171 results on '"Hideaki Ogata"'
Search Results
102. Protein Crystallography Using Free-Electron Lasers: Water Oxidation in Photosynthesis
- Author
-
Hideaki Ogata and Wolfgang Lubitz
- Subjects
Free electron model ,Crystallography ,Photosystem II ,Chemistry ,Lasers ,Free-electron laser ,Water ,Electrons ,General Chemistry ,Photosynthesis ,Laser ,Photochemistry ,Catalysis ,law.invention ,Nanocrystal ,law ,X-ray crystallography ,Oxidation-Reduction - Published
- 2014
103. Purification, crystallization and preliminary X-ray analysis of the dissimilatory sulfite reductase from Desulfovibrio vulgaris Miyazaki F
- Author
-
Yasuhito Shomura, Wolfgang Gärtner, Amrit Pal Kaur, Hideaki Ogata, Aruna Goenka Agrawal, Yoshiki Higuchi, and Wolfgang Lubitz
- Subjects
Models, Molecular ,Inorganic chemistry ,Biophysics ,Hydrogensulfite reductase ,Crystal structure ,Crystallography, X-Ray ,Biochemistry ,law.invention ,Crystal ,chemistry.chemical_compound ,Structural Biology ,law ,Potassium thiocyanate ,Genetics ,Desulfovibrio vulgaris ,Crystallization ,Sulfate-reducing bacteria ,Hydrogensulfite Reductase ,biology ,Condensed Matter Physics ,biology.organism_classification ,Protein Structure, Tertiary ,chemistry ,Crystallization Communications ,bacteria ,Single crystal ,Nuclear chemistry - Abstract
Dissimilatory sulfite reductase (Dsr) plays an important role in sulfate respiration in many sulfate-reducing bacteria. Dsr from Desulfovibrio vulgaris Miyazaki F has been purified and crystallized at 277 K using the sitting-drop vapour-diffusion method with PEG 3350 and potassium thiocyanate as precipitants. A data set was collected to 3.7 Å resolution from a single crystal at 100 K using synchrotron radiation. The Dsr crystal belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 163.26, c = 435.32 Å. The crystal structure of Dsr was determined by the molecular-replacement method based on the three-dimensional structure of Dsr from D. vulgaris Hildenborough. The crystal contained three α(2)β(2)γ(2) units per asymmetric unit, with a Matthews coefficient (V(M)) of 2.35 Å(3) Da(-1); the solvent content was estimated to be 47.7%.
- Published
- 2010
104. Formation of the complex of nitrite with the ferriheme b beta-barrel proteins nitrophorin 4 and nitrophorin 7
- Author
-
Chunmao He, Markus Knipp, and Hideaki Ogata
- Subjects
Hemeproteins ,Stereochemistry ,Resonance Raman spectroscopy ,Heme ,Photochemistry ,Crystallography, X-Ray ,Ligands ,Biochemistry ,Methemoglobin ,chemistry.chemical_compound ,Nitrophorin ,Animals ,Nitrite ,Salivary Proteins and Peptides ,Nitrites ,Chemistry ,Electron Spin Resonance Spectroscopy ,Ligand (biochemistry) ,Dissociation constant ,Heme B ,Kinetics ,Beta barrel ,Rhodnius ,Hemin ,Metmyoglobin - Abstract
The interaction of ferriheme proteins with nitrite has recently attracted interest as a source for NO or other nitrogen oxides in mammalian physiology. However, met-hemoglobin (metHb), which was suggested as a key player in this process, does not convert nitrite unless small amounts of NO are added in parallel. We have recently reported that, in contrast, nitrophorins (NPs) convert nitrite as the sole substrate to form NO even at pH 7.5, which is an unprecedented case among ferrihemes [He, C., and Knipp, M. (2009) J. Am. Chem. Soc. 131, 12042-12043]. NPs, which comprise a class of unique heme b proteins from the saliva of the blood-sucking insect Rhodnius prolixus, appear in a number of concomitant isoproteins. Herein, the first spectroscopic characterization of the initial complexes of the two isoproteins NP4 and NP7 with nitrite is presented and compared to the data reported for metHb and met-myoglobin (metMb). Because upon nitrite binding, NPs, in contrast to metHb and metMb, continue to react with nitrite, resonance Raman spectroscopy and continuous wave electron paramagnetic resonance spectroscopy were applied to frozen samples. As a result, the existence of two six-coordinate ferriheme low-spin complexes was established. Furthermore, X-ray crystallography of NP4 crystals soaked with nitrite revealed the formation of an eta(1)-N nitro complex, which is in contrast to the eta(1)-O-bound nitrite in metMb and metHb. Stopped-flow kinetic experiments show that although the ligand dissociation constants of NP4 and NP7 (15-190 M(-1)) are comparable to those of metHb and metMb, the rates of ligand binding and release are significantly slower. Moreover, not only the reaction kinetics but also electron paramagnetic resonance spectroscopy reveals notable differences between the two isoproteins.
- Published
- 2010
105. The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state)
- Author
-
Petra Kellers, Wolfgang Lubitz, and Hideaki Ogata
- Subjects
Models, Molecular ,Hydrogenase ,Inorganic chemistry ,Iron–sulfur cluster ,Crystal structure ,010402 general chemistry ,Crystallography, X-Ray ,01 natural sciences ,Chromatiaceae ,law.invention ,Metal ,03 medical and health sciences ,chemistry.chemical_compound ,Structural Biology ,law ,Nickel ,Catalytic Domain ,Spectroscopy, Fourier Transform Infrared ,Electron paramagnetic resonance ,Protein Structure, Quaternary ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,biology ,Chemistry ,Electron Spin Resonance Spectroscopy ,Active site ,Bridging ligand ,Electron transport chain ,0104 chemical sciences ,Crystallography ,Protein Subunits ,visual_art ,biology.protein ,visual_art.visual_art_medium ,Desulfovibrio ,Protein Multimerization ,Oxidation-Reduction ,Protein Binding - Abstract
The crystal structure of the membrane-associated [NiFe] hydrogenase from Allochromatium vinosum has been determined to 2.1 A resolution. Electron paramagnetic resonance (EPR) and Fourier transform infrared spectroscopy on dissolved crystals showed that it is present in the Ni-A state (>90%). The structure of the A. vinosum [NiFe] hydrogenase shows significant similarities with [NiFe] hydrogenase structures derived from Desulfovibrio species. The amino acid sequence identity is ∼ 50%. The bimetallic [NiFe] active site is located in the large subunit of the heterodimer and possesses three diatomic non-protein ligands coordinated to the Fe (two CN(-) , one CO). Ni is bound to the protein backbone via four cysteine thiolates; two of them also bridge the two metals. One of the bridging cysteines (Cys64) exhibits a modified thiolate in part of the sample. A mono-oxo bridging ligand was assigned between the metal ions of the catalytic center. This is in contrast to a proposal for Desulfovibrio sp. hydrogenases that show a di-oxo species in this position for the Ni-A state. The additional metal site located in the large subunit appears to be a Mg(2+) ion. Three iron-sulfur clusters were found in the small subunit that forms the electron transfer chain connecting the catalytic site with the molecular surface. The calculated anomalous Fourier map indicates a distorted proximal iron-sulfur cluster in part of the crystals. This altered proximal cluster is supposed to be paramagnetic and is exchange coupled to the Ni(3+) ion and the medial [Fe(3)S(4)](+) cluster that are both EPR active (S=1/2 species). This finding of a modified proximal cluster in the [NiFe] hydrogenase might explain the observation of split EPR signals that are occasionally detected in the oxidized state of membrane-bound [NiFe] hydrogenases as from A. vinosum.
- Published
- 2010
106. [NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism
- Author
-
Yoshiki Higuchi, Wolfgang Lubitz, and Hideaki Ogata
- Subjects
Reaction mechanism ,Carbon Monoxide ,Hydrogenase ,biology ,Chemistry ,Spectrum Analysis ,Active site ,Crystal structure ,Photochemistry ,biology.organism_classification ,Redox ,Catalysis ,Inorganic Chemistry ,Electron transfer ,Crystallography ,biology.protein ,Biocatalysis ,Enzyme Inhibitors ,Desulfovibrio vulgaris ,Oxidation-Reduction - Abstract
[NiFe] hydrogenases catalyze the reversible oxidation of dihydrogen. For this simple reaction the molecule has developed a complex catalytic mechanism, during which the enzyme passes through various redox states. The [NiFe] hydrogenase contains several metal centres, including the bimetallic Ni-Fe active site, iron-sulfur clusters and a Mg(2+) ion. The Ni-Fe active site is located in the inner part of the protein molecule, therefore a number of pathways are involved in the catalytic reaction route. These consist of an electron transfer pathway, a proton transfer pathway and a gas-access channel. Over the last 10-15 years we have been investigating the crystal structures of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F, which is a sulfate-reducing anaerobic bacterium. So far the crystal structures of the oxidized, H(2)-reduced and carbon monoxide inhibited states have been determined at high resolution and have revealed a rather unique structure of the hetero-bimetallic Ni-Fe active site. Furthermore, intensive spectroscopic studies have been performed on the enzyme. Based on the crystal structure, a water-soluble Ni-Ru complex has been synthesized as a functional model for the [NiFe] hydrogenases. The present review gives an overview of the catalytic reaction mechanism of the [NiFe] hydrogenases.
- Published
- 2009
107. Purification, crystallization and preliminary X-ray analysis of adenylylsulfate reductase from Desulfovibrio vulgaris Miyazaki F
- Author
-
Hideaki Ogata, Wolfgang Lubitz, Aruna Goenka Agrawal, Amrit Pal Kaur, Richard Goddard, and Wolfgang Gärtner
- Subjects
Ammonium sulfate ,Molecular Sequence Data ,Biophysics ,chemistry.chemical_element ,Biochemistry ,law.invention ,Crystal ,chemistry.chemical_compound ,Bacterial Proteins ,X-Ray Diffraction ,Structural Biology ,law ,Dissimilatory sulfate reduction ,Genetics ,Oxidoreductases Acting on Sulfur Group Donors ,Desulfovibrio vulgaris ,Crystallization ,biology ,Condensed Matter Physics ,biology.organism_classification ,Sulfur ,Crystallography ,chemistry ,Crystallization Communications ,Single crystal ,Bacteria - Abstract
Sulfur in its various oxidation states is used for energy conservation in many microorganisms. Adenylylsulfate reductase is a key enzyme in the sulfur-reduction pathway of sulfate-reducing bacteria. The adenylylsulfate reductase from Desulfovibrio vulgaris Miyazaki F has been purified and crystallized at 277 K using the vapour-diffusion method with ammonium sulfate as the precipitating agent. A data set was collected to 1.7 A resolution from a single crystal at 100 K using synchrotron radiation. The crystal belonged to space group P3(1), with unit-cell parameters a = b = 125.93, c = 164.24 A. The crystal contained two molecules per asymmetric unit, with a Matthews coefficient (V(M)) of 4.02 A(3) Da(-1); the solvent content was estimated to be 69.4%.
- Published
- 2008
108. Purification, crystallization and preliminary X-ray analysis of the membrane-bound [NiFe] hydrogenase from Allochromatium vinosum
- Author
-
Wolfgang Lubitz, Petra Kellers, and Hideaki Ogata
- Subjects
Hydrogenase ,Protein Conformation ,Biophysics ,chemistry.chemical_element ,Crystallography, X-Ray ,Biochemistry ,law.invention ,chemistry.chemical_compound ,Structural Biology ,law ,Sodium citrate ,Proteobacteria ,Genetics ,Metalloprotein ,Imidazole ,Crystallization ,chemistry.chemical_classification ,Chemistry ,Space group ,Condensed Matter Physics ,Sulfur ,Crystallography ,Crystallization Communications ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,X-ray crystallography ,Chromatography, Gel ,Electrophoresis, Polyacrylamide Gel - Abstract
The membrane-bound [NiFe] hydrogenase is a unique metalloprotein that is able to catalyze the reversible oxidation of hydrogen to protons and electrons during a complex reaction cycle. The [NiFe] hydrogenase was isolated from the photosynthetic purple sulfur bacterium Allochromatium vinosum and its crystallization and preliminary X-ray analysis are reported. It was crystallized by the hanging-drop vapour-diffusion method using sodium citrate and imidazole as crystallization agents. The crystals belong to space group P2(1)2(1)2, with unit-cell parameters a = 205.00, b = 217.42, c = 120.44 A. X-ray diffraction data have been collected to 2.5 A resolution.
- Published
- 2008
109. Crystallization and preliminary X-ray crystallographic studies of the axin DIX domain
- Author
-
Michihiko Kataoka, Yoshiki Higuchi, Hirofumi Komori, Nobuhiro Mizuno, Hideaki Ogata, Akira Kikuchi, Naoki Shibata, Jun Kondo, Sakayu Shimizu, Toru Hanamura, Mai Ueda, Yasufumi Ueda, Ryo Yamamoto, Yasuhito Shomura, Hideki Yamamoto, and Yusuke Tomimoto
- Subjects
Beta-catenin ,Biophysics ,Repressor ,macromolecular substances ,Crystallography, X-Ray ,Biochemistry ,law.invention ,Axin Protein ,Structural Biology ,law ,GSK-3 ,Genetics ,Animals ,Crystallization ,biology ,Chemistry ,Microfilament Proteins ,Wnt signaling pathway ,Intracellular Signaling Peptides and Proteins ,Condensed Matter Physics ,equipment and supplies ,Protein Structure, Tertiary ,Rats ,Repressor Proteins ,Wnt Proteins ,Crystallography ,Crystallization Communications ,biological sciences ,biology.protein ,health occupations ,Phosphorylation ,bacteria ,Signal transduction ,Signal Transduction - Abstract
Axin is a negative regulator of the canonical Wnt signalling pathway that mediates the phosphorylation of beta-catenin by glycogen synthase kinase 3beta. The DIX domain of rat axin, which is important for its homooligomerization and interactions with other regulators in the Wnt pathway, was purified and crystallized by the sitting-drop vapour-diffusion technique using polyethylene glycol 6000 and lithium sulfate as crystallization agents. Crystals belong to space group P6(1) or P6(5), with unit-cell parameters a = b = 91.49, c = 84.92 A. An X-ray diffraction data set has been collected to a nominal resolution of 2.9 A.
- Published
- 2007
110. Promyelocytic crisis of chronic myelogenous leukaemia during imatinib mesylate treatment
- Author
-
Kazuaki Yakushiji, Korenori Otsubo, Rie Imamura, Takashi Okamura, Michio Sata, Kohji Yoshimoto, Eijiro Oku, Shuichiro Nagata, Ritsuko Seki, Hideaki Ogata, Yuka Takata, Koichi Osaki, and Michitoshi Hashiguchi
- Subjects
Male ,Antineoplastic Agents ,Piperazines ,Immunophenotyping ,Myelogenous ,hemic and lymphatic diseases ,Leukemia, Myelogenous, Chronic, BCR-ABL Positive ,medicine ,Humans ,neoplasms ,In Situ Hybridization, Fluorescence ,Aged ,ABL ,medicine.diagnostic_test ,business.industry ,Reverse Transcriptase Polymerase Chain Reaction ,breakpoint cluster region ,Imatinib ,Hematology ,General Medicine ,medicine.disease ,Flow Cytometry ,Leukemia ,Imatinib mesylate ,Pyrimidines ,Karyotyping ,Benzamides ,Cancer research ,Imatinib Mesylate ,business ,medicine.drug ,Fluorescence in situ hybridization - Abstract
An untreated 66-year-old woman with chronic myelogenous leukaemia (CML) in the chronic phase was initially given imatinib mesylate, rapidly achieving a good cytogenetic response with treatment. However, acute promyelocytic leukaemia complicated by a disseminated intravascular coagulation occurred 9 months after beginning imatinib treatment. Promyelocytic crisis of CML was diagnosed by demonstration of both BCR/ABL and PML/RARα chimeric genes in leukaemic cells by karyotypic and fluorescence in situ hybridization analysis. Clonal evolution with addition of the PML/RARα translocation may have arisen in the early chronic phase of CML, with expansion of this clone during imatinib treatment. Promyelocytic crisis of CML is rare; furthermore, we know of no previous report of promyelocytic crisis occurring during treatment with imatinib.
- Published
- 2006
111. Demonstration of reversed flow in segmental branches of the portal vein with hand-held color Doppler ultrasonography after hematopoietic stem cell transplantation
- Author
-
Masakazu Higuchi, K Nagafuji, Kazuaki Yakushiji, Ritsuko Seki, Michitoshi Hashiguchi, Mamoru Harada, Hideaki Ogata, Hisashi Gondo, Kohji Yoshimoto, Shibuya T, Naofumi Ono, Koji Kato, Takashi Okamura, Korenori Otsubo, S Taniguchi, Rie Imamura, Mika Kuroiwa, Eijirou Oku, and Michio Sata
- Subjects
Adult ,Male ,medicine.medical_specialty ,Time Factors ,Adolescent ,medicine.medical_treatment ,Hepatic Veno-Occlusive Disease ,Hematopoietic stem cell transplantation ,Hypertension, Portal ,medicine ,Humans ,Child ,Aged ,Ultrasonography ,Transplantation ,Vascular disease ,business.industry ,Portal Vein ,Liver Diseases ,Ursodeoxycholic Acid ,Hematopoietic Stem Cell Transplantation ,Ultrasonography, Doppler ,Hematology ,Blood flow ,Middle Aged ,medicine.disease ,Surgery ,surgical procedures, operative ,medicine.anatomical_structure ,Graft-versus-host disease ,Treatment Outcome ,Disease Progression ,Portal hypertension ,Female ,Bone marrow ,Complication ,business - Abstract
Hepatic veno-occlusive disease (VOD) is a severe complication of hematopoietic stem cell transplantation (SCT). When monitored with hand-held color Doppler ultrasonography during day -7 to +35 around SCT, reversed blood flow in the segmental branches of the portal vein was detected in nine of 56 patients who had undergone SCT. Three of nine patients had clinical evidence of VOD, but six patients did not fulfill the criteria for diagnosis of VOD initially. Two patients progressed to clinical VOD at a later date and the reversed portal flow disappeared with or without treatment for VOD in the other four patients. Monitoring for reversed portal flow with color Doppler ultrasonography may be a useful tool for the early diagnosis of VOD, and may improve prognosis by allowing early initiation of treatment.
- Published
- 2005
112. Simultaneous hepatic relapse of non-Hodgkin's lymphoma and hepatocellular carcinoma in a patient with hepatitis C virus-related cirrhosis
- Author
-
Eijiro Oku, Kazuaki Yakushiji, Eiji Ando, Michitoshi Hashiguchi, Takashi Okamura, Hideaki Ogata, Ritsuko Seki, Kohji Yoshimoto, Koichi Osaki, Hiroaki Nagamatsu, Rie Imamura, Kazuhide Shimamatsu, Michio Sata, and Korenori Ohtsubo
- Subjects
Oncology ,Liver Cirrhosis ,Male ,Vincristine ,medicine.medical_specialty ,Cirrhosis ,Carcinoma, Hepatocellular ,Hepatitis C virus ,Hepacivirus ,medicine.disease_cause ,Gastroenterology ,immune system diseases ,hemic and lymphatic diseases ,Internal medicine ,medicine ,Humans ,neoplasms ,Aged ,business.industry ,Lymphoma, Non-Hodgkin ,Liver Neoplasms ,Hematology ,General Medicine ,medicine.disease ,digestive system diseases ,Lymphoma ,Non-Hodgkin's lymphoma ,Hepatocellular carcinoma ,Rituximab ,business ,Diffuse large B-cell lymphoma ,medicine.drug - Abstract
We report a 66-year-old man with hepatitis C virus (HCV)-related cirrhosis and simultaneous hepatic relapse of non-Hodgkin’s lymphoma (NHL) and of hepatocellular carcinoma (HCC). Although the liver is frequently involved by NHL, hepatic colocalization of NHL and HCC is rarely detected by imaging techniques. HCV has been suggested to be lymphotrophic as well as hepatotrophic, and therefore has attracted speculation about a causative role in some cases of lymphoma. The patient had a past history of cutaneous diffuse large B cell lymphoma (DLBCL) in concurrence with HCC 32 months previously. Complete remission (CR) had been maintained for both diseases until February 2004, when ultrasonography and computed tomography (CT) showed multiple liver tumors. Two of these, appearing hyperattenuating in the arterial phase of contrast-enhanced CT, were diagnosed histopathologically as HCC, and treated with radiofrequency ablation. The other tumors, hypoattenuating in the portal phase CT, were diagnosed histopathologically as DLBCL, and treated with cyclophosphamide, tetrahydropyranyl-Adriamycin, vincristine and prednisolone (THP-COP) in combination with rituximab. CR was achieved for both DLBCL and HCC. Given the previously demonstrated immune system tropism and perturbation by HCV, the virus might have contributed to the occurrence of the NHL as well as the HCC.
- Published
- 2005
113. A single-crystal ENDOR and density functional theory study of the oxidized states of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F
- Author
-
Yoshiki Higuchi, Olga Schröder, Robert Bittl, Matthias Stein, Maurice van Gastel, Marc Brecht, Friedhelm Lendzian, Hideaki Ogata, and Wolfgang Lubitz
- Subjects
Hydrogenase ,Protein Conformation ,Ligands ,Biochemistry ,law.invention ,Inorganic Chemistry ,Computational chemistry ,law ,Cysteine ,Desulfovibrio vulgaris ,Electron paramagnetic resonance ,Hyperfine structure ,Quantitative Biology::Biomolecules ,Electron nuclear double resonance ,Binding Sites ,biology ,Chemistry ,Electron Spin Resonance Spectroscopy ,Resonance ,Bridging ligand ,biology.organism_classification ,Crystallography ,Density functional theory ,Protons ,Crystallization ,Oxidation-Reduction ,Sulfur - Abstract
The catalytic center of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F in the oxidized states was investigated by electron paramagnetic resonance and electron-nuclear double resonance spectroscopy applied to single crystals of the enzyme. The experimental results were compared with density functional theory (DFT) calculations. For the Ni-B state, three hyperfine tensors could be determined. Two tensors have large isotropic hyperfine coupling constants and are assigned to the beta-CH2 protons of the Cys-549 that provides one of the bridging sulfur ligands between Ni and Fe in the active center. From a comparison of the orientation of the third hyperfine tensor with the tensor obtained from DFT calculations an OH- bridging ligand has been identified in the Ni-B state. For the Ni-A state broader signals were observed. The signals of the third proton, as observed for the "ready" state Ni-B, were not observed at the same spectral position for Ni-A, confirming a structural difference involving the bridging ligand in the "unready" state of the enzyme.
- Published
- 2005
114. The use of doppler ultrasound in evaluation of breast cancer metastasis to axillary lymph nodes
- Author
-
Nobuo Okuyama, Hideaki Ogata, and Hitoshi Murakuni
- Subjects
Cancer Research ,Pathology ,medicine.medical_specialty ,Axillary lymph nodes ,Breast Neoplasms ,Metastasis ,chemistry.chemical_compound ,Breast cancer ,medicine ,Humans ,Lymph node ,Neovascularization, Pathologic ,business.industry ,Cancer ,Ultrasonography, Doppler ,General Medicine ,Middle Aged ,Sentinel node ,medicine.disease ,Vascular endothelial growth factor ,medicine.anatomical_structure ,Oncology ,chemistry ,Lymphatic Metastasis ,Regression Analysis ,Female ,Lymph ,business - Abstract
The formation of microvessels in tumors by angiogenesis is considered to be an important prognostic factor, and closely correlates with lymph node metastasis. We used color Doppler ultrasound to examine the relationship between the amount of blood vessels in tumors and pulsatility index (PI), and tumor size in breast cancers, with and without regional lymph node metastasis. Doppler ultrasound was performed on 80 patients with breast cancer prior to surgery. The concentration of vascular endothelial growth factor (VEGF) within the tumors was measured following surgery in 42 cases chosen at random. In the negative metastatic nodes group, the number of vessels in the tumor correlated positively with tumor diameter. In the positive metastatic nodes group, however, the number of blood vessels in the tumor did not correlate with tumor diameter. Differences in tumor vascularity between node positive and negative groups were useful in determining the status of node metastasis in subsequent analysis. Fifteen of 17 cases of tumors that measured20 mm, and in which there were no blood vessels, were node-negative. There were no node-negative tumors measuring20 mm in diameter (p=0.003). Conversely, in nodes with positive metastasis, blood vessels were observed in 5 of 7 tumors that measured15 mm in diameter (p=0.019). These findings may be useful in estimating the likelihood of metastasis to regional lymph nodes. PI was directly proportional to tumor size in the negative nodes group (r=0.47). There was no such correlation in the positive nodes group. There was no correlation between VEGF concentration in the tumor and the number of blood vessels in that tumor. In conclusion color Doppler analysis of blood vessels appears to be useful in predicting lymph node metastasis, especially for small tumors.
- Published
- 2004
115. Cloning and expression of the enolase gene from Desulfovibrio vulgaris (Miyazaki F)
- Author
-
Yuki Takayama, Masaya Kitamura, Kyoko Kohno, Hideo Inoue, Yoshiki Higuchi, Shuichi Kojima, and Hideaki Ogata
- Subjects
Glycerol ,Enolase ,Molecular Sequence Data ,Biophysics ,Biology ,medicine.disease_cause ,Biochemistry ,law.invention ,Structural Biology ,law ,Genetics ,medicine ,Escherichia coli ,Amino Acid Sequence ,Desulfovibrio vulgaris ,Lactic Acid ,RNA, Messenger ,Cloning, Molecular ,Gene ,chemistry.chemical_classification ,Base Sequence ,Reverse Transcriptase Polymerase Chain Reaction ,Nucleic acid sequence ,Hydrogen-Ion Concentration ,biology.organism_classification ,Molecular biology ,Recombinant Proteins ,Amino acid ,Molecular Weight ,Kinetics ,Glucose ,chemistry ,Methylenetetrahydrofolate dehydrogenase ,Phosphopyruvate Hydratase ,Recombinant DNA - Abstract
The gene encoding an enolase from Desulfovibrio vulgaris (Miyazaki F) was cloned and overexpressed in Escherichia coli. A 2.1-kb DNA fragment, isolated from D. vulgaris (Miyazaki F) by double digestion with PstI and BamHI, contained an enolase gene (eno) and part of the methylenetetrahydrofolate dehydrogenase gene (folD). The nucleotide sequence of eno indicates that the protein monomer is composed of 434 amino acids. An expression system for eno under control of the T7 promoter was constructed in E. coli. The purified His-tagged enolase formed a homooctamer and was active in the formation of phosphoenolpyruvate (PEP) as well as in the reverse reaction, the formation of d -(+)-2-phosphoglyceric acid (2-PGA). The pH dependence and kinetic properties of the recombinant enolase from the sulfate-reducing bacterium were also studied. The amounts of eno mRNA when the bacterium was grown on glycerol or glucose were compared to that when D. vulgaris was grown on lactate.
- Published
- 2004
116. Prognostic significance of the F-box protein Skp2 expression in diffuse large B-cell lymphoma
- Author
-
Michitoshi Hashiguchi, Hideaki Ogata, Rie Imamura, Kazuaki Yakushiji, Ritsuko Seki, Hironori Koga, Kohji Yoshimoto, Takashi Okamura, Takato Ueno, Michio Sata, Masayoshi Kage, and Yutaka Nakashima
- Subjects
Adult ,Male ,Lymphoma, B-Cell ,Cell Cycle Proteins ,medicine.disease_cause ,International Prognostic Index ,Proliferating Cell Nuclear Antigen ,medicine ,SKP2 ,Humans ,S-Phase Kinase-Associated Proteins ,Aged ,biology ,Performance status ,Hematology ,Cell cycle ,Middle Aged ,medicine.disease ,Prognosis ,Immunohistochemistry ,Survival Analysis ,Lymphoma ,Ki-67 Antigen ,Treatment Outcome ,Ki-67 ,Cancer research ,biology.protein ,Female ,Lymphoma, Large B-Cell, Diffuse ,Carcinogenesis ,Diffuse large B-cell lymphoma ,Biomarkers - Abstract
The F-box protein Skp2 positively regulates the G1-S transition by promoting degradation of the cyclin-dependent kinase inhibitor p27kip1 (p27). Recent evidence has suggested an oncogenic role of Skp2 in not only carcinogenesis but also lymphomagenesis. In this study, we performed immunohistochemical analysis on the cell-cycle-associated proteins, Skp2, p27, and Ki-67, in 27 patients with de novo diffuse large B-cell lymphoma (DLBCL), evaluating the correlation between the clinical characteristics and expression levels of these proteins. The patients were classified into two groups according to the positivity for Skp2 expression: a high Skp2 expression group (>60% positive for Skp2 in lymphoma cells) and a low Skp2 expression group (60%). A high level of Skp2 expression significantly correlated with advanced clinical stage (P = 0.029), although the increase did not correlate with age, gender, LDH levels, presence of extranodal disease, or performance status and resulted in no correlation with the International Prognostic Index-based risk grading. However, it was noteworthy that the high Skp2 expression group demonstrated a significantly worse prognosis than the low Skp2 expression group (P = 0.0007). The expression level of Skp2 correlated with that of Ki-67 but not necessarily with that of p27. The p27 expression level did not correlate patients’ prognosis. Taken together, it was suggested that Skp2 was a valuable and independent marker predicting the outcome in DLBCL. Am. J. Hematol. 73:230–235, 2003. © 2003 Wiley-Liss, Inc.
- Published
- 2003
117. Single crystal EPR studies of the reduced active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F
- Author
-
Stefanie Foerster, Matthias Stein, Hideaki Ogata, Marc Brecht, Yoshiki Higuchi, and Wolfgang Lubitz
- Subjects
Models, Molecular ,Hydrogenase ,Protein Conformation ,Crystal structure ,Biochemistry ,Catalysis ,law.invention ,Colloid and Surface Chemistry ,Bacterial Proteins ,law ,Oxidation state ,Desulfovibrio vulgaris ,Electron paramagnetic resonance ,Binding Sites ,biology ,Hydride ,Chemistry ,Electron Spin Resonance Spectroscopy ,General Chemistry ,biology.organism_classification ,Crystallography ,Models, Chemical ,Density functional theory ,Single crystal ,Oxidation-Reduction - Abstract
In the catalytic cycle of [NiFe] hydrogenase the paramagnetic Ni-C intermediate is of key importance, since it is believed to carry the substrate hydrogen, albeit in a yet unknown geometry. Upon illumination at low temperatures, Ni-C is converted to the so-called Ni-L state with markedly different spectroscopic parameters. It is suspected that Ni-L has lost the "substrate hydrogen". In this work, both paramagnetic states have been generated in single crystals obtained from the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. Evaluation of the orientation dependent spectra yielded the magnitudes of the g tensors and their orientations in the crystal axes system for both Ni-C and Ni-L. The g tensors could further be related to the atomic structure by comparison with the X-ray crystallographic structure of the reduced enzyme. Although the g tensor magnitudes of Ni-C and Ni-L are quite different, the orientations of the resulting g tensors are very similar but differ from those obtained earlier for Ni-A and Ni-B (Trofanchuk et al. J. Biol. Inorg. Chem. 2000, 5, 36-44). The g tensors were also calculated by density functional theory (DFT) methods using various structural models of the active site. The calculated g tensor of Ni-C is, concerning magnitudes and orientation, in good agreement with the experimental one for a formal Ni(III) oxidation state with a hydride (H(-)) bridge between the Ni and the Fe atom. Satisfying agreement is obtained for the Ni-L state when a formal Ni(I) oxidation state is assumed for this species with a proton (H(+)) removed from the bridge between the nickel and the iron atom.
- Published
- 2003
118. Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen
- Author
-
Yasutaka Mizoguchi, Hideaki Ogata, Kunio Miki, Noritake Yasuoka, Yoshiki Higuchi, Tatsuhiko Yagi, Shin-ichi Adachi, Shun Hirota, Nobuhiro Mizuno, and Osamu Yamauchi
- Subjects
Models, Molecular ,Hydrogenase ,Stereochemistry ,Protein Conformation ,Resonance Raman spectroscopy ,chemistry.chemical_element ,Crystal structure ,Crystallography, X-Ray ,Spectrum Analysis, Raman ,Biochemistry ,Catalysis ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Nickel ,Atom ,Desulfovibrio vulgaris ,Carbon Monoxide ,Binding Sites ,biology ,Fourier Analysis ,Active site ,General Chemistry ,biology.organism_classification ,Crystallography ,chemistry ,biology.protein ,Spectrophotometry, Ultraviolet ,Carbon monoxide ,Hydrogen - Abstract
The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase in the CO-bound and CO-liberated forms were determined at 1.2-1.4 A resolution. The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe active site. The CO was not replaced with H(2) in the dark at 100 K, but was liberated by illumination with a strong white light. The Ni-C distances and Ni-C-O angles were about 1.77 A and 160 degrees, respectively, except for one case (1.72 A and 135 degrees ), in which an additional electron density peak between the CO and Sgamma(Cys546) was recognized. Distinct changes were observed in the electron density distribution of the Ni and Sgamma(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. The novel structural features found near the Ni and Sgamma(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a role during the initial H(2)-binding process. Anaerobic addition of CO to dithionite-reduced [NiFe]hydrogenase led to a new absorption band at about 470 nm ( approximately 3000 M(-1)cm(-1)). Resonance Raman spectra (excitation at 476.5 nm) of the CO complex revealed CO-isotope-sensitive bands at 375/393 and 430 cm(-1) (368 and 413 cm(-1) for (13)C(18)O). The frequencies and relative intensities of the CO-related Raman bands indicated that the exogenous CO is bound to the Ni atom with a bent Ni-C-O structure in solution, in agreement with the refined structure determined by X-ray crystallography.
- Published
- 2002
119. Colour Doppler ultrasonography of a segmental branch of the portal vein is useful for early diagnosis and monitoring of the therapeutic course of veno-occlusive disease after allogenic haematopoietic stem cell transplantation
- Author
-
Naofumi Ono, Hideaki Ogata, Kazuaki Yakushiji, Michio Sata, Hiroshi Hashimoto, Hiroyasu Ijuin, Kohji Yoshimoto, Michitoshi Hashiguchi, Takashi Okamura, and Rie Imamura
- Subjects
Adult ,Male ,medicine.medical_specialty ,medicine.drug_class ,medicine.medical_treatment ,Hepatic Veno-Occlusive Disease ,Low molecular weight heparin ,Hematopoietic stem cell transplantation ,Hepatic Veins ,medicine ,Humans ,Transplantation, Homologous ,Alprostadil ,Ultrasonography, Doppler, Color ,Chemotherapy ,business.industry ,Portal Vein ,Anticoagulant ,Hematopoietic Stem Cell Transplantation ,Anticoagulants ,Hematology ,Blood flow ,Heparin, Low-Molecular-Weight ,Middle Aged ,Surgery ,Transplantation ,Regional Blood Flow ,Veno-Occlusive Disease ,Hepatic portal vein ,business - Abstract
We report two cases in which visualization of the segmental branch of the hepatic portal vein with the colour Doppler ultrasonography (US) technique was useful for the early diagnosis of veno-occlusive disease. The change in blood flow in the segmental branch of the portal vein occurred 5 and 6 d before the clinical criteria were fulfilled in the two cases. Reverse flow in the segmental branch began partially in the liver at first, and then spread to the whole liver several days later. All the US findings in both cases disappeared after thrombolytic therapy.
- Published
- 2002
120. [A 5'-DFUR + CPA + THP therapy that was effective for paclitaxel-refractory pulmonary metastasis of breast cancer--a case report]
- Author
-
Shinzo, Kitahara, Hideaki, Ogata, Toshio, Katagiri, Kyoei, Nonaka, and Tadaaki, Shiba
- Subjects
Adult ,Lung Neoplasms ,Paclitaxel ,Doxorubicin ,Drug Resistance, Neoplasm ,Antineoplastic Combined Chemotherapy Protocols ,Humans ,Breast Neoplasms ,Female ,Floxuridine ,Antineoplastic Agents, Phytogenic ,Cyclophosphamide ,Drug Administration Schedule - Abstract
What should be the standard treatment for taxane-refractory metastatic breast cancer remains controversial. In this paper, a case in which the 5'-DFUR + CPA + THP therapy was effective for paclitaxel-refractory metastatic breast cancer is reported. A 41-year-old female received pectoral muscle preserved mastectomy under diagnosis of the left breast cancer in May 1996. In June, 1999, a coin lesion of 2.2 cm diameter was found in the left middle lung field with chest X-ray. Paclitaxel 210 mg/m2 (once for three weeks, 8 cycles in total) resulted in marked improvement. The regimen of paclitaxel 70 mg/m2 (medication consecutive once-weekly for three weeks, and withdrawal for next week; 1 cycle) was carried out continuously with the patient ambulatory. Because resistance to the treatment appeared at the time the total dose reached 2,700 mg, 5'-DFUR + CPA + THP therapy (THP 30 mg/m2 (i.v.) x day 1, CPA 77 mg/m2 (p.o.) x 14 days, 5'-DFUR 460 mg/m2 (p.o.) x 14 days; 3 weeks with 1 cycle) was carried out, and definite improvement in the lung findings were observed. 5'-DFUR + CPA + THP therapy may be of use as a second-line therapy in paclitaxel-refractory recurrent breast cancer.
- Published
- 2002
121. P48. Nitrite disproportionation reaction: Investigations on the mechanism of the conversion of nitrite into nitric oxide at the ferriheme center of nitrophorins at blood plasma pH
- Author
-
Markus Knipp, Chunmao He, and Hideaki Ogata
- Subjects
Cancer Research ,chemistry.chemical_compound ,Physiology ,Chemistry ,Clinical Biochemistry ,Inorganic chemistry ,Blood plasma ,Disproportionation ,Nitrite ,Photochemistry ,Biochemistry ,Nitric oxide - Published
- 2011
122. Observation of a metal-hydride in [NiFe] hydrogenase
- Author
-
Wolfgang Lubitz, Hideaki Ogata, and Koji Nishikawa
- Subjects
Inorganic Chemistry ,Materials science ,Structural Biology ,Hydride ,Inorganic chemistry ,General Materials Science ,Physical and Theoretical Chemistry ,NiFe hydrogenase ,Condensed Matter Physics ,Biochemistry - Abstract
Hydrogenases catalyze the reversible hydrogen oxidation process by cleaving dihydrogen heterolytically.(1) For this reaction, the enzyme uses the transition metals Ni and Fe, which are abundant in Nature. Standard [NiFe] hydrogenaes are mainly composed of two subunits (total ~90 kDa) The [NiFe] active site is located in the center of the molecule. The active site of [NiFe] hydrogenase is composed of the dinuclear Ni-Fe center, where the Fe ion is coordinated by non-protein ligands (1CO and 2CN¯ ). Two thiolates of cysteine residues are bridging both metals. Furthermore, the Ni is coordinated to the two thiolates of cysteine residues in a terminal fashion. A third bridging ligand is found between the Ni and Fe atom, depending on the redox state.(1) In the inactive form, a third bridging ligand (OH¯¯¯ ) is found between Ni and Fe. Once the enzyme is activated, the bridging position is supposed to be vacant or bridged by a hydride. A previous X-ray crystallographic study at 1.4 Å resolution revealed that the bridging ligand (OH) is removed upon H2 reduction.(2) Electron paramagnetic resonance (EPR) spectroscopy showed that a hydride is located in the bridge between Ni and Fe, which is lost upon illumination at cryogenic temperature.(3) Here we present a crystallographic analysis of the fully reduced (Ni-R) state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F at 0.89 Å resolution. The ultra-high resolution analysis revealed the presence of the hydride bridge at the NiFe active site in the catalytically active state. Furthermore the CO and CN ligands could be identified and a protonated thiolate sulfur ligand of the Ni is postulated based on the electron density.
- Published
- 2014
123. Human breast cancer MDA-MB-231 cells fail to express the neurofibromin protein, lack its type I mRNA isoform and show accumulation of P-MAPK and activated Ras
- Author
-
Hideaki Ogata, Jun Takatsuka, Hirokazu Sato, and Luigi M. De Luca
- Subjects
MAPK/ERK pathway ,congenital, hereditary, and neonatal diseases and abnormalities ,Cancer Research ,Tumor suppressor gene ,GTPase-activating protein ,Breast Neoplasms ,Nerve Tissue Proteins ,Gene product ,Mice ,Tumor Cells, Cultured ,Animals ,Humans ,RNA, Messenger ,Phosphorylation ,Protein kinase A ,Neurofibromin 1 ,biology ,Autosomal dominant trait ,nervous system diseases ,Cell biology ,Oncology ,Cancer cell ,biology.protein ,Cancer research ,ras Proteins ,Female ,Guanosine Triphosphate ,Rabbits ,Mitogen-Activated Protein Kinases - Abstract
Neurofibromin is a tumor suppressor protein, which is similar in function to the GTPase activating protein (GAP), p120GAP, in that it accelerates inactivation of Ras. Mutations in the NF1 gene cause neurofibromatosis type 1, NF1, an autosomal dominant disease with a diverse spectrum of clinical manifestations, including neurofibromas. Ras activation (GTP binding) is induced by the GTP exchange factor Sos and its inactivation is regulated through the GAPs (p120GAP and neurofibromin). Strikingly, neurofibromin was nearly absent in MB-231 human breast cancer cells and present in the remaining four cell lines studied, with higher levels in BT-474 and MB-453 than in MCF-7 and BT-20 cells, as tested with polyclonal antibodies to both the N-terminal as well as the C-terminal peptides. Coordinated with the near absence of neurofibromin, these cells also presented with much greater levels of P-MAPK and activated Ras. Further, RT-PCR analysis demonstrated the absence of expression of NF1 mRNA type I isoform only in the MB-231 cell lines. This result documents for the first time an altered NF1 expression at the protein and mRNA levels in MDA-MB-231 breast cancer cells.
- Published
- 2001
124. Subject Index Vol. 117, 2007
- Author
-
Giovanni Targher, Maria Teresa Pirrotta, Filomena Cappucci, Maria Rosaria De Cuia, Hirokazu Murakami, Nikolaos Gompakis, Vassilios Kouloulias, Hideo Koh, Takahisa Yamane, Elvira Grandone, Francisco Sicilia, Masamitsu Karasawa, Chang-Ki Min, Fabiana Gentilini, Nicola Cascavilla, Takafumi Matsushima, Younggu Kim, Takashi Okamura, Tatiana Gil Alves Portugal, Jong Weon Choi, Giuliana Alimena, Gyeongsin Park, Anna Levi, Shuichiro Nagata, Seok Lee, Kensuke Ohta, Fiammetta Natalino, Leonora Houet, Chaido Tsantali, Marina Economou, Donatella Raspadori, Maria Keramida, Rosaria Crupi, Hiroshi Handa, Kiyoyuki Hagihara, Yoshihisa Nojima, Hiroyuki Irisawa, Ivan Alvarez, Norifumi Tsukamoto, Takayuki Saitoh, Hideaki Ogata, Donatella Colaizzo, Giuseppe Lippi, Juan Espinosa, Sung-Jin Moon, Hendrik Veelken, Eijiro Oku, Myungshin Kim, Monica Bocchia, Yuka Takata, Hirohisa Nakamae, Alessandro Gozzetti, Masayuki Hino, Koichi Osaki, Jürgen Finke, Michio Sata, Akihiko Yokohama, Ritsuko Seki, Takahiko Nakane, Erina Sakamoto, Massimo Breccia, Elena Carretera, Annamaria Frustaci, Yasunobu Takeoka, Massimo Franchini, Kazuaki Yakushiji, Anna-Katharina Thomas-Kaskel, Maria Rosa Valvano, Jong Wook Lee, Gianna Maria D'Elia, Lorella Melillo, Simona Calabrese, Dong-Gun Lee, Korenori Otsubo, Masataka Sakuraya, Ki-Ryang Koh, Chun-Choo Kim, Dieter Herchenbach, Roberto Latagliata, Rie Imamura, Jose Manuel Calvo-Villas, Miranda Athanasiou-Metaxa, Francesco Lauria, Kohji Yoshimoto, Arito Yamane, Michitoshi Hashiguchi, Ida Carmosino, Woo-Sung Min, and Mika Nakamae
- Subjects
Index (economics) ,Statistics ,Subject (documents) ,Hematology ,General Medicine ,Mathematics - Published
- 2007
125. Contents Vol. 117, 2007
- Author
-
Chang-Ki Min, Fabiana Gentilini, Miranda Athanasiou-Metaxa, Kazuaki Yakushiji, Vassilios Kouloulias, Masamitsu Karasawa, Annamaria Frustaci, Seok Lee, Gyeongsin Park, Masataka Sakuraya, Iván Alvarez, Michitoshi Hashiguchi, Kohji Yoshimoto, Ki-Ryang Koh, Hiroshi Handa, Simona Calabrese, Dong-Gun Lee, Hiroyuki Irisawa, Hendrik Veelken, Sung-Jin Moon, Kiyoyuki Hagihara, Woo-Sung Min, Rie Imamura, Takahisa Yamane, Ida Carmosino, Alessandro Gozzetti, Takashi Okamura, Chaido Tsantali, Elvira Grandone, Roberto Latagliata, Jürgen Finke, Mika Nakamae, Giovanni Targher, Koichi Osaki, Maria Rosaria De Cuia, Maria Teresa Pirrotta, Monica Bocchia, Lorella Melillo, Norifumi Tsukamoto, Hideo Koh, Massimo Franchini, Maria Keramida, Yuka Takata, Chun-Choo Kim, Anna-Katharina Thomas-Kaskel, Shuichiro Nagata, Hirohisa Nakamae, Dieter Herchenbach, Maria Rosa Valvano, Anna Levi, Takafumi Matsushima, Younggu Kim, Tatiana Gil Alves Portugal, Korenori Otsubo, Takahiko Nakane, Elena Carretera, Michio Sata, Kensuke Ohta, Erina Sakamoto, Jong Wook Lee, Rosaria Crupi, Jong Weon Choi, Takayuki Saitoh, Francisco Sicilia, Hirokazu Murakami, Donatella Raspadori, Hideaki Ogata, Giuseppe Lippi, Akihiko Yokohama, Giuliana Alimena, Donatella Colaizzo, Francesco Lauria, Fiammetta Natalino, Marina Economou, Myungshin Kim, Leonora Houet, Jose M. Calvo-Villas, Filomena Cappucci, Massimo Breccia, Gianna Maria D'Elia, Yasunobu Takeoka, Juan Espinosa, Eijiro Oku, Masayuki Hino, Yoshihisa Nojima, Arito Yamane, Ritsuko Seki, Nicola Cascavilla, and Nikolaos Gompakis
- Subjects
Hematology ,General Medicine - Published
- 2007
126. In vitro study of neutrophil apoptosis in liver cirrhosis
- Author
-
Hideaki Ogata, Michio Sata, Nobuhide Kusaba, Kyuichi Tanikawa, and Ryukichi Kumashiro
- Subjects
Adult ,Liver Cirrhosis ,Male ,Programmed cell death ,Pathology ,medicine.medical_specialty ,Cirrhosis ,Neutropenia ,Time Factors ,Neutrophils ,Apoptosis ,DNA Fragmentation ,In Vitro Techniques ,Flow cytometry ,chemistry.chemical_compound ,Internal Medicine ,medicine ,Humans ,fas Receptor ,Aged ,Aged, 80 and over ,Leukopenia ,TUNEL assay ,medicine.diagnostic_test ,business.industry ,General Medicine ,Middle Aged ,medicine.disease ,Microscopy, Electron ,chemistry ,Case-Control Studies ,Trypan blue ,Female ,medicine.symptom ,business - Abstract
Cirrhotic patients frequently manifest neutropenia and are predisposed to bacterial infections. We examined neutrophil apoptosis to determine if neutrophil survival in cirrhotic patients is shortened. Neutrophils isolated from 10 cirrhotic patients and 10 healthy volunteers were cultured for 24 hours. The time course of neutrophil viability was assessed by the trypan blue dye exclusion test and apoptosis was determined morphologically by light and electron microscopy. Apoptotic cells were also confirmed by terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick and labeling (TUNEL) and DNA gel electrophoresis. Fas expression of neutrophils was examined by flow cytometry. Viabilities were significantly decreased in liver cirrhosis (p
- Published
- 1998
127. Subject Index Vol. 116, 2006
- Author
-
Raj Rangineni, Michio Sata, Theodoros Eleftheriadis, Christian Breymann, Ashok K. Malani, Anna Mestice, Lei Wang, Kazuaki Yakushiji, Terri Gelbart, Maria Ditsa, Charalambos Kartsios, Ana Rita Manhani, Rokuo Abe, Eiji Ando, Rívia Mara Morais e Silva, Hongfan Peng, Eijiro Oku, Maria das Graças Carvalho, Rie Imamura, Dimitra Markala, Ritsuko Seki, Kazuei Ogawa, Auro Del Giglio, Paola Carluccio, Yurie Saitoh, Hideaki Ogata, Yukio Maruyama, Michitoshi Hashiguchi, G. Anifandis, Giorgina Specchia, Lauro Mello Vieira, Hiroaki Nagamatsu, Tilo Burkhardt, Margherita Giannoccaro, Georgia Antoniadi, Manuela Leo, Kohji Yoshimoto, Ioannis Stefanidis, Domenico Pastore, Jonathan M. Flanagan, Silvia Sibilla, Ernest Beutler, Vassilios Liakopoulos, Luci Maria Sant'Ana Dusse, Christos Papadopoulos, Gabriela Bencaiova, Vânia Maria Freitas, Takashi Okamura, Fernando Coutinho, Margherita Casanova, Geraldo Majella Medeiros de Paula, Pauline Lee, Tsutomu Shichishima, Alexander Krafft, Vincenzo Liso, Arcangelo Liso, Barbra Sasu, Kazuhide Shimamatsu, Vicram Gupta, Koichi Osaki, Korenori Ohtsubo, Aliki Skirta, and André Aleixo Pereira Hipólito Dantas
- Subjects
Index (economics) ,Statistics ,Subject (documents) ,Hematology ,General Medicine ,Mathematics - Published
- 2006
128. Importance of Hydrogen Bonding in Fine Tuning the [2Fe-2S] Cluster Redox Potential of HydC from Thermotoga maritima.
- Author
-
Birrell, James A., Laurich, Christoph, Reijerse, Edward J., Hideaki Ogata, and Wolfgang Lubitz
- Published
- 2016
- Full Text
- View/download PDF
129. Inflammatory pseudotumor of the liver--MR imaging findings
- Author
-
Tomoyuki Yoshida, Hideaki Ogata, Kensi Koga, Hiroyasu Ijuin, Taku Kusaba, Makoto Kohakura, Naofumi Ono, Makoto Yamawaki, Shiroh Miyazaki, Hiroyuki Ohnishi, Kyuichi Tanikawa, and Kohei Ogawa
- Subjects
Male ,Pathology ,medicine.medical_specialty ,medicine.diagnostic_test ,business.industry ,Liver Diseases ,Magnetic resonance imaging ,General Medicine ,Blood flow ,Middle Aged ,medicine.disease ,Mr imaging ,Magnetic Resonance Imaging ,Granuloma, Plasma Cell ,Contrast medium ,medicine.anatomical_structure ,Granuloma ,Inflammatory pseudotumor ,Medicine ,Humans ,Female ,Stage (cooking) ,business ,Vein ,Aged - Abstract
Using retrospective studies, we have investigated the possibility of obtaining characteristic findings of inflammatory pseudotumor of the liver by magnetic resonance (MR) imaging. We examined 8 patients (involving 8 masses) who had been histologically diagnosed as having an inflammatory pseudotumor in the liver. The histological studies were performed on an excised specimen of 1 mass, and on aspiration needle biopsy specimens and the clinical courses of the other 7 masses. T1 weighted images (T1WI) and T2 weighted images (T2WI) were obtained on MR imaging. MR imagings were analyzed for visualized patterns, patterns of internal structure and patterns of contrast enhancement of dynamic MR imaging. The 8 masses were visualized as hypointense on T1WI and hyperintense on T2WI by MR imaging. Dynamic MR imaging revealed that 1 mass was markedly enhanced peripherally while another mass was homogeneously enhanced, and that enhancement was most marked immediately after injection of contrast medium and then gradually disappeared. Vessels were observed in 4 masses (the portal vein in 2 masses, the hepatic vein in 1 mass, and portal and hepatic veins in 1 mass), and these vessels were clearly visualized on T1WI. The MR imaging findings from the early stage of an inflammatory pseudotumor showed a pattern similar to that of hepatic tumors with rich blood flow. The portal vein or hepatic vein was found in the tumor in half the patients, suggesting that this characteristic was useful for diagnosis of an inflammatory pseudotumor in the liver.
- Published
- 1997
130. P53
- Author
-
Markus Knipp, Hideaki Ogata, and Chunmao He
- Subjects
Cancer Research ,Hemeprotein ,biology ,Physiology ,Chemistry ,Clinical Biochemistry ,Resonance Raman spectroscopy ,Nuclear magnetic resonance spectroscopy ,Biochemistry ,Cofactor ,chemistry.chemical_compound ,biology.protein ,Dismutase ,Nitrite ,Heme ,Peroxidase - Abstract
Background Nitrophorins (NPs) are NO transporting proteins from the saliva of the blood-sucking insect Rhodnius prolixus . The delivery of NO is accomplished by storage on the protein’s ferriheme cofactor and the gas molecule is released when the protein is injected into a victim’s tissue. However, we demonstrated that nitrophorins can also produce NO from nitrite as the only substrate, i.e., in this reaction nitrite serves as both electron donor and electron acceptor. The enzymatic activity was termed nitrite dismutase activity and is now classified with the EC number 1.7.6.1. This study provides insight into the structural features required for the catalytic activity. Methods Proteins were recombinantly expressed in Escherichia coli cells. They were characterized by X-ray crystallography, EPR spectroscopy, UV/vis spectroscopy, resonance Raman spectroscopy, and NMR spectroscopy. The enzymatic reaction was studied by absorbance detected stopped-flow kinetics. Results The binding mode of nitrite to the NP Fe (III) is clearly different compared to that of the globins, i.e., N-bound. Contrary to the globins, the insertion of an H-donating residue (NP4(L130R)) into the protein pocket does not affect the nitrite binding mode; however, it cancels the enzymatic activity. On the other hand, mutation of the proximal Asp70 residue, which is H-bonded via a water to the iron coordinating His59, also affects the enzymatic activity, indicating that the charge distribution on the heme cofactor has a major influence on the iron reactivity. Conclusion The nitrophorins are good model systems for the characterization of the nitrite dismutase catalysis. The absence of H-donating residues and the charge density on the proximal His were identified as important structural features that are required for the nitrite dismutase reaction. Among the many heme proteins expressed in the human organism some might bear a similar catalytic activity. We suggest the group of heme peroxidases as potential candidates for enzymatic “nitrite-only” NO production. Disclosure Supported by the Deutsche Forschungsgemeinschaft (DFG), Grants KN 951-1/1 and 2.
- Published
- 2013
131. Cover Picture: Observation of the FeCN and FeCO Vibrations in the Active Site of [NiFe] Hydrogenase by Nuclear Resonance Vibrational Spectroscopy (Angew. Chem. Int. Ed. 2/2013)
- Author
-
Devrani Mitra, E. Ercan Alp, Saeed Kamali, Jiyong Zhao, Hideaki Ogata, Yoshitaka Yoda, Thomas B. Rauchfuss, Francis E. Jenney, Stephen P. Cramer, Deborah Byrne, Violaine Bonnefoy, Michael W. W. Adams, Brian C. Manor, Hongxin Wang, and Wolfgang Lubitz
- Subjects
Crystallography ,Hydrogenase ,biology ,Chemistry ,Inorganic chemistry ,biology.protein ,Infrared spectroscopy ,Active site ,Cover (algebra) ,General Chemistry ,Nuclear resonance vibrational spectroscopy ,NiFe hydrogenase ,Catalysis - Published
- 2012
132. Titelbild: Detektion von Fe-CN- und Fe-CO-Schwingungen im aktiven Zentrum der [NiFe]-Hydrogenase durch inelastische kernresonante Streuung (Angew. Chem. 2/2013)
- Author
-
Francis E. Jenney, Stephen P. Cramer, Devrani Mitra, Saeed Kamali, Thomas B. Rauchfuss, Yoshitaka Yoda, Jiyong Zhao, Violaine Bonnefoy, Hideaki Ogata, Hongxin Wang, Brian C. Manor, Wolfgang Lubitz, Deborah Byrne, Michael W. W. Adams, and E. Ercan Alp
- Subjects
General Medicine - Published
- 2012
133. Primary Report of Experience using Bevacizumab for Recurrent Breast Cancers
- Author
-
Hironori Kaneko, Toshihide Ito, Yorichika Kubota, Syunsuke Magoshi, Hideaki Ogata, Shinsaku Kanazawa, and Fumi Saito
- Subjects
Oncology ,medicine.medical_specialty ,Lung ,Proteinuria ,genetic structures ,Bevacizumab ,Combination therapy ,Anthracycline ,business.industry ,Hematology ,medicine.disease ,Metastatic breast cancer ,eye diseases ,medicine.anatomical_structure ,Internal medicine ,Invasive lobular carcinoma ,medicine ,medicine.symptom ,skin and connective tissue diseases ,business ,Lymph node ,medicine.drug - Abstract
Introduction American Food and Drug Administration canceled the adaptation of bevacizumab approved in February 2008 for HER2 negative untreated metastatic breast cancer in November 2011. But in Japan, bevacizumab effect was approved for inoperability or recurrent breast cancer in September, 2011. Cases Three cases of Luminal A recurrence breast cancers were treated with bevacizumab combination therapy. In all cases, anthracycline were already given. Case 1: invasive ductal carcinoma, premenopause woman, FEC100 followed DTX was carried out after operation. Lymph node recurrence occurred, and bevacizumab combination therapy was carried out. Case 2: invasive lobular carcinoma, post-menopause woman, operation was carried out after FEC100 followed DTX as primary systemic chemotherapy. Bone and metastases to uterus occurred, and bevacizumab combination therapy was carried out. Case 3: invasive ductal carcinoma, post-menopause woman, operation was carried out after FEC100 followed DTX as primary systemic chemotherapy. Metastases to lung occurred, and bevacizumab combination therapy was carried out. Results In all cases no side-effects such as high blood pressure nor proteinuria that peculiar to bevacizumab were shown and treatments were successful. Discussion It was considered that bevacizumab combination therapy was one of the treatment preferences for the HER2-negative recurrence breast cancers.
- Published
- 2012
134. Structure of [NiFe] hydrogenase fromAllochromatium vinosumin its Ni-A state
- Author
-
P. Kellers, Wolfgang Lubitz, and Hideaki Ogata
- Subjects
Crystallography ,Materials science ,Structural Biology ,Allochromatium vinosum ,Crystal structure ,NiFe hydrogenase - Published
- 2011
135. Comparison of CEUS with Enhanced MR-Mammography in Patients with Breast Cancer
- Author
-
Hironori Kaneko, Nobuyuki Shiraga, Hideaki Ogata, Aki Mitsuda, Yukio Mitsuzuka, Tetsuo Nemoto, Tsutomu Hatori, Syunsuke Magoshi, Fumi Saito, Kazutoshi Shibuya, and Shinsaku Kanazawa
- Subjects
Oncology ,medicine.medical_specialty ,Acoustics and Ultrasonics ,Radiological and Ultrasound Technology ,business.industry ,Biophysics ,medicine.disease ,Breast cancer ,Internal medicine ,medicine ,Radiology, Nuclear Medicine and imaging ,In patient ,Radiology ,business ,Mr mammography - Published
- 2011
136. 1121: Contrast Enhanced Ultrasound of the Breast Using Sonazoid
- Author
-
Kazutoshi Shibuya, Nobuyasu Shiraga, Yukio Mitsuzuka, Tutomu Hatori, Aki Mitsuta, Hideaki Ogata, Shinsaku Kanazawa, and Hironori Kaneko
- Subjects
Acoustics and Ultrasonics ,Radiological and Ultrasound Technology ,business.industry ,Biophysics ,Medicine ,Radiology, Nuclear Medicine and imaging ,Nuclear medicine ,business ,Contrast-enhanced ultrasound - Published
- 2009
137. 1464: Availability of Contrast Enhanced Ultrasound Using Sonazoid for the Breast Cancer Patients Treated with Neoadjuvant Chemotherapy
- Author
-
Kazutoshi Shibuya, Hironori Kaneko, Yukio Mitsuzuka, Syunsuke Magoshi, Shinsaku Kanazawa, Hideaki Ogata, Aki Mitsuda, and Tsutomu Hatori
- Subjects
Oncology ,medicine.medical_specialty ,Chemotherapy ,Acoustics and Ultrasonics ,Radiological and Ultrasound Technology ,business.industry ,medicine.medical_treatment ,Biophysics ,medicine.disease ,Breast cancer ,Internal medicine ,medicine ,Radiology, Nuclear Medicine and imaging ,Radiology ,business ,Contrast-enhanced ultrasound - Published
- 2009
138. Liver Metastasis of a Triple-Negative Breast Cancer and Complete Remission for 5 Years After Treatment With Combined Bevacizumab/Paclitaxel/Carboplatin: Case Report and Review of the Literature.
- Author
-
Hideaki Ogata, Yoshihiro Kikuchi, Kazuhiko Natori, Nobuyuki Shiraga, Masahiro Kobayashi, Shunsuke Magoshi, Fumi Saito, Tadatoshi Osaku, Shinsaku Kanazawa, Yorichika Kubota, Yoshie Murakami, Hironori Kaneko, Ogata, Hideaki, Kikuchi, Yoshihiro, Natori, Kazuhiko, Shiraga, Nobuyuki, Kobayashi, Masahiro, Magoshi, Shunsuke, Saito, Fumi, and Osaku, Tadatoshi
- Published
- 2015
- Full Text
- View/download PDF
139. Role of the non-protein ligand at the Ni-Fe active site of [NiFe] hydrogenase
- Author
-
Hirofumi Komori, Hideaki Ogata, A. Nakahara, Shun Hirota, Yoshiki Higuchi, and Naoki Shibata
- Subjects
Hydrogenase ,biology ,Structural Biology ,Stereochemistry ,Chemistry ,biology.protein ,Active site ,NiFe hydrogenase ,Protein ligand - Abstract
Hydrogenase Yoshiki Higuchi, Hideaki Ogata, Shun Hirota, Asuka Nakahara, Hirofumi Komori, Naoki Shibata, Max-Planck-Institut fur Bioanorganische Chemie, Mulheim, Germany. Department of Life Science, University of Hyogo, Koto, Kamigori-cho, Ako-gun, Hyogo. Department of Physical Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto. RIKEN Harima Institute/SPring-8, Mikazuki-cho, Sayo-gun, Hyogo, Japan. E-mail: hig@sci.uhyogo.ac.jp
- Published
- 2005
140. 3P012 X-ray structural study of the activation mechanisim of the active site of [NiFe]hydrogenase
- Author
-
Naoki Shibata, Shun Hirota, Hirofumi Komori, Yoshiki Higuchi, N. Miyabe, A. Nakahara, and Hideaki Ogata
- Subjects
Crystallography ,Materials science ,biology ,biology.protein ,X-ray ,Active site ,NiFe hydrogenase - Published
- 2005
141. 2P087 Analysis of the interaction between cytochrome c_3 and its physiological partner [NiFe] hydrogenase
- Author
-
Yuki Takayama, T. Saitoh, Hideaki Ogata, Kiyoshi Ozawa, Hideo Akutsu, Naoki Yahata, Yoshiki Higuchi, and A. Nakahara
- Subjects
Cytochrome ,biology ,Stereochemistry ,Chemistry ,biology.protein ,NiFe hydrogenase - Published
- 2004
142. Structural Chemistry of two different states (Ni-A and Ni-B states) of [NiFe]hydrogenase
- Author
-
Naoki Shibata, Shun Hirota, Hideaki Ogata, Yoshiki Higuchi, and A. Nakahara
- Subjects
Crystallography ,Materials science ,NiFe hydrogenase ,Structural chemistry - Published
- 2003
143. New aspects of the structural and spectroscopic chemistry on [NiFe]hydrogenase
- Author
-
T. Yagi, Hideaki Ogata, Yoshiki Higuchi, Shun Hirota, Shin-ichi Adachi, and N. Yasuoka
- Subjects
Hydrogenase ,Structural Biology ,Chemistry ,NiFe hydrogenase ,Combinatorial chemistry - Published
- 2002
144. 1L1645 The structural and spectroscopic chemistry on [NiFe]hydrogenase
- Author
-
Shun Hirota, Noritake Yasuoka, T. Yagi, Yoshiki Higuchi, and Hideaki Ogata
- Subjects
Chemistry ,NiFe hydrogenase ,Photochemistry - Published
- 2002
145. Assignement of the substrate (hydrogen molecule) at the active site of [NiFe] hydrogenase
- Author
-
Yoshiki Higuchi, T. Yagi, Hideaki Ogata, Kunio Miki, Noritake Yasuoka, Shin-ichi Adachi, and N. Mizuno
- Published
- 2000
146. Immunohistochemical study for PIVKA-II in hepatocellular carcinoma
- Author
-
Kenji Hirai, Shotaro Sakisaka, Yasuo Majima, Hideaki Ogata, Ryuichi Nouno, Kyuichi Tanikawa, and Masao Yoshitake
- Subjects
Pathology ,medicine.medical_specialty ,Hepatology ,business.industry ,Hepatocellular carcinoma ,Medicine ,Immunohistochemistry ,business ,medicine.disease - Published
- 1990
147. Expression, Purification, and Solid-State NMR Characterization of the Membrane Binding Heme Protein Nitrophorin 7 in Two Electronic Spin States.
- Author
-
Varghese, Sabu, Fei Yang, Pacheco, Victor, Wrede, Kathrin, Medvedev, Alexander, Hideaki Ogata, Knipp, Markus, and Heise, Henrike
- Published
- 2013
- Full Text
- View/download PDF
148. [NiFe] hydrogenases: structural and spectroscopic studies of the reaction mechanism.
- Author
-
Hideaki Ogata, Wolfgang Lubitz, and Yoshiki Higuchi
- Subjects
- *
HYDROGENASE , *REACTION mechanisms (Chemistry) , *MOLECULAR structure , *TRANSITION metal complexes , *OXIDATION-reduction reaction , *METAL catalysts , *CHARGE exchange , *COMPLEX compounds synthesis - Abstract
[NiFe] hydrogenases catalyze the reversible oxidation of dihydrogen. For this simple reaction the molecule has developed a complex catalytic mechanism, during which the enzyme passes through various redox states. The [NiFe] hydrogenase contains several metal centres, including the bimetallic Ni–Fe active site, iron–sulfur clusters and a Mg2+ion. The Ni–Fe active site is located in the inner part of the protein molecule, therefore a number of pathways are involved in the catalytic reaction route. These consist of an electron transfer pathway, a proton transfer pathway and a gas-access channel. Over the last 10–15 years we have been investigating the crystal structures of the [NiFe] hydrogenase from Desulfovibrio vulgarisMiyazaki F, which is a sulfate-reducing anaerobic bacterium. So far the crystal structures of the oxidized, H2-reduced and carbon monoxide inhibited states have been determined at high resolution and have revealed a rather unique structure of the hetero-bimetallic Ni–Fe active site. Furthermore, intensive spectroscopic studies have been performed on the enzyme. Based on the crystal structure, a water-soluble Ni–Ru complex has been synthesized as a functional model for the [NiFe] hydrogenases. The present review gives an overview of the catalytic reaction mechanism of the [NiFe] hydrogenases. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
149. Prognostic significance of the F-box protein Skp2 expression in diffuse large B-cell lymphoma.
- Author
-
Ritsuko Seki, Takashi Okamura, Hironori Koga, Kazuaki Yakushiji, Michitoshi Hashiguchi, Kohji Yoshimoto, Hideaki Ogata, Rie Imamura, Yutaka Nakashima, Masayoshi Kage, Takato Ueno, and Michio Sata
- Published
- 2003
- Full Text
- View/download PDF
150. Inhibition of the [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F by carbon monoxide: An FTIR and EPR spectroscopic study
- Author
-
Leslie J. Currell, Maria-Eirini Pandelia, Hideaki Ogata, Marco Flores, and Wolfgang Lubitz
- Subjects
Hydrogenase ,Light ,Antimetabolites ,Inorganic chemistry ,Biophysics ,chemistry.chemical_element ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Redox ,law.invention ,Carbon monoxide inhibition ,chemistry.chemical_compound ,Nickel ,law ,Spectroscopy, Fourier Transform Infrared ,[NiFe] hydrogenase ,Desulfovibrio vulgaris ,Electron paramagnetic resonance ,Carbon Monoxide ,biology ,010405 organic chemistry ,Photodissociation ,Electron Spin Resonance Spectroscopy ,Active site ,Spectro-electrochemistry ,Cell Biology ,biology.organism_classification ,0104 chemical sciences ,Kinetics ,Crystallography ,Models, Chemical ,chemistry ,biology.protein ,Rapid-scan FTIR ,EPR ,Carbon monoxide - Abstract
X-ray crystallographic studies [Ogata et al., J. Am. Chem. Soc. 124 (2002) 11628–11635] have shown that carbon monoxide binds to the nickel ion at the active site of the [NiFe] hydrogenase from Desulfovibriovulgaris Miyazaki F and inhibits its catalytic function. In the present work spectroscopic aspects of the CO inhibition for this bacterial organism are reported for the first time and enable a direct comparison with the existing crystallographic data. The binding affinity of each specific redox state for CO is probed by FTIR spectro-electrochemistry. It is shown that only the physiological state Ni–SIa reacts with CO. The CO-inhibited product state is EPR-silent (Ni2+) and exists in two forms, Ni–SCO and Ni–SCOred. At very negative potentials, the exogenous CO is electrochemically detached from the active site and the active Ni–R states are obtained. At temperatures below 100 K, photodissociation of the extrinsic CO from the Ni–SCO state results in Ni–SIa that is identified to be the only light-induced state. In the dark, rebinding of CO takes place; the recombination rate constants are of biexponential character and the activation barrier is determined to be approximately 9 kJ mol−1. In addition, formation of a paramagnetic CO-inhibited state (Ni–CO) was observed that results from the interaction of carbon monoxide with the Ni–L state. It is proposed that the nickel in Ni–CO is in a formal monovalent state (Ni1+).
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.