Biology subjects

Inoue, R.

Publications and source records attributed to Inoue, R..

12 recordsLinked to original sources

bioRxiv2026

An Exploratory Study of Prefrontal Cortex Activation Related to Golf Putting Performance Under Psychological Pressure: A Functional Near-infrared Spectroscopy Approach

Neurofeedback (NF) is a promising method for helping individuals overcome choking under pressure. Identifying relevant neural biomarkers is crucial for developing effective NF. In this exploratory study, we aimed to investigate changes in prefrontal hemodynamic signals associated with golf-putting performance under psychological pressure using functional near-infrared spectroscopy. Participants engaged in a one-on-one golf-putting task against an experimenter, with monetary rewards introduced to induce psychological pressure. This manipulation successfully elicited psychological pressure, leading to impaired performance in some participants. Based on performance changes between the practice and competition sessions, participants were categorized into a non-choking group (performance improved) and a choking group (performance declined). Statistical analysis revealed significantly greater increases in prefrontal activation from practice to competition in the non-choking group than in the choking group, especially in the left superior frontal gyrus. Furthermore, moderate but statistically nonsignificant negative correlations were observed between changes in activation in this region and changes in putting error, indicating that greater activation increases tended to accompany less performance deterioration or greater performance improvement. These exploratory findings suggest that the left superior frontal gyrus warrants further investigation as a candidate biomarker for NF interventions aimed at mitigating choking under pressure.

neuroscience↗

bioRxiv2026

Ecological drivers of social complexity: the role of predation risk and nesting resource in group-living cichlid

Understanding how social complexity responds to environmental variation remains a longstanding challenge in evolutionary biology. Here, we investigated the drivers of social complexity using intraspecific social variation across seven locations of the obligatory shell-brooding cichlid Neolamprologus meeli in Lake Tanganyika. We quantified the number of subordinate individuals per female territory and examined the effects of predation risk, shell availability, and their interaction. Social complexity increased with shell availability under high predation risk but showed little association under low predation risk. A field manipulative-experiment further demonstrated that increasing shell availability led to higher juvenile retention, indicating a causal effect of territory quality. In addition, removal of subordinates reduced shell availability, suggesting the feedback between group size and territory maintenance. We also assessed genetic population structure based on nuclear SNPs obtained by MIG-seq and found only weak genetic differentiation among localities, suggesting that the observed social variation is unlikely to simply reflect strong genetic subdivision. Together, these results show that predation risk promotes group living, whereas nesting resource availability constrains its extent. Our study highlights that social complexity emerges from the interaction between macro- and micro-ecological factors, providing a mechanistic understanding of the evolution of social complexity and philopatry.

ecology↗

bioRxiv2026

Selective activation of LH-dependent transcriptional pathways determines ovulatory follicles in the hierarchical ovary of cloudy catshark

The number of offspring produced per reproductive cycle is generally explained by a luteinizing hormone receptor (LHR)-threshold model, in which only follicles expressing sufficient levels of LHR respond to the LH surge and proceed to ovulation. Using the cloudy catshark as a model, we reveal a distinct mechanism that determines the fate of ovulatory (F1) and non-ovulatory (F2) follicles independently of LHR abundance. The cloudy catshark produces only two eggs per reproductive cycle by ovulating a pair of F1 follicles from its single ovary. Both F1 and F2 follicles express comparable levels of lhr, indicating that both retain the capacity to receive the LH signal. Nevertheless, LH stimulation selectively activated ovulation-associated responses in F1 follicles. These included progesterone production via star2 upregulation, as well as transcriptional programs including RUNX transcription factors, prostaglandin signaling (ptgs2, ptger1), and matrix metalloproteinases. Moreover, direct activation of cAMP pathway, bypassing LHR activation, induced progesterone production in F1 but not F2 follicles, indicating that the critical difference in ovulatory responsiveness lies downstream of cAMP. These results demonstrate that follicular ovulatory fate is determined, at least in part, by follicle-specific transcriptional responses to cAMP, rather than by LHR abundance alone, challenging the prevailing LHR-threshold model of ovulatory regulation in vertebrates.

physiology↗

bioRxiv2026

Kinetic hierarchy of Kai protein complex formation governs the cyanobacterial circadian oscillator

Cyanobacterial circadian oscillations arise from a phosphorylation cycle of KaiC that is coupled to reversible complex formation with KaiA and KaiB. Although representative assemblies such as A2C6, B6C6, and A12B6C6 have been structurally characterized, quantitative understanding of their stoichiometry, affinity, and formation kinetics during the oscillation cycle remains limited. Here, we systematically quantified AC, BC and ABC complex formation using phosphorylation-mimetic KaiC and controlled protein mixing ratios by integrating analytical ultracentrifugation with small-angle X-ray/neutron scattering. A2C6 formation exhibits graded dependence on the phosphorylation state of KaiC and occurs rapidly in solution. In contrast, B6C6 formation behaves in a switch-like manner, showing strong selectivity for the hyperphosphorylation mimic and proceeding on a slow timescale ([~] 6 h). Upon B6C6 formation, KaiA rapidly associates with the complex to generate AnB6C6, with KaiA occupancy n determined by the mixing ratio through fast redistribution among coexisting complexes. This behavior enables dynamic allocation of KaiA among clock complexes. Together, these quantitative insights delineate a hierarchy of assembly dynamics--fast, graded AC exchange; slow, state-selective BC formation; and rapid KaiA redistribution--revealing a mechanistic basis for the dynamic regulation of the Kai oscillator.

biophysics↗

bioRxiv2026

Integrating Segmental Deuteration iCM-SANS with SAXS and MD for Dynamical Analysis of Multi-domain Proteins

Multi-domain proteins (MDPs) adopt diverse conformations arising from cooperative inter-domain motions, and such dynamics are intimately coupled to their biological functions. Quantitative characterization of these motions is crucial for elucidating their functional mechanisms. Although small-angle X-ray scattering (SAXS) provides information on overall domain arrangement, the limited experimental constraints hinder reliable discrimination of conformational ensembles derived from molecular dynamics (MD) simulations. To address this limitation, complementary experimental constraints that enable to observe domain-selective structural information are required. Inverse contrast-matching small-angle neutron scattering (iCM-SANS), combined with segmental deuteration, enables selective visualization of individual domains and thus provides such complementary information. However, practical strategies for preparing segmentally deuterated MDPs with arbitrary domain labelling have yet to be established. Here, we develop an experimental protocol that integrates controlled protein deuteration with high-efficiency multi-step protein ligation to generate a segmentally deuterated MDP in high yield. The combined use of SAXS and iCM-SANS yields complementary structural constraints that enhance discrimination of MD-derived conformational ensembles. This protocol expands the applicability of segment-selective visualization and also provides an opportunity for high-precision analysis of dynamics in complex MDPs. SynopsisSegmental deuteration enabled by high-efficiency multi-step protein ligation, combined with inverse contrast-matching SANS and SAXS, provides structural constraints that improve discrimination of molecular dynamics ensembles of multi-domain proteins. IMPORTANTthis document contains embedded data - to preserve data integrity, please ensure where possible that the IUCr Word tools (available from http://journals.iucr.org/services/docxtemplate/) are installed when editing this document.

biophysics↗

bioRxiv2024

A neuroimaging dataset during sequential color qualia similarity judgments with and without reports

Recent neuroscientific research has advanced our understanding of consciousness, yet the connection between specific qualitative aspects of consciousness, known as "qualia," and particular brain regions or networks remains elusive. Traditional methods that rely on verbal descriptions from participants pose challenges in neuroimaging studies. To address this, our group has introduced a novel "qualia structure" paradigm that leverages exhaustive, structural, and relational comparisons among qualia instead of verbal reports. In this study, we present the first fMRI dataset that captures relational similarity judgments among two out of nine color qualia per trial from 35 participants. This dataset also includes a "no-report" condition in half of the trials to assess the impact of overt reporting. Additionally, each participants color discriminability was evaluated with a hue test conducted outside the scanner. Our data offer valuable insights into the brain functions associated with color qualia and contribute to a deeper understanding of the neural foundations of consciousness.

neuroscience↗

bioRxiv2023

Mechanistic modeling of amyloid oligomer and protofibril formation

Early phase of amyloid formation, where prefibrillar aggregates such as oligomers and protofibrils are often observed, is crucial for elucidating pathogenesis. However, since oligomers and protofibrils form transiently and heterogeneously, the detailed mechanisms of their formation remain unclear. Here, we have investigated the early aggregation process of bovine and human insulin by static and dynamic light scattering in combination with thioflavin T (ThT) fluorescence and Fourier transform infrared (FTIR) spectroscopy. The time dependence of light scattering has revealed that oligomers and protofibrils form in bovine insulin, in contrast to no significant aggregation in human insulin. By focusing on bovine insulin for kinetic analysis, it has been revealed that the protofibril formation process was divided into two steps with reference to fractal dimension. When modeled the experimental data of static and dynamic light scattering based on the Smoluchowski aggregation kinetics with fractal aggregation and end-to-end association, we found the initial formation of spherical oligomers and their subsequent uniaxial docking. Furthermore, the analysis of temperature and salt concentration dependence revealed that the end-to-end association is the rate-limiting step, where structure organization occurred with dehydration. The established model for protofibril formation where oligomers are incorporated as a precursor provides insight into the molecular mechanism how protein molecules assemble during the early stage of amyloid formation. SignificanceAmyloid oligomers and protofibrils have attracted attention as critical causes of neurodegenerative diseases; however, detailed formation processes of these aggregates have been poorly understood. In this study, we established a mechanistic model of oligomer and protofibril formation of bovine insulin based on Smoluchowski aggregation kinetics in terms of static and dynamic light scattering. It has been demonstrated that early aggregation proceeds by initial fractal-like aggregation to form oligomers, and subsequent their end-to-end docking to form protofibrils. The latter step is a rate-limiting step, where structural organization occurs with dehydration. The established model is expected to broadly applicable to a variety of proteins, and thus will provides valuable insights for accelerating therapeutic development and anti-neurodegenerative drug design.

biophysics↗

bioRxiv2022

Orchestration of Proteins in cyanobacterial Circadian Clock System 1

Circadian rhythm by Cyanobacteria is one of the simplest biological clocks: the clock consists of only three proteins, KaiA, KaiB and KaiC. Their oligomers, KaiA dimer (A2), KaiB tetramer (B4) and KaiC hexamer (C6) oscillate an association- disassociation cycle with 24hr period. In a widely accepted model, the oscillation process is as follows. From the viewpoint of a base unit (C6), C6 homo-oligomer [->] A2C6 complex [->] B6C6 complex [->] AnB6C6 complex (n[≤]12) [->]C6 homo-oligomer. In this study, Small-Angle X-ray Scattering, Contrast Matching-Small-Angle Neutron Scattering, Analytical Ultracentrifuge and phosphorylation-analysis PAGE measurements were performed to reveal the kinetics not only of KaiC hexamer but also of all components in a working Kai clock. The complementary analysis disclosed that the oscillation is not the single process as the widely accepted model but composed with synchronized multiple association-dissociation reactions between components. Namely, there are various reactions between components, which proceed simultaneously, in a working Kai-clock.

biophysics↗

bioRxiv2021

Structural development of amyloid precursors in insulin B chain and the inhibition effect by fibrinogen

Amyloid fibrils are abnormal protein aggregates that relate to a large number of amyloidoses and neurodegenerative diseases. The oligomeric precursors, or prefibrillar intermediates, which emerge prior to the amyloid fibril formation, have been known to play a crucial role for the formation. Therefore, it is essential to elucidate the mechanisms of the structural development of the prefibrillar intermediates and ways to prevent its fibril formation. An insulin-derived peptide, insulin B chain, has been known for its stable accumulation of the prefibrillar intermediates. In this study, structural development of B chain prefibrillar intermediates was monitored by transmission electron microscopy and small-angle X-ray scattering combined with size exclusion chromatography and solid-state NMR spectroscopy to elucidate the stability and secondary structure. We further tracked its inhibition process by fibrinogen (Fg), which has been known to effectively prevent the amyloid fibril formation of B chain. We demonstrated that prefibrillar intermediates are wavy structures with low {beta}-sheet content, growing in a multistep manner toward the nucleation for the amyloid fibril formation. In the presence of Fg, the formation of the prefibrillar intermediates slowed down by forming specific complexes. These observations suggest that the prefibrillar intermediates serve as reaction fields for the nucleation and its propagation for the amyloid fibril formation, whereas the inhibition of prefibrillar intermediate elongation by Fg is the significant factor to suppress the fibril formation. We propose that the obtained molecular picture could be a general inhibition mechanism of the amyloid fibril formation by the inhibitors.

biochemistry↗

bioRxiv2021

Spatial, temporal and molecular dynamics of swine influenza virus-specific CD8 tissue resident memory T cells.

We defined naive, central memory, effector memory and terminally differentiated porcine CD8 T cells and analyzed their phenotype in lymphoid and respiratory tissues after influenza infection or immunization using peptide-MHC tetramers of three influenza nucleoprotein (NP) epitopes. The hierarchy of response to the three epitopes changes during the response in different tissues. Most NP-specific CD8 T cells in broncho-alveolar lavage (BAL) and lung are tissue resident memory cells (TRM), that express CD69 and have an effector memory or terminally differentiated phenotype. NP-specific cells isolated from BAL express genes characteristic of TRM, but gene expression differs at 7, 21 and 63 days post infection. The frequency of NP-specific cells declines over 63 days in all tissues but is best maintained in BAL. The pig is a powerful model for understanding how best to induce and harness local immunity to respiratory viruses. One sentence summaryInfluenza NP-specific porcine tissue resident memory CD8 T cells persist in the lung with major changes in gene expression.

immunology↗

bioRxiv2019

Structural Studies of Overlapping Dinucleosomes in Solution

An overlapping dinucleosome (OLDN) is a structure composed of one hexasome and one octasome and appears to be formed through nucleosome collision promoted by nucleosome remodeling factor(s). In the present study, the solution structure of the OLDN was investigated through integration of small-angle X-ray and neutron scattering (SAXS and SANS, respectively), computer modeling, and molecular dynamics simulations. Starting from the crystal structure, we generated a conformational ensemble based on normal mode analysis, and searched for the conformations that well reproduced the SAXS and SANS scattering curves. We found that inclusion of histone tails, which are not observed in the crystal structure, greatly improved model quality. The obtained structural models suggest that OLDNs adopt a variety of conformations stabilized by histone tails situated at the interface between the hexasome and octasome, simultaneously binding to both the hexasomal and octasomal DNA. In addition, our models define a possible direction for the conformational changes or dynamics, which may provide important information that furthers our understanding of the role of chromatin dynamics in gene regulation.\n\nStatement of SignificanceOverlapping dinucleosomes (OLDNs) are intermediate structures formed through nucleosome collision promoted by nucleosome remodeling factor(s). To study the solution structure of OLDNs, a structural library containing a wide variety of conformations was prepared though simulations, and the structures that well reproduced the small angle X-ray and neutron scattering data were selected from the library. Simultaneous evaluation of the conformational variation in the global OLDN structures and in the histone tails is difficult using conventional MD simulations. We overcame this problem by combining multiple simulation techniques, and showed the importance of the histone tails for stabilizing the structures of OLDNs in solution.

biophysics↗

bioRxiv2017

Glucocorticoid receptor-mediated amygdalar metaplasticity underlies adaptive modulation of fear memory by stress

Glucocorticoid receptor (GR) is crucial for signaling mediated by stress-induced high levels of glucocorticoids. The lateral nucleus of the amygdala (LA) is a key structure underlying auditory-cued fear conditioning. Here, we demonstrate that genetic disruption of GR in the LA (LAGRKO) resulted in an auditory-cued fear memory deficit for strengthened conditioning. Furthermore, the suppressive effect of a single restraint stress (RS) prior to conditioning on auditory-cued fear memory in floxed GR (control) mice was abolished in LAGRKO mice. Optogenetic induction of long-term depression (LTD) at auditory inputs to the LA reduced auditory-cued fear memory in RS-exposed LAGRKO mice, and in contrast, optogenetic induction of long-term potentiation (LTP) increased auditory-cued fear memory in RS-exposed floxed GR mice. These findings suggest that prior stress suppresses fear conditioning-induced LTP at auditory inputs to the LA in a GR-dependent manner, thereby protecting animals from encoding excessive cued fear memory under stress conditions.

neuroscience↗