Difference between revisions of "Team:JMU Wuerzburg/Results"

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<div class="column full_size">
 
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<h1>Results</h1>
 
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<p>Here you can describe the results of your project and your future plans. </p>
 
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</div>
 
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<div class="column third_size" >
 
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<h3>What should this page contain?</h3>
 
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<ul>
 
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<li> Clearly and objectively describe the results of your work.</li>
 
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<li> Future plans for the project. </li>
 
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<li> Considerations for replicating the experiments. </li>
 
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</ul>
 
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</div>
 
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<div class="column two_thirds_size" >
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<h3>Describe what your results mean </h3>
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        <div class="content">
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<ul>
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<li> Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for. </li>
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<li> Show data, but remember all measurement and characterization data must be on part pages in the Registry. </li>
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<li> Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project. </li>
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</ul>
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</div>
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            <h3>Bioinformatics</h3>
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            <div>
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                To detect <i>Plasmodium</i> in general we aligned 2080 sequences from NCBI.
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                Our primers and the probe has a consensus of more than 98% and in one case 94,9%.
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                The oligos are located in the mitochondria in a regulatory region.
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                <br>
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                In the case of <i>Plasmodium falciparum</i>, we aligned 1012 sequences of
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                <i>Plasmodium falciparum</i> and our primer set and the probe has a higher
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                consensus than 97,5%. The location of the oligos is in a regulatory region of the mitochondria.
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            </div>
  
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<div class="clear extra_space"></div>
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            <hr>
  
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            <h3>Wet Lab</h3>
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            <div>
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                In general, we can detect <i>Plasmodium</i> in all five cultured <i>Plasmodium</i> strains of <i>Plasmodium falciparum</i>
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                (FCR3, Mali2K, HB3, Dd2 and 3D7 from Tuebingen and Heidelberg).
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                In addition, we can detect our Biobrick (BBa_K2614000)
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                that includes a synthetic template as a positive control for the
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                qPCR that detects <i>Plasmodium</i> in general (figure 1).
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                We can detect less than 1000 copies of our synthetic template with a probe (FAM)
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                and less than 50 copies with SybrGreen.
  
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                <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
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                    <img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/3/3f/T--JMU_Wuerzburg--project-result_fig1.png" alt="fehlt" style="display: block;">
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                    <span style="text-decoration: underline;">Figure 1:</span> qPCR with cultured <i>Plasmodium</i> stems and our BioBrick as a control for <i>Plasmodium</i> general
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                </div>
  
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<div class="column two_thirds_size" >
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                Moreover, we are able to detect <i>P. falciparum</i> in all five cultured <i>Plasmodium</i> strains.
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<h3> Project Achievements </h3>
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                Our BioBrick is a negative control for our qPCR that detects <i>P. falciparum</i>.
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                With the probe (HEX) we detect less than ten copies of our synthetic template. (figure 2)
  
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<p>You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.</p>
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                <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
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                    <img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/d/db/T--JMU_Wuerzburg--project-result_fig2.png" alt="fehlt" style="display: block;">
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                    <span style="text-decoration: underline;">Figure 2:</span> qPCR with cultured <i>Plasmodium stems</i> and our BioBrick as a control for <i>P. falciparum</i>.
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                </div>
  
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<ul>
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                In a multiplex system the two probes (FAM and HEX) also
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<li>A list of linked bullet points of the successful results during your project</li>
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                detect the five cultured <i>Plasmodium</i> strains.
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<li>A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.</li>
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                They detect them with nearly the same cq-mean which means that
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</ul>
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                both qPCRs can detect <i>Plasmodium</i>. With this result we showed that
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                multiplexing is also possible with the two primer/probe pairs (figure 3).
  
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</div>
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                <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
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                    <img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/7/7e/T--JMU_Wuerzburg--project-result_fig3.png" alt="fehlt" style="display: block;">
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                    <span style="text-decoration: underline;">Figure 3:</span> Multiplex qPCR with cultured <i>Plasmodium</i> stems and our BioBrick as a control for <i>Plasmodium</i> general and specific for <i>P. falciparum</i>
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                </div>
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            </div>
  
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            <hr>
  
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            <h3>Human practices</h3>
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            <div>
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                We organised different workshops from scientists about
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                malaria or primer/probe design which were open for
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                all interested students. There was also a pipetting test where
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                more experienced students could give their knowledge to pipetting beginners.
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                <br><br>At our “cake and science” events we presented our project to the public.
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            </div>
  
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<div class="column third_size" >
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            <hr>
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<div class="highlight decoration_A_full">
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<h3>Inspiration</h3>
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<p>See how other teams presented their results.</p>
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<ul>
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<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
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<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
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<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
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</ul>
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</div>
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</div>
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            <h3>Interlab</h3>
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            <div>
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                We participated successfully at the
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                <i>fifth International InterLaboratory Measurement Study</i>
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                in synthetic biology. At the iGEM 2018 Vibrigens InterLab Study
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                from Marburg we also take place.
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            </div>
  
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            <hr>
  
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            <h3>Collaboration</h3>
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            <div>
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                We were able to establish a very pleasant and close
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                collaboration with team Munich. They have mentored us with great
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                care and reliability and answered all our questions.
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                So, it was much easier to start a new iGEM team in Wuerzburg.
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                We also received advice from different members of team Tuebingen
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                who were so kind to exchange some valuable information and experience with us.
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            </div>
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        </div>
  
  
 
</html>
 
</html>

Latest revision as of 15:06, 17 October 2018

Bioinformatics

To detect Plasmodium in general we aligned 2080 sequences from NCBI. Our primers and the probe has a consensus of more than 98% and in one case 94,9%. The oligos are located in the mitochondria in a regulatory region.
In the case of Plasmodium falciparum, we aligned 1012 sequences of Plasmodium falciparum and our primer set and the probe has a higher consensus than 97,5%. The location of the oligos is in a regulatory region of the mitochondria.

Wet Lab

In general, we can detect Plasmodium in all five cultured Plasmodium strains of Plasmodium falciparum (FCR3, Mali2K, HB3, Dd2 and 3D7 from Tuebingen and Heidelberg). In addition, we can detect our Biobrick (BBa_K2614000) that includes a synthetic template as a positive control for the qPCR that detects Plasmodium in general (figure 1). We can detect less than 1000 copies of our synthetic template with a probe (FAM) and less than 50 copies with SybrGreen.
fehlt Figure 1: qPCR with cultured Plasmodium stems and our BioBrick as a control for Plasmodium general
Moreover, we are able to detect P. falciparum in all five cultured Plasmodium strains. Our BioBrick is a negative control for our qPCR that detects P. falciparum. With the probe (HEX) we detect less than ten copies of our synthetic template. (figure 2)
fehlt Figure 2: qPCR with cultured Plasmodium stems and our BioBrick as a control for P. falciparum.
In a multiplex system the two probes (FAM and HEX) also detect the five cultured Plasmodium strains. They detect them with nearly the same cq-mean which means that both qPCRs can detect Plasmodium. With this result we showed that multiplexing is also possible with the two primer/probe pairs (figure 3).
fehlt Figure 3: Multiplex qPCR with cultured Plasmodium stems and our BioBrick as a control for Plasmodium general and specific for P. falciparum

Human practices

We organised different workshops from scientists about malaria or primer/probe design which were open for all interested students. There was also a pipetting test where more experienced students could give their knowledge to pipetting beginners.

At our “cake and science” events we presented our project to the public.

Interlab

We participated successfully at the fifth International InterLaboratory Measurement Study in synthetic biology. At the iGEM 2018 Vibrigens InterLab Study from Marburg we also take place.

Collaboration

We were able to establish a very pleasant and close collaboration with team Munich. They have mentored us with great care and reliability and answered all our questions. So, it was much easier to start a new iGEM team in Wuerzburg. We also received advice from different members of team Tuebingen who were so kind to exchange some valuable information and experience with us.