REFERENCE

REFERENCE

Grant Achknowledgement

MEXT/JSPS KAKENHI Grant Number JP課題番号 “Resonance Bio”成果発表の際は謝辞に必ず記載してください。

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RESONANCE BIO ロゴマーク

 

Figure Sources

Chihara T., Umezawa M., Miyata K., Sekiyama S., Hosokawa N., Okubo K., Kamimura M., Soga K. (2019) Biological Deep Temperature Imaging with Fluorescence Lifetime of Rare-Earth-Doped Ceramics Particles in the Second NIR Biological Window. Scientific Reports, 9: 12806.

Umezawa M., Haruguchi S., Fukushima R., Sekiyama S., Kamimura M., Soga K. (2019) Rapid Increase in Transparency of Biological Organs by Matching Refractive Index of Media to Cell Membrane Using Phosphoric Acid. RSC Advances, 9: 15269–15276.



Sekiyama S., Umezawa M., Iizumi Y., Ube T., Okazaki T., Kamimura M., Soga K. (2019) Delayed Increase in Near-Infrared Fluorescence in Cultured Murine Cancer Cells Labeled with Oxygen-Doped Single-Walled Carbon Nanotubes. Langmuir, 35 (3): 831–837.

Sekiyama S., Umezawa M., Kuraoka S., Ube T., Kamimura M., Soga K. (2018) Temperature Sensing of Deep Abdominal Region in Mice by Using Over-1000 nm Near-Infrared Luminescence of Rare-Earth-Doped NaYF4 Nanothermometer. Scientific Reports, 8: 16979.

Yi X., Son S., Ando R., Miyawaki A., Weiss S. (2019) Moments reconstruction and local dynamic range compression of high order superresolution optical fluctuation imaging, Biomed. Opt. Express, 10 (5): 2430-2445.

Shibata K.I., Tanaka T., Hioki H., Furuta T. (2018) Projection Patterns of Corticofugal Neurons Associated with Vibrissa Movement. eNeuro, 5(5): pii: ENEURO.0190-18.2018.

Hioki H., Sohn J., Nakamura H., Okamoto S., Hwang J., Ishida Y., Takahashi M., Kameda H. (2018) Preferential Inputs from Cholecystokinin-Positive Neurons to the Somatic Compartment of Parvalbumin-Expressing Neurons in the Mouse Primary Somatosensory Cortex. Brain Research, 1695: 18-30.

Okamoto K., Hitora-Imamura N., Hioki H., Ikegaya Y. (2018) GABAergic malfunction in the anterior cingulate cortex underlying maternal immune activation-induced social deficits. Journal of neuroimmunology, 321: 92-96.

Ohara S., Onodera M., Simonsen Ø.W., Yoshino R., Hioki H., Iijima T., Tsutsui K.I., Witter M.P. (2018) Intrinsic Projections of Layer Vb Neurons to Layers Va, III, and II in the Lateral and Medial Entorhinal Cortex of the Rat. Cell Reports, 24(1): 107-116.

Ogasawara A., Kamiya M., Sakamoto K., Kuriki Y., Fujita K., Komatsu T., Ueno T., Hanaoka K., Onoyama H., Abe H., Tsuji Y., Fujishiro M., Koike K., Fukayama M., Seto Y., Urano Y. (2019) Red Fluorescence Probe Targeted to Dipeptidylpeptidase-IV for Highly Sensitive Detection of Esophageal Cancer. Bioconjug. Chem., 30(4): 1055-1060.

Umezawa K., Kamiya M., Urano Y. (2018) A reversible fluorescent probe for real-time live-cell imaging and quantification of endogenous hydropolysulfides. Angew. Chem. Int. Ed. 57(30): 9346-9350.

Kuriki Y., Kamiya M., Kubo H., Komatsu T., Ueno T., Tachibana R., Hayashi K., Hanaoka K., Yamashita S., Ishizawa T., Kokudo N., Urano Y. (2018) Establishment of Molecular Design Strategy To Obtain Activatable Fluorescent Probes for Carboxypeptidases. J. Am. Chem. Soc., 140(5): 1767-1773.

Uno S., Kamiya M., Morozumi A., Urano Y. (2017) A green-light-emitting, spontaneously blinking fluorophore based on intramolecular spirocyclization for dual-colour super-resolution imaging. Chemical Communications, 54(1): 102-105.

Yogo T., Umezawa K., Kamiya M., Hino R., Urano Y. (2017) Development of an Activatable Fluorescent Probe for Prostate Cancer Imaging. Bioconjug Chem., 28(8): 2069-2076.

Iwatate R.J., Kamiya M., Urano Y. (2016) Asymmetric Rhodamine-Based Fluorescent Probe for Multicolour In Vivo Imaging. Chemistry, 22: 1696-1703.

Obashi K., Matsuda A., Inoue Y., Okabe S. (2019) Precise temporal regulation of molecular diffusion within dendritic spines by actin polymers during structural plasticity. Cell Reports, 27(5): 1503-1515. e8.

Sakane A., Yoshizawa S., Yokota H., Sasaki T. (2018) Dancing Styles of Collective Cell Migration: Image-Based Computational Analysis of JRAB/MICAL-L2. Frontiers in Cell and Developmental Biology, 6: 4.

Tamada A. (2019) Chiral Neuronal Motility: The Missing Link between Molecular Chirality and Brain Asymmetry. Symmetry, 11: 102.

Kawasaki A., Okada M., Tamada A., Okuda S., Nozumi M., Ito Y., Kobayashi D., Yamasaki T., Yokoyama R., Shibata T., Nishina H., Yoshida Y., Fujii Y., Takeuchi K., Igarashi M. (2019) Growth Cone Phosphoproteomics Reveals that GAP-43 Phosphorylated by JNK Is a Marker of Axon Growth and Regeneration. iScience, 4: 190-203.

izuguchi T, Yasui M, Nuriya M.(2018) igh-Resolution Plasma Membrane-Selective Imaging by Second Harmonic Generation. iScience, 9, 359-366.

Komatsu N., Terai K., Imanishi A., Kamioka Y., Sumiyama K., Jin T., Okada Y., Nagai T., Matsuda M. (2018) A platform of BRET-FRET hybrid biosensors for optogenetics, chemical screening, and in vivo imaging. Scientific Report, 8: 8984.

Hori Y., Otomura N., Nishida A., Nishiura M., Umeno M., Suetake I., Kikuchi K. (2018) Synthetic-Molecule/Protein Hybrid Probe with Fluorogenic Switch for Live-Cell Imaging of DNA Methylation. J. Am. Chem. Soc., 140 (5): 1686–1690.

Sakamoto H., Ariyoshi T., Kimpara N., Sugao K., Taiko I., Takikawa K., Asanuma D., Namiki S. Hirose K. (2017) Synaptic weight set by Munc13-1 supramolecular assemblies. Nat. Neurosci., 21, 41-49.

Konagaya Y., Terai K., Hirao Y., Takakura K., Imajo M., Kamioka Y., Sasaoka N., Kakizuka A., Sumiyama K., Asano T., Matsuda M. (2017) A Highly Sensitive FRET Biosensor for AMPK Exhibits Heterogeneous AMPK Responses among Cells and Organs. Cell Rep. 21: 2628-2638.

Tanabe A., Hibi T., Ipponjima S., Matsumoto K., Yokoyama M., Kurihara M.,Hashimoto N., Nemoto T. (2016) Transmissive liquid crystal device for correcting primary coma aberration and astigmatism in biospecimen in two-photon excitation laser scanning microscopy, J. Biomed. Opt., 21 (12):121503.

Yang SH., Han XH, Chen YW. (2017) Automatic Segmentation of Cellular/ Nuclear Boundaries Based on the Shape Index of Image Intensity Surfaces. Innovation in Medicine and Healthcare 2017, Eds. Yen-Wei Chen et al., Springer, 66-67.

Hiratsuka T., Sano T., Kato H., Komatsu N., Imajo M., Kamioka Y., Sumiyama K., Banno F., Miyata T., Matsuda M. (2017) Live imaging of extracellular signal-regulated kinase and protein kinase A activities during thrombus formation in mice expressing biosensors based on Förster resonance energy transfer. J Thromb. Haemat. 15(7):1487-1499.

 Nishimura K, *Fumoto S, Fuchigami Y, Hagimori M, Maruyama K, Kawakami S.(2017) Effective Intraperitoneal Gene Transfection System Using Nanobubbles and Ultrasound Irradiation. Drug Delivery, 24 (1), 737-744.

Watanabe T, Seki T, Fukano T, Sakaue-Sawano A, Karasawa S, Kubota M, Kurokawa H, Inoue K, Akatsuka J, Miyawaki A. (2017) Genetic visualization of protein interactions harnessing liquid phase transitions. Sci. Rep., 7: 46380.

Murakoshi H., Shin M., Parra-Bueno P., Szatmari E.M., Shibata A.C., Yasuda R. (2017) Kinetics of endogenous CaMKII required for synaptic plasticity revealed by optogenetic kinase inhibitor. Neuron, 94 (1), 37-47.

Wang J., Han XH., Xu Y., Lin L., Hu H., Jin C., Chen YW. (2017) Sparse codebook model of local structures for retrieval of focal liver lesions using multi-phase medical images. International Journal of Biomedical Imaging, 2017 (2017), Article ID 1413297.

Nakahata Y, Nabekura J, and Murakoshi H.(2016)Dual observation of the ATP-evoked small GTPase activation and Ca2+ transient in astrocytes using a dark red fluorescent protein.Scientific Reports, 6: 39564 .

Sohn J., Takahashi M., Okamoto S., Ishida Y., Furuta T., Hioki H. (2017) A Single Vector Platform for High-Level Gene Transduction of Central Neurons: Adeno-Associated Virus Vector Equipped with the Tet-Off System. PLoS One, 12: e0169611.

Sohn J., Okamoto S., Kataoka N., Kaneko T., Nakamura K., Hioki H. (2016) Differential Inputs to the Perisomatic and Distal-Dendritic Compartments of VIP-Positive Neurons in Layer 2/3 of the Mouse Barrel Cortex. Front Neuroanat, 10: Article 124.


Han XH., Tohsato Y., Kyoda K., Onami S., Nishikawa I., Chen YW. (2016) Nuclear detection in 4D microscope images of a developing embryo using an enhanced probability map of top-ranked intensity-ordered descriptors. IPSJ Trans. Computer Vision and Applications, 8:8.

Sakane A., Yoshizawa S., Nishimura M., Tsuchiya Y., Matsushita N., Miyake K., Horikawa K., Imoto I., Mizuguchi C., Saito H., Ueno T., Matsushita S., Haga H., Deguchi S., Mizuguchi K., Yokota H., Sasaki T. (2016) Conformational plasticity of JRAB/MICAL-L2 provides “law and order” in collective ce+M35ll migration. Mol. Biol. Cell, 27: 3095-3108.

Hamamoto H., Kiyokage E., Sohn J., Hioki H., Harada T., Toida K. (2017) Structural Basis for Cholinergic Regulation of Neural Circuits in the Mouse Olfactory Bulb. J Comp Neurol, 525: 574-591.

Kuramoto E., Pan SX., Furuta T., Tanaka YR., Iwai H., Yamanaka A., Ohno S., Kaneko T., Goto T., Hioki H. (2017) Individual Mediodorsal Thalamic Neurons Project to Multiple Areas of the Rat Prefrontal Cortex: A Single Neuron-Tracing Study Using Virus Vectors. J Comp Neurol, 525: 166-185.

Toyoshima Y., Tokunaga T., Hirose O., Kanamori M., Teramoto T., Jang, M-S., Kuge S., Ishihara T., Yoshida R., Iino Y. (2016) Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space. PLoS computational biology, 12: e1004970.

Kitajima N., Takikawa K., Sekiya H., Satoh K., Asanuma D., Sakamoto H., Takahashi S., Hanaoka K., Urano Y., Namiki S., Iino M., Hirose K. (2020) Real-time in vivo imaging of extracellular ATP in the brain with a hybrid-type fluorescent sensor. eLife, 9:e57544.

Kojima H., Rosendale M., Sugiyama Y., Hayashi M., Horiguchi Y., Yoshihara T., Ikegaya Y., Saneyoshi T., Hayashi Y. (2019) The role of CaMKII-Tiam1 complex on learning and memory. Neurobiol. Learn Mem., 166:107070.

Gao J., Hori Y., Takeuchi O., Kikuchi K. (2020) Live-Cell Imaging of Protein Degradation Utilizing Designed Protein-Tag Mutant and Fluorescent Probe with Turn-Off Switch. Bioconjug Chem. 31: 577-583.

Gao J., Hori Y., Shimomura T., Bordy M., Hasserodt J., Kikuchi K. (2020) Development of Fluorogenic Probes for Rapid High-Contrast Imaging of Transient Nuclear Localization of Sirtuin 3. ChemBioChem., 21: 656-662.

Torii K., Hori Y., Watabe K., Kikuchi K. (2020) Development of photoswitchable fluorescent molecules using arylazopyrazole. Bull. Chem. Soc. Jpn., 93 (7): 821-824.

Kumar N., Hori Y., Nishiura M., Kikuchi K. (2020) Rapid No-Wash Labeling of PYP-Tag Proteins with Reactive Fluorogenic Ligands Affords Stable Fluorescent Protein Conjugates for Long-Term Cell Imaging Studies. Chem Sci., 11: 3694-3701.

Hori Y., Kikuchi K. (2019) Chemical Tools with Fluorescence Switches for Verifying Epigenetic Modifications. Acc. Chem. Res., 52: 2849–2857.

Kumar N., Hori Y., Kikuchi K. (2019) Photoactive Yellow Protein and Its Chemical Probes: an Approach to Protein Labelling in Living Cells. J. Biochem., 166: 121–127.

Kumar N., Hori Y., Kikuchi K. (2018) Live-Cell Imaging of DNA Methylation Based on Synthetic-Molecule/Protein Hybrid Probe. Chem Rec., 18: 1672–1680.


Saitou T., Takanezawa S., Ninomiya H., Watanabe T., Yamamoto S., Hiasa Y., Imamura T. (2018) Tissue Intrinsic Fluorescence Spectra-Based Digital Pathology of Liver Fibrosis by Marker-Controlled Segmentation. Frontiers in Medicine (Lausanne) 5: 350.

Imamura T., Saitou T., Kawakami R. (2018) In vivo optical imaging of cancer cell function and tumor microenvironment. Cancer Science, 109, 912-918.

Saitou T., Kiyomatsu H., Imamura T. (2018) Quantitative Morphometry for Osteochondral Tissues Using Second Harmonic Generation Microscopy and Image Texture Information. Scientific Reports, 8: 2826.

Morozumi A., Kamiya M., Uno S., Umezawa K., Kojima R., Yoshihara T., Tobita S., Urano Y. (2020) Spontaneously blinking fluorophores based on nucleophilic addition/dissociation of intracellular glutathione for live-cell super-resolution imaging. J. Am. Chem. Soc., 142 (21): 9625–9633.

Rivas C., Kamiya M., Urano Y. (2020) A novel sialidase-activatable fluorescence probe with improved stability for the sensitive detection of sialidase. Bioorg. Med. Chem. Lett., 30: 126860.

Yamamoto K., Kamiya M., Urano Y. (2019) Highly sensitive fluorescence imaging of cancer with avidin-protease probe conjugate. Bioorg. Med. Chem. Lett., 9: 126663.

Kawatani M., Yamamoto K., Yamada D., Kamiya M., Miyakawa J., Miyama Y., Kojima R., Morikawa T., Kume H., Urano Y. (2019) Fluorescence Detection of Prostate Cancer by an Activatable Fluorescence Probe for PSMA Carboxypeptidase Activity. J. Am. Chem. Soc. 14, 10409-10416.

Uno S., Kamiya M., Morozumi A., Urano Y. (2018) A green-light-emitting, spontaneously blinking fluorophore based on intramolecular spirocyclization for dual-colour super-resolution imaging. Chem. Comm., 54: 102-105.


Iwatate R.J., Kamiya M., Urano Y. (2016) Asymmetric Rhodamine-Based Fluorescence Probes for Multi-colour In Vivo Imaging. Chem-Eur. J., 22: 1696-1703.

Murakoshi H., Horiuchi H., Kosugi T., Onda M., Sato A., Koga N., Nabekura J. (2019) ShadowR: a novel chromoprotein with reduced non-specific binding and improved expression in living cells. Scientific Reports, 9, 12072.

Murakoshi H., Shibata A.C. (2017) ShadowY: a dark yellow fluorescent protein for FLIM-based FRET measurement. Scientific Reports, 7: 6791.

Kozawa Y., Sato S. (2019) Light needle microscopy with spatially transposed detection for axially resolved volumetric imaging. Scientific Reports, 9: 11687.

Kozawa Y., Matsunaga D., Sato S. (2018) Superresolution imaging via superoscillation focusing of a radially polarized beam. Optica, 5 (2): 86-92.

Matsumoto D., Tamamura H., and Nomura W. (2020) TALEN-Based Chemically Inducible, Dimerization-Dependent, Sequence-Specific Nucleases. Biochemistry, 57: 197-204.

2018

Nomura W., Matsumoto D., Sugii T., Kobayakawa T., Tamamura H. (2018) Efficient and Orthogonal Transcription Regulation by Chemically Inducible Artificial Transcription Factors. Biochemistry, 57: 6452-6459.

Nuriya M., Yoneyama H., Takahashi K., Leproux P., Cuderc V., Yasui M. Kano H. (2019) Characterization of Intra/Extracellular Water States Probed by Ultrabroadband Multiplex Coherent Anti-Stokes Raman Scattering (CARS) Spectroscopic Imaging. The Journal of Physical Chemistry A, 23 (17): 3928-393.

Zhang H., Yarinome K., Kawakami R., Otomo K., Nemoto T., Okamura Y. (2020) Nanosheet wrapping-assisted coverslip-free imaging for looking deeper into a tissue at high resolution. PLoS ONE, 15: e0227650.

Zhang H, Sakagami D, Huang W, Kimura H, Okamura Y. (2020) Measurement and Modelling of Tensile Moduli of Polymer Blend Thin Films with Phase Separated Structures. Polymer, 190: 122233.

Toyoshima Y., Wu S., Kanamori M., Sato H., Jang M. S., Oe S., Murakami Y., Teramoto T., Park C., Iwasaki Y., Ishihara T., Yoshida R., Iino Y. (2020) Neuron ID dataset facilitates neuronal annotation for whole-brain activity imaging of C. elegans. BMC Biology, 18: 30.


Gao J., Hori Y., Nishiura M., Bordy M., Hasserodt J., Kikuchi K. (2020) Engineered Protein-Tag for Rapid Live-Cell Fluorogenic Visualization of Proteins by Anionic Probes. Chem. Lett. 49: 232-235.

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