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| - | .modelling {
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| - | .wetlab {
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| - | </style>
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| - | <body>
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| - | <div class="outer" style="overflow-y: scroll; overflow-x: hidden;">
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| - | <div id="stuff" style="float:left;position:absolute;margin-left:200px;margin-right:100px; margin-top:50px;min-width:645px;">
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| - | <img src="https://static.igem.org/mediawiki/2014/e/e6/Real_Biosensor.jpg" style="position:absolute; width:100%;z-index:-1; border-radius:15px;"/>
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| - | <div style="background-color:#D9D9D9; opacity:0.7; z-index:5; Height:75px; width:100%;font-size:65px;font-family:Helvetica;padding-top:5px; font-weight: 450;margin-top:10px;">
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| - | <div style="background-color:white; opacity:0.9; Height:75px; width:100%;margin-top:5px:margin-bottom:5px;font-size:65px;font-family:Helvetica;padding-top:5px; color:#00000; font-weight: 450;"><br><center><font style="opacity:0.7">Construction</font></center></div>
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| - | <div style="border-bottom-left-radius:10px;border-bottom-right-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;">
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| - | <img src="https://static.igem.org/mediawiki/2014/7/79/Realisation_Biosensor.png" style="width:35%;margin-left:33%;margin-top:-50px;">
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| - | <div style="background-color:white; border-bottom-left-radius:10px;border-radius:10px; padding-left:10px;padding-right:10px;min-width:300px;margin-top:-50px;">
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| - | <a href="#"><img src="https://static.igem.org/mediawiki/2014/5/50/OxigemLabbook.png" style="position:absolute;width:6%;margin-left:84%;margin-top:-13%;z-index:10;"></a>
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| - | <a href="#"><img src="https://static.igem.org/mediawiki/2014/a/a4/OxigemProtocols.png" style="position:absolute;width:6%;margin-left:91%;margin-top:-13%;z-index:10;"></a>
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| - | <div style="position:absolute;background-color:rgba(255,255,255,0.6);border-radius:15px; z-index:5;margin-top:-18.2%; Height:70px; width:20%;font-size:65px;font-family:Helvetica; font-weight: 450;padding-left:10px;padding-right:10px;padding-top:3px;min-width:170px;margin-bottom:3px;">
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| - | <div style="width:100%;"><font style="font-size:15px;font-weight:500;">Show all:</font></div>
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| - | <a href="#showmodelling"><div class="orange_news_block1 showmodelling" style="background: #F9A7B0;border-radius:15px;color:black;float:left;height:40%;width:40%;margin-left:6%;padding-top:5%;margin-top:3px;"><center>
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| - | <h1white><font style="font-size:15px;font-weight:500;">Modelling</font>
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| - | </div></a>
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| - | <a href="#showwetlab"><div class="orange_news_block1 showwetlab" style="background: #ADD8E6;border-radius:15px;color:black;float:left;height:40%;width:40%;padding-top:5%;margin-left:3%;margin-top:3px;"><center>
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| - | <h1white><font style="font-size:15px;font-weight:500;">Wetlab</font>
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| - | <br><br><br><br><br>
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| - | </div>
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| - | <br>
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| - | <h1>Introduction: how we constructed our biosensor</h1>
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| - | In order to be able to use our model and to determine whether DcmR acts as a repressor or activator in the presence of DCM we designed and constructed the following two plasmid system. We primarily used Gibson assembly methods and source most of the necessary DNA from gblocks(synthesised oligonucleotides) we had designed based in the sequenced genome of Methylobacterium DM4. This system will also form the DCM biosensor and will be integrated with an electronic circuit to complement this genetic one:<br><br>
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| - | <div class="row">
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| - | <a href="#show1" class="show" id="show1"><div class="wetlab">
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| - | <h1white>pOXON-2-dcmR-mCherry</h1white>
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| - | <img src="https://static.igem.org/mediawiki/2014/4/4d/Oxford_plus-sign-clip-art.png" style="float:right;position:relative; width:2%;" />
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| - | </div></a>
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| - | <a href="#hide1" class="hide" id="hide1"><div class="wetlab">
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| - | <h1white>pOXON-2-dcmR-mCherry</h1white></div></a>
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| - | <div class="list">
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| - | <div class="white_news_block2">
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| - | <img src="https://static.igem.org/mediawiki/2014/b/b6/Oxford_pOXON-2-dcmR-mCherry_text.png" style="float:left;position:relative; width:100%;" />
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| - | Oxford iGEM 2014
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| - | </div>
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| - | <div class="row">
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| - | <a href="#show2" class="show" id="show2"><div class="modelling">
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| - | <h1white>pSRK-Gm-pdcmAsfGFP</h1white>
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| - | <img src="https://static.igem.org/mediawiki/2014/4/4d/Oxford_plus-sign-clip-art.png" style="float:right;position:relative; width:2%;" />
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| - | </div></a>
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| - | <a href="#hide2" class="hide" id="hide2"><div class="modelling">
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| - | <h1white>pSRK-Gm-pdcmAsfGFP</h1white></div></a>
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| - | <div class="list">
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| - | <div class="white_news_block2">
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| - | <img src="https://static.igem.org/mediawiki/2014/1/12/Oxford_pSRK-Gm-pdcmAsfGFP_text.png" style="float:left;position:relative; width:100%;" />
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| - | Oxford iGEM 2014
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| - | </div>
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| - | </div>
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| - | <div class="row">
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| - | <a href="#show3" class="show" id="show3"><div class="wetlab">
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| - | <h1white>Why these two plasmid backbones?</h1white>
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| - | <img src="https://static.igem.org/mediawiki/2014/4/4d/Oxford_plus-sign-clip-art.png" style="float:right;position:relative; width:2%;" />
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| - | </div></a>
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| - | <a href="#hide3" class="hide" id="hide3"><div class="wetlab">
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| - | <h1white>Why these two plasmid backbones?</h1white></div></a>
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| - | <li>The two plasmids are partitioned during cell division by different systems, thus an equal proportion of each plasmid is maintained in each new daughter cell. </li><br> <li>Different antibiotic resistances will allow us to select for cells that have taken up both plasmids by application of both antibiotics.</li><br> <li>The replication origins compatible with E.coli and pseudomonas strains.</li><br> <li>We have used two plasmids so that we can test each part in isolation before transforming them both into the same cell.</li>
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| - | <a href="#show4" class="show" id="show4"><div class="modelling">
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| - | <h1white>How were the constructs made?</h1white>
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| - | <img src="https://static.igem.org/mediawiki/2014/4/4d/Oxford_plus-sign-clip-art.png" style="float:right;position:relative; width:2%;" />
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| - | </div></a>
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| - | <a href="#hide4" class="hide" id="hide4"><div class="modelling">
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| - | <h1white>How were the constructs made?</h1white></div></a>
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| - | <div class="list">
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| - | <img src="https://static.igem.org/mediawiki/2014/0/08/Oxford_Fran_flowchart2.png" style="float:right;position:relative; width:83%;margin-left:2%;" />
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| - | <img src="https://static.igem.org/mediawiki/2014/8/84/Oxford_Fran_flowchart1.png" style="float:right;position:relative; width:83%;margin-left:2%;" />
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| - | <h1>Building pOXON-1</h1><br>
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| - | <li>The first task in the construction of the pOXON-2-dcmR-mcherry construct was the creation of pOXON-1; pME6010 with tetracycline resistance replaced by kanamycin resistance. (N.B. The KanR gene was amplified with an optimised RBS.)</li><br>
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| - | <li>pOXON-1 was produced using the Gibson assembly method.</li><br>
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| - | <h1>Building pOXON-2 and pOXON-2-dcmR</h1><br>
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| - | <li>pOXON-1 was then used as the vector for the insertion of the three gblock fragment constituting the inducible expression system of dcmR via Gibson assembly.</li><br>
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| - | <li>Upon sequencing of the product, it was determined that the version of the gblock containing the dcmR gene in the construct was actually truncated. This construct with the truncated dcmR is pOXON-2. A second Gibson assembly reaction was used to replace the truncated version with the full length gene also derived from the gblock. The resulting construct was named pOXON-2-dcmR.</li><br>
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| - | <h1>Adding in mCherry</h1><br>
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| - | <li>We then used pOXON-2-dcmR as the vector for the insertion of mCherry downstream of dcmR as a translational fusion by Gibson assembly.</li><br>
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| - | <li>We therefore have a system of expressing dcmR with (pOXON-2-dcmR-mCherry) and without (pOXON-2-dcmR) the mCherry fusion in order to test whether the addition of mCherry affects the action of DcmR. Both will be submitted as BioBricks in the standard pSB1C3 backbone.</li><br>
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| - | <li>All constructs were confirmed by sequencing.</li><br>
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| - | <h1>Building pSRK Gm construct</h1><br>
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| - | <li>Still under construction, we have attempted to make our second construct by inserting the pdcmAsfGFP gblock into the pSRK Gm vector by Gibson assembly. As this is proving difficult the next approach will be to insert the two components separately and to source the DNA from other sources instead of the gblock. Firstly pdcmA will be amplified from Methylobacterium extorquens DM4 genomic DNA and inserted into the pSRKGm vector. sfGFP will them be amplified from a plasmid already containing it and then added the the pSRKGm-pdcmA construct.</li><br>
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| - | <div class="white_news_block2">
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| - | <a href="https://2014.igem.org/Team:Oxford/biosensor_characterisation"><img src="https://static.igem.org/mediawiki/2014/c/ca/Oxford_Characterisation.png" style="float:left;position:relative; width:23%;" /></a>
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| - | <a href="https://2014.igem.org/Team:Oxford/biosensor_realisation"><img src="https://static.igem.org/mediawiki/2014/4/4c/Oxford_Realisation.png" style="float:right;position:relative; width:23%;" /></a>
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| - | <a href="https://2014.igem.org/Team:Oxford/biosensor_construction"><img src="https://static.igem.org/mediawiki/2014/e/ef/Oxford_construction_dark.png" style="float:left;position:relative; width:23%; margin-left: 2.66%" /></a>
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| - | <a href="https://2014.igem.org/Team:Oxford/biosensor_optimisation"><img src="https://static.igem.org/mediawiki/2014/9/93/Oxford_Optimisation.png" style="float:right;position:relative; width:23%; margin-right: 2.66%" /></a>
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| - | <a href="https://2014.igem.org/Team:Oxford/biosensor"><img src="https://static.igem.org/mediawiki/2014/a/a7/Oxford_biosensor_link.png" style="float:left;position:relative;width:50%; margin-top:2%;margin-left:25%;margin-right:25%;" /></a>
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| - | <br><br><br>
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| - | Oxford iGEM 2014
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| - | {{Team:Oxford/templates/footer}}
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