Biology subjects

Ohara, M.

Publications and source records attributed to Ohara, M..

7 recordsLinked to original sources

bioRxiv2025

Albumin-binding dendrimer-conjugated siRNA enables safe and effective gene silencing throughout the central nervous system

Improving siRNA delivery to the central nervous system (CNS) is a major focus for treating the numerous debilitating neurological conditions which have a genetic basis. Here, we present an albumin-binding siRNA based on an amphiphilic dendrimer conjugate (D-siRNA). We demonstrate that D-siRNA achieves effective and homogeneous delivery throughout the CNS following administration into the cerebrospinal fluid (CSF). In mice, a single CSF administration of D-siRNA resulted in potent and durable gene silencing across various brain regions, with effects lasting six months without detectable toxicity. We validate its utility in larger rodents (rats) using intrathecal administration--a clinically relevant route--showing effective and broad delivery and robust silencing. Benchmarking against other clinically relevant siRNA delivery scaffolds revealed that D-siRNA provides comparable delivery and efficacy, with more efficient conversion of gross uptake to functional uptake. These findings support the use of albumin-binding conjugates for brain delivery, and position D-siRNA as a safe, effective, and durable platform for gene silencing in the CNS.

pharmacology and toxicology↗

bioRxiv2025

Transcriptomic insights into the tripartite plant-pathogen-mycoparasite interaction reveal novel mechanisms involving fungal secretomes and plant amino acid metabolism

O_LIThe tomato-Cladosporium fulvum (syn. Fulvia fulva) pathosystem has served as a model for the gene-for-gene concept of effectors and resistance proteins, but this binary framework does not include the potential influence of other microbial participants. Here we describe the dramatic changes in gene expression of all members of the tritrophic interaction among tomato, C. fulvum, and mycoparasitic fungus Hansfordia pulvinata. C_LIO_LITranscriptomic analyses of the mycoparasite H. pulvinata during parasitism of C. fulvum on tomato on planta and in vitro revealed a dramatic upregulation of genes encoding small secreted proteins during mycoparasitism, notably, a Nep1-like protein (HpNlp1) lacked typical necrosis-inducing activity but induced the accumulation of antifungal compounds inhibiting spore germination of C. fulvum. C_LIO_LISimilarly, in C. fulvum parasitized by H. pulvinata, effector genes were highly expressed. Strikingly, effector protein Ecp2 was found to share structural similarity with pathogen killer toxin 4 proteins and had broad-spectrum antifungal activity, indicating a dual function in fungal competition and Cf-ECP2-mediated plant resistance. C_LIO_LIIn tomato plants infected by C. fulvum parasitized by H. pulvinata, primary metabolism and defense-related genes were exclusively activated. These results suggest that in the tritrophic interaction, the mycoparasite simultaneously suppressed the pathogen and induced plant resistance. This study uncovers a multilayered molecular network in which the mycoparasite coordinates pathogen suppression and plant defense within the tritrophic interaction. C_LI

microbiology↗

bioRxiv2025

FOXM1 Expression in Invasive Ductal Breast Carcinoma of No Special Type: Insights from RNA-seq and Immunohistochemical Analysis

BackgroundInvasive ductal carcinoma of no special type (IDC-NST) is the most common subtype of breast cancer, characterized by significant clinical heterogeneity. Forkhead box M1 (FOXM1) is a key transcription factor involved in cell cycle regulation and tumor progression, but its expression profile and clinical significance in IDC-NST remain incompletely understood. MethodsWe analyzed FOXM1 expression in a cohort of 100 IDC-NST patients using RNA sequencing and immunohistochemistry (IHC). FOXM1 mRNA levels were quantified, and protein expression was scored based on the percentage of positive tumor cells. Differentially expressed genes (DEGs) between high and low FOXM1 expression groups were identified, followed by pathway enrichment and protein-protein interaction (PPI) network analyses. The prognostic value of FOXM1 was evaluated by recurrence-free survival (RFS) analysis. ResultsFOXM1 protein expression correlated significantly with mRNA abundance in 22 representative cases (p < 0.05). Receiver operating characteristic (ROC) curve analysis identified a cut-off value of 4.954 CPM for FOXM1 mRNA to predict recurrence (AUC = 0.642). High FOXM1 expression was associated with larger tumor size, higher histological grade, and negative hormone receptor status. Patients with high FOXM1 expression exhibited significantly poorer 5-year RFS (73.6% vs. 92.3%, p < 0.001). Multivariate analysis confirmed FOXM1 as an independent prognostic factor (HR 15.26; p = 0.026). Transcriptomic profiling revealed 190 upregulated and 197 downregulated genes in the FOXM1-high group, enriched in cell cycle and mitotic pathways. PPI network analysis positioned FOXM1 as a central hub coordinating genes involved in chromosomal stability and mitosis. ConclusionsFOXM1 overexpression is a strong independent predictor of poor prognosis in IDC-NST and plays a critical role in tumor proliferation and genome integrity. These findings support FOXM1 as a potential prognostic biomarker and therapeutic target, warranting further investigation into FOXM1-targeted therapies for breast cancer management.

cancer biology↗

bioRxiv2022

Which life history strategy can maintain high genetic diversity in plants?

Classifying a variety of plant life histories is an important step to understand ecological and evolutionary background of life history diversification in plants. Principal component analysis (PCA) of life history traits, as well as elasticity analysis using a ternary diagram, successfully categorized the diverse life histories and clarified their link to various ecological characteristics, such as population dynamics, functional traits, and conservation status. However, the relationships with population genetic properties, including genetic diversity, have not been explored very much. In this study, we overlaid annual change rate of expected heterozygosity{eta} on life history spectrum obtained by PCA and elasticity analysis to examine which life history strategy can maintain high genetic diversity over time. We found that{eta} gradually changed along the fast-slow continuum and that slow-paced life histories maintained high genetic diversity, probably due to generation overlap. Elasticity analysis showed that life histories that highly depend on stasis also maintained genetic diversity. As genetic diversity reflects adaptive potential to environmental changes, our study provides a new genetic perspective on adaptative evolution and population viability to life history study.

ecology↗

bioRxiv2021

Potential effects of life history on demographic genetic structure in stage-structured plant populations

O_LIPredicting temporal dynamics of genetic diversity is important for assessing long-term population persistence. In stage-structured populations, especially in perennial plant species, genetic diversity is often compared among life history stages, such as seedlings, juveniles, and flowerings, using neutral genetic markers. Because individuals in mature stages will die and be replaced by those in more immature stages over the course of time, the comparison among stages (sometimes referred to as demographic genetic structure) has been regarded as a proxy of potential genetic changes that accompany the turnover of constituent individuals. However, because demographic genetic structure had not been theoretically examined, the basic property and the validity of demographic genetic structure remained unclear. C_LIO_LIWe developed a matrix model which was made up of difference equations of expected heterozygosity, a common proxy of genetic diversity, of each life history stage at a neutral locus in stage-structured plant populations. Based on the model, we formulated demographic genetic structure as well as the annual change rate of expected heterozygosity (denoted as{eta} ). We obtained theoretical expectation of demographic genetic structure and{eta} from our model and compared them with computational results of stochastic simulation for randomly generated 3,000 life histories for model validation. We then examined the relationships of demographic genetic structure with effective population size Ne, which is the determinants of diversity loss per generation time, as well as with{eta} . C_LIO_LITheoretical expectations on{eta} and demographic genetic structure fitted well to the results of stochastic simulation, supporting the validity of our model. Demographic genetic structure varied independently of Ne and{eta} , while having a strong correlation with stable stage distribution: expected heterozygosity was lower in stages with fewer individuals. C_LIO_LIOur results indicate that demographic genetic structure strongly reflects stable stage distribution, rather than temporal genetic dynamics, and that inferring future genetic diversity solely from demographic genetic structure would be misleading. Instead of demographic genetic structure, the newly-defined statistics{eta} will be an useful tool to predict genetic diversity at the same time scale as population dynamics, facilitating evaluation on population viability from a genetic point of view. C_LI

genetics↗

bioRxiv2021

Visualization of ecological successions in lakes subdivided by volcanic eruption at Akan Caldera, Hokkaido, Japan

It is not feasible to continuously observe ecological succession in lakes because of the long time-scales generally involved. Thus, the process has been inductively deduced by comparing many lakes with different succession states, or indirectly simulated by tracking studies of smaller water bodies, experiments using microcosms or mesocosms, and reconstruction of lake history by sediment analysis. However, the reality of succession processes in large lakes with slow succession is not well understood, and new approaches are needed. Theoretically, in a group of large and small lakes of similar ages and with similar initial and watershed environments, the rate of nutrient accumulation in each lake depends on the ratio of watershed area to lake size, and the lakes are predicted to evolve to different trophic levels over time. Here, we tested this hypothesis on the 10 lakes of varying sizes in Akan Caldera, Japan, which were formed thousands of years ago by fragmentation due to volcanic eruptions within the caldera. Topographic and water quality studies showed that the ratio of accumulated watershed area to lake size (area and volume), expressed logarithmically, had a positive linear regression with the total phosphorus concentration, an indicator of trophic level. The trophic levels of the lakes were diverse, including oligotrophic, mesotrophic, and eutrophic types in the traditional "lake type" classification based on total phosphorus and chlorophyll-a concentrations. Furthermore, 21 species of aquatic macrophytes were observed by a diving survey, and the plant species composition was classified into five groups corresponding to the trophic status of the lakes, indicating a conventional "hydrarch succession". The diversity of water quality and aquatic vegetation in a group of lakes with similar origins paves the way for new comparative studies of lakes, including large lakes.

ecology↗

bioRxiv2021

Effect of luminal surface structure of decellularized aorta on thrombus formation and cell behavior

As the number of cardiovascular diseases increases, artificial heart valves and blood vessels have been developed. Although cardiovascular application using decellularized tissue have been studied, the mechanism of their functionality is still unknown. To find the important factor for preparing decellularized cardiovascular prothesis which shows good in vivo performance, the effect of luminal surface structure of decellularized aorta on thrombus formation and cell behavior was investigated. Various luminal surface structures of decellularized aorta were prepared by heating, drying and peeling. The luminal surface structure and collagen denaturation was evaluated by immunohistological staining, collagen hybridizing peptide (CHP) staining and scanning electron microscopy (SEM) analysis. To evaluate the effect of luminal surface structure of decellularized aorta on thrombus formation and cell behavior, blood clotting test and recellularization of endothelial cells and smooth muscular cells were performed. The results of blood clotting test showed that the closer the luminal surface structure is to native aorta, the higher the anti-coagulant property. From the result of cell seeding-test, it was suggested that vascular cells recognize the luminal surface structure and regulate adhesion, proliferation and functional expression. These results will provide important factor for preparing decellularized cardiovascular prothesis and lead to future development on decellularized cardiovascular applications.

bioengineering↗