Difference between revisions of "Team:Wageningen UR/Collaboration"
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<section id="delft"> | <section id="delft"> | ||
| + | <p>Our philosophy when it comes to collaboration is that “collaboration leads to codevelopment of the innovation and its full acceptance and use”. Based on this, we did not only collaborate with other iGEM teams, but also with students from the Design Academy Eindhoven. The students from the DAE helped us gain insight into how people perceive our project and synthetic biology in general, while the collaboration with iGEM teams helped us move forward in a scientific way. | ||
| + | We collaborated with two other iGEM teams: TU_Delft and Groningen. During this process, we also learned about their projects and helped each other out with some ideas. We even got some valuable input from both teams. Here’s what we have achieved in collaboration with them.</p> | ||
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<h1><b>Delft</b></h1> | <h1><b>Delft</b></h1> | ||
| − | <p> | + | <p> The team of TU Delft has been working on the creation of a biolaser. This is the name for a biosilica-covered cell expressing fluorescent proteins. The biosilica-layer is able to trap some of the photons sent out by fluorescing proteins that can then be used to excite other fluorescent proteins, leading to an increased overall fluorescence intensity in these cells. |
| − | + | Our task was to test eight different samples: three XXX and expression of GFP with five different promoters. As we ourselves have worked with the platereader extensively during our project to measure fluorescence of samples, we were more than willing to also test these samples, as it also added to our own expertise in handling the platereader. | |
| − | + | The data has been processed by the team of TU Delft, after we have sent them the raw data. Still, as the curious scientists that we are, we had a look at the cells we worked with to get some preliminary results. While some samples did not show high levels of fluorescence, some showed a stunning green colour. Contempt with the results we got and the practice we had gotten through this collaboration, we were happy to have taken this opportunity to help another team. | |
| − | + | Moreover, the Delft team also did some test for us. For our in vitro toxicity assay with fluorophore-filled vesicles, we were longing for a picture proving that we were indeed able to encapsulate fluorophores in vesicles. The results can be found here. | |
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</p> | </p> | ||
</section> | </section> | ||
<section id="groningen"> | <section id="groningen"> | ||
| − | <h1><b>Groningen</b></h1> | + | <h1><b>Groningen</b></h1>For the team of Groningen, we tested and improved their system CryptoGERM. This is a way of encrypting messages in spores, the messages being only decryptable with the belonging key, also in a spore. |
| + | We received spores of Bacillus subtilis with a message encrypted in the genome. As we tested at an early stage, the key was not delivered in spores as well, but we could test our results on a webpage that was able to transform the sequence we obtained into a message for us to read. | ||
| + | The procedure seems to be easy: | ||
| + | 1) Put spores to grow | ||
| + | 2) PCR with the primers delivered with the spores | ||
| + | 3) Put PCR product to sequencing | ||
| + | Unfortunately, the first attempts of PCRing the fragment in question failed. We tried to perform colony PCR and tested different changes in the protocol: longer initial denaturation time, higher dilution of colony, adding of DMSO. However, we could not obtain a PCR fragment. So, we chose to first isolate the genomic sequence of the bacteria. After this, we obtained a nice and distinct band that we sent to sequencing. Thus, we proposed to change the protocol from simple colony PCR to PCR from the isolated genome. | ||
| + | |||
</section> | </section> | ||
Revision as of 18:04, 5 October 2016
Our philosophy when it comes to collaboration is that “collaboration leads to codevelopment of the innovation and its full acceptance and use”. Based on this, we did not only collaborate with other iGEM teams, but also with students from the Design Academy Eindhoven. The students from the DAE helped us gain insight into how people perceive our project and synthetic biology in general, while the collaboration with iGEM teams helped us move forward in a scientific way. We collaborated with two other iGEM teams: TU_Delft and Groningen. During this process, we also learned about their projects and helped each other out with some ideas. We even got some valuable input from both teams. Here’s what we have achieved in collaboration with them.
Delft
The team of TU Delft has been working on the creation of a biolaser. This is the name for a biosilica-covered cell expressing fluorescent proteins. The biosilica-layer is able to trap some of the photons sent out by fluorescing proteins that can then be used to excite other fluorescent proteins, leading to an increased overall fluorescence intensity in these cells. Our task was to test eight different samples: three XXX and expression of GFP with five different promoters. As we ourselves have worked with the platereader extensively during our project to measure fluorescence of samples, we were more than willing to also test these samples, as it also added to our own expertise in handling the platereader. The data has been processed by the team of TU Delft, after we have sent them the raw data. Still, as the curious scientists that we are, we had a look at the cells we worked with to get some preliminary results. While some samples did not show high levels of fluorescence, some showed a stunning green colour. Contempt with the results we got and the practice we had gotten through this collaboration, we were happy to have taken this opportunity to help another team. Moreover, the Delft team also did some test for us. For our in vitro toxicity assay with fluorophore-filled vesicles, we were longing for a picture proving that we were indeed able to encapsulate fluorophores in vesicles. The results can be found here.
Groningen
For the team of Groningen, we tested and improved their system CryptoGERM. This is a way of encrypting messages in spores, the messages being only decryptable with the belonging key, also in a spore. We received spores of Bacillus subtilis with a message encrypted in the genome. As we tested at an early stage, the key was not delivered in spores as well, but we could test our results on a webpage that was able to transform the sequence we obtained into a message for us to read. The procedure seems to be easy: 1) Put spores to grow 2) PCR with the primers delivered with the spores 3) Put PCR product to sequencing Unfortunately, the first attempts of PCRing the fragment in question failed. We tried to perform colony PCR and tested different changes in the protocol: longer initial denaturation time, higher dilution of colony, adding of DMSO. However, we could not obtain a PCR fragment. So, we chose to first isolate the genomic sequence of the bacteria. After this, we obtained a nice and distinct band that we sent to sequencing. Thus, we proposed to change the protocol from simple colony PCR to PCR from the isolated genome.
