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 (2024)
From microscopy data to in silico environments for in vivo-oriented simulations.
In: EURASIP Journal on Bioinformatics and Systems Biology, 2012, 1 (7)
doi: 10.26083/tuprints-00026938
Artikel, Zweitveröffentlichung, Verlagsversion
 | Es ist eine neuere Version dieses Eintrags verfügbar. |
Kurzbeschreibung (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 μ m²/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.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2024 |
| Autor(en): | 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 |
| Art des Eintrags: | Zweitveröffentlichung |
| Titel: | From microscopy data to in silico environments for in vivo-oriented simulations |
| Sprache: | Englisch |
| Publikationsjahr: | 30 April 2024 |
| Ort: | Darmstadt |
| Publikationsdatum der Erstveröffentlichung: | 2012 |
| Ort der Erstveröffentlichung: | Heidelberg |
| Verlag: | Springer |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | EURASIP Journal on Bioinformatics and Systems Biology |
| Jahrgang/Volume einer Zeitschrift: | 1 |
| (Heft-)Nummer: | 7 |
| Kollation: | 11 Seiten |
| DOI: | 10.26083/tuprints-00026938 |
| URL / URN: | https://tuprints.ulb.tu-darmstadt.de/26938 |
| Zugehörige Links: | |
| Herkunft: | Zweitveröffentlichungsservice |
| Kurzbeschreibung (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 μ m²/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. |
| Freie Schlagworte: | Transmission Electron Microscopy Image; Mean Square Displacement; Fluorescence Correlation Spectroscopy; Anomalous Diffusion; Reaction Space |
| ID-Nummer: | Artikel-ID: 7 |
| Status: | Verlagsversion |
| URN: | urn:nbn:de:tuda-tuprints-269388 |
| Zusätzliche Informationen: | Supplements sind auf der Verlagsseite erhältlich: https://bsb-eurasipjournals.springeropen.com/articles/10.1186/1687-4153-2012-7#Sec21 |
| Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 000 Allgemeines, Informatik, Informationswissenschaft > 004 Informatik 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie 600 Technik, Medizin, angewandte Wissenschaften > 621.3 Elektrotechnik, Elektronik |
| Hinterlegungsdatum: | 30 Apr 2024 09:28 |
| Letzte Änderung: | 13 Mai 2024 09:43 |
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| Suche nach Titel in: | TUfind oder in Google |
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- From microscopy data to in silico environments for in vivo-oriented simulations. (deposited 30 Apr 2024 09:28) [Gegenwärtig angezeigt]
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