Difference between revisions of "Team:NRP-UEA-Norwich/Collaborations/kent"

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<p>At the iGEM Westminster Meetup we got into contact with the iGEM Kent team (UKC) and started discussing potential ideas for collaboration. We established an experiment which would address the adherence of <i>S. oneidensis</i> MR-1 onto potential electrode  materials. UKC would provide us access to their Atomic Force Microscopy (AFM), and in return we would model their proteins. </p>
 
<p>At the iGEM Westminster Meetup we got into contact with the iGEM Kent team (UKC) and started discussing potential ideas for collaboration. We established an experiment which would address the adherence of <i>S. oneidensis</i> MR-1 onto potential electrode  materials. UKC would provide us access to their Atomic Force Microscopy (AFM), and in return we would model their proteins. </p>
  
<img src="https://2016.igem.org/File:T--NRP-UEA-Norwich--UKCgraphite.jpg" style="width: 400px;" class="centerMiddle"/>
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<img src="https://static.igem.org/mediawiki/2016/c/c6/T--NRP-UEA-Norwich--UKCgraphite.jpg" style="width: 400px;" class="centerMiddle"/>
<img src="https://2016.igem.org/File:T--NRP-UEA-Norwich--UKCIron.jpg" style="width: 400px;" class="centerMiddle"/>
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<img src="https://static.igem.org/mediawiki/2016/d/d0/T--NRP-UEA-Norwich--UKCIron.jpg" style="width: 400px;" class="centerMiddle"/>
  
 
<p> The AFM results showed that <i>S.oneidensis</i> MR-1 could adhere to graphite, figure 1A. Unfortunately, no <i>S.oneidensis</i> MR-1 adhered to iron which should have been the positive control, figure 1B. After discussions with Kent we determined that this issue could be due to the treatment of the Iron Mica discs used as sample slides for the atomic force microscopy i.e. it could be coated with a material that <i>S.oneidensis</i> could not adhere to. If we were to repeat the experiment we would use untreated iron or manganese as a positive control. </p>
 
<p> The AFM results showed that <i>S.oneidensis</i> MR-1 could adhere to graphite, figure 1A. Unfortunately, no <i>S.oneidensis</i> MR-1 adhered to iron which should have been the positive control, figure 1B. After discussions with Kent we determined that this issue could be due to the treatment of the Iron Mica discs used as sample slides for the atomic force microscopy i.e. it could be coated with a material that <i>S.oneidensis</i> could not adhere to. If we were to repeat the experiment we would use untreated iron or manganese as a positive control. </p>

Revision as of 00:49, 19 October 2016

NRP-UEA-NORWICH iGEM

Collaborations

We have collaborated with UKC to image the adherence of E. coli and S.oneidensis MR-1 onto graphite and iron. In return we offered to model their proteins. This collaboration gave us a better indication of which possible cathode materials could be used in our electrochemical system when we have prepared our modified strains of Shewanella oneidensis MR-1.

At the iGEM Westminster Meetup we got into contact with the iGEM Kent team (UKC) and started discussing potential ideas for collaboration. We established an experiment which would address the adherence of S. oneidensis MR-1 onto potential electrode materials. UKC would provide us access to their Atomic Force Microscopy (AFM), and in return we would model their proteins.

The AFM results showed that S.oneidensis MR-1 could adhere to graphite, figure 1A. Unfortunately, no S.oneidensis MR-1 adhered to iron which should have been the positive control, figure 1B. After discussions with Kent we determined that this issue could be due to the treatment of the Iron Mica discs used as sample slides for the atomic force microscopy i.e. it could be coated with a material that S.oneidensis could not adhere to. If we were to repeat the experiment we would use untreated iron or manganese as a positive control.

We modelled UKC’s native and non-native, proteins using the Phyre 2 server (see figure 2). The protein models showed low alignment, high disorder and low sequence coverage, this is due to the fact there are few proteins with high sequence homology that have crystal structures resolved for the proteins UKC were working with. The models we produced were the best possible approximation of these proteins structures from homology based modelling. Thus, giving our attempt at modelling their structures gave them a rough indication of what their proteins could look like.

The intent behind this modelling aspect of the collaboration was to use our knowledge of homology protein modelling to help UKC approximate the structures their protein models after they attempted to remove the transmembrane region. Simultaneously, they helped us in observing the adherence of S. oneidensis to potential cathode materials. The results on both ends were not what was expected in that while the bacteria did adhere to the graphite they did not adhere to iron, and we did not manage to take these experiments further to start optimising biofilm growth conditions. We demonstrated however that S. oneidensis will adhere to graphite, and this informed our demonstration experiment. Similarly, for UKC we have attempted to model their protein structures to the best possible approximation.

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