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Y Ishino

Publications and source records attributed to Y Ishino.

At least 19 recordsLinked to original sources
PubMed1998

A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase.

We describe here a DNA polymerase family highly conserved in Euryarchaeota, a subdomain of Archaea. The DNA polymerase is composed of two proteins, DP1 and DP2. Sequence analysis showed that considerable similarity exists between DP1 and the second subunit of eukaryotic DNA polymerase delta, a protein essential for the propagation of Eukarya, and that DP2 has conserved motifs found in proteins with nucleotide-polymerizing activity. These results, together with our previous biochemical analyses of one of the members, DNA polymerase II (DP1 + DP2) from Pyrococcus furiosus, implicate the DNA polymerases of this family in the DNA replication process of Euryarchaeota. The discovery of this DNA-polymerase family, aside from providing an opportunity to enhance our knowledge of the evolution of DNA polymerases, is a significant step toward the complete understanding of DNA replication across the three domains of life.

Amino Acid Sequence↗
PubMed1998

A tRNA(Glu) gene from the hyperthermophilic archaeon Pyrococcus furiosus contains the 3'-terminal CCA sequence of the mature tRNA.

We cloned a gene encoding tRNA(Glu) of the hyperthermophilic archaeon Pyrococcus furiosus. This gene contains the CCA sequence corresponding to the 3'-terminus of the mature tRNA. It is known that, like in eukaryal tRNAs, the CCA-termini of archaeal tRNAs are generally not encoded. Therefore, we analyzed all tRNA genes in the genome of Methanococcus jannaschii estimated by its whole genome sequence. Twenty-one of 37 listed tRNA genes contained the 3'-terminal CCA sequence. The corresponding M. jannaschii tRNA(Glu) gene does not contain the CCA sequence, although the tRNA sequences of the M. jannaschii and P. furiosus tRNA(Glu) genes are 86% identical.

Anticodon↗
PubMed1998

Clinical evaluation of irreversible data compression for computed radiography of the chest.

Efficient data compression is essential for practical daily operation of computed radiography (CR) systems. In this study the clinical applicability of type III irreversible high data compression using an FCR 9501 chest unit (Fuji Photo Film, Tokyo, Japan) was evaluated. Sixty-eight normal and 93 various abnormal cases, with an additional 15 cases of lung cancers with solitary lung nodules, were selected from the file. A pair of hard copies of original images and images reconstructed using type III compression was made for each case. Six radiologists evaluated the image quality by visual rating and receiver operating characteristic (ROC) curve analysis. For all five anatomic regions of normal cases, "original equal to compressed" was the most common response, followed by "original significantly better than compressed." When abnormal cases were evaluated for diagnostic information, there was no significant difference between the compressed and original images. ROC curve analysis on lung nodules with lung cancer showed no significant difference between the two. Compressed CR images using the type III irreversible technique are clinically applicable and acceptable despite slight degradation of image quality.

Adenocarcinoma↗
PubMed1998

Adenylosuccinate synthetase genes: molecular cloning and phylogenetic analysis of a highly conserved archaeal gene.

Adenylosuccinate synthetase (PurA) catalyzes the first step in the de novo AMP synthesis and has been extensively studied in both Bacteria and Eukarya. We cloned the purA gene from the hyperthermophilic archaeon, Pyrococcus furiosus. The gene appears to be individually transcribed and encodes a protein of 339 amino acids. The amino acid sequence comparison with other archael PurAs found from recent genome analyses indicated that two deletions, one central and the other C-terminal, are a common feature of archaeal PurAs. None of the 21 PurA homologues analyzed from Eukarya and Bacteria exhibited this feature. Amino acid sequences of PurAs in Archaea showed 64% average identities which were significantly higher than the 50% and 55% calculated for Bacteria and Eukarya, respectively. Several residues conserved in PurAs of both Eukarya and Bacteria and shown to be of catalytic importance are missing in the archaeal PurAs. Phylogenetic analysis using PurA as the marker grouped life into 3 domains, hence it was consistent with results derived from 16-18S ribosomal RNA sequences. The topology within the three domains, in general, portrayed the hitherto accepted evolutionary relationship among the organisms utilized. PurA can, thus, serve as an additional marker to evaluate phylogenetic inferences drawn from sequence data from rRNA and other conserved genes. The presence of two unique deletions in both euryarchaeal and crenarchaeal PurAs, but not in those of Bacteria and Eukarya, is a strong evidence confirming the common lineage of these two subdomains of Archaea.

Adenylosuccinate Synthase↗
PubMed1998

A pilot study on modified endoscopic variceal ligation using endoscopic ultrasonography with color Doppler function.

OBJECTIVE: The purpose of the study was to evaluate feasibility of modified endoscopic variceal ligation (EVL), namely the "intensive ligation" method, using endoscopic ultrasonography with color Doppler function (EUS-CD). METHODS: Forty-five patients with esophageal varices were treated by modified EVL. Variceal hemodynamics in 38 patients were examined using EUS-CD, which showed abdominal hemodynamics in detail under physiological conditions before and after the modified procedure. RESULTS: 1) The median number of treatment sessions was 3.2, and 41 O-rings on average were required per individual patient. 2) The median nonrecurrence period after treatment was 18 months (Kaplan-Meier method). 3) Nine patients with a good response to modified EVL did not have recurrences for 16.9+/-2.8 months, and five with a poor response had recurrences at 5.8+/-2.2 months. Gastric varices were related to the response to modified EVL (p < 0.05, Mann-Whitney's U test). 4) Minor complications in modified EVL as well as standard EVL were experienced; however, we had a patient with the development of meningitis, which was a major septic complication. 5) Before modified EVL, EUS-CD demonstrated that good responders had undeveloped (grade I) gastric varices in five of nine (56%); however, poor responders had developed (grade III) gastric varices in four of five (80%) (p < 0.05, Mann-Whitney's U test]. 6) After modified EVL, EUS-CD revealed that six of nine (67%) good responders and one of five (20%) poor responders showed a decrease in color signals in supplying veins; however, none of the former (0%) and three of the latter (60%) showed an increase (p < 0.05, Mann-Whitney's U test]. CONCLUSION: Modified EVL was safe and effective, at least with regard to intermediate-term outcome, especially when treating patients with undeveloped gastric varices revealed by EUS-CD. Both good and poor responders showed no exacerbation of gastric varices after the modified procedure, ultrasonographically as well as endoscopically.

Adult↗
PubMed1998

A novel DNA polymerase family found in Archaea.

One of the most puzzling results from the complete genome sequence of the methanogenic archaeon Methanococcus jannaschii was that the organism may have only one DNA polymerase gene. This is because no other DNA polymerase-like open reading frames (ORFs) were found besides one ORF having the typical alpha-like DNA polymerase (family B). Recently, we identified the genes of DNA polymerase II (the second DNA polymerase) from the hyperthermophilic archaeon Pyrococcus furiosus, which has also at least one alpha-like DNA polymerase (T. Uemori, Y. Sato, I. Kato, H. Doi, and Y. Ishino, Genes Cells 2:499-512, 1997). The genes in M. jannaschii encoding the proteins that are homologous to the DNA polymerase II of P. furiosus have been located and cloned. The gene products of M. jannaschii expressed in Escherichia coli had both DNA polymerizing and 3'-->5' exonuclease activities. We propose here a novel DNA polymerase family which is entirely different from other hitherto-described DNA polymerases.

Amino Acid Sequence↗
PubMed1998

The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: fact or farce?

Archaea is now recognized as the third domain of life. Since their discovery, much effort has been directed towards understanding the molecular biology and biochemistry of Archaea. The objective is to comprehend the complete structure and the depth of the phylogenetic tree of life. DNA replication is one of the most important events in living organisms and DNA polymerase is the key enzyme in the molecular machinery which drives the process. All archaeal DNA polymerases were thought to belong to family B. This was because all of the products of pol genes that had been cloned showed amino acid sequence similarities to those of this family, which includes three eukaryal DNA replicases and Escherichia coli DNA polymerase II. Recently, we found a new heterodimeric DNA polymerase from the hyperthermophilic archaeon, Pyrococcus furiosus. The genes coding for the subunits of this DNA polymerase are conserved in the euryarchaeotes whose genomes have been completely sequenced. The biochemical characteristics of the novel DNA polymerase family suggest that its members play an important role in DNA replication within euryarchaeal cells. We review here our current knowledge on DNA polymerases in Archaea with emphasis on the novel DNA polymerase discovered in Euryarchaeota.

Amino Acid Sequence↗
PubMed1997

A high-density STS map based on a single contig of YAC and P1 clones in the chromosome 8p12-p21 region.

We have constructed a yeast artificial chromosome (YAC) and P1 contig in the 8p12-p21 region. The contig comprises 16 overlapping YAC clones and 44 overlapping P1 clones. Twelve dinucleotide-repeat polymorphic sequence-tagged site (STS)-markers that were previously isolated mainly from these YAC and P1 clones were genetically mapped. A total of 46 nonpolymorphic STS markers were newly established mainly from the YAC and P1 clone end fragments, and 28 of the 46 nonpolymorphic STSs, as well as the 12 polymorphic STSs, were also mapped physically onto the contig based on STS content analysis of YAC pools and of the P1 and YAC clones. As a result, the YAC and P1 clones were assembled into a single contig covering a minimum of 1.5 Mb physically and 2.8 cM genetically with 12 polymorphic and 28 nonpolymorphic STSs within the 8p12-p21 region. Average STS spacing in the contig was estimated to be 40 kb/STS. In addition, further characterization of the contig suggested that this contig includes a region where genetic recombination occurs frequently. Thus, the resulting cloned region, together with densely mapped STS markers on the contig, should help to promote our understanding of this region.

Bacteriophage P1↗
PubMed1997

A novel DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus: gene cloning, expression, and characterization.

BACKGROUND: In many respects Archaea are much more like eukaryotes than prokaryotes with respect to the conservation of many of the components involved in transcription, translation and DNA replication. So far, only a few DNA polymerases with structures similar to those of eukaryotic DNA polymerase a have been found in Archaea. The identification and characterization of all the DNA polymerases of one archaeon would add considerably to our knowledge of the basic mechanisms of DNA replication in these organisms. RESULTS: We have identified a novel DNA polymerase composed of two proteins, DP1 and DP2, with molecular weights of 69294 Da and 143161 Da, respectively, in the hyperthermophilic archaeon, Pyrococcus furiosus, and have cloned the corresponding genes which are tandemly arranged on the Pyrococcus genome. No significant sequence homology was found between these two proteins and other known DNA polymerases. The pol genes were transcribed as part of a single operon that additionally contained genes homologous to the cdc18+/CDC6 and Dmc1/Rad51 family of proteins. We purified the Pyrococcus DNA polymerase from Escherichia coli strains expressing the cloned genes and characterized its activity. It possesses strong 3' --> 5' exonucleolytic activity and has a template-primer preference which is characteristic of a replicative DNA polymerase. CONCLUSION: In P. furiosus, we identified a second DNA polymerase encoded by two genes, neither of which display significant homology to any other known DNA polymerase. Both the enzymatic properties of the enzyme and the gene organization raise the possibility that this enzyme might be the replicative DNA polymerase of P. furiosus.

Antigens, CD↗
PubMed1997

[Evaluation of left ventricular systolic function using cine MRI--application to hypertrophic cardiomyopathy].

Cine MRI is a useful means to analyse the anatomical and functional changes of hypertrophic cardiomyopathy. The visual evaluation of hypertrophic regions and the motion patterns of their walls is in most cases possible on cine MR images. To complement a subjective method a certain quantitative analysis is necessary. Left ventricular regional systolic function can be quantitatively evaluated using cine MRI images printed on films. There is a good correlation between % thickness of LV wall and its thickness at end diastolic phase. The comparison of % thickness of normal subjects with that of hypertrophic cardiomyopathies shows a tendency of its value being less at the region of more severe hypertrophic change.

Cardiomyopathy, Hypertrophic↗
PubMed1996

Preferential replication-dependent mutagenesis in the lagging DNA strand in Escherichia coli.

The mutation frequencies attributable to -1 frameshift or one-base substitution in the structural genes coding for resistance to chloramphenicol (Cm) and tetracycline (Tc) were followed over several cycles of DNA replication, and found to differ several-fold, depending on the orientation of the gene on the plasmid with respect to the direction of (unidirectional ColE1-type) replication. The mutation frequency was higher when the reporter gene was present in the plasmid in the same orientation as the direction of the origin, i.e., when the transcription template is the lagging daughter strand, than when the gene was inserted in the opposite orientation. This significant difference in reversion frequencies of genes with different polarities was demonstrated only for a brief period of cell growth (several cycles of replication) after induction of the dnaQ49 mutator, but was not observed when an increased number of replication cycles, was permitted, most probably due to fixation of the mutation into both strands. The mutated intermediate DNA which possesses a misaligned basepair in the Cm gene was demonstrated to be replicated into two progeny DNA molecules; one is the chloramphenicol-resistant (CmR) DNA synthesized from the template strand having the mutation and the other is the CmS DNA from the template strand without mutation. Our results suggest that replication-dependent mutagenesis may occur preferentially in the lagging strand.

Bacteriocin Plasmids↗
PubMed1996

Cloning and expression of the BalI restriction-modification system.

BalI, a type II restriction-modification (R-M) system from the bacterium, Brevibacterium albidum, recognizes the DNA sequence 5'-TGGCCA-3'. We cloned the genes encoding the BalI restriction endonuclease and methyltransferase and expressed them in Escherichia coli. The two genes were aligned tail-to-tail and their termination codons overlapped. BalI restriction endonuclease and methyltransferase comprise 260 and 280 amino acids, respectively, and have molecular weights of 29 043 and 31 999 Da. The amino acid sequence of BalI methyltransferase is similar to that of other m6A MTases, although it has been categorized as a m5C methyltransferase. A high expression system for the BalI restriction endonuclease was constructed in E. coli for the production of large quantities of enzyme.

Amino Acid Sequence↗
PubMed1996

Human herpesvirus 6 induces IL-8 gene expression in human hepatoma cell line, Hep G2.

The infectivity of human herpesvirus 6 (HHV-6) in a human hepatoma cell line, Hep G2 cells, and the effect of HHV-6 on production of inflammatory cytokines in these cells were examined to analyze pathogenesis of HHV-6 in the liver. We demonstrated that Hep G2 cells were susceptible to infection with HHV-6, and produced infectious virus. Moreover, infection of Hep G2 cells by HHV-6 induced the expression of IL-8 mRNA, but not IL-1 beta. The effect on induction of IL-8 gene expression was observed only in Hep G2 cells infected with infectious virus, whereas both heat-inactivated HHV-6 and UV-irradiated HHV-6 did not change the IL-8 mRNA level in these cells. These data suggest that HHV-6 may induce the cytokine-mediated inflammatory response by infecting liver cells, which could result in liver dysfunction in vivo.

Antigens, Viral↗
PubMed1996

Clinical evaluation of irreversible data compression for computed radiography in excretory urography.

Efficient data compression is required for practical daily use of digital images in computed radiography (CR). This study investigated the clinical utility of data compression in excretory urography using the FCR 9000 system (Fuji Photo Film, Tokyo, Japan). Type III data compression technique was used, which can achieve a 20:1 to 25:1 compression ratio. To evaluate the degradation of image quality, we compared paired original and compressed CR images. Although a slight deterioration of image quality was noted in the renal calyx including collecting tubules among various anatomical structures, the difference was not significant. Receiver operating characteristics analysis revealed no significant difference among the original and compressed images. We conclude that compressed CR images using Type III data compression technique in excretory urography appear to be clinically applicable and acceptable.

Adolescent↗
PubMed1996

Deficiencies of automatic endoscopic reprocessors: a method to achieve high-grade disinfection of endoscopes.

BACKGROUND: We show that disinfection using the automatic endoscopic reprocessor is not complete and propose a method for high-grade disinfection of endoscopes. METHODS: We used an automatic endoscopic reprocessor, Pyser System 83, and 2% glutaraldehyde. After each endoscopic procedure, the endoscopes were divided into three groups. Endoscopes in group A were washed only by the reprocessor. Group B endoscopes were washed by the reprocessor after the connectors were soaked in glutaraldehyde for 5 minutes. The channels, valves, connecting sections of group C endoscopes, and the connectors of the machine were sprayed with glutaraldehyde before machine-washing. Swabs were taken from all 13 parts of each endoscope and machine for microbiologic culture. RESULTS: Six endoscopes were positive, cumulatively, for bacterial contamination in group A. Among group B endoscopes, one remained contaminated. No endoscope was positive in group C. The difference between group A and C was statistically significant (p < .05). CONCLUSIONS: Machine washing by automatic endoscopic reprocessors may not achieve complete disinfection. Additional procedures are necessary. High-grade disinfection of the connectors is critical. Disinfection of the interface between the connectors is important.

Disinfection↗