Biology subjects

Koyama, H.

Publications and source records attributed to Koyama, H..

13 recordsLinked to original sources

bioRxiv2026

Mechanically competitive regulation of cell volume in cytoplasm-sharing cells connected by intercellular bridges

In multicellular organisms, various cellular structures exhibit cytoplasmic sharing, where cells remain interconnected. While essential for development and function in contexts such as germ cell formation and insect early embryos, the physical basis of cell volume regulation in these systems remains poorly defined. Germline cysts are formed by interconnected sister cells via intercellular bridges. In mice, germline cysts form during gametogenesis in fetal ovaries and testes. In mouse fetal female cysts, cells with numerous bridges preferentially differentiate into oocytes by selectively increasing their volume, a process that may be mediated through cytoplasmic flow. This volume bias may be influenced by hydrostatic pressure within the cytoplasm. Here, we theoretically investigate how the mechanical properties of cells affect cytoplasmic pressure and volume distribution within interconnected cells. Our soap-bubble model revealed that cells with more bridges exhibit increased volume when they have large cell-cell contact areas, as observed in fetal cysts. We found that incorporating cell cycle (including cell growth and cell division) significantly enhances the likelihood of volume bias in favor of cells with more bridges. These theoretical findings suggest that intrinsic mechanical properties, coupled with cell cycle, establish robust cyst development in fetal female germline cysts. Our findings also provide insights into the volume dynamics observed in adult male germline cysts, which are characterized by smaller cell-cell contact areas. Impact statementA theoretical model demonstrates how mechanical properties and cell cycle dynamics regulate volume distribution in germline cysts, providing a physical basis for oocyte differentiation.

developmental biology↗

bioRxiv2025

Emergence of cell polarity by reciprocal interactions between Wnt and core PCP components

Planar cell polarity (PCP) is established by asymmetric localization of core PCP components in each cell. Since some Wnt proteins can induce PCP in vertebrates, it has been proposed that Wnt concentration gradients provide spatial cues for polarization. Here, however, we present evidence that Wnt11 can regulate PCP in a gradient-independent manner. In the neural plate of Xenopus embryos, endogenous Wnt11 does not form an obvious gradient in the direction of PCP, but is polarized at cell boundaries together with core PCP components. Wnt11 polarization is dependent on core PCP components, while polarization of core PCP components can also be induced by Wnt11, indicating a mutual amplification loop between Wnt11 and core PCP components in PCP formation. Furthermore, Wnt11 and core PCP components compose an intercellular loop to coordinate the direction of polarity. Thus, we propose that local and reciprocal interactions between Wnt11 and core PCP components can generate PCP.

developmental biology↗

bioRxiv2025

Early transcriptional divergence underlies cell fate bias in bovine embryos

Developmental plasticity, or the ability of early embryonic cells to contribute to multiple lineages, is traditionally considered equal among sister blastomeres during early cleavage. However, divergence may occur earlier than expected. We performed single-cell RNA sequencing of bovine embryos from the 2- to 8-cell stages to examine transcriptional asymmetry. While gene expression was uniform at the 2-cell stage, variability increased at the 4-cell stage and became pronounced by the 8-cell stage. At this stage, blastomeres showed heterogeneity in MAPK pathway genes (e.g., RAC1, MAPK14) and the trophectoderm marker CDX2. These differences were associated with blastomere size; larger blastomeres more frequently initiated cavity formation, a functional marker of trophectoderm fate. Our findings suggest that both molecular and physical asymmetries contribute to early lineage bias, and that developmental plasticity may be lost in an asynchronous, cell-specific manner before visible morphological events such as compaction.

developmental biology↗

bioRxiv2025

Directional alignment of different cell types organizes planar cell polarity

Planar cell polarity (PCP) refers to unidirectional coordination of cell polarity in the plane of epithelial tissues, whose proper formation is essential for development in various tissues. While imbalances in the amount of core PCP proteins (core proteins) between adjacent cells disrupt PCP in some tissues, other tissues maintain PCP despite containing multiple cell types with different levels of core proteins. How such tissues tolerate these imbalances remains unclear. Here, we theoretically analyzed the contribution of spatial distribution of different cell types to PCP maintenance. We adopted a previously established PCP model on two-dimensional cell sheets, where local protein-protein interactions were assumed. Our systematic simulations revealed that the patterns of cell-type distribution significantly affect the accuracy of PCP maintenance under the condition of imbalanced PCP proteins. To identify the critical patterns, we applied both deep learning techniques and statistical modeling to the simulation data. Consequently, these analyses revealed that orientation of cell-type alignment is a key aspect of cell-type distribution that affects PCP. Such directional cell-type alignment was observed in the mouse oviduct. Our findings highlight the overlooked contribution of spatial distribution of cell types to PCP maintenance in tissues with multiple cell-types.

developmental biology↗

bioRxiv2024

Cell position-based evaluation of mechanical features of cells in multicellular systems

Measurement of mechanical forces of cell-cell interactions is important for studying the emergence of diverse three-dimensional morphologies of multicellular organisms. We previously reported an image-based statistical method for inferring effective pairwise forces of cell-cell interactions (i.e., attractive/repulsive forces), where a cell particle model was fitted to cell tracking data acquired by live imaging. However, because the particle model is a coarse-grained model, it remains unclear how the pairwise forces relates to sub-cellular mechanical components including cell-cell adhesive forces. Here we applied our inference method to cell tracking data generated by vertex models that assumed sub-cellular components. Through this approach, we investigated the relationship between the effective pairwise forces and various sub-cellular components: cell-cell adhesion forces, cell surface tensions, cell-extracellular matrix (ECM) adhesion, traction forces between cells and ECM, cell growth, etc. We found that the cell-cell adhesion forces were attractive, and both the cell surface tensions and cell-ECM adhesive forces were repulsive, etc. These results indicate that sub-cellular mechanical components can contribute to the effective attractive/repulsive forces of cell-cell interactions. This comprehensive analysis provides theoretical bases for linking the pairwise forces to the sub-cellular mechanical components: this showcase is useful for speculating the sub-cellular mechanical components from the information of cell positions, and for interpreting simulation results based on particle models.

biophysics↗

bioRxiv2024

Compatibility of time-lapse dry incubator on in vitro production of bovine embryos

Embryo culture is crucial to achieve successful outcomes in assisted reproductive technology (ART) for cattle. This study explored the innovative use of dry incubators integrated with time-lapse monitoring systems for bovine embryo culture, building on their advantages in human medicine, such as reduced contamination risk, stable temperature control, and lower gas consumption. Our research demonstrates the feasibility of this approach, showing that although the osmotic pressure gradually increases over the culture period, it remains below the critical threshold for developmental impairment. Embryos cultured in dry incubators exhibited morphokinetics comparable to those cultured in conventional humidified time-lapse incubators. Furthermore, RNA-seq revealed that the transcriptomic profiles of blastocysts cultured in dry incubators closely matched those of blastocysts cultured in humidified incubators. These findings highlight the significant potential of dry incubators with time-lapse monitoring systems for the in vitro production of bovine embryos, marking a promising advancement in assisted reproductive technologies for the livestock industry and research setting.

developmental biology↗

bioRxiv2023

Mechanical transapical coupling of endometrial epithelial cells during implantation

Epithelial cells lining the lumen of organs have an apical-basal polarity, and mechanical cell contacts are located in the lateral and basal regions. During early pregnancy in rodents, the luminal space of the uterus is closed, and opposing epithelial cells attach to each other at apical-apical surfaces. Here, we show that cells are mechanically coupled at the apical cell-cell contacts. The apical plasma membrane was intricately intertwined between opposing cells. Extracellular matrix and tight junction molecules were localized at apical contacts. Claudin inhibition resulted in impaired luminal closure, suggesting a functional requirement of claudins for the establishment of transapical coupling. The present results demonstrate a mechanical cell-cell interaction that occurs between apical-apical surfaces in addition to lateral and basal cell junctions. One Sentence SummariesTransapical coupling of epithelial cells mediated by extracellular matrix and tight junction molecules

cell biology↗

bioRxiv2023

Effective mechanical potential of cell-cell interaction in tissues harboring cavity and in cell sheet toward morphogenesis

Measuring mechanical forces of cell-cell interactions is important for studying morphogenesis in multicellular organisms. We previously reported an image-based statistical method for inferring effective mechanical potentials of pairwise cell-cell interactions by fitting cell tracking data with a theoretical model. However, whether this method is applicable to tissues with non-cellular components such as cavities remains elusive. Here we evaluated the applicability of the method to cavity-harboring tissues. Using synthetic data generated by simulations, we found that the effect of expanding cavities was added to the pregiven potentials used in the simulations, resulting in the inferred effective potentials having an additional repulsive component derived from the expanding cavities. Interestingly, simulations by using the effective potentials reproduced the cavity-harboring structures. Then, we applied our method to the mouse blastocysts, and found that the inferred effective potentials can reproduce the cavity-harboring structures. Pairwise potentials with additional repulsive components were also detected in two-dimensional cell sheets, by which curved sheets including tubes and cups were simulated. We conclude that our inference method is applicable to tissues harboring cavities and cell sheets, and the resultant effective potentials are useful to simulate the morphologies.

biophysics↗

bioRxiv2022

An ImageJ-based tool for three-dimensional registration between different types of microscopic images

Three-dimensional (3D) registration (i.e. alignment) between two microscopic images is substantially helpful to study tissues not adhere to substrates such as mouse embryos and organoids which are often three-dimensionally rotated during imaging. However, there is no 3D registration tool easily accessible for experimental biologists. Here we developed an ImageJ-based tool which achieves 3D registration accompanying both quantitative evaluation of the accuracy and reconstruction of 3D rotated images. In this tool, several landmarks are manually provided in two images to be aligned, and 3D rotation is computed so that the distances between the paired landmarks from the two images are minimized. By simultaneously providing multiple points (e.g. all nuclei in the regions of interest) other than the landmarks in the two images, the correspondence of each point between the two images is quantitatively explored: a certain nucleus in one image corresponds to which nucleus in another image. Furthermore, the 3D rotation is applied to one of the two images, resulting in reconstruction of 3D rotated images. We demonstrated that this tool successfully achieved 3D registration and reconstruction of images in mouse pre-implantation embryos, where one image was obtained during live imaging and another image from fixed embryos after live imaging. This approach provides a versatile tool applicable for various tissues and species.

developmental biology↗

bioRxiv2022

Differential cellular stiffness contributes to tissue elongation on an expanding surface

Pattern formation and morphogenesis of cell populations is essential for successful embryogenesis. Steinberg proposed the differential adhesion hypothesis (DAH), and differences in cell-cell adhesion and interfacial tension have proven to be critical for cell sorting. Standard theoretical models such as the vertex model consider not only cell-cell adhesion/tension but also area elasticity of apical cell surfaces and viscous friction forces. However, the potential contributions of the latter two parameters to pattern formation and morphogenesis remain to be determined. In this theoretical study, we analyzed the effect of both area elasticity and the coefficient of friction on pattern formation and morphogenesis. We assumed the presence of two cell populations, one population of which is surrounded by the other. Both populations were placed on the surface of a uniformly expanding environment analogous to growing embryos, in which friction forces are exerted between cell populations and their expanding environment. When the area elasticity or friction coefficient in the cell cluster was increased relative to that of the surrounding cell population, the cell cluster was elongated. In comparison with experimental observations, elongation of the notochord in mice is consistent with the hypothesis based on the difference in area elasticity but not the difference in friction coefficient. Because area elasticity is an index of cellular stiffness, we propose that differential cellular stiffness may contribute to tissue elongation within an expanding environment.

biophysics↗

bioRxiv2019

Effective physical properties of cell-cell interaction explain basic structural units of three-dimensional morphogenesis

Mechanical forces are critical for the emergence of diverse three-dimensional morphologies of multicellular systems. However, it remains unclear what kind of mechanical parameters at cellular level substantially contribute to tissue morphologies. This is largely due to technical limitations of live measurements of cellular forces. Here we developed a framework for inferring and modeling mechanical forces of cell-cell interactions. First, by analogy to coarse-grained models in molecular and colloidal sciences, we approximated cells as particles, where mean forces (i.e. effective forces) of pairwise cell-cell interactions are considered. Then, the forces were statistically inferred by fitting the mathematical model to cell tracking data. This method was validated by using synthetic cell tracking data resembling various in vivo situations. Application of our method to the cells in the early embryos of mice and the nematode Caenorhabditis elegans revealed that cell-cell interaction forces can be written as a pairwise potential energy in a manner dependent on cell-cell distances. Importantly, the profiles of the pairwise potentials were quantitatively different among species and embryonic stages, and the quantitative differences correctly described the differences of their morphological features such as spherical vs. distorted cell aggregates, and tightly vs. non-tightly assembled aggregates. We conclude that the effective pairwise potential of cell-cell interactions is a live measurable parameter whose quantitative differences can be a parameter describing three-dimensional tissue morphologies. Author summaryEmergence of diverse three-dimensional morphologies of multicellular organisms is one of the most intriguing phenomena in nature. Due to the complex situations in living systems (e.g. a lot of genes are involved in morphogenesis.), a model for describing the emergent properties of multicellular systems has not been established. To approach this issue, approximation of the complex situations to limited numbers of parameters is required. Here, we searched for mechanical parameters for describing morphologies. We developed a statistical method for inferring mechanical potential energy of cell-cell interactions in three-dimensional tissues; the mechanical potential is an approximation of various mechanical components such as cell-cell adhesive forces, cell surface tensions, etc. Then, we showed that the quantitative differences in the potential is sufficient to reproduce basic three-dimensional morphologies observed during the mouse and C. elegans early embryogenesis, revealing a direct link between cellular level mechanical parameters and three-dimensional morphologies. Our framework provides a noninvasive tool for measuring spatiotemporal cellular forces, which would be useful for studying morphogenesis of larger tissues including organs and their regenerative therapy.

biophysics↗

bioRxiv2019

Isotropic expansion of external environment induces tissue elongation and collective cell alignment

Cell movement is crucial for morphogenesis in multicellular organisms. Growing embryos or tissues often expand isotropically, i.e., uniformly, in all dimensions. On the surfaces of these expanding environments, which we call \"fields,\" cells are subjected to frictional forces and move passively in response. However, the potential roles of isotropically expanding fields in morphogenetic events have not been investigated well. In this study, we mathematically analyzed the effect of isotropically expanding fields using a vertex model, a standard type of multi-cellular model. We found that cells located on fields were elongated along a similar direction each other. Simultaneously, the cell clusters were also elongated, even though field expansion was absolutely isotropic. We then investigated the mechanism underlying these counterintuitive phenomena. In particular, we asked whether elongation was caused by the properties of the field, the cell cluster, or both. Theoretical analyses involving simplification of the model revealed that cell clusters have an intrinsic ability to asymmetrically deform, leading to their elongation. Importantly, this ability is effective only under the non-equilibrium conditions provided by field expansion. This may explain the elongation of the notochord, located on the surface of the growing mouse embryo. We established that passive cell movement induced by isotropically expanding external environments can contribute to both cell and tissue elongation, as well as collective cell alignment, providing key insight into morphogenesis involving multiple adjacent tissues.\n\nStatement of SignificanceIt is a central question of developmental biology how the symmetric shapes of eggs can develop the asymmetric structures of embryos. Embryos expand through their growth. Simultaneously, elongation of tissues such as the notochord occurs, which is fundamental phenomena of morphogenesis. However, possible relationships between tissue elongation and the expansion of embryos have not been investigated well. Here we mathematically present that, even if the expansion is isotropic, tissues located on the embryos are asymmetrically deformed by the expansion, resulting in elongation. We generalize the effect of expanding environments on tissue elongation through model reduction and uncover the mechanism underlying elongation. This process can be a novel key piece for symmetry breaking of embryos, together with previously established morphogenetic processes.

biophysics↗

bioRxiv2017

Changes in free amino acid concentrations and associated gene expression profiles in the abdominal muscle of kuruma shrimp Marsupenaeus japonicus reared at different salinity

Shrimps inhabiting around the coastal area can survive in a wide range of salinity. However, the molecular mechanisms involved in their adaptation to different environmental salinity have remained largely unknown. In the present study, we reared kuruma shrimp Marsupenaeus japonicus at 1.7 %, 3.4 % and 4.0 % salinity. After rearing for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA-seq analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after rearing for 24 h. Glutamine and alanine concentrations were markedly increased following the increase of salinity. In association with such changes, many genes related to amino acid metabolism changed their expression levels. Notably, the increased glutamine content at high salinity appeared to be relevant to the increase of the expression level of the gene encoding glutamate-ammonia ligase which functions in the glutamine metabolism. Furthermore, the alanine content increased at high salinity was likely to be associated with the decrease in the expression levels of the alanine-glyoxylate transaminase gene. Thus, the changes in the concentration of free amino acids for osmoregulation in kuruma shrimp are considered to be regulated by the changes in the expression levels of genes related to amino acid metabolism.\n\nSummary statesmentKuruma shrimp Marsupenaeus japonicus changes free amino acid contents and associated gene expression levels in their muscle to adjust effectively to different salinity.

zoology↗