• Biomolecules & Therapeutics
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• v.27 no.2
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• pp.193-200
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• 2019

Ceramide metabolism is known to be an essential etiology for various diseases, such as atopic dermatitis and Gaucher disease. Glucosylceramide synthase (GCS) is a key enzyme for the synthesis of glucosylceramide (GlcCer), which is a main ceramide metabolism pathway in mammalian cells. In this article, we developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to determine GCS activity using synthetic non-natural sphingolipid C8-ceramide as a substrate. The reaction products, C8-GlcCer for GCS, could be separated on a C18 column by reverse-phase high-performance liquid chromatography (HPLC). Quantification was conducted using the multiple reaction monitoring (MRM) mode to monitor the precursor-to-product ion transitions of m/z $588.6{\rightarrow}264.4$ for C8-GlcCer at positive ionization mode. The calibration curve was established over the range of 0.625-160 ng/mL, and the correlation coefficient was larger than 0.999. This method was successfully applied to detect GCS in the human hepatocellular carcinoma cell line (HepG2 cells) and mouse peripheral blood mononuclear cells. We also evaluated the inhibition degree of a known GCS inhibitor 1-phenyl-2-decanoylamino-3-morpholino-1-propanol (PDMP) on GCS enzymatic activity and proved that this method could be successfully applied to GCS inhibitor screening of preventive and therapeutic drugs for ceramide metabolism diseases, such as atopic dermatitis and Gaucher disease.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.629-636
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• 2022

Colletotrichum species is known as the major causal pathogen of red pepper anthracnose in Korea and various groups of fungicides are registered for the management of the disease. However, the consistent use of fungicides has resulted in the development of resistance in many red pepper-growing areas of Korea. Effective management of the occurrence of fungicide resistance depends on constant monitoring and early detection. Thus, in this study, various methods such as agar dilution method (ADM), gene sequencing, allele-specific polymerase chain reaction (PCR), and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) were applied for the detection of benzimidazole resistance among 24 isolates of Colletotrichum acutatum s. lat. and Colletotrichum gloeosporioides s. lat. The result of the ADM showed that C. gloeosporioides s. lat. was classified into sensitive and resistant isolates to benomyl while C. acutatum s. lat. was insensitive at ≥1 ㎍/ml of benomyl. The sequence analysis of the β-tubulin gene showed the presence of a single nucleotide mutation at the 198th amino acid position of five isolates (16CACY14, 16CAYY19, 15HN5, 15KJ1, and 16CAYY7) of C. gloeosporioides s. lat. Allele-specific PCR and PCR-RFLP were used to detect point mutation at 198th amino acid position and this was done within a day unlike ADM which usually takes more than one week and thus saving time and resources that are essential in the fungicide resistance management in the field. Therefore, the molecular techniques established in this study can warrant early detection of benzimidazole fungicide resistance for the adoption of management strategies that can prevent yield losses among farmers.

• Biomedical Science Letters
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• v.29 no.4
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• pp.363-370
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• 2023

Human respiratory viral infections such as COVID-19 are highly contagious, so continuous management of airborne viruses is essential. In particular, indoor air monitoring is necessary because the risk of infection increases in poorly ventilated indoors. However, the current method of detecting airborne viruses requires a lot of time from sample collection to confirmation of results. In this study, we proposed a system that can monitor airborne viruses in real time to solve the deficiency of the present method. Air samples were collected in liquid form through a bio sampler, in which case the virus is present in low concentrations. To detect viruses from low-concentration samples, viral RNA was concentrated and extracted using silica-magnetic beads. RNA binds to silica under certain conditions, and by repeating this binding reaction, bulk samples collected from the air can be concentrated. After concentration and extraction, viral RNA is specifically detected through real-time qPCR (quantitative polymerase chain reaction). In addition, based on liquid handling technology, we have developed an automatic machine that automatically performs the entire testing process and can be easily used even by non-experts. To evaluate the system, we performed air sample collection and automated testing using bacteriophage MS2 as a model virus. As a result, the air-collected samples concentrated by 45 times then initial volume, and the detection sensitivity of PCR also confirmed a corresponding improvement.

• Journal of Microbiology and Biotechnology
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• v.33 no.9
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• pp.1228-1237
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• 2023

The CRISPR-Cas system has emerged as the most efficient genome editing technique for a wide range of cells. Delivery of the Cas9-sgRNA ribonucleoprotein complex (Cas9 RNP) has gained popularity. The objective of this study was to develop a quantitative polymerase chain reaction (qPCR)-based assay to quantify the double-strand break reaction mediated by Cas9 RNP. To accomplish this, the dextransucrase gene (dsr) from Leuconostoc citreum was selected as the target DNA. The Cas9 protein was produced using recombinant Escherichia coli BL21, and two sgRNAs were synthesized through in vitro transcription to facilitate binding with the dsr gene. Under optimized in vitro conditions, the 2.6 kb dsr DNA was specifically cleaved into 1.1 and 1.5 kb fragments by both Cas9-sgRNA365 and Cas9-sgRNA433. By monitoring changes in dsr concentration using qPCR, the endonuclease activities of the two Cas9 RNPs were measured, and their efficiencies were compared. Specifically, the specific activities of dsr365RNP and dsr433RNP were 28.74 and 34.48 (unit/㎍ RNP), respectively. The versatility of this method was also verified using different target genes, uracil phosphoribosyl transferase (upp) gene, of Bifidobacterium bifidum and specific sgRNAs. The assay method was also utilized to determine the impact of high electrical field on Cas9 RNP activity during an efficient electroporation process. Overall, the results demonstrated that the qPCR-based method is an effective tool for measuring the endonuclease activity of Cas9 RNP.

• Clinical and Experimental Vaccine Research
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• v.11 no.1
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• pp.104-115
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• 2022

Purpose: In the United States, Pfizer-BioNTech, Moderna, and Janssen's coronavirus disease 2019 (COVID-19) vaccines have been granted Emergency Use Authorization (EUA) with the Pfizer-BioNTech vaccine presently approved by the US Food and Drug Administration. The purpose of this study is to analyze passive surveillance data on COVID-19 vaccine adverse reaction in the United States. Materials and Methods: We analyzed passive surveillance data on COVID-19 vaccine adverse reactions which were retrieved from the Vaccine Adverse Event Reporting System database. Retrieved records on demographic information as well as the top 10 common vaccine adverse events were extracted and assessed from 200 of the most recently reported cases for the study analysis. Results: Local and systemic adverse reactions were reported in the study. A significant difference (p<0.05) was recorded for the top 10 systemic reactions by age category (0.041) and by gender (0.002). Analysis of the top five systemic reactions, stratified by vaccine type yielded a significant difference (p<0.05) for chills (p=0.044), and when stratified by age group and type of vaccination received, it yielded a significant difference (p<0.05) for fatigue (p=0.023). Overall, Pfizer had 182 persons (91.0%) reporting adverse events, Moderna with 13 (6.5%), and Janssen with 5 (2.5%). Conclusion: Mild side effects were reported following vaccination with the EUA COVID-19 vaccines in the United States. Thus, continuous monitoring and reporting of all adverse events are recommended to ensure the safety of vaccination.

• Journal of Sensor Science and Technology
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• v.29 no.2
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• pp.93-99
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• 2020

A colorimetric paper sensor was used to detect volatile nitrogen-containing compounds emitted from spoiled salmon filets to determine their freshness. The sensing mechanism was based on acid-base reactions between acidic pH-indicating dyes and basic volatile ammonia and amines. A sensing layer was simply fabricated by drop-casting a dye solution of bromocresol green (BCG) on a polyvinylidene fluoride substrate, and its color-change response was enhanced by optimizing the amounts of additive chemicals, such as polyethylene glycol, p-toluene sulfonic acid, and graphene oxide in the dye solution. To avoid the adverse effects of water vapor, both faces of the sensing layer were enclosed by using a polyethylene terephthalate film and a gas-permeable microporous polytetrafluoroethylene sheet, respectively. When exposed to basic gas analytes, the paper-like sensor distinctly exhibited a color change from initially yellow, then to green, and finally to blue due to the deprotonation of BCG via the Brønsted acid-base reaction. The use of ammonia analyte as a test gas confirmed that the sensing performance of the optimized sensor was reversible and excellent (detection time of < 15 min, sensitive naked-eye detection at 0.25 ppm, good selectivity to common volatile organic gases, and good stability against thermal stress). Finally, the coloration intensity of the sensor was quantified as a function of the storage time of the salmon filet at 28℃ to evaluate its usefulness in monitoring of the food freshness with the measurement of the total viable count (TVC) of microorganisms in the food. The TVC value increased from 3.2 × 10⁵ to 3.1 × 10⁹ cfu/g in 28 h and then became stable, whereas the sensor response abruptly changed in the first 8 h and slightly increased thereafter. This result suggests that the colorimetric response could be used as an indicator for evaluating the degree of decay of salmon induced by microorganisms.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.17 no.3
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• pp.160-180
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• 2012

We have studied the eukaryotic plankton species diversity to compare the community structure of fresh and brackish waters in the lower reaches of the Nakdong River using metagenomic methods. We constructed 18S rDNA clone libraries of total DNAs extracted from environmental water samples collected at Mulgeum (MG100929, fresh) and Eulsukdo bridge (ES, brackish). Through the steps of colony PCR, PCR-RFLP, sequencing and similarity analysis, we discovered the diverse species composition of eukaryotic plankton. Total 338 clones (170 at MG100929 and 168 at ES) were analyzed, and then we found 74 phylotypes (49 for MG100929 and 25 for ES). From the phylogenetic analysis, we confirmed various eukaryotic plankton of broad range of taxonomic groups, including Stramenopiles, Cryptophyta, Viridiplantae, Alveolata, Rhizaria, Metazoa, and Fungi. We also found several unreported species in Korea and candidates of new taxonomic entities at levels higher than genus. Especially, the cryptic species diversity including unreported phylotypes of Pirsonia (Stramenopiles) and Perkinsea (Alveolata) suggests that the molecular monitoring method can produce new informative biological data in monitoring the changes in the Nakdong River Mouth ecosystem.

• Journal of Plant Biotechnology
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• v.45 no.1
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• pp.77-82
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• 2018

In South Korea, LM crops are not allowed to grow locally, but have been allowed to be imported as food and feed purposes. Currently, the typical LMO imports are continuously increasing in the region of South Korea. In 2014, we carried out a review of the environmental release monitoring of LM maize (Zea mays L.) in Gyeonggi-do of South Korea, and analyzed volunteer samples using strip test kits and polymerase chain reaction (PCR) methods. We thereby collected 44 volunteers of released LM maize in 169 locations around ports, from roadsides, feed factories and stockbreeding farmhouses. We found 4 positive samples at 3 sites using strip test kits. Based on the PCR analysis, the LM maize plants were found using event-specific primers. These results suggested that our monitoring is necessary to detect the presence of released LM maize in the natural environment of South Korea.

• Biomedical Science Letters
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• v.9 no.3
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• pp.139-144
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• 2003

Since water borne infection causes acute diseases and results in spread of diseases by secondary infection, the prevention is very important. Therefore, it is necessary to have a method that is rapid and effective to monitor pathogenic bacteria in drinking water. In this study, we employed a systematic method, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis, to develop an effective monitoring system for possible bacterial contaminants in drinking water. For this purpose, PCR primers were derived from 992 bp region of the 16s rRNA gene that is highly conserved through the different species of prokaryotes. To test whether the PCR primers designed are indeed useful for detecting all the possible microbial contaminants in the water, the primers were used to amplify 16s rRNA regions of different microbial water-borne pathogens such as E. coli, Salmonella, Yersinia, Listeria, and Staphylococcus. As expected, all of tested microorganisms amplified expected size of PCR products indicating designed PCR primers for 16s rRNA indeed can be useful to amplify all different microbial water-borne pathogens in the water. Furthermore, to test whether these 16s rRNA based PCR primers can detect bacterial populations present in the water, water samples taken from diverse sources, such as river, tap, and sewage, were used for amplification. PCR products were for then subjected for cloning into a T-vector to generate a library containing 16s rRNA sequences from various bacteria. With cloned PCR products, RFLP analysis was done using PCR products digested with restriction enzyme such as Hae III to obtain species-specific RFLP profiles. After PCR-RFLP, the bacterial clones which showed the same RFLP profiles were regarded as the same ones, and the clones which showed distinctive RFLP profiles were subsequently subjected for sequence analysis for species identification. By this PCR-RFLP analysis, we were able to reveal diverse populations of bacteria living in water. In brief, in unsterilized natural river water, over 60 different species of bacteria were found. On the other hand, no PCR products were detected in drinking tap-water. The results from this study clearly indicate that the PCR-RFLP-sequence analysis can be a useful method for monitoring diverse, perhaps pathogenic bacteria contaminated in water in a rapid fashion.

• YAKHAK HOEJI
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• v.51 no.2
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• pp.96-102
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• 2007

Measurement of globotriaosylceramide (Gb3, ceramide trihexoside) in urine has clinical importance for monitoring after enzyme replacement therapy in Fabry disease patients. The disease is an X-linked lipid storage disorder that results from a deficiency of the enzyme ${\alpha}$-galactosidase A (${\alpha}$-Gal A). The lack of ${\alpha}$-Gal A causes an intracellular accumulation of glycosphingolipids, mainly Gb3. A simple, rapid, and highly sensitive analytical method for Gb3 in urine was developed without labor-extensive pre-treatment by electrospray ionization MS/MS (ESI-MS/MS). Only simple 5-fold dilution of urine is necessary for the extraction and isolation of Gb3 in urine. Gb3 in diluted urine was dissolved in dioxane containing C17:0 Gb3 as an internal standard. After centrifugation it was directly injected and analyzed through guard column by in combination with multiple reaction monitoring mode of ESI-MS/MS. Eight isoforms of Gb3 were completely resolved from urine matrix. C24:0 Gb3 occupied 50% of total Gb3 as a major component in urine. Linear relationship for Gb3 isoforms was found in the range of 0.005${\sim}$5.0 ${\mu}$g/ml. The limit of detection (S/N=5) was 0.005 ${\mu}$g/ml and limit of quantification was 0.05 ${\mu}$g/ml for C24:0 Gb3 with acceptable precision and accuracy. Correlation coefficient of calibration curves for 8 Gb3 isoforms ranged from 0.9598 to 0.9975. This method could be useful for rapid and sensitive 1st line Fabry disease screening, monitoring and/or diagnostic tool for Fabry disease.