• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.4
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• pp.496-507
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• 2020

Virus infections of apples result in lowered commercial qualities such as low sugar content, weakened tree vigor, and malformed fruits. An effective way to control viruses is to produce virus-free plants based on the development of an accurate and sensitive diagnostic method. In this study, real-time PCR assays based on SYBR Green I and TaqMan probes were developed for detecting ASGV, ASPV, and ApMV viruses. These methods can detect and quantify 10³ to 10¹¹ RNA copies/μL of each virus separately. Compared with methods with two different dyes, the SYBR Green I-based method was efficient for virus detection as well as for assay using the TaqMan probe. Field tests demonstrated that real-time PCR methods developed in this study were applicable to high-throughput diagnoses for virus research and plant quarantine.

• Environmental Engineering Research
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• v.14 no.1
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• pp.63-67
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• 2009

Escherichia coli K-12 (E. coli K-12) is a representative indicator globally used for distinguishing and monitoring dynamic fates of pathogenic microorganisms in the environment. This study investigated how to most critically quantify lacZ ($\beta$-galactosidase) gene in E. coli K-12 by two different real-time polymerase chain reaction (real-time PCR) in association with three different DNA extraction practices. Three DNA extractions, i.e., sodium dodecyl sulfate (SDS)/proteinase K, magnetic beads and guanidium thiocyanate (GTC)/silica matrix were each compared for extracting total genomic DNA from E. coli K-12. Among them, GTC/silica matrix and magnetic beads beating similarly worked out to have the highest (22-23 ng/${\mu}L$) concentration of DNA extracted, but employing SDS/proteinase K had the lowest (10 ng/${\mu}L$) concentration of DNA retrieved. There were no significant differences in the quantification of the copy numbers of lacZ gene between SYBR Green I qPCR and QProbe-qPCR. However, SYBR Green I qPCR obtained somewhat higher copy number as $1{\times}10^8$ copies. It was decided that GTC/silica matrix extraction or magnetic beads beating in combination with SYBR Green I qPCR can be preferably applied for more effectively quantifying specific gene from a pure culture of microorganism.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.22 no.1
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• pp.431-438
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• 2021

To prepare more stringent regulations for USCG Phase II ballast water management, this study investigated the staining efficiency of SYBR Green I(SGI) and SYBR Gold(SG) on the virus-like particle (VLP). A dye with high staining efficiency was applied to the treated water that was passed through the ballast water treatment system (BWTS). VLP staining was observed most clearly under the 100-fold and 200-fold dilution of the stock solution when the volume of filtered samples was 0.5 mL to 2 mL. The staining efficiency of SGI and SG did not show a significant difference. On the other hand, the green fluorescence of viruses in the sample stained with SGI was more pronounced than in the samples stained with SG (expressed yellow fluorescence), making it easier to observe. The abundance of VLP in the test water and control water treatments that did not pass through the two types of BWTS (electrolysis type, UV + electrolysis type) was approximately 109 - 1010 VLP 100 mL-1. In contrast, no stained VLP was observed in the treated water treatments. Moreover, SGI was confirmed to be effectively stained under various salinity conditions, including seawater, brackish water, and freshwater. Further verification tests and development of staining methods under various BWTS are required, but the SGI staining method is believed to be a good alternative to the VLP live/dead determination of the USCG Phase II type approval test.

• Microbiology and Biotechnology Letters
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• v.33 no.2
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• pp.148-153
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• 2005

Malaria is a re-emerging infectious disease that is spreading to areas where it had been eradicated, such as Eastern Europe and Central Asia. To avoid the mortality from malaria, early detection of the parasite is a very important issue. The peripheral blood smear has been the gold standard method for the diagnosis of malaria infection. Recently, several other methods have been introduced for quantitative detection of malaria parasites. Real time PCR that employs fluorescent labels to enable the continuous monitoring of PCR product formation throughout the reaction has recently been used to detect several human malaria parasites. 18S rRNA sequences from malaria parasites have been amplified using Taqman real time PCR assay. Here, a SYBR Green-based real time quantitative PCR assay for the detection of malaria parasite-especially, Plasmodium vivax - was applied for the evaluation of 26 blood samples from Korean malaria patients. Even though SYBR Green-based real time PCR is easier and cheaper than Taqman-based assay, SYBR Green-based assay cannot be used because 18S rRNA cannot be specifically amplified using 1 primer set. Therefore, we used DBP gene sequences from Plasmodium vivax, which is specific for the SYBR Green based assays. We amplified the DBP gene from the 26 blood samples of malaria patients using SYBR Green based assay and obtained the copy numbers of DBP genes for each sample. Also, we selected optimal reference gene between ACTB and B2M using real time assay to get the stable genes regardless of Malaria titer. Using selected ACTB reference genes, we successfully converted the copy numbers from samples into titer, ${\sharp}$ of parasites per microliter. Using the resultant titer from DBP based SYBER Green assay with ACTB reference gene, we compared the results from our study with the titer from Taqman-based assay. We found that our results showed identical tendency with the results of 18S rRNA Taqman assay, especially in lower titer range. Thus, our DBP gene-utilized real time assay can detect Plasmodium vivax in Korean patient group semi-quantitatively and easily.

• Journal of Life Science
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• v.24 no.4
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• pp.428-436
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• 2014

Loop-mediated isothermal amplification (LAMP) technique relies on autocycling strand displacement DNA sysnthesis without template denaturation steps under isothermal conditions. LAMP has more advantages than modern PCR, as it requires only basic laboratory equipment like an isothermal water bath, oven, and heating cabinet. Hence, in this study, five random primers were designed with Streptococcus parauberis, shikimate kinase Arok gene sequences (Genbank accession number: CP0024711). Two primers were selected based on the ladder pattern. Other optimum reaction conditions like temperature, time, and sensitivity were established and confirmed with conventional SYBR-green PCR. Results confirmed that the designed random primers were species specific, without any non-target DNA amplification under isothermal conditions. Hence, this study suggests that LAMP techniques could be used in the diagnosis of fish pathogen, specifically S. parauberis.

• Korean Journal of Clinical Laboratory Science
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• v.48 no.2
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• pp.88-93
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• 2016

Dirofilaria immitis is a filarial nematode parasite that causes cardiopulmonary dirofilariasis in dogs. The purpose of this study was the development of real-time PCR assays for efficient detection of D. immitis. The D. immitis-specific primers confirmed in our previous study and a newly designed TaqMan probe were used for quantitative diagnostics. First, SYBR Green real-time PCR was performed using the specific primers and serially diluted genomic DNA or plasmid DNA, and melting curve analyses were performed after amplification. The melting curve showed one specific peak in each of the genomic and plasmid DNA reactions, suggesting that the primers specifically amplify the D. immitis cytochrome c oxidase subunit I gene. Comparison of SYBR Green and TaqMan real-time PCR using serially diluted plasmid DNA showed higher efficiency and specificity with TaqMan real-time PCR. The real-time PCR assays developed in this study will provide improved diagnostic methods to overcome the limitations of conventional diagnostic tools and facilitate more rapid and accurate diagnoses.

• Journal of Food Hygiene and Safety
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• v.33 no.4
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• pp.280-288
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• 2018

In this study, an approach for the analysis of the five cephalopod species (octopus, long-arm octopus, squid, wet-foot octopus, beka squid) consumed in the Republic of Korea is developed. The samples were collected from the Southeast Asian countries Thailand, Indonesia, Vietnam, and China. The SYBR-green-based real-time qPCR method, based on the mitochondrial DNA genome of the five cephalopods was developed and validated. The intergroup variations in the mitochondrial DNA are evident in the bioinformatic analysis of the mitochondrial genomic DNA sequences of the five groups. Some of the highly-conserved and slightly-variated regions are identified in the mitochondrial cytochrome-c-oxidase subunit I (COI) gene, 16s ribosomal RNA (16s rRNA) gene, and 12s ribosomal RNA (12s rRNA) gene of these groups. To specify each five cephalopod groups, specific primer sets were designed from the COI, 16s rRNA and 12s rRNA regions. The specific primer sets amplified the DNA using the SYBR-green-based real-time PCR system and 11 commercially secured animal tissues: Octopus vulgaris, Octopus minor, Todarodes pacificus, Dosidicus gigas, Sepia esculenta, Amphioctopus fangsiao, Amphioctopus aegina, Amphioctopus marginatus, Loliolus beka, Loligo edulis, and Loligo chinensis. The results confirmed by a conveient way to calculate relative amplification levels between different samples in that it directly uses the threshold cycles (Ct)-value range generated by the qPCR system from these samples. This genomic DNA-based molecular technique provides a quick, accurate, and reliable method for the taxonomic classification of the animal tissues using the real-time qPCR.

• Journal of the Korean Chemical Society
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• v.57 no.1
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• pp.81-87
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• 2013

Staphylococcus aureus is the most important pathogen in nosocomial infections, including bloodstream infections. Prompt identification of S. aureus from blood cultures and detection of methicillin resistance are essential in cases of suspected sepsis. We have studied a new method for the sequence-specific visual detection of minute amounts of nucleic acids using intercalating reaction by addition of SYBR Green to amplicons of LAMP, and it's a unique gene amplification method in which DNA can be isothermally amplified using only one enzyme. Staphylococcus-LAMP, which targets the spa gene, encoding S.aureus-specific protein A, and the mecA gene, encoding penicillin-binding protein-2' for methicillin resistance, detected MRSA and MRSE. In this study, by using LAMP assay, I detected for Staphylococcus aureus and Staphylococcus epidermidis concentration in the clinical sample. The detection of Staphylococcus aureus and Staphylococcus epidermidis was tested by using serial 10-fold dilutions standard solution. I have accurate detected the limit of detection, sensitity, specificity and reproducibility of the assay. The Bio-chip based LAMP assay allowed easy, rapid, accurate and sensitive detection of infection with Staphylococcus and especially applicable in a resource-limited situation.

• Toxicological Research
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• v.21 no.3
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• pp.219-226
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• 2005

• Journal of Environmental Science International
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• v.18 no.12
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• pp.1331-1338
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• 2009

Marine dinoflagellate Alexandrium minutum producing paralytic shellfish toxins is responsible for paralytic shellfish poisoning (PSP). To investigate its temporal distributions in Chinhae Bay where PSP occurs annually, SYBR Green I based A. minutum-specific real-time PCR probe was developed on the LSU rDNA region. Assay specificity and sensitivity were tested against related species, and its specificity was further confirmed by sequencing of field-derived samples. Ten months field survey in 2008 (a total 100 surface water samples) by using the real-time PCR probe showed that A. minutum was detected at very low densities of 1-4 cells $L^{-1}$ in May and June being spring in Chinhae Bay, Korea.