Biology subjects

Kudo, K.

Publications and source records attributed to Kudo, K..

17 recordsLinked to original sources

bioRxiv2026

Single-molecule bouncing at a liquid interface governs presynaptic enrichment

Many cellular processes rely on accumulating highly diffusive cytoplasmic proteins to a specific location within the cell. This spatial enrichment is generally thought to rely on locally immobilizing proteins or slowing diffusion through binding and molecular crowding. Paradoxically, cytoplasmic proteins that are enriched within nerve terminals remain highly diffusive, raising questions about the mechanisms that govern presynaptic enrichment. Here, using in vivo single-molecule microscopy, we tracked the diffusion of a model cytoplasmic protein, -Synuclein (-Syn), and synaptic vesicles (SVs), in motor neuron presynapses of live Drosophila larvae. We demonstrate that -Syn undergoes rapid and frequent "bouncing" events at a presynaptic interface, locally impeding escape from the presynapse. We measured escape probabilities at the interface, and show that impeding escape, without dramatically slowing diffusion, is sufficient to govern presynaptic enrichment. The interface is liquid-like and coincides with the boundary of the SV cluster, which is a necessary scaffold for the presynaptic enrichment of -Syn. Our results provide direct evidence of interfacial reflectivity at the interface of liquid-like compartments, and that this phenomenon can govern the subcellular enrichment of proteins and small organelles at the level of individual particles.

neuroscience↗

bioRxiv2026

Modulating supplementary motor area excitability enhances groove-related pleasure during music listening

Pleasurable urge to move to music is often referred to as groove. Although previous studies have shown an association between the supplementary motor area (SMA) and the groove experience, its causal role remains unclear. Here, we investigated whether the SMA is causally involved in groove experience during music listening using repetitive transcranial magnetic stimulation. Fifteen healthy participants completed three sessions on separate days: excitatory stimulation (intermittent theta burst stimulation; iTBS) over the SMA, inhibitory stimulation (continuous theta burst stimulation; cTBS) over the SMA, and sham stimulation (iTBS or cTBS) over the vertex. After each stimulation session, participants listened to five high-groove and five low-groove musical excerpts and rated urge-to-move and pleasure on a 0-100 scale. Heart rate was additionally recorded as an exploratory physiological measure during music listening. Linear mixed-effects models (LMM) showed that pleasure ratings, but not urge-to-move ratings, were higher following both iTBS and cTBS compared with sham stimulation. In exploratory LMMs, reduced log-transformed heart rate variability (HRV) significantly predicted higher pleasure ratings. These findings suggest that SMA stimulation modulates the pleasurable component of the groove experience, likely via network-level mechanisms rather than a simple linear relationship between SMA excitability and pleasure. They also raise the possibility that reduced parasympathetic activity, reflected by lower HRV, mediates the stimulation-related increase in musical pleasure. Future studies should investigate the causal roles of other brain regions as well as clarify the directionality between autonomic changes and the groove experience.

neuroscience↗

bioRxiv2026

Fragile streak goals induce pressure responses and an inverted-U performance pattern

Psychological pressure is thought to relate to performance in an inverted-U pattern, yet evidence is mixed, possibly because manipulations rarely produce high pressure. We induced scalable pressure using a streak goal that resets after a failure in a force-control task. Participants pursued ten consecutive successes (streak goal) or 100 successes irrespective of sequence (total goal). Under the streak goal, heart rate, pupil size, and perceived pressure rose as participants approached their maximum streak; under the total goal, heart rate and pupil size showed little modulation. Performance followed an inverted-U under the streak goal--improving then declining at the maximum streak--whereas the total goal showed no late-stage drop. This dissociation suggests the late-stage decline reflects pressure, not the streak itself. Despite this clear performance decrement, analyses of movement vigor, feedforward/feedback kinematics, and individual differences in pressure responses revealed no consistent systematic signatures at the group level. Fragile streak goals thus provide a multimodal pressure manipulation and a platform for testing mechanisms underlying choking in human motor control.

neuroscience↗

bioRxiv2025

Individual bounded rationality destabilizes cooperative dynamics in human-AI groups

Cooperative dynamics arise from interactions among individuals, including humans and artificial agents, yet it remains unclear how individual-level cognition and motion shape collective dynamics in such human-AI groups. We combined a dynamic cooperative task, in which one attacker was controlled by a human and two by heuristic artificial agents facing a deep reinforcement learning defender, with counterfactual simulations of artificial groups. Across nine task conditions, groups including a human consistently underperformed relative to groups composed solely of artificial agents. Humans exhibited restricted movement options and probabilistic rather than deterministic action choices, which shifted coordination dynamics towards less symmetric, less organized patterns and reduced performance for both individuals and groups. Embedding these boundedly rational movement and decision parameters into artificial agents reproduced human-like behavior and performance declines. These results demonstrate how limitations of a single individual can destabilize cooperative dynamics and provide insights into the design of robust human-AI systems.

animal behavior and cognition↗

bioRxiv2025

The Paradox of Unpredictability: Trying to Be Unpredictable Makes Sequences More Predictable

Human intuition about randomness is systematically biased. When asked to generate random sequences, people systematically generate too many alternations, yet game theory suggests that being unpredictable to an opponent requires true randomness. In our first experiment (50 Japanese adults), we show that when the goal shifts from being random to being unpredictable, participants do the opposite, generating sequences with a strong repetition bias. In a second experiment, we asked a new sample of 50 Japanese adults to predict two model-derived sequences that were empirically calibrated to the group-level statistics from the first Experiment (Competitive-like vs Random-like). We found a paradox: the repetitive sequences intended to be unpredictable were in fact more predictable than the alternating sequences intended to be random. This paradox appears to stem from an asymmetric reinforcement learning mechanism, whereby success selectively strengthens beliefs in repetition but not alternation. Our findings bridge classic cognitive bias and strategic behavior, suggesting how a fundamental learning mechanism can shape paradoxical predictability.

neuroscience↗

bioRxiv2025

Type I partition-related proteins enhance conjugative transfer through transcriptional activation and oriT region binding

Plasmid partitioning and bacterial conjugation are critical processes ensuring plasmid maintenance and dissemination, respectively, within bacterial populations. Although traditionally regarded as distinct phenomena, these two processes are increasingly recognized as interconnected. While partitioning ensures plasmid inheritance during cell division, its potential influence on conjugative transfer remains poorly understood. A major impediment to understanding their interplay is that partition systems are often essential for plasmid stability, making it difficult to distinguish their direct effects on conjugation. In this study, we addressed this challenge using a mini-conjugative plasmid derived from the Pseudomonas putida NAH7 plasmid. This engineered plasmid, containing all conjugation-related genes, was cloned into an E. coli-compatible vector. Additionally, the par genes from NAH7 were expressed from a separate plasmid to investigate their roles in conjugative transfer. Our results revealed that the par gene cluster plays a significant role in enhancing the conjugative transfer of the mini-conjugative plasmid. Specifically, ParB, a centromere-binding protein, functions as a transcriptional activator of conjugation-related genes with binding parSNAH site. In contrast, ParR, a KorA homolog, was not found to enhance transcription directly but binds extensively to the oriT region. This binding probably facilitates the recruitment or stabilization of the relaxosome, thereby enhancing conjugation efficiency. Together, these findings unveil a previously unappreciated role for partition proteins in stimulating bacterial conjugation, providing new insights into how plasmids coordinate vertical and horizontal dissemination, highlighting that these processes can occur simultaneously within bacterial communities. IMPORTANCEPlasmid partition systems are classified into three types. While some systems have been reported to influence conjugative transfer, this study uncovers a novel mechanism utilized by a Type I system to enhance DNA transfer. Strikingly, repeat sequences perfectly matching the parSNAH site--bound by ParB to activate downstream conjugative transfer genes--were identified on both plasmids and chromosomes across diverse proteobacterial taxa. Furthermore, many of these repeat sequences were localized near genes involved in conjugative transfer and partitioning, suggesting the presence of a conserved regulatory mechanism mediated by these repeats. This study provides important insights into how plasmid partition systems coordinate both vertical and horizontal dissemination. Such knowledge is essential for understanding and mitigating the spread of antibiotic resistance and other plasmid-encoded traits, and it offers a foundation for developing strategies to manage plasmid-associated genetic exchange.

microbiology↗

bioRxiv2024

Secreted phospholipase PLA2G12A-driven lysophospholipid signaling via lipolytic modification of extracellular vesicles facilitates pathogenic Th17 differentiation

Lipogenesis-driven metabolic flux is crucial for differentiation of pathogenic Th17 cells. Although our previous CRISPR-based screening identified PLA2G12A as a key player in this process, it has remained obscure how this secreted phospholipase A2 isoform controls Th17 differentiation. Here we show that global, T cell-specific, or fibroblast-specific deletion of PLA2G12A prevents Th17 differentiation and associated diseases including psoriasis and arthritis. PLA2G12A acts on Th17-derived extracellular vesicles (EVs) to produce lysophospholipids including the ROR{gamma}t activator 1-oleoyl-lysophosphatidylethanolamine. These lysophospholipids are further converted by autotaxin to lysophosphatidic acid (LPA), which assists Th17 differentiation mainly via LPA2 receptor. Moreover, PLA2G12A promotes the secretion and uptake of EVs by Th17 cells and alters their cargo contents. Defective Th17 differentiation by PLA2G12A deficiency is rescued by supplementation with PLA2G12A-modified EVs. Importantly, a PLA2G12A-blocking antibody prevents Th17 differentiation and ameliorates psoriasis and arthritis models. Thus, targeting the PLA2G12A-EV-lysophospholipid axis may be useful for treatment of Th17-related diseases.

immunology↗

bioRxiv2024

RNA G-quadruplexes and calcium ions synergistically induce Tau phase transition in vitro

Tau aggregation is a defining feature of neurodegenerative tauopathies, including Alzheimers disease, corticobasal degeneration, and frontotemporal dementia. This aggregation involves the liquid-liquid phase separation (LLPS) of Tau, followed by its sol-gel phase transition, representing a crucial step in aggregate formation both in vitro and in vivo. However, the precise cofactors influencing Tau phase transition and aggregation under physiological conditions (e.g., ion concentration and temperature) remain unclear. In this study, we unveil that nucleic acid secondary structures, specifically RNA G-quadruplexes (rG4s), and calcium ions (Ca2+) synergistically facilitated the sol-gel phase transition of human Tau under mimic intracellular ion conditions (140 mM KCl, 15 mM NaCl, and 10 mM MgCl2) at 37{square} in vitro. In the presence of molecular crowding reagents, Tau formed stable liquid droplets through LLPS, maintaining fluidity for 24 h under physiological conditions. Notably, cell-derived RNA promoted Tau sol-gel phase transition, with G4-forming RNA emerging as a crucial factor. Surprisingly, polyanion heparin did not elicit a similar response, indicating a distinct mechanism not rooted in electrostatic interactions. Further exploration underscored the significance of Ca2+, which accumulate intracellularly during neurodegeneration, as additional cofactors in promoting Tau phase transition after 24 h. Importantly, our findings demonstrate that rG4s and Ca2+ synergistically enhance Tau phase transition within 1 h when introduced to Tau droplets. In conclusion, our study illuminates the pivotal roles of rG4s and Ca2+ in promoting Tau aggregation under physiological conditions in vitro, offering insights into potential triggers for tauopathy.

biochemistry↗

bioRxiv2023

Structural polymorphism of the nucleic acids in pentanucleotide repeats associated with CANVAS

Short tandem repeats are highly unstable, depending on repeat length, and the expansion of the repeat length in the human genome is responsible for repeat expansion disorders. Pentanucleotide AAGGG and ACAGG repeat expansions in intron 2 of the gene encoding replication factor C subunit 1 (RFC1) cause cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and other phenotypes of late-onset cerebellar ataxia. Herein, we reveal the structural polymorphism of the RFC1 repeat sequences associated with CANVAS in vitro. Single-stranded AAGGG repeat DNA formed a hybrid-type G-quadruplex, whereas its RNA formed a parallel-type G-quadruplex with three layers. The RNA of the ACAGG repeat sequence formed double helical hairpin structures comprising C-G and G-C base pairs with A:A and GA:AG mismatched repeats. Furthermore, both pathogenic repeat RNAs formed more rigid structures than those of the non-pathogenic sequences. These findings provide novel insights into the structural polymorphism of the RFC1 repeat sequences, which may be closely related to the disease mechanism of CANVAS.

biophysics↗

bioRxiv2023

RNA G-quadruplexes forming scaffolds for alpha-synuclein aggregation lead to progressive neurodegeneration

Synucleinopathies, including Parkinsons disease, dementia with Lewy bodies, and multiple system atrophy, are triggered by the aggregation of -synuclein, leading to progressive neurodegeneration1,2,3,4,5,6,7,8. However, the intracellular mechanism of -synuclein aggregation remains unclear. Here we show that assembly of RNA G-quadruplexes forming scaffolds for -synuclein aggregation, contributing to neurodegeneration. Purified -synuclein binds RNA G-quadruplexes directly through the N-terminus. RNA G-quadruplex itself undergoes phase separation and assembly by Ca2+, accelerating the sol-gel phase transition of -synuclein. In -synuclein preformed fibrils-treated neurons, RNA G-quadruplexes assembly composed of synaptic mRNAs co-aggregates with -synuclein upon Ca2+ excess influx into cytoplasm, eliciting synaptic dysfunction. Forced assembly of RNA G-quadruplexes using an optogenetic approach evokes -synuclein aggregation, neuronal dysfunction and neurodegeneration. Administration of 5-aminolevulinic acid, a prodrug of protoporphyrin IX that prevents phase separation of RNA G-quadruplexes9, attenuating -synuclein aggregation, neurodegeneration, and progressive motor deficits in -synuclein preformed fibrils-injected synucleinopathy mice. Together, assembly of RNA G-quadruplexes due to dysregulation of intracellular Ca2+ homeostasis accelerates -synuclein phase transition and aggregation may contribute to pathogenesis of synucleinopathies.

molecular biology↗

bioRxiv2023

Neurophysiological trajectories in Alzheimer's disease progression

Alzheimers disease (AD) is characterized by the accumulation of amyloid-{beta} and misfolded tau proteins causing synaptic dysfunction, and progressive neurodegeneration and cognitive decline. Altered neural oscillations have been consistently demonstrated in AD. However, the trajectories of abnormal neural oscillations in AD progression and their relationship to neurodegeneration and cognitive decline are unknown. Here, we deployed robust event-based sequencing models (EBMs) to investigate the trajectories of long-range and local neural synchrony across AD stages, estimated from resting-state magnetoencephalography. The increases in neural synchrony in the delta-theta band and the decreases in the alpha and beta bands showed progressive changes throughout the stages of the EBM. Decreases in alpha and beta band synchrony preceded both neurodegeneration and cognitive decline, indicating that frequency-specific neuronal synchrony abnormalities are early manifestations of AD pathophysiology. The long-range synchrony effects were greater than the local synchrony, indicating a greater sensitivity of connectivity metrics involving multiple regions of the brain. These results demonstrate the evolution of functional neuronal deficits along the sequence of AD progression.

neuroscience↗

bioRxiv2023

Dynamic functional connectivity MEG features of Alzheimer's disease

Dynamic resting state functional connectivity (RSFC) characterizes time-varying fluctuations of functional brain network activity. While many studies have investigated static functional connectivity, it has been unclear whether features of dynamic functional connectivity are associated with neurodegenerative diseases. Popular sliding-window and clustering methods for extracting dynamic RSFC have various limitations that prevent extracting reliable features to address this question. Here, we use a novel and robust time-varying dynamic network (TVDN) approach to extract the dynamic RSFC features from high resolution magnetoencephalography (MEG) data of participants with Alzheimers disease (AD) and matched controls. The TVDN algorithm automatically and adaptively learns the low-dimensional spatiotemporal manifold of dynamic RSFC and detects dynamic state transitions in data. We show that amongst all the functional features we investigated, the dynamic manifold features are the most predictive of AD. These include: the temporal complexity of the brain network, given by the number of state transitions and their dwell times, and the spatial complexity of the brain network, given by the number of eigenmodes. These dynamic features have high sensitivity and specificity in distinguishing AD from healthy subjects. Intriguingly, we found that AD patients generally have higher spatial complexity but lower temporal complexity compared with healthy controls. We also show that graph theoretic metrics of dynamic component of TVDN are significantly different in AD versus controls, while static graph metrics are not statistically different. These results indicate that dynamic RSFC features are impacted in neurodegenerative disease like Alzheimers disease, and may be crucial to understanding the pathophysiological trajectory of these diseases.

neuroscience↗

bioRxiv2022

Whole brain network analysis of neural synchrony and information flow during transition from wakefulness to light non-rapid eye movement sleep

Sleep is a highly stereotyped phenomenon, requiring robust spatial and temporal coordination of neural activity. How the brain coordinates neural activity with sleep onset can provide insight into the physiological functions subserved by sleep and pathologic phenomena associated with sleep onset. We quantified whole-brain network changes in synchrony and information flow during the transition from wake to non-rapid eye movement (NREM) sleep using magnetoencephalography imaging in healthy subjects. In addition, we performed computational modeling to infer excitatory and inhibitory properties of local neural activity. The sleep transition was identified to be encoded in spatially and temporally specific patterns of local and long-range neural synchrony. Patterns of information flow revealed that mesial frontal regions receive hierarchically organized inputs from broad cortical regions upon sleep onset. Finally, biophysical neural mass modeling demonstrated spatially heterogeneous properties of cortical excitation-to-inhibition from wake to NREM. Together, these findings reveal whole-brain corticocortical structure in the sleep-wake transition and demonstrate the orchestration of local and long-range, frequency-specific cortical interactions that are fundamental to sleep onset.

bioengineering↗

bioRxiv2022

Altered excitatory and inhibitory neuronal subpopulation parameters are distinctly associated with tau and amyloid in Alzheimer's disease

BackgroundNeuronal and circuit level abnormalities of excitation and inhibition are shown to be associated with tau and amyloid-beta (A{beta}) in preclinical models of Alzheimers disease (AD). These relationships remain poorly understood in patients with AD. MethodsUsing empirical spectra from magnetoencephalography (MEG) and computational modeling (neural mass model; NMM) we examined excitatory and inhibitory parameters of neuronal subpopulations and investigated their specific associations to regional tau and A{beta}, measured by positron emission tomography (PET), in patients with AD. ResultsPatients with AD showed abnormal excitatory and inhibitory time-constants and neural gains compared to age-matched controls. Increased excitatory time-constants distinctly correlated with higher tau depositions while increased inhibitory time-constants distinctly correlated with higher A{beta} depositions. ConclusionsOur results provide critical insights about potential mechanistic links between abnormal neural oscillations and cellular correlates of impaired excitatory and inhibitory synaptic functions associated with tau and A{beta} in patients with AD. FundingThis study was supported by the National Institutes of Health grants: K08AG058749 (KGR), F32AG050434-01A1 (KGR), K23 AG038357 (KAV), P50 AG023501, P01 AG19724 (BLM), P50-AG023501 (BLM & GDR), R01 AG045611 (GDR); AG034570, AG062542 (WJ); NS100440 (SSN), DC176960 (SSN), DC017091 (SSN), AG062196 (SSN); a grant from John Douglas French Alzheimers Foundation (KAV); grants from Larry L. Hillblom Foundation: 2015-A-034-FEL and (KGR); 2019-A-013-SUP (KGR); a grant from the Alzheimers Association: (PCTRB-13-288476) (KAV), and made possible by Part the CloudTM, (ETAC-09-133596); a grant from Tau Consortium (GDR & WJJ), and a gift from the S. D. Bechtel Jr. Foundation.

neuroscience↗

bioRxiv2021

Intrinsic network activity in human brain organoids

Human brain organoids replicate much of the cellular diversity and developmental anatomy of the human brain. However, the physiological behavior of neuronal circuits within organoids remains relatively under-explored. With high-density CMOS microelectrode arrays (26,400 electrodes) and shank electrodes (960 electrodes), we probed broadband and three-dimensional extracellular field recordings generated by spontaneous activity of human brain organoids. These recordings simultaneously captured local field potentials (LFPs) and single-unit activity extracted through spike sorting. From spiking activity, we estimated a directed functional connectivity graph of synchronous neural network activity, which showed a large number of weak functional connections enmeshed within a network skeleton of significantly fewer strong connections. Treatment of the organoid with a benzodiazepine induced a reproducible signature response that shortened the inter-burst intervals, increased the uniformity of the firing pattern within each burst and decreased the population of weakly connected edges. Simultaneously examining the spontaneous LFPs and their phase alignment to spiking showed that spike bursts were coherent with theta oscillations in the LFPs. Our results demonstrate that human brain organoids have self-organized neuronal assemblies of sufficient size, cellular orientation, and functional connectivity to co-activate and generate field potentials from their collective transmembrane currents that phase-lock to spiking activity. These results point to the potential of brain organoids for the study of neuropsychiatric diseases, drug mechanisms, and the effects of external stimuli upon neuronal networks.

neuroscience↗

bioRxiv2020

Relationship between serum bilirubin levels, urinary biopyrrin levels, and retinopathy in patients with diabetes

Aims/IntroductionPrevious reports have indicated that serum bilirubin levels may be associated with diabetic retinopathy. However, the detailed mechanism is not fully understood. In this study, we evaluated the relationship between the severity of diabetic retinopathy and various factors including bilirubin levels and factors influencing bilirubin metabolism. MethodsThe study participants consisted of 94 consecutive patients with diabetes mellitus admitted to Kyushu University Hospital from April 2011 to July 2012. The patients were classified into three groups: no retinopathy (NDR), simple retinopathy (SDR), and pre-proliferative or proliferative retinopathy (PDR). The relationship between the severity of retinopathy and various factors was evaluated using univariate and logistic regression analyses. In addition, multivariate regression analysis was performed to evaluate the significant determinants for bilirubin levels. ResultsIn univariate analysis, a significant difference was found among NDR, SDR and PDR in bilirubin levels, duration of diabetes, systolic blood pressure, and macroalbuminuria. Logistic regression analysis showed that PDR was significantly associated with bilirubin levels, duration of diabetes, and systolic blood pressure (OR 0.737, 95% CI 0.570-0.952, P=0.012; OR 1.085, 95% CI 1.024-1.149, P=0.006; OR 1.036, 95% CI 1.011-1.062, P=0.005, respectively). In turn, multivariate regression analysis showed that bilirubin levels were negatively associated with high-sensitivity Creactive protein levels and PDR, but positively correlated with urinary biopyrrin levels, oxidized metabolites of bilirubin. ConclusionsPDR was negatively associated with bilirubin levels. This negative association may be due to a decreased production of bilirubin rather than its increased consumption considering the positive association between bilirubin and biopyrrin levels.

biochemistry↗

bioRxiv2020

Expression of ERV3-1 in Leukocytes of Acute Myelogenous Leukemia Patients

Acute myelogenous leukemia (AML) is one of the major hematological malignancies. In the human genome, several have been found to originate from retroviruses, and some of which are involved in progression of various cancers. Hence, to investigate whether retroviral-like genes are associated with the development of AML, we conducted a transcriptome sequencing analysis of 12 retroviral-like genes of 150 AML patients using The Cancer Genome Atlas database. We found high expression of ERV3-1, an envelope gene of endogenous retrovirus group 3 member 1. In particular, blood and bone marrow cells of the myeloid lineage in AML patients, exhibited higher expression of ERV3-1 than those of the monocytic AML lineage. We also examined the protein expression of ERV3-1 by immunohistochemical analysis and found expression of ERV3-1 protein in 7 out of 12 AML patients, with a particular concentration observed at the membrane of some leukemic cells. Transcriptome analysis further suggested that upregulated ERV3-1 expression may be associated with chromosome 8 trisomy as anomaly was found to be more common among the high expression group compared to the low expression group. However, this finding was not corroborated by the immunohistochemical data. This discrepancy may have been caused, in part, by the small number of samples analyzed in this study. Although the precise associated molecular mechanisms remain unclear, our results suggest that ERV3-1 may be involved in AML development. HighlightsO_LIExpression of 12 retroviral-like genes in the human genome were analyzed using transcriptome data of 150 acute myelogenous leukemia (AML) patients. C_LIO_LIERV3-1, an envelope gene of endogenous retrovirus group 3 member 1, was found to uniquely show high expression level. C_LIO_LIMorphologic characteristics and chromosomal abnormalities are found to be related with the expression of ERV3-1. C_LI

molecular biology↗