• Archives of Pharmacal Research
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• v.29 no.1
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• pp.88-95
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• 2006

Analysis of molecular nature of mitochondrial DNA (mtDNA) could be powerful marker for anthropological studies of modern populations. While population genetic studies on mtDNA have been reported for several ethnic groups, no such study has been documented for the Korean population. We surveyed mtDNA polymorphisms in the HVS I of noncoding D-loop region and its upstream region from 430 unrelated healthy Korean population by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing analysis. PCR product with 2,790 bp spanning the specific mtDNA region (mt13715-16504) was subjected to RFLP analysis using 6 restriction enzyme (Hinf I, Hae III, Alu I, Dde I, Mbo I, Rsa I). On the PAUP analysis of PCR-RFLP results, 38 mtDNA haplotypes (Hap 1-38) were detected in the Korean populations, which were classified into 11 haplogroups (Grp 1-11) of related haplotypes encompassing all 38 haplotypes. In comparison of sequencing data with Anderson's reference sequence, the transition type was more prevalent than the transversion type. Insertions or deletions were not found. In addition, three of the polymorphic sites (A16240C, A16351G, G16384A) in HVS-I region are determined newly. The polymorphic sites were distributed randomly in the region, though the frequency at each site was variable. Thus, this research might be required for the genealogical study of Orientals.

• Development and Reproduction
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• v.19 no.4
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• pp.259-264
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• 2015

Genomic DNA samples isolated from geographical purplish Washington clam (Saxidomus purpuratus) were obtained from three different regions in the Korean Peninsula: Geoje (Geoje population; GJP), Gunsan (Gunsan population; GSP) and a site of North Korea (North Korea population; NKP). The seven primers generated the total 369 loci that can be scored from the GSP clam population. 356 fragments were generated from the NKP clam population. The complexity of the banding patterns varies dramatically between the primers and three localities. In this study, 319 loci were identified in the purplish Washington clam from Geoje and 369 in the clam population from Gunsan: 221 specific loci (69.3%) in the GJP clam population and 300 (81.3%) in the GSP population. These results demonstrate that the primer detected a large quantity of specific fragments, suggesting that the genetic variation in the GSP is higher than in the GJP population. In particular, the BION-28 primer gave DNA profiles with more fragments than the other six primers in the NKP population. The oligonucleotides primer BION-75 produced 21 unique loci to each population, which were ascertaining each population, approximately 250 bp, 300 bp and 400 bp, in the GJP population. Outstandingly, the primer BION-50 detected 21 shared loci by the three populations, major and/or minor fragments of sizes 150 bp, which were matching in all samples. With regard to average bandsharing value (BS) results, individuals from GJP population (0.743) displayed higher bandsharing values than did individuals from GSP population (0.606). In the present study, the dendrogram gained by the seven oligonucleotides primers indicates three genetic clusters: cluster 1 (GEOJE 01 ~ GEOJE 07), cluster 2 (GUNSAN 08 ~ GUNSAN 14), cluster 3 (N.KOREA 15 ~ N.KOREA 21). Among the twenty one clams, the shortest genetic distance that revealed significant molecular differences was between individuals 08 and 09 from the NKP population (genetic distance = 0.073), while the longest genetic distance among the twenty-one individuals that demonstrated significant molecular differences was between individuals GEOJE no. 03 and GUNSAN no. 09 (genetic distance = 0.669). Comparatively, individuals of GJP population were properly closely related to that of NKP population, as revealed in the hierarchical dendrogram of genetic distances. In due course, PCR analysis has revealed the significant genetic distance among three purplish Washington clam populations. PCR fragments discovered in this study could be valuable as a DNA marker of the three geographical clam populations to distinguish.

• BMB Reports
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• v.37 no.2
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• pp.213-222
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• 2004

A randomly amplified polymorphic DNA (RAPD) analysis was used to identify the species- and population-specific markers of abalone; Haliotis asinina, H. ovina, and H. varia in Thai waters. Fifteen species-specific and six population-specific RAPD markers were identified. In addition, an 1650 bp band (UBC195) that was restricted to H. ovina from the Gulf of Thailand (east) was also found. All of the specific RAPD markers were cloned and sequenced. Twenty pairs of primers were designed and specificity-tested (N = 12 and 4 for target and non-target species, respectively). Seven primer pairs (CUHA1, 2, 4, 11, 12, 13, and 14) were specifically amplified by H. asinina DNA, whereas a single pair of primers showed specificity with H. ovina (CUHO3) and H. varia (CUHV1), respectively. Four primer pairs, including CUHA2, CUHA12, CUHO3, and CUHV1, were further examined against 216 individuals of abalone (N = 111, 73, and 32, respectively). Results indicated the species-specific nature of all of them, except CUHO3, with the sensitivity of detection of 100 pg and 20 pg of the target DNA template for CUHA2 and CUHA12 and CUHV1, respectively. The species-origin of the frozen, ethanol-preserved, dried, and boiled H. asinina specimens could also be successfully identified by CUHA2.

• Development and Reproduction
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• v.20 no.2
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• pp.135-140
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• 2016

Genomic DNAs isolated from crucian carp of four rivers, belonging to the family Cyprinidae was amplified by seven oligonucleotides primers. In the present study, we employed hierarchical clustering method in order to reveal genetic distances and variations. Crucian carp was acquired from Hangang river (CAH), Geumgang river (CAG), Nakdonggang river (CAN) and Yeongsangang river (CAY). The primer BION-12 generated the most loci (a total of 50) with an average of 10 in the CAY population. The primer BION-10 generated the least loci (a total of 19), with an average of 3.8 in the CAG population, in comparison to the other primers used. Seven oligonucleotides primers made 16.7 average no. per primer of specific loci in the CAH population, 7.4 in the CAG population, 8.6 in the CAN population and 0.9 in the CAY population, respectively. The specific loci generated by oligonucleotides primers revealed inter-individual-specific characteristics, thus disclosing DNA polymorphisms. The dendrogram obtained by the seven oligonucleotides primers indicates four genetic clusters. The genetic distance that displayed significant molecular differences was between individuals no.06 and no.08 from the CAG population (genetic distance = 0.036), while the genetic distance among the five individuals that displayed significant molecular differences was between individuals no.08 and no.09 from the CAG population (genetic distance = 0.088). With regard to average bandsharing value (BS) results, individuals from CAY population ($0.985{\pm}0.009$) exhibited higher bandsharing values than did individuals from CAH population ($0.779{\pm}0.049$) (P<0.05). Relatively, individuals of CAY population were fairly closely related to that of CAN location (genetic distance between two populations<0.016).

• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.166-171
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• 2002

The genus Leuconostoc is generally recognized as a favorable microorganism associated with a good taste of Kimchi and Lactobacillus plantarum is responsible for the overripening and acidification of Kimchi. A rapid and reliable PCR-based method to monitor the change of these lactic acid bacterial populations during Kimchi fermentation was attempted. A Leuconostoc-specific primer set was chosen from the conserved sequences of 16S rRNA genes among Leuconostoc species. The Lb. plantarum-specific primer set was the internal segments of a Lb. plantarum-specific probe which was isolated after randomly amplified polymorphic DNA (RAPD) analysis and tested for identification. The specificity of this protocol was examined in DNA samples isolated from a single strain. In agarose gel, as little as 10 pg of template DNA could be used to visualize the PCR products, and quantitative determination was possible at the levels of 10 pg to 100 ng template DNA. For the semi-quantitative determination of microbial changes during Kimchi fermentation, total DNAs from the 2 h-cultured microflora of Kimchi were extracted for 16 days and equal amounts of DNA templates were used for PCR. The intensities of DNA bands obtained from PCR using Leuconostoc-specific and Lb. plantarum-specific primer sets marked a dramatic contrast at the 1 ng and 100 ng template DNA levels during Kimchi fermentation, respectively. As the fermentation proceeded, the intensity of the band for Leuconostoc species increased sharply until the 5th day and the levels was maintained until the 11 th day. The sharp increase for Lb. plantarum occurred after 11 days with the decrease of Leuconostoc species. The results of this study indicate that Leuconostoc species were the major microorganisms at the beginning of Kimchi fermentation and reach their highest population during the optimum ripening period of Kimchi.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.4
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• pp.568-572
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• 2015

Acetes chinensis is an economically important shrimp that belongs to the Sergestidae family; following fermentation, A. chinensis' economic value, however, is low in China, and much of the catch in China is exported to Korea at a low price, thus leading to potential false labeling. For this reason, we developed a simple method to identify A. chinensis' origin using allele-specific polymerase chain reaction (PCR). Ten single nucleotide polymorphisms (SNPs) were identified from partial (i.e., 570 bp) DNA sequence analysis of the mitochondrial 16s rRNA gene in 96 Korean and 96 Chinese individual shrimp. Among 10 SNP sites, four sites were observed in populations from both countries, and two sites located in the middle with SNP sites at their 3'-ends were used to design allele-specific primers. Among the eight internal primers, the C220F primer specific to the Chinese A. chinensis population amplified a DNA fragment of 364 bp only from that population. We were able to identify the A. chinensis population origin with 100% accuracy using multiplex PCR performed with two external primers and C220F primers. These results show that the 16S rRNA gene that is generally used for the identification of species can be used for the identification of the origin within species of A. chinensis, which is an important finding for the fair trade of the species between Korea and China.

• The Korean Journal of Malacology
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• v.25 no.1
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• pp.5-13
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• 2009

Genomic DNA isolated from two geographical ark shell (Scapharca subcrenata) populations was amplified several times by PCR reactions. The ark shell population from Daecheon (ASPD) and from Wonsan (ASPW) in the West Sea and the East Sea of Korean Peninsula, respectively, obtained. The seven arbitrarily selected primers OPA-05, OPA-11, OPB-09, OPB-11, OPB-14, OPC-18 and OPD-07 were shown to generate the loci observed per primer, shared loci by each population, specific loci, unique shared loci to each population and shared loci by the two populations which could be clearly scored. Here, 862 loci were identified in the ASPD population, and 1,191 in the ASPW population: 137 specific loci (15.9%) in the Daecheon population and 84 (7.1%) in the Wonsan population. 407 shared loci by each population, with an average of 58.1 per primer, were observed in the ASPD population. 473 shared loci by each population, with an average of 67.6 per primer, were identified in the ASPW population. The numbers of specific loci in the ASPD and ASPW population were 137 and 84, respectively. Consequently, the average bandsharing value of individuals within the ASPW population was much higher than in the ASPD population. The bandsharing value between individuals' no. 08 and no. 13 was 0.628, which was the highest measured between the two geographical populations. The dendrogram obtained by the seven primers indicated three genetic clusters: cluster 1 (DAECHEON 01-DAECHEON 11), cluster 2 (WONSAN 12 and 14) and cluster 3 (WON SAN 13, 15, 16, 17, 18, 19, 20, 21 and 22). The genetic distance between the two geographical populations ranged from 0.043 to 0.499. Especially, individual no. 10 of Daecheon population was most distantly related to no. 14 of Wonsan population (genetic distance = 0.499).

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.3
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• pp.302-306
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• 2001

This study was carried out to construct mapping population and to evaluate the methods involved, including polymorphic DNA marker system and appropriate statistical analysis. As an initial step to establish chicken genome mapping project, White Leghorn (WL) and Korean Ogol chicken (KOC) were used for generating backcross population. From 8 initial parents, total 280 backcross progenies were obtained and 40 were used for genotyping and linkage analysis. For development of novel polymorphic markers for KOC, Random Amplified Polymorphic DNA (RAPD) markers specific for this chicken line were generated. Also included in this study were six microsatellite markers from East Lansing map as reference loci. For segregation analysis, 15 RAPD markers and 6 microsatellites were used to genotype the backcross population. Among the RAPD markers that we developed, 2 pairs of markers were identified to be linked and another 4 RAPD markers showed linkage with microsatellites of known map. In summary, this study showed that our backcross population generated from the mating of KOC to WL serves as a valuable genetic resource for genotyping. Furthermore, RAPD markers are proved to be valuable in linkage mapping analysis.

• Journal of Physiology & Pathology in Korean Medicine
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• v.17 no.5
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• pp.1208-1216
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• 2003

Stress is known to influence the immune function via an effect on the central nervous system. To investigated the effects of Kwibitang water extract (KBT) on the specific immune response in C57BL/6 mice stressed by immobilization, we evaluated the changes in the cell viability, DNA fragmentation and subpopulation of thymocytes and splenocytes. KBT enhanced the cell viability of thymocytes and splenocytes decreased by immobilization stress. Also, KBT decreased DNA fragmentation of thymocytes and splenocytes increased by immobilization stress. KBT decreased the population of CD4/sup +/ cells and CD8/sup +/ cells in thymocytes and Thy1/sup +/ cells in splenocytes increased by immobolization stress, but increased the population of B220/sup +/ cells decreased by immobilization stress. In addition, KBT enhanced the production of ν-interferon and IL-2 decreased by immobilization stress. These results indicate that KBT may be useful for the prevention and treatment of stress via enhancement of the specific immune response

• Fisheries and Aquatic Sciences
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• v.12 no.3
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• pp.171-178
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• 2009

The Perciformes include approximately 40% of all bony fishes and are the largest order of vertebrates. This order includes some of the most economically relevant marine fishes, particularly the red seabream, black seabream and rock bream. A 409 bp fragment of the cytochrome b (cyt b) gene and 403 bp and 518 bp fragments of ribosomal RNA (12S and 16S rRNA, respectively) were sequenced from five populations of natural and cultured red seabreams, natural black seabream, and natural and cultured rock breams. The mitochondrial DNA sequences were utilized for the genetic identification and population structural analyses of these three species. Phylogenetic relationships of intra- and inter-species were elucidated using three types of molecular genetic markers from three species of the order Perciformes in Korea. We noted no significant differences in the intra-specific variation of the cyt b and rRNA genes in each population however, inter-specific divergences were greater than intra-specific variation. Inter-specific variation was induced more by transition than transversion type in the cyt b and rRNA genes. The cyt b gene and rRNA genes make it possible to determine the inter-species divergence. The rRNA genes have more conserved sequences than the cyt b gene. Therefore, these genes are expected to prove useful among species belonging to the different genera or families.