Biology subjects

Inokuchi, K.

Publications and source records attributed to Inokuchi, K..

16 recordsLinked to original sources

bioRxiv2026

Large-scale dimensional behavioral profiling dissociates fear memory from locomotor confounds in mice: The necessity of baseline-normalized metrics

Fear conditioning is widely used to assess associative memory in mice, yet percent freezing conflates memory with baseline locomotor and anxiety-related traits. A systematic survey of recent studies (2020-2025) found that fewer than 1% statistically integrate locomotor activity into freezing analyses. Here, we address this gap using a large-scale dataset of >10,000 mice across >160 comparisons, including genetic mutations, pharmacological interventions and aging, tested in 15 standardized behavioral paradigms. Conventional freezing scores covaried strongly with general locomotor activity, obscuring memory-related phenotypes. Multiple factor analysis identified two principal behavioral dimensions, locomotor activity and learning/memory: conventional freezing aligned with the locomotor dimension, whereas freezing subtraction and the activity suppression ratio mapped onto the memory dimension and improved detection of synaptic plasticity phenotypes. These analyses show that baseline locomotor normalization is essential for interpreting fear conditioning as a memory assay and provide an open framework for selecting and reporting locomotor-normalized metrics.

neuroscience↗

bioRxiv2026

A model of schema learning based on biological dimensionality reduction during sleep

Reorganizing learned knowledge into generalized representations and transferring it to future learning are essential aspects of cognition, often described as schema formation and use. However, the computational and circuit mechanisms underlying these processes remain unclear. Here, we propose a theoretical model in which schemas emerge through the formation and alignment of low-dimensional neural representations. In this model, high-dimensional input patterns are reorganized into low-dimensional manifolds through replay-driven Hebbian nonlinear dimensionality reduction. Manifold alignment simultaneously maps representations with shared task structure onto a common format, enabling downstream readout circuits to be reused across tasks. The model captures three core features of schema learning: rapid learning of similar tasks by reusing low-dimensional representations from prior experience, sleep-dependent generalization to unobserved relationships in transitive inference, and compositional recombination of schemas to solve novel tasks. Together, these results suggest a potential neural mechanism for forming, aligning, and recombining low-dimensional schemas to support future learning.

neuroscience↗

bioRxiv2026

Silent hippocampal engrams shape future memory processing

The hippocampus harbors silent memory traces even when memory recall is absent. It is unknown why these traces persist and whether they remain sensitive to future episodes. We trained mice on the hippocampal-dependent novel object place recognition task and tracked the transition of the engram from a latent to a silent phase, which still held a functional memory trace. When mice were exposed to a weaker, modified version of their original memories, silent engrams led to better consolidation of these new events than their latent predecessors. Bidirectional manipulation of the engrams state, as well as artificially prolonging its latent state, successfully reversed its effect on the second memory. The silent engram state consistently displayed higher neuronal reactivation during the second event compared to the latent one, which may explain its preferential effect on its consolidation. Our results reveal previously unknown cognitive and activation dynamics for this behaviorally silent state.

animal behavior and cognition↗

bioRxiv2026

Sleep neural code perpetuates the evolving negativity bias under stress

Negativity bias is the distorted cognitive processing of how self-experiences are negatively perceived through rumination and overgeneralization. Despite proposed theories of higher-order emotional representation and the involvement of default mode networks, the biological mechanisms underlying how negative emotional bias is persistently generated remain unknown. Here, we show that under negative emotional state, sleep orchestrates neural dynamics to shape persistent negativity bias. A negative emotional state, induced by repeated social defeat stress (SoD), generates negativity bias in both memory-recall and novel experiences such as fear conditioning. Longitudinal Ca2+ imaging of the hippocampus across days revealed that in emotional states, negative schema-like representations that encode the semantic aspect of negativity across experiences are generated. These negative schema-like representations are continuously processed along with dynamic co-reactivations of distinct emotional experiences during sleep. Closed-loop optogenetic silencing of stress experience-tagged cellular ensembles during sleep, but not during awake, prevents negativity bias in future memory-recall and novel experiences. Finally, sleep-active, but not sleep-nonactive, SoD cells predict and decode emotional behaviours during learned and novel situations. Together, these results reveal the biological emergence of semantic-like representations of emotional experiences and sleep causally coordinate neuronal dynamics to persistently shape negativity in future conscious states. These findings offer a new perspective on how higher-order emotional processing during sleep may determine our emotional interpretation of past and future experiences.

neuroscience↗

bioRxiv2025

The medial prefrontal cortex encodes procedural rules as sequential neuronal activity dynamics

The prefrontal cortex plays a crucial role in procedural rule learning; however, the specific neuronal mechanism through which it represents rules is unknown. We hypothesized that sequential neuronal activities in the prefrontal cortex encode these rules. To investigate this, we recorded neuronal activities in the medial prefrontal cortex of mice during rule learning using Ca2+ imaging. We utilized a method based on convolutional negative matrix factorization, iSeq, to automatically detect temporal neuronal sequences in the recorded data. As rule learning advanced, these neuronal sequences began to encode critical information for rule execution. In mice that had mastered the rule, the dynamics of neuronal sequences could predict success and failure of reward acquisition. Furthermore, the composition of cell populations within the neuronal sequences was rearranged throughout the learning process. These findings suggest that as animals learn a rule, the medial prefrontal cortex continually updates its neuronal sequences to assign significance to behavioral actions crucial for reward acquisition.

neuroscience↗

bioRxiv2024

Dual roles of idling moments in past and future memories

Every day, we experience new daily episodes and store new memories. Although memories are stored in corresponding engram cells, how different sets of engram cells are selected for current and next episodes, and how they create their memories, remains unclear. We report that in mice, hippocampal CA1 neurons show an organized synchronous activity in prelearning home cage sleep that correlates with the learning ensembles only in engram cells, termed preconfigured ensembles. Moreover, after learning, a subset of nonengram cells develops population activity, which is constructed during postlearning offline periods through synaptic depression and scaling, and then emerges to represent engram cells for new learning. Together, our findings indicate that during offline periods there are two parallel processes occurring: conserving of past memories through reactivation, and preparation for upcoming ones through offline synaptic plasticity mechanisms.

neuroscience↗

bioRxiv2022

HOTARU: Automatic sorting system for large scale calcium imaging data

Currently, calcium imaging allows long-term recording of large-scale neuronal activity in diverse states. However, it remains difficult to extract neuronal dynamics from recorded imaging data. In this study, we propose an improved constrained nonnegative matrix factorization (CNMF)-based algorithm and an effective method to extract cell shapes with fewer false positives and false negatives through image processing. We also show that the evaluation metrics obtained during image and signal processing can be combined and used for false-positive cell determination. For the CNMF algorithm, we combined cell-by-cell regularization and baseline shrinkage estimation, which greatly improved its stability and robustness. We applied these methods to real data and confirmed their effectiveness. Our method is simpler and faster, detects more cells with lower firing rates and signal-to-noise ratios, and enhances the quality of the extracted cell signals. These advances can improve the standard of downstream analysis and contribute to progress in neuroscience.

neuroscience↗

bioRxiv2022

The hippocampus as a sorter and reverberatory integrator of sensory inputs

In entorhinal-hippocampal networks, the trisynaptic pathway, including the CA3 recurrent circuit, processes episodes of context and space1-3. Recurrent connectivity can generate reverberatory activity4-6, an intrinsic activity pattern of neurons that occurs after sensory inputs have ceased. However, the role of reverberatory activity in memory encoding remains incompletely understood. Here we demonstrate that in mice, synchrony between conditioned stimulus (CS) and unconditioned stimulus (US)-responsible cells occurs during the reverberatory phase, lasting for approximately 15 s, but not during CS and US inputs, in the CA1 and the reverberation is crucial for the linking of CS and US in the encoding of delay-type cued-fear memory. Retrieval-responsive cells developed primarily during the reverberatory phase. Mutant mice lacking N-methyl-D-aspartate receptors (NRs) in CA3 showed a cued-fear memory impairment and a decrease in synchronized reverberatory activities between CS- and US-responsive CA1 cells. Optogenetic CA3 silencing at the reverberatory phase during learning impaired cued-fear memory. Our findings suggest that reverberation recruits future retrieval-responsive cells via synchrony between CS- and US-responsive cells. The hippocampus uses reverberatory activity to link CS and US inputs, and avoid crosstalk during sensory inputs.

neuroscience↗

bioRxiv2021

Cortical cell ensemble control of past experience-dependent memory updating

When processing current sensory inputs, animals refer to related past experiences. Current information is then incorporated into the related neural network to update previously stored memories. However, the neuronal mechanism underlying the impact of memories of prior experiences on current learning is not well understood. Here, we found that a cellular ensemble in the posterior parietal cortex (PPC) that is activated during past experience mediates an interaction between past and current information to update memory through a PPC-anterior cingulate cortex circuit in mice. Moreover, optogenetic silencing of the PPC ensemble immediately after retrieval dissociated the interaction without affecting individual memories stored in the hippocampus and amygdala. Thus, a specific subpopulation of PPC cells represents past information and instructs downstream brain regions to update previous memories.

neuroscience↗

bioRxiv2021

Uncovering long-term existence of a silent short-term memory trace

Active recall of short-term memory (STM) is known to last for a few hours, but whether STM has long-term functions is unknown. Here we show that, STM can be optogenetically retrieved at a time point during which natural recall is not possible, uncovering the long-term existence of a silent STM engram. Moreover, re-training within 3 days led to natural long-term recall, indicating facilitated consolidation. Calcium imaging revealed hippocampal CA1 reactivations of the STM trace during post-learning sleep. Inhibiting offline CA1 activity, N-methyl-D-aspartate receptor activity, or protein synthesis after first exposure to the STM-forming event impaired the future re-exposure-facilitated consolidation, which highlights a role of protein synthesis and sleep in storing a silent STM trace. These results provide evidence that STM is not completely lost within hours and demonstrates a possible two-step STM consolidation, first storage as a silent engram, then transformation into an active state by recurrence within 3 days.

neuroscience↗

bioRxiv2021

Inspiring cognitive inference in a cortical network during REM sleep

Idling brain activity has been proposed to facilitate inference, insight, and innovative problem-solving1-4. However, it remains unclear how and when the subconscious brain can create novel ideas. Here, we show coordinated roles of non-rapid eye movement (NREM) and rapid-eye movement (REM) sleep in weaving inferential information from learned information. In a transitive inference paradigm, mice gained the inference one day, but not shortly, after complete training. Inhibiting the neuronal computations in the anterior cingulate cortex (ACC) during post-learning either NREM or REM sleep, but not wakefulness, disrupted the inference without affecting the learned knowledge. In vivo Ca2+ imaging showed gradual development of inference-related representation, peaking at post-training REM sleep. Neurons representing learned information co-reactivated significantly during post-training NREM sleep, while their co-reactivation with neurons representing inferential information was significantly higher during REM sleep. Furthermore, after insufficient learning, artificial activation of medial entorhinal cortex-ACC dialogue during only REM sleep created inferential knowledge. These findings suggest that NREM sleep organizes the scattered learned knowledge in a complete hierarchy, while REM sleep computes the inferential information from the organized hierarchy. Collectively, our study provides a mechanistic insight on NREM and REM coordination in weaving inferential knowledge, thus highlighting the power of idling brain in cognitive flexibility.

neuroscience↗

bioRxiv2021

Offline knowledge assimilations ensue online obscurity to inspire implicit learning

Passive priming of prior knowledge to assimilate ongoing experiences underlies advanced cognitive processing. However, the necessary neural dynamics of memory assimilation remains elusive. Uninstructed brain could also show boosted creativity, particularly after idling states, yet it remains unclear whether the idling brain can spontaneously spark relevant knowledge assimilations. We established a paradigm that links/separates context-dependent memories according to geometrical similarities. Mice exploring one of four contexts one day before undergoing contextual fear conditioning in a square context showed a gradual fear transfer to pre-exposed geometrically relevant contexts next day, but not after 15 min. Anterior cingulate cortex neurons representing relevant, rather than distinct, memories were significantly co-reactivated during post-conditioning sleep only, before their selective integration next day during testing. Disrupting sleep co-reactivations prevented assimilation while preserving recent memory consolidation. Thus, assimilating pertinent memories during sleep through co-reactivation of their respective engrams represents the neural underpinnings of sleep-triggered implicit cortical learning.

neuroscience↗

bioRxiv2017

Autophagy enhances memory erasure through synaptic destabilization

There is substantial interest in memory reconsolidation as a target for the treatment of anxiety disorders such as post-traumatic stress disorder (PTSD). However, its applicability is restricted by reconsolidation-resistant conditions that constrain the initial memory destabilization. In this study, we investigated whether the induction of synaptic protein degradation through autophagy modulation, a major protein degradation pathway, can enhance memory destabilization upon retrieval and whether it can be utilized to overcome these conditions. Here, using male mice in an auditory fear reconsolidation model, we showed that autophagy contributes to memory destabilization and its induction can be utilized to enhance erasure of a reconsolidation-resistant auditory fear memory that depended on -amino-3-hydroxy-5-methyl4-isoxazolepropionic acid receptor (AMPAR) endocytosis. Using male mice in a contextual fear reconsolidation model, autophagy induction in the amygdala or in the hippocampus enhanced fear or contextual memory destabilization, respectively. The latter correlated with AMPAR degradation in the spines of the contextual memory-ensemble cells. Using male rats in an in vivo long-term potentiation reconsolidation model, autophagy induction enhanced synaptic destabilization in an N-methyl-D-aspartate receptor-dependent manner. These data indicate that induction of synaptic protein degradation can enhance both synaptic and memory destabilization upon reactivation and that autophagy inducers have the potential to be used as a therapeutic tool in the treatment of anxiety disorders.\n\nSignificance StatementIt has been reported that inhibiting synaptic protein degradation prevents memory destabilization. However, whether the reverse relation is true and whether it can be utilized to enhance memory destabilization is still unknown. Here we addressed this question on the behavioral, molecular and synaptic levels, and showed that induction of autophagy, a major protein degradation pathway, can enhance memory and synaptic destabilization upon reactivation. We also show that autophagy induction can be utilized to overcome a reconsolidation-resistant memory, suggesting autophagy inducers as a potential therapeutic tool in the treatment of anxiety disorders.

neuroscience↗

bioRxiv2017

Glucocorticoid receptor-mediated amygdalar metaplasticity underlies adaptive modulation of fear memory by stress

Glucocorticoid receptor (GR) is crucial for signaling mediated by stress-induced high levels of glucocorticoids. The lateral nucleus of the amygdala (LA) is a key structure underlying auditory-cued fear conditioning. Here, we demonstrate that genetic disruption of GR in the LA (LAGRKO) resulted in an auditory-cued fear memory deficit for strengthened conditioning. Furthermore, the suppressive effect of a single restraint stress (RS) prior to conditioning on auditory-cued fear memory in floxed GR (control) mice was abolished in LAGRKO mice. Optogenetic induction of long-term depression (LTD) at auditory inputs to the LA reduced auditory-cued fear memory in RS-exposed LAGRKO mice, and in contrast, optogenetic induction of long-term potentiation (LTP) increased auditory-cued fear memory in RS-exposed floxed GR mice. These findings suggest that prior stress suppresses fear conditioning-induced LTP at auditory inputs to the LA in a GR-dependent manner, thereby protecting animals from encoding excessive cued fear memory under stress conditions.

neuroscience↗

bioRxiv2017

Automatic sorting system for large calcium imaging data

It has become possible to observe neural activity in freely moving animals via calcium imaging using a microscope, which could not be observed previously. However, it remains difficult to extract the dynamics of nerve cells from the recorded imaging data. In this study, we greatly improved the stability, and robustness of the cell activity estimation method via non-negative matrix decomposition with shrinkage estimation of the baseline. In addition, by improving the initial state of the iterative algorithm using a newly proposed method to extract the shape of the cell via image processing, a solution could be obtained with a small number of iterations. These methods were applied to artificial and real data, and their effectiveness was confirmed.

neuroscience↗

bioRxiv2017

Adult Neurogenesis Conserves Hippocampal Learning Capacity

Memory coding strengthens synaptic efficacy in the hippocampus via a long-term potentiation (LTP)-like mechanism. Given that animals are able to store memories of everyday experiences, hippocampal circuits should be able to avoid saturation of overall synaptic weight to preserve learning capacity. However, the underlying mechanism for this is still poorly understood. Here, we show that adult neurogenesis in rats plays a crucial role in the maintenance of the hippocampal learning capacity for learning. Artificial saturation with hippocampal LTP impaired learning capacity in contextual fear conditioning, which then completely recovered after 14 days, when LTP had decayed to the basal level. Ablation of neurogenesis by X-ray irradiation delayed the recovery of learning capacity, while enhancement of neurogenesis using running wheel sped up the recovery. Thus, one benefit of ongoing adult neurogenesis is the maintenance of hippocampal learning capacity through homeostatic renewing of hippocampal memory circuits. Decreased neurogenesis in aged animals may underlie declines in cognitive function with aging.

neuroscience↗