Team:KU Leuven/Project/DataPage

Welcome to our data page! Here we will summarize everything we achieved this summer. Of course, if you want a more extensive explanation you should check out the corresponding wiki page.

Ultimately our project aims to reduce crop loss due to aphid infestations. With an environmental project like ours, the computer is our best friend: through modelling and prediction algorithms we can reduce the real costs of field tests.
Our first step in the modelling was to predict the effect of our pheromones on the environment and the ecosystem through a series of modelling steps. You can find this in our ecological model page. The pheromones E-β-farnesene and methyl salicylate will not only affect the environment but also the bacterial cell itself. To figure out the impact of our system on our E. coli we performed a Flux Balance Analysis. Once we knew that our bacteria could handle the production of the pheromones we tried to predict the exact production amounts and find the rate limiting steps. Here our goal was also to feed wet-lab data into our algorithms. Finally, to optimise the impact of the released pheromones on the aphids and the ladybugs, we designed an oscillating transcription factor network to regulate their production. This oscillator also communicates between cells, enforcing the oscillating rhythm onto the whole colony.
Summarised, these algorithms allow us to model our system from the cellular metabolism throughout to the environmental impact. Based on our models, we adapted the actual building of the system towards the most effective circuit. Finally, our mathematical predictions will provide significant benefits once we prepare our E. coligy for field tests.

Ecology

Two companies (Biobest and pc fruit) specialised in biological pest management, were very interested in our project and invited us to perform experiments at their facilities. These experiments proved to be challenging given the fact that there are quite a few variables when working with plants and insects. Nonetheless, we were able to demonstrate the effect of MeS in inducing plant defence mechanisms and that this has an effect on the aphid population.

(E)-β-farnesene Project

After the whole summer's work, we finally made 5 BioBricks for this section. Our favorites are:
1. BBa_K1060002 contains an open reading frame that codes for (E)-β-farnesene synthase from Artemisia annua. The enzyme converts farnesyl diphosphate into E-β-farnesene. It was a milestone in our project work. We succeeded to remove an EcoRI site in the gene (AY835398.1). This gave us one of the basic parts we needed to create our system.
2. BBa_K1060009 is a construct that constitutively expresses β-farnesene synthase. This was the final device used for our Aphid experiments.
3. BBa_K1060011 is similar to BBa_K1060009. However, in this biobrick we added a lac operator in front of the βfarnesene synthase. This makes it possible to switch of (E)- β-farnesene production by using biosensors expressing LacI.
Our pilot studies with these biobricks and the aphids are promising. Apart from this in vivo characterization, we also initiated an SDS-PAGE analysis. This indicated that the EBF synthase was most likely produced. We can possibly measure the amounts of EBF and MeS produced by our bacteria and use these concentrations to characterize the impact of our synthetic compounds further.

Methyl Salicylate Project

Throughout the summer, we made 4 different BioBricks involved in the production of methyl salicylate.
After finding out that the MIT 2006 brick (BBa_J45700) only produced weak amounts of the wintergreen scent (MeS), we dove into the literature and discovered a possible lack of chorismate present in the bacteria. We tried to overcome this problem by overexpressing aroG in E. coli. In the literature, we found two mutations that could make DAHP synthase insensitive to allosteric inhibition. We succeeded in biobricking the normal aroG gene, which gives future teams the opportunity to introduce mutations themselves to overcome the chorismate problem. We characterized our bricks with a renewed smell test and an SDS-PAGE analysis.

As a result of our unique collaboration between philosophers and scientists within our team, we formulated a new approach, which is bottom-up structured and central is the dialogue between scientists, philosophers and the general public. Therefore, all team members and their supervisors were interviewed about their ethical beliefs. We also explained why we should inform the general public using the ideas of philosopher Hannah Arendt and we examined the responsability of synthetic biologists using the ideas of philosopher Hans Jonas. This is not only a first time in the iGEM competition that these well-known philosophers are read to provide a strong foundation, but has also never been done in the scientific literature!
We consider this bottom-up collaboration between students a new starting point for approaching human practices within the iGEM competition.

To make sure that we have a product that is worth to be launched, we asked Biobest & pcfruit why they were so interested in the BanAphids. Furthermore, we also asked the end users (farmers) whether they would use our BanAphids and the results were definitely positive!

We organized a symposium for the general public for which we also invited the other BeNeLux teams to present their project. We hope that one day this will become a yearly tradition in the iGEM competition.

We also went to schools to teach them about synthetic biology. For this we made our very own Plexiglas "biobricks" which the students can use to work on excercises and we made a 3D-bacterial model, which gives the students an idea of what a bacterium looks like.