Hepatitis C virus genotypes: molecular basis and clinical significance.
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Genome, Viral↗
Biomedical subjects
N Kato
Publications and source records attributed to N Kato.
[Preventive use of interferons for liver neoplasms].
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Hepatitis C↗
A novel sequence found at the 3' terminus of hepatitis C virus genome.
The 3' end region of positive-strand RNA-virus genomes is implicated in the initiation of genomic replication. We analyzed the extreme 3' end of the hepatitis C virus (HCV) genome by primer extension of the 5' end region of the antigenomic strand RNA found in infected liver. We discovered a novel sequence present downstream of the poly(U) stretch that was previously considered to be the 3' end structure of the HCV genome. The novel sequence was 98 nucleotides long and had no significant homology with any known sequences, viral or nonviral. The discovery of this novel tail on the HCV genome should contribute to the study of HCV replication.
Base Sequence↗
Gene of heat shock protein of sulfur-dependent archaeal hyperthermophile Desulfurococcus.
To elucidate thermoresistance, a gene of a hyperthermophilic heat shock protein (HHSP) was isolated from the hyperthermophile Desulfurococcus strain SY which grows at 95 degrees C. The molecular weight of HHSP deduced from the open reading frame was 59,137 (545 amino acid residues). Sequence alignments of peptides reveal similarities (evolutionary distances) to the alpha (0.279) and beta (0.296) subunits of thermosome, TF55 (0.343) and human t-complex polypeptide 1. The structure of a thermophilic heat shock protein TGroEL (Tamada et al. (1991) Biochem, Biophys. Res. Commun. 179, 565) was quite different from that of HHSP. TGroEL and HSP60 have sequences identical to HHSP at its equatorial domain, while those identical to the alpha subunit of F-type ATPase are at its apical domain.
Amino Acid Sequence↗
Solid-phase nested deletion: a new subcloning-less method for generating nested deletions.
We have developed a new subcloning-less method for generating nested deletions which we have termed Solid-Phase Nested Deletion. The basic procedure for this method is as follows. The target DNA fragment is cloned in the multiple cloning site of a cloning vector, pUC or its derivatives, and amplified by PCR using a set of primers, one of which is 5'-biotinylated. The amplified DNA is partially digested by a restriction enzyme with a 4-base recognition sequence. The digested DNA is ligated with a synthetic adapter DNA. Monodiverse beads coupled with streptavidin (Dynabeads M-280 streptavidin) are added to the mixture and the biotinylated DNA fragments are separated by applying magnetic field. The unidirectionally deleted DNA fragments are recovered by PCR from the magnetic beads, and size-fractionated by agarose gel electrophoresis. The DNA fragments are amplified by PCR and used for sequencing. We demonstrate the potential of this method using a 4878-bp EcoRI fragment of lambda phage DNA.
Bacteriophage lambda↗
Gene activation by the Escherichia coli positive regulator OmpR: a mutational study of the DNA-binding domain of OmpR.
The Escherichia coli DNA-binding protein, OmpR, is one of the best characterized of the bacterial positive regulators that enhance the transcriptional ability of RNA polymerase. OmpR, consisting of 239 amino acids, binds to specific sequences located upstream of the cognate ompC and ompF promoters. The C-terminal half of OmpR, consisting of about 120 amino acids, exhibits an inherent DNA-binding ability. To address the issue of DNA binding by OmpR, we selected a set of OmpR mutants, each of which has a single amino acid substitution in the C-terminal half of OmpR. In particular, we characterized a number of OmpR mutants which are defective in DNA binding and thereby result in an OmpF- OmpC phenotype. Among them, a putative positive control OmpR mutant was also obtained, which appears to be defective in phosphorylation-dependent transcriptional activation, but not in DNA binding. These results are discussed with general emphasis on DNA recognition by the E. coli family of OmpR-like regulatory proteins.
Amino Acid Sequence↗
Inhibition of hepatitis C virus replication by antisense oligonucleotide in culture cells.
Oligonucleotides complementary to the sequences containing the initiator codon, AUG, of the core region of positive-stranded hepatitis C virus (HCV) were tested for their effects on viral translation in a cell-free protein synthesis system and on viral replication in a human T-lymphotropic virus type I infected cell line, MT-2C, which was cloned by the limited dilution method from MT-2 cells and showed more efficient HCV replication than an uncloned population of MT-2 cells. Treatment of HCV-infected MT-2C cells with the antisense oligonucleotide (10 microM) had a dramatic inhibitory effect on viral replication. This result suggests that the antisense oligonucleotide complementary to the sequence close to the initiation codon of the core region might be useful as an antiviral agent against HCV replication.
Antiviral Agents↗
Purification and characterization of recombinant hamster tissue complement C1s.
Hamster complement C1s cDNA was inserted into expression plasmid BCMGSNeo, and transfected to SEA7 cells, A31 mouse fibroblasts transformed by polyoma virus. The transfectant secreted a large amount of recombinant C1s that was activated in the serum free culture medium and hydrolyzed acetyl-Gly-L-Lys-naphthyl ester (AGLNE). C1s was purified to a homogeneity from the culture medium of the transfectant by DEAE-Sephadex, Dymatrex orange A and size-exclusion HPLC. Purified hamster C1s consumed human complement in hemolytic assay and hydrolyzed gelatin in enzymography. To investigate the enzymic action of C1s at molecular levels, several antibodies were prepared against hamster C1s. One peptide (amino-acid residues 379-391) and two peptides (amino-acid residues 478-496 and 560-583) corresponding to the heavy and the light chain, respectively, were synthesized. The amino-acid sequences of these regions is not conserved between hamster and human C1s. Antibodies against these peptides were raised in rabbits. The anti-peptide antibodies bound specifically to hamster serum and recombinant C1s but not to human C1s. They inhibited the esterase activity of recombinant C1s to varying degrees depending on each antibody's binding site.
Amino Acid Sequence↗
Synthesis and secretion of tobacco neutral PR-5 protein by transgenic tobacco and yeast.
Tobacco neutral osmotin-like protein was expressed in both homologous and heterologous expression systems. Osmotin-like protein was retained in tobacco cells when expressed as the prepro-form, whereas deletion of the carboxyl-terminal propeptide of 22 amino acids induced its secretion into the extracellular fluid. Without the amino-terminal signal peptide, there was no accumulation of osmotin-like protein. When the construct with both the amino- and carboxyl-terminal peptides was introduced to methylotrophic yeast, divergent osmotin-like protein forms were found in the cell and medium. Results suggest that the amino-terminal signal of the osmotin-like protein is essential for the transport of protein to the endoplasmic reticulum both in tobacco and yeasts but that the carboxyl-terminal propeptide signal is effective only for intracellular retention in tobacco.
Amino Acid Sequence↗
A novel formaldehyde oxidation pathway in methylotrophic yeasts: methylformate as a possible intermediate.
A considerable amount of methylformate accumulated in the culture medium of methanol-grown methylotrophic yeasts. Methylformate is considered as an intermediate in a novel formaldehyde oxidation pathway. Through investigations with Pichia methanolica, methylformate formation was found to be catalysed by a new type of alcohol dehydrogenase, which was named methylformate synthase. When cells were grown on a relatively high concentration of methanol or exposed to a high concentration of formaldehyde, formation of methylformate was enhanced and the level of methylformate synthase in the cells increased. How methylformate synthase is involved in formaldehyde oxidation and formaldehyde detoxification is discussed.
Alcohol Dehydrogenase↗
Sensitive assay for detection of hepatocellular carcinoma associated gene transcription (alpha-fetoprotein mRNA) in blood.
The sensitivity of RT-PCR and nested RT-PCR for detection of circulating hepatocellular carcinoma was assessed by demonstrating the tumor cell-associated gene transcription, alpha-fetoprotein mRNA, in the nuclear cells of peripheral blood. When HepG2 cells were mixed in blood, 100-1000 tumor cells/5ml of blood could be detected by RT-PCR, in contrast to 1-10 tumor cells/5ml of blood by nested RT-PCR. In addition, 2 x 10(4) copies of AFP mRNA were found in one HepG2 cell when analyzed by the quantitative nested RT-PCR assay. Thus, the nested RT-PCR assay could provide a useful tool for detecting a tiny amount of circulating tumor cells in patients with hepatocellular carcinoma presenting extra-hepatic metastasis.
Base Sequence↗
Susceptibility of human T-lymphotropic virus type I infected cell line MT-2 to hepatitis C virus infection.
To obtain a hepatitis C virus (HCV) proliferation system, we examined the susceptibility of various cultured cell lines to HCV infection. We found that a human T-lymphotropic virus type I infected cell line MT-2 was fairly sensitive to HCV infection. Using the polymerase chain reaction, intracellular positive-stranded HCV RNA was detected until at least 15 days postinoculation (p.i.). Intracellular negative-stranded HCV RNA was also detected at 10 days p.i., although not at 7 days p.i., suggesting that HCV is replicating in MT-2 cells 10 days p.i. Sequence analysis of hypervariable region 1 (HVR1) revealed that HVR1 sequences from cells 10 days p.i. had become homogeneous, although HVR1 sequences from the inoculum showed the typical quasi-species. We also found a lack of anti-HVR1 antibody against the HVR1 species which became homogeneous at 10 days p.i., although we easily detected antibody against the other HVR1 species obtained from the inoculum. These findings suggest that MT-2 cells are susceptible to HCV infection and are capable of supporting HCV replication.
Amino Acid Sequence↗
Expression of Saccharomyces adenylate kinase gene in Candida boidinii under the regulation of its alcohol oxidase promoter.
The methylotrophic yeast, Candida boidinii, was investigated as a new efficient host for heterologous gene expression. The Saccharomyces cerevisiae adenylate kinase gene (ADK1) was used as the first example for heterologous enzyme production in C. boidinii. C. boidinii cells were transformed with plasmids harboring the S. cerevisiae ADK1 gene under the alcohol oxidase (C. boidinii AOD1) promoter. The chromosome-integrant strains produced adenylate kinase protein corresponding to 22%-28% of the total soluble proteins in an enzymatically active form. When the three-copy integrative transformant was grown for 60 h on methanol-glycerol medium in a 1.5-l jar fermentor, adenylate kinase was produced intracellularly with a yield of up to 2 milligrams culture medium. As the expression of the S. cerevisiae ADK1 in C. boidinii was under similar regulation to that of the C. boidinii AOD1, the previously cloned 1.7-kb AOD1 promoter fragment was proved to harbor sufficient cis elements for AOD1 regulation and found to be an efficient promoter for heterologous gene expression.
Adenylate Kinase↗
Detection of Bacteroides fragilis in clinical specimens by polymerase chain reaction amplification of the neuraminidase gene.
The polymerase chain reaction (PCR) was used in an attempt to detect Bacteroides fragilis by amplifying a segment of the gene encoding B. fragilis neuraminidase. Forty-five reference strains representing 45 species and 113 clinical isolates were tested. Only B. fragilis was PCR positive, except for Bacteroides merdae ATCC 43184, which gave a band by ethidium bromide staining that showed no signal by Southern hybridization. Using a protocol that employed DNA extraction by Sepa Gene kit and a highly sensitive digoxigenin-chemiluminescence detection system, detection of B. fragilis by PCR was in complete agreement with culture results for 44 clinical specimens from which a wide range of aerobic and anaerobic organisms and fungi were recovered.
Bacterial Infections↗
Suppression of gelatinase production with decreased invasiveness of choriocarcinoma cells by human recombinant interferon beta.
OBJECTIVE: Choriocarcinoma is a highly invasive gynecologic tumor, and hematogenous metastases frequently develop. To establish a molecular basis for antiinvasion therapy of choriocarcinoma, we examined the effects of human recombinant interferons on gelatinase production and invasion by choriocarcinoma cells. STUDY DESIGN: Using five choriocarcinoma cell lines, we measured gelatinase activity by gelatin zymography. The effects of recombinant interferons (rIFN-alpha, rIFN-beta, and rIFN-gamma) were then analyzed by Western blot analysis and chemoinvasion assay. RESULTS: High levels of 72 kd gelatinase activity were detected in the highly invasive choriocarcinoma cell lines, two of which also contained an active form of 72 kd gelatinase with an apparent molecular mass of 68 kd. Gelatinase production was decreased by incubation with rIFN-beta. In the chemoinvasion assay, only rIFN-beta had an inhibitory effect on the invasiveness of tumor cells without a cytotoxic effect. CONCLUSION: Choriocarcinoma cells showed high 72 kd gelatinase activity, which suggested a role for the enzyme in vascular metastasis. Studies on the use of rIFN-beta to inhibit metastasis of choriocarcinoma via suppression of gelatinase production are warranted.
Choriocarcinoma↗
Altered brain contents of neuropeptides in spontaneously epileptic rats (SER) and tremor rats with absence seizures.
Immunoreactive- (IR-) somatostatin (SRIF), neuropeptide Y (NPY) and corticotropin-releasing factor (CRF) contents were investigated in the brain of tremor rats with absence-like seizure and spontaneously epileptic rats (SER), which is a genetically defined double-mutant (zi/zi, tm/tm) obtained by mating zitter homozygote (zi/zi) with tremor heterozygote (tm/+) and shows both absence-like seizure and tonic convulsions. Increased levels of IR-NPY and IR-CRF were observed in several regions including the amygdala and hippocampus in homozygous SER compared to heterozygous SER (zi/zi, tm/+ or +/+). Homozygous tremor rats (tm/tm) showed lower levels of IR-NPY and IR-CRF contents mainly in the hippocampus and mesolimbic system (entorhinal and pyriform cortex and nucleus accumbens) than heterozygous tremor rats. IR-SRIF contents of homozygous SER were higher in frontal cortex than heterozygous SER and in amygdala than homozygous tremor rats. No change of IR-SRIF between groups was noted in the hippocampus among brain structures underlying epileptogenicity. The results suggest that the change of neuropeptide levels, most conspicuous in NPY among three peptides tested, may be involved in the phenotypical manifestation of seizures in SER and tremor rats, and that the development of tonic convulsion and absence seizures may be differently associated with the change of brain neuropeptide levels.
Animals↗
Characteristic difference of hepatocellular carcinoma between hepatitis B- and C- viral infection in Japan.
Characteristics of 205 consecutive patients with hepatocellular carcinoma (HCC) admitted during 1990 to 1993 have been analyzed from the standpoint of hepatitis viral infection in Japan. Among 205 HCC patients, 71% of the patients showed positivity for hepatic C virus (HCV) antibody alone, 13% showed positivity both for HCV and HBV (HCV/HBV) antibody, 11% demonstrated HBsAg alone, and negativity of both HCV and HBV antibody in 4% only. Positivity to both HCV antibody and HBsAg was demonstrated in 1% only. Mean detection age of HCVAb-positive HCC as well as both HCV/HBV antibody-positive HCC was 62 +/- 7 years, in contrast to 52 +/- 13 years in HCC with HBsAg (P < .05). Male-to-female ratio among HCVAb-positive HCC was 3.3:1, in contrast to 5.5:1 among the HCV/HBVAb-positive HCC and 7:1 among HBsAg-positive HCC, but there was no significant difference in the gender distribution between these groups. More than 60% of HCVAb-positive HCC and HCV/HBVAb-positive HCC were classified into the stage of Child B and C, whereas 65% of HBsAg-positive HCC was at the stage of Child A. The severity of liver disease was confirmed by liver histology, indicating that more than 70% of the HCVAb-positive HCC and the HCV/HBVAb-positive HCC showed cirrhosis, in contrast to 50% among the HBsAg-positive HCC. Three-year survival rate of HCV Ab-positive HCC and HBV/HCVAb-positive HCC was 68% and 56%, respectively, in contrast to 47% in HBsAg-positive HCC.(ABSTRACT TRUNCATED AT 250 WORDS)
Adult↗
Effective absorption of nitrogen dioxide with soda lime.
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Absorption↗