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1.
Sci Rep ; 7(1): 14841, 2017 11 01.
Article in English | MEDLINE | ID: mdl-29093526

ABSTRACT

Spermine oxidase (SMOX) catalyzes oxidation of spermine to generate spermidine, hydrogen peroxide (H2O2) and 3-aminopropanal, which is spontaneously converted to acrolein. SMOX is induced by a variety of stimuli including bacterial infection, polyamine analogues and acetaldehyde exposure. However, the physiological functions of SMOX are not yet fully understood. We investigated the physiological role of SMOX in liver cells using human hepatocellular carcinoma cell line HepG2. SMOX localized to the bile canalicular lumen, as determined by F-actin staining. Knockdown of SMOX reduced the formation of bile canalicular lumen. We also found that phospho-Akt (phosphorylated protein kinase B) was localized to canalicular lumen. Treatment with Akt inhibitor significantly reduced the formation of bile canalicular lumen. Acrolein scavenger also inhibited the formation of bile canalicular lumen. PTEN, phosphatase and tensin homolog and an inhibitor of Akt, was alkylated in a SMOX-dependent manner. Our results suggest that SMOX plays a central role in the formation of bile canalicular lumen in liver cells by activating Akt pathway through acrolein production.


Subject(s)
Acrolein/metabolism , Bile Canaliculi/ultrastructure , Oxidoreductases Acting on CH-NH Group Donors/physiology , Actins/metabolism , Aldehydes/metabolism , Alkylation , Bile Canaliculi/chemistry , Hep G2 Cells , Humans , Oxidoreductases Acting on CH-NH Group Donors/analysis , Oxidoreductases Acting on CH-NH Group Donors/genetics , PTEN Phosphohydrolase/metabolism , Phosphorylation , Propylamines/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Polyamine Oxidase
2.
Pathophysiology ; 21(4): 309-16, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25270870

ABSTRACT

INTRODUCTION: The literature described that neural damage caused by ischemia definitely occurs in brain areas. However, few studies have shown real-time changes of extracellular monoamine levels at the time of transient ischemia. METHODS: We examined changes in the responses of dopamine (DA) and serotonin (5-HT) release in the nucleus accumbens (ACC) of rats treated with four-vessel occlusion (4VO) in experiment 1. In the second experiment, we investigated the selective neural vulnerabilities among the ACC, lateral hypothalamus (LH), and frontal cortex (FC) of rats treated with 4VO and four days of reperfusion. RESULTS: The extracellular levels of DA and 5-HT were remarkably increased 200- and 20-fold upon the 10-min clipping of both common carotid arteries in transient cerebral ischemia, respectively. Each increased monoamine release returned to the baseline levels immediately. The release of DA in the ACC and FC was significantly decreased in the rats treated with the coagulation of bilateral vertebral arteries (2VO), compared with that of sham-operated rats. K(+)-induced DA release in the ACC and FC of 4VO-treated rats was increased without alteration of DA content. DISCUSSION: Surviving dopaminergic neurons in the ACC and FC showed neural hyperfunction associated with the monoamine release, serotonergic neurons in particular these areas exhibiting functional resistance to the transient ischemic change. CONCLUSION: It is suggested that the remarkable extracellular release of DA and 5-HT was not the cause of the ischemic delayed neural degeneration in each brain area, and that the functions of neurotransmitter release involved remarkable resistance to the transient ischemia.

3.
Toxicology ; 310: 1-7, 2013 Aug 09.
Article in English | MEDLINE | ID: mdl-23707493

ABSTRACT

Ethanol consumption causes serious liver injury including cirrhosis and hepatocellular carcinoma. Ethanol is metabolized mainly in the liver to acetic acid through acetaldehyde. We investigated the effect of ethanol and acetaldehyde on polyamine metabolism since polyamines are essential factors for normal cellular functions. We found that acetaldehyde induced spermine oxidase (SMO) at the transcriptional level in HepG2 cells. The levels and activities of ornithine decarboxylase (ODC) and spermidine/spermine acetyltransferase (SSAT) were not affected by acetaldehyde. Spermidine content was increased and spermine content was decreased by acetaldehyde treatment. Knockdown of SMO expression using siRNA reduced acetaldehyde toxicity. Acetaldehyde exposure increased free acrolein levels. An increase of acrolein by acetaldehyde was SMO dependent. Our results indicate that cytotoxicity of acetaldehyde involves, at least in part, oxidation of spermine to spermidine by SMO, which is induced by acetaldehyde.


Subject(s)
Acetaldehyde/toxicity , Ethanol/toxicity , Oxidoreductases Acting on CH-NH Group Donors/biosynthesis , Transcription, Genetic , Acetyltransferases/metabolism , Acrolein/metabolism , Blotting, Western , Cell Proliferation/drug effects , Cell Survival/drug effects , Enzyme Induction , Hep G2 Cells , Humans , Ornithine Decarboxylase/metabolism , Oxidation-Reduction , Oxidoreductases Acting on CH-NH Group Donors/genetics , Polyamines/metabolism , RNA, Small Interfering/genetics , Reverse Transcriptase Polymerase Chain Reaction , Polyamine Oxidase
4.
Leg Med (Tokyo) ; 14(3): 121-5, 2012 May.
Article in English | MEDLINE | ID: mdl-22285643

ABSTRACT

In criminal investigations, usually it is necessary to identify whether blood spots found at crime scenes are from humans or not. Nowadays, immunohistochemical methods and DNA analysis are usually used for this purpose. However, such methods and DNA analysis are labor intensive and expensive, and require highly trained skilled technicians. Recently, the genome profiling method (GP method) was developed. However, its use as a human DNA analysis method has not been reported. In this report, an attempt was made to differentiate human blood samples from animal blood samples using the GP method for forensic purposes. DNA extracted from a rat, squirrel, cat, dog, cow, and antelope along with human blood samples were analyzed. Following cluster analysis the human samples clustered into a single group separate from the animal samples. Therefore, although the number of samples was small the results suggest that the GP method might enable us to differentiate human samples from various animal samples. It may become a powerful tool in the field of forensic science.


Subject(s)
Blood , DNA Fingerprinting/methods , Forensic Medicine , Genome/genetics , Animals , Humans
5.
Leg Med (Tokyo) ; 13(5): 265-7, 2011 Sep.
Article in English | MEDLINE | ID: mdl-21684187

ABSTRACT

The identification of sperm at the scene of a sexual crime is important evidence that can be used to prove that a crime took place. We used the new genome profiling (GP) method in this study to identify sperm and vaginal fluid from RNA extracted from bodily fluids. We randomly amplified genes via a PCR approach from these semen and vaginal fluid samples and performed temperature gradient gel electrophoresis between 15-65°C. We identified specific species identification dots (spiddos) for semen and vaginal fluid. The results showed that the GP method is effective for the identification of bodily fluids at the scene of a sex crime.


Subject(s)
RNA , Rape/diagnosis , Semen , Vaginal Smears , Adult , DNA Fingerprinting , Female , Forensic Genetics , Humans , Japan , Male , Middle Aged
6.
J Clin Microbiol ; 49(3): 1122-3, 2011 Mar.
Article in English | MEDLINE | ID: mdl-21248094

ABSTRACT

To evaluate the risk of accidental hepatitis C virus (HCV) infection, we examined whether anti-HCV antibodies and HCV RNA were detectable in HCV-infected blood samples from living donors, cadavers, and bloodstains. We showed that even after blood has left the body for several days, anti-HCV antibodies and HCV RNA may persist in it.


Subject(s)
Blood Stains , Blood/immunology , Blood/virology , Hepacivirus/isolation & purification , Hepatitis C Antibodies/blood , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Occupational Exposure , Risk Assessment , Time Factors
7.
Forensic Sci Int ; 209(1-3): 48-52, 2011 Jun 15.
Article in English | MEDLINE | ID: mdl-21239123

ABSTRACT

Recently, in the field of forensic medicine the number of unidentified cadavers has increased due to mass disasters and international terrorism. In addition to the conventional anthropological methods, a simple and precise method to estimate the age of these unidentified cadavers to assist in the personal identification is necessary. On the other hand, many researchers have reported that mitochondrial respiratory activity decreases with aging because of the production of reactive oxidative species in the process of ATP generation. Therefore, it may be possible for us to estimate human age by analyzing mitochondrial activity. In this report we attempted to analyze cytochrome c oxidase (CCO) activity, and the amount of protein and mRNA expression in various aged rats. The age of human subjects was estimated through the analysis of human CCO activity from 28 actual forensic cases. The CCO activity, the amount of protein and the mRNA expression increased in the 3rd week and decreased afterwards in rats. Furthermore, human CCO activity was decreased gradually with aging. Therefore, CCO activity analysis may be useful for age estimation in forensic cases.


Subject(s)
Aging/metabolism , Electron Transport Complex IV/metabolism , Mitochondrial Proteins/metabolism , RNA, Messenger/metabolism , Adult , Aged , Animals , Blotting, Western , Child , Child, Preschool , Electron Transport Complex IV/genetics , Female , Forensic Medicine , Humans , Infant , Male , Middle Aged , Mitochondria/metabolism , Mitochondrial Proteins/genetics , Myocardium/metabolism , Rats , Rats, Sprague-Dawley , Young Adult
8.
Microbes Infect ; 9(2): 204-13, 2007 Feb.
Article in English | MEDLINE | ID: mdl-17208484

ABSTRACT

BK polyomavirus (BKV) is ubiquitous in human populations, infecting children asymptomatically and then persisting in the kidney, in which it can cause nephropathy in renal transplant patients. BKV isolates are classified into four subtypes (I-IV) using serological or genotyping methods, and subtype I is further divided into four subgroups, Ia, Ib-1, Ib-2, and Ic, based on DNA sequence variations. To clarify whether there is an association between BK virus lineages and human populations, we examined BKV-positive urine samples collected from immunocompetent individuals at various locations in Europe, Africa, and Asia. Partial BKV DNA sequences (n=299) in these samples were determined and subjected to phylogenetic and single nucleotide polymorphism analysis to classify BKV isolates around the world. The validity of the classification was confirmed by analyses based on complete BKV DNA sequences. Subtype I was the major subtype throughout the studied regions, and subtype IV was prevalent only in Asia and Europe. Subtype-I subgroups showed close relationships to major geographical areas. It has recently been shown that JC virus (a human polyomavirus closely related to BKV) co-evolved with human populations, and the present study thus suggests that host-linked evolution is the general mode of polyomavirus evolution. Additionally, our results indicate certain unique aspects of the relationship between BKV and humans.


Subject(s)
BK Virus/classification , BK Virus/genetics , Polyomavirus Infections/virology , Tumor Virus Infections/virology , Africa , Asia , DNA, Viral/chemistry , DNA, Viral/genetics , Europe , Geography , Humans , Phylogeny , Polymorphism, Single Nucleotide , Polyomavirus , Sequence Analysis, DNA , Urine/virology
9.
J Mol Evol ; 63(3): 341-52, 2006 Sep.
Article in English | MEDLINE | ID: mdl-16897259

ABSTRACT

The human polyomavirus BK virus (BKV) is ubiquitous in humans, infecting children asymptomatically. BKV is the only primate polyomavirus that has subtypes (I-IV) distinguishable by immunological reactivity. Nucleotide (nt) variations in a major capsid protein (VP1) gene region (designated the epitope region), probably responsible for antigenic diversity, have been used to classify BKV isolates into subtypes. Here, with all the protein-encoding gene sequences, we attempted to elucidate the evolutionary relationships among 28 BKV isolates belonging to subtypes I, III, and IV (no isolate belonging to subtype II, a minor one, was included). First, using the GTR + Gamma + I model, maximum likelihood trees were reconstructed for individual viral genes as well as for concatenated viral genes. On the resultant trees, the 28 BKV isolates were consistently divided into three clades corresponding to subtypes I, III, and IV, although bootstrap probabilities are not always high. Then we used more sophisticated likelihood models, one of which takes account of codon structure, to elucidate the phylogenetic relationships among BKV subtypes, but the phylogeny of the deep branchings remained ambiguous. Furthermore, the possibility of positive selection in the evolution of BKV was examined using the nonsynonymous/synonymous rate ratio as a measure of selection. An analysis based on entire genes could not detect any strong evidence for positive selection, but that based on the epitope region identified a few sites potentially under positive selection (these sites were among those showing subtype linked polymorphisms).


Subject(s)
BK Virus/genetics , Evolution, Molecular , Genome, Viral , Adaptation, Physiological/genetics , Models, Genetic , Phylogeny , Selection, Genetic , Time Factors
10.
J Gen Virol ; 87(Pt 7): 1893-1901, 2006 Jul.
Article in English | MEDLINE | ID: mdl-16760391

ABSTRACT

BK polyomavirus (BKPyV) is ubiquitous in human populations, infecting children without obvious symptoms and persisting in the kidney. BKPyV isolates have been classified into four subtypes (I-IV) using either serological or genotyping methods. In general, subtype I occurs most frequently, followed by subtype IV, with subtypes II and III rarely detected. As differences in growth capacity in human cells possibly determine the proportion of the four subtypes of BKPyV in human populations, here the growth properties of representative BKPyV strains classified as subtype I or IV in renal proximal tubule epithelial cells (HPTE cells) of human origin were analysed. HPTE cells were transfected with four and three full-length BKPyV DNAs belonging to subtypes I and IV, respectively, and cultivated in growth medium. Virus replication, detected using the haemagglutination assay, was observed in all HPTE cells transfected with subtype I BKPyV DNAs, whereas it was markedly delayed or not detected in those transfected with subtype IV BKPyV DNAs. It was confirmed that the transfected viral DNAs induced virus replication in HPTE cells. Furthermore, it was found that BKPyVs with archetypal transcriptional control regions replicated in HPTE cells, with only the occasional emergence of variants carrying rearranged transcriptional control regions. Essentially the same results as described above were obtained with renal epithelial cells derived from whole kidney. Thus, it was concluded that subtype I BKPyV replicates more efficiently than subtype IV BKPyV in human renal epithelial cells, supporting the hypothesis that growth capacity in human cells is related to the proportion of BKPyV subtypes in human populations.


Subject(s)
BK Virus/classification , BK Virus/physiology , BK Virus/genetics , Cells, Cultured , Chimera/genetics , DNA, Viral/genetics , Epithelial Cells/virology , Genome, Viral , Humans , Kidney/cytology , Kidney/virology , Kidney Tubules, Proximal/cytology , Kidney Tubules, Proximal/virology , Models, Biological , Molecular Sequence Data , Species Specificity , Transcription, Genetic , Transfection , Virus Cultivation , Virus Replication/genetics , Virus Replication/physiology
11.
J Gen Virol ; 87(Pt 2): 303-306, 2006 Feb.
Article in English | MEDLINE | ID: mdl-16432015

ABSTRACT

To clarify the stability of the BK polyomavirus (BKPyV) genome in renal transplant (RT) recipients, three to five complete BKPyV genomes from each of six RT recipients with surviving renal allografts were molecularly cloned. The complete sequences of these clones were determined and compared in each patient. No nucleotide difference was detected among clones in two patients, and a few nucleotide variations were found among those in four patients. In each of these patients a parental sequence (usually the major sequence), from which variant sequences (usually minor sequences) with nucleotide substitutions would have been generated, were identified. A comparison between the parental and variant sequences in each patient identified a single nucleotide substitution in each variant sequence. From these findings, it was concluded that the genome of BKPyV is stable in RT recipients without nephropathy, with only minor nucleotide substitutions in the coding region.


Subject(s)
BK Virus/genetics , Capsid Proteins/genetics , Genetic Variation , Genome, Viral , Kidney Transplantation , BK Virus/physiology , Cytomegalovirus Infections/complications , Humans , Kidney Diseases/virology , Molecular Sequence Data , Phylogeny
12.
Am J Phys Anthropol ; 129(3): 465-72, 2006 Mar.
Article in English | MEDLINE | ID: mdl-16331656

ABSTRACT

Both mtDNA and the Y chromosome have been used to investigate how modern humans dispersed within and out of Africa. This issue can also be studied using the JC virus (JCV) genotype, a novel marker with which to trace human migrations. Africa is mainly occupied by two genotypes of JCV, designated Af1 and Af2. Af1 is localized to central/western Africa, while Af2 is spread throughout Africa and in neighboring areas of Asia and Europe. It was recently suggested that Af1 represents the ancestral type of JCV, which agrees with the African origin of modern humans. To better understand the origin of modern Africans, we examined the phylogenetic relationships among Af2 isolates worldwide. A neighbor-joining phylogenetic tree was constructed based on the complete JCV DNA sequences of 51 Af2 isolates from Africa and neighboring areas. According to the resultant tree, Af2 isolates diverged into two major clusters, designated Af2-a and -b, with high bootstrap probabilities. Af2-a contained isolates mainly from South Africa, while Af2-b contained those from the other parts of Africa and neighboring regions of Asia and Europe. These findings suggest that Af2-carrying Africans diverged into two groups, one carrying Af2-a and the other carrying Af2-b; and that the former moved to southern Africa, while the latter dispersed throughout Africa and to neighboring regions of Asia and Europe. The present findings are discussed with reference to relevant findings in genetic and linguistic studies.


Subject(s)
Emigration and Immigration , JC Virus/genetics , Phylogeny , Africa , Base Sequence , Cluster Analysis , DNA Primers , Genotype , Humans , Molecular Sequence Data , Sequence Analysis, DNA
13.
Biochem Biophys Res Commun ; 333(3): 996-1002, 2005 Aug 05.
Article in English | MEDLINE | ID: mdl-15964545

ABSTRACT

Recently, we found that JC polyomavirus (JCPyV) associated with progressive multifocal leukoencephalopathy (PML) frequently undergoes amino acid substitutions (designated VP1 loop mutations) in the outer loops of the major capsid protein, VP1. To further characterize the mutations, we analyzed the VP1 region of the JCPyV genome in brain-tissue or cerebrospinal fluid samples from 20 PML patients. VP1 loop mutations occurred far more frequently than silent mutations. Polymorphic residues were essentially restricted to three positions (55, 60, and 66) within the BC loop, one (123) within the DE loop, and three (265, 267, and 269) within the HI loop. The mutations at most polymorphic residues showed a trend toward a change to specific amino acids. Finally, we presented evidence that the VP1 loop mutations were associated with the progression of PML. These findings should form the basis for elucidating the biological significance of the VP1 loop mutations.


Subject(s)
JC Virus/genetics , Leukoencephalopathy, Progressive Multifocal/virology , Mutation , Autopsy , Base Sequence , Brain/pathology , Brain/virology , Capsid Proteins/chemistry , Capsid Proteins/isolation & purification , DNA Primers , DNA, Viral/cerebrospinal fluid , DNA, Viral/genetics , Disease Progression , Humans , JC Virus/isolation & purification , Polymerase Chain Reaction
14.
J Gen Virol ; 86(Pt 7): 2035-2045, 2005 Jul.
Article in English | MEDLINE | ID: mdl-15958683

ABSTRACT

JC polyomavirus (JCPyV) causes progressive multifocal leukoencephalopathy (PML) in patients with decreased immune competence. To elucidate genetic changes in JCPyV associated with the pathogenesis of PML, multiple complete JCPyV DNA clones originating from the brains of three PML cases were established and sequenced. Although unique rearranged control regions occurred in all clones, a low level of nucleotide variation was also found in the coding region. In each case, a parental coding sequence was identified, from which variant coding sequences with nucleotide substitutions would have been generated. A comparison between the parental and variant coding sequences demonstrated that all 12 detected nucleotide substitutions gave rise to amino acid changes. Interestingly, seven of these changes were located in the surface loops of the major capsid protein (VP1). Finally, 16 reported VP1 sequences of PML-type JCPyV (i.e. derived from the brain or cerebrospinal fluid of PML patients) were compared with their genotypic prototypes, generated as consensus sequences of representative archetypal isolates belonging to the same genotypes; 13 VP1 proteins had amino acid changes in the surface loops. In contrast, VP1 proteins from isolates from the urine of immunocompetent and immunosuppressed patients rarely underwent mutations in the VP1 loops. The present findings suggest that PML-type JCPyV frequently undergoes amino acid substitutions in the VP1 loops. These polymorphisms should serve as a new marker for the identification of JCPyV isolates associated with PML. The biological significance of these mutations, however, remains unclear.


Subject(s)
Capsid Proteins/chemistry , Capsid Proteins/genetics , JC Virus/genetics , Leukoencephalopathy, Progressive Multifocal/physiopathology , Leukoencephalopathy, Progressive Multifocal/virology , Polymorphism, Genetic , Adult , Amino Acid Substitution , Brain/virology , Cerebrospinal Fluid/virology , Female , Humans , JC Virus/classification , JC Virus/isolation & purification , Male , Middle Aged , Molecular Sequence Data , Phylogeny , Sequence Analysis, DNA , Urine/virology
15.
Am J Phys Anthropol ; 128(1): 185-93, 2005 Sep.
Article in English | MEDLINE | ID: mdl-15778974

ABSTRACT

The JC virus (JCV) genotyping method was used to gain insights into the population history of the Saami and the Finns, both speaking Finno-Ugric languages and living in close geographic proximity. Urine samples from Saami and Finns, collected in northern and southern Finland, respectively, were used to amplify a 610-bp JCV-DNA region containing abundant type-specific mutations. Based on restriction site polymorphisms in the amplified fragments, we classified JCV isolates into one of the three superclusters of JCV, type A, B, or C. All 15 Saami isolates analyzed and 41 of 43 Finnish isolates analyzed were classified as type A, the European type, and two samples from Finns were classified as type B, the African/Asian type. We then amplified and sequenced a 583-bp JCV-DNA region from the type A isolates of Saami and Finns. According to type-determining nucleotides within the region, we classified type A isolates into EU-a1, -a2, or -b. Most type A isolates from Saami were classified as EU-a1, while type A isolates from Finns were distributed among EU-a1, EU-a2, and EU-b. This trend in the JCV-genotype distribution was statistically significant. On a phylogenetic tree based on complete sequences, most of the type A isolates from Saami were clustered in a single clade within EU-a1, while those from Finns were distributed throughout EU-a1, EU-a2, and EU-b. These findings are discussed in the context of the population history of the Saami and the Finns. This study provides new complete JCV DNA sequences derived from populations of anthropological interest.


Subject(s)
Genetic Variation/genetics , JC Virus/genetics , White People/genetics , Adult , Finland/epidemiology , Genetics, Population/methods , Genotype , Humans , Phylogeny , Sequence Analysis, DNA
16.
J Neurovirol ; 10(4): 244-9, 2004 Aug.
Article in English | MEDLINE | ID: mdl-15371154

ABSTRACT

The regulatory regions of JC virus (JCV) DNAs in the brain of patients with progressive multifocal leukoencephalopathy (PML) (designated as PML-type regulatory regions) are hypervariable, whereas those in the urine and renal tissue of individuals without PML have the same basic structure, designated as the archetype. It is thought that JCV strains with the archetypal regulatory region circulate in the human population. Nevertheless, Monaco et al (J Virol 70: 7004-7012, 1996) reported that PML-type regulatory regions occur in human tonsil tissue. The purpose of this study is to confirm their findings. Using nested polymerase chain reaction (PCR), the authors detected the regulatory region of JCV DNA in the tonsil tissue from 14 (44%) of 32 donors with tonsillitis and tonsilar hypertrophy. Sequencing of the detected regulatory regions indicated that they were identical with the archetypal regulatory regions detected previously or, in a few cases, slightly deviated from the archetype. This finding suggests not only that tonsil tissue is the potential site of initial JCV infection but also that archetypal JCV strains circulate in the human population.


Subject(s)
JC Virus/genetics , JC Virus/isolation & purification , Palatine Tonsil/pathology , Palatine Tonsil/virology , Polyomavirus Infections/diagnosis , Regulatory Sequences, Nucleic Acid/genetics , Tonsillitis/virology , Adult , Base Sequence , Cerebrospinal Fluid/virology , Female , Humans , Hypertrophy , Male , Middle Aged , Molecular Sequence Data , Polymerase Chain Reaction , Polyomavirus Infections/cerebrospinal fluid , Replication Origin/genetics , Sequence Alignment , Sequence Homology, Nucleic Acid , Tonsillitis/cerebrospinal fluid
17.
J Gen Virol ; 85(Pt 10): 2821-2827, 2004 Oct.
Article in English | MEDLINE | ID: mdl-15448343

ABSTRACT

BK polyomavirus (BKV) is ubiquitous in the human population, infecting children without obvious symptoms, and persisting in the kidney in a latent state. In immunosuppressed patients, BKV is reactivated and excreted in urine. BKV isolates have been classified into four subtypes (I-IV) using either serological or genotyping methods. To elucidate the subtypes of BKV prevalent in Japan, the 287 bp typing region in the viral genome was PCR-amplified from urine samples of 45 renal transplant (RT) and 31 bone-marrow transplant (BMT) recipients. The amplified fragments were subjected to a phylogenetic or RFLP analysis to determine the subtypes of BKV isolates in urine samples. Subtypes I, II, III and IV were detected, respectively, in 70-80, 0, 2-3 and 10-20 % of the BKV-positive patients in both patient groups. This pattern of distribution was virtually identical to patterns previously demonstrated in England, Tanzania and the United States, suggesting that BKV subtypes are distributed similarly in various human populations. Furthermore, transcriptional control regions (TCRs) were PCR-amplified from the urine samples of 25 RT and 20 BMT recipients, and their nucleotide sequences were determined. The basic TCR structure (the so-called archetype configuration) was observed in most isolates belonging to subtypes I, III and IV (subtype II isolates were not available), albeit with several nucleotide substitutions and a few single-nucleotide deletions (or insertions). Only three TCRs carried extensive sequence rearrangements. Thus, it was concluded that the archetypal configuration of the BKV TCR has been conserved during the evolution of BKV.


Subject(s)
BK Virus/classification , Transcription, Genetic , BK Virus/genetics , Base Sequence , Humans , Japan , Molecular Sequence Data , Phylogeny , Urine/virology
18.
Rev Med Virol ; 14(3): 179-91, 2004.
Article in English | MEDLINE | ID: mdl-15124234

ABSTRACT

A small DNA virus, named JC virus (JCV) and belonging to the Polyomaviridae, is attracting the attention of anthropologists worldwide, as JCV genotyping appears to be a novel means of elucidating human migrations and the origins of various ethnic groups. The basic properties of JCV, the regional distributions of JCV genotypes, and the phylogenetic relationships among various JCV genotypes are described. Then, a study is described in which the origin of the modern Japanese was extensively investigated using the JCV genotyping method. Based on JCV genotypes in neighboring areas, the origins of people who carried JCV genotypes to the Japanese Archipelago are discussed. Finally, the relationships between JCV genotypes and Y-chromosome haplogroups are examined, as genetic variation on the Y chromosome has recently been examined in detail to investigate ancient human migrations and the population structures of human groups.


Subject(s)
JC Virus/genetics , Polyomavirus Infections/virology , Tumor Virus Infections/virology , Chromosomes, Human, Y/genetics , DNA, Viral/chemistry , DNA, Viral/genetics , Emigration and Immigration , Evolution, Molecular , Genotype , Humans , Phylogeny , Polymerase Chain Reaction , Polyomavirus Infections/epidemiology , Polyomavirus Infections/urine , Tumor Virus Infections/epidemiology , Tumor Virus Infections/urine
19.
Microbes Infect ; 6(6): 596-603, 2004 May.
Article in English | MEDLINE | ID: mdl-15158194

ABSTRACT

JC virus (JCV) is a useful marker to trace human dispersal. Two genotypes of JCV (MY and CY) are mainly distributed in Northeast Asia. The population history of people carrying MY has been studied in some detail but that of people carrying CY remains poorly understood. To gain insights into the population history of Northeast Asians carrying CY we analyzed the genetic variation in CY isolates. We constructed a neighbor-joining phylogenetic tree from 28 complete CY DNA sequences: on the resultant tree the CY DNA sequences diverged into two clades, designated CY-a and -b, each clustered with a high bootstrap probability. The split into CY-a and -b was estimated to have occurred about 10 000 years ago, based on K(s) values (synonymous substitutions per synonymous site) and the suggested rate of synonymous nucleotide substitutions. Comparison of the 28 complete CY sequences revealed six nucleotide mismatches between CY-a and -b, one of which showed a restriction fragment length polymorphism (RFLP). We then PCR-amplified a region of the genome containing this polymorphic site from many CY isolates in various Northeast Asian populations and classified the isolates into CY-a or -b according to the RFLP analysis. CY-a was more abundant than CY-b in various Chinese and Japanese populations but CY-b was more abundant than CY-a in South Koreans. On the basis of the present findings we inferred the population history in East Asians carrying CY.


Subject(s)
Asian People/genetics , JC Virus/genetics , JC Virus/isolation & purification , Asia , DNA, Viral/chemistry , DNA, Viral/isolation & purification , Emigration and Immigration , Genetic Variation , Genotype , Humans , Phylogeny , Point Mutation , Polymorphism, Restriction Fragment Length , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid
20.
Am J Phys Anthropol ; 120(2): 125-32, 2003 Feb.
Article in English | MEDLINE | ID: mdl-12541330

ABSTRACT

The Philippines is generally believed to have been established by various peoples who migrated from neighboring areas. To gain new insights into the peopling of the Philippines, we used the JC virus (JCV) genotyping approach. We collected about 50 urine samples on each of two representative islands of the Philippines, Luzon and Cebu. DNA was extracted from the urine samples and used to amplify the 610-bp region (IG region) of the viral genome. For each island, we determined about 20 IG sequences, from which a neighbor-joining phylogenetic tree was constructed to classify the JCV isolates detected into distinct genotypes. The predominant genotype detected was SC, the Southeast Asian genotype. Minor JCV genotypes were SC/Phi, B1-a, and B3. SC/Phi was a subcluster of SC and has not been detected in areas other than the Philippines. B1-a was detected previously in mainland China, Pamalican Island (Palawan, Philippines), and Taiwan (an aboriginal tribe). B3 was classified in this study into two subgroups, one (B3-a) containing three Luzon isolates and several Chinese, Thai, and Uzbek isolates, the other (B3-b) containing two Luzon, one Cebu, and one Indonesian isolate. These findings suggest that the modern Filipino population was formed not only by Southeast Asians carrying SC but also by a few distinct ethnic groups carrying SC/Phi, B1-a, and B3-a or -b.


Subject(s)
DNA, Viral/analysis , Emigration and Immigration/classification , Genetic Variation/genetics , JC Virus/genetics , Polyomavirus Infections/genetics , White People/genetics , Adult , Emigration and Immigration/history , Genotype , History, 20th Century , History, Ancient , Humans , JC Virus/classification , Middle Aged , Philippines/epidemiology , Phylogeny , Polyomavirus Infections/ethnology , Polyomavirus Infections/urine , Polyomavirus Infections/virology , Sequence Analysis, DNA , Urine/virology
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