Biology subjects

Yamaguchi, A.

Publications and source records attributed to Yamaguchi, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Early origin of sugar sensing in jawed vertebrates

Sweet taste guides animals to consume carbohydrate-rich foods, and many different vertebrate groups, from fish to mammals, rely on sugar-rich fruits or nectar produced by flowering plants (angiosperms). Although the genes encoding T1R2-T1R3, the receptor pair that mammals use to sense sugars, exist in the genomes of many vertebrates, their functions are unclear--and whether sugar sensing arose once early in vertebrate evolution or independently in different lineages after angiosperms evolved is currently unknown. Here, we combined ancestral reconstruction and receptor functional profiling to examine the evolutionary history of T1R taste receptors--including recently-described non-canonical receptors--across all major vertebrate clades. Our results pinpoint the origin of sugar sensing to before the emergence of angiosperms and uncover a myriad of alternative T1R-based sugar-sensing mechanisms, suggesting multiple independent T1R trajectories and revealing uncharted sensory diversity across vertebrates.

evolutionary biology↗

bioRxiv2026

Acquisition of Stickland-metabolizing bacteria during infancy prevents Clostridium botulinum infection

Infant botulism is caused by intestinal colonization with Clostridium botulinum, whereas healthy adults are resistant. Although the gut microbiota has long been implicated in protection against C. botulinum, its bacterial basis has remained unknown. Here, we show that specific amino acid-metabolizing bacteria confer resistance to C. botulinum colonization through nutrient competition. Longitudinally collected human infant microbiotas exhibited a transition from susceptibility to resistance after transplantation into germ-free mice. 5-Aminovalerate marked the resistant microbiota, implicating Stickland metabolism. Resistant microbiotas were enriched in Stickland-metabolizing Clostridia, including Clostridioides difficile. Metabolomics revealed overlapping amino acid utilization, and C. difficile suppressed C. botulinum expansion through amino acid competition. These findings demonstrate that acquisition of Stickland-metabolizing Clostridia during infancy prevents C. botulinum infection through competition for shared amino-acid-dependent nutritional niches.

microbiology↗

bioRxiv2026

An Antibiotic-Treated Mouse Model Reveals the Progression of Intestinal Botulism

Intestinal botulism, including infant botulism and adult intestinal toxemia botulism, is a life-threatening disease caused by intestinal infection with Clostridium botulinum (Cb) spores. Infants are particularly susceptible to Cb infection because of their immature gut microbiota, whereas healthy adults are generally protected by gut microbiota-mediated colonization resistance. Thus, immature gut microbiota or gut dysbiosis is thought to permit Cb colonization. However, the mechanisms underlying colonization resistance and disease progression remain poorly characterized. Here, using adult mice with antibiotic-induced dysbiosis, we established a model for studying Cb infection and characterized intestinal colonization, bacterial expansion, BoNT accumulation, and disease progression during intestinal botulism. Intestinal botulism developed in antibiotic-treated mice after intragastric administration of strain 62A spores, whereas untreated adult mice showed no symptoms. In antibiotic-treated mice, Cb expanded over time in fecal samples, followed by accumulation of BoNT/A, which correlated with the progression of botulism symptoms. Cb growth and BoNT/A accumulation occurred mainly in the cecum and colon, but not in the small intestine. Furthermore, this mouse model was applicable to the analysis of intestinal botulism caused by other Cb strains, including 7I03-H, Okra, and Osaka05. Taken together, this mouse model provides a useful platform for elucidating the pathogenesis of intestinal botulism and developing novel therapeutic strategies.

microbiology↗

bioRxiv2026

Identification of loop regions as motifs determining cellular and organ chirality in Myosin 1C

Left-right (LR) asymmetry occurs throughout the animal kingdom, from microscopic to macroscopic scales; however, how microscale LR asymmetry (chirality) is integrated into higher-order structural LR asymmetry remains unclear. In Drosophila, the actin motor proteins Myosin1D and Myosin1C impose opposite chirality states on cell shape and intracellular F-actin flow, thereby directing dextral and sinistral morphogenesis, respectively. However, the protein motifs that confer their distinct activities in specifying chiral states have remained unknown. Here, we show that loop motifs within the myosin head domain that form actin-binding sites determine enantiomeric chirality. By swapping these loop motifs between Myosin1D and Myosin1C, we demonstrate that Myosin1D acquires sinistral activity when carrying Myosin1C loops. AlphaFold3 and molecular dynamics analyses reveal differences in loop structure and actin-binding energetics that may account for the contrasting chiral activities of Myosin1D and Myosin1C. Our findings identify specific protein motifs that dictate the handedness of actin flow and organ asymmetry, providing a mechanistic link between molecular interactions and macroscopic left-right patterning.

cell biology↗

bioRxiv2026

The association of extracellular vesicle (EV)-cargo miR-330-3p with postoperative delirium and a potential mechanism of tau phosphorylation and neuron toxicity

BackgroundPostoperative delirium (POD) is a frequent and severe neurocognitive complication following cardiac surgery, associated with poor long-term outcomes. The underlying mechanisms are unclear, and objective biomarkers are urgently needed. MethodsWe used pre- and post-operative plasma samples from 59 patients undergoing cardiac surgery in three separate studies with rigorous delirium assessment using the Confusion Assessment Method in a case-control design. Small extracellular vesicles (sEVs) were isolated from plasma, and their miRNA cargo was profiled using RNA sequencing. Target miRNAs were validated by qRT-PCR, and digital PCR (dPCR). The functional impact of the lead candidate miRNA was investigated in vitro by assessing tau phosphorylation and cell viability in HT22 neuronal cell line. ResultsThere were no differences in sEV morphology or numbers between patients with and without POD. While three candidate miRNAs were initially validated by qRT-PCR, subsequent dPCR analysis confirmed that only the perioperative change in plasma sEV-cargo miR-330-3p expression was significantly greater in patients who developed POD (n = 20) compared with those who did not (n = 20) (5.22 copies/L plasma; 95% Confidence Interval (CI), 1.187 to 9.256; p = 0.0139). Receiver operating characteristic curve analysis for this change yielded an area under the curve of 0.745 (95% CI, 0.589 to 0.901). In vitro overexpression of miR-330-3p in a neuronal cell line significantly increased the phosphorylation of tau at Ser199 (p < 0.0001) and Ser396 (p < 0.001) and reduced cell viability (p < 0.001). ConclusionsOur findings suggest that sEV-bound miR-330-3p increases in patients with POD after cardiac surgery. In vitro results suggest a potential pathogenic role for miR-330-3p, linking a systemic signal to tau-related neuronal injury. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study identifies a specific perioperative increase in small extracellular vesicle (sEV)-cargo miR-330-3p in patients with postoperative delirium (POD) following cardiac surgery. C_LIO_LIWe provide the first evidence that miR-330-3p directly induces tau hyperphosphorylation and reduces neuronal viability in vitro, establishing a potential mechanistic link between systemic sEV signaling and neurodegeneration. C_LI What Are the Clinical Implications?O_LIThe measurement of perioperative change in miR-330-3p could serve as an objective biological marker to assist in the early identification and risk stratification of patients at high risk for POD. C_LIO_LIThe identified miR-330-3p/tau pathway represents a potential new therapeutic target; future interventions aimed at inhibiting this specific miRNA might help prevent or mitigate POD-related neuronal injury. C_LIO_LIThese findings emphasize the importance of monitoring dynamic sEV-cargo changes to better understand and manage perioperative neurocognitive disorders. C_LI

molecular biology↗

bioRxiv2026

Modeling the pathological brain-gut axis in Parkinson's disease using human iPSC derived brain-intestinal assembloids

Parkinson disease is increasingly recognized as a systemic disorder involving pathological communication along the brain-gut axis, yet the cellular mechanisms underlying inter-organ -synuclein propagation remain poorly defined. Here, we establish a human induced pluripotent stem cell-derived brain-intestinal assembloid that integrates a developmentally specified medullary hindbrain organoid with an enteric neuron-enriched intestinal organoid. Using this model, we show the propagation of -synuclein from brainstem neurons to enteric neurons. Ligand-receptor analysis combined with genetic perturbation identifies NRXN1-NLGN2 signaling as a key mediator of brain-to-gut -synuclein propagation, with NRXN1 being upregulated in Parkinsons disease patient datasets in vivo. Together, these findings establish a human stem cell-based platform for investigating brain-gut communication and uncover molecular mechanisms underlying -synuclein propagation in Parkinsons disease.

neuroscience↗

bioRxiv2026

Tonically active interneurons gate motor output in Drosophila larvae

Tonic inhibition and its transient removal are fundamental neural mechanisms for gating activity, suppressing out-of-phase excitation, and enhancing the temporal precision of behavior. However, their roles within locomotor central pattern generators (CPGs) remain poorly understood. Here, we identify A02l neurons--segmentally repeated excitatory interneurons in the Drosophila larval ventral nerve cord (VNC)--that regulate crawling behavior through tonic inhibition. A02l neurons exhibit high baseline activity and are transiently suppressed during motor output. They provide excitatory input to inhibitory premotor networks, enabling widespread silencing of motor neurons to maintain muscle relaxation. Optogenetic activation of A02l neurons reduced crawling frequency, whereas their inhibition induced transient whole-body contractions. Together, these findings reveal a cellular-resolution mechanism for tonic inhibition within the nerve cord and highlight its importance in gating motor output and maintaining motor quiescence.

neuroscience↗

bioRxiv2025

Molecular Characterization of Parabrachial Neurons in Xenopus laevis and Silurana tropicalis: Evolutionary Conservation and Sex-Specific Differences

Clawed frogs communicate acoustically to coordinate reproduction, with males producing species-specific advertisement calls to attract females. In Xenopus laevis, males generate fast trills composed of clicks repeated at 60 Hz, a feature absent in both Silurana tropicalis males and X. laevis females, whose calls consist of slower click rates (30 Hz and 7 Hz, respectively). In male X. laevis, fast trills are generated by premotor neurons in the parabrachial nucleus (PBN), known as Fast Trill Neurons (FTNs). We hypothesized that FTNs are unique in male X. laevis, and either absent or molecularly distinct in clawed frogs that do not produce fast trills. To test this, we used constellation pharmacology to profile receptor expression of neurons via intracellular Ca{superscript 2} responses to pharmacological agents in PBN neurons from male X. laevis, male S. tropicalis, and female X. laevis. Surprisingly, we found putative FTNs in all three groups, including those that do not produce fast trills. Furthermore, a similar proportion of FTNs across groups expressed fast-kinetic voltage-gated potassium channels known to support rapid firing, indicating that the presence of these channels does not correlate with the ability to produce fast trills. Instead, some of these channels were more prevalent in males of both species compared to female X. laevis, suggesting a potential sex-specific, non-vocal function. The discovery of FTNs with similar molecular profiles in non-fast-trilling individuals suggests that these neurons are conserved across species and sexes, and may serve other functions. In male X. laevis, FTNs may have been repurposed for fast trill production during speciation. These findings provide new insight into understanding how neural circuits evolve and diversify across species and sexes. Summary statementPremotor vocal neurons share molecular profiles across clawed frogs, despite differences in calls, revealing unexpected conservation and functional divergence of homologous neurons underlying evolution of vocal behavior.

neuroscience↗

bioRxiv2025

Thermosensitivity of cellular translation restricts the growth of fission yeast at high temperatures

Living organisms have thermal limits above which they are unable to operate and survive. Our previous genetic screen identified proteins that impede the high-temperature growth of fission yeast, including the RNA-binding protein Dri1 and a fission yeast-specific protein termed Rhs1. Here, we show that Dri1 and Rhs1 form a complex and physically interact with the Ccr4-Not complex, a master regulator of mRNA metabolism. Gene expression analysis revealed that the Dri1-Rhs1 and Ccr4-Not complexes negatively regulate a set of genes implicated in ribosome biogenesis (Ribi genes). Loss of the Dri1-Rhs1 complex results in the augmented expression of Ribi genes, thereby suppressing the accumulation of 80S monosomes and the growth inhibition under high-temperature conditions. The thermosensitivity of the translational processes may be a determinant of the upper limit of the growth temperature in fission yeast.

cell biology↗

bioRxiv2025

The microRNA regulatory landscape of skeletal muscle-derived extracellular vesicles

Skeletal muscle-derived extracellular vesicles (SkM-EVs) have recently been recognized as novel endocrine factors capable of facilitating inter-organ communication between skeletal muscle and distant organs. These vesicles transport various molecular cargoes, including microRNAs (miRNAs), which are essential regulators of post-transcriptional gene expression. In this study, we characterized the miRNA composition of SkM-EVs using small RNA sequencing and elucidated their putative biological roles via comprehensive bioinformatics analyses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the predicted miRNA targets revealed that SkM-EV miRNAs are involved in several key pathways, including the FoxO signaling pathway, the insulin signaling pathway, and cancer-related pathways. Our findings suggest that SkM-EV miRNAs may simultaneously promote muscle differentiation and exert protective effects against diabetes and cancer development. These findings provide new insights into the systemic regulatory roles of SkM-EVs and highlight their therapeutic potential for muscular, metabolic, and oncological disorders.

physiology↗

bioRxiv2025

Class I myosins direct circumferential F-actin flows to define cell chirality

Eukaryotic cells possess intrinsic chirality in their structure, motility, and intracellular dynamics, which are designated cell chirality. Cell chirality participates in the left-right asymmetric morphogenesis and tissue integrity. However, the mechanisms of cell chirality formation remain elusive. In Drosophila, two evolutionarily conserved myosin I genes, Myosin 1D (Myo1D) and Myosin 1C (Myo1C), respectively, dictate the dextral and sinistral chirality of the cells and body. Here, we reported that Myo1D and Myo1C respectively directed the clockwise and counterclockwise circumferential flow of F-actin in Drosophila macrophages. Both induced the corresponding circular cytoplasm flows and depended on Myosin2 (Myo2). In a modified in vitro motility assay using near-physiological actin concentrations, Myo1D triggered the self-organization of the F-actin ring (chiral F-actin ring) that rotated clockwise; conversely, Myo1C induced the random flow of F-actin. The chiral F-actin ring implied that the F-actin bundle was parallelly and annularly polarized concerning its barbed pointed end. Considering that Myo1D and Myo1C are localized to the dorsal plasma membrane of macrophages, Myo1D and Myo1C might organize the parallelly polarized F-actin in macrophages. Our results suggest that Myo2 might drive the clockwise circumferential flow of F-actin along its parallel and annular polarity induced by Myo1D, which may be a molecular basis of cell and organ chirality.

cell biology↗

bioRxiv2025

Low-salinity medium for large-scale biomass production of the marine purple photosynthetic bacterium Rhodovulum sulfidophilum

Marine purple non-sulfur bacteria such as Rhodovulum sulfidophilum are versatile due to their diverse applications in bioremediation, biotechnological production of useful materials, industrial production of value-added compounds, and agricultural fertilizers. Our previous study demonstrated the potential of its lysed and dried biomass as a nitrogen fertilizer for plant production. However, large-scale fertilizer production requires scaling up the culture to larger volumes, which is not cost-effective with currently available options for growth media. In this study, we tested a seawater-based, cost-effective alternative to the commonly used nutrient-rich culture medium for the growth of this bacterium. We found that reducing salinity from 3% to 1.2% had no adverse effects on its heterotrophic growth, dry cell yield, nitrogen content, and total amino acid composition. The nitrogen content and the weight percent of free lysine, aspartic acid, and glutamate increased in the biomass obtained from cultures grown at 1.2% salinity. Under autotrophic conditions, decreasing salinity to 1.2% did not affect cell growth, final dry cell yields, and total carbon assimilation, but N assimilation tended to be higher. Reducing salinity to 1.2% proved to be cost-effective and feasible for the cultivation of R. sulfidophilum without increasing the risk of contamination, providing a viable alternative for its large-scale cultivation and application as a plant nitrogen fertilizer.

microbiology↗

bioRxiv2024

CRASH2p: Closed-loop Two Photon Imaging in Freely Moving Animals

Direct measurement of neural activity in freely moving animals is essential for understanding how the brain controls and represents behaviors. Genetically encoded calcium indicators report neural activity as changes in fluorescence intensity, but brain motion confounds quantitative measurement of fluorescence. Translation, rotation, and deformation of the brain and the movements of intervening scattering or auto-fluorescent tissue all alter the amount of fluorescent light captured by a microscope. Compared to single-photon approaches, two photon microscopy is less sensitive to scattering and off-target fluorescence, but more sensitive to motion, and two photon imaging has always required anchoring the microscope to the brain. We developed a closed-loop resonant axial-scanning high-speed two photon (CRASH2p) microscope for real-time 3D motion correction in unrestrained animals, without implantation of reference markers. We complemented CRASH2p with a novel scanning strategy and a multi-stage registration pipeline. We performed volumetric ratiometrically corrected functional imaging in the CNS of freely moving Drosophila larvae and discovered previously unknown neural correlates of behavior.

neuroscience↗

bioRxiv2024

Adeno-Associated Viral Tools to Trace Neural Development and Connectivity Across Amphibians

The development, evolution, and function of the vertebrate central nervous system (CNS) can be best studied using diverse model organisms. Amphibians, with their unique phylogenetic position at the transition between aquatic and terrestrial lifestyles, are valuable for understanding the origin and evolution of the tetrapod brain and spinal cord. Their metamorphic developmental transitions and unique regenerative abilities also facilitate the discovery of mechanisms for neural circuit remodeling and replacement. The genetic toolkit for amphibians, however, remains limited, with only a few species having sequenced genomes and a small number of transgenic lines available. In mammals, recombinant adeno-associated viral vectors (AAVs) have become a powerful alternative to genome modification for visualizing and perturbing the nervous system. AAVs are DNA viruses that enable neuronal transduction in both developing and adult animals with low toxicity and spatial, temporal, and cell-type specificity. However, AAVs have never been shown to transduce amphibian cells efficiently. To bridge this gap, we established a simple, scalable, and robust strategy to screen AAV serotypes in three distantly-related amphibian species: the frogs Xenopus laevis and Pelophylax bedriagae, and the salamander Pleurodeles waltl, in both developing larval tadpoles and post-metamorphic animals. For each species, we successfully identified at least two AAV serotypes capable of infecting the CNS; however, no pan-amphibian serotype was identified, indicating rapid evolution of AAV tropism. In addition, we developed an AAV-based strategy that targets isochronic cohorts of developing neurons - a critical tool for parsing neural circuit assembly. Finally, to enable visualization and manipulation of neural circuits, we identified AAV variants for retrograde tracing of neuronal projections in adult animals. Our findings expand the toolkit for amphibians to include AAVs, establish a generalizable workflow for AAV screening in non-canonical research organisms, generate testable hypotheses for the evolution of AAV tropism, and lay the foundation for modern cross-species comparisons of vertebrate CNS development, function, and evolution.

neuroscience↗

bioRxiv2023

Pulsed ultrasound promotes secretion of anti-inflammatory extracellular vesicles from skeletal myotubes via elevation of intracellular calcium level

The regulation of inflammatory responses is an important intervention in biological function and macrophages play an essential role during inflammation. Skeletal muscle is the largest organ in the human body and releases various factors which mediate anti-inflammatory/immune modulatory effects. Recently, the roles of extracellular vesicles (EVs) from a large variety of cells are reported. In particular, EVs released from skeletal muscle are attracting attention due to their therapeutic effects on dysfunctional organs and tissues. Also, ultrasound (US) promotes release of EVs from skeletal muscle. In this study, we investigated the output parameters and mechanisms of US-induced EV release enhancement and the potential of US-treated skeletal muscle-derived EVs in the regulation of inflammatory responses in macrophages. High-intensity US (3.0 W/cm2) irradiation increased EV secretion via elevating intracellular Ca2+ level without negative effects. Moreover, US-induced EVs suppressed expression levels of pro-inflammatory factors in macrophages. miRNA sequencing analysis revealed that miR-206-3p and miR-378a-3p were especially abundant in skeletal myotube-derived EVs. In this study we demonstrated that high-intensity US promotes the release of anti-inflammatory EVs from skeletal myotubes and exert anti-inflammatory effects on macrophages.

immunology↗

bioRxiv2023

Two conserved vocal central pattern generators broadly tuned for fast and slow rates generate species-specific vocalizations in Xenopus clawed frogs

Across phyla, species-specific vocalizations are used by males to attract females. Functional analyses of the neural circuitry underlying behavior have been difficult, particularly in vertebrates. However, using an ex vivo brain preparation that produces fictive vocalizations, we previously identified anatomically distinct fast and slow central pattern generators (CPGs) that drive the fast and slow clicks of male courtship calls in male African clawed frogs, Xenopus laevis. To gain insight into the evolution of neural circuits underlying courtship calls, we extended this approach to four additional species. Here, we show that although the exact rate and duration of the clicks are unique to each species, fast and slow CPGs identified in male X. laevis are conserved across species. Further, we show that the development of fast CPGs depends on testosterone in a species-specific manner: testosterone facilitates the development of fast CPGs in a species with a courtship call containing fast clicks, but not in a species with a courtship call made entirely of slow clicks. Finally, we showed that, unlike other vestigial neural circuits that remain latent, the fast CPGs are not inherited by all species; rather, they are possessed only by the species that produce fast clicks. The results suggest that species-specific calls of the genus Xenopus have evolved by utilizing conserved fast or slow CPGs that are broadly tuned to generate fast or slow trains of clicks, the development of which appear to be regulated by a strategic expression of testosterone receptors in the brain of each species.

neuroscience↗

bioRxiv2022

Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis

Kleptoplasts are distinct among photosynthetic organelles in eukaryotes (i.e, plastids) because they are routinely sequestered from prey algal cells and function only temporarily in the new host cell. Therefore, the hosts of kleptoplasts benefit from photosynthesis without constitutive photoendosymbiosis. Here, we report that the euglenozoan Rapaza viridis has only kleptoplasts derived from a specific strain of green alga, Tetraselmis sp., but no canonical plastids like those found in its sister group, the Euglenophyceae. R. viridis showed a dynamic change in the accumulation of cytosolic polysaccharides in response to light- dark cycles, and 13C isotopic labeling of ambient bicarbonate demonstrated that these polysaccharides originate in situ via photosynthesis; these data indicate that the kleptoplasts of R. viridis are functionally active. We also identified 247 sequences encoding putative plastid-targeting proteins and 35 sequences of presumed kleptoplast transporters in the transcriptome of R. viridis. These genes originated in a wide range of algae other than Tetraselmis sp., the source of the kleptoplasts, suggesting a long history of repeated horizontal gene transfer events from different algal prey cells. Many of the kleptoplast proteins, as well as the protein-targeting system, in R. viridis were shared with members of the Euglenophyceae, providing evidence that the early stages in the endosymbiotic origin of euglenophyte plastids also involved kleptoplasty.

evolutionary biology↗

bioRxiv2021

Homogeneity of antibody-drug conjugates critically impacts the therapeutic efficacy in brain tumors

Glioblastoma multiforme (GBM) is characterized by aggressive growth and the poorest prognosis of all brain tumor types. Most therapies rarely provide clinically meaningful improvements in outcomes of patients with GBM. Antibody-drug conjugates (ADCs) are emerging chemotherapeutics with stunning success in cancer management. Although promising, clinical studies of three ADCs for treating GBM, including Depatux-M, have been discontinued because of safety concerns and limited therapeutic benefits. Here, we report that ADC homogeneity is a critical parameter to maximize the therapeutic potential in GBM therapy. We demonstrate that homogeneous conjugates generated using our linker show enhanced drug delivery to intracranial brain tumors. Notably, compared to heterogeneous ADCs, including a Depatux-M analog, our ADCs provide greatly improved antitumor effects and survival benefits in orthotopic brain tumor models, including a patient-derived xenograft model of GBM. Our findings warrant the future development of homogeneous ADCs as promising molecular entities toward cures for intractable brain tumors.

bioengineering↗