Kyung-Yong Kim

Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost

A thermophilic, spore-forming rod isolated from hay compost in Korea was subjected to a taxonomic study. The micro-organism, designated strain SK-1(T), was identified as being aerobic, Gram-positive, motile and rod-shaped. Growth of the isolate was observed at 45-70 degrees C (optimum 60 degrees C) and pH 6.0-9.0 (optimum pH 7.5). The G+C content of the genomic DNA was 43.9 mol%. Chemotaxonomic characteristics of the isolate included the presence of mesodiaminopimelic acid in the cell wall and iso-C15:0 and iso-C17:0 as the major cellular fatty acids. The predominant isoprenoid quinone was MK-7. The chemotaxonomic characteristics of strain SK-1(T) were the same as those of the genus Geobacillus. Phylogenetic analysis based on 16S rDNA sequences showed that strain SK-1(T) is most closely related to Geobacillus thermoglucosidasius. However, the phenotypic properties of strain SK-1(T) were clearly different from those of G. thermoglucosidasius. The level of DNA-DNA relatedness between strain SK-1(T) and the type strain of G. thermoglucosidasius was 27%. On the basis of the phenotypic traits and molecular systematic data, strain SK-1(T) represents a novel species within the genus Geobacillus, for which the name Geobacillus toebii sp. nov. is proposed. The type strain is strain SK-1(T) (= KCTC 0306BP(T) - DSM 14590(T)).

Preventive effects of chebulic acid isolated from Terminalia chebula on advanced glycation endproduct-induced endothelial cell dysfunction

AIM OF THE STUDY The aqueous extract of Terminalia chebular fruits was reported to have anti-hyperglycemia and anti-diabetic complication effects. The present study therefore investigated the protective mechanism of chebulic acid, a phenolcarboxylic acid compound isolated from the ripe fruits of Terminalia chebula against advanced glycation endproducts (AGEs)-induced endothelial cell dysfunction. MATERIALS AND METHODS To investigate the protective mechanism of chebulic acid against vascular endothelial dysfunction human umbilical vein endothelial cells (HUVEC) were treated with chebulic acid in the presence/absence of glyceraldehyde-related AGEs (glycer-AGEs). RESULTS HUVEC incubated with 100 μg/ml of glycer-AGEs had significantly enhanced reactive oxygen species formation, whereas the treatment of chebulic acid dose-dependently reduced glycer-AGE-induced formation to 108.2 ± 1.9% for 25 μM versus 137.8 ± 1.1% for glycer-AGEs treated alone. The transendothelial electrical resistance (TER) value of the glycer-AGEs group was dramatically decreased to 76.9 ± 2.2% compared to the control, whereas chebulic acid treatment prevented glycer-AGE-induced TER change with a value of 91.3 ± 5.3%. The incubation of confluent HUVEC with 100 μg/ml of glycer-AGEs for 24h remarkably increased the adhesion of human monocytic THP-1 cells compared to non-stimulated HUVEC. These increases in HUVEC adhesiveness were dose-dependently reduced by chebulic acid. CONCLUSIONS The present study shows the effects of chebulic acid against the progression of AGE-induced endothelial cell dysfunction suggesting that this compound may constitute a promising intervention agent against diabetic vascular complications.

A Western Eurasian Male Is Found in 2000-Year-Old Elite Xiongnu Cemetery in Northeast Mongolia

We analyzed mitochondrial DNA (mtDNA), Y-chromosome single nucleotide polymorphisms (Y-SNP), and autosomal short tandem repeats (STR) of three skeletons found in a 2,000-year-old Xiongnu elite cemetery in Duurlig Nars of Northeast Mongolia. This study is one of the first reports of the detailed genetic analysis of ancient human remains using the three types of genetic markers. The DNA analyses revealed that one subject was an ancient male skeleton with maternal U2e1 and paternal R1a1 haplogroups. This is the first genetic evidence that a male of distinctive Indo-European lineages (R1a1) was present in the Xiongnu of Mongolia. This might indicate an Indo-European migration into Northeast Asia 2,000 years ago. Other specimens are a female with mtDNA haplogroup D4 and a male with Y-SNP haplogroup C3 and mtDNA haplogroup D4. Those haplogroups are common in Northeast Asia. There was no close kinship among them. The genetic evidence of U2e1 and R1a1 may help to clarify the migration patterns of Indo-Europeans and ancient East-West contacts of the Xiongnu Empire. Artifacts in the tombs suggested that the Xiongnu had a system of the social stratification. The West Eurasian male might show the racial tolerance of the Xiongnu Empire and some insight into the Xiongnu society.

Knowledge and attitudes of Korean parents towards their son's circumcision: a nationwide questionnaire study

Objective To evaluate knowledge about the foreskin and circumcision, and to understand the attitudes of parents to circumcision in Korea, where circumcision in childhood is widely practised with no particular religious or medical background.

Technical note: Improved ancient DNA purification for PCR using ion‐exchange columns

A novel method of ancient DNA (aDNA) purification was developed using ion-exchange columns to improve PCR-amplifiable DNA extraction from ancient bone samples. Thirteen PCR-resistant ancient bone samples aged 500-3,300 years were tested to extract aDNA using a recently reported, silica-based aDNA extraction method and an ion-exchange column method for the further purification. The PCR success rates of the aDNA extracts were evaluated for the amplification ability of the fragments of mitochondrial DNA, a high-copy DNA, and amelogenin, a low-copy DNA. The results demonstrate that the further purification of silica-based aDNA extracts using ion-exchange columns considerably improved PCR amplification. We suggest that the ion-exchange column-based method will be useful for the improvement of PCR-amplifiable aDNA extraction, particularly from the poorly preserved, PCR-resistant, ancient samples.

Localization of peripheral dopamine D1 and D2 receptors in rat corpus cavernosum

Objective  To detect and locate anatomically peripheral dopamine D1 and D2 receptors in rat cavernosa, as dopamine is important in sexual drive and penile erection through receptors located in the central nervous system.

Mycobacterium parakoreense sp. nov., a slowly growing non-chromogenic species related to Mycobacterium koreense, isolated from a human clinical specimen.

A previously undescribed, slowly growing, non-chromogenic Mycobacterium strain (299(T)) was isolated from the sputum sample of a patient with a symptomatic pulmonary infection. Phenotypically, strain 299(T) was generally similar to Mycobacterium koreense DSM 45576(T) and Mycobacterium triviale ATCC 23292(T). The 16S rRNA gene sequence of strain 299(T) was similar to that of M. koreense DSM 45576(T) (GenBank accession no. AY734996, 99.5% similarity); however, it differed substantially from that of M. triviale ATCC 23292(T) (X88924, 98.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 299(T) clustered together with M. koreense DSM 45576(T) and M. triviale ATCC 23292(T), supported by high bootstrapping values (99%). Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 299(T) represents a novel mycobacterial species, for which the name Mycobacterium parakoreense sp. nov. is proposed. The type strain is 299(T) (=DSM 45575(T)=KCTC 19818(T)).

A real-time PCR-based amelogenin Y allele dropout assessment model in gender typing of degraded DNA samples

Allelic dropout due to stochastic variation in degraded small quantity DNA appears to be one of the most serious genotyping errors. Most methods require PCR replication to address this problem. The small amounts of valuable samples are often a limitation for such replications. We report a real-time PCR-based amelogonin Y (AMELY) allele dropout estimation model in an AMEL-based gender typing. We examined 915 replicates of AMELY-positive modern male DNA with varying amounts of DNA and humic acid. A male-specific AMEL fragment (AMELy) dropped out in 143 genuine male replicates, leading to gender typing errors. By graphing a scatter plot of the crossing point versus the end cycle fluorescence of the male replicates, a standard graph model for the estimation of the AMELy allele dropout was constructed with the dropout-prone and dropout-free zones. This model was then applied to ancient DNA (aDNA) samples. Nine samples identified as female were found in the dropout-prone zone; with higher DNA concentrations, six were shifted to the dropout-free zone. Among them, two female identifications were converted to male. All the aDNA gender was confirmed by sex-determination region Y marker amplification. Our data suggest that this model could be a basic approach for securing AMELy allele dropout-safe data from the stochastic variation of degraded inhibitory DNA samples.

Pes anserinus and anserine bursa: anatomical study

This study investigated the boundary of anserine bursa with the recommended injection site and shape on the insertion area of pes anserinus (PA), with the aim of improving clinical practice. Eighty six legs from 45 Korean cadavers were investigated. The mixed gelatin solution was injected to identify the shape of anserine bursa, and then the insertion site of the PA tendons was exposed completely and carefully dissected to identify the shape of the PA. The sartorius was inserted into the superficial layer and gracilis, and the semitendinosus was inserted into the deep layer on the medial surface of the tibia. The number of the semitendinosus tendons at the insertion site varied: 1 in 66% of specimens, 2 in 31%, and 3 in 3%. The gracilis and semitendinosus tendons were connected to the deep fascia of leg. Overall, the shape of the anserine bursa was irregularly circular. Most of the anserine bursa specimens reached the proximal line of the tibia, and some of the specimens reached above the proximal line of the tibia. In the medial view of the tibia, the anserine bursa was located posteriorly and superiorly from the tibias midline, and it followed the lines of the sartorius muscle. The injection site for anserine bursa should be carried out at 20° from the vertical line medially and inferiorly, 15 or 20 mm deeply, and at the point of about 20 mm medial and 12 mm superior from inferomedial point of tibial tuberosity.

Sex determination using upper limb bones in Korean populations.

The purpose of this research is to establish metric standards for the determination of sex from the upper limb bones of Korean. We took a set of eleven measurements on each of 175 right sides of adult skeletons chosen at Korean sample. Classification accuracy dropped only one or two individuals when only vertical head diameter of humerus is used. Variables in relation with maximal length were less accurate than head diameter of humerus. Two variables were selected by the stepwise procedure: maximal length of humerus, vertical head diameter of humerus. The combined accuracy was 87%. This study of modern Korean skeletons underscores the need for population-specific techniques, not only for medicolegal investigations, but also for the study of population affinities and factors affecting bone configurations.