoCpi construct cloning was completed </span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
 +
</section>
</section>
<section id="11">
<section id="11">
<div class="date">August 11<sup>th</sup> 2012</div></br>
<div class="date">August 11<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">pTrcHis2A vector transformation into <i>E.coli</i> MG1655 cell</div>
 +
 +
<div id="content_note" >
 +
<b>Procedure</b></br></br>
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">pBAD/mycHisC-FDH transformation into TOP10</div>
 +
 +
<div id="content_note" >
 +
 +
</br>
 +
</div>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">Bxb1 pTrcHis2A, pBADmycHisC plasmid DNA mini-prep</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
<span id="little">single cut check</span></br></br>
 +
<div align="center"><img id="figure" alt="2_0811Fig1" src="https://static.igem.org/mediawiki/2012/d/db/KAIST_2nd_08112012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
 +
 +
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">pPoC and pPoCpi nested PCR</div>
 +
 +
<div id="content_note" >
 +
 +
 +
<b>Results</b></br></br>
 +
<span id="little">nested PCR to prepare more insert DNA</span></br></br>
 +
<div align="center"><img id="figure" alt="2_0811Fig2" src="https://static.igem.org/mediawiki/2012/1/11/KAIST_2nd_08112012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
 +
 +
</br>
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
 +
 +
<section id="12">
<section id="12">
<div class="date">August 12<sup>th</sup> 2012</div></br>
<div class="date">August 12<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">colony PCR check of pTrcHis2A inserted FDH gene</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0812Fig1" src="https://static.igem.org/mediawiki/2012/8/80/KAIST_08122012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">We checked the presence of FDH gene by conducting colony PCR. Correct size of band appeared at about 1115bp, which means formate dehydrogenase is inserted correctly. </span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">pBAD FDH MG1655 electroporation</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
 +
<span id="little">Fail</span>
 +
<!--여기 쓸말 더 있으면 써줘요 지환오빠 ㅋㅋ-->
 +
</br>
 +
</div>
 +
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="13">
<section id="13">
<div class="date">August 13<sup>th</sup> 2012</div></br>
<div class="date">August 13<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">FDH pBAD MG1655 electroporation</div>
 +
 +
<div id="content_note" >
 +
<b>Procedure</b></br></br>
 +
 +
<span id="little">We seeded cells on 7:10 AM and did cell-down on 10:00AM. And then we plated cells on 1:00PM and checked colony on 8/14 5:00AM</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
<!--
 +
<div align="center"><img id="figure" alt="08##Fig#" src="#"></img></div>
 +
<div style="clear:both;"></div>    Colony pic.-->
 +
</br>
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">FDH pTrc MG1655 expression check (sampling and induction)</div>
 +
 +
<div id="content_note" >
 +
<b>Procedure</b></br></br>
 +
 +
<span id="little">We seeded cells (500λ of cells put into 50mL LB with 50λ Ampicillin) on 7 : 30 AM and checked Optical Density on 10:30pm. According to the O.D. value, we induced 37℃ sample on 10:30PM and did sampling on 4:30pm. Also, we induced 30℃ sample on 11:30pm and did sampling on 5:30pm. (6 hour induction) Each temperature samples were induced by different conditions ; 2mM and 3mM of IPTG.</span>
 +
</br></br>
 +
</div>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">pPoCpi cloning into pSB1C3</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Cloning was done by remaining DNA samples. </span>
 +
</br></br>
 +
 +
</div>
 +
 +
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="14">
<section id="14">
<div class="date">August 14<sup>th</sup> 2012</div></br>
<div class="date">August 14<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">colony PCR check of pBADmycHisC inserted FDH gene</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0814Fig1" src="https://static.igem.org/mediawiki/2012/e/e2/KAIST_08142012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<b>Discussion</b></br></br>
 +
 +
<span id="little">We checked the presence of FDH gene by conducting colony PCR. Correct size of band appeared at about 1115 bp, which means formate dehydrogenase is inserted correctly. </span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Expression check of Formate dehydrogenase on pTrcHis2A vector (Result)</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0814Fig2" src="https://static.igem.org/mediawiki/2012/6/64/KAIST_08142012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">For each samples of different induction conditions, we run SDS-PAGE gel and checked the presence of 43.7 kDa protein, formate dehydrogenase. The band appeared significantly on the correct size. </span>
 +
 +
</br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
<div class="note-title">FDH pBAD MG1655 seeding for expression check</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Procedure</b></br></br>
 +
 +
<span id="little">We seeded cell on 7:00PM, so we’ll incubate cell about 16hours. (This means we have to do next seeding on 11:00AM. )</span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Primer design for the insertion of <i>1202</i> and <i>0109</i></div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0814Fig3" src="https://static.igem.org/mediawiki/2012/b/bd/KAIST_08142012_Fig3.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">To eliminate uncertain spacer between genes, we inserted </span>
 +
<!--쓰다가 말았네;;-->
 +
</br>
 +
</div>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">Bxb1 pTrcHis2A and pPoCpi ligated products transformation</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">The products were transformed into TOP10</span>
 +
</br></br>
 +
 +
</div>
 +
 +
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
 +
</section>
</section>
<section id="15">
<section id="15">
<div class="date">August 15<sup>th</sup> 2012</div></br>
<div class="date">August 15<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">FDH pBAD MG1655 expression check</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Procedure</b></br></br>
 +
 +
<span id="little">We seeded cells on 11 : 30 AM and checked Optical Density on 1:30pm. According to the O.D. value, we induced 37℃ sample on 1:40pm and did sampling on 7:40pm. Also, we induced 30℃ sample on 3:30pm and did sampling on 9:30pm. (6 hour induction) Each temperature samples were induced by different conditions: 10mM of arabinose and 30mM of arabinose.</span>
 +
 +
</br>
 +
 +
</div>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">pPoCpi colony PCR</div>
 +
 +
<div id="content_note" >
 +
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_08##Fig#" src="https://static.igem.org/mediawiki/2012/c/cd/KAIST_2nd_08152012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">Among colonies #1~10, four colonies were inoculated.
 +
#1, 3, 4, 7
 +
</span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Bxb1 pTrcHis2A colony PCR</div>
 +
 +
<div id="content_note" >
 +
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0815Fig2" src="https://static.igem.org/mediawiki/2012/9/9d/KAIST_2nd_08152012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">Among colonies #1~20, three colonies were inoculated.
 +
#2, 5, 19
 +
</span>
 +
 +
</br>
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
 +
<section id="16">
<section id="16">
<div class="date">August 16<sup>th</sup> 2012</div></br>
<div class="date">August 16<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">PCR amplification of <i>1201</i>, <i>1202</i>, <i>1203</i>, <i>1198</i> and <i>1191</i></div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0816Fig1" src="https://static.igem.org/mediawiki/2012/8/86/KAIST_08152012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<b>Discussion</b></br></br>
 +
 +
<span id="little">Primers arrived, and we began to do additional PCR amplification on the preparation for Gibson assembly. Each PCR sample has the correct size of oligonucleotides except <i>Moth 1202</i> gene.</br></br>
 +
<ul>
 +
<li><i>1191</i> : 921bp</br></li>
 +
<li><i>1198</i> : 972bp + about 400bp = 1300 bp </br></li>
 +
<li><i>1201</i> : 1341bp + ?</br></li>
 +
<li><i>1202</i> : 2190bp + </br></li>
 +
<li><i>1203</i> : 2025bp + 1600bp = 3625bp</br></li>
 +
</ul>
 +
</br>
 +
We did PCR purification on the PCR product and the concentration/purity result was as shown below.
 +
</span>
 +
</br></br>
 +
 +
<div align="center"><img id="figure" alt="0816Fig2" src="https://static.igem.org/mediawiki/2012/3/30/KAIST_08162012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Pre-culture of <i>0109</i></div>
 +
 +
<div id="content_note" >
 +
 +
<b>Discussion</b></br></br>
 +
 +
<span id="little">There was no vector prepared for Moth 0109, so we did 5ml pre-culture on 10ml tube. Cell was grown about 16hours after pre-culture, and we did vector mini-prep on the sample. The concentration of the mini-prepped vector is 726.8ng/ul and the purity(A<sub>260</sub>/A<sub>280</sub>) was 1.86.</span>
 +
</br>
 +
</div>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">pPoC and pPoCpi electro-transformation into MG1655</div>
 +
 +
<div id="content_note" >
 +
 +
<span>Strain: MG1655</br></br>
 +
Plasmid source:</br></br>
 +
<ul style="list-style-type:square">
 +
<li>pPoC: from DH5α-pPoC colony #1 and TOP10-pPoC colony #1</li>
 +
<li>pPoCpi: from TOP10-pPoC colony #1 and #3</li>
 +
</ul>
 +
</br></br>
 +
</span>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
 +
</section>
</section>
<section id="17">
<section id="17">
<div class="date">August 17<sup>th</sup> 2012</div></br>
<div class="date">August 17<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">Expression check of Formate dehydrogenase.</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0817Fig1" src="https://static.igem.org/mediawiki/2012/3/34/KAIST_08172012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">For each samples of different induction conditions, we run SDS-PAGE gel and checked the presence of 40.xx kDa protein, formate dehydrogenase. The band appeared more significantly than the case of pTrcHis2A vector. Therefore, using pBAD promoter seems to produce more proteins.</span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">PCR amplification – second trial</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0817Fig2" src="https://static.igem.org/mediawiki/2012/5/5b/KAIST_08172012_Fig2.png" /></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">As the band was not significant for <i>1203</i> and <i>1198</i> on previous trial and purity was low for <i>1191</i>, we tried secondary PCR amplification on samples for Gibson assembly; <i>1202</i>, <i>1203</i>, <i>1198</i>, <i>1191</i>. Particularly for <i>1202</i> gene, we tried additional colony PCR, so that we could check any problem with vector mini-prep. (PCR solution for <i>1202</i> colony PCR was : 22ul </span>
 +
 +
</br></br>
 +
<div align="center"><img id="figure" alt="0817Fig3" src="https://static.igem.org/mediawiki/2012/e/e7/KAIST_08172012_Fig3.png" /></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
</div>
 +
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">MG1655-pPoC, MG1655-pPoCpi streaking</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">We could not distinguish single colony from plates. Therefore we scraped cells and streaked onto new plates.</span>
 +
</br></br>
 +
<b>Discussions</b></br></br>
 +
 +
<span id="little">Wild-type <i>E.coli</i> showed more reddish and yellowish color than competent strains, DH5α and TOP10. The promoter BBa_J23119 may show different strength in-between strains.</span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">TOP10-pTrcHis2A_Bxb1 expression check </div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">TOP10 containing pTrcHis2A was cultured in 30mL of LB with 1% of Ampicillin.</br></span>
 +
<span id="little">IPTG induced when OD = 0.4</br></span>
 +
<span id="little">Sampling: 8 hours after induction, 1010 cells.</br></span>
 +
<span id="little">Only soluble fractions were PAGEed.</br></span>
 +
</br>
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
</section>
</section>
<section id="18">
<section id="18">
<div class="date">August 18<sup>th</sup> 2012</div></br>
<div class="date">August 18<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:262px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title">PCR amplification of <i>1202</i>, <i>0109</i> gene with original primer and Gibson primers</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/b/b0/KAIST_08182012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">Each lane indicates:</br></br>
 +
<ul>
 +
<li><i>Moth_1202_1</i> : Gibson forward + original reverse</li>
 +
<li><i>Moth_1202_2</i> : Gibson reverse + original forward</li>
 +
<li><i>Moth_0109_1</i> : Gibson forward + original reverse</li>
 +
<li><i>Moth_0109_2</i> : Gibson reverse + original forward</li>
 +
</ul>
 +
</br>
 +
There was correct size and unspecific size of band on <i>1202_1</i> sample. Although there are also unspecific band, <i>1202_2</i> sample has large band of correct size. <i>0109_1</i> sample has only unspecific band and <i>0109_2</i> sample has right size of band.
 +
</span>
 +
 +
</br></br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">When the PCR was unsuccessful, we first thought it might be problem of forward primer as in the case of <i>1199</i> and <i>1191</i>. Our guess was correct, and we’re going to fix the problem with forward primers. </span>
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title"><i>1202</i> and <i>0109</i> forward primer design</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">We designed new forward primer hoping no problem with it. </span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/6/64/120818_1202_0109_primer_design.PNG"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">Newly designed primers contain overlapping region with former DNA fragments, artificial ribosome binding site, and overlapping region with 1202 and 0109 each. </br></br>
 +
</span>
 +
 +
</div>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">MG1655-pPoC, MG1655-pPoCpi colony inoculation</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Two colonies from each plate were inoculated into 3mL of LB containing 1% of chloramphenicol.</span>
 +
</br></br>
 +
<b>Discussions</b></br></br>
 +
 +
 +
<span id="little">In 12 hours, cell cultures show colors compared to another common <i>E.coli</i> culture. When they are centrifuged, pellet shows clear and definite yellow or red color.</span>
 +
 +
</br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">pTrcHis2A_Bxb1 electro-transformation into MG1655-pPoC, MG1655-pPoCpi</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">pTrcHis2A_Bxb1 is electro-transformed into MG1655 containing pPoC and pPoCpi.</br></br>
 +
  Plasmid source: TOP10-pTrcHis2A_Bxb1</span>
 +
</br></br>
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
 +
</section>
</section>
<section id="19">
<section id="19">
<div class="date">August 19<sup>th</sup> 2012</div></br>
<div class="date">August 19<sup>th</sup> 2012</div></br>
 +
<div id="content_note" >
 +
<span id="little">No Special Event!</span>
 +
</br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="20">
<section id="20">
<div class="date">August 20<sup>th</sup> 2012</div></br>
<div class="date">August 20<sup>th</sup> 2012</div></br>
 +
<div id="content_note" >
 +
<span id="little">No Special Event!</span>
 +
</br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="21">
<section id="21">
<div class="date">August 21<sup>st</sup> 2012</div></br>
<div class="date">August 21<sup>st</sup> 2012</div></br>
 +
<div id="content_note" >
 +
<span id="little">No Special Event!</span>
 +
</br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="22">
<section id="22">
<div class="date">August 22<sup>nd</sup> 2012</div></br>
<div class="date">August 22<sup>nd</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">Primer design for Bxb1 integrase cloning</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Primers for Bxb1 integrase cloning were designed. For controlling basal transcription level optimization, a mutant primer which has GTG rather than ATG for its start codon was also ordered.</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0822Fig1" src="https://static.igem.org/mediawiki/2012/9/92/KAIST_2nd_08222012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
</section>
</section>
<section id="23">
<section id="23">
<div class="date">August 23<sup>rd</sup> 2012</div></br>
<div class="date">August 23<sup>rd</sup> 2012</div></br>
 +
<div id="content_note" >
 +
<span id="little">No Special Event!</span>
 +
</br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="24">
<section id="24">
<div class="date">August 24<sup>th</sup> 2012</div></br>
<div class="date">August 24<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title"> <i>0109</i>, <i>1191</i> PCR with new primers</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/1/10/120824_0109_1191_pcr_gel_picture.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">PCR product of Moth 0109 gene and 1191 gene has run on the gel. There was only faint band of 0109 fragment but the product band of 1191 gene was significantly shown on the gel. After gel electrophoresis, we tried PCR of 0109 once more and got significant amount of fragments.  </span>
 +
 +
</div>
 +
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="25">
<section id="25">
<div class="date">August 25<sup>th</sup> 2012</div></br>
<div class="date">August 25<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">pPoC-Bxb1 double transformants inoculation for prep & PCR check</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Double transformants 1 through 24 were inoculated into 3ml of LB containing 1% of Cm and Ap. For our convenience, three colonies were inoculated in one culture tube.</span>
 +
</br></br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
</section>
</section>
 +
<section id="26">
<section id="26">
<div class="date">August 26<sup>th</sup> 2012</div></br>
<div class="date">August 26<sup>th</sup> 2012</div></br>
 +
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">pPoC-Bxb1 double transformants plasmid DNA miniprep & PCR check</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Inoculated cultures were mipi-preped. And Bxb1-pTrc plasmid was checked by PCR. In case of pPoC, it would be check by color.</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
<span id="little">Vector</span></br></br>
 +
<div align="center"><img id="figure" alt="2_0826Fig1" src="https://static.igem.org/mediawiki/2012/3/38/KAIST_2nd_08252012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
<span id="little">Confirm PCR</span></br></br>
 +
<div align="center"><img id="figure" alt="2_0826Fig2" src="https://static.igem.org/mediawiki/2012/b/b9/KAIST_2nd_08252012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussions</b></br></br>
 +
<span id="little">In confirm PCR, all the colonies seem to have Bxb1 vector. Colony #1, 4, 7, 10, 13, 14, 16, 19 and 22 will be inoculated.</span></br>
 +
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Bxb1 PCR with new primers</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">For cloning of Bxb1 into pBAD and mutating its start codon from ATG to GTG, we PCR pGEM-B1-Bxb1 vector as template. Samples were duplicated</br></br></span>
 +
<span>
 +
PCR conditions
 +
<ol>
 +
<li>95℃ for 3min</li>
 +
<li>95℃ for 30sec</li>
 +
<li>55℃ for 30sec</li>
 +
<li>72℃ for 1min 30sec</li>
 +
Step 2 to 4: 34 cycles
 +
<li>72℃ for 10min</li>
 +
<li>12℃ forever</li>
 +
</ol>
 +
</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0826Fig3" src="https://static.igem.org/mediawiki/2012/6/61/KAIST_2nd_08262012_Fig3.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little">Duplicated samples were purified in one DNA binding column.</br></br>ATG: 297.9ng/uL (purity: 1.90)</br>GTG: purify failed. Sample lost</br></span>
 +
 +
</br>
 +
<b>Discussions</b></br></br>
 +
<span id="little">There were multiple bands in our PCR products. We will PCR again Bxb1-GTG with different conditions. Template vector may show larger bands.</span>
 +
</br>
 +
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">pGEM-Bxb1 template vector gel electrophoresis</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">To check whether the undesired bands were template vector, we diluted template vector with same conditions of PCR, 50X, and electrophoresized.</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0826Fig4" src="https://static.igem.org/mediawiki/2012/e/ea/KAIST_2nd_08262012_Fig4.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussion</b></br></br>
 +
 +
<span id="little">The band was different from undesired bands from Bxb1 ATG, GTG PCR products.</span>
 +
 +
</br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Insert DNA (Bxb1 integrase) and vector (pTrc and pBAD) cloning</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little"></span>
 +
</div>
 +
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
</section>
</section>
 +
<section id="27">
<section id="27">
<div class="date">August 27<sup>th</sup> 2012</div></br>
<div class="date">August 27<sup>th</sup> 2012</div></br>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">Bxb1-pTrc and Bxb1-pBAD electrotransformation into MG1655</div>
 +
 +
<div id="content_note" >
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Bxb1 PCR with changed conditions</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">For cloning of Bxb1 into pBAD and mutating its start codon from ATG to GTG, we PCR pGEM-B1-Bxb1 vector as template. Samples were duplicated</span>
 +
</br></br>
 +
<div align="center">
 +
<table style="border:0px;background-color:transparent;">
 +
<tr>
 +
<td style="padding:5px 20px 5px 20px;"><b>PCR conditions #1</b></td> <td style="padding:5px 20px 5px 20px;"><b>PCR conditions #2</b></td>
 +
</tr>
 +
<tr>
 +
<td style="padding:5px 20px 5px 20px;">1) 95℃ for 3min</td> <td style="padding:5px 20px 5px 20px;">1) 95℃ for 3min</td>
 +
</tr>
 +
<tr>
 +
<td style="padding:5px 20px 5px 20px;">2) 95℃ for 30sec</td> <td style="padding:5px 20px 5px 20px;">2) 95℃ for 30sec</td>
 +
</tr>
 +
<tr>
 +
<td style="padding:5px 20px 5px 20px;">3) 56.5℃ for 30sec</td> <td style="padding:5px 20px 5px 20px;">3) 58℃ for 30sec</td>
 +
</tr>
 +
<tr>
 +
<td style="padding:5px 20px 5px 20px;">4) 72℃ for 1min 30sec</br>　　(Step 2 to 4: 34 cycles)</td> <td style="padding:5px 20px 5px 20px;">4) 72℃ for 1min 30sec</br>　　(Step 2 to 4: 34 cycles)</td>
 +
</tr>
 +
<tr>
 +
<td style="padding:5px 20px 5px 20px;">5) 72℃ for 10min</td> <td style="padding:5px 20px 5px 20px;">5) 72℃ for 10min</td>
 +
</tr>
 +
<tr>
 +
<td style="padding:5px 20px 5px 20px;">6) 12℃ forever </td> <td style="padding:5px 20px 5px 20px;">6) 12℃ forever</td>
 +
</tr>
 +
 +
</table>
 +
 +
</div>
 +
</br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0827Fig1" src="https://static.igem.org/mediawiki/2012/a/a5/KAIST_2nd_08272012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussions</b></br></br>
 +
 +
<span id="little">Still, undesired bands appeared. We do not know where they come from. We decide to extract desired DNA with gel extraction.</span>
 +
 +
</br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Bxb1, with GTG as start codon, PCR product gel extraction</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">PCR products were gel extracted.</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
<ul style="list-style-type:square">
 +
<li>Bxb1 GTG cond. #1 - #1: 128.2ng/uL (purity: 1.89)</li>
 +
<li>Bxb1 GTG cond. #1 - #2: 79.0ng/uL (purity: 1.89)</li>
 +
<li>Bxb1 GTG cond. #2 - #1: 110.7ng/uL (purity: 1.89)</li>
 +
<li>Bxb1 GTG cond. #2 - #2: 66.7ng/uL (purity: 1.94)</li>
 +
</ul>
 +
 +
</br></br>
 +
<b>Discussions</b></br></br>
 +
<span id="little"> Bxb1 GTG cond. #1 - #1 and Bxb1 GTG cond. #2 - #1 will be used to cloning.</span></br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Insert DNA (Bxb1 GTG) and vector (pTrc and pBAD) cloning</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Insert DNA: Bxb1 integrase mutated by primer.</span></br>
 +
<span id="little">Vectro DNA: pTrcHis2A, pBAD-mycHisC</span></br></br>
 +
<span id="little">Prepared DNA concentration:</span></br></br>
 +
<span>
 +
<ul style='list-style-type:square'>
 +
<li>Bxb1 GTG cond. #1 - #1: 128.2ng/uL (purity: 1.89)</li>
 +
<li>Bxb1 GTG cond. #2 - #1: 110.7ng/uL (purity: 1.89)</li>
 +
<li>pTrcHis2A: 116.1ng/uL</li>
 +
<li>pBAD-mycHisC: 128.7ng/uL</li>
 +
</ul>
 +
</span>
 +
</br></br>
 +
<span id="little">Enzyme digestion: 37℃ for 1hr 30min, 80℃ for 20min</span></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0827Fig2" src="https://static.igem.org/mediawiki/2012/c/c7/KAIST_2nd_08272012_Fig2.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
 +
<span id="little">Dephosphorylation: 37℃ for 30min, 70℃ for 5min</span></br></br>
 +
<div align="center"><img id="figure" alt="2_0827Fig3" src="https://static.igem.org/mediawiki/2012/6/67/KAIST_2nd_08272012_Fig3.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<span id="little">Ligation: 16℃ overnight</span></br></br>
 +
<div align="center"><img id="figure" alt="2_0827Fig4" src="https://static.igem.org/mediawiki/2012/8/8b/KAIST_2nd_08272012_Fig4.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Bxb1, pPoC double transformants colony PCR</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">Colony #1, 4, 7, 10, 13, 14, 16, 19 and 22 from master plate</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0827Fig5" src="https://static.igem.org/mediawiki/2012/4/45/KAIST_2nd_08272012_Fig5.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussions</b></br></br>
 +
 +
<span id="little">The gel showed that all the colonies have Bxb1-pTrc vector. And also they all have pPoC or pPoCpi, because they show color.</span>
 +
 +
</br>
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
 +
</section>
</section>
<section id="28">
<section id="28">
<div class="date">August 28<sup>th</sup> 2012</div></br>
<div class="date">August 28<sup>th</sup> 2012</div></br>
 +
<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">Bxb1-GTG-pTrc and Bxb1-GTG-pBAD electrotransformation into MG1655</div>
 +
 +
<div id="content_note" >
 +
 +
</div>
 +
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Bxb1-pTrc and Bxb1-pBAD transformants check</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<span>Bxb1-pTrc: No colony</br>
 +
Bxb1-pBAD: Colonies appeared and incoculated into 3mL of LB containing 1% of Ap</br>
 +
</span>
 +
 +
</br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Bxb1-pTrc and Bxb1-pBAD transformants colony PCR</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
<div align="center"><img id="figure" alt="2_0828Fig1" src="https://static.igem.org/mediawiki/2012/1/15/KAIST_2nd_08282012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
 +
</br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">Bxb1-pTrc and Bxb1-pBAD transformants plasmid DNA miniprep</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
<span>Colony #2: 109.8ng/uL, purity = 1.87</br>
 +
Colony #3: 138.9ng/uL, purity = 1.74</br>
 +
</span>
 +
</br></br>
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
 +
<div class="note-title">mRFP, GFP 30mL culture and sampling</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
 +
<section id="29">
<section id="29">
<div class="date">August 29<sup>th</sup> 2012</div></br>
<div class="date">August 29<sup>th</sup> 2012</div></br>
 +
</br><div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
 +
<div class="note-title">Bxb1 pBADmycHisC prepped plasmid DNA RE cut check</div>
 +
 +
<div id="content_note" >
 +
 +
<span id="little">mini-prepped plasmid DNAs were cut with SnaBI</br></br>
 +
expected size : 5.6kb
 +
</span>
 +
</br></br>
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="2_0829ig1" src="https://static.igem.org/mediawiki/2012/4/45/KAIST_2nd_08292012_Fig1.png"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br>
 +
 +
<span id="little"></span>
 +
 +
</br>
 +
<img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
 +
<div class="note-title"> <i>1202</i> PCR to make fragments for Gibson assembly</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/7/7c/120829.PNG"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">PCR for Moth 1202 gene has failed. No band for Moth 1202 gene has appeared on the gel.</span>
 +
 +
</div>
 +
</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
 +
<div class="note-title"> Gibson assembly – assembly of pcr fragments.</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
<span id="little">Among three methods to assemble DNA fragments, we chose first method, which is assembly of PCR amplified DNA fragments. </br>
 +
0.2umoles of each fragments are added into the reaction sample, and volume to be added for each fragments has calculated on the assumption that average MW of each base is 660Da. Table below is the result of calculation.</br>
 +
Fragment 1</br>
 +
</span>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/d/d8/120829_table.PNG"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
<span id="little">Fragment 2</br>
 +
</span>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/3/34/120829_table2.PNG"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/9/98/120829-2.PNG"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">As we can only assemble the fragments through Gibson Assembly method and not amplify them, there would be very small amount of template remaining in the tube. We thought that’s why we couldn’t see any band on the gel. So we did PCR purification of the fragment once more and saw if the band appears on the gel. </span>
 +
 +
</div>
 +
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
 +
</section>
</section>
<section id="30">
<section id="30">
<div class="date">August 30<sup>th</sup> 2012</div></br>
<div class="date">August 30<sup>th</sup> 2012</div></br>
 +
<img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:35px;float:bottom;"id="packman" src='https://static.igem.org/mediawiki/2012/0/03/KAIST_PACKMAN.png'/>　PACKMAN<img style="height:3px;width:262px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></br>
 +
<div class="note-title"> Gibson Assembly product – Amplification by nested PCR</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/6/67/120830.PNG"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">There was no right size of the band but just unspecific bands on the gel.
 +
There might be several reasons why the Gibson assembly ended with failure. So we decided to change the method of Gibson assembly; we will assemble fragments in the presence of vectors, so that assembly product can become stable, circular form. To cut the cost used in experiment, we will not design primers, but digest the vector with restriction enzymes to make it linear form.</span>
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 +
</div>
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</br><div align="center"><img style="width:670px; height:2px;" src="https://static.igem.org/mediawiki/2012/7/7f/Horizontal_line_kaist.png"></img></div></br>
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<div class="note-title"> Gibson primer second design 2</div>
 +
 +
<div id="content_note" >
 +
 +
<b>Results</b></br></br>
 +
 +
<div align="center"><img id="figure" alt="0818Fig1" src="https://static.igem.org/mediawiki/2012/b/b7/120830table.PNG"></img></div>
 +
<div style="clear:both;"></div>
 +
 +
</br></br>
 +
<b>Discussion</b></br></br>
 +
<span id="little">We designed primers again for another trial of Gibson Assembly. As stated before, We’ll use vector-involved assembly method to stabilize the assembly product and amplify them by in vivo system. </br>Like the method we used before, we’ll assemble 5 fragments first and assemble those 5-fragment-long two fragments into full construct. </br></span>
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</div>
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<div id="linegray" align="center" style="font-size:15px; font-weight:bold; color:#888;"><img style="height:3px;width:269px;margin:0px 5px 0px 0px; "src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/><img style="width:40px; height:28px;float:bottom;"id="flipflop" src='https://static.igem.org/mediawiki/2012/2/22/KAIST_FlipFlop.png'/>　Flip Flop<img style="height:3px;width:269px; margin:0px 0px 0px 5px;"src="https://static.igem.org/mediawiki/2012/1/1b/KAIST_horizontal_gray.png"/></div></br>
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<div class="note-title">Double transformants expression SDS-PAGE</div>
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<div id="content_note" >
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<span id="little">Gel composition: 20%</span>
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</br></br>
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<b>Results</b></br></br>
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<span>pPoC</span><br><br>
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<div align="center"><img id="figure" alt="2_0830Fig1" src="https://static.igem.org/mediawiki/2012/b/b6/KAIST_2nd_08302012_Fig1.png"></img></div>
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<div style="clear:both;"></div>
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</br>
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<span>pPoCpo</span><br><br>
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<div align="center"><img id="figure" alt="2_0830Fig2" src="https://static.igem.org/mediawiki/2012/a/a7/KAIST_2nd_08302012_Fig2.png"></img></div>
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<div style="clear:both;"></div>
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</br>
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<b>Results</b></br></br>
 +
<span id="little">We cannot see expression level change of fluorescent protein in SDS-PAGE.</span>
 +
</br>
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 +
</div>
 +
<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
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</section>
</section>
<section id="31">
<section id="31">
<div class="date">August 31<sup>st</sup> 2012</div></br>
<div class="date">August 31<sup>st</sup> 2012</div></br>
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<div id="content_note" >
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<span id="little">No Special Event!</span>
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</br>
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</div>
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<a id="back_to_the_calender" style="font-size:12px;color:#111;text-decoration:none;float:right;margin:20px 0px 0px 5px;" href="https://2012.igem.org/wiki/index.php?title=Team:KAIST_Korea/Notebook_Labnote"><img src="https://static.igem.org/mediawiki/2012/e/e3/KAIST_calendar_icon.png" style="width:60px;height:60px;display:none;"/>Back to the Calendar</a>
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</section>
</br></br>
</br></br>
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Latest revision as of 02:20, 27 October 2012

KAIST Korea 2012 iGEM

Notebook : Labnote-August

Labnote

August

August 1st 2012

　PACKMAN

PCR amplification of Moth_1191, 1199 gene : decreasing annealing temperature down to 45℃
To make sure there’s no problem with unspecific binding or annealing temperature, we decreased annealing condition down to 45℃.

Results

0801Fig1

There was no band and it became certain that there are no problems with annealing procedure.


Induction of Moth_0109 gene (sampling) and running SDS-PAGE gel.
We induced Moth_0109 gene in pBAD/myc vector with different Arabinose conditions and temperature: 10mM, 30mM and 37℃, 30℃. And then, we run the sample into SDS-PAGE gel. The gel is stained with coomassie blue for 1 hour and de-stained for overnight.



PCR amplification of Moth_1191, 1199 gene with Gibson and TOPO primer
To see whether there are any problem with Gibson primers that we’ve designed, we did one more pcr amplification. Primers for Gibson assembly and TOPO cloning are mixed, and we could see any problems with forward or reverse primers.

Results

0801Fig2

Each lane indicates:

  • Moth_1191_1 : TOPO forward primer and Gibson reverse primer
  • Moth_1191_2 : Gibson forward primer and TOPO reverse primer
  • Moth_1199_1 : Gibson forward primer and TOPO reverse primer
  • Moth_1199_2 : TOPO forward primer and Gibson reverse primer

Correct size of band appeared when topo forward primer and Gibson reverse primer was used in amplification of both genes. Therefore, we can conclude that there is some unknown problem with forward primers.

　Flip Flop

pPoC and pPoCpi OE PCR with changed primers
Results

2_0801Fig1

→ Gel extracted
Back to the Calendar
August 2nd 2012

　PACKMAN

Primer design for FDH derived from Candida boidinii mutant
Results

0802Fig1

Discussion

These primers are universial primer that can be used for insertion of this gene into both pTrcHis2A vector and pBAD/mycHisC vector.


Expression check of Moth_0109 gene on pBAD/mycHisC vector (Result)
For each samples of different induction conditions, we run SDS-PAGE gel and checked the presence of 59.94 kDa protein, formate tetrahydrofolate ligase.

Results

0802Fig2

Discussion

The band of PAGE gel was not certain, so we

　Flip Flop

pPoC and pPoCpi cloning - Digestion
Restriction enzyme digestion

  • Enzyme pre-mix / each reaction – 37℃ 1hr, 80℃ 20min

    • 2_0802Fig1

  • Digestion mixture – 37℃ 1hr, 80℃ 20min

    • 2_0802Fig2


Bxb1 integrase transformation
Synthesized gene arrived.
 Transformed into DH5α 
Back to the Calendar
August 3rd 2012

　Flip Flop

Bxb1 integrase-DH5α streaking
Discussions

Synthesized gene was cloned into pGEM-B1 vector. It seems the vector concentration is too high so that too much colonies may appeared.


pPoC and pPoCpi cloning - Ligation
Ligation - 16℃ overnight

2_0803Fig3

Transformed into DH5α chemically competent cell.


BBa_J04450 transformation into DH5α
For pSB1C3 vector amplification
Back to the Calendar
August 4th 2012

　PACKMAN

1191 and 1199 forward primer design
We designed new forward primers for both 1191 and 1199 gene that are thought to solve problems appeared during PCR amplification.

Results

0804Fig1


　Flip Flop

BBa_J04450 and Bxb1-pGEM colony picking and inoculation.
Made master plates and inoculated in 3mL of LB.
Back to the Calendar
August 5th 2012

No Special Event!
Back to the Calendar
August 6th 2012

　Flip Flop

BBa_J04450 Plasmid miniprep
BBa_J04450(pSB1C3): 285.8ng/uL
purity:2.10


Requested part arrived
Each parts were streaked on appropriate plates.

  • BBa_I11020
  • BBa_I11022
  • BBa_I11023
  • BBa_I11030
  • BBa_K137007
  • BBa_K137008
  • BBa_K137010
  • BBa_K112001
  • BBa_K112141
  • BBa_K112142



BBa_K381001(GFP) and BBa_K398005(pSB1C3) transformation
BBa_K381001(GFP): for GFP control
BBa_K398005(pSB1C3): for pSB1C3 template

Back to the Calendar
August 7th 2012

　PACKMAN

FDH gene PCR amplification
Results

0807Fig1

Discussion

We amplified 2 samples of formate dehydrogenase gene with the primers we designed. From gel electrophoresis picture, we can say that oligonucleotides with the proper size 1100bp are present in the sample.
0807Fig2



　Flip Flop

BBa_J04450(pSB1C3) enzyme cut check(single cut with EcoRI)
Results

2_0807Fig1

Vector was double digested. The insert and vector sizes were correct


pPoC and pPoCpi OE PCR product nested PCR
Results

2_0807Fig2

→ Gel extracted


BBa_K398005 Plasmid miniprep & single cut check with EcoRI
Results

2_0807Fig3



Overlapping PCR
pPoC insert

2_0807Fig4

  • HSTaq Pol MM : 25uL
  • DW : 1uL
  • templates : 22uL
  • primers : 2uL


pPoCpi insert

2_0807Fig4

  • HSTaq Pol MM : 25uL
  • templates : 23.2uL
  • primers : 2uL

Results

2_0807Fig5

→ Concentration after gel extraction was not sufficient for cloning



Overlapping PCR template preparation
2_0807Fig6

2_0807Fig7

Back to the Calendar
August 8th 2012

　PACKMAN

FDH gene and pTrcHis2A, pBAD/mycHisC vector enzyme digestion
Procedure

We mixed restriction enzymes and buffers with DNA samples as shown below.

0808Fig1

After mixing the enzymes and buffer with the sample, we incubated the sample on 37℃ for 1 hour and then on 65℃ for 20minutes.


pTrcHis2A, pBAD/myc vector dephosphorylation
Procedure

We mixed phosphatidase and buffer with DNA sample as shown below.

0808Fig2

After mixing the enzyme and buffer with the sample, we incubated the sample on 37℃ for 1 hour 20minutes and then on 70℃ for 5minutes.


ligation of FDH gene with pTrcHis2A and pBAD/mycHisC vectors
Procedure

We mixed ligase and buffer with DNA sample as shown below.

0808Fig3

After mixing the enzyme and buffer with the sample, we incubated the sample on 16℃ for 16 hours.


Primer amplification of 1191 and 1199
Results

0808Fig4

Discussion



　Flip Flop

Overlapping PCR
pPoC insert

2_0808Fig2

pPoCpi insert

2_0808Fig3


  • HSTaq Pol MM : 25uL
  • DW : 5.2uL
  • templates : 19.8uL
  • primers : 2uL
  • pfu-x : 0.1uL

Results

2_0808Fig1

→ Gel extraction


Overlapping PCR template preparation
Results

2_0808Fig4

Back to the Calendar
August 9th 2012

　PACKMAN

vector transformation into TOP10 cell
Transformation of pTrcHis2A vector into TOP10 cell was successful. So we did vector mini-preparation after the transformation. However, transformation of pBAD vector has failed, so we ligated the samples again.

Results

0809Fig1

This is gel picture to confirm that FDH is well inserted into TOP10 cells. 3 wells on the left are PCR product of

　Flip Flop

Bxb1 integrase cloning into pTrcHis2a and pBADmycHisC
Bxb1 integrase: 1515bp

Results

2_0809Fig1

→ Gel extracted


Extracted OE PCR product cloning into pSB1C3
pSB1C3 was originated from BBa_K398005.

Transformed into TOP10

Results

Transformed colony was grown in LB media. No colony shows fluorescence.

Discussions

We think cloning failed.

Back to the Calendar
August 10th 2012

　Flip Flop

Bxb1-pTrc, pBAD colony inoculation


Overlapping PCR
In this time, PCR was done first 18 cycles without any primer.
After that, we add 1uL of primers. And then PCR was done 20 cycles more.

Results

2_0810Fig1

Discussions

With this OE PCR conditions, yield was better than previous conditions.


pPoC, pPoCpi insert cloning into pSB1C3
pSB1C3 was derived from BBa_K398005

  1. Digestion – 37℃ 1hr, 80℃ 20min
    2. 2_0810Fig5

  2. Dephosphorylation – 37℃ 30min, 80℃ 10min
    3. 2_0810Fig6

  3. Ligation – 37℃ 2hr
    4. 2_0810Fig7

Ligated products were transformed into DH5α.



Transformed cell inoculation and colony PCR
Results

2_0810Fig8

Discussions

only pPoCpi construct cloning was completed 
Back to the Calendar
August 11th 2012

　PACKMAN

pTrcHis2A vector transformation into E.coli MG1655 cell
Procedure



pBAD/mycHisC-FDH transformation into TOP10


　Flip Flop

Bxb1 pTrcHis2A, pBADmycHisC plasmid DNA mini-prep
Results

single cut check

2_0811Fig1



pPoC and pPoCpi nested PCR
Results

nested PCR to prepare more insert DNA

2_0811Fig2


Back to the Calendar
August 12th 2012

　PACKMAN

colony PCR check of pTrcHis2A inserted FDH gene
Results

0812Fig1

Discussion

We checked the presence of FDH gene by conducting colony PCR. Correct size of band appeared at about 1115bp, which means formate dehydrogenase is inserted correctly.


pBAD FDH MG1655 electroporation
Results

Fail
Back to the Calendar
August 13th 2012

　PACKMAN

FDH pBAD MG1655 electroporation
Procedure

We seeded cells on 7:10 AM and did cell-down on 10:00AM. And then we plated cells on 1:00PM and checked colony on 8/14 5:00AM

Results




FDH pTrc MG1655 expression check (sampling and induction)
Procedure

We seeded cells (500λ of cells put into 50mL LB with 50λ Ampicillin) on 7 : 30 AM and checked Optical Density on 10:30pm. According to the O.D. value, we induced 37℃ sample on 10:30PM and did sampling on 4:30pm. Also, we induced 30℃ sample on 11:30pm and did sampling on 5:30pm. (6 hour induction) Each temperature samples were induced by different conditions ; 2mM and 3mM of IPTG.


　Flip Flop

pPoCpi cloning into pSB1C3
Cloning was done by remaining DNA samples.

Back to the Calendar
August 14th 2012

　PACKMAN

colony PCR check of pBADmycHisC inserted FDH gene
Results

0814Fig1

Discussion

We checked the presence of FDH gene by conducting colony PCR. Correct size of band appeared at about 1115 bp, which means formate dehydrogenase is inserted correctly.


Expression check of Formate dehydrogenase on pTrcHis2A vector (Result)
Results

0814Fig2

Discussion

For each samples of different induction conditions, we run SDS-PAGE gel and checked the presence of 43.7 kDa protein, formate dehydrogenase. The band appeared significantly on the correct size.


FDH pBAD MG1655 seeding for expression check
Procedure

We seeded cell on 7:00PM, so we’ll incubate cell about 16hours. (This means we have to do next seeding on 11:00AM. )


Primer design for the insertion of 1202 and 0109
Results

0814Fig3

Discussion

To eliminate uncertain spacer between genes, we inserted

　Flip Flop

Bxb1 pTrcHis2A and pPoCpi ligated products transformation
The products were transformed into TOP10

Back to the Calendar
August 15th 2012

　PACKMAN

FDH pBAD MG1655 expression check
Procedure

We seeded cells on 11 : 30 AM and checked Optical Density on 1:30pm. According to the O.D. value, we induced 37℃ sample on 1:40pm and did sampling on 7:40pm. Also, we induced 30℃ sample on 3:30pm and did sampling on 9:30pm. (6 hour induction) Each temperature samples were induced by different conditions: 10mM of arabinose and 30mM of arabinose.

　Flip Flop

pPoCpi colony PCR
Results

2_08##Fig#

Among colonies #1~10, four colonies were inoculated. #1, 3, 4, 7


Bxb1 pTrcHis2A colony PCR
Results

2_0815Fig2

Among colonies #1~20, three colonies were inoculated. #2, 5, 19
Back to the Calendar
August 16th 2012

　PACKMAN

PCR amplification of 1201, 1202, 1203, 1198 and 1191
Results

0816Fig1

Discussion

Primers arrived, and we began to do additional PCR amplification on the preparation for Gibson assembly. Each PCR sample has the correct size of oligonucleotides except Moth 1202 gene.

  • 1191 : 921bp
  • 1198 : 972bp + about 400bp = 1300 bp
  • 1201 : 1341bp + ?
  • 1202 : 2190bp +
  • 1203 : 2025bp + 1600bp = 3625bp

We did PCR purification on the PCR product and the concentration/purity result was as shown below.

0816Fig2



Pre-culture of 0109
Discussion

There was no vector prepared for Moth 0109, so we did 5ml pre-culture on 10ml tube. Cell was grown about 16hours after pre-culture, and we did vector mini-prep on the sample. The concentration of the mini-prepped vector is 726.8ng/ul and the purity(A260/A280) was 1.86.

　Flip Flop

pPoC and pPoCpi electro-transformation into MG1655
Strain: MG1655

Plasmid source:

  • pPoC: from DH5α-pPoC colony #1 and TOP10-pPoC colony #1
  • pPoCpi: from TOP10-pPoC colony #1 and #3
Back to the Calendar
August 17th 2012

　PACKMAN

Expression check of Formate dehydrogenase.
Results

0817Fig1

Discussion

For each samples of different induction conditions, we run SDS-PAGE gel and checked the presence of 40.xx kDa protein, formate dehydrogenase. The band appeared more significantly than the case of pTrcHis2A vector. Therefore, using pBAD promoter seems to produce more proteins.


PCR amplification – second trial
Results

0817Fig2

Discussion

As the band was not significant for 1203 and 1198 on previous trial and purity was low for 1191, we tried secondary PCR amplification on samples for Gibson assembly; 1202, 1203, 1198, 1191. Particularly for 1202 gene, we tried additional colony PCR, so that we could check any problem with vector mini-prep. (PCR solution for 1202 colony PCR was : 22ul

0817Fig3


　Flip Flop

MG1655-pPoC, MG1655-pPoCpi streaking
We could not distinguish single colony from plates. Therefore we scraped cells and streaked onto new plates.

Discussions

Wild-type E.coli showed more reddish and yellowish color than competent strains, DH5α and TOP10. The promoter BBa_J23119 may show different strength in-between strains.


TOP10-pTrcHis2A_Bxb1 expression check
TOP10 containing pTrcHis2A was cultured in 30mL of LB with 1% of Ampicillin.
 IPTG induced when OD = 0.4
 Sampling: 8 hours after induction, 1010 cells.
 Only soluble fractions were PAGEed.
Back to the Calendar
August 18th 2012

　PACKMAN

PCR amplification of 1202, 0109 gene with original primer and Gibson primers
Results

0818Fig1

Each lane indicates:

  • Moth_1202_1 : Gibson forward + original reverse
  • Moth_1202_2 : Gibson reverse + original forward
  • Moth_0109_1 : Gibson forward + original reverse
  • Moth_0109_2 : Gibson reverse + original forward

There was correct size and unspecific size of band on 1202_1 sample. Although there are also unspecific band, 1202_2 sample has large band of correct size. 0109_1 sample has only unspecific band and 0109_2 sample has right size of band.

Discussion

When the PCR was unsuccessful, we first thought it might be problem of forward primer as in the case of 1199 and 1191. Our guess was correct, and we’re going to fix the problem with forward primers.


1202 and 0109 forward primer design
We designed new forward primer hoping no problem with it.

Results

0818Fig1

Newly designed primers contain overlapping region with former DNA fragments, artificial ribosome binding site, and overlapping region with 1202 and 0109 each.


　Flip Flop

MG1655-pPoC, MG1655-pPoCpi colony inoculation
Two colonies from each plate were inoculated into 3mL of LB containing 1% of chloramphenicol.

Discussions

In 12 hours, cell cultures show colors compared to another common E.coli culture. When they are centrifuged, pellet shows clear and definite yellow or red color.


pTrcHis2A_Bxb1 electro-transformation into MG1655-pPoC, MG1655-pPoCpi
pTrcHis2A_Bxb1 is electro-transformed into MG1655 containing pPoC and pPoCpi.

Plasmid source: TOP10-pTrcHis2A_Bxb1

Back to the Calendar
August 19th 2012

No Special Event!
Back to the Calendar
August 20th 2012

No Special Event!
Back to the Calendar
August 21st 2012

No Special Event!
Back to the Calendar
August 22nd 2012

　Flip Flop

Primer design for Bxb1 integrase cloning
Primers for Bxb1 integrase cloning were designed. For controlling basal transcription level optimization, a mutant primer which has GTG rather than ATG for its start codon was also ordered.

Results

2_0822Fig1

Back to the Calendar
August 23rd 2012

No Special Event!
Back to the Calendar
August 24th 2012

　PACKMAN

0109, 1191 PCR with new primers
Results

0818Fig1


Discussion

PCR product of Moth 0109 gene and 1191 gene has run on the gel. There was only faint band of 0109 fragment but the product band of 1191 gene was significantly shown on the gel. After gel electrophoresis, we tried PCR of 0109 once more and got significant amount of fragments.
Back to the Calendar
August 25th 2012

　Flip Flop

pPoC-Bxb1 double transformants inoculation for prep & PCR check
Double transformants 1 through 24 were inoculated into 3ml of LB containing 1% of Cm and Ap. For our convenience, three colonies were inoculated in one culture tube.

Back to the Calendar
August 26th 2012


　Flip Flop

pPoC-Bxb1 double transformants plasmid DNA miniprep & PCR check
Inoculated cultures were mipi-preped. And Bxb1-pTrc plasmid was checked by PCR. In case of pPoC, it would be check by color.

Results

Vector

2_0826Fig1

Confirm PCR

2_0826Fig2


Discussions

In confirm PCR, all the colonies seem to have Bxb1 vector. Colony #1, 4, 7, 10, 13, 14, 16, 19 and 22 will be inoculated.


Bxb1 PCR with new primers
For cloning of Bxb1 into pBAD and mutating its start codon from ATG to GTG, we PCR pGEM-B1-Bxb1 vector as template. Samples were duplicated

 PCR conditions
  1. 95℃ for 3min
  2. 95℃ for 30sec
  3. 55℃ for 30sec
  4. 72℃ for 1min 30sec
    5. Step 2 to 4: 34 cycles
  5. 72℃ for 10min
  6. 12℃ forever

Results

2_0826Fig3

Duplicated samples were purified in one DNA binding column.

ATG: 297.9ng/uL (purity: 1.90)
GTG: purify failed. Sample lost
Discussions

There were multiple bands in our PCR products. We will PCR again Bxb1-GTG with different conditions. Template vector may show larger bands.


pGEM-Bxb1 template vector gel electrophoresis
To check whether the undesired bands were template vector, we diluted template vector with same conditions of PCR, 50X, and electrophoresized.

Results

2_0826Fig4


Discussion

The band was different from undesired bands from Bxb1 ATG, GTG PCR products.


Insert DNA (Bxb1 integrase) and vector (pTrc and pBAD) cloning
Back to the Calendar
August 27th 2012


　Flip Flop

Bxb1-pTrc and Bxb1-pBAD electrotransformation into MG1655


Bxb1 PCR with changed conditions
For cloning of Bxb1 into pBAD and mutating its start codon from ATG to GTG, we PCR pGEM-B1-Bxb1 vector as template. Samples were duplicated

PCR conditions #1 PCR conditions #2
1) 95℃ for 3min 1) 95℃ for 3min
2) 95℃ for 30sec 2) 95℃ for 30sec
3) 56.5℃ for 30sec 3) 58℃ for 30sec
4) 72℃ for 1min 30sec
　　(Step 2 to 4: 34 cycles)		 4) 72℃ for 1min 30sec
　　(Step 2 to 4: 34 cycles)
5) 72℃ for 10min 5) 72℃ for 10min
6) 12℃ forever 6) 12℃ forever

Results

2_0827Fig1


Discussions

Still, undesired bands appeared. We do not know where they come from. We decide to extract desired DNA with gel extraction.


Bxb1, with GTG as start codon, PCR product gel extraction
PCR products were gel extracted.

Results

  • Bxb1 GTG cond. #1 - #1: 128.2ng/uL (purity: 1.89)
  • Bxb1 GTG cond. #1 - #2: 79.0ng/uL (purity: 1.89)
  • Bxb1 GTG cond. #2 - #1: 110.7ng/uL (purity: 1.89)
  • Bxb1 GTG cond. #2 - #2: 66.7ng/uL (purity: 1.94)


Discussions

Bxb1 GTG cond. #1 - #1 and Bxb1 GTG cond. #2 - #1 will be used to cloning.


Insert DNA (Bxb1 GTG) and vector (pTrc and pBAD) cloning
Insert DNA: Bxb1 integrase mutated by primer.
Vectro DNA: pTrcHis2A, pBAD-mycHisC

Prepared DNA concentration:

  • Bxb1 GTG cond. #1 - #1: 128.2ng/uL (purity: 1.89)
  • Bxb1 GTG cond. #2 - #1: 110.7ng/uL (purity: 1.89)
  • pTrcHis2A: 116.1ng/uL
  • pBAD-mycHisC: 128.7ng/uL

Enzyme digestion: 37℃ for 1hr 30min, 80℃ for 20min

2_0827Fig2


Dephosphorylation: 37℃ for 30min, 70℃ for 5min

2_0827Fig3


Ligation: 16℃ overnight

2_0827Fig4



Bxb1, pPoC double transformants colony PCR
Colony #1, 4, 7, 10, 13, 14, 16, 19 and 22 from master plate

Results

2_0827Fig5


Discussions

The gel showed that all the colonies have Bxb1-pTrc vector. And also they all have pPoC or pPoCpi, because they show color.
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August 28th 2012

　Flip Flop

Bxb1-GTG-pTrc and Bxb1-GTG-pBAD electrotransformation into MG1655


Bxb1-pTrc and Bxb1-pBAD transformants check
Results

Bxb1-pTrc: No colony
Bxb1-pBAD: Colonies appeared and incoculated into 3mL of LB containing 1% of Ap


Bxb1-pTrc and Bxb1-pBAD transformants colony PCR
Results

2_0828Fig1





Bxb1-pTrc and Bxb1-pBAD transformants plasmid DNA miniprep
Results

Colony #2: 109.8ng/uL, purity = 1.87
Colony #3: 138.9ng/uL, purity = 1.74



mRFP, GFP 30mL culture and sampling
Results

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August 29th 2012


　Flip Flop

Bxb1 pBADmycHisC prepped plasmid DNA RE cut check
mini-prepped plasmid DNAs were cut with SnaBI

expected size : 5.6kb

Results

2_0829ig1


　PACKMAN

1202 PCR to make fragments for Gibson assembly
Results

0818Fig1


Discussion

PCR for Moth 1202 gene has failed. No band for Moth 1202 gene has appeared on the gel.


Gibson assembly – assembly of pcr fragments.
Results

Among three methods to assemble DNA fragments, we chose first method, which is assembly of PCR amplified DNA fragments.
0.2umoles of each fragments are added into the reaction sample, and volume to be added for each fragments has calculated on the assumption that average MW of each base is 660Da. Table below is the result of calculation.
Fragment 1
0818Fig1
Fragment 2
0818Fig1
0818Fig1


Discussion

As we can only assemble the fragments through Gibson Assembly method and not amplify them, there would be very small amount of template remaining in the tube. We thought that’s why we couldn’t see any band on the gel. So we did PCR purification of the fragment once more and saw if the band appears on the gel.
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August 30th 2012

　PACKMAN
Gibson Assembly product – Amplification by nested PCR
Results

0818Fig1


Discussion

There was no right size of the band but just unspecific bands on the gel. There might be several reasons why the Gibson assembly ended with failure. So we decided to change the method of Gibson assembly; we will assemble fragments in the presence of vectors, so that assembly product can become stable, circular form. To cut the cost used in experiment, we will not design primers, but digest the vector with restriction enzymes to make it linear form.


Gibson primer second design 2
Results

0818Fig1


Discussion

We designed primers again for another trial of Gibson Assembly. As stated before, We’ll use vector-involved assembly method to stabilize the assembly product and amplify them by in vivo system.
Like the method we used before, we’ll assemble 5 fragments first and assemble those 5-fragment-long two fragments into full construct.
　Flip Flop

Double transformants expression SDS-PAGE
Gel composition: 20%

Results

pPoC

2_0830Fig1

pPoCpo

2_0830Fig2

Results

We cannot see expression level change of fluorescent protein in SDS-PAGE.
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August 31st 2012

No Special Event!
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