36 results on '"Yoshimi Oka"'
Search Results
2. Fluorescence Imaging of Disrupted Interfaces between Liquid-Ordered and Liquid-Disordered Domains by a Flavin-Labeled PNA Duplex
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Yoshimi Oka and Hisae Shishino
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Chemistry ,QD1-999 - Published
- 2017
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3. Exclusion of Anchor-Matched Peptide Nucleic Acid from Liquid-Ordered Domains by Hybridization with Complementary Flavin-Labeled DNA
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Yoshimi Oka
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General Chemical Engineering ,General Chemistry - Published
- 2022
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4. Photogenerated Radical Pair between Flavin and a Tryptophan-Containing Transmembrane-Type Peptide in a Large Unilamellar Vesicle
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Tomoaki Miura, Yoshimi Oka, and Tadaaki Ikoma
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Quenching (fluorescence) ,010304 chemical physics ,biology ,Chemistry ,Vesicle ,Tryptophan ,Flavoprotein ,Biological membrane ,Electrons ,Flavin group ,010402 general chemistry ,Photochemistry ,01 natural sciences ,0104 chemical sciences ,Surfaces, Coatings and Films ,Microviscosity ,Electron Transport ,0103 physical sciences ,Materials Chemistry ,biology.protein ,Cage effect ,Singlet state ,Physical and Theoretical Chemistry ,Peptides ,Unilamellar Liposomes - Abstract
Electron-transfer (ET) reactions in biological systems, such as those with magnetic sensors based on flavoproteins and electron transport at biomembrane interfaces, are interesting and important issues that require understanding. As a model system of flavoproteins in biomimetic environments, we report the dynamics of the radical pair generated by photoinduced ET between riboflavin tetrabutylate (RFTB) and tryptophan (Trp) residues in a transmembrane-type polypeptide, both of which are distributed in a large unilamellar vesicle of 1,2-dimyristoyl-sn-glycero-3-phosphocholine. The Trp residues locate near the hydrophilic membrane interface, as confirmed by a dual-fluorescence quenching assay. The fluorescence and transient absorption upon photoexcitation of RFTB indicate that ET from both the singlet and triplet excited states occurs at the hydrophilic interface, whereas the RFTB in the hydrophobic region does not contribute to ET. The ET efficiency and the magnetic field effect (MFE) on the RFTB anion increase significantly above the gel-to-liquid crystal phase transition temperature due to a decrease in microviscosity. The MFE analysis indicates that the radical pair generated from the triplet ET channel exhibits a long lifetime as those in micellar systems due to the strong cage effect of the vesicle.
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- 2021
5. Fluorescence Quenching of Alexa Fluor 488-labeled DNA by Complementary Trp-containing PNA Partitioned in Liquid-ordered Domains
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Hisae Shishino and Yoshimi Oka
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0301 basic medicine ,Quenching (fluorescence) ,Chemistry ,Analytical chemistry ,Stacking ,General Chemistry ,010402 general chemistry ,Photochemistry ,01 natural sciences ,Fluorescence ,0104 chemical sciences ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,DNA ,Alexa Fluor - Abstract
We demonstrate Trp-containing PNA/Alexa Fluor 488 (AL488)-labeled DNA hybrid partitions preferentially into liquid-ordered (lo) microdomains of GUV. The Trp quenches the fluorescence of AL488 microscopically. The mechanism involved collisional and static quenching, both of which proceeded effectively. The static quenching indicates an AL488–Trp complex through a stacking interaction.
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- 2017
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6. Gigantic Magnetic Field Effect on the Long-Lived Intermolecular Charge-Separated State Created at the Nonionic Bilayer Membrane
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Tadaaki Ikoma, Kiminori Maeda, Tomoaki Miura, and Yoshimi Oka
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chemistry.chemical_classification ,Materials science ,Bilayer ,Intermolecular force ,Supramolecular chemistry ,Viologen ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Surfaces, Coatings and Films ,Metal ,Membrane ,chemistry ,Chemical physics ,visual_art ,Materials Chemistry ,visual_art.visual_art_medium ,medicine ,Molecule ,Physical and Theoretical Chemistry ,0210 nano-technology ,Alkyl ,medicine.drug - Abstract
For realization of low-cost organic photon-energy conversion, the supramolecular approach has been a focus of attention as a counter approach to precise synthesis of covalently linked donor (D)-acceptor (A) molecules. Here we report photogeneration of a long-lived (∼3 μs) intermolecular charge-separated (CS) state of metal porphyrins (D) and an alkyl viologen (A) at an interface of a vesicle membrane formed by self-assembly of nonionic surfactant and cholesterol molecules. The yield of escaped free radicals is negligibly low as in the case of CS states in covalently linked D-A systems. Furthermore, the transient concentration of the CS state dramatically increases by ∼100% upon application of a magnetic field of 250 mT at room temperature. The simulation of the spin dynamics of the CS state indicates that fast (∼107 s-1) spin-selective recombination and slow (105-106 s-1) dissociation-re-encounter dynamics are the key processes for the long CS-state lifetime and the gigantic magnetic field effect. It has turned out that such dynamics are sharply dependent on temperature and alkyl chain length of the viologen. The present results would lead to the development of future materials for light energy conversion, drug delivery, and microscopic bioprobes.
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- 2018
7. Structure of silver(I) complex prepared from azobenzenonaphthalenophane, photochemical coordination change of silver(I) and silver(I)-induced acceleration of Z?E thermal isomerization of azobenzene unit
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Yoshimi Oka and Tamaoki, Nobuyuki
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Benzene -- Chemical properties ,Silver -- Chemical properties ,Silver -- Optical properties ,Naphthalene -- Chemical properties ,Organometallic compounds -- Structure ,Organometallic compounds -- Chemical properties ,Organometallic compounds -- Optical properties ,Chemistry - Published
- 2010
8. Long-Range Magnetic Ordering at 5.5 K for Cobalt(II)–Hydroxide Diamond Chains Isolated by 17 Å with α-Phenylcinnamate
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Mohamedally Kurmoo, Yoshimi Oka, Katsuya Inoue, and Hitoshi Kumagai
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Models, Molecular ,Range (particle radiation) ,Chemistry ,Temperature ,Diamond ,Cobalt ,engineering.material ,Crystallography, X-Ray ,Hydrothermal circulation ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,Magnetic Fields ,Nuclear magnetic resonance ,Octahedron ,Cinnamates ,Hydroxides ,Organometallic Compounds ,engineering ,Physical and Theoretical Chemistry ,Cobalt(II) hydroxide - Abstract
[Co(4)(phcina)(6)(OH)(2)(H(2)O)(4)]·2H(2)O (1) (phcina = α-phenylcinnamate), obtained as pink needles by hydrothermal technique, consists of two edge-sharing pairs of octahedral CoO(6) connected by their apexes to form diamond-chains. The magnetic chains are isolated from one another without chemical bond at 17 Å by the nonmagnetic bulky organic ligand. It exhibits hidden canting below the long-range antiferromagnetic (AF) ordering at 5.5 K. A metamagnetic critical field of only 30 Oe at 2 K suffices to overcome the weak through space magnetic interaction between chains and reverse the moments within the chains to give a canted AF reaching only (1)/(4) of the required moment for all parallel moment alignment. The anisotropy measured on aligned crystals, using dc and ac modes, estimates g(||b) = 6.5 and g(⊥b) = 3.25, thus eliminating an Ising or a Heisenberg magnetic dimensionality while suggesting an easy-plane AF. Weak frequency dependence of the ac-susceptibilities below the transition temperature is associated with domain structure in the ordered state, and absence of it well above T(N) eliminates single-chain magnetism. It is inferred that the competition between the strong AF coupling between the edge-sharing pairs, which dominates the high temperature susceptibility, and the ferromagnetic coupling within the pairs, results in a canting of the moments within each chain, where the moments are out of the ac-plane by an estimated 13°. In zero-field the moments of adjacent chains are antiparallel resulting in a compensated system, i.e., hidden canting.
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- 2013
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9. Competitive Allele-Specific Hairpin Primer PCR for Extremely High Allele Discrimination in Typing of Single Nucleotide Polymorphisms
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Kazuhiko Nakatani, Masako Igarashi, Yoshimi Oka, Yusuke Koga, and Fumie Takei
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Genetics ,Base Pair Mismatch ,Homozygote ,Organic Chemistry ,Single-nucleotide polymorphism ,Biology ,Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Biochemistry ,Humans ,Molecular Medicine ,Aryl Hydrocarbon Hydroxylases ,Typing ,Primer (molecular biology) ,Allele ,Variants of PCR ,Molecular Biology ,Alleles ,Allele specific ,Cytochrome P-450 CYP2C9 ,DNA Primers - Published
- 2012
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10. Collagen type I-mediated mechanotransduction controls epithelial cell fate conversion during intestinal inflammation
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Sakurako Kobayashi, Nobuhiko Ogasawara, Satoshi Watanabe, Yosuke Yoneyama, Sakura Kirino, Yui Hiraguri, Masami Inoue, Sayaka Nagata, Yoshimi Okamoto-Uchida, Satoshi Kofuji, Hiromichi Shimizu, Go Ito, Tomohiro Mizutani, Shinichi Yamauchi, Yusuke Kinugasa, Yoshihito Kano, Yasuhiro Nemoto, Mamoru Watanabe, Kiichiro Tsuchiya, Hiroshi Nishina, Ryuichi Okamoto, and Shiro Yui
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YAP/TAZ-TEAD axis ,Fetal-like reprogramming ,Regenerative and inflammatory response ,Inflammatory bowel disease ,Mechanotransduction ,Pathology ,RB1-214 - Abstract
Abstract Background The emerging concepts of fetal-like reprogramming following tissue injury have been well recognized as an important cue for resolving regenerative mechanisms of intestinal epithelium during inflammation. We previously revealed that the remodeling of mesenchyme with collagen fibril induces YAP/TAZ-dependent fate conversion of intestinal/colonic epithelial cells covering the wound bed towards fetal-like progenitors. To fully elucidate the mechanisms underlying the link between extracellular matrix (ECM) remodeling of mesenchyme and fetal-like reprogramming of epithelial cells, it is critical to understand how collagen type I influence the phenotype of epithelial cells. In this study, we utilize collagen sphere, which is the epithelial organoids cultured in purified collagen type I, to understand the mechanisms of the inflammatory associated reprogramming. Resolving the entire landscape of regulatory networks of the collagen sphere is useful to dissect the reprogrammed signature of the intestinal epithelium. Methods We performed microarray, RNA-seq, and ATAC-seq analyses of the murine collagen sphere in comparison with Matrigel organoid and fetal enterosphere (FEnS). We subsequently cultured human colon epithelium in collagen type I and performed RNA-seq analysis. The enriched genes were validated by gene expression comparison between published gene sets and immunofluorescence in pathological specimens of ulcerative colitis (UC). Results The murine collagen sphere was confirmed to have inflammatory and regenerative signatures from RNA-seq analysis. ATAC-seq analysis confirmed that the YAP/TAZ-TEAD axis plays a central role in the induction of the distinctive signature. Among them, TAZ has implied its relevant role in the process of reprogramming and the ATAC-based motif analysis demonstrated not only Tead proteins, but also Fra1 and Runx2, which are highly enriched in the collagen sphere. Additionally, the human collagen sphere also showed a highly significant enrichment of both inflammatory and fetal-like signatures. Immunofluorescence staining confirmed that the representative genes in the human collagen sphere were highly expressed in the inflammatory region of ulcerative colitis. Conclusions Collagen type I showed a significant influence in the acquisition of the reprogrammed inflammatory signature in both mice and humans. Dissection of the cell fate conversion and its mechanisms shown in this study can enhance our understanding of how the epithelial signature of inflammation is influenced by the ECM niche.
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- 2022
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11. A Light-Controlled Molecular Brake with Complete ON-OFF Rotation
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Yoshimi Oka, Meethale C. Basheer, Nobuyuki Tamaoki, and Manoj Mathews
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Photoisomerization ,Organic Chemistry ,General Chemistry ,Planar chirality ,Photochemistry ,Catalysis ,chemistry.chemical_compound ,Azobenzene ,chemistry ,Moiety ,Racemization ,Isomerization ,Cis–trans isomerism ,Cyclophane - Abstract
A light-controlled molecular machine based on cyclic azobenzenophanes consisting of a dioxynaphthalene rotating unit and a photoisomerizable dioxyazobenzene unit bridged by methylene spacers is reported. In compounds 1 and 2, 1,5- and 2,6-dioxynaphthalene moieties, respectively, are linked to p-dioxyazobenzene by different methylene spacers (n=2 in 1a and 2; n=3 in 1b), whereas a 1,5-dioxynaphthalene moiety is bonded to m-dioxyazobenzene by bismethylene spacers in 3. In 1b and 2, the naphthalene ring can rotate freely in both the trans and cis states at room temperature. The rotation speed can be controlled either by photoinduced reversible trans-cis (E-Z) isomerization of the azobenzene or by keeping the system at low temperature, as is evident from its NMR spectra. Furthermore, for the first time, we demonstrate a light-controlled molecular brake, wherein the rotation of the naphthalene moiety through the cyclophane is completely OFF in the trans isomer of compound 3 due to its smaller cavity size. Such restricted rotation imparts planar chirality to the molecule, and the corresponding enantiomers could be resolved by chiral HPLC. However, the rotation of the naphthalene moiety is rendered ON in the cis isomer due to its increased cavity size, and it is manifested experimentally by the racemization of the separated enantiomers by photoinduced E-Z isomerization.
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- 2010
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12. Enhanced in vivo antitumor efficacy of fenretinide encapsulated in polymeric micelles
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Yuriko Higuchi, Tomoyuki Okuda, Taku Satoh, Shigeru Kawakami, Masayuki Yokoyama, Yoshimi Oka, Mitsuru Hashida, and Fumiyoshi Yamashita
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Male ,Fenretinide ,Cell Survival ,Polymers ,medicine.drug_class ,Melanoma, Experimental ,Pharmaceutical Science ,macromolecular substances ,Pharmacology ,Micelle ,Dosage form ,Cell Line ,Polyethylene Glycols ,Mice ,chemistry.chemical_compound ,Drug Delivery Systems ,In vivo ,medicine ,Animals ,Retinoid ,Particle Size ,Micelles ,Controlled release ,Mice, Inbred C57BL ,carbohydrates (lipids) ,chemistry ,Biophysics ,bacteria ,Emulsions ,Peptides ,Drug carrier ,Ethylene glycol - Abstract
Fenretinide (N-(4-hydroxyphenyl)retinamide, 4-HPR) is a synthetic retinoid with high antitumor activity against a variety of malignant cells in vitro, and is a promising candidate for cancer chemoprevention and chemotherapy. To enhance the antitumor efficacy of 4-HPR in vivo, 4-HPR were encapsulated into polymeric micelles for tumor targeting by enhanced permeability and retention effects. 4-HPR encapsulated in poly(ethylene glycol)-poly(benzyl aspartate) block copolymer micelles were prepared by the evaporation method. The mean particle size of 4-HPR encapsulated in polymeric micelles was about 173 nm. After intravenous injection into tumor-bearing mice, the delivery of 4-HPR by polymeric micelles increased the blood concentration and enhanced the tumor accumulation of 4-HPR over the injection of the 4-HPR encapsulated in oil-in-water (O/W) emulsions. Tumor growth was significantly delayed following treatment by 4-HPR encapsulated in polymeric micelles, which demonstrated the improved in vivo antitumor efficacy of 4-HPR. In addition, 4-HPR encapsulated in polymeric micelles did not cause any body weight loss. These results suggest that polymeric micelles are a promising and effective carrier of 4-HPR in order to enhance tumor delivery and have potential application in the treatment of solid tumor.
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- 2009
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13. Transplantation of Nasal Mucosa into the Middle Ear for the Treatment of Adhesive Otitis media
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Hiroaki Hashimoto, Jun-Ichi Suzuki, Noriyuki Fukushima, and Yoshimi Oka
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Transplantation ,medicine.medical_specialty ,medicine.anatomical_structure ,business.industry ,medicine ,Middle ear ,Dentistry ,Mucous membrane of nose ,Adhesive otitis media ,business ,Surgery - Published
- 2015
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14. 2D molecular square grid of Cobalt(II) with tridentate phenylglycinate and mandelate: structure and magnetism
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Mohamedally Kurmoo, Yoshimi Oka, Katsuya Inoue, and Hitoshi Kumagai
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Magnetism ,chemistry.chemical_element ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Magnetization ,Crystallography ,chemistry.chemical_compound ,chemistry ,Hydrothermal synthesis ,Molecule ,General Materials Science ,Carboxylate ,Cobalt ,Single crystal - Abstract
The hydrothermal synthesis, single crystal X-ray structures and magnetic properties of two layered cobalt-carboxylate complexes, ∞2[CoII(O2C∗CH(OH)C6H5)2] (1) and ∞2[CoII(O2C∗CH(NH2)C6H5)2] (2), where O2CCH(OH)C6H5 is mandalate and O2CCH(NH2)C6H5 is phenylglycinate, are described. Pale pink crystals of 1 and 2 were obtained by the reaction of cobalt nitrate and the enantiomer-pure acids at 120 °C. In each case, the structure consists of stacks of quasi square-grid polymeric sheets consisting of carboxylato- bridges, M–O–C–O–M, and the presence of both d - and l -enantiomers of the ligands segregated on each face of the layer. The ligands exhibit both chelating and bridging functions with the carboxylate group adopting an anti–anti mode. The magnetic properties are characteristic of weakly interacting paramagnets where the moments are elevated by an important orbital contribution via spin-orbit coupling.
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- 2004
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15. Hydrothermal synthesis, crystal structure and characterization of a new hexanuclear cobalt(II) complex comprised of octahedral and tetrahedral cobalt ions
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Hisashi Ōkawa, Masaaki Ohba, Yoshimi Oka, Hitoshi Kumagai, Satoshi Kawata, Katsuya Inoue, and Mohamedally Kurmoo
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Magnetic moment ,chemistry.chemical_element ,Crystal structure ,Hydrothermal circulation ,Ion ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,Octahedron ,chemistry ,Sodium hydroxide ,Materials Chemistry ,Hydrothermal synthesis ,Physical and Theoretical Chemistry ,Cobalt - Abstract
Reaction of Co(II) with phenylcinnamic acid and sodium hydroxide under hydrothermal conditions yields a new hexanuclear Co(II) complex, [Co6(OH)2(L)10] (L=phenylcinnamate). [Co6(OH)2(L)10] consists of two edge-sharing octahedral {CoO6} and four tetrahedral {CoO4} units linked through μ-carboxylate ligands and μ-hydroxide ions. The magnetic moment shows a large decrease from 300 to 25 K which amounts to antiferromagnetic coupling between cobalt ions in octahedral and tetrahedral sites leading to an s=3 ground-state at low temperatures.
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- 2003
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16. Hydrothermal synthesis and characterization of a two-dimensional nickel(II) complex containing benzenehexacarboxylic acid (mellitic acid)
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Katsuya Inoue, Motoko Akita-Tanaka, Hitoshi Kumagai, and Yoshimi Oka
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Hydrogen bond ,Coordination polymer ,Dimer ,chemistry.chemical_element ,Crystal structure ,Inorganic Chemistry ,chemistry.chemical_compound ,Crystallography ,Nickel ,chemistry ,Materials Chemistry ,Hydrothermal synthesis ,Mellitic acid ,Physical and Theoretical Chemistry ,Single crystal - Abstract
The hydrothermal synthesis, single crystal X-ray structure and magnetic properties of a two-dimensional (2-D) coordination polymer, [Ni4(C6(COO)6)(OH)2(H2O)6] (1), is described. Complex 1 consists of dimer motifs of pseudo octahedral NiO6 linked through μ3-OH to generate one-dimensional (1-D) chains which are further bridged by the mellitate ligands to form non interpenetrated undulating sheet structure. The sheets are further connected by hydrogen bonding interaction to yield a three-dimensional (3-D) structure. The temperature dependence of magnetic susceptibilities revealed the presence of antiferromagnetic interaction between nickel centers.
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- 2002
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17. Hydrothermal Synthesis and Structural and Magnetic Characterization of the Coordination Bonding Network Co II (H 2 O) 2 carboxy-cinnamate
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Nathalie Kyritsakas, Katsuya Inoue, Hitoshi Kumagai, Mohamedally Kurmoo, and Yoshimi Oka
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Coordination polymer ,Stereochemistry ,chemistry.chemical_element ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Magnetic susceptibility ,chemistry.chemical_compound ,Crystallography ,Magnetization ,chemistry ,Hydrothermal synthesis ,General Materials Science ,Carboxylate ,Cobalt ,Monoclinic crystal system - Abstract
The hydrothermal synthesis, single crystal X-ray structure and magnetic properties of a new cobalt(II)-carboxy-cinnamate complex is described. Reaction of Co(II), Carboxy-cinnamic acid (C 10 H 8 O 4 ) and NaOH at 120°C yield the coordination network, Co(H 2 O) 2 carboxy-cinnamate ( 1 ). 1 crystallizes in the monoclinic system, a =11.3236(4), b =6.6084(4), c =7.2011(6) A, g =101.948(5)°, V =527.2(1) A 3 , space group P 2 1 /c, Z =2. 1 possesses a three-dimensional coordination-bonding network consisting of layers of CoO 6 bridged by the tetra-dendate carboxy-cinnamate. Its magnetic moment decreases on lowering temperature due to spin-orbit coupling and no interaction between cobalt ions is observed. carboxylate cobalt coordination polymer magnetic properties
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- 2002
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18. Secondary-Structure-Inducible Ligand Fluorescence Coupled with PCR
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Yoshimi Oka, Masako Igarashi, Kazuhiko Nakatani, Fumie Takei, Yoshihiro Soya, and Masaki Hagihara
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Base Sequence ,Chemistry ,Stereochemistry ,Ligand ,DNA, Single-Stranded ,General Medicine ,General Chemistry ,Ligands ,Polymerase Chain Reaction ,Fluorescence ,Molecular biology ,Catalysis ,law.invention ,chemistry.chemical_compound ,law ,Primer dimer ,Multiplex polymerase chain reaction ,Nucleic Acid Conformation ,Protein secondary structure ,Nested polymerase chain reaction ,DNA ,Polymerase chain reaction - Published
- 2009
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19. Structure of silver(I) complex prepared from azobenzenonaphthalenophane, photochemical coordination change of silver(I) and silver(I)-induced acceleration of Z-E thermal isomerization of azobenzene unit
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Nobuyuki Tamaoki and Yoshimi Oka
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Bridged-Ring Compounds ,Models, Molecular ,Denticity ,Silver ,Photoisomerization ,Molecular Structure ,Ligand ,Photochemistry ,Temperature ,Stereoisomerism ,Crystallography, X-Ray ,Inorganic Chemistry ,chemistry.chemical_compound ,Azobenzene ,chemistry ,Thermal ,Organometallic Compounds ,Physical and Theoretical Chemistry ,Isomerization ,Azo Compounds - Abstract
A Ag(I) complex was prepared from azobenzenonaphthalenophane as a photoreactive multidentate ligand. The coordination of Ag(I) was reversibly controlled by photoisomerization of the azobenzene unit, and at the same time, Ag(I) accelerated the Z-E thermal isomerization of the azobenzene unit.
- Published
- 2010
20. Transformation of cytosine to uracil in single-stranded DNA via their oxime sulfonates
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Kazuhiko Nakatani, Fumie Takei, and Yoshimi Oka
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Benzoyl peroxide ,Medicinal chemistry ,Catalysis ,chemistry.chemical_compound ,Cytosine ,Oximes ,Materials Chemistry ,medicine ,Organic chemistry ,heterocyclic compounds ,Uracil ,Chemistry ,organic chemicals ,Metals and Alloys ,General Chemistry ,DNA ,Oxime ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Transformation (genetics) ,Sulfonate ,Ceramics and Composites ,Sulfonic Acids ,medicine.drug - Abstract
The novel transformation of cytosine oxime sulfonate (C*) to uracil sulfonate (U*) proceeded by a Co(II)-assisted benzoyl peroxide reaction, eventually leading to the conversion of cytosine to uracil.
- Published
- 2010
21. Synthesis and reaction of DNA oligomers containing modified cytosines related to bisulfite sequencing
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Tao Peng, Yoshimi Oka, Kazuhiko Nakatani, and Fumie Takei
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DNA synthesis ,Molecular Structure ,Oligonucleotide ,Organic Chemistry ,Bisulfite sequencing ,Oligonucleotides ,DNA ,Biochemistry ,Combinatorial chemistry ,Catalysis ,Bisulfite ,chemistry.chemical_compound ,Cytosine ,Hydroxylamine ,chemistry ,Duplex (building) ,Physical and Theoretical Chemistry - Abstract
The synthesis of DNA oligomers containing N(4)-hydroxy-5,6-dihydrocytosine-6-sulfonate by using ligand-induced base flipping of cytosine followed by the simultaneous addition of bisulfite and hydroxylamine is reported. In contrast to C, the flipped-out 5-methylcytosine was selectively oxidized over thymines and cytosines in the duplex by potassium permanganate. Ligand-induced base flipping is a convenient and powerful strategy for the synthesis of modified cytosines and 5-methylcytosines related to bisulfite sequencing at the predetermined site of DNA.
- Published
- 2009
22. The reaction of cytosine with bisulfite by base flipping from the duplex
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Fumie Takei, Tao Peng, Yoshimi Oka, and Kazuhiko Nakatani
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congenital, hereditary, and neonatal diseases and abnormalities ,Stereochemistry ,Guanine ,Base Pair Mismatch ,General Medicine ,DNA ,Hydroxylamine ,Molecular biology ,nervous system diseases ,Adduct ,Bisulfite ,chemistry.chemical_compound ,5-Methylcytosine ,Cytosine ,chemistry ,Duplex (building) ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Sulfites ,Carbamates ,Naphthyridines ,Chromatography, High Pressure Liquid - Abstract
Methylation of cytosine at the C5-position in DNA plays a major role in epigenetic gene control. The detection of 5-methylcytosine was designed with the base flipping from the duplex using NC and CGG/CGG triad. Using bisulfite and hydroxylamine, the reaction of cytosine in 11-mer duplex produced the adduct of bisulfite and hydroxylamine, which was isolated by HPLC and identified by MALDI-TOF MS. The duplex containing (5m)C in (5m)CGG/(5m)CGG did not react with bisulfite and hydroxylamine under the same conditions. Further this method enables cytosine adjacent to mismatch guanine to react with bisulfite and hydroxylamine selectively.
- Published
- 2008
23. Knotted network consisting of 3-threads and a zwitterionic one-dimensional polymorphs of trans-3-(3-pyridyl)acrylate of cobalt and nickel, MII(C8H6NO2)2(H2O)2
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Hitoshi Kumagai, Yoshimi Oka, Mohamedally Kurmoo, Katsuya Inoue, and Claude Estournès
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Denticity ,Stereochemistry ,chemistry.chemical_element ,Crystal structure ,Triclinic crystal system ,Inorganic Chemistry ,Crystallography ,chemistry.chemical_compound ,Nickel ,chemistry ,Pyridine ,Carboxylate ,Physical and Theoretical Chemistry ,Cobalt ,Monoclinic crystal system - Abstract
We present the hydrothermal synthesis, characterization (IR, DT-TGA), single-crystal structures, and magnetic properties of two polymorphs of trans-3(3-pyridyl)acrylate of cobalt(II) and of nickel(II), M(II)(C(8)H(6)NO(2))(2)(H(2)O)(2). Hydrothermal reaction at 120 or 170 degrees C results exclusively in the different polymorphs. The infrared spectra and thermogravimetric analyses of the complexes are almost similar for the two polymorphs but show a difference between cobalt and nickel in energies of the vibrational modes and in the decomposition temperatures. The crystal structures of the two polymorphs are quite different; one crystallizes in a monoclinic space group and the other in a triclinic. This major difference is due to the different stereochemistry, cis or trans, of the coordination at the metal sites. When it is trans-MN(2)O(4), it results in the monoclinic cell consisting of a 3D-network of metals bridged by the ligands through single bonds (M-N and M-O). There is threading of three sublattices up to 2a x 4b x 2c, at which point the three sublattices are knotted into one infinite framework. When it is cis-MN(2)O(4), it results in the triclinic cell and consists of Zwitterionic linear chains of metals bridged by one single ligand via the pyridine and a bidentate carboxylate group and the other ligand is bonded only via the pyridine while its carboxylate end is free. All four compounds are paramagnetic with Weiss constants suggesting weak interactions.
- Published
- 2005
24. Ion microprobe U-Pb dating of phosphates in lunar basaltic breccia, Elephant Moraine 87521
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Tomoyo Saiki, Kentaro Terada, Yoshimi Oka, Yuji Sano, and Yasutaka Hayasaka
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Basalt ,Lunar meteorite ,geography ,geography.geographical_feature_category ,Geochemistry ,Volcanic rock ,Igneous rock ,Paleontology ,Geophysics ,Impact crater ,Meteorite ,Moraine ,Breccia ,General Earth and Planetary Sciences ,Geology - Abstract
[1] We report ion microprobe U-Pb dating of phosphates in lunar meteorite “Elephant Moraine 87521 (EET87521),” which is a fragmental breccia consisting of Very-Low Ti (VLT) basaltic clasts and a small component of highland-derived materials. The observed Pb-Pb age of phosphates in EET87521 is 3503 ± 140 Ma, which is distinct from the results from previous chronological studies on VLT mare basalt of 3.2–3.3 Ga for LUNA-24. This suggests that the VLT basalt volcanism appears to have been prolonged on the Moon. Moreover, the age is apparently different from those of other VLT meteorites (3.8 Ga for QUE94281 and 4.0 & 4.4 Ga for Yamato793274), which are proposed to have been launched by a single impact event based on the similarity of launching ages, mineralogical and geochemical signatures. This evidence questions the validities of bulk age analyses for the Yamato & QUE meteorites in the literature and/or the hypothesis of a single-crater origin.
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- 2005
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25. Age-dependent motor dysfunction due to neuron-specific disruption of stress-activated protein kinase MKK7
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Tokiwa Yamasaki, Norie Deki-Arima, Asahito Kaneko, Norio Miyamura, Mamiko Iwatsuki, Masato Matsuoka, Noriko Fujimori-Tonou, Yoshimi Okamoto-Uchida, Jun Hirayama, Jamey D. Marth, Yuji Yamanashi, Hiroshi Kawasaki, Koji Yamanaka, Josef M. Penninger, Shigenobu Shibata, and Hiroshi Nishina
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Medicine ,Science - Abstract
Abstract c-Jun N-terminal kinase (JNK) is a member of the mitogen-activated protein kinase family and controls various physiological processes including apoptosis. A specific upstream activator of JNKs is the mitogen-activated protein kinase kinase 7 (MKK7). It has been reported that MKK7-JNK signaling plays an important regulatory role in neural development, however, post-developmental functions in the nervous system have not been elucidated. In this study, we generated neuron-specific Mkk7 knockout mice (MKK7 cKO), which impaired constitutive activation of JNK in the nervous system. MKK7 cKO mice displayed impaired circadian behavioral rhythms and decreased locomotor activity. MKK7 cKO mice at 8 months showed motor dysfunctions such as weakness of hind-limb and gait abnormality in an age-dependent manner. Axonal degeneration in the spinal cord and muscle atrophy were also observed, along with accumulation of the axonal transport proteins JNK-interacting protein 1 and amyloid beta precursor protein in the brains and spinal cords of MKK7 cKO mice. Thus, the MKK7-JNK signaling pathway plays important roles in regulating circadian rhythms and neuronal maintenance in the adult nervous system.
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- 2017
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26. Studies on the Restriction of Feed Supply for Meat-type Pullet
- Author
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Kiyoshi Yamanishi, Hideshi Furuichi, Akira Kawasaki, Naokata Funakoshi, Masahiro Matushima, Tadayoshi Inoue, and Yoshimi Oka
- Subjects
Type (biology) ,Animal breeding ,Ecology ,media_common.quotation_subject ,Zoology ,Sexual maturity ,Appetite ,Biology ,media_common - Published
- 1972
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27. Studies on the Restriction of Feed Supply for Growing Mealt-type Pullet
- Author
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Masami Iwao, Yoshimi Oka, Makoto Aoyama, Masahiro Matushima, Tadayoshi Inoue, and Naokata Funakoshi
- Subjects
Animal science ,Hatching ,media_common.quotation_subject ,embryonic structures ,Sexual maturity ,Appetite ,Anatomy ,Biology ,Body weight ,media_common - Abstract
Collaborative experiments at 6 Prefectural Poultry Experiment Station with 1, 444 White Plymouth Rock pullets were carried out to study the effect of regulation of body weight by restricting the daily supply of feed. Feed supply was so restricted that body weight of pullets at 24 weeks of age was either 80, 70 or 60% of that of control pullets fed ad libitum in each Experiment Station. After 24 weeks of age, all the pullets were fed the layer diet full.1. Pullets kept their body weight at 80% level started to lay almost simultaneously and with similar egg weight to the control pullets. In average, they produced hatching egg at the rate of 5.6% higher with 1.5yen/egg less feed cost than those of the control did.2. Pullets kept their body weight at 70% level delayed in sexual maturity by 5 days and layed a significantly heavier first egg. The production of hatching egg was 9.7% higher and feed cost per hatching egg was 2.0 yen lower then those of the control, the difference being significant at 1 and 5% levels, respectively.3. Pullets kept their body weight at 60% level delayed in sexual maturity by 16 days and layed a significantly heavier first egg. The production of hatching egg was 7.3% higher and feed cost per hatching egg was 3.8 yen lower than those of the control, the difference being significant at 5 and 1% levels, respectively.4. Summarizing all of the data, it was suggested that body weight at 24 weeks of age should be kept at the level less than 70% of the control to get better performance in laying period.Little effect on mortality of the pullet was observed among the different feeding programs.
- Published
- 1970
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- View/download PDF
28. Synthesis and Reaction of DNA Oligomers Containing Modified Cytosines Related to Bisulfite Sequencing.
- Author
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Yoshimi Oka, Tao Peng, Fumie Takei, and Kazuhiko Nakatani
- Subjects
- *
ORGANIC synthesis , *OLIGOMERS , *DNA , *PYRIMIDINES , *SULFITES , *CHEMICAL reactions , *HYDROXYLAMINE - Abstract
The synthesis of DNA oligomers containing N4-hydroxy-5,6-dihydrocytosine-6-sulfonate by using ligand-induced base flipping of cytosine followed by the simultaneous addition of bisulfite and hydroxylamine is reported. In contrast to C, the flipped-out 5-methylcytosine was selectively oxidized over thymines and cytosines in the duplex by potassium permanganate. Ligand-induced base flipping is a convenient and powerful strategy for the synthesis of modified cytosines and 5-methylcytosines related to bisulfite sequencing at the predetermined site of DNA. [ABSTRACT FROM AUTHOR]
- Published
- 2009
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29. Drugs causing severe ocular surface involvements in Japanese patients with Stevens–Johnson syndrome/toxic epidermal necrolysis
- Author
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Nahoko Kaniwa, Mayumi Ueta, Ryosuke Nakamura, Yoshimi Okamoto-Uchida, Emiko Sugiyama, Keiko Maekawa, Yukitoshi Takahashi, Hirokazu Furuya, Akiko Yagami, Setsuko Matsukura, Zenro Ikezawa, Kayoko Matsunaga, Chie Sotozono, Michiko Aihara, Shigeru Kinoshita, and Yoshiro Saito
- Subjects
Immunologic diseases. Allergy ,RC581-607 - Published
- 2015
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- View/download PDF
30. Ceramics utilizing glass fiber-reinforced plastic as civil engineering materials to counteract the heat island phenomenon
- Author
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Yusuke YASUDA, Hiroyuki KINOSHITA, Kentaro YASUI, Toshifumi YUJI, Yoshimi OKAMURA, Mitsuhiro SEZAKI, and Ryuusuke KAWAMURA
- Subjects
ceramics ,recycling ,waste gfrp ,pavement block ,radiant heat-reducing effect ,Mechanical engineering and machinery ,TJ1-1570 - Abstract
This study is aimed at the development of civil engineering materials such as pavement blocks and building tiles that can moderate the heat island phenomenon. This is achieved by exploiting properties such as the material porous structure, high water absorption capacity and high strength of ceramics produced by mixing clay and crushed waste glass fiber-reinforced plastic (GFRP) before firing. Fundamental properties, such as pore size distribution, water absorption capacity, solution pH after ceramic immersion, bending strength, freezing resistance performance and thermal conductivity of ceramic specimens with varying ratios of clay and GFRP were clarified. The radiant heat reduction performance of the ceramic was examined by measuring the surface temperatures of a ceramic sample made from clay, a ceramic sample made by mixing 20% GFRP with clay, and a mortar sample in water-saturated and dry states while their surfaces were irradiated with infrared light. To clarify the difference in temperature-reducing ability by evaporation heat on each sample, the amount of water evaporated from a sample that had absorbed water and was irradiated with infrared light was measured. The rate of heat-absorption from the sample by water evaporation was estimated. The temperature-reducing effect by evaporation heat of the sample during water-absorption was verified quantitatively by thermal conductivity analysis using finite element methods. While water-saturated, a 20% GFRP/clay ceramic sample could reduce the increase in temperature caused by radiant heat considerably, and for an extended duration. It is expected that such ceramics could be used in civil engineering materials to counteract the heat island phenomenon.
- Published
- 2016
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31. Hydrothermal synthesis and characterization of a two-dimensional cobalt (II) complex containing cinnamate anion
- Author
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Katsuya Inoue, Mohamedally Kurmoo, Hitoshi Kumagai, and Yoshimi Oka
- Subjects
chemistry.chemical_classification ,Coordination polymer ,Stereochemistry ,Carboxylic acid ,chemistry.chemical_element ,General Chemistry ,Crystal structure ,Condensed Matter Physics ,Magnetic susceptibility ,Hydrothermal circulation ,Cinnamic acid ,chemistry.chemical_compound ,chemistry ,Polymer chemistry ,Hydrothermal synthesis ,General Materials Science ,Cobalt - Abstract
Synthesis, structure and magnetic properties of the hydrothermal reaction product of cobalt (II) ion and the mono-carboxylic acid, trans -cinnamic acid, (cina) are described. The 2-D coordination polymer, [Co(cina) 2 (H 2 O) 2 ] n , consists of square-grid layers with O-C-O bridging the cobalt atoms sandwich by m CHCHC 6 H 5 in the galleries. The temperature dependence of the magnetic moment revealed a lowering at low temperatures due to the presence of spin orbit coupling. cobalt cinnamic acid hydrothermal layered
32. Hydrothermal synthesis, structure and magnetism of square-grid cobalt(II)-carboxylate layered compounds with and without pillars
- Author
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Hitoshi Kumagai, Mohamedally Kurmoo, Katsuya Inoue, and Yoshimi Oka
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Magnetic moment ,Magnetism ,chemistry.chemical_element ,Mineralogy ,General Chemistry ,Magnetic field ,chemistry.chemical_compound ,Crystallography ,chemistry ,Hydrothermal synthesis ,Coupling (piping) ,Carboxylate ,Single crystal ,Cobalt - Abstract
The hydrothermal synthesis, single crystal X-ray structures and magnetic properties of two layered cobalt(II)-carboxylate complexes, 2∞[CoII(H2O)2(O2CCHCHC6H5)2] (1) and 2∞[CoII(H2O)2(O2CCHCHC6H4CO2)2/2] (2), are described. Pale red crystals of Co(H2O)2L2, L = trans-cinnamate (C9H7O2−) (1) or L2 = 4-carboxycinnamate (C10H6O42−) (2), were obtained at 120 °C. The structures consist of square-grid 2D-coordination polymeric sheets, ⋯–OCO–Co(H2O)2–OCO–Co(H2O)2–⋯, separated by C6H5–CHCH– for (1) or pillared by –C6H4–CHCH– for (2). The magnetism was studied as a function of temperature and magnetic field. In both cases the magnetic moment decreases on lowering the temperature due to spin–orbit coupling and no interaction between cobalt ions. The data can alternatively be fitted to an unrealistic quadratic layer model for S = 3/2 without taking into account the effect of spin–orbit.
33. Studies on Structures and Magnetic Properties of Low-Dimensional Co (II) Complexes with Phenylcinnamic Acid
- Author
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Yoshimi, OKA
- Abstract
第1章では分子磁性体の背景及び本研究の目的について述べた。分子磁性体は分子がスピンを担うため、構造を適切に組み立てることによって磁性を設計、制御できる可能性を秘めている。錯体化学の分野では1)相互作用の型、2)次元数、3)スピン量子数、4)配位数、配位構造の異なる多くの有機-無機融合系について合成され物性の評価がなされてきた。近年、磁気緩和現象は分子磁性の分野で最も注目されている現象のひとつであり、低次元性や異方性を有する遷移金属錯体における構造-磁性の関係について興味が高まっている。本研究では、Co(II)イオンが一般的にイジング型スピンを取ること、水熱合成法によって通常の合成方法では得られない化合物の単結晶が得られ、フラストレーションを示すヒドロキソ錯体が得られる場合が多いことに着目した。α-フェニルケイ皮酸(phcinaH)を用いた6種類の低次元Co(II)錯体を主に水熱合成法で合成し、構造と磁性について調べた。 第2章では合成と構造について述べた。3核錯体[Co3(phcina)6(quin)2](1)、2種類 6核錯体[Co6(OH)2(phcina)10](2)と[Co6(OH)2(phcina)10(phcinaH)2(actn)2](3)、3種類の1次元錯体、[Co(phcina)2](4)、[Co2(OH)(phcina)3(H2O)](5)、[Co4(OH)2(phcina)6(H2O)4]・2H2O(6)(quin = quinoline)について述べた。1次元錯体4は交互鎖構造を取るのに対し、5及び6は2重鎖構造を取っている。これらのモデル図を以下に示した。 モデル図省略 第3章では磁気物性について述べ、構造を考慮に入れた考察を行った。3核錯体1は基底状態S = 9/2をとっている。さらに、磁化率の温度変化について、オクタヘドラル構造を持つCoII(HS)の軌道角運動量を考慮したLinesのモデルに基づいたフイッテイングを行い、J/kB:17K、J’/kB=2Kと求まり、クラスター内及びクラスター間に強磁性的相互作用が働いていることがわかった。2及び3は構造から、すべてCoII(HS)の6核錯体であり、磁化の磁場依存からS = 3に近い状態をとっている。化合物2についてはJ1/kB~5K、J2/kB = 30K、J3/kB = -90K、化合物3についてはJ1/kB~0 K、J2/kB = 40K、J3/kB = -90Kと求まり、スピンフラストレーションの可能性を持つことがわかった。1次元錯体4と5はそれぞれTN=20K、TN=25Kの反強磁性体であり、4について1次元イジングモデルを用いてJ/kB = -52Kを得た。 2重鎮構造を持つ6はメタ磁性を示し、1次元鎖方向、b軸方向が磁化容易軸となっている。6には配位環境の異なる2種類のCoII(HS)が存在し、このgの値が異なる2種のスピンが反強磁性的に相互作用することによって、2重鎮内にフェリ磁性が生じる。また、ゼロ磁場下においては2重鎖間には反強磁性的相互作用が存在し、TN=5.5Kの反強磁性体であるが、H>Hc:20 Oeではフェリ磁性へと転移を示す。この臨界磁場から鎖間(J’)と鎖内(J)の交換相互作用の比はJ’/J~10-5と与えられ、2重鎖同士は広い温度領域において磁気的に十分孤立しているとみなせる。ゼロ磁場下における交流磁化率は4K付近に周波数依存を示すピークを持ち、反強磁性状態での磁壁の移動による磁気緩和現象が観測された。アレニウス則を用いることにより、エネルギー障壁及び緩和時間は、//b方向についてEa/kB=64K、τo = 1.9×10-11s、⊥b方向についてEa/kB = 89K、τo = 1.8×10-11sと求まった。さらに、30 Oeの正磁場を印加したときも同様にフェリ磁性状態での磁壁の移動による磁気緩和現象が観測され、Ea/kB=27K、τo= 3.1×10-7s(//b方向)、Ea/kB=176K、τo=1.7×10-19s(⊥b方向)を得た。このことは、1次元鎖方向の交換相互作用が2重鎮間と比較して大きいため、磁壁の移動が若干起こりやすく、フェリ磁性状態では1次元鎖方向に磁区が成長していく様子を示していると考えられる。 第4章では、α-フェニルケイ皮酸(phcinaH)を用いた6種類の低次元Co(II)錯体の構造-磁性の関係についてまとめた。本研究では同じ配位子phcinaを有する6種類の錯体について理論モデルを用いCoII(HS)錯体の磁性の解析を行い、磁気的相互作用の大きさを見積もった。また、2重鎖構造等の珍しい構造を得ることに成功し、1次元系特有の磁壁の移動がメタ磁性転移前後の両方で観測された従来報告のない例について考察を行った。
34. Reaction of cytosine with bisulfite and hydroxylamine
- Author
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Fumie Takei, Yoshimi Oka, and Kazuhiko Nakatani
- Subjects
chemistry.chemical_classification ,Ketone ,Uracil ,General Medicine ,Hydroxylamine ,Oxime ,Medicinal chemistry ,Bisulfite ,chemistry.chemical_compound ,Potassium permanganate ,Cytosine ,chemistry ,Oligodeoxyribonucleotides ,Reagent ,Organic chemistry ,Sulfites ,Sulfonic Acids - Abstract
The synthesis of DNA oligomer containing N(4)-hydroxy-5,6-dihydrocytosine-6-sulfonate by the simultaneous addition of bisulfite and hydroxylamine under mild conditions is reported. To the best of our knowledge, the reaction of the oxime into the ketone, N(4)-hydroxy-5,6-dihydrocytosine-6-sulfonate into 5,6-dihydrouracil-6-sulfonate or uracil has not been reported. Moreover, this issue contains the difficulty in specific reactivity of oxime derivative from DNA bases include (5m)C toward reagent; for example, T also reacts to potassium permanganate known as a reagent for oxime into ketone. Here we examined the transformation of DNA containing N(4)-hydroxy-5,6-dihydrocytosine-6-sulfonate into 5,6-dihydrouracil 6-sulfonate and the following elimination of sulfonate.
35. A Modified Murine Embryonic Stem Cell Test for Evaluating the Teratogenic Effects of Drugs on Early Embryogenesis.
- Author
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Ruoxing Yu, Norio Miyamura, Yoshimi Okamoto-Uchida, Norie Arima, Mari Ishigami-Yuasa, Hiroyuki Kagechika, and Hiroshi Nishina
- Subjects
Medicine ,Science - Abstract
Mammalian fetal development is easily disrupted by exogenous agents, making it essential to test new drug candidates for embryotoxicity and teratogenicity. To standardize the testing of drugs that might be used to treat pregnant women, the U.S. Food and Drug Administration (FDA) formulated special grade categories, labeled A, B, C, D and X, that define the level of risk associated with the use of a specific drug during pregnancy. Drugs in categories (Cat.) D and X are those with embryotoxic and/or teratogenic effects on humans and animals. However, which stages of pregnancy are affected by these agents and their molecular mechanisms are unknown. We describe here an embryonic stem cell test (EST) that classifies FDA pregnancy Cat.D and Cat.X drugs into 4 classes based on their differing effects on primitive streak formation. We show that ~84% of Cat.D and Cat.X drugs target this period of embryogenesis. Our results demonstrate that our modified EST can identify how a drug affects early embryogenesis, when it acts, and its molecular mechanism. Our test may thus be a useful addition to the drug safety testing armamentarium.
- Published
- 2015
- Full Text
- View/download PDF
36. A Single Amino Acid Substitution in the Virus-Encoded Replicase of Tomato Mosaic Tobamovirus Alters Host Specificity
- Author
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Hiroshi Hamamoto, Yuichiro Watanabe, Hiroshi Kamada, and Yoshimi Okada
- Subjects
Microbiology ,QR1-502 ,Botany ,QK1-989 - Abstract
Introduction of a single amino acid substitution (Gln979 to Ile) into the 130- and 180-kDa proteins of tomato mosaic tobamovirus (ToMV) rendered the mutant virtually unable to replicate in tomato cells while it replicated perfectly in tobacco cells. The mechanism of this change in host specificity is discussed.
- Published
- 1997
- Full Text
- View/download PDF
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