Hiroi, N. ; Klann, M. ; Iba, K. ; Heras Ciechomski, P. de ; 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.
In: EURASIP Journal on Bioinformatics and Systems Biology, 2012 (1)
doi: 10.1186/1687-4153-2012-7
Article, Bibliographie
This is the latest version of this item.
Abstract
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 (Dnro) and the anomaly in the tracer diffusion (α). For Dnro=21.96 to 44.49 μm2/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.
| Item Type: | Article |
|---|---|
| Erschienen: | 2012 |
| Creators: | Hiroi, N. ; Klann, M. ; Iba, K. ; Heras Ciechomski, P. de ; Yamashita, S. ; Tabira, A. ; Okuhara, T. ; Kubojima, T. ; Okada, Y. ; Oka, K. ; Mange, R. ; Unger, M. ; Funahashi, A. ; Koeppl, H. |
| Type of entry: | Bibliographie |
| Title: | From microscopy data to in silico environments for in vivo-oriented simulations |
| Language: | English |
| Date: | January 2012 |
| Journal or Publication Title: | EURASIP Journal on Bioinformatics and Systems Biology |
| Volume of the journal: | 2012 |
| Issue Number: | 1 |
| DOI: | 10.1186/1687-4153-2012-7 |
| URL / URN: | http://bsb.eurasipjournals.com/CONTENT/2012/1/7 |
| Corresponding Links: | |
| Abstract: | 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 (Dnro) and the anomaly in the tracer diffusion (α). For Dnro=21.96 to 44.49 μm2/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. |
| Divisions: | 18 Department of Electrical Engineering and Information Technology 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications > Bioinspired Communication Systems 18 Department of Electrical Engineering and Information Technology > Institute for Telecommunications |
| Date Deposited: | 04 Apr 2014 12:56 |
| Last Modified: | 13 May 2024 09:43 |
| PPN: | |
| Export: | |
| Suche nach Titel in: | TUfind oder in Google |
Available Versions of this Item
-
From microscopy data to in silico environments for in vivo-oriented simulations. (deposited 30 Apr 2024 09:28)
- From microscopy data to in silico environments for in vivo-oriented simulations. (deposited 04 Apr 2014 12:56) [Currently Displayed]
 |
Send an inquiry |
Options (only for editors)
 |
Show editorial Details |
Drucken
Impressum