Biology subjects

Shimbo, A.

Publications and source records attributed to Shimbo, A..

3 recordsLinked to original sources

bioRxiv2026

A visualization framework for cell division activity and orientation in pre-anthesis ovaries of Prunus species

Fruit size and shape, which influence horticultural quality, are determined by the number and the size of the cells in the local region. In fruit trees, however, the difficulty of applying molecular genetic approaches has hindered a detailed understanding of the localization and orientation of cell division in developing fruit tissues. In this study, we established a novel framework to visualize cell division in pre-anthesis ovaries of three drupe crops, peach (Prunus persica), Japanese apricot (P. mume) and the interspecific hybrid Japanese apricot (P. salicina x P. mume), providing clear insight into the spatial distribution and orientation of dividing cells. We systematically optimized a 5-ethynyl-2'-deoxyuridine (EdU) labeling protocol for thick ovary tissues by adjusting infiltration conditions and fixation methods. In addition, electron microscopy combined with wide-view tiling visualization was applied to directly identify dividing cells, including those undergoing chromosome segregation and cell plate formation. By combining with machine learning-based detection, we efficiently and objectively identified dividing cells. Using these complementary approaches, we found that cell division activity was broadly distributed throughout pre-anthesis ovaries in all three crops, without pronounced spatial restriction. In contrast, analysis of division orientation revealed region-specific patterns: cells in the outermost exocarp divided predominantly anticlinally, whereas cells in the mesocarp divided largely periclinally, consistent with subsequent ovary (fruit) enlargement. The integrated framework presented here provides a foundation for understanding the spatial and three-dimensional regulation of fruit development and for future studies in fruit morphogenesis and horticulture.

plant biology↗

bioRxiv2025

Spatially resolved analysis of growth dynamics in pome and drupe fruits of Rosaceae using 3D Gaussian Splatting

Fruit growth has long been described using single- or double-sigmoid curves; however, these temporal models cannot fully capture the spatial heterogeneity that ultimately shapes a fruit. Here, we present a three-dimensional analysis pipeline that non-destructively tracks spatial fruit growth dynamics from field-collected imaginary. Surface landmarks were drawn, and video recordings were taken throughout development for three pome fruits, apple (Malus x domestica), Japanese pear (Pyrus pyrifolia) and European pear (Pyrus communis), and two drupe fruits, peach (Prunus persica) and Japanese apricot (Prunus mume), to track their motion. Using 3D Gaussian Splatting, we successfully reconstructed 3D models of the fruits, and the landmark displacement could be measured with high accuracy, with R2 [≥] 0.98 when compared to manual recordings. We found a common spatial growth gradient in the longitudinal growth shared in the pomes and drupes of the Rosaceae; proximal (stem-end) regions exhibited more pronounced growth than the distal (stylar) end. An exception was found in European pear Bartlett, which showed relatively vigorous growth in the distal region, explaining its distinct shape with expanded distal end. Transverse expansion varied far less than longitudinal expansion, with a possible association with initial fruit morphology. Inter-fruit growth variability peaked in the fastest-growing regions, particularly in the distal area of the European pear, highlighting the link between growth vigor and phenotypic variance. These results provide foundational insights into the developmental dynamics of both pome and drupe fruits of the Rosaceae family, contributing to the optimization of fruit size, shape, and uniformity.

plant biology↗

bioRxiv2024

Synchronous processing of temporal information across the hippocampus, striatum, and orbitofrontal cortex

Information processing for interval timing is supported by several brain regions, including the hippocampus, basal ganglia, and frontal cortical areas. However, little is known about the mechanism by which temporal information is processed cooperatively in the distributed brain network. Here, we investigated the neuronal processing of temporal information in the hippocampal CA1, dorsal striatum, and orbitofrontal cortex by simultaneously recording neuronal activity during a temporal bisection task. We found time cells representing elapsed time during the interval period across all three regions. Seeking a potential mechanism for the correlative representation of time, we found that theta oscillations were dominant in these areas and modulated the activity of these time cells. Moreover, the synchronization of the time cell pairs across the areas was also regulated by theta oscillations. Taken together, these results demonstrated the presence of synchronous activity of time cells across the three areas on a fine time scale, which was supported by theta oscillations. In addition, decoding analysis revealed that the activity of the time cells in these areas correlated with the rats decisions based on their internal time estimation, with the decoded time also showing correlations across the three regions. Thus, the cooperative activity of time-cell assemblies in the three regions reflected the recognition of elapsed time in the rats. In conclusion, these results demonstrate the pivotal role of neuronal synchronization of time cells in supporting temporal processing in the distributed brain network.

neuroscience↗