Biology subjects

Nakamura, F.

Publications and source records attributed to Nakamura, F..

15 recordsLinked to original sources

bioRxiv2026

Inflammatory restraint and membrane lipid integrity protect hematopoietic stem cells under stress

Life-long production of blood requires the preservation of hematopoietic stem cell (HSCs) regenerative capacity during inflammation. The cytokine, Thrombopoietin (THPO), is essential for HSC maintenance yet its role during inflammatory stress remains incompletely understood. Long-term repopulating potential was rapidly depleted in THPO-deficient HSCs upon poly(I:C) administration through inflammatory pyroptosis. Transcriptomic and chromatin accessibility analyses revealed constitutive interferon (IFN) pathway activation in THPO-deficient HSCs, characterized by enhanced STAT1 signaling, increased accessibility of STAT and IRF motifs, and elevated expression of IFN-stimulated genes. Lipidomic profiling further identified selective shifts in sphingomyelin (SM) species and enrichment of features associated with increased bilayer rigidity. THPO-deficient HSCs displayed elevated membrane SM incorporation, impaired membrane fluidity and altered membrane ultrastructure. Genetic ablation of Stat1 normalized membrane lipid abnormalities and reduced pyroptotic activation and restored HSC survival and regenerative function under inflammatory stress. Together, these findings identify a STAT1 and SM metabolism as critical THPO downstream to protect HSCs from inflammatory pyroptosis. Our results reveal membrane lipid homeostasis as a fundamental mechanism through which cytokine signaling safeguards HSC function during stress.

cell biology↗

bioRxiv2025

The nucleocytoplasmic translocation of HINT1 regulates the maturation of cell density

Cell contact inhibition progresses through three stages: (i) increasing cell density leads to reduced movement while mitosis continues; (ii) a rapid shift to epithelial morphology; and (iii) ongoing division with decreased cell size. This transition involves reorganizing the actin cytoskeleton from stress fibers to a cortical network, stabilizing cell shape, and strengthening cell-cell connections. However, the signaling pathways regulating the final stage remain unclear. We identified histidine triad nucleotide-binding protein 1 (HINT1), also known as protein kinase C inhibitor 1 (PKCI-1), as essential for monolayer maturation. At low density, HINT1 is located in the nucleus, binding to open chromatin. As density increases, exportin-1 relocates HINT1 to the cytoplasm, where it inhibits PKC and remodels the actin cytoskeleton. While monolayer formation can occur without HINT1, its presence is necessary for fully confining cells and achieving a mature monolayer. Additionally, MARCKS phosphorylation decreases in high-density cells, and loss of HINT1 leads to increased cell area, similar to hypertrophic conditions in patients with low HINT1 levels. Summary blurbHistidine triad nucleotide-binding protein 1 shuttles between the nucleus and cytoplasm based on cell density, regulating gene expression in the nucleus and inhibiting protein kinase C in the cytoplasm to remodel actin.

cell biology↗

bioRxiv2023

Hot spots in a cold river synchronize temporarily separated salmon runs in their offsprings development

The identification of thermal heterogeneity in the environment and its inclusion in adaptive strategies are key to habitat management of cold-water fish, including salmonid species. This study tested the hypothesis that upwelling of groundwater (GW) from a tributary catchment through a relatively deep aquifer (tributary GW) affects salmon redds selection in an urbanized gravel-bed river, and that the spawning preference of such areas depends on the seasonal context. The field study was conducted between 2001 and 2015 in an approximately 6-km long segment of the Toyohira River, Northern Japan. Chum salmon redds distribution data over 15 years (2001-2015) were combined with spatial distribution data of hyporheic water affected by tributary GW in the riverbed to examine seasonally variable redds site selection in relation to the presence of unique GW. Furthermore, models that predicted the hyporheic water thermal regime were coupled with redds count data to estimate the approximate timing of fry emergence from the riverbed. The redds site selection was seasonally variable, with a higher dependence on tributary-GW-affected areas with a decrease in water temperature. The time until fry emergence from spawning was shortened when the tributary-GW area was chosen during the cold winter. Overall, the present study identified hotspots for salmon spawning redds in winter with a disproportionately high level of site selection because of their warmer temperature compared to surface river water in winter. Thermally diverse spawning habitats allow the diversification of spawner strains in synchronized descents to the sea. Signs of tributary-GW pollution was suggested, and thus the conservation of the groundwater pathway and its sources, followed by improvements in quality, can be beneficial to the Chum salmon populations in the Toyohira River.

ecology↗

bioRxiv2023

Cryptic connectivity between hyporheic and riparian zones via winged aquatic insects revealed by DNA barcoding

How subsurface hyporheic zone (HZ) of rivers is connected to riparian zones remains largely unknown. We collected benthic macroinvertebrates and adult aquatic insects for six years, including those at 30-cm depth in the HZ to identify insect taxa having a high level of habitat affinity for HZ (HZ taxa). Adults of HZ taxa were identified with the aid of CO1 gene barcoding, and the relative abundance of HZ taxa in the riparian zone was quantified. In addition to the previously known stonefly Alloperla ishikariana, three species of stonefly Leuctridae and one caddisfly species of Philopotamidae were identified as HZ taxa. At the annual scale, HZ taxa accounted for approximately 38% of the total aquatic insects in the family of stoneflies (Plecoptera), caddisflies (Trichoptera), and mayflies (Ephemeroptera) in abundance and 26% of biomass, with their seasonal peaks in early spring and mid-summer (60% in abundance and 47% in biomass). Few individuals of HZ taxa were found in benthic samples (<0.1%), and hyporheic samples quantified more but erroneously estimated relative abundances of adult HZ taxa, with Leuctridae and Philopotamidae being substantially underrepresented relative to their adult abundance. Cryptic biological connectivity between subsurface and riparian zones via winged HZ-taxa adults is substantial. DNA-based species identification combined with community surveys of adult HZ-taxa complementarily used with benthic data can substantially improve the effectiveness of biomonitoring programs and outcomes of habitat conservation based on more complete picture of ecosystem health.

ecology↗

bioRxiv2023

Recruitment status and host-fish-limitation threats to endangered freshwater pearl mussel (Margaritifera laevis) in eastern Hokkaido, northern Japan

Recruitment failure is a major threat to freshwater mussel (Order Unionoida) populations worldwide. Assessments of the recruitment status and determining the bottleneck factors of mussel recruitment are crucial for preventing future declines in mussel populations. In this study, we investigated the recruitment status (i.e., size structure and the proportion of juveniles within a population) of the endangered freshwater pearl mussel Margaritifera laevis in 22 rivers in eastern Hokkaido, northern Japan. We also quantified the density of the host fish Oncorhynchus masou masou and examined the relationship between the proportion of juveniles and host-fish density to assess host-limitation threats to M. laevis recruitment. Our assessments showed that 13 (59.1%) rivers had no signs of recent recruitment within 10 years, with a low mean proportion of juveniles (mean:0.02 [range:0.00-0.09] fraction), indicating that these populations are threatened by sustained recruitment failure. The proportion of juveniles was positively associated with host-fish density, suggesting that host-fish limitation could be a bottleneck factor for M. laevis recruitment. These results highlight the urgent need for prompt conservation measures, including the enhancement of host-fish availability, to sustain M. laevis populations in the study region.

ecology↗

bioRxiv2022

Long-term recoveries of forest ecosystem components after shallow landslides were asynchronized among slope positions

Landslides are a common disturbance in mountainous areas of the world. Transporting and accumulating landslide debris, i.e., disturbance legacies, such as coarse woody debris (CWD), vegetation patches, and surface soils, generate a heterogeneous environment along slopes (zones), which are suggested to affect forest recovery. However, the long-term changes in forest ecosystems after landslides remain unknown, particularly zone-dependent change patterns. We aimed to reveal the differences in the changes in live trees, understory vegetation, CWD, and soils among zones by surveying forests with landslide ages (years since the landslide) ranging from 3 to 74 years and reference stands. The increase in live tree aboveground biomass occurred at a faster rate at the lower part of the slopes where the disturbance legacies were rich and surface soils were stabilized due to the smaller slope angle. Chronological patterns of understory vegetation amounts were determined by the differences in disturbance legacy richness and the timing of subsequent canopy closure. The amounts and decay-class diversity of CWD were determined by the differences in legacy richness and mortality through stand development. These zone-dependent chronological changes influenced litter production and determined the recovery rates of surface soil carbon stocks and nitrogen contents. The increase in the dominance rates of forest herbaceous species was faster in the lower part of the slopes due to the faster surface soil development and canopy closure. Our results illustrate that long-term forest ecosystem succession and recovery after landslides occurs more rapidly at the lower parts than at the upper parts of slopes. HighlightsO_LIRich landslide legacies and low slope angles promoted vegetation and soil recovery C_LIO_LILegacy richness and timing of canopy closure determined changes in the understory C_LIO_LILandslide mortality and stand development mortality determined changes in dead wood C_LI

ecology↗

bioRxiv2022

Relationship between salmon egg subsidy and the distribution of an avian predator

As a spatial subsidy, which is the phenomenon of transferring resources from a donor system to a recipient system, anadromous salmonids contribute to the supply of marine-derived nutrients to freshwater and terrestrial systems. Live salmon and salmon carcasses and eggs are utilized by various organisms and affect their abundance and distribution. However, the evaluation of the effect of salmon subsidies on the abundance and distribution of terrestrial animals is biased towards predators or scavengers that utilize spawning adults and carcasses, and few studies have focused on the effect of salmon eggs as a subsidy. To avoid underestimating the function of salmon subsidies, the response to the availability of salmon eggs in various systems should be investigated. Here, we investigated the abundance and feeding behaviour of the brown dipper Cinclus pallasii, as salmon egg a consumer, based on the hypothesis that the availability of salmon eggs affects the diet composition and stream distribution of this small predator. In addition, to test whether changes in the abundance of brown dippers are determined by salmon spawning, their abundance was compared upstream and downstream of the dam. Brown dippers used salmon eggs during the spawning season (53.7% of diet composition), and their abundance increased as the number of spawning redds increased. In contrast, this pattern was not observed upstream of the dam. These results suggested that the abundance and stream distribution of brown dippers vary according to the variation in the spatiotemporal availability of salmon eggs.

ecology↗

bioRxiv2022

Inferring future changes in gene flow under climate change in riverscapes

Global climate change poses a significant threat to the habitat connectivity of cold-water-adapted organisms, leading to species extinctions. Because gene flow is itself a functional connectivity among wild populations, if gene flow is modeled by landscape variables, changes in population connectivity could be predicted. In this study, using a model-based riverscape genetics technique and a hydrological model to estimate water temperature, we inferred the determinants of and future changes in gene flow of the fluvial sculpin Cottus nozawae in the upstream section of the Sorachi River, Hokkaido, Japan. As a result of model selection, stream order, water temperature, slope, and distance were detected as landscape variables affecting the strength of gene flow in each stream section. In particular, the trend of greater gene flow in sections with higher stream order and lower temperature fluctuations or summer water temperatures was pronounced. The map from the model showed that gene flow is overall prevented in small tributaries in the southern area, where spring-fed environments are less prevalent. Estimating future changes in gene flow using future water temperature predictions, genetic connectivity was predicted to decrease dramatically until the end of the 21st century under IPCC representative concentration pathway scenario 8.5 (RCP8.5).

ecology↗

bioRxiv2022

The role of geology in creating stream climate-change refugia along climate gradients

Identifying climate-change refugia is a key adaptation strategy for reducing global warming impacts. Knowledge of the effects of underlying geology on thermal regime along climate gradients and the ecological responses to the geology-controlled thermal regime is essential to plan appropriate climate adaptation strategies. The dominance of volcanic rocks in the watershed is used as a landscape-scale surrogate for cold groundwater inputs to clarify the importance of underlying geology. Using statistical models, we explored the relationship between watershed geology and the mean summer water temperature of mountain streams along climate gradients in the Japanese archipelago. Summer water temperature was explained by the interaction between the watershed geology and climate in addition to independent effects. The cooling effect associated with volcanic rocks was more pronounced in streams with less summer precipitation or lower air temperatures. We also examined the function of volcanic streams as cold refugia under contemporary and future climatic conditions. Community composition analyses revealed that volcanic streams hosted distinct stream communities composed of more cold-water species compared with non-volcanic streams. Scenario analyses revealed a geology-related pattern of thermal habitat loss for cold-water species. Non-volcanic streams rapidly declined in thermally suitable habitats for lotic sculpins even under the lowest emission scenario (RCP 2.6). In contrast, most volcanic streams will be sustained below the thermal threshold, especially for low and mid-level emission scenarios (RCP 2.6, 4.5). However, the distinct stream community in volcanic streams and geology-dependent habitat loss for lotic sculpins was not uniform and was more pronounced in areas with less summer precipitation or lower air temperatures. Although further studies are needed to understand underlying mechanisms of the interplay of watershed geology and climate, findings highlight that watershed geology, climate variability, and their interaction should be considered simultaneously for effective management of climate-change refugia in mountain streams.

ecology↗

bioRxiv2021

Multiple stressors and recruitment failure of long-lived endangered freshwater mussels with a complex life cycle

O_LIMultiple stressors can interactively affect the population of organisms; however, the process by which they affect recruitment efficiency remains unclear for empirical populations. Recruitment efficiency can be regulated at multiple stages of life, particularly in organisms with complex life cycles. Understanding the interactive effects of multiple stressors on recruitment efficiency and determining the bottleneck life stages is imperative for species conservation. C_LIO_LIThe proportion of <20-year-old juveniles of the endangered freshwater pearl mussel Margaritifera togakushiensis, which has an obligate parasitic larval stage, was investigated in 24 rivers from eastern Hokkaido, northern Japan to reveal the influence of nutrients, fine sediment, and their combined effects on juvenile recruitment efficiency. The following indices for recruitment at adult, parasitic, and post-parasitic juvenile stages were obtained from 11 of these rivers: gravid female density, glochidia density (the number of glochidia infections per stream area), and juvenile survival rate. This study explored the bottleneck stages of recruitment efficiency and the interactive effects of the two stressors on these stages. C_LIO_LITwenty-four population status assessments determined that the proportion of juveniles ranged from 0.00 to 0.53, and juveniles were absent from four rivers. The results showed that the parasitic and post-parasitic juvenile stages were bottlenecks for recruitment efficiency. Juvenile survival rates had a more significant positive effect on recruitment efficiency in rivers with a high glochidia density. Juvenile survival rate was decreased by the synergistic interaction of nutrients and fine sediment, although factors limiting glochidia density were not found. C_LIO_LIThe nutrient concentration of rivers in the study region was well explained by the proportion of agricultural land cover and urban areas in the watersheds, but no relationship was detected between fine sediment abundance and land use. C_LIO_LIThis study suggests that nutrient management at a catchment scale can be effective for re-establishing the recruitment of M. togakushiensis, particularly in rivers with a high content of fine sediments. The results also emphasise the importance of considering both parasitic and post-parasitic juvenile stages of mussels to maximise the positive effects of stressor mitigation. C_LI

ecology↗

bioRxiv2021

A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded unexpected results and provided important insights for conservation.

ecology↗

bioRxiv2020

No evidence that androgen regulation of pulmonary TMPRSS2 explains sex-discordant COVID-19 outcomes

The sex discordance in COVID-19 outcomes has been widely recognized, with males generally faring worse than females and a potential link to sex steroids. A plausible mechanism is androgen-induced expression of TMPRSS2 and/or ACE2 in pulmonary tissues that may increase susceptibility or severity in males. This hypothesis is the subject of several clinical trials of anti-androgen therapies around the world. Here, we investigated the sex-associated TMPRSS2 and ACE2 expression in human and mouse lungs and interrogated the possibility of pharmacologic modification of their expression with anti-androgens. We found no evidence for increased TMPRSS2 expression in the lungs of males compared to females in humans or mice. Furthermore, in male mice, treatment with the androgen receptor antagonist enzalutamide did not decrease pulmonary TMPRSS2. On the other hand, ACE2 and AR expression was sexually dimorphic and higher in males than females. ACE2 was moderately suppressible with enzalutamide therapy. Our work suggests that sex differences in COVID-19 outcomes attributable to viral entry are independent of TMPRSS2. Modest changes in ACE2 could account for some of the sex discordance.

physiology↗

bioRxiv2020

Belowground changes to community structure alter methane-cycling dynamics in Amazonia

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with changes to ecosystem processes, including substantial increases in soil methane (CH4) emission. The drivers of this change in CH4 flux are not well understood. To address this knowledge gap, we measured soil CH4 flux, environmental conditions, and belowground microbial community attributes across a land use change gradient (old growth primary forest, cattle pasture, and secondary forest regrowth) in two Amazon Basin regions. Primary forest soils exhibited CH4 uptake at modest rates, while pasture soils exhibited CH4 emission at high but variable rates. Secondary forest soils exhibited low rates of CH4 uptake, suggesting that forest regrowth following pasture abandonment could reverse the CH4 sink-to-source trend. While few environmental variables were significantly associated with CH4 flux, we identified numerous microbial community attributes in the surface soil that explained substantial variation in CH4 flux with land use change. Among the strongest predictors were the relative abundance and diversity of methanogens, which both increased in pasture relative to forests. We further identified individual taxa that were associated with CH4 fluxes and which collectively explained ~50% of flux variance. These taxa included methanogens and methanotrophs, as well as taxa that may indirectly influence CH4 flux through acetate production, iron reduction, and nitrogen transformations. Each land type had a unique subset of taxa associated with CH4 fluxes, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, our results suggest that changes in CH4 flux from agricultural conversion could be driven by microbial responses to land use change in the surface soil, with both direct and indirect effects on CH4 cycling. This demonstrates the central role of microorganisms in mediating ecosystem responses to land use change in the Amazon Basin.

ecology↗

bioRxiv2020

Histone modification dynamics as revealed by a multicolor immunofluorescence-based single-cell analysis

Post-translational modifications on histones can be stable epigenetic marks and transient signals that can occur in response to internal and external stimuli. Levels of histone modifications fluctuate during the cell cycle and vary among different cell types. Here we describe a simple system to monitor the levels of multiple histone modifications in single cells by multicolor immunofluorescence using directly labeled modification-specific antibodies. We first analyzed histone H3 and H4 modifications during the cell cycle. Levels of active marks, such as acetylation and H3K4 methylation, were increased during the S phase, in association with chromatin duplication. By contrast, levels of some repressive modifications gradually increased during the G2 and the next G1 phases. We applied this method to validate the target modifications of various histone demethylases in cells using a transient overexpression system. We also screened chemical compounds in marine organism extracts that affect histone modifications and identified psammaplin A, which was previously reported to inhibit histone deacetylases. Thus, the method presented here is a powerful and convenient tool for analyzing the changes in histone modifications.

cell biology↗

bioRxiv2019

Intra-individual variability of sleep and nocturnal cardiac autonomic activity in elite female soccer players during an international tournament

PurposeThis study provides insights into the individual sleep patterns and nocturnal cardiac autonomic activity responses of elite female soccer players during an international tournament.\n\nMaterials and methodsTwenty elite female soccer players (aged 25.2{+/-}3.1 years) wore wrist actigraph units and heart rate (HR) monitors during night-sleep throughout 9 consecutive days (6 day-time training sessions [DT], 2 day-time matches [DM], and 1 evening-time match [EM]) of an international tournament. Training and match loads were monitored using the session-rating of perceived exertion (s-RPE) and wearable 18-Hz GPS (total distance covered [TD], training and match exposure time, and high-speed running [HSR]) to characterize training and match loads.\n\nResultsIndividually, s-RPE, TD, exposure time, and HSR during training sessions ranged from 20 to 680 arbitrary units (AU), 892 to 5176 m, 20 to 76 min, and 80 to 1140 m, respectively. During matches, s-RPE, TD, exposure time, and HSR ranged from 149 to 876 AU, 2236 to 11210 m, 20 to 98 min, and 629 to 3213 m, respectively. Individually, players slept less than recommended (<7 hours) on several days of the tournament, especially after EM (n=8; TST ranging between 6:00-6:54 h). Total sleep time coefficient of variation (CV) ranged between 3.1 and 18.7%. However, all players presented good sleep quality (i.e., sleep efficiency [≥]75%; individual range between: 75-98%) on each day of the tournament. Most of the players presented small fluctuations in nocturnal cardiac autonomic activity (individual nocturnal heart rate variability [HRV] ranged from 3.91-5.37 ms and HRV CV ranged from 2.8-9.0%), while two players presented higher HRV CV (11.5 and 11.7%; respectively).\n\nConclusionOverall, elite female soccer players seemed to be highly resilient to training and match schedules and loads during a 9 day international tournament.

physiology↗