• International Journal of Oral Biology
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• v.38 no.2
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• pp.43-49
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• 2013

The objective of this study was to develop PCR primers that are specific for Streptococcus sanguinis, Streptococcus parasanguinis, and Streptococcus gordonii. We designed the S. sanguinis-, S. parasanguinis-, and S. gordonii-specific primers, Ssa21-F3/Ssa21-R2, Spa17-F/Spa17-R, and Sgo41-F1/Sgo41-R1 respectively, based on the nucleotide sequences of the Ssa21, Spa17, and Sgo41 DNA probes that were screened using inverted dot blot hybridization (IDBH). The species-specificity of these primers was assessed against 43 strains of mitis group streptococci, including clinical strains of S. sanguinis, S. parasanguinis, and S. gordonii. The resulting PCR data revealed that species-specific amplicons had been obtained from all strains of the target species tested, and that none of these amplicons occurred in any other strains from other species. These results suggest that the Ssa21-F3/Ssa21-R2, Spa17-F/Spa17-R, and Sgo41-F1/Sgo41-R1 primers may be useful in detecting S. sanguinis, S. parasanguinis, and S. gordonii at the species level, respectively.

• Journal of Environmental Impact Assessment
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• v.32 no.2
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• pp.94-111
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• 2023

In order to establish an effective management strategy for invasive species early detection and regular monitoring are required to assess their introduction or dispersal. Environmental DNA (eDNA) is actively applied to evaluate the fauna including the presence of invasive species as it has high detection sensitivity and can detect multiple species simultaneously. In Korea, the applicability evaluation of metabarcoding is being conducted mainly on fish, and research on other taxa is insufficient. Therefore, this study identified the feasibility of detecting invasive species in Korea using eDNA metabarcoding. In addition, to confirm the possibility of detection by taxa, the detection of target species was evaluated using four universal primers (MiFish, MiMammal, Mibird, Amp16S) designed for fish, mammals, birds, and amphibians. As a result, target species (Trachemys scripta, 3 sites; Cervus nippon, 3 sites; Micropterus salmoides, 7 sites; Rana catesbeiana, 4 sites) were detected in 17 of the total 55 sites. Even in the selection of dense sampling sites within the study area, there was a difference in the detection result by reflecting the ecological characteristics of the target species. A comparison of community structures (species richness, abundance and diversity) based on the presence of invasive species focused on M.salmoides and T.scripta, showed higher diversity at the point where invasive species were detected. Also, 1 to 4 more species were detected and abundance was also up to 1.7 times higher. The results of invasive species detection through metabarcoding and the comparison of community structures indicate that the accumulation of large amounts of monitoring data through eDNA can be efficiently utilized for multidimensional ecosystem evaluation. In addition, it suggested that eDNA can be used as major data for evaluation and prediction, such as tracking biological changes caused by artificial and natural factors and environmental impact assessment.

• Journal of Surface Science and Engineering
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• v.51 no.2
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• pp.133-137
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• 2018

Plasma devices such as jets, pencils, and torches have been developed as new tools that help penetration of target agents and applied to plasma medicine. However, these devices cannot be used in a large area. Therefore, we introduced a flexible plasma device, which can be treated of large area and designed as bendable plasma. In additional, in vitro model based on agarose gel was prepared that can be show effectiveness in the depth of penetration. Plasma treatment conditions such as power, time and distance can be optimized on the agarose gel wound model. The chemical structure of changed polysaccharides was predicted due to reactive excited atoms and molecules, UV photons, charged particles and reactive oxygen and nitrogen species (RONS).

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.32 no.3
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• pp.257-265
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• 1996

The combined hydroacoustic and bottom trawl surveys were conducted in the Cheju southeastern area by the training ship "KAYA" belong to Pukyong National University in July 1995 and the traning ship "NAGASAKI MARl]" belong to Nagasaki University in April 1994, respectively. The main purpose of the investigations was to provide the basic data for the management and the biomass estimation of commercially important demersal fish stocks in this area. Fish samples were collected by bottom trawling from 10 trawl stations randomly selected in the survey area, and the species and length compositions of trawl catches were examined. The fish school target strength for demersal fish aggregations was related to the catchability of trawl net with a 90 mm mesh codend. The most abundant species in the 1995 trawl stations were Japanese flying squid, sword tip squid and red horsehead and that of the 1994 trawl stations Japanese flying squid and blackmouth goosefish. The average weight per cubic meter of trawl catches collected by bottom trawling in the Cheju southeastern area were $1.0791{\times}lO^-4$kg/$m^3$ in the 1994 survey area and $1.3636{\times}lO^-4$kg/$m^3$ in the 1995 survey area, respectively. The catch data by cover net suggest that the efficiency of trawl net could affect the weight normalized target strength values for demersal fish aggregations. That is, the average target strength per unit of weight dropped from - 33.1 dB/kg using the total catch by codend and cover net to - 30.5 dB/kg using only the catch data by codend, and a change of2.6 dB/kg was observed.ange of2.6 dB/kg was observed.

• Ocean and Polar Research
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• v.39 no.1
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• pp.13-21
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• 2017

Temporal changes in the number of zooplankton species are important information for understanding basic characteristics and species diversity in marine ecosystems. The aim of the present study was to estimate the optimal monitoring frequency (OMF) to guarantee and predict the minimum number of species occurrences for studies concerning marine ecosystems. The OMF is estimated using the temporal number of zooplankton species through bi-weekly monitoring of zooplankton species data according to operational taxonomic units in the Tongyoung coastal sea. The optimal model comprises two terms, a constant (optimal mean) and a cosine function with a one-year period. The confidence interval (CI) range of the model with monitoring frequency was estimated using a bootstrap method. The CI range was used as a reference to estimate the optimal monitoring frequency. In general, the minimum monitoring frequency (numbers per year) directly depends on the target (acceptable) estimation error. When the acceptable error (range of the CI) increases, the monitoring frequency decreases because the large acceptable error signals a rough estimation. If the acceptable error (unit: number value) of the number of the zooplankton species is set to 3, the minimum monitoring frequency (times per year) is 24. The residual distribution of the model followed a normal distribution. This model can be applied for the estimation of the minimal monitoring frequency that satisfies the target error bounds, as this model provides an estimation of the error of the zooplankton species numbers with monitoring frequencies.

• Journal of the Korean Institute of Landscape Architecture
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• v.38 no.4
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• pp.106-127
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• 2010

Although multi-layer planting methods are more widely used as a method for clustered planting and environmental programs such as plant remediation, difficulties have been faced in applying those to planting design. This study develops a basic planting model that can be applied to multi-layer planting in basis on an analysis of forest structures in the Seoul area. An optimal number of clusters was determined through the ISA (Indicator Species Analysis), and 7 basic clusters were found through a cluster analysis by using PC ORD 4.0 software specifically developed for ecological analysis. The 7 basic clusters include the following communities: the Quercus acutissima Community, Sorbus alnifolia-Quercus mongolica Community, Pinus rigida-Pinus densifiora Community, Rododendron mucronulatum var. mucronulatum-Quercus mongolica Community, Juniperus rigida-Quercus mongolica Community, Rododendron mucronulatum var. mucronulatum-Pinus densiflora Community, and Rododendron sclippenbachii-Quercus mongolica Community. The study also selected 57 species with at least a 10% frequency among the plant species existing in the Seoul area and suggested both a companion species and available similar alternative species by conducting an additional interspecific association analysis. This study may help to enhance usefulness of the model in architectural planting design. In addition, the two results named above were synthesized to develop a multi-layer planting model that can be utilized in landscape planting design by selecting similar alternative species through the interspecific association analysis, which includes 7 clusters of natural plants. The multi-layer planting model can be widely applied to design planting because the model has an average target cover range based on the average value of a transformed likelihood.

• Korean Journal of Veterinary Service
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• v.34 no.4
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• pp.417-428
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• 2011

Species-specific PCR assay was developed for detection of cattle, sheep, goat, horse, dog, pig, chicken, duck, goose, and turkey using mitochondrial 12S rRNA and 16S rRNA as target genes. Also, an internal positive control was used to detect possible false negatives by using 18S rRNA gene. We designed species-specific primers with amplicon length of 190, 219, 350, 467, 241, 119, 171, 229, 111 and 268 bp for cattle, sheep, goat, horse, dog, pig, chicken, duck, goose, and turkey respectively. The specificity of the primers was tested against the other 10 non-target animal species and a cross-reaction was not observed. We developed two multiplex PCR assays for the simultaneous identification of Korea's major livestock species (cattle, pig, chicken and duck) and poultry species (chicken, duck, goose and turkey) from analogous samples, retaining the same specificity. The limit of detection of the multiplex PCR assay (cattle, pig, chicken and duck) ranged between 1 pg and 0.1 pg of template DNA extracts from raw meat. Applying multiplex PCR assays to DNA extracts from experimental pork/beef and pork/chicken tested raw and heat-treated ($120^{\circ}C$ for 30 min) mixtures respectively, detection limit was 0.1% level beef in pork, pork in beef and chicken in pork and 1.0% level pork in chicken. In conclusion, this assay using gel-based capillary electrophoresis would be very useful in highly sensitive and rapid identification of animal species or ingredients in minced meat and other meat products.

• Journal of Ecology and Environment
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• v.33 no.4
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• pp.377-389
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• 2010

Understanding the factors relevant to endangerment and the patterns of habitat locations in relation to protected areas is critically important for the conservation of rare species. Although 64 plant species have recently been listed as endangered species in Korea, this information has, until now, not been available, making appropriate management and conservation strategies impossible to devise. Thus, we collected information on potentially threatening factors, as well as information on the locations in which these species were observed. The potentially threatening factors were classified into seven categories. National parks, provincial parks, ecosystem conservation areas, and wetland conservation areas were defined as protected conservation areas. Korean digital elevation model data, along with the maps of all protected areas were combined with the maps of endangered plant species, and analyzed via Geographic Information Systems (GIS). Excluding the category of "small population", endangered plant species in Korea were associated more frequently with extrinsic factors than intrinsic factors. Considering land surface only, all conservation areas in Korea totaled 4.9% of the land, far lower than International Union for Conservation of Nature and Natural Resources (IUCN)'s 10% coverage target. At the species level, 69% of the endangered plant species were detected in conservation areas, mostly in national parks. However, this result demonstrates that 31% of endangered species inhabit areas outside the conservation zones. Furthermore, at the habitat level, a large proportion of endangered species were found to reside in unprotected areas, revealing "gaps" in protected land. In the face of rapid environmental changes such as population increases, urbanization, and climate changes, converting these gap areas to endangered species' habitats, or at least including them in habitat networks, will help to perpetuate the existence of endangered species.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.47 no.6
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• pp.945-959
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• 2014

This study was conducted to provide basic data for optimal fisheries management through the accurate understanding the catches, fishing level, species composition, distribution characteristics and fisheries status of trammel net in Gangwon Province. As the results of trammel net survey, Pisces were collected 77 species, 1,983.0 kg, Crustacea 9 species, 569.0 kg, Cephalopoda 5 species, 75.3 kg, Gastropoda 12 species, 16.5 kg in the coastal waters of Sokcho and Pisces 55 species, 3,681.5 kg, Crustacea 6 species, 2,229.8 kg, Gastropoda 10 species, 72.8 kg, Cephalopoda 4 species, 10.1 kg in the coastal waters of Donghae, respectively. The catches of important species with season and depths showed that the main target species is Pleuronectidae spp. at all depth and Aptocyclus ventricosus at <100 m in Sokcho, Liparis spp. and Dasycottus setiger at 200-500 m in Donghae, respectively. The mean total length (cm) of Gadus macrocephalus and Aptocyclus ventricosus didn't appear significant difference, but the mean total length of Pleuronectidae spp., Liparis spp. and D. setiger in Donghae is bigger than in Sokcho. From the cluster and MDS analysis based on Bray-Curtis similarity matrix of fourth root transformed, catches data of dominant species in the coastal waters of Sokcho and Donghae was divided into three different groups of the demersal organisms community in 12 survey of Donghae (Group A) and Jul., Oct.-Dec. survey of Sokcho (Group B) and Jan.-Jun. and Aug.-Sep. survey of Sokcho (Group C).

• Korean Journal of Veterinary Service
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• v.35 no.3
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• pp.215-222
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• 2012

Species-specific $TaqMan^{(R)}$ probe-based real-time PCR assays were developed for detection of beef, pork, chicken, duck, goose and turkey. The primer and probe sets used in this study were designed to be complementary to fibroblast growth factor (FGF) for cattle and pig, mitochondrial NADH dehydrogenase (ND) subunit 3 and ND2 for chicken and duck, 12S rRNA for goose and turkey, respectively. As internal positive control we used conserved region in the ribosomal 18S RNA gene to ensure the accuracy of the detection of target DNA by real-time PCR. We confirmed that real-time PCR assays with the primer and probe sets were positive for cattle, pig and chicken intended target animal species with no cross-reactivity with other non-target animal species. Only >50 ng DNA of beef show cross-reactivity in the determination of duck. Using species-specific primer and probe sets, it was possible to detect amounts of 0.1 ng DNA of cattle and pig, 1.0 pg DNA of chicken, duck and turkey, and 0.1 pg DNA of goose for raw samples, respectively. The detection limits were 0.1 ng DNA of cattle, 1.0 ng DNA of pig and 1.0 pg DNA of chicken for DNA mixtures (beef, pork and chicken) extracted from heat-treated ($121^{\circ}C$/5 min) meat samples. In conclusion, it can be suggested that the $TaqMan^{(R)}$ probe-based assay developed in this study might be a rapid and specific method for the identification of meat species in raw or cooked meat products.