Biology subjects

Ando, H.

Publications and source records attributed to Ando, H..

13 recordsLinked to original sources

bioRxiv2026

Systematic Comparison of Indicator and Pathogenic Viruses Using High-Throughput qPCR Identifies Pepper Mild Mottle Virus as a Robust Indicator of Virus Removal in Wastewater Treatment

The selection of appropriate viral indicators for evaluating wastewater treatment performance remains challenging because candidate markers have rarely been compared systematically within a unified analytical framework. Here, we collected influent and effluent samples monthly for one year from two wastewater treatment plants in Japan and conducted, to our knowledge, the first comprehensive comparison of 19 viral targets and one protozoan target using high-throughput quantitative PCR. Pepper mild mottle virus (PMMoV) was consistently detected at high concentrations, showed limited seasonal variability, and exhibited an approximately 1.0 log10 reduction, comparable to those observed for pathogenic viruses. In contrast, Carjivirus, formerly known as crAssphage, was present at the highest concentrations but showed significantly greater reduction than pathogenic viruses. Tomato brown rugose fruit virus (ToBRFV), despite its high abundance and emerging recognition as a potential marker, exhibited pronounced seasonal fluctuations. Other Tobamovirus species, such as cucumber green mottle mosaic virus and tobacco mild green mosaic virus, exhibited similar removal but lower prevalence compared with PMMoV. Overall, PMMoV demonstrated the most balanced performance in terms of abundance, stability, and removal behavior, supporting its use as a robust indicator for monitoring virus removal in wastewater treatment.

microbiology↗

bioRxiv2026

Population genomics reveal genetic variants associated with lunar-regulated spawning time in grass puffer

High and low tides occur twice a day (every [~]12.4 hours), with the largest tidal ranges during spring tides around new and full moons (every [~]14.765 days). Although lunar cycles shape diverse animal phenotypes, particularly the reproduction of coastal animals, the genetic basis of lunar-related rhythms remains unclear. Since phenotypic variation is a valuable resource for elucidating such mechanisms, we examined geographic variation in the lunar-regulated mass spawning of the grass puffer (Takifugu alboplumbeus) along the Japanese coast. Western populations spawned during the first half of the spring tides, whereas eastern populations spawned during the second half. Furthermore, the spawning was restricted to a narrow daily time window that occurred earlier in the western populations than in the eastern ones. Assuming that spawning is regulated by circadian gating, this geographic shift in the daily spawning window could account for the population difference in semilunar spawning timing. Consistent with this hypothesis, the free-running circadian period ({tau}), which can affect the phase of the gating window, was shorter in the western populations. Mathematical modeling recapitulated the observed geographic difference in the spawning time window based on variation in {tau}. To identify candidate genes responsible for these differences, we conducted population genomics analysis and identified proline-rich transmembrane protein 1-like (prrt1l) as a candidate. Expression of prrt1l was observed in the circadian pacemaker suprachiasmatic nucleus, and triple CRISPR F0 knockout of prrt1l shortened the free-running period in larvae. These findings suggest a potential mechanism underlying the geographic variation in lunar-synchronized spawning behavior. HighlightsO_LIThe geographic variation exists in the lunar-regulated spawning of the grass puffer, with differences in spawning dates and times between western and eastern Japan. C_LIO_LIThe free-running period of western populations is shorter than that of eastern populations, which is consistent with their earlier spawning timing. C_LIO_LIPopulation genomics analysis identified prrt1l as a candidate gene harboring population-specific missense mutations, the knockout of which shortens the free-running period. C_LI

evolutionary biology↗

bioRxiv2026

Soil Microbial Diversity of the Imperial Palace Outer Gardens, Tokyo

The Imperial Palace in Tokyo serves as a significant reservoir of biodiversity within the urban landscape; however, its soil microbial communities remain uncharacterized despite decades of macro-biological surveys. This study presents the first dataset profiling the soil microbiome of the Imperial Palace Outer Gardens, utilizing both 16S rRNA amplicon and shotgun metagenomic sequencing to fill this knowledge gap. We collected bulk soil samples from four distinct sites, including pond sediments and soils beneath ginkgo and pine trees, to capture a range of environmental conditions within this conserved greenspace. Both 16S rRNA amplicon sequencing and shotgun metagenomic sequencing revealed that Pseudomonadota and Actinomycetota were the predominant phyla across all samples. Notably, sites with monoculture vegetation, such as those beneath pine trees, exhibited lower microbial diversity than other locations. Functional annotation identified core metabolic pathways and detected specific antimicrobial resistance and virulence factor genes in selected samples. These datasets provide a critical baseline for future research into urban ecosystem dynamics, soil health, and the intersection of environmental conservation and public health.

microbiology↗

bioRxiv2025

Pathological Angiogenesis Precedes the Onset of Aortic Dissection

Aortic dissection (AD) is a severe, life-threatening disease that occurs abruptly1. Although remodeling and inherent vulnerability of the aortic media, as observed in heritable connective tissue disorders such as Marfan syndrome, have been implicated in the onset of AD, the precise pathological mechanisms underlying the non-heritable form, which accounts for most cases, remains largely unknown2. Here, using hyperacute AD patient-derived samples, we show that pathological angiogenesis within the aortic media precedes the onset of dissection. Integrating single-cell transcriptomic analysis of aortic medial endothelial cells with high-resolution imaging revealed temporal changes preceding dissection. Hypoxic alterations in the media triggered osteochondrogenic changes in smooth muscle cells, promoted hydroxyapatite deposition, and induced angiogenesis via VEGF secretion from AD-specific CD14+CD68+CD163+MRC1(CD206)neg-low macrophages. Atomic force microscopy revealed that these processes culminated in the formation of a soft capillary layer, potentially concentrating stress on this region and contributing to AD onset. H&E staining of archived specimens revealed that non-heritable AD can be classified into angiogenic or non-angiogenic subtypes, with more than half exhibiting the former. In contrast, acute AD cases associated with Marfan syndrome typically exhibit a non-angiogenic pattern, suggesting distinct underlying mechanisms. This study reports angiogenesis as a key pathological driver in non-heritable AD and highlight potential targets for early diagnosis, prevention, and treatment.

pathology↗

bioRxiv2024

Extracellular vesicles adhere to cells predominantly through the interaction of CD151-associated integrin heterodimers and GM1 with laminin

Tumor-derived extracellular vesicles (EVs) have attracted significant attention, yet the molecular mechanisms that govern their specific binding to recipient cells remain elusive. Our in vitro study utilizing single-particle tracking demonstrated that integrin heterodimers comprising 6{beta}4 and 6{beta}1 and ganglioside, GM1 are responsible for the binding of small-EV (sEV) subtypes to laminin. EVs derived from four distinct tumor cell lines, regardless of size, exhibited high binding affinities for laminin but not for fibronectin, although fibronectin receptors are abundant in EVs and have functional roles in EV-secreting cells. Our findings revealed that integrins in EVs bind to laminin via the conventional molecular interface, facilitated by CD151 rather than by inside-out signaling of talin-1 and kindlin-2. Super-resolution movie observation revealed that sEV integrins bind only to laminin on living recipient cells. Furthermore, sEVs bound to HUVEC and induced cell branching morphogenesis in a laminin-dependent manner. Thus, we demonstrated that EVs predominantly bind to laminin on recipient cells, which is indispensable for cell responses. SummaryQuantitative assessments using single-molecule imaging and super-resolution microscopy revealed that all extracellular vesicle subtypes derived from four distinct tumor cell lines, regardless of size, bind to laminin predominantly via CD151-facilitated integrin heterodimers and GM1, leading to response of recipient cells.

cell biology↗

bioRxiv2024

The uptake of small extracellular vesicles by recipient cells is facilitated by paracrine adhesion signaling

Small extracellular vesicles (sEVs) play crucial roles in intercellular communication. However, the internalization of individual sEVs by recipient cells has not yet been directly observed. Here, we examined these mechanisms using state-of-the-art imaging techniques. Single-molecule imaging showed that tumor-derived sEVs can be classified into several subtypes. Simultaneous single-sEV particle tracking and observation of super-resolution movies of membrane invaginations in living cells revealed that all sEV subtypes were internalized via clathrin-independent endocytosis mediated by galectin-3 and LAMP-2C, while some subtypes that recruited raft markers were internalized through caveolae. Integrin {beta}1 and talin-1 accumulated in recipient cell plasma membranes beneath all sEV subtypes. Paracrine, but not autocrine, sEV binding triggered Ca2+ mobilization induced by the activation of Src family kinases and PLC{gamma}. Subsequent Ca2+-induced activation of calcineurin-dynamin promoted sEV internalization, leading to the recycling pathway. Thus, we have clarified the detailed mechanisms of sEV internalization driven by paracrine adhesion signaling.

cell biology↗

bioRxiv2023

Phylogenomics reveals the demography of reverse colonization in a rail species

AimIslands have recently been recognized as potential sources of biodiversity, challenging the traditional view that their small population sizes and low genetic diversity limit such roles. This raises the question of how insular genetic variation becomes incorporated into continental populations, contrary to expectations of unidirectional colonization. Here, we investigate whether and how island-derived genetic variation has influenced a continental population through population establishment and gene flow in a bird species where frequent trans-ocean dispersal is expected. LocationContinental East Asia (Russian Far East), Japanese Archipelago TaxonSwinhoes Rail (Coturnicops exquisitus) Materials and MethodsWe apply integrative phylogenomics to reconstruct the spatiotemporal history of the species. Colonization sequences and gene flow are inferred by comparing four different phylogenetic reconstruction methods, using mitochondrial sequences obtained by Sanger sequencing and genome-wide data obtained by genotyping by sequencing (MIG-seq). We assess a history of colonization and gene flow based on summary statistics, demographic trajectory inference by Stairway Plot2, demographic modeling by fastsimcoal2, and species distribution modeling. ResultsAnalyses collectively supported asymmetric gene flow from the island to the continental population, following divergence around the Middle Pleistocene. Post-divergence, the island maintained a large and stable population, while the continental population underwent a severe bottleneck, suggesting a significant evolutionary role of the island for the continental population. Additionally, evidence of recent re-establishment of the island by continental individuals indicates dynamic exchange and persistence within a continent-island metapopulation. Main conclusionsThe maintenance of insular genetic variation within a dynamic continent-island metapopulation may have enabled the island to act as a genetic and demographic reservoir for the continental population. Thus, continent-island metapopulation dynamics may be a key evolutionary pathway through which island populations contribute to continental genetic diversity.

evolutionary biology↗

bioRxiv2023

Inhibitory effect of Ephedra herba on human norovirus infection in human intestinal organoids

Human norovirus (HuNoV) is a major cause of acute gastroenteritis and foodborne diseases worldwide with public health concern, yet no antiviral therapies have been developed. In this study, we aimed to screen crude drugs, which are components of Japanese traditional medicine, Kampo" to see their effects on HuNoV infection using a reproducible HuNoV cultivation system, stem-cell derived human intestinal organoids/enteroids (HIOs). Among the 23 crude drugs tested, Ephedra herba significantly inhibited HuNoV infection in HIOs. A time-of-drug addition experiment indicated that this crude drug likely targets post-entry step for the inhibition. To our knowledge, this is the first anti-HuNoV inhibitor screen targeting crude drugs, and Ephedra herba was identified as a novel inhibitor candidate that merits further study.

microbiology↗

bioRxiv2023

Mass cytometry identifies characteristic immune cell subsets in bronchoalveolar lavage fluid from interstitial lung diseases

Immune cells have been implicated in interstitial lung diseases (ILDs), although their phenotypes and effector mechanisms remain poorly understood. To better understand these cells, we conducted an exploratory mass cytometry analysis of immune cell subsets in bronchoalveolar lavage fluid (BALF) from patients with idiopathic pulmonary fibrosis (IPF), connective-tissue disease (CTD)-related ILD, and sarcoidosis, using two panels including 64 markers. Among myeloid cells, we observed the expansion of CD14+ CD36hi CD84hi monocyte populations in IPF. These CD14+ CD36hi CD84hi subsets were also increased in ILDs with a progressive phenotype, particularly in a case of acute exacerbation (AEx) of IPF. Analysis of B cells revealed the presence of cells at various stages of differentiation in BALF, with a higher percentage of IgG memory B cells in CTD-ILDs and a trend toward more FCRL5+ B cells. These FCRL5+B cells were also present in the patient with AEx-IPF and sarcoidosis with advanced lung lesions. Among T cells, we found increased levels of IL-2R+TIGIT+ LAG3+ CD4+T cells in IPF, increased levels of CXCR3+ CD226+ CD4+ T cells in sarcoidosis, and increased levels of PD1+ TIGIT+ CD57+ CD8+ T cells in CTD-ILDs. Together, these findings underscore the diverse immunopathogenesis of ILDs.

immunology↗

bioRxiv2022

Gene model correction for PVRIG in single cell and bulk sequencing data enables accurate detection and study of its functional relevance

Single cell RNA sequencing (scRNA-seq) has gained increased popularity in recent years and has revolutionized the study of cell populations; however, this technology presents several caveats regarding specific gene expression measurement. Here we examine the expression levels of several immune checkpoint genes, which are currently assessed in clinical studies. We find that unlike in most bulk sequencing studies, PVRIG, a novel immune-modulatory receptor in the DNAM-1 axis, suffers from poor detection in 10x Chromium scRNA-seq and other types of assays that utilize the GENCODE transcriptomic reference (gene model). We show that the default GENCODE gene model, typically used in the analysis of such data, is incorrect in the PVRIG genomic region and demonstrate that fixing the gene model recovers genuine PVRIG expression levels. We explore computational strategies for resolving multi-gene mapped reads, such as those implemented in RSEM and STARsolo and find that they provide a partial solution to the problem. Our study provides means to better interrogate the expression of PVRIG in scRNA-seq and emphasizes the importance of optimizing gene models and alignment algorithms to enable accurate gene expression measurement in scRNA-seq and bulk sequencing. The methodology applied here for PVRIG can be applied to other genes with similar issues.

bioinformatics↗

bioRxiv2020

Isolation and characterization of a novel phage SaGU1 that infects Staphylococcus aureus clinical isolates from patients with atopic dermatitis

The bacterium Staphylococcus aureus, which grows on healthy human skin, may cause diseases such as atopic dermatitis (AD). Treatment for such AD cases involves antibiotic use; however, alternate treatments are preferred owing to the development of antimicrobial resistance. This study aimed to characterize the novel bacteriophage SaGU1 as a potential agent for phage therapy to treat S. aureus infections. SaGU1 that infects S. aureus strains previously isolated from the skin of patients with AD was screened from sewage samples in Gifu, Japan. Its genome was sequenced and analyzed using bioinformatics tools, and the morphology, lytic activity, stability, and host range of the phage were determined. The SaGU1 genome consisted of 140,909 bp with an average GC content of 30.2%. The viral chromosome contained putative 225 protein-coding genes and four tRNA genes, carrying neither toxic nor antibiotic resistance genes. Electron microscopy analysis revealed that SaGU1 belongs to the Myoviridae family. Stability tests showed that SaGU1 was heat-stable under physiological and acidic conditions. Host-range testing revealed that SaGU1 could infect a broad range of S. aureus clinical isolates present on the skin of patients with AD, whereas it did not kill strains of Staphylococcus epidermidis, which are symbiotic bacteria in the human skin microbiota. Our data suggest that SaGU1 is a potential candidate for developing a phage therapy to treat AD caused by pathogenic S. aureus.

microbiology↗

bioRxiv2019

Effective connectivity during autobiographical memory search

Autobiographical memory (AM) retrieval is known to recruit a widely distributed network of brain regions but much less is known regarding how these regions interact during the various phases that presumably take place during episodic memory retrieval in general and AM retrieval in particular. Here, we used dynamic causal modeling (DCM) to examine effective connectivity during cued AM search in a sub-network consisting of six major regions within this large network. Functional MRI data was acquired while participants were visually presented verbal cues describing common life events and requested to search for a personal memory that could be associated with each cue. We examined directed couplings between the ventromedial (vmPFC), dorsomedial (dmPFC) and dorsolateral prefrontal cortices (dlPFC), hippocampus, angular gyrus and a region in the posterior midline cortex (RSC/PCC/Prec), all located in the left hemisphere. Results indicated that during AM search, the vmPFC, dlPFC and RSC/PCC/Prec acted as primary drivers of activity in the rest of the network. Moreover, when AM search was completed successfully (Hits), an up-modulation of the effective connectivity of the hippocampus in the vmPFC and angular gyrus was observed. In the same way, there was an increase in the influence of the RSC/PCC/Prec in the activity of the dlPFC and dmPFC. Furthermore, during Hits the angular gyrus showed to have an inhibitory effect in all other nodes of the network. These results are consistent with the notion that midline cortical regions are crucial in supporting the retrieval of AMs, and highlight the interplay between the vmPFC and the RSC/PCC/Prec and the dlPFC during AM search.

neuroscience↗

bioRxiv2019

Engineering Phage Host-Range and Suppressing Bacterial Resistance Through Phage Tail Fiber Mutagenesis

The rapid emergence of antibiotic-resistant infections is prompting increased interest in phage-based antimicrobials. However, acquisition of resistance by bacteria is a major issue in the successful development of phage therapies. Through natural evolution and structural modeling, we identified host-range determining regions (HRDR) in the T3 phage tail fiber protein and developed a high-throughput strategy to genetically engineer these regions through site-directed mutagenesis. Inspired by antibody specificity engineering, this approach generates deep functional diversity (>107 different members), while minimizing disruptions to the overall protein structure, resulting in synthetic \"phagebodies\". We showed that mutating HRDRs yields phagebodies with altered host-ranges. Select phagebodies enable long-term suppression of bacterial growth by preventing the appearance of resistance in vitro and are functional in vivo using a mouse skin infection model. We anticipate this approach may facilitate the creation of next-generation antimicrobials that slow resistance development and could be extended to other viral scaffolds for a broad range of applications.\n\nHighlightsO_LIVastly diverse phagebody libraries containing 107 different members were created.\nC_LIO_LIStructure-informed engineering of viral tail fibers efficiently generated host-range alterations.\nC_LIO_LIPhagebodies prevented the development of bacterial resistance across long timescales in vitro and are functional in vivo.\nC_LI

synthetic biology↗