Biology subjects

Kodama, H.

Publications and source records attributed to Kodama, H..

7 recordsLinked to original sources

bioRxiv2026

Differential associations of insulin resistance with anterior hippocampal volume in mild cognitive impairment and Alzheimer's disease

Insulin resistance is increasingly recognized as a metabolic factor associated with Alzheimers disease (AD); however, its relevance to hippocampal structural changes--a key pathological feature of AD--across disease stages is not fully understood. To address this issue, we investigated the relationship between insulin resistance, hippocampal gray matter volume, and cognitive performance using data from the Alzheimers Disease Neuroimaging Initiative (ADNI), a large-scale neuroimaging dataset. Insulin resistance was assessed using the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR), and its relationship with brain structure and cognitive performance was evaluated across diagnostic groups. In the mild cognitive impairment (MCI) group, higher insulin resistance was associated with larger anterior hippocampal gray matter volume, whereas in the AD group this association was reversed in direction. Furthermore, in the MCI group, anterior hippocampal gray matter volume was also positively associated with higher Mini-Mental State Examination (MMSE) scores, and an exploratory mediation analysis suggested a significant indirect association linking HOMA-IR, anterior hippocampal volume, and cognitive performance through anterior hippocampal volume. These findings suggest that the relationship between insulin resistance and AD-related brain changes differs across diagnostic groups, highlighting the importance of considering metabolic alterations in relation to disease status.

neuroscience↗

bioRxiv2026

Moderate overexpression of PROTON GRADIENT REGULATION 5 improves photosynthetic performance and plant growth under fluctuating low light in Arabidopsis thaliana

Cyclic electron transport (CET) around photosystem I (PSI) is essential for maintaining photosynthetic efficiency by balancing ATP/NADPH production and protecting PSI from photoinhibition. Although the PROTON GRADIENT REGULATION 5 (PGR5)-dependent CET pathway is known to be critical under high or fluctuating light conditions, its role under fluctuating low light remains poorly understood. In natural environments, plants frequently experience prolonged low irradiance interspersed with brief sunflecks, making fluctuating low light a physiologically relevant condition. Here, we investigated Arabidopsis thaliana lines with graded PGR5 expression levels to evaluate the dose-dependent contribution of PGR5 to CET activity, photosynthetic regulation, and growth performance under both low light and fluctuating low light conditions. Moderate increase in the PGR5 protein level enhanced CET activity, accelerated photosynthetic induction, improved PSI protection and increased biomass accumulation under fluctuating low light. In contrast, excessive PGR5 accumulation impaired photosynthetic performance and reduced plant growth, indicating that optimal CET capacity requires precise tuning of PGR5 abundance. These results reveal a non-linear relationship between PGR5 protein levels and photosynthetic performance and demonstrate that moderate enhancement of CET improves plant productivity under fluctuating low light. Our findings highlight the importance of optimizing CET capacity to match dynamic light environments and suggest that fine-tuning PGR5 expression could be a promising strategy for improving crop performance under natural canopy conditions. Significance statementModerate increase in the PGR5 improves plant productivity, whereas excessive PGR5 accumulation impaired photosynthetic performance and reduced plant growth. Therefore, optimizing CET capacity by the fine-tuning PGR5 expression is important for improving crop productivity.

plant biology↗

bioRxiv2026

Cyclic electron transport via the NDH complex sustains photosynthesis and productivity under fluctuating and sub-optimal environments

The chloroplast NADH dehydrogenase-like (NDH) complex mediates cyclic electron transport (CET) around photosystem I (PSI) and contributes to photosynthetic regulation and photoprotection under various environmental stresses. Although NDH function has been extensively characterized under controlled conditions, NDH-deficient mutants often show only subtle phenotypes in such environments, leaving its physiological importance under naturally fluctuating field conditions poorly understood. Here, we evaluated growth, yield, and photosynthetic performance of NDH-deficient rice cultivated under field conditions. Mutant plants exhibited reduced biomass accumulation and grain yield compared with wild type. Detailed physiological analyses revealed that NDH deficiency markedly decreased PSI electron transport and CO2 assimilation, particularly under low temperature and sub-saturating irradiance. At moderate and high temperatures, reductions in carbon fixation were largely confined to low-light conditions, whereas at low temperatures, impairment extended across nearly the entire light response range. Under repetitive fluctuating light regimes, NDH-deficient plants showed progressive declines in photosynthesis accompanied by a selective decrease in PSI photochemical capacity without changes in PSII maximum efficiency, indicating PSI-specific photoinhibition. These findings demonstrate that NDH-dependent CET plays a crucial role in sustaining photosynthetic efficiency and crop productivity in dynamic field environments by stabilizing PSI redox balance and maintaining long-term carbon gain. Summary StatementNDH-dependent cyclic electron transport supports photosynthesis and yield in field-grown rice by maintaining PSI function under fluctuating light, low temperature, and sub-saturating irradiance.

plant biology↗

bioRxiv2026

Avatar facial expressions enhance social presence and inter-brain synchronization in virtual reality

Virtual reality (VR) has become a prominent medium for computer-mediated social interaction, yet the psychological and neural mechanisms underpinning avatar-mediated communication remain insufficiently understood. This study investigated how dynamically modulated avatar facial expressions shape interpersonal interaction in VR. Pairs of participants engaged in a collaborative creativity task while interacting via avatars whose facial expressions were either amplified, natural, or expressionless. We collected subjective measures of body ownership, social presence, and interpersonal attraction, while simultaneously recording neural activity using functional near-infrared-spectroscopy-based hyperscanning to assess inter-brain synchrony (IBS). Avatars displaying facial expressions, particularly amplified ones, significantly enhanced body ownership, social presence, and interpersonal attraction compared to expressionless avatars. At the neural level, visible avatar facial expressions were associated with IBS in the right temporo-parietal junction (TPJ) and the dorsolateral prefrontal cortex (dlPFC), regions that are commonly implicated in social-cognitive processes such as mentalizing and executive control. Although task performance did not differ across conditions, social presence was positively correlated with creative performance, suggesting that psychological connectedness supports collaborative creativity. Together, these findings indicate that avatar facial expressivity functions as a critical nonverbal social cue that facilitates affective and cognitive alignment between interaction partners. By linking subjective experience with inter-brain neural dynamics, this study provides empirical guidance for the design of virtual environments that promote social engagement and effective collaboration.

neuroscience↗

bioRxiv2025

Cyt b6/f Complex Fine-Tunes PSI Stability and Photosynthetic Capacity Under Fluctuating Light

Plants encounter dynamic light fluctuations in natural habitats, requiring robust mechanisms to protect Photosystem I (PSI) against photoinhibition. The cytochrome (Cyt) b6/f complex plays a pivotal role in regulating electron flow and ensuring PSI stability under fluctuating light. However, its precise role in balancing PSI protection and photosynthetic capacity remains unclear. In this study, transgenic tobacco (Nicotiana tabacum L. W38) with reduced Cyt b6/f content was used to examine PSI tolerance to photoinhibition and photosynthetic performance under fluctuating light. Notably, the reduced Cyt b6/f content conferred significant protection of PSI against photoinhibition induced by fluctuating light, albeit at the expense of the electron transport capacity. Remarkably, PSI stability was maintained even under extreme fluctuating light conditions in the plants with lowest Cyt b6/f contents, highlighting a trade-off between photoprotection and photosynthetic capacity. These findings reveal that a reduction in Cyt b6/f content enhances PSI protection while adjusting electron transport capacity, making plants more adaptable in environments dominated by low light and transient sunflecks. This study provides new insights into the adaptive strategies of plants under dynamic light environments and underscores the potential of targeting Cyt b6/f for enhancing crop tolerance to fluctuating light conditions.

plant biology↗

bioRxiv2024

A Computational Approach to Interpreting the Embedding Space of Dimension Reduction

Nonlinear dimension reduction methods are widely applied in studies analyzing gene and protein expression, by revealing patterns of discrete groups and continuous orders in high-dimensional data. However, the tools are limited to understanding the obtained embedding structures of biological mechanisms, hindering the full exploitation of data. Here, we propose a novel framework to interpret embedding systematically by identifying and mapping associated biological functions. The method performs statistical tests and visualizes significantly enriched functions essential for the organization of the embedding structure, by applying it to the embedding results of two datasets: the Genotype Tissue Expression dataset and a Caenorhabditis elegans embryogenesis dataset, one capturing distinct cluster structures and the other capturing continuous developmental trajectories. We identified the associated functions for interpreting the two embeddings and confirmed it as a useful explainable AI tool in exploratory data analysis by providing annotations to the embedding space.

bioinformatics↗

bioRxiv2024

Systematic identification of exercise-induced anti-aging processes involving intron retention

Exercise is one of the most promising anti-aging interventions for maintaining skeletal muscle health in older adults. Nine "Aging Hallmarks", proposed by Lopez-Otin, offer insights into the aging process; however, the link between these hallmarks and exercise is not fully elucidated. In this study, we conducted a systematic multi-omics analysis of skeletal muscles, focusing on aging and exercise, based on gene signatures for aging hallmarks. It is posited that mRNA splicing activity, linked to genomic instability, constitutes a fundamental hallmark of aging, and it exhibits divergent expression patterns in response to aging and exercise. Additionally, we analysed splicing events and discovered that intron retention (IR) is significantly impacted by aging, exhibiting contrasting changes to those induced by resistance training in the older cohort. The isoforms characterised by IR are notably enriched in mitochondrial functions. Conclusively, our results underscore the significance of splicing mechanisms as a novel aspect of aging hallmarks in skeletal muscles and propose a new mechanism by which exercise exerts its anti-aging effects on skeletal muscles through intron retention. Key points summaryO_LISkeletal muscle aging involves significant structural and functional changes, including loss of muscle mass, decline in strength, and mitochondrial dysfunction, all influenced by genomic instability. C_LIO_LIExercise has been identified as a key intervention that counters genomic instability and modulates mRNA splicing patterns, particularly through the regulation of Intron Retention, to mitigate aging effects in skeletal muscle. C_LIO_LIWe reveal the novel role of IR, especially in principal isoforms, where it is linked to critical cellular processes like mitochondrial function, suggesting a targeted pathway through which exercise exerts its anti-aging effects. C_LIO_LIThe findings provide new insights into the molecular mechanisms underlying the beneficial effects of exercise on aging skeletal muscle. C_LIO_LIThis study lays the groundwork for future research on exercise-induced modulation of mRNA splicing as a therapeutic strategy for aging and potentially age-related diseases, pointing towards a significant shift in how we approach aging intervention strategies. C_LI

systems biology↗