From microscopy data to in silico environments for in vivo-oriented simulations

Noriko Hiroi, Michael Klann, Keisuke Iba, Pablo De Heras Ciechomski, Shuji Yamashita, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Yasunori Okada, Kotaro Oka, Robin Mange, Michael Unger, Akira Funahashi, Heinz Koeppl

研究成果: Article

5 引用 (Scopus)

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In our previous study, we introduced a combination methodology of Fluorescence Correlation Spectroscopy (FCS) and Transmission Electron Microscopy (TEM), which is powerful to investigate the effect of intracellular environment to biochemical reaction processes. Now, we developed a reconstruction method of realistic simulation spaces based on our TEM images. Interactive raytracing visualization of this space allows the perception of the overall 3D structure, which is not directly accessible from 2D TEM images. Simulation results show that the diffusion in such generated structures strongly depends on image post-processing. Frayed structures corresponding to noisy images hinder the diffusion much stronger than smooth surfaces from denoised images. This means that the correct identification of noise or structure is significant to reconstruct appropriate reaction environment in silico in order to estimate realistic behaviors of reactants in vivo. Static structures lead to anomalous diffusion due to the partial confinement. In contrast, mobile crowding agents do not lead to anomalous diffusion at moderate crowding levels. By varying the mobility of these non-reactive obstacles (NRO), we estimated the relationship between NRO diffusion coefficient (D nro) and the anomaly in the tracer diffusion (α). For D nro=21.96 to 44.49 μ m 2/s, the simulation results match the anomaly obtained from FCS measurements. This range of the diffusion coefficient from simulations is compatible with the range of the diffusion coefficient of structural proteins in the cytoplasm. In addition, we investigated the relationship between the radius of NRO and anomalous diffusion coefficient of tracers by the comparison between different simulations. The radius of NRO has to be 58 nm when the polymer moves with the same diffusion speed as a reactant, which is close to the radius of functional protein complexes in a cell.

元の言語English
記事番号7
ジャーナルEurasip Journal on Bioinformatics and Systems Biology
2012
発行部数1
DOI
出版物ステータスPublished - 2012

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Computer Science Applications
  • Computational Mathematics

フィンガープリント From microscopy data to in silico environments for in vivo-oriented simulations' の研究トピックを掘り下げます。これらはともに一意のフィンガープリントを構成します。

  • これを引用

    Hiroi, N., Klann, M., Iba, K., Heras Ciechomski, P. D., Yamashita, S., Tabira, A., Okuhara, T., Kubojima, T., Okada, Y., Oka, K., Mange, R., Unger, M., Funahashi, A., & Koeppl, H. (2012). From microscopy data to in silico environments for in vivo-oriented simulations. Eurasip Journal on Bioinformatics and Systems Biology, 2012(1), [7]. https://doi.org/10.1186/1687-4153-2012-7