Biology subjects

Okazaki, S.

Publications and source records attributed to Okazaki, S..

5 recordsLinked to original sources

bioRxiv2025

The Freshwater Sounds Archive

Freshwater ecosystems are full of underwater sounds produced by amphibians, aquatic arthropods, reptiles, plants, fishes, and methane bubbles escaping from the sediment. Although much headway has been made in recent years investigating the overall soundscapes of various freshwater ecosystems around the world, there remains a significant knowledge gap in our collective inability to accurately and reliably link recorded sounds with the species that produced them. Here, we present The Freshwater Sounds Archive, a new global initiative, which seeks to address this knowledge gap by collating species-specific freshwater sound recordings into a publicly available database. By means of metadata collection, we also present a snapshot of the species studied, the recording equipment, and recording parameters used by freshwater ecoacousticians globally. In total, 61 entries were submitted to the archive between the 4th of March 2023 and the 30th of April 2025, representing 16 countries and 6 continents. The most numerous taxonomic group was arthropods (29 entries), followed by fishes (14 entries), amphibians (10 entries), macrophytes (7 entries), and a freshwater mollusk (1 entry). The majority of the submissions were from European countries (27 entries), of which the United Kingdom was the most represented with 14 entries. The next most represented region was North America (11 entries), followed by South America (8 entries), Oceania and Asia (5 entries each), Africa (3 entries), and the Middle East and Central America with 1 entry each. The global south, polar regions, and areas with an elevation >500 m (asl) were underrepresented. The field of freshwater ecoacoustics to date has largely focused on the analysis of sound types due to a current lack of knowledge of species-specific sounds. The Freshwater Sounds Archive presents an opportunity to move beyond the sound type approach, and towards an approach with higher taxonomic resolution, ultimately resulting in species-specific descriptions. Furthermore, The Freshwater Sounds Archive will provide freshwater ecoacousticians with one of the main tools required to start creating annotated training datasets for machine learning models from soundscape recordings by referring to known species sounds present in the archive. In the long-term, this will result in the automatic detection and classification of species-specific freshwater sounds from soundscape recordings, such as indicator, invasive, and endangered species.

ecology↗

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↗

bioRxiv2022

Apoplast-localized β-Glucosidase Elevates Isoflavone Accumulation in the Soybean Rhizosphere

Plant specialized metabolites (PSMs) are often stored as glycosides within cells and released from the roots with some chemical modifications. While isoflavones are known to function as symbiotic signals with rhizobia and to modulate the soybean rhizosphere microbiome, the underlying mechanisms of root-to-soil delivery are poorly understood. In addition to transporter-mediated secretion, the hydrolysis of isoflavone glycosides in the apoplast by an isoflavone conjugate-hydrolyzing {beta}-glucosidase (ICHG) has been proposed but not yet verified. To clarify the role of ICHG in isoflavone supply to the rhizosphere, we have isolated two independent mutants defective in ICHG activity from a soybean high-density mutant library. In the ichg mutants, the isoflavone contents and composition in the root apoplast and root exudate significantly changed. When grown in a field, the lack of ICHG activity considerably reduced isoflavone aglycone contents in roots and the rhizosphere soil, although the transcriptomes showed no distinct differences between the ichg mutants and WTs. Despite the change in isoflavone contents and composition of the root and rhizosphere of the mutants, root and rhizosphere bacterial communities were not distinctive from those of the WTs. Root bacterial communities and nodulation capacities of the ichg mutants did not differ from the WTs under nitrogen-deficient conditions, either. Taken together, these results indicate that ICHG elevates the accumulation of isoflavones in the soybean rhizosphere but is not essential in isoflavone-mediated plant-microbe interactions.

plant biology↗

bioRxiv2022

RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex

The type III-E Cas7-11 effector nuclease forms a complex with a CRISPR RNA (crRNA) and the putative caspase-like protease Csx29, catalyzes crRNA-guided target RNA cleavage, and has been used for RNA targeting in eukaryotic cells. Here, we report cryo-electron microscopy structures of the Cas7-11-crRNA-Csx29 complex with and without target RNA, and demonstrate that target RNA binding induces a conformational change in Csx29 and results in the protease activation. Biochemical analysis confirmed that Cas7-11-bound Csx29 cleaves Csx30 in a target RNA-dependent manner. Reconstitution of the system in bacteria uncovered Csx30-dependent cellular toxicity regulated by Csx31, and that Csx29-mediated cleavage produces toxic Csx30 fragments, promoting cell death. We find that Csx30 can bind both Csx31 and the associated sigma factor RpoE, suggesting Csx30 can inhibit RpoE and modulate cellular stress response towards infection. Overall, the RNA-guided nuclease-protease activities of the Cas7-11-Csx29 effector complex facilitate protease-based programmed cell death.

molecular biology↗

bioRxiv2022

High-throughput platform for depolarization-induced Ca2+ release for skeletal muscle disease mutation validation and drug discovery

In skeletal muscle excitation-contraction (E-C) coupling, depolarization of the plasma membrane triggers Ca2+ release from the sarcoplasmic reticulum (SR), referred to as depolarization-induced Ca2+ release (DICR). DICR occurs via the type 1 ryanodine receptor (RyR1), which physically interacts with the dihydropyridine receptor Cav1.1 subunit in specific machinery formed with additional essential components including {beta}1a, Stac3 adaptor protein and junctophilins. Exome sequencing has accelerated the discovery of many novel mutations in genes encoding DICR machinery in various skeletal muscle diseases. However, functional validation is time-consuming because it must be performed in a skeletal muscle environment. In this study, we established a platform of the reconstituted DICR in HEK293 cells. The essential components were effectively transduced into HEK293 cells expressing RyR1 using baculovirus vectors, and Ca2+ release was quantitatively measured with R-CEPIA1er, a fluorescent ER Ca2+ indicator, without contaminant of extracellular Ca2+ influx. In these cells, [K+]-dependent Ca2+ release was triggered by chemical depolarization with the aid of inward rectifying potassium channel, indicating a successful reconstitution of DICR. Using the platform, we evaluated several Cav1.1 mutations that are implicated in malignant hyperthermia and myopathy. We also tested several RyR1 inhibitors; whereas dantrolene and Cpd1 inhibited DICR, procaine had no effect. Furthermore, twitch potentiators such as perchlorate and thiocyanate shifted the voltage dependence of DICR to more negative potentials without affecting Ca2+-induced Ca2+ release. These results well reproduced the findings with the muscle fibers and the cultured myotubes. Since the procedure is simple and reproducible, the reconstituted DICR platform will be highly useful for validation of mutations and drug discovery for skeletal muscle diseases. SummaryMutations in essential components for depolarization-induced Ca2+ release (DICR) are implicated into various skeletal muscle diseases. Murayama et al. establish a reconstituted DICR platform in nonmuscle cells for evaluation of disease-causing mutations and drug discovery.

physiology↗