Biology subjects

Sato, M.

Publications and source records attributed to Sato, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Neuromedin U Receptor 2 orchestrates sleep continuity and circadian entrainment

Neuromedin S signaling has recently been identified as a modulator of both sleep and circadian rhythms in the central nervous systems of mammals. Nevertheless, the involvement of its preferred receptor, NMUR2, in sleep and circadian regulation remains elusive. Here, employing its only selective antagonist R-PSOP, we demonstrate that NMUR2 function in the mouse brain is essential for physiological sleep architecture under baseline conditions, as well as for responses to homeostatic and circadian challenges. Using a combination of pharmacological, neuronal tagging, brain clearing and chemogenetic tools, we identified and functionally validated a group of PVH neurons as one of the targets mediating the effect of R-PSOP on sleep. These findings establish NMUR2 as a potential therapeutic target for the integral treatment of sleep and circadian neurological disorders. HIGHLIGHTSSelective NMUR2 antagonism via R-PSOP disrupts vigilance state continuity in a dose- and circadian phase-dependent manner R-PSOP administration delays circadian phase entrainment and hinders sleep homeostasis recovery PVH neurons are activated by R-PSOP and boost wake-to-NREM sleep transitions in the active period

neuroscience↗

bioRxiv2025

Feasibility of an eDNA-based educational program for high school students

O_LIEnvironmental education plays a crucial role in raising public awareness of ecosystem conservation. Environmental DNA (eDNA) analysis is a promising environmental education tool because it enables easy and comprehensive biodiversity assessment through simple water sampling. Despite several citizen-based surveys using eDNA analysis, minimal attention has been paid to its educational effectiveness. C_LIO_LIIn this study, we examined the educational feasibility of eDNA analysis by conducting an environmental education program that incorporated eDNA-based local fish surveys in three high schools in Japan. Through detailed questionnaire surveys conducted before and after the program, we verified whether our program increased student interest in biodiversity and ecosystem services. C_LIO_LIIn the program, students proactively identified diverse fish species living in the survey area by simply collecting water. The questionnaire survey results showed that student knowledge of and interest in biodiversity and ecosystem services increased after the program. Students became aware of local fish diversity and expressed their motivation to engage in conservation activities. We confirmed the educational impact of the program not only at the end but also immediately following the water sampling experience. C_LIO_LISynthesis and applications. These results provide the first empirical evidence of the positive effects of eDNA analysis on student environmental awareness and engagement. Our program provides a feasible model for eDNA-based environmental education. Because eDNA analysis can be applied to diverse target taxa that are unique to a given area, similar environmental education programs can be conducted for various citizen groups worldwide. Our research also suggested that eDNA-based environmental education was effective for younger generations with varying levels of interest and experience in nature, showing significant potential for addressing the extinction of natural experiences and motivating citizens to participate in ecosystem conservation activities. C_LI

scientific communication and education↗

bioRxiv2025

Mitorubin, berberrubine-based compounds that improve mitochondrial function, exhibit cardioprotective effects against age-related cardiac dysfunction

Mitochondria play a central role in cellular energy metabolism and homeostasis, and their dysfunction is closely linked to the progression of age-related diseases. The mitochondrial ubiquitin ligase MITOL (also known as MARCHF5) is a key regulator of mitochondrial dynamics and function, and reduced MITOL expression in the mouse heart has been implicated in mitochondrial dysfunction and cardiac aging. In this study, we identified berberrubine as a compound that promotes MITOL expression and activates mitochondria. We further assembled a group of berberrubine-based compounds, including its quinoid form and a newly developed water-soluble derivative, and collectively named them "Mitorubin" as mitochondria-activating compounds with therapeutic potential. While conventional berberrubine has poor water solubility, the addition of acetic acid significantly improved its solubility, enabling formulation as a solution. Mitorubin enhanced MITOL expression in cultured cells, increased mitochondrial DNA content and expression of mitochondrial proteins, and promoted mitochondrial respiration. In a model of age-related cardiac dysfunction, oral administration of Mitorubin restored mitochondrial function, improved cardiac performance, suppressed myocardial hypertrophy, and alleviated pulmonary congestion. Moreover, Mitorubin did not shorten lifespan in aged mice and significantly extended lifespan in high-fat diet-fed mice, suggesting both safety and efficacy under chronic administration. These findings suggest that Mitorubin is a promising mitochondrial activator and may represent a novel therapeutic strategy for age-related diseases.

biochemistry↗

bioRxiv2024

Becker muscular dystrophy mice showed site-specific decay of type IIa fibers with capillary change in skeletal muscle

Becker muscular dystrophy (BMD), an X-linked muscular dystrophy, is mostly caused by an in-frame deletion of DMD. BMD severity varies from asymptomatic to severe, associated with the genotype of DMD. However, the underlying mechanisms remain unclear. We established BMD mice carrying three representative exon deletions: ex45-48 del., ex45-47 del., and ex45-49 del. (d45-48, d45-47 and d45-49), with high frequencies and different severities in the human BMD hotspot. All three BMD mice showed muscle weakness, muscle degeneration, and fibrosis, but these changes appeared at different times for each exon deletion, consistent with the severities obtained by the natural history study of BMD. BMD mice showed site-specific muscle changes, unlike mdx mice, which showed diffuse muscle changes, and we demonstrated selective type IIa fiber reduction in BMD mice. Furthermore, BMD mice showed sarcolemmal neuronal nitric oxide synthase (nNOS) reduction and morphological capillary changes around type IIa fibers. These results suggest that capillary changes caused by nNOS reduction may be associated with the mechanism of skeletal muscle degeneration and type IIa fiber reduction in BMD mice. BMD mice may be useful in elucidating the pathomechanisms and developing vascular targeted therapies for human BMD.

genetics↗

bioRxiv2024

Mitigating nitrous oxide emission by an ultra-fast bioprocess enabling the removal of high concentration N2O

Nitrous oxide (N2O) is known as a greenhouse gas as well as an ozone-depleting substance. Wastewater treatment process is one of the sources of N2O emission, and the high concentrations of N2O in off-gas were reported from an anaerobic ammonium oxidation process. This study developed a novel N2O removal process using a down-flow hanging sponge reactor to remove high concentrations of N2O. More than 96% removal efficiencies were achieved for up to 300 ppm N2O with 3 min gas retention time (GRT), and more than 99% removal efficiency was obtained for 2,000 ppm N2O with 18 min GRT. A maximum removal rate of 161 {+/-} 26 mg-N/L-reactor/day was achieved, that was over 10 times faster than the pioneering process. Kinetic analysis indicated that the N2O dissolution rate is a crucial factor in determining the N2O removal rate in the reactor. Various N2O reducers belonging to both clade I and II were detected in reactors, and Azonexus was thought to play a key role.

microbiology↗

bioRxiv2024

Enabling Epitope Analysis of Glycoproteins via HDX-MS Using Antigens with Uni-formed N-linked Glycans

Hydrogen deuterium exchange mass spectrometry (HDX-MS) is widely used for epitope analysis of the antibodies. However, epitope analysis of glycoproteins is challenging because of the heterogeneity of attached N-linked glycans. Recent studies have reported methods where N-linked glycans were removed at low pH following hydrogen deuterium exchange reactions, but the methods for glycoproteins remain controversial. Here, we demonstrate the utility of using antigens with uniformed N-linked glycans in glycoprotein epitope analysis by HDX-MS. By treating HEK293 cells with kifunensine, we were able to prepare antigens mainly with N-linked high-mannose-type glycans. Analysis of epitopes of a monoclonal antibody S309 using antigens prepared with this method allowed us to identify an epitope that included the previously reported N-linked glycan attachment sites for this anti-body. We propose that using antigens with uniformed glycans should be effective for epitope analysis of glycoproteins, such as virus spike proteins covered by glycan shields. Moreover, we believe that this approach accelerates research on vaccines and neutralizing antibodies against viruses that escape host immunity through glycan shields or mutations.

biochemistry↗

bioRxiv2024

Amyloid-β-induced Alteration of Fast and Localized Calcium Elevations in Cultured Astrocytes

Alzheimers disease (AD) is a progressive neurodegenerative disorder that causes cognitive decline. Uncovering the mechanisms of neurodegeneration in the early stages is essential to establish a treatment for AD. Recent research has proposed the hypothesis that amyloid-{beta} (A{beta}) oligomers elicit an excessive glutamate release from astrocytes toward synapses through intracellular free Ca2+ ([Ca2+]i) elevations in astrocytes, finally resulting in neuronal dendritic spine loss. Under physiological conditions, astrocytic [Ca2+]i elevations range spatially from microdomains to network-wide propagation and temporally from milliseconds to tens of seconds. Astrocytic localized and fast [Ca2+]i elevations might correlate with glutamate release; however, the A{beta}-induced alteration of localized, fast astrocytic [Ca2+]i elevations remains unexplored. In this study, we quantitatively investigated the A{beta} dimers-induced changes in the spatial and temporal patterns of [Ca2+]i in a primary culture of astrocytes by two-photon excitation spinning-disk confocal microscopy. The frequency of fast [Ca2+]i elevations occurring locally in astrocytes ([≤]0.5 s, [≤]35 {micro}m2) and [Ca2+]i event occupancy relative to cell area significantly increased after exposure to A{beta} dimers. The effect of A{beta} dimers appeared dose-dependently above 500 nM, and these A{beta} dimers-induced [Ca2+]i elevations were primarily mediated by a metabotropic purinergic receptor (P2Y1 receptor) and Ca2+ release from the endoplasmic reticulum. Our findings suggest that the A{beta} dimers-induced alterations and hyperactivation of astrocytic [Ca2+]i is a candidate cellular mechanism in the early stages of AD.

neuroscience↗

bioRxiv2024

Effectiveness of Exercise Intervention in Preventing Active Arthritis Exacerbation in an SKG Mouse Model of Rheumatoid Arthritis

ObjectivesTo investigate the effects of low-intensity exercise on active arthritis in an SKG mouse model of human rheumatoid arthritis (RA) pathology. MethodsTwenty-four female SKG mice were divided into three groups: sedentary (control), AR (induced arthritis), and AREx (induced arthritis plus low-intensity exercise). Arthritis was induced via intraperitoneal administration of mannan. After a 2-week inflammation period, low-intensity treadmill exercise was performed only in the AREx group. Arthritis was assessed weekly during the rearing period. After 4 weeks of exercise, histological and bone morphometric analyses of the right ankle joint were performed. A histological analysis of the gastrocnemius muscle was also performed. Bulk mRNA sequencing was conducted on the left synovial membrane-fat pad (SM-FP) complex. ResultsThe synovitis score showed no change; however, the arthritis score was significantly lower in the AREx group than in the AR group (p<0.05), indicating that low-intensity exercise suppressed arthritis exacerbation. The calcaneal and talar bone volumes decreased in the AR group, whereas the AREx group showed no significant change. In the SM-FP complex tissue, the gene expression of inflammatory cytokines decreased in the AREx group compared with the AR group, particularly the suppression of IL6/Jak/Stat3. Immunohistochemical analysis revealed significantly decreased expression of pro-inflammatory cytokines and increased expression of anti-inflammatory cytokines in the synovium of the AREx group compared with the AR group (p<0.05). ConclusionLow-intensity exercise therapy for active RA showed anti-inflammatory and suppressive effects on arthritis exacerbation in SKG mice, a mouse model of human RA pathology. Key messagesO_LIExercise had an anti-inflammatory effect on SKG mice, a mouse model of rheumatoid arthritis. C_LIO_LIExercise suppresses pro-inflammatory cytokine pathways such as IL6/Jak/Stat3 signalling in the synovial-fat complex tissue. C_LIO_LIExercise therapy is effective in improving the pathophysiology of active rheumatoid arthritis. C_LI

molecular biology↗

bioRxiv2024

Multiomics-based assessment of the impact of airflow on diverse plant callus cultures

Plant cell culture has multiple applications in biotechnology and horticulture, from plant propagation to the production of high-value biomolecules. However, the interplay between cellular diversity and ambient conditions influences the metabolism of cultured tissues; understanding these factors in detail will inform efforts to optimize culture conditions. This study presents multiomics datasets from callus cultures of tobacco (Nicotiana tabacum), rice (Oryza sativa), and two bamboo species (Phyllostachys nigra and P. bambusoides). Over four weeks, calli were cultured under continuous moisture without airflow or gradually reduced ambient moisture with airflow. For each sample, gene expression was profiled with high-throughput RNA sequencing, 442 metabolites were measured using liquid chromatography (LC) with triple-quadrupole mass spectrometry (LC-QqQMS), and 31 phytohormones were quantified using ultra-performance LC coupled with a tandem quadrupole mass spectrometer equipped with an electrospray interface (UPLC-ESI-qMS/MS) and ultra-high-performance LC- orbitrap MS (UHPLC-Orbitrap MS). These datasets highlight the impact of airflow on callus cultures, revealing differences between and within species, and provide a comprehensive resource to explore the physiology of callus growth.

plant biology↗

bioRxiv2024

Dual roles of idling moments in past and future memories

Every day, we experience new daily episodes and store new memories. Although memories are stored in corresponding engram cells, how different sets of engram cells are selected for current and next episodes, and how they create their memories, remains unclear. We report that in mice, hippocampal CA1 neurons show an organized synchronous activity in prelearning home cage sleep that correlates with the learning ensembles only in engram cells, termed preconfigured ensembles. Moreover, after learning, a subset of nonengram cells develops population activity, which is constructed during postlearning offline periods through synaptic depression and scaling, and then emerges to represent engram cells for new learning. Together, our findings indicate that during offline periods there are two parallel processes occurring: conserving of past memories through reactivation, and preparation for upcoming ones through offline synaptic plasticity mechanisms.

neuroscience↗

bioRxiv2024

Delineating neural contributions to electroencephalogram-based speech decoding

Speech Brain-computer interfaces (BCIs) have emerged as a pivotal technology in facilitating communication for individuals with speech impairments. Utilizing electroencephalography (EEG) for noninvasive speech BCIs offers an accessible and affordable solution, potentially benefiting a broader audience. However, EEG-based speech decoding remains controversial especially for overt speech, due to difficulties in separating speech-related neural activities from myoelectric potential artifacts generated during articulation. Here we aim to delineate the extent of the neural contributions by employing Explainable AI techniques to a convolutional neural network predicting spoken words based on signals obtained by ultra-high-density (uhd)-EEG. We found that electrode-wise contributions to the decoding cannot be explained by their mutual information with electromyography (EMG). Furthermore, contributing periods of speech to EEG-based decoding are distinct from those to decoding solely relying on EMG. In contrast, there are significant overlaps in signal timings contributing to EEG-based decoding, regardless of vocal conditions such as overt or covert speech. Notably, the denoising process successfully enhanced the decoding contribution from electrodes within speech-related brain areas for all speech conditions. Altogether, our findings support the idea that, with appropriate preprocessing, EEG becomes a valuable tool for decoding spoken words based on underlying neural activities.

neuroscience↗

bioRxiv2024

Prediction of antibiotic resistance mechanisms using a protein language model

MotivationAntibiotic resistance has emerged as a major global health threat, with an increasing number of bacterial infections becoming difficult to treat. Predicting the underlying resistance mechanisms of antibiotic resistance genes (ARGs) is crucial for understanding and combating this problem. However, existing methods struggle to accurately predict resistance mechanisms for ARGs with low similarity to known sequences and lack sufficient interpretability of the prediction models. ResultsIn this study, we present a novel approach for predicting ARG resistance mechanisms using Protein-BERT, a protein language model based on deep learning. Our method outperforms state-of-the-art techniques on diverse ARG datasets, including those with low homology to the training data, highlighting its potential for predicting the resistance mechanisms of unknown ARGs. Attention analysis of the model reveals that it considers biologically relevant features, such as conserved amino acid residues and antibiotic target binding sites, when making predictions. These findings provide valuable insights into the molecular basis of antibiotic resistance and demonstrate the interpretability of protein language models, offering a new perspective on their application in bioinformatics. AvailabilityThe source code is available for free at https://github.com/hmdlab/ARG-BERT. The output results of the model are published at https://waseda.box.com/v/ARG-BERT-suppl. Contactmhamada@waseda.jp

bioinformatics↗

bioRxiv2024

Coatomer complex I is required for the transport of SARS-CoV-2 progeny virions from the endoplasmic reticulum-Golgi intermediate compartment

SARS-CoV-2 undergoes budding within the lumen of the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and delivers progeny virions to the cell surface by employing vesicular transport. However, the molecular mechanisms remain poorly understood. Using three-dimensional electron microscopic analysis, such as array tomography and electron tomography, we found that virion-transporting vesicles possessed a coated protein on their membrane and demonstrated that the coated protein was coatomer complex I (COPI). During the later stages of SARS-CoV-2 infection, we observed a notable alteration in the distribution of COPI and ERGIC throughout the cytoplasm. Depletion of COPB2, a key component of COPI, led to the confinement of SARS-CoV-2 structural proteins in the perinuclear region, where progeny virions were accumulated within the ERGIC. While the expression levels of viral proteins within cells were comparable, this depletion significantly reduced the efficiency of virion release, leading to the significant inhibition of viral replication. Hence, our findings suggest COPI as a critical player in facilitating the transport of SARS-CoV-2 progeny virions from the ERGIC. Thus, COPI could be a promising target for the development of antivirals against SARS-CoV-2.

microbiology↗

bioRxiv2024

Dynamic population coding of social novelty in the insular cortex

The familiarity of socially interacting peers has a profound impact on behavior1-3, but little is known about the neuronal representations distinguishing familiar from novel conspecifics. The insular cortex (IC) regulates social behavior4-9, and our previous study revealed that neurons in the agranular IC (aIC) encode ongoing social interactions10. To elucidate how these neurons discriminate between interactions with familiar and novel conspecifics, we monitored neuronal activity in mice by microendoscopic calcium imaging during social recognition memory (SRM) and linear chamber social discrimination (LCSD) tasks. In the SRM task, repeated interactions with the same target activated largely nonoverlapping cells during each session. The fraction of cells associated with social investigation (social cells) decreased as the subject repeatedly interacted with the same target, whereas substitution of a second novel target and subsequent exchange with the first familiar target recruited more new social cells. In the LCSD task, the addition of a novel target to an area containing a familiar target transiently increased the number of cells responding to both targets, followed by an eventual increase in the number of cells responding to the novel target. These results support the view that the aIC dynamically encodes social novelty, rather than consistently encode social identity, by rapidly reorganizing the neural representations of conspecific information.

neuroscience↗

bioRxiv2024

BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks

BackgroundChemical bioproduction has attracted attention as a key technology in a decarbonized society. In computational design for chemical bioproduction, it is necessary to predict changes in metabolic fluxes when up-/down-regulating enzymatic reactions, that is, responses of the system to enzyme perturbations. Structural sensitivity analysis (SSA) was previously developed as a method to predict qualitative responses to enzyme perturbations on the basis of the structural information of the reaction network. However, the network structural information can sometimes be insufficient to predict qualitative responses unambiguously, which is a practical issue in bioproduction applications. To address this, in this study, we propose BayesianSSA, a Bayesian statistical model based on SSA. BayesianSSA extracts environmental information from perturbation datasets collected in environments of interest and integrates it into SSA predictions. ResultsWe applied BayesianSSA to synthetic and real datasets of the central metabolic pathway of Escherichia coli. Our result demonstrates that BayesianSSA can successfully integrate environmental information extracted from perturbation data into SSA predictions. In addition, the posterior distribution estimated by BayesianSSA can be associated with the known pathway reported to enhance succinate export flux in previous studies. ConclusionsWe believe that BayesianSSA will accelerate the chemical bioproduction process and contribute to advancements in the field.

bioinformatics↗

bioRxiv2024

Discovery of anti-SARS-CoV-2 S2 protein antibody CV804 with broad-spectrum reactivity with various beta coronaviruses and analysis of its pharmacological properties in vitro and in vivo

SARS-CoV-2 pandemic alerts us that spillovers of various animal coronaviruses to human in the future may bring us enormous damages. Thus, there is a significant need of antibody-based drugs to treat patients infected with previously unseen coronaviruses.CV804 against the S2 domain of the spike protein, which is less prone to mutations. CV804 shows not only broad cross-reactivities with representative 20 animal-origin coronaviruses but also with diseases-associated human beta coronaviruses including SARS-CoV, MERS-CoV, HCoV-OC43, HCoV-HKU1 and mutant strains of SARS-CoV-2. Other than that, the main characteristics of CV804 are that it has strong antibody-dependent cellular cytotoxicity (ADCC) activity to SARS-CoV2 spike protein-expressed cells in vitro and completely lacks virus-neutralization activity. Comprehensively in animal models, CV804 suppressed disease progression by SARS-CoV-2 infection. Structural studies using HDX-MS and point mutations of recombinant spike proteins revealed that CV804 binds to a unique epitope within the highly conserved S2 domain of the spike proteins of various coronaviruses. Based on the overall data, we suggest that the non-neutralizing CV804 antibody recognizes the conformational structure of the spike protein expressed on the surface of the infected cells and weakens the viral virulence by supporting host immune cells attack through ADCC activity in vivo. CV804 epitope identified in this study is not only useful for the design of pan-corona antibody therapeutics but also to design next-generation coronavirus vaccines and antiviral drugs.

microbiology↗

bioRxiv2024

A new paradigm considering multicellular adhesion, repulsion and attraction represent diverse cellular tile patterns

Cell sorting by differential adhesion is one of the basic mechanisms explaining spatial organization of neurons in early stage brain development of fruit flies. The columnar arrangements of neurons determine the large scale patterns in the fly visual center. Experimental studies indicate that hexagonal configurations regularly appear while tetragonal configurations can be induced in mutants. Mathematical models based on macroscopic approximations of agent based models (ARA models) are shown to produce a similar behavior changing from hexagonal to tetragonal steady configurations when medium range repulsion and longer-range attraction between individuals is incorporated in previous successful models for cell sorting based on adhesion and volume constraints. We analyse the angular configurations of these patterns based on angle summary statistics and compare between experimental data and parameter fitted ARA models showing that intermediate patterns between hexagonal and tetragonal configuration are common in experimental data as well as in our ARA mathematical model. Our studies indicate an overall qualitative agreement of ARA models in tile patterning and pave the way for their quantitative studies. 2010 MSC92C17, 92C37, 35Q92

developmental biology↗

bioRxiv2024

Human color constancy in cast shadows

Most natural scenes contain cast shadows to a varying extent. Illuminant conditions inside and outside the shadow typically differ largely both in intensity and in chromaticity. Nevertheless, our daily experiences suggest that colored materials appear to have the same color in shadows even though the reflected light from the material might be very different. Two experiments were conducted to reveal mechanisms that support human color constancy in cast shadows. In all experiments we built a real scene that consisted of colored hexagons illuminated by two independent liquid crystal projectors simulating "sunlight" and "skylight", respectively. A part of the scene included a cast shadow under which observers were instructed to change the luminance and the chromaticity of a test field so that it appeared as a full-white paper under the shadow. The color of the skylight was manipulated, testing if our visual system uses a prior that the skylight is typically bluish or yellowish to achieve color constancy. We also created a condition where a cast shadow is not recognized as a shadow. Results showed that color constancy generally holds well in shadows and changing skylight color had little effect. Recognizing a cast shadow as a shadow also had no effect. Overall, these results are consistent with our daily experiences that we stably judge objects color even in shadows, providing a key step to reveal mechanisms of color perception in real-world scenes where lighting conditions spatially vary.

neuroscience↗