Biology subjects

Nonaka, S.

Publications and source records attributed to Nonaka, S..

12 recordsLinked to original sources

bioRxiv2026

Extrinsic MMPs drive epithelial shape change via basal ECM disassembly in the Drosophila wing disc

Epithelial morphogenesis generates complex tissue architectures with remarkable reproducibility, yet how such self-organized shape transformations are triggered in vivo remains poorly understood. Here, we show that epithelial morphogenesis during early pupal development of the Drosophila wing disc is regulated non-autonomously through remodeling of the basal extracellular matrix (ECM) by neighboring tissues. Live imaging analyses reveal a previously unrecognized epithelial shape transition at the larval-to-pupal stage, in which the wing disc epithelium transforms from a concave to a convex configuration. Rather than being driven autonomously by the epithelium, this morphogenetic transition depends on adjacent non-epithelial cell populations, including myoblasts and tracheal cells. Mechanistically, systemic ecdysone signaling activates Mmp1 and Mmp2 in these neighboring tissues, leading to spatially restricted basal ECM disassembly that permits collective epithelial shape reorganization. Together, our findings establish ECM remodeling at tissue interfaces as a non-autonomous regulatory layer that enables epithelial self-organization during development.

developmental biology↗

bioRxiv2025

Three-dimensional and molecular brain atlas of the hagfish reveals the evolutionary origin and early diversification of the vertebrate brain

Hagfish and lampreys form the clade cyclostomes, the earliest branching lineage of the vertebrates. Although hagfish are generally assumed to have experienced intense modifications, its brain development shows certain ancestral patterns that are secondarily lost in the lamprey. Therefore, hagfish provides key insights into the evolutionary origin and early diversification of the vertebrate brain. However, neuroanatomical information of the hagfish brain is substantially limited today due to its sources based on old-fashioned methodology alone. Here, we provide a detailed brain atlas of the adult hagfish, based on three-dimensional reconstruction and expression analysis of genetic markers for major neuronal transmitters. Through our analyses, we found the following key characteristics. First, the dopaminergic system appears to be distributed more broadly than previously thought in the hagfish brain, implying that dopamine is involved in various neural functions. Second, the previously suggested "primordial cerebellum" area in hagfish shows notable affinity to the cerebellum-like octavolateral structures of the jawed vertebrate hindbrain. Last, the gene expression profile suggests a hippocampus-equivalent brain region in hagfish, that is, the ventrolateral subnucleus of the central prosencephalic complex (NCvl). This study highlights conserved and diversified neuroarchitecture of the hagfish brain, providing a pivotal reference for further studies.

evolutionary biology↗

bioRxiv2025

Longitudinal analysis of antibody titers after primary and booster mRNA COVID-19 vaccination can identify individuals at risk for breakthrough infection

A key issue in the post-COVID-19 era is the ongoing administration of COVID-19 vaccines. Repeated vaccination is essential for preparing against currently circulating and newly emerging SARS-CoV-2 variants while enabling people to continue with daily life. Optimizing vaccination strategies is crucial to efficiently manage medical resources and establish an effective vaccination framework. Therefore, it is important to quantitatively understand vaccine-induced immunity dynamics and to be able to identify poor responders with lower sustained antibody titers as potential priorities for revaccination. We investigated longitudinal antibody titer data in a cohort of 2,526 people in Fukushima, Japan, from April 2021 to November 2022 for whom basic demographic and health information was available. Using mathematical modeling and machine learning, we stratified the time-course patterns of antibody titers after 2 primary doses and 1 booster dose of mRNA COVID-19 vaccines. We identified 3 notable populations, which we refer to as the durable, the vulnerable, and the rapid-decliner populations, approximately half of which remained in the same population after the booster dose. Notably, the rapid-decliner population experienced earlier infections than the others. Furthermore, when comparing IgG(S) titers, IgA(S) titers, and T-spot counts between participants who experienced breakthrough infections after booster vaccination and those who did not, we found that IgA(S) titers were significantly lower in breakthrough infected participants during the early stage after booster vaccination. Our computational approach is adaptable to various types of vaccinations. This flexibility can inform policy decisions on vaccine distribution to enhance immunity both in future pandemics and in the post-COVID-19 era.

immunology↗

bioRxiv2024

A long shelf-life melon created via CRISPR/Cas9 RNP-based in planta genome editing

We developed a non-culture and DNA-free genome editing technique for melon using in plant Particle Bombardment (iPB-RNP). The method was employed to create CmACO1 mutants. One of the mutant lines exhibited an extended shelf life due to ethylene deficiency during fruit ripening. As no cell culture step is involved, the iPB-RNP method is expected to overcome limitations associated with conventional genome editing, such as genotype dependency and somatic variations. Thus, this methodology holds significant potential for application in commercial melon breeding and across a wide range of Cucurbitaceae species.

plant biology↗

bioRxiv2023

Discovery of essential kinetoplastid-insect adhesion proteins and their function in Leishmania-sand fly interactions

Leishmania species, members of the kinetoplastid parasites, cause leishmaniasis, a neglected tropical disease, in millions of people worldwide1. Leishmania has a complex life cycle with multiple developmental forms, as it cycles between a sand fly vector and a mammalian host; understanding their life cycle is critical to understanding disease spread2. One of the key life cycle stages is the haptomonad form, which is attached to the insect through its flagellum. This adhesion, which is conserved across kinetoplastid parasites, is implicated to have an important function within their life cycles and hence on disease transmission3-5. Here, we discovered kinetoplastid-insect adhesion proteins (KIAPs), which are localised in the attached haptomonad flagellum. Deletion of these KIAPs impaired cell adhesion in vitro and prevented Leishmania from colonising the stomodeal valve in the sand fly, without affecting cell growth. This result will provide important insights for a comprehensive understanding of the Leishmania life cycle.

microbiology↗

bioRxiv2023

Left-right asymmetry is formed in the basal bodies of the mouse node cilia in a cilia motility-dependent manner

Laterality of the shapes and arrangements of the visceral organs in mice is determined in the node, a small cavity found at the ventral side of 7.5 dpc (days post coitum) embryos. On the node cells, motile cilia which are tilted toward the posterior side of the embryos show clockwise movement and thus produce fluid flow in the node toward the left side of the embryos. This left-ward flow regulates left/right (L/R) asymmetric gene expressions and L/R asymmetric morphogenesis in later stages. Structurally, node cilia have the characteristics of primary cilia and their basal body (mother centriole) is accompanied by a daughter centriole. Here, to obtain insights into the process of symmetry breaking by node cilia, we investigated whether the structure of the cilia themselves have L/R asymmetry, and found that positions of the daughter centrioles become biased to the right side of the mother centrioles in a stage-dependent manner. We found that this L/R asymmetry of the basal bodies is absent in iv mutant mice, in which node cilia are immotile, suggesting that formation of this L/R asymmetry in the basal bodies requires cilia motility. It has been reported that culturing embryos in a flow chamber with artificial counter-flow, which is toward the opposite direction to the endogenous leftward flow in the node, results in reversed laterality of the visceral organs in later stages. However, we found that applying such artificial counter-flow did not reverse the L/R asymmetry of the basal bodies, and the daughter centrioles were still biased to the right side of the mother centrioles, suggesting that the L/R asymmetry of the basal bodies is formed independently from the direction of the fluid flow in the node and that it is independent from the laterality of the visceral organs. Although the biological significance of this phenomenon is unknown so far, these results suggest that node cilia have a previously unknown mechanism to produce L/R asymmetry in the basal bodies inside the cells in early development, independently from the canonical fluid flow-dependent L/R determining pathway.

developmental biology↗

bioRxiv2022

Formation and three-dimensional architecture of Leishmania adhesion in the sand fly vector

Attachment to a substrate to maintain position in a specific ecological niche is a common strategy across biology, especially for eukaryotic parasites. During development in the sand fly vector, the eukaryotic parasite Leishmania adheres to the stomodeal valve, as the specialised haptomonad form. Dissection of haptomonad adhesion is a critical step for understanding parasite transmission. Nevertheless, haptomonad studies are limited, as this is a technically challenging life cycle form to investigate. Here, we have combined three-dimensional electron microscopy approaches, including serial block face scanning electron microscopy (SBFSEM) and serial tomography to dissect the organisation and architecture of haptomonads in the sand fly. We showed that the attachment plaque contains distinct structural elements. Using time-lapse light microscopy, we identified five stages of haptomonad differentiation, and showed that calcium is necessary for haptomonad adhesion to the surface. This study provides the structural and regulatory foundations of the haptomonad form, which are critical for a holistic understanding of Leishmania transmission.

microbiology↗

bioRxiv2022

Epigenetically distinct synaptic architecture in clonal compartments in the teleostean dorsal pallium

The dorsal telencephalon (i.e. the pallium) exhibits high anatomical diversity across vertebrate classes. The mammalian dorsal pallium accommodates a six layered-structure, the neocortex, whereas the teleostean dorsal pallium possesses various compartmentalized structures among species. The development, function and evolution of the fish dorsal pallium remain unillustrated. Here, we analyzed the structure and epigenetic landscapes of cell lineages in the telencephalon of medaka fish (Oryzias latipes) which possesses a clearly delineated dorsal pallium (the Dd2 region). We found that different pallial regions, including Dd2, are formed by mutually exclusive clonal units, and that each pallium compartment exhibits a distinct epigenetic landscape. In particular, Dd2 possesses a unique open chromatin pattern that preferentially targets synapse-related genes. Indeed, Dd2 shows a high density of synapses, which might reflect strong plasticity. Finally, we identified several transcription factors as candidate regulators for the Dd2, which are partially shared with the human neocortex and hippocampus.

neuroscience↗

bioRxiv2020

Brain hierarchy score: Which deep neural networks are hierarchically brain-like?

Achievement of human-level image recognition by deep neural networks (DNNs) has spurred interest in whether and how DNNs are brain-like. Both DNNs and the visual cortex perform hierarchical processing, and correspondence has been shown between hierarchical visual areas and DNN layers in representing visual features. Here, we propose the brain hierarchy (BH) score as a metric to quantify the degree of hierarchical correspondence based on the decoding of individual DNN unit activations from human brain activity. We find that BH scores for 29 pretrained DNNs with varying architectures are negatively correlated with image recognition performance, indicating that recently developed high-performance DNNs are not necessarily brain-like. Experimental manipulations of DNN models suggest that relatively simple feedforward architecture with broad spatial integration is critical to brain-like hierarchy. Our method provides new ways for designing DNNs and understanding the brain in consideration of their representational homology.

neuroscience↗

bioRxiv2020

Visualizing ATP Dynamics in Live Mice

ABSTRACTAnalysis of the dynamics of adenosine triphosphate (ATP) is vital to quantitatively define the actual roles of ATP in biological activities. Here, we applied a genetically encoded Förster resonance energy transfer biosensor “GO-ATeam” and created a transgenic mouse model that allows systemic ATP levels to be quantitatively, sensitively, noninvasively, and spatiotemporally measured under physiological and pathological conditions. We used this model to readily conduct intravital imaging of ATP dynamics under three different conditions: during exercise, in all organs and cells; during myocardial infarction progression; and in response to the application of cardiotoxic drugs. These findings provide compelling evidence that the GO-ATeam mouse model is a powerful tool to investigate the multifarious functions of cellular ATP in vivo with unprecedented spatiotemporal resolution in real-time. This will inform predictions of molecular and morphological responses to perturbations of ATP levels, as well as the elucidation of physiological mechanisms that control ATP homeostasis.One Sentence Summary Intravital real-time imaging of ATP dynamics in multiple organs using GO-ATeam mice, can be used to quantitatively, sensitively, noninvasively, and spatiotemporally measure systemic ATP levels and provide a platform for preclinical pharmacological studies.Competing Interest StatementM.Yamamoto is involved in a pending patent related to GO-ATeam mice. H.I. holds a patent for ATeam probe. All other authors declare no competing interests.View Full Text

physiology↗

bioRxiv2018

Improved G-AgarTrap: A highly efficient transformation method for intact gemmalings of the liverwort Marchantia polymorpha

Liverworts are key species for studies of plant evolution, occupying a basal position among the land plants. Marchantia polymorpha has emerged as a highly studied model liverwort, and many relevant techniques, including genetic transformation, have been established for this species. Agrobacterium-mediated transformation is widely used in many plant species because of its low cost. Recently, we developed a simplified Agrobacterium-mediated method for transforming M. polymorpha, known as AgarTrap (agar-utilized transformation with pouring solutions). The AgarTrap procedure, which involves culturing the liverwort tissue in various solutions on a single solid medium, yields up to a hundred independent transformants. AgarTrap is a simple procedure, requiring minimal expertise, cost, and time.\n\nHere, we investigated four factors that influence AgarTrap transformation efficiency: (1) humidity, (2) surfactant in the transformation buffer, (3) Agrobacterium strain, and (4) light/dark condition. We adapted the AgarTrap protocol for transforming intact gemmalings, achieving an exceptionally high transformation efficiency of 97%. The improved AgarTrap method will enhance the molecular biological study of M. polymorpha. The present study also provides new possibilities for improving transformation techniques for a variety of plant species.

plant biology↗

bioRxiv2018

System level analyses of motor-related neural activities in larval Drosophila

The way in which the central nervous system (CNS) governs animal movement is complex and difficult to solve solely by the analyses of muscle movement patterns. We tackle this problem by observing the activity of a large population of neurons in the CNS of larval Drosophila. We focused on two major behaviors of the larvae, forward and backward locomotion, and analyzed the neuronal activity related to these behaviors during fictive locomotion that spontaneously occurs in the isolated CNS. We expressed genetically-encoded calcium indicator, GCaMP, and a nuclear marker in all neurons and used digital scanned light-sheet microscopy to record neural activities in the entire ventral nerve cord at a fast frame rate. We developed image processing tools that automatically detect the cell position based on the nuclear staining and allocate the activity signals to each detected cell. We also applied a machine learning-based method that we developed recently to assign motor status in each time frame. Based on these methods, we find cells whose activity is biased to forward versus backward locomotion and vice versa. In particular, we identified a group of neurons near the boundary of subesophageal zone (SEZ) and thoracic neuromeres, which are strongly active during an early phase of backward but not forward fictive locomotion. Our experimental procedure and computational pipeline enable systematic identification of neurons to show characteristic motor activities in larval Drosophila.

neuroscience↗