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

Line 8: Line 8:
  
  
−
        <div class="content">
+
      <div class="content">
  
 
             <h3>Bioinformatics</h3>
 
             <h3>Bioinformatics</h3>
 
             <div>
 
             <div>
 
                 To detect <i>Plasmodium</i> in general we aligned 2080 sequences from NCBI.  
 
                 To detect <i>Plasmodium</i> in general we aligned 2080 sequences from NCBI.  
−
                 Our primers and the probe has a consensus of more than 98%  
+
                 Our primers and the probe has a consensus of more than 98% and in one case 94,9%.  
−
                and in one case 94,9%. The oligos are located in the  
+
                The oligos are located in the mitochondria in a regulatory region.  
−
                mitochondria in a regulatory region.  
+
                <br>
−
                 In the case of <i>Plasmodium falciparum</i>, we aligned 1012 sequences  
+
                 In the case of <i>Plasmodium falciparum</i>, we aligned 1012 sequences of
−
                 of <i>Plasmodium falciparum</i> and our primer set and the probe has a  
+
                 <i>Plasmodium falciparum</i> and our primer set and the probe has a higher
−
                 higher consensus than 97,5%. The location of the oligos  
+
                 consensus than 97,5%. The location of the oligos is in a regulatory region of the mitochondria.
−
                is in a regulatory region of the mitochondria.
+
 
             </div>
 
             </div>
  
 
             <hr>
 
             <hr>
−
           
+
 
 
             <h3>Wet Lab</h3>
 
             <h3>Wet Lab</h3>
 
             <div>
 
             <div>
−
                 In general, wWe can detect <span style="font-style: italic;">Plasmodia</span> in general in all five cultured <span style="font-style: italic;">Plasmodia</span> stems of  
+
                 In general, we can detect <i>Plasmodium</i> in all five cultured <i>Plasmodium</i> strains of <i>Plasmodium falciparum</i>  
−
                <span style="font-style: italic;">Plasmodium</span> falciparum (FCR3, Mali2K, HB3, Dd2 and 3D7 from Tuebingen and Heidelberg).
+
                (FCR3, Mali2K, HB3, Dd2 and 3D7 from Tuebingen and Heidelberg).  
−
                 In addition, we can detect our Biobrick (BBa_K2614000) that includes a  
+
                 In addition, we can detect our Biobrick (BBa_K2614000)  
−
                synthetic template as a positive control for the qPCR that detects <span style="font-style: italic;">Plasmodium</span> in general (figure 1).
+
                that includes a synthetic template as a positive control for the  
 +
                qPCR that detects <i>Plasmodium</i> in general (figure 1).  
 
                 We can detect less than 1000 copies of our synthetic template with a probe (FAM)  
 
                 We can detect less than 1000 copies of our synthetic template with a probe (FAM)  
 
                 and less than 50 copies with SybrGreen.
 
                 and less than 50 copies with SybrGreen.
Line 38: Line 38:
 
                 </div>
 
                 </div>
  
−
                 Moreover, we are able to detect P.
+
                 Moreover, we are able to detect <i>P. falciparum</i> in all five cultured <i>Plasmodium</i> strains.  
−
                falciparum in all five cultured <span style="font-style: italic;">Plasmodia</span> stems.
+
                 Our BioBrick is a negative control for our qPCR that detects <i>P. falciparum</i>.  
−
                 Our BioBrick is a negative control for our qPCR that detects P.
+
                 With the probe (HEX) we detect less than ten copies of our synthetic template. (figure 2)
−
                falciparum.
+
−
                 With the probe (HEX) we detect less than ten copies of our synthetic template.
+
−
                (figure 2)
+
  
 
                 <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
 
                 <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
Line 50: Line 47:
 
                 </div>
 
                 </div>
  
−
                 In a multiplex system the two probes (FAM and HEX) also detect the five cultured <span style="font-style: italic;">Plasmodium</span> stems.
+
                 In a multiplex system the two probes (FAM and HEX) also  
−
                 They detect them with nearly the same cq-mean which means that both qPCRs can detect <span style="font-style: italic;">Plasmodium</span>.
+
                detect the five cultured <i>Plasmodium</i> strains.  
−
                With this result we showed that multiplexing is also possible with the two primer/probe pairs (figure 3).
+
                 They detect them with nearly the same cq-mean which means that  
 +
                both qPCRs can detect <i>Plasmodium</i>. With this result we showed that  
 +
                multiplexing is also possible with the two primer/probe pairs (figure 3).
  
 
                 <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
 
                 <div style="border-style: solid; border-color: #CCC; border-width: 1px; margin: 2em auto; width: 80%;">
Line 64: Line 63:
 
             <h3>Human practices</h3>
 
             <h3>Human practices</h3>
 
             <div>
 
             <div>
−
                 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.  
+
                 We organised different workshops from scientists about  
−
                 <br><br>
+
                malaria or primer/probe design which were open for  
−
                At our “cake and science” events we presented our project to the public.
+
                all interested students. There was also a pipetting test where  
 +
                more experienced students could give their knowledge to pipetting beginners.  
 +
                 <br><br>At our “cake and science” events we presented our project to the public.
 
             </div>
 
             </div>
  
Line 73: Line 74:
 
             <h3>Interlab</h3>
 
             <h3>Interlab</h3>
 
             <div>
 
             <div>
−
                 We participated successfully at the <span style="font-style: italic;">fifth International InterLaboratory Measurement Study</span> in synthetic biology. At the iGEM 2018 Vibrigens InterLab Study from Marburg we also take place.
+
                 We participated successfully at the
 +
                <i>fifth International InterLaboratory Measurement Study</i>  
 +
                in synthetic biology. At the iGEM 2018 Vibrigens InterLab Study  
 +
                from Marburg we also take place.
 
             </div>
 
             </div>
  
Line 80: Line 84:
 
             <h3>Collaboration</h3>
 
             <h3>Collaboration</h3>
 
             <div>
 
             <div>
−
                 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.
+
                 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.
 
             </div>
 
             </div>
 
         </div>
 
         </div>
−
 
  
  
  
 
</html>
 
</html>

Revision as of 11:34, 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.