Biology subjects

Kodama, H.

Publications and source records attributed to Kodama, H..

3 recordsLinked to original sources

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↗