Biology subjects

Hoshino, T.

Publications and source records attributed to Hoshino, T..

11 recordsLinked to original sources

bioRxiv2026

A Proof-of-Concept Study on Attached Spirulina Cultivation Under Microgravity and Partial Gravity Aboard the ISS

Microalgal attached cultivation circumvents gas-liquid separation issues of liquid-suspended cultivation, yet performance under reduced gravity remains unevaluated. As a proof-of-concept, we evaluated Arthrospira platensis (Spirulina) cultivation under artificial 1G, 1/6G, and microgravity ({micro}G) on the International Space Station. Spirulina expanded without cell detachment, medium floating, or component separation, with relative radial growth rates of 0.28%0.5 day-1 (1G), 0.22%0.5 day-1 (1/6G), and 0.17-0.21%0.5 day-1 ({micro}G), demonstrating feasibility in space.

bioengineering↗

bioRxiv2025

Linking sediment porosity to taxon-specific patterns of eDNA preservation in a temperate, semi-enclosed bay

Sedimentary environmental DNA provides unique insights into past community dynamics. However, the influence of physical sediment properties, such as porosity, on taxon-specific eDNA preservation remains poorly understood, particularly in temperate inner-bay environments. Therefore, here, we characterized eukaryotic communities in sediment cores from the surface to 6-m depth in the inner and mouth regions of the Uranouchi Bay, a semi-enclosed embayment in temperate Japan. Both 18S rRNA and mitochondrial cytochrome c oxidase subunit I gene metabarcoding revealed marked spatial variation; specifically, inner-bay sediments were enriched in terrestrial plant DNA and dinoflagellates, whereas mouth sediments contained higher proportions of marine diatoms. Vertical profiles further highlighted differences in DNA persistence, with terrestrial and particle-associated taxa retained deeper in the inner-bay sediments. Land-sea connectivity and basin geography strongly shape sedimentary eDNA composition, reflecting both ecological sourcing and preservation bias. We further systematically analyzed the relationship between sediment porosity, a critical physical property governing pore water mobility and solute diffusion, and taxon-specific sedimentary eDNA preservation. To highlight effects of porosity independent of burial depth, we modeled porosity as a function of depth and correlated the residual porosity with the relative abundances of individual phyla. Notably, the phyla exhibited contrasting preservation patterns: Dinoflagellata, Euglenozoa, and Rotifera showed weak to moderate positive correlations with porosity, whereas Chlorophyta and Ochrophyta displayed weak negative correlations. When depth correlations were examined jointly, multiple distinct pattern groups emerged: some taxa (e.g., Dinoflagellata) exhibited negative depth but positive porosity correlations, whereas others showed opposite or neutral patterns. These divergent responses suggest that DNA preservation in marine sediments involves multiple taxon-specific mechanisms rather than a single universal process, with porosity acting as an independent determinant of burial depth. Our results highlight the importance of integrating physical properties of sediments into sedimentary environmental DNA-based paleoenvironmental reconstructions.

ecology↗

bioRxiv2025

Evolutionary stasis and homogeneous selection structure microbial communities in the deep subseafloor sedimentary biosphere

The subseafloor biosphere, one of the Earths largest and most stable microbial habitats, mainly consists of energy-limited sediments where microbial life persists over geological timescales. However, the mechanisms governing microbial community assembly and evolution under condition of extreme energy limitation remains unclear. Here, we analysed a 296 m sediment core off the Shimokita Peninsula using amplicon sequencing, metagenomics, and genome-resolved analyses from 31 depth intervals spanning [~]480 kyr. The microbial community composition was governed primarily by homogeneous selection, consistent with persistent environmental uniformity during burial. Genome-resolved analyses of 224 high-quality metagenome-assembled genomes revealed highy conserved gene repertoires and uniformly low ratios of non-synonymous-to-synonymous substitutions, suggesting strong purifying selection with minimal genomic changes over this timescale. Our results indicate that evolutionary stasis is a pervasive feature of microbial life in deep subseafloor sediments, and propose a conceptual framework linking long-term environmental stability to genomic preservation in the Earths most persistent biosphere.

ecology↗

bioRxiv2025

Kernel-Based Style Transfer Mapping for Cross-Subject Biological Signal Classification

AO_SCPLOWBSTRACTC_SCPLOWOwing to pronounced inter-individual variability in biological signals, transfer learning has emerged as a widely used strategy to reduce calibration requirements for new users. Among the various approaches, style transfer mapping (STM) is distinguished by its ability to align the data distribution of target users directly with that of source users, thereby enabling the reuse of pretrained classifiers without retraining. However, STM is constrained by its inherent assumption of linear relationships between the target and source domains, which is often unrealistic given the complex and nonlinear nature of biological signals. To address this problem, we propose a novel kernel-based STM (k-STM) method that incorporates nonlinear kernel functions to capture complex inter-user variability more effectively. We evaluated the proposed k-STM method using four publicly available electromyogram and electroencephalogram datasets: MyoDataset, NinaProDB5, OpenBMI, and BCI Competition IV-2a, and four backbone classifiers: logistic regression, support vector machine, random forest, and multilayer perceptron. The experimental results demonstrate that k-STM significantly improves classification accuracy over the original STM, particularly when nonlinear kernels are employed. Statistical analyses confirm the superiority of the proposed approach across diverse datasets and classifiers. Furthermore, we examined the impact of the number of prototypes (i.e., mapping destinations) on the performance of both STM and k-STM, and found that using fewer prototypes than previously recommended can yield higher classification accuracy. Overall, the proposed k-STM constitutes a versatile, efficient, and robust nonlinear transfer-learning framework, enhancing its practical applicability in cross-subject biosignal classification.

bioengineering↗

bioRxiv2024

Transcriptomic analysis of the juvenile to adult transition in the mouse corpus callosum

The corpus callosum, a major white matter tract in the brain, undergoes age-related functional changes. To extend our investigation of age-related gene expression dynamics in the mouse corpus callosum, we compared RNA-seq data from 2-week-old and 12-week-old wild-type C57BL/6J mice and identified the differentially expressed genes (e.g., Serpinb1a, Ndrg1, Dnmt3a, etc.) between these ages. Interestingly, we found that genes highly expressed in myelinating oligodendrocytes were upregulated in 12-week-old mice compared to 2-week-old mice, while genes highly expressed in oligodendrocyte precursor cells (OPCs) and newly formed oligodendrocytes were downregulated. Furthermore, by comparing these genes with the datasets from 20-week-old and 96-week-old mice, we identified novel sets of genes with age-dependent variations in the corpus callosum. These gene expression changes potentially affect key biological pathways and may be closely linked to age-related neurological disorders, including dementia and stroke. Therefore, our results provide an additional dataset to explore age-dependent gene expression dynamics of oligodendrocyte lineage cells in the corpus callosum.

neuroscience↗

bioRxiv2023

Extracellular Histone Promotes Calcium Phosphate-Dependent Calcification in Mouse Vascular Smooth Muscle Cells

Vascular calcification, a major risk factor for cardiovascular events, is associated with a poor prognosis in chronic kidney disease (CKD) patients. This process is often associated with the transformation of vascular smooth muscle cells (VSMCs) into cells with osteoblast-like characteristics. Damage-associated molecular patterns (DAMPs), such as extracellular histones released from damaged or dying cells, are suspected to accumulate at calcification sites. To investigate the potential involvement of DAMPs in vascular calcification, we assessed the impact of externally added histones (extracellular histones) on calcium and inorganic phosphate-induced calcification in mouse VSMCs. Our study found that extracellular histones intensified calcification. We also observed that the histones decreased the expression of VSMC marker genes, while simultaneously increasing the expression of osteoblast marker genes. Additionally, histones treated with DNase I, which degrades dsDNA, attenuated this calcification, compared with the non-treated histones, suggesting a potential involvement of dsDNA in this process. Elevated levels of dsDNA were also detected in the serum of CKD model mice, underlining its potential role in vascular calcification in CKD. Our findings suggest that extracellular histones could play a pivotal role in the vascular calcification observed in CKD. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/555403v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@19c3239org.highwire.dtl.DTLVardef@1a563fdorg.highwire.dtl.DTLVardef@1479cd1org.highwire.dtl.DTLVardef@886219_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Copy number of the eukaryotic rRNA gene can be counted comprehensively

Gene sequence has been widely used in molecular ecology. For instance, the ribosomal RNA (rRNA) gene has been widely used as a biological marker to understand microbial communities. The variety of the detected rRNA gene sequences reflects the diversity of the microorganisms existing in the analyzed sample. Their biomass also can be estimated by applying quantitative sequencing with the information of rRNA gene copy numbers in genomes, however, the information on rRNA gene copy number is still limited. Especially, the copy number in microbial eukaryotes is much less understood than that of prokaryotes, possibly because of the large and complex structure of eukaryotic genomes. In this communication, we report an alternative approach that is more appropriate from the existing method of quantitative sequencing and demonstrate that the copy number of eukaryotic rRNA can be measured efficiently and comprehensively. By applying this approach widely, information on the eukaryotic rRNA copy number can be determined, and their community structures can be depicted and compared more efficiently.

microbiology↗

bioRxiv2021

Apparent digestibility of captive colobines in relation to stomach types with special reference to fibre digestion

Colobine monkeys are known for the anatomical complexity of their stomachs, making them distinct within the primate order. Amongst foregut fermenters, they appear peculiar because of the occurrence of two different stomach types, having either three ( tripartite) or four ( quadripartite, adding the praesaccus) chambers. The functional differences between tri and quadripartite stomachs largely remain to be explained. In this study, we aim to compare the apparent digestibility (aD) in tripartite and quadripartite colobines. Hence, we measured the aD in two colobine species, Nasalis larvatus (quadripartite) and Trachypithecus cristatus (tripartite), in two zoos. We also included existing colobine literature data on the aD and analysed whether the aD of fibre components is different between the stomach types to test the hypothesis of whether quadripartite colobines show higher aD of fibre components than tripartite colobines did. Our captive N. larvatus specimen had a more distinctively varying nutrient intake across seasons with a larger seasonal variation in aD than that of a pair of T. cristatus, which mostly consumed commercial foods with a lower proportion of browse and less seasonal variation. We observed higher aD of dry matter (DM), neutral detergent fibre (NDF) and acid detergent fibre (ADF) in the N. larvatus specimen, suggesting a higher gut capacity of N. larvatus provided by the additional praesaccus forestomach chamber. Based on the analysis of literature data for aD, we also found that quadripartite species achieved higher fibre digestibility at similar dietary fibre levels compared with tripartite species, supporting the hypothesis that the additional gut capacity offered by the praesaccus facilitates a longer retention and hence more thorough microbial fermentation of plant fibre.

zoology↗

bioRxiv2020

Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro.

In December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, Hubei Province, China. No specific treatment has been established against coronavirus disease-2019 (COVID-19) so far. Therefore, it is urgently needed to identify effective antiviral agents for the treatment of this disease, and several approved drugs such as lopinavir have been evaluated. Here, we report that nelfinavir, an HIV-1 protease inhibitor, potently inhibits replication of SARS-CoV-2. The effective concentrations for 50% and 90% inhibition (EC50 and EC90) of nelfinavir were 1.13 {micro}M and 1.76 {micro}M respectively, the lowest of the nine HIV-1 protease inhibitors including lopinavir. The trough and peak serum concentrations of nelfinavir were three to six times higher than EC50 of this drug. These results suggest that nelfinavir is a potential candidate drug for the treatment of COVID-19 and should be assessed in patients with COVID-19.

microbiology↗

bioRxiv2019

Comprehensive biological interpretation of gene signatures using semantic distributed representation

Recent rise of microarray and next-generation sequencing in genome-related fields has simplified obtaining gene expression data at whole gene level, and biological interpretation of gene signatures related to life phenomena and diseases has become very important. However, the conventional method is numerical comparison of gene signature, pathway, and gene ontology (GO) overlap and distribution bias, and it is not possible to compare the specificity and importance of genes contained in gene signatures as humans do. This study proposes the gene signature vector (GsVec), a unique method for interpreting gene signatures that clarifies the semantic relationship between gene signatures by incorporating a method of distributed document representation from natural language processing (NLP). In proposed algorithm, a gene-topic vector is created by multiplying the feature vector based on the genes distributed representation by the probability of the gene signature topic and the low frequency of occurrence of the corresponding gene in all gene signatures. These vectors are concatenated for genes included in each gene signature to create a signature vector. The degrees of similarity between signature vectors are obtained from the cosine distances, and the levels of relevance between gene signatures are quantified. Using the above algorithm, GsVec learned approximately 5,000 types of canonical pathway and GO biological process gene signatures published in the Molecular Signatures Database (MSigDB). Then, validation of the pathway database BioCarta with known biological significance and validation using actual gene expression data (differentially expressed genes) were performed, and both were able to obtain biologically valid results. In addition, the results compared with the pathway enrichment analysis in Fishers exact test used in the conventional method resulted in equivalent or more biologically valid signatures. Furthermore, although NLP is generally developed in Python, GsVec can execute the entire process in only the R language, the main language of bioinformatics.

bioinformatics↗

bioRxiv2017

Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus ×- yedoensis 'Somei-yoshino' across the Japanese archipelago

Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the \"Ohanami Project\", to obtain environmental DNA samples from petal surfaces of Cerasus x yedoensis Somei-yoshino across the Japanese archipelago during spring 2015. C. x yedoensis is the most popular garden cherry species in Japan and clones of this cultivar bloom simultaneously every spring. Data collection spanned almost every prefecture and totaled 577 DNA samples from 149 collaborators. Preliminary amplicon-sequencing analysis showed the rapid attachment of environmental DNA onto the petal surfaces. Notably, we found DNA of other common plant species in samples obtained across a wide distribution; this DNA likely originated from pollen of the Japanese cedar. Our analysis supports our belief that petal surfaces after blossoming are a promising target to reveal the dynamics of environmental DNA in nature. The success of our experiment also shows that crowdsourced environmental DNA analyses have considerable value in ecological studies.

microbiology↗