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

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number7
JournalEurasip Journal on Bioinformatics and Systems Biology
Volume2012
Issue number1
DOIs
Publication statusPublished - 2012

Fingerprint

Microscopy
Computer Simulation
Microscopic examination
Diffusion Coefficient
Anomalous Diffusion
Transmission Electron Microscopy
Radius
Simulation
Fluorescence
Anomaly
Spectroscopy
Protein
Crowding
Fluorescence Spectrometry
Ray Tracing
Smooth surface
Mobile Agent
Transmission electron microscopy
Post-processing
Range of data

ASJC Scopus subject areas

  • Medicine(all)
  • Computer Science(all)
  • Signal Processing
  • Statistics and Probability
  • General

Cite this

Hiroi, N., Klann, M., Iba, K., Heras Ciechomski, P. D., Yamashita, S., Tabira, 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

From microscopy data to in silico environments for in vivo-oriented simulations. / Hiroi, Noriko; Klann, Michael; Iba, Keisuke; Heras Ciechomski, Pablo De; Yamashita, Shuji; Tabira, Akito; Okuhara, Takahiro; Kubojima, Takeshi; Okada, Yasunori; Oka, Kotaro; Mange, Robin; Unger, Michael; Funahashi, Akira; Koeppl, Heinz.

In: Eurasip Journal on Bioinformatics and Systems Biology, Vol. 2012, No. 1, 7, 2012.

Research output: Contribution to journalArticle

Hiroi, N, Klann, M, Iba, K, Heras Ciechomski, PD, 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, vol. 2012, no. 1, 7. https://doi.org/10.1186/1687-4153-2012-7
Hiroi, Noriko ; Klann, Michael ; Iba, Keisuke ; Heras Ciechomski, Pablo De ; Yamashita, Shuji ; Tabira, Akito ; Okuhara, Takahiro ; Kubojima, Takeshi ; Okada, Yasunori ; Oka, Kotaro ; Mange, Robin ; Unger, Michael ; Funahashi, Akira ; Koeppl, Heinz. / From microscopy data to in silico environments for in vivo-oriented simulations. In: Eurasip Journal on Bioinformatics and Systems Biology. 2012 ; Vol. 2012, No. 1.
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