Biology subjects

Abe, K.

Publications and source records attributed to Abe, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

High-speed atomic force microscopy reveals surface-catalyzed elongation mechanism of fungal functional amyloid, hydrophobin RolA

Hydrophobins, a type of functional amyloid, are conserved in filamentous fungi and act as a protective coat in the fibrous form called rodlet. Rodlets form hierarchical structures where they are bundled and densely aligned, contributing to the hydrophobicity of the mycelium surface. However, the formation mechanism of the hierarchical structures is completely unknown. In this study we used high-speed atomic force microscopy to directly observe the structural dynamics of hierarchical structure formation by hydrophobin RolA from the industrial fungus Aspergillus oryzae at a single-fibril level and revealed its mechanism. The elongation of rodlets occurred at both ends and was discontinuous, alternating between periods when they could elongate (growth state) and could not elongate (pause state). This suggests an equilibrium of two distinct structural states at the rodlet ends. We also discovered an aggregation pathway, termed "surface-catalyzed elongation", in which elongation is promoted by lateral interactions between bundled rodlets. Surface-catalyzed elongation decreased the energy barrier of both structural switching between growth and pause states and elongation at rodlet ends, doubling the elongation rate in bundled rodlets. The rodlet surface could be considered as a catalyst for the elongation of neighboring rodlets. Surface-catalyzed elongation could contribute to rodlet bundling, whereby rodlets tend to form oriented domain structures, and our Monte Carlo simulations confirmed this. Surface-catalyzed elongation may be a universal concept to explain the hierarchical assembly mechanism of amyloid fibrils, so it could contribute to the advancement of amyloid research in general.

biophysics↗

bioRxiv2025

Intermingled representation of oral cavity in mouse trigeminal ganglion

Somatotopy serves as a fundamental principle underlying sensory information processing, traditionally emphasized in the study of the cerebral cortex. However, little effort has been directed towards unraveling the spatial organization characterizing the earlier stages of sensory pathways. In this study, we developed a novel methodology to visualize individual neurons within the trigeminal ganglion--a crucial cluster of cell bodies of sensory neurons innervating the face. Our investigations revealed a reliable sensory response to stimulation of the lower teeth or lip within this ganglion. The responsive neurons were confined to a specific portion of the trigeminal ganglion, consistent with innervation of the lower oral cavity by the mandibular nerve. Contrary to our expectations, we did not observe a discernible map delineating specific regions of the oral cavity. Instead, the spatial representation of the teeth and lips exhibited unexpected intermingling. These findings challenge conventional understandings rooted in cortical maps and suggest that such conceptual frameworks may not be applicable to earlier stages of sensory pathways for the oral cavity. Our study sheds light on the complex spatial organization of sensory processing in the trigeminal system, highlighting the need for further research to elucidate the underlying mechanisms and implications for sensory perception and clinical interventions. Impact statementIn vivo calcium imaging revealed that neurons responding to tooth stimulation are sparsely distributed in the trigeminal ganglion, intermixed with neurons responding to lip stimulation.

neuroscience↗

bioRxiv2025

Anti-amyloid beta therapy resolves stroke recovery impairment caused by Alzheimer's disease

Stroke and dementia are common comorbidities and a growing concern causing disability in aging societies worldwide. Although anti-amyloid beta (anti-A{beta}) antibodies have recently been anticipated to relieve preclinical Alzheimers disease pathology, we discovered that post-stroke administration of anti-A{beta} antibodies restored neural repair for stroke recovery impeded by cerebral A{beta} accumulation. Neuronal recovery-associated gene expression for stroke recovery was considerably impaired even by slight A{beta} accumulation in murine and human brain. Slight A{beta} accumulation had less impact on neurons without stroke but caused a unique myeloid immunity after an ischemic stroke that enhanced the inflammatory cascades impeding neural repair for stroke recovery. Aducanumab administration after ischemic stroke prevented formation of this malignant myeloid immunity, resolving the impairment of post-stroke neural repair caused by cerebral A{beta} accumulation. Thus, our study has revealed the ability of anti-A{beta} therapies to restore functional recovery after a stroke with cerebral A{beta} accumulation.

neuroscience↗

bioRxiv2025

Consolidation of a recurrent choice pattern into a fixed action schema requires the orbitofrontal cortex

Our actions are crystallized by repetition, warranting the efficiency, reproducibility and stability of decisions. Unlike a habit that is formally defined as insensitive to reward value, such persistency in choice can still be shaped and executed in a goal-directed manner, which underlies many volitional behaviors in animals. Yet, largely due to the absence of an established procedure that accesses non-habitual but persistent patterns of choice in animal models, empirical findings that identify its neural substrates are lacking. Using a cost-benefit conflicting decision paradigm in rodents, we here introduce an experimental procedure involving extensive decision opportunities in a fixed contingency, whereby mice acquire a recurrent pattern of choice and shape it into a fixed schema of goal-directed action to guide behavior. A subsequent functional screening of neural circuitry by chemogenetic inhibition reveals the orbitofrontal cortex (OFC) as a candidate for this form of choice. Notably, we found that OFC plays a specific role in embedding the recurrent choice pattern into the fixed schema for action selection, but not in merely defining conflicting choice. Consistently, we uncover that OFC ablation leaves animals ability intact to make a conflicting choice, but selectively disrupts the formation of the fixed action schema. These findings suggest that OFC is crucial to ensure persistency in action selection by solidifying extensive history of recurrent choices into a firmly established schema of action selection, providing novel insights into how the stability and persistency of behavior are held in the brain.

neuroscience↗

bioRxiv2025

Astringent flavanol fires the locus-noradrenergic system, regulating neurobehavior and autonomic nerves

Astringent flavanols (FLs) have shown enhanced cognitive function in a large intervention trial, but their mechanism remains unclear due to poor bioavailability. An oral dose of FLs increased spontaneous locomotion and memory, with activation of the sympathetic-adrenergic-medullary (SAM) and hypothalamic-pituitary-adrenal (HPA) axis, as shown by increased urinary catecholamine concentrations and corticotropin-releasing hormone (CRH) mRNA expression in the paraventricular nucleus (PVN) of mice. MS imaging showed high intensity of noradrenaline (NA) in the locus coeruleus (LC), which plays a key role in learning and memory, the hypothalamus lateral preoptic area, which affects sleep and arousal, and the brainstem as the origin of the sympathetic nervous system, immediately after FLs administration. Subsequent in situ hybridization (ISH) analysis showed that these NAs originated from LC. Astringent compounds like FLs influence brain function and physiological changes. Furthermore, the present series of results presents novel mechanisms by which food sensory properties maintain homeostasis. Highlights- A oral dose of astringent flavanols (FLs) immediately fires locus coeruleus-noradrenaline axis - FLs enhance spontaneous locomotion and short-term memory in mice - SAM and HPA axis are also activated by an oral dose of FLs - FLs astringency affects the brain and body, contributing to homeostasis.

synthetic biology↗

bioRxiv2025

High-Throughput Assessment of Vocal Modulation Following Chemogenetic Inhibition in Songbirds

Chemogenetic tools that enable temporary and repeatable manipulation of neuronal activity have become essential for studying the precise neural underpinning of animal behavior. However, their application has so far been limited to songbirds, which are widely used to study behaviors related to vocal communication. In this study, we applied and evaluated designer receptors exclusively activated by designer drugs (DREADD)-mediated neural suppression in songbirds brains, focusing on its impacts on vocalizations. We found that neuronal activity in zebra finches (Taeniopygia guttata) can be effectively suppressed both in vitro and in vivo using the inhibitory DREADD by its ligand deschloroclozapine (DCZ). By establishing a high-throughput system for recording and analyzing their vocalizations, we systematically assessed the effects of DREADD-mediated suppression on song behavior. Inhibiting HVC in zebra finches led to a reduction in song production number for approximately 90 min and altered phonological features over a longer time course. Notably, the concentration of DCZ required to induce robust effects on song behaviors was higher than doses typically used in mice. Furthermore, suppression of HVC or Area X in Bengalese finches (Lonchura striata domestica) produced a distinct effect on song features, suggesting species-specific responses to chemogenetic intervention. These findings refine the use of chemogenetic tools in songbirds and provide new insights into the neural mechanisms underlying vocal communication.

neuroscience↗

bioRxiv2025

Linear ubiquitination triggers Amph-mediated T-tubule biogenesis

T-tubules are specialized invaginations of the plasma membrane essential for muscle contraction. While their physiological importance is well established, the mechanisms underlying T-tubule formation remain elusive. Here, we identify LUBEL/RNF31, a ubiquitin E3 ligase responsible for linear (M1-linked) ubiquitination, as a key regulator of T-tubule biogenesis through proximity proteomics and RNAi screening in Drosophila. Loss of LUBEL leads to the formation of Amphiphysin (Amph)-positive membrane sheets instead of tubular networks in muscle cells. Mechanistically, the ubiquitin ligase activity of LUBEL, and direct interaction with Amph, a BAR domain protein involved in membrane tubule extension, are crucial for proper T-tubule morphology. LUBEL and M1-linked ubiquitin chains assemble into condensates on membranes, facilitating Amph-mediated membrane tubulation. Notably, the Amph-LUBEL/RNF31 interaction is evolutionarily conserved across a broad range of species, underscoring a fundamental role for linear ubiquitination in membrane remodeling. Our findings uncover a previously unrecognized role for linear ubiquitination in membrane deformation driven by BAR domain proteins.

cell biology↗

bioRxiv2025

Single-AAV CRISPR editing of skeletal muscle in non-human primates with NanoCas, an ultracompact nuclease

CRISPR gene editing is a transformative technology for addressing genetic diseases, but delivery constraints have largely limited its therapeutic applications to liver-targeted and ex vivo therapies. Here, we present the discovery and engineering of NanoCas, an ultracompact CRISPR nuclease capable of extending CRISPRs reach in vivo beyond liver targets. We experimentally screened 176 ultracompact CRISPR systems found in metagenomic data and applied protein engineering approaches to enhance the editing efficiency of NanoCas. The optimized NanoCas exhibits potent editing capabilities across various cell systems and tissues in vivo when administered via adeno-associated viral (AAV) vectors. This is accomplished despite NanoCas being approximately one-third the size of conventional CRISPR nucleases. In proof-of-concept experiments, we observed robust editing with our optimized NanoCas in mouse models targeting Pcsk9, a gene involved in cholesterol regulation, and targeting exon splice sites in dystrophin to address Duchenne muscular dystrophy (DMD) mutations. We further tested the efficacy of our NanoCas system in vivo in non-human primates (NHPs) resulting in editing levels above 30% in muscle tissues. The compact size of NanoCas, in combination with robust nuclease editing, opens the door for single-AAV editing of non-liver tissues in vivo, including the use of newer editing modalities such as reverse transcriptase (RT) editing, base editing, and epigenetic editing.

bioengineering↗

bioRxiv2024

mmVelo: A deep generative model for estimating cell state-dependent dynamics across multiple modalities

Single-cell multiomics provides unique insight into the regulatory relationships across different biological layers such as the transcriptome and regulome. However, single-cell multiomics is limited by its ability to capture only static snapshots at the time of observation, restricting the reflection of dynamic state changes orchestrated across modalities. RNA velocity analysis of single cells allows for the prediction of temporal changes in the transcriptome; however, the inferred dynamics cannot be applied across all biological layers, specifically in the regulome. Therefore, to address this limitation, we developed multimodal velocity of single cells (mmVelo), a deep generative model designed to estimate cell state-dependent dynamics across multiple modalities. mmVelo estimates cell state dynamics based on spliced and unspliced mRNA expression, and uses multimodal representation learning to project these dynamics onto chromatin accessibility, inferring chromatin velocity at a single-peak resolution. We applied mmVelo to single-cell multiomics data from a developing mouse brain and validated the accuracy of the estimated chromatin accessibility dynamics. Furthermore, using the estimated dynamics, we identified the transcription factors that are crucial for chromatin accessibility regulation in mouse skin. Finally, using multiomics data as a bridge, we demonstrated that during human brain development, the dynamics of missing modalities can be inferred from single-modal data via cross-modal generation. Overall, mmVelo enhances our understanding of the dynamic interactions between modalities, offering insights into the regulatory relationships across molecular layers.

bioinformatics↗

bioRxiv2024

scSurv: a deep generative model for single-cell survival analysis

Single-cell omics analysis has unveiled the heterogeneity of various cell types within tumors. However, no methodology currently reveals how this heterogeneity influences cancer patient survival at single-cell resolution. Here, we introduce scSurv, combining a Cox proportional hazards model with a deep generative model of single-cell transcriptome, to estimate individual cellular contributions to clinical outcomes. The accuracy of scSurv was validated using both simulated and real datasets. This method identifies cells associated with favorable or adverse prognoses and extracts genes correlated with their contribution levels. In melanoma, scSurv reproduces known prognostic macrophage classifications and facilitates hazard mapping through spatial transcriptomics in renal cell carcinoma. We also identified genes consistently associated with prognosis across multiple cancers and demonstrated the applicability of this method to infectious diseases. scSurv is a novel framework for quantifying the heterogeneity of individual cellular effects on clinical outcomes.

bioinformatics↗

bioRxiv2024

Tertiary lymphoid structure as a therapeutic target of Crohns disease: modulation by TNFα blockade

Inflammatory diseases, such as Crohns disease (CD), are primarily treated with therapies aimed at alleviating inflammation. Notably, biological agents like TNF inhibitors have transformed the management of these conditions. Previous research has indicated that TNF inhibitors affect the cells in the lamina propria. However, this study demonstrates that infliximab, a type of TNF inhibitor, reduces the presence of tertiary lymphoid structures (TLS) and alleviates inflammation of CD by targeting follicular dendritic cells and macrophages within these structures. TLS could also be a potential target for various biological agents used to treat inflammatory diseases beyond CD. Furthermore, our study suggests that the status of TLS may serve as a predictor for the response to TNF inhibitor treatment. Our research could pave the way for new treatment strategies and the advancement of personalized medicine for inflammatory diseases.

immunology↗

bioRxiv2024

Altered renal vascular patterning reduces ischemic kidney injury and limits vascular loss associated with aging

The kidney vasculature has a complex arrangement, which runs in both series and parallel to perfuse the renal tissue and appropriately filter plasma. Recent studies have demonstrated that the development of this vascular pattern is dependent on netrin-1 secreted by renal stromal progenitors. Mice lacking netrin-1 develop an arterial tree with stochastic branching, particularly of the large interlobar vessels. The current study investigated whether abnormalities in renal vascular pattern altered kidney function or response to injury. To examine this, we analyzed kidney function at baseline as well as in response to recovery from a model of bilateral ischemic injury and measured vascular dynamics in aged mice. We found no differences in kidney function or morphology at baseline between mice with an abnormal arterial pattern compared to control. Interestingly, male and female mutant mice with stochastic vascular patterning showed a reduction in tubular injury in response to ischemia. Similarly, mutant mice also had a preservation of perfused vasculature with aging compared to a reduction in the control group. These results suggest that guided and organized patterning of the renal vasculature may not be required for normal kidney function; thus, modulating renal vascular patterning may represent an effective therapeutic strategy. Understanding how patterning and maturation of the arterial tree affects physiology and response to injury or aging has important implications for enhancing kidney regeneration and tissue engineering strategies.

cell biology↗

bioRxiv2024

Multi-color fluorescence live-cell imaging in Dictyostelium discoideum

The cellular slime mold Dictyostelium discoideum, a member of the Amoebozoa, has been extensively studied in cell and developmental biology. D. discoideum is unique in that they are genetically tractable, with a wealth of data accumulated over half a century of research. Fluorescence live-cell imaging of D. discoideum has greatly facilitated studies on fundamental topics, including cytokinesis, phagocytosis, and cell migration. Additionally, its unique life cycle places Dictyostelium at the forefront of understanding aggregative multicellularity, a recurring evolutionary trait found across the Opisthokonta and Amoebozoa clades. The use of multiple fluorescent proteins (FP) and labels with separable spectral properties is critical for tracking cells in aggregates and identifying co-occurring biomolecular events and factors that underlie the dynamics of the cytoskeleton, membrane lipids, second messengers, and gene expression. However, in D. discoideum, the number of frequently used FP species is limited to two or three. In this study, we explored the use of new-generation FP for practical 4- to 5-color fluorescence imaging of D. discoideum. We showed that the yellow fluorescent protein Achilles and the red fluorescent protein mScarlet-I both yield high signals and allow sensitive detection of rapid gene induction. The color palette was further expanded to include blue (mTagBFP2 and mTurquosie2), large Stoke-shift LSSmGFP, and near-infrared (miRFP670nano3) FPs, in addition to the HaloTag ligand SaraFluor 650T. Thus, we demonstrated the feasibility of deploying 4- and 5- color imaging of D. discoideum using conventional confocal microscopy.

cell biology↗

bioRxiv2024

Unsupervised alignment reveals structural commonalities and differences in neural representations of natural scenes across individuals and brain areas

Neuroscience research has extensively explored the commonality of neural representations of sensory stimuli across individuals to uncover universal neural mechanisms in the encoding of sensory information. To compare neural representations across different brains, Representational Similarity Analysis (RSA) has been used, which focuses on the similarity structures of neural representations for different stimuli. Despite the broad applicability and utility of RSA, one limitation is that its conventional framework assumes that neural representations of particular stimuli correspond directly to those of the same stimuli in different brains. This assumption excludes the possibility that neural representations correspond differently and limits the exploration of finer structural similarities. To overcome this limitation, we propose to use an unsupervised alignment framework based on Gromov-Wasserstein Optimal Transport (GWOT) to compare similarity structures without presupposing stimulus correspondences. This method allows for the identification of optimal correspondence between neural representations of stimuli based solely on internal neural representation relationships, and thereby provides a more detailed comparison of neural similarity structures across individuals. We applied this unsupervised alignment to investigate the commonality of representational similarity structures of natural scenes, using large datasets of Neuropixels recordings in mice and fMRI recordings in humans. We found that the similarity structure of neural representations in the same visual cortical areas can be well aligned across individuals in an unsupervised manner in both mice and humans. In contrast, we found that the degree of alignment across different brain areas cannot be fully explained by proximity in the visual processing hierarchy alone, but also found some reasonable alignment results, such that the similarity structures of higher-order visual areas can be well aligned with each other but not with lower-order visual areas. We expect that our unsupervised approach will be useful for revealing more detailed structural commonalities or differences that may not be captured by the conventional supervised approach.

neuroscience↗

bioRxiv2024

The Role of Morphological Adaptability in Vibrio cholerae's Motility and Pathogenicity

Vibrio cholerae, the etiological agent of cholera, exhibits remarkable adaptability to different environmental conditions by undergoing morphological changes that significantly contribute to its pathogenicity and impact the epidemiology of the disease globally. This study investigates the morphological adaptability of the clinically isolated V. cholerae O1 strain, specifically focusing on the motility and pathogenicity differences between the filamentous and original comma-shaped forms within diverse viscosity conditions. Utilizing the El Tor strain of V. cholerae O1, we induced the transformation into the filamentous form and performed a comparative analysis with the canonical comma-shaped morphology. Our approach involved assessing motility patterns, swimming speeds, rotation rates, kinematics, and reversal frequencies through dark-field microscopy and high-speed imaging techniques. The findings reveal that filamentous V. cholerae cell retains enhanced motility in viscous environments. This suggests an evolutionary adaptation enabling survival across a range of habitats, notably the human gastrointestinal tract. Filamentous forms demonstrated increased reversal behavior at mucin interfaces, hinting at an advantage in penetrating the mucus layer. Rabbit intestinal loop assays further showed that both morphological forms exhibit similar fluid accumulation ratios, thus indicating comparable pathogenic potentials. These results underscore the significance of V. choleraes morphological flexibility in adapting to environmental viscosity changes, shedding light on the bacteriums intricate survival and infection strategies. Our study provides critical insights into the dynamics of cholera, underlining the importance of considering bacterial morphology in developing effective cholera control strategies.

microbiology↗

bioRxiv2024

LineageVAE: Reconstructing Historical Cell States and Transcriptomes toward Unobserved Progenitors

AO_SCPLOWBSTRACTC_SCPLOWSingle-cell RNA sequencing (scRNA-seq) enables comprehensive characterization of the cell state. However, its destructive nature prohibits measuring gene expression changes during dynamic processes such as embryogenesis. Although recent studies integrating scRNA-seq with lineage tracing have provided clonal insights between progenitor and mature cells, challenges remain. Because of their experimental nature, observations are sparse, and cells observed in the early state are not the exact progenitors of cells observed at later time points. To overcome these limitations, we developed LineageVAE, a novel computational methodology that utilizes deep learning based on the property that cells sharing barcodes have identical progenitors. This approach transforms scRNA-seq observations with an identical lineage barcode into sequential trajectories toward a common progenitor in a latent cell state space. Using hematopoiesis and reprogrammed fibroblast datasets, we demonstrate the capability of LineageVAE to reconstruct unobservable cell state transitions, historical transcriptome, and regulatory dynamics toward progenitor cell states at single-cell resolution.

bioinformatics↗

bioRxiv2024

Beta-Glucanase superfamily identified by sequential, functional, and structural analyses

{beta}-1,2-Glucans are natural glucose polymers that play important physiological roles, including as symbiotic or pathogenic factors and in osmoregulation. Phylogenetically new glycoside hydrolase (GH) families have recently been identified from {beta}-1,2-glucanase (SGL) sequences from bacteria (GH144) and a fungus (GH162). In this study, we identified four phylogenetically new groups (Groups 1-4), and determined that these families, together with GH144, GH162, and GH189, a family of transglycosylase domains in cyclic {beta}-1,2-glucan synthases, form a superfamily. Biochemical analysis of six proteins in these groups revealed that the proteins in Groups 1-3 showed hydrolytic activity specific to {beta}-1,2-glucan. The kinetic parameters of the enzymes of Groups 1-3 were similar to GH144 and GH162 SGLs, indicating that these enzymes were SGLs. Optical rotation analysis revealed that the SGLs followed an anomer-inverting mechanism. Structural analysis and prediction of the proteins in Groups 1-4, GH144, GH162, and GH189 suggested that Groups 1-3 and GH144 had the same reaction mechanism. Nevertheless, Groups 1-3 were dispersed irregularly in the superfamily. Overall, we determined that Groups 1-3 were new GH families, GHxxx, GHyyy, and GHzzz, respectively, and proposed that this superfamily be called an SGL superfamily because of the phylogenetical, functional, and structural relationships within the superfamily. HighlightsWide variety of glycoside hydrolases is far beyond our understanding. Functional and structural analysis identified three new glycoside hydrolase families. Molecular evolution with irregular changes in reaction mechanism was revealed.

biochemistry↗

bioRxiv2023

MCFBM: a behavioral analysis system enabling objective inference of songbirds' attention during social interactions

Understanding animal behavior is crucial in behavioral neuroscience, which aims to unravel the mechanism driving these behaviors. A milestone in this field is the analysis of behavioral reactions among animals engaging in social interactions. Although many studies have revealed the fundamental roles of social interaction in social learning, the behavioral aspects of these interactions remain poorly understood, largely due to the lack of tools for analyzing complex behaviors and the attention of subjects in naturalistic, free-moving conditions. Here, we introduce a high-precision system for behavior analysis in songbirds using a marker-based motion capture technique. This system accurately tracks the body location and head direction of freely moving finches and is applicable to multiple subjects during social interaction. With this system, we have quantitatively analyzed behaviors of zebra finches (Taeniopygia guttata) related to visual attention. Our analysis revealed variations in the use of right and left eyes, as well as the duration of sight, among the individuals presented. Further analysis and comparison of their behaviors during both virtual and live presentation identified the similarities and differences in their behavioral reactions. Additionally, we observed changes in their behavioral reactions during a conditioned learning paradigm. This system provides an efficient and easy-to-use tool for advanced behavioral analysis in songbirds, providing an objective method to infer their focus of attention.

animal behavior and cognition↗