Biology subjects

Hosoda, K.

Publications and source records attributed to Hosoda, K..

9 recordsLinked to original sources

bioRxiv2026

Modeling Time to Visual Insight in Mooney Image Recognition with a Chaotic Recurrent Neural Network

Insight is often described as a sudden shift in or formation of a conceptual representation, enabling humans to restructure existing knowledge and solve problems beyond conventional analytical approaches. Although prior computational studies have modeled aspects of insight using deep neural networks (DNNs) or reinforcement learning, few have captured the dynamic emergence of insight through autonomous neural computation. Here, we present a neural network model that simulates the time required to reach visual insight in the Mooney image recognition task, a widely used paradigm for studying visual insight and perceptual reorganization. The model couples a DNN module for perceptual feature extraction with a recurrent neural network (RNN) that implements a chaotic search process for recognition. The RNN is formulated as a continuous-time dynamical system, autonomously explores internal states, and stabilizes when the missing visual features required for recognition are internally reconstructed. Using the same image set as in human psychophysical experiments, the model reproduces key statistical properties of human search times (STs), including (i) lognormal-like ST distributions across participants for each image, (ii) a proportional relationship between the log-scale mean and standard deviation estimated from lognormal fits across images, and (iii) discrete levels of the fitted log-scale mean across images (a proxy for image difficulty). Importantly, these properties emerge without assuming any lognormal distribution for participant-to-participant variability, whereas previous models reproduced similar signatures by positing lognormal-distributed individual differences. We further show that lognormal-like signatures can arise from exponential search dynamics when combined with both standard experimental preprocessing and finite observation windows, highlighting the need to distinguish generative mechanisms from measurement and analysis effects. Together, these results motivate a mechanistic link between chaotic neural dynamics and insight-related search and provide a computational framework for implementing insight in artificial systems.

neuroscience↗

bioRxiv2025

Structural basis for MurJ inhibition by phage lysis protein SglPP7 suggesting convergence

Some bacteriophages encode lysis proteins that inhibit essential bacterial processes, the elucidation of which is valuable for developing antibacterial strategies against drug-resistant pathogens. We determined the cryo-EM structure of the complex between the essential E. coli lipid II flippase MurJ and a phage lysis protein, SglPP7. MurJ was locked in an outward-facing conformation by SglPP7, similar to the MurJ/LysM complex; however, distinct interactions suggest convergent evolution among phage lysis proteins.

molecular biology↗

bioRxiv2025

Phage lysis protein LysM acts as a wedge to block MurJ conformational changes

Many antibiotics target essential cellular processes. To combat multidrug-resistant bacteria, new antibacterial strategies are needed. In the peptidoglycan biogenesis pathway in Escherichia coli, MurJ, the lipid II flippase, is an essential membrane protein. The 37-residue protein M from the Levivirus phage, known as LysM or SglM, targets MurJ and induces cell lysis; however, its molecular mechanism remains unclear. Here, we present the cryo-EM structure of the MurJ/LysM (JM) complex at 3.09 [A] resolution, revealing that LysM interacts with the crevasse between TM2 and TM7 of MurJ, locking MurJ in an outward-facing conformation, with LysM acting like a wedge. Alanine-scanning mutagenesis and pull-down assays revealed key residues responsible for LysM function, and molecular dynamics simulations showed that LysM stabilizes MurJs outward-facing state. These findings demonstrate an unprecedented phage-derived mechanism for blocking lipid II transport, providing a structural framework for designing MurJ-targeted antimicrobial agents.

molecular biology↗

bioRxiv2025

Superior colliculus coordinates whole-brain dynamics for sudden unconscious visual insight

The human capacity for sudden insight, often marked by abrupt and illuminating "eureka" moments, has long intrigued neuroscientists seeking to understand its elusive neural basis1-6. Mooney image recognition offers a compelling behavioral paradigm of this phenomenon, in which ambiguous black-and-white patterns are abruptly perceived as coherent objects7-13. Whole-brain cortical involvement, which is mainly revealed by the contrast between recognition and nonrecognition, is well established8,14-27. However, the neural dynamics underlying the transition from nonrecognition to recognition, particularly the contributions of noncortical structures, have remained largely unknown. Here, we show that the transition in whole-brain dynamics can be effectively characterized by three large-scale activity patterns and that the superior colliculus (SC) emerges as a structure with a distinct temporal profile that is potentially critical for insight. Using functional clustering of functional magnetic resonance imaging data comprising 41,446 time points from 14 human participants performing this insight task, we identified three distinct functional clusters exhibiting stimulus-driven activation, suppression, and recognition-associated patterns. Notably, the SC in the third cluster displayed a distinct activation peak immediately before the recognition response. Furthermore, empirical dynamic modeling revealed that the SC was the only region in the whole brain that exhibited mutual positive directed interactions with all three clusters and was functionally embedded within higher-order cortical interactions mediating the transformation from stimulus input to motor output. Our findings provide compelling experimental evidence that the SC plays a critical role in orchestrating whole-brain dynamics for sudden insight, calling for a reappraisal of this evolutionarily conserved structure as a key player supporting unconscious but high-level cognitive processing.

neuroscience↗

bioRxiv2024

Odor source localization behavior of an insect enhanced by intermittent intake strategy

This study investigated odor acquisition strategies to enhance odor plume tracking performance. Efficient odor plume tracking is a crucial ability for organisms, affecting their survival, including for insects with relatively simple nervous systems. Insects can use odor cues to locate food sources or potential mates. Odors released from a source disperse in complex patterns owing to air currents and collisions with objects, making their spread unpredictable. Organisms must therefore engage in active odor acquisition behaviors to effectively gather spatial information from this highly uncertain odor environment. This study focused on odor acquisition via wing flapping in a male silk moth and its relationship with female localization. Given the difficulty of directly intervening in wing flapping, we employed an insect-mounted robotic system to engineer interventions and investigate the relationship between wing-flapping-induced odor acquisition and localization. We found that the difference between air inflow and stoppage in odor attraction was large, and that the odor plume tracking performance was highest at 10 Hz, where odor attraction can be performed at high frequencies. Although constant strong odor acquisition improves localization performance, it increases the likelihood of movement in directions other than that of the odor source. This suggests that periodic wing flapping helps to suppress undesired movements.

animal behavior and cognition↗

bioRxiv2023

Transcription-coupled changes in higher-order genomic structure and transcription hub viscosity prolong enhancer-promoter connectivity

The orchestration of our genes heavily relies on a coordinated communication between enhancers and promoters, yet how this dynamic interplay remains elusive while transcription is active. Here, we investigated enhancer-promoter (E-P) interactions and relative to transcriptional bursting in mouse embryonic stem cells using sequential DNA/RNA/immunofluorescence (IF)-FISH analyses and computational simulations. Our data reveal that the active state of specific genes is characterized by higher-order genomic structures and local condensates of transcriptional regulatory factors, leading to an elevation in local viscosity that highly stabilizes the duration of E-P interactions. Our study underscores the pivotal role of viscosity in transcriptional dynamics and paves the way for a more nuanced understanding of gene-specific regulatory mechanisms.

molecular biology↗

bioRxiv2023

Precise immunofluorescence canceling for highly multiplexed imaging capturing specific cell state

Cell states are regulated by the response of signaling pathways to receptor ligand-binding and inter-cellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we developed Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes.

cell biology↗

bioRxiv2021

Analysis of Multisensory-Motor Integration in Olfactory Navigation of Silkmoth, Bombyx mori, using Virtual Reality System

Most animals survive and thrive due to navigation behavior to reach their destinations. In order to navigate, it is important for animals to integrate information obtained from multisensory inputs and use that information to modulate their behavior. In this study, by using a virtual reality (VR) system for an insect, we investigated how an adult silkmoth integrates visual and wind direction information during female search behavior (olfactory behavior). According to the behavioral experiments using the VR system, the silkmoth had the highest navigation success rate when odor, vision, and wind information were correctly provided. However, we found that the success rate of the search significantly reduced if wind direction information was provided that was incorrect from the direction actually detected. This indicates that it is important to acquire not only odor information, but also wind direction information correctly. In other words, Behavior was modulated by the degree of co-incidence between the direction of arrival of the odor and the direction of arrival of the wind, and posture control (angular velocity control) was modulated by visual information. We mathematically modeled the modulation of behavior using multisensory information and evaluated it by simulation. As a result, the mathematical model not only succeeded in reproducing the actual female search behavior of the silkmoth, but can also improve search success relative to the conventional odor source search algorithm.

systems biology↗

bioRxiv2020

A model ecosystem of twelve cryopreservable microbial species allowing for a non-invasive approach

Simultaneous understanding of both individual and ecosystem dynamics is crucial in an era marked by the degradation of ecosystem services. Herein, we present a high-throughput synthetic microcosm system comprising 12 functionally and phylogenetically diverse microbial species. These species are axenically culturable, cryopreservable, and can be measured noninvasively via microscopy, aided by machine learning. This system includes prokaryotic and eukaryotic producers and decomposers, and eukaryotic consumers to ensure functional redundancy. Our model system displayed both positive and negative interspecific interactions and higher-order interactions that surpassed the scope of any two-species interaction. Although complete species coexistence was not our primary objective, we identified several conditions under which at least one species from the producers, consumers, and decomposers groups, and one functionally redundant species, persisted for over six months. These conditions set the stage for detailed investigations in the future. Given its designability and experimental replicability, our model ecosystem offers a promising platform for deeper insights into both individual and ecosystem dynamics, including evolution and species interactions.

microbiology↗