Biology subjects

Murayama, M.

Publications and source records attributed to Murayama, M..

12 recordsLinked to original sources

bioRxiv2026

Meso2EM: a cross-scale CLEM workflow linking mesoscale functional imaging to targeted electron microscopy

Meso2EM is a correlative light and electron microscopy workflow that transfers neurons selected from mesoscale functional images to targeted electron microscopy. We recorded Ca{superscript 2} signals from layer 2/3 neurons across a contiguous 3 x 3 mm cortical field in awake mice and reidentified a selected neuron after fixation and tangential sectioning. Lectin-labeled vascular architecture served as a shared landmark across in vivo two-photon imaging, confocal microscopy, laboratory micro-CT of resin-embedded tissue, and block-surface scanning electron microscopy, guiding focused-ion-beam scanning electron microscopy to the target cell body. The same progressive-targeting principle also supported serial ATUM-SEM reconstruction of an in vivo-tracked dendrite and serial transmission electron microscopy of optically selected dendrites from a patch-clamp-recorded Martinotti cell. Meso2EM therefore provides a practical route for preserving target identity across large changes in scale and specimen state while restricting electron-microscopy acquisition to a selected region.

neuroscience↗

bioRxiv2026

Multi-area single-cell calcium imaging dataset of the mouse cortex across wakefulness, sleep, and anesthesia

We present a reusable dataset of neuronal population activity from multiple cortical areas, recorded from layers 2/3 of the mouse cortex at single-cell resolution during wakefulness, natural sleep (including NREM and REM sleep), and isoflurane anesthesia. Using wide-field two-photon microscopy, we recorded approximately 4,000 to 10,000 neurons per session at 7.65 Hz and provided the spatial coordinates of individual neurons. The repository provides both processed datasets and the corresponding raw imaging movies (TIFF) and electrophysiological recordings (MATLAB format). Processed data are distributed in MATLAB format and include {Delta} F/F fluorescence signals, deconvolved spike estimates, Gaussian-smoothed spike estimates, behavioral state annotations, and metadata. This dataset supports reuse in studies of cortical population dynamics, brain-state-dependent activity, and spatially distributed neuronal organization. It should also be useful for method development, benchmarking, and comparative analyses of large-scale neuronal activity across physiological and pharmacological brain states.

neuroscience↗

bioRxiv2026

Prior experience establishes a proactive cortical filter that blocks redundant associations

Prior experience allows selective learning by filtering out redundant cues, as exemplified by blocking, in which prior learning about one cue prevents a novel but redundant cue from being learned during subsequent compound conditioning. Top-down cortico-cortical pathways have been implicated in sensory filtering, but whether, how, and when they contribute to blocking remain unknown. Here we establish a head-fixed blocking paradigm in mice in which prior auditory cue-reward learning prevents a redundant somatosensory cue-reward association during subsequent compound conditioning. We found that a projection from anterior cingulate cortex (ACC) to primary somatosensory cortex (S1) facilitates blocking. Prior auditory learning establishes ACC-driven inhibitory control over S1 via parvalbumin neurons, before explicit somatosensory experience, thereby suppressing burst responses to the somatosensory cue, limiting network plasticity, and promoting blocking. These findings propose a proactive cortical filter that preconfigures inhibitory sensory bias to constrain future learning about redundant cues. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/736748v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@6e1c4org.highwire.dtl.DTLVardef@1d01b49org.highwire.dtl.DTLVardef@1af67fdorg.highwire.dtl.DTLVardef@d42d8d_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Repetitive Hibernation-Like State Suppresses the Progression of Amyloid Pathology

Alzheimers disease (AD) is characterized by the gradual accumulation of amyloid pathology before the onset of cognitive impairment, yet effective strategies to alter disease progression remain limited. Here, we tested whether induction of a hibernation-like physiological state can slow amyloid pathology in an AD mouse model. To achieve sustained effects, we developed a protocol for repeated induction of a hypometabolic/hypothermic state and found that it significantly slowed plaque accumulation in a duration-dependent manner. This intervention also attenuated neuroinflammation and the formation of dystrophic neurites associated with plaques. Notably, this approach does not target specific molecular pathways but instead modulates global brain state. Our findings establish a proof-of-concept for a brain-state- based therapeutic paradigm for modifying disease progression in AD.

neuroscience↗

bioRxiv2025

Linking sediment porosity to taxon-specific patterns of eDNA preservation in a temperate, semi-enclosed bay

Sedimentary environmental DNA provides unique insights into past community dynamics. However, the influence of physical sediment properties, such as porosity, on taxon-specific eDNA preservation remains poorly understood, particularly in temperate inner-bay environments. Therefore, here, we characterized eukaryotic communities in sediment cores from the surface to 6-m depth in the inner and mouth regions of the Uranouchi Bay, a semi-enclosed embayment in temperate Japan. Both 18S rRNA and mitochondrial cytochrome c oxidase subunit I gene metabarcoding revealed marked spatial variation; specifically, inner-bay sediments were enriched in terrestrial plant DNA and dinoflagellates, whereas mouth sediments contained higher proportions of marine diatoms. Vertical profiles further highlighted differences in DNA persistence, with terrestrial and particle-associated taxa retained deeper in the inner-bay sediments. Land-sea connectivity and basin geography strongly shape sedimentary eDNA composition, reflecting both ecological sourcing and preservation bias. We further systematically analyzed the relationship between sediment porosity, a critical physical property governing pore water mobility and solute diffusion, and taxon-specific sedimentary eDNA preservation. To highlight effects of porosity independent of burial depth, we modeled porosity as a function of depth and correlated the residual porosity with the relative abundances of individual phyla. Notably, the phyla exhibited contrasting preservation patterns: Dinoflagellata, Euglenozoa, and Rotifera showed weak to moderate positive correlations with porosity, whereas Chlorophyta and Ochrophyta displayed weak negative correlations. When depth correlations were examined jointly, multiple distinct pattern groups emerged: some taxa (e.g., Dinoflagellata) exhibited negative depth but positive porosity correlations, whereas others showed opposite or neutral patterns. These divergent responses suggest that DNA preservation in marine sediments involves multiple taxon-specific mechanisms rather than a single universal process, with porosity acting as an independent determinant of burial depth. Our results highlight the importance of integrating physical properties of sediments into sedimentary environmental DNA-based paleoenvironmental reconstructions.

ecology↗

bioRxiv2023

Single-cell resolution functional networks during sleep aresegregated into spatially intermixed modules

The common neural mechanisms underlying the reduction of consciousness during sleep and anesthesia remain unclear. Previous studies have examined changes in network structure only using recordings with limited spatial resolution, which has hindered the investigation of the critical spatial scales from the micro (single neurons) to the meso (groups of neurons) for the reduction of consciousness. To address this issue, by leveraging fast, single-cell resolution, and wide-field two-photon microscopy, we recorded calcium signals from approximately 10,000 neurons across multiple cortical regions in awake, sleeping, and anesthetized mice. This single-cell resolution data enabled us to investigate the scales at which changes in network structure compared to an awake state are commonly observed during sleep and anesthesia. We found that at the single-cell scale, both sleep and anesthesia exhibited higher network modularity, indicating a segregated network, compared to an awake state. Despite this segregation, modules were spatially intermixed in all three states. In contrast, at the mesoscale, there were no consistent differences in modularity between states, and modules were spatially localized. Our multi-scale analysis provides novel insights into the cellular-scale organization of functional networks commonly associated with the reduction of consciousness and highlights a scale-dependent organization of network structures.

neuroscience↗

bioRxiv2023

Dynamics of motor direction representation in the primate premotor and primary motor cortices during sensorimotor learning

Sensorimotor learning requires reorganization of neuronal activity in the premotor cortex (PM) and primary motor cortex (M1). However, how PM- and M1-specific reorganization occurs in primates remains unclear. We conducted calcium imaging of these areas in common marmosets while they learned a two-target reaching (pull/push) task. Throughout learning, the dorsorostral PM (PMdr) showed peak activity earlier than the dorsocaudal PM (PMdc) and M1. PMdr showed decreased representation of newly introduced (push) movement, whereas PMdc and M1 maintained high representation. Many task-related neurons in PMdc and M1 exhibited a strong preference to either movement direction. PMdc neurons dynamically switched their preferred direction, whereas M1 neurons stably retained their preferred direction. Differences in preferred direction between adjacent neurons in PMdc increased during learning. These results suggest that in primate sensorimotor learning, dynamic motor representation in PMdc converts the cognitive sensorimotor signals of PMdr to stable and specific motor representation of M1.

neuroscience↗

bioRxiv2023

Emotional association enhances perceptual memory through amygdalo-cortical inputs during NREM sleep

Emotional arousal is thought to enhance the consolidation of associated memories by activating the basolateral amygdala (BLA) and its projections to memory-storing regions1-4. Although the importance of both rapid eye movement (REM) and non-REM (NREM) sleep-state specific BLA activity for emotional memory processing has been proposed5-9, how and when the BLA interacts with other brain regions to enhance memory consolidation remains unclear10. Here, by adding emotional information to a perceptual recognition task that relies on top-down inputs from frontal to sensory cortices, we demonstrated that the BLA not only associates emotional information with perceptual information, but also enhances the retention of associated perceptual memory through BLA-frontal projections. Electrophysiological recordings revealed that emotional association increases the reactivation of coordinated activity across the BLA-frontal-sensory region during NREM sleep, but not during REM sleep. Notably, this inter-regional coordinated reactivation during NREM sleep was entrained to the BLA high-frequency oscillations in the emotional condition, suggesting that the BLA triggers inter-regional interaction. Optogenetic silencing of BLA terminals in the frontal cortex during NREM sleep, but not REM sleep, disrupted the enhanced retention of the perceptual memory, but not the association itself or the emotional component of associative memory. Our results indicate that the inter-regional coordination through the BLA-cortical inputs during NREM sleep is causally required for memory enhancement by emotional arousal.

neuroscience↗

bioRxiv2023

A multicolor suite for deciphering population coding in calcium and cAMP in vivo

cAMP is a pivotal second messenger regulated by various upstream pathways including Ca2+ and G protein-coupled receptors (GPCRs). To decipher in vivo cAMP dynamics, we rationally designed cAMPinG1, an ultrasensitive genetically encoded green cAMP indicator that outperformed its predecessors in both dynamic range and cAMP affinity. Two-photon cAMPinG1 imaging detected cAMP transients in the somata and dendritic spines of neurons in the mouse visual cortex on the order of tens of seconds. In addition, multicolor imaging with a highly sensitive new red Ca2+ indicator RCaMP3 allowed simultaneous measurement of population patterns in Ca2+ and cAMP in hundreds of neurons. We identified Ca2+-induced cAMP responses that represented specific information, such as direction selectivity in vision and locomotion, as well as GPCR-induced cAMP responses. Overall, our multicolor suite revealed that information encoded in Ca2+ and GPCRs signaling is integrated and stored as cAMP transients for longer periods in vivo. HighlightsO_LIDeveloping an ultrasensitive cAMP indicator, cAMPinG1, for visualizing cAMP transients in somata and dendritic spines in vivo. C_LIO_LIDeveloping a highly sensitive red Ca2+ indicator, RCaMP3, for visualizing Ca2+ transients in large neuronal population. C_LIO_LIDual-color Ca2+ and cAMP imaging for dissecting Ca2+-induced and GPCR-induced cAMP responses. C_LIO_LISingle-cell, single-timepoint cAMP imaging for GRCR biology and drug screening. C_LI

neuroscience↗

bioRxiv2020

Fast scanning high optical invariant two-photon microscopy for monitoring a large neural network activity with cellular resolution

Fast and wide imaging with single-cell resolution, high signal-to-noise ratio and no optical aberration has the potential to open up new avenues of investigation in biology. However, this imaging is challenging because of the inevitable tradeoffs among those parameters. Here, we overcome the tradeoffs by combining a resonant scanning system, a large objective with low magnification and high numerical aperture, and highly sensitive large-aperture photodetectors. The result is a practically aberration-free, fast scanning high optical invariant two-photon microscopy (FASHIO-2PM) that enables calcium imaging from a large network composed of [~]16k neurons at 7.5 Hz in a 9 mm2 contiguous image plane including more than 10 sensory-motor and higher-order regions of the cerebral cortex in awake mice. Through a network analysis based on single-cell activities, we discover that the brain exhibits small-world-ness rather than scale-freeness. FASHIO-2PM will enable revealing biological dynamics by simultaneous monitoring of macroscopic activity and its composing elements.

neuroscience↗

bioRxiv2020

Brain/MINDS Beyond Human Brain MRI Study: Multi-Site Harmonization for Brain Disorders Throughout the Lifespan

Psychiatric and neurological disorders are afflictions of the brain that can affect individuals throughout their lifespan. Many brain magnetic resonance imaging (MRI) studies have been conducted; however, imaging-based biomarkers are not yet well established for diagnostic and therapeutic use. This article describes an outline of the planned study, the Brain/MINDS Beyond human brain MRI project (FY2018 [~] FY2023), which aims to establish clinically-relevant imaging biomarkers with multi-site harmonization by collecting data from healthy traveling subjects (TS) at 13 research sites. Collection of data in psychiatric and neurological disorders across the lifespan is also scheduled at 13 sites, whereas designing measurement procedures, developing and analyzing neuroimaging protocols, and databasing are done at three research sites. The Harmonization protocol (HARP) was established for five high-quality 3T scanners to obtain multimodal brain images including T1 and T2-weighted, resting state and task functional and diffusion-weighted MRI. Data are preprocessed and analyzed using approaches developed by the Human Connectome Project. Preliminary results in 30 TS demonstrated cortical thickness, myelin, functional connectivity measures are comparable across 5 scanners, providing high reproducibility and sensitivity to subject-specific connectome. A total of 75 TS, as well as patients with various psychiatric and neurological disorders, are scheduled to participate in the project, allowing a mixed model statistical harmonization. The HARP protocols are publicly available online, and all the imaging, demographic and clinical information, harmonizing database will also be made available by 2024. To the best of our knowledge, this is the first project to implement a rigorous, prospective harmonization protocol with multi-site TS data. It explores intractable brain disorders across the lifespan and may help to identify the disease-specific pathophysiology and imaging biomarkers for clinical practice.

neuroscience↗

bioRxiv2018

Low Computational-cost Cell Detection Method for Calcium Imaging Data

The rapid progress of calcium imaging has reached a point where the activity of tens of thousands of cells can be recorded simultaneously. However, the huge amount of data in such records makes it difficult to carry out cell detection manually. Consequently, because the cell detection is the first step of multicellular data analysis, there is a pressing need for automatic cell detection methods for large-scale image data. Automatic cell detection algorithms have been pioneered by a handful of research groups. Such algorithms, however, assume a conventional field of view (FOV) (i.e. 512 x 512 pixels) and need a significantly higher computational power for a wider FOV to work within a practical period of time. To overcome this issue, we propose a method called low computational-cost cell detection (LCCD), which can complete its processing even on the latest ultra-large FOV data within a practical period of time. We compared it with two previously proposed methods, constrained non-negative matrix factorization (CNMF) and Suite2P. We found that LCCD makes it possible to detect cells from a huge-amount of high-density imaging data within a shorter period of time and with an accuracy comparable to or better than those of CNMF and Suite2P.

neuroscience↗