Team:TUDelft/Contribution
Contribution
iGEM git guide
COVID-19 has had a profound influence on the lives of people all over the world. During these difficult times many of us are looking for solutions to help adapt to the new norm. This often involves having to work from home and this change has not exempted those competing in iGEM. For the time being, this is not likely to change in the future either. One of the tools that we found to be incredibly useful was Git. Git is a platform that allows you to track changes and collaborate on single or multiple pieces of code.
Throughout our project, we have made extensive use of git to collaborate and share ideas from our homes. It has been a vital tool for us to accomplish both our model for phage infection and toxin production, as well as our 2D biofilm simulation. We’re grateful to the flexibility that the platform provides and we wanted to share what we have learned to make sure that as many teams as possible can benefit from this enabling technology. Therefore, we have developed an Introductory Git Guide to help iGEM teams get acquainted with the platform and the accompanied workflow. We also discuss how GitHub is used within iGEM, so that teams have a good understanding of the many valuable iGEM resources at their disposal.
PHOCUS phage troubleshooting
The scientific method is a vital part of good scientific procedure. We encountered several engineering challenges throughout our project. One of the most prominent were the challenges that we faced when trying to engineer a bacteriophage. To show that we can successfully engineer a phage we made a proof of concept using the bacteriophage T7 and E. coli BL21 (DE3). We thought it could be of great help to scientists and the iGEM community to provide a short and simple guide about troubleshooting phage engineering .
BPUL (BBa_K863000) modifications for enhanced phenol and guaiacol degradation
The aggregation of locusts is (partially) triggered by aggregation pheromones. The predominant compounds in nymphal and young adult faeces are phenol and guaiacol, whereas older adults also contain phenylacetonitrile [1]. The production of these compounds have been associated with the locust gut bacteria [2]. To reverse this swarming behaviour, we researched enzymes that degrade the compounds phenol and guaiacol.
Our initial idea was to express and improve the enzyme laccase, from Bacillus pumilus (BPUL, BBa_K863000), as it is an enzyme capable of oxidizing both phenolic and non-phenolic lignin related compounds. In literature we found that by performing site directed mutagenesis to introduce the mutations L386Q, G417R, V482G we could enhance the oxidation reaction [3], thereby increasing the rate at which the laccase degrades guaiacol.But after talking to experts about our approach, they recommended us to not reverse this swarming behaviour but to kill the locust instead.
Despite not using BPUL BBa_K863000 we decided to add some literature information that we found to be really relevant into the registry page (BBa_K863000), as well as propose an approach to obtain the desired mutations. We hope that another iGEM team will find this suggestions on how to improve the laccase activity useful.
References
- Obeng-Ofori, D., Torto, B., Njagi, P. G. N., & Hassanali, A. (1998). Aggregation pheromone complex of the desert locust, Schistocerca Gregaria (Forskal) (Orthoptera: Acrididae): Current Status. Journal of the Ghana Science Association, 1(1), 69–83. https://doi.org/10.4314/jgsa.v1i1.17787
- Dillon, R. J., Vennard, C. T., & Charnley, A. K. (2000). Pheromones: Exploitation of gut bacteria in the locust. Nature. https://doi.org/10.1038/35002669
- Ihssen, J., Jankowska, D., Ramsauer, T., Reiss, R., Luchsinger, R., Wiesli, L., … Faccio, G. (2017). Engineered Bacillus pumilus laccase-like multi-copper oxidase for enhanced