Single-Cell Biophysics: Measurement, Modulation, and Modeling

Single-Cell Biophysics: Measurement, Modulation, and Modeling

Poster Abstracts

1-POS Board 1 Modelling Intracellular Transport in Realistic Environments Vesa Aho 1 , Markko Myllys 1 , Thomas Kühn 2,3 , Jussi Timonen 1 , Keijo Mattila 1,4 , Carolyn A. Larabell 5,6 , Maija Vihinen-Ranta 1 . 1 University of Jyväskylä, Jyväskylä, Finland, 4 Tampere University of Technology, Tampere, Finland, 2 University of Eastern Finland, Kuopio, Finland, 5 University of California, San Francisco, CA, USA, 6 Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 3 Finnish Meteorological Institute, Kuopio, Finland, The environment inside a cell is highly complex including, e.g., the chromatin network and membrane structures. In order to realistically model intracellular transport, the essential features of this environment must be captured and incorporated into a model. Here we describe our recent studies in computational modelling of intracellular transport utilizing realistic environments reconstructed from images obtained with microscopy methods. We first present our research of modelling diffusion through the nuclear envelope [1]. In this study the permeability of the nuclear envelope to a fluorescent molecule is determined by comparing simulated changes in fluorophore distribution to changes measured in a fluorescence microscopy experiment. Secondly, we present our modelling results for the diffusive motion of herpes simplex virus 1 capsids towards the nuclear envelope through the chromatin network that is characterized using soft x-ray tomography imaging [2,3]. In conclusion, we show that simulating the motion of particles in the reconstructions of their actual environments allows us to gain new insights into intracellular transport phenomena. [1] Aho, V., K. Mattila, T. Kühn, P. Kekäläinen, O. Pulkkinen, R. Brondani Minussi, M. Vihinen-Ranta, and J. Timonen. 2016. Diffusion through thin membranes: Modeling across scales. Phys. Rev. E. 93: 043309 [2] Myllys, M., V. Ruokolainen, V. Aho, E. A. Smith, S. Hakanen, P. Peri, A. Salvetti, J. Timonen, V. Hukkanen, C. A. Larabell, and M. Vihinen-Ranta. 2016. Herpes simplex virus 1 induces egress channels through marginalized host chromatin. Sci. Rep. 6:28844 [3] Aho, V., M. Myllys, V. Ruokolainen, S. Hakanen, E. Mäntylä, J. Virtanen, V. Hukkanen, T. Kühn, J. Timonen, K. Mattila, C. A. Larabell, and M. Vihinen-Ranta. 2017. Chromatin organization regulates viral egress dynamics. Submitted for publication in Scientific Reports.

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