• Korean Journal of Ichthyology
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• v.34 no.3
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• pp.208-217
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• 2022

We wanted to develop a real-time PCR assay capable of detecting Liobagrus obesus in environmental DNA (eDNA) extracted from freshwater samples using a pair of species-specific primers and probe for the endangered fish, L. obesus. The species-specific primers and probe were designed in consideration of single nucleotide polymorphisms between 65 species of freshwater fish living in the Republic of Korea within the cytochrome b (cytb) gene of mitochondrial DNA. The species-specific primers and probe, in the real-time PCR assay, showed high specificity as only the L. obesus genomic DNA (gDNA) was found to be positive in the specificity verification using 65 species gDNA of freshwater fish in the Republic of Korea. In addition, in the detection limit analysis using the serial dilution concentrations of L. obesus gDNA, it was found that it was possible to detect up to 0.2 pg, showing high sensitivity. Afterwards, using the species-specific primers and probe, real-time PCR assay was performed on freshwater samples obtained from 8 stations in the mid-upper basin of Geum River. As a result, the cytb gene of L. obesus was detected in total 5 stations including all 3 stations where this species was collected at the time of field survey. Therefore, the species-specific primers and probe developed in present study, and the real-time PCR assay using them, can accurately detect the cytb gene of L. obesus from eDNA samples, which can be utilized to monitor the existing habitats of this species and to discover potential new habitats.

• Journal of Life Science
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• v.12 no.2
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• pp.158-163
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• 2002

For axenic isolation of the cyanobacterium Microcystis aeruginosa, water bloom at the Mulgum station from the Nakdong River was pretreated by shaking with distilled water. Removal of bacteria was accomplished using antibiotics (150 $\mu$g/$m\ell$ ampicillin and 25 $\mu$g/$m\ell$ neomycin) and colonizing on CB solid medium prepared from 0.7% agarose at 3$0^{\circ}C$ under 40 $\mu$ mol m$^{-2}$ s$^{-1}$ light. Among 26 strains of the Microcystis species, only three strains were axenically established. The three strains were examined by PCR-amplified 16S rRNA gene and 16S rRNA sequencing. The similarities were 99.5 ~100% with M. aeruginosa AF 139292.

• Journal of Food Hygiene and Safety
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• v.26 no.2
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• pp.114-119
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• 2011

In this study, two duplex real-time PCR approach with melting curve analysis is presented for the detection of Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp. and Staphylococcus aureus, which are important food-borne bacterial pathogens usually present in fresh and/or minimally processed vegetables. Reaction conditions were adjusted for the simultaneous amplification and detection of specific fragments in the ${\beta}$-glucuronidase (uidA, E. coli), thermonuclease (nuc, S. aureus), hemolycin (hly, L. monocytogenes) and tetrathionate reductase (ttr, Salmonella spp.) genes. Melting curve analysis using a SYBR Green I real-time PCR approach showed characteristic $T_m$ values demonstrating the specific and efficient amplification of the four pathogens; $80.6{\pm}0.9^{\circ}C$, $86.9{\pm}0.5^{\circ}C$, $80.4{\pm}0.6^{\circ}C$ and $88.1{\pm}0.11^{\circ}C$ for S. aureus, E. coli O157:H7, L. monocytogenes and Salmonella spp., respectively. For all the pathogens, the two duplex, real-time PCR was equally sensitive to uniplex real-time PCR, using same amounts of purified DNA, and allowed detection of 10 genome equivalents. When our established duplex real-time PCR assay was applied to artificially inoculated fresh lettuce, the detection limit was $10^3$ CFU/g for each of these pathogens without enrichment. The results from this study showed that the developed duplex real-time PCR with melting curve analysis is promising as a rapid and cost-effective test method for improving food safety.

• Clinical and Experimental Reproductive Medicine
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• v.23 no.3
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• pp.341-349
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• 1996

초기배의 성판정은 대상가축의 성을 선발하는 수단으로써 뿐만아니라 인간의 유전적 질병의 조기진단법으로서 매우 가치가 크다. 체외수정 소 초기배의 성을 결정하기 위해 PCR과 PRINS를 이용하였으며 성판정에 이용된 8 세포${\sim)$배반포기 초기배는 체외수정후 난관상피세포와의 공배양에 의해 생산되었다. 초기배 의 DNA는 $200{\mu}g/ml$ proteinase K가 함유된 PCR lysis buffer에 하나의 초기배를 부유한 후 $50^{\circ}C$에서 1시간동안 처리하여 준비하였다. 중기 염색체 spreads는 초기배를 nocodazole로 처리한 후 air-drying 방법을 이용하여 준비하였다. 가능한 false positive signals을 배제하기 위해 소특이 및 Y 염색체 특이 primers를 이용하여 PCR을 수행한 결과, 웅성 초기배에서는 두 개의 증폭산물 (소특이 및 Y 염색체 특이)이 합성된 반면 자성 초기배에서는 하나의 증폭산물만 합성되었다. 한편 중기염색체상의 Y 염색체를 동정하기 위해 FISH와 PRINS를 수행한 결과, FISH에서보다 PRINS에서 더 강한 Y 염색체 특이 형광 signals이 탐지되었다. 이러한 결과는 PCR에 의한 체외생산 소 초기배의 신속정확하고 효율적인 성판정이 가능함을 보여주었다. 또한 PRINS를 통해 PCR 에 이용된 Y 특이 probe의 신뢰성이 염색체 수준에서 확인되었다.

• Journal of Life Science
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• v.13 no.5
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• pp.651-657
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• 2003

Randomly amplified polymorphic DNA (RAPD) analysis was used to study genetic relationships among C. polykrikoides, G. impudicum and G. catenatum, which possess similar morphological features. Four of 12 primers were selected and 59 amplification products ranged from 0.2 kb to 3.0 kb. The number of polymorphic products in C. polykrikoides, G. impudicum and G. catenatum was 16 (27.1%), 8 (13.5%), and 16 (27.1%), respectively, while 17 were monomorphic. Number of species-specific bounds was 26 (44.0%), 34 (57.6%), 26 (44.0%) in C. polykrikoides, G. impudicum and G. catenatum, respectively. The genetic similarity between C. polykrikoides and G. impudicum/G. catenatum was 0.83, whereas G. impudicum and G. catenatum was 0.78. Our results suggest that C. polykrikoides, G. impudicum and G. catenatum are extremely different on the basis of RAPD analysis, despite similarity based on their morphology. The RAPD technique appears to be efficient in detecting genetic variation in these dinoflagellates.

• Korean Journal of Plant Tissue Culture
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• v.27 no.1
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• pp.7-12
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• 2000

Explants of lettuce (Lactuca sativa L.) were co-cultivated with Agrobacterium tumifacience GV 3101 strain containing nptII gene and cold regulated gene (BN115) from Brassica napus for transformation. Multiple shoots were obtained from the explants in the selection medium (MS basal medium supplemented with 100 mg/L kanamycin, 500 mg/L carbenicillin, 0.1 mg/L NAA, 0.5 mg/L kinetin) after 3 to 4 weeks of co-culture. The putative transgenic shoots were transferred to rooting medium (1/2 MS basal medium supplemented with 100 mg/L kanamycin and 250 mg/L carbenicillin). The selected shoots were tested with PCR analysis using nptll, BN115 primers whether cold-regulated gene was introduced to genome of the plants. The vir G primers were particularly used to check contamination of Agrobacterium during PCR analysis. The nptII and BN115 primers produced the specific PCR bands in the putative transgenic lines but the vir G primers did not. These results confirmed that the PCR products were not the result of contamination with Agrobacterium. Additionally the Southern analysis of the PCR products and RT-PCR analysis proved that the cold-regulated gene was successfully integrated and transcribed in the putative transgenic lettuce plants.

• Journal of Food Hygiene and Safety
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• v.35 no.6
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• pp.561-566
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• 2020

Nowadays, with increase of seafood consumption, there have been increasing reports of defective seafood products. There have been incidents of red drum (Sciaenops ocellatus) being sold as red seabream (Pagrus major). In this study, we sought to develop and validate species-specific PCRs to differentiate between P. major and S. ocellatus to prevent the sale of S. ocellatus as P. major. Primers for P. major were designed to bind 12s rRNA and those for S. ocellatus were designed to bind 16s rRNA. Multiplex PCR showed a 468 bp amplicon for P. major and a 181 bp amplicon for S. ocellatus. The limit of detection of P. major and S. ocellatus was present at 1 ng each. The developed primers were validated with 19 P. major samples of food items purchased through the internet. Using this monitoring method, the experimental results and tested species were in agreement. Hence, the developed multiplex PCR method is considered reliable to authenticate P. major and S. ocellatus.

• Parasites, Hosts and Diseases
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• v.56 no.5
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• pp.419-427
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• 2018

This study aimed to develop a new multiplex real-time PCR detection method for 3 species of waterborne protozoan parasites (Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis) identified as major causes of traveler's diarrhea. Three target genes were specifically and simultaneously detected by the TaqMan probe method for multiple parasitic infection cases, including Cryptosporidium oocyst wall protein for C. parvum, glutamate dehydrogenase for G. lamblia, and internal transcribed spacer 1 for C. cayetanensis. Gene product 21 for bacteriophage T4 was used as an internal control DNA target for monitoring human stool DNA amplification. TaqMan probes were prepared using 4 fluorescent dyes, $FAM^{TM}$, $HEX^{TM}$, $Cy5^{TM}$, and CAL Fluor $Red^{(R)}$ 610 on C. parvum, G. lamblia, C. cayetanensis, and bacteriophage T4, respectively. We developed a novel primer-probe set for each parasite, a primer-probe cocktail (a mixture of primers and probes for the parasites and the internal control) for multiplex real-time PCR analysis, and a protocol for this detection method. Multiplex real-time PCR with the primer-probe cocktail successfully and specifically detected the target genes of C. parvum, G. lamblia, and C. cayetanensis in the mixed spiked human stool sample. The limit of detection for our assay was $2{\times}10$ copies for C. parvum and for C. cayetanensis, while it was $2{\times}10^3$ copies for G. lamblia. We propose that the multiplex real-time PCR detection method developed here is a useful method for simultaneously diagnosing the most common causative protozoa in traveler's diarrhea.

• Korean Journal of Microbiology
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• v.34 no.3
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• pp.132-136
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• 1998

Molecular analyses of natural microbial communities are often dependent upon the obtainments of pure nucleic acids. The four methods (elution after agarose gel electrophoresis, G-75 microspin columns, hydroxyapatite mi-crospin columns, and polyvinylpolypyrrolidone (PVPP) microspin columns) were compared for the removal of PCR-inhibitory humic substances from the crude DNA extracts of marine sediment samples. The PVPP microspin columns have shown superior removal of humic substances from the crude DNA extract of marine sediment samples, with yield of $4.8{\mu}g/g$ (dry weight of sediment). The purified DNA by this rapid method was pure enough to amplify 1.5 kb fragment corresponding almost full length of 16S rRNA genes.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.9
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• pp.1237-1243
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• 2002

We have developed a reliable and noninvasive method for swine genotyping of single locus nuclear gene with aged single hair follicles delivered by general mail. The method is based on booster and nested PCR amplification with step-wise increase of primers and dNTPs concentrations followed by restriction endonuclease digestion. To establish this method, the ryanodine receptor (RYR 1) locus which is an economically important trait in swine industry was employed for genotyping experiment. The 3-step PCR amplication method is much less dependent on the quantity and quality of template DNA and produces enough amplification product for the detection on the ethidium bromide-stained gel such as RFLP analysis. A total of 120 pigs were subjected to the RYR 1 genotyping analysis using three-step PCR method which amplified enough quantity of PCR products from the aged single hair follicles for RFLP analysis and genotyping results were identical to the results of the corresponding ethanol-fixed skeletal muscle tissue. This approach will be a great help for porcine breeders and investigators in genotyping of swine. They can receive genotyping results later by simply plucking single hairs of their pigs at farm and sending them in general mail to the diagnostic laboratory which eliminates the inconveniences to collect ear tissue or blood cells from pigs, or the investigator's need for travel to farms in order to collect fresh hair samples.