We wanted our modelling approach to be integrated with different aspects of our project. On one hand, we decided to model the degradation process in order to get a solid start in the lab and to explore the possibilities to implement our idea in different ways. On the other hand, we wanted a different perspective and look at the problem of plastic contamination at a bigger scale. For this reason, we chose three different methodologies to shape our dry lab plan.
Metagenomics - Putting microbial waste degradation into perspective.
First, we collected literature data from different shotgun metagenomic experiments so that we could converge them and find abundance of bacterial species, and the functionality of the communities, in different landfills or wastewater collections around the world. Our goal was to collect a database that could serve both to our purposes, but also as benchmark for future researchers to be able to come back and provide a perspective of the potential of microbial plastic degradation. Furthermore, this helped us to get a better overview of the research that has been carried out in the topic so far. a better overview of the research that has been carried out in the topic so far.
Kinetic model – analysing our pathway step by step.
Secondly, we decided to model the degradation of the elastane fibres, the main goal of our project (See Project Description), using an Ordinary Differential Equation (ODE) model. By simulating the degradation, we could find the bottlenecks of the process. By targeting the bottlenecks in the lab, it would be possible to accelerate the degradation of elastane.
Genome Scale Modelling – exploring the capabilities of our bacterial chassis.
Lastly, we wanted to look at the complete metabolic network of E. coli, to learn how efficiently the strain could degrade our substrate or how we could tweak the bacterial metabolism to optimize the production of the enzymes. For this purpose, we used a genome scale model (GEM) to simulate the whole metabolism of the bacteria, adding the enzymes of interest in silico.
Reproducible research - The issue of reproducibility.
Recently, a lot of light has been shed towards the issue of reproducibility in science. Under the reproducibility tab, you can read about how we ensured our modeling would be reproducible for other scientists.
