Team:EPF Lausanne/Overview

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            <!-- RESULTS -->
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                <h1 class="cntr"> RESULTS </h1>
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                <br /><br />
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                <h2> <b><u>Characterisation of the spatiotemporal dynamics of the CpxR - split IFP 1.4 stress sensor </u> </b> </h2>
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                <br /><br />
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                <h3> <b>Experiment 1: </b> Promoter characterisation and folding ability of fused GFP to CpxR via 10 amino acid 2 x (GGGGS) flexible linker </h3>
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                <p>This construct aimed to evaluate the expression and correct folding of our CpxR construct, and the function of the arabinose promoter in <i>E. coli</i> by fusing a superfolder GFP protein to the N terminus of CpxR. The sfGFP was chosen because of its higher intensity compared to GFP. </p>
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                <p>Not knowing if CpxR would react the same way if sfGFP were attached to the N or C terminus, 2 biobricks were built, one with each of the orientations: <a target="_blank" href="http://parts.igem.org/Part:BBa_K1486002">BBa_K1486002 (N terminus)</a> and <a target="_blank" href="http://parts.igem.org/Part:BBa_K1486005">BBa_K1486005 (C terminus)</a>.
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                An experiment on both possible CpxR - sfGFP orientations was launched to determine whether the proteins were well expressed and folded, and if the arabinose promoter worked well. It was also done on a microfluidic chip. The N terminus GFP biobrick results can be seen below; fluorescence intensity plotted against time.
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                  <a href="https://static.igem.org/mediawiki/2014/4/4c/Gfp_ara.png" data-lightbox="img1"><img src="
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                  https://static.igem.org/mediawiki/2014/4/4c/Gfp_ara.png" width="50%"></a>
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                  <p>Here are scans of the chip at t = 0 (no arabinose) and t = 300 min (Upper half has arabinose, lower half doesn't).</p>
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                  <a href="https://static.igem.org/mediawiki/2014/0/0d/Truc2.png" data-lightbox="img1"><img src="https://static.igem.org/mediawiki/2014/0/0d/Truc2.png" width="30%"></a>
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                  <a href="https://static.igem.org/mediawiki/2014/0/0d/Truc3.png" data-lightbox="img1"><img src="https://static.igem.org/mediawiki/2014/0/0d/Truc3.png" width="30%"></a>
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                <a href="https://static.igem.org/mediawiki/2014/f/f7/Truc5.png" data-lightbox="img1"><img src="https://static.igem.org/mediawiki/2014/f/f7/Truc5.png" class="pull-left img-left img-responsive img-border"></a>
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                <br/><br/><br/><br/><br/>
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                <p>The increasing standard deviation for the cells with arabinose can be explained as some chambers did not have a lot of cells and so there was a low intensity. As it can be seen in the following picture :</p>
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                <p>These are chambers with arabinose in the medium, you can see that there are different cell density and thus different intensity in the chambers. Inducing a high standard deviation</p>
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                <br/><br/><br/><br/>
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                <h3><b>Experiment 2: </b>CpxR dimerization & Dimerization Orientation </h3>
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                <p>
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                <u>Introduction</u> <br />
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                CpxR is the relay protein in the stress resonsive CpxAR two component regulatory system. It has been shown by split beta galactosidase assay that CpxR dimerizes when phosphorylated (activated) in yersinia pseudotuberculosis. Moreover, following other in vitro FRET studies, it was shown that <i>E. coli</i> CpxR interacted with itself.  We therefore hypothesised that dimerization would also be true in vivo in <i>E. coli</i>.</p>
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                <p>
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                <u>Aim</u> <br />
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                This experiment aimed to determine if and how CpxR dimerised in vivo in <i>E. coli</i>. This experiment intended to get a first idea of the real-time temporal dynamics of the activation of CpxR (the cytoplasmic relay protein of the CpxA-R pathway) by KCl stress via CpxA (the periplasmic sensor protein of the CpxA-R pathway). This experiment is a first of its kind.
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                </p>
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                <p>
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                <u>Methods</u> <br />
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                To evaluate if and how CpxR dimerized under KCl stress, we built by gibson assembly four constructs with the various possible orientations that the split IFP1.4 fragments could have with CpxR: IFP[1] and IFP[2] on the N-terminus of CpxR, IFP[1] on the N-terminus of CpxR and IFP[2] on the C-terminus of CpxR, and finally IFP[1] and IFP[2] on the N-terminus of CpxR. The split IFP fragments were provided by the Michnick Lab, and the CpxR coding region was amplified by PCR from extracted <i>E. coli</i> genome (Bacterial Genomic Miniprep Kit from Sigma Aldrich). The protocol for stressing the cells and reading the fluorescence can be downloaded <a href="https://static.igem.org/mediawiki/2014/a/a5/EPFL_Protocol_IFP_stress_1.pdf">here</a>.
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                </p>
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                <u>Results</u> <br />
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                As seen in the graph bellow, induction of the signal was done at minute 24 (marked via a vertically spoted line). The construct with IFP fragments on the C-termina responded immediately to stress. In a fact we observed a 3 fold signal increase in 2 minutes. All other constructs we observed a low baseline signal non responsive to KCl stress. It is to be noted that the C-termina constructs always had higher signal levels than the other constructs. This leads us to believe that the PBS used to resuspend our cultures led to small levels of stress (the PBS we use does not contain KCl but traces of NaCl). The 30-fold signal increase from the baseline allows us to assert that our constructs responds to KCl stress.
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                </p>
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                  <img src="https://static.igem.org/mediawiki/2014/c/c2/KCL_Construct_Comparison.jpg" alt="Construct Comparison" class="img-responsive">
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                </div>
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                <p>
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                <u>Discussion</u> <br />
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                We successfully proved that CpxR dimerized in vivo and that dimerization led to close interaction of its C-terminus. This finding suggests that CpxR binds via its C-termina. This leads us to hypothesise that the CpxR dimerisation mechanisms is the same for other members of the highly conserved OmpR/PhoB subfamily. This hypothesis could allow the development of similar system that could the study other components of the OmpR/PhoB subfamily and thus lead to a new generation of highly senstitive and reactive biosensors.
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                </p>
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                <h3><b> Experiment 3: </b>Signal induction by various concentrations of KCl & signal shutdown by centrifugation </h3>
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                <p>
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                <u>Aim</u> <br />
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                Having found that KCl was a good signal inducer for our signal, we decided to characterise our biobrick by testing if the signal could be modulated by various concentrations of KCl and if we were able to remove the signal by centrifugation and medium change.
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                To do so, we read  our signal for 20 minutes without stress and then added KCl. At minute 144 we centrifuged our cells and replaced the medium with PBS to be able to get a shutdown of the signal.
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                </p>
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                <p>
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                <u>Methods</u> <br />
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                To evaluate if a modulation in KCl concentrations affected the intensity of the intensity of the fluorescent signal, and if a change in medium by centrifugation shutdown the signal; we read our signal on a plate reader for 20 minutes without stress and then added KCl. At minute 144 we centrifuged our cells and replaced the medium with PBS to be able to get a shutdown of the signal. The protocol for this experiment can be downloaded <a href="https://static.igem.org/mediawiki/2014/a/a5/EPFL_Protocol_IFP_stress_1.pdf">here</a>.
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                </p>
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                <p>
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                <u>Results</u> <br />
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                We successfully showed that increasing concentrations of KCl led to stronger signals up to a saturation concentration of about 80 mM KCl. Moreover we were able to shut the signal down, thus proving the reversibility of our system. These results prove the reversibility of the split IFP1.4 and suggest that real-time temporal dynamics analysis are possible for our system.
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                </p>
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                <div class="cntr">
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                  <img src="https://static.igem.org/mediawiki/2014/6/61/KCL_titration_green_small_EPFL.jpg" alt="GA1 Shutdown" class="img-responsive">
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                </div>
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                <br /><br />
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                <h3><b> Experiment 4: </b>Visualization of the the CpxR split IFP1.4 activation by KCl stress  </h3>
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                <p>
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                <u>Aim</u> <br />
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                Having shown that we were able to monitor the temporal dynamics of our construct, we wanted to see if we were able to analyze the spatial dynamics by microscopy.
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                </p>
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                <p>
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                <u>Methods</u> <br />
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                To visualize the activation of our construct, we prepared cells as above for the previous plate-reader experiments, spread 10 µl on a glass slide added a coverslip and imaged them on a Zeiss Axioplan with a x100 objective and a APC (Cy5.5) filter. The pictures shown bellow were taken with a 5.1(s) integration time.
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                </p>
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                <p>
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                <u>Results</u> <br />
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                As seen in the pictures bellow, we were able to distinguish specific patterns within bacteria. We observed two phenotypes within our population: elongated and normal cells. The difference in these phenotypes was noticed in previous experiments and is most certainly due to the CpxR overexpression as we observed this also in non-stressed conditions. In the first phenotype (elongated) we were able to distinguish several bands that seem fairly uniformly distributed. In the second phenotype (normal) we observed a single band in the center of the bacteria. These observations led us to believe that CpxR might be involved in the division process of <i>E. coli</i> as it seems coherent for cells to slow down division upon stress. After looking into the literature, similar bands were visualizable in <i>E. coli</i> for factors related to septum formation such as ftsZ or pbpB. Nevertheless when comparing our patterns to the ftsZ and pbpB patterns, we noticed that CpxR might be localized in opposition to these factors. Further experiments comparing the sub-localization of CpxR and ftsZ could help the scientific community better understand how <i>E. coli</i> monitor division under various environments.
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                </p>
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  <a href="https://static.igem.org/mediawiki/2014/0/07/EPFL_2014_03_10_2014_Experiment-46.jpg" data-lightbox="results" data-title="Results"><img src="https://static.igem.org/mediawiki/2014/0/07/EPFL_2014_03_10_2014_Experiment-46.jpg" alt="results" width="45%" class="pull-left"></a>
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  <a href="https://static.igem.org/mediawiki/2014/e/ec/EPFL_2014_03_10_2014_Experiment-24.jpg" data-lightbox="results" data-title="Results"></a>
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  <a href="https://static.igem.org/mediawiki/2014/d/de/EPFL_2014_03_10_2014_Experiment-34.jpg" data-lightbox="results" data-title="Results"></a>
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                <h2> <b><u>Characterisation of the split luciferase </u> </b> </h2>
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                <h3><b>Experiment 1: </b>CheY/CheZ fused to split Firefly/Renilla luciferase, and full Firefly/Renilla luciferase characterisation </h3>
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                <p><u>Introduction</u> <br />
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                CheY and CheZ are two proteins involved in the bacterial chemotaxis pathway. It has been shown by split luciferase complementation assay that these two proteins are not interacting in presence of chemoattractant, but start to interact (CheZ being the phosphatase of CheY) in absence of chemoattractant or presence of chemorepellent. Based on the work of Waldor<sup><a href="#ref1">1</a></sup> Laboratory, we wanted to redo and adapt the experiment to test our own splits.<br /> <br /></p>
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                This experiment aimed to test the efficiency of split Renilla luciferase and split Firefly luciferase. We wanted to study the speed of the signal and the amount of substrate needed to have a performant response. <br /> <br />
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          <a href="#" class="dropdown-toggle active" data-toggle="dropdown">Achievements <span class="caret"></span></a>
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            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Results">Results</a></li>
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                <u>Method</u> <br />
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            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Data">Data</a></li>
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                To proceed to this complementation assay, we built two constructs, one to test split Renilla Luciferase and the other for split Firefly Luciferase The CheY was fused to the N-terminal part of each split, while the CheZ was fused to the C-terminal part. We used the full luciferases (Renilla : <a href="http://parts.igem.org/Part:BBa_K1486022"> BBa_K1486022 </a> and Firefly : <a href="http://parts.igem.org/Part:BBa_K325108"> BBa_K325108 </a> from Cambridge 2010 team) as positive controls and the non-fused splits (Renilla : <a href="http://parts.igem.org/Part:BBa_K1486021"> BBa_K1486021 </a> and Firefly : <a href="http://parts.igem.org/Part:BBa_K1486018"> BBa_K1486018 </a>) as negative controls.<br /> <br />
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            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Judging">Judging</a></li>
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                The bioluminescence assay was performed as described <a href="https://static.igem.org/mediawiki/2014/6/6d/Protocol_-_Bioluminescence_assay.pdf">here</a>. <br />
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                The constructs were designed and assembled as described <a href="https://static.igem.org/mediawiki/2014/3/3b/Constructs_design_CheYCheZ.pdf">here</a>.<br /><br /> <br />
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                <p><u>Results</u> <br />
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                As shown in the graphs below (fig.1A and 1B), we couldn't really observe a high signal for our complementation assay. However, the signal being higher than the blanks, it is an encouraging sign that the splits luciferase can be used for other experiments of this kind. A possible explanation for these results is that arabinose being a chemoattractant, we might need to do more wash steps with PBS to get rid of the arabinose before taking the measurements. Moreover, CheY and CheZ being endogenously expressed in bacteria, the edogenous proteins could interfere with our fusion proteins and weaken our signal. This complementation assay should be tested with CheY/CheZ knock out strains, as it was done in Waldor Laboratory.<br />
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                <a href="https://static.igem.org/mediawiki/2014/3/30/Renilla-CheYCheZexp.png" data-lightbox="cheYcheZ" data-title="Renilla"><img src="https://static.igem.org/mediawiki/2014/3/30/Renilla-CheYCheZexp.png" alt="cheYcheZ" width="45%"></a>
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            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Safety">Bio Safety</a></li>
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                <a href="https://static.igem.org/mediawiki/2014/f/f9/Firefly-CheYCheZexp.png" data-lightbox="cheYcheZ" data-title="Firefly"><img src="https://static.igem.org/mediawiki/2014/f/f9/Firefly-CheYCheZexp.png" alt="cheYcheZ" width="45%"></a>
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                We also could determine which of the luciferases would best suit our following experiments. As shown in fig. 2, for the same concentration of substrate, we see that firefly luciferase has a more stable and higher signal.  Moreover, the difference between the background noise (negative control, non fused split luciferase) and the full luciferase is bigger for Firefly luciferase, which is also preferable.<br />
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          <a href="#" class="dropdown-toggle" data-toggle="dropdown">Notebook <span class="caret"></span></a>
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            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Bacteria">Bacteria</a></li>
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                <h2> <b><u>Microfluidic Achievements </u> </b> </h2>
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                <h3><b>Experiment 1: </b></h3>
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                <h3>Microfluidic Accomplishments</h3>
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                      <th>MITOMI</th>
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            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook">Timeline</a></li>
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                      <th>MITOMI modified</th>
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            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Team">Meet us!</a></li>
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                      <th>SmashColi</th>
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             <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Attributions">Attributions</a></li>
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                      <th>BioPad</th>
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            <li><a href="https://2014.igem.org/Team:EPF_Lausanne/Acknowledgments">Acknowledgments</a></li>
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                      <th>FilterColi</th>
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                      <th>CleanColi</th>
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                      <td>Full chip</td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/a/ab/Mitomi11.png" data-lightbox="chips" data-title="MITOMI"><img src="https://static.igem.org/mediawiki/2014/a/ab/Mitomi11.png" width="70%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/6/64/Mitomimodif1.png" data-lightbox="chips" data-title="MITOMI Modified"><img src="https://static.igem.org/mediawiki/2014/6/64/Mitomimodif1.png" width="70%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/1/15/Smash1.png" data-lightbox="chips" data-title="SmashColi"><img src="https://static.igem.org/mediawiki/2014/1/15/Smash1.png" width="70%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/d/db/Biopad1.png" data-lightbox="chips" data-title="BioPad"><img src="https://static.igem.org/mediawiki/2014/d/db/Biopad1.png" width="70%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/d/db/Filter1.png" data-lightbox="chips" data-title="FilterColi"><img src="https://static.igem.org/mediawiki/2014/d/db/Filter1.png" width="70%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/e/e1/Clean1.png" data-lightbox="chips" data-title="CleanColi"><img src="https://static.igem.org/mediawiki/2014/e/e1/Clean1.png" width="70%"/></a><br /></td>
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                      <td>Unit Cell</td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/0/0f/MitomiUnit1.png" data-lightbox="chips" data-title="MITOMI Unit"><img src="https://static.igem.org/mediawiki/2014/0/0f/MitomiUnit1.png" width="50%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/7/78/MitomimodifUnit.png" data-lightbox="chips" data-title="MITOMI Modified Unit"><img src="https://static.igem.org/mediawiki/2014/7/78/MitomimodifUnit.png" width="70%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/3/3a/Smahsunit1.png" data-lightbox="chips" data-title="SmashColi Unit"><img src="https://static.igem.org/mediawiki/2014/3/3a/Smahsunit1.png" width="30%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/6/60/Biopadunit1.png" data-lightbox="chips" data-title="BioPad Unit"><img src="https://static.igem.org/mediawiki/2014/6/60/Biopadunit1.png" width="70%"/></a><br /></td>
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                      <td class="cntr"><a href="https://static.igem.org/mediawiki/2014/9/9e/FilterUnit.png" data-lightbox="chips" data-title="FilterColi Unit"><img src="https://static.igem.org/mediawiki/2014/9/9e/FilterUnit.png" width="70%"/></a><br /></td>
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                      <td>Designed</td>
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                      <td>Mold fabrication</td>
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                      <td>Fabrication of the chip</td>
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                      <td>Application</td>
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                      <td>Reference</td>
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                      <td ><a href="http://link.springer.com/protocol/10.1007%2F978-1-61779-292-2_6">MITOMI paper</a><br /></td>
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                <h3><b>Experiment 2: Culturing <i>E. coli</i> with constitutive GFP on chip</b></h3>
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                <p>We loaded <i>E. coli</i>, which contained constitutive GFP, in the chip. By using LabVIEW, a protocol was launched overnight to ensure the growth of the cells (the protocol can be found <a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Microfluidics">here</a>).
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                <p>The next morning, a scan of the chip was done to see the intensity of the GFP in the chip.<br /></p>
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                    <img src="https://static.igem.org/mediawiki/2014/f/fe/Gfp.png" width="300">
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                <br />
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                <h3><b>Experiment 3: Inducing the pBAD promoter of our <i>E. coli</i> that has CpxR linked with GFP</b></h3>
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                <p>The experiment that was done on wetbench to show that CpxR linked with GFP was expressed with an arabinose promoter was replicated on a MITOMI chip.
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                LB medium with arabinose was flowed in the upper half whereas LB medium without arabinose was flowed in the lower half. We scanned every hour for 5h (to know how it was done click <a href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Microfluidics">here</a>).</p>
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                <p><img src="https://static.igem.org/mediawiki/2014/4/4e/Truc2.png" alt="" class="img-responsive" /></p>
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                <p><strong>Figure 1.</strong> Scan of the microfluidic chip at t = 0min. No signal is detected</p>
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                <p>&nbsp;</p>
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                <p><img src="https://static.igem.org/mediawiki/2014/3/32/Truc3.png" alt="" class="img-responsive" /></p>
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                <p><strong>Figure 2.</strong> Scan of the microfluidic chip at t = 300min.</p>
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                <p>We analysed the scans and obtained the following results.</p>
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                <p><img src="https://static.igem.org/mediawiki/2014/4/4c/Gfp_ara.png" alt="" class="img-responsive" /></p>
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                <p><strong>Figure 3.&nbsp;</strong>Evolution of CpxR-GFP fluorescence over time</p>
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                <h2> <b><u>Yeast stuff ?</u> </b> </h2>
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                <h3><b>Experiment 1: </b></h3>
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                <p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus</p>
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                <h4> References </h4>
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                <p>
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                <a id="ref1"></a>1: S.K. Hatzios, S. Ringgaard, B. M. Davis, M. K. Waldor (2012, August 15). Studies of Dynamic Protein-Protein Interactions in Bacteria Using Renilla Luciferase Complementation Are Undermined by Nonspecific Enzyme Inhibition. <i>Plos One</i>.
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 +
<!-- PARTS -->
 +
 
 +
 
 +
<div id="parts">
 +
<div class="align-left">
 +
 
 +
<h1 class="cntr">PARTS</h1>
 +
 
 +
 
 +
 
 +
<section id="dna">
 +
<h3 class="section-heading">DNA parts submitted by the 2014 EPFL iGEM team</h3>
 +
<p class="lead">
 +
Our team submitted a total of 55 Biobricks (biobrick 51 does not exist).</p>
 +
<p class="lead">
 +
In addition, 4 microfluidic designs have also been submitted to the registry.</p>
 +
<table class="table table-striped table-hover" id="biobricks_list">
 +
  <tr>
 +
    <th>Biobrick</th>
 +
    <th>What it is</th>
 +
    <th>Function</th>
 +
    <th>Why do we use it?</th>
 +
    <th>Group</th>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486000</td>
 +
    <td>CpxR coding sequence</td>
 +
    <td>Transcription factor</td>
 +
    <td>To make most of our biobricks!</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486001</td>
 +
    <td>CpxR under arabinose promoter</td>
 +
    <td>Treanscription factor</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486002</td>
 +
    <td>PAra + sfGFP CpxR [Nterm]</td>
 +
    <td>Expresses fused protein</td>
 +
    <td>Test CpxR expression & Ara promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486003</td>
 +
    <td>Flexible linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486004</td>
 +
    <td>Flexible linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486005</td>
 +
    <td>PAra + CpxR sfGFP [Cterm]</td>
 +
    <td>Expresses fused protein</td>
 +
    <td>Test CpxR expression & Ara promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486006</td>
 +
    <td>IFP[1]</td>
 +
    <td>N terminus of split IFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486007</td>
 +
    <td>IFP[2]</td>
 +
    <td>C terminus of split IFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486008</td>
 +
    <td>CxpR & Split IFP1.4 [Cterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each C terminus attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486009</td>
 +
    <td>CxpR & Split IFP1.4 [Nterm + Nterm]</td>
 +
    <td>Two CpxR CDS, each N terminus attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486010</td>
 +
    <td>CxpR & Split IFP1.4 [Nterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486011</td>
 +
    <td>CxpR & Split IFP1.4 [Cterm + Nterm]</td>
 +
    <td>Two CpxR CDS, each attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486012</td>
 +
    <td>CpxR + IFP[1]</td>
 +
    <td>CpxR with the Nterm moiety of IFP attached at its C terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486013</td>
 +
    <td>CpxR + IFP[2]</td>
 +
    <td>CpxR with the Cterm moiety of IFP attached at its C terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486014</td>
 +
    <td>IFP[1] + CpxR</td>
 +
    <td>CpxR with the Nterm moiety of IFP attached at its N terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486015</td>
 +
    <td>IFP[2] + CpxR</td>
 +
    <td>CpxR with the Cterm moiety of IFP attached at its N terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486016</td>
 +
    <td>fLuc[1]</td>
 +
    <td>N terminus moiety of the firefly luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486017</td>
 +
    <td>fLuc[2]</td>
 +
    <td>C terminus moiety of the firefly luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486018</td>
 +
    <td>PAra + fLuc[1] + fLuc[2]</td>
 +
    <td>Split firefly luciferase under arabinose promoter</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486019</td>
 +
    <td>rLuc[1]</td>
 +
    <td>C terminus moiety of the renilla luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486020</td>
 +
    <td>rLuc[2]</td>
 +
    <td>N terminus moiety of the renilla luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486021</td>
 +
    <td>PAra + rLuc[1] + rLuc[2]</td>
 +
    <td>Split renilla luciferase under arabinose promoter</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486022</td>
 +
    <td>rLuc</td>
 +
    <td>Full renilla luciferase</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486023</td>
 +
    <td>Yeast sfGFP</td>
 +
    <td>Superfolder GFP for yeast cells</td>
 +
    <td>Reporter</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486024</td>
 +
    <td>Kan</td>
 +
    <td>Yeast kanamycin resistance gene</td>
 +
    <td>Selection marker</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486025</td>
 +
    <td>ADH1 terminator</td>
 +
    <td>Terminator</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486026</td>
 +
    <td>Yeast sfGFP + Kan</td>
 +
    <td>Yeast sfGFP attached to the yeast kanamycin resistance gene</td>
 +
    <td>Control the expression of pbs2</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486027</td>
 +
    <td>rLuc + Kan</td>
 +
    <td>Renilla luciferase attached to the kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486028</td>
 +
    <td>Yeast sfGFP[1]</td>
 +
    <td>N terminal moiety of split yeast sfGFP</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486029</td>
 +
    <td>sfGFP[1] + kan</td>
 +
    <td>Nterm moiety of split yeast sfGFP attached to yeast kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486030</td>
 +
    <td>rLuc[1] + kan</td>
 +
    <td>Nterm moiety of split renilla luciferase attached to yeast kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486031</td>
 +
    <td>Ura</td>
 +
    <td>CDS for Uracil (yeast selective purposes)</td>
 +
    <td>Confer resistance to Uracil-deprived medium</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486032</td>
 +
    <td>Yeast sfGFP + Ura</td>
 +
    <td>Yeast sfGFP attached to the Uracil CDS</td>
 +
    <td>Control the expression of hog1</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486033</td>
 +
    <td>rLuc + Ura</td>
 +
    <td>Renilla luciferase attached to the Uracil CDS</td>
 +
    <td>Control the expression of hog1</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486034</td>
 +
    <td>yeast sfGFP[2]</td>
 +
    <td>C terminal moiety of split the yeast sfGFP</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486035</td>
 +
    <td>yeast sfGFP[2] + Ura</td>
 +
    <td>Cterm moiety of split yeast sfGFP attached to the Uracil CDS</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486036</td>
 +
    <td>rLuc[2] + Ura</td>
 +
    <td>Cterm moiety of split renilla luciferase attached to the Uracil CDS</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486037</td>
 +
    <td>linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486038</td>
 +
    <td>sfGFP[1]</td>
 +
    <td>N terminus moiety of split superfolder GFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486039</td>
 +
    <td>sfGFP[2]</td>
 +
    <td>C terminus moiety of split superfolder GFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486040</td>
 +
    <td>sfGFP[1] + CpxR</td>
 +
    <td>N terminus moiety of split sfGFP attached to CpxR</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486041</td>
 +
    <td>sfGFP[2] + CpxR</td>
 +
    <td>C terminus moiety of split sfGFP attached to CpxR</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486042</td>
 +
    <td>LZip</td>
 +
    <td>Monomer of leucine zipper TF</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486043</td>
 +
    <td>LZip + split rLuc</td>
 +
    <td>Two Leucine Zipper monomers, each attached to a different split rLuc moiety</td>
 +
    <td>Control for split rLuc assays</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486044</td>
 +
    <td>mut IFP[1]</td>
 +
    <td>Biobrick-compatible IFP[1]</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486045</td>
 +
    <td>mut IFP[2]</td>
 +
    <td>Biobrick-compatible IFP[2]</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486046</td>
 +
    <td>CpxR promoter FW</td>
 +
    <td>CpxR binding-region in forward direction</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486047</td>
 +
    <td>CpxR promoter RV</td>
 +
    <td>CpxR binding-region in reverse direction</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486048</td>
 +
    <td>CpxR reporter</td>
 +
    <td>Calgary's CpxR reporter repaired (sequence was missing)</td>
 +
    <td>To see when CpxR is active</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486049</td>
 +
    <td>CpxR promoter FW + RFP</td>
 +
    <td>Reporter of CpxR</td>
 +
    <td>Test the direction of the complete CpxR promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486050</td>
 +
    <td>CpxR promoter RV + RFP</td>
 +
    <td>Reporter of CpxR</td>
 +
    <td>Test the direction of the complete CpxR promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486052</td>
 +
    <td>Spacer</td>
 +
    <td>40 bases placed between constructs</td>
 +
    <td>Separate two constructs in the same plasmid</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486053</td>
 +
    <td>Linker</td>
 +
    <td>10 amino-acid linker</td>
 +
    <td>Attach CheY/Z to split luciferases</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486054</td>
 +
    <td>CheY/CheZ rLuc</td>
 +
    <td>CheY and CheZ, each attached to a moiety of split renilla luciferase</td>
 +
    <td>Positive control for the split rLuc</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486055</td>
 +
    <td>CheY/CheZ fLuc</td>
 +
    <td>CheY and CheZ, each attached to a moiety of split firefly luciferase</td>
 +
    <td>Positive control for the split fLuc</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486056</td>
 +
    <td>CxpR & Split mut IFP1.4 [Cterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each C terminus attached to a moiety of the biobrick-compatible IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
</table>
 +
 
 +
</section>
 +
 
 +
<br /><br />
 +
 
 +
 
 +
<section id="microfluidics">
 +
<h3 class="section-heading">Microfluidics parts (chips created)</h3>
 +
<p class="lead">
 +
Our team designed and made 4 microfluidic chips. At the beginning, we also used the <a target="_blank" href="http://link.springer.com/protocol/10.1007%2F978-1-61779-292-2_6">MITOMI chip</a>.</p>
 +
<p class="lead">When designing the chips, the team took into account the future users and the current iGEM classification of parts. We considered it best to construct our chips as composite microfluidic parts, so their sub-parts could be used and combined in multiple ways. The flow and control layers can be separated and reused, as well as all the basic structures (chamber + connecting channel), nodes, array parts,...</p>
 +
 
 +
 
 +
<!-- send all lines here: https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Designing -->
 +
<table class="table table-striped table-hover" id="chips_list">
 +
  <tr>
 +
    <th>Name</th>
 +
    <th>Main Function</th>
 +
  </tr>
 +
  <tr>
 +
    <td>MITOMI modified</td>
 +
    <td>By using the MITOMI chip as a template, we designed our first chip that could squish the cells in the chamber.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>SmashColi</td>
 +
    <td>To be able to separate the chip in 4 different compartments and apply 4 different pressures on each row of chambers.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>BioPad</td>
 +
    <td>A large and simple microfluidic chip containing 6400 chambers in which the cells are contained in. Each chamber acts as a pixel for the BioPad project.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>CleanColi</td>
 +
    <td>As a result of our Safety page, we decided to create a chip that is able to seal the bacteria in the chip, preventing them to leave the chip.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>FilterColi</td>
 +
    <td>To successfully immerse cells in a certain solution, this chip was designed to flow in the new medium in the chambers instead of doing it by diffusion.</td>
 +
  </tr>
 +
</table>
 +
</section>
 +
 
 +
 
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<br /><br />
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<!-- PARTS -->
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<div id="parts">
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<div class="align-left">
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<h1 class="cntr">PARTS</h1>
 +
 +
 +
 +
<section id="dna">
 +
<h3 class="section-heading">DNA parts submitted by the 2014 EPFL iGEM team</h3>
 +
<p class="lead">
 +
Our team submitted a total of 55 Biobricks (biobrick 51 does not exist).</p>
 +
<p class="lead">
 +
In addition, 4 microfluidic designs have also been submitted to the registry.</p>
 +
<table class="table table-striped table-hover" id="biobricks_list">
 +
  <tr>
 +
    <th>Biobrick</th>
 +
    <th>What it is</th>
 +
    <th>Function</th>
 +
    <th>Why do we use it?</th>
 +
    <th>Group</th>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486000</td>
 +
    <td>CpxR coding sequence</td>
 +
    <td>Transcription factor</td>
 +
    <td>To make most of our biobricks!</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486001</td>
 +
    <td>CpxR under arabinose promoter</td>
 +
    <td>Treanscription factor</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486002</td>
 +
    <td>PAra + sfGFP CpxR [Nterm]</td>
 +
    <td>Expresses fused protein</td>
 +
    <td>Test CpxR expression & Ara promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486003</td>
 +
    <td>Flexible linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486004</td>
 +
    <td>Flexible linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486005</td>
 +
    <td>PAra + CpxR sfGFP [Cterm]</td>
 +
    <td>Expresses fused protein</td>
 +
    <td>Test CpxR expression & Ara promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486006</td>
 +
    <td>IFP[1]</td>
 +
    <td>N terminus of split IFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486007</td>
 +
    <td>IFP[2]</td>
 +
    <td>C terminus of split IFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486008</td>
 +
    <td>CxpR & Split IFP1.4 [Cterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each C terminus attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486009</td>
 +
    <td>CxpR & Split IFP1.4 [Nterm + Nterm]</td>
 +
    <td>Two CpxR CDS, each N terminus attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486010</td>
 +
    <td>CxpR & Split IFP1.4 [Nterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486011</td>
 +
    <td>CxpR & Split IFP1.4 [Cterm + Nterm]</td>
 +
    <td>Two CpxR CDS, each attached to a moiety of IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486012</td>
 +
    <td>CpxR + IFP[1]</td>
 +
    <td>CpxR with the Nterm moiety of IFP attached at its C terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486013</td>
 +
    <td>CpxR + IFP[2]</td>
 +
    <td>CpxR with the Cterm moiety of IFP attached at its C terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486014</td>
 +
    <td>IFP[1] + CpxR</td>
 +
    <td>CpxR with the Nterm moiety of IFP attached at its N terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486015</td>
 +
    <td>IFP[2] + CpxR</td>
 +
    <td>CpxR with the Cterm moiety of IFP attached at its N terminus</td>
 +
    <td>Intermediate & control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486016</td>
 +
    <td>fLuc[1]</td>
 +
    <td>N terminus moiety of the firefly luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486017</td>
 +
    <td>fLuc[2]</td>
 +
    <td>C terminus moiety of the firefly luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486018</td>
 +
    <td>PAra + fLuc[1] + fLuc[2]</td>
 +
    <td>Split firefly luciferase under arabinose promoter</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486019</td>
 +
    <td>rLuc[1]</td>
 +
    <td>C terminus moiety of the renilla luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486020</td>
 +
    <td>rLuc[2]</td>
 +
    <td>N terminus moiety of the renilla luciferase</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486021</td>
 +
    <td>PAra + rLuc[1] + rLuc[2]</td>
 +
    <td>Split renilla luciferase under arabinose promoter</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486022</td>
 +
    <td>rLuc</td>
 +
    <td>Full renilla luciferase</td>
 +
    <td>Control</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486023</td>
 +
    <td>Yeast sfGFP</td>
 +
    <td>Superfolder GFP for yeast cells</td>
 +
    <td>Reporter</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486024</td>
 +
    <td>Kan</td>
 +
    <td>Yeast kanamycin resistance gene</td>
 +
    <td>Selection marker</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486025</td>
 +
    <td>ADH1 terminator</td>
 +
    <td>Terminator</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486026</td>
 +
    <td>Yeast sfGFP + Kan</td>
 +
    <td>Yeast sfGFP attached to the yeast kanamycin resistance gene</td>
 +
    <td>Control the expression of pbs2</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486027</td>
 +
    <td>rLuc + Kan</td>
 +
    <td>Renilla luciferase attached to the kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486028</td>
 +
    <td>Yeast sfGFP[1]</td>
 +
    <td>N terminal moiety of split yeast sfGFP</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486029</td>
 +
    <td>sfGFP[1] + kan</td>
 +
    <td>Nterm moiety of split yeast sfGFP attached to yeast kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486030</td>
 +
    <td>rLuc[1] + kan</td>
 +
    <td>Nterm moiety of split renilla luciferase attached to yeast kanamycin resistance gene</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486031</td>
 +
    <td>Ura</td>
 +
    <td>CDS for Uracil (yeast selective purposes)</td>
 +
    <td>Confer resistance to Uracil-deprived medium</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486032</td>
 +
    <td>Yeast sfGFP + Ura</td>
 +
    <td>Yeast sfGFP attached to the Uracil CDS</td>
 +
    <td>Control the expression of hog1</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486033</td>
 +
    <td>rLuc + Ura</td>
 +
    <td>Renilla luciferase attached to the Uracil CDS</td>
 +
    <td>Control the expression of hog1</td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486034</td>
 +
    <td>yeast sfGFP[2]</td>
 +
    <td>C terminal moiety of split the yeast sfGFP</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486035</td>
 +
    <td>yeast sfGFP[2] + Ura</td>
 +
    <td>Cterm moiety of split yeast sfGFP attached to the Uracil CDS</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
<tr>
 +
    <td class="biobrick_name">BBa_K1486036</td>
 +
    <td>rLuc[2] + Ura</td>
 +
    <td>Cterm moiety of split renilla luciferase attached to the Uracil CDS</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486037</td>
 +
    <td>linker</td>
 +
    <td>Attaches two proteins together</td>
 +
    <td> </td>
 +
    <td>Yeast</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486038</td>
 +
    <td>sfGFP[1]</td>
 +
    <td>N terminus moiety of split superfolder GFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486039</td>
 +
    <td>sfGFP[2]</td>
 +
    <td>C terminus moiety of split superfolder GFP</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486040</td>
 +
    <td>sfGFP[1] + CpxR</td>
 +
    <td>N terminus moiety of split sfGFP attached to CpxR</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486041</td>
 +
    <td>sfGFP[2] + CpxR</td>
 +
    <td>C terminus moiety of split sfGFP attached to CpxR</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486042</td>
 +
    <td>LZip</td>
 +
    <td>Monomer of leucine zipper TF</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486043</td>
 +
    <td>LZip + split rLuc</td>
 +
    <td>Two Leucine Zipper monomers, each attached to a different split rLuc moiety</td>
 +
    <td>Control for split rLuc assays</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486044</td>
 +
    <td>mut IFP[1]</td>
 +
    <td>Biobrick-compatible IFP[1]</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486045</td>
 +
    <td>mut IFP[2]</td>
 +
    <td>Biobrick-compatible IFP[2]</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486046</td>
 +
    <td>CpxR promoter FW</td>
 +
    <td>CpxR binding-region in forward direction</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486047</td>
 +
    <td>CpxR promoter RV</td>
 +
    <td>CpxR binding-region in reverse direction</td>
 +
    <td> </td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486048</td>
 +
    <td>CpxR reporter</td>
 +
    <td>Calgary's CpxR reporter repaired (sequence was missing)</td>
 +
    <td>To see when CpxR is active</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486049</td>
 +
    <td>CpxR promoter FW + RFP</td>
 +
    <td>Reporter of CpxR</td>
 +
    <td>Test the direction of the complete CpxR promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486050</td>
 +
    <td>CpxR promoter RV + RFP</td>
 +
    <td>Reporter of CpxR</td>
 +
    <td>Test the direction of the complete CpxR promoter</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486052</td>
 +
    <td>Spacer</td>
 +
    <td>40 bases placed between constructs</td>
 +
    <td>Separate two constructs in the same plasmid</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486053</td>
 +
    <td>Linker</td>
 +
    <td>10 amino-acid linker</td>
 +
    <td>Attach CheY/Z to split luciferases</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486054</td>
 +
    <td>CheY/CheZ rLuc</td>
 +
    <td>CheY and CheZ, each attached to a moiety of split renilla luciferase</td>
 +
    <td>Positive control for the split rLuc</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486055</td>
 +
    <td>CheY/CheZ fLuc</td>
 +
    <td>CheY and CheZ, each attached to a moiety of split firefly luciferase</td>
 +
    <td>Positive control for the split fLuc</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
  <tr>
 +
    <td class="biobrick_name">BBa_K1486056</td>
 +
    <td>CxpR & Split mut IFP1.4 [Cterm + Cterm]</td>
 +
    <td>Two CpxR CDS, each C terminus attached to a moiety of the biobrick-compatible IFP</td>
 +
    <td>Characterize CpxR dimerization</td>
 +
    <td>Bacteria</td>
 +
  </tr>
 +
</table>
 +
 +
</section>
 +
 +
<br /><br />
 +
 +
 +
<section id="microfluidics">
 +
<h3 class="section-heading">Microfluidics parts (chips created)</h3>
 +
<p class="lead">
 +
Our team designed and made 4 microfluidic chips. At the beginning, we also used the <a target="_blank" href="http://link.springer.com/protocol/10.1007%2F978-1-61779-292-2_6">MITOMI chip</a>.</p>
 +
<p class="lead">When designing the chips, the team took into account the future users and the current iGEM classification of parts. We considered it best to construct our chips as composite microfluidic parts, so their sub-parts could be used and combined in multiple ways. The flow and control layers can be separated and reused, as well as all the basic structures (chamber + connecting channel), nodes, array parts,...</p>
 +
 +
 +
<!-- send all lines here: https://2014.igem.org/Team:EPF_Lausanne/Microfluidics/Designing -->
 +
<table class="table table-striped table-hover" id="chips_list">
 +
  <tr>
 +
    <th>Name</th>
 +
    <th>Main Function</th>
 +
  </tr>
 +
  <tr>
 +
    <td>MITOMI modified</td>
 +
    <td>By using the MITOMI chip as a template, we designed our first chip that could squish the cells in the chamber.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>SmashColi</td>
 +
    <td>To be able to separate the chip in 4 different compartments and apply 4 different pressures on each row of chambers.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>BioPad</td>
 +
    <td>A large and simple microfluidic chip containing 6400 chambers in which the cells are contained in. Each chamber acts as a pixel for the BioPad project.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>CleanColi</td>
 +
    <td>As a result of our Safety page, we decided to create a chip that is able to seal the bacteria in the chip, preventing them to leave the chip.</td>
 +
  </tr>
 +
  <tr>
 +
    <td>FilterColi</td>
 +
    <td>To successfully immerse cells in a certain solution, this chip was designed to flow in the new medium in the chambers instead of doing it by diffusion.</td>
 +
  </tr>
 +
</table>
 +
</section>
 +
 +
 +
<br /><br />
 +
</div>
 +
</div>
 +
 +
</div>
 +
</div>
 +
 +
<div class="col col-md-3">
 +
<nav id="affix-nav" class="sidebar hidden-sm hidden-xs">
 +
    <ul class="nav sidenav box" data-spy="affix" data-offset-top="200" data-offset-bottom="400">
 +
        <li class="active"><a href="#dna">DNA Parts</a></li>
 +
        <li><a href="#microfluidics">Microfluidics Parts</a></li>
 +
    </ul>
 +
</nav>
 +
</div>
 +
</div>
 +
</div>
 +
<!-- END ABSTRACT -->
 +
 +
<script type="text/javascript">
 +
    $(document).ready(function() {
 +
      $('#biobricks_list tr').click(function (e) {
 +
        text = $(this).children('td.biobrick_name').first().text();
 +
        if (text != '') {
 +
          return window.open('http://parts.igem.org/Part:' + text, '_blank');
 +
        }
 +
      });
 +
    });
 +
</script>
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Revision as of 13:14, 15 October 2014

PARTS

DNA parts submitted by the 2014 EPFL iGEM team

Our team submitted a total of 55 Biobricks (biobrick 51 does not exist).

In addition, 4 microfluidic designs have also been submitted to the registry.

Biobrick What it is Function Why do we use it? Group
BBa_K1486000 CpxR coding sequence Transcription factor To make most of our biobricks! Bacteria
BBa_K1486001 CpxR under arabinose promoter Treanscription factor Bacteria
BBa_K1486002 PAra + sfGFP CpxR [Nterm] Expresses fused protein Test CpxR expression & Ara promoter Bacteria
BBa_K1486003 Flexible linker Attaches two proteins together Bacteria
BBa_K1486004 Flexible linker Attaches two proteins together Bacteria
BBa_K1486005 PAra + CpxR sfGFP [Cterm] Expresses fused protein Test CpxR expression & Ara promoter Bacteria
BBa_K1486006 IFP[1] N terminus of split IFP Bacteria
BBa_K1486007 IFP[2] C terminus of split IFP Bacteria
BBa_K1486008 CxpR & Split IFP1.4 [Cterm + Cterm] Two CpxR CDS, each C terminus attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486009 CxpR & Split IFP1.4 [Nterm + Nterm] Two CpxR CDS, each N terminus attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486010 CxpR & Split IFP1.4 [Nterm + Cterm] Two CpxR CDS, each attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486011 CxpR & Split IFP1.4 [Cterm + Nterm] Two CpxR CDS, each attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486012 CpxR + IFP[1] CpxR with the Nterm moiety of IFP attached at its C terminus Intermediate & control Bacteria
BBa_K1486013 CpxR + IFP[2] CpxR with the Cterm moiety of IFP attached at its C terminus Intermediate & control Bacteria
BBa_K1486014 IFP[1] + CpxR CpxR with the Nterm moiety of IFP attached at its N terminus Intermediate & control Bacteria
BBa_K1486015 IFP[2] + CpxR CpxR with the Cterm moiety of IFP attached at its N terminus Intermediate & control Bacteria
BBa_K1486016 fLuc[1] N terminus moiety of the firefly luciferase Bacteria
BBa_K1486017 fLuc[2] C terminus moiety of the firefly luciferase Bacteria
BBa_K1486018 PAra + fLuc[1] + fLuc[2] Split firefly luciferase under arabinose promoter Control Bacteria
BBa_K1486019 rLuc[1] C terminus moiety of the renilla luciferase Bacteria
BBa_K1486020 rLuc[2] N terminus moiety of the renilla luciferase Bacteria
BBa_K1486021 PAra + rLuc[1] + rLuc[2] Split renilla luciferase under arabinose promoter Control Bacteria
BBa_K1486022 rLuc Full renilla luciferase Control Bacteria
BBa_K1486023 Yeast sfGFP Superfolder GFP for yeast cells Reporter Yeast
BBa_K1486024 Kan Yeast kanamycin resistance gene Selection marker Yeast
BBa_K1486025 ADH1 terminator Terminator Yeast
BBa_K1486026 Yeast sfGFP + Kan Yeast sfGFP attached to the yeast kanamycin resistance gene Control the expression of pbs2 Yeast
BBa_K1486027 rLuc + Kan Renilla luciferase attached to the kanamycin resistance gene Yeast
BBa_K1486028 Yeast sfGFP[1] N terminal moiety of split yeast sfGFP Yeast
BBa_K1486029 sfGFP[1] + kan Nterm moiety of split yeast sfGFP attached to yeast kanamycin resistance gene Yeast
BBa_K1486030 rLuc[1] + kan Nterm moiety of split renilla luciferase attached to yeast kanamycin resistance gene Yeast
BBa_K1486031 Ura CDS for Uracil (yeast selective purposes) Confer resistance to Uracil-deprived medium Yeast
BBa_K1486032 Yeast sfGFP + Ura Yeast sfGFP attached to the Uracil CDS Control the expression of hog1 Yeast
BBa_K1486033 rLuc + Ura Renilla luciferase attached to the Uracil CDS Control the expression of hog1 Yeast
BBa_K1486034 yeast sfGFP[2] C terminal moiety of split the yeast sfGFP Yeast
BBa_K1486035 yeast sfGFP[2] + Ura Cterm moiety of split yeast sfGFP attached to the Uracil CDS Yeast
BBa_K1486036 rLuc[2] + Ura Cterm moiety of split renilla luciferase attached to the Uracil CDS Yeast
BBa_K1486037 linker Attaches two proteins together Yeast
BBa_K1486038 sfGFP[1] N terminus moiety of split superfolder GFP Bacteria
BBa_K1486039 sfGFP[2] C terminus moiety of split superfolder GFP Bacteria
BBa_K1486040 sfGFP[1] + CpxR N terminus moiety of split sfGFP attached to CpxR Bacteria
BBa_K1486041 sfGFP[2] + CpxR C terminus moiety of split sfGFP attached to CpxR Bacteria
BBa_K1486042 LZip Monomer of leucine zipper TF Bacteria
BBa_K1486043 LZip + split rLuc Two Leucine Zipper monomers, each attached to a different split rLuc moiety Control for split rLuc assays Bacteria
BBa_K1486044 mut IFP[1] Biobrick-compatible IFP[1] Bacteria
BBa_K1486045 mut IFP[2] Biobrick-compatible IFP[2] Bacteria
BBa_K1486046 CpxR promoter FW CpxR binding-region in forward direction Bacteria
BBa_K1486047 CpxR promoter RV CpxR binding-region in reverse direction Bacteria
BBa_K1486048 CpxR reporter Calgary's CpxR reporter repaired (sequence was missing) To see when CpxR is active Bacteria
BBa_K1486049 CpxR promoter FW + RFP Reporter of CpxR Test the direction of the complete CpxR promoter Bacteria
BBa_K1486050 CpxR promoter RV + RFP Reporter of CpxR Test the direction of the complete CpxR promoter Bacteria
BBa_K1486052 Spacer 40 bases placed between constructs Separate two constructs in the same plasmid Bacteria
BBa_K1486053 Linker 10 amino-acid linker Attach CheY/Z to split luciferases Bacteria
BBa_K1486054 CheY/CheZ rLuc CheY and CheZ, each attached to a moiety of split renilla luciferase Positive control for the split rLuc Bacteria
BBa_K1486055 CheY/CheZ fLuc CheY and CheZ, each attached to a moiety of split firefly luciferase Positive control for the split fLuc Bacteria
BBa_K1486056 CxpR & Split mut IFP1.4 [Cterm + Cterm] Two CpxR CDS, each C terminus attached to a moiety of the biobrick-compatible IFP Characterize CpxR dimerization Bacteria


Microfluidics parts (chips created)

Our team designed and made 4 microfluidic chips. At the beginning, we also used the MITOMI chip.

When designing the chips, the team took into account the future users and the current iGEM classification of parts. We considered it best to construct our chips as composite microfluidic parts, so their sub-parts could be used and combined in multiple ways. The flow and control layers can be separated and reused, as well as all the basic structures (chamber + connecting channel), nodes, array parts,...

Name Main Function
MITOMI modified By using the MITOMI chip as a template, we designed our first chip that could squish the cells in the chamber.
SmashColi To be able to separate the chip in 4 different compartments and apply 4 different pressures on each row of chambers.
BioPad A large and simple microfluidic chip containing 6400 chambers in which the cells are contained in. Each chamber acts as a pixel for the BioPad project.
CleanColi As a result of our Safety page, we decided to create a chip that is able to seal the bacteria in the chip, preventing them to leave the chip.
FilterColi To successfully immerse cells in a certain solution, this chip was designed to flow in the new medium in the chambers instead of doing it by diffusion.


Sponsors

Copyright © iGEM EPFL 2014. All Rights Reserved

PARTS

DNA parts submitted by the 2014 EPFL iGEM team

Our team submitted a total of 55 Biobricks (biobrick 51 does not exist).

In addition, 4 microfluidic designs have also been submitted to the registry.

Biobrick What it is Function Why do we use it? Group
BBa_K1486000 CpxR coding sequence Transcription factor To make most of our biobricks! Bacteria
BBa_K1486001 CpxR under arabinose promoter Treanscription factor Bacteria
BBa_K1486002 PAra + sfGFP CpxR [Nterm] Expresses fused protein Test CpxR expression & Ara promoter Bacteria
BBa_K1486003 Flexible linker Attaches two proteins together Bacteria
BBa_K1486004 Flexible linker Attaches two proteins together Bacteria
BBa_K1486005 PAra + CpxR sfGFP [Cterm] Expresses fused protein Test CpxR expression & Ara promoter Bacteria
BBa_K1486006 IFP[1] N terminus of split IFP Bacteria
BBa_K1486007 IFP[2] C terminus of split IFP Bacteria
BBa_K1486008 CxpR & Split IFP1.4 [Cterm + Cterm] Two CpxR CDS, each C terminus attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486009 CxpR & Split IFP1.4 [Nterm + Nterm] Two CpxR CDS, each N terminus attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486010 CxpR & Split IFP1.4 [Nterm + Cterm] Two CpxR CDS, each attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486011 CxpR & Split IFP1.4 [Cterm + Nterm] Two CpxR CDS, each attached to a moiety of IFP Characterize CpxR dimerization Bacteria
BBa_K1486012 CpxR + IFP[1] CpxR with the Nterm moiety of IFP attached at its C terminus Intermediate & control Bacteria
BBa_K1486013 CpxR + IFP[2] CpxR with the Cterm moiety of IFP attached at its C terminus Intermediate & control Bacteria
BBa_K1486014 IFP[1] + CpxR CpxR with the Nterm moiety of IFP attached at its N terminus Intermediate & control Bacteria
BBa_K1486015 IFP[2] + CpxR CpxR with the Cterm moiety of IFP attached at its N terminus Intermediate & control Bacteria
BBa_K1486016 fLuc[1] N terminus moiety of the firefly luciferase Bacteria
BBa_K1486017 fLuc[2] C terminus moiety of the firefly luciferase Bacteria
BBa_K1486018 PAra + fLuc[1] + fLuc[2] Split firefly luciferase under arabinose promoter Control Bacteria
BBa_K1486019 rLuc[1] C terminus moiety of the renilla luciferase Bacteria
BBa_K1486020 rLuc[2] N terminus moiety of the renilla luciferase Bacteria
BBa_K1486021 PAra + rLuc[1] + rLuc[2] Split renilla luciferase under arabinose promoter Control Bacteria
BBa_K1486022 rLuc Full renilla luciferase Control Bacteria
BBa_K1486023 Yeast sfGFP Superfolder GFP for yeast cells Reporter Yeast
BBa_K1486024 Kan Yeast kanamycin resistance gene Selection marker Yeast
BBa_K1486025 ADH1 terminator Terminator Yeast
BBa_K1486026 Yeast sfGFP + Kan Yeast sfGFP attached to the yeast kanamycin resistance gene Control the expression of pbs2 Yeast
BBa_K1486027 rLuc + Kan Renilla luciferase attached to the kanamycin resistance gene Yeast
BBa_K1486028 Yeast sfGFP[1] N terminal moiety of split yeast sfGFP Yeast
BBa_K1486029 sfGFP[1] + kan Nterm moiety of split yeast sfGFP attached to yeast kanamycin resistance gene Yeast
BBa_K1486030 rLuc[1] + kan Nterm moiety of split renilla luciferase attached to yeast kanamycin resistance gene Yeast
BBa_K1486031 Ura CDS for Uracil (yeast selective purposes) Confer resistance to Uracil-deprived medium Yeast
BBa_K1486032 Yeast sfGFP + Ura Yeast sfGFP attached to the Uracil CDS Control the expression of hog1 Yeast
BBa_K1486033 rLuc + Ura Renilla luciferase attached to the Uracil CDS Control the expression of hog1 Yeast
BBa_K1486034 yeast sfGFP[2] C terminal moiety of split the yeast sfGFP Yeast
BBa_K1486035 yeast sfGFP[2] + Ura Cterm moiety of split yeast sfGFP attached to the Uracil CDS Yeast
BBa_K1486036 rLuc[2] + Ura Cterm moiety of split renilla luciferase attached to the Uracil CDS Yeast
BBa_K1486037 linker Attaches two proteins together Yeast
BBa_K1486038 sfGFP[1] N terminus moiety of split superfolder GFP Bacteria
BBa_K1486039 sfGFP[2] C terminus moiety of split superfolder GFP Bacteria
BBa_K1486040 sfGFP[1] + CpxR N terminus moiety of split sfGFP attached to CpxR Bacteria
BBa_K1486041 sfGFP[2] + CpxR C terminus moiety of split sfGFP attached to CpxR Bacteria
BBa_K1486042 LZip Monomer of leucine zipper TF Bacteria
BBa_K1486043 LZip + split rLuc Two Leucine Zipper monomers, each attached to a different split rLuc moiety Control for split rLuc assays Bacteria
BBa_K1486044 mut IFP[1] Biobrick-compatible IFP[1] Bacteria
BBa_K1486045 mut IFP[2] Biobrick-compatible IFP[2] Bacteria
BBa_K1486046 CpxR promoter FW CpxR binding-region in forward direction Bacteria
BBa_K1486047 CpxR promoter RV CpxR binding-region in reverse direction Bacteria
BBa_K1486048 CpxR reporter Calgary's CpxR reporter repaired (sequence was missing) To see when CpxR is active Bacteria
BBa_K1486049 CpxR promoter FW + RFP Reporter of CpxR Test the direction of the complete CpxR promoter Bacteria
BBa_K1486050 CpxR promoter RV + RFP Reporter of CpxR Test the direction of the complete CpxR promoter Bacteria
BBa_K1486052 Spacer 40 bases placed between constructs Separate two constructs in the same plasmid Bacteria
BBa_K1486053 Linker 10 amino-acid linker Attach CheY/Z to split luciferases Bacteria
BBa_K1486054 CheY/CheZ rLuc CheY and CheZ, each attached to a moiety of split renilla luciferase Positive control for the split rLuc Bacteria
BBa_K1486055 CheY/CheZ fLuc CheY and CheZ, each attached to a moiety of split firefly luciferase Positive control for the split fLuc Bacteria
BBa_K1486056 CxpR & Split mut IFP1.4 [Cterm + Cterm] Two CpxR CDS, each C terminus attached to a moiety of the biobrick-compatible IFP Characterize CpxR dimerization Bacteria


Microfluidics parts (chips created)

Our team designed and made 4 microfluidic chips. At the beginning, we also used the MITOMI chip.

When designing the chips, the team took into account the future users and the current iGEM classification of parts. We considered it best to construct our chips as composite microfluidic parts, so their sub-parts could be used and combined in multiple ways. The flow and control layers can be separated and reused, as well as all the basic structures (chamber + connecting channel), nodes, array parts,...

Name Main Function
MITOMI modified By using the MITOMI chip as a template, we designed our first chip that could squish the cells in the chamber.
SmashColi To be able to separate the chip in 4 different compartments and apply 4 different pressures on each row of chambers.
BioPad A large and simple microfluidic chip containing 6400 chambers in which the cells are contained in. Each chamber acts as a pixel for the BioPad project.
CleanColi As a result of our Safety page, we decided to create a chip that is able to seal the bacteria in the chip, preventing them to leave the chip.
FilterColi To successfully immerse cells in a certain solution, this chip was designed to flow in the new medium in the chambers instead of doing it by diffusion.


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