Biology subjects

Kurihara, Y.

Publications and source records attributed to Kurihara, Y..

16 recordsLinked to original sources

bioRxiv2026

Genomic and phenotypic consequences of long-term isolation and small population size in Yakushima macaques

The relative roles of genetic drift, inbreeding, and natural selection in island evolution have been fundamental themes in evolutionary biology for nearly a century. However, empirical studies have yet to reach a consensus, and research integrating both genotypes and phenotypes in primates remains limited. The present study aims to estimate the demographic history of an island primate population, the Yakushima macaque (Macaca fuscata yakui), and evaluate the genomic and morphological consequences of its isolation. To this end, we conducted population genetic analyses based on whole-genome sequencing and geometric morphometric analyses of cranial shape. Our results indicate that M. f. yakui has been isolated with an effective population size of several thousand individuals for over 100,000 years. Although we detected signatures of purifying selection, deleterious alleles have not been sufficiently purged. The degree of fluctuating asymmetry in males was slightly, yet significantly, higher in M. f. yakui than in mainland populations, whereas this trend was not observed in females. Marginal evidence of directional selection was found for cranial size, but not for shape. Overall, our findings suggest that due to long-term isolation, genetic drift and inbreeding have exerted a substantial influence on shaping genotypic and phenotypic variation in this island population.

evolutionary biology↗

bioRxiv2026

Soil bacterium Massilia secretes metabolites that promote Leptospira growth

Understanding pathogen metabolism is critical for identifying key functions for drug targeting, establishing effective in vitro experimental systems, etc., particularly for metabolically unique organisms such as Leptospira. Pathogenic Leptospira are thought to infect humans from environmental sources; however, direct isolation from environmental samples remains technically challenging and is not yet well established. Here, we report that a ubiquitous environmental bacterium, Massilia sp., produces metabolites that promote the growth of Leptospira interrogans, encountered through an incidental contamination event, and identified in this study. Gas chromatography-tandem mass spectrometry (GC-MS/MS) analysis showed demonstrated that cultivating of Massilia sp. in R2A medium resulted in the accumulation of metabolites, including branched-chain amino acid (BCAA) intermediates, compared to fresh medium. By combining genome-scale metabolic modeling with experimental validation using cell-free culture supernatant supplementation assays, we demonstrate that BCAA intermediates, particularly 2-ketoisocaproic acid (4-methyl-2-oxopentanoate; 4MOP), a leucine biosynthetic intermediate produced by Massilia sp., enhance Leptospira growth. To investigate the metabolic role of 4MOP, we incorporated transcriptomic data into a genome-scale metabolic network model to generate condition-specific models. Resulted flux distributions indicated that Leptospira catabolized imported 4MOP to produce acetyl-CoA. Our results reveal a previously unrecognized metabolic interaction where metabolites produced by environmental bacteria support the growth of pathogenic Leptospira, offering mechanistic insight into its metabolic requirement. These findings have implications to understand the environmental persistence of Leptospira through its metabolic dependencies on coexisting microbes, and they also help develop better strategies for this pathogen. ImportancePathogenic Leptospira persist in environmental reservoirs, yet the mechanisms supporting their growth remain poorly defined. Here, we find that metabolites produced by common environmental bacteria, Massilia sp., can promote Leptospira growth, suggesting a previously unrecognized metabolic dependency on coexisting microbes. Importantly, this study indicates that combining genome-scale metabolic modeling with experimental validation provides a useful framework for identifying metabolic interactions that are otherwise difficult to resolve using conventional culture-based approaches. Current strategy may facilitate the systematic identification of growth-supporting metabolites and provide a basis for improving selective cultivation for uncultured or difficult to culture organisms. Determination of growth promoting metabolites advances our understanding of pathogen persistence in natural environments and offers a generalized framework to study metabolically dependent microorganisms.

microbiology↗

bioRxiv2026

Theta Dual-Brain Stimulation of rTPJ Shapes Joint Agency

Joint agency, the shared feeling of "we are doing this together", has been linked to inter-brain synchrony, but its causal role in shaping this experience remains unclear. We applied dual transcranial alternating current stimulation (dual-tACS) over the right temporo-parietal junction (rTPJ) to 13 dyads performing an alternating tapping task (target ITI = 0.5 s; 180 deg. relative phase), manipulating in- and anti-phase coupling at theta (6 Hz), alpha (10 Hz), and beta (20 Hz). As a result, tapping in the theta anti-phase condition was significantly slower than the memorized reference tempo, whereas the other stimulation conditions did not influence the inter-tap interval. Meanwhile, the relative phase remained close to 180 deg. across all conditions. In the theta condition, anti-phase stimulation produced significantly lower joint agency than in-phase stimulation. Furthermore, mediation analysis suggested that the inter-tap interval may partially account for the effect of theta dual-brain stimulation on joint agency, although this indirect pathway did not reach statistical significance. These findings suggest that anti-phase theta stimulation over the rTPJ lowers joint agency, possibly by reducing coordination efficiency while preserving the overall 180 deg. alternation structure.

neuroscience↗

bioRxiv2026

Large-scale brain network differences during deliberate and spontaneous mind-wandering in a sustained attention task: An electroencephalography source-level connectivity study

Mind-wandering (MW), the shift of attention away from an ongoing task, can be classified as either deliberate or spontaneous, depending on whether these internal thoughts arise intentionally or unintentionally. Previous functional magnetic resonance imaging-based resting state studies have shown that spontaneous MW traits are positively correlated with coupling within the default mode network (DMN), whereas deliberate MW traits are positively correlated with coupling both within the DMN and between the DMN and control-or attention-related networks. However, state-based functional connectivity during each MW episode remains unknown. Addressing this knowledge gap, we investigated how deliberate and spontaneous MW differentially involve state-based large-scale network interactions during a sustained attention task using electroencephalography (EEG), which captures rapid network dynamics. Thirty-one participants performed the gradual-onset continuous performance task using 64-channel EEG. Mental states were classified via experience-sampling probes as on-task, deliberate, or spontaneous MW. EEG data from 1-s pre-probe epochs were analyzed using source estimation and the weighted phase lag index to assess functional connectivity within and across the DMN, control network (CN), dorsal attention network (DAN), and salience network (SN) in the delta, theta, alpha, and beta frequency bands. Relative to both spontaneous MW and the on-task state, deliberate MW was characterized by significantly stronger alpha band functional connectivity. A prominent connectivity cluster was centered on the right frontal operculum-insula of the SN, linking regions across the SN, CN, and DMN. In addition, deliberate MW exhibited enhanced SN-DAN-DMN coupling compared with the on-task state. By contrast, spontaneous MW did not show significant connectivity differences relative to the on-task state in any frequency band. Taken together, these results suggest that alpha band network interactions centered on the SN may contribute to the intentional regulation of internally directed thought during deliberate MW.

neuroscience↗

bioRxiv2025

Revisiting the in vivo Functions of Coilin in Mice

Cajal bodies (CBs), first identified in the early 20th century, are classic nuclear structures organized primarily by the protein coilin. Although CBs have long been implicated in snRNA modification and maturation, their precise roles in mice remain unclear. Here, we revisit the functions of CBs by using genome editing to generate mice that lack nearly the entire coilin protein, retaining only the first seven amino acids. Mass-spectrometry analyses showed reduced 2'-O-methylation of U2 snRNA in coilin mutant liver; however, these reductions had minimal impact on overall gene expression and pre-mRNA splicing patterns. Additionally, detailed analysis recapitulated previously reported testicular size reductions and newly revealed decreased proportions of high-quality sperm. We also identified novel coilin-containing condensates distinct from genuine CBs in the nuclear pocket of elongating spermatids. Our findings implicate that coilin orchestrates membraneless organelles in various compartments, playing multifunctional roles beyond classical CB formation.

molecular biology↗

bioRxiv2025

Hox - Meis-relayed topographical genetic switch underlies cardiopharyngeal neural crest diversification, revealed by multimodal analysis

Neural crest cells (NCCs) are multipotent migratory cells essential for cardiac development, yet the lineage trajectories and gene regulatory networks (GRNs) underlying their differentiation in the cardiopharyngeal region remain unclear. Here, we integrate single-cell RNA-seq, spatial transcriptomics, and multiomic analyses to construct a comprehensive map of NCC lineages in developing mouse cardiopharyngeal tissues. We identify a transition from Hox-positive pharyngeal NCCs to Hox-negative intracardiac populations associated with the outflow tract cushion, accompanied by a shift in Meis transcription factor binding and GRN architecture. By contrast, NCCs forming the aorticopulmonary septum and great vessel smooth muscle retain distinct Hox-codes. A Meis2-Sox9-Scx GRN defines a skeletogenic progenitor-like intermediate state that gives rise to coronary artery smooth muscle and semilunar valves. Our findings suggest that the loss of Hox-dependent regional identity enables pharyngeal NCCs to acquire new fates upon entering the cardiac cushion, providing insight into the developmental origins of coronary and valvular calcification.

developmental biology↗

bioRxiv2025

Locations of consecutive G·C base-pairs direct genomic nucleosome positioning

The nucleosome is a structural and functional subunit of chromatin, and its positioning and dynamics in the eukaryotic genomes serves as a key platform for gene regulation. Here, we determine the positions of fully wrapped nucleosomes across the yeast genome by chemical mapping through the histone H2A-A122C residue, which cleaves near the DNA entry/exit sites. This approach reveals the most refined sequence-dependent profile of nucleosomes reported to date. Comparison of H2A-A122C with the H3-Q85C and H4-S47C methods clearly shows a sequence preference for the chemical cleavage site, and mapping results suggest that the nucleosome locations are dynamic in vivo. More importantly, we find that the depletion of CC and GG dinucleotides at nucleotide positions -11 to -9 and +9 to +11 bp, respectively, from the nucleosome dyad position (0) is inextricably associated with the enrichment of AA/AT/TA/TT dinucleotides in both yeast and mouse genomes. Introducing consecutive C*G base pairs to the corresponding sites in the 601 sequence shifts the nucleosomes to less frequent positions without altering thermal stability, implying a structural constraint imposed by DNA sequence. Thus, CC and GG dinucleotides in the major groove blocks at superhelix locations (SHL) -1.0 and +1.0, respectively, destabilize histone-DNA interactions, serving as intrinsic determinants of nucleosome positioning in eukaryotic genomes.

molecular biology↗

bioRxiv2024

Synchronization between chloroplastic and cytosolic protein synthesis for photosynthesis complex assembly

Through symbiosis, subunits of chloroplastic complexes are encoded in distinct genomes in the nucleus and organelles. For plant cells to maintain the stoichiometry of subunits and respond to environmental cues, the orchestration of the nuclear and organellar gene expression systems is an essential task. However, the mechanism maintaining chloroplastic complexes remains largely enigmatic. Here, we simultaneously assessed the translatomes of the chloroplast and the cytoplasm via ribosome profiling and revealed the differential mechanisms employed by these two systems to cope with acute light/dark transitions: in chloroplasts, translational regulation is employed, whereas in the cytoplasm, control of the mRNA abundance is implemented. This strategy is widely conserved in land plants (Arabidopsis and the grass plant Brachypodium) and green algae (Chlamydomonas). The translational control in chloroplasts may be established based on organelle symbiosis; the primitive chloroplast in Glaucophyta (Cyanophora) was found to have already acquired translational control, whereas cyanobacteria (Synechocystis) control the mRNA abundance. Moreover, reduced plastoquinones and active cytosolic protein synthesis drive chloroplastic translation of the complex subunits in the light. Our work reveals an early origin of coordination of chloroplast and nuclear/cytoplasmic gene expression upon light exposure.

molecular biology↗

bioRxiv2023

In vivo visualization of intracellular pH gradient in brain using PET imaging

Intracellular pH (pHi) is a valuable index for predicting hypoxic brain damage. However, no positron emission tomography (PET) probe is currently available for monitoring pHi in vivo. In this study, we developed a new approach for visualizing monoacylglycerol lipase (MAGL) activity in the brain. This approach used PET with a new probe [11C]HC-A, an azetidine carbamate inhibitor, whose uptake and residence depended on the pHi gradient was evaluated with in silico, in vitro, and in vivo assessments. Molecular dynamics simulations predicted that complex (complex-A) between HC-A and MAGL would be difficult to hydrolyze under acidic conditions. In vitro assessment using rat brain homogenate showed that [11C]HC-A reacted with MAGL to yield [11C]complex-A, which was rapidly hydrolyzed to liberate 11CO2. The 11CO2 liberation rate was slower at lower pH. In PET with [11C]HC-A using ischemic rats, the radioactivity clearance rate, which reflects the production rate of 11CO2 in the brain, was lower in a remarkably hypoxic area than in the contralateral region. In conclusion, we successfully visualized the pHi gradient in the brain using PET imaging.

neuroscience↗

bioRxiv2023

The topology of interpersonal neural network in weak social ties

People often have opportunities to engage in social interactions with strangers, which have been reported to contribute to their well-being. Although strategies for social interaction between strangers differ from those between acquaintances, the differences in neural basis of social interaction have not been fully elucidated. In this study, we examined the geometrical properties of interpersonal neural networks in pairs of strangers and acquaintances during joint tapping using dual electroencephalography (EEG). Twenty-one pairs of participants performed antiphase joint tapping under four different conditions. Intra-brain synchronizations were calculated using the weighted phase lag index (wPLI) for all possible intra-brain pairs of the 29 channels (29C2 = 406), and inter-brain synchronizations were calculated using the phase locking value (PLV) for all possible inter-brain pairs of the 29 channels (29 x 29 = 841) in the theta, alpha, and beta frequency bands. Electrode pairs with larger wPLI and PLV than their surrogates were defined as the nodes (EEG channels) and edges (connections between nodes) of the neural networks. We then calculated the global efficiency, local efficiency, clustering coefficient, and modularity derived from graph theory for the combined intra- and inter-brain networks of each pair. No significant differences in the tapping phase variance were identified between the stranger and acquaintance pairs. However, in the combined intra- and inter-brain theta EEG (4-7 Hz) networks, stranger pairs showed larger local efficiency and cluster coefficients than acquaintance pairs, indicating that the two brains of stranger pairs were more densely connected. Moreover, in the beta EEG bands, the modularity of the two brains was low in the fast condition, indicating that the two brains were coupled when the task demand was high. Our results show that weak social ties promote more extensive social interactions and result in dense brain-to-brain coupling.

neuroscience↗

bioRxiv2023

The Effect of Evaluating Self's Emotions on Frontal Alpha Asymmetry

In this research to assess emotions from biometric signals, participants are asked to evaluate the emotions they subjectively experienced in order to confirm whether the assumed emotions were actually elicited. However, the evaluation of emotions is not routinely performed in daily life, and it is possible that this evaluation may alter biological signals. In fMRI studies, evaluation has been shown to activate the amygdala, which is said to be related to emotional expression. However, electroencephalography (EEG) studies do not take into consideration the effects of such evaluations, and it is unclear how these evaluations affect emotion-related brain activity observed in EEG. We hypothesized that emotion evaluations would amplify emotions and c alter Frontal Alpha Asymmetry (FAA), which has been shown to be related to emotional pleasantness and unpleasantness. We suspect this is because in order to evaluate ones emotions, one must pay attention to ones internal state, and this self-focused attention has been found to enhance the subjective emotional experience. We measured a 29-channel EEG when presented with unpleasant and highly arousing images from the International Affective Picture System (IAPS) from 40 healthy male and female participants. The results revealed that FAA was significantly lower in the condition in which participants rated their own emotions compared to the condition in which they did not. Similar to fMRI studies, this result indicates that emotion-related brain activity is amplified on an EEG. This paper provides a cautionary note regarding the use of such evaluations in EEG emotion estimation studies.

neuroscience↗

bioRxiv2022

Cardiac neural crest lineage diversity and underlying gene regulatory networks revealed by multimodal analysis

Neural crest cells (NCCs), a multipotent stem cell population, contribute to cardiac development as a source of the outflow septum, vascular smooth muscle and semilunar valves. However, genetic programs underlying lineage diversification of cardiac NCCs remain largely unknown. Using single-cell (sc) and spatial transcriptomics, we demonstrate multiple NCC subpopulations with distinct gene expression signatures; smooth muscle(-like), non-muscle mesenchymal, and Schwann cell progenitor/melanoblast-like cells. Integrative scRNA-seq and scATAC-seq analyses predict lineage trajectories starting from immature NCCs, which bifurcate into smooth muscle(-like) and non-muscle mesenchymal lineages in association with hierarchical transcription factor networks. Combinatory analyses with Cre-mediated genetic lineage tracing characterize intermediate NCCs at the bifurcation as Sox9+/Scx+ tendon and cartilage progenitor-like cells with genetic programs, some of which are common to skeletal tissues whereas others are unique to cardiac NCCs. These findings provide a basis for understanding the roles of NCCs in cardiac development and pathogenesis particularly associated with calcification.

developmental biology↗

bioRxiv2022

Brain Activity During Constraint Relaxation in the Insight Problem-Solving Process: An fNIRS Study

People solve insight problems that they encounter daily with a sudden sense of aha! to reach a solution. Chunk decomposition, which decomposes the factors of the problem, and constraint relaxation, which manipulates filters to organize the information necessary to solve the problem, are important in insight problem-solving. Although there have been many studies on brain activity during chunk decomposition, few have examined brain activity during constraint relaxation. Particularly, no study has observed the changes over time due to constraint relaxation during insight problem-solving. This study used a slot machine task as an insight problem to measure brain activity using functional Near-Infrared Spectroscopy (fNIRS), and eye movements to estimate constraint relaxation. The results showed that the right dorsolateral prefrontal cortex (DLPFC) and right superior temporal gyrus (STG) were activated over time in participants in whom constraint relaxation was induced. The right inferior temporal gyrus (ITG) of participants who were able to solve the insight problem after constraint relaxation was also activated. The analysis of brain activity during constraint relaxation in insight problem-solving may be useful for advancing research on the aha! phenomenon and creativity.

neuroscience↗

bioRxiv2022

Thoracic crop formation is spatiotemporally coordinated with flight muscle histolysis during claustral colony foundation of a Lasius japonicus queen

In a majority of ants, a newly mated queen independently founds a colony and claustrally raises her first brood without foraging outside the nest. During claustral independent colony foundation (ICF) in several ants, the esophagus of the founding queen expands and develops into a thoracic crop, which is then filled with a liquid substrate for larval feeding. It has been suggested that these substrates are converted from her body reserves (e.g., histolyzed flight muscles) or redistributed from a gastral crop. Here, we examined thoracic crop development in Lasius japonicus during claustral ICF. The foundresses claustrally fed their larvae from week 2 to 5 after ICF onset, and the first worker emerged at week 6. The development proceeded as follows: in week 0, foundress dorsal esophagus wall was pleated and thickened. Then, from week 2 to 5, the esophagus expanded dorsally toward where flight muscles had been present, following flight muscle histolysis. Gastral crop expansion followed esophagus expansion. Thus, thoracic crop formation may be spatiotemporally coordinated with flight muscle histolysis in Lasius japonicus queens, and similar developmental regulations might be common in other claustral ICF ants.

zoology↗

bioRxiv2021

The Relationship between Stability of Interpersonal Coordination and Inter-Brain EEG Synchronization during Anti-phase Tapping

Inter-brain synchronization is enhanced when individuals perform rhythmic interpersonal coordination tasks, such as playing instruments in music ensembles. Experimentally, synchronization has been shown to correlate with the performance of joint tapping tasks. However, it is unclear whether inter-brain synchronization is related to the stability of interpersonal coordination represented as the standard deviation of relative phase (SDRP). In this study, we simultaneously recorded electroencephalograms of two paired individuals during anti-phase tapping in three speed conditions: slow (reference inter-tap interval [ITI]: 0.5 s), fast (reference ITI: 0.25 s), and free (preferred ITI). We calculated the inter-brain synchronization within six regions of interest: frontal, central, left/right temporal, parietal, and occipital regions. We found that synchronization of the central-temporal regions was positively correlated with SDRP in the theta and alpha bands, while synchronization of the frontal-frontal and frontal-central was positively correlated with SDRP in the beta band. These results demonstrate that inter-brain synchronization occurs only when task requirements are high, and that it increases with the instability of the coordination. This may be explained by the stronger mutual prediction required in unstable coordination than that in stable coordination, which increases inter-brain synchronization.

neuroscience↗

bioRxiv2018

Craniofacial traits determined by neural crest cells-restricted expression of Dlx5/6: probing the origin of matching functional jaws

Gnathostome jaws derive from the first pharyngeal arch (PA1), a complex structure constituted by Neural Crest Cells (NCCs), mesodermal, ectodermal and endodermal cells. Here, to determine the regionalized morphogenetic impact of Dlx5/6 expression, we specifically target their inactivation or overexpression to NCCs. NCC-specific Dlx5/6 inactivation (NCC{Delta}Dlx5/6) generates severely hypomorphic lower jaws that present typical maxillary traits. Therefore, differently from the symmetric jaws obtained after constitutive Dlx5/6 inactivation, NCC{Delta}Dlx5/6 embryos present a strikingly asymmetric mouth. Reciprocally, forced Dlx5 expression in maxillary NCCs provokes the appearance of distinct mandibular characters in the upper jaw. We conclude that: 1) Dlx5/6 activation in NCCs invariably determines lower jaw identity; 2) the morphogenetic processes that generate functional matching jaws depend on the harmonization of Dlx5/6 expression in NCCs and in distinct ectodermal territories. The co-evolution of synergistic opposing jaws requires the coordination of distinct regulatory pathways involving the same transcription factors in distant embryonic territories.

developmental biology↗