Biology subjects

Suzuki, R.

Publications and source records attributed to Suzuki, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Correlation-resolved sum-frequency generation microscopy of biological tissue with bright twin beams

Sum-frequency generation (SFG) driven by bright twin beams generated through high-gain parametric down-conversion comprises a coherent component arising from correlated mode pairs and an incoherent component arising from interactions between uncorrelated modes. Modal correlations can enhance coherent SFG in anisotropic nonlinear media, for example by extending the effective interaction length. Whether such correlations can likewise benefit image formation in heterogeneous biological tissue remains unknown. Here we address this question by performing SFG imaging of biological tissue using bright twin beams as the excitation source. Spectral decomposition of the SFG signal separates its coherent and incoherent components, allowing us to reconstruct co-registered images and examine how twin-beam correlations influence image formation. In mouse skeletal muscle, the coherent-component image revealed sarcomere periodicity with a Bragg-spot-to-background ratio of approximately 310, compared with 7.5 in the incoherent-component image. In fresh human dermis, the coherent-component image showed greater Fourier power than the incoherent-component image in the 0.30-0.50 \mu m^{-1} band and a greater fractional autocovariance decay at short spatial lags. These results demonstrate that twin-beam correlations can enhance contrast and detectability at selected spatial frequencies in heterogeneous tissue. Correlation-resolved SFG microscopy thus offers a route for exploiting bright quantum-light sources in nonlinear optical bioimaging.

biophysics↗

bioRxiv2026

Amide I kurtosis maps cardiac amyloid in human tissue by ultrabroadband multiplex coherent anti-Stokes Raman scattering (CARS) microscopy

Cardiac amyloidosis is caused by deposits of misfolded proteins in the heart and can lead to heart failure. Histological confirmation typically involves staining tissue sections with Congo red and examining them under polarized light for apple-green birefringence; however, achieving an interpretable, label-free, and observer-independent assessment remains challenging. Here we show that Pearson kurtosis of channel intensities within the amide I window provides an interpretable, fitting-free contrast for cardiac amyloid in unstained human cardiac tissue sections from ten participants imaged by ultrabroadband multiplex coherent anti-Stokes Raman scattering (CARS). In a discovery participant, high-kurtosis regions corresponded with Congo red-positive tissue in two CARS-histology pairs of adjacent sections (descriptive spatial AUCs, 0.79 and 0.73). Across 15 fields from nine additional participants, field-level kurtosis values did not overlap between severe-deposition and Congo red-negative tissue fields. Among the descriptors examined, kurtosis showed the largest standardized participant-level separation. Exploratory multivariate curve resolution yielded a deposit-associated component with aromatic-residue features shared with reagent transthyretin. In one field from the discovery participant, the second harmonic generation (SHG) signal, acquired simultaneously with CARS, showed a broadly inverse spatial pattern relative to the amide I kurtosis map, revealing distinct tissue-architectural contrast. Together, these findings support a potential label-free approach to detecting cardiac amyloid deposits that combines amide I kurtosis derived from broadband CARS with SHG-derived architectural contrast.

biophysics↗

bioRxiv2026

Global transcriptional rewiring provides recurrent evolutionary routes to insect-Escherichia coli mutualism

Microbial symbionts often evolve specialized functions that compensate for host nutritional deficiencies, yet the evolutionary routes by which such mutualisms arise remain poorly understood. Here, using an experimental symbiosis between the stinkbug Plautia stali and Escherichia coli, we investigated the early evolution of insect-bacterium mutualism. Among 144 independently evolved bacterial lineages, six acquired the ability to improve host performance. Four lineages carried independent disruptive mutations in cyaA, disabling carbon catabolite repression and thereby increasing the essential amino acid tryptophan. The remaining two lineages evolved through nonsynonymous mutations in rpoB or rpoD, encoding core components of the transcriptional machinery. Transcriptomic analyses revealed extensive regulatory rewiring in both mutants, including marked upregulation of biosynthetic pathways for branched-chain essential amino acids. Our results identify global transcriptional regulatory systems as major evolutionary targets for the emergence of mutualism and demonstrate how large-effect regulatory mutations can rapidly generate host-beneficial traits. (146 < 150 words)

evolutionary biology↗

bioRxiv2026

Comprehensive dissection of GPCR signaling using a NanoBiT-based platform

G-protein-coupled receptors (GPCRs) signal through multiple heterotrimeric G proteins, {beta}-arrestins, GPCR kinases (GRKs), and downstream effectors, whose combinatorial interactions shape cellular responses. These events are typically measured with separate assay formats that each capture only part of the network, making comparison across signaling layers difficult. Here, we consolidate a broad set of previously reported GPCR signaling interactions and assay concepts, together with newly designed sensors, into a single NanoBiT split-luciferase framework, allowing multiple layers of signal transduction to be examined side by side in living cells. We show that rational sensor engineering, in particular the positioning of NanoBiT fragments and targeted modification of the tagged proteins, is essential for detecting transient protein-protein interactions. The framework implements assays for G-protein dissociation, {beta}-arrestin recruitment, conformational activation and trafficking, and GRK recruitment, and extends to G-protein-effector and inter-effector interactions across diverse G, G{beta}, G{gamma}, {beta}-arrestin, GRK, adenylyl cyclase, PLC{beta}, and RhoGEF subtypes. It also enables real-time monitoring of the difficult-to-access G12/13-RhoGEF-RhoA pathway. Together, these assays provide a unified NanoBiT readout for systematic, side-by-side dissection of GPCR signaling.

pharmacology and toxicology↗

bioRxiv2026

Spatiotemporal Patterns of Active Deformation Reveal Downregulation of Cell-Cell Adhesion in Patient-Derived Colorectal Cancer Organoids with BRAF Mutation

Colorectal cancer (CRC) is the second most common cause of cancer-related mortality. At the molecular level, CRC is associated with genetic mutations and epigenetic modifications that dysregulate various signaling networks. From the biophysical viewpoint, invasive and metastatic cell migration need to be empowered by mechanical forces. In this study, we analyze the dynamic deformation of patient-derived CRC organoids in Fourier space and demonstrate how organoids with protooncogene BRAF mutation exhibit deformation phenotypes at an early stage. The organoids with BRAFmut have significantly lower elasticity and higher viscosity than those with BRAFWT, which mathematically indicated as the weakening of cell-cell adhesion. Immunohistochemical images, qRT-PCR, and TCGA data analysis confirm the downregulation of E-cadherin (CDH1) in BRAFmut organoids as well as in BRAFmut CRC, suggesting that the decrease in cell-cell adhesion in BRAFmut CRC facilitates invasive and metastatic migration. Notably, the recovery of CDH1 expression by pharmacological inhibition of DNA methylation can quantitatively be detected as the change in mechanical properties, suggesting that the complementary combination of dynamic phenotyping, mathematical modelling, and molecular-level analyses has a potential to unravel the mechanistic causality of the critical gene mutation and CRCs prognosis and the response to therapeutic interventions.

biophysics↗

bioRxiv2026

Cromolyn inhibits PGE2-mediated sensitisation of TRPV1 in a GPR35-dependent manner in sensory neurons

There is a pressing need for effective alternatives to opioid analgesics, the development of which requires the identification of novel anti-nociceptive drug targets. Here, we have further investigated the anti-nociceptive properties of a GPR35 agonist, cromolyn, in an in vitro model of inflammatory sensitisation. We used ratiometric Ca2+ imaging of cultured sensory neurons to examine the effect of cromolyn on prostaglandin E2 (PGE2)-mediated sensitisation of the pro-nociceptive ion channel, transient receptor potential cation channel, subfamily V, member 1 (TRPV1). The sensitisation of TRPV1 by PGE2 was inhibited by cromolyn in a GPR35-dependent manner. These observations provide further evidence in support of an anti-nociceptive role for GPR35, highlighting the potential use of GPR35 agonists as analgesics.

neuroscience↗

bioRxiv2026

A Scalable, High-Throughput Optomotor Response Pipeline for Quantitative Analysis of Vision Using Infinity-Pools

The optomotor response (OMR) provides a robust readout assay for evaluating visually guided locomotion and has been widely applied to various animal models. We present a scalable, high-throughput OMR platform with tuneable and moving stripe patterns simultaneously projected to the side of 50 petri dishes. The setup is optimized for hatchling-stage medaka (Oryzias latipes and Oryzias sakaizumii) and larval stage zebrafish (Danio rerio) and integrates custom software for automated generation of visual stimuli and specimen detection, enabling precise and automated quantification of optomotor behaviour across thousands of individuals. Using this platform, we systematically assess the visual performance of zebrafish and five medaka strains. By varying stripe width, direction, speed, contrast, and colour, we address spatial resolution, contrast, and colour sensitivity. Albino mutant medaka exhibited the highest sensitivity, responding at lower stripe widths and across a broader range of contrasts and chromatic conditions. Interestingly, some Cab and HO5 hatchlings displayed uni-directional response, revealing strain-specific visuomotor differences. Our platform enables reliable detection of OMR behaviour already at hatching and supports robust analysis of visuomotor function. The modular design, automated detection, analysis pipeline, and capacity for large sample numbers make it a powerful tool for comparative vision research, high-throughput genetic screening, and systematic behavioural profiling.

animal behavior and cognition↗

bioRxiv2025

High-Density Microdroplet Cultivation Reveals the Essential Role of Microbial Interactions in the Growth of Environmental Microbes

The significance of microbial interactions in nature is not well understood because of the limitations of techniques to assess microbial growth at the single-cell level under conditions of high cell density (more than 107 cells/mL). To address this limitation for further solution of microbial uncultivability, we developed a Gel Microdroplet Aggregate in Oil (GMD-agg) cultivation method. This method provides a high inoculum cell density (>108 cells/mL) but maintains pure cultures of each growth unit. Millions of hydrogel particles (10-30 {micro}m in diameter) entrapping single cells with medium softly aggregated in oil (GMD-oil cultivation) is the key structure of this method. In this study, to assess the effect of microbial interactions on the cultivation of environmental microorganisms, soil and activated sludge samples were cultured, and colony formation and diversity during cultivation in GMDs were investigated. Results showed that the cultivation efficiency of GMD-agg was approximately 10 times higher than that of the method in which microbial interactions were canceled. In addition, the growth of taxonomies containing many uncultured microorganisms, such as Verrucomicrobia, Planctomycetia, Acidobacteria, and Vicinimibacteria, was observed. Furthermore, when isolated strains were co-cultured at high cell densities with either inter-or intra-species, we observed a higher cultivation efficiency than when microbial interactions were canceled. Rebuilding growth-promoting microbial interactions using isolated strains demonstrated that microbial interactions positively influence microbial growth. These findings indicate the effectiveness of this cultivation method, reveal the crucial role of microbial interactions in the growth of environmental microorganisms, and contribute to solving the issue of microbial uncultivability. IMPORTANCEThe overwhelming majority of environmental microbes remain uncultured, limiting our understanding of their physiology and ecological roles. Although microbial interactions have been predicted as one of the key factors for the growth of uncultivable microbial types, the effect of these interactions on cultivability remains poorly understood. In this study, we developed a new droplet-based co-cultivation approach that promotes microbial interactions while maintaining pure cultures and enables growth tracking at the single-cell level. This method significantly improved cultivability (approximately 10 times), including the growth of taxa that are difficult to cultivate. Direct observation of microbial growth in the community using this method clearly demonstrated that microbial interactions are essential for the growth of diverse microbial types. These findings underscore the importance of microbial interactions in cultivation and offer a basis for radically expanding microbial bioresources, manipulating microbial communities, and exploring previously unrecognized microbial interactions.

microbiology↗

bioRxiv2025

A non-spike nucleocapsid R204P mutation in SARS-CoV-2 Omicron XEC enhances inflammation and pathogenicity

The global circulation of SARS-CoV-2 in human populations has driven the emergence of Omicron subvariants, which have become highly diversified through recombination. In late 2024, SARS-CoV-2 Omicron XEC variant emerged from the recombination of two JN.1 progeny, KS.1.1 and KP.3.3, and became predominant worldwide. Here, we investigated virological features of the XEC variant. Epidemic dynamics modeling suggested that spike substitutions in XEC mainly contribute to its increased viral fitness. Additionally, four licensed antivirals were effective against XEC. Although the fusogenicity of XEC spike is comparable to that of the JN.1 spike, the intrinsic pathogenicity of XEC in hamsters was significantly higher than that of JN.1. Notably, we found that the nucleocapsid R204P mutation of XEC enhanced inflammation through NF-{kappa}B activation. Recent studies suggest that the evolutionary potential of spike protein is reaching its limit. Indeed, our findings highlight the critical role of non-spike mutations in the future evolution of SARS-CoV-2.

microbiology↗

bioRxiv2025

Discovery and characterisation of gene by environment and epistatic genetic effects in a vertebrate model

Phenotypic variation arises from the interplay between genetic and environmental factors. However, disentangling these interactions for complex traits remains challenging in observational cohorts such as human biobanks. Instead, model organisms where genetic (G) and environmental (E) variation can be controlled offer a valuable complement to human studies in the analysis of higher-order genetic effects such as GxE interactions, dominance, and epistasis. Here, we utilized 76 medaka strains of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel, to compare heart rate plasticity across temperatures. An F2 segregation analysis identified 16 quantitative trait loci (QTLs), with many exhibiting dominance, GxE, GxG, and GxGxE interactions. We experimentally validated four candidate genes using gene editing, revealing their temperature-sensitive impact on heart function. Finally, we devised simulations to assess how GWAS discovery power is influenced by the choice of statistical models, showing that the apparent additivity in human GWAS is to be expected given study design and sample sizes of current studies. This work demonstrates the value of controlled model organism studies for dissecting the genetics of complex traits and provides guidance on the design of genetic association studies.

genetics↗

bioRxiv2025

Deep learning predicts tissue outcomes in retinal organoids

Retinal organoids have become important models for studying development and disease, yet stochastic heterogeneity in the formation of cell types, tissues, and phenotypes remains a major challenge. This limits our ability to precisely experimentally address the early developmental trajectories towards these outcomes. Here, we utilize deep learning to predict the differentiation path and resulting tissues in retinal organoids well before they become visually discernible. Our approach effectively bypasses the challenge of organoid-related heterogeneity in tissue formation. For this, we acquired a high-resolution time-lapse imaging dataset comprising about 1,000 organoids and over 100,000 images enabling precise temporal tracking of organoid development. By combining expert annotations with advanced image analysis of organoid morphology, we characterized the heterogeneity of the retinal pigmented epithelium (RPE) and lens tissues, as well as global organoid morphologies over time. Using this training set, our deep learning approach accurately predicts the emergence and size of RPE and lens tissue formation on an organoid-by-organoid basis at early developmental stages, refining our understanding of when early lineage decisions are made. This approach advances knowledge of tissue and phenotype decision-making in organoid development and can inform the design of similar predictive platforms for other organoid systems, paving the way for more standardized and reproducible organoid research. Finally, it provides a direct focus on early developmental time points for in-depth molecular analyses, alleviated from confounding effects of heterogeneity.

developmental biology↗

bioRxiv2025

Evolution of BA.2.86 to JN.1 reveals functional changes in non-structural viral proteins are required for fitness of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), is still circulating among humans, leading to the continuous evolution. SARS-CoV-2 Omicron JN.1 evolved from a distinct SARS-CoV-2 lineage, BA.2.86, spread rapidly worldwide. It is unclear why BA.2.86 did not become dominant and was quickly replaced by JN.1, which possesses one amino acid substitution in the spike protein (S:L455S) and two in the non-spike proteins NSP6 and ORF7b (NSP6:R252K and ORF7b:F19L) compared to BA.2.86. Here, we utilized recombinant viruses to elucidate the impact of these mutations on the virological characteristics of JN.1. We found that the mutation in the spike attenuated viral replication, but the non-spike mutations enhanced replication, suggesting the mutations in the non-spike proteins compensate for the one in the spike to improve viral fitness, as the mutations in the spike contribute to further immune evasion. Our findings suggest that functional changes in both the spike and non-spike proteins are necessary in the evolution of SARS-CoV-2 to enable evasion of adaptive immunity within the human population while sustaining replication. IMPORTANCEBecause the spike protein is strongly associated with certain virological properties of SARS-CoV-2, such as immune evasion and infectivity, most previous studies on SARS-CoV-2 variants have focused on spike protein mutations. However, the non-spike proteins also contribute to infectivity, as observed throughout the evolution of Omicron subvariants. In this study, we demonstrate a "trade-off" strategy in SARS-CoV-2 Omicron JN.1 in which the reduced infectivity caused by spike mutation is compensated by non-spike mutations. Our results provide insight into the evolutionary scenario of the emerging virus in the human population.

microbiology↗

bioRxiv2025

Humidity-driven ABA depletion determines plant-pathogen competition for leaf water

Bacterial phytopathogens, such as Pseudomonas syringae pv. tomato (Pst) DC3000, induce water-soaked lesions in the leaf apoplast under high humidity, facilitating infection. However, it remains largely unclear how plants regulate their resistance to restrict bacterial infection in response to humidity. Here, we demonstrate that abscisic acid (ABA)-catabolizing ABA 8-hydroxylase, encoded by CYP707A3, plays a critical role in this resistance in Arabidopsis thaliana. Elevated humidity induces CYP707A3 expression, which is essential for reducing ABA levels and promoting stomatal opening, thereby limiting bacterial water-soaking and infection following leaf invasion. High humidity also increases cytosolic Ca2+ levels via the Ca2+ channels CNGC2 and CNGC4, with partial involvement from CNGC9, activating the calmodulin-binding transcription activator CAMTA3 to drive CYP707A3 induction. However, Pst DC3000 counteracts this defense response using type III secretion effectors, particularly AvrPtoB, facilitating water-soaking. These findings provide insights into the mechanisms underlying the competition between plants and bacteria for leaf water under elevated humidity.

plant biology↗

bioRxiv2024

Involvement of Hepatitis B Core-Related Antigen in Viral Genome Integration in Patients With Prior Hepatitis B Virus Infection

BackgroundThe incidence of non-B non-C hepatocellular carcinoma (NBNC-HCC), which is negative for hepatitis B surface antigen and hepatitis C virus antibodies, is on the rise. Relatively high numbers of NBNC-HCC patients are hepatitis B core antibody (HBcAb) positive, suggesting that previous HBV infection may play a role in NBNC-HCC development, though the exact mechanisms are unclear. This study aimed to investigate whether HBV genomes are integrated into the host genome of HBcAb-positive NBNC-HCC cases and how these integrations may contribute to cancer development and progression. MethodsHBV detection PCR using HBV-specific primers on DNA extracted from HBcAb-positive NBNC-HCC tissue samples was performed. Positive samples were further examined for HBV integration sites using viral DNA-capture sequencing. Additionally, hepatitis B core-related antigen (HBcrAg) serum levels were measured to assess whether they could be predictive for HBV detection PCR results. ResultsAmong 90 HBcAb-positive NBNC-HCC samples, HBV genome amplification was detected in 18 samples, and elevated HBcrAg levels were associated with the HBV detection PCR results. Seventeen of these samples exhibited HBV integration. The HBV genome was integrated near the TERT gene in 7 samples, resulting in significantly increased TERT mRNA levels; in the KMT2B gene (2 samples); and downstream of LOC441666 (2 samples). ConclusionThe integration sites we identified in our samples have been previously reported in HBV-related HCC, suggesting that HBV integration may also contribute to hepatocarcinogenesis in HBcAb-positive NBNC-HCC. Furthermore, HBcrAg could serve as a potential, noninvasive marker for detecting HBV integration in these cases.

microbiology↗

bioRxiv2024

Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans

We develop a data harmonization approach for C. elegans volumetric microscopy data, still or video, consisting of a standardized format, data pre-processing techniques, and a set of human-in-the-loop machine learning based analysis software tools. We unify a diverse collection of 118 whole-brain neural activity imaging datasets from 5 labs, storing these and accompanying tools in an online repository called WormID (wormid.org). We use this repository to train three existing automated cell identification algorithms to, for the first time, enable accuracy in neural identification that generalizes across labs, approaching human performance in some cases. We mine this repository to identify factors that influence the developmental positioning of neurons. To facilitate communal use of this repository, we created open-source software, code, web-based tools, and tutorials to explore and curate datasets for contribution to the scientific community. This repository provides a growing resource for experimentalists, theorists, and toolmakers to (a) study neuroanatomical organization and neural activity across diverse experimental paradigms, (b) develop and benchmark algorithms for automated neuron detection, segmentation, cell identification, tracking, and activity extraction, and (c) inform models of neurobiological development and function.

neuroscience↗

bioRxiv2024

Structural and Dynamic Insights into the Biased Signaling Mechanism of the Human Kappa Opioid Receptor

The {kappa}-opioid receptor (KOR) is a member of the G protein-coupled receptor (GPCR) family, responsible for modulating cellular responses through transducers such as G proteins and arrestins. G protein-biased KOR agonists hold promise due to their potential to mitigate side effects such as drug aversion and sedation while preserving analgesic and antipruritic effects. Here, we shed light on the structural dynamics of the human KOR-Gi signaling complex bound with either nalfurafine (a G-protein-biased agonist) or U-50,488H (a balanced agonist) using cryo-electron microscopy (cryo-EM). Cryo-EM structures of the KOR-Gi signaling complexes identify the ligand binding mode in the activated state. Vibrational spectroscopy analysis reveals changes in the ligand-binding pocket upon binding to these ligands. Cell-based mutant experiments pinpoint four amino acids (K2275.40, C2866.47, H2916.52, and Y3127.34; Ballesteros-Weinstein numbering is shown in superscript) that play crucial roles in arrestin recruitment. Among these four amino acids, H2916.52 and Y3127.34 are also implicated in G-protein coupling. Our findings pave the way for targeting specific residues in the KOR ligand-binding pocket to enhance KOR-mediated therapeutic effects while mitigating unwanted side effects.

biophysics↗

bioRxiv2024

Characterizing medaka visual features using a high-throughput optomotor response assay

Medaka fish (Oryzias latipes) is a powerful model to study genetics underlying the developmental and functional traits of the vertebrate visual system. We established a simple and high-throughput optomotor response (OMR) assay utilizing medaka larvae to study visual functions including visual acuity and contrast sensitivity. Our assay presents multiple adjustable stripes in motion to individual fish in a linear arena. For that the OMR assay employs a tablet display and the Fish Stripes software to adjust speed, width, color, and contrast of the stripes. Our results demonstrated that optomotor responses were robustly induced by black and white stripes presented from below in the linear-pool-arena. We detected robust strain specific differences in the OMR when comparing long established medaka inbred strains. We observed an interesting training effect upon the initial exposure of larvae to thick stripes, which allowed them to better respond to narrower stripes. The OMR setup and protocol presented here provide an efficient tool for quantitative phenotype mapping, addressing visual acuity, trainability of cortical neurons, color sensitivity, locomotor response, retinal regeneration and others. Our open-source setup presented here provides a crucial prerequisite for ultimately addressing the genetic basis of those processes.

animal behavior and cognition↗

bioRxiv2023

Virological characteristics of the SARS-CoV-2 BA.2.86 variant

In late 2023, a lineage of SARS-CoV-2 emerged and was named the BA.2.86 variant. BA.2.86 is phylogenetically distinct from other Omicron sublineages identified so far, displaying an accumulation of over 30 amino acid mutations in its spike protein. Here, we performed multiscale investigations to reveal the virological characteristics of the BA.2.86 variant. Our epidemic dynamics modeling suggested that the relative reproduction number of BA.2.86 is significantly higher than that of EG.5.1. Experimental studies showed that four clinically-available antivirals were effective against BA.2.86. Although the fusogenicity of BA.2.86 spike is similar to that of the parental BA.2 spike, the intrinsic pathogenicity of BA.2.86 in hamsters was significantly lower than that of BA.2. Since the growth kinetics of BA.2.86 is significantly lower than that of BA.2 in both in vitro cell cultures and in vivo, it is suggested that the attenuated pathogenicity of BA.2.86 is due to its decreased replication capacity.

microbiology↗