PubMed Health⌕ Search

Biomedical subjects

Kazuo Umetsu

Publications and source records attributed to Kazuo Umetsu.

At least 19 recordsLinked to original sources
PubMed2006

Origin and evolution of gene for prolactin-induced protein.

Prolactin-induced protein (PIP) is a small protein secreted into the fluid in several glands. We determined the PIP coding sequences of 5 hominoid species and estimated the numbers of synonymous and nonsynonymous substitutions for each branch of the mammalian PIP gene tree. The branch connecting hominoids and Old World monkeys showed significantly higher nonsynonymous than synonymous substitutions. These changes tended to be accumulated in the fibronectin-binding domain. Many other primate branches also showed higher nonsynonymous than synonymous substitutions, thus suggesting that the PIP genes of primates have experienced some kind of positive selection. We also considered the phylogenetic relationship of the PIP gene with the alpha-2-macroglobulin gene family. The results indicate that the PIP gene arose by partial gene duplication from a member of the alpha-2-macroglobulin gene family after the divergence between amphibians and other tetrapods.

Amino Acid Sequence↗
PubMed2006

Two universal primer sets for species identification among vertebrates.

The aim of this study was to develop a simple method using universal primers for species identification based on direct PCR sequencing. Two primer sets were designed based on the conserved regions of the 12S and 16S rRNA loci detected by the comprehensive sequence comparison among 30 mammalian whole mitochondrial genomes. In humans, the expected sizes of PCR products of the 12S and 16S rRNAs were 215 and 244 bp, respectively. Both primer sets successfully amplified the expected PCR products from various kinds of vertebrates including mammals, birds, reptiles, amphibians, and fish, and the sequenced segments contained sufficient nucleotide differences to identify each animal species. A case example of the identification of a piece of buried bone of unknown species is presented, and the species was identified as a pig by this method.

Animals↗
PubMed2006

The structure and diversity of alpha1-acid glycoprotein/orosomucoid gene in Africans.

Human orosomucoid (ORM), or alpha(1)-acid glycoprotein, is known to be controlled by duplicated and triplicated genes on chromosome 9, encoding ORM1 and ORM2 proteins. In this study, the structure and diversity of the ORM gene were investigated in 16 Sub-Saharan Africans, who originated from widely dispersed locations in Africa. The duplicated ORM1-ORM2 gene was observed in all 16 samples. ORM1*S1(2), characterized by an ORM2 gene-specific sequence in intron 5, was common in Africans. Three Africans showed the duplication of the ORM1 gene. The organization of the triplicated ORM1A-ORM1B-ORM2 gene was established in two Africans. The recombination breakpoints resulting in the ORM1 duplication lay within a small genomic interval around exon 1 of the ORM1B gene. The duplication of the ORM2 gene reported previously was not detected in this population sample. Several single-nucleotide polymorphisms were observed in the ORM2 gene. The rearrangement of the ORM gene is likely to occur often in Africans.

Alu Elements↗
PubMed2005

Small heat shock protein 27 mutation in a Japanese patient with distal hereditary motor neuropathy.

Heat shock protein 27 (HSP27) belongs to a family of small heat shock proteins that play significant roles in the cellular stress response and are also involved in the control of protein-protein interactions as chaperons. Mutation in HSP27 has been identified as the cause of axonal Charcot-Marie-Tooth disease (CMT) and distal hereditary motor neuropathy (HMN). Heat shock protein 22 (HSP22) is a molecular counterpart of HSP27, and its mutation is another cause of distal HMN. We screened the mutation of HSP27 and HSP22 in 68 Japanese patients with axonal CMT or unclassified CMT and six Japanese patients with distal HMN. We detected a heterozygous P182S mutation of HSP27 in a patient with distal HMN, but we found no mutations in HSP22. Mutation in HSP27 may impair the formation of the stable neurofilament network that is indispensable for the maintenance of peripheral nerves.

Adolescent↗
PubMed2005

Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations.

We present a reliable, rapid, and economical multiplex amplified product-length polymorphism (APLP) method for analyzing the haplogroup-diagnostic mitochondrial single-nucleotide polymorphisms (mtSNPs) in East Asian populations. By examining only 36 haplogroup-specific mtSNPs in the coding region by using four 9-multiplex polymerase chain reaction (PCR) and subsequent electrophoresis, we could safely assign 1815 individuals from 8 populations of Japanese, Korean, Chinese, and Germans to 45 relevant haplogroups. This multiplex APLP analysis of coding-region mtSNPs for haplogrouping is especially useful not only for molecular phylogenetic studies but also for large-scale association studies due to its rapid and economical nature. This is the first panel of mtSNPs in the coding region to be used for haplogrouping of East Asian populations.

Asian People↗
PubMed2005

Molecular aspects of biochemical markers.

This review summarizes present knowledge of the molecular basis for certain serum protein and red cell enzyme markers that have played important roles in forensic individualization and paternity tests. Most genes have nucleotide variations at two or more mutations sites, and their alleles exist as haplotypes. Allelic diversity is generated by various mechanisms including point mutation, intragenic recombination, gene conversion, and alternative splicing. Deficient and null alleles arise from point mutation and deletion. The value of genomic information on allelic diversity is also discussed.

Crossing Over, Genetic↗
PubMed2005

Recent progress in mitochondrial DNA analysis.

In this review, we describe the current state of knowledge of mitochondrial genetics of East Asian populations and its application to forensic science. Recent advances in mitochondrial DNA (mtDNA) phylogeny have identified haplogroup-specific single nucleotide polymorphisms (SNPs) and the control region motifs of haplogroups. By analyzing haplogroup-specific SNPs, we can rapidly and accurately connect the mtDNA under study to the relevant haplogroup. Haplogroups are fairly continent- and/or region-specific; therefore, we can infer the ethnic background of that mtDNA. In addition, errors in hypervariable region sequences can be detected by means of haplogroup motif analysis.

Animals↗
PubMed2005

Neonatal hyperbilirubinemia and the bilirubin uridine diphosphate-glucuronosyltransferase gene: the common -3263T > G mutation of phenobarbital response enhancer module is not associated with the neonatal hyperbilirubinemia in Japanese.

BACKGROUND: Neonatal hyperbilirubinemia is frequent and severe in Japanese newborns. Previously, it has been reported that half of the Japanese neonates with severe hyperbilirubinemia carried the 211G > A (p.G71R) mutation of the bilirubin uridine diphosphate-glucuronosyltransferase (UGT1A1) gene causing Gilbert syndrome. Recently, it was reported that the -3263T > G mutation in the phenobarbital response enhancer module in UGT1A1 was associated with the majority of cases of Gilbert syndrome. The gene frequency of the -3263T > G mutation was determined and the relation with neonatal hyperbilirubinemia in Japanese was studied. METHODS: UGT1A1 in 119 neonates born at Yamagata University Hospital, Yamagata, Japan, and 26 subjects who had undergone phototherapy due to severe hyperbilirubinemia at four other hospitals were studied. The gene frequency of -3263T > G mutation in Japanese, Korean, Chinese and German healthy adult controls was also determined. Hyperbilirubinemia was assessed with a Jaundice Meter and UGT1A1 was analyzed by sequence determination or restriction enzyme method. RESULTS: The gene frequency of the -3263T > G mutation was 0.26 in Japanese subjects and was similar to the prevalence in Korean, Chinese and German populations. However, there was no significant increase in the gene frequency of the mutation in the neonates who required phototherapy for hyperbilirubinemia compared to that in the neonates without severe hyperbilirubinemia. In addition, neonates with or without the mutation did not show a significant change in the level of bilirubin and the mutation also did not show a synergic effect with the 211G > A mutation on the level of bilirubin. CONCLUSION: The -3263T > G mutation is not likely to be associated with the neonatal hyperbilirubinemia in Japanese.

Asian People↗
PubMed2004

Association of alpha2-HS glycoprotein (AHSG, fetuin-A) polymorphism with AHSG and phosphate serum levels.

Alpha2-HS glycoprotein (AHSG), also known as fetuin-A, is a plasma protein displaying high-affinity interaction with calcium phosphate, by which ectopic vascular calcification is prevented. This investigation has attempted to evaluate the relationship between AHSG polymorphism and serum levels of AHSG and calcium-related parameters. AHSG levels in unrelated individuals were measured by quantitative rocket immunoelectrophoresis and were 581+/-38, 542+/-31, and 494+/-23 mg/l for three major genotypes of AHSG1 homozygotes (n=99), heterozygotes (n=55), and AHSG2 homozygotes (n=22), respectively (differences were significant: P<0.001). The circulating AHSG level was therefore influenced by the genetic polymorphism with the additive reduction in the AHSG2 allele. Statistical analysis of simple and multiple regression models revealed no associations between AHSG levels and serum values of total calcium, albumin-corrected total calcium, and ionized calcium. However, the AHSG levels demonstrated a significant negative correlation with free phosphate levels (P<0.001), indicating that AHSG is a novel determinant of serum phosphate. The AHSG polymorphism is attributable to the hereditary variation of AHSG and phosphate serum levels, which may affect skeletal development and chronic disorders such as vascular calcification.

Adult↗
PubMed2004

Mitochondrial GTPase mitofusin 2 mutation in Charcot-Marie-Tooth neuropathy type 2A.

Charcot-Marie-Tooth disease (CMT) has been classified into two types, CMT1 and CMT2, demyelinating and axonal forms, respectively. CMT2 has been further subdivided into eight groups by linkage studies. CMT2A is linked to chromosome 1p35-p36 and mutation in the kinesin family member 1B-beta (KIF1B) gene had been reported in one pedigree. However, no mutation in KIF1B was detected in other pedigrees with CMT2A and the mutations in the mitochondrial fusion protein mitofusin 2 (MFN2) gene were recently detected in those pedigrees. MFN2, a mitochondrial transmembrane GTPase, regulates the mitochondrial network architecture by fusion of mitochondria. We studied MFN2 in 81 Japanese patients with axonal or unclassified CMT and detected seven mutations in seven unrelated patients. Six of them were novel and one of them was a de novo mutation. Most mutations locate within or immediately upstream of the GTPase domain or within two coiled-coil domains, which are critical for the functioning or mitochondrial targeting of MFN2. Formation of a mitochondrial network would be required to maintain the functional peripheral nerve axon.

Adult↗
PubMed2004

MATP polymorphisms in Germans and Japanese: the L374F mutation as a population marker for Caucasoids.

Inference of the population and ancestry to which an individual belongs is important in forensic individualization and personal identification. In this study, five polymorphisms of the membrane-associated transporter protein (MATP) gene were investigated in German and Japanese populations. The L374F mutation was present at an allele frequency as high as 0.96 in the German population, whereas it was completely absent in the Japanese population. This extreme difference in allele frequency suggests that the L374F mutation is valuable as a population and ancestry informative marker for Caucasoids.

Antigens, Neoplasm↗
PubMed2004

Mitochondrial genome variation in eastern Asia and the peopling of Japan.

To construct an East Asia mitochondrial DNA (mtDNA) phylogeny, we sequenced the complete mitochondrial genomes of 672 Japanese individuals (http://www.giib.or.jp/mtsnp/index_e.html). This allowed us to perform a phylogenetic analysis with a pool of 942 Asiatic sequences. New clades and subclades emerged from the Japanese data. On the basis of this unequivocal phylogeny, we classified 4713 Asian partial mitochondrial sequences, with <10% ambiguity. Applying population and phylogeographic methods, we used these sequences to shed light on the controversial issue of the peopling of Japan. Population-based comparisons confirmed that present-day Japanese have their closest genetic affinity to northern Asian populations, especially to Koreans, which finding is congruent with the proposed Continental gene flow to Japan after the Yayoi period. This phylogeographic approach unraveled a high degree of differentiation in Paleolithic Japanese. Ancient southern and northern migrations were detected based on the existence of basic M and N lineages in Ryukyuans and Ainu. Direct connections with Tibet, parallel to those found for the Y-chromosome, were also apparent. Furthermore, the highest diversity found in Japan for some derived clades suggests that Japan could be included in an area of migratory expansion to Continental Asia. All the theories that have been proposed up to now to explain the peopling of Japan seem insufficient to accommodate fully this complex picture.

DNA, Mitochondrial↗
PubMed2004

Molecular basis of ESD*5 and ESD*7 and haplotype analysis with new polymorphisms in introns.

The two polymorphic alleles of esterase D (ESD), ESD*5 and ESD*7, are specific to Europeans and Asians, respectively. In this study the molecular basis was characterized: ESD*5, arising from ESD*1, has a G to A transition, resulting in Gly257(GGT) --> Asp(GAT); and ESD*7, originating from ESD*2, has an A to G transition, resulting in Asp231(GAT) --> Gly(GGT). Glycine is also involved in the common ESD*1/ESD*2 polymorphism [Gly190(GGA) --> Glu(GAA)]. Haplotype analysis using a few novel intragenic polymorphisms showed strong associations among polymorphic sites, suggesting that recombination has been less frequent in the human ESD gene, although it spans about 25 kb from exon 1 to exon 10. A marked difference was observed in the distribution of haplotype frequencies between Germans and Japanese.

Animals↗
PubMed2004

Sudden infant death syndrome is not associated with the mutation of PHOX2B gene, a major causative gene of congenital central hypoventilation syndrome.

Sudden infant death syndrome (SIDS) is a major cause of infant death, but its etiology is unknown. There are several independent risk factors for SIDS, and prone sleeping is a major risk factor. SIDS is probably based on a compromise in arousal response to breathing or blood pressure during sleep. Congenital central hypoventilation syndrome (CCHS or Ondine's curse) is a disorder characterized by an idiopathic failure of the autonomic control of breathing and has been regarded as one of the compromised conditions in SIDS. Recently, mutations of the PHOX2B gene have been detected in half to two-thirds of CCHS patients. We therefore analyzed the PHOX2B gene in 23 cases of SIDS and did not find any mutations, except for three polymorphic nucleotidic substitutions. The mutation of PHOX2B is thus not likely associated with SIDS.

Female↗
PubMed2004

[Haplotype analysis of single nucleotide polymorphisms of mitochondrial DNA].

Mitochondrial DNA (mtDNA) mutations observed in both non-coding control and coding regions are being used widely to characterize human evolution and for identification. Several methodological approaches have been available for detection of single nucleotide polymorphisms (SNPs). SNPs of the non-coding region were mainly analyzed by means of direct sequencing. Especially, sequence analysis of D-loop is often the final resort in forensic and ancient personal identification. However, sequencing is relatively expensive and time-consuming. Furthermore, because the mtDNA molecule is a single linked unit, the statistical significance in forensic cases requires mtDNA matching in comparison with large sequence data. In this study, we developed a procedure of technique simultaneous typing to 11 SNPs and 2 tandem repeat sites in the non-coding and coding region by use of allele-specific amplification. In an analysis to 631 unrelated Japanese individuals the 180 haplotypes were defined in this study, and the level of haplotypic diversity and random mach probability was similar to that obtained by sequencing of the human hypervariable region 1 in mtDNA. These results show the usefulness of mtDNA haplotype analysis by the presented method for personal identification.

Alleles↗
PubMed2003

Evolution of the cystatin B gene: implications for the origin of its variable dodecamer tandem repeat in humans.

The human cystatin B gene contains a variable number of 12-bp tandem repeats in its promoter region, of which the common alleles contain two or three copies and unusual expansion causes progressive myoclonus epilepsy of the Unverricht-Lundborg type. We undertook a comprehensive analysis of the genomic sequence to address the evolutionary events of this variable repeat. By examination of a contiguous genome sequence spanning 5.0 kb and linkage analysis of detected polymorphic changes, we identified six major intragenic haplotypes in unrelated Japanese subjects. The number of normal repeats was closely correlated with these alleles, indicating that changes in the array should be comparatively rare events during human evolution. To examine the origin of the repeat array further, we also analyzed five primate genomes. Repetitive polymorphism was unlikely in hominoids, and the array originated with the dodecamer itself in the course of primate evolution. The variability conceivably developed after the separation to humans.

Cystatin B↗
PubMed2003

Novel paternity testing by distinguishing parental alleles at a VNTR locus in the differentially methylated region upstream of the human H19 gene.

Conventional PCR-based genotyping is useful for forensic testing but cannot be used to determine parental origins of alleles in DNA specimens. Here we describe a novel method of combined conventional genotyping and PIA typing (parentally imprinted allele typing) at a minisatellite region upstream from the H19 locus. The PIA typing uses two sets of primers and DNA digested with methylation-sensitive Hha I enzyme. The first amplification produces only the methylated fragment of paternal H19 allele, and the second detects polymorphism in the minisatellite. Hence, this distinguishes paternal and maternal alleles by difference in the DNA methylation. Furthermore, the polymorphism in this polymorphic locus was examined using 199 unrelated Japanese and 171 unrelated Germans, their polymorphism information content being 0.671 and 0.705, respectively. Feasibility of this typing is demonstrated for six families, and the usefulness is shown by application to paternity testing.

Alleles↗