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Book ; Online: Frontiers in Protein Folding and Related Areas - in Memory of Professor Sir Christopher M. Dobson (1949-2019)

Kuwajima, Kunihiro / Okamoto, Yuko / Knowles, Tuomas / Vendruscolo, Michele

2023

Keywords	Research & information: general ; Biology, life sciences ; 14-3-3 proteins ; molecular chaperone ; amyloid β ; α-synuclein ; NMR spectroscopy ; amyloid fibril ; amyloidogenesis ; aggregation ; adsorption ; Aβ 1-40 peptide ; boundary of liquid phase ; self-assembly ; extraction ; solubilization ; toxic oligomers ; Parkinson's disease ; familial mutations ; α-helical structure ; amyloid-beta ; mutants ; cholesterol ; simulations ; X-ray crystallography ; phospholipase A1 ; homodimer ; dimerization domain ; catalytic triad ; plant protein ; molecular dynamics simulation ; replica permutation method ; amyloid-β ; disaggregation ; β-sheet ; α-helix ; interface ; inhibitor ; polyphenol ; high-temperature reversible oligomerization ; amyloidogenicity ; oligomeric interface residues ; thermal denaturation ; mutational analysis ; RHIM ; TRIF ; necroptosis ; functional amyloid ; fibrils ; RIPK ; turbulent mixing ; continuous flow ; fluorescence ; reaction mechanism ; protein folding ; protein-ligand interactions ; protein design ; reverse fold ; minimum frustration ; protein structure prediction ; sequence-structure alignment ; template-based modeling ; conditional random fields ; boosted regression trees ; CASP ; hydrogen/deuterium exchange ; dimethylsulfoxide ; nuclear magnetic resonance ; chaperonin ; GroEL ; protease ; Lon protease ; proteomics ; proteostasis ; Hfq hexamer ; mutations ; unfolding intermediates ; thermodynamics ; amyloid ; insulin B chain ; nucleation ; prefibrillar aggregates ; protofibrils ; bacterial amyloid ; biofilm ; curli ; FapC ; imperfect repeats ; neurodegeneration ; oligomerisation ; native-like ; micelle ; globular protein ; rigid native state ; molten globule ; intrinsically disordered ; functional state ; unfolded state ; coil ; post-translational modifications ; membrane ; chaperone ; statistical mechanical model ; WSME model ; folding kinetics ; folding intermediates ; protein dynamics ; amyloid fibrils ; amorphous aggregation ; β2-microglobulin ; protein misfolding ; solubility ; supersaturation ; ultrasonication ; cryo-electron microscopy ; fibril ; ganglioside ; cancer ; prion ; folding ; pathway ; interdiction ; peptide ; enhanced sampling method ; molecular force fields ; van der Waals interaction ; CHARMM36m ; NBFIX ; intrinsically disordered proteins ; crowding simulations
Language	English
Size	1 electronic resource (418 pages)
Publisher	MDPI - Multidisciplinary Digital Publishing Institute
Publishing place	Basel
Document type	Book ; Online
Note	English
HBZ-ID	HT030376814
ISBN	9783036573205 ; 3036573208
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Oncostatin M’s Involvement in the Pathogenesis of Chronic Rhinosinusitis

Chie Ishikawa / Sachio Takeno / Yukako Okamoto / Tomohiro Kawasumi / Takashi Kakimoto / Kota Takemoto / Manabu Nishida / Takashi Ishino / Takao Hamamoto / Tsutomu Ueda / Akio Tanaka

Biomedicines, Vol 11, Iss 12, p

Focus on Type 1 and 2 Inflammation

2023 Volume 3224

Abstract: Objectives: The cytokine oncostatin M (OSM) elicits pathogenic effects involving disruption ...

Abstract	Objectives: The cytokine oncostatin M (OSM) elicits pathogenic effects involving disruption of the epithelial barrier function as a part of immunological response networks. It is unclear how these integrated cytokine signals influence inflammation and other physiological processes in the pathology of chronic rhinosinusitis (CRS). We investigated the expression and distribution of OSM and OSM receptor (OSMR) in CRS patients’ sinonasal specimens, and we compared the results with a panel of inflammatory cytokine levels and clinical features. Patients and Methods: We classified CRS patients as eosinophilic (ECRS, n = 36) or non-eosinophilic (non-ECRS, n = 35) based on the Japanese Epidemiological Survey of Refractory Eosinophilic Chronic Rhinosinusitis phenotypic criteria and compared their cases with those of 20 control subjects. We also examined OSM’s stimulatory effects on cytokine receptor expression levels using the human bronchial epithelium cell line BEAS-2B. Results: RT-PCR showed that the OSM mRNA levels were significantly increased in the CRS patients’ ethmoid sinus mucosa. The OSM mRNA levels were positively correlated with those of TNF-α, IL-1β, IL-13, and OSMR-β. In BEAS-2B cells, OSM treatment induced significant increases in the OSMRβ, IL-1R1, and IL-13Ra mRNA levels. Conclusions: OSM is involved in the pathogenesis of CRS in both type 1 and type 2 inflammation, suggesting the OSM signaling pathway as a potential therapeutic target for modulating epithelial stromal interactions.
Keywords	paranasal sinus ; chronic rhinosinusitis ; CRS ; epithelial cell ; eosinophil ; oncostatin M ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Genetic Characterization of CTX-M-2-Producing

Tsuka, Takeshi / Ozaki, Hiroichi / Saito, Daisuke / Murase, Toshiyuki / Okamoto, Yoshiharu / Azuma, Kazuo / Osaki, Tomohiro / Ito, Norihiko / Murahata, Yusuke / Imagawa, Tomohiro

Frontiers in veterinary science

2021 Volume 8, Page(s) 659222

Abstract: CTX-M-2-producing ...

Abstract	CTX-M-2-producing
Language	English
Publishing date	2021-05-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2834243-4
ISSN	2297-1769
ISSN	2297-1769
DOI	10.3389/fvets.2021.659222
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Article ; Online: M-type phospholipase A2 receptor-associated membranous nephropathy in a patient with Noonan-like syndrome with loose anagen hair.

Fujishige, Shuta / Ogawa, Yayoi / Aoyagi, Hayato / Okamoto, Takayuki

Pediatrics international : official journal of the Japan Pediatric Society

2023 Volume 65, Issue 1, Page(s) e15643

MeSH term(s)	Humans ; Glomerulonephritis, Membranous/diagnosis ; Receptors, Phospholipase A2 ; Loose Anagen Hair Syndrome ; Noonan Syndrome ; Autoantibodies
Chemical Substances	Receptors, Phospholipase A2 ; Autoantibodies
Language	English
Publishing date	2023-12-26
Publishing country	Australia
Document type	Journal Article
ZDB-ID	1470376-2
ISSN	1442-200X ; 1328-8067
ISSN (online)	1442-200X
ISSN	1328-8067
DOI	10.1111/ped.15643
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Article ; Online: Clinical usefulness of anti-M-type phospholipase-A-receptor antibodies in patients with membranous nephropathy and the comparison of three quantification methods.

Katsumata, Yasuhiro / Okamoto, Yuko / Moriyama, Takahito / Moriyama, Rina / Kawamoto, Manabu / Hanaoka, Masanori / Uchida, Keiko / Nitta, Kosaku / Harigai, Masayoshi

Immunological medicine

2020 Volume 43, Issue 1, Page(s) 47–56

Abstract: Associations between anti-M-type phospholipase A2 receptor (PLA2R) antibodies and disease activity ...

Abstract	Associations between anti-M-type phospholipase A2 receptor (PLA2R) antibodies and disease activity and prognosis have been suggested in primary membranous nephropathy (MN); however, more evidence is needed. We aimed to establish a clinically useful method to measure anti-PLA2R antibodies. We developed a western blot assay and a cell-based enzyme-linked immunosorbent assay (ELISA). Anti-PLA2R antibodies were evaluated retrospectively using these assays and the commercial solid-phase ELISA. Anti-PLA2R antibodies were detected in 12, 6, and 12 out of 23 Japanese patients with biopsy-proven primary MN using the western blot, the cell-based ELISA, and the solid-phase ELISA, respectively. The samples of the lupus MN patients tested negative. The levels of proteinuria correlated moderately with the titres of anti-PLA2R antibodies measured by the three methods (
MeSH term(s)	Antibodies/blood ; Biomarkers/blood ; Enzyme-Linked Immunosorbent Assay/methods ; Glomerulonephritis, Membranous/diagnosis ; Glomerulonephritis, Membranous/immunology ; Humans ; Receptors, Phospholipase A2/immunology
Chemical Substances	Antibodies ; Biomarkers ; PLA2R1 protein, human ; Receptors, Phospholipase A2
Language	English
Publishing date	2020-01-07
Publishing country	England
Document type	Comparative Study ; Journal Article
ISSN	2578-5826
ISSN (online)	2578-5826
DOI	10.1080/25785826.2019.1710079
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Article ; Online: Fyn Accelerates M Phase Progression by Promoting the Assembly of Mitotic Spindle Microtubules.

Okamoto, Mai / Nakayama, Yuji / Kakihana, Ayana / Yuki, Ryuzaburo / Yamaguchi, Noritaka / Yamaguchi, Naoto

Journal of cellular biochemistry

2016 Volume 117, Issue 4, Page(s) 894–903

Abstract: ... In this study, we studied the role of Fyn in spindle formation and effects on M-phase progression. Re-expression ... on the kinase activity. Furthermore, Fyn accelerates the M phase progression of cells from nocodazole arrest ... polymerization, resulting in the acceleration of M-phase progression. ...

Abstract	The mitotic spindle is the major piece of cellular machinery essential for faithful chromosome segregation. Whereas Fyn, a member of Src-family kinases, is known to be localized to the meiotic and mitotic spindle microtubules, the role of Fyn in mitotic spindle formation has not yet been completely elucidated. In this study, we studied the role of Fyn in spindle formation and effects on M-phase progression. Re-expression of Fyn induced increases in the fluorescence intensity of mitotic spindle microtubules in SYF cells having triple knock-out mutations of c-Src, c-Yes, and Fyn. Cold treatment results showed that Fyn increases the maximum length of microtubules in HeLa S3 cells in a manner dependent on Fyn kinase activity. Complete depolymerization of microtubules under cold treatment and the following release into 37 °C revealed that the increase in the microtubule length in Fyn-expressing cells may be attributed to the promotion of microtubule polymerization. After cold treatment, Fyn promotes the accumulation of EB1, which is a plus-end tracking protein and facilitates microtubule growth, in a manner dependent on the kinase activity. Furthermore, Fyn accelerates the M phase progression of cells from nocodazole arrest. These results suggest that Fyn facilitates mitotic spindle formation through the increase in microtubule polymerization, resulting in the acceleration of M-phase progression.
MeSH term(s)	Animals ; Cell Line ; Chromosome Segregation ; Cold Temperature ; Fibroblasts/metabolism ; Fibroblasts/ultrastructure ; Gene Expression Regulation ; HeLa Cells ; Humans ; Mice ; Microtubules/metabolism ; Microtubules/ultrastructure ; Mitosis ; Polymerization ; Proto-Oncogene Proteins c-fyn/genetics ; Proto-Oncogene Proteins c-fyn/metabolism ; Proto-Oncogene Proteins c-yes/genetics ; Proto-Oncogene Proteins c-yes/metabolism ; Signal Transduction ; Spindle Apparatus/metabolism ; Spindle Apparatus/ultrastructure ; src-Family Kinases/genetics ; src-Family Kinases/metabolism
Chemical Substances	CSK tyrosine-protein kinase (EC 2.7.10.2) ; FYN protein, human (EC 2.7.10.2) ; Proto-Oncogene Proteins c-fyn (EC 2.7.10.2) ; Proto-Oncogene Proteins c-yes (EC 2.7.10.2) ; YES1 protein, human (EC 2.7.10.2) ; src-Family Kinases (EC 2.7.10.2)
Language	English
Publishing date	2016-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.25373
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Zs.A 1114: Show issues

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Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Acute infection by hepatitis E virus with a slight immunoglobulin M antibody response.

Inagaki, Yuki / Oshiro, Yukio / Imanishi, Mamiko / Ishige, Kazunori / Takahashi, Masaharu / Okamoto, Hiroaki / Ohkohchi, Nobuhiro

Clinical journal of gastroenterology

2015 Volume 8, Issue 4, Page(s) 247–252

Abstract: The anti-hepatitis E virus (HEV) immunoglobulin (Ig) M antibody response is generally regarded ...

Abstract	The anti-hepatitis E virus (HEV) immunoglobulin (Ig) M antibody response is generally regarded as a useful marker for diagnosing primary infection. However, in some cases, this antibody is not detected during the acute phase of infection. An 81-year-old man with stable membranous nephropathy who presented with asymptomatic acute liver dysfunction came to our hospital. HEV RNA of genotype 3 was detected in his serum, and he was diagnosed with acute hepatitis E. According to an enzyme-linked immunosorbent assay, high-level positivity for anti-HEV IgG and IgA antibodies was observed, but the assay was negative for IgM antibody throughout the clinical course of infection. The patient was not immunosuppressed. We further investigated the presence of IgM antibody using two other polyclonal antibodies against human IgM as secondary antibodies and another recombinant ORF2 protein of genotype 3 as an immobilized antigen. IgM was weakly detected in the serum during the acute phase only by the test with the antigen of genotype 3. Multi-genotype antigens can detect a slight IgM antibody response; however, anti-HEV IgA is more useful in diagnosing primary HEV infection, particularly in cases with a low IgM antibody response.
MeSH term(s)	Aged, 80 and over ; Enzyme-Linked Immunosorbent Assay ; Genotype ; Hepatitis Antibodies/blood ; Hepatitis E/diagnosis ; Hepatitis E/virology ; Hepatitis E virus/genetics ; Hepatitis E virus/immunology ; Humans ; Immunoglobulin A/blood ; Immunoglobulin M/blood ; Male ; RNA, Viral/blood
Chemical Substances	Hepatitis Antibodies ; Immunoglobulin A ; Immunoglobulin M ; RNA, Viral
Language	English
Publishing date	2015-08
Publishing country	Japan
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2429411-1
ISSN	1865-7265 ; 1865-7257
ISSN (online)	1865-7265
ISSN	1865-7257
DOI	10.1007/s12328-015-0589-4
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Article ; Online: A multi-institutional observational study on the effects of three-dimensional radiotherapy and weekly 40-mg/m

International journal of clinical oncology

2018 Volume 24, Issue 5, Page(s) 575–582

Abstract: ... dimensional radiotherapy (3DRT) and weekly 40-mg/m: Methods: We conducted a retrospective multi ... who had been treated with both 3DRT and weekly 40-mg/m: Results: The eligible 96 patients were analyzed ... The outcomes of concurrent chemoradiotherapy (CCRT) using weekly 40-mg/m ...

Abstract	Background: The aim of this study was to evaluate the effects of treatment with both three-dimensional radiotherapy (3DRT) and weekly 40-mg/m Methods: We conducted a retrospective multi-institutional chart review of postoperative uterine cervical cancer patients with high-risk prognostic factors who had been treated with both 3DRT and weekly 40-mg/m Results: The eligible 96 patients were analyzed. The median follow-up period was 61 months. The 3-year relapse-free survival, overall survival (OS), and locoregional relapse-free survival (LRFS) rates were 76%, 90%, and 88%, respectively. In multivariate analysis, the histological finding of either adenocarcinoma or adenosquamous carcinoma was a significant risk factor for both OS and LRFS. The percentage of patients with grade ≥ 3 acute hematologic toxicity, acute lower gastrointestinal toxicity (GIT), and late lower GIT were 45%, 19%, and 17%, respectively. Conclusions: The outcomes of concurrent chemoradiotherapy (CCRT) using weekly 40-mg/m
MeSH term(s)	Adenocarcinoma/drug therapy ; Adenocarcinoma/mortality ; Adenocarcinoma/radiotherapy ; Adenocarcinoma/surgery ; Adult ; Antineoplastic Agents/administration & dosage ; Antineoplastic Agents/therapeutic use ; Carcinoma, Adenosquamous/drug therapy ; Carcinoma, Adenosquamous/mortality ; Carcinoma, Adenosquamous/radiotherapy ; Carcinoma, Adenosquamous/surgery ; Chemoradiotherapy/adverse effects ; Chemoradiotherapy/methods ; Cisplatin/administration & dosage ; Cisplatin/therapeutic use ; Drug Administration Schedule ; Female ; Humans ; Middle Aged ; Neoplasm Recurrence, Local/drug therapy ; Postoperative Period ; Prognosis ; Retrospective Studies ; Survival Rate ; Treatment Outcome ; Uterine Cervical Neoplasms/drug therapy ; Uterine Cervical Neoplasms/mortality ; Uterine Cervical Neoplasms/radiotherapy ; Uterine Cervical Neoplasms/surgery
Chemical Substances	Antineoplastic Agents ; Cisplatin (Q20Q21Q62J)
Language	English
Publishing date	2018-12-22
Publishing country	Japan
Document type	Journal Article ; Multicenter Study ; Observational Study
ZDB-ID	1400227-9
ISSN	1437-7772 ; 1341-9625
ISSN (online)	1437-7772
ISSN	1341-9625
DOI	10.1007/s10147-018-01380-z
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Zs.A 4828: Show issues

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Book ; Online: Respiratory Disease in the COVID-19 Era

Okamoto, Masaki

2023

Keywords	Medicine ; Epidemiology & medical statistics ; heart rate ; COVID-19 ; pulmonary rehabilitation ; COVID-19 vaccines ; adult ; pneumonia ; risk ; SARS-CoV-2 ; Pneumocystis jirovecii pneumonia ; interstitial pneumonia ; steroids ; immunosuppressive drugs ; spontaneous pneumomediastinum ; subcutaneous emphysema ; therapeutic plasma exchange ; ARDS ; inflammatory markers ; survival ; immunocompromised host ; Bruton's tyrosine kinase ; persistent infection ; pulmonary paragonimiasis ; Paragonimus westermani ; post-COVID-19 condition ; delayed diagnosis ; case cluster ; Bamlanivimab ; Etesevimab ; lung ultrasound ; RT-qPCR ; HRCT ; diabetes mellitus ; computed tomographic severity score ; immunocompromised ; coronavirus disease 2019 ; hydroxychloroquine ; severe acute respiratory syndrome ; n/a ; diaphragm ; thoracic mobilization ; respiratory function
Language	English
Size	1 electronic resource (112 pages)
Publisher	MDPI - Multidisciplinary Digital Publishing Institute
Publishing place	Basel
Document type	Book ; Online
Note	English
HBZ-ID	HT030376929
ISBN	9783036579177 ; 3036579176
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Genetic Characterization of CTX-M-2-Producing Klebsiella pneumoniae and Klebsiella oxytoca Associated With Bovine Mastitis in Japan

Takeshi Tsuka / Hiroichi Ozaki / Daisuke Saito / Toshiyuki Murase / Yoshiharu Okamoto / Kazuo Azuma / Tomohiro Osaki / Norihiko Ito / Yusuke Murahata / Tomohiro Imagawa

Frontiers in Veterinary Science, Vol

2021 Volume 8

Abstract: CTX-M-2-producing Klebsiella oxytoca (K. oxytoca) has not received much attention ... These results suggest that the CTX-M-2-producing K. oxytoca strain with the above-mentioned characteristics ...

Abstract	CTX-M-2-producing Klebsiella oxytoca (K. oxytoca) has not received much attention in animal husbandry compared with Klebsiella pneumoniae (K. pneumoniae), a major reservoir of extended-spectrum β-lactamase (ESBL) genes. Bacteriological examinations of 1,466 mastitic milk samples between October 2012 and December 2014 were conducted. Ninety-five K. pneumoniae isolates (total prevalence: 6.5%) and 81 K. oxytoca isolates (total prevalence: 5.5%) were obtained. Seventeen K. pneumoniae isolates obtained from 15 animals reared on 11 farms and 9 K. oxytoca isolates obtained from 9 animals reared on the same farm were phenotypically confirmed to be ESBL producers. All nine ESBL-producing K. oxytoca isolates were obtained from one farm between June and November 2013 and related to a significantly (p < 0.05) higher monthly prevalence of mild mastitis (in June, August, September, October, and November 2013). Pulsed-field gel electrophoresis (PFGE) patterns of ESBL-producing K. pneumoniae isolates were distinguished from each other by more than 6-band differences except for two isolates from two animals, whereas all nine K. oxytoca isolates showed an identical PFGE pattern. Transferability of the blaCTX−M−2 gene was found in 14 K. pneumoniae and 9 K. oxytoca isolates by conjugation analysis. Of these isolates, the blaCTX−M−2 gene was detected on plasmids belonging to the incompatibility (Inc) groups P and N derived from five K. pneumoniae and nine K. oxytoca isolates, respectively, although the plasmids from the remaining nine K. pneumoniae were untypeable. All the transconjugants exhibited elevated minimum inhibitory concentrations of ampicillin, cefotaxime, and ceftiofur compared with those in the wild-type, recipient strain. Restriction fragment length polymorphism analysis demonstrated that the IncN plasmids extracted from eight of nine transconjugants, which received resistance against β-lactams from K. oxytoca, showed an identical DraI digestion pattern. These results suggest that the CTX-M-2-producing K. oxytoca strain with the above-mentioned characteristics may have clonally spread within a farm, whereas the blaCTX−M−2 gene in K. pneumoniae possibly disseminated among the farms through different plasmids. Thus, monitoring of ESBL genes, including the blaCTX−M−2 gene, among causative agents of bacterial mastitis in cows can help to develop relevant treatments and control practices.
Keywords	bovine ; CTX-M-2 ; Klebsiella oxytoca ; Klebsiella pneumoniae ; mastitis ; Veterinary medicine ; SF600-1100
Subject code	630
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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