Biology subjects

Hashimoto, K.

Publications and source records attributed to Hashimoto, K..

At least 37 records · Page 2Linked to original sources

bioRxiv2022

A descending inhibitory mechanism of nociception mediated by an evolutionarily conserved neuropeptide system in Drosophila

Nociception is a neural process that animals have developed to avoid potentially tissue-damaging stimuli. While nociception is triggered in the peripheral nervous system, its modulation by the central nervous system is a critical process in mammals, whose dysfunction has been extensively implicated in chronic pain pathogenesis. The peripheral mechanisms of nociception are largely conserved across the animal kingdom. However, it is unclear whether the brain-mediated modulation is also conserved in non-mammalian species. Here, we show that Drosophila has a descending inhibitory mechanism of nociception from the brain, mediated by the neuropeptide Drosulfakinin (DSK), a homolog of cholecystokinin (CCK) that plays an important role in the descending control of nociception in mammals. We found that mutants lacking dsk or its receptors are hypersensitive to noxious heat. Through a combination of genetic, behavioral, histological, and Ca2+ imaging analyses, we subsequently revealed neurons involved in DSK-mediated nociceptive regulation at a single-cell resolution and identified a DSKergic descending neuronal pathway that inhibits nociception. This study provides the first evidence for a descending modulatory mechanism of nociception from the brain in a non-mammalian species that is mediated by the evolutionarily conserved CCK system, raising the possibility that the descending inhibition is an ancient mechanism to regulate nociception.

neuroscience↗

bioRxiv2021

Severe disturbance overflows the stabilizing buffer of variable biotic interactions

Recent studies have revealed that biotic interactions in ecological communities vary over time, possibly mediating community responses to anthropogenic disturbances. This study investigated the heterogeneity of such variability within a real community and its impact on population stability in the face of pesticide application, particularly focusing on density-dependence of the interaction effect. Using outdoor mesocosms with a freshwater community, we found considerable heterogeneity in density-dependent interaction variability among links in the same community. This variability mediated the stability of recipient populations, with negative density-dependent interaction variability stabilizing whereas positive density-dependence and density-independent interaction variability destabilizing populations. Unexpectedly, the mean interaction strength, which is typically considered crucial for stability, had no significant effect, suggesting that how organisms interact on average is insufficient to predict the ecological impacts of pesticides. Our findings emphasize the multifaceted role of interaction variability in predicting the ecological consequences of anthropogenic disturbances such as pesticide application.

ecology↗

bioRxiv2021

Transient induction of cell cycle promoter Fam64a improves cardiac function through regulating Klf15-dependent cardiomyocyte differentiation in mice

The introduction of fetal or neonatal signatures such as cell cycle promoting genes into damaged adult hearts has been vigorously pursued as a promising strategy for stimulating proliferation and regeneration of adult cardiomyocytes, which normally cannot divide. However, cell division of cardiomyocytes requires preceding dedifferentiation with sarcomere disassembly and calcium dysregulation, which, in principle, compromises contractile function. To overcome this intrinsic dilemma, we explored the feasibility of optimizing the induction protocol of the cell cycle promoter in mice. As a model of this approach, we used Fam64a, a fetal-specific cardiomyocyte cell cycle promoter that we have recently identified. We first analyzed transgenic mice maintaining long-term cardiomyocyte-specific expression of Fam64a after birth, when endogenous expression was abolished. Despite having an enhanced proliferation of postnatal cardiomyocytes, these mice showed age-related cardiac dysfunction characterized by sustained cardiomyocyte dedifferentiation, which was reminiscent of the dilemma. Mechanistically, Fam64a inhibited glucocorticoid receptor-mediated transcriptional activation of Klf15, a key regulator that drives cardiomyocyte differentiation, thereby directing cardiomyocytes toward immature undifferentiated states. In contrast, transient induction of Fam64a in cryoinjured wildtype adult mice hearts improved functional recovery with augmented cell cycle activation of cardiomyocytes. These data indicate that optimizing the intensity and duration of the stimulant to avoid excessive cardiomyocyte dedifferentiation could pave the way toward developing efficient strategy for successful heart regeneration.

physiology↗

bioRxiv2021

Spatial metabolomics using imaging mass spectrometry to identify the localization of asparaptine in Asparagus officinalis

Spatial metabolomics uses imaging mass spectrometry (IMS) to localize metabolites within tissue section. Here, we performed matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance-IMS (MALDI-FTICR-IMS) to identify the localization of asparaptine, a naturally occurring inhibitor of angiotensin-converting enzyme, in green spears of asparagus (Asparagus officinalis). Spatial metabolome data were acquired with an untargeted manner. Segmentation analysis using the data characterized tissue-type-dependent and - independent distribution patterns in cross-sections of asparagus spears. Moreover, asparaptine accumulated at high levels in developing lateral shoot tissues. Quantification of asparaptine in lateral shoots using liquid chromatography-tandem mass spectrometry (LC-MS/MS) validated the IMS analysis. These results provide valuable information for understanding the function of asparaptine in asparagus, and identify the lateral shoot as a potential region of interest for multiomic studies to examine gene-to-metabolite associations in asparaptine biosynthesis.

plant biology↗

bioRxiv2020

Asymbiotic mass production of the arbuscular mycorrhizal fungus Rhizophagus clarus

Arbuscular mycorrhizal (AM) symbiosis is a mutually beneficial interaction between fungi and land plants and promotes global phosphate cycling in terrestrial ecosystems. AM fungi are recognised as obligate symbionts that require root colonisation to complete a life cycle involving the production of propagules, asexual spores. Recently it has been shown that Rhizophagus irregularis can produce infection-competent secondary spores asymbiotically by adding a fatty acid, palmitoleic acid. Further, asymbiotic growth can be supported using myristate as a carbon and energy source for their asymbiotic growth to increase fungal biomass. However, spore production and the ability of these spores to colonise host roots were still limited compared to co-culture of the fungus with plant roots. Here we show that a combination of two plant hormones, strigolactone and methyl jasmonate, induces production of a large number of infection-competent spores in asymbiotic cultures of Rhizophagus clarus HR1 in the presence of myristate and organic nitrogen. Inoculation of asymbiotically-generated spores promoted the growth of Welsh onions, as observed for spores produced by symbiotic culture system. Our findings provide a foundation for elucidation of hormonal control of the fungal life cycle and development of new inoculum production schemes.

microbiology↗

bioRxiv2020

Centriole and PCM cooperatively recruit CEP192 to spindle poles to promote bipolar spindle assembly

The pericentriolar material (PCM) that accumulates around the centriole expands during mitosis and nucleates microtubules. While centrosomes facilitate bipolar spindle formation, the individual functions of the centriole and PCM in mitosis remain elusive. Herein, we show the redundant roles of the centriole and PCM in bipolar spindle formation in human cells. Upon depletion of the PCM scaffold components, pericentrin and CDK5RAP2, centrioles remained able to recruit CEP192 onto their walls, which was sufficient for bipolar spindle formation. In contrast, through centriole removal, we found that pericentrin and CDK5RAP2 recruited CEP192 at the acentriolar spindle pole and facilitated bipolar spindle formation in mitotic cells with one centrosome. Furthermore, the chemical perturbation of polo-like kinase 1, a critical kinase for PCM assembly, efficiently suppressed the proliferation of various cancer cell lines from which centrioles were removed. Overall, these data suggest that the centriole and PCM cooperatively recruit CEP192 to spindle poles and facilitate bipolar spindle formation in human cells.

cell biology↗

bioRxiv2020

Perception of and anxiety about COVID-19 infection and risk behaviors for spreading infection: An international comparison

To control the spread of the newly developed corona viral infection diseases (COVID-19), peoples appropriate precautionary behaviors should be promoted. We conducted a series of online questionnaire survey, to gather a total of 8,000 citizens responses on March 27-28, 2020 in Japan and April 17-21 in the UK and Spain. Compared to Japan, the knowledge and anxiety level and the frequency of precautionary behaviors were higher in the UK and Spain. Participants with infected acquaintances were more concerned about COVID-19. However, participants in the UK rarely wore a medical mask. Participants in the UK and Spain were eager to get information about COVID-19 compared to those in Japan. The participants in Spain tended not to trust official information and to believe specialists' comments instead. The urgency of the spread of COVID-19, cultural backgrounds, and recent political situations appear to contribute to the differences among countries revealed herein.

scientific communication and education↗

bioRxiv2020

Non-allelic homologous recombination of Alu and LINE-1 elements generates somatic complexity in human genomes.

Millions of Alu and L1 copies in our genomes contribute to evolution and genetic disorders via non-allelic homologous recombination, but the somatic extent of these rearrangements has not been systematically investigated. Here we combine short and long DNA reads sequencing of repeat elements with a new bioinformatic pipeline to show that somatic recombination of Alu and L1 elements is common in human genomes. We report new tissue-specific recombination hallmarks, and show that retroelements acting as recombination hotspots are enriched in centromeres and cancer genes. We compare recombination profiles in human induced pluripotent stem cells and differentiated neurons and show that neuron-specific recombination of repeat elements accompanies chromatin changes during cell-fate determination. Finally, we find that somatic recombination profiles are altered in Parkinsons and Alzheimers disease, indicating a link between retroelements recombination and genomic instability in neurodegeneration. This work shows that somatic recombination of repeat elements contributes massively to genomic diversity in health and disease.

genomics↗

bioRxiv2020

Climate, species richness, and body size drive geographical variation in resource specialization of herbivorous butterflies

AimIt is generally assumed that the degree of resource specialization in herbivorous insects increases towards lower latitudes. However, latitudinal patterns in herbivore diet breadth at large spatial scales remain poorly understood. In this work, we investigated drivers of latitudinal variation in lepidopteran "fundamental" resource specialization, which we defined as the host breadth when not limited by interspecific interactions at the same trophic level. LocationThe Japanese archipelago (22{degrees}N-45{degrees}N), including hemiboreal, temperate, and subtropical zones. TaxonHerbivorous butterflies. MethodsSpecies-specific fundamental host breadth was calculated based on pooled geographical occurrence and host-use records. We investigated the latitudinal pattern and significant drivers of the degree of specialization in regional species pools at a 10-km grid level. As potential drivers, we focused on geography, current climate, and diversity and body size of butterflies. Through Bayesian structural equation modeling, we investigated the complicated relationships between these variables and community-level resource specialization represented by three different indices of host breadth. ResultsWe found that fundamental resource specialization of butterfly communities increases toward higher latitudes. This pattern is contrary to the presumed general trend found in studies based on realized resource specialization within local communities. We found that the observed pattern is driven mainly by factors related to climate, butterfly diversity, and body size in each community. Above all, annual mean temperature most strongly drove community-level fundamental host breadth of butterflies. Main conclusionsOur findings suggest that fundamental resource specialization may show different latitudinal patterns from the conventional prediction based on knowledge of realized resource specialization. Our results emphasize the importance of the current climate as a major factor regulating butterfly morphology and fundamental host breadth, regardless of whether the impact is direct or indirect.

ecology↗

bioRxiv2019

DUX4 regulates oocyte to embryo transition in human

During the human oocyte-to-embryo transition, the fertilized oocyte undergoes final maturation and the embryo genome is gradually activated during the first three cell divisions. How this transition is coordinated in humans is largely unknown. We show that the double homeodomain transcription factor DUX4 contributes to this transition. DUX4 knockdown in human zygotes caused insufficient transcriptome reprogramming as observed three days after fertilization. Induced DUX4 expression in human embryonic stem cells activated transcription of thousands of newly identified bi-directional transcripts, including putative enhancers for embryonic genome activation genes such as LEUTX. DUX4 protein interacted with transcriptional modifiers that are known to couple enhancers and promoters. Taken together, our results reveal that DUX4 is a pioneer regulating oocyte-to-embryo transition in human through activation of intergenic genome, especially enhancers, and hence setting the stage for early human embryo development.

developmental biology↗

bioRxiv2019

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes and yet, their functions remain largely unknown. We systematically knockdown 285 lncRNAs expression in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNA exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest to-date lncRNA knockdown dataset with molecular phenotyping (over 1,000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

genomics↗

bioRxiv2019

Basicity of N5 in semiquinone enhances the rate of respiratory electron outflow in Shewanella oneidensis MR-1

Extracellular electron transport (EET) occurs in environmental iron-reducing bacteria and is mediated by an outer membrane multi-heme cytochrome complex (Cyts). It has critical implications for global mineral cycling and electrochemical microbial catalysis. The rate of EET mediated by multiple heme redox centers significantly increases in the presence of flavins and quinones. Their electron free energy does not entirely account for the fact that differential effects on EET rate enhancement vary significantly by factors [≥]100. Here, we report on whole-cell electrochemical analysis of Shewanella oneidensis MR-1 using six flavin analogs and four quinones. We demonstrated that protonation of the nitrogen atom at position 5 (N5) of the isoalloxazine ring is essential for electron outflow acceleration as a bound non-covalent cofactor of Cyts. EET mediated by Cyts was accelerated at a rate dependent on pKa(N5). The EET rate largely decreased in response to the addition of deuterated water (D2O), while low concentration of D2O (4 %) had little impact on electron free energy difference of the heme and non-covalent bound cofactors, strongly suggesting that the protonation of N5 limits the rate of EET. Our findings directly link EET kinetics to proton transport reaction via N5 and provide a basis for the development of novel strategies for controlling EET-associated biological reactions.\n\nSignificance statementThe potential of various small molecules such as flavins and quinones to enhance the rate of extracellular electron transport (EET) has been exploited to develop environmental energy conversion systems. Flavins and quinones have similar molecular structures but their abilities to enhance EET vary by >100x in Shewanella oneidensis MR-1. These large differences are inconsistent with conventional models, which rely on redox potentials or diffusion constant of shuttling electron mediators. In this study, we demonstrated that the basicity of the nitrogen atom of the isoalloxazine ring (N5) enhances the rate of electron outflow when a flavin or quinone is a non-covalent cofactor of S. oneidensis MR-1 outer membrane c-type cytochromes.

biochemistry↗

bioRxiv2019

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodelling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However, they still present some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.

genomics↗

bioRxiv2019

The first functional characterization of ancient interleukin-15-like (IL-15L) reveals shared and distinct functions of the IL-2, -15 and -15L family cytokines

The ancient cytokine interleukin 15-like (IL-15L) was lost in humans and mice but not throughout mammals. This is the first study to describe IL-15L functions, namely in the fish rainbow trout. Fish have only one -chain receptor gene IL-15R, whereas in mammalian evolution this gene duplicated and evolved into IL-15R plus IL-2R. Trout IL-2, IL-15 and IL-15L all could bind IL-15R and were able to induce phosphorylation of transcription factor STAT5. Reminiscent of the mammalian situation, trout IL-15 was more dependent on \"in trans\" presentation by IL-15R than IL-2. However, whereas trout IL-15 could also function as a free cytokine as known for mammalian IL-15, trout IL-15L function showed a total dependency on in trans presentation by IL-15R. Trout lymphocytes from the mucosal tissues gill and intestine were sensitive to IL-15, but refractory to IL-2 and IL-15L, which is reminiscent of sensitivities to IL-15 in mammals. Distinguishing engagement of the IL-2R/IL-15R receptor chain may explain why IL-2 and IL-15 were selected in evolution as major growth factors for regulatory T cells and lymphocytes in mucosal tissues, respectively. Trout IL-15L efficiently induced expression of IL-4 and IL-13 homologues in CD4-CD8-IgM- splenocytes, and we speculate that the responsive cells within that population were type 2 innate lymphoid cells (ILC2). In contrast, trout IL-15 efficiently induced expression of interferon {gamma} and perforin in CD4-CD8-IgM- splenocytes, and we speculate that in this case the responsive cells were natural killer (NK) cells. In fish, in apparent absence of IL-25, IL-33 and TSLP, primitive IL-15L may have an important role early in the type 2 immunity cytokine cascade. Among trout thymocytes, only CD4-CD8- thymocytes were sensitive to IL-15L, and different than in mammals the CD4+CD8+ thymocytes were quite sensitive to IL-2. In addition, the present study provides (i) the first molecular evidence for inter-species cytokine with receptor chain interaction across fish-mammal borders, and (ii) suggestive evidence for a tendency of IL-2/15/15L cytokines to form homodimers as an ancient family trait. This is the first comprehensive study on IL-2/15/15L functions in fish and it provides important insights into the evolution of this cytokine family.

evolutionary biology↗

bioRxiv2019

Single-cell transcriptomics reveals expansion of cytotoxic CD4 T-cells in supercentenarians

Supercentenarians, people who have reached 110 years of age, are a great model of healthy aging. Their characteristics of delayed onset of age-related diseases and compression of morbidity imply that their immune system remains functional. Here we performed single-cell transcriptome analysis of 61,202 peripheral blood mononuclear cells (PBMCs), derived from seven supercentenarians and five younger controls. We identified a marked increase of cytotoxic CD4 T-cells (CD4 CTLs) coupled with a substantial reduction of B-cells as a novel signature of supercentenarians. Furthermore, single-cell T-cell receptor sequencing of two supercentenarians revealed that CD4 CTLs had accumulated through massive clonal expansion, with the most frequent clonotypes accounting for 15% to 35% of the entire CD4 T-cell population. The CD4 CTLs exhibited substantial heterogeneity in their degree of cytotoxicity as well as a nearly identical transcriptome to that of CD8 CTLs. This indicates that CD4 CTLs utilize the transcriptional program of the CD8 lineage while retaining CD4 expression. Our study reveals that supercentenarians have unique characteristics in their circulating lymphocytes, which may represent an essential adaptation to achieve exceptional longevity by sustaining immune responses to infections and diseases.\n\nSignificanceExceptionally long-lived people such as supercentenarians tend to spend their entire lives in good health, implying that their immune system remains active to protect against infections and tumors. However, their immunological condition has been largely unexplored. We profiled thousands of circulating immune cells from supercentenarians at single-cell resolution, and identified a large number of CD4 T-cells that have cytotoxic features. This characteristic is very unique to supercentenarians, because generally CD4 T-cells have helper, but not cytotoxic, functions under physiological conditions. We further profiled their T-cell receptors, and revealed that the cytotoxic CD4 T-cells were accumulated through clonal expansion. The conversion of helper CD4 T-cells to a cytotoxic variety might be an adaptation to the late stage of aging.

immunology↗

bioRxiv2019

Presynaptic MAST Kinase Controls Bidirectional Post-SynapticResponses to Convey Stimulus Valence in C. elegans

Presynaptic plasticity is known to modulate the strength of synaptic transmission. However, it remains unknown whether regulation in presynaptic neurons alters the directionality -positive or negative-of postsynaptic responses. We report here that the C. elegans homologs of MAST kinase, Stomatin and Diacylglycerol kinase act in a thermosensory neuron to elicit in its postsynaptic neuron an excitatory or inhibitory response that correlates with the valence of thermal stimuli. By monitoring neural activity of the valence-coding interneuron in freely behaving animals, we show that the alteration between excitatory and inhibitory responses of the interneuron is mediated by controlling the balance of two opposing signals released from the presynaptic neuron. These alternative transmissions further generate opposing behavioral outputs necessary for the navigation on thermal gradients. Our findings reveal the previously unrecognized capability of presynaptic regulation to evoke bidirectional postsynaptic responses and suggest a molecular mechanism of determining stimulus valence.

neuroscience↗

bioRxiv2019

Disease-associated mutations hyperactivate KIF1A motility and anterograde axonal transport of synaptic vesicle precursors

KIF1A is a kinesin-family motor involved in the axonal transport of synaptic vesicle precursors (SVPs) along microtubules. In humans, more than ten point mutations in KIF1A are associated with the motor neuron disease, hereditary spastic paraplegia (SPG). However, not all of these mutations appear to inhibit the motility of the KIF1A motor, and thus, a clear molecular explanation for how KIF1A mutations lead to neuropathy is not available. In this study, we established in vitro motility assays with purified full-length human KIF1A and found that KIF1A mutations associated with the pure form of spastic paraplegia hyperactivate motility of the KIF1A motor. Introduction of the corresponding mutations into Caenorhabditis elegans KIF1A homologue unc-104 revealed abnormal accumulation of SVPs at the tips of axons and increased anterograde axonal transport of SVPs. Our data reveal that hyper-activation of kinesin motor activity, rather than its loss-of-function, is a novel cause of motor neuron disease in humans.\n\nSignificance StatementAnterograde axonal transport supplies organelles and protein complexes throughout axonal processes to support neuronal morphology and function. It has been observed that reduced anterograde axonal transport is associated with neuronal diseases. In contrast, here we show that particular disease-associated mutations in KIF1A, an anterograde axonal motor for synaptic vesicle precursors, induce hyperactivation of KIF1A motor activity and increased axonal transport of synaptic vesicle precursors. Our results advance the knowledge of the regulation of motor proteins and axonal transport and cell biology of motor neuron diseases.

cell biology↗

bioRxiv2019

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances reprogramming to epithelial lineages

Mesenchymal-to-epithelial transition (MET) is an important step in cell reprogramming from fibroblasts (a cell type frequently used for this purpose) to various epithelial cell types. However, the mechanism underlying MET induction in fibroblasts remains to be understood. The present study aimed to identify the transcription factors (TFs) that efficiently induce MET in dermal fibroblasts. OVOL2 was identified as a potent inducer of key epithelial genes, and OVOL2 cooperatively enhanced MET induced by HNF1A, TP63, and KLF4, which are known reprogramming TFs to epithelial lineages. In TP63/KLF4-induced keratinocyte-like cell-state reprogramming, OVOL2 greatly facilitated the activation of epithelial and keratinocyte-specific genes. This was accompanied by enhanced changes in chromatin accessibility across the genome. Mechanistically, motif enrichment analysis revealed that the target loci of KLF4 and TP63 become accessible upon induction of TFs, whereas the OVOL2 target loci become inaccessible. This indicates that KLF4 and TP63 positively regulate keratinocyte-associated genes whereas OVOL2 suppresses fibroblast-associated genes. The exogenous expression of OVOL2 therefore disrupts fibroblast lineage identity and facilitates fibroblast cell reprogramming into epithelial lineages cooperatively with tissue-specific reprogramming factors. Identification of OVOL2 as a MET inducer and an epithelial reprogramming enhancer in fibroblasts provides new insights into cellular reprogramming improvement for future applications.

cell biology↗