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Deisenhofer J, Epp O, Miki K, Huber R, Michel H. X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis. J Mol Biol 1984; 180:385-98. [PMID: 6392571 DOI: 10.1016/s0022-2836(84)80011-x] [Citation(s) in RCA: 1284] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
X-ray analysis of three-dimensional crystals of the photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis led to an electron density distribution at 3 A resolution calculated with phases from multiple isomorphous replacement. The protein subunits of the complex were identified. An atomic model of the prosthetic groups of the reaction center complex (4 bacteriochlorophyll b, 2 bacteriopheophytin b. 1 non-heme iron, 1 menaquinone, 4 heme groups) was built. The arrangement of the ring systems of the bacteriochlorophyll b and bacteriopheophytin b molecules shows a local 2-fold rotation symmetry; two bacteriochlorophyll b form a closely associated, non-covalently linked dimer ("special pair"). A different local 2-fold symmetry axis is observed for the heme groups of the cytochrome part.
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Tsujino H, Kondo E, Fukuoka T, Dai Y, Tokunaga A, Miki K, Yonenobu K, Ochi T, Noguchi K. Activating transcription factor 3 (ATF3) induction by axotomy in sensory and motoneurons: A novel neuronal marker of nerve injury. Mol Cell Neurosci 2000; 15:170-82. [PMID: 10673325 DOI: 10.1006/mcne.1999.0814] [Citation(s) in RCA: 623] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Activating transcription factor 3 (ATF3), a member of ATF/CREB family of transcription factors, is induced in a variety of stressed tissue. ATF3 regulates transcription by binding to DNA sites as a homodimer or heterodimer with Jun proteins. The purpose of this study was to examine the expression and regulation of ATF3 after axonal injury in neurons in dorsal root ganglia (DRG) and spinal cord. In naive rats, ATF3 was not expressed in the DRG and spinal cord. Following the cut of peripheral nerve, ATF3 was immediately induced in virtually all DRG neurons and motoneurons that were axotomized, and the time course of induction was dependent on the distance between the injury site and the cell body. Double labeling using immunohistochemistry revealed that the population of DRG neurons expressing ATF3 included those expressing c-jun, and in motoneurons ATF3 and c-jun were concurrently expressed after axotomy. In contrast to c-jun, ATF3 was not induced transsynaptically in spinal dorsal horn neurons. We conclude that ATF3 is specifically induced in sensory and motoneurons in the spinal cord following nerve injury and should be regarded as an unique neuronal marker of nerve injury in the nervous system.
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Misumi Y, Misumi Y, Miki K, Takatsuki A, Tamura G, Ikehara Y. Novel blockade by brefeldin A of intracellular transport of secretory proteins in cultured rat hepatocytes. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67398-3] [Citation(s) in RCA: 597] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Dinis-Ribeiro M, Areia M, de Vries AC, Marcos-Pinto R, Monteiro-Soares M, O'Connor A, Pereira C, Pimentel-Nunes P, Correia R, Ensari A, Dumonceau JM, Machado JC, Macedo G, Malfertheiner P, Matysiak-Budnik T, Megraud F, Miki K, O'Morain C, Peek RM, Ponchon T, Ristimaki A, Rembacken B, Carneiro F, Kuipers EJ. Management of precancerous conditions and lesions in the stomach (MAPS): guideline from the European Society of Gastrointestinal Endoscopy (ESGE), European Helicobacter Study Group (EHSG), European Society of Pathology (ESP), and the Sociedade Portuguesa de Endoscopia Digestiva (SPED). Endoscopy 2012; 44:74-94. [PMID: 22198778 PMCID: PMC3367502 DOI: 10.1055/s-0031-1291491] [Citation(s) in RCA: 475] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Atrophic gastritis, intestinal metaplasia, and epithelial dysplasia of the stomach are common and are associated with an increased risk for gastric cancer. In the absence of guidelines, there is wide disparity in the management of patients with these premalignant conditions. The European Society of Gastrointestinal Endoscopy (ESGE), the European Helicobacter Study Group (EHSG), the European Society of Pathology (ESP) and the Sociedade Portuguesa de Endoscopia Digestiva (SPED) have therefore combined efforts to develop evidence-based guidelines on the management of patients with precancerous conditions and lesions of the stomach (termed MAPS). A multidisciplinary group of 63 experts from 24 countries developed these recommendations by means of repeat online voting and a meeting in June 2011 in Porto, Portugal. The recommendations emphasize the increased cancer risk in patients with gastric atrophy and metaplasia, and the need for adequate staging in the case of high grade dysplasia, and they focus on treatment and surveillance indications and methods.
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475 |
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Asaka M, Kimura T, Kudo M, Takeda H, Mitani S, Miyazaki T, Miki K, Graham DY. Relationship of Helicobacter pylori to serum pepsinogens in an asymptomatic Japanese population. Gastroenterology 1992; 102:760-6. [PMID: 1537513 DOI: 10.1016/0016-5085(92)90156-s] [Citation(s) in RCA: 409] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A seroepidemiologic study of the prevalence of Helicobacter pylori infection in Japan was performed, and the relationship between serum pepsinogen I and II levels (markers of gastritis and gastric atrophy) and H. pylori infection was investigated. Four hundred and eighteen asymptomatic children and adults were studied. The prevalence of anti-H. pylori immunoglobulin G antibody increased with age. For persons born after 1950, the frequency of H. pylori infection increased at approximately 1% per year; for those born before 1950 the prevalence was high (70%-80%) and relatively constant. Serum pepsinogen I and II levels were significantly higher in H. pylori-infected volunteers than in H. pylori-uninfected volunteers [51.6 +/- 3 vs. 42.9 +/- 2 ng/mL (P less than 0.05) for pepsinogen I; 16.0 +/- 1 vs. 7.5 +/- 0.8 ng/mL (P less than 0.001) for pepsinogen II]. The ratio of pepsinogen I to pepsinogen II was significantly lower in H. pylori-infected volunteers (3.5 +/- 0.2) than in uninfected volunteers (6.3 +/- 0.3; P less than 0.001). The apparent decrease in prevalence of H. pylori accompanying the Westernization of Japan may eventually be accompanied by a reduction in the frequency of atrophic gastritis, the precursor lesion of the epidemic form of gastric carcinoma, and ultimately result in a decrease in the incidence of gastric carcinoma in Japan.
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409 |
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Fukasawa M, Miura T, Hasegawa A, Morikawa S, Tsujimoto H, Miki K, Kitamura T, Hayami M. Sequence of simian immunodeficiency virus from African green monkey, a new member of the HIV/SIV group. Nature 1988; 333:457-61. [PMID: 3374586 DOI: 10.1038/333457a0] [Citation(s) in RCA: 285] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Some wild African green monkeys are known to be naturally infected with a retrovirus related to human immunodeficiency virus (HIV) without having any apparent symptoms of an AIDS-like disease. This simian immunodeficiency virus, designated SIVAGM, may be helpful in clarifying the evolution and pathogenicity of HIV. Some virus strains that were previously reported to be isolated from African green monkeys were shown to be laboratory contaminations of SIVMAC (SIV from a rhesus macaque) Here we report the complete DNA sequence of authentic SIVAGM, which was isolated from a naturally infected African green monkey of Kenyan origin. Comparison of the genome of SIVAGM with those of known HIV/SIVs indicates that the virus is a new simian lentivirus that is approximately equally distantly related to HIV-1 and HIV-2 in contrast to SIVMAC, which is much closer to HIV-2 than to HIV-1 (refs 5, 9).
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Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S. Structural genomics projects in Japan. NATURE STRUCTURAL BIOLOGY 2000; 7 Suppl:943-5. [PMID: 11103994 DOI: 10.1038/80712] [Citation(s) in RCA: 280] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Two major structural genomics projects exist in Japan. The oldest, the RIKEN Structural Genomics Initiative, has two major goals: to determine bacterial, mammalian, and plant protein structures by X-ray crystallography and NMR spectroscopy and to perform functional analyses with the target proteins. The newest, the structural genomics project at the Biological Information Research Center, focuses on human membrane proteins.
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Higuchi Y, Ogata H, Miki K, Yasuoka N, Yagi T. Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure 1999; 7:549-56. [PMID: 10378274 DOI: 10.1016/s0969-2126(99)80071-9] [Citation(s) in RCA: 242] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND The active site of [NiFe] hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in Desulfovibrio vulgaris Miyazaki F hydrogenase. RESULTS The X-ray crystal structure of the reduced form of D. vulgaris Miyazaki F [NiFe] hydrogenase has been solved at 1.4 A resolution and refined to a crystallographic R factor of 21.8%. The overall structure is very similar to that of the oxidized form, with the exception that the third monatomic bridge observed at the Ni-Fe site in the oxidized enzyme is absent, leaving this site unoccupied in the reduced form. CONCLUSIONS The unusual ligand structure found in the oxidized form of D. vulgaris Miyazaki F [NiFe] hydrogenase was confirmed in the reduced form of the enzyme, with the exception that the electron density assigned to the monatomic sulfur bridge had almost disappeared. On the basis of this finding, as well as the observation that H2S is liberated from the oxidized enzyme under an atmosphere of H2 in the presence of its electron carrier, it was postulated that the monatomic sulfur bridge must be removed for the enzyme to be activated. A possible mechanism for the catalytic action of the hydrogenase is proposed.
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Miki K, Ichinose M, Shimizu A, Huang SC, Oka H, Furihata C, Matsushima T, Takahashi K. Serum pepsinogens as a screening test of extensive chronic gastritis. GASTROENTEROLOGIA JAPONICA 1987; 22:133-41. [PMID: 3596151 DOI: 10.1007/bf02774209] [Citation(s) in RCA: 216] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The serum level of pepsinogen I (PG I) and pepsinogen II (PG II), and the PG I/PG II ratio were compared with the surface area of the fundic mucosa, as determined endoscopically by the Congo red staining method. Reduction in the area of the fundic mucosa due to gastritis was associated with stepwise reduction in the PG I levels and the PG I/PG II ratios. Reduction in the area of the fundic mucosa was also associated with decreases in the basal acid output, maximal acid output (MAO), the basal pepsin output and the stimulated pepsin output. The best sensitivity and specificity levels for the diagnosis of normal mucosa and severe gastritis were obtained with the PG I/PG II ratio and the MAO. A retrospective study of 58 patients with gastric cancer and 162 cancer-free patients showed that a PG I/PG II ratio identified 86.2% of all carcinomas and 87.5% of early carcinomas. Although this test gave a positive rate of 36% among the cancer-susceptible age group controls, its use would lower the cost of mass screening by targeting a smaller test population.
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Kubota K, Makuuchi M, Kusaka K, Kobayashi T, Miki K, Hasegawa K, Harihara Y, Takayama T. Measurement of liver volume and hepatic functional reserve as a guide to decision-making in resectional surgery for hepatic tumors. Hepatology 1997; 26:1176-81. [PMID: 9362359 DOI: 10.1053/jhep.1997.v26.pm0009362359] [Citation(s) in RCA: 198] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The respective volumes of hepatic tumors and nontumorous parenchyma of 50 patients requiring hepatectomy of more than one segment of Healey for tumor removal were measured using computed tomography (Vol-CT). The volume estimated by Vol-CT was found to correlate with the real weight resected (P < .0001) with a mean absolute error of 64.9 mL. The ratio of the nontumorous parenchymal volume of the resected liver to that of the whole liver (R2) in 15 patients who underwent right or extended right hepatic lobectomy was 43% +/- 15%. Eight of 15 patients with R2s < 60% underwent the procedures without right portal vein embolization (PE). The other seven with R2s exceeding 60% or an indocyanine green retention rate after 15 minutes (ICG15) of 10% to 20% underwent PE: in six of seven, the nontumorous parenchyma of the right hepatic lobe became atrophic and in all seven, the volume of the remaining left hepatic lobe increased with a decrease in the mean R2 from 62% +/- 14% to 55% +/- 8% (P = .0006). In the remaining 35 who underwent other hepatectomy procedures, R2s also remained <60%. Overall, at surgery, in 27 with normal liver function (ICG15 < 10%), R2s exceeded 60% in one, remained at 50% to 60% in five, and <50% in 21, whereas 23 patients except for one with an ICG15 exceeding 10%, had R2s of <50%. The postoperative serum total bilirubin levels in 84% of the patients remained within the normal range and there was no surgery-related mortality. In conclusion, 1) Vol-CT can accurately assess the extent of liver resection, 2) individuals with normal liver function can undergo resection of up to 60% of the nontumorous parenchyma without the need for PE, and 3) PE can be used to reduce the size of the resected tissue and increase the volume of the remnant liver to approximate the target limits in individuals with large tumors or minimally abnormal liver function.
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Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K. Crystal structure of DNA photolyase from Anacystis nidulans. NATURE STRUCTURAL BIOLOGY 1997; 4:887-91. [PMID: 9360600 DOI: 10.1038/nsb1197-887] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The crystal structure at 1.8 A resolution of 8-HDF type photolyase from A. nidulans shows a backbone structure similar to that of MTHF type E. coli photolyase but reveals a completely different binding site for the light-harvesting cofactor.
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171 |
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Asaka M, Kimura T, Kato M, Kudo M, Miki K, Ogoshi K, Kato T, Tatsuta M, Graham DY. Possible role of Helicobacter pylori infection in early gastric cancer development. Cancer 1994; 73:2691-4. [PMID: 8194007 DOI: 10.1002/1097-0142(19940601)73:11<2691::aid-cncr2820731107>3.0.co;2-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND Gastric cancer is the most frequently diagnosed malignancy in Japan. The possible relationship between Helicobacter pylori infection and gastric cancer in Japan was evaluated. METHODS H. pylori infection was identified by the presence of anti-H. pylori IgG. The frequency of H. pylori infection was compared in 213 patients with gastric cancer and the same number of asymptomatic control subjects matched for age and sex. RESULTS The presence of IgG antibody to H. pylori was significantly more prevalent (P < 0.001) in those with gastric cancer compared with asymptomatic control subjects (88.2% versus 74.6%). H. pylori positive rates were significantly greater in patients with the intestinal type (90.4%, P < 0.001) and diffuse type (86.4%, P < 0.05) of gastric cancer than in control subjects. Ninety-three percent of the patients with early gastric cancer tested positive for H. pylori (P < 0.001 compared with control subjects), whereas no significant difference was observed between those with advanced gastric cancer and control subjects. The intestinal type of early gastric cancer showed only the significantly increased frequency of high titer (optical density > 1.50) of H. pylori IgG antibody (P < 0.001) compared with control subjects without cancer. CONCLUSIONS These results suggest that H. pylori infection may be associated with the development of early gastric cancer in Japan.
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Dinis-Ribeiro M, Yamaki G, Miki K, Costa-Pereira A, Matsukawa M, Kurihara M. Meta-analysis on the validity of pepsinogen test for gastric carcinoma, dysplasia or chronic atrophic gastritis screening. J Med Screen 2005; 11:141-7. [PMID: 15333273 DOI: 10.1258/0969141041732184] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AIM To assess the validity of the measurement of pepsinogen I and II as a screening test for gastric cancer and pre-malignant lesions, namely low-grade dysplasia, both in the general population and in selected groups of patients. METHODS A meta-analysis of sensitivity and specificity results from individual papers on the use of the pepsinogen test. An intrinsic cut-off effect was assumed and a random effect model was used for pooling. RESULTS Forty-two data sets were included: 27 (64%) population-based screening studies (n=296,553) and 15 (36%) sets of selected individuals (n=4385). Homogenous sensitivity and diagnostic odds ratio (DOR) estimates were found in studies using both pepsinogen I levels and pepsinogen I/II ratio calculations. Pooled pairs of sensitivity and false positive rates (FPr) for pepsinogen I < or = 70; pepsinogen I/II ratio < or = 3, pepsinogen I < or =50; pepsinogen I/II ratio < or = 3, and pepsinogen I < or = 30; pepsinogen I/II ratio < or = 2, were sensitivity 77%/FPr 27%, sensitivity 68%/FPr 31%, and sensitivity 52%/FPr 84%, respectively. Positive predictive values (PPV) varied between 0.77% and 1.25%, and negative predictive values (NPV) varied between 99.08% and 99.90%. In selected groups, pooling was only possible when considering pepsinogen I < or = 70; pepsinogen I/II ratio < or = 3: giving sensitivity 57%, specificity 80%, PPV 15% and NPV 83%. As for the diagnosis of dysplasia, studies considering pepsinogen I <50; pepsinogen I/II ratio <3 obtained sensitivity 65% and specificity ranging from 74%-85%, both with NPV >95%. CONCLUSION Pepsinogen test definition should include pepsinogen I/II ratio as consistency was obtained, both in population based studies and in selected groups for those studies that used pepsinogen I serum levels together with pepsinogen I/II ratio for screening for gastric cancer in high-incidence regions other than Japan. Further studies of this test in the management of high-risk patients seem to be worthwhile.
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Research Support, Non-U.S. Gov't |
20 |
146 |
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Ohkura N, Hijikuro M, Yamamoto A, Miki K. Molecular cloning of a novel thyroid/steroid receptor superfamily gene from cultured rat neuronal cells. Biochem Biophys Res Commun 1994; 205:1959-65. [PMID: 7811288 DOI: 10.1006/bbrc.1994.2900] [Citation(s) in RCA: 143] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Brain neuronal cells in primary culture provide one system for the analysis of neuronal development, including apoptosis. By PCR amplification, with primers designed from conserved sequences among nuclear receptors, a novel member of the thyroid/steroid receptor superfamily was identified from forebrain neuronal cells undergoing apoptosis and designated as NOR-1 (neuron derived orphan receptor). A cDNA clone of NOR-1 encodes a 68kDa, 628 amino acid residue-containing protein, with an amino acid sequence highly homologous to the Nur77 family in its DNA-binding domain and moderately so in its putative ligand-binding domain. Using mobility shift assay, we showed that the NOR-1 protein binds to the B1a response-element which has been identified as the target sequence of the Nur77 family, suggesting that three members of the Nur77 family may transactivate common target gene(s) at different situations.
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MESH Headings
- Amino Acid Sequence
- Animals
- Apoptosis
- Base Sequence
- Cells, Cultured
- Cloning, Molecular
- DNA Primers/genetics
- DNA, Complementary/genetics
- DNA-Binding Proteins/genetics
- Molecular Sequence Data
- Multigene Family
- Nerve Tissue Proteins
- Neurons/cytology
- Neurons/metabolism
- Nuclear Proteins/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 1
- Nuclear Receptor Subfamily 4, Group A, Member 2
- Polymerase Chain Reaction
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Receptors, Cytoplasmic and Nuclear
- Receptors, Steroid/genetics
- Receptors, Thyroid Hormone/genetics
- Sequence Homology, Amino Acid
- Transcription Factors/genetics
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Ishibashi T, Miki K, Sorgente N, Patterson R, Ryan SJ. Effects of intravitreal administration of steroids on experimental subretinal neovascularization in the subhuman primate. ARCHIVES OF OPHTHALMOLOGY (CHICAGO, ILL. : 1960) 1985; 103:708-11. [PMID: 2581536 DOI: 10.1001/archopht.1985.01050050100026] [Citation(s) in RCA: 135] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To elucidate the role of inflammation in the occurrence of experimental subretinal neovascularization caused by high-intensity laser photocoagulation, we investigated the effects of vitreal infusion of steroids on laser lesions in a primate model. Dexamethasone, with or without triamcinolone, was infused continuously for two weeks through an indwelling cannula system. The animals were followed up clinically for up to eight weeks. The frequency of subretinal neovascularization in the steroid-treated animals was significantly lower than that in a control group of untreated animals. Although steroids have multiple effects, these results suggest that the inflammatory response, possibly macrophage infiltration, may plan an important role in the occurrence of subretinal neovascularization in our experimental model.
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Nogi T, Fathir I, Kobayashi M, Nozawa T, Miki K. Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer. Proc Natl Acad Sci U S A 2000; 97:13561-6. [PMID: 11095707 PMCID: PMC17615 DOI: 10.1073/pnas.240224997] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reaction center (RC) of photosynthetic bacteria is a membrane protein complex that promotes a light-induced charge separation during the primary process of photosynthesis. In the photosynthetic electron transfer chain, the soluble electron carrier proteins transport electrons to the RC and reduce the photo-oxidized special-pair of bacteriochlorophyll. The high-potential iron-sulfur protein (HiPIP) is known to serve as an electron donor to the RC in some species, where the c-type cytochrome subunit, the peripheral subunit of the RC, directly accepts electrons from the HiPIP. Here we report the crystal structures of the RC and the HiPIP from Thermochromatium (Tch.) tepidum, at 2.2-A and 1.5-A resolution, respectively. Tch. tepidum can grow at the highest temperature of all known purple bacteria, and the Tch. tepidum RC shows some degree of stability to high temperature. Comparison with the RCs of mesophiles, such as Blastochloris viridis, has shown that the Tch. tepidum RC possesses more Arg residues at the membrane surface, which might contribute to the stability of this membrane protein. The RC and the HiPIP both possess hydrophobic patches on their respective surfaces, and the HiPIP is expected to interact with the cytochrome subunit by hydrophobic interactions near the heme-1, the most distal heme to the special-pair.
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research-article |
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128 |
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Fujihashi M, Zhang YW, Higuchi Y, Li XY, Koyama T, Miki K. Crystal structure of cis-prenyl chain elongating enzyme, undecaprenyl diphosphate synthase. Proc Natl Acad Sci U S A 2001; 98:4337-42. [PMID: 11287651 PMCID: PMC31836 DOI: 10.1073/pnas.071514398] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2000] [Indexed: 11/18/2022] Open
Abstract
Undecaprenyl diphosphate synthase (UPS) catalyzes the cis-prenyl chain elongation onto trans, trans-farnesyl diphosphate (FPP) to produce undecaprenyl diphosphate (UPP), which is indispensable for the biosynthesis of bacterial cell walls. We report here the crystal structure of UPS as the only three-dimensional structure among cis-prenyl chain elongating enzymes. The structure is classified into a protein fold family and is completely different from the so-called "isoprenoid synthase fold" that is believed to be a common structure for the enzymes relating to isoprenoid biosynthesis. Conserved amino acid residues among cis-prenyl chain elongating enzymes are located around a large hydrophobic cleft in the UPS structure. A structural P-loop motif, which frequently appears in the various kinds of phosphate binding site, is found at the entrance of this cleft. The catalytic site is determined on the basis of these structural features, from which a possible reaction mechanism is proposed.
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Kita A, Kita S, Fujisawa I, Inaka K, Ishida T, Horiike K, Nozaki M, Miki K. An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2. Structure 1999; 7:25-34. [PMID: 10368270 DOI: 10.1016/s0969-2126(99)80006-9] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Catechol dioxygenases catalyze the ring cleavage of catechol and its derivatives in either an intradiol or extradiol manner. These enzymes have a key role in the degradation of aromatic molecules in the environment by soil bacteria. Catechol 2, 3-dioxygenase catalyzes the incorporation of dioxygen into catechol and the extradiol ring cleavage to form 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase (metapyrocatechase, MPC) from Pseudomonas putida mt-2 was the first extradiol dioxygenase to be obtained in a pure form and has been studied extensively. The lack of an MPC structure has hampered the understanding of the general mechanism of extradiol dioxygenases. RESULTS The three-dimensional structure of MPC has been determined at 2.8 A resolution by the multiple isomorphous replacement method. The enzyme is a homotetramer with each subunit folded into two similar domains. The structure of the MPC subunit resembles that of 2,3-dihydroxybiphenyl 1,2-dioxygenase, although there is low amino acid sequence identity between these enzymes. The active-site structure reveals a distorted tetrahedral Fe(II) site with three endogenous ligands (His153, His214 and Glu265), and an additional molecule that is most probably acetone. CONCLUSIONS The present structure of MPC, combined with those of two 2,3-dihydroxybiphenyl 1,2-dioxygenases, reveals a conserved core region of the active site comprising three Fe(II) ligands (His153, His214 and Glu265), one tyrosine (Tyr255) and two histidine (His199 and His246) residues. The results suggest that extradiol dioxygenases employ a common mechanism to recognize the catechol ring moiety of various substrates and to activate dioxygen. One of the conserved histidine residues (His199) seems to have important roles in the catalytic cycle.
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Renganathan V, Miki K, Gold MH. Multiple molecular forms of diarylpropane oxygenase, an H2O2-requiring, lignin-degrading enzyme from Phanerochaete chrysosporium. Arch Biochem Biophys 1985; 241:304-14. [PMID: 4026322 DOI: 10.1016/0003-9861(85)90387-x] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Three different molecular forms of the H2O2-requiring heme enzyme, diarylpropane oxygenase, were isolated from the extracellular medium of Na-acetate buffered, agitated cultures of Phanerochaete chrysosporium. Forms I, II, and III were separated by DEAE-Sepharose and further purified on Sephadex G-100. Absorption maxima of the native, reduced, and a variety of ligand complexes of the three enzyme forms are essentially identical, indicating similar heme environments. All forms also have similar, but not identical, reactivity. The homogeneous proteins oxidized a diarylpropane, an olefin, a beta-aryl ether dimer, a phenylpropane, phenylpropane diols, and veratryl alcohol. Identical products were produced from each form. However, the specific activities of the three homogeneous enzymes for veratryl alcohol oxidation were 18.75, 11.80, and 8.48 mumol min-1 mg-1. In the presence of one equivalent of H2O2 the Soret maximum of diarylpropane oxygenase II shifted from 408 to 418 nm, and two additional maxima appeared at 526 and 553 nm, indicating the presence of an Fe(IV)-oxo species equivalent to horseradish peroxidase II. This oxidized species could be reduced back to the native form by veratryl alcohol and several reducing agents (e.g., Na2S2O4, NH2NH2, thiourea, or NADH). The molecular weights of diarylpropane oxygenases I, II, and III were approximately 39,000, 41,000, and 43,000, respectively. The major form (II) (85% of the activity) contained approximately 6% neutral carbohydrate. The affinity of the forms for concanavalin A-agarose suggests that they all are glycoenzymes.
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Miki K, Fukuoka T, Tokunaga A, Noguchi K. Calcitonin gene-related peptide increase in the rat spinal dorsal horn and dorsal column nucleus following peripheral nerve injury: up-regulation in a subpopulation of primary afferent sensory neurons. Neuroscience 1998; 82:1243-52. [PMID: 9466443 DOI: 10.1016/s0306-4522(97)00258-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Calcitonin gene-related peptide in sensory primary afferent neurons has an excitatory effect on postsynaptic neurons and potentiates the effect of substance P in the rat spinal dorsal horn. It has been established that calcitonin gene-related peptide expression in dorsal root ganglion neurons is depressed, and the effect of calcitonin gene-related peptide on dorsal horn neurons is attenuated, following peripheral nerve injury. We report here that a subpopulation of injured dorsal root ganglion neurons show increased expression of calcitonin gene-related peptide. Using in situ hybridization and the retrograde tracer, FluoroGold, we detected an increased number of medium- to large-sized rat dorsal root ganglion neurons projecting to the gracile nucleus that expressed alpha-calcitonin gene-related peptide messenger RNA following spinal nerve transection. Immunohistochemistry revealed a significant increase in calcitonin gene-related peptide immunoreactivity in the gracile nucleus and in laminae III-IV of the spinal dorsal horn. These results indicate that a subpopulation of dorsal root ganglion neurons express alpha-calcitonin gene-related peptide messenger RNA in response to peripheral nerve injury, and transport this peptide to the gracile nucleus and to laminae III-IV of the spinal dorsal horn. The increase of the excitatory neuropeptide, calcitonin gene-related peptide, in sites of primary afferent termination may affect the excitability of postsynaptic neurons, and have a role in neuronal plasticity following peripheral nerve injury.
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Dong ZC, Guo XL, Trifonov AS, Dorozhkin PS, Miki K, Kimura K, Yokoyama S, Mashiko S. Vibrationally resolved fluorescence from organic molecules near metal surfaces in a scanning tunneling microscope. PHYSICAL REVIEW LETTERS 2004; 92:086801. [PMID: 14995803 DOI: 10.1103/physrevlett.92.086801] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Indexed: 05/24/2023]
Abstract
Intrinsic molecular fluorescence from porphyrin molecules on Au(100) has been realized by using a nanoscale multimonolayer decoupling approach with nanoprobe excitation in the tunneling regime. The molecular origin of luminescence is established by the observed well-defined vibrationally resolved fluorescence spectra. The molecules fluoresce at low "turn-on" voltages for both bias polarities, suggesting an excitation mechanism via hot electron injection from either tip or substrate. The excited molecules decay radiatively through Franck-Condon pi(*)-pi transitions.
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Fujiwara H, Tatsumi K, Miki K, Harada T, Miyai K, Takai S, Amino N. Congenital hypothyroidism caused by a mutation in the Na+/I- symporter. Nat Genet 1997; 16:124-5. [PMID: 9171822 DOI: 10.1038/ng0697-124] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Kohri M, Miki K, Waite DE, Nakajima H, Okabe T. In vitro stability of biphasic calcium phosphate ceramics. Biomaterials 1993; 14:299-304. [PMID: 8386558 DOI: 10.1016/0142-9612(93)90122-i] [Citation(s) in RCA: 108] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Biphasic calcium phosphate ceramics consist of both beta-tricalcium phosphate and hydroxyapatite. This study was performed to examine the in vitro stability of biphasic calcium phosphate ceramics in deionized distilled water and in physiological solutions. Biphasic calcium phosphates of two different molar ratios and pure hydroxyapatite and pure beta-tricalcium phosphate granules were tested. X-ray diffraction data were obtained before and after immersion. Surface morphology was compared using scanning electron microscopy. The pure beta-tricalcium phosphate and the beta-tricalcium phosphate in the biphasic calcium phosphate ceramics gradually converted to apatite. Needle-like apatite crystals were observed on the surface of biphasic calcium phosphate and beta-tricalcium phosphate, but hydroxyapatite showed no change.
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Omari TI, Miki K, Fraser R, Davidson G, Haslam R, Goldsworthy W, Bakewell M, Kawahara H, Dent J. Esophageal body and lower esophageal sphincter function in healthy premature infants. Gastroenterology 1995; 109:1757-64. [PMID: 7498639 DOI: 10.1016/0016-5085(95)90741-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND & AIMS Gastroesophageal reflux is a common problem in premature infants. The aim of this study was to use a novel manometric technique to measure esophageal body and lower esophageal sphincter pressures in premature infants. METHODS Micromanometric feeding assemblies (OD, < or = 2 mm) incorporating 4-9 manometric channels were used in 49 studies of 27 premature neonates. Esophageal body motility was recorded at three sites for 20 minutes after feeding. Twenty attempts (one per minute) were made to stimulate swallowing via facial stimulation (Santmyer reflex). In 32 studies lower esophageal sphincter pressures were recorded (sleeve) for 15 minutes before and after feeding. RESULTS Peristaltic motor patterns were less common than non-peristaltic motor patterns (26.6% vs. 73.4%; P < 0.0001) that comprised 31.1% synchronous, 34.6% incomplete, and 6.3% retrograde pressure waves. Reflex swallowing was elicited more frequently in neonates older than 34 weeks postconceptional age than in younger infants (33.4% vs. 20.4%; P < 0.05). Mean lower esophageal sphincter pressure was 20.5 +/- 1.7 mm Hg before and 13.7 +/- 1.3 mm Hg after feeding (P < 0.0005). CONCLUSIONS Premature infants show nonperistaltic esophageal motility that may contribute to poor clearance of refluxed material. In contrast, the lower esophageal sphincter mechanisms seem well developed.
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Imai H, Nakamoto Y, Asakura K, Miki K, Yasuda T, Miura AB. Spontaneous glomerular IgA deposition in ddY mice: an animal model of IgA nephritis. Kidney Int 1985; 27:756-61. [PMID: 4021309 DOI: 10.1038/ki.1985.76] [Citation(s) in RCA: 104] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
It was found that ddY mice derived from non-inbred dd-stock mice brought from Germany before 1920 and then raised in Japan developed spontaneously IgA dominant deposition in the glomerular mesangium. In this report we give a detailed natural history of the renal pathology of those mice. The animals were fed rodent laboratory chow and sacrificed in groups of 9 to 10 at 6, 10, 16, 24, 28, 40, and 59 weeks of age. The bladder urine was analyzed, serum immunoglobulins were measured, and the kidney specimens were evaluated with light, fluorescent, and electron microscopy. Proteinuria was (plus) to (2 plus) after 28 weeks and (2 plus) to (3 plus) at 59 weeks with negative hematuria. Mesangial cell proliferation began to appear at 16 weeks, then progressed to a definite proliferative glomerulonephritis. At 59 weeks an additional increase of the mesangial matrix occurred. By immunofluorescence, there were IgG of (2 plus), IgM (plus) to (2 plus), IgA (plus) and C3 (plus) in the glomeruli until 28 weeks. However, IgA started to be dominant at 40 weeks and the glomerular pattern was IgA (2 plus) to (3 plus), IgG (plus) to (2 plus), IgM (+/-) to (plus) and C3 (plus) to (2 plus) at 59 weeks. Polyclonal IgA and IgG2a among immunoglobulins steeply rose at 40 weeks, and at 59 weeks IgA increased by 850%, IgG2a by 280%, IgG1 by 170%, IgG2b by 90%, and IgM by 60%, as compared with their level at 6 weeks. There was no anti-nuclear antibody. Thus, ddY mice, at least after the age of 40 weeks, can be used as a new animal model for spontaneous IgA nephritis. The probable origin of IgA is also discussed.
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