• Journal of Ginseng Research
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• v.41 no.4
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• pp.469-476
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• 2017

Background: Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion: Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.

• Journal of Life Science
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• v.18 no.12
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• pp.1733-1738
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• 2008

SLC6A18, one of the neurotransmitters, was reported the possible relationship to hypertension, and it contained eight blocks of minisatellites. In this study, SLC6A18-MS5 sequence which showed the highest heterozygosity among seven minisatellites was analyzed using the Transfac software, the putative binding sites for the transcription factor Pax4 and HNF4 were discovered as a result. The HNF4 is involved in the diabetes pathway and suggested the relationship to hypertension. Thus, we investigated the putative functional significance of allelic variation in this minisatellites with respect to susceptibility for hypertension. To address this possibility, we analyzed genomic DNA from the blood of 301 hypertension-free controls and 184 cases with hypertension. A statistically significant association was not identified between the allelic distribution of SLC6A18-MS5 and occurrence of hypertension. We then examined the meiotic segregation of SLC6A18-MS5 and it was transmitted following Mendelian inheritance. Therefore, this locus could be useful markers for paternity mapping and DNA fingerprinting. Moreover, we undertook a comprehensive analysis of the genomic sequence to address the evolutionary events of these variable repeats. SLC6A18 minisatellites regions are only conserved in human and primates. This result suggestedthat intronic minisatellites analysis is powerful evolution marker for the non-coding regions in primates and can provide a great insight to the molecular evolution of repeated region in primates.

• The Korean Journal of Physiology and Pharmacology
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• v.19 no.2
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• pp.119-124
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• 2015

The aim of the present study was to assess whether exposure to the combination of an extremely low frequency magnetic field (ELF-MF; 60 Hz, 1 mT or 2 mT) with a stress factor, such as ionizing radiation (IR) or $H_2O_2$, results in genomic instability in non-tumorigenic human lung epithelial L132 cells. To this end, the percentages of G2/M-arrested cells and aneuploid cells were examined. Exposure to 0.5 Gy IR or 0.05 mM $H_2O_2$ for 9 h resulted in the highest levels of aneuploidy; however, no cells were observed in the subG1 phase, which indicated the absence of apoptotic cell death. Exposure to an ELF-MF alone (1 mT or 2 mT) did not affect the percentages of G2/M-arrested cells, aneuploid cells, or the populations of cells in the subG1 phase. Moreover, when cells were exposed to a 1 mT or 2 mT ELF-MF in combination with IR (0.5 Gy) or $H_2O_2$ (0.05 mM), the ELF-MF did not further increase the percentages of G2/M-arrested cells or aneuploid cells. These results suggest that ELF-MFs alone do not induce either G2/M arrest or aneuploidy, even when administered in combination with different stressors.

• Korean Journal of Biological Psychiatry
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• v.13 no.3
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• pp.170-177
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• 2006

Objectives : Disturbances of serotonergic system might be related to the possible mechanism of social phobia. This study was to investigate the association of serotonin transporter gene and social phobia. Methods : Sixty nine patients with social phobia(51 male(73.9%), mean age $35.17{\pm}11.89$ years) and seventy four normal controls(54 male(73.0%), mean age $33.46{\pm}9.63$ years) were tested for serotonin transporter gene-linked polymorphic region(5-HTTLPR) polymorphism. Additionally, patients were grouped into 46 generalized(GEN) and 23 nongeneralized(NGEN) subgroups and 5-HTTLPR polymorphism was compared with that of normal controls. The genotypes and allele frequencies of the 5-HTTLPR polymorphism between social phobia and the control group were compared. Genomic DNA was extracted from their blood and 5-HTTLPR polymorphisms were determined by using polymerase chain reaction. Results : Significant association was observed between the S(ss) genotype and social phobia, by functional classification(p=.010). In allele frequency analysis, a significant association was also observed between the short allele and social phobia(p=.030). A significant associations between S genotype and each subgroup were observed(GEN p=.045 ; NGEN p=.033), but there were no differences in allele frequency. And, no differences in genotype and allele distribution between two subgroups were found. Conclusion : The results in our Korean sample suggest that S genotype of 5-HTTLPR may be associated with social phobia and s allele may be an important genetic factor that activates social phobic symptoms. But, further studies including large number of samples are necessary to elucidate these present findings.

• Development and Reproduction
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• v.13 no.2
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• pp.97-103
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• 2009

Genomic DNA samples isolated from four geographical freshwater crab (Eriocheir sinensis) populations collected in the inland of the Korean Peninsula (Gunsan, Paju, and Nampo) and a Chinese site, were used for PCR amplification. Seven decamer primers generated 19 specific loci (19/243 loci, 7.81%) in the Gunsan population, 32 (32/215 loci, 14.88%) in the Paju population, 19 (19/231 loci, 8.23%) in the Nampo population and 62 (62/340 loci, 18.24%) in a Chinese population. The average 8.9 specific loci exhibited inter-individual-specific characteristics, thus revealing DNA polymorphisms in the Chinese population. The number of unique shared loci to each population and number of shared loci by the four populations were generated by molecular analysis using seven primers in four populations. 35 unique shared loci to each population, with an average of 5.0 per primer, were observed in the Gunsan population, and 50 loci, with an average of 7.1 per primer, were observed in the Chinese population. The hierarchical dendrogram indicates three main branches: cluster 1 (GUNSAN 01$\sim$GUNSAN 05, PAJU 06$\sim$PAJU 10 and NAMPO 11$\sim$NAMPO 15) and cluster 2 (CHINESE 16, 17, 18, 19 and 20). Conclusively individual no. 20 of the PAJU 10 freshwater crab was most distantly related to CHINESE no. 20 (genetic distance = 0.667). Taken together, these results demonstrate the potential of RAPD analysis to identify diagnostic markers for the identification of four freshwater crab populations.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1710-1720
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• 2008

A comprehensive genome profiling study was undertaken based on automated genotyping and analysis of 20 microsatellite markers that involved 155 birds representing eight different populations. The distribution of microsatellite markers in each of these breeds helped us to decipher genetic heterogeneity, population genetic structure and evolutionary relationships of the present day chicken populations in India. All the microsatellite loci utilized for the analysis were polymorphic and reasonably informative. A total of 285 alleles were documented at 20 loci with a mean of 14.25 alleles/locus. A total of 103 alleles were found to be population/strain specific of which, only 30 per cent had a frequency of more than 10. The mean PIC values ranged from 0.39 for the locus ADL158 to 0.71 for loci MCW005 or ADL267 across the genomes and 0.55 in Dahlem Red to 0.71 in Desi (non-descript), among the populations. The overall mean expected and observed heterozygosity estimates for our populations were 0.68 and 0.64, respectively. The overall mean inbreeding coefficients (FIS) varied between -0.05 (Babcock) and 0.16 (Rhode Island Red). The pairwise FST estimates ranged from 0.06 between Aseel and Desi (non-descript) to 0.14 between Dahlem Red and Babcock. The Nei's genetic distance varied from 0.30 (WLH-IWD and WLH-IWF) to 0.80 (Dahlem Red and Babcock. Phylogenetic analysis grouped all the populations into two main clusters, representing i) the pure breeds, Dahlem Red and Rhode Island Red, and ii) the remaining six populations/strains. All the chicken populations studied were in the state of mild to moderate inbreeding except for commercial birds. A planned breeding is advised for purebreds to revive their genetic potential. High genetic diversity exists in Desi (non-descript), local birds, which can be exploited to genetically improve the birds suitable for backyard poultry.

• The Korean Journal of Physiology and Pharmacology
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• v.1 no.2
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• pp.195-200
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• 1997

Water transport in highly-permeable membranes is facilitated by some specialized pathways, which are called aquaporins (AQP). AQP1 (AQP-CHIP) is the first recognized aquaporin identified from red cells and renal proximal tubules. Up until now 4 other aquaporin homologs have been reported. Each aquaporin has its unique tissue distribution and regulatory mechanims. To elucidate molecular mechanisms for their transcription regulation and tissue-specific expression isolation of aquaporin genes is required. To clone promoters of the AQP family mouse genomic library was screened by the 1st exon-specific probe of AQP4, and 5 different plaques were positively hybridized. Phage DNAs were purified and characterized by restriction mapping and sequencing. One of them is the mouse AQP-CD gene. The gene was consisted of 4 exons and the exon-intron boundaries of mouse AQP-CD gene were identified at identical positions in other related genes. The 5'-flanking region of AQP-CD gene contains one classic TATA box, a GATA consensus sequence, an E-box and a cyclic AMP-responsive element. The cloning of the mouse AQP-CD gene, of which product is expressed in the collecting duct and is responsible for antidiuresis by vasopressin, will contribute to understand the molecular mechanisms of tissue-specific expression and regulation of AQP-CD gene under various conditions.

• The Korean Journal of Malacology
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• v.24 no.1
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• pp.11-24
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• 2008

GDNA was isolated from the jedo venus clam (Protothaca jedoensis, Lischke) from Boryeong (jedo venus clam from Boryeong JVCB) and Wonsan (jedo venus clam from Wonsan; JVCW) located in the West Sea and the East Sea of Korean Peninsula, respectively and we performed clustering analyses, DNA polymorphisms and the populations genetic variations. In the present study, the seven decamer primer generated the one hundred and eleven major/minor specific bands in JVCB population and ninety four-specific bands in JVCW population. Seven primers generated the unique shared bands to each population of one hundred and seventy-six, on average of 25,1, in JVCB population from Boryeong and three hundred thirty, on average of 47,1, in JVCW population from Wonsan, respectively. The dendrogram obtained by the seven oligonucleotides primers, indicates two genetic clusters. Especially, two Protothaca between the individual WONSAN no. 12 and BORYEONG no. 10 showed the longest genetic distance (0.537) in comparison with other individuals used. Accordingly, RAPD analysis showed that the JVCB was a little more genetically diverse than the JVCW population. This result implies the genetic similarity owing to rearing in the same and/or similar circumstances or inbreeding within the JVCW population. So to speak, JVCB population may have high levels of genomic DNA variability owing to the introduction of the wild individuals from the other sites to sampling sites although it may be the geographically diverse distribution of this species. However, it was confirmed that it did not appear like that really in this study. We feel convinced that RAPD analysis discovered a significant genetic distance between two Protothaca population pairs (P<0.001). The existence of population discrimination and genetic diversity between two Protothaca populations was identified by RAPD analysis.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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• pp.9621-9625
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• 2014

XRCC (X-ray cross-complementing group) genes contribute to important DNA repair mechanisms that play roles in the repair of single strand breaks (SSBs) induced by a variety of external and internal factors, including ionizing radiation, alkylating agents and reactive oxygen species. These repair genes have a pivotal role in maintaining genomic stability through different pathways of base excision repair (BER). The aim of this study was to investigate the XRCC3 Thr241Met gene polymorphism in colorectal cancer (CRC) in Kashmir. We investigated the genotype distribution of XRCC3 gene in 120 CRC cases in comparison with 150 healthy subjects and found a significant association between XRCC3 genotypes and CRC ($p{\leq}0.05$). Both heterozygous genotype (Thr/Met) as well as homozygous variant genotype (Met/Met) were moderately associated with elevated risk of CRC [OR=2.53; OR=2.29 respectively]. Also, Thr/Met and Met/Met genotypes demonstrated a significant association with the risk of CRC (p = 0.003). This study displayed a significantly elevated risk for CRC in individuals with XRCC3 Thr/Met and Met/Met Genotype of about 2.5 times that with the Thr/Thr wild genotype.

• Korean Journal of Veterinary Service
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• v.32 no.4
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• pp.315-323
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• 2009

Foot-and-mouth disease (FMD) virus exists in seven serotypes and is known to be a highly contagious disease that is hard to eradicate from the world. The O, A, Asia1 and SAT2 serotypes commonly infected cattle, sheep and goats during 2007~2009 throughout the world. In particular, the outbreak of the Asia1 serotype in China appeared in all areas from 2005 and is still present. Surprisingly, in 2009, Taiwan reported the first outbreak of the type O serotype since 2001. Then type A appeared in China for the first time since the early 1960s. The virus shows a close relationship to the viruses from Southeast Asia suggesting one or more recent introductions into China in the OIE reports. Recently the subtype of A/Iran05 spread to nearby countries exhibiting genomic evolution. The use of molecular epidemiology is an important tool in understanding and consequently controlling the FMD virus. The phylogenetic analysis with VP1 gene was especially useful for molecular epidemiological studies and showed the same pattern which matches with serotype classification. This paper describes basic information about the disease, and the serotype-specific characteristics and evolution to perform molecular epidemiological analysis. Furthermore, we show the importance of the genetic evolution on the FMD serotypes in global surveillance and molecular epidemiology of FMD for outbreak investigation.