Team:Wageningen UR/Collaborations

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Wageningen UR iGEM 2016

 

Collaborations

Our philosophy when it comes to collaboration is that “collaboration leads to development 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 in the form of a a biosilica-covered cell expressing fluorescent proteins. The biosilica-layer traps some of the photons sent out by fluorescent proteins that can be used to excite other fluorescent proteins. This leads to increased overall fluorescence intensity in the cells. We measured their strains in our plate reader.

During our own project, we have worked with the microplate reader extensively. We tested eight different constructs in a microplate reader: three different BioBricks for expression of fluorescent proteins and expression of GFP with five different promoters. In short, we are content with the results we got and the practice we got through this collaboration, and we are happy about this opportunity to help another team.

Figure 1. We grew and tested 8 different strains from Delft. The figures they made with our data can be found in Figure 1 on their Collaborations page.

Moreover, the Delft team did some experiments for us. For our in vitro toxicity assay with fluorophore-filled vesicles, we were hoping for a picture proving that we were indeed able to encapsulate fluorophores in vesicles. The TU Delft team helped us by making nice pictures of our vesicles using an electron microscope!

Figure 2. TEM images of BBMVs. The images of Varroa destructor vesicles were made by the iGEM team from Delft. (a) Tenebrio molitor (b) Varroa destructor

Groningen

For the Groningen iGEM team, we tested and improved their system "CryptoGERM". CryptoGERM was developed to encrypt messages in the DNA of Bacillus subtilis spores, that can only be decoded using a key that is also in a spore. We received a message to decrypt from Groningen. As we tested the system in an early stage, when it was not fully developed, we used a translator webpage instead of spores containing the key.

The procedure is as follows:

  1. Grow spores.
  2. PCR the encoded message.
  3. Sequence the PCR product.

Unfortunately, the first attempts of PCR amplifying the message failed. We tried to perform colony PCR and tested different adjustments of the protocol: longer initial denaturation time, less DNA as template and addition of DMSO. However, we could not obtain the correct PCR fragment. Subsequently, we tried to isolate the genomic sequence of the bacteria first. After doing this we obtained a nice PCR product that was sent for sequencing. Thus, we proposed to change the protocol from colony PCR to PCR from isolated and purified genomic DNA.

Figure 3. On the left one of the four attempts of colony PCR. No bands are visual. After purification of the genomic DNA, PCR succeeded resulting in a band around 900 basepairs as can be seen in the right figure.

The sequence we obtained was entered into their decoder, leaving us with the following message: …..