Difference between revisions of "Team:Wageningen UR/Collaborations"

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The sequence we obtained was entered into their <a href="https://2016.igem.org/Team:Groningen/Decoding#carlos">decoder</a>, leaving us with the following message: <i>The world is full of obvious things which nobody by any chance ever observes. </i>
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The sequence we obtained was entered into their <a href="https://2016.igem.org/Team:Groningen/Decoding#carlos">decoder</a>, leaving us with the following message: <br><i>The world is full of obvious things which nobody by any chance ever observes. </i>
 
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Revision as of 19:27, 19 October 2016

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Wageningen UR iGEM 2016

 

Collaborations

We believe that collaboration leads to development of the innovation and its full acceptance and use. Therefore, we collaborated with two other iGEM teams: TU Delft and Groningen. During this process, we learned a lot about their projects and helped each other out with experiments and ideas. The beauty of this is that we got some valuable input from both teams. Here you will find more details of these two collaborations

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 some of 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 various fluorescent proteins and five different devices for the expression of GFP, each with a different promoter. The protocol used for this experiment can be found here.

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.

On top of that, the Delft team performed an experiment for us. An essential part of our in vitro toxicity assay were vesicles made from the gut membrane of Varroa mites. We were hoping for a picture showing the presence of these vesicles. The TU Delft team helped us with this by making pictures of our vesicles using an transmission electron microscopy!The pictures as shown in Figure 2. In short, we are content with the results we got and the practice we had through this collaboration.

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 the Groningen team. 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.
  • 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:
The world is full of obvious things which nobody by any chance ever observes.