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+ | <div class="content"> | ||
+ | |||
+ | <h3>Bioinformatics</h3> | ||
+ | <div> | ||
+ | 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% and in one case 94,9%. | ||
+ | The oligos are located in the mitochondria in a regulatory region. | ||
+ | <br> | ||
+ | In the case of <i>Plasmodium falciparum</i>, we aligned 1012 sequences of | ||
+ | <i>Plasmodium falciparum</i> 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. | ||
+ | </div> | ||
+ | |||
+ | <hr> | ||
− | |||
<h3>Wet Lab</h3> | <h3>Wet Lab</h3> | ||
<div> | <div> | ||
− | In general, | + | In general, we can detect <i>Plasmodium</i> in all five cultured <i>Plasmodium</i> strains of <i>Plasmodium falciparum</i> |
− | + | (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) |
− | + | 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. | ||
<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%;"> | ||
− | <img style="width: 100%;" src=" | + | <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;"> |
− | <span style="text-decoration: underline;">Figure 1:</span> qPCR with cultured < | + | <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 |
</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. |
− | + | 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) |
− | + | ||
− | With the probe (HEX) we detect less than ten copies of our synthetic template. | + | |
− | + | ||
<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%;"> | ||
− | <img style="width: 100%;" src=" | + | <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;"> |
− | <span style="text-decoration: underline;">Figure 2:</span> qPCR with cultured < | + | <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>. |
</div> | </div> | ||
− | In a multiplex system the two probes (FAM and HEX) also detect the five cultured < | + | 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 < | + | detect the five cultured <i>Plasmodium</i> strains. |
− | + | 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%;"> | ||
− | <img style="width: 100%;" src=" | + | <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;"> |
− | <span style="text-decoration: underline;">Figure 3:</span> Multiplex qPCR with cultured < | + | <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> |
</div> | </div> | ||
</div> | </div> | ||
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<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 |
− | + | 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> | ||
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<h3>Interlab</h3> | <h3>Interlab</h3> | ||
<div> | <div> | ||
− | We participated successfully at the < | + | 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> | ||
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<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> |
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.
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.
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)
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).
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.
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.