• Korean Journal of Microbiology
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• v.42 no.3
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• pp.199-204
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• 2006

Streptococcosis of olive flounder(Paralichthys olivaceus) is an important bacterial disease in Jeju island. In this study, we investigated monthly infection pattern of this disease in different size of the flounder fish. Even though the disease occurred throughout the year, the infection ratio was relatively higher in the months with warm water season. The infection was more prevalent in adult flounder over 30 cm total length compare to these of small size fish. Two infectious species of streptococcosis pathogens were detected by multiplex PCR assay. Detection ratios of Streptococcus iniae and S. parauberis reached up to 46% and 54%, respectively, from June 2003 to May 2005 in Jeju island. S. iniae occurred intensively from September to October, whereas S. parauberis reported from March to May. S. iniae and S. parauberis infections of cultured flounder share some common features, but clinical findings showed considerable differences between two diseases. Distended abdomen, protruded anus and ascitic fluid in the peritoneal cavity are evident lesions detected in S. iniae infection, whereas, flounders infected by S. parauberis showed prominent lesions such as darkened surface and haemorrhaging in the non-ocular side. Both streptococcosis pathogens were sensitive to antibiotics, such as ampicillin and amoxicillin. However, S. iniae strains were more sensitive to doxycycline, erythromycin and oxytetracycline than S. parauberis strains.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.22 no.1
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• pp.31-44
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• 2017

Pfiesteria piscicida is one of heterotrophic dinoflagellate having toxic metaboliges, and it is difficult to detect and quantify this dinoflagellate via light microscope due to small size and morphological similarity with Pfiesteria-like dinoflagellate (PLD) species. Alternatively, we developed quantitative real-time PCR assay based on EvaGreen and determined field accessibility throughout the investigation of distribution in the entire Korean coastal waters and population dynamics in Shihwa Lake. The P. piscicida-specific primers based on internal transcribed spacer 1 (ITS 1) were designed and the specificity of primers was confirmed by PCR with other genomic DNAs which have genetic similarity with target species. Through real-time PCR assay, a standard curve which had a significant linear correlation between log cell number and $C_T$ value ($r^2{\geq}0.999$) and one informative melting peak ($88^{\circ}C$) were obtained. These results implies that developed real-time PCR can accurately detect and quantify P. piscicida. Throughout the field applications of real-time PCR assay, P. piscicida was distributed in western (Mokpo and Kimje) and easthern (Gangneng) Korean coastal water even though light microscopy failed to identify P. piscicida. In the investigation of population dynamics in Shihwa Lake, the density of P. piscicida was peaked in June, July and August 2007 at St. 1 where salinity (${\leq}15psu$) was lower than the other 2 sites. In this study, we successed to develop EvaGreen bassed real-time PCR for detection and quantification of P. piscicida in fields, so this developed assay will be useful for various ecological studies in the future.

• Pediatric Infection and Vaccine
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• v.27 no.2
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• pp.90-101
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• 2020

Purpose: The multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) test developed recently can help detect enteric pathogens of acute gastroenteritis (AGE). This study aimed to investigate the epidemiology of pathogens in children with AGE using the multiplex RT-PCR. Methods: From May 2015 to June 2018, multiplex RT-PCR tests were performed to identify pathogens in the feces of pediatric patients diagnosed with AGE at a secondary hospital in Seoul, Korea. Results: Of the 1,366 stool samples examined for viral pathogens, 483 (35.3%) tested positive for ≥1 pathogen. Group A rotavirus (RV) was detected in 106 cases (7.8%). The positivity rate increased annually from 3.0% (8/263) to 16.7% (48/288) and surged in 2018 (P<0.001). Norovirus (NoV) GII was the most common viral pathogen (263/1,366, 19.3%), and the positivity rate did not increase during the 3 years. Of the 304 stool samples tested for bacterial pathogens, Campylobacter spp. was the most common bacterial pathogen (32/304, 10.5%), followed by Clostridium difficile (22/304, 7.2%) and Salmonella spp. (17/304, 5.6%). The positivity rate of these bacterial pathogens did not change significantly during the study period. Conclusions: NoV GII is the main pathogen in childhood AGE since the introduction of RV vaccine, yet the number of rotavirus-infected patients increased during our study, especially in 2018. Therefore, further research is needed including the possibility of emergence of novel RV strains. Campylobacter spp. is the predominant cause of bacterial AGE in children. For proper treatment, the clinical characteristics of the bacteria should be taken into consideration, and continuous monitoring is necessary.

• 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.

• Clinical and Experimental Reproductive Medicine
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• v.34 no.4
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• pp.275-283
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• 2007

Objective: This study was performed to investigate the expressions of endometriosis related genes in shed endometrial tissues from menstrual blood of patients with or without endometriosis. Methods: The shed endometrial tissues were collected on 2$^{nd}$ or 3$^{rd}$ day of menstrual cycle with Wallace catheter in patients with endometriosis (n=16) and without endometriosis (n=26). The mRNA expressions of twelve kinds of endometriosis related genes were compared between two groups using semi-quantitative RT-PCR. Results: The collected shed endometrium was confirmed by histological observation. Expressions of telomerase, c-kit and aromatase mRNA were not detected by RT-PCR in shed endometrial tissues. The mRNA expressions of apoptosis related genes (fas, fas ligand, bcl-2, bax), stem cell factor, estrogen receptor-$\alpha$/$\alpha$, endometriosis protein-I and secretory leukocyte protease inhibitor gene were similar between shed endometrial tissues with endometriosis and without endometriosis. Conclusion: We could not find the difference of mRNA expressions of tested endometriosis related genes between shed endometrial tissues with or without endometriosis by semi-quantitative RT-PCR analysis. It may be related to the dynamical changes of gene expressions in the endometrium with menstrual cycle.

• Research in Plant Disease
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• v.11 no.1
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• pp.56-65
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• 2005

To establish taxonomic system of morphologically similar species of small-spored Alternaria, phylogenetic analysis of internal transcribed spacer (ITS 1, ITS 2 and 5.8S rDNA) and mitochondrial small subunit (mt SSU) rDNA sequences and URP-PCR fingerprinting analysis from 11 species ofAlternaria were performed. Phylogenetic analysis of ITS and mt SSU rDNA sequences revealed that 10 out of 11 species of the smallspored Alternaria were phylogenetically identical with a bootstrap value of 100%. A. infectoria only was phylogenetically differentiated from the other species. The results suggest that the 10 small-spored Alternaria species are very closely related evolutionally and the markers can not be used for differentiation of the smallspored Alternaria species. URP-PCR fingerprinting analysis from eleven species of smallspored Alternaria using 10 URP primers showed that it was possible to differentiate the species, although genetic similarities were found among the species. The Alternaria sp. from common pokeweed could be distinguished from other species by URP-PCR analysis, and it was considered as a new species. A. infectoria could be easily distinguished from the other 10 species by phylogenetic analysis of ITS and mt SSU rDNA sequences and the URPPCR fingerprinting analysis.

• Korean Journal of Food Science and Technology
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• v.40 no.4
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• pp.406-411
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• 2008

This study was conducted to examine the quality enhancement of fermented soybean pastes (cheonggukjang) using microorganisms with high enzyme activities and proper experimental design. The microorganisms for soybean paste fermentation were selected from a specific area of Gyeonggi and were idenlified by 16S rDNA sequence analysis. To prepare the cheonggukjang, an optimum mixing ratio of selected microorganisms was determined using contour plots and numerical optimization methods. A total of 39 microorganisms were isolated from the soybean paste, consisting primarily of Bacillus subtilis and Bacillus licheniformis, and no mold was found. Three microorganisms showing high enzyme activities were selected and used to formulate an optimum mixing ratio for cheonggukjang preparation. Based on levels of amino-nitrogen, ammonium-nitrogen, antioxidant activity values, and sensory preference results, the optimum mixing ratio of 50% of Bacillus sp. SC-1 and 50% SC-3 was suggested for the manufacture of high quality of cheonggukjang.

• Korean Journal of Microbiology
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• v.45 no.2
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• pp.208-214
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• 2009

To avoid ambiguity in counting the number of colony, about 1,500 of colonies grown on B. cereus selective agar plates were grouped into 12 types by morphological difference and then identified by biochemical and 16S rDNA nucleotide sequence. Among them, seven colony types with 11 to 15 mm diameters of halo were identified as B. cereus or B. cereus subsp. cytotoxis. Five mm sized colonies with no halo, which have not been considered as B. cereus according to the manufacturer's manual, were identified as B. cereus. A colony type with double halos of only 6 mm in diameter was also B. cereus. Other three types were proven to be Enterococcus sp., Brevibacillus sp., and B. subtilis, respectively. PCR results showed that only 9 types that are identified as B. cereus strains harbor at least one of B. cereus toxin genes.

• Journal of Food Hygiene and Safety
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• v.35 no.1
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• pp.45-50
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• 2020

In this study, seafood products (n=26) sold on sushi buffet restaurants in the city of Wonju were monitored by analyzing sequences of DNA barcode markers (cytochrome c oxidase subunit I and 16S ribosomal RNA genes). NCBI BLAST database was screened with the barcode sequences analyzed as a query for species identification. The BLAST search revealed that fifteen samples (58%) analyzed were consistent with their labeling information; however, the ingredients used in seven samples (27%) were not compliant with their label information. In the case of these mislabeled products, ingredients for sutchi catfish sushi and cherry bass sashimi were identified as Pangasianodon hypophthalmus and Lampris guttatus, respectively. For Japanese flying-fish roe sushi and Pacific herring roe sushi, roe of Mallotus villosus was used as an ingredient. Amphioctopus fangsiao and A. membranaceus were used in octopus sushi and soybean-marinated squid products, respectively. This monitoring result can contribute to the protection of consumer rights and the reduction of fraudulent practices in the food industry.

• Korean Journal of Ecology and Environment
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• v.40 no.1
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• pp.143-148
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• 2007

The introduced exotic species has often caused severe problems to the native ecosystem. One of such species is the freshwater fish gengorobuna (Carassius cuvieri) introduced from Japan. The first step to assess harmful effects of this species on the Korean freshwater ecosystem is to discriminate it from the most similar native crucian carp (Carassius auratus). Because traditional morphological identification often gives unreliable results due to their highly similar phenotype, a new more efficient method is needed. For this purpose, molecular markers produced by the efficient one-step PCR method using three primers (DDF, DDR and DDR1) were developed and tested in the present study. This molecular marker will play an important role in monitoring fish community of Korean freshwater ecosystem.