Biology subjects

Inagaki, M.

Publications and source records attributed to Inagaki, M..

10 recordsLinked to original sources

bioRxiv2026

SorCS1 promotes synaptic and cognitive resilience despite amyloid pathology in Alzheimer's disease model mice

Alzheimer's disease (AD) lacks effective therapies despite extensive efforts targeting amyloid {beta} (A{beta}) and its precursor processing. Synapse loss is the strongest correlate of cognitive decline, driven partly by A{beta} oligomers (A{beta}Os), which bind multiple synaptic membrane proteins including the synaptic organizer neurexin and disrupt synaptic integrity and function. The protein sorting receptor SorCS1 blocks interactions between A{beta}Os and {beta}-isoforms of neurexins ({beta}-Nrxns), but its therapeutic relevance in vivo remains unclear. Using 5xFAD mice, which overproduce A{beta}Os, combined with forebrain specific neuronal SorCS1 overexpression, we show that SorCS1 preserves working memory, synaptic integrity, and basal excitatory transmission without altering amyloid deposition, in part by restoring synaptic {beta}-Nrxn expression. SorCS1 also reduces tau hyperphosphorylation in 5xFAD synaptosomes and binds the tau kinase GSK3{beta}. These results identify SorCS1 as an AD resilience promoting factor that maintains synaptic connectivity and attenuates tau pathology, revealing a therapeutic strategy that operates independently of amyloid reduction.

neuroscience↗

bioRxiv2025

Cdc25-mediated activation of the small GTPase RasB is essential for hyphal fusion and symbiotic infection of Epichloë festucae

Epichloe festucae is a filamentous endophytic fungus that symbiotically colonizes the intercellular spaces of aerial tissues in perennial ryegrass (Lolium perenne) without causing disease symptoms. This mutualistic association enhances host resistance to both biotic and abiotic stresses. Balanced and coordinated growth of E. festucae with its host is essential for the establishment and long-term maintenance of the symbiotic relationship. Various E. festucae mutants defective in symbiosis with host plants have been isolated, and notably, many of these symbiosis-defective mutants also lack hyphal fusion ability under culture conditions, supporting a close functional connection between signal transduction required for hyphal fusion and symbiosis establishment. Using a plasmid insertional mutagenesis approach, we identified Cdc25 as an essential regulator of hyphal fusion in E. festucae. Cdc25 encodes a guanine nucleotide exchange factor (GEF) that activates the small GTPase Ras. The{Delta} cdc25 strain lost both hyphal fusion ability and the capacity to infect host plants. Furthermore, yeast two-hybrid assays revealed that Cdc25 specifically interacts with RasB, one of the five Ras proteins in E. festucae. Expression of constitutively active (CA) RasB in the{Delta} cdc25 strain restored both hyphal fusion and host infection, whereas expression of CA-RasB in the{Delta} mpkB deletion strain failed to rescue its defect in hyphal fusion, suggesting that the Cdc25-RasB signaling module acts upstream of the MAPK cascade. In pathogenic fungi, this signaling module is known to regulate infection-related morphogenesis. These findings indicate that E. festucae has evolutionarily repurposed the conserved Cdc25-RasB module to coordinate hyphal fusion and maintain a stable mutualistic interaction with its host.

microbiology↗

bioRxiv2024

From phenotype to receptor: validating physiological clustering of Escherichia coli phages through comprehensive receptor analysis

Understanding the relationship between bacteriophage (phage) classification and target receptors is crucial for phage ecology and applied research. In this study, we compared 13 previously isolated Escherichia coli phages based on physiological characteristics, whole-genome sequences, and tail fiber protein phylogenetics. We improved our previously proposed physiological clustering method by optimizing the bacterial panel for host range assessment, implementing appropriate distance metrics for mixed data types, and applying silhouette coefficient analysis for objective determination of optimal cluster numbers. We combined genomic analysis and lipopolysaccharide (LPS) structural analysis of phage-resistant E. coli strains to identify target receptors of the phages. Complementation experiments further confirmed the direct involvement of identified genes in phage reception. The results revealed that phylogenetically distinct E. coli phages target different sites in the LPS R-core region (modified by WaaV, WaaW, WaaT, and WaaY), membrane proteins (NfrB, TolA, YhaH), or flagella. Our analysis revealed that, subtle chemical modifications of LPS (such as Heptose phosphorylation) were shown to be important for E. coli phage recognition. Furthermore, physiological characteristics, tail fiber phylogenetics, and whole genome analysis independently classified the phages with high correlation to target receptor specificity. The addition of three phages with known receptors further validated our approach. Our results suggest that grouping based on physiological characteristics (such as lysis dynamics and host range) and genotypes (tail fiber phylogenetics or whole genome analysis) independently classified phages with high correlation to target receptor specificity. Here, we elucidated the diversity and specificity of E. coli phage target receptors, providing new insights into the classification of E. coli phages and phage-host interactions. ImportancePhage therapy is gaining attention as an alternative treatment for antibiotic-resistant bacteria. Developing effective phage cocktails requires combining phages with different target receptors, but traditional methods for identifying target receptors are labor-intensive. This study demonstrates that E. coli phages targeting the TK001 strain with different target receptors can be grouped based on their physiological characteristics, tail fiber sequences, or whole genomes. Our approach was enhanced through systematic bacterial panel selection for host range assessment, optimized distance metrics for physiological characteristics, and objective cluster determination using silhouette coefficient analysis for all three classifications. This insight can be used to more efficiently create diverse phage cocktails. Additionally, we identified phages targeting diverse sites, including different regions of LPS, membrane proteins, and flagella. These findings deepen our understanding of phage host recognition mechanisms, enabling the rapid preparation of effective phage cocktails and contributing to new advancements in bacterial infection treatment.

microbiology↗

bioRxiv2024

Multi-objective computational optimization of human 5' UTR sequences

The computational design of mRNA sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of 5' UTR sequences, key upstream elements of mRNA. However, fully automated design of 5' UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human 5' UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.

bioinformatics↗

bioRxiv2024

The frontal cortex adjusts striatal integrator dynamics for flexible motor timing

Flexible control of motor timing is crucial for behavior. Before volitional movement begins, the frontal cortex and striatum exhibit ramping spiking activity, with variable ramp slopes anticipating movement onsets. This activity in the cortico-basal ganglia loop may function as an adjustable timer, triggering actions at the desired timing. However, because the frontal cortex and striatum share similar ramping dynamics and are both necessary for timing behaviors, distinguishing their individual roles in this timer function remains challenging. To address this, we conducted perturbation experiments combined with multi-regional electrophysiology in mice performing a flexible lick-timing task. Following transient silencing of the frontal cortex, cortical and striatal activity swiftly returned to pre-silencing levels and resumed ramping, leading to a shift in lick timing close to the silencing duration. Conversely, briefly inhibiting the striatum caused a gradual decrease in ramping activity in both regions, with ramping resuming from post-inhibition levels, shifting lick timing beyond the inhibition duration. Thus, inhibiting the frontal cortex and striatum effectively paused and rewound the timer, respectively. These findings suggest the striatum is a part of the network that temporally integrates input from the frontal cortex and generates ramping activity that regulates motor timing.

neuroscience↗

bioRxiv2023

Analysis of convolutional neural networks reveals the computational properties essential for subcortical processing of facial expression

Perception of facial expression is crucial in the social life of primates. This visual information is processed along the ventral cortical pathway and the subcortical pathway. Processing of face information in the subcortical pathway is inaccurate, but the architectural and physiological properties that are responsible remain unclear. We analyzed the performance of convolutional neural networks incorporating three prominent properties of this pathway: a shallow layer architecture, concentric receptive fields at the first processing stage, and a greater degree of spatial pooling. The neural networks designed in this way could be trained to classify seven facial expressions with a correct rate of 51% (chance level, 14%). This modest performance was gradually improved by replacing the three properties, one-by-one, two at a time, or all three simultaneously, with the corresponding features in the cortical pathway. Some processing units in the final layer were sensitive to spatial frequencies (SFs) in the retina-based coordinate, whereas others were sensitive to object-based SFs, similar to neurons in the amygdala. Replacement of any one of these properties affected the SF coordinate of units. All three properties constrain the accuracy of facial expression information in the subcortical pathway, and are essential for determining the coordinate of SF representation.

neuroscience↗

bioRxiv2021

A mosaic adeno-associated virus vector as a versatile tool that exhibits high levels of transgene expression and neuron specificity in primate brain

Recent emphasis has been placed on gene transduction mediated through recombinant adeno-associated virus (AAV) vector to manipulate activity of neurons and their circuitry in the primate brain. In the present study, we created a novel AAV vector of which capsid was composed of capsid proteins derived from the serotypes 1 and 2 (AAV1 and AAV2). Following the injection into the frontal cortex of macaque monkeys, this mosaic vector, termed AAV2.1 vector, was found to exhibit the excellence in transgene expression (for the AAV1 vector) and neuron specificity (for the AAV2 vector) simultaneously. To explore its applicability to chemogenetic manipulation and in vivo calcium imaging, the AAV2.1 vector expressing excitatory DREADDs or GCaMP was injected into the striatum or the visual cortex of macaque monkeys, respectively. Our results have defined that such vectors secure intense and stable expression of the target proteins and yield conspicuous modulation and imaging of neuronal activity.

neuroscience↗

bioRxiv2020

Infrared absorptions as indicators for Pseudomonas aeruginosa and Acinetobacter baumannii

There is clinical demand for simple and contact-free diagnosis techniques in medical practice. This study shows that the infrared absorptions of volatile metabolites can be used to distinguish between the air around Pseudomonas aeruginosa, Acinetobacter baumannii, other bacteria, and normal room air. Gas samples were collected from the air surrounding single and mixed laboratory cultures, and preliminary data on human breath samples are also presented. The infrared spectra of a variety of gasses are measured with a high resolution of 0.5 cm-1 to obtain information about the wavenumber position of the key bands. Hence, it is not necessary to specify the molecular species of biomarkers. This work also shows that discrimination rates can be improved by observing additional infrared absorptions caused by different characteristic volatile molecules. The significance of this work is that the specific wavenumber positions of the key bands that allow the application of infrared lasers are provided. As a result, it is considered that Pseudomonas aeruginosa and Acinetobacter baumannii can be monitored more sensitively and easily. With further research and development, this simple approach could be used in future applications to identify infections in healthcare settings.

microbiology↗

bioRxiv2017

Low-dimensional and monotonic preparatory activity in mouse anterior lateral motor cortex

Neurons in multiple brain regions fire trains of action potentials anticipating specific movements, but this preparatory activity has rarely been compared across behavioral tasks in the same brain region. We compared preparatory activity in auditory and tactile delayed-response tasks, with directional licking as the output. The anterior lateral motor cortex (ALM) is necessary for motor planning in both tasks. Multiple features of ALM preparatory activity during the delay epoch were similar across tasks. First, majority of neurons showed direction-selective activity and spatially intermingled neurons were selective for either movement direction. Second, many cells showed mixed coding of sensory stimulus and licking direction, with a bias toward licking direction. Third, delay activity was largely monotonic and low-dimensional. Fourth, pairs of neurons with similar direction selectivity showed high spike-count correlations. Our study forms the foundation to analyze the neural circuits underlying preparatory activity in a genetically tractable model organism.

neuroscience↗

bioRxiv2017

Rapid responses of amygdala neurons discriminate facial expressions

The amygdala plays a critical role in detecting potential danger through sensory input [1, 2]. In the primate visual system, a subcortical pathway through the superior colliculus and the pulvinar is thought to provide the amygdala with rapid and coarse visual information about facial emotions [3-6]. A recent electrophysiological study in human patients supported this hypothesis by showing that intracranial event-related potentials discriminated fearful faces from other faces very quickly (within [~]74 ms) [7]. However, several aspects of the hypothesis remain debatable [8]. Critically, evidence for short-latency, emotion-selective responses from individual amygdala neurons is lacking [9-12], and even if this type of response existed, how it might contribute to stimulus detection is unclear. Here, we addressed these issues in the monkey amygdala and found that ensemble responses of single neurons carry robust information about emotional faces-- especially threatening ones--within [~]50 ms after stimulus onset. Similar rapid response was not found in the temporal cortex from which the amygdala receives cortical inputs [13], suggesting a subcortical origin. Additionally, we found that the rapid amygdala response contained excitatory and suppressive components. The early excitatory component might be useful for quickly sending signals to downstream areas. In contrast, the rapid suppressive component sharpened the rising phase of later, sustained excitatory input (presumably from the temporal cortex) and might therefore improve processing of emotional faces over time. We thus propose that these two amygdala responses that originate from the subcortical pathway play dual roles in threat detection.

neuroscience↗