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Biomedical subjects

Y Ishino

Publications and source records attributed to Y Ishino.

At least 19 recordsLinked to original sources
PubMed2005

Helicobacter pylori eradication induces marked increase in H+/K+-adenosine triphosphatase expression without altering parietal cell number in human gastric mucosa.

BACKGROUND AND AIMS: Gastric acid secretion is downregulated by Helicobacter pylori infection and upregulated after its eradication, but the mechanisms are still unclear. We examined the effects of H pylori eradication on the number of parietal cells and on expression of molecules functioning in acid secretion in the human gastric mucosa. METHODS: We enrolled 111 consecutive men with chronic gastritis induced by H pylori. Biopsy specimens were endoscopically obtained before and 12 weeks after successful eradication of H pylori and parietal cell numbers were counted. mRNA expression levels of H+/K+-adenosine triphosphatase (H+/K+-ATPase), anion exchanger 2, M3 muscarinic receptor, intrinsic factor, and interleukin 1beta were determined with a real time reverse transcriptase-polymerase chain reaction method. The severity of gastric atrophy was evaluated using the serum pepsinogen I/II ratio. RESULTS: No significant difference was observed in parietal cell numbers before and after H pylori eradication. Median mRNA expression levels of H+/K+-ATPase in the gastric mucosa increased 250-fold after H pylori eradication accompanied by attenuation of interleukin 1beta. A large increase in H+/K+-ATPase expression was observed even in patients with severe atrophic gastritis. In contrast, fold increases in mRNA expression levels, including intrinsic factor, anion exchanger 2, and M3 muscarinic receptor, after eradication therapy, were limited to 1.4, 2.3, and 2.5 times, respectively. CONCLUSIONS: In the absence of alteration of parietal cell number, gastric H+/K+-ATPase mRNA expression was markedly restored after successful H pylori eradication, suggesting a central role for the restoration of H+/K+-ATPase expression in gastric acid secretion recovery after H pylori eradication.

Chronic Disease↗
PubMed2005

Contamination with hepatitis B virus DNA in gastrointestinal endoscope channels: risk of infection on reuse after on-site cleaning.

BACKGROUND AND STUDY AIMS: The incidence of viral contamination in the air, water and suction/accessory channels of gastrointestinal endoscopes was examined in order to evaluate the risk of infection. MATERIALS AND METHODS: After endoscopic examinations, including biopsy procedures, in 17 patients who were positive for hepatitis B virus surface antigen and eight patients who were positive for hepatitis C virus antibody, the endoscopes were cleaned on site by suctioning and flushing the air and water channels with an enzyme detergent. First samples were then collected by flushing 5 ml of sterile water through each channel. After mechanical reprocessing, second samples were collected in the same way. Virological studies were carried out with real-time polymerase chain reactions for hepatitis B virus DNA and hepatitis C virus RNA. RESULTS: Hepatitis B virus DNA was detected in five of the first samples recovered from the suction/accessory channels of the endoscopes (titers of 1.3 x 10 (4) to 2.5 x 10 (5) copies/ml), while no contamination was detected after reprocessing ( P = 0.0445). The first samples from one water channel and three air channels were also positive for hepatitis B virus DNA, but were negative after reprocessing ( P > 0.5, P = 0.227, respectively). No hepatitis C virus RNA was detected in any of the samples. CONCLUSIONS: These results indicate that all of the channels were potential sources of viral infection.

Biopsy↗
PubMed2005

Histamine-2 receptor expression in gastric mucosa before and after Helicobacter pylori cure.

BACKGROUND: Helicobacter pylori infection prevents the occurrence of the tolerance phenomenon of Histamine-2 (H2) receptor antagonists. Gastro-esophageal reflux disease develops in some cases with the restoration of acid secretion after H. pylori eradication therapy. AIM: To clarify the mechanisms of H2 receptor restoration after the eradication of H. pylori on parietal cells. METHODS: We enrolled 80 consecutive asymptomatic male patients with H. pylori infection, having chronic gastritis with or without the presence of peptic ulcers. Biopsy specimens from the greater curvatures at the mid-corpus of the stomach were obtained endoscopically from all subjects before and 12 weeks after the eradication of H. pylori. Degrees of gastric atrophy were evaluated by serum pepsinogen levels. The amounts of mRNA expression of H2 receptor were evaluated in each subject's gastric mucosa by real time reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS: H2 receptor mRNA expression levels significantly correlated with serum pepsinogens I and II ratios. The expression level of H2 receptor mRNA was lower in subjects with hypergastrinemia. The median expression level of H2 receptor after H. pylori eradication was threefold greater than prior to treatment. In addition, its restoration became more pronounced in subjects with severe gastric atrophy. However, a comparatively low restoration of H2 receptor mRNA was found in subjects with hypergastrinemia. CONCLUSIONS: H2 receptor mRNA levels decrease with the progression of gastric atrophy induced by H. pylori infection, and are restored after H. pylori eradication. Such expression levels of H2 receptor may explain a part of the tolerance phenomenon to H2 receptor antagonists.

Anti-Bacterial Agents↗
PubMed2003

Change in apoptosis in the gastric surface epithelium and glands after eradication of Helicobacter pylori.

BACKGROUND: Change in apoptosis in gastric glands after eradication of Helicobacter pylori has never been reported. AIMS: The purpose of this paper is to investigate the change in apoptosis in gastric glands after eradication of Heliobacter pylori. PATIENTS AND METHODS: We studied 23 Heliobacter pylori-positive patients with duodenal and gastric ulcers, who were monitored for 6-12 months after eradication, and eight controls. Biopsies were taken from the antrum and body. Apoptosis was evaluated immunohistochemically using anti-single stranded DNA antibody. Apoptotic index was calculated by counting immunostained cells in surface epithelial and glandular cells. RESULTS: In the surface epithelium, Apoptotic indexes were significantly higher in patients than in controls. In the upper portion of fundic glands, apoptotic indexes were significantly higher in patients with gastric ulcers (14.2% (9.3, 17.8)) (median (1st quartile, 3rd quartile)) than in controls (8.0% (2.0, 9.0), p < 0.01) and decreased significantly after eradication (3.4% (2.0, 5.3)), p < 0.01). In pyloric glands, apoptotic indexes were no different between patients and controls. In the lower portion of fundic glands, apoptotic indexes were very low, both in patients and in controls. CONCLUSIONS: Our results showed that apoptosis, not only of surface epithelial cells but also of glandular cells in the upper portion of fundic glands, increased in Heliobacter pylori-positive patients with gastric ulcers and decreased to normal levels after eradication of Heliobacter pylori.

Adult↗
PubMed2003

Improvement of the automatic endoscopic reprocessor: self-cleaning disinfecting connectors between endoscope and reprocessor.

BACKGROUND AND STUDY AIMS: We have previously pointed out a defect of automatic endoscopic reprocessors, i. e. the contamination of the connecting part between the endoscope and the reprocessor. We evaluated a newly designed connector (MH-861; Olympus, Tokyo, Japan) with a self-cleaning and disinfection mechanism, which enabled cleaning and disinfection of both the connector itself and its interface with the suction and air/water valves during a reprocessing cycle, which was not previously possible. METHODS: Ten upper gastrointestinal endscopes were examined in the study. Swabs were taken from the suction and air/water valves for microbiological culture before and after reprocessing by the washer-disinfector. The numbers of contaminated endoscopes before and after reprocessing with the new connector were compared. RESULTS: Before the procedure there were five contaminated endoscopes and none after the procedure. When the new connector was used, the difference in cleaning and disinfection of the connecting parts was significant (P = 0.0325). CONCLUSIONS: We conclude that the newly developed connector permits effective cleaning and disinfection by automatic reprocessors.

Automation↗
PubMed2001

Mg-promoted regio- and stereoselective C-acylation of aromatic alpha,beta-unsaturated carbonyl compounds.

[reaction: see text]. Treatment of aromatic alpha,beta-unsaturated carbonyl compounds with Mg turnings in the presence of acid anhydrides/TMSCl or acyl chlorides in DMF brought about a facile and efficient cross-coupling to give C-acylation products, which are useful 1,4-dicarbonyl compounds, in good to excellent yields in a regio- and stereoselective manner. The reaction may be initiated by electron transfer from magnesium to the substrates.

Journal Article↗
PubMed2001

The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus.

We characterized the primase complex of the hyperthermophilic archaeon, Pyrococcus furiosus. The two proteins, Pfup41 and Pfup46, have similar sequences to the p48 and p58 subunits, respectively, of the eukaryotic DNA polymerase alpha-primase complex. Unlike previously reported primases, the Pfup41 preferentially utilizes deoxyribonucleotides for its de novo synthesis, and moreover, it synthesizes up to several kilobases in length in a template-dependent manner (Bocquier, A., Liu, L., Cann, I., Komori, K., Kohda, D., and Ishino, Y. (2001) Curr. Biol. 11, 452-456). The p41-p46 complex showed higher DNA binding activity than the catalytic p41 subunit alone. In addition, the amount of DNA synthesized by the p41-p46 complex was much more abundant and shorter in length than that by Pfup41 alone. The activity for RNA primer synthesis, which was not detected with Pfup41, was observed from the reaction using the p41-p46 complex in vitro. The in vitro replication of M13 single-stranded DNA by the P. furiosus proteins was stimulated by ATP. Observation of the labeled primers by using [gamma-(32)P]ATP in the substrates suggests ATP as the preferable initiating nucleotide for the p41-p46 complex. These results show that the primer synthesis activity of Pfup41 is regulated by Pfup46, and the p41-p46 complex may function as the primase in the DNA replication machinery of P. furiosus, in a similar fashion to the eukaryotic polymerase alpha-primase complex.

Adenosine Triphosphate↗
PubMed2001

In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin.

Although genome analyses have suggested parallels between archaeal and eukaryotic replication systems, little is known about the DNA replication mechanism in Archaea. By two-dimensional gel electrophoreses we positioned a replication origin (oriC) within 1 kb in the chromosomal DNA of Pyrococcus abyssi, an anaerobic hyperthermophile, and demonstrated that the oriC is physically linked to the cdc6 gene. Our chromatin immunoprecipitation assays indicated that P. abyssi Cdc6 and minichromosome maintenance (MCM) proteins bind preferentially to the oriC region in the exponentially growing cells. Whereas the oriC association of MCM was specifically inhibited by stopping DNA replication with puromycin treatment, Cdc6 protein stayed bound to the replication origin after de novo protein synthesis was inhibited. Our data suggest that archaeal and eukaryotic Cdc6 and MCM proteins function similarly in replication initiation and imply that an oriC association of MCM could be regulated by an unknown mechanism in Archaea.

Base Sequence↗
PubMed2001

Expansion of the zinc metallo-hydrolase family of the beta-lactamase fold.

Recently, the zinc metallo-hydrolase family of the beta-lactamase fold has grown quite rapidly, accompanied by the accumulation of sequence and structure data. The variety of the biological functions of the family is higher than expected. In addition, the members often have mosaic structures with additional domains. The family includes class B beta-lactamase, glyoxalase II, arylsulfatase, flavoprotein, cyclase/dehydrase, an mRNA 3'-processing protein, a DNA cross-link repair enzyme, a DNA uptake-related protein, an alkylphosphonate uptake-related protein, CMP-N-acetylneuraminate hydroxylase, the romA gene product, alkylsulfatase, and insecticide hydrolases. In this minireview, the functional and structural varieties of the growing protein family are described.

Amino Acid Sequence↗
PubMed2001

Dissection of the regional roles of the archaeal Holliday junction resolvase Hjc by structural and mutational analyses.

Hjc is an archaeal DNA endonuclease, which resolves the Holliday junction in the presence of divalent metals. Combined with mutational analyses, the x-ray structure of the Pyrococcus furiosus Hjc crystal grown in the presence of ammonium sulfate revealed a positively charged interface, rich in conserved basic residues, and the catalytic center (Nishino, T., Komori, K., Tsuchiya, D., Ishino, Y., and Morikawa, K. (2001) Structure 9, 197-T204). This structural study also suggested that the N-terminal segment and some loops of Hjc play crucial roles in the cleavage of DNA. However, a structural view of the interaction between these regions and DNA remains elusive. To clarify the regional roles of Hjc in the recognition of the Holliday junction, further structural and biochemical analyses were carried out. A new crystal form of Hjc was obtained from a polyethylene glycol solution in the absence of ammonium sulfate, and its structure has been determined at 2.16-A resolution. A comparison of the two crystal structures has revealed that the N-terminal segment undergoes a serious conformational change. The site-directed mutagenesis of the sulfate-binding site within the segment caused a dramatic decrease in the junction binding, but the mutant was still capable of cleaving DNA with a 20-fold lower efficiency. The kinetic analysis of Hjc-Holliday junction interaction indicated that mutations in the N-terminal segment greatly increased the dissociation rate constants of the Hjc-Holliday junction complex, explaining the decreased stability of the complex. This segment is also responsible for the disruption of base pairs near the junction center, through specific interactions with them. Taken together, these results imply that, in addition to the secondary effects of two basic loops, the flexible N-terminal segment plays predominant roles in the recognition of DNA conformation near the crossover and in correct positioning of the cleavage site to the catalytic center of the Hjc resolvase.

Amino Acid Sequence↗
PubMed2001

Replication protein A in Pyrococcus furiosus is involved in homologous DNA recombination.

Single-stranded DNA-binding protein in Bacteria and replication protein A (RPA) in Eukarya play crucial roles in DNA replication, repair, and recombination processes. We identified an RPA complex from the hyperthermophilic archaeon, Pyrococcus furiosus. Unlike the single-peptide RPAs from the methanogenic archaea, Methanococcus jannaschii and Methanothermobacter thermoautotrophicus, P. furiosus RPA (PfuRPA) exists as a stable hetero-oligomeric complex consisting of three subunits, RPA41, RPA14, and RPA32. The amino acid sequence of RPA41 has some similarity to those of the eukaryotic RPA70 subunit and the M. jannaschii RPA. On the other hand, RPA14 and RPA32 do not share homology with any known open reading frames from Bacteria and Eukarya. However, six of eight archaea, whose total genome sequences have been published, have the open reading frame homologous to RPA32. The PfuRPA complex, but not each subunit alone, specifically bound to a single-stranded DNA and clearly enhanced the efficiency of an in vitro strand-exchange reaction by the P. furiosus RadA protein. Moreover, immunoprecipitation analyses showed that PfuRPA interacts with the recombination proteins, RadA and Hjc, as well as replication proteins, DNA polymerases, primase, proliferating cell nuclear antigen, and replication factor C in P. furiosus cells. These results indicate that PfuRPA plays important roles in the homologous DNA recombination in P. furiosus.

Amino Acid Sequence↗
PubMed2001

Archaeal primase: bridging the gap between RNA and DNA polymerases.

In the evolution of life, DNA replication is a fundamental process, by which species transfer their genetic information to their offspring. DNA polymerases, including bacterial and eukaryotic replicases, are incapable of de novo DNA synthesis. DNA primases are required for this function, which is sine qua non to DNA replication. In Escherichia coli, the DNA primase (DnaG) exists as a monomer and synthesizes a short RNA primer. In Eukarya, however, the primase activity resides within the DNA polymerase alpha-primase complex (Pol alpha-pri) on the p48 subunit, which synthesizes the short RNA segment of a hybrid RNA-DNA primer. To date, very little information is available regarding the priming of DNA replication in organisms in Archaea. Available sequenced genomes indicate that the archaeal DNA primase is a homolog of the eukaryotic p48 subunit. Here, we report investigations of a p48-like DNA primase from Pyrococcus furiosus, a hyperthermophilic euryarchaeote. P. furiosus p48-like protein (Pfup41), unlike hitherto-reported primases, does not catalyze by itself the synthesis of short RNA primers but preferentially utilizes deoxynucleotides to synthesize DNA fragments up to several kilobases in length. Pfup41 is the first DNA polymerase that does not require primers for the synthesis of long DNA strands.

DNA↗
PubMed2001

Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition.

BACKGROUND: Homologous recombination is a crucial mechanism in determining genetic diversity and repairing damaged chromosomes. Holliday junction is the universal DNA intermediate whose interaction with proteins is one of the major events in the recombinational process. Hjc is an archaeal endonuclease, which specifically resolves the junction DNA to produce two separate recombinant DNA duplexes. The atomic structure of Hjc should clarify the mechanisms of the specific recognition with Holliday junction and the catalytic reaction. RESULTS: The crystal structure of Hjc from the hyperthermophilic archaeon Pyrococcus furiosus has been determined at 2.0 A resolution. The active Hjc molecule forms a homodimer, where an extensive hydrophobic interface tightly assembles two subunits of a single compact domain. The folding of the Hjc subunit is clearly different from any other Holliday junction resolvases thus far known. Instead, it resembles those of type II restriction endonucleases, including the configurations of the active site residues, which constitute the canonical catalytic motifs. The dimeric Hjc molecule displays an extensive basic surface on one side, which contains many conserved amino acids, including those in the active site. CONCLUSIONS: The architectural similarity of Hjc to restriction endonucleases allowed us to construct a putative model of the complex with Holliday junction. This model accounts for how Hjc recognizes and resolves the junction DNA in a specific manner. Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA.

Amino Acid Sequence↗
PubMed2001

Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus.

An archaeal clamp loader, replication factor C (RFC), consists of two proteins, the small subunit (RFCS) and large subunit (RFCL), whose sequences are both highly homologous to those of the eukaryotic RFC components. We have investigated the oligomeric structure of RFCS from Pyrococcus furiosus by electron microscopy using single-particle analysis. RFCS forms mostly ring-shaped hexamers at pH 9.0, although it tends to form C-shaped tetramers or pentamers at a lower pH (pH 5.5). The three-dimensional (3D) structure of the RFCS hexamer was obtained by random conical tilt reconstruction at 24.0-A resolution. RFCS forms a hexameric ring with outer and inner diameters of 117 and 27 A, respectively, and with a height of about 55 A. The six subunits are arranged in a twisted manner with a sixfold symmetry around the channel. The 3D map revealed that the six subunits are arranged in a head-to-tail configuration. Although the RFC complex consists of RFCS and RFCL in vivo, RFCS alone, together with PCNA, substantially enhanced the DNA synthesizing activity of P. furiosus DNA polymerase I in vitro. The 3D reconstruction of RFCS with catalytic activity provides important insights into the organization mechanism and the functional state of the RFC complex.

Archaeal Proteins↗
PubMed2001

Investigation of Corneal Autofluorescence in Diabetic Patients.

Purpose: The investigation of corneal autofluorescence in diabetic patients.Objects and Methods: Corneal autofluorescence was investigated with a newly-developed fluorophotometer (wave length: excitation, 290-390 nm; emission, 430-630 nm) having, fluorescence characteristics involving those of reduced pyridine nucleotides (PN) and advanced glycation endoproduct (AGE) except pentosidine and pyrraline. Twenty-eight patients with non-insulin-dependent diabetes mellitus and sixty-seven healthy volunteers were studied.Results: The corneal autofluorescence was 1.65 times higher than that of controls (P <.0001). In non-insulin-dependent diabetes mellitus, the corneal autofluorescenece was not correlated significantly with various diabetic parameters in blood (r < 0.4). In controls, the corneal autofluorescence was correlated significantly with age (r = 0.438).Conclusion: The corneal autofluorescence has some relation with PN and AGE accumulation in the cornea.

Journal Article↗
PubMed2001

Atomic structure of the clamp loader small subunit from Pyrococcus furiosus.

In eukaryotic DNA replication, replication factor-C (RFC) acts as the clamp loader, which correctly installs the sliding clamp onto DNA strands at replication forks. The eukaryotic RFC is a complex consisting of one large and four small subunits. We have determined the crystal structure of the clamp loader small subunit (RFCS) from Pyrococcus furiosus. The six subunits, of which four bind ADP in their canonical nucleotide binding clefts, assemble into a dimer of semicircular trimers. The crescent-like architecture of each subunit formed by the three domains resembles that of the delta' subunit of the E. coli clamp loader. The trimeric architecture of archaeal RFCS, with its mobile N-terminal domains, involves intersubunit interactions that may be conserved in eukaryotic functional complexes.

Amino Acid Sequence↗
PubMed2001

The expression of osteopontin with condylar remodeling in growing rats.

It is suggested that osteopontin may promote osteoclast binding to resorptive sites by interacting with the alphavbeta3 receptor on osteoclasts. However, the role of osteopontin in functional remodeling of bony structures remains unclear. The present study was conducted to examine the distribution of osteopontin on the condyle and explore the role in condylar remodeling in growing rats using an immunohistochemical method. Twenty Wistar strain male rats aged 7, 14, 28 and 56 days were used. In 7- and 14-day-old rats, no immunoreaction to osteopontin was detected in the cartilage cells. In 28-day-old rats initiating mastication, the thickness of condylar cartilage was decreased abruptly as compared to the younger rats. High immunoreaction to osteopontin was found in the cytoplasm of hypertrophic chondrocytes and on the trabecular bone surfaces of primary spongiosa adjacent to the osteoclasts or chondroclasts. The immunoreactions to osteopontin in the cytoplasm of hypertrophic chondrocytes were less in 56-day-old rats than in 28-day-old rats. It is shown that the alteration in mechanical loading on the mandibular condyle due to functional changes from weaning to mastication correlates with the localization of osteopontin in growing rats. Furthermore, it is suggested that osteopontin may stimulate osteoclastic resorption of calcified matrix by mediating the attachment of osteoclasts and/or chondroclasts during growth-related functional remodeling of the condyle.

Journal Article↗