Biology subjects

Fukasawa, Y.

Publications and source records attributed to Fukasawa, Y..

7 recordsLinked to original sources

bioRxiv2026

Decoupling species richness and interaction frequency reveals how fungal interactions regulate wood decomposition

Wood decay fungi play a central role in forest carbon cycling, yet the mechanisms linking fungal biodiversity to decomposition remain unclear because species richness and interspecific interactions are rarely separated. Here, these effects were experimentally disentangled using a laboratory wood decomposition microcosm with four common wood-decay fungi. By manipulating the spatial arrangements of pre-colonized wood blocks, fungal species richness and the frequency of interspecific interactions were independently varied. Wood mass loss was quantified, and lignin and carbohydrate analyses were conducted to examine the changes in decay strategies and the potential accumulation of recalcitrant fungal products. Both fungal species richness and interspecific interactions enhanced wood decomposition, but their effects depended on species identity and combinations. Selection effects were observed when competitively dominant species replaced weaker competitors. Several species combinations showed decomposition rates exceeding those of pure cultures, indicating complementarity and facilitation by interspecific interactions. Generalized linear mixed models revealed that interaction frequency and species richness independently influenced decay rates in a species-specific manner. Chemical analyses revealed that interspecific interactions altered the relative loss of lignin and carbohydrates, indicating shifts in the enzymatic allocation and/or production of acid-insoluble fungal metabolites during competition. Our results indicate that competitive interactions among wood decay fungi often accelerate decomposition to offset energetic costs. However, deadlock interactions among basidiomycetes may promote the accumulation of recalcitrant fungal compounds, potentially slowing decomposition over longer timescales. We propose the "accumulated inhibitor hypothesis" to reconcile contrasting fungal diversity-decomposition relationships and highlight the importance of interaction frequency in fungal biodiversity-ecosystem functioning research.

ecology↗

bioRxiv2026

Heterogeneous Nuclear Ribonucleoprotein A1 as a Key Regulator in Pulmonary Arterial Hypertension Development

BackgroundAlthough plexiform lesion (PL) formation in severe pulmonary arterial hypertension (PAH) is a therapeutic target, the mechanisms underlying their formation have not been fully elucidated. This study aimed to identify candidate proteins involved in PL formation by examining differentially expressed proteins (DEPs) in PAH lesions. MethodsProteomic remodeling was assessed before and after the formation of PLs in a SU5416 combined with hypoxia (SuHx) rat model of severe PAH using laser-capture microdissection coupled with mass spectrometry. Unobstructed pulmonary arteries with medial hypertrophy (UMHPAs) and PLs from SuHx rats were subjected to qualitative and quantitative proteomics, revealing DEPs between these structures. ResultsWe identified 718 proteins with 58 DEPs, of which 31 were upregulated in UMHPAs and 27 were upregulated in PLs. Immunostaining confirmed that DEPs detected in our proteomic analysis were differentially expressed between UMHPAs and PLs. Among them, we focused on heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) as a candidate protein that may be strongly associated with PL formation because of its strong association with cell proliferation. siRNA knockdown of hnRNPA1 in hypoxia-treated pulmonary artery smooth muscle cells reduced pyruvate kinase M2 expression and significantly decreased proliferative capacity. Treatment of SuHx rats with hnRNPA1 inhibitors also suppressed pulmonary artery remodeling in PAH and PL formation. ConclusionsSeveral DEPs associated with PL formation but with unclear relevance to pulmonary artery remodeling in PAH were discovered. Among these, hnRNPA1, which was not detected in transcriptome analysis, may be important in PL formation. What are the Clinical Implications?The prognosis for pulmonary arterial hypertension (PAH) with plexiform lesions (PLs) is poor. Although PLs are therapeutic targets, the mechanisms of PL formation have not been fully elucidated, and there have been no direct examinations of proteomic remodeling before and after their formation. We identified several differentially expressed proteins (DEPs) that may be strongly associated with PL formation. Of these, heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) was examined as a candidate protein involved in PA remodeling in PAH and PLs. Inhibition of hnRNPA1 in a severe PAH model not only suppressed pulmonary artery remodeling in PAH but also reduced PL formation. Several DEPs involved in pulmonary artery remodeling in PAH may be of significant value in the search for new therapeutic targets.

cell biology↗

bioRxiv2025

Electrical information flows across the sporocarps of two ectomycorrhizal fungi in the field

We measured the extracellular bioelectrical activities of two ectomycorrhizal basidiomycete species belonging to the genus Hebeloma in a field to examine the potential information flow across the sporocarps and its reponse to artificial stimulation. The 37 sporocarps (29 H. danicum and 8 H. cylindrosporum) occurring within a 5 m x 5 m quadrat on the forest floor of an oak-dominated stand were measured for their electrical potential every second for 3.5 days using subdermal stainless electrodes. Causality analysis of electrical potential during a period without artificial stimulation indicated that the magnitude of potential information flow across the sporocarps was not restricted to the sporocarps belonging to the same genet (clone) nor within a species. Howeverm this was still negatively associated with genetic as well as spatial distances. The effects of artificial stimulation (water and urine addition) on the average magnitude of information flow across the sporocarps were positive when tap water was added locally to a certain sporocarp but were negative when tap water was added to all the sporocarps. In contrast, the addition of urine had minimal effect on the magnitude of information flow. These results indicate the presence of underground electrical information flows across fungal sporocarps which respond vigorously to the environmental conditions.

ecology↗

bioRxiv2025

Genome complexity, not ploidy, dictates long-read variant-calling accuracy

Accurate characterization of genetic variation is fundamental to genomics. While long-read sequencing technologies promise to resolve complex genomic regions and improve variant detection, their application in complex genomes has not been well validated. Here, we systematically investigate the factors influencing variant calling accuracy using accurate long reads. Using human trio data with known variants to simulate variable ploidy levels (diploid, tetraploid, hexaploid), we demonstrate that while variant sites can often be identified accurately, genotyping accuracy decreases with increasing ploidy due to allelic dosage uncertainty. This highlights a specific challenge in assigning correct allele counts in polyploids even with high depth, separate from the initial variant discovery. We then assessed genotyping and variant detection performance in real genomes with varying complexity: the relatively simple diploid Fragaria vesca, the tetraploid Solanum tuberosum, and the highly repetitive diploid Zea mays. Our results reveal that overall variant calling accuracy is influenced strongly by inherent genome complexity (e.g., repeat content). Furthermore, we identify a critical mechanism impacting variant discovery: structural variations between the reference and sample genomes, particularly those containing repetitive elements, can induce spurious read mapping. This effect is likely exacerbated by the length and accuracy of long reads. This leads to false variant calls, constituting a distinct and more dominant source of error than allelic-dosage uncertainty. Our findings underscore the multifaceted challenges in long-read variant analysis and highlight the need for ploidy-aware genotypers and bias-aware mapping strategies to fully realize the potential of long reads in diverse organisms.

bioinformatics↗

bioRxiv2022

Mushrooms arising from the mole latrine reveal the life of talpid moles: proposals of myco-talpology and habitat-cleaning symbiosis

Myco-talpology is the science of moles and mushrooms based on our discovery in 1976 that underground nests of talpid moles can be located by the aboveground fruiting of the agarics Hebeloma danicum or Hebeloma sagarae, a Japanese sibling species of European Hebeloma radicosum. Hyphae of these mushrooms specifically colonise mole latrines near nests, forming ectomycorrhizas with the roots of their host trees. By this process, the hyphae and roots absorb, transform, and translocate the nutrients from mole excretions, cleaning the moles habitat. The mushrooms fruit on the ground with thick root-like tissue stretching up from the ectomycorrhizas. The presence of the fruit bodies serves as the only indicator for underground mole nests, enabling us to provide novel insights into mole ecology. We excavated 74 H. sagarae or H. danicum sites in Japan and 13 H. radicosum sites in Europe and identified the nesting species. These investigations provided new perspectives on latrine making, nest structure, breeding and nestlings, the neighbouring presence of different Talpini species, and long-term nesting at the same site with inhabitant changes. Moreover, they suggested that a tripartite habitat-cleaning symbiosis among moles, mushrooms, and mushroom-host trees in the latrine must have existed for a long time in Japanese and European forests. While moles are traditionally considered inhabitants of open areas, their special relationship with mushrooms and trees suggests they may originally be forest inhabitants.

ecology↗

bioRxiv2022

Lipid Droplets Fuel Small Extracellular Vesicle Biogenesis

Despite an increasing gain of knowledge regarding small extracellular vesicle (sEV) composition and functions in cell-cell communication, the mechanism behind their biogenesis remains unclear. Here, we revealed for the first time that the sEV biogenesis and release into the microenvironment are tightly connected with another important organelle: Lipid Droplets (LD). We have observed this correlation using different human cancer cell lines as well as patient-derived colorectal cancer stem cells (CR-CSCs). Our results showed that the use of external stimuli such as radiation, pH, hypoxia, or lipid interfering drugs, known to affect the LD content, had a similar effect in terms of sEV secretion. Additional validations were brought using multiple omics data, at the mRNA and protein levels. Altogether, the possibility to fine-tune sEV biogenesis by targeting LDs, could have a massive impact on the amount, the cargos and the properties of those sEVs, paving the way for new clinical perspectives. Significance Statement

cancer biology↗

bioRxiv2021

LeafGo: Leaf to Genome, a quick workflow to produce high-quality De novo genomes with Third Generation Sequencing technology

Recent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a complete de novo plant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two different Eucalyptus species E. rudis, and E. camaldulensis to chromosome level without using additional scaffolding technologies. For the rapid production of de novo genome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.

genomics↗