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Takashi Miura Last modified date:2022.07.15

Professor / Department of Anatomy and Cell Biology
Department of Basic Medicine
Faculty of Medical Sciences

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Academic Degree
Ph. D
Field of Specialization
Developmental Biology, Mathematical Biology
Research Interests
  • Mathematical modeling of biological pattern formation phenomena and their experimental verification
    keyword : Pattern formation, mathematical modeling, reaction-diffusion, particle system, developmental biology
Academic Activities
1. Yoshie Endo, Daisuke Asanuma, Shigeyuki Namiki, Kei Sugihara, Kenzo Hirose, Akiyoshi Uemura, Yoshiaki Kubota, Takashi Miura, Quantitative modeling of regular retinal microglia distribution, Scientific Reports, 10.1038/s41598-021-01820-3, 11, 1, 2021.12, AbstractMicroglia are resident immune cells in the central nervous system, showing a regular distribution. Advancing microscopy and image processing techniques have contributed to elucidating microglia’s morphology, dynamics, and distribution. However, the mechanism underlying the regular distribution of microglia remains to be elucidated. First, we quantitatively confirmed the regularity of the distribution pattern of microglial soma in the retina. Second, we formulated a mathematical model that includes factors that may influence regular distribution. Next, we experimentally quantified the model parameters (cell movement, process formation, and ATP dynamics). The resulting model simulation from the measured parameters showed that direct cell–cell contact is most important in generating regular cell spacing. Finally, we tried to specify the molecular pathway responsible for the repulsion between neighboring microglia..
2. Mari Kawamura, Kei Sugihara, Hisako Takigawa-Imamura, Toshiyuki Ogawa, Takashi Miura, Mathematical Modeling of Dynamic Cellular Association Patterns in Seminiferous Tubules, Bulletin of Mathematical Biology, 10.1007/s11538-021-00863-x, 83, 4, 33-33, 2021.04, In vertebrates, sperm is generated in testicular tube-like structures called seminiferous tubules. The differentiation stages of spermatogenesis exhibit a dynamic spatiotemporal wavetrain pattern. There are two types of pattern-the vertical type, which is observed in mice, and the helical type, which is observed in humans. The mechanisms of this pattern difference remain little understood. In the present study, we used a three-species reaction-diffusion model to reproduce the wavetrain pattern observed in vivo. We hypothesized that the wavelength of the pattern in mice was larger than that in humans and undertook numerical simulations. We found complex patterns of helical and vertical pattern frequency, which can be understood by pattern selection using boundary conditions. From these theoretical results, we predicted that a small number of vertical patterns should be present in human seminiferous tubules. We then found vertical patterns in histological sections of human tubules, consistent with the theoretical prediction. Finally, we showed that the previously reported irregularity of the human pattern could be reproduced using two factors: a wider unstable wavenumber range and the irregular geometry of human compared with mouse seminiferous tubules. These results show that mathematical modeling is useful for understanding the pattern dynamics of seminiferous tubules in vivo..
3. Kei Sugihara, Yoshimi Yamaguchi, Shiori Usui, Yuji Nashimoto, Sanshiro Hanada, Etsuko Kiyokawa, Akiyoshi Uemura, Ryuji Yokokawa, Koichi Nishiyama, Takashi Miura, A new perfusion culture method with a self-organized capillary network, PLOS ONE, 10.1371/journal.pone.0240552, 15, 10, e0240552-e0240552, 2020.10, A lack of perfusion has been one of the most significant obstacles for three-dimensional culture systems of organoids and embryonic tissues. Here, we developed a simple and reliable method to implement a perfusable capillary network in vitro. The method employed the self-organization of endothelial cells to generate a capillary network and a static pressure difference for culture medium circulation, which can be easily introduced to standard biological laboratories and enables long-term cultivation of vascular structures. Using this culture system, we perfused the lumen of the self-organized capillary network and observed a flow-induced vascular remodeling process, cell shape changes, and collective cell migration. We also observed an increase in cell proliferation around the self-organized vasculature induced by flow, indicating functional perfusion of the culture medium. We also reconstructed extravasation of tumor and inflammatory cells, and circulation inside spheroids including endothelial cells and human lung fibroblasts. In conclusion, this system is a promising tool to elucidate the mechanisms of various biological processes related to vascular flow..
4. Kei Sugihara, Saori Sasaki, Akiyoshi Uemura, Satoru Kidoaki, Takashi Miura, Mechanisms of endothelial cell coverage by pericytes: computational modelling of cell wrapping and in vitro experiments, Journal of The Royal Society Interface, 10.1098/rsif.2019.0739, 17, 162, 20190739-20190739, 2020.01, Pericytes (PCs) wrap around endothelial cells (ECs) and perform diverse functions in physiological and pathological processes. Although molecular interactions between ECs and PCs have been extensively studied, the morphological processes at the cellular level and their underlying mechanisms have remained elusive. In this study, using a simple cellular Potts model, we explored the mechanisms for EC wrapping by PCs. Based on the observed
in vitro
cell wrapping in three-dimensional PC–EC coculture, the model identified four putative contributing factors: preferential adhesion of PCs to the extracellular matrix (ECM), strong cell–cell adhesion, PC surface softness and larger PC size. While cell–cell adhesion can contribute to the prevention of cell segregation and the degree of cell wrapping, it cannot determine the orientation of cell wrapping alone. While atomic force microscopy revealed that PCs have a larger Young’s modulus than ECs, the experimental analyses supported preferential ECM adhesion and size asymmetry. We also formulated the corresponding energy minimization problem and numerically solved this problem for specific cases. These results give biological insights into the role of PC–ECM adhesion in PC coverage. The modelling framework presented here should also be applicable to other cell wrapping phenomena observed
in vivo
5. Yuji Nashimoto, Tomoya Hayashi, Itsuki Kunita, Akiko Nakamasu, Yu-Suke Torisawa, Masamune Nakayama, Hisako Takigawa-Imamura, Hidetoshi Kotera, Koichi Nishiyama, Takashi Miura, Ryuji Yokokawa, Integrating perfusable vascular networks with a three-dimensional tissue in a microfluidic device., Integrative biology : quantitative biosciences from nano to macro, 10.1039/c7ib00024c, 9, 6, 506-518, 2017.06, Creating vascular networks in tissues is crucial for tissue engineering. Although recent studies have demonstrated the formation of vessel-like structures in a tissue model, long-term culture is still challenging due to the lack of active perfusion in vascular networks. Here, we present a method to create a three-dimensional cellular spheroid with a perfusable vascular network in a microfluidic device. By the definition of the cellular interaction between human lung fibroblasts (hLFs) in a spheroid and human umbilical vein endothelial cells (HUVECs) in microchannels, angiogenic sprouts were induced from microchannels toward the spheroid; the sprouts reached the vessel-like structures in a spheroid to form a continuous lumen. We demonstrated that the vascular network could administer biological substances to the interior of the spheroid. As cell density in the spheroid is similar to that of a tissue, the perfusable vasculature model opens up new possibilities for a long-term tissue culture in vitro..
6. Takumi Higaki, Natsumaro Kutsuna, Kae Akita, Hisako Takigawa-Imamura, Kenji Yoshimura, Takashi Miura, A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells, PLOS COMPUTATIONAL BIOLOGY, 10.1371/journal.pcbi.1004833, 12, 4, e1004833, 2016.04, Plant leaf epidermal cells exhibit a jigsaw puzzle-like pattern that is generated by interdigitation of the cell wall during leaf development. The contribution of two ROP GTPases, ROP2 and ROP6, to the cytoskeletal dynamics that regulate epidermal cell wall interdigitation has already been examined; however, how interactions between these molecules result in pattern formation remains to be elucidated. Here, we propose a simple interface equation model that incorporates both the cell wall remodeling activity of ROP GTPases and the diffusible signaling molecules by which they are regulated. This model successfully reproduces pattern formation observed in vivo, and explains the counterintuitive experimental results of decreased cellulose production and increased thickness. Our model also reproduces the dynamics of three-way cell wall junctions. Therefore, this model provides a possible mechanism for cell wall interdigitation formation in vivo..
7. Miura, T., Hartmann, D., Kinboshi, M., Komada, M., Ishibashi, M., Shiota, K., The cyst-branch difference in developing chick lung results from a different morphogen diffusion coefficient, Mechanisms of Development, 10.1016/j.mod.2008.11.006, 126, 3-4, 160-172, 2009.04, The developing avian lung is formed mainly by branching morphogenesis, but there is also a unique cystic structure, the air sac, in the ventral region. It has been shown that mesenchymal tissue is responsible for the differential development of a cystic or branched structure, and that the transcription factor Hoxb may be involved in determining this regional difference. We have previously developed two scenarios for branch-cyst transition, both experimentally and theoretically: increased production or increased diffusion of FGF. The aim of the present study was to discover whether one of these scenarios actually operates in the ventral region of the chick lung. We found that the FGF10 level was lower while the diffusion of FGF10 was more rapid in the ventral lung, indicating that the second scenario is more plausible. There are two possibilities as to why the diffusion of FGF10 differs between the two regions: (1) diffusion is facilitated by the looser tissue organisation of the ventral lung mesenchyme; (2) stronger expression of heparan sulphate proteoglycan ( HSPG) in the dorsal lung traps FGF and decreases the effective diffusion coefficient. Mathematical analysis showed that the dorsal-ventral difference in the amount of HSPG is not sufficient to generate the observed difference in pattern, indicating that both extracellular matrix and tissue architecture play a role in this system. These results suggest that the regional cystic-branched difference within the developing chick lung results from a difference in the rate of diffusion of morphogen between the ventral and dorsal regions due to differential levels of HSPG and a different mesenchymal structure. (C) 2008 Elsevier Ireland Ltd. All rights reserved..
8. Takashi Miura, Kohei Shiota, TGFβ2 acts as an 'activator' molecule in reaction-diffusion model and is involved in cell sorting phenomenon in mouse limb micromass culture, Developmental Dynamics, 10.1002/(SICI)1097-0177(200003)217:3<241::AID-DVDY2>3.0.CO;2-K, 217, 3, 241-249, 2000.04, It was previously speculated that TGFβ acts as an 'activator'-molecule in chondrogenic pattern formation in the limb micromass culture system, but its precise role and relationship with the cell sorting phenomenon have not been properly studied. In the present study, we examined whether the TGFβ2 molecule satisfies the necessary conditions for an 'activator'-molecule in the reaction-diffusion model. Firstly, we showed that TGFβ2 became localized at chondrogenic sites during the establishment of a chondrogenic pattern, and exogenous TGFβ2 promoted chondrogenesis when added in the culture medium. Secondly, TGFβ2 protein was shown to promote the production of its own mRNA after 3 hr, indicating that a positive feedback mechanism exists which may be responsible for the emergence of the chondrogenic pattern. We then found that when locally applied with beads, TGFβ2 suppressed chondrogenesis around the beads, indicating it induces the lateral inhibitory mechanism, which is a key element for the formation of the periodic pattern. We also examined the possible effects of TGFβ2 on the cell sorting phenomenon and found that TGFβ2 exerts differential chemotactic activity on proximal and distal mesenchyme cells of the limb bud, and at very early phases of differentiation TGFβ2 promotes the expression of N-cadherin protein which is known to be involved in pattern formation in this culture system. These findings suggest that TGFβ2 acts as an 'activator'-like molecule in chondrogenic pattern formation in vitro, and is possibly responsible for the cell sorting phenomenon. (C) 2000 Wiley- Liss, Inc..
Membership in Academic Society
  • Japanese Society for Mathematical Biologists
Educational Activities
Cell Biology
Human Anatomy