Biology subjects

Ogasawara, M.

Publications and source records attributed to Ogasawara, M..

11 recordsLinked to original sources

bioRxiv2026

Acoustic detection of a rarely vocalising invasive mammal from sparse data

O_LIMonitoring and limiting the spread of invasive species on islands requires efficient detection and population estimation methods. However, elusive species can be difficult to monitor using traditional methods, making autonomous approaches such as camera trapping and acoustic monitoring increasingly valuable. C_LIO_LIOn the island of Okinawa, Japan, the small Indian mongoose ( Urva auropunctata) threatens many native species since its introduction in 1910. Listed among the worlds worst invasive species, effective monitoring of U. auropunctata in Okinawa is critical. The Okinawa Environmental Observation Network (OKEON) uses camera traps to detect U. auropunctata, but success depends on precise placement. Though OKEON also includes a high-resolution acoustic monitoring programme, no audio classification model currently exists for U. auropunctata. Developing such a model could improve substantially our capacity to detect and manage the species. C_LIO_LIUsing sparse U. auropunctata vocalisations collected from camera trap videos, we built a lightweight Convolutional Neural Network distilled from a more complex model for classifying contact calls and alarm calls of U. auropunctata. Our distilled model performed similarly to the full model at detecting vocalisations from training data, but was considerably faster. C_LIO_LIWe applied the distilled classifier to [~]486 hrs of audio collected over eight years from southern Okinawa, where we successfully detected U. auropunctata a handful of times in each year of recording. In spite of strong model performance on test data, our model did not transfer well to unseen data, perhaps owing to the rarity of U. auropunctata calls and consequent small training dataset size, limiting its utility for ecological monitoring. C_LIO_LIPractical implication. The use of sparse audio data from camera trap videos to train an acoustic classifier had limited utility to detect the rarely vocalising U. auropunctata from passive acoustic monitoring data. We provide several recommendations for enhancing classifier performance to provide robust actionable insights into the distribution and spread of U. auropunctata, and aid targeted conservation efforts for Okinawas threatened biodiversity. C_LI

ecology↗

bioRxiv2026

Structural basis for site-specific histone H3 acetylation-dependent regulation of RNAPII transcription through nucleosomes

Acetylation of histone H3 regulates chromatin dynamics and transcription, but how specific acetylation sites affect RNA polymerase II (RNAPII) transcription through nucleosomes remains unclear. Here, we found that H3 acetylation at Lys56 and Lys122 markedly enhances RNAPII transcription through nucleosomes, whereas acetylation at Lys64 has little effect. To elucidate the structural basis for these functional differences, we determined cryo-electron microscopy (cryo-EM) structures of nucleosomes bearing site-specific acetylation at H3K56, H3K64, or H3K122. The cryo-EM structures revealed that H3K56ac and H3K122ac locally weaken histone-DNA interactions at the DNA entry/exit region and near the dyad, respectively, while H3K64ac induces no detectable structural changes. These structural differences correlate with the observed transcriptional outcomes, indicating that acetylation at H3K56 and H3K122, but not H3K64, alleviates the nucleosomal barrier to RNAPII progression. Our findings provide direct structural evidence that specific acetylations within the histone fold domain of H3 finetune nucleosome dynamics to facilitate RNAPII transcription.

molecular biology↗

bioRxiv2026

Establishing genetically controlled, closed 1 colonies of an ascidian

Recent technological advances have made many "non-model" organisms accessible for experimental studies. However, reference inbred strains were not necessarily available, especially in marine invertebrates, and genetic background of organisms used for experiments are often non-uniform. This situation potentially affects experimental reproducibility. Although ascidians, Ciona intestinalis (type A, or C. robusta), are a widely used marine animal for many areas of experimental biology including developmental studies, no reference strains have been obtained despite extensive efforts. As an alternative way to improve reproducibility, we have established and maintained ascidian colonies through intra-population breeding every year from 2016 to 2020, and monitored genomic variants of these colonies. This method does not reduce genetic variations but instead manages and monitors genetic variations in the colonies, providing an easy and cost-effective way of increasing experimental reproducibility. Furthermore, we recently upgraded these genetically isolated, closed colonies that were re-established every year, and have maintained them for more than three years only through intra-population breeding and occasional back-cross using cryopreserved sperm. Genetic variants that we revealed using 3.7 tera-bases of sequence data will help to design future experiments in this species. Our data also show that two wild-populations, which were used to establish the colonies, have maintained distinct genetic backgrounds, although their habitats are directly linked to the Pacific Ocean and only 170 km apart. More importantly, genetic information regarding these colonies will undoubtedly improve experimental reproducibility and traceability, and our method will provide a realistic solution for performing reproducible experiments using non-model organisms.

developmental biology↗

bioRxiv2025

Structural basis of asymmetric transcription through a composite nucleosome formed by a hexasome and an octasome

The overlapping dinucleosome (OLDN), a composite chromatin particle consisting of a hexasome and a canonical octasome, forms immediately downstream of transcription start sites, likely through chromatin remodeling activity, and has been proposed to act as a transient regulatory intermediate during transcription. However, how RNA polymerase II (RNAPII) engages with and transcribes through this unusual structure remains unclear. Here, we reconstituted OLDNs in vitro and performed transcription assays with RNAPII. We found that transcription efficiency was markedly higher when RNAPII initiated from the hexasome side than from the octasome side. Cryo-electron microscopy further revealed that transcription from the hexasome side induced pronounced conformational rearrangements, in which RNAPII progression dramatically opened the hexasome-octasome interface. These results uncover the mechanism by which RNAPII senses the intrinsic transcriptional polarity of OLDNs and suggest that OLDNs function as dynamic, directionally sensitive regulators of transcription elongation.

molecular biology↗

bioRxiv2025

High-throughput phenomics of global ant biodiversity

The big data era in biology is underway, but the study of organismal form has been slow to capitalize on advances in imaging and computation. Modern imaging can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Within the open science initiative Antscan, we applied high-throughput synchrotron X-ray microtomography to capture phenotypes across a diverse and ecologically dominant insect group -- ants. We provide 2193 whole-body 3D ant datasets from 792 species to broadly cover the ant phylogeny with a global scope, also pairing phenomic data with genome sequencing projects. Scans acquired with standardized parameters facilitate automated analysis and free access to data can broaden the audience and incentivize methods development. Antscan presents a scalable approach to create libraries of diverse anatomies, heralding a new era of studies on the evolution, structure, and function of organismal phenotypes.

zoology↗

bioRxiv2025

Structural basis of RNA polymerase II transcription on the H3-H4 octasome

The H3-H4 octasome is a nucleosome-like particle in which two DNA gyres are wrapped around each H3-H4 tetramer disk, forming a clamshell-like configuration. In the present study, we performed in vitro RNAPII transcription assays with the H3-H4 octasome and found that RNAPII transcribed the H3-H4 octasome more efficiently than the nucleosome. RNAPII paused at only one position, superhelical location (SHL) -4 in the H3-H4 octasome, in contrast to pausing at the SHL(-5), SHL(-2), and SHL(-1) positions in the nucleosome. Cryo-electron microscopy analysis revealed that two H3-H4 tetramer disks are retained when the RNAPII paused at the SHL(-4) position of the H3-H4 octasome. However, when RNAPII reached the SHL(-0.5) position, five base pairs before the dyad position of the H3-H4 octasome, the proximal H3-H4 tetramer was disassembled but the distal H3-H4 tetramer still remained on the DNA. Therefore, RNAPII efficiently transcribes the H3-H4 octasome by stepwise H3-H4 tetramer disassembly.

molecular biology↗

bioRxiv2023

Retrospective Evaluation of the Eye Irritation Potential of Agrochemical Formulations

While multiple in vitro eye irritation methods have been developed and adopted as OECD health effects test guidelines, only one is considered a complete replacement for the in vivo rabbit eye test for classification and labelling for eye irritation hazard. Additionally, for most of the adopted methods there is a data gap on the applicability to predict the ocular irritation potential of agrochemical formulations. To overcome this data gap, a retrospective evaluation of 192 agrochemical formulations with in vivo (OECD TG 405) or in vitro (OECD TG 437, 439, or 492) data was conducted to determine if the in vitro methods could accurately assign United Nations Globally Harmonized System for Classification and Labelling of Chemicals (GHS) eye irritation hazard classifications. In addition, for each of the final formulations and their individual components, we also conducted an evaluation of the GHS concentration threshold (CT) approach. The results herein suggest that the four individual methods and GHS CT approach were highly predictive of formulations that would not require classification for eye irritation hazard. Given most agrochemical formulations fall into this category, methods that accurately identify not classified mixtures could significantly reduce the use of animals for this endpoint.

pharmacology and toxicology↗

bioRxiv2023

Breakdown in seasonal dynamics of ant communities with land-cover change

Concerns about widespread human-induced declines in insect populations are mounting, yet little is known about how land-use change modifies the dynamics of insect communities, particularly in understudied biomes. Here, we examine how the seasonal patterns of ant activity--key drivers of terrestrial ecosystem functioning--vary with human-induced land cover change on a subtropical island landscape. Using trap captures sampled biweekly from a biodiversity monitoring network covering Okinawa Island, Japan, we processed 1.2 million individuals and reconstructed activity patterns within and across habitat types. Forest communities exhibited greater variability than those in more developed areas. Using time-series decomposition to deconstruct this pattern, we found that ant communities at sites with greater human development exhibited diminished seasonality, reduced synchrony, and higher stochasticity compared to those at sites with greater forest cover. Our results cannot be explained by variation in either regional or in situ temperature patterns, or by differences in species richness or composition among sites. We conclude that the breakdown of natural seasonal patterns of functionally key insect communities may comprise an important and underappreciated consequence of global environmental change that must be better understood across Earths biomes.

ecology↗

bioRxiv2022

Voltage-Sensing Phosphatase (VSP) Regulates Endocytosis-Dependent Nutrient Absorption in Chordate Enterocytes

Voltage-sensing phosphatase (VSP) is a unique membrane protein that translates membrane electrical activities into the changes of phosphoinositide profiles. VSP orthologs from various species have been intensively investigated toward their biophysical properties, primarily using a heterologous expression system. In contrast, the physiological role of VSP in native tissues remains largely unknown. Here we report that zebrafish VSP (Dr-VSP) is functionally expressed on the endomembranes of lysosome-rich enterocytes (LREs) that mediate dietary protein absorption via endocytosis in the zebrafish mid-intestine. Dr-VSP-deficient LREs were remarkably defective in forming endosomal vacuoles after initial uptake of dextran and mCherry. Dr-VSP-deficient zebrafish exhibited growth restriction and higher mortality during the critical period when zebrafish larvae rely primarily on exogenous feeding via intestinal absorption. Furthermore, our comparative study on marine invertebrate Ciona intestinalis VSP (Ci-VSP) revealed co-expression with endocytosis-associated genes in absorptive epithelial cells of the Ciona digestive tract, corresponding to zebrafish LREs. These findings signify a crucial role of VSP in regulating endocytosis-dependent nutrient absorption in specialized enterocytes across animal species. Summary statementVoltage-sensing phosphatase (VSP) is identified in absorptive enterocytes, revealing its crucial role in promoting endocytosis and nutrient absorption during early development.

cell biology↗

bioRxiv2021

A stepwise route to domesticate rice by controlling seed shattering and panicle shape

Asian rice (Oryza sativa L.) is consumed by more than half of the worlds population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (O. rufipogon Griff.) acquired non-seed-shattering behaviour, allowing humans to increase grain yield. Previous studies argued that the sh4 mutation triggered a reduction in seed shattering during rice domestication; but our experiments using wild introgression lines of O. rufipogon show that the domesticated sh4 allele alone is insufficient for shattering loss. Here, we identified the interaction between three key mutations associated with the interruption of abscission layer formation and panicle architecture that were causal in early rice domestication. An interruption of abscission layer formation requires both sh4 and qSH3 mutations, presenting an apparent barrier to the selection of shattering loss. We identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we demonstrated that seed shattering alone did not significantly impact yield; rather yield increases were observed with closed panicle formation controlled by SPR3, which is further augmented by the integration of sh4 and qSH3 alleles. Complementary manipulation of seed shattering and panicle shape result in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which led to the loss of shattering. Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as those in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 alone is insufficient and other genes, such as qSH3, are required to cause abscission layer disruption. The evolution of non-seed-shattering therefore required multiple mutations. Furthermore, shattering loss in genetic backgrounds of wild rice does not correspondingly increase yields. We have identified an interaction in which a second trait, closed panicle formation controlled by SPR3, that both increases the yield and facilitates recruitment of sh4 and qSH3, which synergistically augment yield, leading to a stepwise model for rice domestication.

plant biology↗

bioRxiv2021

CatSper mediates the chemotactic behavior and motility of the ascidian sperm

Sperm motility, including chemotactic behavior, is regulated by changes in the intracellular Ca2+ concentration. The cation channel of sperm (CatSper), plays an important role in the regulation of intracellular Ca2+ concentration. In mammals, CatSper is the only Ca2+ channel that functions in the sperm, and the mice that lack the genes for the subunits of CatSper, which make up the pore region of the Ca2+ channel, are infertile due to the inhibition of hyperactivation of the sperm. CatSper is also thought to be involved in chemotaxis in sea urchins. In contrast, in the ascidian, Ciona intestinalis, the sperm-activating and -attracting factor (SAAF) interacts with Ca2+/ATPase, which is a Ca2+-pump. Although the existence of CatSper genes has been reported, it is not clear whether CatSper is the specific Ca2+ channel that functions in the ascidian sperm. Therefore, in this study, we generated Catsper3 knockout (KO) animals that found that they were significantly less motile, with few motile sperms not exhibiting any chemotactic behavior. These results suggest that CatSper plays important roles in the spermatogenesis and basic motility mechanisms of sperms in both ascidians and mammals.

developmental biology↗