Biology subjects

Yamane, H.

Publications and source records attributed to Yamane, H..

8 recordsLinked to original sources

bioRxiv2026

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↗

bioRxiv2026

Photosynthesis-derived carbohydrate supply sustains CuCl2-induced phytoalexin production in rice leaves

Phytoalexins are antimicrobial metabolites whose biosynthesis is triggered by signaling activated by both biotic and abiotic elicitors, but the physiological conditions that sustain their production remain poorly understood. Here, we examined how light and carbohydrate availability affect CuCl2-induced production of diterpenoid (phytocassanes and momilactones) and flavonoid (sakuranetin) phytoalexins in rice (Oryza sativa L.) leaf disks. Darkness strongly suppressed both the accumulation of all three phytoalexin groups and the induction of their biosynthetic genes. In darkness, endogenous sucrose, glucose, and fructose declined to 3%-8% of the levels in the light, whereas early accumulation of jasmonic acid and jasmonoyl-L-isoleucine (JA-Ile) was not detectably reduced. Exogenous sucrose restored phytoalexin accumulation in darkness in a dose-dependent manner, together with the expression of the suppressed biosynthetic genes, whereas equimolar mannitol had no effect. Glucose also restored sakuranetin accumulation in darkness but only partially restored diterpenoid accumulation, whereas the glucose analog 2-deoxy-D-glucose did not, and it suppressed CuCl2-induced accumulation in the light in a dose-dependent manner. In the light, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosynthetic electron transport, depleted soluble sugars and suppressed phytoalexin accumulation, and sucrose reversed this suppression. Sugars alone induced little phytoalexin accumulation, indicating that carbohydrates act permissively rather than as elicitors. Diterpenoid phytoalexins depended more strongly on light than sakuranetin, yet both classes depended on carbohydrate availability. These results indicate that photosynthesis-derived carbohydrate supply sustains elicitor-induced phytoalexin production in rice leaves and largely accounts for its light dependence.

plant biology↗

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

Weak SLP-76-PLC-γ1 interaction in the LAT-nucleated multi-protein complex fine-tunes TCR signal strength to optimize T cell responsiveness

Upon TCR engagement several protein tyrosine kinases are recruited and activated, and adapter proteins and enzymes are phosphorylated on tyrosine residues, leading to further events characterizing activated T cells. Phosphorylation of the LAT adapter protein enables binding of the enzyme PLC-{gamma}1 and of a dimer of two additional adapter proteins Gads and SLP-76, forming a tetrameric structure. Within this heterotetramer there is a weak interaction between SLP-76 and PLC-{gamma}1, and the relevant binding sites of SLP-76 and PLC-{gamma}1 are highly conserved in vertebrates. To address the biological relevance of this weak interaction, we introduced a mutation in the SLP-76 that enhanced its affinity for PLC-{gamma}1 and found that this mutation increased PLC-{gamma}1 activity and altered thymocyte development and peripheral T cell responses due to enhanced TCR signal strength. The conserved weak SLP-76-PLC-{gamma}1 interaction is critical for the controlled activation of PLC-{gamma}1, thus fine-tuning TCR signal strength to optimize T cell-mediated immunity.

immunology↗

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↗

bioRxiv2025

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↗

bioRxiv2022

Generation of anti-tumor chimeric antigen receptors incorporating T cell signaling motifs

Chimeric antigen receptors (CAR) T cells have been successfully used to treat lymphoma, leukemia, and multiple myeloma, but adverse effects due to cytokine secretion, CAR-T cell exhaustion, and loss of target antigen have limited their potential. Furthermore, while CARs have been designed to harness T Cell Receptor (TCR) signaling, they are significantly less sensitive than TCRs, resulting in suboptimal signaling. We have developed novel Chimeric Adapter Proteins (CAPs) that are designed to trigger signaling downstream of the TCR{zeta} chain. CAPs are chimeric molecules that contain adapter domains in tandem with the kinase domain of ZAP70, fused to an extracellular targeting domain. We hypothesized that CAPs would be more potent than CARs because kinetic proofreading steps that define the signaling threshold and the inhibitory regulation of upstream molecules are bypassed. Indeed, second generation CAPs exhibited high anti-tumor efficacy, and significantly enhanced long-term in vivo tumor clearance in leukemia-bearing NSG mice as compared with conventional CD19-28{zeta} CAR-T. Mechanistically, CAPs were activated in an Lck-independent manner and displayed slower phosphorylation kinetics and a longer duration of signaling compared with 28{zeta}-CAR. The unique signaling properties of CAPs may therefore be harnessed to improve the in vivo efficacy of T cells engineered to express an anti-tumor chimeric receptor.

immunology↗

bioRxiv2019

Targeting of RBM10 to S1-1 Nuclear Bodies: Targeting Sequences and its Biological Significance

RBM10 is an RNA-binding protein that regulates alternative splicing (AS). It localizes to the extra-nucleolar nucleoplasm and S1-1 nuclear bodies (NBs) in the nucleus. We investigated the biological significance of this localization in relation to its molecular function. Our analyses, employing deletion mutants, revealed that RBM10 possesses two S1-1 NB-targeting sequences (NBTSs), one in the KEKE motif region and another in the C2H2 Zn finger (ZnF). These NBTSs act synergistically to localize RBM10 to S1-1 NBs. The C2H2 ZnF not only acts as an NBTS, but is also essential for AS regulation by RBM10. Moreover, RBM10 does not participate in S1-1 NB formation, and without alterations of RBM10 protein levels, its NB-localization changes, increasing as cellular transcriptional activity declines, and vice versa. These results indicate that RBM10 is a transient component of S1-1 NBs and is sequestered in NBs via its NBTSs when cellular transcription decreases. We propose that the C2H2 ZnF exerts its NB-targeting activity when RBM10 is unbound by pre-mRNAs, and that NB-localization of RBM10 is a mechanism to control its AS activity in the nucleus. Note that the previous title of this manuscript was Targeting of RBM10 to S1-1 Nuclear Bodies: Targeting Sequences and its Biological Significance.

molecular biology↗