Difference between revisions of "Team:Exeter/Collaborations"

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     <span style="margin-bottom:4px;">Lab</span>
 
     <span style="margin-bottom:4px;">Lab</span>
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<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Project">Lab Project</a></li>
 
<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Project">Lab Project</a></li>
 
     <li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Labbook">Lab Book</a></li>
 
     <li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Labbook">Lab Book</a></li>
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Safety">Safety</a></li>
 
  
 
   </ul>
 
   </ul>
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<li ><a id="links"href="https://2016.igem.org/Team:Exeter/Parts">Parts</a></li>
 
<li ><a id="links"href="https://2016.igem.org/Team:Exeter/Parts">Parts</a></li>
 
<li ><a id="links"href="https://2016.igem.org/Team:Exeter/Team">Team</a></li>
 
<li ><a id="links"href="https://2016.igem.org/Team:Exeter/Team">Team</a></li>
<li ><a id="links" href="https://2016.igem.org/Team:Exeter/Interlab">InterLab</a></li>
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<li><a id="links" href="https://2016.igem.org/Team:Exeter/Interlab">InterLab</a></li>
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     <span style="margin-bottom:4px;">Human Practices</span>
 
     <span style="margin-bottom:4px;">Human Practices</span>
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<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Human_Practices">Human Practices Homepage</a></li>
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    <li><a id="links" style="margin:10px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Integrated_Practices">Integrated</a></li>
    <li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Integrated_Practices">Integrated</a></li>
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<li><a id="links" style="background:none;line-height:0.7vh;margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Engagement">Public Engagement<br /><br /><br /> & Education</a></li><li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Log">Log</a></li>
<li><a id="links" style="background:none;line-height:0.7vh;margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Engagement">Public Engagement<br /><br /><br /> & Education</a></li>
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<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Log">Log</a></li>
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   </ul>
 
   </ul>
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<li ><a id="links"href="https://2016.igem.org/Team:Exeter/Attributions">Attributions</a></li>
 
<li ><a id="links"href="https://2016.igem.org/Team:Exeter/Attributions">Attributions</a></li>
  
<li><div id="links" style="margin:0;" class="dropdown">
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     <span style="margin-bottom:4px;">Awards</span>
 
     <span style="margin-bottom:4px;">Awards</span>
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<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Awards">Medals</a></li>
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<li><a id="links" style="margin:10px 0 30px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/Awards">Awards</a></li>
<li><span style="margin:10px 0 30px 2px;padding:0;"><u>Special pages</u></span></li>
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<li><span style="margin:10px 0 30px 2px;padding:0;">Special pages</span></li>
 
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/HP/Silver">HP Silver</a></li>
 
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/HP/Silver">HP Silver</a></li>
 
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/HP/Gold">HP Gold</a></li>
 
<li><a id="links" style="margin:30px 0 10px 2px;padding:0;font-size:1.8vh;" href="https://2016.igem.org/Team:Exeter/HP/Gold">HP Gold</a></li>
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<a href="#section_1" class="banner_link col-xs-6 col-sm-2"><span class="oneline">Newcastle</span></a>
 
<a href="#section_1" class="banner_link col-xs-6 col-sm-2"><span class="oneline">Newcastle</span></a>
 
<a href="#section_2" class="banner_link col-xs-6 col-sm-2"><span class="oneline">Purdue</span></a>
 
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<a href="#section_3" class="banner_link col-xs-6 col-sm-4"><span class="oneline">Glasgow</span></a>
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<a href="#section_3" class="banner_link col-xs-6 col-sm-2"><span class="oneline">Glasgow</span></a>
 
<a href="#section_4" class="banner_link col-xs-6 col-sm-2"><span class="oneline">Edinburgh</span></a>
 
<a href="#section_4" class="banner_link col-xs-6 col-sm-2"><span class="oneline">Edinburgh</span></a>
<a href="#section_5" class="banner_link twoline col-xs-6 col-sm-2"><span class="oneline">Stanford <br />Brown</span></a>
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<a href="#section_5" class="banner_link col-xs-6 col-sm-2"><span class="oneline">Stanford&nbsp;Brown</span></a>
 
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<!--Left picture (the teal line on left)-->
 
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                 <p id="pp">A 0.65m insulated copper wire (cross-sectional area, 0.05m<sup>2</sup>) was passed through the centre of a 50mL falcon tube containing the liquid medium to be measured, suspended in a water bath (Fig. 1b). Three thermocouples (Pico Technology TC-08) were attached, one to the wire in contact with the insulation using blue tack, one suspended in the liquid medium 5mm from the wire, and one in the water bath. Power was supplied to the wire at 5A, 1.8V for 600s, generating a small temperature increase of approximately 2&deg;C above room temperature (23 &plusmn; 1&deg;C) to avoid convection effects. Our experimental setup was calibrated to the thermal conductivity of <a href="http://www2.bren.ucsb.edu/~dturney/WebResources_13/WaterSteamIceProperties/PropOfWaterFrom0to100Celcius.pdf">water</a> at 20&deg;C, 598.4 $\frac{mW}{Km}\text{ }$. Measurements of two growth media, liquid broth (LB) and M9 were repeated at least in quintuple.</p>
 
                 <p id="pp">A 0.65m insulated copper wire (cross-sectional area, 0.05m<sup>2</sup>) was passed through the centre of a 50mL falcon tube containing the liquid medium to be measured, suspended in a water bath (Fig. 1b). Three thermocouples (Pico Technology TC-08) were attached, one to the wire in contact with the insulation using blue tack, one suspended in the liquid medium 5mm from the wire, and one in the water bath. Power was supplied to the wire at 5A, 1.8V for 600s, generating a small temperature increase of approximately 2&deg;C above room temperature (23 &plusmn; 1&deg;C) to avoid convection effects. Our experimental setup was calibrated to the thermal conductivity of <a href="http://www2.bren.ucsb.edu/~dturney/WebResources_13/WaterSteamIceProperties/PropOfWaterFrom0to100Celcius.pdf">water</a> at 20&deg;C, 598.4 $\frac{mW}{Km}\text{ }$. Measurements of two growth media, liquid broth (LB) and M9 were repeated at least in quintuple.</p>
  
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        <img src="https://static.igem.org/mediawiki/2016/e/e8/T--Exeter--Template_Colab_setup.jpg"
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<img src="https://static.igem.org/mediawiki/2016/e/e8/T--Exeter--Template_Colab_setup.jpg">
style="max-width:100%;margin:auto;display:block;">
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<span>Figure 1a - experimental setup of the transient hot wire method.</span>
            <span class="caption">Figure 1a - experimental setup of the transient hot wire method.</span>
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</div>
<br>
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<div class="graph_box col-xs-12">
<br>
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<img src="https://static.igem.org/mediawiki/2016/2/23/T--Exeter--Colab_2.jpg">
    </div>
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<span>Figure 1b - arrangement of thermocouples within the falcon tube measuring thermal conductivity using the transient hot-wire method.</span>
<div class="col-xs-6" style="padding:5px 10% 5px 2%;margin:0; text-align:center">
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        <img src="https://static.igem.org/mediawiki/2016/2/23/T--Exeter--Colab_2.jpg"
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            <span class="caption">Figure 1b - arrangement of thermocouples within the falcon tube measuring thermal conductivity using the transient hot-wire method.</span>
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                 <p id="pp">Nagasaka and Nagashima noted that wire insulation has negligible impact on the measurement of the thermal conductivity of saline solutions (Nagasaka and Nagashima 1981) and thus can be described by the equation: $$ \lambda = \frac{Q}{4\pi\Delta T}\ \ln{(t)}$$ where $Q$ is the power per unit length of the wire, $Q = \frac{(I \times V)}{Length}$, and $\Delta T$ is the change in temperature over time $t$. A linear fit of a $T$ vs. $ln(t)$ plot following only the reading from the liquid medium thermocouple will yield the conductivity (Fig. 2).</p>
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<img src="https://static.igem.org/mediawiki/2016/4/40/Thermal_conductivity_rep_plot_EXE2016.png">
 +
<span>Figure 2 - representative plots of temperature against natural log of time for water, liquid broth and M9 media. A fit was applied from the point where the relationship becomes linear to extract the thermal conductivities.</span>
 +
</div>
 +
<div class="col-xs-6">
 +
<p id="pp">Nagasaka and Nagashima noted that wire insulation has negligible impact on the measurement of the  
 +
thermal conductivity of saline solutions (Nagasaka and Nagashima 1981) and thus can be described by the equation:  
 +
$$ \lambda = \frac{Q}{4\pi\Delta T}\ \ln{(t)}$$ where $Q$ is the power per unit length of the wire,  
 +
$Q = \frac{(I \times V)}{Length}$, and $\Delta T$ is the change in temperature over time $t$.  
 +
</p>
  
                <p id="pp">We found the thermal conductivity of LB and M9 to be similar to that of water, at 605 $\pm$ 20 $\frac{mW}{Km}\text{ }$ and 570 $\pm$ 30 $\frac{mW}{Km}\text{ }$ respectively.</p>
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<br />
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            </div>
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</div>
  
 +
  <p id="pp">We found the thermal conductivity of LB and M9 to be similar to that of water,
 +
  at 605 $\pm$ 20 $\frac{mW}{Km}\text{ }$ and 570 $\pm$ 30 $\frac{mW}{Km}\text{ }$ respectively.
 +
  A linear fit of a $T$ vs. $ln(t)$ plot following only the reading from the liquid medium thermocouple
 +
will yield the conductivity (Fig. 2).</p>
 +
  
<div class="col-xs-12" style="padding:0;margin:0;text-align:center">
 
            <img src="https://static.igem.org/mediawiki/2016/4/40/Thermal_conductivity_rep_plot_EXE2016.png" style="max-width:50%;margin:auto;display:block;">
 
            <span class="caption">Figure 2 - representative plots of temperature against natural log of time for water, liquid broth and M9 media. A fit was applied from the point where the relationship becomes linear to extract the thermal conductivities.</span>
 
<br>
 
<br>
 
    </div>
 
</div>
 
  
<h5>References</h5>
+
<h5 style="padding-top:15px;"><u>References</u></h5>
<ol style="font-size:100%;">
+
<ol style="font-size:100%;font-weight:600;">
<li>Healy, J.J, de Groot, J.J and Kestin, J, The Theory of the Transient Hot-Wire Method for Measuring Thermal Conductivity,<i>Physica</i> <b>82C</b>: 392-408 (1976)
+
<li>Healy, J.J, de Groot, J.J and Kestin, J, The Theory of the Transient Hot-Wire Method for
<li>Nagasaka Y, Nagashima A. Absolute measurement of the thermal conductivity of electrically conducting liquids by the transient hot-wire method. Journal of Physics E: Scientific Instruments. 1981 Dec;14(12):1435–40.</li>
+
Measuring Thermal Conductivity,<i>Physica</i> <b>82C</b>: 392-408 (1976)
 +
<li>Nagasaka Y, Nagashima A. Absolute measurement of the thermal conductivity of electrically  
 +
conducting liquids by the transient hot-wire method. Journal of Physics E: Scientific Instruments. 1981 Dec;14(12):1435–40.</li>
 
</ol>
 
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                 <p id="pp">We collaborated with Glasgow iGEM 2016 to test the efficiency of the T7 Promoter we were using to construct the KillerRed, KillerOrange and Lysozyme kill switches. We new that it was leaky and we speculated that it was reducing the efficiency of our project but we needed proof that the leakiness of the promoter could affect our project. In return they gave us a DH5α.Z1 strain in the hopes it would improve the efficiency of our promoter. After subsequent testing we were unable to express our KillerRed and KillerOrange proteins in this strain. This is the report they sent us for the test of the T7 promoter:</p>
 
                 <p id="pp">We collaborated with Glasgow iGEM 2016 to test the efficiency of the T7 Promoter we were using to construct the KillerRed, KillerOrange and Lysozyme kill switches. We new that it was leaky and we speculated that it was reducing the efficiency of our project but we needed proof that the leakiness of the promoter could affect our project. In return they gave us a DH5α.Z1 strain in the hopes it would improve the efficiency of our promoter. After subsequent testing we were unable to express our KillerRed and KillerOrange proteins in this strain. This is the report they sent us for the test of the T7 promoter:</p>
  
                 <h5>Exeter and Glasgow iGEM 2016 Collaboration: <br \>
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                 <br>
 
                 <br>
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<h5>
 
                 KillerRed and KillerOrange Promoter Efficiency Experiment
 
                 KillerRed and KillerOrange Promoter Efficiency Experiment
 
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                 </h5>
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<p id="pp">Fluorescence scan image from the Typhoon with labels for which samples are in each well.</p>
 
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                 <p id="pp">Fluorescence scan image from the Typhoon with labels for which samples are in each well.</p>
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                 <p id="pp">Both plasmids had the BioBrick prefix, and the correct sequence for both KillerRed and KillerOrange open reading frame, according to the papers cited on the Exeter 2016 iGEM wiki. The sequence between the prefix and the ATG start codon, we checked against lac-repressible promoters in the iGEM registry. We found a match to R0184, which is a T7 lac-repressible promoter. T7 promoters require T7 polymerase to be transcribed, as they are not recognised by E. coli polymerases. This results confirms the result of the fluorescence measurements. No KillerRed or KillerOrange protein was observed by fluorescence, as neither gene was being transcribed by either DH5α or DH5α.Z1 as neither strain produces the required T7 polymerase. A protein overexpression E. coli strain such as BL21<DE3> which has the T7 polymerase gene inserted into its genome is designed to use T7 promoters would have been able to express these KillerRed and KillerOrange constructs.</p>
 
                 <p id="pp">Both plasmids had the BioBrick prefix, and the correct sequence for both KillerRed and KillerOrange open reading frame, according to the papers cited on the Exeter 2016 iGEM wiki. The sequence between the prefix and the ATG start codon, we checked against lac-repressible promoters in the iGEM registry. We found a match to R0184, which is a T7 lac-repressible promoter. T7 promoters require T7 polymerase to be transcribed, as they are not recognised by E. coli polymerases. This results confirms the result of the fluorescence measurements. No KillerRed or KillerOrange protein was observed by fluorescence, as neither gene was being transcribed by either DH5α or DH5α.Z1 as neither strain produces the required T7 polymerase. A protein overexpression E. coli strain such as BL21<DE3> which has the T7 polymerase gene inserted into its genome is designed to use T7 promoters would have been able to express these KillerRed and KillerOrange constructs.</p>
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                 <h6>Conclusion:</h6>
 
                 <h6>Conclusion:</h6>
  
                 <p id="pp">Glasgow iGEM did fantastic work for us, providing us with detailed analysis of the T7 promoter and suggestions for improving the efficiency of our project. Whilst their data on the DH5alpha Z1 strain is accurate and in accordance with subsequent research and advice, we have since noted there is expression of KillerRed and KillerOrange in DH5alpha lab tests.  </p>
+
                 <p id="pp">Glasgow iGEM did fantastic work for us, providing us with detailed analysis of the T7 promoter and suggestions for improving the efficiency of our project. Whilst their data on the DH5alpha Z1 strain is accurate and in accordance with subsequent research and advice, we have since noted there is expression of KillerRed and KillerOrange in DH5alpha in lab tests.  </p>
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<p id="pp">We are proud and grateful in saying that we have helped and been helped by various other teams in this years iGEM competition. Utilising other teams equipment and different ways of thinking towards solving problems has provided us all with some great data and innovative solutions to some problems we have encountered. We are confident that what we have achieved will benefit the iGEM competition as a whole. </p>
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<p id="pp">We are proud and grateful in saying that we have helped and been helped by various other teams in this years iGEM competition. Utilising other teams equipment and different ways of thinking towards solving problems has provided us all with some great data and innovative solutions to some problems we have encountered. We are confident that what we have achieved will benefit the iGEM competition as a whole. </p>
  
<p id="pp">Good inter-team communication is a vital factor in all disciplines and at the core of the iGEM spirit. We hope to have contributed to this in several ways. </p>
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<p id="pp">Good inter-team communication is a vital factor in all disciplines and at the core of the iGEM spirit. We hope to have contributed to this in several ways. </p>
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Theory: Edinburgh
 
Theory: Edinburgh
 
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<h6>Optimising methods of data mutation detection in BabbleBlocks</h6>
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<h6>Optimising methods of data mutation detection in BabbleBlocks</h6>
 
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<p id="pp">
 
Storing information on DNA offers many advantages over current methods, however mutations  
 
Storing information on DNA offers many advantages over current methods, however mutations  
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If continued further, research should also be done in to the reconstruction of data after it has been lost.
 
If continued further, research should also be done in to the reconstruction of data after it has been lost.
 
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Stanford Brown
 
 
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Stanford Brown
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                <p id="pp">
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                      We initiated contact with Stanford-Brown this year with the intention of interviewing one of their supervisors, Prof. Lynn Rothschild. We were interested in hearing       
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                      about her opinions as well as experiences with diversity and equality in science. Unfortunately we were never able to find a mutually suitable date to carry out the   
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                      interview. However we were able to organise a collaboration with her team.
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                      The Stanford-Brown team have helped our podcast and YouTube series by making their own edition of Desert Island… Science? Which is now available on our   
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<p id="pp">
                      YouTube and SoundCloud channels.  
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  We initiated contact with Stanford-Brown this year with the intention of interviewing one of their supervisors, Prof. Lynn Rothschild. We were interested in hearing       
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  about her opinions as well as experiences with diversity and equality in science. Unfortunately we were never able to find a mutually suitable date to carry out the   
                <p id="pp">
+
  interview. However we were able to organise a collaboration with her team.
                      We are very grateful to Stanford-Brown for their contribution, as it has helped our work get further recognition on an international scale.  
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  The Stanford-Brown team have helped our podcast and YouTube series by making their own edition of Desert Island… Science? Which is now available on our   
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  YouTube and SoundCloud channels.  
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  We are very grateful to Stanford-Brown for their contribution, as it has helped our work get further recognition on an international scale.  
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Revision as of 23:03, 19 October 2016