Biology subjects

Okamura, H.

Publications and source records attributed to Okamura, H..

13 recordsLinked to original sources

bioRxiv2026

Long-term Population Dynamics and Conservation of Proboscis Monkeys (Nasalis larvatus) in the Lower Kinabatangan, Sabah, Malaysia

Long-term ecological monitoring is essential for evaluating the effectiveness of conservation actions for long-lived tropical primates, yet few studies have integrated repeated population censuses with habitat-change analyses. We evaluated long-term population and habitat dynamics of the endangered proboscis monkey (Nasalis larvatus) in the Lower Kinabatangan, Sabah, Malaysian Borneo, by integrating a landscape-wide population survey conducted in 2025 with previous surveys from 2005 and 2014, long-term monitoring at three representative sites, and spatial analyses of land-use and land-cover change. Standardized late-afternoon boat-based surveys covering approximately 223 km of the Kinabatangan River and its tributaries recorded an estimated 2,420 individuals in 174 social groups, representing an increase of approximately 66% and 72% respectively compared with the 2005 survey. Group sizes (number of individuals per social group) remained largely unchanged despite the overall increase in population size. Long-term monitoring at three representative sites indicated stable population trajectories throughout the study period. Habitat analyses further revealed an increase in natural vegetation and limited conversion of forest to oil palm within protected areas between 2005 and 2025. Together, these independent lines of evidence indicate that the Lower Kinabatangan proboscis monkey population has recovered while maintaining overall demographic stability under long-term habitat protection. Nevertheless, substantial areas of suitable habitat remain outside the protected-area network, highlighting opportunities for additional habitat restoration and improved landscape connectivity. Our findings demonstrate the value of integrating long-term ecological monitoring with landscape-scale habitat assessment to inform adaptive conservation management in fragmented tropical landscapes.

ecology↗

bioRxiv2026

The slow-acting G-protein Gz defines the duration of circadian rest time

Duration of nightly rest is a trait that varies between individuals, influenced by a complex interplay between multiple genetic and environmental factors. The central circadian clock that orchestrates daily rhythm in behavior/sleep resides in the suprachiasmatic nucleus (SCN). Yet, how the SCN encodes the "length" of the circadian rest phase ({rho}) remains an open question. Here we demonstrate that the unique G-protein-subtype Gz contributes to this process by sculpting the waveform of the circadian cAMP-PKA activity rhythm within the SCN. Genetic deletion and subsequent rescue of Gz expression reversibly altered the {rho} duration, shifting it from [~]10 h in Gz+/+ mice to [~]7.5 h in Gz-/-; mice, accompanied by proportional changes in peak cAMP-PKA activity duration and transcriptome remodeling in the SCN. Notably, intra-SCN cAMP activation led to behavioral rest, with Gz specifically shaping this response without affecting 24-h rhythmicity. These findings suggest that the SCN is not merely a rhythm-generator, but actively allocates the {rho}-rest period via Gz signaling.

neuroscience↗

bioRxiv2026

Robustness and management performance of MSY reference points derived from the hockey-stick stock-recruitment model under structural uncertainty

The hockey-stick (HS) stock recruitment relationship (SRR) has been widely used as an empirical alternative to conventional SRRs such as the Beverton-Holt (BH) and Ricker (RI) models. However, the management performance and risks associated with estimating maximum-sustainable-yield (MSY) reference points (RPs) based on HS remain insufficiently understood. This study first defines deterministic and stochastic MSY RPs under the HS model and provides an overview of their properties. We then conduct simulation experiments to investigate the bias and management consequences that arise when MSY RPs are estimated from the HS model (HS-derived MSY RPs) rather than from the true SRR (e.g., BH) across a range of biological and stochastic parameters, with particular focus on scenarios with insufficient data contrast. Our results show that HS-derived MSY RPs tend to exhibit higher bias but lower variance than MSY RPs derived from the true SRR. Management strategy evaluation simulations further reveal that management procedures combining HS-derived MSY RPs with adaptive model learning and some precautionary measures gradually reduce this bias and achieve average spawning biomass and yield that are comparable to those obtained under management based on the true BH SRR. We also show that the management effectiveness of the precautionary measures depends on life-history traits and recruitment variability. These findings indicate that although HS-derived MSY RPs may be biased and require cautious use, combining them with appropriate precautionary measures allows management to remain robust while limiting variability and yield losses. This broadens the range of management options that are available for supporting sustainable fisheries management.

ecology↗

bioRxiv2025

EC-isHCR: a rapid method for in situ hybridization chain reaction in diverse animal samples

The in situ hybridization chain reaction (isHCR) visualizes RNA across multiple spatial scales, from organs to subcellular structures, in diverse samples. We previously proposed a rapid protocol, EC-isHCR, for Drosophila embryos and ovaries. Whether EC-isHCR retains the features of conventional isHCR, including wide-spatial-scale analyses in various samples, however, has remained unclear. Here, we show that EC-isHCR enables robust RNA detection in a broad range of samples, such as whole-mount fruit fly, parasitoid wasp, and aphid preparations; paraffin sections of trout; frozen mouse sections; and human cultured cells. Moreover, EC-isHCR enabled detection of subcellular RNA localization. EC-isHCR also visualized co-localization of RNA with phase-separated condensates in fruit fly embryos and detected the protrusion-enriched mRNA in HeLa cells. To broaden the applicability of EC-isHCR, we developed an automated probe design tool (https://github.com/ShuntaYorimoto/hcrkit). By combining this tool with EC-isHCR, we provide a fast and versatile framework to visualize mRNAs. This framework will help reduce the barrier to using fast isHCR and thereby facilitate research across diverse areas of the life sciences. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/696653v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1852584org.highwire.dtl.DTLVardef@621682org.highwire.dtl.DTLVardef@1b3bf5corg.highwire.dtl.DTLVardef@1d86841_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- EC-isHCR enables rapid acquisition of high-contrast images. - EC-isHCR preserves features of conventional isHCR, including versatile sample compatibility and high-resolution imaging. - An automated probe design tool was developed for EC-isHCR. - EC-isHCR/probe tool framework will help reduce the barrier to using fast isHCR.

bioengineering↗

bioRxiv2025

Bent Hockey-Stick Stock-Recruitment Function

The hockey-stick is a simple and widely applicable stock-recruitment function. One drawback is its non-differentiability at the breakpoint, which can be especially problematic when using state-space models for stock assessment. Here, we develop a new bent hockey-stick model that retains the desirable properties of the original hockey-stick function while providing a differentiable breakpoint. We also propose a new algorithm for estimating MSY under multiplicative process stochasticity in the stock-recruitment relationship. Simulation studies demonstrate the utility of these approaches, which can substantially enhance the robustness and sustainability of fisheries management.

ecology↗

bioRxiv2023

Forecasting fish recruitment using machine learning methods: A case study of arabesque greenling

Fish recruitment prediction is a central topic in fisheries science. We use a machine learning method for predicting the recruitment of Arabesque greenling in Hokkaido, Japan. Biological, fisheries-related, and environmental factors were included in the predictive models as feature variables. A gradient boosting model (GBM) showed better predictive performance compared with a linear regression model (LRM) and a random forest model (RFM) in terms of relative bias and relative root mean square error for recruitment prediction in the last 5 years. The most influential feature for GBM was spawning stock biomass in the last year, followed by the fishing rate for older fish. The sea surface temperature (SST) was a very weak predictor in the GBM but was the most influential feature in the LRM. The difference among models suggests the importance of nonlinearity and variable interactions. Machine learning methods will greatly contribute to fish recruitment forecast and thereby sustainable fisheries management.

ecology↗

bioRxiv2022

Spatio-temporal model and machine learning method reveal process of phenological shift under climate change of North Pacific spiny dogfish

Climate change has disrupted natural phenological patterns, including migration. Despite extensive studies of phenological shifts in migration by climate change and driving factors of migration, a few issues remain unresolved. In particular, little is known about the complex effects of driving factors on migration with interactions and nonlinearity, and partitioning of the effects of factors into spatial, temporal, and spatio-temporal effects. The Pacific spiny dogfish Squalus suckleyi (hereafter "spiny dogfish") is a coastal elasmobranchii that migrates southward for parturition and northward for feeding in the western North Pacific. Here, to elucidate the migration patterns as well as the driving factors under climate change, we first examined long-term changes in the timing and geographic location of migration by applying a spatio-temporal model to ca. 5-decade time series data for the presence/absence of spiny dogfish in the western North Pacific. We then evaluated the spatial, temporal, and spatio-temporal effects of driving factors (sea surface temperature [SST], depth, productivity, and magnetic fields) on seasonal occurrence patterns using a machine learning model. We found that the migration area did not change over ca. 5 decades, whereas the migration timing advanced by a month after 2000. The spatial effects of magnetic fields and depth were consistently large and the spatial and spatio-temporal effects of SST increased in the migration season, even though temporal effect of SST was always weak. These results suggest that the migration area of spiny dogfish was stable over time because their spatial distribution was determined by geographic features, whereas the migration timing advanced by tracking a suitable SST location which increased steeply after 2000. Therefore, temperature as well as other factors influence migration simultaneously under climate change and underline the importance of paying attention biotic/abiotic factors including temperature and process-based understanding to predict future impacts of climate change on phenological shifts.

ecology↗

bioRxiv2021

Gpr19 is a circadian clock-controlled orphan GPCR with a role in modulating free-running period and light resetting capacity of the circadian clock

Background and PurposeGpr19 encodes an evolutionarily conserved orphan G-protein-coupled receptor (GPCR) with no established physiological function in vivo. The purpose of this study was to determine the role of Gpr19 in the circadian clock system. Experimental ApproachWe examined whether and how the master circadian clock neurons in the suprachiasmatic nucleus (SCN) express Gpr19. By analysing Gpr19-deficient (Gpr19-/-) mice, we asked whether Gpr19 has a role in modulating free-running period and light resetting capacity of the circadian clock. Key ResultsCompared with the known common core clock genes, Gpr19 was identified to show several distinct yet limited features related to the circadian clock. Gpr19 mRNA was mainly expressed in the middle-to-dorsal region of the SCN. A conserved cAMP-responsive element within the Gpr19 promoter drove the circadian expression of Gpr19. Gpr19-/- mice exhibited a prolonged circadian period and a delayed initiation of daily locomotor activity in a 12-h light/12-h dark cycle. Gpr19 deficiency caused the downregulation of several genes that normally peak during the night, including Bmal1 and Gpr176. Gpr19-/- mice had a reduced capacity for phase shift to early subjective night light. The defect was only observed for phase-delay, but not phase-advance, and accompanied by reduced response of c-Fos expression in the dorsal region of the SCN, while apparently normal in the ventral part of the SCN, in Gpr19-/- mice. Conclusion and ImplicationsGpr19 is an SCN-enriched orphan GPCR with a distinct role in circadian regulation and thus may be a potential target for alleviating circadian clock disorders. O_LIWhat is already known: Gpr19 is an evolutionarily conserved class-A orphan receptor with no established physiological role in vivo. The SCN is a light-entrainable master circadian pacemaker governing daily rhythms of behaviour and physiology. C_LIO_LIWhat this study adds: Gpr19 is an SCN-enriched orphan GPCR whose levels fluctuate in a circadian fashion. Gpr19 is a functional clock modulator involved in period determination and phase resetting. C_LIO_LIClinical significance: Targeting the orphan receptor Gpr19 may provide a therapeutic approach for alleviating circadian clock disorders. C_LI

neuroscience↗

bioRxiv2020

Evaluating a harvest control rule to improve the sustainability of Japanese fisheries

Fisheries management in Japan is currently at a turning point. MSY based reference points have historically been rejected because of impacts on the fishing industry that would result from their adoption. We propose and evaluate a new harvest control rule (HCR) that uses the biological reference points based on sustainable yield from the stochastic hockey-stick stock recruitment relationship. Management strategy evaluation simulations conditioned on data from Japanese stocks demonstrate that the new HCR avoided recruitment overfishing while providing stable and near maximum catch. The new HCR outperformed Japans traditional HCR in terms of conservation, and it outperformed an alternative HCR which is widely used around the world in terms of initial catch reduction and future catch variation. For forecasting and hindcasting simulations, the new HCR showed considerable improvements over traditional HCRs in terms of biomass and catch. This new management procedure can improve the current and future status of many overfished stocks in Japan as well as increase economic efficiency and better protect ecosystems.

ecology↗

bioRxiv2020

State-space Modeling Clarifies Productivity Regime Shifts of Japanese Flying Squid

Regime shifts of climatic and environmental conditions potentially affect productivity of fisheries resources, posing challenging issues to stock management. The stocks of the Japanese flying squid (Todarodes pacificus) are suspected to suffer from regime shifts, but their detection is difficult and possibly doubtful because the nature of short-lived species readily makes the effect of regime shifts confounded with observation errors. Here we developed a new state-space assessment model to evaluate the influence of regime shifts on spawner-recruitment relationship of the Japanese flying squid. The model simultaneously estimates the population dynamics of multiple stocks that could share some life history parameters, making parameter inference stable. We demonstrate that two-time regime shifts of productivity around 1991 and 2015 caused two-to three-fold changes of maximum sustinabile yields. The model with regime shifts clarifies the relationship between fishing pressure and spawner abudance that is difficult to detect in a model with no regime shift. The state-space approach will be a promising tool to accurately assess stock status by separating recruitment process from observation errors and contribute tothe management of marine biological resources sensitive to regime shifts.

ecology↗

bioRxiv2020

Spatio-temporal model reduces species misidentification bias of spawning eggs in stock assessment of spotted mackerel in the western North Pacific

Species identification based on morphological characteristics includes species misidentification, leading to estimation bias of population size. The eggs of spotted mackerel Scomber australicus and chub mackerel S. japonicus in the western North Pacific has been identified based on egg diameter. Recent density of spotted mackerel was considerably high despite its low stock biomass. A possibility of this phenomenon is due to overestimation because the difference in egg diameter has become ambiguous between two species. However, we cannot test this possibility using DNA analysis because the eggs are fixed with formalin. Here, we estimated the index of egg density of spotted mackerel using a spatio-temporal model that incorporates the effect of egg density of chub mackerel on the catchability of spotted mackerel, using 15 years data of spawning eggs. We then examined how retrospective biases in estimated stock abundance were reduced when using the index from the model. The index estimated from the model decreased temporal fluctuation and showed smooth patterns. Especially, the recent index was considerably revised down rather than the nominal index. Additionally, the retrospective bias decreased ca. half compared with the nominal index. Therefore, incorporating species misidentification bias should be an essential process for improving stock assessment.

ecology↗

bioRxiv2020

Estimating maximum sustainable yield of snow crab (Chionoecetes opilio) off Tohoku Japan via a state-space assessment model with time-varying natural mortality

Yield from fisheries is a tangible benefit of ecosystem services and sustaining or restoring a fish stock level to achieve a maximum sustainable yield (MSY). Snow crab (Chionoecetes opilio) off Tohoku has been managed by a total allowable catch since 1996, although their abundance has not increased even after 2011, when fishing pressure rapidly decreased because of the Great East Japan Earthquake. This implies that their biological characteristics, such as recruits, natural mortality coefficient (M), and terminal molting probabilities (p), might have changed. We developed "just another state-space stock assessment model (JASAM)" to estimate the MSY of the snow crab off Tohoku, Japan, considering interannual variations in M and p. The multi-model inference revealed that M increased from 0.2 in 1997 to 0.59 in 2018, although it was not different among the instars, sex, nor terminal molt of crabs. The parameter p also increased by 1.34-2.46 times depending on the instar growth stages from 1997 to 2018. We estimated the MSYs in three scenarios, which drastically changed if M and p were set as they were in the past or at the current values estimated from this study. This result indicated that the MSY of snow crab would also be time-varying based on their time-varying biological characteristics.

ecology↗

bioRxiv2019

The methyl cycle is a conserved regulator of biological clocks.

The methyl cycle is a universally conserved metabolic pathway operating in prokaryotes and eukaryotes. In this pathway, the amino acid methionine is used to synthesize S-adenosylmethionine, the methyl donor co-substrate in the methylation of nucleic acids, histone and non-histone proteins and many other molecules within the cell. The methylation of nucleic acids and proteins is the foundation of epigenetic and epitranscriptomic regulations of gene expression, but whether the methyl cycle centrally regulates gene expression and function by controlling the availability of methyl moieties is poorly understood.\n\nFrom cyanobacteria to humans, a circadian clock that involves an exquisitely regulated transcription-translation-feedback loop driving oscillations in gene expression and orchestrating physiology and behavior has been described. We reported previously that inhibition of the methyl cycle in mammalian cells caused the lengthening of the period of these oscillations, suggesting the methyl cycle may indeed act as a central regulator of gene expression, at least in mammals. Here, we investigated whether the methyl cycle, given its universal presence among living beings, regulates the circadian clock in species across the phylogenetic tree of life.\n\nWe reveal a remarkable evolutionary conservation of the link between the methyl cycle and the circadian clock. Moreover, we show that the methyl cycle also regulates the somite segmentation clock, another transcription-translation negative feedback loop-based timing mechanism that orchestrate embryonic development in vertebrates, highlighting the methyl cycle as a master regulator of biological clocks.\n\nSIGNIFICANCE STATEMENTHere we reveal that the methyl cycle, a universal metabolic pathway leading to the synthesis of S-adenosylmethionine, the methyl donor co-substrate in virtually all transmethylation reactions within the cell, is a conserved regulator of biological clocks. These discoveries highlight the methyl cycle as a metabolic hub that regulates gene expression via the availability of methyl moieties for the methylation of nucleic acids, proteins and many other molecules with the cell.

evolutionary biology↗