Abstract
Bacterial conjugation is a cell-cell communication by which neighbor cells transmit circular DNA strands called plasmids. The transmission of these plasmids has been traditionally modeled using differential equations. Recently agent-based systems with spatial resolution have emerged as a promising tool that we use in this work to assess three different schemes for modeling the bacterial conjugation. The three schemes differ basically in which point of cell cycle the conjugation is most prone to happen. One alternative is to allow a conjugative event occurs as soon a suitable recipient is found, the second alternative is to make conjugation equally like to happen throughout the cell cycle and finally, the third one technique to assume that conjugation is more likely to occur in a specific point late in the cell cycle.
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Notes
- 1.
A value of \(-1\) set the model to conjugate as soon an infected cell finds a susceptible one. Setting the parameter to \(0\) will randomize the conjugation time between \(t_0\) and \(G\). Finally using a value greater than zero indicates the specific point in the cell cycle for conjugation. A polynomic equation fitted to the experimental time series where the dependent variable is equal to \(T/(T+R)\) rate.
- 2.
The Type IV secretion systems (T4SS) is a sort of transmembrane protein responsible, amongst other things, for the mating pair stabilization and the injection of single strand DNA into the target recipient cell.
- 3.
The expression comes from the common expression for estimate the standard deviation of uniform distribution which is given by \((b-a)/\sqrt{(}12)\) or \((b-a)/3.464102\).
- 4.
generated using the model parameter \(param(\gamma _0)\) and assuming again a coefficient of variation equals to \(0.1\) (\( Z(\gamma _0)= 0.1 \gamma _0 Z + \gamma _0\)).
- 5.
This plasmid is based on the R388 backbone.
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Acknowledgments
This work was supported by the European FP7-ICT-FET EU research project 612146 (PLASWIRES “Plasmids as Wires” project) www.plaswires.eu and by Spanish Government (MINECO) research grant TIN2012-36992.
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García, A.P., Rodríguez-Patón, A. (2015). A Preliminary Assessment of Three Strategies for the Agent-Based Modeling of Bacterial Conjugation. In: Overbeek, R., Rocha, M., Fdez-Riverola, F., De Paz, J. (eds) 9th International Conference on Practical Applications of Computational Biology and Bioinformatics. Advances in Intelligent Systems and Computing, vol 375. Springer, Cham. https://doi.org/10.1007/978-3-319-19776-0_1
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