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Masuda, R.

Publications and source records attributed to Masuda, R..

16 recordsLinked to original sources

Population-level, state-dependent response as a trait predicting species redistribution under climate change

Species change their population sizes and distributions in response to fluctuating environments. Predicting such changes across space, particularly distributional shifts under climate change, is a central challenge in ecology and conservation1. Traditionally, static traits such as habitat preferences, or performance traits such as abundance-environment relationships, have been used to characterize species responses to the environment2,3. However, these approaches assume fixed relationships between species and their environments, overlooking the inherently state-dependent nature of ecosystems. Here, we show that population-level, state-dependent responses of species to environments can serve as a novel trait to better represent population dynamics in nature, which we term a dynamic response trait. Using nonlinear time-series analysis4,5 and long-term marine fish community data collected from Kyoto, Japan6, we identify causal influences of water temperature on about one hundred fish species. Species with higher latitudinal centers generally show negative dynamic responses to warming, whereas those with lower latitudinal centers show positive ones. Intriguingly, these dynamic response traits quantified at a single location explain the fish species poleward range shift velocities estimated from public biodiversity records; species with negative dynamic responses to warming shift poleward more rapidly, whereas those with positive ones tend to remain. Our findings establish dynamic response traits as a new dimension of trait-based ecology, capturing state-dependent species responses. By linking local population dynamics to broad-scale distributional shifts, this approach provides a powerful basis for guiding ecology and conservation under climate change.

ecology↗

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↗

Nuclear α1A-Adrenergic Receptor Regulation of cAMP Production by an Inside-Out MAP Kinase Signaling Pathway in Cardiac Myocytes

Sympathetic stimulation produces beneficial changes in cardiac function through {beta}-adrenergic receptor ({beta}AR) production of cAMP and subsequent alteration of electrical and mechanical activity. Long term activation of cAMP production also contributes to cardiac remodeling and detrimental changes associated with heart failure. However, sympathetic responses are mediated by the endogenous neurotransmitter norepinephrine (NE), which is also a potent 1-adrenergic receptor (1AR) agonist, and 1AR activation can produce significant effects on the heart as well. What is less clear is how 1- and {beta}-adrenergic responses interact with one another. Previous studies have demonstrated that 1AR activation can inhibit {beta}-adrenergic regulation of electrical and mechanical activity of cardiac myocytes, although the signaling mechanisms involved were not previously known. In the present study, we used FRET-based biosensors in adult rat ventricular myocytes to demonstrate that this crosstalk effect involves inhibition of cAMP production by nuclear 1AARs acting on {beta}ARs found on the plasma membrane. Furthermore, we established that this inside-out signaling mechanism involves a mitogen-activated protein kinase (MAPK) pathway that uncouples {beta}ARs from downstream signaling in a G protein coupled receptor kinase (GRK)/arrestin-dependent manner. These results reveal a novel, non-canonical signaling mechanism contributing to 1AR responses in the heart, and that this effect limits {beta}AR production of cAMP by NE. This mechanism may contribute to the cardioprotective effect previously ascribed to 1AAR activation. These findings also clearly demonstrate the importance of considering the contributions of 1 and {beta}ARs together when studying the influence of the sympathetic nervous system on the heart.

pharmacology and toxicology↗

Triple-helical ligands selectively targeting the closed αI domain of integrin α2β1

Integrins 1{beta}1, 2{beta}1, 10{beta}1, and 11{beta}1 are known to recognize the GxxGEx motif of the collagen triple helix through their I domains, with the Glu residue engaging the domain via a divalent metal cation. The binding amino acid sequences containing these motifs, identified from native collagen, exhibit low subtype selectivity. Here we identify novel triple-helical peptides that selectively bind the 2I domain independently of Glu and metal ions. Yeast two-hybrid screening of randomized triple-helical peptide libraries yielded non-natural sequences in which the canonical Glu was replaced by aliphatic residues such as Met. X-ray crystal structural analysis of the representative variant GFOGMR in complex with the 2I domain revealed a new binding mode. In this mode, peptides are recognized by the closed, inactive conformation of the 2I domain without metal coordination. This cryptic interaction, likely unused by native ligands, provides a new basis for the design of subtype-specific ligands targeting collagen-binding integrins.

biochemistry↗

Whole-genome sequencing revealed local genetic differences and multi-layered genetic structure in brown bear (Ursus arctos) populations

A multi-layered genetic structure shaped by multiple demographic events across different time periods has been well documented in some species. However, evaluating this pattern remains challenging in many wide-ranging wildlife because genome-wide datasets with broad geographic coverage are still scarce. Brown bears are genetically differentiated among regional populations, but the genomic data are still limited and the demographic events remain incompletely understood. Here, we generated whole-genome resequencing data from brown bears in Asian local populations previously reported to show significant variation and combined these data with ancient samples for population genomic analyses. Our results support previously reported demographic events, such as the early divergence of Central Asian populations. Furthermore, we found genetic differences among Asian brown bear populations, suggesting that population-specific demographic histories occurring at different times have contributed to their unique genetic characteristics. In the Central and West Asian populations, divergence times estimated from autosomal genomes differed by hundreds of thousands of years from those inferred from mitochondrial DNA and Y-chromosomal DNA haplotypes, suggesting that gene flow continued after regional dispersal. In addition, the Y-chromosomal phylogeny and f4 statistics indicated genetic differentiation between the Kazakhstan and Tibetan populations, likely resulting from male-biased introgression into the Tibetan population. Finaly, the Hokkaido and Etorofu (Iturup) populations retained alleles derived from hybridization with polar bears, likely due to the limited impact of post-LGM population expansion. These findings indicate that the genetic variation among brown bear populations is shaped by multiple demographic events occurring at different times, resulting in a multi-layered genetic structure. Significance StatementMulti-layered genetic structure is well known in some species, but remains poorly understood in wild species due to limited genomic data. In this study, we newly sequenced nine brown bears in Asia which included bears that genome data in their area is unreported. By combining these with modern and ancient genomes, we conducted population genomic analyses to characterize local genetic variation and detect hybridization with related species such as the polar bear. We identified (1) substantial divergence time gaps in Central and West Asian populations between autosomal genomes and mitochondrial and Y-chromosomal haplotypes, (2) male-biased introgression into the Tibetan population, and (3) limited impact of recent expansion between island and Eurasian continental populations. These findings suggest that the genetic structure of the populations has been shaped by multiple demographic events at different times, resulting in a multi-layered genetic structure and providing new insights into how wildlife genetic diversity is shaped.

evolutionary biology↗

The disruption of CtBP regulates DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells

After fertilization, maternally deposited mRNA is cleared, and de novo mRNA is transcribed from the zygotic genome through zygotic genome activation (ZGA), a process known as maternal-to-zygotic transition (MZT) occurring in the mouse at 2-cell (2C) stage. 2C-like cells (2CLCs) marked by MERVL expression are transcriptionally similar to 2C embryos spontaneously emerge from mouse embryonic stem cells (mESCs). Although the emergence of 2CLCs completely depends on DUX function, a recent knockout study clearly showed that DUX is dispensable for mouse embryos, suggesting that DUX-independent molecular pathways are not recapitulated in 2CLCs. We present here that the disruption of C-terminal binding protein 1/2 (Ctbp1/2) activates DUX-dependent and -independent molecular pathway associated with the development of early mouse embryos mediated by the upregulation of Preferentially expressed antigen of melanoma family-like 7 (PRAMEL7). Furthermore, the abnormality of the gene expression profile caused by Dux KO is partially rescued by the overexpression of PRAMEL7 in mESCs. Our study provides new insights into the DUX-independent molecular pathway for the activation of early embryonic genes in mESCs.

cell biology↗

A yeast two-hybrid system to obtain triple-helical ligands from combinatorial random peptide libraries

Many bioactive proteins interact with collagen, recognizing amino acid sequences displayed on the triple helix. We report here a selection strategy to obtain triple-helical peptides that interact with the proteins from a combinatorial random library constructed in yeast cells. This system enables us to select them using the standard two-hybrid protocol, detecting interactions between triple-helical peptides and target proteins fused to the GAL4-activating and binding domains, respectively. The library was constructed having triple-helical peptides with a "host-guest" design in which host helix-stabilizing regions flanked guest random sequences. Using this system, we selected peptides that bind to pigment epithelium-derived factor (PEDF), a collagen-binding protein that shows anti-angiogenic and neurotrophic activities, from the libraries. Two-step selections from the total random library and subsequently from the second focused library yielded new PEDF-binding sequences that exhibited a comparable affinity to or more potent than that of the native PEDF-binding sequence in collagen. The obtained sequences also contained a variant of the PEDF-binding motif that did not match the known motif identified from the native collagen sequences. This combinatorial library system allows the chemical space of triple-helical peptides to be screened more widely than that found in native collagen, thus increasing the expectation of obtaining more specific and high-affinity peptides.

biochemistry↗

A novel spawning survey: identifying spawning times and locations of jack mackerel in a semi-closed bay using environmental DNA analysis

Understanding spawning ecology is important for species/population management and conservation. However, conventional surveys are often time- and labour-consuming and invasive. To address these challenges, environmental DNA (eDNA) analysis has emerged as a promising method for spawning surveys. This study investigated the spawning season and diurnal changes in eDNA concentrations targeted Japanese jack mackerel in Maizuru Bay, Japan, to assess the potential of eDNA-based spawning surveys in the marine environment. First, to estimate the spawning season, eDNA concentrations at sunset and sunrise were compared monthly for one year at three sites. As Japanese jack mackerel are nocturnal spawners, eDNA concentration will increase at night during the spawning season. A significant increase in eDNA concentration was observed between sunset and sunrise in July, suggesting that this period corresponded to the spawning season. This was confirmed by egg collection surveys using a plankton net. Second, to investigate diurnal changes in eDNA concentrations during the spawning season, time-series sampling was conducted every three hours for 24 hours in July. The results indicated that eDNA concentration showed a significant diurnal change with a peak between 9 PM and midnight, which is suggested to be their spawning time window. This study successfully estimated the spawning season of Japanese jack mackerel and demonstrated the potential of eDNA-based spawning surveys for the first time in marine environments. These surveys are expected to contribute to the advancement of this field as a new approach to overcoming traditional challenges in marine spawning surveys. HighlightsO_LIThe potential of eDNA for spawning surveys was assessed in jack mackerel. C_LIO_LIMonthly morning and evening eDNA sampling identified spawning activity in July. C_LIO_LIEgg surveys using a plankton net confirmed the spawning event. C_LIO_LITime-series sampling showed a diurnal change in eDNA concentrations in July. C_LIO_LIeDNA analysis is thus applicable for detecting spawning in marine species. C_LI

ecology↗

Clinical prediction of wound re-epithelisation outcomes in non-severe burn injury using the plasma lipidome

Whilst wound repair in severe burns has received substantial research attention, non-severe burns (<20% total body surface area) remain relatively understudied, despite causing considerable physiological impact and constituting most of the hospital admissions for burns. Early prediction of healing outcomes would decrease financial and patient burden, and aid in preventing long-term complications from poor wound healing. Lipids have been implicated in inflammation and tissue repair and may play essential roles in burn wound healing. In this study, plasma samples were collected from 20 non-severe burn patients over 6 weeks from admission, including surgery, and analysed by liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance spectroscopy to detect 850 lipids and 112 lipoproteins. Orthogonal projections to latent structures-discriminant analysis was performed to identify changes associated with re-epithelialisation and delayed re-epithelisation. We demonstrated that the lipid and lipoprotein profiles at admission could predict re-epithelisation outcomes at 2 weeks post-surgery, and that these discriminatory profiles were maintained up to 6 weeks post-burn. Inflammatory markers GlycB and C-reactive protein indicated divergent systemic responses to the burn injury at admission. Triacylglycerols, diacylglycerols and low-density lipoprotein subfractions were associated with delayed wound closure (p-value <0.02, Cliffs delta >0.7), whilst high-density lipoprotein subfractions, phosphatidylinositols, phosphatidylcholines, and phosphatidylserines were associated with re-epithelisation at 2 weeks post-surgery (p-value <0.01, Cliffs delta <-0.7). Further model validation will potentially lead to personalised intervention strategies to reduce the risk of chronic complications post-burn injury.

systems biology↗

Metabolic consequences of non-severe burn injury are associated with increased plasma markers of inflammation and cardiovascular disease risk.

Globally, burns are a significant cause of injury that can cause substantial acute trauma as well as lead to increased incidence of chronic co-morbidity and disease. To date, research has primarily focused on the systemic response to severe injury, with little in the literature reported on impact of non-severe injuries (<15% total burn surface area; TBSA). To elucidate the metabolic consequences of non-severe burn injury, longitudinal plasma was collected from adults (n=35) who presented at hospital with a non-severe burn injury at admission, and at 6 week follow up. A cross-sectional baseline sample was also collected from non-burn control participants (n=14). Samples underwent multiplatform metabolic phenotyping using 1H nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry to quantify 112 lipoprotein and glycoproteins signatures and 852 lipid species from across 20 subclasses. Multivariate data modelling (Orthogonal projection to latent structures-discriminate analysis) revealed alterations in lipoprotein and lipid metabolism when comparing baseline control to hospital admission samples, with the phenotypic signature found to be sustained at follow up. Univariate (Mann-Whitney U) testing and OPLS-DA indicated specific increases in GlycB (p-value <1.0e-4), low density lipoprotein-2 subfractions (Variable importance in projection score; VIP >6.83e-1) and monoacyglyceride (20:4)(p-value <1.0e-4) and decreases in circulating anti-inflammatory high-density lipoprotein-4 subfractions (VIP >7.75e-1), phosphatidylcholines, phosphatidylglycerols, phosphatidylinositols and phosphatidylserines. The results indicate a persistent systemic metabolic phenotype that occurs even in cases of non-severe burn injury. The phenotype is indicative of an acute inflammatory profile which continues to be sustained post-injury, suggesting an impact on systems health beyond the site of injury. The phenotypes contained metabolic signatures consistent with chronic inflammatory states reported to have elevated incidence post-burn injury. Such phenotypic signatures may provide patient stratification opportunities, to identify individual responses to injury, personalise intervention strategies and improve acute care, reducing risk of chronic co-morbidity.

systems biology↗

Temperature sensitivity of the interspecific interaction strength of coastal marine fish communities

The effects of temperature on interaction strengths are important for understanding and forecasting how global climate change impacts marine ecosystems; however, tracking and quantifying interactions of marine fish species is practically difficult especially under field conditions, and thus, how temperature influences their interaction strengths under field conditions remains poorly understood. We herein performed quantitative fish environmental DNA (eDNA) metabarcoding on 550 seawater samples that were collected twice a month from 11 coastal sites for two years in the Boso Peninsula, Japan, and analyzed eDNA monitoring data using nonlinear time-series analytical tools. We detected fish-fish interactions as information flow between eDNA time series, reconstructed interaction networks for the top 50 frequently detected species, and quantified pairwise, fluctuating interaction strengths. Although there was a large variation, water temperature influenced fish-fish interaction strengths. The impact of water temperature on interspecific interaction strengths varied among fish species, suggesting that fish species identity influences the temperature effects on interactions. For example, interaction strengths that Halichoeres tenuispinis and Microcanthus stringatus received strongly increased with water temperature, while those of Engraulis japonicus and Girella punctata decreased with water temperature. An increase in water temperature induced by global climate change may change fish interactions in a complex way, which consequently influences marine community dynamics and stability. Our research demonstrates a practical research framework to study the effects of environmental variables on interaction strengths of marine communities in nature, which would contribute to understanding and predicting natural marine ecosystem dynamics.

ecology↗

Analysis of the persistence and particle size distributional shift of sperm-derived environmental DNA to monitor Jack Mackerel spawning activity

Environmental DNA (eDNA) analysis holds great promises as an efficient and noninvasive method to monitor not only the presence and biomass of organisms but also their spawning activity. In eDNA analysis-based monitoring of spawning activity, the detection of sperm-derived eDNA is a key point; however, its characteristics and dynamics are completely unknown. The present study focuses on the persistence and particle size distribution (PSD) of eDNA derived from the sperm of Japanese jack mackerel. First, we investigated the time-dependent degradation and the PSD of sperm-derived eDNA by artificially adding sperm to fish eDNA-free seawater. Next, we kept fish in tanks and examined the changes in DNA concentration and PSD before and after spawning. The data obtained from the two experiments showed that the degradation of sperm-derived eDNA proceeded rapidly, with PSD shifting to a smaller size, regardless of the DNA region (Cyt b or ITS1). Additionally, it was shown that the nuclei and mitochondria released from sperm through degradation had a size distribution that was not simply dependent on each organelle size. The results of this study will contribute to elucidating the characteristics and dynamics of eDNA specifically during the spawning season and to further developing eDNA analysis as a powerful tool for the monitoring of spawning activity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/483695v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@15a91e8org.highwire.dtl.DTLVardef@1212566org.highwire.dtl.DTLVardef@11e5e95org.highwire.dtl.DTLVardef@d39a36_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

An efficient early-pooling protocol for environmental DNA metabarcoding

Environmental DNA (eDNA) metabarcoding, a method that applies high-throughput sequencing and universal primer sets to eDNA analysis, has been a promising approach for efficient, comprehensive biodiversity monitoring. However, significant money-, labor-, and time-costs are still required for performing eDNA metabarcoding. In the present study, we assessed the performance of an "early-pooling" protocol (a protocol based on the 1st PCR indexing) to reduce the experimental costs of the library preparation for eDNA metabarcoding. Specifically, we performed three experiments to test the effects of 1st PCR and 2nd PCR indexing protocols on the community composition revealed by eDNA metabarcoding, of post-1st-PCR exonuclease purification on index-hopping, and of the number of PCR replicates and eDNA template volume on the number of detected OTUs. By analyzing 204 eDNA libraries from 3 natural aquatic ecosystems and 1 mock eDNA sample, we show that (i) the 1st PCR indexing does not cause clear biases in the outcomes of eDNA metabarcoding, (ii) post-1st-PCR exonuclease purification reduces the risk of index-hopping, and (iii) increasing the eDNA template volume can increase the number of detected OTUs and reduce the variations in detected community compositions, as can increasing the number of the 1st PCR replicates. Our results show that an early-pooling protocol with post-1st-PCR exonuclease purification and an increased amount of DNA template will reduce the risk of index-hopping, the costs for consumables and reagents, and the handling time in the library preparation, and that it produces comparable results to a 2nd-PCR-indexing protocol. Therefore, once a target metabarcoding region is determined and a set of indexed-1st-PCR primers is prepared, the early-pooling protocol provides a cost-, labor-, and time-efficient way to process a large number of samples.

ecology↗

Learning for angling: an advanced learning capability for avoidance of angling gear in red sea bream juveniles

Angling has been the cause of mortality for fish since ancient. The avoidance learning for angling gear could be considered as a survival strategy against the mortality by angling. Whereas some studies indicated the possibility of avoidance learning for angling gear, most studies investigated the avoidance learning by using groups of fish, in which it is difficult to reveal the process and mechanisms of the learning. The present study elucidated the avoidance learning for angling gear by experiment of single fish in a tank using red sea bream Pagrus major juveniles. Individuals with only once or twice of experience for angling avoided angling gear while showing the feeding motivation for pellets, representing avoidance learning for the angling gear. Most of the experienced individuals avoided the krill attached with a fishing line, but not krill and pellets near the angling gear. Feeding rate for prey on a fishing line at two month after the angling trial demonstrated that approximately half of fish kept the memory for angling gear. A series of experiment for angling gear elucidated that red sea bream juveniles are equipped with considerable learning capability for angling gear, suggesting a cognitive evolution for angling.

animal behavior and cognition↗

Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

We propose a general framework of abundance estimation based on spatially replicated quantitative measurements of environmental DNA in which production, transport, and degradation of DNA are explicitly accounted for. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. These findings indicate the ability of environmental DNA to reliably reflect population abundance of aquatic macroorganisms and may o[ff]er a new avenue for population monitoring based on the fast, cost-e[ff]ective, and non-invasive sampling of genetic information.

ecology↗

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Therefore, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time- and effort-consuming and costly. Recent studies have shown that environmental DNA (eDNA), which is released to the environment from macro-organisms living in a habitat, contains information about species identity and abundance. Thus, analyzing eDNA would be a promising approach for more efficient biodiversity monitoring. In the present study, we added internal standard DNAs (i.e., known amounts of short DNA fragments from fish species that have never been observed in a sampling area) to eDNA samples, which were collected weekly from a coastal marine ecosystem in Maizuru-Bay, Kyoto, Japan (from April 2015 to March 2016), and performed metabarcoding analysis using Illumina MiSeq to simultaneously identify fish species and quantify fish eDNA copy numbers. A correction equation was obtained for each sample using the relationship between the number of sequence reads and the added amount of the standard DNAs, and this equation was used to estimate the copy numbers from the sequence reads of non-standard fish eDNA. The calculated copy numbers showed significant positive correlation with those determined by quantitative PCR, suggesting that eDNA metabarcoding with standard DNA enabled useful quantification of eDNA. Furthermore, for samples that show a high level of PCR inhibition, our method might allow more accurate quantification than qPCR because the correction equations generated using internal standard DNAs would include the effect of PCR inhibition. A single run of Illumina MiSeq produced > 70 quantitative fish eDNA time series in our study, showing that our method could contribute to more efficient and quantitative monitoring of biodiversity.

ecology↗