Team:Wageningen UR/Collaborations


Group Photo


During the summer, we embarked on the journey to find a cure for Xylella fastidiosa. To improve our project, to help other teams do the same, and to improve knowledge on synthetic biology we collaborated with multiple different teams. We performed wet-lab collaborations with TU Eindhoven and MSP Maastricht. Human practices collaborations included attending meetups, filling in surveys and joining other non-scientific collaborations. We also started our very own outreach project: The voice of iGEM. A song contest, that encouraged teams to make song parodies that would help engage people in synthetic biology in a fun way.

MSP Maastricht — The RocKit

During our wetlab collaboration MSP Maastricht reproduced our findings of a fluorescence loss assay we performed. The graphs shows the repression of mRFP and GFP fluorescence by dCas12a. mrfp and gfp were under the control of the early transcripts regulatory region of phage Lambda. The importance of the experiment was to show the reproducibility of our approach to gain control of phage gene expression and proliferation via targeted operon repression. In this way, MSP Maastricht confirmed our findings and contributed to the characterization of our parts BBa_K3286040, BBa_K3286041, and BBa_K3286046.

iGEM Maastricht 2019 Logo
iGEM MSP Maastricht 2019
Fluorescence Loss Assay Graph
Alba and Abraham
The relative mRFP and GFP fluorescence downstream native bacteriophage phage Lambda's early transcripts regulatory region, targeted by dCas12a. Samples were normalized to a control sample lacking the dCas12 spacer array. Six spacer arrays were used, a non-targeting (NT) and different combinations of spacers targeting the promoter PL, P RM and P R of the early transcripts regulatory region. Data represent the averages of five biological replicates.
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    In return, MSP Maastricht asked us to repeat a transformation experiment for them. The plasmid names were dCas9-AID and dCas9-eAID which contain several proteins that were necessary for the functionality of this mutation mechanism. AID is activation induced deaminase and chemically alters DNA by changing Cytosine to Uracil. eAID does the same type of mutations but on a larger locus of the DNA. The transformations of the AID and eAID plasmids showed no colonies. We contributed to their project by troubleshooting the transformation of these plasmids using their protocols. This collaboration enriched their project with knowledge of how reproducible it is to transform this plasmid that contain the following parts: BBa_K3218005, BBa_K3218006, BBa_K3218007 and BBa_K3218008. Sadly, we could not successfully transform cells with the ligation mix of iGEM MSP Maastricht.

    Transformation of AID and e-AID plasmids
    Electro- and Heat Shock Transformation of plasmids carrying aid and enhanced(e)-aid. The two plasmids carrying either eaid or aid where transformed both via electro- and heat shock. After the recovery phase 50 and 200 µL of transformation reaction were spread on LB-Amp100 plates and incubated at 37 °C for 14 hours. puc19 (NEBN3041) was used as a positive control. Dots visible on plates which are not control plates are air bubbles in the media which appeared due to temperature changes.
    Team picture when we received the package.

TU Eindhoven

Xylencer is focused on using genetically engineered bacteriophages to optimize phage therapy against Xylella fastidiosa. iGEM Eindhoven is the other Dutch team that choose to work with phages. They are working on a bacteriophage-based system to detect specific (pathogenic) bacterial strains. Detection takes place by a bioluminescent signal after detection of a specific region of the phage DNA. As we are the two Dutch teams that work with phages, we immediately started discussing our projects.

During the whole iGEM experience, we discussed our projects both at meetups and in emails. The first thing we discussed was the possibility to work with bacteriophages in our respective labs. We both had trouble with this, as the chances of contamination are large. In Wageningen we could solve this by working in an ML-2 lab. Sadly, this was not possible for TU Eindhoven, as they did not have access to such a lab. They found a solution by performing all their phage work at the QAMH in Brussels. They offered to ask questions regarding phages in plants on our behalf.

iGEM Eindhoven 2019 Logo
iGEM Eindhoven 2019
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    We also discussed our troubles with protein expression. Eindhoven had already conquered a problem with lack of expression of their protein. For small proteins, we also experienced a lack of expression. The Eindhoven team proposed three options: sonification of the cells, inducing with a lower concentration of IPTG and codon optimizing the proteins. The proteins were already codon optimized and we used sonification to lyse the cells. We tried inducing expression with a lower concentration of IPTG, which could reduce toxic effects. Sadly, this did not have an effect on our expression levels.

    Eindhoven struggled with a high level of background fluorescence. We did not have any experience with this ourselves, but we proposed lowering the concentration of the proteins and checking for autofluorescence. Tweaking with the concentrations of different compounds finally helped solve their problems.

    Early on in the competition, we also discussed the potential for collaboration. iGEM Eindhoven proposed to detect our engineered bacteriophages using their detection system. This would allow TU Eindhoven to test whether their system would work with genetically engineered bacteriophages. It might be possible to differentiate between the genetically engineered and normal bacteriophages using this system. If this would prove to work, we would be able to detect if we have generated a genetically engineered bacteriophage. We would also be able to detect the presence of Xylella fastidiosa on plants and compare it to our own detection tool specialized on insects. We would perform this research on phage lambda, our model organism phage.

    One of the biggest issues the TU Eindhoven team faced in their project was the ability to work with bacteriophages in their lab in Eindhoven. As we are allowed to work with phages in our lab, we could test whether the device would work with phages. This would benefit us both.

    Unfortunately, due to time issues and problems generating results for both teams, it was not possible to actually perform the experiment in Wageningen. Still, we are very grateful for the help in discussing and troubleshooting both of our projects.

The Voice of iGEM

This year, our team decided to organize a song contest. We asked any team that wanted to participate to make a parody song from either a popular song or a completely new one. In other words, they had to write lyrics for a song, which would talk about their iGEM experience or about science in general. To see the sent in songs, visit the Voice of iGEM page.

mic Voice of iGEM

Other Collaborations