Biology subjects

Sakai, M.

Publications and source records attributed to Sakai, M..

17 recordsLinked to original sources

bioRxiv2026

Age-associated erosion of organ-specific endothelial programs compromises tissue function and resilience

Endothelial cells (ECs) express organ-specific gene programs supporting tissue homeostasis and resilience. However, the mechanisms by which aging reshapes these organ-specific endothelial programs and how the resulting changes affect tissue homeostasis, resilience, and disease susceptibility remain largely unknown. Herein, we performed single-cell RNA sequencing of ECs harvested from five organs across the lifespan and found that aging progressively erodes organ-specific endothelial programs while inducing shared interferon-responsive and antigen-presentation programs across organs. Although vascular subtype identity and conserved capillary subset identity were mostly preserved, these organ-specific transcriptional programs were broadly attenuated with aging, indicating erosion of organ-specific endothelial identity to be a fundamental feature of endothelial aging. Importantly, these alterations were associated with declines in specialized EC functions, including alveolar barrier maintenance in the lung, scavenging activity in the liver, angiogenic capacity in the heart, and homeostatic programs in the kidneys and the brain, suggesting that age-related EC alterations compromise tissue homeostasis and resilience in multiple organs. Furthermore, we established a single-cell aging index for alveolar capillary ECs in mice and humans, revealing stress-associated endothelial activation to potentially be an intermediate state linking functional deterioration to cellular senescence, and also demonstrating marked heterogeneity in aging states even among ECs from animals of the same chronological age. Notably, alveolar capillary ECs exhibited progressive functional decline before reaching a senescent-like state, suggesting endothelial dysfunction to precede overt cellular senescence as the organism ages. Collectively, our findings establish progressive erosion of organ-specific endothelial programs as a central feature of vascular aging and provide a conceptual framework for elucidating how endothelial aging contributes to tissue dysfunction and reduced resilience across organs.

physiology↗

bioRxiv2026

Cycling persister clones with elevated NR2F1-mediated cholesterol biosynthesis cause chemotherapy resistance

While a subpopulation termed cycling persisters (CPs) that is characterized by sustained proliferation, even under chemotherapy drug exposure, contributes more directly to tumor relapse, the molecular basis for the emergence of CPs has been unclear. Here, we used the human tongue cancer organoid (TCO) library to continuously track the in vitro fate of individual cancer cell clones during and after chemotherapy exposure using time-lapse imaging. Among the heterogeneous clones, we identified CPs that formed larger clusters than the others, which barely grew and remained small (non-CPs). Using differences in cell cluster size as an indicator, thousands of CP and non-CP clones were directly sampled from 3D matrix organoid cultures and were analyzed. Notably, tumor-intrinsic interferon (IFN) signaling and hypoxic pathways were inactivated, whereas the NR2F1-mediated cholesterol biosynthesis pathway was distinctly activated in CPs compared to non-CPs. Indeed, inhibiting cholesterol biosynthesis with simvastatin significantly suppressed the appearance of CP clones, showing that elevated cholesterol biosynthesis is essential for the emergence of CPs. These findings suggest that clonal-level variations in the intensity of these signaling pathways determine the fate of individual tumor cells exposed to chemotherapeutic agents, which may provide insights into cancer relapse mechanisms and identify potential molecular targets of CPs.

cancer biology↗

bioRxiv2026

A single conserved residue in FlhA couples export gate activation to substrate specificity switching

FlhA is a core component of the bacterial flagellar type III secretion system that functions as both an export engine and a switch regulator of substrate specificity. How these two processes are mechanistically coupled remains unclear. Here we identify a single conserved residue in FlhA, Arg-391, as a key molecular node that links export gate activation to substrate specificity switching. The R391A substitution blocks the transition from hook-type to filament-type secretion, resulting in polyhooks lacking filaments. An intermolecular salt-bridge formation of Arg-391 with Glu-351 of an adjacent FlhA subunit stabilizes the filament-type FlhA ring. Suppressor mutations in FlhA and the ruler protein FliK restore this interaction, indicating that FliK promotes the intermolecular salt-bridge formation during export switching. Moreover, Arg-391 is required for efficient ATPase-independent activation of the export gate. Together, these findings reveal an electrostatic mechanism by which FlhA coordinates export gate activation and substrate specificity switching during flagellar assembly.

microbiology↗

bioRxiv2026

Radiocesium Uptake in Two Fungal Bed-cultivated Edible Mushroom Species in Forests in Fukushima, Japan

In Japan, mushrooms have long been valued as food resources, but the Fukushima nuclear accident disrupted production and shipment due to radiocesium contamination. Limited knowledge has particularly hindered outdoor fungal bed cultivation. To address this, we conducted cultivation experiments with Lyophyllum decastes and Lepista nuda across 14 broad-leaved deciduous forest sites in Fukushima Prefecture. Air dose rates at 1 m height ranged from 0.04 to 0.89 {micro}Sv/h. Radiocesium concentrations (combined 137Cs and 134Cs, expressed as Bq/kg at 90% water content) in fruit bodies were 0.4-12 (mean 2.3) for Ly. decastes and 0.2-43 (mean 8.1) for Le. nuda. Both species remained below Japans food safety threshold of 100 Bq/kg, indicating that safe cultivation is feasible across broad areas. Uptake patterns differed: concentrations in Ly. decastes correlated with contamination in litter and multiple soil layers, whereas in Le. nuda it correlated only with litter contamination. These findings suggest that clean soil fills for Ly. decastes and clean litter covers for Le. nuda could serve as mitigation strategies tailored to each species. Aggregated transfer factors (2.76 x 10-5 m2/kg for Ly. decastes and 6.60 x 10-5 m2/kg for Le. nuda) were lower than those reported for wild mushrooms. Overall, this study provides new insights into reducing radiocesium assimilation by cultivated mushrooms and supports the revival of outdoor fungal bed cultivation in contaminated landscapes.

ecology↗

bioRxiv2025

Weak and tunable adhesion-clutch drives rapid cell migration and glioblastoma motility

To move forward, migrating cells must exert backward forces against the extracellular environment. Recent studies have highlighted the importance of integrin-independent forces for cell migration; but the molecular machinery that exerts forces remains unclear. Here, we show that the clutch-linker molecule shootin1 and the cell adhesion molecule L1 transmit the backward force of treadmilling actin filaments to the adhesive environment for rapid dendritic cell migration. Notably, shootin1 and L1 transmit weak traction forces, [~]100 times weaker than integrin-based forces, by constituting an integrin-independent slippery adhesion-clutch. This adhesion-clutch system is tunable in response to the chemoattractant CCL19 and the adhesive ligand laminin and mediates chemotaxis through its polarized activation within cells. Furthermore, its aberrant activity enhances glioblastoma cell motility. Our results show that the weak adhesion-clutch is well-suited for rapid cell migration, without forming strong adhesions that impede cell motility, and provides a potential target for inhibiting abnormal cell motility.

cell biology↗

bioRxiv2024

A single amino acid substitution in the Borna disease virus glycoprotein enhances the infectivity titer of vesicular stomatitis virus pseudotyped virus by altering membrane fusion activity

Borna disease virus 1 (BoDV-1) causes acute fatal encephalitis in mammals, including humans. Despite its importance, research on BoDV-1 cell entry has been hindered by low viral particle production in cells and the lack of cytopathic effects. To address these issues, we developed a method to efficiently produce vesicular stomatitis virus (VSV) pseudotyped with glycoprotein (G) of the genus Orthobornavirus, including BoDV-1. We discovered that optimal G expression is required to obtain a high infectivity titer of the VSV pseudotyped virus. Remarkably, the infectivity of the VSV pseudotyped virus with G from the BoDV-1 strain huP2br was significantly higher than that of the VSV pseudotyped virus with G from the He/80 strain. Mutational analysis demonstrated that the BoDV-1-G residue 307 determines the infectivity titer of VSV pseudotyped with BoDV-1-G (VSV-BoDV-1-G). A cell-cell fusion assay indicated that this residue plays a pivotal role in membrane fusion, thus suggesting that high membrane fusion activity and a broad pH range for membrane fusion are crucial for achieving a high infectivity titer of VSV-BoDV-1-G. This finding may be extended to increase the infectivity titer of VSV pseudotyped virus with other orthobornavirus G. Our study also contributes to identifying functional domains of BoDV-1-G and provides insight into G-mediated cell entry.

microbiology↗

bioRxiv2024

STOP1 dominates Arabidopsis tolerance to ammonium over NRT1.1/NPF6.3/CHL1

The Arabidopsis nitrate transceptor NITRATE TRANSPORTER 1.1 (NRT1.1/NPF6.3/CHL1) plays significant roles even in the absence of nitrate. The loss-of-function of NRT1.1 alleviates growth suppression and chlorosis under toxic levels of ammonium as the sole nitrogen source. Recently, we reported that acidic stress-inducible genes are downregulated by NRT1.1 deficiency under ammonium toxicity conditions, implying that NRT1.1 may exacerbate ammonium-dependent acidic stress. The transcription factor SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) enhances Arabidopsis tolerance to ammonium and acidic stresses. Furthermore, STOP1 directly activates NRT1.1 transcription. These previous findings prompted us to analyze the association between NRT1.1 and STOP1 on ammonium tolerance. Here, we show that ammonium-inducible STOP1 plays a dominant role over NRT1.1 in ammonium tolerance and expression of direct target genes of STOP1. We present a novel scheme in which NRT1.1 and STOP1 jointly regulate common target(s) associated with ammonium tolerance.

plant biology↗

bioRxiv2023

Simple ways to avoid collecting highly 137Cs-contaminated Aralia elata buds

Collection and cooking of wild vegetables have provided seasonal enjoyments for Japanese local people as provisioning and cultural ecosystem services. However, the Fukushima Daiichi Nuclear Power Plant accident in March 2011 caused extensive radiocesium contamination of wild vegetables. Restrictions on commercial shipments of wild vegetables have been in place for the last 10 years. Some species, including buds of Aralia elata, are currently showing radiocesium concentrations both above and below the Japanese reference level for food (100 Bq/kg), suggesting that there are factors decreasing and increasing the 137Cs concentration. Here, we evaluated easy-to-measure environmental variables (dose rate at the soil surface, organic soil layer thickness, slope steepness, and presence/absence of decontamination practices) and the 137Cs concentrations of 40 A. elata buds at 38 locations in Fukushima Prefecture to provide helpful information on avoiding collecting highly contaminated buds. The 137Cs concentrations in A. elata buds increased significantly with increases in the dose rate at the soil surface. Meanwhile, the 137Cs concentration in A. elata buds were not reduced by decontamination practices. These findings suggest that measuring the latest dose rate at the soil surface at the base of A. elata plants is a helpful way to avoid collecting buds with higher 137Cs concentrations and aid in the management of species in polluted regions.

ecology↗

bioRxiv2023

Genome-scale CRISPR-Cas9 screen identifies novel host factors as potential therapeutic targets for SARS-CoV-2 infection.

Although many host factors important for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection have been reported, the mechanisms by which the virus interacts with host cells remain elusive. Here, we identified tripartite motif containing (TRIM) 28, TRIM33, euchromatic histone lysine methyltransferase (EHMT) 1, and EHMT2 as novel proviral factors involved in SARS-CoV-2 infection by CRISPR-Cas9 screening. We demonstrated that TRIM28 plays a role(s) in viral particle formation and that TRIM33, EHMT1, and EHMT2 are involved in viral transcription and replication using cells with suppressed gene expression. UNC0642, a compound that specifically inhibits the methyltransferase activity of EHMT1/2, strikingly suppressed SARS-CoV-2 growth in cultured cells and reduced disease severity in a hamster infection model. This study suggests that EHMT1/2 may be a novel therapeutic target for SARS-CoV-2 infection.

microbiology↗

bioRxiv2023

Identical tau filaments in subacute sclerosing panencephalitis and chronic traumatic encephalopathy

Subacute sclerosing panencephalitis (SSPE) occurs in some individuals after measles infection, following a symptom-free period of several years. It resembles chronic traumatic encephalopathy (CTE), which happens after repetitive head impacts or exposure to blast waves, following a symptom-free period. As in CTE, when present, the neurofibrillary changes of SSPE are concentrated in superficial cortical layers. Here we used electron cryo-microscopy of tau filaments from two cases of SSPE to show that the tau folds of SSPE and CTE are identical. Two types of filaments were each made of two identical protofilaments with an extra density in the {beta}-helix region. Like in CTE, the vast majority of tau filaments were Type I, with a minority of Type II filaments. These findings suggest that the CTE tau fold can be caused by different environmental insults, which may be linked by inflammatory changes.

neuroscience↗

bioRxiv2022

Systematic analysis of transcriptional and epigenetic effects of genetic variation in Kupffer cells enables discrimination of cell intrinsic and environment-dependent mechanisms

Noncoding genetic variation is a major driver of phenotypic diversity but determining the underlying mechanisms and the cell types in which it acts remain challenging problems. Here, we investigate the impact of natural genetic variation provided by phenotypically diverse inbred strains of mice on gene expression and epigenetic landscapes of Kupffer cells. Analysis of gene expression in Kupffer cells and other liver cell types derived from C57BL/6J, BALB/cJ and A/J mice provided evidence for strain-specific differences in environmental factors influencing Kupffer cell phenotypes, including preferential Leptin signaling in BALB/cJ Kupffer cells. Systematic analysis of transcriptomic and epigenetic data from F1 hybrids of these mice, and transcriptomic data from strain-specific Kupffer cells engrafted into a common host enabled quantitative assessment of cis versus trans effects of genetic variation on gene expression and an estimate of cell autonomous versus non cell autonomous effects. Under homeostatic conditions, trans effects of genetic variation were dominant, with the majority of trans regulation being non cell autonomous. In contrast, strain specific responses to acutely administered LPS were primarily associated with genetic variation acting in cis to modify response elements for lineage determining and signal dependent transcription factors. Collectively, these findings reveal cell intrinsic and environmental effects of natural genetic variation on gene expression, demonstrate the use of enhancers as detectors of trans effects of genetic variation, and provide a new resource for understanding the impact of genetic variation on gene expression in Kupffer cells.

genomics↗

bioRxiv2021

Seasonal variations of 137Cs concentration in freshwater charr through uptake and metabolism in 1-2 years after the Fukushima accident

Understanding the factors influencing 137Cs concentrations in freshwater salmonids is crucial for reviving inland fisheries in polluted regions. We studied seasonal variations of 137Cs concentration in charr (Salvelinus leucomaenis) through uptake and metabolism in forested headwaters at Fukushima and Gunma sites. Charr consumed both terrestrial and aquatic animals, and terrestrial prey was predated more in summer at both sites. The 137Cs concentrations in litter, which is a dominant basal food resource of both forest and stream ecosystems, differed between forest and stream due to 137Cs leaching effect on litter submerged in streams. The concentration difference in both litter and prey was greater at Fukushima site than at Gunma site. The estimated prey 137Cs concentration at Fukushima site peaked in summer when terrestrial preys are most available, whereas it remained relatively constant at Gunma site because of the small difference of 137Cs concentrations in between terrestrial and aquatic preys. The specific metabolic rate of charr was commonly changed with stream water temperature, greatest in summer and lowest in winter at both sites. Because both prey 137Cs concentrations and specific metabolic rates peaked in summer, the combination of uptake and metabolism at Fukushima site largely negated seasonal 137Cs fluctuations in charr, whereas specific metabolic rate fluctuations could be the major determinant of charr 137Cs concentrations at Gunma site. Our results suggested that 137Cs concentrations in prey items, whose seasonality are varied due to initial 137Cs fallout volume, were expected to be an important determinant for 137Cs concentrations in charr.

ecology↗

bioRxiv2020

Catalytic Promiscuity of Rice 2-Oxoglutarate/Fe(II)-Dependent Dioxygenases Supports Xenobiotic Metabolism

The rice 2-oxoglutarate/Fe(II)-dependent dioxygenase HIS1 mediates the catalytic inactivation of five distinct {beta}-triketone herbicides (bTHs). During a search for potential inhibitors of HIS1, we found that it mediates the hydroxylation of trinexapac-ethyl (TE) in the presence of Fe2+ and 2-oxoglutarate. TE is a plant growth regulator that blocks gibberellin biosynthesis, and we observed that its addition to culture medium induced growth retardation of rice seedlings in a concentration-dependent manner. Similar treatment with hydroxylated TE revealed that hydroxylation greatly attenuated the inhibitory effect of TE on plant growth. Forced expression of HIS1 in a rice his1 mutant also reduced its sensitivity to TE compared with that of the nontransformant. These results indicated that HIS1 metabolizes TE and thereby markedly reduces its ability to slow plant growth. Furthermore, testing of five HIS1-related proteins (HSLs) of rice revealed that OsHSL2 and OsHSL4 also metabolize TE in vitro. HSLs from wheat and barley also showed such activity. In contrast, OsHSL1, which shares the highest amino acid sequence identity with HIS1 and metabolizes the bTH tefuryltrione, did not manifest TE-metabolizing activity. Site-directed mutagenesis of OsHSL1 informed by structural models showed that substitution of three amino acids with the corresponding residues of HIS1 conferred TE-metabolizing activity similar to that of HIS1. Our results thus reveal a catalytic promiscuity of HIS1 and its related enzymes that supports xenobiotic metabolism in plants. One-sentence summaryThe rice 2-oxoglutarate/Fe(II)-dependent dioxygenase HIS1 and related enzymes show broad substrate specificity and mediate metabolism of the growth regulator trinexapac-ethyl as well as of herbicides.

plant biology↗

bioRxiv2020

Unique habitat and macroinvertebrate assemblage structures in spring-fed streams: a comparison among lowland tributaries and mainstreams in northern Japan

The stable flow and temperature regimes of spring-fed streams are distinct from the dynamic regimes of other streams. We investigated differences in habitat and macroinvertebrate assemblages among three stream types (spring-fed tributary, non-spring-fed tributary and mainstream) in a clastic lowland of northern Japan. Current velocity was the slowest in the spring-fed reach, where the percent of fine sediment deposition was also 3.8-11.4 times higher than in the other stream types. The standing stock of detritus was also greater in the spring-fed reach. These results suggest that the stable flow regime in the spring-fed stream leads to the accumulation of fine sediment and detritus on the streambed. Oligochaeta and chironomids, which are burrower-gatherers, were remarkably abundant in the spring-fed reach. Total macroinvertebrate abundance was 3.8-12.2 times greater in the spring-fed reach than in the other stream types. Sprawler-grazer ephemeropterans were the most abundant in the mainstream reaches, likely due to higher primary productivity. Allomyia sp, which depend on cool spring-fed habitats, were found only in the spring-fed reach. The indicator species analysis also indicated multiple taxa of detritivores and Allomyia sp. for the spring-fed tributary. The macroinvertebrate assemblage in the spring-fed reach was characterized by numerous burrowers, collector-gatherers, and crenobiont taxa, highlighting the uniqueness and its contribution to enhance beta diversity in river networks.

ecology↗

bioRxiv2020

Spring-fed streams as flow refugia: Changes in fish assemblages after a rainfall event

Understanding the migratory community dynamics of river networks is important for maintaining lotic system integrity. River animals migrate to their preferred habitats in spatiotemporally heterogeneous river environments. Spring-fed habitats are uniquely characterized by stable temperature and flow regimes, which create suitable spawning habitats for the chum salmon Oncorhynchus keta. O. keta exhibits "run up" to its birthplace for spawning, especially during floods. Because the eggs deposited by this anadromous fish are nutritious and actively consumed by freshwater animals, the location and timing of O. keta spawning events affect the spatiotemporal accumulation of mobile consumers. In this study, we examined changes in temporal population density in spawning O. keta and a mobile consumer (juvenile O. masou masou) in a lowland, spring-fed tributary in northern Japan during a 48.5-mm autumn rainfall event. In both species, population density increased, and then decreased, after the rainfall event. In O. keta, these changes were closely associated with rainfall intensity, whereas in O. masou masou the peak was delayed until 3 days after the rainfall event. A comparison of the gut contents of O. masou masou sampled from a spring-fed tributary and an adjacent non-spring-fed tributary indicated greater consumption of O. keta eggs in the spring-fed tributary. These results suggested that preferential migration of O. keta into spring-fed tributaries for spawning induces subsequent accumulation of juvenile O. masou masou, in turn increasing O. keta egg consumption. These findings improve our understanding of community dynamics during floods in a heterogeneous river network environment.

ecology↗

bioRxiv2019

Seasonal and annual fluctuations of deer populations estimated by a Bayesian state-space model

Deer overabundance is a contributing factor in the degradation of plant communities and ecosystems worldwide. The management and conservation of the deer-affected ecosystems requires us to urgently grasp deer population trends and to identify the factors that affect them. In this study, we developed a Bayesian state-space model to estimate the population dynamics of sika deer (Cervus nippon) in a cool-temperate forest in Japan, where wolves (Canis lupus hodophilax) are extinct. The model was based on field data collected from block count surveys, road count surveys by vehicles, mortality surveys during the winter, and nuisance control for 12 years (2007-2018). We clarified the seasonal and annual fluctuation of the deer population. We found two peaks of deer abundance (2007 and 2010) over 12 years. In 2011 the estimated deer abundance decreased drastically and has remained at a low level then. The deer population increased from spring to autumn and decreased from autumn to winter in most years. The seasonal fluctuation we detected could reflect the seasonal migration pattern of deer and the population recruitment through fawn births in early summer. In our model, snowfall accumulation, which can be a lethal factor for deer, may have slightly affected their mortality during the winter. Although we could not detect a direct effect of snow on population dynamics, snowfall decrease due to global warming may decelerate the winter migration of deer; subsequently, deer staying on-site may intensively forage evergreen perennial plants during the winter season. The nuisance control affected population dynamics. Even in wildlife protection areas and national parks where hunting is regulated, nuisance control could be effective in buffering the effect of deer browsing on forest ecosystems.

ecology↗

bioRxiv2019

Morphological differences between phyllosoma larvae from the midwestern and eastern Pacific populations of the pronghorn spiny lobster Panulirus penicillatus

The pronghorn spiny lobster Panulirus penicillatus is known to have the widest distribution among palinurid lobster species, occurring in tropical and sub-tropical areas of the Indo-Pacific Ocean. In the Pacific Ocean, mitochondrial DNA analyses have revealed that the western-central and eastern populations are genetically isolated. We performed morphological investigations on mid- to late-stage phyllosoma larvae collected in these two areas. The larvae of the western-central population had a significantly narrower cephalic shield, shorter abdomen, and longer eyestalk than those of the eastern population. Additionally, for larvae larger than about 25-mm body length, the widest position of the cephalic shield in the western-central population was located closer to the middle of the median line of the cephalic shield than that in the eastern population. The ratio of width to length of cephalic shield and the ratio of cephalic shield width to thorax width are key traits for distinguishing between the larvae of the two populations.

ecology↗