Biology subjects

Hori, Y.

Publications and source records attributed to Hori, Y..

At least 19 recordsLinked to original sources

bioRxiv2025

Dynamic Tuning of Genetic Circuit Gain via Controllable Plasmid Copy Number

Plasmid copy number directly influences gene expression strength in synthetic genetic circuits and serves as a tunable parameter for adjusting circuit gain and output levels. Building upon recent progress in copy number control, this report presents a genetic circuit that enables dynamic regulation of circuit gain through the regulation of plasmid copy numbers. To illustrate the underlying concept, we first developed a mathematical model describing the relationship between plasmid copy number and circuit gain and simulated the circuit dynamics to examine how gain responds to copy number changes. We then constructed the circuit and experimentally confirmed that plasmid copy number, i.e., circuit gain, can be externally controlled in E. coli. In particular, we demonstrate communication-based gain control using AHL-mediated quorum sensing from co-cultured cells. These results support the feasibility of plasmid copy number control as a practical and predictable strategy for tuning synthetic gene circuit behavior.

synthetic biology↗

bioRxiv2025

Modular dynamics of conscious and unconscious states in marmoset cortex

General anesthetics are routinely used to induce unconsciousness. While much is known about their effects on receptor function and the activity of individual neurons, much less is known about how these local effects are manifest at the level of largescale, distributed brain networks. Using functional magnetic resonance imaging (fMRI) with the common marmoset (Callithrix jacchus) we investigated the effects of the anaesthetic isoflurane on functional brain networks and their temporal dynamics, comparing network measures during wakeful rest and induced unconsciousness. The anaesthetic condition was characterised by weak functional networks that were more similar to anatomical structure and more fragmented than during wakeful rest. Conversely, the awake condition was characterised by coordinated network reconfiguration and more distinct subnetwork composition. Our findings are consistent with the view that consciousness is an emergent property of the dynamics of functional brain networks, and that anaesthetics impoverish these dynamics by reducing the efficacy of synaptic transmission.

neuroscience↗

bioRxiv2025

Establishment of a second-generation transgenic marmoset model of polyglutamine disease recapitulating neurological symptoms and pathology

Neurodegenerative diseases, including polyglutamine diseases, remain a major clinical challenge, partly because of limited animal models that recapitulate human disease. Here, we describe a second-generation transgenic marmoset model of spinocerebellar ataxia 3 (SCA3), a polyglutamine disease, which stably expresses expanded CAG repeats in ATXN3. All five offspring of the founder marmoset harbored the transgene with reduced transgene integration sites and without repeat instability or genetic mosaicism, offering improved construct validity. Three of the five marmosets developed progressive motor impairments that segregated into two distinct phenotypes: early onset with rapid progression and late onset with mild progression, accompanied by corresponding patterns in body weight gain and grip strength. Pathological analysis revealed cerebellar Purkinje cell loss, spinal cord neurodegeneration, and widespread intranuclear inclusions. The severity of motor phenotypes correlated with transgene expression levels in disease-relevant brain regions, including the cerebellum, spinal cord, and striatum. By overcoming the common translational limitations of rodent systems, our second-generation model offers a powerful platform for investigating disease mechanisms and testing potential therapeutic interventions. Our results advance the utility of transgenic marmosets as clinically relevant models of neurodegenerative diseases. Summary StatementSecond-generation transgenic marmoset models of spinocerebellar ataxia 3 replicated the progressive motor deficits and neuropathology of the founder marmoset, providing a powerful platform for studying disease mechanisms and developing therapies.

neuroscience↗

bioRxiv2025

Inhibition of NF-κB signaling pathway in astrocytes facilitates amyloid-β clearance by kallikrein-related peptidase 7

Alzheimer disease (AD) is characterized by the deposition of amyloid-{beta} peptide (A{beta}). Decreased A{beta} clearance is observed in sporadic AD patients, suggesting that enhancing A{beta} clearance is a potential therapeutic approach for AD. We identified kallikrein-related peptidase 7 (KLK7) as an astrocyte-derived A{beta}-degrading protease, and its mRNA expression is reduced in AD brains. Memantine, an N-methyl-D-aspartate (NMDA) receptor antagonist, upregulates KLK7 expression in astrocytes; however, the regulatory mechanism remains unclear. Here, we show that the NMDA receptor signaling negatively regulates KLK7 mRNA expression via nuclear factor-{kappa}B (NF-{kappa}B). Inhibition of NF-{kappa}B signaling pathway in astrocytes increases KLK7 expression and promotes A{beta} degradation. Moreover, the mRNA expression level of the NF-{kappa}B family is elevated in AD brains and shows a negative correlation with KLK7 mRNA expression. Finally, the injection of an NF-{kappa}B inhibitor significantly upregulates Klk7 expression and reduces A{beta} levels in vivo. These findings suggest that the NMDA receptor-NF-{kappa}B signaling axis in astrocytes negatively regulates KLK7 expression and modulates KLK7-mediated A{beta} clearance.

neuroscience↗

bioRxiv2025

Remote Cortical Network for Frontal Cognitive Symptoms derived from Tau Accumulation in Progressive Supranuclear Palsy

Progressive Supranuclear Palsy (PSP) is a neurodegenerative disorder characterized by impaired movement and frontal cognitive dysfunctions. While motor symptoms have been linked with subcortical tau deposits, network mechanisms underlying the frontal cognitive symptoms remain unclear because pathological tau accumulation is quite limited within the frontal cortex and heterogeneously distributed primarily in the subcortical regions. Here, we combined tau-PET using a high-contrast probe we have recently developed with normative connectome to resolve this issue. Tau-deposition sites were connected to a common cortical network that could not be identified through similar analyses based on atrophy detected by structural MRI. This network was predominantly overlapped with canonical action-mode and frontoparietal networks, which jointly support adaptive and goal-directed behavior. Critically, while the degree of subcortical primary tau deposition correlated with motor symptoms, only the degree of connectivity from tau-deposition sites to the derived cortical network explained the frontal cognitive deficits of individual patients. These findings suggest a novel mechanism that frontal cognitive impairments, but not motor deficits, in PSP are derived from remote effects of tau deposits, independent of atrophy, through the convergent connectivity to the identified common cortical network.

neuroscience↗

bioRxiv2024

Longitudinal assessment of DREADD expression and efficacy in the monkey brain

Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) offer a powerful means for reversible control of neuronal activity through systemic administration of inert actuators. Because chemogenetic control relies on DREADD expression levels, understanding and quantifying the temporal dynamics of their expression is crucial for planning long-term experiments in monkeys. In this study, we longitudinally quantified in vivo DREADD expression in macaque monkeys using positron emission tomography with the DREADD-selective tracer [11C]deschloroclozapine (DCZ), complemented by functional studies. Twenty macaque monkeys were evaluated after being injected with adeno-associated virus vectors expressing the DREADDs hM4Di or hM3Dq, whose expression was quantified as changes in [11C]DCZ binding potential from baseline levels. Expression levels of both hM4Di and hM3Dq peaked around 60 days post-injection, remained stable for about 1.5 years, and declined gradually after two years. Significant chemogenetic control of neural activity and behavior persisted for about two years. The presence of protein tags significantly influenced expression levels, with co-expressed protein tags reducing overall expression levels. These findings provide valuable insights and guidelines for optimizing the use of DREADDs in long-term primate studies and potential therapeutic applications.

neuroscience↗

bioRxiv2024

Embryological cellular origins and hypoxia-mediated mechanisms in PIK3CA-Driven refractory vascular malformations

Congenital vascular malformations, affecting 0.5% of the population, often occur in the head and neck, complicating treatment due to the critical functions in these regions. Our previous research identified distinct developmental origins for blood and lymphatic vessels in these areas, tracing them to the cardiopharyngeal mesoderm (CPM), which contributes to the development of the head, neck, and cardiovascular system in both mouse and human embryos. In this study, we investigated the pathogenesis of these malformations by expressing Pik3caH1047R in the CPM. Mice expressing Pik3caH1047R in the CPM developed vascular abnormalities restricted to the head and neck. Single-cell RNA sequencing revealed that Pik3caH1047R upregulates Vegf-a expression in endothelial cells through HIF-mediated hypoxia signaling. Human samples supported these findings, showing elevated HIF-1 and VEGF-A in malformed vessels. Notably, inhibition of HIF-1 and VEGF-A in the mouse model significantly reduced abnormal vasculature. These results highlight the role of embryonic origins and hypoxia-driven mechanisms in vascular malformations, providing a foundation for the development of therapies targeting these difficult-to-treat conditions.

molecular biology↗

bioRxiv2024

Formation of brain-wide neural geometry during visual item recognition in monkeys

Neural dynamics assumes to reflect computations that relay and transform information in the brain. Previous studies have identified the neural population dynamics in many individual brain regions as a trajectory geometry, preserving a manifest of computational motifs. However, whether these populations share particular geometric patterns across brain-wide neural populations remains unclear. Here, by mapping neural dynamics widely across temporal/frontal/limbic regions in the cortical and subcortical structures of monkeys, we show that 10 neural populations, including 2,500 neurons, propagate visual item information in a stochastic manner. We found that visual inputs predominantly evoked rotational dynamics in the higher-order visual area, TE and its downstream striatum tail, while curvy/straight dynamics appeared frequently downstream in the orbitofrontal/hippocampal network. These geometric changes were not deterministic but rather stochastic according to their respective emergence rates. Our meta-analysis results indicated that visual information propagates as a heterogeneous mixture of stochastic neural population signals in the brain.

neuroscience↗

bioRxiv2023

Distinct roles of monkey OFC-subcortical pathways in adaptive behavior

To be the most successful, primates must adapt to changing environments and optimize their behavior by making the most beneficial choices. At the core of adaptive behavior is the orbitofrontal cortex (OFC) of the brain, which updates choice value through direct experience or knowledge-based inference. Here, we identify distinct neural circuitry underlying these two separate abilities. We designed two behavioral tasks in which macaque monkeys updated the values of certain items, either by directly experiencing changes in stimulus-reward associations, or by inferring the value of unexperienced items based on the tasks rules. Chemogenetic silencing of bilateral OFC combined with mathematical model-fitting analysis revealed that monkey OFC is involved in updating item value based on both experience and inference. In vivo imaging of chemogenetic receptors by positron emission tomography allowed us to map projections from the OFC to the rostromedial caudate nucleus (rmCD) and the medial part of the mediodorsal thalamus (MDm). Chemogenetic silencing of the OFC-rmCD pathway impaired experience-based value updating, while silencing the OFC-MDm pathway impaired inference-based value updating. Our results thus demonstrate a dissociable contribution of distinct OFC projections to different behavioral strategies, and provide new insights into the neural basis of value-based adaptive decision-making in primates.

neuroscience↗

bioRxiv2023

Multimodal imaging for validation and optimization of ion channel-based chemogenetics in nonhuman primates

Chemogenetic tools provide an opportunity to manipulate neuronal activity and behavior selectively and repeatedly in nonhuman primates (NHPs) with minimal invasiveness. Designer Receptors Exclusively Activated by Designer Drugs are one example that is based on mutated muscarinic acetylcholine receptors. Another channel-based chemogenetic system available for neuronal modulation in NHPs uses Pharmacologically Selective Actuator Modules (PSAMs), which are selectively activated by Pharmacologically Selective Effector Molecules (PSEMs). To facilitate the use of the PSAM/PSEM system, the selection and dosage of PSEMs should be validated and optimized for NHPs. To this end, we used a multimodal imaging approach. We virally expressed excitatory PSAM (PSAM4-5HT3) in the striatum and the primary motor cortex of two macaque monkeys, and visualized its location through positron emission tomography (PET) with the reporter ligand [18F]ASEM. Chemogenetic excitability of neurons triggered by two PSEMs (uPSEM817 and uPSEM792) was evaluated using [18F]fluorodeoxyglucose-PET imaging, with uPSEM817 being more efficient than uPSEM792. Pharmacological magnetic resonance imaging showed that increased brain activity in the PSAM4-expressing region began approximately 13 min after uPSEM817 administration and continued for at least 60 min. Our multimodal imaging data provide valuable information regarding the manipulation of neuronal activity using the PSAM/PSEM system in NHPs, facilitating future applications. Significance statementLike other chemogenetic tools, the ion channel-based system called Pharmacologically Selective Actuator Module/Pharmacologically Selective Effector Molecule (PSAM/PSEM) allows remote manipulation of neuronal activity and behavior in living animals. Nevertheless, its application in non-human primates (NHPs) is still limited. Here, we used multi-tracer positron emission tomography (PET) imaging and pharmacological magnetic resonance imaging (MRI) to visualize an excitatory chemogenetic ion channel (PSAM4-5HT3) and validate its chemometric function in macaque monkeys. Our results provide the optimal agonist, dose, and timing for chemogenetic neuronal manipulation, facilitating the use of the PSAM/PSEM system and expanding the flexibility and reliability of circuit manipulation in NHPs in a variety of situations.

neuroscience↗

bioRxiv2023

Reduced serotonergic transmission alters sensitivity to cost and reward via 5-HT1A and 5-HT1B receptors in monkeys

Deficiency of the serotonin (5-HT) system is considered one of the core biological pathologies of depression and other psychiatric disorders whose key symptom is decreased motivation. Yet, the exact role of 5-HT in motivation remains controversial and elusive. Here, we pharmacologically manipulated the 5-HT system and quantified effects on motivation in terms of incentives and costs for goal-directed action in monkeys. Reversible inhibition of 5-HT synthesis increased refusal responses and reaction times in goal-directed task performance, indicating decreased motivation that could be separated into value-dependent and -independent components. To identify the receptor subtypes involved in these components, we systemically administered antagonists specific for four major 5-HT receptor subtypes: 5-HT1A, 5-HT1B, 5-HT2A, and 5-HT4. Positron emission tomography visualized the unique distribution of each subtype in limbic brain regions and determined the systemic antagonist dose that achieved approximately 30% occupancy. We found that blockade of 5-HT1A, but not other receptor subtypes, increased sensitivity to future workload and time-delay to reward, and decreased motivation in a value-independent manner. Moreover, blocking only 5-HT1B receptors reduced the impact of incentive value on motivation. These results suggest that two distinct processes, mediated by 5-HT1A and 5-HT1B receptors, lead to reduced motivation in 5-HT system deficiency.

neuroscience↗

bioRxiv2022

A red fluorescent genetically encoded biosensor for extracellular L-lactate

L-Lactate, traditionally recognized as a waste product of metabolism, is now appreciated as a key intercellular energy currency in mammals. To enable investigations of intercellular shuttling of L-lactate, we have previously reported eLACCO1.1, a green fluorescent genetically encoded biosensor for extracellular L-lactate. eLACCO1.1 enables cellular resolution imaging of extracellular L-lactate in cultured mammalian cells and brain tissue. However, eLACCO1.1 spectrally overlaps with commonly used optical biosensors and actuators, limiting its application for multiplexed imaging or combined use with optogenetic actuators. Here, we report a red fluorescent extracellular L-lactate biosensor, designated R-eLACCO2. R-eLACCO2 is the end-product of extensive directed evolution and exhibits a large fluorescence response to L-lactate with high molecular specificity in vitro. We demonstrate that R-eLACCO2 with optimized leader and anchor sequences shows a large fluorescence change in response to extracellular L-lactate on the membrane of live mammalian cells. R-eLACCO2 should enable multicolor imaging of extracellular L-lactate in combination with other fluorescent probes and optogenetic actuators.

bioengineering↗

bioRxiv2022

Chemogenetic disconnection between the orbitofrontal cortex and the rostromedial caudate nucleus disrupts motivational control of goal-directed action

The orbitofrontal cortex (OFC) and its major downstream target within the basal ganglia--the rostromedial caudate nucleus (rmCD)--are involved in reward-value processing and goal-directed behavior. However, a causal contribution of the pathway linking these two structures to goal-directed behavior has not been established. Using the chemogenetic technology of Designer Receptors Exclusively Activated by Designer Drugs with a crossed inactivation design, we functionally and reversibly disrupted interactions between the OFC and rmCD in two male macaque monkeys. We injected an adeno-associated virus vector expressing an inhibitory designer receptor (hM4Di) into the OFC and contralateral rmCD, the expression of which was visualized in vivo by positron emission tomography (PET) and confirmed by post-mortem immunohistochemistry. Functional disconnection of the OFC and rmCD resulted in a significant and reproducible loss of sensitivity to the cued reward value for goal-directed action. This decreased sensitivity was most prominent when monkeys had accumulated a certain amount of reward. These results provide causal evidence that the interaction between the OFC and the rmCD is needed for motivational control of action on the basis of the relative reward value and internal drive. This finding extends current understanding of the physiological basis of psychiatric disorders in which goal-directed behavior is affected, such as obsessive-compulsive disorder. Significance StatementIn daily life, we routinely adjust the speed and accuracy of our actions on the basis of the value of expected reward. Abnormalities in these kinds of motivational adjustments might be related to behaviors seen in psychiatric disorders such as obsessive-compulsive disorder. In the current study, we show that the connection from the orbitofrontal cortex to the rostromedial caudate nucleus is essential formotivational control of action in monkeys. This finding expands our knowledge about how the primate brain controls motivation and behavior and provides a particular insight into disorders like obsessive-compulsive disorder, in which altered connectivity between the orbitofrontal cortex and the striatum has been implicated.

neuroscience↗

bioRxiv2022

A parametric logistic equation with light flux and media concentration for cultivation planning of microalgae

Microalgae are considered to be promising producers of bioactive chemicals, feeds, and fuels from carbon dioxide by photosynthesis. Thus, the prediction of microalgal growth profiles is important for the planning of cost-effective and sustainable cultivation-harvest cycles. This paper proposes a mathematical model capable of predicting the effect of light flux into culture and medium concentration on the growth profiles of microalgae by incorporating these growth-limiting factors into the logistic equation. The specific form of the equation is derived based on the experimentally measured growth profiles of Monoraphidium sp., a microalgal strain isolated by the authors, under 16 conditions consisting of the combinations of incident light fluxes into culture and initial medium concentrations. Using a cross-validation method, it is shown that the proposed model has the ability to predict necessary incident light flux into culture and initial medium concentration for harvesting target biomass at target time. Finally, the model-guided cultivation planning is performed and is evaluated by comparing the result with the experimental data.

systems biology↗

bioRxiv2022

Self-organization, quality control, and preclinical studies of human iPSC-derived retinal sheets for tissue-transplantation therapy

Three-dimensional retinal organoids (3D-retinas) are a promising graft source for transplantation therapy. We previously developed self-organizing culture for 3D-retina generation from human pluripotent stem cells (hPSCs). Here we present a quality control method and preclinical studies for tissue-sheet transplantation. Self-organizing hPSCs differentiated into both retinal and off-target tissues. Gene expression analyses identified the major off-target tissues as eye-related, cortex-like, and spinal cord-like tissues. For quality control, we developed a qPCR-based test in which each hPSC-derived neuroepithelium was dissected into two tissue-sheets: inner-central sheet for transplantation and outer-peripheral sheet for qPCR to ensure retinal tissue selection. During qPCR, tissue-sheets were stored for 3-4 days using a newly developed preservation method. In a rat tumorigenicity study, no transplant-related adverse events were observed. In retinal degeneration model rats, retinal transplants differentiated into mature photoreceptors and exhibited light responses in electrophysiology assays. These results demonstrate our rationale toward self-organizing retinal sheet transplantation therapy.

neuroscience↗

bioRxiv2022

Anatomical variability, multi-modal coordinate systems, and precision targeting in the marmoset brain

Localising accurate brain regions needs careful evaluation in each experimental species due to their individual variability. However, the function and connectivity of brain areas is commonly studied using a single-subject cranial landmark-based stereotactic atlas in animal neuroscience. Here, we address this issue in a small primate, the common marmoset, which is increasingly widely used in systems neuroscience. We developed a non-invasive multi-modal neuroimaging-based targeting pipeline, which accounts for intersubject anatomical variability in cranial and cortical landmarks in marmosets. This methodology allowed creation of multi-modal templates (MarmosetRIKEN20) including head CT and brain MR images, embedded in coordinate systems of anterior and posterior commissures (AC-PC) and CIFTI grayordinates. We found that the horizontal plane of the stereotactic coordinate was significantly rotated in pitch relative to the AC-PC coordinate system (10 degrees, frontal downwards), and had a significant bias and uncertainty due to positioning procedures. We also found that many common cranial and brain landmarks (e.g., bregma, intraparietal sulcus) vary in location across subjects and are substantial relative to average marmoset cortical area dimensions. Combining the neuroimaging-based targeting pipeline with robot-guided surgery enabled proof-of-concept targeting of deep brain structures with an accuracy of 0.2 mm. Altogether, our findings demonstrate substantial intersubject variability in marmoset brain and cranial landmarks, implying that subject-specific neuroimaging-based localization is needed for precision targeting in marmosets. The population-based templates and atlases in grayordinates, created for the first time in marmoset monkeys, should help bridging between macroscale and microscale analyses. HighlightsO_LIAchieved sub-millimeter localization accuracy of subject-wise brain region C_LIO_LIPropose a dedicated non-invasive multi-modal subject-specific registration pipeline C_LIO_LIConstruct brain coordinate system in AC-PC and grayordinate spaces C_LIO_LIEstablish multi-modal MRI and CT brain and cortical templates, MarmosetRIKEN20 C_LIO_LIQuantify intersubject variabilities in marmoset brain C_LIO_LISignificant bias and uncertainty exist in marmoset stereotactic positioning C_LI

neuroscience↗

bioRxiv2022

Comparison of neural population dynamics in the regression subspace between continuous and categorical task parameters

Neural population dynamics, presumably fundamental computational units in the brain, provide a key framework for understanding information processing in the sensory, cognitive, and motor functions. However, neural population dynamics is not explicitly related to the conventional analytic framework for single-neuron activity, i.e., representational models that analyze neuronal modulations associated with cognitive and motor parameters. In this study, we applied a recently developed state-space analysis to incorporate the representational models into the dynamic model in combination with these parameters. We compared neural population dynamics between continuous and categorical task parameters during two visual recognition tasks, using the datasets originally designed for a single-neuron approach. We successfully extracted neural population dynamics in the regression subspace, which represent modulation dynamics for both continuous and categorical task parameters with reasonable temporal characteristics. Furthermore, we combined the classical optimal-stimulus analysis paradigm for the single-neuron approach (i.e., stimulus identified as maximum neural responses) into the dynamic model, and found that the most prominent modulation dynamics at the lower dimension were derived from these optimal responses. Thus, our approach provides a unified framework for incorporating knowledge acquired with the single-neuron approach into the dynamic model as a standard procedure for describing neural modulation dynamics in the brain.

neuroscience↗

bioRxiv2021

Metrics of High Cofluctuation and Entropy to Describe Control of Cardiac Function in the Stellate Ganglion

Stellate ganglia within the intrathoracic cardiac control system receive and integrate central, peripheral, and cardiopulmonary information to produce postganglionic cardiac sympathetic inputs. Pathological anatomical and structural remodeling occurs within the neurons of the stellate ganglion (SG) in the setting of heart failure. A large proportion of SG neurons function as interneurons whose networking capabilities are largely unknown. Current therapies are limited to targeting sympathetic activity at the cardiac level or surgical interventions such as stellectomy, to treat heart failure. Future therapies that target the stellate ganglion will require understanding of their networking capabilities to modify any pathological remodeling. We observe SG networking by examining cofluctuation and specificity of SG networked activity to cardiac cycle phases. We investigate network processing of cardiopulmonary transduction by SG neuronal populations in porcine with chronic pacing-induced heart failure and control subjects during extended in-vivo extracellular microelectrode recordings. We find that information processing and cardiac control in chronic heart failure by the SG, relative to controls, exhibits: i) more frequent, short-lived, high magnitude cofluctuations, ii) greater variation in neural specificity to cardiac cycles, and iii) neural network activity and cardiac control linkage that depends on disease state and cofluctuation magnitude.

bioengineering↗