Difference between revisions of "Team:Stuttgart/Collaborations"

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                 <h2 class="title is-5">Hamburg (<i>E. coli</i> DH5-&alpha;)</h2>
 
                 <h2 class="title is-5">Hamburg (<i>E. coli</i> DH5-&alpha;)</h2>
 
                 <canvas id="team-hamburg"></canvas>
 
                 <canvas id="team-hamburg"></canvas>
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                 <p>As seen in Fig. 1, the E.&nbsp;coli grew on all three mediums. The PhyCoVi medium including
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                 <p>As seen in Fig. 1, <i>E.&nbsp;coli</i> was able to grow in all three media. The PhyCoVi medium including
 
                     additional soy peptone and the high salt LB medium show similar growth curves after 45&nbsp;minutes.
 
                     additional soy peptone and the high salt LB medium show similar growth curves after 45&nbsp;minutes.
 
                     The PhyCoVi medium without supplements shows a very long lag phase, growth occurs after 135 minutes.
 
                     The PhyCoVi medium without supplements shows a very long lag phase, growth occurs after 135 minutes.
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                 <h2 class="title is-5">T&uuml;bingen (<i>E. coli</i> Nissle 1917)</h2>
 
                 <h2 class="title is-5">T&uuml;bingen (<i>E. coli</i> Nissle 1917)</h2>
 
                 <canvas id="team-tuebingen"></canvas>
 
                 <canvas id="team-tuebingen"></canvas>
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                 <p>Fig. 2 shows the attempted growth curves by Team T&uuml;bingen. Probably due to algae lipid residues
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                 <p>Fig. 2 shows the growth curves by Team T&uuml;bingen. Probably due to algae lipid residues
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                     in the PhyCoVi medium samples, the OD values are corrupted and appear in negative values. But still,
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                     in the PhyCoVi medium samples, OD(600) measurements reveal negative values. But still,
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                     a growth of the Nissle 1917 strain can be observed in the medium with soy peptone additive. As
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                     growth of <i>E. coli</i> Nissle 1917 can be observed in the PhyCoVi medium supplemented with soy peptone. As
 
                     described <a href="#link-2"><sup>2</sup></a>, this wildtype strain has a low tolerance for high salt medium,
 
                     described <a href="#link-2"><sup>2</sup></a>, this wildtype strain has a low tolerance for high salt medium,
 
                     therefore the reduced
 
                     therefore the reduced
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                 <h2 class="title is-5">TU Dresden (<i>E. coli</i> GB05)</h2>
 
                 <h2 class="title is-5">TU Dresden (<i>E. coli</i> GB05)</h2>
 
                 <canvas id="team-dresden"></canvas>
 
                 <canvas id="team-dresden"></canvas>
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                 <p>The results of the iGEM Team TU Dresden shows very low growth for all three mediums, possibly caused
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                 <p>The results of the iGEM Team TU Dresden shows very low growth for all three media, possibly caused
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                     by the high salt concentrations (Fig. 3). After the long lag phase, only the LB medium manages a
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                     by the high salt concentrations (Fig. 3). After a long adaptation phase, <i>E. coli</i> GB05 was able to grow in high salt LB
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                     nice growth curve. Also, the PhyCoVi medium with additional soy peptone shows high deviations,
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                     medium. Growth in PhyCoVi medium supplemented with soy peptone shows high fluctuations,
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                     probably due to the already discussed problem with insoluble medium components. The used strain is
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                     probably due to the already discussed problem with insoluble medium compounds. The used strain is
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                     able to take up linear DNA fragments but seems not to be able to cope with high salt mediums
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                     able to take up linear DNA fragments but seems not to be able to cope with high salt media
 
                     <a href="#link-3"><sup>3</sup></a>.</p>
 
                     <a href="#link-3"><sup>3</sup></a>.</p>
 
             </div>
 
             </div>
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                 <h2 class="title is-5">TU Darmstadt (<i>E. coli</i> BL21 (DE3))</h2>
 
                 <h2 class="title is-5">TU Darmstadt (<i>E. coli</i> BL21 (DE3))</h2>
 
                 <canvas id="team-darmstadt"></canvas>
 
                 <canvas id="team-darmstadt"></canvas>
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                 <p>The BL21 (DE3) strain shows a growth pattern strongly influenced by the PhyCoVi medium (Fig. 4).
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                 <p>
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                    While the LB medium reaches high OD values, both algae-based mediums show very slow growth and long
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                    While <i>E. coli</i> BL21 (DE3) in High Salt LB medium reaches high OD values, growth in both algae-based mediums is very slow with long
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                     lag phases. Also, the SD values show high differences during the measurement. These are, as already
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                     adaptation phases (Fig. 4). Also, the OD(600) values exhibit high standard deviations. As already discussed, this can be explained by algea remnants, such as lipids and cell wall remnants, which had not been removed properly. The strain is
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                    discussed, remnants of the lipids and cell wall, which had not been removed properly. The strain is
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                     one of the most frequent used <i>E. coli</i> strains and it grows best on low salt medium
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                     one of the most frequent used <i>E. coli</i> strains and as stated in growths best on low salt medium
+
 
                     <a href="#link-4"><sup>4</sup></a>.</p>
 
                     <a href="#link-4"><sup>4</sup></a>.</p>
 
             </div>
 
             </div>
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                 <h2 class="title is-5">Freiburg (<i>E. coli</i> DH5-&alpha;)</h2>
 
                 <h2 class="title is-5">Freiburg (<i>E. coli</i> DH5-&alpha;)</h2>
 
                 <canvas id="team-freiburg"></canvas>
 
                 <canvas id="team-freiburg"></canvas>
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                 <p>This measurement was conducted in a 96-well plate reader (Fig. 5). Both algae-based mediums are
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                 <p>This measurement was conducted in a 96-well plate reader. The quality of both algae-based media are
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                     affected by the lipid and cell wall remnants and therefore show negative values. But highly
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                     impaired by algea lipid and cell wall remnants and therefore show negative growth rates. But thank you, Team Freiburg,
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                     appreciated is the measurement length of 15 hours. <br/><br/>
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                     for conducting the experiment over such a long time course. <br/><br/>
 
                 </p>
 
                 </p>
 
             </div>
 
             </div>
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         <div class="column">
 
         <div class="column">
 
             <h2 class="title is-5">Conclusion</h2>
 
             <h2 class="title is-5">Conclusion</h2>
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             <p> In conclusion, the collaboration was a full success, as it showed us that bacteria do indeed grow on
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             <p> In conclusion, the collaboration was a full success! It showed that different strains are able to grow in
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                 our medium. Also, we increased our clean-up efforts for lipids and cell wall aggregates by including
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                 our developed PhyCoVi medium. After evaluating the collaboration results, we increased our clean-up efforts during the production of our medium. Algea lipids and cell wall aggregates were removed by including
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                 an additional step of autoclaving and centrifugation of the medium, as many aggregates formed during
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                 an additional autoclavation step followed by centrifugation of the medium.
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                an initial sterilization by autoclaving.</p>
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</p>
 
             <figure class="image">
 
             <figure class="image">
 
                 <img style="width: 350px; margin: 0 auto;"
 
                 <img style="width: 350px; margin: 0 auto;"
 
                     src="https://2019.igem.org/wiki/images/thumb/8/89/T--Stuttgart--Collab_Fig7.png/800px-T--Stuttgart--Collab_Fig7.png"/>
 
                     src="https://2019.igem.org/wiki/images/thumb/8/89/T--Stuttgart--Collab_Fig7.png/800px-T--Stuttgart--Collab_Fig7.png"/>
 
             </figure>
 
             </figure>
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             <p>The result is visible as seen in <a target="_blank"
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             <p>The result of this improvement can be seen in <a target="_blank"
 
                                                   href="https://2019.igem.org/wiki/images/thumb/8/89/T--Stuttgart--Collab_Fig7.png/800px-T--Stuttgart--Collab_Fig7.png">Fig.
 
                                                   href="https://2019.igem.org/wiki/images/thumb/8/89/T--Stuttgart--Collab_Fig7.png/800px-T--Stuttgart--Collab_Fig7.png">Fig.
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                 7</a> with left being the
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                 7.</a> The left part shows the old version of our medium, which exhibits a higher turbidity as the advanced medium seen in the right part of <a target="_blank"
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                old medium version, while on the right, our new advanced medium can be seen.</p>
+
                                                  href="https://2019.igem.org/wiki/images/thumb/8/89/T--Stuttgart--Collab_Fig7.png/800px-T--Stuttgart--Collab_Fig7.png">Fig.
 +
                7.</a>
 +
            </p>
 
         </div>
 
         </div>
 
     </div>
 
     </div>

Revision as of 16:38, 21 October 2019

Collaboration

Validation of our new algae based PhyCoVi medium

Besides our own experiments with the algae extract, we wanted to have a cross-validation from other iGEM teams and their organisms. Through this, we can make sure, that everybody can work with our medium and also improve the product itself, if problems occur. Kindly, the iGEM teams of Hamburg, Tübingen, TU Darmstadt, Freiburg, and TU Dresden offered their help. Therefore, we prepared 15 ml tubes with two variations of PhyCoVi and a LB control dry medium and sent them to the teams, respectively. Additionally, they received a SOP for their growth curve including an Excel sheet to plot their results directly. Before we discuss their results individually, it can be said, that we are happy with every result and already improved the product concerning the issues that occurred for some teams.

Hamburg (E. coli DH5-α)

As seen in Fig. 1, E. coli was able to grow in all three media. The PhyCoVi medium including additional soy peptone and the high salt LB medium show similar growth curves after 45 minutes. The PhyCoVi medium without supplements shows a very long lag phase, growth occurs after 135 minutes. The DH5-α strain is very robust and optimized for optimal transformation 1. These optimizations also seem to have a positive effect on high salt concentrations.

Tübingen (E. coli Nissle 1917)

Fig. 2 shows the growth curves by Team Tübingen. Probably due to algae lipid residues in the PhyCoVi medium samples, OD(600) measurements reveal negative values. But still, growth of E. coli Nissle 1917 can be observed in the PhyCoVi medium supplemented with soy peptone. As described 2, this wildtype strain has a low tolerance for high salt medium, therefore the reduced growth is expected.

TU Dresden (E. coli GB05)

The results of the iGEM Team TU Dresden shows very low growth for all three media, possibly caused by the high salt concentrations (Fig. 3). After a long adaptation phase, E. coli GB05 was able to grow in high salt LB medium. Growth in PhyCoVi medium supplemented with soy peptone shows high fluctuations, probably due to the already discussed problem with insoluble medium compounds. The used strain is able to take up linear DNA fragments but seems not to be able to cope with high salt media 3.

TU Darmstadt (E. coli BL21 (DE3))

While E. coli BL21 (DE3) in High Salt LB medium reaches high OD values, growth in both algae-based mediums is very slow with long adaptation phases (Fig. 4). Also, the OD(600) values exhibit high standard deviations. As already discussed, this can be explained by algea remnants, such as lipids and cell wall remnants, which had not been removed properly. The strain is one of the most frequent used E. coli strains and it grows best on low salt medium 4.

Freiburg (E. coli DH5-α)

This measurement was conducted in a 96-well plate reader. The quality of both algae-based media are impaired by algea lipid and cell wall remnants and therefore show negative growth rates. But thank you, Team Freiburg, for conducting the experiment over such a long time course.

Conclusion

In conclusion, the collaboration was a full success! It showed that different strains are able to grow in our developed PhyCoVi medium. After evaluating the collaboration results, we increased our clean-up efforts during the production of our medium. Algea lipids and cell wall aggregates were removed by including an additional autoclavation step followed by centrifugation of the medium.

The result of this improvement can be seen in Fig. 7. The left part shows the old version of our medium, which exhibits a higher turbidity as the advanced medium seen in the right part of Fig. 7.

References