| Title |
From microscopy data to in silico environments for in vivo-oriented simulations
|
|---|---|
| Published in |
EURASIP Journal on Bioinformatics & Systems Biology, June 2012
|
| DOI | 10.1186/1687-4153-2012-7 |
| Pubmed ID | |
| Authors |
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 |
| 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. |
Mendeley readers
The data shown below were compiled from readership statistics for 13 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Japan | 1 | 8% |
| Unknown | 12 | 92% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 5 | 38% |
| Student > Ph. D. Student | 3 | 23% |
| Other | 1 | 8% |
| Student > Bachelor | 1 | 8% |
| Student > Master | 1 | 8% |
| Other | 1 | 8% |
| Unknown | 1 | 8% |
| Readers by discipline | Count | As % |
|---|---|---|
| Engineering | 4 | 31% |
| Computer Science | 3 | 23% |
| Agricultural and Biological Sciences | 2 | 15% |
| Chemistry | 1 | 8% |
| Unknown | 3 | 23% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 08 December 2012.
All research outputs
#20,657,128
of 25,374,917 outputs
Outputs from EURASIP Journal on Bioinformatics & Systems Biology
#33
of 53 outputs
Outputs of similar age
#138,597
of 177,446 outputs
Outputs of similar age from EURASIP Journal on Bioinformatics & Systems Biology
#3
of 5 outputs
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So far Altmetric has tracked 53 research outputs from this source. They receive a mean Attention Score of 3.1. This one is in the 22nd percentile – i.e., 22% of its peers scored the same or lower than it.
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