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Article ; Online: Differential metabolic secretion between mdx mouse-derived spindle cell sarcomas and rhabdomyosarcomas drives tumor type development.

Niba, Emma Eko Tabe / Awano, Hiroyuki / Nishimura, Noriyuki / Koide, Hiroshi / Matsuo, Masafumi / Shinohara, Masakazu

American journal of physiology. Cell physiology

2024

Abstract: ... ...

Abstract	The
Language	English
Publishing date	2024-04-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	392098-7
ISSN	1522-1563 ; 0363-6143
ISSN (online)	1522-1563
ISSN	0363-6143
DOI	10.1152/ajpcell.00523.2023
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Book ; Online: Novel transition dynamics of topological solitons

Nishimura, Kentaro / Sogabe, Noriyuki

2023

Abstract: Continuous phase transitions can be classified into ones characterized by local order parameters and others that need additional topological constraints. The critical dynamics near the former transitions have been extensively studied, but the latter is ... ...

Abstract	Continuous phase transitions can be classified into ones characterized by local order parameters and others that need additional topological constraints. The critical dynamics near the former transitions have been extensively studied, but the latter is less understood. We fill this gap in knowledge by studying the transition dynamics to a parity-breaking topological ground state called the chiral soliton lattice in quantum chromodynamics at finite temperature, baryon chemical potential, and external magnetic field. We find a slowing down of the soliton's translational motion as the critical magnetic field approaches while the local dissipation rate remains finite. Therefore, the characteristic time it takes to converge to the stationary state associated with a finite topological number strongly depends on the initial configuration: whether it forms a solitonic structure or not. Comment: 6 pages, 3 figures; affiliation updated
Keywords	High Energy Physics - Theory ; Condensed Matter - Materials Science ; High Energy Physics - Phenomenology ; Nuclear Theory
Subject code	539
Publishing date	2023-04-03
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Manipulation of Macrophage Uptake by Controlling the Aspect Ratio of Graft Copolymer Micelles.

Sakamoto, Yusuke / Fujii, Shota / Takano, Shin / Fukushima, Jokichi / Ando, Mitsuru / Kodera, Noriyuki / Nishimura, Tomoki

Nano letters

2024

Abstract: Nanostructures of drug carriers play a crucial role in nanomedicine due to their ability to influence drug delivery. There is yet no clear consensus regarding the optimal size and shape (e.g., aspect ratio) of nanoparticles for minimizing macrophage ... ...

Abstract	Nanostructures of drug carriers play a crucial role in nanomedicine due to their ability to influence drug delivery. There is yet no clear consensus regarding the optimal size and shape (e.g., aspect ratio) of nanoparticles for minimizing macrophage uptake, given the difficulties in controlling the shape and size of nanoparticles while maintaining identical surface properties. Here, we employed graft copolymer self-assembly to prepare polymer micelles with aspect ratios ranging from 1.0 (spherical) to 10.8 (cylindrical) and closely matched interfacial properties. Notably, our findings emphasize that cylindrical micelles with an aspect ratio of 2.4 are the least susceptible to macrophage uptake compared with both their longer counterparts and spherical micelles. This reduced uptake of the short cylindrical micelles results in a 3.3-fold increase in blood circulation time compared with their spherical counterparts. Controlling the aspect ratio of nanoparticles is crucial for improving drug delivery efficacy through better nanoparticle design.
Language	English
Publishing date	2024-04-25
Publishing country	United States
Document type	Journal Article
ISSN	1530-6992
ISSN (online)	1530-6992
DOI	10.1021/acs.nanolett.4c01054
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Article ; Online: Alignment and use of microbeam with full-field x-ray microscopes.

Shibazaki, Yuki / Wakabayashi, Daisuke / Suzuki, Yoshio / Nishimura, Ryutaro / Hirano, Keiichi / Sugiyama, Hiroshi / Igarashi, Noriyuki / Funamori, Nobumasa

The Review of scientific instruments

2023 Volume 94, Issue 1, Page(s) 13102

Abstract: Demonstration tests of the alignment of Fresnel zone plate focusing optics using a full-field x-ray microscope and microbeam x-ray diffraction measurements combined with the full-field x-ray microscope were performed. It was confirmed that the full-field ...

Abstract	Demonstration tests of the alignment of Fresnel zone plate focusing optics using a full-field x-ray microscope and microbeam x-ray diffraction measurements combined with the full-field x-ray microscope were performed. It was confirmed that the full-field x-ray microscope enables direct two-dimensional observation of a microbeam with sub-micrometer spatial resolution. This allowed visualization of the misalignment of the focusing optics, resulting in accurate alignment of the optics within a short time. In addition, the microscope could be used to observe the sample as well as the microbeam, which enabled clarification of the position and two-dimensional shape of the microbeam on the sample. This realized a measurement procedure that a 100-μm-size sample was imaged with sub-micrometer spatial resolution, and then, microbeam-use measurements were performed for only the region of interest determined by the microscope, which has been difficult with conventional microbeam applications. The combination of observations by a full-field x-ray microscope and measurements using a microbeam is expected to open a new style of measurement.
Language	English
Publishing date	2023-01-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/5.0123780
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Article ; Online: X-ray zooming optics for analyzer-based multi-contrast computed tomography.

Hirano, Keiichi / Sugiyama, Hiroshi / Nishimura, Ryutaro / Wakabayashi, Daisuke / Suzuki, Yoshio / Igarashi, Noriyuki / Funamori, Nobumasa

Journal of synchrotron radiation

2022 Volume 29, Issue Pt 3, Page(s) 787–793

Abstract: An X-ray analyzer-based optics with a zoom function is proposed for observing various samples with apparent-absorption contrast, phase contrast and scattering contrast. The proposed X-ray optics consists of a collimator crystal and an analyzer crystal ... ...

Abstract	An X-ray analyzer-based optics with a zoom function is proposed for observing various samples with apparent-absorption contrast, phase contrast and scattering contrast. The proposed X-ray optics consists of a collimator crystal and an analyzer crystal arranged in a nondispersive (+, -) geometry with a sample placed between them. For the implementation of the zoom function, an asymmetrically cut crystal in the rotated-inclined geometry was used for the analyzer. Proof-of-principle experiments were performed at the vertical wiggler beamline BL-14B of the Photon Factory. First, the magnification was set to 1×, and then it was zoomed into the optimal magnification (10×). At these magnifications, tri-modal contrast cross-sectional images of a sample were obtained by computed tomography. It was confirmed that the image quality at 10× was superior to that at 1×. This achievement opens up new possibilities for observing an entire sample or regions of interest within a sample at optimal magnification, and is expected to be useful for materials science, condensed matter physics, archeology and biomedical science.
Language	English
Publishing date	2022-03-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2021413-3
ISSN	1600-5775 ; 0909-0495
ISSN (online)	1600-5775
ISSN	0909-0495
DOI	10.1107/S1600577522001412
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Article ; Online: Measurement of the Caspase-1-Like Activity of Vacuolar Processing Enzyme in Plants.

Hatsugai, Noriyuki / Hara-Nishimura, Ikuko

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1743, Page(s) 163–171

Abstract: Caspase-like activities are essential to regulate programed cell death in plants. Although no caspase orthologous enzymes with aspartic acid specificity have been identified in plants, vacuolar processing enzyme (VPE) exhibits a caspase-1-like activity. ... ...

Abstract	Caspase-like activities are essential to regulate programed cell death in plants. Although no caspase orthologous enzymes with aspartic acid specificity have been identified in plants, vacuolar processing enzyme (VPE) exhibits a caspase-1-like activity. In this chapter, we introduce two methods for the measurement of the caspase-1-like/VPE activity. These methods are based on the cleavage of caspase-1 specific synthetic substrates and on monitoring the active forms of VPE using a biotinylated-inhibitor blot analysis. Both methods are also adaptable to other plant caspase-like activities.
MeSH term(s)	Apoptosis ; Caspase 1/metabolism ; Caspase Inhibitors/pharmacology ; Cysteine Endopeptidases/metabolism ; Peptides/metabolism ; Plant Proteins/metabolism ; Plants/drug effects ; Plants/enzymology ; Plants/metabolism
Chemical Substances	Caspase Inhibitors ; Peptides ; Plant Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; vacuolar processing enzyme (EC 3.4.22.-) ; Caspase 1 (EC 3.4.22.36)
Language	English
Publishing date	2018-01-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7668-3_15
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Article ; Online: Dynamic Solution Structures of Whole Human NAP1 Dimer Bound to One and Two Histone H2A-H2B Heterodimers Obtained by Integrative Methods.

Ohtomo, Hideaki / Yamane, Tsutomu / Oda, Takashi / Kodera, Noriyuki / Kurita, Jun-Ichi / Tsunaka, Yasuo / Amyot, Romain / Ikeguchi, Mitsunori / Nishimura, Yoshifumi

Journal of molecular biology

2023 Volume 435, Issue 15, Page(s) 168189

Abstract: Nucleosome assembly protein 1 (NAP1) binds to histone H2A-H2B heterodimers, mediating their deposition on and eviction from the nucleosome. Human NAP1 (hNAP1) consists of a dimerization core domain and intrinsically disordered C-terminal acidic domain ( ... ...

Abstract	Nucleosome assembly protein 1 (NAP1) binds to histone H2A-H2B heterodimers, mediating their deposition on and eviction from the nucleosome. Human NAP1 (hNAP1) consists of a dimerization core domain and intrinsically disordered C-terminal acidic domain (CTAD), both of which are essential for H2A-H2B binding. Several structures of NAP1 proteins bound to H2A-H2B exhibit binding polymorphisms of the core domain, but the distinct structural roles of the core and CTAD domains remain elusive. Here, we have examined dynamic structures of the full-length hNAP1 dimer bound to one and two H2A-H2B heterodimers by integrative methods. Nuclear magnetic resonance (NMR) spectroscopy of full-length hNAP1 showed CTAD binding to H2A-H2B. Atomic force microscopy revealed that hNAP1 forms oligomers of tandem repeated dimers; therefore, we generated a stable dimeric hNAP1 mutant exhibiting the same H2A-H2B binding affinity as wild-type hNAP1. Size exclusion chromatography (SEC), multi-angle light scattering (MALS) and small angle X-ray scattering (SAXS), followed by modelling and molecular dynamics simulations, have been used to reveal the stepwise dynamic complex structures of hNAP1 binding to one and two H2A-H2B heterodimers. The first H2A-H2B dimer binds mainly to the core domain of hNAP1, while the second H2A-H2B binds dynamically to both CTADs. Based on our findings, we present a model of the eviction of H2A-H2B from nucleosomes by NAP1.
MeSH term(s)	Humans ; Histones/metabolism ; Nucleosome Assembly Protein 1/genetics ; Nucleosome Assembly Protein 1/chemistry ; Nucleosome Assembly Protein 1/metabolism ; Scattering, Small Angle ; X-Ray Diffraction ; Nucleosomes ; Protein Binding
Chemical Substances	Histones ; Nucleosome Assembly Protein 1 ; nucleic acid probe 1 ; Nucleosomes
Language	English
Publishing date	2023-06-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168189
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Article ; Online: Time-course changes in mental distress and their predictors in response to the coronavirus disease 2019 (COVID-19) pandemic: A longitudinal multi-site study of hospital staff.

Kameno, Yosuke / Nishimura, Tomoko / Naito, Yumi / Asai, Daisuke / Inoue, Jun / Mochizuki, Yosuke / Isobe, Tomoyo / Hanada, Atsuko / Enomoto, Noriyuki / Yamasue, Hidenori

PloS one

2023 Volume 18, Issue 10, Page(s) e0292302

Abstract: The coronavirus disease 2019 (COVID-19) pandemic provides a unique opportunity studying individual differences in the trajectory of mental distress to relatively homogeneous stressors by longitudinally examining time-course changes between pandemic waves. ...

Abstract	The coronavirus disease 2019 (COVID-19) pandemic provides a unique opportunity studying individual differences in the trajectory of mental distress to relatively homogeneous stressors by longitudinally examining time-course changes between pandemic waves. For 21 months, we tested the effects of COVID-19 waves on mental health among 545 staffs at 18 hospitals treating COVID-19 patients in Shizuoka Prefecture, Japan. Contrary to increasing new infected cases as waves progressed, initially elevated psychological distress (K6) and fear of COVID-19 (FCV-19S) were decreased among waves (K6: B = -.02, 95% confidence interval [CI] = -.03 to -.01; FCV-19S: B = -.10, 95% CI = -.16 to -.04). This initial increase and subsequent decrease in K6 and FCV-19S were more prominent in individuals with high trait anxiety (K6: B = 1.55, 95% CI = 1.18 to 1.91; FCV-19S: B = 4.27, 95% CI = 2.50 to 6.04) and in occupations other than physicians or nurses. The current study revealed time-course changes in psychological distress and fear regarding COVID-19 in each pandemic wave and across waves, and indicated the usefulness of trait anxiety and occupation as predictors of mental health outcomes.
MeSH term(s)	Humans ; Anxiety/epidemiology ; Anxiety Disorders ; COVID-19/epidemiology ; Pandemics ; Personnel, Hospital ; Longitudinal Studies
Language	English
Publishing date	2023-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0292302
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Article ; Online: Dynamic Solution Structures of Whole Human NAP1 Dimer Bound to One and Two Histone H2A-H2B Heterodimers Obtained by Integrative Methods

Ohtomo, Hideaki / Yamane, Tsutomu / Oda, Takashi / Kodera, Noriyuki / Kurita, Junʼichi / Tsunaka, Yasuo / Amyot, Romain / Ikeguchi, Mitsunori / Nishimura, Yoshifumi

Journal of Molecular Biology. 2023 Aug., v. 435, no. 15 p.168189-

2023

Abstract	Nucleosome assembly protein 1 (NAP1) binds to histone H2A-H2B heterodimers, mediating their deposition on and eviction from the nucleosome. Human NAP1 (hNAP1) consists of a dimerization core domain and intrinsically disordered C-terminal acidic domain (CTAD), both of which are essential for H2A-H2B binding. Several structures of NAP1 proteins bound to H2A-H2B exhibit binding polymorphisms of the core domain, but the distinct structural roles of the core and CTAD domains remain elusive. Here, we have examined dynamic structures of the full-length hNAP1 dimer bound to one and two H2A-H2B heterodimers by integrative methods. Nuclear magnetic resonance (NMR) spectroscopy of full-length hNAP1 showed CTAD binding to H2A-H2B. Atomic force microscopy revealed that hNAP1 forms oligomers of tandem repeated dimers; therefore, we generated a stable dimeric hNAP1 mutant exhibiting the same H2A-H2B binding affinity as wild-type hNAP1. Size exclusion chromatography (SEC), multi-angle light scattering (MALS) and small angle X-ray scattering (SAXS), followed by modelling and molecular dynamics simulations, have been used to reveal the stepwise dynamic complex structures of hNAP1 binding to one and two H2A-H2B heterodimers. The first H2A-H2B dimer binds mainly to the core domain of hNAP1, while the second H2A-H2B binds dynamically to both CTADs. Based on our findings, we present a model of the eviction of H2A-H2B from nucleosomes by NAP1.
Keywords	atomic force microscopy ; dimerization ; gel chromatography ; histones ; humans ; models ; molecular biology ; molecular dynamics ; mutants ; nuclear magnetic resonance spectroscopy ; nucleosomes ; small-angle X-ray scattering ; histone chaperone ; NMR ; molecular dynamics simulation ; SAXS ; AFM ; TROSY ; HSQC ; MD ; SEC ; MALS
Language	English
Dates of publication	2023-08
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168189
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Fibroblast activation protein-targeted near-infrared photoimmunotherapy depletes immunosuppressive cancer-associated fibroblasts and remodels local tumor immunity.

Akai, Masaaki / Noma, Kazuhiro / Kato, Takuya / Nishimura, Seitaro / Matsumoto, Hijiri / Kawasaki, Kento / Kunitomo, Tomoyoshi / Kobayashi, Teruki / Nishiwaki, Noriyuki / Kashima, Hajime / Kikuchi, Satoru / Ohara, Toshiaki / Tazawa, Hiroshi / Choyke, Peter L / Kobayashi, Hisataka / Fujiwara, Toshiyoshi

British journal of cancer

2024

Abstract: Background: Cancer-associated fibroblasts (CAFs) in the tumor microenvironment (TME) play a critical role in tumor immunosuppression. However, targeted depletion of CAFs is difficult due to their diverse cells of origin and the resulting lack of ... ...

Abstract	Background: Cancer-associated fibroblasts (CAFs) in the tumor microenvironment (TME) play a critical role in tumor immunosuppression. However, targeted depletion of CAFs is difficult due to their diverse cells of origin and the resulting lack of specific surface markers. Near-infrared photoimmunotherapy (NIR-PIT) is a novel cancer treatment that leads to rapid cell membrane damage. Methods: In this study, we used anti-mouse fibroblast activation protein (FAP) antibody to target FAP Results: FAP-targeted NIR-PIT induced specific cell death in CAFs without damaging adjacent normal cells. Furthermore, FAP-targeted NIR-PIT treated mice showed significant tumor regression in the CAF-rich tumor model accompanied by an increase in CD8 Conclusions: Cancers with FAP-positive CAFs in their TME grow rapidly and FAP-targeted NIR-PIT not only suppresses their growth but improves tumor immunosuppression. Thus, FAP-targeted NIR-PIT is a potential therapeutic strategy for selectively targeting the TME of CAF
Language	English
Publishing date	2024-03-30
Publishing country	England
Document type	Journal Article
ZDB-ID	80075-2
ISSN	1532-1827 ; 0007-0920
ISSN (online)	1532-1827
ISSN	0007-0920
DOI	10.1038/s41416-024-02639-1
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