Genetic variation for three Y-STR loci: DYS390, DYS518, and DYS643.

Y chromosome short tandem repeats (Y-STRs) are commonly used to analyze male-specific DNA. Although biallelic patterns due to duplication events have been detected at some loci, Y-STRs generally appear as a single peak except for DYS385 because the Y chromosome is haploid. STR loci in regions of segmental duplication by homologous recombination on the Y chromosome exhibit double allelic peaks, rather than single peaks. In this study, we report a bi- and triallelic pattern observed simultaneously in DYS390, DYS518, and DYS643. A bi- and triallelic pattern has not previously been observed simultaneously for these three loci. We also identified the copy number variation in the region including these loci by the microarray-based analysis. Given the peak balance pattern, the copy number variation, and the close position of these three loci on the Y chromosome, we consider that this phenomenon is caused by a segmental duplication in the euchromatin region. By ruling out mixed samples, a common interpretation of multiple peaks, these results have practical implications for the interpretation of Y-STR results in forensics analyses.

Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra.

The mottled skate, Beringraja pulchra is one of the commercially important fishes in the market today. However, B. pulchra identification methods have not been well developed. The current study reports a novel real-time PCR method based on TaqMan technology developed for the genetic identification of B. pulchra. The mitochondrial cytochrome oxidase subunit 1 (COI) nucleotide sequences of 29 B. pulchra, 157 skates and rays reported in GenBank DNA database were comparatively analyzed and the COI sequences specific to B. pulchra was identified. Based on this information, a system of specific primers and Minor Groove Binding (MGB) TaqMan probe were designed. The assay successfully discriminated in 29 specimens of B. pulchra and 27 commercial samples with unknown species identity. For B. pulchra DNA, an average Threshold Cycle (Ct) value of 19.1±0.1 was obtained. Among 27 commercial samples, two samples showed average Ct values 19.1±0.0 and 26.7±0.1, respectively and were confirmed to be B. pulchra based on sequencing. The other samples tested showed undetectable or extremely weak signals for the target fragment, which was also consistent with the sequencing results. These results reveal that the method developed is a rapid and efficient tool to identify B. pulchra and might prevent fraud or mislabeling during the distribution of B. pulchra products.

Application of volume-of-fluid method to analyze the viscosity effect on the spine formation of bloodstains.

In bloodstain pattern analysis, the blood droplet volume and surface impact velocity play an important role, and many related experimental studies have been carried out. If an appropriate computational fluid dynamics (CFD) model that could solve bloodstain patterns, especially spine formation bloodstain patterns, can be obtained, the blood droplet volume and impact speeds at various crime scenes can be predicted more accurately. For this purpose, Flow-3D software using the volume-of-fluid method was applied to analyze the behavior of human blood droplets during an impact event, especially focusing on the viscous effect on splashing, which forms the spine which can be used to predict the impact velocity. To obtain a non-Newtonian viscosity model of blood for a computational fluid dynamic analysis, the venous blood samples of 163 people were tested using a hemorheology instrument. Among the venous blood samples of 163 people, 37 samples for which all blood test results were in a normal range were selected for the non-Newtonian viscosity modeling. From the CFD analysis, it could be concluded that a non-Newtonian viscosity model is more appropriate than a constant viscosity model for predicting splashing that forms the spine. The gradient of the non-Newtonian model at a high shear rate has more of an effect on spine formation than that at a low shear rate. The lowest viscosity with a high velocity at the outer front of the radiating flow plays an important role in forming the splashing pattern.

Mechanisms of phytoestrogen biochanin A-induced vasorelaxation in renovascular hypertensive rats.

BACKGROUND: The plant-derived estrogen biochanin A is known to cause vasodilation, but its mechanism of action in hypertension remains unclear. This study was undertaken to investigate the effects and mechanisms of biochanin A on the thoracic aorta in two-kidney, one clip (2K1C) renovascular hypertensive rats. METHODS: Hypertension was induced by clipping the left renal artery, and control age-matched rats were sham treated. Thoracic aortae were mounted in tissue baths to measure isometric tension. RESULTS: Biochanin A caused concentration-dependent relaxation in aortic rings from 2K1C hypertensive and sham-treated rats, which was greater in 2K1C rats than in sham rats. Biochanin A-induced relaxation was significantly attenuated by removing the endothelium in aortic rings from 2K1C rats, but not in sham rats. N (ω)-Nitro-l-arginine methyl ester, a nitric oxide synthase inhibitor, or indomethacin, a cyclooxygenase inhibitor, did not affect the biochanin A-induced relaxation in aortic rings from 2K1C and sham rats. By contrast, treatment with glibenclamide, a selective inhibitor of adenosine triphosphate-sensitive K(+) channels, or tetraethylammonium, an inhibitor of Ca(2+)-activated K(+) channels, significantly reduced biochanin A-induced relaxation in aortic rings from both groups. However, 4-aminopyridine, a selective inhibitor of voltage-dependent K(+) channels, inhibited the relaxation induced by biochanin A in 2K1C rats, whereas no significant differences were observed in sham rats. CONCLUSION: These results suggest that the enhanced relaxation caused by biochanin A in aortic rings from hypertensive rats is endothelium dependent. Vascular smooth muscle K(+) channels may be involved in biochanin A-induced relaxation in aortae from hypertensive and normotensive rats. In addition, an endothelium-derived activation of voltage-dependent K(+) channels contributes, at least in part, to the relaxant effect of biochanin A in renovascular hypertension.

A large population genetic study of 15 autosomal short tandem repeat loci for establishment of Korean DNA profile database.

Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications.

Population genetic polymorphisms of 17 Y-chromosomal STR loci in South Koreans.

Haplotypes and allele frequencies of 17 Y-chromosomal STR loci included in the AmpFlSTR(®) Yfiler(®) system were obtained from a sample of 1021 unrelated individuals living in 6 provinces of South Korea. A total of 938 haplotypes were observed in the 1021 individuals studied, of which 885 were unique. The overall haplotype diversity for the 17 Y-STR loci was 0.9998, and the discrimination capacity was 0.9187. We found 11 atypical alleles (null, duplicated, triplicated, and microvariant alleles), that have not previously been reported in South Korean populations. It seems that these 17 loci are useful genetic markers for forensic personal identification and paternity testing in the South Korean population.

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Mutational analysis of whole mitochondrial DNA in patients with MELAS and MERRF diseases.

Mitochondrial diseases are clinically and genetically heterogeneous disorders, which make the exact diagnosis and classification difficult. The purpose of this study was to identify pathogenic mtDNA mutations in 61 Korean unrelated families (or isolated patients) with MELAS or MERRF. In particular, the mtDNA sequences were completely determined for 49 patients. From the mutational analysis of mtDNA obtained from blood, 5 confirmed pathogenic mutations were identified in 17 families, and 4 unreported pathogenically suspected mutations were identified in 4 families. The m.3243A>G in the tRNA(Leu(UUR))was predominantly observed in 10 MELAS families, and followed by m.8344A>G in the tRNA(Lys) of 4 MERRF families. Most pathogenic mutations showed heteroplasmy, and the rates were considerably different within the familial members. Patients with a higher rate of mutations showed a tendency of having more severe clinical phenotypes, but not in all cases. This study will be helpful for the molecular diagnosis of mitochondrial diseases, as well as establishment of mtDNA database in Koreans.

Genetic polymorphisms of 16 Y chromosomal STR loci in Korean population.

Allele frequencies and haplotypes of 16 Y chromosomal STR loci included in the AmpFlSTR((R)) Yfilertrade mark system were obtained from a sample of 526 unrelated Korean male individuals. A total of 478 haplotypes were observed in the 526 individuals studied, of which 440 were unique. The overall haplotype diversity for the 16 Y-STR loci was 0.9996, and the discrimination capacity was 0.9087. We found 13 atypical alleles, including null, duplicated and microvariant alleles. Microvariants have been characterized by sequencing, 14.1 allele at DYS458 showing the flanking site mutation, 13.1 and 15.2 allele at DYS385a/b showing changes in the repeat structure.

Haplotypes for 12 Y-chromosomal STR loci in a Korean population (the central region).

Haplotypes and allele frequencies of 12 STR loci included in the PowerPlex Y system (DYS391, DYS389I, DYS439, DYS389II, DYS438, DYS437, DYS19, DYS392, DYS393, DYS390, and DYS385a/b) were obtained from a sample of 569 unrelated individuals living in the central region of Korea. A total of 473 haplotypes were observed in the 569 individuals studied, of which 426 (90.06%) were unique. The overall haplotype diversity for the 12 Y-STR loci was 0.9985, and the discrimination capacity was 0.8313. In DYS439, we found a new intermediate-sized allele that added an A at base 3 upstream from the repeat region's first GATA motif. The allele was named 11 (U3Ains) according to its sequence structure.

Population database on nine STR loci of the AmpFlSTR Profiler kit in Koreans.

Allele frequencies for nine STR loci included in the AmpFlSTR Profiler Kit (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820), were obtained from a sample of 1206 unrelated individuals living in the central region of Korea.

Population genetics of nine STR loci: TH01, TPOX, CSF1PO, vWA, FESFPS, F13A01, D13S317, D7S820 and D16S539 in a Korean population.

Allele frequencies for nine STR loci namely, TH01, TPOX, CSF1PO, vWA, FESFPS, F13A01, D13S317, D7S820 and D16S539 were obtained from a sample of 437 unrelated individuals living in Chungcheong-do, South Korea.