Biology subjects

Fujimoto, S.

Publications and source records attributed to Fujimoto, S..

At least 19 recordsLinked to original sources

bioRxiv2026

GSDMD transcript levels are higher in endothelial than cardiomyocyte compartments across three human heart cohorts

Cardiac GSDMD research has largely centred on cardiomyocytes. We quantified donor-level endothelial-minus-cardiomyocyte differences in two single-nucleus cohorts and one GeoMx spatial cohort, retaining assay-specific scales. GSDMD was higher in endothelial compartments in 42/42, 38/38 and 27/32 donors and ranked, post hoc, at the 94.9th, 95.1st and 97.4th percentiles of the corresponding within-cohort signed-contrast distributions. Although positive direction and complete donor concordance were not unique transcriptome-wide, this hypothesis-led target retained high rank across markedly different reference backgrounds and assay modalities. A fixed eight-transcript panel included both endothelial- and cardiomyocyte-shifted members, arguing against a uniform panel-wide directional shift or simple detection failure. GeoMx provided the most discriminating transcriptome background but remained composition-sensitive. GSDMD transcripts are therefore recurrently higher in endothelial than cardiomyocyte compartments across human-heart cohorts, showing that a cardiomyocyte-only interpretation of human-heart GSDMD transcript signals is incomplete.

cell biology↗

bioRxiv2026

Osmotic-stress-inducible nuclear condensates restrict gene inducibility

Plants, as sessile organisms, have developed various mechanisms to respond to environmental stress conditions. The plant hormone abscisic acid (ABA) is necessary for the plant to adapt to osmotic stress conditions. However, the molecular mechanisms preceding ABA accumulation remain largely unknown. To isolate transcriptional complexes on the promoter region of NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) encoding a rate-limiting enzyme in the ABA biosynthetic pathway in planta, we developed the insertional chromatin immunoprecipitation (iChIP) screen method. The identified ALBA proteins formed condensates through liquid-liquid phase separation (LLPS) in response to osmotic stress conditions. ALBA4 directly binds to stress-inducible genes, including NCED3, and suppresses their stress inducibility. Our results demonstrate how plants respond to osmotic stress at early timepoints before ABA biosynthesis through condensate formation as osmo-sensors.

plant biology↗

bioRxiv2026

A nucleus-vacuole junction in fission yeast enriches the HMG-CoA reductase Hmg1 and INSIG protein Ins1

Membrane contact sites (MCSs) enable communication between organelles and play central roles in lipid metabolism. In budding yeast, the nucleus-vacuole junction (NVJ) functions as a dynamic platform that integrates lipid metabolism and stress responses. However, it remains unclear whether NVJ structure and function are broadly conserved across eukaryotes, particularly because Nvj1, the key membrane tethering factor that mediates NVJ formation in budding yeast, is absent in higher eukaryotes. Here, we investigated whether an MCS analogous to the NVJ in budding yeast exists in fission yeast (Schizosaccharomyces pombe), which lacks Nvj1. We show that an NVJ is present in fission yeast and serves as a platform for the accumulation of sterol synthesis factors, including the HMG-CoA reductase Hmg1 and the INSIG homolog Ins1. We further demonstrate that the localization of these factors depends on the membrane protein insertase Snd302 and is dynamically regulated by nutrient conditions. Our findings reveal that, despite the absence of Nvj1, the NVJ is functionally conserved as a site for sterol synthesis in fission yeast, suggesting a conserved role of spatial organization in lipid metabolism.

cell biology↗

bioRxiv2026

Genetic polymorphisms in a mate choice locus are maintained by balancing selection in a wild medaka population

Sexual selection arises from individual differences in reproductive success, which can drive the maintenance of genetic polymorphisms in genes subject to balancing selection by the pleiotropic effects that trade-off between survival and reproduction. However, the extent to which sexual selection maintains genetic polymorphisms in wild populations remains unclear. Here, we explored on genomic signatures of balancing selection and selective sweep in the northern medaka, Oryzias sakaizumii in Japan by performing whole-genome resequencing of wild individuals. In addition, we re-evaluated the population genetic structure and admixture of Oryzias latipes and O. sakaizumii across the Japanese archipelago and detected genomic regions affected by introgression. Regions with signatures of selection from multiple statistics were located on eleven chromosomes. In particular, a region spanning 4.25 to 6.80 Mb on chromosome 18 showed high genetic diversity that could not be explained by sex differentiation or introgression from O. latipes in Eastern Japan. This pattern suggests that balancing selection maintains genetic polymorphisms in O. sakaizumii. Specifically, because a previously reported quantitative trait locus associated with female mating behavior overlaps with this region, we infer that sexual selection contributes to the maintenance of genetic polymorphism at this locus.

evolutionary biology↗

bioRxiv2026

Spatial transcriptomics identifies a translayer architecture of pyroptosis-related transcription in systemic sclerosis skin

Anatomical-layer enrichment does not establish cellular attribution, so correspondence with major-cell-class expression must be tested gene by gene. Systemic sclerosis (SSc) skin is informative because inflammasome- and pyroptosis-related molecules have been reported across epidermal, fibroblast-associated and vascular contexts. Spatial transcriptomics of SSc and control skin, with same-donor single-nucleus profiles from 10 SSc donors, revealed gene-specific correspondence. Across 13 discovery sections, NLRP1, PYCARD and CASP4 were epidermally biased, whereas GSDMD was dermally biased. An independent 10-section SSc cohort supported epidermal NLRP1 (q = 0.0078) and PYCARD (q = 0.043), with directional, non-significant support for CASP4 and GSDMD. Despite epidermal NLRP1 bias, endothelial class-pseudobulk exceeded keratinocyte class-pseudobulk in all 10 donors. Restricted three-class reconstruction reproduced the NLRP1 direction in 1 and 0 of 10 donors under the two fixed dermal weightings and in 0-8 of 10 across a post hoc sweep of the dermal endothelial share; PYCARD and GSDMD were concordant in most donors at every weighting, and CASP4 in no more than 4 of 10. Thus, tissue layer and major cell class are gene-specifically non-equivalent axes of spatial interpretation.

immunology↗

bioRxiv2026

Msc1 facilitates glucose starvation-induced remodeling of the nucleus-vacuole junction

The nucleus-vacuole junction (NVJ) is a membrane contact site between the nuclear envelope and the vacuole in yeast that undergoes dynamic remodeling in response to nutrient starvation. Here, we report that Msc1 is a glucose starvation (GS)-responsive NVJ factor. GS strongly induced Msc1 expression and promoted its accumulation at the NVJ. Although Msc1 is not essential for NVJ formation itself, loss of Msc1 impaired GS-dependent functional maturation of the NVJ, including stabilization and recruitment of multiple NVJ-associated proteins. Notably, GS-induced transcriptional activation of NVJ1 was markedly attenuated in msc1{Delta} cells, suggesting that proper NVJ remodeling contributes to the execution of stress-responsive transcriptional programs. Together, these findings establish Msc1 as an upstream regulator linking GS to functional remodeling of the NVJ and associated transcriptional responses.

cell biology↗

bioRxiv2026

Three-dimensional redistribution of pelagic fish aggregations associated with floating offshore wind farms

Floating offshore wind farms (F-OWFs) are rapidly expanding into offshore pelagic environments, yet their ecological consequences remain poorly resolved because quantitative, non-invasive monitoring is challenging at sea. Here, we integrated environmental DNA (eDNA) metabarcoding and scientific echosounding to assess fish community composition and three-dimensional aggregation structure around a commercial-scale F-OWF off the Goto Islands, Japan. We compared four stations adjacent to turbines with four offshore control stations under comparable environmental conditions across five sampling periods (April and August 2024; May, June, and August 2025) and three depth layers (5, 50, and 80-160 m). eDNA metabarcoding detected 126 fish species, and community structure based on the 30 most frequently detected taxa did not differ significantly between the F-OWF and control areas (Bray-Curtis PERMANOVA, p = 0.60). Species richness varied strongly with sampling period and water layer, with a significant water layer x period interaction, whereas overall richness did not differ between areas (Mann-Whitney U test, p = 0.18). In contrast, acoustic surveys revealed a marked difference in vertical structuring of fish aggregations: in the control area, NASC per mile increased with depth, while this depth-dependence disappeared near turbines. Moreover, the weighted mean normalized depth (WMND) indicated a shallower vertical center of aggregation in the F-OWF area (0.34) than in the control area (0.24), consistent with turbine-associated redistribution in the water column. Although voyage-level integrated NASC per mile did not differ significantly between areas (t-test, p = 0.83), mean values were higher near turbines. Together, these results indicate that F-OWFs can be associated with changes in the three-dimensional organization of fish aggregations without producing pronounced shifts in dominant taxonomic composition. Our study demonstrates the value of combining eDNA metabarcoding and acoustics for evaluating ecological effects of offshore renewable-energy infrastructures and provides a framework for standardized, long-term monitoring as F-OWF deployment accelerates globally.

ecology↗

bioRxiv2025

Better Safe Than Sorry: Leg Amputations as a Prophylactic Wound Care Behaviour in Carpenter Ants

Animals often sustain injuries, which are susceptible to lethal infections. In social insects, wound care behaviours have evolved to reduce these risks. But the limits of wound care behaviours remain unclear. Here we investigated the wound care behaviours of the ant Camponotus maculatus. Our findings show that amputation of legs infected with Pseudomonas aeruginosa significantly reduced mortality. However, nestmates do not differentiate between infected and sterile injuries, providing similar treatments regardless of infection. Even though we show that early amputation correlates with higher survival rates, nestmates amputate indiscriminately on legs with fresh or old wounds. Additionally, cuticular hydrocarbon profiles differed between ants with infected or sterile wounds only 24 hours post-injury, a timepoint when amputations are no longer effective. We propose that C. maculatus workers perform prophylactic amputations regardless of injury state or age. This is in sharp contrast to previous studies which showed clear capabilities to treat infected wounds differently in ants using antimicrobial compounds. This work therefore shows the limits of wound care behaviours in social insects, allowing us to better understand the evolutionary drivers of this unique behaviour.

animal behavior and cognition↗

bioRxiv2025

Glucose Starvation Sensing through Membrane Remodeling at theNucleus-Vacuole Junction Coordinates Ergosterol Biosynthesis

Membrane contact sites (MCSs), where organelle membranes come into close proximity, function as dynamic hubs for lipid metabolism in response to metabolic and stress signals. In yeast, the nucleus-vacuole junction (NVJ) expands during glucose starvation through the recruitment of stress-specific proteins, but the underlying mechanisms and physiological significance remained unclear. Here, we identify the yeast INSIG homologs Nsg1, Nsg2, along with the aspartyl protease Ypf1 as glucose starvation-specific NVJ-localized factors. Ypf1 promotes the recruitment of INSIG proteins and the HMG-CoA reductases Hmg1 and Hmg2 to the NVJ, likely in response to nuclear membrane remodeling induced by changes in very long-chain fatty acid (VLCFA) metabolism. We further demonstrate that this membrane remodeling destabilizes Nsg1, promoting the NVJ localization and activation of Hmg1, while stabilizing Nsg2, which counteracts Hmg1 activation. These findings reveal that Nsg1 and Nsg2, previously known as regulators of Hmg2 stability, also act as negative regulators of Hmg1. Based on these results, we propose a model in which VLCFAs modulate the physical properties of the nuclear membrane, enabling cells to sense glucose starvation and regulate sterol metabolism during glucose starvation. Overall, our study provides new insights into MCS-mediated metabolic stress responses and highlights the role of membrane properties as active regulators of lipid homeostasis.

cell biology↗

bioRxiv2025

Floating offshore wind farms cause Japanese horse mackerel to congregate

Floating offshore wind farms (F-OWFs) are becoming key components of renewable energy production, yet their ecological impacts on marine ecosystems remain largely unexplored. Using environmental DNA (eDNA) analysis in the East China Sea, this study investigated the tendency for Japanese horse mackerel (Trachurus japonicus) to congregate beneath F-OWFs. Water samples were collected at stations near an F-OWF and control stations farther away at various depths and seasons. A total of 115 samples were analyzed, and eDNA of T. japonicus was detected in 83% of all samples. eDNA concentrations were significantly higher near an F-OWF (F-OWF stations) than at control stations. The highest recorded eDNA concentration reached 2,280 copies/L at an F-OWF station, whereas the maximum concentration at control stations was 783 copies/L. Seasonal variations were also observed, with lower concentrations in summer and higher concentrations from autumn to spring. Generalized linear model (GLM) analysis further revealed that wind turbines had a significant influence on eDNA concentration, whereas other environmental variables, such as water temperature and depth, were not significant. These findings suggest that F-OWFs may function as artificial reefs, providing habitat for commercially important fish and influencing fish distributions at both spatial and temporal scales. However, potential conflicts with fisheries due to spatial restrictions, displacement of fishery resources, and increased navigation costs necessitate further long-term ecological and socio-economic assessments. Integrating eDNA monitoring with traditional survey methods, such as acoustic surveys and ROV observations, is crucial for coexistence of adaptive offshore wind farm management and sustainable fisheries. Future research should also explore the long-term effects of F-OWFs on fish assemblages and biodiversity to support evidence-based decision-making for offshore energy development.

ecology↗

bioRxiv2024

Isotonic and minimally invasive optical clearing media for live cell imaging ex vivo and in vivo

Tissue clearing has been widely used for fluorescence imaging of fixed tissues, but not for live tissues due to its toxicity. Here we develop minimally invasive optical clearing media for fluorescence imaging of live mammalian tissues. Light scattering is minimized by adding spherical polymers with low osmolarity to the extracellular medium. A clearing medium containing bovine serum albumin (SeeDB-Live) is minimally invasive to live cells, allowing for structural and functional imaging of live tissues, such as spheroids, organoids, acute brain slices, and the mouse brain in vivo. SeeDB-Live minimally affects the electrophysiological properties and sensory responses of neurons. We demonstrate its utility for widefield imaging of subcellular voltage dynamics, such as backpropagating action potentials, in acute brain slices. We also utilize SeeDB-Live for widefield voltage imaging of dozens of dendrites in vivo, demonstrating population dynamics. Thus, SeeDB-Live expands the scale and modalities of fluorescence imaging of live mammalian tissues.

neuroscience↗

bioRxiv2024

Lipogenic Lung Fibroblast-derived Extracellular Vesicles Mitigate Cigarette Smoke-Induced Chronic Obstructive Pulmonary Disease Pathologies through LAT1-mediated Alveolar Type II Cell Restoration

Emerging research has revealed specific cellular aberrations in Chronic Obstructive Pulmonary Disease (COPD), with a particular focus on alveolar type 2 (AT2) cells, which play a pivotal role in the restoration of damaged lung tissue and promotion of normal cellular differentiation. Lipofibroblasts (LipoFBs), which are stromal fibroblasts that house lipid droplets, have been identified in close proximity to AT2 cells and have been demonstrated to support AT2 function. In this study, we present a comprehensive investigation into the therapeutic potential of extracellular vesicles (EVs) derived from LipoFBs (LipoFB-EVs) in COPD treatment. They effectively mitigate key COPD pathologies such as cellular senescence and inflammatory responses in lung epithelial cells. This is achieved by reducing reactive oxygen species (ROS) levels and modulating DNA damage response pathways. Moreover, LipoFB-EVs demonstrate antifibrotic properties by inhibiting TGF-{beta}-induced myofibroblast differentiation, surpassing conventional antifibrotic drugs. They also aid in restoring impaired AT2 stem cells, which are crucial for lung homeostasis, by enhancing their viability, colony-forming ability, and proliferation. Furthermore, we identify the presence of L-type amino acid transporter 1 (LAT1) within LipoFB-EVs, which mediates amino acid uptake, particularly leucine transport, and contributes to the restoration of AT2 cell dysfunction. Importantly, the administration of LipoFB-EVs in murine models of COPD resulted in significant improvements in airway inflammation, remodeling, obstruction, cellular senescence, and alveolar emphysema induced by both short- and long-term CS exposure. Overall, our findings highlight the therapeutic potential of LipoFB-EVs as a novel regenerative therapy for COPD, offering promising avenues for future clinical interventions.

molecular biology↗

bioRxiv2024

Brown Adipose Tissue and Skeletal Muscle Coordinately Contribute to Thermogenesis in Mice

Endotherms increase the rate of metabolism in metabolic organs as one strategy to cope with a decline in temperature of the external environment. However, an additional major contributor to maintenance of body temperature in a cold environment is contraction-based thermogenesis in skeletal muscle. Here, we show that impairment of hind limb muscle contraction by cast immobilization induced a loss of function of skeletal muscle and activated brown adipose tissue (BAT) thermogenesis as a compensatory mechanism. BAT utilizes free branched-chain amino acids (BCAAs) derived from skeletal muscle as an energy substrate for thermogenesis, and interleukin-6 released by skeletal muscle stimulates BCAAs production in muscle for support of BAT thermogenesis. Additionally, this thermoregulatory system between BAT and skeletal muscle may also play an important role in response to cold temperatures or acute stress. Our findings suggest that BAT and skeletal muscle cooperate to maintain body temperature in endotherms.

molecular biology↗

bioRxiv2023

Environmental DNA Reveals the Geographic Distributions of Two Eel Species, Anguilla japonica and A. marmorata, in Western Kyushu, Japan

Anguillid eels migrate thousands of kilometres from their spawning grounds, dispersing across a vast geographic area to fresh and brackish water habitats, where they settle and grow. Japanese eels (Anguilla japonica) and giant mottled eels (A. marmorata) are both found in Japan, although their distributions differ. However, details of these differences are unknown. We hypothesised that distribution patterns of Japanese and giant mottled eels must be different between and within rivers along the northwest coast of Kyushu, Japan. Environmental DNA (eDNA) analysis was conducted at 87 sites in 23 rivers. Japanese eel eDNA was detected in 19 rivers (82.6%) and that of giant mottled eels was detected in 8 (34.8%). eDNA for Japanese eels was detected at 6 of 9 sites in the North (66.7%), 13 of 23 sites in Omura (56.5%) and 37 of 55 sites in the South (67.3%). In contrast, giant mottled eel eDNA was detected at 1 of 9 sites in the North (11.1%), no sites in Omura and 15 of 55 sites in the South (27.3%). There was no correlation between eDNA concentrations of the two species at 10 sites in the five rivers where eDNA of both species was detected, implying that their habitat preference differ. This partially reveals dispersal and settlement mechanisms of these eel species.

ecology↗

bioRxiv2022

Automated neuronal reconstruction with super-multicolour fluorescence imaging

Fluorescence imaging is widely used for the mesoscopic mapping of neuronal connectivity. However, neurite reconstruction is challenging, especially when neurons are densely labelled. Here we report a strategy for the fully automated reconstruction of densely labelled neuronal circuits. Firstly, we established stochastic "super-multicolour" labelling with up to seven different fluorescent proteins using the Tetbow method. With this method, each neuron was labelled with a unique combination of fluorescent proteins, which were then imaged and separated by linear unmixing. We also established an automated neurite reconstruction pipeline based on the quantitative analysis of multiple dyes (QDyeFinder). To classify colour combinations, we used a newly developed unsupervised clustering algorithm, dCrawler, in which data points in multi-dimensional space were clustered based on a given threshold distance. Our new strategy allows for the reconstruction of neurites for up to hundreds of neurons at a millimetre scale without manual tracing.

neuroscience↗

bioRxiv2021

CUX2 mutations in temporal lobe epilepsy; increased kainate susceptibility and excitatory input to hippocampus in deficient mice

CUX2 gene encodes a transcription factor that controls neuronal proliferation, dendrite branching and synapse formation, locating at the epilepsy-associated chromosomal region 12q24 that we previously identified by a genome-wide association study (GWAS) in Japanese population. A CUX2 recurrent de novo variant p.E590K has been described in patients with rare epileptic encephalopathies and the gene is a candidate for the locus, however the mutation may not be enough to generate the genome-wide significance in the GWAS and whether CUX2 variants appear in other types of epilepsies and physiopathological mechanisms are remained to be investigated. Here in this study, we conducted targeted sequencings of CUX2, a paralog CUX1 and its short isoform CASP harboring a unique C-terminus on 271 Japanese patients with a variety of epilepsies, and found that multiple CUX2 missense variants, other than the p.E590K, and some CASP variants including a deletion, predominantly appeared in patients with temporal lobe epilepsy (TLE). The CUX2 variants showed abnormal localization in human cell culture analysis. While wild-type CUX2 enhances dendritic arborization in fly neurons, the effect was compromised by some of the variants. Cux2- and Casp-specific knockout mice both showed high susceptibility to kainate, increased excitatory cell number in the entorhinal cortex, and significant enhancement in glutamatergic synaptic transmission to the hippocampus. CASP and CUX2 proteins physiologically bound to each other and co-expressed in excitatory neurons in brain regions including the entorhinal cortex. These results suggest that CUX2 and CASP variants contribute to the TLE pathology through a facilitation of excitatory synaptic transmission from entorhinal cortex to hippocampus.

neuroscience↗

bioRxiv2021

Rapid inactivation of SARS-CoV-2 variants by continuous and intermittent irradiation with a deep-ultraviolet light-emitting diode (DUV-LED) device

More than 1 year has passed since social activities have been restricted due to the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More recently, novel SARS-CoV-2 variants have been spreading around the world, and there is growing concern of higher transmissibility of the variants and weaker protective efficacy of vaccine against the variants. Immediate measures are needed to reduce human exposure to the virus. In this study, the antiviral efficacy of deep-ultraviolet light-emitting diode (DUV-LED) irradiation (280 {+/-} 5 nm, 3.75 mW/cm2) against three SARS-CoV-2 variants was evaluated. For the B.1.1.7, B.1.351, and P.1 strains, the infectious titer reduction rates of 96.3%, 94.6%, and 91.9%, respectively, were already recognized with the irradiation of virus stocks for 1 s, and the rates increased to 99.9%, 99.9%, and 99.8%, respectively, with irradiation for 5 s. We also tested the effect of pulsed DUV-LED irradiation (7.5 mW/cm2, duty rate: 50%, frequency: 1 KHz) under the same output conditions as continuous irradiation, and found that the antiviral efficacy of pulsed and continuous irradiation was the same. These findings suggest that SARS-CoV-2 may be instantly inactivated by DUV-LED irradiation if the DUV-LED device is further developed and optimized to increase its output.

microbiology↗

bioRxiv2020

Rapid inactivation of SARS-CoV-2 with ozone water

Although ozone water is one of the promising candidates for hand hygiene to prevent fomite infection, the detailed effects of ozone water on SARS-CoV-2 have not been clarified. We evaluated the inactivating effect of ozone water against SARS-CoV-2 by its concentration and exposure time. The reduction rates of virus titer after 5 sec treatment with ozone concentrations of 1, 4, 7, and 10 mg/L were 81.4%, 93.2%, 96.6%, and 96.6%, respectively. No further decrease in virus titer was observed by the extended exposure time over 5 sec. High-concentration ozone water was considered to be effective in promptly inactivating SARS-CoV-2 virus.

microbiology↗