Biology subjects

Fujii, Y.

Publications and source records attributed to Fujii, Y..

13 recordsLinked to original sources

bioRxiv2026

Secretory ferritins mediate iron delivery during magnetite tooth formation in chitons

Iron is essential to most organisms, yet unbound iron is toxic, necessitating tight regulation of its storage and transport. Chitons concentrate extraordinary amounts of iron in radular tissue to form magnetite-mineralized teeth, but how iron is supplied to developing teeth remains unclear. Here, synchrotron radiation X-ray fluorescence mapping resolved the spatiotemporal redistribution of iron from the radular epithelium toward developing teeth. Integrated transcriptomic and proteomic analyses identified secretory ferritin subunits in radular tissue whose genes were highly expressed in the midgut gland and whose proteins were also present in the hemolymph. In vivo fluorescence tracking showed that circulating ferritin was selectively taken up by the radular epithelium, and following injection of Ag-loaded hemolymph ferritin, Ag was detected in developing teeth. Together, these findings support a model in which secretory ferritins produced in the midgut gland transport iron through the hemolymph to the radula, enabling the pronounced iron accumulation required for tooth mineralization.

molecular biology↗

bioRxiv2025

From model to field: predictive design of microbial communities for resilient crop performance

Synthetic microbial communities (SynComs) represent a promising approach to enhance crop growth and stress resilience through microbiome engineering. However, the systematic design and field validation of SynComs remain limited. Here, we present a predictive framework for SynCom optimization, integrating plant phenotyping, microbial genomics, and machine learning. Using tomato as a model, we tested over 800 SynCom-temperature combinations consisting of root endophytic bacteria and rhizosphere metabolites. An Elastic Net regression model trained on plant biomass data accurately predicted the performance of unseen SynComs, with prediction accuracy plateauing at [~]5% (301/6144) of all possible SynCom-temperature combinations. Incorporating genomic features significantly improved model performance, whereas microbiome compositional data alone were not informative. We applied the model to design novel SynComs, which were tested in both laboratory and field conditions using a commercial tomato cultivar. The model-informed SynCom enhanced plant growth in field trials and improved heat stress tolerance under controlled laboratory conditions. Multi-omics analyses and feature importance metrics identified specific microbial taxa, including Sphingobium sp., whose enrichment was linked to host plant metabolite (e.g., tomatine) and stress-responsive gene expression. Our results demonstrate a scalable strategy for the predictive design of beneficial microbiomes to improve resilient crop performance under real-world conditions.

systems biology↗

bioRxiv2025

Mycn Reactivates the Cell Cycle in Adult Cardiomyocytes and Promotes Cardioprotection in Myocardial Infarction

BackgroundAdult mammalian cardiomyocytes are terminally differentiated and possess minimal capacity for cell cycle re-entry. However, recent studies have shown that a rare population of cycling cardiomyocytes may confer cardioprotective effects following myocardial infarction (MI). The Myc family--Myc, Mycl, and Mycn--plays central roles in regulating cell cycle progression and cellular plasticity. This raises the possibility that specific Myc isoforms could reactivate the cardiomyocyte cell cycle and promote cardioprotective responses in the ischemic heart. This study aimed to systematically evaluate the effects of Myc, Mycl, and Mycn on cardiomyocyte cell cycle activation and cardiac outcomes following MI. MethodsCardiomyocyte-specific overexpression of Myc, Mycl, or Mycn was achieved in adult mice via adeno-associated virus 9 vectors driven by the cardiac troponin T promoter. Cardiomyocyte cell cycle activity, structural remodeling, and functional outcomes were assessed using RNA sequencing, immunohistochemistry, and transthoracic echocardiography. Cardioprotective effects were evaluated in MI model mice. ResultsWhile all three Myc family members activated cell cycle-related gene expression to varying degrees, Mycn elicited the most robust response. Mycn overexpression significantly enhanced cardiomyocyte cell cycle re-entry, as demonstrated by increased 5-bromo-2-deoxyuridine incorporation and phosphorylation of histone H3. Mycn also induced hypertrophic growth, reflected by increased cardiomyocyte size and heart mass. Transcriptomic analyses revealed that Mycn uniquely upregulated genes associated with extracellular matrix remodeling and paracrine signaling, typically enriched in neonatal cardiomyocytes and previously linked to cardioprotection. Functionally, Mycn expression preserved cardiac contractility after MI, reduced infarct size, and increased capillary density in peri-infarct regions. ConclusionsThese findings identify Mycn as a functionally distinct member of the Myc family in the adult heart, capable of reactivating the cardiomyocyte cell cycle and promoting cardiac protection after ischemic injury. The cardioprotective effects appear to be mediated, in part, by the induction of a neonatal-like gene expression program supporting a stress-adaptive cardiac microenvironment.

molecular biology↗

bioRxiv2025

Astringent flavanol fires the locus-noradrenergic system, regulating neurobehavior and autonomic nerves

Astringent flavanols (FLs) have shown enhanced cognitive function in a large intervention trial, but their mechanism remains unclear due to poor bioavailability. An oral dose of FLs increased spontaneous locomotion and memory, with activation of the sympathetic-adrenergic-medullary (SAM) and hypothalamic-pituitary-adrenal (HPA) axis, as shown by increased urinary catecholamine concentrations and corticotropin-releasing hormone (CRH) mRNA expression in the paraventricular nucleus (PVN) of mice. MS imaging showed high intensity of noradrenaline (NA) in the locus coeruleus (LC), which plays a key role in learning and memory, the hypothalamus lateral preoptic area, which affects sleep and arousal, and the brainstem as the origin of the sympathetic nervous system, immediately after FLs administration. Subsequent in situ hybridization (ISH) analysis showed that these NAs originated from LC. Astringent compounds like FLs influence brain function and physiological changes. Furthermore, the present series of results presents novel mechanisms by which food sensory properties maintain homeostasis. Highlights- A oral dose of astringent flavanols (FLs) immediately fires locus coeruleus-noradrenaline axis - FLs enhance spontaneous locomotion and short-term memory in mice - SAM and HPA axis are also activated by an oral dose of FLs - FLs astringency affects the brain and body, contributing to homeostasis.

synthetic biology↗

bioRxiv2025

Evaluation of anti-noroviral compounds on human norovirus replication using 2D monolayers of human intestinal organoids

We evaluated the anti-noroviral effects of compounds including molnupiravir, on human norovirus (HuNoV) replication using 2D monolayers of human intestinal organoids (HIOs), which have been widely used in HuNoV infection studies. We found that these compounds exhibited lower antiviral activity in 2D HIO monolayers compared with that in apical-out 3D HIOs, a recently developed culture system for HuNoV. This suggests that the anti-noroviral efficacy of these compounds may vary depending on the assay system used.

microbiology↗

bioRxiv2024

Mapping single-cell rheology of ascidian embryos in the cleavage stages using AFM

During early embryo development, cell division is highly organized and synchronized. Understanding the mechanical properties of embryonic cells as a material is crucial for elucidating the physical mechanism underlying embryogenesis. Previous atomic force microscopy (AFM) studies on developing embryos revealed that single cells of ascidian embryos in the cleavage stage stiffened and softened during cell division. However, how embryonic cells, as a compliant material, exhibit viscoelastic properties during the cell cycle remains poorly characterized. In this study, we investigated the rheological properties of embryonic cells in the animal hemisphere in the cleavage stages using stress-relaxation AFM and approach-retraction force curve AFM techniques. The AFM measurements revealed that developing single cells followed a power-law rheology observed in single-cell rheology in vitro. The embryonic cells increased the modulus (stiffness) and decreased the fluidity (the power-law exponent) towards cell division. We found three rheological states in developing embryos during the cell cycle. The correlation between the cell modulus and the fluidity during the cell cycle was collapsed onto a master curve with a negative correlation, indicating that embryonic cells tightly interacting with the neighboring cells conserved the universality of rheological behavior observed in single cells in vitro. SIGNIFICANCEUnderstanding the rheological properties of embryonic cells is crucial to elucidate the origin and mechanism of the functional and morphological changes in cells during embryogenesis. AFM-based microrheology revealed that single cells of ascidian embryos in the animal hemisphere in the cleavage stages followed a single power-law rheology, which has no characteristic time scale. Furthermore, the rheological parameters, such as cell stiffness and fluidity, were collapsed onto a master curve with a negative correlation during the cell cycle. These rheological behaviors are similar to those observed in single cells in vitro, indicating that the embryonic cells tightly interacting with each other conserved the intrinsic rheological behaviors of isolated single cells.

cell biology↗

bioRxiv2024

Single-nucleus transcriptional and chromatin accessibility analyses of maturing mouse Achilles tendon uncover the molecular landscape of tendon stem/progenitor cells

Tendons and ligaments are crucial connective tissues linking bones and muscles, yet achieving full functional recovery after injury remains challenging. We investigated the characteristics of tendon stem/progenitor cells (TSPCs) by focusing on the declining tendon repair capacity with growth. Using single-cell RNA sequencing on Achilles tendon cells from 2-and 6-week-old mice, we identified Cd55 and Cd248 as novel surface antigen markers for TSPCs. Combining single-cell RNA sequencing with single-nucleus RNA and ATAC sequencing analyses revealed that Cd55 and Cd248 positive fractions in tendon tissue represent TSPCs, as confirmed by their expression of established TSPC markers, with this population decreasing at 6 weeks. We also identified candidate upstream transcription factors regulating these fractions. Functional analyses of isolated CD55/CD248 positive cells demonstrated high clonogenic potential and tendon differentiation capacity, forming functional tendon-like tissue in vitro. This study establishes CD55 and CD248 as novel TSPC surface antigens, potentially advancing tendon regenerative medicine and contributing to the development of new treatment strategies for tendon and ligament injuries.

developmental biology↗

bioRxiv2024

Dual expansion routes likely underlie the present-day population structure in a Parnassius butterfly across the Japanese Archipelago

The Japanese Archipelago, comprising a series of isolated yet interconnected islands, had been geographically separated from the Eurasian continent. The linear topography presents a unique biogeographic context for dispersing organisms from the continent. In this study, we utilized mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) variation to elucidate the dispersal history of the Japanese clouded butterfly Parnassius glacialis across the Japanese Archipelago, including North Island (Hokkaido), Main Island (Honshu) and Shikoku Island. Our analysis of mtDNA (COI, COII) at 1192 base pairs (bps) revealed 49 haplotypes and identified three distinct haplotype groups in the network. These groups correspond geographically to East Japan, West Japan, and Chugoku-Shikoku. The Chugoku-Shikoku group is the most ancient lineage. Interestingly, the Chugoku-Shikoku lineage showed a closer network connection to the East Japan lineage than the geographically proximate West Japan lineage. Divergence time estimates suggest that the Chugoku-Shikoku lineage diverged from the continental P. glacialis approximately 3.05 million years ago (MYA). Subsequently, from the Chugoku-Shikoku lineage, the East Japan and West Japan lineages diverged around 1.05 MYA, with the subsequent divergence between the East and West Japan lineages occurring at approximately 0.62 MYA. Based on the 3067 SNP genotypes, population structure analysis revealed five distinct genetic structures within the Japanese Archipelago, indicating geographical differentiation. From the analyses by mtDNA and SNP variations, four primary genetic barriers were identified: between Hokkaido and Honshu, between East and Central Japan, within the Kansai region, and within the Chugoku region. The former three lines corresponded to the Blakiston Line, the Itoigawa-Shizuoka Tectonic Line, and Lake Biwa, respectively. These findings suggest that P. glacialis diverged from the continental P. glacialis and expanded its range across the Japanese Archipelago via the North and South routes, establishing its current distribution.

molecular biology↗

bioRxiv2023

Mechanistic modeling of amyloid oligomer and protofibril formation

Early phase of amyloid formation, where prefibrillar aggregates such as oligomers and protofibrils are often observed, is crucial for elucidating pathogenesis. However, since oligomers and protofibrils form transiently and heterogeneously, the detailed mechanisms of their formation remain unclear. Here, we have investigated the early aggregation process of bovine and human insulin by static and dynamic light scattering in combination with thioflavin T (ThT) fluorescence and Fourier transform infrared (FTIR) spectroscopy. The time dependence of light scattering has revealed that oligomers and protofibrils form in bovine insulin, in contrast to no significant aggregation in human insulin. By focusing on bovine insulin for kinetic analysis, it has been revealed that the protofibril formation process was divided into two steps with reference to fractal dimension. When modeled the experimental data of static and dynamic light scattering based on the Smoluchowski aggregation kinetics with fractal aggregation and end-to-end association, we found the initial formation of spherical oligomers and their subsequent uniaxial docking. Furthermore, the analysis of temperature and salt concentration dependence revealed that the end-to-end association is the rate-limiting step, where structure organization occurred with dehydration. The established model for protofibril formation where oligomers are incorporated as a precursor provides insight into the molecular mechanism how protein molecules assemble during the early stage of amyloid formation. SignificanceAmyloid oligomers and protofibrils have attracted attention as critical causes of neurodegenerative diseases; however, detailed formation processes of these aggregates have been poorly understood. In this study, we established a mechanistic model of oligomer and protofibril formation of bovine insulin based on Smoluchowski aggregation kinetics in terms of static and dynamic light scattering. It has been demonstrated that early aggregation proceeds by initial fractal-like aggregation to form oligomers, and subsequent their end-to-end docking to form protofibrils. The latter step is a rate-limiting step, where structural organization occurs with dehydration. The established model is expected to broadly applicable to a variety of proteins, and thus will provides valuable insights for accelerating therapeutic development and anti-neurodegenerative drug design.

biophysics↗

bioRxiv2022

EPI-589, a redox-active neuroprotectant, potently protects cultured cells from oxidative stress and alleviates symptomatic and pathological progression of motor neuron disease in the wobbler mouse

Oxidative stress is believed to play a significant role in the pathophysiology of amyotrophic lateral sclerosis (ALS), the most common form of motor neuron disease. The present study aims to firstly investigate the antioxidant activities of EPI-589, a small-molecule quinone derivative, under cell-free or cell culture conditions, and explore the in vivo efficacy of EPI-589 in the wobbler mouse model of human motor neuron disease. The reduced form of EPI-589 showed hydroxyl radical scavenging activities, whereas the oxidized form i.e. EPI-589 did not. In cellular models utilizing ALS patient-derived fibroblasts carrying mutations in the fused in sarcoma (FUS) gene or superoxide dismutase 1 (SOD1) gene, EPI-589 potently protected cells from oxidative stress induced by buthionine sulfoximine and ferric citrate. Protective effect of EPI-589 was also observed in culture of mouse immortalized striatal STHdHQ7/Q7 cells with cystine deprivation. In wobbler mice, oral administration of dietary EPI-589 provided long-lasting amelioration of both of deterioration of the rotarod walking performance and progression of forelimb deformity in wobbler mice throughout the treatment. In separate studies, we found that EPI-589 significantly suppressed changes of pathophysiological markers such as plasma phosphorylated neurofilament heavy chain, urinary 8-hydroxy-2-deoxyguanosine, and cervical N-acetylaspartate in untreated wobbler mice. Thus, the present study firstly demonstrates that EPI-589 is a highly potent, redox-active neuroprotectant and robustly delays the symptomatic and pathophysiological progression of motor neuron disease in the wobbler mouse, and these findings strongly encourage further exploration of the therapeutic potential of EPI-589 for the treatment of ALS.

pharmacology and toxicology↗

bioRxiv2021

Identification of general acid catalyst for the ATPase activity of Lynch syndrome-related MutL homologs

Mutations of mismatch repair MutL homologs are causative of a hereditary cancer, Lynch syndrome. Investigation of MutL facilitates genetic diagnoses essential for cancer risk managements and therapies. We characterized MutL homologs from human and a hyperthermophile, Aquifex aeolicus, (aqMutL) to reveal the catalytic mechanism for the ATPase activity. Although existence of a general acid catalyst had not been conceived in the mechanism, analysis of the pH dependence of the aqMutL ATPase activity revealed that the reaction is accelerated by general acid-base catalysis. Analyses of mutant aqMutLs showed that Lys79 is the general acid, and the corresponding residues were confirmed to be critical for activities of human homologs, on the basis of which a catalytic mechanism for MutL ATPase is proposed. These and other results described here would contribute to evaluating the pathogenicity of Lynch syndrome-associated missense mutations.

biochemistry↗

bioRxiv2021

Dasabuvir inhibits human norovirus infection in human intestinal enteroids

Human noroviruses (HuNoVs) are acute viral gastroenteritis pathogens that affect all age groups, yet no approved vaccines and drugs to treat HuNoV infection are available. In this study, with a human intestinal enteroid (HIE) culture system where HuNoVs are able to replicate reproducibly, we screened an antiviral compound library to identify compound(s) showing anti-HuNoV activity. Dasabuvir, which has been developed as an anti-hepatitis C virus agent, was found to inhibit HuNoV infection in HIEs at micromolar concentrations. Dasabuvir also inhibited severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human A rotavirus (RVA) infection in HIEs. To our knowledge, this is the first study to screen an antiviral compound library for HuNoV using HIEs and we successfully identified dasabuvir as a novel anti-HuNoV inhibitor that warrants further investigation.

microbiology↗

bioRxiv2019

Chloroplast cold-avoidance response in Marchantia polymorpha occurs independently of changes in endogenous phototropin expression

When exposed to fluctuating light intensity, chloroplasts move towards weak light (accumulation response), and away from strong light (avoidance response). In addition, cold treatment (5{degrees}C) induces the avoidance response even under weak light conditions (cold-avoidance response). These three responses are mediated by the phototropin (phot), which is a blue-light photoreceptor and has also been found to act as a thermosensory protein that perceives temperature variation. Our previous report indicated that cold-induced changes in phot biochemical activity initiate the cold-avoidance response. In this study, we further explored the induction mechanism of the cold-avoidance response in the liverwort Marchantia polymorpha and examined the relationship between changes in the amount of phot and the induction of the cold-avoidance response. The switch between the accumulation and avoidance responses occurs at a so-called transitional light intensity. Our physiological experiments revealed that a cold-mediated decrease in the transitional light intensity leads to the induction of the cold-avoidance response. While artificial overexpression of phot decreased the transitional light intensity as much as cold treatment did, the amount of endogenous phot remained unchanged by cold treatment in wild-type M. polymorpha. Taken together, these findings show that the cold-avoidance response is initiated by a cold-mediated reduction of the transitional light intensity, independent of the amount of endogenous phot. This study provides a clue to understand the mechanism underlying the switch in direction of chloroplast relocation in response to light and temperature.

plant biology↗