Physiological environment induce quick response - slow exhaustion reactions
In vivo environments are highly crowded and inhomogeneous, which may affect reaction processes in cells. In this study we examined the effects of intracellular crowding and an inhomogeneity on the behavior of in vivo reactions by calculating the spectral dimension (ds), which can be translated into...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2011-09-01
|
| Series: | Frontiers in Physiology |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fphys.2011.00050/full |
| _version_ | 1811202360037343232 |
|---|---|
| author | Noriko eHiroi James eLu Keisuke eIba Akito eTabira Shuji eYamashita Yasunori eOkada Flamm eChristoph Kotaro eOka Gottfried eKöhler Akira eFunahashi |
| author_facet | Noriko eHiroi James eLu Keisuke eIba Akito eTabira Shuji eYamashita Yasunori eOkada Flamm eChristoph Kotaro eOka Gottfried eKöhler Akira eFunahashi |
| author_sort | Noriko eHiroi |
| collection | DOAJ |
| description | In vivo environments are highly crowded and inhomogeneous, which may affect reaction processes in cells. In this study we examined the effects of intracellular crowding and an inhomogeneity on the behavior of in vivo reactions by calculating the spectral dimension (ds), which can be translated into the reaction rate function. We compared estimates of anomaly parameters obtained from Fluorescence Correlation Spectroscopy (FCS) data with fractal dimensions derived from Transmission Electron Microscopy (TEM) image analysis. FCS analysis indicated that the anomalous property was linked to physiological structure. Subsequent TEM analysis provided an in vivo illustration; soluble molecules likely percolate between intracellular clusters, which are constructed in a self-organizing manner. We estimated a cytoplasmic spectral dimension ds to be 1.39 ± 0.084. This result suggests that in vivo reactions initially run faster than the same reactions in a homogeneous space; this conclusion is consistent with the anomalous character indicated by FCS analysis. We further showed that these results were compatible with our Monte-Carlo simulation in which the anomalous behavior of mobile molecules correlates with the intracellular environment, leading to description as a percolation cluster, as demonstrated using TEM analysis. We confirmed by the simulation that the above-mentioned in vivo like properties are different from those of homogeneously concentrated environments. Additionally, simulation results indicated that crowding level of an environment might affect diffusion rate of reactant. Such knowledge of the spatial information enables us to construct realistic models for in vivo diffusion and reaction systems. |
| first_indexed | 2024-04-12T02:38:26Z |
| format | Article |
| id | doaj.art-43c11639d49445edb1b780000d130617 |
| institution | Directory Open Access Journal |
| issn | 1664-042X |
| language | English |
| last_indexed | 2024-04-12T02:38:26Z |
| publishDate | 2011-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Physiology |
| spelling | doaj.art-43c11639d49445edb1b780000d1306172022-12-22T03:51:24ZengFrontiers Media S.A.Frontiers in Physiology1664-042X2011-09-01210.3389/fphys.2011.0005011658Physiological environment induce quick response - slow exhaustion reactionsNoriko eHiroi0James eLu1Keisuke eIba2Akito eTabira3Shuji eYamashita4Yasunori eOkada5Flamm eChristoph6Kotaro eOka7Gottfried eKöhler8Akira eFunahashi9Keio UniversitySwiss Federal Institute of TechnologyKeio UniversityKeio UniversityKeio UniversityKeio UniversityUniversity of ViennaKeio UniversityUniversity of ViennaKeio UniversityIn vivo environments are highly crowded and inhomogeneous, which may affect reaction processes in cells. In this study we examined the effects of intracellular crowding and an inhomogeneity on the behavior of in vivo reactions by calculating the spectral dimension (ds), which can be translated into the reaction rate function. We compared estimates of anomaly parameters obtained from Fluorescence Correlation Spectroscopy (FCS) data with fractal dimensions derived from Transmission Electron Microscopy (TEM) image analysis. FCS analysis indicated that the anomalous property was linked to physiological structure. Subsequent TEM analysis provided an in vivo illustration; soluble molecules likely percolate between intracellular clusters, which are constructed in a self-organizing manner. We estimated a cytoplasmic spectral dimension ds to be 1.39 ± 0.084. This result suggests that in vivo reactions initially run faster than the same reactions in a homogeneous space; this conclusion is consistent with the anomalous character indicated by FCS analysis. We further showed that these results were compatible with our Monte-Carlo simulation in which the anomalous behavior of mobile molecules correlates with the intracellular environment, leading to description as a percolation cluster, as demonstrated using TEM analysis. We confirmed by the simulation that the above-mentioned in vivo like properties are different from those of homogeneously concentrated environments. Additionally, simulation results indicated that crowding level of an environment might affect diffusion rate of reactant. Such knowledge of the spatial information enables us to construct realistic models for in vivo diffusion and reaction systems.http://journal.frontiersin.org/Journal/10.3389/fphys.2011.00050/fullanomalous diffusionDiffusion Limited Aggregationfractal dimensionintracellular crowdinginvasive percolationspectral dimension |
| spellingShingle | Noriko eHiroi James eLu Keisuke eIba Akito eTabira Shuji eYamashita Yasunori eOkada Flamm eChristoph Kotaro eOka Gottfried eKöhler Akira eFunahashi Physiological environment induce quick response - slow exhaustion reactions Frontiers in Physiology anomalous diffusion Diffusion Limited Aggregation fractal dimension intracellular crowding invasive percolation spectral dimension |
| title | Physiological environment induce quick response - slow exhaustion reactions |
| title_full | Physiological environment induce quick response - slow exhaustion reactions |
| title_fullStr | Physiological environment induce quick response - slow exhaustion reactions |
| title_full_unstemmed | Physiological environment induce quick response - slow exhaustion reactions |
| title_short | Physiological environment induce quick response - slow exhaustion reactions |
| title_sort | physiological environment induce quick response slow exhaustion reactions |
| topic | anomalous diffusion Diffusion Limited Aggregation fractal dimension intracellular crowding invasive percolation spectral dimension |
| url | http://journal.frontiersin.org/Journal/10.3389/fphys.2011.00050/full |
| work_keys_str_mv | AT norikoehiroi physiologicalenvironmentinducequickresponseslowexhaustionreactions AT jameselu physiologicalenvironmentinducequickresponseslowexhaustionreactions AT keisukeeiba physiologicalenvironmentinducequickresponseslowexhaustionreactions AT akitoetabira physiologicalenvironmentinducequickresponseslowexhaustionreactions AT shujieyamashita physiologicalenvironmentinducequickresponseslowexhaustionreactions AT yasunorieokada physiologicalenvironmentinducequickresponseslowexhaustionreactions AT flammechristoph physiologicalenvironmentinducequickresponseslowexhaustionreactions AT kotaroeoka physiologicalenvironmentinducequickresponseslowexhaustionreactions AT gottfriedekohler physiologicalenvironmentinducequickresponseslowexhaustionreactions AT akiraefunahashi physiologicalenvironmentinducequickresponseslowexhaustionreactions |