• Journal of Wetlands Research
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• v.22 no.2
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• pp.100-105
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• 2020

Northern pipevine (Aristolochia contorta) commonly inhabits marginal areas between waterside and terrestrial vegetation. In particular, A. contorta is ecologically important in the marginal areas as a food plant of dragon swallowtail butterfly (Sericinus montela), which is designated as vulnerable species in the Republic of Korea. For long-term sustainability of the plant population, assessment of the genetic diversity of exist populations should be conducted. Genomic DNA of A. contorta leaf samples were extracted from four populations where the vigorous growth were observed in the South Korea. Intra-population genetic diversity and inter-population genetic distance were assessed using randomly amplified polymorphic DNA (RAPD) with five polymorphic random primers. Overall genetic diversity was lower, compared to other wetland species (h: 0.0607 ~ 0.1401; I: 0.0819 ~ 0.1759), while GP showed the highest intra-population genetic diversity. Despite of the geographical distance, GP showed the larger genetic distance from other populations. This result seemed to be caused by the fragmented habitat and lower sexual reproduction of A. controta. Mixture of the different source populations and construction of the proper environmental condition such as shade and physical support for sexual reproduction should be considered for conservation of A. contorta population.

• Journal of Mushroom
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• v.17 no.4
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• pp.171-178
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• 2019

Agaricus bisporus is a functional food and among the most widely cultivated mushrooms in the world. In this study, we analyzed the genetic diversity and population structure of 23 Korean and 42 foreign A. bisporus cultivars using SSR (Simple sequence repeat) markers. Genetic diversity of A. bisporus cultivars was as follows: number of alleles was approximately 13; observed and expected heterozygosity were approximately 0.59 and 0.74, respectively; and polymorphic information content value was about 0.71. A. bisporus cultivars were divided into three groups using distance-based analysis. Genetic diversity of Group 2, which consisted of cultivars from various countries, was high. In addition, model-based subpopulations were divided into two, and the genetic diversity of Pop2 (Population 2), which had many cultivars, was high. The results of this study could be used in a breeding program for A. bisporus, such as the development of new genetic resources and securing diversity.

• Journal of Life Science
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• v.20 no.7
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• pp.983-990
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• 2010

Genus Spiraea is a woody species primarily distributed throughout Asia. Many species of this genus are important plants medicinally and ecologically. I evaluated a representative sample of the sixteen taxa with random amplified polymorphic DNA (RAPD) markers to estimate genetic relationships within genus Spiraea. In addition, RAPD analysis was also conducted to estimate the genetic diversity and population structure of these species. As the typical populations of Spiraea were small, isolated, and patchily distributed for natural populations, they maintained a low level of genetic diversity for polymorphic primers. The mean H was 0.117 across species. The Korean endemic species (S. chartacea) and patchily distributed species (S. betulifolia) showed fewer alleles per locus (mean 1.240 vs. 1.297), lower percent polymorphic locus (24.0 vs. 29.7), and lower diversity (0.092 vs. 0.121) than a relatively widely spread species. An assessment of the proportion of diversity present within species, $H_{POP}/H_{SP}$, indicated that about 87.8% the total genetic diversity was among species. Thus, the majority of genetic variation (87.8%) resided within species. The phylogenic tree showed three distinct groups. One clade includes S. prunifolia for. simpliciflora, S. thunbergii, S. chamaedryfolia var. ulmifolia, S. media, and S. cantoniensis. Another clade includes S. blumei, S. pubescens, S. chartacea, and S. chinensis. The other clade is the remaining seven species.

• Journal of Life Science
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• v.29 no.2
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• pp.152-157
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• 2019

Porphyra yezoensis is a red algal species in the genus Porphyra. The phenetics and genetic diversity of four populations of P. yezoensis in Korea were reconstructed using random amplified polymorphic DNA (RAPD) markers. Overall, 55 fragments were generated among the tested P. yezoensis array with 20 OPERON primers. A total of 30(54.5%) of these bands were polymorphic. The OPA-18-02 band was amplified in the samples of Nakdong population and absent in them of other three populations. The OPA-20-02 band was only amplified in the Seocheon population. Both bands exhibited distinctive patterns in specific populations. The effective number of alleles per locus (Ae) ranged from 1.161 to 1.293 with a mean of 1.366. The Seocheon population had a high expected diversity (0.163). The Nakdong population was an isolated endemic and intertidal zone. Thus the narrow distributed Nakdong population had a low expected diversity (0.092). Shannon's index of phenotypic diversity (I) of the Seocheon population (0.238) was the highest among all populations. Total genetic diversity ($H_T$) varied between 0.132 for OPA-02 and 0.420 for OPA-19. The interlocus variation of genetic diversity ($H_S$) was 0.059 for OPA-18 and 0.339 for OPA-19. On a per locus basis, the proportion of total genetic variation due to differences among populations ($G_{ST}$) ranged from 0.012 for OPA-11 to 0.762 for OPA-18 with a mean of 0.415, indicating that 42% of the total variation was found among these populations. In an assessment of the proportion of diversity present within this species, 58.5% (100%-41.5%) of genetic variation resided within the populations studied. The Nm was estimated to be low (0.705).

• Genomics & Informatics
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• v.17 no.4
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• pp.48.1-48.6
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• 2019

Over the last decade, genome-wide association studies (GWASs) have provided an unprecedented amount of genetic variations that are associated with various phenotypes. However, previous GWAS were mostly conducted in European populations, and these biased results for non-Europeans may result in a significant reduction in risk prediction for non-Europeans. An issue with the early GWAS was the winner's curse problem, which led to misleading results when constructing the polygenic risk scores (PRS). Therefore, more non-European population-based studies are needed to validate reported variants and improve genetic risk assessment across diverse populations. In this study, we validated 422 variants independently associated with glycemic indexes, liver enzymes, and type 2 diabetes in 125,872 samples from a Korean population, and further validated the results by assessing publicly available summary statistics from European GWAS (n = 898,130). Among the 422 independently associated variants, 284, 320, and 361 variants were replicated in Koreans, Europeans, and either one of the two populations. In addition, the effect sizes for Koreans and Europeans were moderately correlated (r = 0.33-0.68). However, 61 variants were not replicated in both Koreans and Europeans. Our findings provide valuable information on effect sizes and statistical significance, which is essential to improve the assessment of disease risk using PRS analysis.

• Journal of Microbiology and Biotechnology
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• v.28 no.2
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• pp.284-292
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• 2018

A novel ${\beta}$-agarase, AgaJ5, was identified from an agar-degrading marine bacterium, Gayadomonas joobiniege G7. It belongs to the glycoside hydrolase family 86 and is composed of 805 amino acids with a 30-amino-acid signal peptide. Zymogram analysis showed that purified AgaJ5 has agarase activity. The optimum temperature and pH for AgaJ5 activity were determined to be $30^{\circ}C$ and 4.5, respectively. AgaJ5 was an acidic ${\beta}$-agarase that had strong activity at a narrow pH range of 4.5-5.5, and was a cold-adapted enzyme, retaining 40% of enzymatic activity at $10^{\circ}C$. AgaJ5 required monovalent ions such as $Na^+$ and $K^+$ for its maximum activity, but its activity was severely inhibited by several metal ions. The $K_m$ and $V_{max}$ of AgaJ5 for agarose were 8.9 mg/ml and 188.6 U/mg, respectively. Notably, thin-layer chromatography, mass spectrometry, and agarose-liquefication analyses revealed that AgaJ5 was an endo-type ${\beta}$-agarase producing neoagarohexaose as the final main product of agarose hydrolysis. Therefore, these results suggest that AgaJ5 from G. joobiniege G7 is a novel endo-type neoagarohexaose-producing ${\beta}$-agarase having specific biochemical features that may be useful for industrial applications.

• Korean Journal of Plant Taxonomy
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• v.43 no.4
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• pp.245-251
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• 2013

Paeonia lactiflora is a valuable natural resource for horticulture and traditional Chinese medicine. To propose conservation strategy and future utility of the wild Paeonia lactiflora populations recently found around the Gyeongju National Park, genetic diversity analysis using microsatellite markers were performed. Three populations in and near the Gyeongju N.P. and one population from Jilin, China were analyzed for five microsatellite markers, producing 61 alleles with mean observed heterozygosity($H_o$) of 0.452. $F_{ST}$ value (0.11642) suggested moderate level of genetic differentiation among the populations, and hierarchical AMOVA suggested most of the genetic variation resides within/among the individuals rather than among-population. While AMOVA with $F_{ST}$ suggested lack of genetic differentiation between the regional (Korean vs. Chinese) populations, AMOVA with $R_{ST}$, which incorporates the allele sizes, suggested considerable differentiation between them, but without significant statistical support. STRUCTURE analysis also suggested segregation of regional populations with presence of gene flow among the three Gyeongju N.P. populations. Considering small population size and scarcity of mature individuals, further protection and long-term monitoring are needed.

• FLOWER RESEARCH JOURNAL
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• v.16 no.1
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• pp.28-35
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• 2008

Eleven accessions of Hedera helix, three accessions of Hedera rhombea, one accession of Fatshedera lizei, and one accession of Fatsia japonica were collected and their genetic diversity was measured by using 10 RAPD primers. Approximately ninety seven percentage of polymorphism was detected, because broad germplasm, three genus, was used. Total 97 bands were scored and a dendrogram was constructed by using an UPGMA method. Accessions belonging to Hedera helix tightly clustered in one group: eight accessions showed extremely narrow genetic differences and the other three accessions also showed significant similarity. Despite of their genetic similarity, they showed morphological variations. The morphological variation with a narrow genetic differences indicated that the ivy cultivars have been indeed developed from a mutation breeding program. Genetically most unrelated Fatsia japonica showed a genetic distance of 0.63 on the average between other species. An accession from Fatshedera lizei developed by crossing between two genus, Hedera helix and Fatsia japonica, was allocated together with accessions from Hedera rhombea.

• BMB Reports
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• v.36 no.1
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• pp.1-11
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• 2003

The causative role of polycyclic aromatic hydrocarbons (PAH) in human carcinogenesis is undisputed. Measurements of PAH-DNA adduct levels in easily accessible white blood cells therefore represent useful early endpoints in exposure intervention of chemoprevention studies. The successful applicability of DNA adducts as early endpoints depends on several criteria:i.adduct levels in easily accessible surrogate tissues should reflect adduct levels in target-tissues, ii. toxicokinetics and the temporal relevance should be properly defined.iii. sources of inter- and intra-individual variability must be known and controllable, and finally iv. adduct analyses must have advantages as compared to other markers of PAH-exposure. In general, higher DNA adduct levels or a higher proportion of subjects with detectable DNA adduct levels were found in exposed individuals as compared with non-exposed subjects, but saturation may occur at high exposures. Furthermore, DNA adduct levels varied according to changes in exposure, for example smoking cessation resulted in lower DNA adduct levels and adduct levels paralleled seasonal variations of air-pollution. Intra-individual variation during continuous exposure was low over a short period of time (weeks), but varied significantly when longer time periods (months) were investigated. Inter-individual variation is currently only partly explained by genetic polymorphisms in genes involved in PAH-metabolism and deserves further investigation. DNA adduct measurement may have three advantages over traditional exposure assessment: i. they can smooth the extreme variability in exposure which is typical for environmental toxicants and may integrate exposure over a longer period of time. Therefore, DNA adduct assessment may reduce the monitoring effort. ii. Biological monitoring of DNA adducts accounts for all exposure routes. iii. DNA adducts may account for inter-individual differences in uptake, elimination, distribution, metabolism and repair amongst exposed individuals. In conclusion, there is now a sufficiently large scientific basis to justify the application of DNA adduct measurement as biomarkers in exposure assessment and intervention studies. Their use in risk-assessment, however, requires further investigation.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2009.04a
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• pp.392-395
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• 2009

응답면 기법을 활용하여 댐구조물과 같은 사회간접자본 시설물의 파괴확률을 구할 수 있다. 본 위험성 평가과정에서 응답면기법으로 구성한 한계상태 방정식을 유전자알고리즘의 적합도 방정식으로 사용하면, 핵심타입이나 지반종류, 지반다짐정도 등의 입력설계변수의 최적화 과정 속도를 더욱 신속화 시킬 수 있다. 제안된 응답면 기법과 유전자알고리즘의 복합해석기법은 신뢰성기반 최적화프로그램으로 기존의 유전자알고리즘의 수렴속도를 더욱 빠르게 하여주고, 특히 입력변수의 상하한계가 불확실한 경우에도 만족스러운 수렴성을 보장하여준다. 한계상태 방정식의 목표신뢰도 지수를 변화시켜면 해당하는 입력변수의 최적값을 출력하여주므로, 입력변수의 제약조건에 가격함수와 같은 가중치를 벌칙함수로 부여하면 가격최적화 프로그램으로 작용하게 되며, 시설물 운영자에게는 목표신뢰도에 대한 유지관리 기법과 정도를 의사결정 할 수 있도록 하여주는 기능을 가지게 된다. 조사된 많은 댐구조물의 파괴모드가 시간에 독립적으로 시공중 또는 시공완료 후 5년이내에 다수 발생하는바, 파괴모드를 조사하고 중요한 파괴모드인 파이핑 현상에 대해서 파괴확률을 계산하고 최적유지관리를 위한 개선된 유전자알고리즘 최적화 연산을 수행하였다. 기존 댐구조물과 같이 설계변수와 하중의 변동성을 알기가 어려운 경우에 유지관리비용 최소화를 위해서 본 제안 프로그램의 확장된 버젼은 중요한 기준을 제시하여줄 것으로 기대한다.