Difference between revisions of "Team:Bielefeld-CeBiTec/Collaborations"

 
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During the mentorship we picked certain topics for every skype meeting. Those topics covered technical and practical advices concerning the wiki and important points for human practice among others. Together we discussed all the gold medal criteria and gave tips how to fulfill them. Furthermore we discussed organizational aspects of travel and stay in Boston. During one skype call our HTML programming expert Maximilian Edich answered questions concerning HTML coding. <br>
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During the mentorship we picked certain topics for every skype meeting. Those topics covered technical and practical advices concerning the wiki and important points for human practice among others. Together we discussed all the gold medal criteria and gave tips how to fulfill them. Furthermore we discussed organizational aspects of travel and stay in Boston. During one skype call our HTML programming expert Maximilian answered questions concerning HTML coding. <br>
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In return for the mentorship, iGEM <a target="_blank" href="https://2017.igem.org/Team:UNIFI">UNIFI</a> helped us characterizing two BioBricks. To make sure that <i>Escherichia coli</i> is able to take up the unnatural nucleoside triphosphates from the cultivation media we had to introduce a heterologous transporter. This is due to a lack of nucleotide transporters in <i>E. coli</i>. One of the BioBricks encodes a complete  nucleotide transporter <i>pt</i>NTT2 (<a target="_blank" href="http://parts.igem.org/Part:BBa_K2201000">BBa_K2201000</a>) originated from the algae <i>Phaeodactylum tricornutum</i>. The second BioBrick is a truncated version missing the N-terminal signal peptide (<a target="_blank" href="http://parts.igem.org/Part:BBa_K2201001">BBa_K2201001</a>). This N-terminal signal peptide leads to some kind of toxicity in <i>E. coli</i>. Through cultivation experiments we wanted to investigate the extent of the toxicity by comparing the growth of the strain expressing the full version of <i>Pt</i>NTT2 to the ones expressing the truncated version. <br>
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In return for the mentorship, iGEM <a target="_blank" href="https://2017.igem.org/Team:UNIFI">UNIFI</a> helped us characterizing two BioBricks. To make sure that <i>Escherichia coli</i> is able to take up the unnatural nucleoside triphosphates from the cultivation media we had to introduce a heterologous transporter. One of the BioBricks encodes a complete  nucleotide transporter <i>Pt</i>NTT2 (<a target="_blank" href="http://parts.igem.org/Part:BBa_K2201004">BBa_K2201004</a>) originated from the algae <i>Phaeodactylum tricornutum</i>. The second BioBrick is a truncated version missing the N-terminal signal peptide (<a target="_blank" href="http://parts.igem.org/Part:BBa_K2201001">BBa_K2201001</a>). This N-terminal signal peptide leads to some kind of toxicity in <i>E. coli</i>. Through cultivation experiments we wanted to investigate the extent of the toxicity by comparing the growth of the strain expressing the full version of <i>Pt</i>NTT2 to the ones expressing the truncated version. <br>
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We started to cultivate the different strains in 50 mL media using flasks and measured the OD<SUB>600</SUB> every 30 minutes during the exponential growing phase. Due to manual measurements our results showed big error values for the maximum growing rate µmax. This makes it hard to get a valid conclusion. iGEM <a target="_blank" href="https://2017.igem.org/Team:UNIFI">UNIFI</a> has the capacity to do the same cultivation experiment using a microscale bioreactor. This ensures automatic measurements for OD<SUB>600</SUB> values which would decrease errors concerning µmax. This characterization from iGEM <a target="_blank" href="https://2017.igem.org/Team:UNIFI">UNIFI</a> would lead to a more accurate estimation of the toxicity of a full length version compared to a truncated version of <i>Pt</i>NTT2.
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iGEM <a target="_blank" href="https://2017.igem.org/Team:UNIFI">UNIFI</a> had the capacity to perform the same cultivation experiment we performed using a microscale bioreactor. This ensured automatic measurements for OD<SUB>600</SUB> values which would decrease errors concerning µ<sub>max</sub>. This characterization from iGEM <a target="_blank" href="https://2017.igem.org/Team:UNIFI">UNIFI</a> led to a more accurate estimation of the toxicity of a full length version compared to a truncated version of <i>Pt</i>NTT2.
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<img class="figure image" src="https://static.igem.org/mediawiki/2017/0/02/T--Bielefeld-CeBiTec--microcultivation96_well.jpeg">
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<p class="figure subtitle"><b>Cultivation performed by iGEM team UNIFI as part of our collaboration</b><br> </p>
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<p class="figure subtitle"><b>Figure 8:</b> Collection of the postcards of iGEM teams from around the world. Our card is the black one in the lower middle.</p>
 
<p class="figure subtitle"><b>Figure 8:</b> Collection of the postcards of iGEM teams from around the world. Our card is the black one in the lower middle.</p>
 
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<h4>Labnotes Creator</h4>
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To make it easier for this years and future iGEM teams to write and upload their lab journals to the wiki, we developed the <a href="https://2017.igem.org/Team:Bielefeld-CeBiTec/Notebook/LabnotesGenerator">Labnotes Creator</a>. After initial testing performed by our team, we reached out to other iGEM teams to test the software. We would like to thank our beta testers team <a href="https://2017.igem.org/Team:TU_Darmstadt">TU Darmstadt</a> and team <a href="https://2017.igem.org/Team:Cologne-Duesseldorf">Duesseldorf-Cologne</a>. Team Duesseldorf-Cologne provided some valuable feedback, while team TU Darmstadt actively tested and validated our software. A big thank you to both team!
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Latest revision as of 02:39, 2 November 2017

Collaboration

Short Summary

The main idea of iGEM is an easy way of biological engineering realized by standard biological parts (BioBricks) and an open source database. These make synthetic biology accessible to everyone. The whole concept of BioBricks is based on sharing parts freely across the community. The community connects different iGEM teams to help each other, learn from each other and finally to achieve their desired goals. The collaboration of individual teams is one of the most important aspects in iGEM. For our iGEM project we worked with several other iGEM teams. We collaborated extensively with the iGEM team UNIFI 2017 and CU Boulder 2017. Team UNIFI participates for the first time in the iGEM competition and our aim was to help them getting jump started into the iGEM competition and coaching them in order to direct them towards a successful project. iGEM UNIFI helped us with the characterization of the transporter ptNTT2, using their more precise equipment to recording growth rates. Next to this collaboration we sent plasmids from former iGEM Bielefeld-CeBiTec Teams to iGEM SDU Denmark 2017 and to several other researchers worldwide.

Collaboration – Mentoring iGEM Team UNIFI 2017

The iGEM team UNIFI is representing the University of Florence and is participating for the first time in the iGEM competition. As the only Italian team this year, they took the chance to collaborate with other iGEM teams beyond their own country borders. We met the iGEM team UNIFI at the European iGEM Meetup in Delft on 7th to 8th July and initiated the mentoring. Afterwards, we started this collaboration, with weekly skype conferences (Figure 1) in addition to intensive communication via email.

Figure 1: Skype meetings with iGEM UNIFI for a two-way collaboration.

During the mentorship we picked certain topics for every skype meeting. Those topics covered technical and practical advices concerning the wiki and important points for human practice among others. Together we discussed all the gold medal criteria and gave tips how to fulfill them. Furthermore we discussed organizational aspects of travel and stay in Boston. During one skype call our HTML programming expert Maximilian answered questions concerning HTML coding.
In return for the mentorship, iGEM UNIFI helped us characterizing two BioBricks. To make sure that Escherichia coli is able to take up the unnatural nucleoside triphosphates from the cultivation media we had to introduce a heterologous transporter. One of the BioBricks encodes a complete nucleotide transporter PtNTT2 (BBa_K2201004) originated from the algae Phaeodactylum tricornutum. The second BioBrick is a truncated version missing the N-terminal signal peptide (BBa_K2201001). This N-terminal signal peptide leads to some kind of toxicity in E. coli. Through cultivation experiments we wanted to investigate the extent of the toxicity by comparing the growth of the strain expressing the full version of PtNTT2 to the ones expressing the truncated version.
iGEM UNIFI had the capacity to perform the same cultivation experiment we performed using a microscale bioreactor. This ensured automatic measurements for OD600 values which would decrease errors concerning µmax. This characterization from iGEM UNIFI led to a more accurate estimation of the toxicity of a full length version compared to a truncated version of PtNTT2.

Cultivation performed by iGEM team UNIFI as part of our collaboration

Collaboration - Lokalization Study and Part Exchange with CU Boulder 2017

This year the iGEM team CU Boulder works with artificial compartments which consist of shell proteins containing a photoswitch amino acid. These compartments are supposed to break up into separate shell proteins releasing the protein captured inside the compartment. This could potentially act as next-generation drug delivery systems, biosensors, or as a solution to sequester diffuse and harmful environmental toxins. The iGEM team CU Boulder 2016 submitted the BioBrick containing the aminoacyl tRNA synthetase (aaRS) for the photoswitch amino acid. This year’s team helped us to realize our photoswitching project by sending us their aaRS and a small amount of the amino acid AzeF. In return, we transformed their parts EutS (BBa_K2129001) and EutC-tagged FusionRed in E.coli DH5α and performed localization studies by fluorescence microscopy with our confocal laser scan microscope.

Figure 2: 3D-Animation of the fluorescence signal of E.coli cells transformed with EutC-tagged FusionRed from CU Boulder. The fluorescence is present in the whole cell.

Figure 3: 3D-Animation of the fluorescence signal of three E.coli cells cotransformed with shell protein EutS and EutC-tagged FusionRed from CU Boulder. The fluorescence is concentrated in the EutS-compartments.

As you can see above the parts work perfectly. The cells only containing FusionRed have a bright fluorescence in the cytoplasm (Figure 2) and the cotransformats show the fluorescence concentrated in the EutS compartments (Figure 3). We send CU Boulder the stacked pictures and combined the stacks to 3D-animations.
We are very happy that they provided their aaRS to us to expand our toolkit and we hope that our results of the localization study are helpful for their further work.

Networking

Beside the collaborations mentioned above, our team got in contact with many people from all over the world throughout the year. We would like to give a little impression of how we benefited from the iGEM community.

22.04 - March for Science in Bonn

In April we were invited to participate in the March for Science in Bonn. We answered this call and met with other iGEM teams from the region to stand up for the importance of science and reliable facts in our modern society. It was a great event and we had a lot of fun and got to know the team Cologne Duesseldorf, with which we held close contact throughout the whole year.

Figure 4: Daniel Bergen at the March for Science in Bonn at the 22nd April with members of the team Cologne Duesseldorf and other iGEM teams.

13.05, 15.07 - Meetings with Team Cologne Duesseldorf

After participating in the March for Science in Bonn, the iGEM team Cologne Duesseldorf invited us to a team meet-up. Thus, on the 13th of May, some of our team members drove to Dusseldorf and had a very fun and exciting day in this beautiful city. We also wanted to offer the team Cologne Duesseldorf the opportunity to visit us in Bielefeld in return. Some team members visited us at the 15th of July and we had a delicious BBQ and showed them the city, the CeBiTec, and our lab.

Figure 5: Impressions of our meet ups with the team Cologne Duesseldorf. Our visit in Dusseldorf left and the meet up in Bielefeld right.

30.06 - German Meet-up in Dresden

On the 30th of June, we participated in the German Meet-up in Dresden and represented our team and our project. It was the first time we presented our project to the public which is why the presentation was very exciting for our speaker Chris. It was also interesting to see what other teams planned to work on over the year and we are very curious to see what they and we will achieve until the Giant Jamboree in November.

Figure 6: Our speaker Chris Whitford at the German meet-up in Dresden, presenting our project to the public for the first time.

06-08.07 - European Meet-up in Delft

From the 6th to the 8th of July, six of our team members drove to the beautiful city of Delft to participate in the European iGEM meet-up organized by the TU Delft team. We were astonished by the very interesting presentations from a lot of speakers at the faculty of aerospace engineering at the TU Delft and were very excited about our first poster session. It was great to meet people from all over Europe and especially our friends from Munich and the Team Unifi with whom we started the mentoring partnership. After the official end of the meet-up, we met with some members of the team Cologne Duesseldorf and had a wonderful afternoon at the seaside.

Figure 7: Six of our team members at the European meet-up in delft.

Postcards

Just like last year, the team Cologne Duesseldorf organized a campaign to promote synthetic biology by inviting other iGEM teams to design interesting postcards related to synthetic biology. We were thrilled by this idea and started with the design of our own postcard. Since we were then in a time of intense cloning which consumed a huge amount of agarose gels, we decided to collect the nicest and most terrible gel pictures of our current work. We liked the funny design of the final card, and this little distraction motivated us to work even harder.

Figure 8: Collection of the postcards of iGEM teams from around the world. Our card is the black one in the lower middle.

Labnotes Creator

To make it easier for this years and future iGEM teams to write and upload their lab journals to the wiki, we developed the Labnotes Creator. After initial testing performed by our team, we reached out to other iGEM teams to test the software. We would like to thank our beta testers team TU Darmstadt and team Duesseldorf-Cologne. Team Duesseldorf-Cologne provided some valuable feedback, while team TU Darmstadt actively tested and validated our software. A big thank you to both team!