Biology subjects

Matsumoto, N.

Publications and source records attributed to Matsumoto, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Task-specific ISS reduction and network balance during Stroop task performance in older adults

Declines in the cognitive inhibition that comes with aging impacts daily life and independence. It is still debated whether overactivation during cognitive inhibition tasks in older adults is due to compensation or neural noise. To address this question, we examined age-related changes in inter-subject similarity (ISS) of functional connectivity from task-based and resting-state fMRI. Using Bayesian hierarchical modeling, we identified 27 Stroop task-related regions of interest and found that ISS in these regions was significantly reduced in older adults during task performance. Furthermore, aging is associated with a loss of consistent functional connectivity patterns in frontal regions, accompanied by the emergence of a convergent compensatory mechanism within visual attention regions. Principal component analysis of individual activation deviations from the group-mean pattern showed that task performance in older adults cannot be explained by overall task-related brain activation, but rather by a specific spatial component involving suppression of the default mode network and increased activity in visual attention regions. These findings indicate that task-related brain overactivation in older adults is not due to uniform noise or uniform compensation, but rather a spatially specific pattern of functional reorganization.

neuroscience↗

bioRxiv2026

EcoXAI: Autonomous Agentic Ecosystem for Explainable Artificial Intelligence and Biomedical Discovery

Motivation: As biomedical datasets and knowledge graphs continue to grow in size, complexity, and heterogeneity, navigating and extracting actionable insights from them presents a major bottleneck for researchers. There is a clear need for autonomous analytical solutions that can utilize recent advancements in agentic AI such as agent harnessing and loop engineering without introducing hallucination or workflow fragmentation. Researchers, regardless of technical expertise, need tools that streamline complex data analysis and deliver meaningful, actionable insights grounded in both data and established biomedical knowledge. EcoXAI addresses this by introducing a modular, customizable, containerized multi-agent system that structures analysis into explicit pipeline execution stages, lowering the computational barrier for clinical and translational researchers. Result: EcoXAI replaces monolithic AI text interfaces with an autonomous execution-driven framework with specialized bioinformatics agents for delivering proactive, data-driven insights grounded in established biological knowledge. Unlike purely LLM-driven or less integrated AI solutions prone to hallucinations or biologically implausible outcomes, EcoXAI's multi-agent framework, which leverages modern agentic management and explicit knowledge graph integration, provides greater transparency and verifiability in its reasoning. In our use case in drug repurposing for Alzheimer's Disease, EcoXAI evaluated 103 drug candidates and identified 79 novel candidates whose predictive models exceeded a randomized baseline, including the CCR5 antagonist Maraviroc, whose generated hypothesis was subsequently supported by the literature. These results demonstrate the potential of knowledge graph-grounded AI agents to accelerate hypothesis-driven biomedical research.

bioinformatics↗

bioRxiv2026

Turn-taking-like temporal coordination of ultrasonic vocalizations during close-range social interactions in Mongolian gerbils (Meriones unguiculatus)

Vocal communication depends not only on the acoustic features and rate of vocalizations, but also on their timing relative to the vocalizations of others. In this study, we examined whether ultrasonic vocalizations (USVs) produced by adult female Mongolian gerbils during freely moving social interactions are temporally related to the vocal timing of a partner. Using USVCAM, we assigned each USV to an individual caller and evaluated whether brief USVs exhibit turn-taking-like temporal organization by analyzing response latency after partner calls, call overlap rate, and circular-shift surrogate data. The offset-to-onset gaps of alternating vocalizations were concentrated within a short time range, with a median of 130 ms. In addition, the call overlap rate was significantly lower in the observed data than in the circularly shifted surrogate data, indicating that USVs occurred with short latencies after partner calls while being less likely to overlap with ongoing partner calls. Furthermore, USV counts were reduced in unoperated Ctrl animals that interacted with devocalized Mute animals. These findings suggest that gerbil USVs may be coordinated in relation to partner vocal timing and vocal input. This study provides a basis for understanding rodent USVs not merely as individual vocal outputs, but as temporally organized dyadic social signals.

animal behavior and cognition↗

bioRxiv2026

Ramelteon facilitates hippocampal ripple occurrence and amplitude in mice

The hippocampus is essential for memory consolidation, a process mediated by high-frequency oscillations known as ripples during non-rapid eye movement (NREM) sleep. Ramelteon, a selective MT1/MT2 receptor agonist, has been reported to possess cognitive-enhancing properties; however, its impact on the fine-scale dynamics of hippocampal ripples remains unclear. We performed chronic local field potential recordings from the dorsal hippocampus and prefrontal cortex in mice. Following the intraperitoneal administration of either vehicle or ramelteon, we evaluated sleep architecture and characterized ripple properties, including occurrence rate, amplitude, instantaneous frequency, and duration during NREM sleep. Ramelteon administration significantly increased NREM sleep occupancy. Notably, we found that ramelteon significantly enhanced both the occurrence rate and amplitude of hippocampal ripples compared to the control group. While a slight increase in intra-ripple frequency was observed, other structural features, such as ripple duration and asymmetry index, remained unaffected. Our findings demonstrate that ramelteon facilitates hippocampal ripple dynamics by increasing their occurrence and synchrony during NREM sleep. Given the critical role of ripples in memory consolidation, these neurophysiological changes may underlie the procognitive effects of ramelteon. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=55 SRC="FIGDIR/small/723673v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@77b58org.highwire.dtl.DTLVardef@132dbc1org.highwire.dtl.DTLVardef@1f98dc1org.highwire.dtl.DTLVardef@c9a3f2_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2026

Enzyme activity as an actionable axis for small-molecule precision oncology

Current precision oncology--molecular targeted therapies and immunotherapies--relies on genomic or expressed biomarkers, yet most cancer patients remain ineligible for these treatments. Here, we establish enzyme activity as an actionable and orthogonal axis for precision cancer medicine. Strategic activity-based screening of mouse organs and human clinical specimens with a panel of enzyme-reactive fluorescence probes identified {beta}-galactosidase 1 (GLB1) and {beta}-hexosaminidases (HEX) as broadly elevated tumor-selective biomarkers. Leveraging these activities, we developed 7-ethyl-10-hydroxycamptothecin (SN38)-based GLB1-and HEX-reactive prodrugs. These prodrugs exhibited dramatically reduced systemic toxicities and improved therapeutic windows, compared to a clinically used SN38-based prodrug, irinotecan (CPT-11). Both prodrugs demonstrated activity-dependent therapeutic efficacy, affording a dramatic reduction of tumor volumes across multiple in vivo models, including a subcutaneous patient-derived xenograft (PDX) of lung squamous cell carcinoma that lacked genetic alterations targeted by current precision medicine. Furthermore, this strategy is broadly applicable across various cytotoxic payloads, establishing a generalizable platform for small-molecule precision medicines. Our results define an enzyme-targeting paradigm for precision oncology, in which fluorescence probes serve as companion diagnostic tools to guide development and selection of appropriately targeted prodrugs, which are expected to provide safer and more efficacious treatment options for cancer patients with elevated enzyme activities.

cancer biology↗

bioRxiv2026

Autophagy induction requires the suppression of potassium influx mediated by phosphatases

Potassium is an essential element for all living organisms. As the most abundant intracellular cation, it is vital for osmoregulation, maintenance of membrane potential, macromolecule transport and enzyme function. In this study, we identify potassium homeostasis as a previously unknown regulator of autophagy through the phosphatase activities of Ppz1 and Ppz2. We find that overexpression of either Ppz1 or Ppz2 triggers autophagy under nutrient-replete conditions, whereas the loss of both causes severe autophagy defects. Strikingly, deletion of the potassium transporters Trk1 and Trk2, which are substrates of Ppz1 and Ppz2-mediated dephosphorylation, restores autophagic activity in ppz1{Delta} ppz2{Delta} cells. Furthermore, intracellular potassium concentrations declined during autophagy induction in wild-type cells but remained stable in ppz1{Delta} ppz2{Delta} mutants. Collectively, these findings establish Ppz1 and Ppz2 as pivotal regulators of autophagy and underscore intracellular potassium reduction as a primary determinant of this process. Summary statementThis study demonstrates that potassium regulation by the phosphatases, Ppz1 and Ppz2, which suppress the major potassium transporters Trk1 and Trk2, is indispensable for autophagy induction in yeast.

molecular biology↗

bioRxiv2025

Human spastin functions as an ATPase-independent microtubule nucleator via ring-stack formation

Microtubule severing enzyme spastin plays pivotal roles in cytokinesis and neuronal outgrowth, and its mutations cause hereditary spastic paraplegia (HSP). Here we show that, at physiological tubulin concentrations, human spastin behaves predominantly as an ATPase- independent microtubule nucleator rather than a severase. Biochemical and structural analyses revealed that spastin assembles tubulin into stacked-ring intermediates via strategically positioned microtubule-binding domains, thereby generating nucleation-competent sites for polymerization. Tubulin subunits within these spastin-induced rings adopt a straight, microtubule-like interface, in marked contrast to the twisted tubulin spirals characteristic of depolymerizing microtubule ends. Our results redefine the mechanistic landscape of multifaceted spastin functions and provide insights that may inform the pathological basis of HSP and guide future therapeutic strategies.

biophysics↗

bioRxiv2025

Nonlinear hippocampal coding of the pair-bonded partner in prairie voles

Neural representation of specific opposite-sex partners remains largely unexplored. Using monogamous prairie voles, we demonstrated that partner preference required the ventral hippocampus, in which 3-4 Hz oscillations were enhanced following partner interaction. We identified ventral hippocampal neurons responding selectively to the pair-bonded partner and stranger, which encoded identity-related information in a nonlinear manner, shedding light upon how mammalian brains create distinct neural representations of romantic opposite-sex partners.

neuroscience↗

bioRxiv2025

Adapting a commercial anti-Aspergillus IgG ELISA kit for penguin sera: A novel approach using anti-chicken IgY antibody for the detection of anti-Aspergillus IgY titer

Penguins are susceptible to aspergillosis and are affected by the causative fungal pathogens Aspergillus spp., under immunocompromised conditions. Currently, there are limited serological tests available for diagnosing Aspergillus infections in penguins, highlighting the need for new diagnostic methods. While an anti-Aspergillus IgG detection kit using ELISA is commercially available and widely used in human medicine, it is not applicable for penguins because it incorporates anti-human antibodies as the secondary antibody for detection. To address this issue, an anti-chicken IgY antibody was incorporated into a commercial anti-Aspergillus IgG detection ELISA kit. First, anti-chicken IgY antibody was examined for cross-reactivity to penguin IgY, and the antibody recognized IgY from King, Gentoo, and African penguins in sera. Subsequently, serum samples from healthy penguins and penguins with aspergillosis were examined using anti-chicken IgY antibody incorporated into the anti-Aspergillus IgG ELISA kit. The results suggest that the combination method is applicable for the detection of anti-Aspergillus penguin IgY antibodies. However, because background titers can vary among individuals, we propose that routine monitoring could aid in the early detection of aspergillosis, even before the onset of symptoms.

microbiology↗

bioRxiv2025

Theanine boosts frontal theta and hippocampal beta and gamma oscillations for familiarity in object recognition

Theanine, a non-proteinogenic amino acid derivative from green tea leaves, enhances object recognition memory in rats through facilitated neurogenesis. In this sense, the cellular mechanism for the theanine-enhanced object recognition memory has been elucidated to some extent, but physiological evidence still remains unclear. To tackle this issue, we chronically fed mice with theanine (or tap water) for three weeks, implanted electrodes into the hippocampus and frontal cortex, both of which are responsible for object recognition memory. We then recorded the local field potentials from the two regions during the novel object recognition task, evaluated the task performance, and broke down the neural signals in the hippocampus and frontal cortex into delta, theta, beta, low gamma, and high gamma frequency bands. The discrimination ratio of theanine-treated mice was higher than that of vehicle-treated mice. We also found that theta oscillations in the frontal cortex and beta and low gamma oscillations in the hippocampus in theanine-treated mice were simultaneously enhanced for familiar objects. These results shed light on the new physiological underpinnings of object recognition memory enhanced by exogenous substances.

pharmacology and toxicology↗

bioRxiv2025

Enhanced Tactile Coding in Rat Neocortex Under Darkness

Sensory systems are known for their adaptability, responding dynamically to changes in environmental conditions. A key example of this adaptability is the enhancement of tactile perception in the absence of visual input. Despite behavioral studies showing visual deprivation can improve tactile discrimination, the underlying neural mechanisms, particularly how tactile neural representations are reorganized during visual deprivation, remain unclear. In this study, we explore how the absence of visual input alters tactile neural encoding in the rat somatosensory cortex (S1). Rats were trained on a custom-designed treadmill with distinct tactile textures (rough and smooth), and local field potentials (LFPs) were recorded from S1 under light and dark conditions. Machine learning techniques, specifically a convolutional neural network, were used to decode the high-dimensional LFP signals. We found that the neural representations of tactile stimuli became more distinct in the dark, indicating a reorganization of sensory processing in S1 when visual input was removed. Notably, conventional amplitude-based analyses failed to capture these changes, highlighting the power of deep learning in uncovering subtle neural patterns. These findings offer new insights into how the brain rapidly adapts tactile processing in response to the loss of visual input, with implications for multisensory integration.

neuroscience↗

bioRxiv2025

Ophiobolin A selectively alters mitochondria, metabolism and redox biology in breast cancer and mammary epithelial cells which have undergone epithelial to mesenchymal transition

Breast cancer progression is facilitated by the epithelial to mesenchymal transition (EMT), generating cancer cells with enhanced metastatic capacity and resistance to chemotherapeutics. EMT is known to impart changes in metabolic pathways and mitochondrial function. Here, we show a natural product possesses EMT-specific cytotoxic activity via alterations in metabolic and mitochondrial functions. The fungus-derived sesterterpenoid, ophiobolin A (OpA), possesses nanomolar cytotoxic activity and a high therapeutic index, although its target and mechanism of action remain unknown. Here, we utilized a model of mammary epithelial cells and breast cancer cell lines with and without EMT features to characterize the mechanism of selectivity towards EMT(+) cells by OpA and to identify novel targets for the treatment of EMT-enriched breast cancer. Proteins interacting with OpA in EMT(+) cells were identified through proteomic studies. We utilized trans-mitochondrial cybrids to determine that mitochondria mediate sensitivity to OpA. Furthermore, we report effects on glycolysis, oxidative metabolism, and disruption of metabolite abundance in the TCA cycle. Alterations to mitochondrial iron concentrations and glutathione production, mediated partly by OpA engagement with the metabolic proteins CISD3 and SLC25A40, were also detected in EMT(+) cells. Antioxidant mechanisms are activated by OpA in EMT(+) cells via the NRF2-ARE pathway, verified by decreased cytotoxicity in EMT(+) cells pretreated with the NRF2 activator CDDO. Collectively, we conclude that OpA selectivity toward EMT is mediated by the mitochondria, and at sub-cytotoxic levels, generates a metabolic shift leading to cell death countered by antioxidant mechanisms.

cancer biology↗

bioRxiv2024

Dopamine-induced Relaxation of Connectivity Diversifies Burst Patterns in Cultured Hippocampal Networks

The intricate interplay of neurotransmitters orchestrates a symphony of neural activity in the hippocampus, with dopamine emerging as a key conductor in this complex ensemble. Despite numerous studies uncovering the cellular mechanisms of dopamine, its influence on hippocampal neural networks remains elusive. Combining in vitro electrophysiological recordings of rat embryonic hippocampal neurons, pharmacological interventions, and computational analyses of spike trains, we found that dopamine induces a relaxation in network connectivity, characterised by a reduction in spike coherence. This relaxation expands the repertoire of burst dynamics within these hippocampal networks, a phenomenon notably absent under the administration of dopamine antagonists. Our study provides a thorough understanding of the roles of dopamine signalling in shaping functional networks of hippocampal neurons.

neuroscience↗

bioRxiv2024

Diffusion model-based image generation from rat brain activity

Brain-computer interface (BCI) technology has gained recognition in various fields, including clinical applications, assistive technology, and human-computer interaction research. BCI enables communication, control, and monitoring of the affective/cognitive states of users. Recently, BCI has also found applications in the artistic field, enabling real-time art composition using brain activity signals, and engaging performers, spectators, or an entire audience with brain activity-based artistic environments. Existing techniques use specific features of brain activity, such as the P300 wave and SSVEPs, to control drawing tools, rather than directly reflecting brain activity in the output image. In this study, we present a novel approach that uses a latent diffusion model, a type of deep neural network, to generate images directly from continuous brain activity. We demonstrate this technology using local field potentials from the neocortex of freely moving rats. This system continuously converted the recorded brain activity into images. Our end-to-end method for generating images from brain activity opens up new possibilities for creative expression and experimentation.

neuroscience↗

bioRxiv2024

Fetal Kidney Transplantation for In Utero Fetuses

Potter sequence, characterized by bilateral renal agenesis, oligohydramnios, and consequent pulmonary hypoplasia, presents a significant challenge in the management of affected neonates. Due to their prematurity and associated abdominal complications, these infants often fail to reach a stage where dialysis can be safely initiated and sustained, leading to an exceedingly high mortality rate. Therefore, there is hopeful anticipation that interventions serving as a bridge to achieve a state where dialysis can be safely performed will markedly improve life expectancy. We have developed a unique approach of "transplantation of fetal kidneys from a different species during the fetal period" as a bridge therapy until stable dialysis therapy can be implemented. This is a new concept of fetal therapy, targeting the fetus in utero and utilizing fetal kidneys of an appropriate size for transplantation. In this study, we first validated the approach using allogeneic transplantation. Fetal kidneys with bladders from GFP-expressing rats (gestational age 14.0-16.5 days) were transplanted subcutaneously into allogeneic rat fetuses in utero (gestational age 18.0-18.5 days) using a special needle transuterinally, and live pups were successfully obtained. The transplanted fetal kidneys with bladders were confirmed to have urine production capability. By periodic aspiration of the subcutaneous urinary cyst after birth, urine produced by the transplanted fetal kidney was successfully drained outside the body for an extended period (up to 150 days). Biochemical tests confirmed the solute removal capacity of the transplanted fetal kidney. Furthermore, despite allogeneic transplantation, long-term urine production was sustained without the use of immunosuppressants, confirming that organ transplantation into fetuses is associated with lower rejection compared to adult transplantation. Next, xenotransplantation was performed. When GFP-expressing mouse fetal kidneys (gestational age 13.0-13.5 days) were transplanted into rat fetuses in utero, maturation of renal tissue structures was confirmed even in the interspecies setting.

bioengineering↗

bioRxiv2023

Neural correlates of category learning in monkey inferior temporal cortex

We trained two monkeys implanted with multi-electrode arrays to categorize natural images of cats and dogs, in order to observe changes in neural activity related to category learning. We recorded neural activity from area TE, which is required for normal learning of visual categories based on perceptual similarity. Neural activity during a passive viewing task was compared pre- and post-training. After the category training, the accuracy of abstract category decoding improved. Specifically, the proportion of single units with category selectivity increased, and units sustained their category-specific responses for longer. Visual category learning thus appears to enhance category separability in area TE by driving changes in the stimulus selectivity of individual neurons and by recruiting more units to the active network.

neuroscience↗

bioRxiv2023

Slow gamma oscillations in the mouse olfactory bulb are correlated with sniffing in the dark period

Neural activity in the olfactory bulb is reflected in local field potentials (LFPs). Functionally, LFPs in the olfactory bulb are categorized into different frequency bands: 1-4 Hz, 6-12 Hz, 25-50 Hz, and 65-130 Hz, which respectively correspond to respiration, sniffing, slow gamma, and fast gamma oscillations. While gamma oscillations in the olfactory bulb are modulated by respiration and sniffing, it remains unknown how and whether the modulation of LFP oscillations is affected by the time of day. To address this question, we recorded LFPs in the olfactory bulb, hippocampus, and neocortex of unrestrained mice for up to 3 d. For each recording site, we calculated the correlation coefficients of normalized LFP powers between pairs of frequency bands in the three regions during the dark and light periods. We then compared these correlations with those generated by surrogate data to investigate whether the correlation was statistically significant. We found that the correlation between sniffing and slow gamma oscillations was higher in the dark period than in the light period. Our finding has the potential to shed light on the coding scheme of olfactory information that is dependent on the light/dark cycle.

neuroscience↗

bioRxiv2022

Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing

Next-generation DNA sequencing (NGS) in short-read mode has been recently used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, focusing mostly on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains mostly unexplored despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions using 10 genome sequence features on the basis of real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). We used the obtained metrics, designated "UNMET score," along with other lines of structural information of the human genome to identify difficult-to-sequence genomic regions using conventional NGS. Thus, the UNMET score could provide appropriate caveats to address potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.

genomics↗