Team:Athens/Timeline

iGEM Athens

TIMELINE

From the beginning, the focus of the project was the production of a structurally coloured biomaterial with a variety of applications as an alternative to toxic and widely used synthetic dyes. Therefore, the main dry lab idea was to gain an insight into the mechanisms involved in the production of such a type of colour by modeling the spatial arrangement of the bacterial cells into the biofilm. Many different approaches were researched and tested and each one of them was a step closer to the final result. These approaches can be linked to our constantly improving understanding of the concept of structural colour itself and were affected by conversations with experts and continuous literature research that had an impact on both the final idea of the project and the modeling approach to it.

Initially, the idea of the project was to use E. coli cells for the production of a structurally coloured biofilm to use as a biomaterial. For that purpose the bacteria had to be adapted in specific patterns into the biofilm. A continuous cell to cell adhesion model of the cell self-organised cultures was our first approach. Building the simulation, finite differences method was used to solve ODEs that describe the cell density of the colonies. However, discussions on the matter with Dr. Mihalis Kavousanakis, made us realize that a continuous approach could not inform us about the periodicities in the micron scale, which are necessary to produce structural colouration. In order to describe these periodicities, we had to create a model that contains individual cells. For that reason, the research focused on individual-based models for better prediction on the microscale.

At this time, we also had a virtual conversation with Dr Colin Ingham, who proposed that using Flavobacteriia, which naturally produce iridescent colonies, would be more convenient for the production of the coloured biomaterial. Therefore, the idea of using these bacteria for creating a material based on bacterial cellulose was adapted. Compucell3D was the next step.

CompuCell3D is C++ software environment that is based on the cellular Potts model (CPM), a stochastic lattice-based model, and could simulate bacteria interactions in a biofilm. Unfortunately, the capabilities of the environment could not satisfy our modeling criteria.

Thus the construction of a novel stochastic model in Python beginned, while still searching the literature for different theoretical biology models. The model would include processes that occur during formation of the biofilm such as mitosis, growth, adhesion, transitional and rotational movement.But this idea was eventually replaced.

While searching the literature, we found out that the biophysics of the movement of the F. johnsoniae is similar to the ones of M. xanthus. Thus, we began searching for relevant models. After thorough examination of the prospective models, we decided that the optimum way is to extend the model proposed by Janulevivius et al. for M. xanthus[1], to include the specificities of F. johnsoniae. The original model is a Mass-Spring Model (MSM) which reduces the dimensions of the problem by considering each bacterium as a number of particles bound together by a complex network of springs. In order to properly understand this method, we studied the physics behind it, and then we aimed to build a simulator to get the expected results. However, due to the lack of information available for MSMs, we had to get through numerous computational challenges while developing the simulator. After a lot of debugging, and some help from Dr. Mihalis Kavousanakis, we succeeded in building a computationally stable and inexpensive algorithm to solve this model. The final step was to extend the model so that it would be valid for F. johnsoniae. We also built a simulation for the gliding motility mechanism using a popular game engine. More detailed information about the model can be found in the Background and in the Model sections.

"Detail of a blue morpho" by Tambako the Jaguar is licensed under CC BY-ND 2.0

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