Updated on 2025/07/06

写真a

 
TAINAKA Kazuki
 
Organization
Brain Research Institute Professor
Title
Professor
External link

Degree

  • 博士(工学) ( 2006.3   京都大学 )

Research Interests

  • Bioorganic Chemistry

  • Photochemistry

  • 組織透明化

  • 神経病理学

  • ケミカルバイオロジー

  • イメージング

Research Areas

  • Life Science / Anatomy and histopathology of nervous system

  • Nanotechnology/Materials / Bio chemistry

Research History (researchmap)

  • Niigata University   Brain Research Institute   Professor

    2021.6

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    Country:Japan

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  • Niigata University   Brain Research Institute   Tenure-track Professor

    2018.10 - 2021.5

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  • Niigata University   Brain Research Institute   Specially Appointed Professor

    2017.1 - 2018.9

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  • The University of Tokyo   Lecturer

    2013.4 - 2016.12

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  • 理化学研究所   生命システム研究センター   研究員

    2010.10 - 2013.3

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  • Kyoto University   Institute of Advanced Energy   Assistant Professor

    2008.2 - 2010.9

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  • Osaka University   The Institute of Scientific and Industrial Research

    2007.4 - 2008.1

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  • Osaka University   The Institute of Scientific and Industrial Research

    2006.10 - 2007.3

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  • 理化学研究所   岡本独立主幹研究ユニット   ユニット研究員

    2006.4 - 2006.9

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  • Kyoto University

    2003.4 - 2006.3

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Research History

  • Niigata University   Brain Research Institute Basic Neuroscience Branch   Professor

    2020.4

  • Niigata University   Brain Research Institute Center for Bioresources   Professor

    2018.10 - 2020.3

  • Niigata University   Brain Research Institute   Specially Appointed Professor

    2017.1 - 2018.9

Education

  • Kyoto University   工学研究科   合成・生物化学専攻

    2001.4 - 2006.3

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  • Kyoto University   Faculty of Engineering   School of Industrial Chemistry

    1997.4 - 2001.3

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Professional Memberships

  • JAPANESE SOCIETY FOR CHEMICAL BIOLOGY

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  • THE JAPANESE PHOTOCHEMISTRY ASSOCIATION

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  • THE JAPANESE PHARMACOLOGICAL SOCIETY

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  • THE CHEMICAL SOCIETY OF JAPAN

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  • THE JAPANESE SOCIETY OF NEUROPATHOLOGY

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Papers

  • Blood-brain barrier dysfunction in multiple system atrophy: A human postmortem study. International journal

    Ramil Gabdulkhaev, Hiroshi Shimizu, Masato Kanazawa, Yasuko Kuroha, Arika Hasegawa, Jiro Idezuka, Kazuki Tainaka, Osamu Onodera, Akiyoshi Kakita

    Neuropathology : official journal of the Japanese Society of Neuropathology   45 ( 3 )   210 - 222   2025.6

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    Multiple system atrophy (MSA) is a rare neurodegenerative disease characterized by an accumulation of phosphorylated α-synuclein (p-αsyn) in oligodendrocytes in the form of glial cytoplasmic inclusions (GCIs). In MSA, not only mature oligodendrocytes but also oligodendrocyte precursor cells (OPCs) are affected. The latter play an important role in remyelination by differentiating into mature oligodendrocytes, as well as maintaining the blood-brain barrier (BBB) by promoting the expression of tight junction proteins. We have hypothesized that in MSA, the BBB is impaired as a result of aberrant interactions between affected OPCs and the cerebral vasculature. To verify this hypothesis, we conducted a neuropathological examination of postmortem brains from MSA patients and control subjects, focusing on the primary motor area, one of the main regions affected in MSA. Using double immunofluorescence, we quantified the expression of tight junction protein claudin-5 in capillary endothelial cells and found that it was significantly lower in MSA than in controls in both the gray matter and white matter. Furthermore, a significantly higher amount of fibrinogen was extravasated into the brain parenchyma in MSA patients than in controls. In addition, leakage of IgG was detected almost specifically in MSA brain parenchyma, as visualized in three dimensions by combining techniques of chemical tissue clearing and light sheet microscopy. Finally, we confirmed accumulation of p-αsyn-positive GCIs along the cerebral vasculature within OPCs. These results suggest that BBB dysfunction and associated fibrinogen extravasation are constant findings in MSA, presumably triggered by the deposition of p-αsyn in perivascular OPCs.

    DOI: 10.1111/neup.13021

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  • Imaging Heterogeneous Patterns of Aminopeptidase N Activity in Hierarchical Tissue Structures Through High-Resolution Whole-Organ 3D Mapping. International journal

    Bo Yi, Hiroyuki Yatabe, Daichi M Sakamoto, Iori Tamura, Yutaro Saito, Naoki Yamada, Ruki Ashikaga, Masafumi Kuroda, Shimpei I Kubota, Kazuki Tainaka, Shinsuke Sando

    Angewandte Chemie (International ed. in English)   64 ( 22 )   e202504668   2025.5

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    Enzymes play a crucial role in regulating physiological functions, and abnormal enzyme activity is associated with various pathological conditions. Precise imaging of enzyme activity in tissues, providing detailed spatial and quantitative information, advances our understanding of physiological and pathological processes. Despite their importance, there is still a lack of methods for high-resolution 3D imaging of enzyme activity across entire tissues. In this research, we report a methodology for high-resolution, whole-organ 3D mapping of enzyme activity, which combines tissue clearing with an activity-based covalent chemical probe. Focusing on aminopeptidase N (APN) as a representative target of peptidase, we developed ANA-o-BODIPY, an activity-based covalent fluorescent probe compatible with tissue clearing for imaging APN activity. Upon activation by APN, ANA-o-BODIPY produces a reactive intermediate, aza-quinone methide, which covalently binds to proximal proteins. This covalent probe is successfully utilized to record the location of APN activity during the tissue-clearing process. By combining the probe with tissue clearing, we have achieved high-resolution 3D mapping of APN activity across whole organs for the first time. Moreover, this advancement allowed us to visualize the heterogeneity of APN activity in individual tubular structures and to uncover the inhibitory effects of different APN inhibitors.

    DOI: 10.1002/anie.202504668

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  • Nature visible only digitally. International journal

    Yasuhiro Iba, Aya Kubota, Yusuke Takeda, Mehmet Oguz Derin, Shin Ikegami, Jörg Mutterlose, Takahiro Harada, Tomonori Takeuchi, Kazuki Tainaka

    Patterns (New York, N.Y.)   6 ( 4 )   101210 - 101210   2025.4

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    Recent progress in imaging technology has enabled paleontologists to visualize all fossils inside solid rocks. Consequently, we can now imagine the natural worlds hidden not only inside our research materials but also within the opaque solids of everyday life. Here, we introduce the unique visual-spatial worlds that emerge from inside rocks and the creativity this discovery fosters.

    DOI: 10.1016/j.patter.2025.101210

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  • The activation of the piriform cortex to lateral septum pathway during chronic social defeat stress is crucial for the induction of behavioral disturbance in mice. International journal

    Yuki Okuda, Dongrui Li, Yuzuki Maruyama, Hirokazu Sonobe, Tomoyuki Mano, Kazuki Tainaka, Ryota Shinohara, Tomoyuki Furuyashiki

    Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology   50 ( 5 )   828 - 840   2025.4

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    Chronic stress induces neural dysfunctions and risks mental illnesses. Clinical and preclinical studies have established the roles of brain regions underlying emotional and cognitive functions in stress and depression. However, neural pathways to perceive sensory stimuli as stress to cause behavioral disturbance remain unknown. Using whole-brain imaging of Arc-dVenus neuronal response reporter mice and machine learning analysis, here we unbiasedly demonstrated different patterns of contribution of widely distributed brain regions to neural responses to acute and chronic social defeat stress (SDS). Among these brain regions, multiple sensory cortices, especially the piriform (olfactory) cortex, primarily contributed to classifying neural responses to chronic SDS. Indeed, SDS-induced activation of the piriform cortex was augmented with repetition of SDS, accompanied by impaired odor discrimination. Axonal tracing and chemogenetic manipulation showed that excitatory neurons in the piriform cortex directly project to the lateral septum and activate it in response to chronic SDS, thereby inducing behavioral disturbance. These results pave the way for identifying a spatially defined sequence of neural consequences of stress and the roles of sensory pathways in perceiving chronic stress in mental illness pathology.

    DOI: 10.1038/s41386-024-02034-7

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  • CRISPR/CasRx suppresses KRAS-induced brain arteriovenous malformation developed in postnatal brain endothelial cells in mice

    Shoji Saito, Yuka Nakamura, Satoshi Miyashita, Tokiharu Sato, Kana Hoshina, Masayasu Okada, Hitoshi Hasegawa, Makoto Oishi, Yukihiko Fujii, Jakob Körbelin, Yoshiaki Kubota, Kazuki Tainaka, Manabu Natsumeda, Masaki Ueno

    JCI Insight   9 ( 22 )   2024.11

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    Publishing type:Research paper (scientific journal)   Publisher:American Society for Clinical Investigation  

    DOI: 10.1172/jci.insight.179729

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  • CRISPR/CasRx suppresses KRAS-induced brain arteriovenous malformation developed in postnatal brain endothelial cells in mice. International journal

    Shoji Saito, Yuka Nakamura, Satoshi Miyashita, Tokiharu Sato, Kana Hoshina, Masayasu Okada, Hitoshi Hasegawa, Makoto Oishi, Yukihiko Fujii, Jakob Körbelin, Yoshiaki Kubota, Kazuki Tainaka, Manabu Natsumeda, Masaki Ueno

    JCI insight   9 ( 22 )   2024.11

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    Brain arteriovenous malformations (bAVMs) are anomalies forming vascular tangles connecting the arteries and veins, which cause hemorrhagic stroke in young adults. Current surgical approaches are highly invasive, and alternative therapeutic methods are warranted. Recent genetic studies identified KRAS mutations in endothelial cells of bAVMs; however, the underlying process leading to malformation in the postnatal stage remains unknown. Here we established a mouse model of bAVM developing during the early postnatal stage. Among 4 methods tested, mutant KRAS specifically introduced in brain endothelial cells by brain endothelial cell-directed adeno-associated virus (AAV) and endothelial cell-specific Cdh5-CreERT2 mice successfully induced bAVMs in the postnatal period. Mutant KRAS led to the development of multiple vascular tangles and hemorrhage in the brain with increased MAPK/ERK signaling and growth in endothelial cells. Three-dimensional analyses in cleared tissue revealed dilated vascular networks connecting arteries and veins, similar to human bAVMs. Single-cell RNA-Seq revealed dysregulated gene expressions in endothelial cells and multiple cell types involved in the pathological process. Finally, we employed CRISPR/CasRx to knock down mutant KRAS expression, which efficiently suppressed bAVM development. The present model reveals pathological processes that lead to postnatal bAVMs and demonstrates the efficacy of therapeutic strategies with CRISPR/CasRx.

    DOI: 10.1172/jci.insight.179729

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  • Sensory-motor circuit is a therapeutic target for dystonia musculorum mice, a model of hereditary sensory and autonomic neuropathy 6. International journal

    Nozomu Yoshioka, Masayuki Kurose, Hiromi Sano, Dang Minh Tran, Satomi Chiken, Kazuki Tainaka, Kensuke Yamamura, Kenta Kobayashi, Atsushi Nambu, Hirohide Takebayashi

    Science advances   10 ( 30 )   eadj9335   2024.7

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    Mutations in Dystonin (DST), which encodes cytoskeletal linker proteins, cause hereditary sensory and autonomic neuropathy 6 (HSAN-VI) in humans and the dystonia musculorum (dt) phenotype in mice; however, the neuronal circuit underlying the HSAN-VI and dt phenotype is unresolved. dt mice exhibit dystonic movements accompanied by the simultaneous contraction of agonist and antagonist muscles and postnatal lethality. Here, we identified the sensory-motor circuit as a major causative neural circuit using a gene trap system that enables neural circuit-selective inactivation and restoration of Dst by Cre-mediated recombination. Sensory neuron-selective Dst deletion led to motor impairment, degeneration of proprioceptive sensory neurons, and disruption of the sensory-motor circuit. Restoration of Dst expression in sensory neurons using Cre driver mice or a single postnatal injection of Cre-expressing adeno-associated virus ameliorated sensory degeneration and improved abnormal movements. These findings demonstrate that the sensory-motor circuit is involved in the movement disorders in dt mice and that the sensory circuit is a therapeutic target for HSAN-VI.

    DOI: 10.1126/sciadv.adj9335

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  • Click3D: Click reaction across deep tissues for whole-organ 3D fluorescence imaging. International journal

    Iori Tamura, Daichi M Sakamoto, Bo Yi, Yutaro Saito, Naoki Yamada, Jumpei Morimoto, Yoichi Takakusagi, Masafumi Kuroda, Shimpei I Kubota, Hiroyuki Yatabe, Minoru Kobayashi, Hiroshi Harada, Kazuki Tainaka, Shinsuke Sando

    Science advances   10 ( 29 )   eado8471   2024.7

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    Click chemistry offers various applications through efficient bioorthogonal reactions. In bioimaging, pretargeting strategies have often been used, using click reactions between molecular probes with a click handle and reporter molecules that make them observable. Recent efforts have integrated tissue-clearing techniques with fluorescent labeling through click chemistry, allowing high-resolution three-dimensional fluorescence imaging. Nevertheless, these techniques have faced a challenge in limited staining depth, confining their use to imaging tissue sections or partial organs. In this study, we introduce Click3D, a method for thoroughly staining whole organs using click chemistry. We identified click reaction conditions that improve staining depth with our custom-developed assay. The Click3D protocol exhibits a greater staining depth compared to conventional methods. Using Click3D, we have successfully achieved whole-kidney imaging of nascent RNA and whole-tumor imaging of hypoxia. We have also accomplished whole-brain imaging of hypoxia by using the clickable hypoxia probe, which has a small size and, therefore, has high permeability to cross the blood-brain barrier.

    DOI: 10.1126/sciadv.ado8471

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  • descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Reviewed International journal

    Kohei Otomo, Takaki Omura, Yuki Nozawa, Steven J Edwards, Yukihiko Sato, Yuri Saito, Shigehiro Yagishita, Hitoshi Uchida, Yuki Watakabe, Kiyotada Naitou, Rin Yanai, Naruhiko Sahara, Satoshi Takagi, Ryohei Katayama, Yusuke Iwata, Toshiro Shiokawa, Yoku Hayakawa, Kensuke Otsuka, Haruko Watanabe-Takano, Yuka Haneda, Shigetomo Fukuhara, Miku Fujiwara, Takenobu Nii, Chikara Meno, Naoki Takeshita, Kenta Yashiro, Juan Marcelo Rosales Rocabado, Masaru Kaku, Tatsuya Yamada, Yumiko Oishi, Hiroyuki Koike, Yinglan Cheng, Keisuke Sekine, Jun-Ichiro Koga, Kaori Sugiyama, Kenichi Kimura, Fuyuki Karube, Hyeree Kim, Ichiro Manabe, Tomomi Nemoto, Kazuki Tainaka, Akinobu Hamada, Hjalmar Brismar, Etsuo A Susaki

    Nature communications   15 ( 1 )   4941 - 4941   2024.6

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    Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.

    DOI: 10.1038/s41467-024-49131-1

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  • Trial Analysis of Brain Activity Information for the Presymptomatic Disease Detection of Rheumatoid Arthritis. International journal

    Keisuke Maeda, Takahiro Ogawa, Tasuku Kayama, Takuya Sasaki, Kazuki Tainaka, Masaaki Murakami, Miki Haseyama

    Bioengineering (Basel, Switzerland)   11 ( 6 )   2024.5

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    This study presents a trial analysis that uses brain activity information obtained from mice to detect rheumatoid arthritis (RA) in its presymptomatic stages. Specifically, we confirmed that F759 mice, serving as a mouse model of RA that is dependent on the inflammatory cytokine IL-6, and healthy wild-type mice can be classified on the basis of brain activity information. We clarified which brain regions are useful for the presymptomatic detection of RA. We introduced a matrix completion-based approach to handle missing brain activity information to perform the aforementioned analysis. In addition, we implemented a canonical correlation-based method capable of analyzing the relationship between various types of brain activity information. This method allowed us to accurately classify F759 and wild-type mice, thereby identifying essential features, including crucial brain regions, for the presymptomatic detection of RA. Our experiment obtained brain activity information from 15 F759 and 10 wild-type mice and analyzed the acquired data. By employing four types of classifiers, our experimental results show that the thalamus and periaqueductal gray are effective for the classification task. Furthermore, we confirmed that classification performance was maximized when seven brain regions were used, excluding the electromyogram and nucleus accumbens.

    DOI: 10.3390/bioengineering11060523

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  • Whole-Body and Whole-Organ 3D Imaging of Hypoxia Using an Activatable Covalent Fluorescent Probe Compatible with Tissue Clearing

    Daichi M. Sakamoto, Iori Tamura, Bo Yi, Sho Hasegawa, Yutaro Saito, Naoki Yamada, Yoichi Takakusagi, Shimpei I. Kubota, Minoru Kobayashi, Hiroshi Harada, Kenjiro Hanaoka, Masayasu Taki, Masaomi Nangaku, Kazuki Tainaka, Shinsuke Sando

    ACS Nano   18 ( 6 )   5167 - 5179   2024.2

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    Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/acsnano.3c12716

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  • In situ Microinflammation Detection Using Gold Nanoclusters and a Tissue-clearing Method. International journal

    Fayrouz Naim, Rie Hasebe, Shintaro Hojyo, Yukatsu Shichibu, Asuka Ishii, Yuki Tanaka, Kazuki Tainaka, Shimpei I Kubota, Katsuaki Konishi, Masaaki Murakami

    Bio-protocol   13 ( 7 )   e4644   2023.4

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    Microinflammation enhances the permeability of specific blood vessel sites through an elevation of local inflammatory mediators, such as interleukin (IL)-6 and tumor necrosis factor (TNF)-α. By a two-dimensional immunohistochemistry analysis of tissue sections from mice with experimental autoimmune encephalomyelitis (EAE), an animal model for multiple sclerosis (MS), we previously showed that pathogenic immune cells, including CD4+ T cells, specifically accumulate and cause microinflammation at the dorsal vessels of the fifth lumbar cord (L5), resulting in the onset of disease. However, usual pathological analyses by using immunohistochemistry on sections are not effective at identifying the microinflammation sites in organs. Here, we developed a new three-dimensional visualization method of microinflammation using luminescent gold nanoclusters (AuNCs) and the clear, unobstructed brain/body imaging cocktails and computational analysis (CUBIC) tissue-clearing method. Our protocol is based on the detection of leaked AuNCs from the blood vessels due to an enhanced vascular permeability caused by the microinflammation. When we injected ultrasmall coordinated Au13 nanoclusters intravenously (i.v.) to EAE mice, and then subjected the spinal cords to tissue clearing, we detected Au signals leaked from the blood vessels at L5 by light sheet microscopy, which enabled the visualization of complex tissue structures at the whole organ level, consistent with our previous report that microinflammation occurs specifically at this site. Our method will be useful to specify and track the stepwise development of microinflammation in whole organs that is triggered by the recruitment of pathogenic immune cells at specific blood vessels in various inflammatory diseases.

    DOI: 10.21769/BioProtoc.4644

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  • Cerebrospinal fluid-contacting neuron tracing reveals structural and functional connectivity for locomotion in the mouse spinal cord. International journal

    Yuka Nakamura, Miyuki Kurabe, Mami Matsumoto, Tokiharu Sato, Satoshi Miyashita, Kana Hoshina, Yoshinori Kamiya, Kazuki Tainaka, Hitoshi Matsuzawa, Nobuhiko Ohno, Masaki Ueno

    eLife   12   2023.2

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    Cerebrospinal fluid-contacting neurons (CSF-cNs) are enigmatic mechano- or chemosensory cells lying along the central canal of the spinal cord. Recent studies in zebrafish larvae and lampreys have shown that CSF-cNs control postures and movements via spinal connections. However, the structures, connectivity, and functions in mammals remain largely unknown. Here we developed a method to genetically target mouse CSF-cNs that highlighted structural connections and functions. We first found that intracerebroventricular injection of adeno-associated virus with a neuron-specific promoter and Pkd2l1-Cre mice specifically labeled CSF-cNs. Single-cell labeling of 71 CSF-cNs revealed rostral axon extensions of over 1800 μm in unmyelinated bundles in the ventral funiculus and terminated on CSF-cNs to form a recurrent circuitry, which was further determined by serial electron microscopy and electrophysiology. CSF-cNs were also found to connect with axial motor neurons and premotor interneurons around the central canal and within the axon bundles. Chemogenetic CSF-cNs inactivation reduced speed and step frequency during treadmill locomotion. Our data revealed the basic structures and connections of mouse CSF-cNs to control spinal motor circuits for proper locomotion. The versatile methods developed in this study will contribute to further understanding of CSF-cN functions in mammals.

    DOI: 10.7554/eLife.83108

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  • Detection and Morphological Analysis of Micro-Ruptured Cortical Arteries in Subdural Hematoma: Three-Dimensional Visualization Using the Tissue-Clearing Clear, Unobstructed, Brain/Body Imaging Cocktails and Computational Analysis Method. International journal

    Kazuhisa Funayama, Kazuki Tainaka, Akihide Koyama, Rieka Katsuragi-Go, Natsumi Nishikawa-Harada, Ryoko Higuchi, Takashi Aoyama, Hiraku Watanabe, Naoya Takahashi, Hisakazu Takatsuka

    Diagnostics (Basel, Switzerland)   12 ( 11 )   2022.11

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    One of the causes of bleeding in subdural hematoma is cortical artery rupture, which is difficult to detect at autopsy. Therefore, reports of autopsy cases with this condition are limited and hence, the pathogenesis of subdural hematoma remains unclear. Herein, for the detection and morphological analysis of cortical artery ruptures as the bleeding sources of subdural hematoma, we used the tissue-clearing CUBIC (clear, unobstructed, brain/body imaging cocktails and computational analysis) method with light-sheet fluorescence microscopy and reconstructed the two-dimensional and three-dimensional images. Using the CUBIC method, we could clearly visualize and detect cortical artery ruptures that were missed by conventional methods. Indeed, the CUBIC method enables three-dimensional morphological analysis of cortical arteries including the ruptured area, and the creation of cross-sectional two-dimensional images in any direction, which are similar to histopathological images. This highlights the effectiveness of the CUBIC method for subdural hematoma analysis.

    DOI: 10.3390/diagnostics12112875

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  • General Design Strategy to Precisely Control the Emission of Fluorophores via a Twisted Intramolecular Charge Transfer (TICT) Process. International journal

    Kenjiro Hanaoka, Shimpei Iwaki, Kiyoshi Yagi, Takuya Myochin, Takayuki Ikeno, Hisashi Ohno, Eita Sasaki, Toru Komatsu, Tasuku Ueno, Motokazu Uchigashima, Takayasu Mikuni, Kazuki Tainaka, Shinya Tahara, Satoshi Takeuchi, Tahei Tahara, Masanobu Uchiyama, Tetsuo Nagano, Yasuteru Urano

    Journal of the American Chemical Society   144 ( 43 )   19778 - 19790   2022.11

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    Fluorogenic probes for bioimaging have become essential tools for life science and medicine, and the key to their development is a precise understanding of the mechanisms available for fluorescence off/on control, such as photoinduced electron transfer (PeT) and Förster resonance energy transfer (FRET). Here we establish a new molecular design strategy to rationally develop activatable fluorescent probes, which exhibit a fluorescence off/on change in response to target biomolecules, by controlling the twisted intramolecular charge transfer (TICT) process. This approach was developed on the basis of a thorough investigation of the fluorescence quenching mechanism of N-phenyl rhodamine dyes (commercially available as the QSY series) by means of time-dependent density functional theory (TD-DFT) calculations and photophysical evaluation of their derivatives. To illustrate and validate this TICT-based design strategy, we employed it to develop practical fluorogenic probes for HaloTag and SNAP-tag. We further show that the TICT-controlled fluorescence off/on mechanism is generalizable by synthesizing a Si-rhodamine-based fluorogenic probe for HaloTag, thus providing a palette of chemical dyes that spans the visible and near-infrared range.

    DOI: 10.1021/jacs.2c06397

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  • Cerebrocortical activation following unilateral labyrinthectomy in mice characterized by whole-brain clearing: implications for sensory reweighting. International journal

    Ryota Kai, Kuniyuki Takahashi, Kazuki Tainaka, Yuriko Iwakura, Hisaaki Namba, Nae Saito, Toshikuni Sasaoka, Shun Yamaguchi, Hiroyuki Nawa, Arata Horii

    Scientific reports   12 ( 1 )   15424 - 15424   2022.9

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    Posture and gait are maintained by sensory inputs from the vestibular, visual, and somatosensory systems and motor outputs. Upon vestibular damage, the visual and/or somatosensory systems functionally substitute by cortical mechanisms called "sensory reweighting". We investigated the cerebrocortical mechanisms underlying sensory reweighting after unilateral labyrinthectomy (UL) in mice. Arc-dVenus transgenic mice, in which the gene encoding the fluorescent protein dVenus is transcribed under the control of the promoter of the immediate early gene Arc, were used in combination with whole-brain three-dimensional (3D) imaging. Performance on the rotarod was measured as a behavioral correlate of sensory reweighting. Following left UL, all mice showed the head roll-tilt until UL10, indicating the vestibular periphery damage. The rotarod performance worsened in the UL mice from UL1 to UL3, which rapidly recovered. Whole-brain 3D imaging revealed that the number of activated neurons in S1, but not in V1, in UL7 was higher than that in sham-treated mice. At UL7, medial prefrontal cortex (mPFC) and agranular insular cortex (AIC) activation was also observed. Therefore, sensory reweighting to the somatosensory system could compensate for vestibular dysfunction following UL; further, mPFC and AIC contribute to the integration of sensory and motor functions to restore balance.

    DOI: 10.1038/s41598-022-19678-4

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  • Elucidating the role of neurotransmission via D1 and D2 dopamine receptors in the mechanisms of motor control, learning, and memory Reviewed

    Nae Saito, Makoto Itakura, Kazuki Tainaka, Tom Macpherson, Takatoshi Hikida, Shun Yamaguchi, Asako Sato, Tadashi Okubo, Satomi Chiken, Atsushi Nambu, Toshikuni Sasaoka

    Japanese Journal of Biological Psychiatry   33 ( 3 )   100 - 105   2022.9

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    Language:Japanese   Publishing type:Research paper (scientific journal)  

    DOI: 10.11249/jsbpjjpp.33.3_100

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  • Spatiotemporal dynamics of clonal selection and diversification in normal endometrial epithelium. International journal

    Manako Yamaguchi, Hirofumi Nakaoka, Kazuaki Suda, Kosuke Yoshihara, Tatsuya Ishiguro, Nozomi Yachida, Kyota Saito, Haruka Ueda, Kentaro Sugino, Yutaro Mori, Kaoru Yamawaki, Ryo Tamura, Sundaramoorthy Revathidevi, Teiichi Motoyama, Kazuki Tainaka, Roel G W Verhaak, Ituro Inoue, Takayuki Enomoto

    Nature communications   13 ( 1 )   943 - 943   2022.2

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    It has become evident that somatic mutations in cancer-associated genes accumulate in the normal endometrium, but spatiotemporal understanding of the evolution and expansion of mutant clones is limited. To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we sequence 1311 endometrial glands from 37 women. By collecting endometrial glands from different parts of the endometrium, we show that multiple glands with the same somatic mutations occupy substantial areas of the endometrium. We demonstrate that "rhizome structures", in which the basal glands run horizontally along the muscular layer and multiple vertical glands rise from the basal gland, originate from the same ancestral clone. Moreover, mutant clones detected in the vertical glands diversify by acquiring additional mutations. These results suggest that clonal expansions through the rhizome structures are involved in the mechanism by which mutant clones extend their territories. Furthermore, we show clonal expansions and copy neutral loss-of-heterozygosity events occur early in life, suggesting such events can be tolerated many years in the normal endometrium. Our results of the evolutionary dynamics of mutant clones in the human endometrium will lead to a better understanding of the mechanisms of endometrial regeneration during the menstrual cycle and the development of therapies for the prevention and treatment of endometrium-related diseases.

    DOI: 10.1038/s41467-022-28568-2

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  • Using a new three-dimensional CUBIC tissue-clearing method to examine the brain during experimental cerebral malaria Reviewed

    Julia Matsuo-Dapaah, Michelle Sue Jann Lee, Ken J Ishii, Kazuki Tainaka, Cevayir Coban

    International Immunology   33 ( 11 )   587 - 594   2021.10

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Cerebral malaria (CM) is a life-threatening complication of the malaria disease caused by Plasmodium falciparum infection and is responsible for the death of half a million people annually. The molecular pathogenesis underlying CM in humans is not completely understood, although sequestration of infected erythrocytes in cerebral microvessels is thought to play a major role. In contrast, experimental cerebral malaria (ECM) models in mice have been thought to be distinct from human CM, and are mainly caused by inflammatory mediators. Here, to understand the spatial distribution and the potential sequestration of parasites in the whole-brain microvessels during a mouse model of ECM, we utilized the new tissue-clearing method CUBIC (Clear, Unobstructed, Brain/Body Imaging Cocktails and Computational analysis) with light-sheet fluorescent microscopy (LSFM), and reconstructed images in three dimensions (3D). We demonstrated significantly greater accumulation of Plasmodium berghei ANKA (PbANKA) parasites in the olfactory bulb (OB) of mice, compared with the other parts of the brain, including the cerebral cortex, cerebellum and brainstem. Furthermore, we show that PbANKA parasites preferentially accumulate in the brainstem when the OB is surgically removed. This study therefore not only highlights a successful application of CUBIC tissue-clearing technology to visualize the whole brain and its microvessels during ECM, but it also shows CUBIC’s future potential for visualizing pathological events in the whole ECM brain at the cellular level, an achievement that would greatly advance our understanding of human cerebral malaria.

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  • Mechanical load regulates bone growth via periosteal Osteocrin. International journal

    Haruko Watanabe-Takano, Hiroki Ochi, Ayano Chiba, Ayaka Matsuo, Yugo Kanai, Shigetomo Fukuhara, Naoki Ito, Keisuke Sako, Takahiro Miyazaki, Kazuki Tainaka, Ichiro Harada, Shingo Sato, Yasuhiro Sawada, Naoto Minamino, Shu Takeda, Hiroki R Ueda, Akihiro Yasoda, Naoki Mochizuki

    Cell reports   36 ( 2 )   109380 - 109380   2021.7

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    Mechanical stimuli including loading after birth promote bone growth. However, little is known about how mechanical force triggers biochemical signals to regulate bone growth. Here, we identified a periosteal-osteoblast-derived secretory peptide, Osteocrin (OSTN), as a mechanotransducer involved in load-induced long bone growth. OSTN produced by periosteal osteoblasts regulates growth plate growth by enhancing C-type natriuretic peptide (CNP)-dependent proliferation and maturation of chondrocytes, leading to elongation of long bones. Additionally, OSTN cooperates with CNP to regulate bone formation. CNP stimulates osteogenic differentiation of periosteal osteoprogenitors to induce bone formation. OSTN binds to natriuretic peptide receptor 3 (NPR3) in periosteal osteoprogenitors, thereby preventing NPR3-mediated clearance of CNP and consequently facilitating CNP-signal-mediated bone growth. Importantly, physiological loading induces Ostn expression in periosteal osteoblasts by suppressing Forkhead box protein O1 (FoxO1) transcription factor. Thus, this study reveals a crucial role of OSTN as a mechanotransducer converting mechanical loading to CNP-dependent bone formation.

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  • Three-dimensional understanding of the morphological complexity of the human uterine endometrium Reviewed

    Manako Yamaguchi, Kosuke Yoshihara, Kazuaki Suda, Hirofumi Nakaoka, Nozomi Yachida, Haruka Ueda, Kentaro Sugino, Yutaro Mori, Kaoru Yamawaki, Ryo Tamura, Tatsuya Ishiguro, Teiichi Motoyama, Yu Watanabe, Shujiro Okuda, Kazuki Tainaka, Takayuki Enomoto

    iScience   24 ( 4 )   102258 - 102258   2021.4

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    DOI: 10.1016/j.isci.2021.102258

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  • 世界結核デーにちなんで、世界の結核・抗酸菌症研究のこれまでと今 結核菌北京株のゲノム解析と組織透明化/3次元イメージング「CUBIC」による抗酸菌感染の生体内モニタリング

    袴田 真理子, 瀧原 速仁, 尾関 百合子, 西山 晃史, 立石 善隆, 大橋 璃子, 奥田 修二郎, 田井中 一貴, 菊地 利明, 松本 壮吉

    日本細菌学雑誌   76 ( 1 )   65 - 65   2021.2

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  • 病原因子と生態防御(感染モデル・寄生・免疫・ワクチン)/病原体と感染症 組織透明化/3次元イメージング「CUBIC」による抗酸菌感染の生体内モニタリング

    袴田 真理子, 井内 絵梨奈, 横山 晃, 尾関 百合子, 西山 晃史, 立石 善隆, 大橋 璃子, 菊地 利明, 田井中 一貴, 松本 壮吉

    日本細菌学雑誌   76 ( 1 )   59 - 59   2021.2

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  • Whole-organ analysis of TGF-β-mediated remodelling of the tumour microenvironment by tissue clearing International journal

    Shimpei I. Kubota, Kei Takahashi, Tomoyuki Mano, Katsuhiko Matsumoto, Takahiro Katsumata, Shoi Shi, Kazuki Tainaka, Hiroki R. Ueda, Shogo Ehata, Kohei Miyazono

    Communications Biology   4 ( 1 )   294 - 294   2020.12

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    <title>Abstract</title>Tissue clearing is one of the most powerful strategies for a comprehensive analysis of disease progression. Here, we established an integrated pipeline that combines tissue clearing, 3D imaging, and machine learning and applied to a mouse tumour model of experimental lung metastasis using human lung adenocarcinoma A549 cells. This pipeline provided the spatial information of the tumour microenvironment. We further explored the role of transforming growth factor-β (TGF-β) in cancer metastasis. TGF-β-stimulated cancer cells enhanced metastatic colonization of unstimulated-cancer cells in vivo when both cells were mixed. RNA-sequencing analysis showed that expression of the genes related to coagulation and inflammation were up-regulated in TGF-β-stimulated cancer cells. Further, whole-organ analysis revealed accumulation of platelets or macrophages with TGF-β-stimulated cancer cells, suggesting that TGF-β might promote remodelling of the tumour microenvironment, enhancing the colonization of cancer cells. Hence, our integrated pipeline for 3D profiling will help the understanding of the tumour microenvironment.

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  • Neurotransmission through dopamine D1 receptors is required for aversive memory formation and Arc activation in the cerebral cortex. Reviewed International journal

    Nae Saito, Kazuki Tainaka, Tom Macpherson, Takatoshi Hikida, Shun Yamaguchi, Toshikuni Sasaoka

    Neuroscience Research   156   58 - 65   2020.5

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    Dopaminergic neurotransmission is considered to play an important role not only in reward-based learning, but also in aversive learning. Here, we investigated the role of dopaminergic neurotransmission via dopamine D1 receptors (D1Rs) in aversive memory formation in a passive avoidance test using D1R knockdown (KD) mice, in which the expression of D1Rs can conditionally and reversibly be controlled by doxycycline (Dox) treatment. We also performed whole-brain imaging after aversive footshock stimulation in activity-regulated cytoskeleton protein (Arc)-dVenus D1RKD mice, which were crossbred from Arc-dVenus transgenic mice and D1RKD mice, to examine the distribution of Arc-controlled dVenus expression in the hippocampus and cerebral cortex during aversive memory formation. Knockdown of D1R expression following Dox treatment resulted in impaired performance in the passive avoidance test and was associated with a decrease in dVenus expression in the cerebral cortex (visual, somatosensory, and motor cortices), but not the hippocampus, compared with control mice without Dox treatment. These findings indicate that D1R-mediated dopaminergic transmission is critical for aversive memory formation, specifically by influencing Arc expression in the cerebral cortex.

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  • Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues. Reviewed International journal

    Etsuo A Susaki, Chika Shimizu, Akihiro Kuno, Kazuki Tainaka, Xiang Li, Kengo Nishi, Ken Morishima, Hiroaki Ono, Koji L Ode, Yuki Saeki, Kazunari Miyamichi, Kaoru Isa, Chihiro Yokoyama, Hiroki Kitaura, Masako Ikemura, Tetsuo Ushiku, Yoshihiro Shimizu, Takashi Saito, Takaomi C Saido, Masashi Fukayama, Hirotaka Onoe, Kazushige Touhara, Tadashi Isa, Akiyoshi Kakita, Mitsuhiro Shibayama, Hiroki R Ueda

    Nature Communications   11 ( 1 )   1982 - 1982   2020.4

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    Whole-organ/body three-dimensional (3D) staining and imaging have been enduring challenges in histology. By dissecting the complex physicochemical environment of the staining system, we developed a highly optimized 3D staining imaging pipeline based on CUBIC. Based on our precise characterization of biological tissues as an electrolyte gel, we experimentally evaluated broad 3D staining conditions by using an artificial tissue-mimicking material. The combination of optimized conditions allows a bottom-up design of a superior 3D staining protocol that can uniformly label whole adult mouse brains, an adult marmoset brain hemisphere, an ~1 cm3 tissue block of a postmortem adult human cerebellum, and an entire infant marmoset body with dozens of antibodies and cell-impermeant nuclear stains. The whole-organ 3D images collected by light-sheet microscopy are used for computational analyses and whole-organ comparison analysis between species. This pipeline, named CUBIC-HistoVIsion, thus offers advanced opportunities for organ- and organism-scale histological analysis of multicellular systems.

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  • Rapid chemical clearing of white matter in the post-mortem human brain by 1,2-hexanediol delipidation. Reviewed

    Inoue M, Saito R, Kakita A, Tainaka K

    Bioorganic Medicinal Chemistry Letters   29 ( 15 )   1886 - 1890   2019.8

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  • Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents Reviewed International journal

    Kazuki Tainaka, Tatsuya C. Murakami, Etsuo A. Susaki, Chika Shimizu, Rie Saito, Kei Takahashi, Akiko Hayashi-Takagi, Hiroshi Sekiya, Yasunobu Arima, Satoshi Nojima, Masako Ikemura, Tetsuo Ushiku, Yoshihiro Shimizu, Masaaki Murakami, Kenji F. Tanaka, Masamitsu Iino, Haruo Kasai, Toshikuni Sasaoka, Kazuto Kobayashi, Kohei Miyazono, Eiichi Morii, Tadashi Isa, Masashi Fukayama, Akiyoshi Kakita, Hiroki R. Ueda

    Cell Reports   24 ( 8 )   2196 - 2210.e9   2018.8

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    We describe a strategy for developing hydrophilic chemical cocktails for tissue delipidation, decoloring, refractive index (RI) matching, and decalcification, based on comprehensive chemical profiling. More than 1,600 chemicals were screened by a high-throughput evaluation system for each chemical process. The chemical profiling revealed important chemical factors: salt-free amine with high octanol/water partition-coefficient (logP) for delipidation, N-alkylimidazole for decoloring, aromatic amide for RI matching, and protonation of phosphate ion for decalcification. The strategic integration of optimal chemical cocktails provided a series of CUBIC (clear, unobstructed brain/body imaging cocktails and computational analysis) protocols, which efficiently clear mouse organs, mouse body including bone, and even large primate and human tissues. The updated CUBIC protocols are scalable and reproducible, and they enable three-dimensional imaging of the mammalian body and large primate and human tissues. This strategy represents a future paradigm for the rational design of hydrophilic clearing cocktails that can be used for large tissues.

    DOI: 10.1016/j.celrep.2018.07.056

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  • A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing Reviewed

    Tatsuya C. Murakami, Tomoyuki Mano, Shu Saikawa, Shuhei A. Horiguchi, Daichi Shigeta, Kousuke Baba, Hiroshi Sekiya, Yoshihiro Shimizu, Kenji F. Tanaka, Hiroshi Kiyonari, Masamitsu Iino, Hideki Mochizuki, Kazuki Tainaka, Hiroki R. Ueda

    Nature Neuroscience   21 ( 4 )   625 - 637   2018.4

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    DOI: 10.1038/s41593-018-0109-1

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  • Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock Reviewed

    Yuta Shinohara, Yohei M. Koyama, Maki Ukai-Tadenuma, Takatsugu Hirokawa, Masaki Kikuchi, Rikuhiro G. Yamada, Hideki Ukai, Hiroshi Fujishima, Takashi Umehara, Kazuki Tainaka, Hiroki R. Ueda

    MOLECULAR CELL   67 ( 5 )   783 - +   2017.9

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    DOI: 10.1016/j.molcel.2017.08.009

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  • Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution Reviewed

    Shimpei I. Kubota, Kei Takahashi, Jun Nishida, Yasuyuki Morishita, Shogo Ehata, Kazuki Tainaka, Kohei Miyazono, Hiroki R. Ueda

    CELL REPORTS   20 ( 1 )   236 - 250   2017.7

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    DOI: 10.1016/j.celrep.2017.06.010

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  • Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling Reviewed

    Kazuki Tainaka, Akihiro Kuno, Shimpei I. Kubota, Tatzya Murakami, Hiroki R. Ueda

    ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 32   32   713 - 741   2016

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    DOI: 10.1146/annurev-cellbio-111315-125001

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  • Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging Reviewed

    Etsuo A. Susaki, Kazuki Tainaka, Dimitri Perrin, Hiroko Yukinaga, Akihiro Kuno, Hiroki R. Ueda

    NATURE PROTOCOLS   10 ( 11 )   1709 - 1727   2015.11

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    DOI: 10.1038/nprot.2015.085

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  • Whole-Body Imaging with Single-Cell Resolution by Tissue Decolorization Reviewed

    Kazuki Tainaka, Shimpei I. Kubota, Takeru Q. Suyama, Etsuo A. Susaki, Dimitri Perrin, Maki Ukai-Tadenuma, Hideki Ukai, Hiroki R. Ueda

    CELL   159 ( 4 )   911 - 924   2014.11

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    DOI: 10.1016/j.cell.2014.10.034

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  • Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis Reviewed

    Etsuo A. Susaki, Kazuki Tainaka, Dimitri Perrin, Fumiaki Kishino, Takehiro Tawara, Tomonobu M. Watanabe, Chihiro Yokoyama, Hirotaka Onoe, Megumi Eguchi, Shun Yamaguchi, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Shimizu, Atsushi Miyawaki, Hideo Yokota, Hiroki R. Ueda

    CELL   157 ( 3 )   726 - 739   2014.4

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  • Non-Enzymatic DNA Cleavage Reaction Induced by 5-Ethynyluracil in Methylamine Aqueous Solution and Application to DNA Concatenation Reviewed

    Shuji Ikeda, Kazuki Tainaka, Katsuhiko Matsumoto, Yuta Shinohara, Koji L. Ode, Etsuo A. Susaki, Hiroki R. Ueda

    PLOS ONE   9 ( 3 )   e92369   2014.3

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  • Positional Effects of Phosphorylation on the Stability and Morphology of Tau-Related Amyloid Fibrils Reviewed

    Masafumi Inoue, Takashi Konno, Kazuki Tainaka, Eiji Nakata, Hiro-o Yoshida, Takashi Morii

    BIOCHEMISTRY   51 ( 7 )   1396 - 1406   2012.2

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    DOI: 10.1021/bi201451z

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  • Generation of Singlet Oxygen during Photosensitized One-Electron Oxidation of DNA Reviewed

    Yasuko Osakada, Kiyohiko Kawai, Takashi Tachikawa, Mamoru Fujitsuka, Kazuki Tainaka, Shozo Tero-Kubota, Tetsuro Majima

    CHEMISTRY-A EUROPEAN JOURNAL   18 ( 4 )   1060 - 1063   2012.1

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  • ICON probes: Synthesis and DNA methylation typing Reviewed

    Kazuki Tainaka, Akimitsu Okamoto

    Current Protocols in Nucleic Acid Chemistry   Chapter 8 ( 47 )   1 - 17   2011

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    DOI: 10.1002/0471142700.nc0807s47

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  • Sequence Dependence of Excess Electron Transfer in DNA Reviewed

    Kazuki Tainaka, Mamoru Fujitsuka, Tadao Takada, Kiyohiko Kawai, Tetsuro Majima

    JOURNAL OF PHYSICAL CHEMISTRY B   114 ( 45 )   14657 - 14663   2010.11

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  • Design Strategies of Fluorescent Biosensors Based on Biological Macromolecular Receptors Reviewed

    Kazuki Tainaka, Reiko Sakaguchi, Hironori Hayashi, Shun Nakano, Fong Fong Liew, Takashi Morii

    SENSORS   10 ( 2 )   1355 - 1376   2010.2

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    DOI: 10.3390/s100201355

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  • Construction of the Artificial Enzyme for Using Solar Energy Reviewed

    Shun Nakano, Masatora Fukuda, Kazuki Tainaka, Takashi Morii

    Green Energy and Technology   44   176 - 180   2010

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    DOI: 10.1007/978-4-431-99779-5_27

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  • An In Vivo Fluorescent Sensor Reveals Intracellular Ins(1,3,4,5)P-4 Dynamics in Single Cells Reviewed

    Reiko Sakaguchi, Kazuki Tainaka, Naoko Shimada, Shun Nakano, Masafumi Inoue, Shigeki Kiyonaka, Yasuo Mori, Takashi Morii

    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION   49 ( 12 )   2150 - 2153   2010

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    DOI: 10.1002/anie.200903951

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  • A single circularly permuted GFP sensor for inositol-1,3,4,5-tetrakisphosphate based on a split PH domain Reviewed

    Reiko Sakaguchi, Takashi Endoh, Seigo Yamamoto, Kazuki Tainaka, Kenji Sugimoto, Nobutaka Fujieda, Shigeki Kiyonaka, Yasuo Mori, Takashi Morii

    BIOORGANIC & MEDICINAL CHEMISTRY   17 ( 20 )   7381 - 7386   2009.10

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  • Osmium Complexation of Mismatched DNA: Effect of the Bases Adjacent to Mismatched 5-Methylcytosine Reviewed

    Akiko Nomura, Kazuki Tainaka, Akimitsu Okamoto

    BIOCONJUGATE CHEMISTRY   20 ( 3 )   603 - 607   2009.3

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    DOI: 10.1021/bc800531z

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  • Osmium complex binding to mismatched methylcytosine: effect of adjacent bases. Reviewed

    Nomura A, Tainaka K, Okamoto A

    Nucleic acids symposium series (2004)   ( 53 )   207 - 208   2009

  • 2TA1-06 Positional effects of phosphorylation upon fibrillation of tau derived peptide(The 47th Annual Meeting of the Biophysical Society of Japan)

    Konno Takashi, Inoue Masafumi, Tainaka Kazuki, Morii Takashi

    Seibutsu Butsuri   49   S39   2009

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    DOI: 10.2142/biophys.49.S39_5

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  • The amyloid fibrillization of phosphorylated human tau core peptides

    Inoue Masafumi, Tainaka Kazuki, Hirata Akiyoshi, Konno Takashi, Morii Takashi

    Trans. Mat. Res. Soc. Japan   34 ( 3 )   517 - 520   2009

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    Post-translational phosphorylation of the microtubule-associated protein tau is believed to have close relevance to the pathogenesis of Alzheimers disease. The growth of amyloid fibrils of the short peptide segment VQIVY<sub>310</sub>K (PHF6) corresponding to the core part of tau fibril formation is strongly affected by the phospholylation at Tyr310 via its electrostatic pairing with the neighboring charged lysine. Herein, we studied the propensity of resultant fibrils from PHF6 derivative peptides with charged aromatic amino acid residue at Tyr310. The results showed that the phosphorylation at Tyr310 contributed to significant enhancement of the amyloidogenicity and the stability of fibrillar aggregates. The physical origin of remarkable stabilization of fibrils by tyrosine phosphorylation is plausibly attributed to the charge pairing with the adjacent lysine residue in a similar fashion to the phosphorylation effect on the growth of amyloid fibril.

    DOI: 10.14723/tmrsj.34.517

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  • Charge-Pairing Mechanism of Phosphorylation Effect upon Amyloid Fibrillation of Human Tau Core Peptide Reviewed

    Masafumi Inoue, Akiyoshi Hirata, Kazuki Tainaka, Takashi Morii, Takashi Konno

    BIOCHEMISTRY   47 ( 45 )   11847 - 11857   2008.11

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  • Synthesis of bipyridine-adenine conjugates for DNA methylation analysis Reviewed

    Tainaka Kazuki, Okamoto Akimitsu

    Chemistry of Nucleic Acid Components   10   146 - 149   2008

  • An Osmium-DNA interstrand complex: Application to facile DNA methylation analysis Reviewed

    Kazuo Tanaka, Kazuki Tainaka, Tadashi Umemoto, Akiko Nomura, Akimitsu Okamoto

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   129 ( 46 )   14511 - 14517   2007.11

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  • Direct labeling of 5-methylcytosine and its applications Reviewed

    Kazuo Tanaka, Kazuki Tainaka, Taku Kamei, Akimitsu Okamoto

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   129 ( 17 )   5612 - 5620   2007.5

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  • Synthesis and fluorescence properties of dimethylaminonaphthalene-deoxyuridine conjugates as polarity-sensitive probes Reviewed

    Akimitsu Okamoto, Kazuki Tainaka, Tomo Unzai, Isao Saito

    TETRAHEDRON   63 ( 17 )   3465 - 3470   2007.4

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  • PRODAN-conjugated DNA: Synthesis and photochemical properties Reviewed

    Kazuki Tainaka, Kazuo Tanaka, Shuji Ikeda, Ken-ichiro Nishiza, Tomo Unzai, Yoshimasa Fujiwara, Isao Saito, Akimitsu Okamoto

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   129 ( 15 )   4776 - 4784   2007.4

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  • Methylcytosine-selective fluorescence quenching by osmium complexation Reviewed

    Kazuo Tanaka, Kazuki Tainaka, Akimitsu Okamoto

    BIOORGANIC & MEDICINAL CHEMISTRY   15 ( 4 )   1615 - 1621   2007.2

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    DOI: 10.1016/j.bmc.2006.12.023

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  • Selective oxidation of methylcytosine in single base pair mismatches by osmium complex. Reviewed

    Nomura A, Tainaka K, Okamoto A

    Nucleic acids symposium series (2004)   ( 51 )   299 - 300   2007

  • Chemistry of osmium-DNA complexes. Reviewed

    Umemoto T, Tainaka K, Tanaka K, Okamoto A

    Nucleic acids symposium series (2004)   ( 51 )   175 - 176   2007

  • DNA methylation analysis using metal complex formation. Reviewed

    Okamoto A, Tanaka K, Tainaka K, Umemoto T, Nomura A

    Nucleic acids symposium series (2004)   ( 51 )   27 - 28   2007

  • Nile Red nucleoside: Design of a solvatofluorochromic nucleoside as an indicator of micropolarity around DNA Reviewed

    A Okamoto, K Tainaka, Y Fujiwara

    JOURNAL OF ORGANIC CHEMISTRY   71 ( 9 )   3592 - 3598   2006.4

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  • Simple SNP typing assay using a base-discriminating fluorescent probe Reviewed

    A Okamoto, K Tainaka, Y Ochi, K Kanatani, Saito, I

    MOLECULAR BIOSYSTEMS   2 ( 2 )   122 - 126   2006.2

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  • Synthesis and properties of novel PRODAN-labeled uridine. Reviewed

    Tainaka K, Ikeda S, Tanaka K, Nishiza K, Unzai T, Okamoto A, Saito I

    Nucleic acids symposium series (2004)   ( 50 )   131 - 132   2006

  • Development of bipyridine-modified nucleobase for methylcytosine-selective crosslink reaction. Reviewed

    Tainaka K, Tanaka K, Okamoto A

    Nucleic acids symposium series (2004)   ( 50 )   129 - 130   2006

  • Photochemical evaluation of dual fluorescence of a novel DNA groove binder. Reviewed

    Tanaka K, Tainaka K, Fujishima S, Okamoto A

    Nucleic acids symposium series (2004)   ( 50 )   137 - 138   2006

  • Fluorescence quenching by methylcytosine-metal complexation. Reviewed

    Tanaka K, Tainaka K, Okamoto A

    Nucleic acids symposium series (2004)   ( 50 )   139 - 140   2006

  • Development of novel PRODAN-labeled nucleosides as base-discriminating fluorescent probes. Reviewed

    Tainaka K, Ikeda S, Tanaka K, Nishiza K, Fujiwara Y, Okamoto A, Saito I

    Nucleic acids symposium series (2004)   ( 50 )   133 - 134   2006

  • Development of fluorescence-labeling method for methylcytosine with metal complexation. Reviewed

    Tanaka K, Tainaka K, Kamei T, Okamoto A

    Nucleic acids symposium series (2004)   ( 50 )   135 - 136   2006

  • Development of electrochemical detection for methylcytosine and its application. Reviewed

    Tanaka K, Tainaka K, Kamei T, Okamoto A

    Nucleic acids symposium series (2004)   ( 50 )   141 - 142   2006

  • Luminescence properties of dual fluorescent pyrene derivatives used as DNA probe molecule. Reviewed

    Kodate S, Wada H, Suzuka I, Okamoto A, Tainaka K, Saito Y, Saito I

    Nucleic acids symposium series (2004)   ( 50 )   211 - 212   2006

  • Sequence-selective osmium oxidation of DNA: efficient distinction between 5-methylcytosine and cytosine Reviewed

    A Okamoto, K Tainaka, T Kamei

    ORGANIC & BIOMOLECULAR CHEMISTRY   4 ( 9 )   1638 - 1640   2006

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    DOI: 10.1039/b600401f

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  • A dielectric-sensitive fluorescent DNA probe for monitoring polarities on the interior of a DNA-binding protein Reviewed

    A Okamoto, K Tainaka, Saito, I

    BIOCONJUGATE CHEMISTRY   16 ( 5 )   1105 - 1111   2005.9

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    DOI: 10.1021/bc050077i

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  • Monitoring DNA structures by dual fluorescence of pyrene derivatives Reviewed

    A Okamoto, K Tainaka, K Nishiza, Saito, I

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   127 ( 38 )   13128 - 13129   2005.9

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    DOI: 10.1021/ja053609e

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  • Design of highly selective fluorescent nucleobases for SNP typing: Base-discriminating fluorescent (BDF) probe Reviewed

    Saito, I, Y Saito, A Okamoto, T Ichiba, K Kanatani, K Tainaka

    Chemistry of Nucleic Acid Components   7   57 - 64   2005

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  • SNPs typing by base-discriminating fluorescence DNA probe. Reviewed

    Okamoto A, Tainaka K, Ochi Y, Saito I

    Nucleic acids symposium series (2004)   ( 49 )   201 - 202   2005

  • Nile Red nucleoside: novel nucleoside analog with a fluorophore replacing the DNA base. Reviewed

    Tainaka K, Fujiwara Y, Okamoto A

    Nucleic acids symposium series (2004)   ( 49 )   155 - 156   2005

  • Sequence-selective 5-methylcytosine oxidation for epigenotyping. Reviewed

    Okamoto A, Tainaka K

    Nucleic acids symposium series (2004)   ( 49 )   45 - 46   2005

  • Development of a novel solvatochromic pyrimidine analog for probing local dielectric environment of DNA polymerase. Reviewed

    Tainaka K, Okamoto A, Saito I

    Nucleic acids symposium series (2004)   ( 48 )   31 - 32   2004

  • Synthesis and properties of a novel fluorescent nucleobase, naphthopyridopyrimidine Reviewed

    A Okamoto, K Tainaka, Saito, I

    TETRAHEDRON LETTERS   44 ( 36 )   6871 - 6874   2003.9

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    DOI: 10.1016/S0040-4039(03)01740-4

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  • Detection of A/G single nucleotide alteration in RNA using base-discriminating fluorescent oligodeoxynucleotides Reviewed

    A Okamoto, K Tainaka, Saito, I

    CHEMISTRY LETTERS   32 ( 8 )   684 - 685   2003.8

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    DOI: 10.1246/cl.2003.684

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  • Clear distinction of purine bases on the complementary strand by a fluorescence change of a novel fluorescent nucleoside Reviewed

    A Okamoto, K Tainaka, Saito, I

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   125 ( 17 )   4972 - 4973   2003.4

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    DOI: 10.1021/ja034090u

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  • Oligonucleotides containing 7-vinyl-7-deazaguanine as a facile strategy for expanding the functional diversity of DNA Reviewed

    A Okamoto, T Taiji, K Tainaka, Saito, I

    BIOORGANIC & MEDICINAL CHEMISTRY LETTERS   12 ( 15 )   1895 - 1896   2002.8

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    DOI: 10.1016/S0960-894X(02)00334-7

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  • A facile incorporation of the aldehyde function into DNA: 3-Formylindole nucleoside as an aldehyde-containing universal nucleoside Reviewed

    Akimitsu Okamoto, Kazuki Tainaka, Isao Saito

    Tetrahedron Letters   43 ( 26 )   4581 - 4583   2002.6

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    DOI: 10.1016/S0040-4039(02)00888-2

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MISC

  • Whole-organ pathological profiling with single-cell resolution

    久保田晋平, 高橋恵生, 田井中一貴, 江幡正悟, 上田泰己, 宮園浩平

    日本病理学会会誌   110 ( 1 )   2021

  • Whole-organ profiling of cancer metastasis by tissue clearing and light-sheet fluorescent microscopy

    Kubota Shimpei I., Takahashi Kei, Nishida Jun, Ehata Shogo, Tainaka Kazuki, Ueda Hiroki R., Miyazono Kohei

    Proceedings for Annual Meeting of The Japanese Pharmacological Society   93 ( 0 )   1 - YIA-16   2020

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    <p>It has been recognized that interactions between cancer cells and stroma are important for survival of cancer cells and metastasis at distant organs. In addition, the complexity within tumor microenvironment contributes to resistance of conventional therapy. Therefore, despite decades of cancer researches, it is still difficult to elucidate the complexity of tumor microenvironment at whole organ or whole body level. To understand tumor microenvironment and overcome cancer, it is necessary to detect and quantify sparsely distributed metastatic cells throughout the body or organ at single-cell resolution. </p><p>Here, we demonstrate that CUBIC (clear, unobstructed brain/body imaging cocktails and computational analysis)-based cancer (CUBIC-Cancer) analysis with refractive-indices (RI) optimized protocol enables comprehensive cancer cell profiling in whole body and organs. We applied CUBIC-Cancer analysis to a dozen mouse models using several cancer cells and spatio-temporal quantification of metastatic cancer progression at single-cell resolution. As a result, metastatic foci can be observed and quantified through whole organ or whole body at single-cell resolution. In addition, three-dimensional (3D) monitoring revealed that the patterns of metastasis were dependent upon cancer cell or metastatic organs. Comparing two cancer cell lines, we quantified the difference of metastatic processes between angiogenesis and vessel cooption. Whole-organ profiling with single-cell resolution also enables to quantify the early steps of lung metastasis formation and rejection.CUBIC-Cancer analysis suggests that the epithelial-mesenchymal transition promotes not only extravasation but also cell survival at metastatic sites. CUBIC-Cancer analysis is applicable to pharmacotherapeutic profiling of anti-tumor drugs. CUBIC-Cancer analysis is compatible with in vivo bioluminescence imaging and 2D histology.We suggest that a scalable analytical pipeline with these three modalities may contribute to addressing currently incurable metastatic diseases.</p>

    DOI: 10.1254/jpssuppl.93.0_1-YIA-16

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  • CUBIC-癌分析法を用いた癌転移の全身/全組織的特性解析(Whole-body/organ profiling of cancer metastasis with CUBIC-Cancer analysis)

    久保田 晋平, 高橋 恵生, 西田 純, 江幡 正悟, 田井中 一貴, 上田 泰己, 宮園 浩平

    生命科学系学会合同年次大会   2017年度   [2P - 1450]   2017.12

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  • CUBIC-癌分析法を用いた癌転移の全身/全組織的特性解析(Whole-body/organ profiling of cancer metastasis with CUBIC-Cancer analysis)

    久保田 晋平, 高橋 恵生, 西田 純, 江幡 正悟, 田井中 一貴, 上田 泰己, 宮園 浩平

    生命科学系学会合同年次大会   2017年度   [2P - 1450]   2017.12

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  • Pharmacological analysis of sleep consolidation mechanisms in mammals

    Qianhui Zhang, Hiroko Yukinaga, Dimitri Perrin, Kazuki Tainaka, Hiroki R. Ueda

    JOURNAL OF PHARMACOLOGICAL SCIENCES   130 ( 3 )   S140 - S140   2016.3

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  • タンパク質可視化・制御の新技術 細胞局所から個体まで CUBIC 化学混合液を用いた単一細胞レベルでの全器官と全組織のイメージング法(CUBIC: whole-organ, whole-body imaging with single-cell resolution using chemical cocktails)

    田井中 一貴, 洲崎 悦生, 久保田 晋平, 上田 泰己

    日本生化学会大会・日本分子生物学会年会合同大会講演要旨集   88回・38回   [2S4 - 5]   2015.12

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  • マウスの臓器・個体を丸ごと1細胞解像度でイメージングする新技術

    田井中一貴

    臨床免疫・アレルギー科   64 ( 3 )   281 - 284   2015.9

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  • 1細胞解像度全身・組織丸ごとイメージング

    上田 泰己, 田井中 一貴

    日本免疫学会ニュースレター45号   22 - 23   2015.4

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  • 次世代生物学の扉を開く一細胞解析法 1細胞解像度個体全身三次元イメージング

    久保田晋平, 田井中一貴, 上田泰己

    細胞工学   34 ( 3 )   278 - 282   2015.2

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  • CUBICを用いた全身三次元病理解析

    須山 孟, 田井中 一貴, 上田 泰己

    心臓   47 ( 2 )   285 - 291   2015

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    Language:Japanese   Publisher:公益財団法人 日本心臓財団  

    DOI: 10.11281/shinzo.47.285

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  • マウス全脳・全身を透明化し1細胞解像度で観察する新技術を開発:アミノアルコールを含む化合物カクテルと高速イメージング・画像解析を組み合わせた「CUBIC」技術を実現

    久野 朗広, 洲崎 悦生, 田井中 一貴, 上田 泰己

    化学と生物   53 ( 11 )   737 - 740   2015

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    Language:Japanese   Publisher:公益社団法人 日本農芸化学会  

    DOI: 10.1271/kagakutoseibutsu.53.737

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  • 脳を透明化して観察するCUBIC法-透明化溶剤と画像解析による新技術

    田井中一貴, 洲崎悦生, 上田泰己

    化学   69 ( 10 )   24 - 27   2014.10

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  • 全脳全細胞を観察対象とする新規技術CUBIC

    洲崎悦生, 田井中一貴, PERRIN Dimitri, 上田泰己

    日本薬理学会関東部会プログラム・要旨集   130th   50   2014

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    J-GLOBAL

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  • 生体組織透明化・脱色化試薬による一細胞解像度個体丸ごとイメージング技術の開発 2

    久保田晋平, 田井中一貴, 上田泰己

    日本薬理学会関東部会プログラム・要旨集   131st   67   2014

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    J-GLOBAL

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  • 生体組織透明化・脱色化試薬による一細胞解像度個体丸ごとイメージング技術の開発 1

    田井中一貴, 久保田晋平, 上田泰己

    日本薬理学会関東部会プログラム・要旨集   131st   66   2014

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    J-GLOBAL

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  • 全組織スキャンニングによるシステミックな3次元遺伝子発現プロファイリング

    洲崎悦生, 田井中一貴, 渡邉朋信, 清成寛, 阿部高也, 宮脇敦史, 今井猛, 上田泰己

    日本分子生物学会年会プログラム・要旨集(Web)   36th   3P-0737 (WEB ONLY)   2013

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    J-GLOBAL

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  • 概日時計におけるタンパク質リン酸化反応の意義

    中嶋正人, 小山洋平, 田井中一貴, 上田泰己

    時間生物学   17 ( 2 )   146   2011.11

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    J-GLOBAL

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  • Structural aspects of the fluorescence intensity changes of the ATP-binding ribonucleopeptide sensor

    Nakano, S, Mashima, T, Tainaka, K, Katahira, M, Morii, T

    The 37th International Symposium on Nucleic Acids Chemistry 2010,   2010.11

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  • 可視光照射により光電流応答を示すDNA自己組織化膜の作製 Reviewed

    丹佳夫, 田井中一貴, 藤枝伸宇, 森井孝

    日本化学会第89春季年会,日本大学,2009.3.27-30   2009

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  • 蛍光タンパク質をもとにしたイノシトール四リン酸センサーの設計 Reviewed

    藤枝伸宇, 山本誠吾, 遠藤太志, 坂口怜子, 田井中一貴, 森井孝

    日本化学会第89春季年会,日本大学,2009.3.27-30   2009

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  • Construction of a stable functional ribonucleopeptide complex by the covalent linking method. Reviewed

    M. Fukuda, S. Nakano, K. Tainaka, N. Fujieda, T. Morii

    Nucleic acids symposium series (2004)   ( 52 )   195 - 196   2008

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  • Selective recognition of a tetra-amino-acid motif containing phosphorylated tyrosine residue by ribonucleopeptide. Reviewed

    S. Nakano, T. Hasegawa, M. Fukuda, N. Fujieda, K. Tainaka, T. Morii

    Nucleic acids symposium series (2004)   ( 52 )   199 - 200   2008

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  • Development of ribonucleopeptide-based fluorescent sensors for biologically active amines based on the stepwise molding strategy. Reviewed

    K. Tainaka, T. Hasegawa, M. Fukuda, S. Nakano, N. Fujieda, T. Morii

    Nucleic acids symposium series (2004)   ( 52 )   201 - 202   2008

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  • Highly Selective Fluorescent Nucleobases for Designing Base-Discriminating Fluorescence Probe.

    齋藤 烈, Saito, I, Saito, Y, Hanawa, K, Hayashi, K, Motegi, K, Bag, S. S, Dohno, C, Ichiba, T, Tainaka, K, Okamoto, A

    Pure. Appl. Chemistry,   78 ( 12 )   2305 - 2312   2006

  • Effect of Single Nucleotide Alteration in Hybridized RNA on Fluorescence Intensity of Dimethylaminonaphthalene-labeled DNA.

    齋藤 烈, A. Okamoto, K. Tainaka, I. Saito

    Photomedicine & Photobiology   ( 28 )   31 - 32   2006

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  • Development of novel modified nucleobases as a fluorescence probe for detection of single nucleotide polymorphisms.

    K Tainaka, A Okamoto, Saito, I

    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   224   U33 - U33   2002.8

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  • DNAの一塩基変異検出法の最近の進歩

    齋藤 烈, 田井中一貴

    未来材料   ( 2 )   32 - 37   2002.2

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Presentations

  • CUBIC: Whole-organ, whole-body imaging with single-cell resolution using chemical cocktails

    TAINAKA Kazuki

    2019.8 

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  • 組織透明化による3D神経病理学 Invited

    田井中 一貴

    第16回日本病理学会カンファレンス  2019.8 

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  • Comprehensive 3D Imaging by Tissue Clearing Technique CUBIC International conference

    TAINAKA Kazuki

    Neuro2019  2019.7 

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  • 3D神経病理学に向けたホールマウント染色手法の開発

    田井中一貴, 齋藤理恵, 井上雅文, 柿田明美

    第60回日本神経病理学会総会学術研究会  2019.7 

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  • CUBIC: 組織透明化技術による3Dイメージング Invited

    田井中 一貴

    第60回新潟生化学懇話会  2019.7 

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  • CUBIC:生体組織透明化による包括的3Dイメージング技術 Invited

    田井中 一貴

    第738回新潟医学会  2019.4 

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  • CUBIC: Whole-brain/body imaging with single-cell resolution using hydrophilic chemical cocktails Invited International conference

    TAINAKA Kazuki

    The International Symposium of Biofuctional Chemistry  2019.4 

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  • CUBIC: Whole-brain/body imaging with single-cell resolution using hydrophilic chemical cocktails Invited International conference

    TAINAKA Kazuki

    The 9th BRI International Symposium  2019.3 

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  • 水溶性試薬による組織透明化の化学 Invited

    田井中 一貴

    ERATO浜地プロジェクト:ニューロ分子技術講演会2019-1  2019.1 

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  • 組織透明化技術CUBICによる個体・臓器丸ごと3Dイメージング Invited

    田井中 一貴

    ChemBioレクチャー  2018.12 

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  • 組織透明化技術CUBIC による3D神経病理学 Invited

    田井中 一貴

    第107回日本病理学会総会  2018.6 

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  • 組織透明化技術と包括的3Dイメージング Invited

    田井中 一貴

    イメージング技術の融合による医学・生命科学の新たな地平の開拓  2018.2 

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  • 生体組織透明化技術CUBIC Invited

    田井中 一貴

    第15回 新潟内耳疾患研究会  2017.7 

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  • 組織透明化技術と脳コネクトーム Invited

    田井中 一貴

    第47回新潟神経学夏期セミナー  2017.7 

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  • CUBIC:生体組織透明化による包括的3Dイメージング技術 Invited

    田井中 一貴

    北海道大学遺伝子病制御研究所セミナー  2017.6 

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  • CUBIC: whole-organ, whole-body imaging with single-cell resolution using chemical cocktals. Invited International conference

    田井中 一貴

    BMB2015 Biochemistry and Molecular Biology in Kobe, Japan.  2015.12 

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  • CUBIC: Whole-organ, whole-body imaging with single-cell resolution using hydrophilic chemical cocktails. Invited International conference

    田井中 一貴

    International Conference on Systems Biology of Human Disease 2015 in Heidelberg, German.  2015.7 

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    *Lecture of the Anne Heidenthal Prize for Fluorescence Research

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  • 生体組織透明化技術 CUBIC Invited

    田井中一貴

    バイオガレージセミナー「生体・組織イメージングの最先端」  2014.10 

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Industrial property rights

  • 骨を含む生物試料を透明化する方法、骨を含む生物試料の屈折率を調整する方法、及び、骨を含む生物試料を透明化するためのキット

    田井中一貴, 三國貴康, 内ケ島基政, 劉歆儀

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    Applicant:国立大学法人新潟大学

    Application no:PCT/JP2025/012465  Date applied:2025.3

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  • 骨を含む生物試料を透明化する方法、骨を含む生物試料の屈折率を調整する方法、及び、骨を含む生物試料を透明化するためのキット

    田井中一貴, 三國貴康, 内ケ島基政, 劉歆儀

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    Applicant:国立大学法人新潟大学

    Application no:特願特願2024-061116  Date applied:2024.4

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  • 光透過性に優れた生物材料を調製するための組成物およびその利用(国内出願)

    上田泰己, 田井中一貴, 村上達哉

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    Application no:特願2016-092025  Date applied:2016.4

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  • 光透過性に優れた生物材料を調製するための組成物およびその利用(国内出願)

    洲崎悦生, 田井中一貴, 上田泰己

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    Application no:特願2013-168705  Date applied:2013.8

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  • 非天然型塩基を含むオリゴデオキシヌクレオチドの切断による5’末端リン酸化オリゴデオキシヌクレオチドの製造方法(PCT出願)

    上田泰己, 池田修二, 田井中一貴

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    Application no:PCT/JP2013/058349  Date applied:2013.3

    Announcement no:WO2013150902 A1  Date announced:2013.10

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  • 非天然型塩基を含むオリゴデオキシヌクレオチドの切断による5’末端リン酸化オリゴデオキシヌクレオチドの製造方法(国内出願)

    上田泰己, 池田修二, 田井中一貴

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    Application no:特願2012-084249  Date applied:2012.4

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  • メチルシトシンの簡便検出法(PCT出願)

    岡本晃充, 田井中一貴, 田中一生, 亀井琢

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    Application no:PCT/JP2006/306359  Date applied:2006.3

    Announcement no:WO2006132022 A1  Date announced:2006.12

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  • プロダン含有ヌクレオシド及びその応用(国内出願)

    岡本晃充, 田井中一貴, 齋藤 烈, 高橋則彦

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    Application no:特願2005-335005  Date applied:2005.11

    Announcement no:特開2006-169240  Date announced:2006.6

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  • プロダン含有ヌクレオシド及びその応用(PCT出願)

    岡本晃充, 田井中一貴, 齋藤 烈, 高橋則彦

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    Application no:US 11/135,368  Date applied:2005.5

    Announcement no:US20060142311 A1  Date announced:2006.6

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  • ポリヌクレオチド誘導体およびその利用

    齋藤 烈, 岡本晃充, 田井中一貴, 飯田 満, 加藤輝久

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    Application no:特願2002-333326  Date applied:2002.11

    Announcement no:特開2004-168672  Date announced:2004.6

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  • メチルシトシンの簡便検出法(国内出願)

    岡本晃充, 田井中一貴, 田中一生, 亀井琢

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    Application no:特願2007-520033 

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  • 光透過性に優れた生物材料を調製するための組成物およびその利用(PCT出願)

    洲崎悦生, 田井中一貴, 上田泰己

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    Application no:PCT/JP2014/070618 

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Awards

  • 第58回日本神経病理学会総会学術研究会 優秀ポスター賞

    2017.6  

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  • Anne Heidenthal Prize for Fluorescence Research at International Conference on Systems Biology of Human Disease 2015

    2015.7  

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  • 日本化学会第88春季年会 優秀講演賞

    2008.3  

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  • 日本化学会第84春季年会 学生講演賞

    2004.3  

    田井中 一貴

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Research Projects

  • ひとてんかん原性病態機序を知りこれを制御する

    Grant number:23H00434

    2023.4 - 2026.3

    System name:科学研究費助成事業

    Research category:基盤研究(A)

    Awarding organization:日本学術振興会

    柿田 明美, 他田 真理, 北浦 弘樹, 田井中 一貴, 池田 昭夫

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    Grant amount:\47320000 ( Direct Cost: \36400000 、 Indirect Cost:\10920000 )

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  • 炎症シグナルによる皮質神経回路形成の攪乱とリモデリング

    Grant number:22H02728

    2022.4 - 2026.3

    System name:科学研究費助成事業

    Research category:基盤研究(B)

    Awarding organization:日本学術振興会

    那波 宏之, 竹林 浩秀, 武井 延之, 田井中 一貴

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    Grant amount:\17030000 ( Direct Cost: \13100000 、 Indirect Cost:\3930000 )

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  • Development of neuroregeneration therapy mediated by peripheral blood mononuclear cell-derived exosomes through cell modification.

    Grant number:22H03183

    2022.4 - 2026.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (B)

    Awarding organization:Japan Society for the Promotion of Science

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    Grant amount:\17420000 ( Direct Cost: \13400000 、 Indirect Cost:\4020000 )

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  • Whole human brain pathological analysis by 3D imaging with single cell resolution

    Grant number:22H02937

    2022.4 - 2025.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (B)

    Awarding organization:Japan Society for the Promotion of Science

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    Grant amount:\17550000 ( Direct Cost: \13500000 、 Indirect Cost:\4050000 )

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  • 脳内修復におけるミクログリアによるタウ排泄機序の解明

    Grant number:21K19441

    2021.7 - 2024.3

    System name:科学研究費助成事業

    Research category:挑戦的研究(萌芽)

    Awarding organization:日本学術振興会

    金澤 雅人, 田井中 一貴, 清水 宏, 上野 将紀

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    Grant amount:\6240000 ( Direct Cost: \4800000 、 Indirect Cost:\1440000 )

    認知症の原因となるタウ蛋白蓄積が生じる能血管障害モデルをもとに,タウ蓄積とその排泄に関して機序の解明を行う.脳血管障害に伴うタウ蛋白蓄積を解明することのみならず,その障害の基盤を解明する研究である.ミクログリアで,タウ蓄積を軽減し,認知機能を改善することができれば,高血圧,糖尿病,高脂血症治療薬を用いて,ミクログリアを保護的に修飾し,タウ排泄促進するかを検討する.これにて,ドラッグ・リポジショニングの応用が可能である.さらに,異常蛋白蓄積による神経変性疾患にも応用可能な提案であり,他の蛋白排泄機序の解明につながり,他の神経疾患研究にも展開する.

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  • Research on the role of tissue-resident NK cells in cancer immune-surveillance

    Grant number:21H02783

    2021.4 - 2025.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (B)

    Awarding organization:Japan Society for the Promotion of Science

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    Grant amount:\17290000 ( Direct Cost: \13300000 、 Indirect Cost:\3990000 )

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  • Visualization of microenvironments of malignant glioma utilizing 7T-MRI and 3D tissue clearing technology

    Grant number:21H03042

    2021.4 - 2024.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (B)

    Awarding organization:Japan Society for the Promotion of Science

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    Grant amount:\17420000 ( Direct Cost: \13400000 、 Indirect Cost:\4020000 )

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  • Development of novel forensic technology by tissue clearing-based 3D imaging

    Grant number:20K21246

    2020.7 - 2022.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Challenging Research (Exploratory)

    Awarding organization:Japan Society for the Promotion of Science

    Tainaka Kazuki

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    Grant amount:\6500000 ( Direct Cost: \5000000 、 Indirect Cost:\1500000 )

    The objective of this study is to establish a novel method for determining the exact cause of death by highly cleared human postmortem specimens while preserving their morphology, and by performing high-resolution and comprehensive 3D imaging of injured organs. We have developed a new tissue clearing protocol applicable to large human postmortem specimens, and have succeeded in achieving a high degree of transparency in large 3-5 cm cubic postmortem human tissue specimens. In addition, 3D imaging analysis was performed on a lesion site of a subdural hematoma caused by cortical artery rupture, and it was found that cortical artery rupture could be successfully detected, even ruptures that had been missed by conventional method.

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  • Design strategy for specific chemical probes visualizing multimolecular crowding biosystems

    Grant number:20H04700

    2020.4 - 2022.3

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Awarding organization:Japan Society for the Promotion of Science

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    Grant amount:\4940000 ( Direct Cost: \3800000 、 Indirect Cost:\1140000 )

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  • 慢性ストレスによる心不全の分子病態解明に関する研究

    2019.10 - 2022.3

    System name:循環器病の予防法・治療法開発のための分子病態解明に関する研究

    Awarding organization:国立研究開発法人日本医療研究開発機構

    村上 正晃

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    Grant type:Competitive

    Grant no. 19ek0210125h0001

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  • デジタル3D神経病理学の創成

    2019.8 - 2022.3

    System name:挑戦的研究(開拓)

    Awarding organization:文部科学省

    柿田 明美

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    Grant type:Competitive

    Grant no. 19H05559

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  • てんかん原性病巣の病態機序と制御:外科標本のイメージングプラクティス

    2019.4 - 2022.3

    System name:基盤研究(A)

    Awarding organization:文部科学省

    柿田 明美

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    Grant type:Competitive

    Grant no. 19H01061

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  • 脳小血管病の3D病理解析基盤の確立

    2018.7 - 2019.3

    System name:挑戦的研究(萌芽)

    Awarding organization:文部科学省

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

    Grant no. 18K19373

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  • ヒト脳組織特異的染色による先進的3D神経病理学の確立

    2018.4 - 2022.3

    System name:基盤研究(B)

    Awarding organization:文部科学省

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

    Grant no. 18H02105

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  • D1/D2ドーパミン受容体発現操作マウスによる運動制御と学習記憶機構の理解

    2018.4 - 2021.3

    System name:基盤研究(B)

    Awarding organization:文部科学省

    笹岡 俊邦

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    Grant type:Competitive

    Grant no. 18H02540

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  • 組織夾雑系の理解を目的としたケミカルプローブの設計戦略

    2018.4 - 2020.3

    System name:新学術領域研究(研究領域提案型)

    Awarding organization:文部科学省

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

    分子夾雑の生命化学, Grant no. 18H04543

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  • ヒト脳組織膨潤・透明化技術による神経病理学的解析

    2018

    System name:2018年度医学系研究助成(精神・神経・脳領域)

    Awarding organization:公益財団法人武田科学振興財団

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

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  • ゲートウェイ反射に基づく病原体侵入口形成機構の解明

    2017.8 - 2020.3

    System name:感染症研究革新イニシアティブ(J-PRIDE)

    Awarding organization:国立研究開発法人日本医療研究開発機構

    村上 正晃

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    Grant type:Competitive

    Grant no. JP17fm0208023

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  • 3D免疫染色によるタンパク質の老化基盤の解析

    2017.4 - 2019.3

    System name:新学術領域研究(研究領域提案型)

    Awarding organization:文部科学省

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

    脳タンパク質老化と認知症制御, Grant no. 17H05688

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  • ヒト脳組織特異的染色に向けたケミカルプローブの包括的プロファイリング

    2017

    System name:2017年度研究奨励金

    Awarding organization:公益財団法人ノバルティス科学振興財団

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

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  • 3D神経病理学に向けた組織透明化技術の開発

    2017

    System name:2017年度 内藤記念科学奨励金・研究助成

    Awarding organization:公益財団法人内藤記念科学振興財団

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

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  • 3 次元神経病理学の基盤となる染色技術の開発

    2017

    System name:平成29年度 研究奨励金(II)

    Awarding organization:公益財団法人東京生化学会

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

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  • 3Dイメージングによる脳小血管病の病態解析

    2017

    System name:平成30年度研究助成

    Awarding organization:公益財団法人細胞科学研究財団

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

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  • 細胞機能の変容により曝露物質の毒性を評価する新規安全性試験技術の開発

    2016.4 - 2018.3

    System name:挑戦的萌芽研究

    Awarding organization:文部科学省

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

    Grant no. 16K15124

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  • 全身・臓器丸ごとイメージング技術によるバイオ医薬品の時間的・空間的な体内動態可視化技術の開発

    2015.10 - 2016.12

    System name:革新的バイオ医薬品創出基盤技術開発事業

    Awarding organization:国立研究開発法人日本医療研究開発機構

    上田 泰己

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    Grant type:Competitive

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  • 全脳イメージング技術を用いた統合失調症治療薬投与時の脳内神経活動変化解析

    2015

    System name:平成27年度研究助成

    Awarding organization:公益財団法人薬理研究会

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

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  • 全身丸ごとイメージング技術を用いた炎症制御機構の解析基盤の確立

    2015

    System name:平成27年度医学研究助成

    Awarding organization:一般財団法人東京医学会

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

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  • 哺乳類概日振動体の構成的な理解

    2013.4 - 2016.12

    System name:科学研究費補助金(基盤研究(S))

    Awarding organization:日本学術振興会

    上田 泰己

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    Grant type:Competitive

    Grant no. 25221004

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  • プロドラッグを利用した細胞ネットワークにおける薬理活性評価システムの開発

    2013

    System name:平成25年度研究助成

    Awarding organization:一般財団法人島原科学振興会

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

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  • 可視光照射により酸化反応を触媒する太陽光駆動型オキシダーゼの開発

    2010.4 - 2013.3

    System name:科学研究費補助金(若手研究(B))

    Awarding organization:日本学術振興会

    田井中 一貴

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    Authorship:Principal investigator  Grant type:Competitive

    Grant no. 22750152

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  • 太陽光駆動型人工酵素の作製

    2010

    System name:2010年研究助成

    Awarding organization:公益財団法人国際科学技術財団

    田井中 一貴

      More details

    Authorship:Principal investigator  Grant type:Competitive

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  • Development of the light-driven artificial reductase

    2008 - 2013

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    Grant type:Competitive

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  • A modular strategy to construct functional RNA-protein complexes

    Grant number:20241051

    2008 - 2011

    System name:Grants-in-Aid for Scientific Research

    Research category:Grant-in-Aid for Scientific Research (A)

    Awarding organization:Japan Society for the Promotion of Science

    MORII Takashi, TAINAKA Kazuki

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    Grant amount:\49400000 ( Direct Cost: \38000000 、 Indirect Cost:\11400000 )

    A stable complex of a peptide and RNA, ribonucleopeptide(RNP), provides a new framework to construct a macromolecular receptor for small molecules. The RRE RNA and the Rev peptide form a structurally well-characterized stable RNP complex that is suitable for a stepwise functionalization. In vitro selection of the RNP pool originating from an RRE-based RNA library and the Rev peptide affords RNP receptors specific for nucleotide triphosphates, for a phosphotyrosine residue in defined amino acid sequence, and for dopamine. A new ATP-binding motif for the ATP-binding RNP was characterized by a combination of biochemical and NMR studies. The RNP receptor functionalized by a fluorophore-labeled Rev peptide exerts optical signals associated with the ligand binding events. Replacing the Rev peptide of the ATP-binding RNP with a fluorophore-modified Rev peptide affords a series of fluorescent ATP sensors. This strategy to generate tailor-made fluorescent sensors is applied for a selective detection of a specific phosphorylated tyrosine residue within a defined amino acid sequence.

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  • 生体内シグナル伝達分子を標的とした蛍光バイオセンサーの創製

    Grant number:19021023

    2007 - 2008

    System name:科学研究費助成事業

    Research category:特定領域研究

    Awarding organization:日本学術振興会

    森井 孝, 田井中 一貴

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    Grant amount:\4800000 ( Direct Cost: \4800000 )

    (1) 二種類の標的分子を同時計測できるデュアルバイオセンサーの構築
    異なった波長で応答する二種類のバイオセンサーを使用する事により、二元同時センサーを作製した。Cy5をN末端に導入したペプチドを用いて作製した光応答性ATPリセプターライブラリーから、効率よく光応答する蛍光性センサーを得た。GTPに対しても同様に、フルオレセインを導入した光応答性GTPリセプターライブラリーから光応答するセンサーを選出した。得られたリボヌクレオペプチドセンサーのRNAサブユニット3'末端を参加し、蛍光性RevペプチドのC末端に導入したヒドラジド基と反応させることにより、共有結合で連結された蛍光性RNPセンサーを合成した。異なった波長で応答するATPセンサーとGTPセンサーを同時に用いることにより、ATPとGTPを同時に計測できる二元同時センサーの作製に成功した。異なった波長で応答する二種類のバイオセンサーを使用する事により、二元同時センサーを作製した。Cy5をN末端に導入したペプチドを用いて作製した光応答性ATPリセプターライブラリーから、効率よく光応答する蛍光性センサーを得た。GTPに対しても同様に、フルオレセインを導入した光応答性GTPリセプターライブラリーから光応答するセンサーを選出した。得られたリボヌクレオペプチドセンサーのRNAサブユニット3'末端を参加し、蛍光性RevペプチドのC末端に導入したヒドラジド基と反応させることにより、共有結合で連結された蛍光性RNPセンサーを合成した。異なった波長で応答するATPセンサーとGTPセンサーを同時に用いることにより、ATPとGTPを同時に計測できる二元同時センサーの作製に成功した。
    (2) 細胞抽出液中でのセンシング
    上記(2)で合成した共有結合性ATPセンサーとGTPセンサーは、ヌクレアーゼ耐性が向上した。それぞれのセンサーは、細胞抽出液中でも効率よくATPもしくはGTPを検出・定量する事が可能であった。
    (3) 細胞内イノシトール四リン酸動態のリアルタイム計測
    天然タンパク質を基にIP4に対する蛍光性センサーを構築し、試験管内および細胞内においてIP4濃度変化の検出に成功した。また、IP4センサーとカルシウムセンサーfura-2を同時に用いて、IP4とCa2+挙動の単一細胞内リアルタイム検出に成功した。

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