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Ota, N.

Publications and source records attributed to Ota, N..

12 recordsLinked to original sources
bioRxiv2026

A Novel Conjugation System in AMR-associated pELF-type Linear Plasmids of Enterococcus faecium.

The pELF-type linear plasmid is a unique transconjugative plasmid that disseminates various antimicrobial resistance (AMR) genes (e.g., vancomycin resistance in vancomycin-resistant Enterococcus faecium, [VRE]), leading to hospital outbreaks worldwide. Despite evidence of its role in AMR gene expansion, the molecular mechanisms underlying conjugative transfer of pELF-type plasmids have been poorly understood due to their unique linear structure and the lack of convenient genetic engineering tools adapted to E. faecium strain. Herein, we focused on a putative transconjugation-associated gene cluster, named the trapELF cluster, encoded on pELF2, a vanA-type vancomycin resistance gene-harboring plasmid. RNA-seq analysis of the pELF2 plasmid identified a putative operon containing an ftsK-like ATPase-encoding gene and an additional 10 genes as candidates for conjugative transfer of pELF-type linear plasmids. We constructed isogenic deletion mutants for these 10 genes and revealed that two genes, designated traC and traD, are essential for the conjugative transfer of pELF2 to a recipient strain. Inducible overexpression of the tra genes in trans from an ectopic shuttle vector confirmed the essentiality of traC and traD for conjugative transfer. Promoter assay using a luciferase reporter plasmid revealed that the upstream region of the putative tra operon possesses functional promoter activity characterized by constitutive strong transcriptional expression. Furthermore, we observed membrane localization for a fluorescent protein fusion of TraC, but not for that of TraD. Based on these findings, we propose a working model for the unique molecular machinery for the transconjugation of pELF-type linear plasmids. Author SummaryEnterococci are among the opportunistic pathogens of greatest global concern due to their multidrug resistance, and it is well established that various plasmids mediate horizontal transfer of resistance genes in this species, converting susceptible strains into resistant ones. While most enterococcal plasmids have a circular structure, a linear pELF-type plasmid was recently discovered. Since then, pELF-type plasmids have been reported worldwide as important vehicles for antimicrobial resistance genes, but their mechanism of transfer has remained unknown. In this study, we have, for the first time, successfully identified the genes required for the conjugative transfer of pELF-type plasmids. We confirmed that these genes are absent from known conjugative plasmids, yet are highly conserved among pELF-type plasmid sequences deposited in public databases. Taken together, these findings suggest that pELF-type plasmids possess a unique transfer mechanism that reflects their distinctive molecular architecture.

microbiology↗
bioRxiv2024

Multi-timescale neural adaptation underlying long-term musculoskeletal reorganization.

The central nervous system (CNS) can effectively control body movements despite environmental changes. While much is known about adaptation to external environmental changes, less is known about responses to internal bodily changes. This study investigates how the CNS adapts to long-term alterations in the musculoskeletal system using a tendon transfer model in non-human primates. We surgically relocated finger flexor and extensor muscles to examine how the CNS adapts its strategy for finger movement control by measuring muscle activities during grasping tasks. Two months post-surgery, the monkeys demonstrated significant recovery of grasping function despite the initial disruption. Our findings suggest a two-phase CNS adaptation process: an initial phase enabling function with the transferred muscles, followed by a later phase abandoning this enabled function and restoring a control strategy that, while potentially less conflicted than the maladaptive state, resembled the original pattern, possibly representing a good enough solution. These results highlight a multi-phase CNS adaptation process with distinct time constants in response to sudden bodily changes, offering potential insights into understanding and treating movement disorders. SIGNIFICANCE STATEMENTAfter major changes to the bodys mechanics, the nervous system adapts using strategies on multiple timescales. Our primate tendon transfer study shows that core muscle synergy groupings remain stable, reflecting a default to modular control. However, the activation of these synergies changes dramatically; an initial, rapid swap of their timing proves to be maladaptive, impairing motor function. This conflict is only resolved through the gradual development of slower, compensatory strategies over several weeks. This process highlights the fundamental tension the CNS faces when its reliance on stable motor modules conflicts with the need for flexible control, offering insights into neural plasticity and staged rehabilitation.

neuroscience↗
bioRxiv2023

Evidence that recent climatic changes have expanded the potential geographic range of the Mediterranean fruit fly

The species distributions migration poleward and into higher altitudes in a warming climate is especially concerning for economically important insect pest species, as their introduction can potentially occur in places previously considered unsuitable for year-round survival. We explore the expansion of the climatically suitable areas for a horticultural pest, the Mediterranean fruit fly (medfly) Ceratitis capitata (Diptera, Tephritidae), with an emphasis on Europe and California. We reviewed and refined a published CLIMEX model for C. capitata, taking into consideration new records in marginal locations, with a particular focus on Europe. To assess the model fit and to aid in interpreting the meaning of the new European distribution records, we used a time series climate dataset to explore the temporal patterns of climate suitability for C. capitata from 1970 to 2019. At selected bellwether sites in Europe, we found statistically significant trends in increasing climate suitability, as well as a substantial northward expansion in the modelled potential range. In California, we also found a significant trend of northward and altitudinal expansion of areas suitable for C. capitata establishment. These results provide further evidence of climate change impacts on species distributions and the need for innovative responses to increased invasion threats.

ecology↗
bioRxiv2022

Deep learning for histopathological subtyping and grading of lung adenocarcinoma

The histopathological distinction of lung adenocarcinoma (LADC) subtypes is subject to high inter-observer variability, which can compromise the optimal assessment of the patient prognosis. Therefore, this study developed convolutional neural networks (CNNs) capable of distinguishing LADC subtypes and predicting disease-specific survival, according to the LADC tumour grades established recently by the International Association for the Study of Lung Cancer pathology committee. Consensus LADC ground truth histopathological images were obtained from seventeen expert pulmonary pathologists and one pathologist in training. Two deep learning models (AI-1 and AI-2) were trained with EfficientNet b3 architecture to predict eight different LADC classes (lepidic, acinar, papillary, micropapillary, solid, invasive mucinous adenocarcinoma, other carcinoma types, and no carcinoma cells). Furthermore, the trained models were tested on an independent cohort of 133 patients. The models achieved high precision, recall, and F1-scores exceeding 0.90 for most of the LADC classes. Clear stratification of the three LADC grades was reached in predicting the disease-specific survival by the two models. Moreover, the grading prediction of one of the trained models was more accurate than those of 14 out of 15 pulmonary pathologists involved in the study (p=0.0003). Both trained models showed high stability in the segmentation of each pair of predicted grades with low variation in the hazard ratio across 200 bootstrapped samples. These findings indicate that the trained CNNs improve the diagnostic accuracy of the pathologist, standardise LADC subtype recognition, and refine LADC grade assessment. Thus, the trained models are promising tools that may assist in the routine evaluation of LADC subtypes and grades in clinical practice.

pathology↗
bioRxiv2022

PNPO-PLP Axis Senses Prolonged Hypoxia by Regulating Lysosomal Activity

Oxygen is critical for all metazoan organisms on the earth and impacts various biological processes in physiological and pathological conditions. While oxygen sensing systems inducing acute hypoxic response, including HIF pathway, have been identified, those operating in prolonged hypoxia remain to be elucidated. Here, we show that pyridoxine 5-phosphate oxidase (PNPO) that catalyzes bioactivation of vitamin B6 serves as an oxygen sensor and regulates lysosomal activity in macrophages. Decline of PNPO activity under prolonged hypoxia reduced an active form of vitamin B6, pyridoxal 5-phosphate (PLP), and inhibited lysosomal activity, leading to the augmentation of inflammatory response of macrophages. The PNPO-PLP axis creates a distinct layer of oxygen sensing, which gradually turns down and up the PLP-dependent metabolism according to prolonged changes in oxygen availability.

biochemistry↗
bioRxiv2021

The PAF1 complex cell-autonomously promotes oogenesis in Caenorhabditis elegans

The RNA polymerase II-associated factor 1 complex (PAF1C) is a protein complex that consists of LEO1, RTF1, PAF1, CDC73, and CTR9, and has been shown to be involved in Pol II-mediated transcriptional and chromatin regulation. Although it has been shown to regulate a variety of biological processes, the precise role of the PAF1C during germ line development has not been clarified. In this study, we found that reduction in the function of the PAF1C components, LEO-1, RTFO-1, PAFO-1, CDC-73, and CTR-9, in Caenorhabditis elegans affects cell volume expansion of oocytes. Defects in oogenesis were also confirmed using an oocyte maturation marker, OMA-1::GFP. While four to five OMA-1::GFP-positive oocytes were observed in wild-type animals, their numbers were significantly decreased in pafo-1 mutant and leo-1(RNAi), cdc-73(RNAi), and pafo-1(RNAi) animals. Expression of a functional PAFO-1::mCherry transgene in the germline significantly rescued the oogenesis-defective phenotype of the pafo-1 mutants, suggesting that expression of the PAF1C in germ cells is required for oogenesis. Notably, overexpression of OMA-1::GFP partially rescued the oogenesis defect in the pafo-1 mutants. Based on our findings, we propose that the PAF1C promotes oogenesis in a cell-autonomous manner by positively regulating the expression of genes involved in oocyte maturation.

developmental biology↗
bioRxiv2021

Non-invasive human skin transcriptome analysis using mRNA in skin surface lipids

Non-invasive acquisition of mRNA data from the skin would be extremely useful for understanding skin physiology and diseases. Inspired by the holocrine process, in which the sebaceous glands secrete cell contents into the sebum, we focused on the possible presence of mRNAs in skin surface lipids (SSLs). We found that measurable human mRNAs exist in SSLs, where sebum protects them from degradation by RNases. The AmpliSeq transcriptome analysis was modified to measure SSL-RNAs, and our results revealed that SSL-RNAs predominantly contained mRNAs derived from sebaceous glands, epidermis, and hair follicles. Analysis of SSL-RNAs non-invasively collected from patients with atopic dermatitis revealed significantly increased expression of inflammation-related genes and decreased expression of terminal differentiation-related genes, consistent with the results of previous reports. Further, we found that lipid synthesis-related genes were downregulated in the sebaceous glands of patients with atopic dermatitis. These results indicate that the analysis of SSL-RNAs is promising to understand the pathophysiology of skin diseases.

molecular biology↗
bioRxiv2020

Overlapping and non-overlapping roles of the class-I histone deacetylase-1 corepressors, LET-418, SIN-3, and SPR-1 in Caenorhabditis elegans embryonic development

Histone deacetylases (HDACs) are divided into four classes. Class-I HDAC, HDAC-1 forms three types of complexes, namely the Nucleosome Remodeling Deacetylase complex, the Sin3 complex, and the CoREST complex, with specific corepressor component Mi2/CHD-3, Sin3, and RCOR1 in human, respectively. The functions of these HDAC-1 complexes are regulated by their corepressors, however, their exact mechanistic roles in several biological processes remain unexplored, such as in embryonic development. Here, we report that each of the corepressors, LET-418, SIN-3, and SPR-1, the homologous of Mi2, Sin3, and RCOR1, respectively, were expressed throughout Caenorhabditis elegans embryonic development and served essential roles in the process. Moreover, genetic analysis suggested that three pathways (i.e., LET-418- SIN-3-SPR-1, SIN-3-SPR-1, and LET-418) participated in embryonic development. Our terminal-phenotype observations of single mutants of each corepressor implied that LET-418, SIN-3, and SPR-1 played similar roles in promoting advancement to the middle and late embryonic stages. Genome-wide comparative-transcriptome analysis indicated that 47.5% and 42.3% of genes were commonly increased and decreased in sin-3 and spr-1 mutants, respectively. These results suggest that among the three pathways studied, the SIN-3-SPR-1 pathway mainly serves to regulate embryonic development. Comparative-Gene Ontology analysis indicated that these three pathways played overlapping and distinct roles in regulating C. elegans embryonic development.

developmental biology↗
bioRxiv2020

Enhancer Remodeling Promotes Tumor-Initiating Activity in NRF2-Activated Non-Small Cell Lung Cancers

Transcriptional dysregulation, which can be caused by genetic and epigenetic alterations, is a fundamental feature of many cancers. A key cytoprotective transcriptional activator, NRF2, is often aberrantly activated in non-small cell lung cancers (NSCLCs) and supports both aggressive tumorigenesis and therapeutic resistance. Herein, we found that persistently activated NRF2 in NSCLCs generates enhancers at gene loci that are not normally regulated by transiently activated NRF2 under physiological conditions. Elevated accumulation of CEBPB in NRF2-activated NSCLCs was found to be one of the prerequisites for establishment of the unique NRF2-dependent enhancers, among which NOTCH3 enhancer was shown to be critical for the promotion of tumor-initiating activity. Enhancer remodeling mediated by NRF2-CEBPB cooperativity promotes tumor-initiating activity and drives malignancy of NRF2-activated NSCLCs via establishment of the NRF2-NOTCH3 regulatory axis.

cancer biology↗
bioRxiv2018

Coffee polyphenols prevent cognitive dysfunction and suppress amyloid β plaques in APP/PS2 transgenic mouse

Epidemiological studies have found that habitual coffee consumption may reduce the risk of Alzheimers disease. Coffee contains numerous phenolic compounds (coffee polyphenols) such as chlorogenic acids. However, evidence demonstrating the contribution of chlorogenic acids in preventing cognitive dysfunction induced by Alzheimers disease is limited. In this study, we investigated the effect of chlorogenic acids on prevention of cognitive dysfunction in APP/PS2 transgenic mouse model of Alzheimers disease. Five-week-old APP/PS2 mice were administered a diet supplemented with coffee polyphenols daily for 5 months. The memory and cognitive function of mice was determined using the novel object recognition test, the Morris water maze test, and the step-through passive avoidance test. We found that chronic treatment with coffee polyphenols prevented cognitive dysfunction and significantly reduced hippocampal A{beta} deposition. We then determined the effect of 5-caffeoylquinic acid, one of the primary components of coffee polyphenols, on A{beta} formation. 5-Caffeoylquinic acid did not inhibit A{beta} fibrillation, but degraded A{beta} fibrils in a dose-dependent manner. In conclusion, these results demonstrate that coffee polyphenols prevented cognitive deficits and alleviated A{beta} plaque deposition via disaggregation of A{beta} in APP/PS2 mouse.

animal behavior and cognition↗
bioRxiv2018

Supporting global biodiversity assessment through high-resolution macroecological modelling: Methodological underpinnings of the BILBI framework

AimGlobal indicators of change in the state of terrestrial biodiversity are often derived by intersecting observed or projected changes in the distribution of habitat transformation, or of protected areas, with underlying patterns in the distribution of biodiversity. However the two main sources of data used to account for biodiversity patterns in such assessments - i.e. ecoregional boundaries, and vertebrate species ranges - are typically delineated at a much coarser resolution than the spatial grain of key ecological processes shaping both land-use and biological distributions at landscape scale. Species distribution modelling provides one widely used means of refining the resolution of mapped species distributions, but is limited to a subset of species which is biased both taxonomically and geographically, with some regions of the world lacking adequate data to generate reliable models even for better-known biological groups.\n\nInnovationMacroecological modelling of collective properties of biodiversity (e.g. alpha and beta diversity) as a correlative function of environmental predictors offers an alternative, yet highly complementary, approach to refining the spatial resolution with which patterns in the distribution of biodiversity can be mapped across our planet. Here we introduce a new capability - BILBI (the Biogeographic Infrastructure for Large-scaled Biodiversity Indicators) - which has implemented this approach by integrating advances in macroecological modelling, biodiversity informatics, remote sensing and high-performance computing to assess spatial-temporal change in biodiversity at ~1km grid resolution across the entire terrestrial surface of the planet. The initial implementation of this infrastructure focuses on modelling beta-diversity patterns using a novel extension of generalised dissimilarity modelling (GDM) designed to extract maximum value from sparsely and unevenly distributed occurrence records for over 400,000 species of plants, invertebrates and vertebrates.\n\nMain conclusionsModels generated by BILBI greatly refine the mapping of beta-diversity patterns relative to more traditional biodiversity surrogates such as ecoregions. This capability is already proving of considerable value in informing global biodiversity assessment through: 1) generation of indicators of past-to-present change in biodiversity based on observed changes in habitat condition and protected-area coverage; and 2) projection of potential future change in biodiversity as a consequence of alternative scenarios of global change in drivers and policy options.

ecology↗