Biology subjects

Arai, M.

Publications and source records attributed to Arai, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Analysis of Rare Coding Variation Identifies New Genetic Contributors to Schizophrenia

In this study, we present the largest rare coding variant association study of schizophrenia to date, with 87,959 schizophrenia cases and 150,587 controls. We identify 16 genes at exome-wide significance: SETD1A, ZMYM2, HERC1, RB1CC1, SCAF1, XPO7, SP4, FYN, PPP3CA, CUL1, HDAC9, JARID2, ATP9A, PTK2, STAG1, and SCN2A, and an additional 24 at a 5% false discovery rate. Cases carrying ultra-rare, damaging variants, primarily protein-truncating and deleterious missense mutations, show strong enrichment in constrained genes with consistent effects across ancestries. Half of the 40 identified genes overlap with those implicated in developmental delay, autism, or bipolar disorder, underscoring shared neurodevelopmental risk. All 40 genes identified are highly expressed in excitatory and inhibitory neurons, and their expression patterns span diverse developmental stages. Functionally, the identified genes implicate chromatin regulation, protein degradation, and synaptic function. Overall, our results advance understanding of the genetic architecture of schizophrenia, provide a foundation for modeling risk genes in cellular and animal systems, and offer a framework for future work toward biologically informed patient stratification.

genetics↗

bioRxiv2026

Chronic trazodone treatment consolidates sleep, improves memory, and reduces amyloid pathology in a mouse model of Alzheimer's disease

Sleep disturbance in Alzheimers disease (AD), particularly the reduction of slow wave sleep (SWS), has been proposed as a novel therapeutic target, with disease-modifying potential. Trazodone, an antidepressant with robust SWS-promoting properties, is currently the most prescribed sleep-promoting medication in the United States. Here, we demonstrate that chronic trazodone administration consolidates sleep in the APPNL-F knock-in mouse model of AD, increasing NREM sleep duration and slow wave power during the rest phase while promoting wake during the active phase. These sleep consolidating effects were accompanied by lower regional glial activation and amyloid burden, particularly in male mice. Most notably, hippocampal amyloid plaque burden was 45% lower in mice treated from 14 to 16 months of age than in vehicle-treated controls. Chronic trazodone treatment was also associated with better short-term and long-term recognition memory. Together, these findings support the potential of repurposing trazodone as a well-tolerated, disease-modifying therapeutic for AD, capable of enhancing sleep quality, improving cognition, and lowering AD-relevant neuropathology.

neuroscience↗

bioRxiv2026

Lid speculum as effective active and reference electrodes for electroretinography recording in normal rabbits

PurposeAlthough electroretinography (ERG) is vital for evaluating retinal function, conventional corneal electrodes slide or detach in animals. This study aimed to investigate the effectiveness of a novel approach to ERG recording using a metal eyelid speculum for both active and reference electrodes in conjunction with a skin electrode-based ERG device. MethodsWe tested a stainless-steel eyelid speculum as both active and reference electrodes with a skin-electrode ERG system (HE-2000vet) in six healthy Japanese White rabbits. Dark-adapted rod and maximal responses and light-adapted cone and 30 Hz flicker ERGs were recorded in three weekly sessions. ResultsReproducible waveforms with identifiable a- and b-waves were obtained in every eye; rod b-waves reached 50-90 {micro}V and cone b-waves 40-55 {micro}V. Intraclass correlation coefficients revealed substantial interocular agreement and moderate-to-substantial inter-session reproducibility for b-wave amplitude and implicit time, whereas a-wave metrics were less reliable owing to lower amplitudes. The advantages of speculum electrode over corneal electrodes are that it requires no fur shaving, maintains stable contact regardless of globe orientation, and allows real-time observation. ConclusionsThis study demonstrated that an eyelid-speculum electrode is a practical, non-invasive alternative for veterinary and experimental ERG recordings, producing signal quality sufficient for longitudinal and interocular analyses while avoiding cosmetic and technical drawbacks of conventional methods.

neuroscience↗

bioRxiv2025

Predator-driven local convergence fosters global microbial community divergence

Understanding the rules that govern microbial community assembly is essential for predicting ecosystem function. While microbial predators are key biotic agents that shape bacterial communities through predation, yet their ecological consequences have been studied mostly in isolated and in vitro systems1-3. In contrast, large-scale studies of microbial diversity have primarily emphasized abiotic factors as drivers of community assembly 4-7, while the role of microbial predators modulating global microbial divergence and convergence patterns remains largely neglected. Here, we show that bacterivorous protists (predators) exert dual, scale-dependent effects on microbial communities: promoting local convergence by suppressing dominant bacterial taxa, while generating global divergence through species-specific predation effects. By integrating global meta-analyses, controlled field experiments, and reconstructions of natural and synthetic communities, we find that predator identity and prey susceptibility jointly determine convergence outcomes. Communities dominated by predator-resistant taxa exhibit reduced convergence under predation pressure, revealing a predictable trait-based filtering mechanism. This framework reconciles previous contradictory findings3,8-11 and highlights predators as selective, context-dependent agents of microbial biogeography. Predator-driven convergence suggests new opportunities for microbiome engineering 12: targeted use of predators may steer microbial communities toward functional configurations that enhance soil health, disease suppression, carbon cycling, and ecosystem resilience 2,13,14.

ecology↗

bioRxiv2025

Generation of antigen-specific and functionally stable Treg cells from effector/memory T cells for cell therapy of immunological diseases

One strategy for antigen-specific immunosuppression is to convert antigen-specific conventional T cells (Tconvs) into Foxp3+ regulatory T cells (Tregs) that are as stably suppressive as naturally occurring Tregs (nTregs). To achieve the conversion in vitro for mice and humans, we induced high Foxp3 expression in antigen- and IL-2-stimulated Tconvs by CDK8/19 inhibition, and established Treg-specific epigenetic changes by depriving CD28 co-stimulation during in vitro Treg induction to specifically promote the expression of Treg signature genes, especially Foxp3. Repeating this process, with intermittent resting cultures containing IL-2 only, enabled in a short duration efficient conversion of naive as well as effector/memory CD4+ Tconvs, including Th1, Th2 and Th17 cells, into Foxp3+ Tregs, which were similar to nTregs in transcription and epigenetic modification. Induced Tregs (iTregs) thus generated were indeed functionally and phenotypically stable in vivo and effectively suppressed inflammatory bowel disease and graft-versus-host disease in mouse models. Adoptive cell therapy with such effector/memory Tconv-derived, functionally stable, iTregs would be able to achieve antigen- and disease-specific treatment of immunological diseases. One Sentence SummaryAntigen-specific and functionally stable Treg cells can be generated in vitro from effector/memory T cells for cell therapy of immunological diseases.

immunology↗

bioRxiv2025

Combinative protein expression of immediate early genesc-Fos, Arc, and Npas4 along aversive- and reward-related neural networks

AbstractExpression of immediate early genes (IEGs) is critical for memory formation and has been widely used to identify the neural substrate of memory traces, termed memory engram cells. Functions of IEGs have been known to be different depending on their types. However, there is limited knowledge about the extent to which different types of IEGs are selectively or concurrently involved in the formation of memory engram. To address this question, we investigated the combinative expression of c-Fos, Arc, and Npas4 proteins using immunohistochemistry following aversive and rewarding experiences across subregions in the prefrontal cortex (PFC), basolateral amygdala (BLA), hippocampal dentate gyrus (DG), and retrosplenial cortex (RSC). Using an automated cell detection algorithm, we found that expression patterns of c-Fos, Npas4, and Arc varied across different brain areas, with a higher increase of IEG expressing cells in the PFC and posterior BLA than in the DG. The combinative expression patterns, along with their learning-induced changes, also differed across brain areas; the co-expression of IEGs increased in the PFC and BLA following learning whereas the increase was less pronounced in the DG and RSC. Furthermore, we demonstrate that different area-to-area functional connectivity networks were extracted by different IEGs. These findings provide insights into how different IEGs and their combinations identify engram cells, which will contribute to a deeper understanding of the functional significance of IEG-tagged memory engram cells.

neuroscience↗

bioRxiv2025

Oral antigen exposure under co-stimulation blockade generates Treg cells to establish immune tolerance despite prior sensitization

Antigen-specific oral tolerance is effective in preventing harmful immune responses in antigen-non-sensitized animals but difficult to be induced in those already antigen-primed. Here, we show in mice that feeding of antigen-containing diet generates peripherally derived regulatory T (pTreg) cells that exhibit a tissue-adapted effector phenotype. The antigen feeding also enables the generated pTreg cells to acquire Treg-specific epigenomic changes in Treg signature genes including Foxp3, hence the stability of Treg-specific function. Cessation of antigen feeding, however, results in decline in oral tolerance with diminution of pTreg cells. Transcriptomic analysis has revealed that the induced pTreg cells predominantly express CD101. CD101+ Treg cells with a similar phenotype and epigenetic alterations can also be generated in vitro from antigen-primed naive CD4+ T cells by blockade of CD28-mediated co-stimulation during TGF-{beta}-dependent Treg induction. Furthermore, in vivo CD28 signal blockade by CTLA-4-immunoglobulin fusion protein (CTLA4-Ig) before antigen feeding can establish oral tolerance in the mice precedingly antigen-sensitized by a non-oral route. The blockade facilitates differentiation of antigen-specific conventional T cells into CD101+ pTreg cells. Thus, continuous oral antigen administration combined with CD28 co-stimulation blockade generates CD101+ antigen-specific functionally stable pTreg cells, which can establish long-term systemic antigen-specific immune tolerance even in antigen-pre-sensitized animals.

immunology↗

bioRxiv2025

The Effects of Acute Trazodone Administration on Sleep in Mice

Study ObjectivesTrazodone is an antidepressant with robust hypnotic effects, frequently prescribed off-label to treat insomnia. Trazodone has gained recent attention in the context of neurodegenerative diseases because sleep has been proposed as a novel target for disease-modifying therapeutics. Preclinical research in rodents examining the effects of trazodone on sleep is limited, so here we aimed to develop a translationally-focused protocol to study the sleep-promoting effects of trazodone in mice. MethodsWe investigated the effects of voluntary oral trazodone administration at doses of 0 mg/kg, 10 mg/kg, 40 mg/kg, and 60 mg/kg on sleep in C57BL/6J mice (n = 15; females = 6; age 10-13 months). Mice were dosed with trazodone for 6 consecutive nights, while being recorded with intracranially implanted 2-channel electroencephalogram (EEG) and electromyography (EMG). EEG/EMG recordings were analyzed for time spent in each vigilance state and power spectra. ResultsA single dose of trazodone, administered prior to the onset of the 12-h rest phase, dose-dependently increased non-rapid eye movement (NREM) sleep and delta power during NREM sleep, at the expense of rapid eye movement (REM) sleep. These effects on sleep persisted after six consecutive days of dosing, albeit to a lesser extent. ConclusionWe have validated a novel voluntary oral administration protocol for trazodone use in mice and have shown that trazodone effectively promotes NREM in mice. Our novel protocol will be useful for future research investigating the effects of trazodone on sleep in mouse models of disease. Statement of significanceTrazodone is an antidepressant known to increase slow wave sleep in humans. Slow wave sleep promotion is being explored as a disease-modifying therapeutic target for neurodegenerative diseases, such as Alzheimers disease. We have developed a novel translationally-focused protocol for administering trazodone to mice, which overcomes some of the challenges of using trazodone for preclinical sleep research. Using our protocol we have demonstrated for the first time that trazodone dose-dependently increases the amount of NREM sleep and delta power in mice, recapitulating the enhancement of slow wave sleep in humans treated with trazodone.

neuroscience↗

bioRxiv2025

Fine root endophytes forming winter mycorrhiza

Arbuscular mycorrhizal fungi, classified in the subphylum Glomeromycotina, are obligate symbionts that depend on photosynthetic products from plants. There is substantial evidence that AMF support plant and crop growth in natural and agricultural ecosystems. Fine root endophytes (FRE) also co-occur in plant roots with AMF in all but tropical environments. However, their presence remains poorly recognised, and their lifestyle and functionality remain largely unknown. Our analysis demonstrates that, in contrast to AMF, FRE colonise plants during the winter season, when photosynthesis is more challenging. It is also noteworthy that FRE was unable to colonise the roots of spring-sown crops. The results of our laboratory pot experiments demonstrated that low temperatures are not sufficient for FRE colonisation. Furthermore, we observed that FRE, in contrast to AMF, exhibited increased colonisation in soils containing metabolically inactive plants. Our results suggest that FRE does not contribute to the increase of ecosystem biomass through direct photosynthesis in summer, but may play an overlooked role in the formation of mycorrhiza-based soil ecosystems in winter. However, this winter ecosystem can be disrupted by conventional bare fallow management of the field, interrupting the annual cycle.

plant biology↗

bioRxiv2024

Automated cell detection for immediate early gene-expressing neurons using inhomogeneous background subtraction in fluorescent images

Although many methods for automated fluorescent-labeled cell detection have been proposed, not all of them assume a highly inhomogeneous background arising from complex biological structures. Here, we propose an automated cell detection algorithm that accounts for and subtracts the inhomogeneous background by avoiding high-intensity pixels in the blur filtering calculation. Cells were detected by intensity thresholding in the background-subtracted image, and the algorithms performance was tested on NeuN- and c-Fos-stained images in the mouse prefrontal cortex and hippocampal dentate gyrus. In addition, applications in c-Fos positive cell counting and the quantification for the expression level in double-labeled cells were demonstrated. Our method of automated detection after background assumption (ADABA) offers the advantage of high-throughput and unbiased analysis in regions with complex biological structures that produce inhomogeneous background. Highlights- We proposed a method to assume and subtract inhomogeneous background pattern. (79/85) - Cells were automatically detected in the background-subtracted image. (71/85) - The automated detection results corresponded with the manual detection. (73/85) - Detection of IEG positive cells and overlapping with neural marker were demonstrated. (85/85)

neuroscience↗

bioRxiv2024

Impact of Optogenetic Activation of the Thalamic Reticular Nucleus on Sleep Architecture in Mice

Alzheimers disease (AD) is a progressive neurodegenerative disorder affecting millions worldwide and is often accompanied by significant sleep disturbances, such as sleep fragmentation, early awakenings, decreased sleep efficiency, and insomnia. It has been suggested that the alterations in activity of the thalamic reticular nucleus (TRN) are closely associated with sleep disruptions in AD. Evidence suggests that activating neurons expressing gamma-aminobutyric acid (GABA) within the TRN may enhance sleep quality and potentially ameliorate neuropathology associated with AD. However, the precise mechanisms through which TRN influences sleep disruptions and AD pathophysiology remain poorly understood. In this study, we investigated whether activating GABAergic TRN neurons could alter sleep architecture in wild-type mice. Utilizing optogenetic stimulation, we observed that activation of these neurons did not significantly alter sleep state durations or delta wave power, a key indicator of Slow Wave Sleep (SWS). Furthermore, the application of a two-virus strategy inadvertently led to non-specific opsin expression beyond the targeted TRN area. We discuss the potential factors that contributed to these outcomes, providing directions for future investigations to better delineate the role of the TRN in sleep and AD.

neuroscience↗

bioRxiv2024

A large pocket structure surrounding the catalytic center in the BCG protein from Mycobacterium tuberculosis

The widespread prevalence of tuberculosis and the need for extensive chemotherapy in its treatment are caused by the ability of tuberculosis (TB) bacteria to enter a dormant state. Therefore, it is crucial to develop effective compounds that can inhibit the growth of TB bacteria in both the active and dormant states. Previous research has identified agelasine D (marine sponge-derived diterpene alkaloid) capable of resisting dormant mycobacteria. Additionally, BCG3185c has been designated as a target mycobacterial protein. In this study, the crystal structure of BCG3185c was determined at a resolution of 1.86 [A]. Analysis of this crystal structure revealed a large pocket toward the catalytic center of BCG3185c, which is potentially adequate for agelasine D binding. Based on the results of the interaction analysis between agelasine D and Bacillus Calmette-Guerin (BCG) proteins, it was inferred that the binding of agelasine D to this large pocket is crucial for suppressing the growth of Mycobacterium tuberculosis.

biochemistry↗

bioRxiv2024

Healthy dietary choices involve prefrontal mechanisms associated with long-term reward maximization but not cognitive control

Taste and health are critical factors to be considered when choosing foods. Prioritizing healthiness over tastiness requires self-control. It has also been suggested that self-control is guided by cognitive control. We then hypothesized that neural mechanisms underlying healthy food choice are associated with both self-control and cognitive control. Human participants performed a food choice task and a working memory (WM) task during functional MRI scanning. Their degree of self-control was assessed behaviorally by the value discount of delayed monetary rewards in intertemporal choice. Prioritizing healthiness in food choice was associated with greater activity in the superior, dorsolateral, and medial prefrontal cortices. Importantly, the prefrontal activity was greater in individuals with smaller delay discounting (i.e., high self-control) who preferred a delayed larger reward to an immediate smaller reward in intertemporal choice. On the other hand, WM activity did not show a correlation with delay discounting or food choice activity, which was further supported by supplementary results that analyzed data from the Human Connectome Project. Our results suggest that the prefrontal cortex plays a critical role in healthy food choice, which requires self-control, but not cognitive control, for maximization of reward attainments in a remote future.

neuroscience↗

bioRxiv2023

Single-cell transcriptome landscape of circulating CD4+ T cell populations in human autoimmune diseases

CD4+ T cells are a key mediator of various autoimmune diseases; however, how they contribute to disease development remains obscure primarily because of their cellular heterogeneity. Here, we evaluated CD4+ T cell subpopulations by decomposition-based transcriptome characterization together with canonical clustering strategies. This approach identified 12 independent transcriptional gene programs governing whole CD4+ T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell data sets of over 1.8M peripheral CD4+ T cells from 953 individuals by projecting cells onto the reference and cataloged cell frequency and qualitative alterations of the populations in 20 diseases. The analyses revealed that the 12 transcriptional programs were useful in characterizing each autoimmune disease and predicting its clinical status. Moreover, genetic variants associated with autoimmune diseases showed disease-specific enrichment within the 12 gene programs. The results collectively provide a landscape of single-cell transcriptomes of CD4+ T cell subpopulations involved in autoimmune disease.

immunology↗

bioRxiv2023

Reentrant condensation of a multicomponent complex system of biomolecules induced by polyphosphate

Reentrant condensation (RC) is a phase behavior of protein solution comprising at least two components. In RC, a protein state varies from one phase to two phases and then back to one phase as the concentration of one component monotonically increases. To understand the phase behavior of multicomponent complex solutions of biomolecules, it is worth constructing an experimental multicomponent system that exhibits RC behavior. Here, we used a cola/milk mixture to investigate RC of a multicomponent complex system and explained the RC mechanism by reducing the system to two pure components, polyphosphate (polyP) and casein. In the multicomponent complex system, RC was observed with 20-60% cola and 1% milk. In the pure system, RC occurred with 0.01-2 mM tetraphosphate and 0.5 mg/ml casein. Moreover, the phase diagram showed that the condensation of casein depended on the chain length of the polyP. The present study succeeded in experimentally inducing RC in a multicomponent system and reproducing RC even when the system was reduced to its pure components. The fact that RC can be experimentally induced using common materials will provide important insights into the understanding of phase-separation behavior of biomolecules.

biochemistry↗

bioRxiv2022

Structure and Function of Gli123 Involved in Mycoplasma mobile Gliding

Mycoplasma mobile is a fish pathogen that glides on solid surfaces by means of a unique mechanism. The gliding machinery of M. mobile is composed of internal and surface structures. In the present study, we focused on the function and structure of Gli123, a surface protein that is essential for the localization of other surface proteins. The amino acid sequence of Gli123, which is 1128 amino acids long, contains lipoprotein-specific repeats. We isolated the native Gli123 protein from M. mobile cells and a recombinant protein, rGli123, from Escherichia coli. The isolated rGli123 complemented a non-binding and non-gliding mutant of M. mobile that lacked Gli123. Circular dichroism and rotary-shadowing electron microscopy (EM) showed that rGli123 has a structure that is not significantly different from that of the native protein. Rotary-shadowing EM suggested that the molecules changed their shape between globular and rod-like structures, depending on the ionic strength of the solution. Negative-staining EM coupled with single-particle analysis revealed that Gli123 forms a globular structure featuring a small protrusion with dimensions of 20.0, 14.5, and 16.0 nm. Small-angle X-ray scattering analyses indicated a rod-like structure composed of several tandem globular domains with total dimensions of approximately 34 nm length and 4 nm width. Both molecular structures were suggested to be dimers based on the predicted molecular size and structure. Gli123 may have evolved by multiplication of repeating lipoprotein units and acquired clumping role of surface proteins. IMPORTANCEMycoplasmas are pathogenic bacteria that are widespread in animals. They are characterized by small cell and genome sizes but are equipped with unique abilities to escape host immunity, such as surface variation and gliding. Here, we focused on a surface-localizing protein that is essential for Mycoplasma mobile gliding. The findings of this study suggested that the protein undergoes drastic conformational changes between its rod-like and globular structures. These changes may be caused by a repetitive structure common in the surface proteins that is responsible for the modulation of the cell surface structure and related to the assembly process for the surface gliding machinery. An evolutionary process for this unique mycoplasma gliding mechanism has also been suggested in the present study.

microbiology↗

bioRxiv2022

Hit-and-run silencing of endogenous DUX4 by targeting DNA hypomethylation on D4Z4 repeats in facioscapulohumeral muscular dystrophy

Facioscapulohumeral muscular dystrophy (FSHD), a progressive skeletal muscle disorder, is epigenetically characterized by DNA hypomethylation of the D4Z4 repeats in the 4q35 region, which enables aberrant DUX4 expression. Sustainable DUX4 suppression is thus a promising therapeutic strategy by which to prevent disease progression, but most of the supposed methods to achieve this depend on the expression of a mediator biochemical entity that would potentially narrow the quality of life of individuals with FSHD in the clinical context. In this study, we report that by applying hit-and-run silencing with dCas9-mediated epigenetic editing targeting DNA hypomethylation on D4Z4 repeats, we could achieve the suppression of endogenous DUX4 in our FSHD patient-derived iPSC model. Notably, DNA methylation was significantly upregulated in FSHD cells and suppression effects were observed for at least two weeks after intervention, which was not the case with transient treatments of typical dCas9-KRAB alone. Off-target analysis showed that despite the potential genome-wide risk for DNA methylation, the impact on the transcriptome was limited. We propose that hit-and-run silencing could be a promising option to prevent disease progression with minimum intervention for individuals with FSHD, motivating further study for clinical development. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/487997v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@19e85dforg.highwire.dtl.DTLVardef@672798org.highwire.dtl.DTLVardef@58717dorg.highwire.dtl.DTLVardef@83044b_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2021

Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma

Myasthenia gravis (MG) is a neurological disease caused by autoantibodies against neuromuscular-associated proteins. While MG is frequently developed in thymoma patients, the etiologic factors for MG are not well understood. Here, by constructing a comprehensive atlas of thymoma using bulk and single-cell RNA-seq, we identified ectopic expression of neuromuscular molecules in MG-associated thymoma (MG-thymoma). These molecules were originated from a distinct subpopulation of medullary thymic epithelial cells (mTECs), which we named neuromuscular mTECs (nmTECs). MG-thymoma also exhibited microenvironments dedicated to autoantibody production, including ectopic germinal center formation, T follicular helper cell accumulation, and type 2 conventional dendritic cell migration. Cell-cell interaction analysis also predicted the interaction between nmTECs and T/B cells via CXCL12-CXCR4. The enrichment of nmTECs presenting neuromuscular molecules within MG-thymoma was further confirmed by immunohistochemically and by cellular composition estimation from MG-thymoma transcriptome. Altogether, this study suggests that nmTECs play a significant role in MG pathogenesis via ectopic expression of neuromuscular molecules.

immunology↗