Biology subjects

Matsui, T.

Publications and source records attributed to Matsui, T..

67 records · Page 4Linked to original sources

bioRxiv2021

Why do some primate mothers carry their infant's corpse? A cross-species comparative study

Non-human primates respond to the death of a conspecific in diverse ways, some which may present phylogenetic continuity with human thanatological behaviours. Of these responses, infant corpse carrying by mothers (ICC) is the most-frequently reported. Despite its prevalence, quantitative analyses of this behaviour are scarce and inconclusive. We compiled a database of 409 published cases across 50 different primate species of mothers responses to their infants deaths to test hypotheses proposed to explain between- and within-species variation in corpse carrying. Using Bayesian phylogenetic regressions, we preliminarily identified three factors as possible predictors of ICC occurrence. However, using an information-theoretic approach, no combination of these predictors performed better than the null model, offering no support for any of the hypotheses we tested. In contrast, for those cases where infants corpses were carried, infant age affected ICC duration, with longer ICC observed for younger infants. This result may provide support for hypotheses that suggest that ICC is a by-product of a strong mother-infant bond. The results are discussed in the context of the evolution of emotion and their implications for evolutionary thanatology are considered.

animal behavior and cognition↗

bioRxiv2020

Canopy micrometeorology monitoring in diverse climates innovatively improves the evaluation heat-induced sterility of rice under climate change

This study is the first and unique of open-field studies to assess the determination process of heat-induced spikelet sterility (HISS) of rice by using the same variety and the same monitoring system, MINCER (Micrometeorological Instrument for Near Canopy Environment of Rice), covering the major-rice growing regions from Sub-Saharan Africa, South, Southeast, and East Asia, and USA. Applying the observation data from the monitoring network, MINCERnet, to the canopy heat balance model, IM2PACT, it was quantitatively corroborated in open-field conditions worldwide that the canopy and panicle transpiration and their evaporative cooling effect played a great role on the micrometeorological gap between the ambient air temperature and the panicle temperature, and that the sterility rate due to HISS in open-fields can be evaluated accurately in diverse climates by the mean panicle temperature at flowering hours in the flowering period. The heat balance structure suggested that the risk of HISS should be higher in high humidity climates rather than in dry climates also in the future, which lead to the importance of the humidity accuracy as well as of the air temperature in climate scenarios and their spatial downscaling for future prediction of rice heat stress and production. Applying the heat-tolerant variety was suggested to be able to keep the sterility due to HISS low in all climates. It is needed of the approach using the panicle temperature as indicator of HISS by intervening sub-model and/or monitoring of micrometeorology inside the canopy to reduce uncertainties in future rice yield prediction under various adaptation measures.

plant biology↗

bioRxiv2020

ALIX and ceramide differentially control polarized exosome release from epithelial cells

Exosomes, new players in cell-cell communication, are extracellular vesicles of endocytic origin. Although single cells are known to release various kinds of exosomes (referred to as exosomal heterogeneity), very little is known about the mechanisms by which they are produced and released. Here, we established methods for studying exosomal heterogeneity by using polarized epithelial cells and showed that distinct types of exosomes are differentially secreted from the apical and basolateral sides. We also identified GPRC5C (G protein-coupled receptor class C group 5 member C) as an apical-exosome-specific protein. We further demonstrated that basolateral exosome release depends on ceramide, whereas ALIX, an ESCRT (endosomal sorting complexes required for transport)-related protein, not the ESCRT machinery itself, is required for apical exosome secretion. Thus, two independent machineries, the ALIX-Syntenin1- Syndecan1 machinery (apical side) and the sphingomyelinase-dependent ceramide production machinery (basolateral side), are likely to be responsible for the polarized exosome release from epithelial cells.

cell biology↗

bioRxiv2020

Genetic architecture of a mutation's expressivity and penetrance

Genetic background often influences the phenotypic consequences of mutations, resulting in variable expressivity. How standing genetic variants collectively cause this phenomenon is not fully understood. Here, we comprehensively identify loci in a budding yeast cross that impact the growth of individuals carrying a spontaneous missense mutation in the nuclear-encoded mitochondrial ribosomal gene MRP20. Initial results suggested that a single large effect locus influences the mutations expressivity, with one allele causing inviability in mutants. However, further experiments revealed this simplicity was an illusion. In fact, many additional loci shape the mutations expressivity, collectively leading to a wide spectrum of mutational responses. These results exemplify how complex combinations of alleles can produce a diversity of qualitative and quantitative responses to the same mutation.

genetics↗

bioRxiv2019

A Bacterial Surface Layer Protein Exploits Multi-step Crystallization for Rapid Self-assembly

Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular self-assembly by crystallizing when exposed to an environmental trigger. However, molecular mechanisms governing rapid protein crystallization in vivo or in vitro are largely unknown. Here, we demonstrate that the C. crescentus SLP readily crystallizes into sheets in vitro via a calcium-triggered multi-step assembly pathway. This pathway involves two domains serving distinct functions in assembly. The C-terminal crystallization domain forms the physiological 2D crystal lattice, but full-length protein crystallizes multiple orders of magnitude faster due to the N-terminal nucleation domain. Observing crystallization using time-resolved electron cryo-microscopy (Cryo-EM) reveals a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Dynamic flexibility between the two domains rationalizes efficient S-layer crystal nucleation on the curved cellular surface. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials.\n\nSignificance StatementMany microbes assemble a crystalline protein layer on their outer surface as an additional barrier and communication platform between the cell and its environment. Surface layer proteins efficiently crystallize to continuously coat the cell and this trait has been utilized to design functional macromolecular nanomaterials. Here, we report that rapid crystallization of a bacterial surface layer protein occurs through a multi-step pathway involving a crystalline intermediate. Upon calcium-binding, sequential changes occur in the structure and arrangement of the protein, which are captured by time-resolved small angle x-ray scattering and transmission electron cryo-microscopy. We demonstrate that a specific domain is responsible for enhancing the rate of self-assembly, unveiling possible evolutionary mechanisms to enhance the kinetics of 2D protein crystallization in vivo.

biophysics↗

bioRxiv2019

Characterization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus

Bacterial diversity associated with corals has been studied extensively, however, localization of bacterial associations within the holobiont is still poorly resolved. Here we provide novel insight into the localization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus. In total, 318 and 308 CAMAs were characterized via histological and fluorescent in situ hybridization (FISH) approaches respectively, and shown to be distributed extensively throughout coral tissues collected from five sites in Japan and Australia. The densities of CAMAs within the tissues were negatively correlated with the distance from the coastline (i.e. lowest densities at offshore sites). CAMAs were randomly distributed across the six coral tissue regions investigated. Within each CAMA, bacterial cells had similar morphological characteristics, but bacterial morphologies varied among CAMAs, with at least five distinct types identified. Identifying the location of microorganisms associated with the coral host is a prerequisite for understanding their contributions to fitness. Localization of tissue-specific communities housed within CAMAs is particularly important, as these communities are potentially important contributors to vital metabolic functions of the holobiont.

microbiology↗

bioRxiv2018

Astrocytes in the mouse visual cortex reliably respond to visual stimulation

Astrocytes are known to contact with a great number of synapses and may integrate sensory inputs. In the ferret primary visual cortex, astrocytes respond to a visual stimulus with a delay of several seconds with respect to the surrounding neurons. However, in the mouse visual cortex, it remains unclear whether astrocytes respond to visual stimulations. In this study, using dual-color simultaneous in vivo two-photon Ca2+ imaging of neurons and astrocytes in the awake mouse visual cortex, we examined the visual responsiveness of astrocytes and their precise response timing relative to the surrounding neurons. Neurons reliably responded to visual stimulations, whereas astrocytes often showed neuromodulator-mediated global activities, which largely masked small periodic activities. Administration of the selective 1-adrenergic receptor antagonist prazosin substantially reduced such global astrocytic activities without affecting the neuronal visual responses. In the presence of prazosin, astrocytes showed weak but consistent visual responses mostly at their somata. Cross-correlation analysis estimated that the astrocytic visual responses were delayed by approximately 5 s relative to the surrounding neuronal responses. In conclusion, our research demonstrated that astrocytes in the primary visual cortex of awake mice responded to visual stimuli with a delay of several seconds relative to the surrounding neurons, which may indicate the existence of a common mechanism of neuron-astrocyte communication across species.\n\nHighlightsO_LIWe performed dual-color in vivo two-photon Ca2+ imaging of neurons and astrocytes.\nC_LIO_LI1-adrenoblocker prazosin substantially reduced global astrocytic activities.\nC_LIO_LIAstrocytes showed weak but reliable visual responses in the awake mouse visual cortex.\nC_LIO_LIAstrocytic visual responses were delayed by 5 s relative to the neuronal ones.\nC_LI

neuroscience↗

bioRxiv2018

Molecular typing and macrolide resistance analyses of Treponema pallidumin heterosexuals and men who have sex with men communities in Japan, 2017.

In recent years, syphilis notifications have increased dramatically in Japan. We performed molecular typing and analyzed macrolide resistance of Treponema pallidum samples collected from four clinics and a hospital in Tokyo and Osaka prefectures in 2017.\n\nMacrolide resistant strain type 14d/f was found significantly more in heterosexual syphilis cases compared with those strains identified in men who have sex with men (MSM) syphilis cases. The proportion of 14d/f among heterosexuals was 79% (31/39) compared to 37% (7/19) among MSM [OR, 6.6 (95% CI, 1.7 to 26.7); P=0.002]. 83% (50/60) of the strains were identified as macrolide resistant with an A2058G mutation at the 23S rRNA gene. 90% (35/39) of the heterosexual strains were macrolide resistant, relative to 58% (11/19) of MSM strains; the odds of having the resistant mutation was considerably higher in heterosexuals compared with MSM [OR, 6.4 (95% CI, 1.3 to 33.5); P=0.02]. Heterosexual females and males showed similar distributions, and the results remained the same when restricted to men.\n\nThe strain type distribution and frequency of macrolide resistance differed substantially between heterosexual and MSM syphilis samples, suggesting distinct epidemiologic profiles for the two communities and insight into syphilis transmission dynamics in Japan.

epidemiology↗

bioRxiv2018

A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios

Abstract.To support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land use and climate change on biodiversity and ecosystem services (i.e. natures contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs) to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenarios selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem service models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modelling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modelling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.

ecology↗

bioRxiv2018

Noise-resistant developmental reproducibility in vertebrate somite formation

The reproducibility of embryonic development is remarkable, although molecular processes are intrinsically stochastic at the single-cell level. How the multi-cellular system resists the inevitable noise to acquire developmental reproducibility constitutes a fundamental question in developmental biology. Toward this end, we focused on vertebrate somitogenesis as a representative system, because somites are repeatedly reproduced within a single embryo whereas such reproducibility is lost in segmentation clock gene-deficient embryos. However, the effect of noise on developmental reproducibility has not been fully investigated, because of the technical difficulty in manipulating the noise intensity in experiments. In this study, we developed a computational model of ERK-mediated somitogenesis, in which bistable ERK activity is regulated by an FGF gradient, cell-cell communication, and the segmentation clock, subject to the intrinsic noise. The model simulation generated our previous in vivo observation that the ERK activity was distributed in a step-like gradient in the presomitic mesoderm, and its boundary was posteriorly shifted by the clock in a stepwise manner, leading to regular somite formation. Here we showed that this somite regularity was robustly maintained against the noise. Removing the clock from the model predicted that the stepwise shift of the ERK activity occurs at irregular timing with irregular distance owing to the noise, resulting in somite size variation. Through theoretical analysis, we presented a mechanism by which the clock reduces the inherent somite irregularity observed in clock-deficient embryos. Therefore, this study indicates a novel role of the segmentation clock in noise-resistant developmental reproducibility.

developmental biology↗

bioRxiv2017

Size-reduced embryos reveal a gradient scaling based mechanism for zebrafish somite formation

Little is known about how the sizes of animal tissues are controlled. A prominent example is somite size which varies widely both within an individual and across species. Despite intense study of the segmentation clock governing the timing of somite generation, how it relates to somite size is poorly understood. Here we examine somite scaling and find that somite size at specification scales with the length of the presomitic mesoderm (PSM) despite considerable variation in PSM length across developmental stages and in surgically size-reduced embryos. Measurement of clock period, axis elongation speed, and clock gene expression patterns demonstrate that existing models fail to explain scaling. We posit a \"clock and scaled gradient\" model, in which somite boundaries are set by a dynamically scaling signaling gradient across the PSM. Our model not only explains existing data, but also makes a unique prediction that we experimentally confirm--the formation of periodic \"echoes\" in somite size following perturbation of the size of one somite. Our findings demonstrate that gradient scaling plays a central role both in progression and size control of somitogenesis.\n\nSummary statementBy comparing patterning in zebrafish embryos of different size we show that a dynamically scaling gradient in the presomitic mesoderm regulates somite size control.

developmental biology↗

bioRxiv2017

Neuronal origin of the temporal dynamics of spontaneous BOLD activity correlation

Resting-state functional connectivity (FC) has become a major fMRI method to study network organization of human brains. There has been recent interest in the temporal fluctuations of FC calculated using short time windows (\"dynamic FC\") because this method could provide information inaccessible with conventional \"static\" FC, which is typically calculated using the entire scan lasting several tens of minutes. Although multiple studies have revealed considerable temporal fluctuations in FC, it is still unclear whether the fluctuations of FC measured in hemodynamics reflect the dynamics of underlying neural activity. We addressed this question using simultaneous imaging of neuronal calcium and hemodynamic signals in mice and found coordinated temporal dynamics of calcium FC and hemodynamic FC measured in the same short time windows. Moreover, we found that variation in transient neuronal coactivation patterns (CAPs) was significantly related to temporal fluctuations of sliding window FC in hemodynamics. Finally, we show that the observed dynamics of FC cannot be fully accounted for by simulated data assuming stationary FC. These results provide evidence for the neuronal origin of dynamic FC and further suggest that information relevant to FC is condensed in temporally sparse events that can be extracted using a small number of time points.

neuroscience↗

bioRxiv2017

The stress-inducible peroxidase TSA2 enables Chromosome IV duplication to be conditionally beneficial in Saccharomyces cerevisiae

Although chromosomal duplications are often deleterious, in some cases they enhance cells abilities to tolerate specific genetic or environmental challenges. Identifying the genes that cause particular chromosomal duplications to confer these conditionally beneficial effects can improve our understanding of the genetic and molecular mechanisms that enable certain aneuploidies to persist in cell populations and contribute to disease and evolution. Here, we perform a screen for spontaneous mutations that improve the tolerance of haploid Saccharomyces cerevisiae to hydrogen peroxide. Chromosome IV duplication is the most frequent mutation, as well as the only change in chromosomal copy number, seen in the screen. Using a genetic mapping strategy that involves systematically deleting segments of a duplicated chromosome, we show that the Chromosome IV duplications effect is largely due to the generation of a second copy of the stress-inducible cytoplasmic thioredoxin peroxidase TSA2. This finding is consistent with a growing literature indicating that the conditionally beneficial effects of chromosomal duplications tend to reflect the contributions of small numbers of genes that enhance tolerance to specific stresses when their copy number is increased.\n\nArticle summaryChanges in karyotype play an important role in evolution and health. Although these aneuploidization events are usually deleterious, in some instances they show conditionally beneficial effects by enabling cells to tolerate specific mutations or environmental stresses. The mechanisms underlying these protective effects of aneuploidization are not fully understood. To provide insights into this problem, we identify and characterize a conditionally beneficial chromosomal duplication that makes haploid yeast more tolerant to oxidative stress. We determine that the effect of the chromosomal duplication on oxidative stress tolerance is largely explained by duplication of a single stress-inducible gene.

genetics↗