Team:EPF Lausanne/Results

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                 <h1 class="cntr"> <b>RESULTS</b> </h1>
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                 <h1 class="cntr"> RESULTS </h1>
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<!--replaced the title : Characterisation of the spatiotemporal dynamics of the CpxR - split IFP 1.4 stress sensor -->
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                <h2 id="IFP_Exp" class="cntr"> <b> Characterisation of the spatiotemporal dynamics of the CpxR stress sensor  </b> </h2
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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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                <h3> <b>Experiment 1: </b> Characterisation of the AraC/PBad Promoter and folding ability GFP fused to CpxR </h3>
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                 <h3 id="IFP_Exp2"><b>Demonstration of CpxR's dimerization & Elucidation of its dimerization orientation</b></h3>
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                <p>This construct aimed to evaluate the expression of our construct and the characteristics 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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Previous in vitro experiments (FRET) have shown that CpxR dimerizes. Currently little in vivo information about CpxR’s dimerization is available. To  characterize our stress responsive bacteria, we had to confirm that CpxR dimerized in vivo as well as elucidate CpxR’s dimerization orientation.
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                An experiment on both possible CpxR - sfGFP orientations was launched to determine whether the proteins were well expressed and if the arabinose promoter worked well. It was also done on a microfluidic chip and on the wet bench. The N terminus GFP biobrick results can be seen below; fluorescence intensity  plotted as a function of time.
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We synthesized four constructs with combinations of the split IFP1.4 fragments fused to the C or N terminal of CpxR.  
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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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As seen in the graph below, induction of IFP1.4 signal by 50 mM KCl was done at t=24min. We clearly see that the construct with IFP fragments on the C-terminal immediately responded to stress by emitting fluorescence. In fact we observe a 3 fold signal increase in 2 minutes. On the other hand, the three other orientations were non-responsive to KCl stress.</p>
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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/c/c2/KCL_Construct_Comparison.jpg" data-lightbox="chips" data-title="Construct Comparison"><img src="https://static.igem.org/mediawiki/2014/c/c2/KCL_Construct_Comparison.jpg" width="80%"/></a><br />
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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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                <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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This 30-fold signal increase in little time from the baseline allows us to assert that only the strain synthesizing the IFP fragments on the C-terminals of CpxR responded to KCl stress. For a further analysis of this experiment check out <a target="_blank" href="https://2014.igem.org/Team:EPF_Lausanne/Results/IFP_experiments">this link!</a>
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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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                <h3><b>Experiment 2: </b>CpxR dimerization & Dimerization Orientation </h3>
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<p>
                 <u>Introduction</u> <br />
                 <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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                 CpxR is the relay protein in the stress responsive 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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                 <u>Aim</u> <br />
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                 <u>Methods</u> <br />
                 <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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                 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 target="blank" href="https://static.igem.org/mediawiki/2014/a/a5/EPFL_Protocol_IFP_stress_1.pdf">here</a>.
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                 <u>Results</u> <br />
                 <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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                 As seen in the graph below, 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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                  <img src="https://static.igem.org/mediawiki/2014/c/c2/KCL_Construct_Comparison.jpg" alt="Construct Comparison" class="img-responsive">
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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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                 <h3><b> Experiment 3: </b>Signal induction by various concentrations of KCl & signal shutdown by centrifugation </h3>
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                 <h3 id="IFP_Exp3"> <b>Signal induction by various concentrations of KCl & signal shutdown by centrifugation</b></h3>
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Having confirmed that KCl was a good inducer for our signal, we tested different concentration of KCl to modulate the signal and better characterize our biobrick. We also aimed to shut down the signal by centrifugation and medium change. The signal was measured on a plate reader 20 minutes, before the addition of KCl. After 2 hours of measurement we centrifuged the cells for ten minutes and replaced the medium with PBS to be able to get a shutdown of the signal.</p>
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                  <a target="_blank" href="https://static.igem.org/mediawiki/2014/6/61/KCL_titration_green_small_EPFL.jpg" data-lightbox="chips" data-title="The split-IFP are linked to cpxR on the C-terminal. During the experiment it was possible to shut down the signal"><img src="https://static.igem.org/mediawiki/2014/6/61/KCL_titration_green_small_EPFL.jpg" width="80%"/></a><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 drastically shut down the signal. These results prove the reversibility of the split IFP1.4 and suggest that real-time temporal dynamics analysis is possible for our system. For a thorough analysis of this experiment check out <a target="_blank" href="https://2014.igem.org/Team:EPF_Lausanne/Results/IFP_experiments">this link!</a>
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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.
                 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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                 <u>Methods</u> <br />
                 <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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                 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 target="_blank" href="https://static.igem.org/mediawiki/2014/a/a5/EPFL_Protocol_IFP_stress_1.pdf">here</a>.
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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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                 <h3><b> Experiment 4: </b>Visualization of the the CpxR split IFP1.4 activation by KCl stress </h3>
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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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                 <h3 id="IFP_Exp4"><b>Visualization of the the CpxR split IFP1.4 activation by KCl stress </b></h3>
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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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                <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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Having shown that we were able to monitor the temporal dynamics of CpxR activation, we wanted to see if we could analyze CpxR’s spatial dynamics by microscopy. 10μl of our cells, previously stressed with 80 mM KCl were spread on a glass slide and imaged with a x100 objective and a APC (Cy5.5) filter.
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We noticed various characteristics of the cells from the picture below. First, IFP signal was much more present in stressed bacteria rather than in non-stressed bacteria. Secondly, we distinguished two specific phenotypes within bacteria: elongated and normal cells. We noticed that this difference was due to CpxR overexpression as we saw this phenomenon also in non-stressed conditions.<br /><br />
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In elongated cells, we were able to distinguish several bright bands of IFP signal that seem fairly uniformly distributed. In the normal phenotype we distinguished a single band in the centre of the bacteria. These observations led us to believe that CpxR might be involved in the division process of E. coli as it seems coherent for cells to slow down division upon stress. <br /><br />
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After looking into the literature, similar bands were visualizable in E. coli 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 E. coli monitor division under various environments. For a thorough analysis of this experiment check out <a target="_blank" href="https://2014.igem.org/Team:EPF_Lausanne/Results/IFP_experiments">this link!</a>
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<figcaption class="cntr">To the left: unstressed cells. To the right: stressed cells.</figcaption>
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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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                 <h3 id=“CpxR-promoter"><b>RFP under CpxR promoter to investigate time delay between transcription factor activation and protein synthesis</b></h3>
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<p>To mesure the time it takes a cell to react to a stress input and if our modified CpxR still has its function as a transcription factor, we wanted to investigate the RFP expression of stressed cells that we co-transformed our CpxR-split-IPF construct with the <a target="_blank" href="http://parts.igem.org/Part:BBa_K339007">BBa_K339007</a>. Unfortunately we realised that the regulatory sequence of the RFP, the CpxR responsive promoter, was missing. So we constructed the biobrick <a target="_blank" href="http://parts.igem.org/Part:BBa_K1486048">BBa_K1486048</a> which contains the regulatory sequence. After a few experiments we realised that KCl stress, which we have found to be a good signal inducer, did not work, even in cells expressing native CpxR. So we developed the biobricks <a target="_blank" href="http://parts.igem.org/Part:BBa_K1486049">BBa_K1486049</a> and <a target="_blank" href="http://parts.igem.org/Part:BBa_K1486050">BBa_K1486050</a>, which encode for RFP regulated by the CpxR responsive promoter, how it is found in the genome. In the figure below you see that neither of the three constructs was stress induced.</p>
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<a href="https://static.igem.org/mediawiki/2014/9/91/BBa_K1486049_BBa_K1486048.png" data-lightbox="cpxr" data-title="CpxR promoted RFP under stress">
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<img src="https://static.igem.org/mediawiki/2014/9/91/BBa_K1486049_BBa_K1486048.png" alt="CpxR promoted RFP under stress" class="img-responsive" /></a>
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<figcaption class="cntr">To the left: unstressed cells. To the right: stressed cells.</figcaption>
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 +
 
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<br/><br/><br/>
 +
-->
 +
 
 +
 
 +
                <h3 id="IFP_Exp5"><b>Activation of CpxR - split IFP1.4 on microfluidic chip by chamber crushing </b></h3>
 +
 
 +
<p>
 +
Knowing that we were able to able to visualize CpxR-IFP activation under a microscope, we proceeded to trying to activate the pathway by mechanical stress on a microfluidic chip - the ultimate barrier to building a functional BioPad !<br /><br />
 +
 
 +
To induce this stress, we turned on the buttons of our SmashColi microfluidic chip at a pressure of 25 psi. We imaged chambers before stress and after stress (10 min after button activation). A drastic increase in signal was detected !</p>
 +
 
 +
<div class="cntr">
 +
 
 +
<div class="pull-left" style="width: 45%">
 +
  <a href="https://static.igem.org/mediawiki/2014/d/dc/Button_IFP_non_stressed_2_Cy5.jpg" data-lightbox="results_button" data-title="Image of IFP signal in non stressed cells in a microfluidic chamber (Cy5 filter)">
 +
<img src="https://static.igem.org/mediawiki/2014/d/dc/Button_IFP_non_stressed_2_Cy5.jpg" alt="results" width="100%">
 +
</a>
 +
<figcaption class="cntr">non stressed</figcaption>
 +
</div>
 +
 
 +
<div class="pull-right" style="width: 45%">
 +
  <a href="https://static.igem.org/mediawiki/2014/7/77/Button_IFP_non_stressed_2.jpg" data-lightbox="results_button" data-title="Image of IFP signal in non stressed cells in a microfluidic chamber (Cy5 filter)"></a>
 +
  <a href="https://static.igem.org/mediawiki/2014/9/99/Button_IFP_stressed_2.jpg" data-lightbox="results_button" data-title="Image of IFP signal in stressed cells in a microfluidic chamber (Cy5 filter)"></a>
 +
 
 +
  <a href="https://static.igem.org/mediawiki/2014/f/f8/Button_IFP_stressed_2_Cy5.jpg" data-lightbox="results_button" data-title="Image of IFP signal in stressed cells in a microfluidic chamber (Cy5 filter)"><img src="https://static.igem.org/mediawiki/2014/f/f8/Button_IFP_stressed_2_Cy5.jpg" alt="results" width="100%"> 
 +
</a>
 +
<figcaption class="cntr">stressed</figcaption>
 +
</div>
 +
</div>
 +
 
 +
<div class="clearfix"></div>
 +
<br /><br />
 +
 
 +
 
 +
                <h3 id="IFP_Exp1"> <b> Characterisation of the pBAD promoter and folding ability of GFP fused to CpxR </b></h3><br />
 +
                <div class="cntr">
 +
                  <a href="https://static.igem.org/mediawiki/2014/0/06/Sfgfpcpxr_gradient.jpg" data-lightbox="img1"><img src="
 +
                  https://static.igem.org/mediawiki/2014/0/06/Sfgfpcpxr_gradient.jpg" width="70%"></a>
 +
                </div> <br /><br />
 +
 
 +
                <p>This construct aimed to evaluate the expression of our construct and the characteristics of the arabinose promoter in <i>E. coli</i> by fusing a superfolder GFP protein to CpxR. The sfGFP was chosen because of its higher intensity compared to GFP. </p>
 +
                <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>.
 +
                </p>
 +
                <p>
 +
We tested both constructs CpxR-sfGFP and sfGFP-CpxR on a plate reader to characterize the pBAD promoter, measuring the sfGFP signal in function of the arabinose concentration. We also measured the signal in a microfluidic chip. You can see in the graph below that the signal is increasing as the concentration of the arabinose increases. The construct with sfGFP at the C terminal lead to a higher GFP signal.
 +
                </p>
 +
                <div class="cntr">
 +
                  <a href="https://static.igem.org/mediawiki/2014/a/ac/Nterm_and_Cterm_log.png" data-lightbox="hellopony"><img src="
 +
                  https://static.igem.org/mediawiki/2014/a/ac/Nterm_and_Cterm_log.png" width="50%"></a>
 +
                </div>
 +
                <br/><br/>
 +
<hr/>
 +
 
 +
</div>
 +
 
 +
<div class="whitebg box">
 +
 
 +
                 <h2 id="Characterisation_of_the_split_luciferase" class="cntr"> <b>Characterisation of the split luciferase </b> </h2>
 +
 
 +
                <h3 id="Characterisation_of_the_split_luciferase"><b>Split luciferase complementation assay using CheY and CheZ chemotaxis proteins </b> </h3>
 +
 
 +
<p>
 +
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 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 the experiment to test our own splits, with firefly (<a target="_blank" href="http://parts.igem.org/Part:BBa_K1486055">BBa_K1486055</a>) and renilla (<a target="_blank" href="http://parts.igem.org/Part:BBa_K1486054">BBa_K1486054</a>) luciferases.
 +
</p>
 +
 
 +
<p>As shown in the graphs (fig.1A and 1B), we didn't observe a high signal for our 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 we didn't completely get rid of the arabinose, which acts as a chemoattractant. Moreover, CheY and CheZ being endogenously expressed in bacteria, there could be interferences with our fusion proteins and weakening of our signal. This should be tested again with CheY/CheZ knock out strains.<br />
 +
                </p>
 +
                <br />
 +
                <div class="cntr">
 +
                <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>
 +
                <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>
 +
                </div><br />
 +
                <br />
 +
                <p>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.</p><br />
 +
                <div class="cntr">
 +
                  <p>
 +
                  <div class="cntr">
 +
                    <a href="https://static.igem.org/mediawiki/2014/f/f7/Controls-CheYCheZexp.png" data-lightbox="chips" data-title="Bioluminescence assay"><img src="https://static.igem.org/mediawiki/2014/f/f7/Controls-CheYCheZexp.png" width="80%"/></a><br />
 +
                  </div>
 +
                  </p>
 +
                </div>
 +
                <br />
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<!--
 +
<div class="cntr">
 +
                <h2 id="Characterisation_of_the_split_luciferase"> <b><u>Characterisation of the split luciferase </u> </b> </h2>
 +
</div>
 +
<br /><br />
 +
 
 +
                 <h3 id="Characterisation_of_the_split_luciferase"><b>Experiment 1: </b>CheY/CheZ fused to split Firefly/Renilla luciferase, and full Firefly/Renilla luciferase characterisation </h3>
                 <p><u>Introduction</u> <br />
                 <p><u>Introduction</u> <br />
                 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>
                 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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                 <p>
                 <p>
                 <u>Method</u> <br />
                 <u>Method</u> <br />
-
                 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 />
+
                 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 target="_blank" href="http://parts.igem.org/Part:BBa_K1486022"> BBa_K1486022 </a> and Firefly : <a target="_blank" 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 target="_blank" href="http://parts.igem.org/Part:BBa_K1486021"> BBa_K1486021 </a> and Firefly : <a target="_blank" href="http://parts.igem.org/Part:BBa_K1486018"> BBa_K1486018 </a>) as negative controls.<br /> <br />
-
                 The bioluminescence assay was performed as described <a href="https://static.igem.org/mediawiki/2014/6/6d/Protocol_-_Bioluminescence_assay.pdf">here</a>. <br />
+
                 The bioluminescence assay was performed as described <a target="_blank" href="https://static.igem.org/mediawiki/2014/6/6d/Protocol_-_Bioluminescence_assay.pdf">here</a>. <br />
-
                 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 />
+
                 The constructs were designed and assembled as described <a target="_blank" href="https://static.igem.org/mediawiki/2014/3/3b/Constructs_design_CheYCheZ.pdf">here</a>.<br /><br /> <br />
                 </p>
                 </p>
                 <p><u>Results</u> <br />
                 <p><u>Results</u> <br />
-
                 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 />
+
                 As shown in the graphs below (fig.1A and 1B), we couldn't really observe a high signal for our 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 />
                 </p>
                 </p>
                 <br />
                 <br />
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                 </div>
                 </div>
                 <br />
                 <br />
-
                 <h2> <b><u>Microfluidic Achievements </u> </b> </h2>
+
-->
-
                 <h3><b>Experiment 1: </b></h3>
+
 
-
                 <h3>Microfluidic Accomplishments</h3>
+
 
 +
             
 +
              </div>
 +
              <div class="whitebg box">
 +
 
 +
                 <h2 id="Yeast_experiments"  class="cntr"> <b>The PBS2-HOG1 split-GFP & split Renilla Luciferase stress response
 +
</b> </h2>
 +
 
 +
<br/><br/>
 +
               
 +
                <h3 id="Yeast_exp1"><b>Confirmation of successful transformation via the R. Luciferase tag </b></h3>
 +
<br/>
 +
                 <p>
 +
               
 +
Since we had never transformed <i>S. cerevisiae</i>, we first needed to confirm our protein tag transformations as a positive control for subsequent experiments.  We cultured the two strains we got from the transformation, the HOG1-rLuc  (<a target="_blank" href="http://parts.igem.org/Part:BBa_K1486033">BBa_K1486033</a> ) and PBS2-rLuc (<a target="_blank" href="http://parts.igem.org/Part:BBa_K1486027">BBa_K1486027</a>), put them in a 96 well plate and tested their luminescence using a plate reader.</p>
 +
<p>
 +
 
 +
The test was performed using two different concentrations of the substrate, coelenterazine-h(benzyl coelenterazine): 1μM and 5μM so that we could determine the optimal concentration we would use for the next assays. The plate started to be read directly after addition of the substrate in the dark and measures were taken every 56 seconds thereafter. Three wells for each sample were measured and below are shown the graphs of their average luminescence plotted over time. We observed a signal-to-noise ratio of 4 at 1μM of substrate and 10 at 5μM for the PBS2-rLuc strain. The HOG1-rLuc strain seemed problematic and died within the plate. Unable to verify the correct transformation, we reproduced the strain but were unable to confirm its validity before the wiki deadline.</p>
 +
 
 +
<div class="cntr">
 +
                  <p>
 +
                  <div class="cntr">
 +
                    <a href="https://static.igem.org/mediawiki/2014/0/0e/Pbslucprettycomparaison_.png" data-lightbox="chips" data-title=""><img src="https://static.igem.org/mediawiki/2014/0/0e/Pbslucprettycomparaison_.png" class="img-responsive"></a>
 +
                  </div>
 +
                  </p>
 +
                </div>
 +
 
 +
<p>
 +
There is a clear luminescence generated by the cells, providing us with confirmation that our designs are correct and we determined which concentration of substrate to use to have a decent signal-to-background ratio.
 +
</p>
 +
 
 +
 
 +
 
 +
<h3 id="Yeast_exp2"><b>The split-sfGFP strain stress-response</b></h3>
 +
                <p>
 +
         
 +
 
 +
Having confirmed that our design for yeast transformations was correct via the previous experiment, we performed stress-response tests upon our PBS2-HOG1-splitGFP (<a target="_blank" href="http://parts.igem.org/Part:BBa_K1486029">BBa_K1486029</a>) and (<a target="_blank" href="http://parts.igem.org/Part:BBa_K1486035">BBa_K1486035</a>) strain to determine whether the pathway is reactive to stress as theorized. A co-transformation was performed using linear fragments produced in the same way as for the first experiment to obtain the strain. The N-terminal split of the superfolder GFP was tagged onto PBS2 and the C-terminal onto HOG1. The strain was then tested along with non-transformed cells in a 96 well plate with various stresses (e.g. Acetic Acid, Ethanol, Glucose...). The cells were centrifuged and resuspended in PBS before loading into the plate.
 +
</p>
 +
 
 +
 
 +
<div class="cntr">
 +
               
 +
<div class="cntr">
 +
 
 +
                    <img src="https://static.igem.org/mediawiki/2014/1/1d/Splitgfpgraph.png" class="img-responsive">
 +
                  </div>
 +
                  </p>
 +
                </div>
 +
<p>
 +
The most reactive of stresses turned out to be Acetic Acid 3.6% (shown above). Ethanol 10% was also very efficient. Other stresses tested did not seem to show conclusive results and we were unable to determine more reactants before the wiki freeze deadline. To further assess the fluorescence 10μl of our  cells were spread on a glass slide and imaged with a x63 objective and a Green LP filter
 +
(Excitation BP 450-490, Dichroïc FT 510, Emission LP 515). Below is shown a comparison of before and after 3.6% Acetic Acid stress in the microscopy image merged with the fluorescence.
 +
</p>
 +
 
 +
<div class="cntr">
 +
                  <p>
 +
                  <div class="cntr">
 +
<a href="https://static.igem.org/mediawiki/2014/3/3b/Splitgfpyeast.jpg" data-lightbox="caca" data-title="Image of our split sfGFP expressing cells before and after the 3.6% acetic acid stress (x63 objective and a Green LP filter)">
 +
                    <img src="https://static.igem.org/mediawiki/2014/3/3b/Splitgfpyeast.jpg" class="img-responsive"></a>
 +
                  </div>
 +
                  </p>
 +
                </div>
 +
 
 +
 
 +
<div class="cntr">
 +
                  <p>
 +
For a more quantitative measure, the fluorescent cells to total cells ratio was calculated and illustrated below.
 +
                  <div class="cntr">
 +
                    <img src="https://static.igem.org/mediawiki/2014/8/81/Splitgfpcount.png" class="img-responsive">
 +
                  </div>
 +
                  </p>
 +
                </div>
 +
 
 +
<p>
 +
 
 +
 
 +
From the data shown above, we can see that fluorescence increases within cells in our split sfGFP strain in response to stress while it does not in non-transformed cells. We can thus conclude that the orientation of the split sfGFP constructs added to PBS2 and HOG1 allows proper re-assembly upon interaction of the two proteins. This result shows promise for the actual application of the project as a Biopad using yeast cells. <b>It is the first time a split gets succesfully implemented in the HOG1 pathway by direct attachment to proteins of the kinase cascade</b>. Detection of protein–protein interactions within the pathway were previously studied <a target="_blank" href="http://onlinelibrary.wiley.com/doi/10.1002/yea.320080602/abstract"> using vesicle targeting</a>.
 +
 
 +
<p/>
 +
 
 +
 
 +
 
 +
 
 +
 
 +
<h3 id="Yeast_exp3"><b>The split-Luciferase strain stress-response</b></h3>
 +
                 <p>
 +
After determining that the pathway is reactive to certain stresses and that the split-GFP strain increases its fluorescence, we performed the same test in the obtained split-luciferase (<a target="_blank" href="http://parts.igem.org/Part:BBa_K1486030">BBa_K1486030</a>) and (<a target="_blank" href="http://parts.igem.org/Part:BBa_K1486036">BBa_K1486036</a>) strain. Unfortunately, due to the difficult nature of detecting an instantaneous luminescence signal and the unstable nature of coelenterazine-Luciferase reaction in different conditions (inhibition due to various molecules such as glucose), our attempts in detecting it on the plate reader failed. Further tests are planned, including an experiment in the microfluidic chips, to directly measure the effect of mechanical pressure, but will not be done before the wiki freeze.         
 +
</p>
 +
 
 +
</div>
 +
<div class="whitebg box">
 +
 
 +
<a id="Microfluidics_experiments"></a>
 +
 
 +
               
 +
 
 +
                <h2 id="Micro_exp1"  class="cntr"><b>Microfluidic achievements</b></h2>
 +
<br/>
                 <table class="table table-striped valign-middle table-center">
                 <table class="table table-striped valign-middle table-center">
                   <thead>
                   <thead>
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                     <tr>
                     <tr>
                       <td>Full chip</td>
                       <td>Full chip</td>
-
                       <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>
+
                       <td class="cntr"><a target="_blank" 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>
                       <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>
                       <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>
                       <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>
                       <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>
                       <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>
                       <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>
                       <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>
                       <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 class="cntr"><a href="https://static.igem.org/mediawiki/2014/b/b0/Screen_Shot_2014-10-16_at_22.15.39.png" data-lightbox="chips" data-title="CleanColi"><img src="https://static.igem.org/mediawiki/2014/b/b0/Screen_Shot_2014-10-16_at_22.15.39.png" width="70%"/></a><br /></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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<br/> <p>To start our microfluidic experiments, we used the <a target="_blank" href="http://link.springer.com/protocol/10.1007%2F978-1-61779-292-2_6">MITOMI chip</a> that was designed in the laboratory of Prof. Maerkl.</p><br/>
                 <br/>
                 <br/>
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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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 +
 
 +
 
 +
 
 +
                 <h3 id="Micro_exp2"><b>Culturing <i>E. coli</i> with constitutive GFP on chip</b></h3>
 +
                 <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 target="_blank" href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Microfluidics#growth">here</a>).
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                  https://static.igem.org/mediawiki/2014/e/e4/Growth_small.gif" width="50%"></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>
                 <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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                  <a href="https://static.igem.org/mediawiki/2014/f/fe/Gfp.png" data-lightbox="prout"><img src="
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                  https://static.igem.org/mediawiki/2014/f/fe/Gfp.png" width="50%" class="img-responsive"></a>
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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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 +
 
 +
 
 +
                 <h3 id="Micro_exp3"><b>CpxR linked with GFP on the N terminal, induced by arabinose in <i>E. coli</i></b></h3>
                 <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.
                 <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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                 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 target="_blank" href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Microfluidics#date-08-21-2014">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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                <div class="col col-md-6"><a href="https://static.igem.org/mediawiki/2014/4/4e/Truc2.png" data-lightbox="chips" data-title="Scan of the microfluidic chip at t = 0min. No signal is detected."><img src="https://static.igem.org/mediawiki/2014/4/4e/Truc2.png" alt="" class="img-responsive" /></a><br />
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                <strong>Figure 1.</strong> Scan of the microfluidic chip at t = 0min. No signal is detected
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                 <p><strong>Figure 2.</strong> Scan of the microfluidic chip at t = 300min.</p>
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                <a href="https://static.igem.org/mediawiki/2014/3/32/Truc3.png" data-lightbox="chips" data-title="Scan of the microfluidic chip at t = 300min."><img src="https://static.igem.org/mediawiki/2014/3/32/Truc3.png" alt="" class="img-responsive" /></a><br />
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                <strong>Figure 2.</strong> Scan of the microfluidic chip at t = 300min.</div></div>
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                 <p>We analysed the scans and obtained the following results.</p>
                 <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><a href="https://static.igem.org/mediawiki/2014/4/4c/Gfp_ara.png" data-lightbox="chips" data-title="Figure 3. Evolution of CpxR-GFP fluorescence over time"><img src="https://static.igem.org/mediawiki/2014/4/4c/Gfp_ara.png" alt="" class="img-responsive" /></a></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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<div class="cntr">              
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                 <h3><b>Experiment 1: </b></h3>
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<strong>Figure 3.&nbsp;</strong> Evolution of CpxR-GFP fluorescence over time
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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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                 <h3 id="Micro_exp4"><b>On chip infrared detection</b></h3>
 +
                <p>As we focused part of our work on the IFP1.4, we needed confirmation of this signal detection in our microfluidic chips. Thus the aim of this experiment was to prove this fluorescence detection capability. Bacteria were loaded in the smash-coli chip. The first batch was KCl stressed and the second batch was unstressed. We then simply scanned the chip and analysed the results using ImageJ. For more details, please visit our <a target="_blank" href="https://2014.igem.org/Team:EPF_Lausanne/Notebook/Microfluidics#date-10-03-2014">notebook</a>. </p>
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                <div class="col col-md-6"><a href="https://static.igem.org/mediawiki/2014/c/cf/No_KCl_red.png" data-lightbox="chips" data-title="Figure 1. Cy5 scan of a chamber containing non-stressed CpxR-IFP bacteria"><img src="https://static.igem.org/mediawiki/2014/c/cf/No_KCl_red.png" alt="" class="img-responsive" /></a><br />
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                <strong>Figure 1.</strong> Cy5 scan of a chamber containing non-stressed CpxR-IFP bacteria.
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                <a href="https://static.igem.org/mediawiki/2014/c/c2/KCL_red.png" data-lightbox="chips" data-title="Figure 2. Cy5 scan of a chamber containing KCl-stressed CpxR-IFP bacteria"><img src="https://static.igem.org/mediawiki/2014/c/c2/KCL_red.png" alt="" class="img-responsive" /></a><br />
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                <strong>Figure 2.</strong> Cy5 scan of a chamber containing KCl-stressed CpxR-IFP bacteria.</div></div>
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                 <p>We analysed the scans and obtained the following results.</p>
 +
                <p><img src="https://static.igem.org/mediawiki/2014/2/24/KCl_stack.PNG" alt="" class="img-responsive" /></p>
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                <strong>Figure 3.&nbsp;</strong> Histogram of KCl stressed cells and non-stressed cells.
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 +
<h3>BioPad Detector: Detection of sfGFP</h3>
 +
 
 +
<p> To get a first idea of how our BioPad was able to detect signal, we attempted to detect sfGFP signal emission by exciting our sfGFP with a 470 nm emitting LED and acquiring the images through our device. A sample of the video taken can be seen here below: </p>
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<video width="500" height="300" controls>
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  <source src="https://static.igem.org/mediawiki/2014/2/2f/Gfptracking_EPFL.mp4" type="video/mp4">
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<p>
 +
To learn more about how the detector works check out our <a href="https://2014.igem.org/Team:EPF_Lausanne/Hardware"> Hardware page!</a>
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                 <!--<h4> References </h4>
                 <p>
                 <p>
                 <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>.
                 <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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               <li><a href="#general_medal" class="active">General Medal</a>
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               <li class="active"><a href="#IFP_Exp">Characterization of spatiotemporal dynamics of the CpxR stress sensor</a>
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                <li><a href="#general_bronze">Bronze</a></li>
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                <li><a href="#general_silver">Silver</a></li>
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                          <li><a href="#IFP_Exp3">Titration of KCl & signal shutdown </a></li>
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                          <li><a href="#IFP_Exp4"></b>Microscopy of KCl stress </a></li>
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                          <li><a href="#IFP_Exp5"></b>Mechanical stress on microfluidic chip</a></li>
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<li><a href="#IFP_Exp1">AraC/PBad Promoter & GFP fused to CpxR</a></li>
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             <li><a href="#microfluidics_medal">Microfluidics Medal</a>
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               <li><a href="#Yeast_exp1">Confirmation of successful transformation via the rLuc tag</a></li>
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               <li><a href="#Yeast_exp2">The split-GFP strain stress-response </a></li>
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               <li><a href="#Yeast_exp3">The split-Luciferase strain stress response</a></li>
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              <li><a href="#Micro_exp1">Chips</a></li>
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              <li><a href="#Micro_exp2">Culturing <i>E.coli</i> </a></li>
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              <li><a href="#Micro_exp3">sfGFP-CpxR fusion under pBAD</a></li>
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              <li><a href="#Micro_exp4">On chip infrared detection</a></li>
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Latest revision as of 03:28, 18 October 2014

RESULTS


Characterisation of the spatiotemporal dynamics of the CpxR stress sensor



Demonstration of CpxR's dimerization & Elucidation of its dimerization orientation

Previous in vitro experiments (FRET) have shown that CpxR dimerizes. Currently little in vivo information about CpxR’s dimerization is available. To characterize our stress responsive bacteria, we had to confirm that CpxR dimerized in vivo as well as elucidate CpxR’s dimerization orientation.


We synthesized four constructs with combinations of the split IFP1.4 fragments fused to the C or N terminal of CpxR. As seen in the graph below, induction of IFP1.4 signal by 50 mM KCl was done at t=24min. We clearly see that the construct with IFP fragments on the C-terminal immediately responded to stress by emitting fluorescence. In fact we observe a 3 fold signal increase in 2 minutes. On the other hand, the three other orientations were non-responsive to KCl stress.




This 30-fold signal increase in little time from the baseline allows us to assert that only the strain synthesizing the IFP fragments on the C-terminals of CpxR responded to KCl stress. For a further analysis of this experiment check out this link!



Signal induction by various concentrations of KCl & signal shutdown by centrifugation

Having confirmed that KCl was a good inducer for our signal, we tested different concentration of KCl to modulate the signal and better characterize our biobrick. We also aimed to shut down the signal by centrifugation and medium change. The signal was measured on a plate reader 20 minutes, before the addition of KCl. After 2 hours of measurement we centrifuged the cells for ten minutes and replaced the medium with PBS to be able to get a shutdown of the signal.




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 drastically shut down the signal. These results prove the reversibility of the split IFP1.4 and suggest that real-time temporal dynamics analysis is possible for our system. For a thorough analysis of this experiment check out this link!



Visualization of the the CpxR split IFP1.4 activation by KCl stress

Having shown that we were able to monitor the temporal dynamics of CpxR activation, we wanted to see if we could analyze CpxR’s spatial dynamics by microscopy. 10μl of our cells, previously stressed with 80 mM KCl were spread on a glass slide and imaged with a x100 objective and a APC (Cy5.5) filter.

We noticed various characteristics of the cells from the picture below. First, IFP signal was much more present in stressed bacteria rather than in non-stressed bacteria. Secondly, we distinguished two specific phenotypes within bacteria: elongated and normal cells. We noticed that this difference was due to CpxR overexpression as we saw this phenomenon also in non-stressed conditions.

In elongated cells, we were able to distinguish several bright bands of IFP signal that seem fairly uniformly distributed. In the normal phenotype we distinguished a single band in the centre of the bacteria. These observations led us to believe that CpxR might be involved in the division process of E. coli as it seems coherent for cells to slow down division upon stress.

After looking into the literature, similar bands were visualizable in E. coli 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 E. coli monitor division under various environments. For a thorough analysis of this experiment check out this link!

results results
To the left: unstressed cells. To the right: stressed cells.


Activation of CpxR - split IFP1.4 on microfluidic chip by chamber crushing

Knowing that we were able to able to visualize CpxR-IFP activation under a microscope, we proceeded to trying to activate the pathway by mechanical stress on a microfluidic chip - the ultimate barrier to building a functional BioPad !

To induce this stress, we turned on the buttons of our SmashColi microfluidic chip at a pressure of 25 psi. We imaged chambers before stress and after stress (10 min after button activation). A drastic increase in signal was detected !

results
non stressed
results
stressed


Characterisation of the pBAD promoter and folding ability of GFP fused to CpxR




This construct aimed to evaluate the expression of our construct and the characteristics of the arabinose promoter in E. coli by fusing a superfolder GFP protein to CpxR. The sfGFP was chosen because of its higher intensity compared to GFP.

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: BBa_K1486002 (N terminus) and BBa_K1486005 (C terminus).

We tested both constructs CpxR-sfGFP and sfGFP-CpxR on a plate reader to characterize the pBAD promoter, measuring the sfGFP signal in function of the arabinose concentration. We also measured the signal in a microfluidic chip. You can see in the graph below that the signal is increasing as the concentration of the arabinose increases. The construct with sfGFP at the C terminal lead to a higher GFP signal.




Characterisation of the split luciferase

Split luciferase complementation assay using CheY and CheZ chemotaxis proteins

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 in absence of chemoattractant or presence of chemorepellent. Based on the work of Waldor1 Laboratory, we wanted to redo the experiment to test our own splits, with firefly (BBa_K1486055) and renilla (BBa_K1486054) luciferases.

As shown in the graphs (fig.1A and 1B), we didn't observe a high signal for our 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 we didn't completely get rid of the arabinose, which acts as a chemoattractant. Moreover, CheY and CheZ being endogenously expressed in bacteria, there could be interferences with our fusion proteins and weakening of our signal. This should be tested again with CheY/CheZ knock out strains.


cheYcheZ cheYcheZ


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.




The PBS2-HOG1 split-GFP & split Renilla Luciferase stress response



Confirmation of successful transformation via the R. Luciferase tag


Since we had never transformed S. cerevisiae, we first needed to confirm our protein tag transformations as a positive control for subsequent experiments. We cultured the two strains we got from the transformation, the HOG1-rLuc (BBa_K1486033 ) and PBS2-rLuc (BBa_K1486027), put them in a 96 well plate and tested their luminescence using a plate reader.

The test was performed using two different concentrations of the substrate, coelenterazine-h(benzyl coelenterazine): 1μM and 5μM so that we could determine the optimal concentration we would use for the next assays. The plate started to be read directly after addition of the substrate in the dark and measures were taken every 56 seconds thereafter. Three wells for each sample were measured and below are shown the graphs of their average luminescence plotted over time. We observed a signal-to-noise ratio of 4 at 1μM of substrate and 10 at 5μM for the PBS2-rLuc strain. The HOG1-rLuc strain seemed problematic and died within the plate. Unable to verify the correct transformation, we reproduced the strain but were unable to confirm its validity before the wiki deadline.

There is a clear luminescence generated by the cells, providing us with confirmation that our designs are correct and we determined which concentration of substrate to use to have a decent signal-to-background ratio.

The split-sfGFP strain stress-response

Having confirmed that our design for yeast transformations was correct via the previous experiment, we performed stress-response tests upon our PBS2-HOG1-splitGFP (BBa_K1486029) and (BBa_K1486035) strain to determine whether the pathway is reactive to stress as theorized. A co-transformation was performed using linear fragments produced in the same way as for the first experiment to obtain the strain. The N-terminal split of the superfolder GFP was tagged onto PBS2 and the C-terminal onto HOG1. The strain was then tested along with non-transformed cells in a 96 well plate with various stresses (e.g. Acetic Acid, Ethanol, Glucose...). The cells were centrifuged and resuspended in PBS before loading into the plate.

The most reactive of stresses turned out to be Acetic Acid 3.6% (shown above). Ethanol 10% was also very efficient. Other stresses tested did not seem to show conclusive results and we were unable to determine more reactants before the wiki freeze deadline. To further assess the fluorescence 10μl of our cells were spread on a glass slide and imaged with a x63 objective and a Green LP filter (Excitation BP 450-490, Dichroïc FT 510, Emission LP 515). Below is shown a comparison of before and after 3.6% Acetic Acid stress in the microscopy image merged with the fluorescence.

For a more quantitative measure, the fluorescent cells to total cells ratio was calculated and illustrated below.

From the data shown above, we can see that fluorescence increases within cells in our split sfGFP strain in response to stress while it does not in non-transformed cells. We can thus conclude that the orientation of the split sfGFP constructs added to PBS2 and HOG1 allows proper re-assembly upon interaction of the two proteins. This result shows promise for the actual application of the project as a Biopad using yeast cells. It is the first time a split gets succesfully implemented in the HOG1 pathway by direct attachment to proteins of the kinase cascade. Detection of protein–protein interactions within the pathway were previously studied using vesicle targeting.

The split-Luciferase strain stress-response

After determining that the pathway is reactive to certain stresses and that the split-GFP strain increases its fluorescence, we performed the same test in the obtained split-luciferase (BBa_K1486030) and (BBa_K1486036) strain. Unfortunately, due to the difficult nature of detecting an instantaneous luminescence signal and the unstable nature of coelenterazine-Luciferase reaction in different conditions (inhibition due to various molecules such as glucose), our attempts in detecting it on the plate reader failed. Further tests are planned, including an experiment in the microfluidic chips, to directly measure the effect of mechanical pressure, but will not be done before the wiki freeze.

Microfluidic achievements


MITOMI MITOMI modified SmashColi BioPad FilterColi CleanColi
Full chip





Unit Cell




Designed
Mold fabrication
Fabrication of the chip
Application

To start our microfluidic experiments, we used the MITOMI chip that was designed in the laboratory of Prof. Maerkl.



Culturing E. coli with constitutive GFP on chip

We loaded E. coli, 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 here).

The next morning, a scan of the chip was done to see the intensity of the GFP in the chip.


CpxR linked with GFP on the N terminal, induced by arabinose in E. coli

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. 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 here).


Figure 1. Scan of the microfluidic chip at t = 0min. No signal is detected

Figure 2. Scan of the microfluidic chip at t = 300min.

We analysed the scans and obtained the following results.

Figure 3.  Evolution of CpxR-GFP fluorescence over time

On chip infrared detection

As we focused part of our work on the IFP1.4, we needed confirmation of this signal detection in our microfluidic chips. Thus the aim of this experiment was to prove this fluorescence detection capability. Bacteria were loaded in the smash-coli chip. The first batch was KCl stressed and the second batch was unstressed. We then simply scanned the chip and analysed the results using ImageJ. For more details, please visit our notebook.


Figure 1. Cy5 scan of a chamber containing non-stressed CpxR-IFP bacteria.

Figure 2. Cy5 scan of a chamber containing KCl-stressed CpxR-IFP bacteria.

We analysed the scans and obtained the following results.

Figure 3.  Histogram of KCl stressed cells and non-stressed cells.


BioPad Detector: Detection of sfGFP

To get a first idea of how our BioPad was able to detect signal, we attempted to detect sfGFP signal emission by exciting our sfGFP with a 470 nm emitting LED and acquiring the images through our device. A sample of the video taken can be seen here below:

To learn more about how the detector works check out our Hardware page!

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