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Nishiyama, S.

Publications and source records attributed to Nishiyama, S..

9 recordsLinked to original sources

Accumulation of two distinct alleles causes astringency loss in cultivated polyploid persimmon

Persimmon fruit accumulates high levels of proanthocyanidins (PAs), causing extreme astringency. In pollination-constant and non-astringent (PCNA) cultivars, PA accumulation ceases early in fruit development. Although the PCNA trait is recessively controlled by the ASTRINGENCY (AST) locus, its causal gene has remained unknown. Using haplotype-resolved forward genetics in a hexaploid genetic background, we identified the previously uncharacterized TANNIN (TAN) as the causal gene. Long-read sequencing revealed that PCNA originated through the accumulation of independently derived ast alleles that cause transcriptional deficiency of TAN. These findings resolve the complex genetic basis of natural astringency loss in persimmon and provide a framework for molecular breeding. Further investigation of TAN function would uncover mechanisms underlying massive accumulation of PAs in persimmon fruit and insight into specialized metabolite sequestration.

plant biology↗

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↗

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↗

Spatially resolved analysis of longitudinal fruit growth in persimmon (Diospyros kaki) via three-dimensional phenotyping

Understanding fruit development patterns is essential, as they are directly linked to fruit size and shape, which ultimately determine final yield and quality. While conventional models describe fruit development based on growth parameters for the whole fruit, it remains unclear how tissue growth at different fruit portions is coordinated to promote overall fruit development. Therefore, in this study, we investigated the relationship between differences in developmental rates among fruit portions and fruit morphology in persimmon (Diospyros kaki), a species known for its high morphological diversity. Starting two weeks after blooming (WAB), surface landmarks were routinely drawn along the calyx-apex line on fruits of four persimmon cultivars with diverse shapes, and the landmark displacement was quantified every two weeks using 3D phenotyping. Consistent with previous studies, all cultivars exhibited active development in the regions near the calyx, with the greatest difference in growth rates between the calyx and apex occurring at 6-8 WAB. However, the extent of these spatial differences varied among cultivars. In elongated fruits, a gradual growth gradient was observed from the calyx toward the apex, with relatively high growth rates even near the apex. In contrast, in flattened fruits, growth was highly concentrated near the calyx, while development in other regions remained minimal. The findings of this study provide a foundation for future research on fruit shape regulation and the elucidation of physiological disorders in persimmon. HighlightsO_LISpatially resolved 3D phenotyping quantified growth dynamics in persimmon fruit C_LIO_LIGrowth rates varied along the fruit axis, with active growth near the calyx in all tested cultivars C_LIO_LIGrowth gradients were linked to final fruit shape C_LI

plant biology↗

Ubiquilin-2 liquid droplets catalyze α-synuclein fibril formation

Liquid-liquid phase separation (LLPS) and subsequent liquid-gel/solid transition are considered common aggregation mechanisms of proteins linked to neurodegenerative diseases. -synuclein (-syn), the main component of Parkinsons disease pathology, has been reported to undergo LLPS, thereby accelerating aggregate formation. However, the precise molecular events involved in the early stages of -syn aggregation remain controversial. In this study, we show that -syn aggregation is promoted by droplets formed by ubiquilin-2 (UBQLN2), rather than by -syn LLPS itself. During the liquid-gel/solid transition of UBQLN2 droplets, -syn within the droplets transformed into pathogenic fibrils both in vitro and in cells. Immunohistochemistry of brain sections from sporadic Parkinsons disease patients revealed UBQLN2 in substantia nigra Lewy bodies, implicating UBQLN2 in -syn aggregation in vivo. Furthermore, the small compound SO286 inhibited both UBQLN2 self-association and its interaction with -syn by binding to the STI1 domain, thereby suppressing -syn aggregation. These findings demonstrate that UBQLN2 droplets catalyze -syn fibrillization and suggest that small molecules targeting fibril-catalyzing proteins such as UBQLN2 may represent a novel therapeutic approach for neurodegenerative diseases.

biochemistry↗

Three-dimensional fruit growth analysis clarifies developmental mechanisms underlying complex shape diversity in persimmon fruit

How fruit size and shape are determined is of research interest in agriculture and developmental biology. Fruit typically exhibits three-dimensional structures with genotype-dependent geometric features. Although minor developmental variations have been recognized, little research has fully visualized and measured these variations throughout fruit growth. In this study, a high-resolution 3D scanner was used to investigate the fruit development of 51 persimmon (Diospyros kaki) cultivars with various complex shapes. We obtained 2,380 3D fruit models that fully represented fruit appearance, and enabled precise and automated measurements of unique geometric features throughout fruit development. The 3D fruit model analysis identified key stages that determined the shape attributes at maturity. Typically, genetic diversity in vertical groove development was found, and such grooves can be filled by tissue expansion in the carpal fusion zone during fruit development. Furthermore, transcriptome analysis of fruit tissues from groove/non-groove tissues revealed gene co-expression networks that were highly associated with groove depth variation. The presence of YABBY homologs was most closely associated with groove depth and indicated the possibility that this pathway is a key molecular contributor to vertical groove depth variation. These results demonstrate the validity of fruit 3D growth analysis, which is a powerful tool for identifying the developmental mechanisms of fruit shape variation and the molecular basis of this diversity.

plant biology↗

Molecular and genetic mechanisms conferring dissolution of dioecy in Diospyros oleifera Cheng

Dioecy, a sexual system of single-sex (gynoecious/androecious) individuals, is rare in flowering plants. This rarity may be a result of the frequent transition from dioecy into systems with co-sex individuals. Here, we report potential molecular and genetic mechanisms that underlie the dissolution of dioecy to monoecy and andro(gyno)monoecy, based on multiscale genome-wide investigations of 150 accessions of Diospyros oleifera. All co-sex D. oleifera plants, including monoecious and andro(gyno)monoecious individuals, possessed the male determinant gene OGI, implying that genetic factors control gynoecia development in genetically male D. oleifera. In both single- and co-sex plants, female function was expressed in the presence of a genome-wide decrease in methylation levels, along with sexually distinct regulatory networks of smRNAs and their targets. Furthermore, a genome-wide association study (GWAS) identified a genomic region and a DUF247 gene cluster strongly associated with the monoecious phenotype, as well as several regions that may contribute to andromonoecy. Collectively, our findings imply stable breakdown of the dioecious system in D. oleifera, presumably a result of the genomic features of the sex-linked region.

plant biology↗

Correcting the Hebbian Mistake: Toward a Fully Error-Driven Hippocampus

The hippocampus plays a critical role in the rapid learning of new episodic memories. Many computational models propose that the hippocampus is an autoassociator that relies on Hebbian learning (i.e., "cells that fire together, wire together"). However, Hebbian learning is computationally suboptimal as it modifies weights unnecessarily beyond what is actually needed to achieve effective retrieval, causing more interference and resulting in a lower learning capacity. Our previous computational models have utilized a powerful, biologically plausible form of error-driven learning in hippocampal CA1 and entorhinal cortex (EC) (functioning as a sparse autoencoder) by contrasting local activity states at different phases in the theta cycle. Based on specific neural data and a recent abstract computational model, we propose a new model called Theremin (Total Hippocampal ERror MINimization) that extends error-driven learning to area CA3 -- the mnemonic heart of the hippocampal system. In the model, CA3 responds to the EC monosynaptic input prior to the EC disynaptic input through dentate gyrus (DG), giving rise to a temporal difference between these two activation states, which drives error-driven learning in the EC[->]CA3 and CA3{leftrightarrow}CA3 projections. In effect, DG serves as a teacher to CA3, correcting its patterns into more pattern-separated ones, thereby reducing interference. Results showed that Theremin, compared with our original model, has significantly increased capacity and learning speed. The model makes several novel predictions that can be tested in future studies. Author SummaryExemplified by the famous case of patient H.M. (Henry Molaison) who had his hippocampus surgically removed, the hippocampus is critical for learning and remembering about everyday events -- what is typically called "episodic memory." The dominant theory for how it learns is based on the intuitive principle stated by Donald Hebb in 1949, that neurons that "fire together, wire together" -- when two neurons are active at the same time, the strength of their connection increases. We show in this paper that using a different form of learning based on correcting errors (error-driven learning) results in significantly improved episodic memory function in a biologically-based computational model of the hippocampus. This model also provides a significantly better account of behavioral data on the testing effect, where learning by testing with partial cues is better than learning with the complete set of information.

neuroscience↗

Role of microRNA-21 in hypertrophic cardiac remodeling

Hypertension is a major public health problem among with aging population worldwide. It causes cardiac remodeling, including hypertrophy and interstitial fibrosis, which leads to development of hypertensive heart disease (HHD). Although microRNA-21 (miR-21) is associated with fibrogenesis in multiple organs, its impact on hypertrophic cardiac remodeling in hypertension is not known. Circulating miR-21 level was higher in patients with HHD than that in the control subjects. It also positively correlated with serum myocardial fibrotic markers. MiR-21 expression levels were significantly upregulated in the mice hearts after angiotensin II (Ang II) infusion or transverse aortic constriction (TAC) compared with control mice. Expression level of programmed cell death 4 (PDCD4), a main target of miR-21, was significantly decreased in Ang II infused mice and TAC mice compared with control mice. Expression levels of transcriptional activator protein 1 (AP-1) and transforming growth factor-{beta}1 (TGF-{beta}1), which were downstream targets of PDCD4, were increased in Ang II infused mice and TAC mice compared with control mice. In vitro, mirVana-miR-21-specific inhibitor attenuated Ang II-induced PDCD4 downregulation and contributed to subsequent deactivation of AP-1/TGF-{beta}1 signaling pathway in neonatal rat cardiomyocytes. Thus, suppression of miR-21 prevents hypertrophic cardiac remodeling by regulating PDCD4, AP-1, and TGF-{beta}1 signaling pathway.

molecular biology↗