Biology subjects

Ban, H.

Publications and source records attributed to Ban, H..

12 recordsLinked to original sources

bioRxiv2026

The time course of co-speech gesture production: An MEG study

People frequently gesture while speaking, even when listeners cannot see them--for instance, during phone calls or behind barriers. Congenitally blind individuals also gesture, indicating that gestures serve functions beyond visual communication. Previous models of gesture production (e.g., Kita & Ozyurek, 2003; Rauscher et al., 1996) suggest that gestures facilitate speech, but they rely heavily on behavioural data and provide limited insight into temporal dynamics. This study used magnetoencephalography (MEG), a neuroimaging technique with high temporal resolution, to investigate when gestures influence speech. Twenty-three native Japanese speakers took part in a storytelling task under two conditions: Gesture-Required (gesture use instructed) and Gesture-Prohibited (hands kept still). Participants described cartoon clips across multiple sessions (30 trials x 3 sessions per condition). Using speech onset as the reference point, we compared root mean square (RMS) values within a -0.25 to 0 second window. RMS values were higher in the Gesture-Prohibited condition, with increased activity in the bilateral anterior temporal lobes (Left ATL: p = .049; Right ATL: p = .027), but not in motor regions (p = .29). These findings suggest that gestures reduce neural load in language-related regions before articulation. Co-speech gestures may support speech planning by facilitating lexical retrieval or semantic structuring. The lack of motor region effects indicates that this influence is linguistic rather than motoric. This study provides direct direct neurophysiological evidence of the timing of gesture-speech interaction, supporting models that view gestures as an integral part of speech production.

neuroscience↗

bioRxiv2026

Correlation-based binocular disparity computations induce representational bottlenecks at the population level

Binocular stereopsis depends on comparing the images seen by the two eyes. Although correlation-based models explain responses of individual binocular neurons in primary visual cortex (V1), it remains elusive whether population representations formed by local correlation activity patterns can support depth perception under ambiguous inputs. Using psychophysics, fMRI, and neural network modeling, we tested human stereopsis with dynamic anticorrelated stimuli that were dominated by binocular mismatches. Humans reliably perceived reversed depth as predicted by correlation-based computations, yet population representations consistent with this percept were detected in V3A, not V1. Shallow and deep neural networks constrained by correlation-like binocular interactions did not capture the full pattern of human depth judgments. Analyses of their internal representations showed greater representational overlap, whereas deep architectures not constrained to explicit correlation interactions exhibited less entangled representations and better aligned with human behavior. These findings suggest that biological stereopsis may rely on population coding beyond correlation-like computations. Significance StatementThe brain must infer depth from binocular inputs that are inherently ambiguous. Although correlation-based models explain disparity tuning of individual neurons in primary visual cortex (V1), whether these local mechanisms support perceptual inference at the population level remains unclear. Using psychophysics, fMRI, and neural network modeling, we show that population representations consistent with perceived depth under ambiguity were detected in mid-dorsal area V3A, not V1. Analyses of how neural networks encode multiple features showed that correlation-based computations represent features into overlapping activity patterns that may constrain downstream readout and degrade depth estimates. In contrast, models not constrained by explicit interocular correlation maintained more distinct population codes and closely matched human perception. These findings suggest that architectures constrained to explicit correlation-like processing can form population representations that are suboptimal to explain human stereopsis, motivating hybrid mechanisms.

neuroscience↗

bioRxiv2026

Rapid diversification of a natural Heterosigma akashiwo virus population during a host bloom

Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Most knowledge on their population genetic dynamics is derived from a small number of laboratory-based experiments, whereas patterns in nature are rarely observed. To overcome this limitation, we traced genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan, by integrating cell counting, metabarcoding, metagenomic and metatranscriptomic sequencing. Our study revealed that HaV dominated the giant virus community in most samples, with the relative abundances of up to 56%. Despite the high abundances, the HaV population exhibited a relatively low level of microdiversity but with a high pN/pS ratio compared to other giant viruses in the study site. Microdiversity increased during the early sampling period, reached a maximum at mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, possibly driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Together, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variation.

ecology↗

bioRxiv2026

Cross-strain transferability of CRISPRi systems and design rules from laboratory to clinical Escherichia coli strains

CRISPR interference (CRISPRi) has emerged as a versatile approach for targeted gene repression in many organisms, including microbes and bacteria, due to the simple design of sequence-specific transcriptional silencing of gene expression. However, the strain-specific effects on repression efficiency and the host when translating a CRISPRi system from a laboratory strain to non-model strains are not well understood, yet they can present important limitations to its use. Here, we investigated the repression efficiency and toxicity of three CRISPRi systems (one dCas9 and two dCas12a variants) across four different Escherichia coli strains, including a laboratory K-12 strain (MG1655) and three non-model strains that are clinical isolates (probiotic Nissle 1917, uropathogenic CFT073, and uropathogenic UMN026). We evaluated the repression in each strain using sets of guide RNAs (gRNAs) targeting along the gene sequence and assayed cytotoxicity of expressing each dCas protein. Growth toxicity from expression of the different dCas proteins notably differed and showed high variation between some host strains. We also observed variable repression among the strains and notably poorer repression in multiple clinical strains. Therefore, we developed a dual gRNA CRISPRi system for enhanced gene silencing among the strains, which achieved up to 824-fold repression in CFT073. The results demonstrate that strain-specific design considerations can arise when a CRISPRi genetic system is transferred to a closely related bacterial strain. These findings provide insight into the relationships between criteria used for CRISPRi genetic design and in vivo activity across non-model E. coli strains, providing guidelines for diverse applications of these tools.

synthetic biology↗

bioRxiv2025

Giant viruses specific to deep oceans show persistent presence and activity

Giant viruses (GVs) of the phyla Nucleocytoviricota and Mirusviricota are large double-stranded DNA viruses that infect diverse eukaryotic hosts and impact biogeochemical cycles. Their diversity and ecological roles have been well studied in the photic layer of the ocean, but less is known about their activity, population dynamics, and adaptive strategies in the aphotic layers. Here, we conducted eight seasonal time-series samplings of the surface and mesopelagic layers at a coastal site in Muroto, Japan, and integrated 18S metabarcoding, metagenomic, and metatranscriptomic data to investigate deep-sea GVs and their potential hosts. The analysis identified 48 GV genomes including six that were exclusively detected in the mesopelagic layer. Notably, these mesopelagic-specific GVs showed persistent activity across seasons. To investigate the global deep-sea-specific GV distribution, we compiled GV reference genomic data from the OceanDNA MAG project and other resources, and analyzed 1,890 marine metagenomes. This revealed 101 deep-sea-specific GVs, distributed across the GV phylogenetic tree, indicating that adaptation to deep-sea environments has occurred in multiple lineages. One clade enriched with deep-sea-specific GVs included one GV identified in our Muroto sampling, which displayed a wide geographic distribution. Seventy-six KEGG orthologs and 74 Pfam domains were specifically enriched in deep-sea-specific GVs, encompassing functions related to the ubiquitin system, energy metabolism, and nitrogen acquisition. These findings support the scenario that distinct GV lineages have adapted to hosts in aphotic marine environments by altering their gene repertoire to thrive in this unique habitat. IMPORTANCEGiant viruses are widespread in the ocean surface and are key in shaping marine ecosystems by infecting phytoplankton and other protists. However, little is known about their activity and adaptive strategies in deep-sea environments. In this study, we performed metagenomic and metatranscriptomic analyses of seawater samples collected from a coastal site in Japan and discovered giant virus genomes showing persistent transcriptional activity across seasons in the deep-sea water. Using a global marine dataset, we further uncovered the widespread existence of deep-sea-specific giant viruses and characterized their unique gene repertoire, which likely facilitates adaptation to the limited availability of light and organic compounds in the aphotic zone. These findings expand our understanding of giant virus ecology in the dark ocean.

genomics↗

bioRxiv2025

Infection signatures of multiple Nucleocytoviricota virus lineages in the brown algae Undaria pinnatifida revealed by population-wide genome analysis

Undaria pinnatifida is a large brown algae native to the northwest Pacific. It has been introduced to numerous countries and is listed among the worlds 100 worst invasive species. However, it is also edible and produces various bioactive compounds, making it commercially important. Despite its ecological and economic value, the viruses that infect U. pinnatifida remain unknown. In this study, a population-wide genome analysis was performed to investigate viral infection signatures in U. pinnatifida. A nearly complete 551-Kb giant endogenous viral element of a Nucleocytoviricota virus was identified on a pseudochromosome in the Korean strain genome Upin_Kr2015. This viral region contained viral hallmark genes and auxiliary metabolic genes, including kinases and GDP-mannose dehydrogenase. Additionally, we detected viral hallmark genes in all 43 whole-genome assemblies analyzed, with origins tracing to the orders Pandoravirales, Algavirales, or Imitevirales. Our findings provide strong evidence of frequent U. pinnatifida infections by multiple Nucleocytoviricota viruses.

genomics↗

bioRxiv2024

Correlation and Matching Representations of Binocular Disparity across the Human Visual Cortex

Seeing three-dimensional objects requires multiple stages of representational transformation, beginning in the primary visual cortex (V1). Here, neurons compute binocular disparity from the left and right retinal inputs through a mechanism similar to local cross-correlation. However, correlation-based representation is ambiguous because it is sensitive to disparities in both similar and dissimilar features between the eyes. Along the visual pathways, the representation transforms to a cross-matching basis, eliminating responses to falsely matched disparities. We investigated this transformation across the human visual areas using functional magnetic resonance imaging (fMRI) and computational modeling. By fitting a linear weighted sum of cross-correlation and cross-matching model representations to the brains representational structure of disparity, we found that areas V1-V3 exhibited stronger cross-correlation components, V3A/B, V7, and hV4 were slightly inclined towards cross-matching, and hMT+ was strongly engaged in cross-matching. To explore the underlying mechanism, we identified a deep neural network optimized for estimating disparity in natural scenes that matched human depth judgment in the random-dot stereograms used in the fMRI experiments. Despite not being constrained to match fMRI data, the network units responses progressed from cross-correlation to cross-matching across layers. Activation maximization analysis on the network suggests that the transformation incorporates three phases, each emphasizing different aspects of binocular similarity and dissimilarity for depth extraction. Our findings suggest a systematic distribution of both components throughout the visual cortex, with cross-matching playing a greater role in areas anterior to V3, and that the transformation exploits responses to false matches rather than discarding them. Significant StatementHumans perceive the visual world in 3D by exploiting binocular disparity. To achieve this, the brain transforms neural representation from the cross-correlation of signals from both eyes into a cross-matching representation, filtering out responses to disparities from falsely matched features. The location and mechanism of this transformation in the human brain are unclear. Using fMRI, we demonstrated that both representations were systematically distributed across the visual cortex, with cross-matching exerting a stronger effect in cortical areas anterior to V3. A neural network optimized for disparity estimation in natural scenes replicated human depth judgment in various stereograms and exhibited a similar transformation. The transformation from correlation to matching representation may be driven by performance optimization for depth extraction in natural environments.

neuroscience↗

bioRxiv2023

Global distribution and diversity of marine Parmales

Parmales (Bolidophyceae) is a minor eukaryotic phytoplankton group, sister to diatoms, that exists as two distinct forms of unicellular organisms: silicified cells and naked flagellates. Since their discovery, many field studies of Parmales have been performed, but their global distribution remains under-investigated. Here, we compile over 3,000 marine DNA metabarcoding datasets targeting the V4 region of the 18S rRNA gene from the EukBank database. By linking this large dataset with the latest morphological and genetic information, we provide updated estimates on the diversity and distribution of Parmales in the global ocean at a fine taxonomic resolution. Parmalean amplicon sequence variants (ASVs) were detected in nearly 90% of the analyzed samples. However, the relative abundance of parmaleans in the eukaryotic community is less than 0.2% on average, and the estimated true richness of parmalean ASVs is about 316 ASVs, confirming their low abundance and low diversity. Phylogenetic analysis clearly divides these algae into four clades, and three known morphotypes of silicified cells were classified into three different clades. The abundance of Parmales is generally high in the pole and decreases toward the tropics, and individual clades/subclades show further distinctions in distributions. Overall, our results suggest their clade/subclade-specific adaptation to different ecological niches.

microbiology↗

bioRxiv2023

Intestelligence: A pharmacological neural network using intestine data

A neural network is a machine learning algorithm that can learn and make predictions by adjusting the strength of the connections between nodes. The sigmoid function is commonly used as an activation function in these nodes. This study explores the potential applicability of biological materials in the development of alternative activation functions. Inspired by the fact that acetylcholine induces intestinal contractions that follow a sigmoid function, we used pharmacological data obtained from guinea pig ilea in a layered neural network for image classification tasks. We found that the intestinal data-based neural network with the same structure as a conventional three-layer perceptron achieved an impressive classification accuracy of 85.7% {+/-} 0.6% based on the MNIST handwritten digit dataset (chance = 10%). Additionally, the neural network was trained to determine whether objects in photographs collected from the internet were digestible, achieving an accuracy of 88.5% {+/-} 0.9% (chance = 50%). Our approach highlights the potential applicability of intestine data in neural computations based on pharmacological mechanisms.

bioengineering↗

bioRxiv2022

Genome analysis of Parmales, a sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

The order Parmales (Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compared the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans were predicted to be phago-mixotrophs. By contrast, diatoms have undergone loss of genes related to phagocytosis, indicating the ecological specialization from phago-mixotroph to photoautotroph in the early evolution of diatoms. Furthermore, diatoms showed significant enrichment in gene sets involved in silica metabolism, nutrient uptake capacity, carbon concentrating mechanisms, and iron uptake in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.

microbiology↗

bioRxiv2019

Splicing factor Rbm10 facilitates heterochromatin assembly in fission yeast

Splicing factors have recently been shown to be involved in heterochromatin formation, but their role in controlling heterochromatin structure and function remains poorly understood. In this study, we identified a fission yeast homologue of human splicing factor RBM10, which has been linked to TARP syndrome. Overexpression of Rbm10 in fission yeast leads to strong global intron retention. Rbm10 also interacts with splicing factors in a pattern resembling that of human RBM10, suggesting that the function of Rbm10 as a splicing regulator is conserved. Surprisingly, our deep-sequencing data showed that deletion of Rbm10 caused only minor effect on genome-wide gene expression and splicing. However, the mutant displays severe heterochromatin defects. Further analyses indicated that the heterochromatin defects in the mutant did not result from mis-splicing of heterochromatin factors. Our proteomic data revealed that Rbm10 associates with the histone deacetylase Clr6 complex and chromatin remodelers known to be important for heterochromatin silencing. Deletion of Rbm10 results in significant reduction of Clr6 in heterochromatin. Our work together with previous findings further suggests that different splicing subunits may play distinct roles in heterochromatin regulation.

molecular biology↗

bioRxiv2018

Layer-specific ultra-high field 7T fMRI showing that threat anticipation is mediated by the pulvinar input to the superficial layers of primary visual cortex (V1)

The perceptual system gives priority to threat-relevant signals with survival value. Its mechanism may not only include the processing initiated in the presence of threat signals but also in the mere anticipation of such signals. Here, we show that the pulvinar modulates activity in the early visual cortex (V1) specifically in threat anticipation. Using ultra-high-field 7T fMRI, we examined the layer-specific interaction between V1 and the pulvinar, while taking advantage of the fact that the directionality of such interaction is anatomically constrained in specific V1 layers. Only in anticipation of a fearful face target, but not of a control happy face target, was false perception of anticipated-yet-unpresented target face accompanied by stronger activity in the V1 superficial-cortical-depth (layers 1-3), which was preceded by pre-target-onset pulvinar activity. The pulvinar may contribute to the visual processing initiated in the anticipation of threat, and play an important role in anxiety.

neuroscience↗