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K Umene

Publications and source records attributed to K Umene.

At least 37 records · Page 2Linked to original sources
PubMed1995

A new genome type of human parvovirus B19 present in sera of patients with encephalopathy.

The possible involvement of human parvovirus B19 infection in encephalopathy has been reported. To determine the characteristics of B19 viruses involved in such cases, we molecularly cloned a part of the B19 DNAs derived from the sera of three patients with encephalopathy (B19 strains N80, N81 and N82), following amplification by PCR. The nucleotide (nt) sequences of the cloned DNAs (nt 3147-3405) were then determined. The nucleotide sequence of N80 was similar to that of the known genome type of group II. The nucleotide sequences of N81 and N82 were similar to each other, but distinctly different from those of other B19 strains reported previously. Almost the entire genome of strain N81 (nt 229-4812) was molecularly cloned following amplification by PCR. Analyses of the restriction site polymorphisms of the cloned N81 DNAs showed that N81 is distantly related to other B19 strains. Therefore, the two strains of N81 and N82 were defined as belonging to a new genome type, group V. Group V B19 virus has so far been isolated only from patients with encephalopathy.

Base Composition↗
PubMed1994

Preparation of herpes simplex virus type 1 genomic markers to differentiate strains of predominant genotypes.

Analyses of restriction fragment length polymorphism (RFLP) of herpes simplex virus type 1 (HSV-1) isolated in Japan using restriction endonucleases recognizing 6-base pairs revealed the presence of two predominant genotypes of F1 and F35. Therefore, the possibility that the two predominant genotypes may differ in clinical manifestations had to be considered. To address the question of whether differences in genotype would reflect clinical presentations of HSV-1 infection, RFLP markers to differentiate strains of predominant genotypes are required. In the present work, DNAs of 66 HSV-1 strains were analyzed, using restriction endonucleases recognizing 4-base pairs of HaeIII, HhaI, and MboI, the objective being to detect a large number of RFLP. The relationship between the 154 identified RFLPs and each predominant genotype of F1 and F35 was traced. RFLPs closely related to each predominant genotype were manifested, as the first case of a set of RFLPs diagnostic for the predominant genotypes. These diagnostic RFLPs will facilitate knowledge on association of predominant genotypes with clinical manifestations by efficiently identifying HSV-1 strains of a genotype, and, in addition, HSV-1 strains of a predominant genotype derived from a common ancestor.

Animals↗
PubMed1994

Quantitative analysis of genomic polymorphism of herpes simplex virus type 1 strains from six countries: studies of molecular evolution and molecular epidemiology of the virus.

Using the presence or absence of 63 variable restriction endonuclease (RE) sites selected from 225 sites with six REs, genomic polymorphism of 242 herpes simplex virus type 1 (HSV-1) strains from six countries (Japan, Korea, China, Sweden, U.S.A. and Kenya) was quantitatively analysed. Twenty-five of the 63 sites were found to differ between Korean and Kenyan strains. In contrast, only three and six sites were found to differ between isolates from Sweden and the U.S.A. and between those from Korea and China, respectively, suggesting that they are closely related to each other. In this way, characterization of 63 sites enabled us to categorize 186 distinct HSV-1 genotypes from 242 individuals. Some strains from Japan, Korea and China shared the same genotypes, indicating that they are phylogenetically closely related. Many significant correlation coefficients (magnitude of > 0.42; P < 0.01) between pairs of sites were found in isolates from the three Asian countries (Japan, Korea and China) as well as in those from Sweden and the U.S.A., suggesting that HSV-1 strains from within the same ethnic groups are evolutionarily closer. The average number of nucleotide substitutions per nucleotide, as defined by nucleotide diversity (pi), was estimated for HSV-1 genomes within (pi x or pi y) and between (pi xy) countries. On the basis of 225 sites, nucleotide diversity for Kenyan isolates was 0.0056, almost three times higher than that for Korean isolates, implying that Kenyan HSV-1 genomes are much more diverse than those from Korea. In addition, the diversity between HSV-1 isolates from different countries (pi xy) was highest between isolates from the three Asian countries and Kenya (0.0075 to 0.0081) and lowest among those from the three Asian countries (0.0032 to 0.0040). The mutation rate (lambda) for HSV-1 was estimated to be 3.5 x 10(-8)/site/year. All these findings show that the evolution of HSV-1 may be host-dependent and very slow.

Biological Evolution↗
PubMed1994

Excision of DNA fragments corresponding to the unit-length a sequence of herpes simplex virus type 1 and terminus variation predominate on one side of the excised fragment.

DNA fragments corresponding to the unit-length a sequence of herpes simplex virus type 1 (HSV-1) were identified in HSV-1 DNA preparations extracted by the method of Hirt. The DNA fragments were molecularly cloned, and nucleotide sequences were determined. Most termini of the fragments were at sites on DR1 corresponding to the termini of linear HSV-1 DNA generated by the cleavage-packaging system. In one-step growth experiments, DNA fragments of the unit-length a sequence appeared simultaneously with the termini of linear HSV-1 DNAs produced by cleavage of circular and concatemeric DNAs. Therefore, excision of the unit-length a sequence appeared closely related to the cleavage-packaging system. Termini of the excised DNA fragments of the variant a sequence with two DR2 arrays varied on the L-component side, while termini on the S-component side were at the site on DR1 corresponding to the authentic cleavage site. It is thus assumed that the cleavage-packaging system functions adequately on the DR1 second distal from the S component, and cleavages of other DR1 are rare and less accurate. If this notion is tenable, then most termini on the S-component side of the excised DNA fragments are derived from the second DR1 properly cleaved and should be constant, while termini on the L-component side are from regions on and around the DR1 third distal from the S component and may be variable. Cleavage of DR1 is likely to be affected by the topological relationship with the S component.

Animals↗
PubMed1993

Partial nucleotide sequencing and characterization of human parvovirus B19 genome DNAs from damaged human fetuses and from patients with leukemia.

While human parvovirus B19 is associated with fetal damage and chronic suppression of bone marrow in patients with leukemia, much less is known of the genomic characteristics of B19 isolated from damaged human fetuses and leukemia patients. B19 genome DNAs from human fetal organs and fluids and sera from leukemia patients were amplified by the polymerase chain reaction. The nucleotide sequences of amplified products in the region between nucleotide (nt) 3141 and nt3411 were determined following molecular cloning in M13 phage. The genome types of B19 from the fetuses and leukemia patients were similar to the types from patients with aplastic crisis and an asymptomatic individual. Wide diversity of the nucleotide sequence, i.e., six or more (6-11) substitutions, were evident in ten M13 phage clones of each DNA source from fetal materials, while substitutions in sera from patients with leukemia and aplastic crisis and of an asymptomatic individual numbered four or fewer (0-4). This wide diversity of B19 viruses in the fetus, revealed after many rounds of DNA replication, probably depends on a persistent state of infection.

Adolescent↗
PubMed1993

The US 9, 10, 11, and 12 genes of herpes simplex virus type 1 are of no importance for its neurovirulence and latency in mice.

We have studied the pathogenic and latency/reactivation potential of a herpes simplex virus type 1 (HSV-1) variant (N38) which has a deletion of four genes, US9, US10, US11, and US12, in the short unique region of the HSV-1 genome. N38 was as pathogenic as the parental wild-type virus following intracerebral infection of mice and replicated with wild-type kinetics in the brain. After intraperitoneal infection, some restricted replication of N38 was observed in the adrenal gland and the deletion virus was about 20-fold less virulent than the parental virus. There was no significant difference between two viruses in the frequency of reactivation or in reactivation time. The results indicate that US9, US10, US11, and US12 gene products are dispensable for its neurovirulence and latency in mice.

Animals↗
PubMed1993

Genomic characterization of two predominant genotypes of herpes simplex virus type 1.

Genomic profiles of 66 strains of herpes simplex virus type 1 (HSV-1) isolated in Japan were investigated with regard to restriction fragment length polymorphism (RFLP) and length variation of fragments containing reiterations. There were two predominant genotypes of F1 and F35, and the genomic characteristics of each were studied. The nucleotide change between F1 and F35 was estimated to be 1.5%. An RFLP marker (VR23) peculiar to genotype F35 was identified as the first case of genomic marker specific to a predominant genotype of HSV-1, and is the diagnostic marker of F35. The a sequences (repeating in an HSV-1 genome and containing reiterations) of F35 were cleaved by SacII on the DR4 (direct repeat 4) stretch, while a sequences of F1 had a rearranged DR4 and were resistant to SacII digestion. Thus, analyses of fragments containing reiterations, such as a sequences, can serve to classify HSV-1 strains as well as for purpose of differentiation. The proportion of strains derived from primary infection to those from recurrent infection was higher in strains of F35 than in those of F1, and this genotypic difference within HSV-1 may possibly influence clinical manifestations.

Animals↗
PubMed1993

Herpes simplex virus type 1 variant a sequence generated by recombination and breakage of the a sequence in defined regions, including the one involved in recombination.

A herpes simplex virus type 1 clone, GN29, having exclusively the variant a sequence was isolated. This a sequence was composed of unique (U) and directly repeated (DR) elements DR1, Ub, (DR2)14, Ucd, Ubd, (DR2)5, DR4n2, and Uc and was assumed to be generated by recombination between sites in Ub and Uc. Unusual DNA fragments containing parts of the a sequence, present in the DNA preparations of GN29, were molecularly cloned. Almost all termini of the cloned unusual DNA fragments were situated in defined regions assumed to be recombinogenic: (i) a site in the inverted repeat of the L component, (ii) DR1, (iii) DR2, (iv) the DR4 stretch, and (v) the novel recombination stretch in the variant a sequence of GN29. The termini of unusual DNA fragments, possibly produced by strand breaks, can serve as free DNA ends to initiate recombination of the a sequence. These results support the model of double-strand-break repair for recombination of the a sequence. Sequence-specific enhancement of the recombination of the a sequence probably depends on the presence of recombinogenic elements apt to break, such as DR2 repeats and the DR4 stretch.

Base Sequence↗
PubMed1991

Homogeneity and diversity of genome polymorphism in a set of herpes simplex virus type 1 strains classified as the same genotypic group.

Restriction fragment length polymorphism (RFLP) of 327 strains of herpes simplex virus type 1 (HSV-1) isolated in Japan were analyzed using six restriction endonucleases (REs) recognizing 6 base pairs (BamHI, HindIII, KpnI, PvuII, SalI, XhoI). The presence of strains with the same RFLP profile became evident. Fifteen strains of each of the two predominant sets with the same RFLP profile were further analyzed using two different methods, that is analyses of RFLP using 3 restriction endonucleases recognizing 4 base pairs (4-bp REs) (HaeIII, HhaI, MboI) and analyses of the variation of 3 reiterated sequences (reiterations I, IV, VII). Most of the epidemiologically unrelated strains could be differentiated by variation of the reiterations. RFLPs differentiating the strains were detected with the 4-bp REs, and epidemiologically related strains shared a specific RFLP, thereby confirming the relationship. These results verified the utility of the two methods for use in molecular epidemiological studies. Homogeneity of RFLP among the strains suggested derivation from a common ancestor (making up a genotypic group) while diversity in strains of the same genotypic group was indicative of a separate replication.

Animals↗
PubMed1991

Genetic diversity of human parvovirus B19 determined using a set of restriction endonucleases recognizing four or five base pairs and partial nucleotide sequencing: use of sequence variability in virus classification.

Analysis of the restriction site polymorphism (RSP) of human parvovirus B19 using 12 restriction endonucleases (REs) recognizing four or five bp sequences (4- or 5-bp REs) revealed a significant difference between strains previously classified as being of the same genome type, and a relationship between two strains of different genome types, thereby indicating a global spread of B19 virus strains. These findings demonstrate the advantage of this set of 4- and 5-bp REs for the calculation of the degree of genetic diversity and clearly it is necessary to amend the taxonomy of B19 virus strains using these REs. We examined the nucleotide (nt) sequence between nt 3141 and 3411, at the N terminus of the VP2 protein coding region, in 12 B19 virus strains. The pattern of distribution of nucleotide differences between the strains confirmed the classification by RSP analysis. Between nt 3293 and nt 3364, a region in which an antigenic epitope may be encoded, there was no evidence of a nucleotide change causing an amino acid change. Thus, the amino acid sequence in this potential epitope is probably conserved.

Cloning, Molecular↗
PubMed1991

Recombination of the internal direct repeat element DR2 responsible for the fluidity of the a sequence of herpes simplex virus type 1.

A series of herpes simplex virus type 1 derivatives, having a sequences composed of DR1, Ub, (DR2)3-7, DR4t (a truncated form of DR4), and Uc were isolated and examined. The derivative having a sequences with six copies of DR2 generated progeny viruses having a sequences with the same number (six copies) of DR2. Another derivative, having a sequences with three and seven copies of DR2, generated progeny viruses having a sequences with varied numbers (4, 5, 8, and 10 copies) of DR2, besides the original DR2 arrays (three and seven copies). Therefore, the variation in copy number of DR2 was assumed to be caused mainly by recombination between DR2 arrays rather than by slippage within a DR2 array during DNA replication. The presence of DR2-like sequences in internal direct repeat elements of DR4 and DR3.5 supported the hypothesis of the recombinogenic property of DR2. The equal distribution of divergence of a sequences to both ends of the virus genome favors the double-strand break and gap repair model to explain gene conversion and amplification of the a sequence.

Animals↗
PubMed1990

The genome type of human parvovirus B19 strains isolated in Japan during 1981 differs from types detected in 1986 to 1987: a correlation between genome type and prevalence.

The genome DNAs of 12 strains of human parvovirus B19, isolated in Japan at two different times, 1981 and 1986 to 1987, were molecularly cloned in the plasmid pUC18. The cloned B19 DNAs were analysed by cleaving with restriction endonucleases, and were classified into several groups by genome type. The restriction endonuclease cutting patterns of B19 strains isolated during 1981 were similar to that of the group IV genome type, and the patterns of those isolated later were similar to that of group II, suggesting a correlation between the genome type and the prevalence. We conclude that the prevalences of B19 infection in Japan during 1981 and in 1986 to 1987 were caused by viruses differing in genome type, and that B19 viruses with similar genome types disseminated widely in Japan during each prevalence.

DNA, Viral↗
PubMed1989

Reiterated sequences of herpes simplex virus type 1 (HSV-1) genome can serve as physical markers for the differentiation of HSV-1 strains.

The stability of regions containing tandemly reiterated sequences in the S component of the herpes simplex virus type 1 (HSV-1) genome was determined, by comparing restriction fragments of the regions among sets of HSV-1 isolates derived from a single source. The 6 reiterations examined were grouped into three. Reiteration VII (within protein coding regions of genes US10 and US11) and reiteration IV (within introns of genes US1 and US12) were stable between the isolates (group 1). Regions containing one of four other reiterations were detected as a set of ladder-like fragments. Reiteration II (between "a" sequence and IE 175 gene) and reiteration VI (within an intergenic region on the 3' side of the 3' co-terminal family of genes US10, US11, and US12) (group 3) were more unstable than reiteration I (within "a" sequence) and reiteration III (between "a" sequence and IE175 gene) (group 2). The mode of fluctuation of the reiterations observed within a set of HSV-1 strains isolated from an individual was similar to that observed between HSV-1 single-plaque clones separated in cultured cells. These reiterations, except for group 3, can serve as sensitive and convenient markers for differentiating HSV-1 strains.

Animals↗
PubMed1989

Short, duplicated sequence indicative of the recombinogenicity of the junction between a unique and an inverted repeat sequence in the S component of the herpes simplex virus type 1 genome.

A herpes simplex virus type 1 (HSV-1) strain, B3, was found to have a short duplication on the left junction between the unique sequence (US) and the inverted repeat sequence (RS) in the S component of the genome DNA. A short region of RS contiguous to the left US-RS junction was duplicated in B3. Based on the nucleotide sequences in and around the US-RS junctions of B3 and other HSV-1 strains, a concept of junction stretch was proposed. The organization of junction stretch is RS side 5'-(G or A stretch)AGC-3' US side. Introduction of the concept of junction stretch led to a definition of the structure in and around the US-RS junction, in the form common to HSV-1 strains. The right end of US in the HSV-1 genome was the A of the ATG initiation codon of gene US12, and thus the ATG triplet may act as a buffer to prevent expansion of RS, as is the case with HSV-2. The duplication in B3 was generated by a crossover event between a point on RS and the US side end of the left junction stretch. These observations suggest that the US side end of the junction stretch possesses the property of recombinogenicity, responsible for generation of the duplication in strain B3 and also for the formation of the US-RS junction of HSV.

Animals↗