Team:TU Delft-Leiden/Modeling/Curli/Reflection

Critical Reflection on our Model

For the conductive curli module, we have successfully created a model that models our system in the way that we envision it. We are fairly confident that the system will show some of the behavior that we modeled. We think that it is valuable to be critical on our own workings. Also, we want you to know that we understand the strong and weak points of our model. Therefore, we have made a short list of things that could be improved in further adaptations of our model.

Gene Level Modeling

• At the gene level, we created a simplified model that only modeled the creation of curli. However, we have not taken into account for instance the maturation of CsgB. It might as well be that our response is delayed. Luckily, we found that CsgB fastens the production of CsgA [1].
• Another point that is interesting to look at, is the restraining of the amount of CsgB that is permitted on the cell surface. We do not know what exactly happens at the cell level, but in order to have adequately long wires, we had to decrease the CsgB production drastically.
• The drastically decrease of CsgB production makes the system especially sensitive to leakage of CsgB. Unfortunately, the experiments that the wetlab performed (see Module Landmine Detection), show that the promoter we use is especially leaky. This means that there will most likely already form curli before the promoter is activated. Then, the steep increase in the amount of curli that is observed in our model, will probably not happen. Instead, the curli are just formed over time. If this is true, then we strongly doubt that there will be any noticeable difference between a weakly and strongly induced promoter at all. However, switching the CsgB production on or off is in our opinion not a good idea. From our colony model, it seems that abundance of CsgA is necessary.

Cell Level Modeling

• Modelling the cell level was maybe the hardest part of our modeling effort. The kinetics of the adding of curli subunits to a growing curli fibrils remains largely unknown to us. We tried to keep it as simple as possible, and still obtain some useful information for the colony level. Our first intention was to actually model each wire and look at the percolation between the wires. Subsequently, we would look at the conductance as function of the radius due to the percolation between the wires. We even created an algorithm that could find clusters of connected curli fibrils. However, in the end this approach was deemed infeasible. For instance, we do not know the exact thickness of the curli fibrils. Also, we could not incorporate physical interactions between the curli fibrils, since this would be computationally too heavy.
• At the cell level, we also made the assumption that curli can only grow and never break. Furthermore, in literature [2] we have found that the assumption that the starting point of the curli is random on the cell surface is not true. It appears that they are clustered. However, distinguishing between the radial axis of the cell would make it very complicated for the colony level. For the same reason, we made the assumption that our E. coli are spherical rather than rod-shaped.
  Both these assumptions decrease the variation per cell. However, from the percolation simulations at the colony level, we see that individual cell variations have small influence on the outcome. Therefore, we still think that our simplifications give reasonable results.

Colony Level Modeling

• At the colony level, we regret that we had to scale down the cell density. The memory necessary to find the resistance between \( N \) cells goes with \( N^2 \). Simulation times increase even more drastically. For higher cell densities, we expect a similar characteristic response, but with a higher conductance. It might also be nice to see what would happen if cells are permitted to lie on top of each other, thereby increasing the number of dimensions of the model from two to three. But then again, physical interactions are hard to incorporate in a model.
• A more fundamental difference between our model and reality is that we look at connections from one cell to another. In reality, it is the stuff in between the cells that makes them conductive or not, ie. the electrons will not go through the cells.

All together we are very proud of what we have achieved with our models. Especially in the time that was given. We think that this model is a good addition to our project and we hope that you enjoyed reading about it.

References

[1] N.D. Hammer & M.R. Chapman, "The C-terminal repeating units of CsgB direct bacterial functional amyloid nucleation", J. Mol. Biol. 422, 3, 2012.

[2] E.A. Epstein, M.A. Reizian & M.R. Chapman, "Spatial clustering of the curlin secretion lipoprotein requires curli fiber assembly", J. Bacteriol. 191, 2, 2009.