Biology subjects

Miyake, Y.

Publications and source records attributed to Miyake, Y..

8 recordsLinked to original sources

bioRxiv2026

Structural Basis of H-NS-Mediated Temperature-Dependent Stimulation of Initial Growth in Escherichia coli.

Bacteria have evolved sophisticated mechanisms to sense and adapt to environmental shifts, particularly when transitioning into the stable, warm temperatures of a host organism. Escherichia coli, a primary inhabitant of the warm-blooded host gut, must rapidly initiate growth upon entry to ensure reproductive success. In this study, we demonstrate that the specific growth rate at the onset of the logarithmic phase (defined as at ODratio=0.2) is specifically stimulated across a medium temperature range (30{degrees}C-42{degrees}C), peaking near the physiological temperature of 37{degrees}C. This adaptive response is strain-specific and depends on both the histone-like nucleoid-associated protein (NAP) H-NS and the presence of the Rac prophage. Using high-frequency automated growth monitoring and statistical modeling, we redefine H-NS not merely as a gene silencer but as a critical "nucleoid structural organizer". Our results indicate that H-NS undergoes a conformational switch at approximately 37{degrees}C, transitioning into a parallel form that provides the necessary physical scaffold for nucleoid reorganization. This reorganization is essential for coordinating transcription and replication during the rapid onset of growth. Crucially, we resolve the "silencing paradox": while H-NS silencing is traditionally thought to be weakened at 37{degrees}C, hns-deficient mutants grow significantly slower because they lack this essential structural scaffold. We conclude that the H-NS-mediated physical organization of the genome is more critical for host adaptation than the mere de-repression of the genomic reservoir, enabling E. coli to effectively transition into a high-growth state for successful host colonization.

microbiology↗

bioRxiv2026

Single-molecule spatial genomics reveals the multi-scale organization and plasticity of extrachromosomal DNA in glioblastoma

Extrachromosomal DNA (ecDNA) is a major driver of intratumoral heterogeneity and is associated with poor clinical outcomes across cancers, yet how individual ecDNA molecules are organized and regulated within intact tumors remains unknown. Here, we leveraged single-molecule, multi-modal spatial genomics to resolve the three-dimensional chromatin organization and transcriptional activity of individual EGFR-containing ecDNA molecules in glioblastoma (GBM) cells in vitro, in orthotopic xenografts, and in patient-derived GBM tissue. At the larger scale, we find that distinct GBM molecular and functional states emerge depending on the local cellular environment. EGFR expression was markedly different between GBM subpopulations, and perturbations of EGFR dosage shifted GBM cellular states. ecDNA expression was modulated by multiple mechanisms, including variation in copy number, chromatin organization, DNA sequence, and chromosomal reintegration, which were simultaneously measured within the same cells. At the single-molecule scale, ecDNA adopts a physically expanded chromatin configuration with larger ecDNA molecules having higher transcriptional activity and interaction with active transcriptional machinery. ecDNA regulation was coordinated within cells and across GBM states, and ecDNA copy number, structure, and transcription were spatially organized across the tumor architecture. Co-culturing GBM cells with neurons recapitulated key features of infiltrative regions, including lower EGFR expression, reduced ecDNA copy number, and increased chromosomal reintegration, suggesting a causal role for the microenvironment in shaping ecDNA regulation. Collectively, these findings support a model in which GBM states and ecDNA are linked, plastic, and influenced by microenvironmental contexts, revealing a previously inaccessible layer of genome organization underlying tumor heterogeneity and malignant cell behavior.

genomics↗

bioRxiv2025

Dysregulated circRNA expression profile and associated miRNA sponging in abnormal lung development in congenital diaphragmatic hernia

RationaleCircular RNAs (circRNAs) can function as disease biomarkers. Their profile in abnormal lung development in congenital diaphragmatic hernia (CDH) is unknown. ObjectiveTo evaluate circRNA expression profile in CDH-associated abnormal lung development. MethodsWe profiled circRNAs in rat CDH and control lungs at embryonic day (E)15 and E21 by microarray. We validated identified circRNAs using back-splice junction amplicon sequencing, RT-qPCR, and in situ hybridization. We modified a CircRNA Function prediction Tool to predict CircRNA::micro(mi)RNA::messenger(m)RNA interactions and compared these with Oxford Nanopore RNA sequencing and existing human CDH datasets. Measurements and Main ResultsMicroarrays revealed a unique circRNA biosignature during CDH lung development. CircAnp32e was expressed in a sex-specific and spatiotemporal expression pattern in the epithelium at E15. The predicted mature sequence of circAnp32e overlapped >90% with its human orthologue. CircRNA::miRNA::mRNA interaction networks in E15 and E21 revealed enrichment in inflammation/infection, smooth muscle cell function, cell proliferation/cell cycle regulation, and response to hypoxia pathways. Parental genes of differential expressed circRNAs at E15 enriched pathways linked to cell proliferation/cell cycle/cancer, while at end-gestation, inflammation and cardiovascular processes were also overrepresented. Rat and human CDH lungs showed overlapping pathways with additional enrichment for RNA processing and protein binding/modification in humans. ConclusionA unique circRNA signature during abnormal lung development in CDH may mediate inflammatory responses, smooth-muscle-cell function, and cell proliferation regulation via miRNA sponging. Overlap of downstream pathways in rat and human CDH suggest conserved functions across species. CircRNAs may serve as biomarkers to guide prenatal management and mitigate aberrant lung development in CDH.

developmental biology↗

bioRxiv2024

Influenza A virus exploits the motility of membrane cytoskeletal actomyosin filaments for its genome packaging in the host cell

Influenza A virus encodes its genome in eight segments of viral ribonucleoproteins (vRNPs) replicated in the host cell nucleus. Our understanding of host factors involved in driving vRNP selective packaging remains incomplete. To address this, we used advanced immuno-freeze-etch electron microscopy to visualise the vRNP packaging process and atomic force live-cell imaging (AFM) to examine the motility of membrane cytoskeletal actin filaments. In the cytoplasm, vRNPs were mainly localised on mottled membrane-like structures, suggesting intracellular trafficking through such structures. After reaching the cytoplasmic side surface of the plasma membrane, vRNPs formed many aggregates while associating with actin filaments. Antibody labelling also detected myosin along actin filaments entangled in vRNPs. Blocking myosin activity with blebbistatin prevented the active movement of membrane cytoskeletal actin filaments just below the plasma membrane visualised by AFM and abrogated proper aggregation of vRNPs. Thus, actomyosin motility appears to be crucial for the selective packaging of vRNPs.

cell biology↗

bioRxiv2023

Overactivated epithelial NF-κB disrupts lung development in human and nitrofen CDH

Background & ObjectiveAbnormal lung development is the main cause of morbidity and mortality in neonates with congenital diaphragmatic hernia (CDH), a common birth defect (1:2500) of largely unknown pathobiology. Recent studies discovered that inflammatory processes, and specifically NF-{kappa}B associated pathways are enriched in human and experimental CDH. However, the molecular signaling of NF-{kappa}B in abnormal CDH lung development and its potential as a therapeutic target requires further investigation. Methods & ResultsUsing sections and hypoplastic lung explant cultures from the nitrofen rat model of CDH and human fetal CDH lungs, we demonstrate that NF-{kappa}B and its downstream transcriptional targets are hyperactive during abnormal lung formation in CDH. NF-{kappa}B activity was especially elevated in the airway epithelium of nitrofen and human CDH lungs at different developmental stages. Fetal rat lung explants had impaired pseudoglandular airway branching after exposure to nitrofen, together with increased phosphorylation and transcriptional activity of NF-{kappa}B. Dexamethasone, the broad and clinically applicable anti-inflammatory NF-{kappa}B antagonist, rescued lung branching and normalized NF-{kappa}B signaling in hypoplastic lung explants. Moreover, specific NF-{kappa}B inhibition with curcumenol similarly rescued ex vivo lung hypoplasia and restored NF-{kappa}B signaling. Lastly, we showed that prenatal intraperitoneal dexamethasone administration to pregnant rat dams carrying fetuses with hypoplastic lungs, significantly improves lung branching and normalizes NF-{kappa}B in vivo. Conclusions: Our results indicate that NF-{kappa}B is aberrantly activated in human and nitrofen CDH lungs. Anti-inflammatory treatment with dexamethasone and/ or specific NF-{kappa}B inhibition should be investigated further as a therapeutic avenue to target lung hypoplasia in CDH.

developmental biology↗

bioRxiv2019

Prior physical synchrony enhances rapport and inter-brain synchronization during subsequent educational communication

Physical synchrony has been suggested to have positive effects on not only concurrent but also subsequent communication, but the underlying neural processes are unclear. Using functional near-infrared spectroscopy (fNIRS) hyperscanning, we tested the effects of preceding physical synchrony on subsequent dyadic teaching-learning communication. Thirty-two pairs of participants performed two experimental sessions. In each session, they underwent a rhythmic arm movement block with synchronous or asynchronous conditions, and then taught/learned unknown words to/from each other according to a given scenario. Neural activities in their medial and left lateral prefrontal cortex (PFC) were measured and inter-brain synchronization (IBS) during the teaching-learning blocks was evaluated. Participants rated their subjective rapport during the teaching-learning blocks, and took a word memory test. The analyses revealed that (1) prior physical synchrony enhanced teacher-learner rapport; (2) prior physical synchrony also enhanced IBS in the lateral PFC; and (3) IBS changes correlated positively with rapport changes. Physical synchrony did however not affect word memory performance. These results suggest that IBS can be useful to measure the effects of social-bonding facilitation activities for educational communication.

neuroscience↗

bioRxiv2019

Inertial Measurement Unit-Based Estimation of Foot Trajectory for Clinical Gait Analysis

Gait analysis is used widely in clinical practice for the evaluation of abnormal gait caused by disease. Conventionally, medical professionals use motion capture systems or make visual observations to evaluate a patients gait. Recent biomedical engineering studies have proposed easy-to-use gait analysis methods involving wearable sensors with inertial measurement units (IMUs). IMUs placed on the shanks just above the ankles allow for the long-term monitoring of gait because the participant can walk with or without shoes during the analysis. As far as the authors know, there is no report of the gait analysis method that estimates stride length, gait speed, stride duration, stance duration, and swing duration at the same time. In this study, we tested a proposed gait analysis method that uses IMUs attached on the shanks to estimate foot trajectory and temporal gait parameters. We evaluated this proposed method by analyzing the gait of 10 able-bodied participants (mean age 23.1 years, nine men and one woman). Wearable sensors were attached to the participants shanks, and we measured three-axis acceleration and three-axis angular velocity with the sensors to estimate foot trajectory during walking. We compared gait parameters estimated from the foot trajectory obtained with the proposed method and those measured with a motion capture system. Mean accuracy (mean {+/-} standard deviation) was -0.046 {+/-} 0.026 m for stride length, -0.036 {+/-} 0.026 m/s for gait speed, -0.002 {+/-} 0.019 s for stride duration, -0.000 {+/-} 0.016 s for stance duration, and -0.002 {+/-} 0.022 s for swing duration. These results suggest that the proposed method is useful for evaluation of clinical gait parameters.

physiology↗

bioRxiv2018

Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

Conventional morphology-based identification is commonly used for routine assessment of freshwater ecosystems. However, cost and time efficient techniques such as high-throughput sequencing (HTS) based approaches may resolve the constraints encountered in conducting morphology-based surveys. Here, we characterized stream macroinvertebrate species diversity and community composition via metabarcoding and morphological analysis from environmental samples collected from the Shigenobu River Basin in Ehime Prefecture, Japan. We compared diversity metrics and assessed both approaches ability to evaluate the relationship between macroinvertebrate community and environmental variables. In total, we morphologically identified 45 taxa (3 families, six subfamilies, 31 genera, and five species) from 8,276 collected individuals from ten study sites. We detected 44 species by metabarcoding, with 35 species collapsed into 11 groups matching the morphologically identified taxa. A significant positive correlation between logged depth (number of HTS reads) and abundance of morphological taxa was observed, which implied that quantitative data can be used for subsequent analyses. Relatively higher estimates of alpha diversity were calculated from the metabarcoding data in comparison to morphology-based data. However, beta diversity estimates between metabarcoding and morphology data based on both incidence and abundance-based matrices were correlated proving that community differences between sampling sites were preserved in the molecular data. Also, both models were significant, but metabarcoding data (93%) explained a relatively higher percentage of variation in the relationship between community composition and the environmental variables than morphological data (91%). Overall, we present both the feasibility and limitations of HTS-driven estimations of taxonomic richness, community composition, and diversity metrics, and that metabarcoding was proven comparable and more sensitive against morphology-based analysis for stream macroinvertebrate biodiversity assessment and environmental monitoring.

ecology↗