Biology subjects

Shimada, Y.

Publications and source records attributed to Shimada, Y..

18 recordsLinked to original sources

bioRxiv2026

Oxidized EGCG redirects α-synuclein aggregation through shear-selected interactions

-Synuclein (Syn) aggregation is central to Parkinson's disease pathology, and the green-tea polyphenol epigallocatechin gallate (EGCG) has been studied as an inhibit fibril formation. However, EGCG autoxidation and analyses under static, non-fibrillating conditions have obscured whether activity arises from EGCG itself or oxidized species and which interactions persist during Syn assembly. Here we combine HPLC, LC-MS, TEM and solution NMR to compare unoxidized and oxidized EGCG (oxEGCG), while Rheo-NMR monitors Syn during shear-promoted assembly. Unoxidized EGCG showed no detectable binding under static, reducing conditions, whereas oxEGCG bound Syn, inhibited fibrillation and remodeled fibrils. Under shear flow, many oxEGCG-dependent perturbations partially reverted toward free Syn, whereas interactions near the NAC-C-terminal boundary were preferentially retained, coinciding with formation of oligomers and short, thick fibrils. These findings identify oxidation state and flow as determinants of EGCG action on Syn and show that Rheo-NMR distinguishes interactions that persist during shear-promoted assembly.

biochemistry↗

bioRxiv2026

An integrated Rheo-NMR platform for real-time, site-specific kinetic analysis of amyloid formation

Amyloid fibrils are protein aggregates associated with neurodegenerative diseases. Their formation proceeds through protein- and condition-dependent microscopic pathways that can generate structurally and biologically distinct aggregates, yet these pathways are inferred from ensemble-averaged measurements. Amyloid formation is often slow under quiescent conditions, prompting agitation. However, conventional agitation precludes simultaneous high-resolution solution nuclear magnetic resonance (NMR) spectroscopy, limiting site-specific kinetic analysis of microscopic aggregation pathways. Here we present an integrated Rheo-NMR platform combining controlled shear flow, time-resolved NMR spectroscopy and mechanistic kinetic modeling to quantify site-specific amyloid-formation kinetics in a single, continuously monitored reaction. Applied to -synuclein under dilute and polyethylene glycol (PEG)-induced liquid-liquid phase separation (LLPS) conditions, the method revealed environment-dependent redistribution of kinetic signatures associated with primary nucleation-elongation and secondary nucleation-elongation pathways across the sequence. The platform distinguishes changes in overall aggregation rates from differences in residue-specific kinetic profiles, providing a quantitative framework for dissecting environment-dependent amyloid formation.

biochemistry↗

bioRxiv2026

Chromosome-level assembly of the Arabian killifish as a novel biomedical model species.

The Arabian killifish (Aphaniops dispar) is an excellent model for studying human diseases such as fungal infections and cancer progression. The embryos possess a transparent chorion for live imaging and display an extended period of independent feeding (13 days post-fertilisation). They also exhibit broad thermal tolerance which enables live imaging at physiologically relevant human temperatures. However, omics resources for this species remain limited and restricts its use in genomics studies. We generated a 1.45 GB high-quality reference assembly with 24 chromosome-level scaffolds and N50 score of 60.64 Mb by combining long-read, long-range, and short-read sequencing. The A. dispar genome exhibits a high level of homozygosity (95.6%) with BUSCO gene completeness scores of 99.2% and 97.5% for the Actinopterygii and Cyprinodontiformes lineages, respectively. The genome is highly repetitive (58.7%) and the majority of these are DNA transposons. The mitochondrial genome is 81.55% similar to that of Aphanius iberus (the Spanish toothcarp), with minor structural modifications. A. dispar exhibits highly conserved synteny with Fundulus heteroclitus within the Cyprinodontoidei clade. Together, these findings provide a valuable genomic resource for comparative genomics within the teleost community.

genomics↗

bioRxiv2026

Title: A de novo transcriptomic atlas of early embryo development in the Arabian killifish

The Arabian killifish (Aphaniops dispar) is new tractable vertebrate model system for developmental, ecological and biomedical research, including drug screening, pharmacological and infection biology studies. It is a relatively small euryhaline teleost with broad thermal tolerance and adaptability across a wide range of salinities from freshwater to hypersaline habitats. The embryos and early larvae are tolerant to environmental stressors and exhibit a delayed period of nutritional independence before hatching. This advantage offers an extended window for experimenting on the early developmental processes. Here, we describe time-course gene expression profiling of Arabian killifish embryos across nine developmental time points, from the 1-cell stage to the larval pre-hatching stage. Clustering of dynamic expression profiles for 27,564 Trinity genes revealed coordinated transcriptional modules corresponding to the maternal, blastula, maternal-to-zygotic transition (MZT)-related, gastrulation, organogenesis and larval maturation stages. The maternal stage displayed a highly distinct expression profile, dominated by maternal-specific transcripts that are rapidly degraded during the MZT. The later stages, from 48 hpf onward, revealed a shift from early regulatory mechanisms to the expression of organogenesis-related genes. The ZGA stage showed the conserved up-regulation of many zinc finger-associated genes, consistent with zebrafish and other teleost genomes. Overall, embryo development in A. dispar is slower than in zebrafish, with equivalent stages occurring several hours later. We propose a delayed onset of zygotic genome activation (ZGA) in the blastula stage, corresponding to 6 hpf in the Arabian killifish. Taken together, this study provides a transcriptomic resource for mining embryo development-related genes in the Arabian killifish.

genomics↗

bioRxiv2026

Globin digest and its constituent peptides promote skeletal muscle hypertrophy and enhance physical performance

Globin digest (GD), an acidic protease hydrolysate of hemoglobin, has been recognized for its anti-obesity and glucose-modulating effects; however, its direct anabolic potential in skeletal muscle remains uncharacterized. We evaluated the effects of GD and its constituent peptides on muscle hypertrophy and motor function using zebrafish, mice, and C2C12 myoblasts. Adult zebrafish administered GD (400 mg/kg BW/d) for 1 week showed significantly increased swimming distance (p < 0.05). Similarly, oral administration of GD (1 g/kg BW/d) to C57BL/6J mice for 4 weeks enhanced grip strength and rotarod performance, accompanied by a 1.5-fold increase in myofiber diameter and upregulation of fast-twitch Myh1 (1.9-fold) and Myh2 (1.8-fold) mRNA levels. In vitro, GD dose-dependently (1-100 g/mL) stimulated C2C12 differentiation and MyHC accumulation. Notably, GD did not merely serve as a nutritional nitrogen source; instead, it functioned as a signaling modulator via a specific "relay-like" peptide orchestration. Among six identified sequences, Peptides 3 (WTQR) and 5 (WGK) primarily initiated early-stage commitment by upregulating MyoD and Myf5, whereas Peptides 2 (VVYP) and 6 (FES) accelerated mid-stage maturation. This stage-specific synergy achieved robust myotube hypertrophy that exceeded the efficacy of individual components. These findings demonstrate that GD promotes skeletal muscle hypertrophy and motor function through direct myogenic signaling, establishing a novel foundation for precision sports nutrition to optimize muscle maintenance and physical performance. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/728339v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@94675borg.highwire.dtl.DTLVardef@10dbbfaorg.highwire.dtl.DTLVardef@b026eforg.highwire.dtl.DTLVardef@cc4058_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2026

Gut microbiome composition and predicted functions relate to growth and behavior in a Japanese preschool cohort

Early childhood is a period of rapid brain maturation and gut microbiome assembly, when emerging behavioral difficulties can shape later mental health and learning trajectories. Microbiota-gut-brain communication has been implicated in neurodevelopment through microbial metabolites and immune signaling. However, most pediatric evidence comes from high-risk or clinically referred cohorts, and gut microbiome-related correlates of typical behavioral variation in community-based preschool children remain poorly defined. In a cross-sectional sample of typically developing Japanese preschool children, here we show that behavioral variation within normative ranges is associated with distinct microbiome configurations: internalizing domains cluster with signatures consistent with higher inflammatory potential and elevated nucleotide biosynthesis, whereas somatic complaints and withdrawn behavior associate with reduced respiratory and fermentative activity. Sleep-related difficulties show the broadest predicted functional footprint, including enrichment of pathways related to methyl-donor and heme biosynthesis, while externalizing domains associate with pathways involved in cell-envelope and carbohydrate remodeling. In contrast, age, height, and weight track canonical maturation of gut microbiome composition, indicating that behavioral associations are not simple proxies of growth. Together, these findings extend early-life microbiome research by resolving domain-specific associations in a low-risk Asian community sample and highlighting pathway-level candidates that may interface with neurodevelopment.

microbiology↗

bioRxiv2026

A macrocyclic peptide-based fusion inhibitor targeting SARS-CoV-2 Spike S2 subunit

Continuous emergence of SARS-CoV-2 variants carrying mutations in Spike presents a significant challenge for durable antiviral agents. Here we screen for random 13-amino acid non-mimetic macrocyclic peptides that bind to Spike and identify PA-001 that inhibits SARS-CoV-2 infection with high potency at 0.23-2.9 nM as 50% inhibitory concentration (IC50). PA-001 bound to Spike S2 subunit and inhibited the membrane fusion during virus entry. Through drug-resistant selection, we revealed that PA-001 targeted the fusion peptide proximal region (FPPR) in S2, which has not been recognized as a drug target to date. Consistent with its highly conserved amino acid sequences beyond strains, PA-001 exhibited broad antiviral activity against all tested SARS-CoV-2 variants, in contrast to clinically-approved S1-targeting antibodies that lost activity to Omicron variants. PA-001 suppressed SARS-CoV-2 propagation and disease progression in mouse- and hamster-infection models, both by administration prophylactically and therapeutically. Combination therapy with remdesivir further enhanced antiviral profiles. In clinical phase-I trial, PA-001 was well-tolerated and showed high systemic exposure, with 4,300-10,300-fold concentration of IC50 as maximum plasma concentration by single administration to healthy volunteers. These evidence propose FPPR as an unexpected antiviral drug target accessible by macrocyclic peptides and identify PA-001 as a potent anti-SARS-CoV-2 fusion inhibitor.

microbiology↗

bioRxiv2026

Histo-anatomical atlas and thermal tolerance of Garra rufa: A novel small teleost model adaptable to human body temperature

Garra rufa, commonly known as the doctor fish, is a small freshwater cyprinid notable for its exceptional tolerance to high temperatures, surviving even at around the human body temperature of 37 {degrees}C, and has emerging potential as a novel laboratory model for human cancer xenotransplantation and infectious disease research. To establish a foundation for its experimental use, we conducted comprehensive anatomical and histological analyses across major organ systems. The overall body organization and tissue architecture of G. rufa are broadly similar to those of zebrafish (Danio rerio), indicating a conserved cyprinid body plan. However, several organ systems in G. rufa exhibited species-specific differences compared with zebrafish, including a well-developed adhesive disc around the oral region, a long and coiled intestine, and a distinct dark pigmentation of the peritoneum. These species-specific traits may reflect ecological and behavioral adaptations of G. rufa, including benthic scraping in warm, flowing habitats. Physiological assays confirmed that G. rufa maintains high survival rates and normal swimming activity at 37 {degrees}C, whereas zebrafish exhibit significant mortality and reduced locomotion under the same conditions. Collectively, this work provides a comprehensive histo-anatomical atlas of G. rufa, highlighting its unique morphological specializations while establishing an essential reference for the development of this species as a novel experimental fish model.

zoology↗

bioRxiv2026

Systems-level Investigation of the Anxiolytic Gut-Brain Interactions induced by Paraprobiotic Lactobacillus brevis SBC8803 in Zebrafish

Anxiety disorders are among the most prevalent mental health conditions worldwide, and interest in psychobiotics--live or inactivated microorganisms that beneficially modulate the microbiota-gut-brain axis--is increasing. Heat-killed Lactobacillus brevis SBC8803 enhances serotonin (5-hydroxytryptamine; 5-HT) signaling and ameliorates stress-related phenotypes in mammals, although the gut-brain pathways mediating these effects remain incompletely defined. Here, we investigated the anxiolytic effects and underlying molecular mechanisms of oral SBC8803 administration in adult zebrafish. Adult male AB-strain zebrafish were fed a diet containing heat-killed SBC8803 for 4 weeks, and anxiety-like behavior was evaluated using the novel tank test. SBC8803-treated fish exhibited a shorter latency to enter the upper half of the tank and more frequent transitions into the upper half, consistent with reduced anxiety-like behavior. To explore underlying mechanisms, we performed brain RNA sequencing and 16S rRNA gene sequencing of intestinal contents, followed by integrative multi-omics analyses. Brain transcriptomic profiling identified differentially expressed genes and enrichment of serotonin receptor, CREB, and oxytocin signaling pathways, suggesting enhanced monoaminergic and plasticity-related signaling. Microbiome functional prediction indicated SBC8803-associated shifts in lipid and vitamin metabolism, including pathways related to riboflavin (vitamin B2) and tryptophan. Gene set variation analysis combined with DIABLO-based data integration revealed coordinated changes between microbial metabolic and brain signaling pathways, consistent with a vitamin B-serotonin-anti-inflammatory axis linking gut metabolism to neural regulation. Furthermore, residual correlation analysis showed innate gut-brain coordination independent of SBC8803 effect, such as the coupling between brain arachidonic acid and gut histidine metabolism. These findings support the biological validity of SBC8803 administration-associated interactions observed in the multi-omics analyses. Collectively, these findings indicate that the paraprobiotic SBC8803 exerts anxiolytic-like effects in zebrafish and reshapes gut-brain network states at behavioral, microbial, and transcriptomic levels, providing a mechanistic framework for considering heat-killed SBC8803 as a candidate psychobiotic for anxiety-related conditions.

microbiology↗

bioRxiv2025

ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment

Short interspersed nuclear elements (SINEs) are abundant non-autonomous transposable elements derived from RNA polymerase III (POL III)-transcribed short non-coding RNAs. SINEs retain sequence features recognized by the POL III machinery and constitute a substantial portion of vertebrate genomes. Despite their impact on genome stability and evolution, the mechanisms governing SINE transcription remain poorly understood. Although DNA methylation and heterochromatin formation have been implicated in their repression, we find these pathways play only a minor role in mouse embryonic stem cells. Instead, we identify the ChAHP complex as a key repressor of SINE B2 elements. ChAHP directly inhibits POL III transcription by blocking TFIIIB recruitment without affecting TFIIIC binding. This selective interference prevents transcription initiation and highlights a distinct regulatory mechanism. Our findings establish ChAHP as a non-canonical repressor of POL III-dependent SINE transcription, offering new insights into the control of this pervasive class of non-coding genomic elements.

molecular biology↗

bioRxiv2025

Induced tolerance to UV stress drives survival heterogeneity in isogenic E. coli cell populations

The emergence of transiently tolerant bacterial subpopulations challenges our understanding of stress tolerance mechanisms. While much is known about antibiotic tolerance, it remains unclear whether similar mechanisms contribute to survival under ultraviolet (UV) stress. Here, we employed a modified Luria-Delbruck fluctuation test to investigate the presence of pre-existing UV-tolerant subpopulations in Escherichia coli. Our results showed no significant evidence of pre-stress UV tolerance. Instead, the data suggest that survival is primarily driven by inducible DNA repair responses activated after UV exposure. Furthermore, sequential low-dose UV exposures yielded higher-than-expected survival, suggesting that transient tolerance can be induced following initial UV exposure, likely through active DNA repair processes. These findings indicate that E. coli survives UV stress via an induced, rather than pre-existing, mechanism of tolerance.

microbiology↗

bioRxiv2025

Chromosome-level genome assembly of the doctor fish (Garra rufa)

Garra rufa, commonly known as doctor fish, is a small freshwater cyprinid fish recognized for its high-temperature tolerance. G. rufa is primarily known for its role in ichthyotherapy, in which it helps remove keratinized skin from human hands and feet. However, in recent years, its high-temperature tolerance has attracted attention owing to its potential use as a model for human disease research, including infectious diseases and cancer xenograft models. Despite this interest, the genomic basis underlying high-temperature tolerance remains largely unexplored, primarily because of the limited availability of genomic resources, which hinders its development as an experimental model. In the present study, a high-quality chromosome-level genome assembly of G. rufa was generated using a combination of PacBio HiFi long-read sequencing and Hi-C technology. We generated a chromosome-level genome assembly with 25 chromosomes, 1.38 Gb in total length, and scaffold N50 of 49.3 Mb. Approximately 59% of the genome comprises repetitive elements, with DNA and LTR elements being particularly abundant. In total, 27,352 protein-coding genes were annotated, of which 26,900 genes (98.3%) were functionally annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark for genome assembly and gene annotation demonstrated 94.5% and 94.7% of complete BUSCOs, respectively. We identified two heat shock transcription factor (HSF) and 239 heat shock protein (HSP)-related genes. Heat shock elements, which are HSF-binding motifs, were present within 3 kb upstream of 944 genes, with statistically significant enrichment of HSP-related genes in this set. Furthermore, molecular phylogenetic analysis and whole-genome comparisons revealed that G. rufa is evolutionarily closely related to species in the Labeoninae subfamily of the Cyprinidae family. This chromosome-level reference genome provides a valuable resource for future research aimed at elucidating the molecular mechanisms underlying high-temperature tolerance in G. rufa and establishing it as a model organism for human biomedical studies.

genomics↗

bioRxiv2024

Transcriptome Analysis Identified SPP1+ Monocytes as a Key in Extracellular Matrix Formation in Thrombi

Thrombi follow various natural courses. They are known to become harder over time and may persist long-term; some of them can also undergo early spontaneous dissolution and disappearance. Hindering thrombus stability may contribute to the treatment of thrombosis and the prevention of embolisms. However, the detailed mechanisms underlying thrombus maturation remain unknown. Using RNA sequencing, we revealed the transcriptional landscape of thrombi retrieved from the cerebral vessels and identified SPP1 as a hub gene related to extracellular matrix formation. Immunohistochemistry confirmed the expression of osteopontin in monocytes/macrophages in the thrombi, particularly in older thrombi. Single-cell RNA sequencing of thrombi from the pulmonary artery revealed increased communication between SPP1-high monocytes/macrophages and fibroblasts. These data suggest that SPP1-high monocytes/macrophages play a crucial role in extracellular matrix formation in thrombi and provide a basis for new antithrombotic therapies targeting thrombus maturation. TeaserSPP1+ monocytes play a key role in thrombus maturation, which can be a potential target for novel antithrombotic therapies.

molecular biology↗

bioRxiv2020

Erythropoietin production?by the kidney and the liver in response to severe hypoxia evaluated by Western blotting with deglycosylation

The detection of erythropoietin (Epo) protein by Western blotting has required pre-purification of the sample. We developed a new Western blot method to detect plasma and urinary Epo using deglycosylation. Epo in urine and tissue and erythropoiesis-stimulating agents (ESAs) in urine were directly detected by our Western blotting. Plasma Epo and ESAs were detected by our Western blotting after deglycosylation. The broad bands of Epo and ESAs were shifted to 22 kDa by deglycosylation except PEG-bound epoetin {beta} pegol. The 22 kDa band from anemic patient urine was confirmed by Liquid Chromatography/Mass Spectrometry (LC/MS) to contain human Epo. Sever hypoxia (7% O2, 4 hr) caused a 400-fold increase in deglycosylated Epo expression in rat kidneys, which is consistent with the increases in both Epo gene expression and plasma Epo concentration. Immunohistochemistry showed Epo expression in nephrons but not in interstitial cells under control conditions, and hypoxia increased Epo expression in interstitial cells but not in tubules. These data show that intrinsic Epo and all ESAs can be detected by Western blot either directly in urine or after deglycosylation in blood, and that the kidney is the main and sole site of Epo production in control and severe hypoxia. Our method will completely change Epo doping and detection.

physiology↗

bioRxiv2019

A fully automated deep learning pipeline for high-throughput colony segmentation and classification

BackgroundAdenine auxotrophy is a commonly used non-selective genetic marker in yeast research. It allows investigators to easily visualize and quantify various genetic and epigenetic events by simply reading out colony color. However, manual counting of large numbers of colonies is extremely time-consuming, difficult to reproduce and possibly inaccurate.\n\nResultsUsing cutting-edge neural networks, we have developed a fully automated pipeline for colony segmentation and classification, which speeds up white/red colony quantification 100-fold over manual counting by an experienced researcher.\n\nConclusionsOur approach uses readily available training data and can be smoothly integrated into existing protocols, vastly speeding up screening assays and increasing the statistical power of experiments that employ adenine auxotrophy.

bioinformatics↗

bioRxiv2019

RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this Toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection

BackgroundThe function of Toll-like receptor 2 (TLR2) in host defense against pathogens, especially Mycobacterium tuberculosis (Mtb) is poorly understood. To investigate the role of TLR2 during mycobacterial infection, we analyzed the response of tlr2 zebrafish mutant larvae to infection with Mycobacterium marinum (Mm), a close relative to Mtb, as a model for tuberculosis. We measured infection burdens and transcriptome responses using RNA deep sequencing in mutant and control larvae.\n\nResultstlr2 mutant embryos at 2 dpf do not show morphological alterations or differences in the number of macrophages and neutrophils when compared to control embryos. However, we found substantial changes in gene expression in these mutants, particularly in developmental and metabolic pathways, when compared with the heterozygote tlr2+/- control. After Mm infection, bacterial burden was six to ten fold higher in tlr2-/- larvae than in tlr2+/-, or tlr2+/+ larvae, indicating that Tlr2 acts as a protective factor in zebrafish host defense. RNAseq analysis of infected tlr2-/- versus tlr2+/- shows that the number of up-regulated and down-regulated genes in response to infection was greatly diminished in tlr2 mutants by at least 2 fold and 10 fold, respectively. Analysis of the transcriptome data and qPCR validation shows that Mm infection of tlr2 mutants leads to decreased mRNA levels of genes involved in inflammation and immune responses, including il1b, tnfb, cxcl11aa/ac, fosl1a, and cebpb. Furthermore, RNAseq analyses revealed that the expression of genes for Maf family transcription factors, vitamin D receptors, and Dicps proteins is significantly altered in tlr2 mutants with or without infection. In addition, the data indicate a function of Tlr2 in the control of induction of cytokines and chemokines, such as the CXCR3-CXCL11 signaling axis.\n\nConclusionThe transcriptome and infection burden analyses give support for a function of TLR2 in host defense against mycobacteria. Transcriptome analysis revealed tlr2-specific pathways involved in Mm infection, which are related to responses to Mtb infection in human macrophages. Considering its dominant function in control of transcriptional processes that govern defense responses and metabolism, the TLR2 protein can be expected to be also of importance for other infectious diseases and interactions with the microbiome.

immunology↗

bioRxiv2019

Long read sequencing reveals a novel class of structural aberrations in cancers: identification and characterization of cancerous local amplifications

Here we report identification of a new class of local structural aberrations in lung cancers. The whole-genome sequencing of cell lines using a long read sequencer, PromethION, demonstrated that typical cancerous mutations, such as point mutations, large deletions and gene fusions can be detected also on this platform. Unexpectedly, we revealed unique structural aberrations consisting of complex combinations of local duplications, inversions and micro deletions. We further analyzed and found that these mutations also occur in vivo, even in key cancer-related genes. These mutations may elucidate the molecular etiology of patients for whom causative cancerous events and therapeutic strategies remain elusive.

genomics↗

bioRxiv2018

Harmonization of resting-state functional MRI data across multiple imaging sites via the separation of site differences into sampling bias and measurement bias

When collecting large neuroimaging data associated with psychiatric disorders, images must be acquired from multiple sites because of the limited capacity of a single site. However, site differences represent the greatest barrier when acquiring multi-site neuroimaging data. We utilized a traveling-subject dataset in conjunction with a multi-site, multi-disorder dataset to demonstrate that site differences are composed of biological sampling bias and engineering measurement bias. Effects on resting-state functional MRI connectivity because of both bias types were greater than or equal to those because of psychiatric disorders. Furthermore, our findings indicated that each site can sample only from among a subpopulation of participants. This result suggests that it is essential to collect large neuroimaging data from as many sites as possible to appropriately estimate the distribution of the grand population. Finally, we developed a novel harmonization method that removed only the measurement bias by using traveling-subject dataset and achieved the reduction of the measurement bias by 29% and the improvement of the signal to noise ratios by 40%.

neuroscience↗