• The Korean Journal of Mycology
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• v.44 no.2
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• pp.103-107
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• 2016

To establish a rapid and accurate detection of Phytophthora pinifolia, which is a quarantine pathogenic fungus in Korea, a species-specific primer was developed based on the ras-related protein (Ypt1) gene. Species-specific primer based on the DNA sequences of Ypt1 gene amplified 193 bp polymerase chain reaction (PCR) product for P. pinifolia. The primer pair yielded the predicted PCR product size exactly in testing with target pathogen DNAs, but not from the other 10 species of Phytophthora and 14 species of other phytopathogenic fungi. The primer pair also showed only the species-specific amplification curve on realtime PCR on target pathogen DNA. The detection sensitivity of real time PCR using species-specific primer pair was 10 to 100 times higher than conventional PCR, with 1 to $10pg/{\mu}L$.

• Journal of Animal Science and Technology
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• v.50 no.1
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• pp.9-18
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• 2008

Species-specific polymorphisms in chicken, pheasant, turkey, and quail were identified by cloning and sequencing of the immunoglobulin constant domain (IgLC). A set of species-specific primers were then designed on the basis of polymorphisms in the IgLC between species, as well as two additional sets of primers for the cytochrome b and tapasin genes, for the purpose of species identification. Together, the primers successfully distinguished specific species from chicken by species-specific PCR. This simple but unambiguous method may be used to screen avian inter-species germline chimeras, which are valuable models for the conservation of endangered species.

• Journal of the Korean Institute of Landscape Architecture
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• v.39 no.1
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• pp.11-21
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• 2011

In this paper, in order to select specialist butterfly species that inhabit Haneul and Noeul Parks, previously landfill areas, we verified the reciprocal relationships between nectar plants and butterflies. While we will design the butterfly habitats, this paper will provide the foundation data for selecting the plants. The completed survey indicated that there were a total of 5 families, 23 species and 1,129 individuals. Butterflies of the main action were feeding on nectar, and such behavior was 36% of the total actions. Therefore, these parks play an important role in butterflies feeding on nectar. The correlation between butterflies and the nectar plants' color was not significant; Therefore, it is not necessary to consider flower color when choosing plants to attract the butterflies. In addition, butterflies prefer naturalized plants for feeding on nectar. Thus, when creating butterfly habitats, there is no use in attracting the butterflies by classifying the naturalized plants and native plants. However, if some areas that are need to plant native plants such as Inkigofera pseudo-tinctoria, Lespedeza bicolor, Aster koraiensis make use it, there could be taken an advantage to attract the butterflies. According to the algebraic curve model of curve estimation regression analysis, we were able to classify the generalist species and specialist species by regression analysis. As a result, Colias erate, Artogeia rapae and Parnara guttata were classified as generalist species, where as Rapala caerulea, Pieris melete, Zizera maha and Celastrina argiolus were classified as specialist species. Rapala caerulea prefers hills and forest for its habitat; therefore, it is clearly distinct from Pieris melete, Zizera maha and Celastrina argiolus which prefer grassland for habitats. These results show that Rapala caerulea is high conservation value in a landfill area where is developing ecological succession from grasslands to wood lands. In conclusion, these research are able to contribute to select the target species and suitable species that consider a singularity between butterflies and nectar plants, when we are creating the butterfly habitats, moreover these research will contribute to maintain a stable habitats.

• Journal of Ecology and Environment
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• v.29 no.3
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• pp.191-203
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• 2006

To understand the effect of forest fragmentation on forest-dwelling birds, it is more effective to analyze on the selected specialists than on the whole bird community. We investigated the edge preference of forest-dwelling birds to discriminate habitat specialist species in the interior and on the edge of temperate deciduous forests in central Korea. Point count and line transect census were conducted at Gwangneung forest from February to October. Our result shows that there was no consistent tendency in abundance of birds between in the interior and on the edge because of the different landscape characteristics and the high proportion of habitat generalists. Five habitat specialists in 73 bird species were identified by the differences in both population densities; three forest interior and two forest edge specialists. Asian Stubtail Warblers (Urosphena squameiceps), Pale Thrushes (Turdus pallidus) and Coal Tits (Parus ater) were included in the forest interior group, but Black-billed Magpies (Pica pica) and Black-naped Orioles (Oriolus chinensis) were classified as the forest edge group. We suppose that a selective monitoring on patterns and changes in spatial use of these five habitat specialists is needed to estimate the effects of forest fragmentation in temperate deciduous forests. And, moreover, systematic monitoring methods for field survey should be established based on the point count method and line transect census to ensure the equality of data.

• Journal of Life Science
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• v.26 no.9
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• pp.1007-1014
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• 2016

A highly efficient, rapid, and reliable multiplex polymerase chain reaction based method for distinguishing ten species of genus Cynoglossus (C. senegalensis, C. abbreviates, C. macrolepidotus, C. arel, C. semilaevis, C. interruptus, C. joyneri, C. lingua, C. robustus, and C. monodi) is described. The species-specific primer sets were designed base on the cytochrome oxidase subunit I gene (1,500 bp). The optimal PCR conditions and primers were selected for ten of Cynoglossus species to determine target base sequences using single PCR. Multiplex PCR using the ten pairs of primers either specifically amplified a DNA fragment of a unique size or failed, depending on each species DNA. The length of amplification fragment of 208 bp for C. senegalensis, 322 bp for C. abbreviates, 493 bp for C. macrolepidotus, 754 bp for C. arel, 874 bp for C. semilaevis, 952 bp for C. interruptus, 1,084 bp for C. joyneri, 1,198 bp for C. lingua, 1,307 bp for C. robustus, and 1,483 bp for C. monodi with the species-specific primers, visualized by agarose gel electrophoresis, allowed perfectly distinction of the Cynoglossus species. The multiplex PCR assay can be easily performed on multiple samples and attain final results in less than 6 hours. This technique should be a useful addition to the molecular typing tools for the tentative identification of Cynoglossus species.

• Korean Journal of Ecology and Environment
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• v.53 no.2
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• pp.173-184
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• 2020

Irrigation ponds, 'dumbeong', which are artificially constructed water resources for traditional farming, serve as a biological shelter connecting seasonally created rice paddy fields to local freshwater ecosystems. This 2018 study surveyed 143 irrigation ponds in the western Civilian Control Zone (CCZ) area from August to September, revealing species diversity and community characteristics of benthic macroinvertebrates. A total of 13,454 individuals of macroinvertebrates were captured and classified into 3 phyla, 5 classes, 17 orders, 59 families, 192 species. Among Insecta, the most frequently recorded order was Odonata, 55 spp.(33.7%), followed by Coleoptera, 52 spp. (31.9%), Hemiptera, 34 spp. (20.8%), Diptera, 17 spp. (9.8%), Ephemeroptera, 3 spp. (2.4%), Trichoptera, 1 spp. (0.6%) and Lepidoptera, 1 spp. (0.6%). Taxon of non-Insecta consisted of Mollusca, 14 spp. (48.2%), Annelida, 11 spp. (37.9%) and Arthropoda, 4 spp. (3.4%). The analysis of Diversity Index (H'), Species Richness Index (RI), Dominance Index (DI) and Evenness Index (J') revealed the general stability of communities in the study sites. A total of 28 rare species were found in 98 study sites, including three endangered species designated by the Ministry of Environment. These results showed that the species diversity and rarity of macroinvertebrates in the study area were greater than those of previous research on lentic wetlands (lake, etc.) and national conserved wetlands(Upo-swamp, etc.) in Korea. A conservation planning of aquatic ecosystems in the western CCZ area, therefore, should focus on conservation of irrigation ponds.

• The Korean Journal of Mycology
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• v.36 no.2
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• pp.138-143
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• 2008

Botrytis cinerea, gray mold pathogen, causes serious losses in greenhouse tomato crop. In this study, a primer set was developed for identification and specific PCR detection of B. cinerea from tomato plants. The primer pair (BTF1/BTR1) was designed from polymorphic sequence region in pyruvate carboxylase gene (pyc) of B. cinerea. A PCR product (112 bp) was amplified on genomic DNA of 13 B. cinerea isolates from 10 different host plants, but not on those from 6 other Botrytis spp., 4 Botryotinia spp., 5 Sclerotinia spp. and 16 other genus of phytopathogenic fungi. The sensitivity limit of the primer set was 2 pg of genomic DNA of B. cinerea, approximately. The PCR assay using species-specific primer set was specifically able to detect the pathogen on naturally infected tomato plants and artificially infected plants. These results suggest that the sensitivity and specificity of this primer set can be applied in a rapid and accurate diagnosis of tomato disease caused by B. cinerea.

• Journal of Life Science
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• v.27 no.11
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• pp.1331-1339
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• 2017

DNA barcoding is the identification of a species based on the DNA sequence of a fragment of the cytochrome C oxidase subunit I (COI) gene in the mitochondrial genome. It is widely applied to assist with the sustainable development of fishery-product resources and the protection of fish biodiversity. This study attempted to verify horse-head fish (Branchiostegus japonicus) and fake horse-head fish (Branchiostegus albus) species, which are commonly consumed in Korea. For the validation of the two species, a real-time PCR method was developed based on the species' mitochondrial DNA genome. Inter-species variations in mitochondrial DNA were observed in a bioinformatics analysis of the mitochondrial genomic DNA sequences of the two species. Some highly conserved regions and a few other regions were identified in the mitochondrial COI of the species. In order to test whether variations in the sequences were definitive, primers that targeted the varied regions of COI were designed and applied to amplify the DNA using the real-time PCR system. Threshold-cycle (Ct) range results confirmed that the Ct ranges of the real-time PCR were identical to the expected species of origin. Efficiency, specificity and cross-reactivity assays showed statistically significant differences between the average Ct of B. japonicus DNA ($21.85{\pm}3.599$) and the average Ct of B. albus DNA ($33.49{\pm}1.183$) for confirming B. japonicus. The assays also showed statistically significant differences between the average Ct of B. albus DNA ($22.49{\pm}0.908$) and the average Ct of B. japonicus DNA ($33.93{\pm}0.479$) for confirming B. albus. The methodology was validated by using ten commercial samples. The genomic DNA-based molecular technique that used the real-time PCR was a reliable method for the taxonomic classification of animal tissues.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.21-28
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• 2004

모든 생명체의 genetic information에는 보존적 염기서열과 다형적 염기서열이 존재한다. 다형적 염기서열과 보존적 염기서열은 하나의 종(species)을 감별하거나, 여러 종류의 종을 동시에 감별할 수 있는 genotyping의 표지자로 각각 이용될 수 있다. 본 논문은 병원성 감염질환 세균, 식중독 유발 세균, 생물의약품 오염 유발 세균 및 환경오염 세균 등 세균의 존재 유무와 속과 종 감별을 위해 대부분 세균 종의 보존적 염기서열과 다형적인 염기서열을 포함하고 있는 23S rDNA 유전자의 표적 염기 서열로부터 고안된 세균 특이적(bacterial-specific), 속 특이적(genus-specific), 종 특이적(species-specific) 올리고 뉴클레오티드프로브와 프라이머를 디자인하는 시스템을 소개한다. 시스템을 통해서 얻어진 프로브와 프라이머들은 PCR을 통한 검증단계를 거쳐서 디자인 결과의 정확성을 확인하였다. 본 시스템의 이용으로 프로브와 프라이머를 디자인하는데 몇 주가 소요되는 시간을 몇 일 내로 줄일 수 있었으며, 체계적인 데이터의 관리로 결과의 정확성을 높일 수 있었다.

• Proceedings of the KSAR Conference
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• 2003.06a
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• pp.48-48
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• 2003

본 실험은 spermatogonia 단계에 발현하는 유전자를 찾기 위하여 suppression subtractive hybridization를 수행하였다. 기존에 mouse에서는 spermatogonia 특이적인 유전자들이 밝혀져 있기 때문에 pig에 특이적인 유전자를 찾기 위하여 pig 250days testis와 pig 60days testis를 재료로 하여 실험하였다. SSH를 통하여 254days testis에 특이적으로 발현되는 후보유전자를 7개 찾았고 25days testis와 60days testis 의 Northern blot을 통하여 25days에 과발현하고 60days에 발현의 양이 대폭 줄어드는 spermatogonia 유전자로 생각되는 후보유전자 2개를 선택하여 pig tissue northern blot, genomic DNA southern blot, RT-PCR 그리고 In-situ hybridization을 수행하였다. Tissue northern blot과 RT-PCR을 통하여 후보자 1번은 간과 폐, 난소, 정소에서 발현하고, 후보유전자 15번은 난소와 정소에서만 특이적으로 발현함을 알았다. DNA sequence analysis와 NCBI Blast search를 통하여 후보자 1번은 다른 종에서 밝혀진 유전자였고 후보유전자 15번은 어느 종에서도 밝혀지지 않은 새로운 유전자였다. Degenerated primer를 통하여 후보자 1번의 pig full sequence를 밝히고 NCBI에 등록하였다. 그리고 In-situ hybridization을 통하여 후보유전자득이 20일째 testis의 Leydic cell에서 많이 발현되고 adult testis에서는 발현이 감소하는 결과를 얻었다. 이것으로 보아 위의 두 후보유전자는 spermatogonia에 직접 관련된 유전자이기 보다는 spermatogonia의 발달에 영향을 주는 leydic cell 특이발현을 가진 유전자로 사료되어진다.