• The Plant Pathology Journal
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• v.18 no.5
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• pp.251-258
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• 2002

A potyvirus was isolated from cultivated Iris plants showing leaf streak mosaic symptom. Reverse transcription and polymerase chain reaction (RT-PCR) product of 1 kb long which encoded partial nuclear inclusion B and N-terminal region of viral coat protein (CP) genes for potyviruses was successfully amplified with a set of potyvirus-specific degenerate primers with viral RNA samples from the infected leaves: The RT-PCR product was cloned into the plasmid vector and its nucleotide sequences were determined. The nucleotide sequence of a CDNA clone revealed that the virus was an isolate of Ornithogalum moseic virus (OrMV) based on BLAST search analysis and was denoted as OrMV Korean isolate (OrMV-Ky). To further characterize the CP gene of the virus, a pair of OrMV-specific primers was designed and used for amplification of the entire CP gene of OrMV-Kr, The virus was easily and reliably detected from virus-infected Iris leaves by using the RT-PCR with the set of virus-specific primers. The RT-PCR product of the CP gene of the virus was cloned and its sequences were determined from selected recombinant CDNA clones. Sequence analysis revealed that the CP of OrMV-Kr consisted of 762 nucleotides, which encoded 253 amino acid residues. The CP of OrMV-Ky has 94.1-98.0% amino acid sequence identities (20 amino acid alterations) with that of other three isolates of OrMV, Two NT rich potential N-glycosylation motif sequences, NCTS and NWTM, and a DAC triple box responsible for aphid transmission were conserved in CPs of all the strains of OrMV. The virus has 58.5-86.2% amino acid sequence identities with that of other 16 potyviruses, indicating OrMV to be a distinct species of the genus. OrMV-Ky was the most related with Pterostylia virus Yin the phylogenetic tree analysis of CP at the amino acid level. This is the first report on the occurrence of OrMV in Iris plants in Korea. Data in this study indicate that OrMV is found in cultivated Iris plants, and may have mixed infection of OrMV and Iris severe mosaic virus in Korea.

• Molecules and Cells
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• v.26 no.3
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• pp.314-318
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• 2008

Korean long-tailed goral (Nemorhaedus caudatus) is one of the most endangered species in South Korea. However, detailed species distribution and sex ratio data on the elusive goral are still lacking due to difficulty of identification of the species and sex in the field. The primary aim of this study was to develop an economical PCR-RFLP method to identify species using invasive or non-invasive samples from five Korean ungulates: goral (N. caudatus), roe deer (Capreolus pygargus), feral goat (Capra hircus), water deer (Hydropotes inermis) and musk deer (Moschus moschiferus). The secondary aim was to find more efficient molecular sexing techniques that may be applied to invasive or non-invasive samples of ungulate species. We successfully utilized PCR-RFLP of partial mitochondrial cytochrome b gene (376 bp) for species identification, and sex-specific amplification of ZFX/Y and AMELX/Y genes for sexing. Three species (goral, goat and water deer) showed distinctive band patterns by using three restriction enzymes (Xbal, Stul or Sspl). Three different sexing primer sets (LGL331/335 for ZFX/Y gene; SE47/48 or SE47/53 for AMELX/Y gene) produced sex-specific band patterns in goral, goat and roe deer. Our results suggest that the molecular analyses of non-invasive samples might provide us with potential tools for the further genetic and ecological study of Korean goral and related species.

• Journal of Life Science
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• v.21 no.11
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• pp.1549-1557
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• 2011

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) can selectively induce apoptosis in many types of transformed cells; however, some human hepatocellular carcinoma cells are particularly resistant to the effects of TRAIL. Although genistein, a natural isoflavonoid phytoestrogen, has been shown to have pro-apoptotic activity against human cancer cell lines, little is known about the mechanism of genistein in terms of TRAIL-induced apoptosis. In the present study, it was investigated whether or not combined treatment with genistein and TRAIL synergistically induced apoptosis in Hep3B hepatocarcinoma cells. Results indicate that treatment with TRAIL in combination with nontoxic concentrations of genistein sensitized TRAIL-resistant Hep3B cells to TRAIL-induced apoptosis, which was associated with mitochondrial dysfunction. Further, the inhibition of p38 mitogen-activated protein kinase (MAPK) activation markedly decreased genistein and TRAIL-induced cell viability and apoptosis by enhanced truncation of Bid, increase of pro-apoptotic Bax, decrease of anti-apoptotic Bcl-2, and release of cytochrome c from mitochondria to cytoplasm. Activation of caspases and degradation of poly (ADP-ribose) polymerase induced by the combined treatment was also markedly increased by the inhibition of p38 MAPK, through the mitochondrial amplification step. In conclusion, our data suggest that genistein sensitizes TRAIL-induced-apoptosis via p38 MAPK-dependent pathway.

• Journal of Life Science
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• v.24 no.1
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• pp.1-7
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• 2014

Eukaryotic gene expression is an important process, which is initiated by several transcription factors and RNA polymerases that occupy the promoter region of genomic DNA. Although there are many experiments to identify the promoter region in a gene, it is time and labor consuming to finalize it. In this study, we utilized bioinformatic programs, including Ensembl, NCBI, and CpG plots, to identify the cloning promoter region in SETDB1 genomic DNA. We performed PCR amplification to obtain the SETDB1 promoter on an approximately 2 kb region upstream from the TSS named SETDB1-P1. The PCR product was ligated with TA cloning vectors, and we confirmed the insert size using restriction enzyme digestion. Sequentially, the insert was subcloned into a pGL3-luc vector to produce pGL3-SETDB1- P1-luc and then confirmed by DNA sequencing. We also obtained a fragmented PCR product called P2 and P3 and performed a luciferase assay using pGL3-SETDB1-P1-luc transfection. We found that several anticancer drugs, including taxol, 4-FU, and doxorubicin, decreased the promoter activity of SETDB1. We obtained consistent data on the regulation of SETDB1 gene expression after anticancer drug treatment using Western blot analysis and RT-PCR. Our results suggest that promoter cloning of the human SETDB1 gene utilizing bioinformatics is a very useful and timesaving approach to study gene expression.

• Korean Journal of Microbiology
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• v.38 no.2
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• pp.127-132
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• 2002

In this study, the bacterial communities distributed in sea water of the whitening areas of Gangjeong and Seongsan, Jeju-do have been analysed using the PCR amplification of 16S rRNA to obtain fundamental data and information on relationship of the whitening phenomenon and microbial ecosystem. In Gangjeong, diverse bacteria such as Alcanivorax, Paracoccus, Damselae, Pseudomonas, Rhodowlum, Silicibacter, Suiftobacter, and Roseobacter have been found, and Alcanivorax was the most abundant clone. The most abundant clone from Seongsan was Pseudomonas, of which Pseudomonas tolaasii and Pseudomonas mandeli were most abundantly occurred in the frequency of approx44% and 24%, respectively. Approx4% of the bacterial clones closest to Verrucomicrobiales and other unidentified clones were also fecund in Seongsan, suggesting there is a great discrepancy between bacterial communities from the whitening areas of Seongsan and Gangjeong. The mean temperature, chlorine concentration, pH, and dissolved oxygen (DO) of the sea water of Gangieong and Seongsan in August of 2001 (sampling period) was $27^{\circ}C$~$27.5^{\circ}C$, 30.24~30.60%, pH 8.23~8.36,7 .20~7.28 mg/ι, suggesting other environmental factors except far the factors mentioned above might result in difference of bacterial communities distributed in both areas.

• Journal of Korean Society of Coastal and Ocean Engineers
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• v.23 no.4
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• pp.313-325
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• 2011

Finite element grid system using h-refinement on the Yellow Sea was constructed based on previous study (Suh, 1999b) from 14 K to 210 K and special attention was concentrated on refining the coastal zone. In grid generation, depth change between adjacent points and non-dimensional tidal wave length ratio were considered. As a result approximately a quarter of the total nodes are located nearby 5 m of shallow area. Accurate bathymetry data using 30's and ETOPO1 with open boundary conditions of 8 major tidal constituents extracted automatically from FES2004 have been applied. In tidal simulation a 3-dimensional nonlinear harmonic model was setup and tidal amplification due to changes in vertical turbulent and bottom friction were simulated. In this study not only 8 major tidal constituents but also nonlinear shallow tides $M_4,$, $MS_4$ and long period $M_f,$, $M_{sf}$ were reproduced. It is found that implication of spatial variation of friction coefficient plays a very important role in reproduction of astronomical and shallow tides which are computed by iterative computation of nonlinear terms. Also it should be considered differently with respect to tidal periods. To understand the distribution of tidal asymmetry, amplitude ratio of $M_4/M_2$ and phase differences $2g(M_2)-g(M_4)$ were calculated. Tidal distortion ratio marks up to 0.2 on the west coast showing shallow coastal characteristics and somewhat wide range of ebb-dominances in front of Mokpo area are reproduced.

• Journal of Life Science
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• v.21 no.2
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• pp.235-241
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• 2011

The purpose of this study was to isolate soy curd forming bacterial strains. Soy curd forming bacteria were isolated from Kimchi, a traditional Korean vegetable food that is fermented using lactic acid bacteria. Among 196 bacterial strains, ten isolates (strain No. 2-2-2, 2-15-2, 2-18-1, 2-19-2, 3-4-1, 3-4-2, 3-8-1, 3-8-3, 3-17-1, 4-39-5) formed firm soy curd. The isolated bacterial strains were identified by molecular biological and biochemical analyses. The genomic DNAs extracted from the isolated bacterial strains were used as a template for PCR amplification of 16S rDNA region. By comparing the results of the 16s rDNA sequences with GenBank data, the isolated strains were identified as Leuconostoc mesenteroides group and Lactobacillus sakei group. The phylogenetic position of soy curd forming strains and their related taxa were investigated using neighbor-joining method. L. mesenteroides group was further identified as L. mesenteroides subsp. dextranicum based on biochemical properties. L. sakei group was named Lactobacillus sp., because it showed a variety of biochemical properties.

• Journal of Advanced Navigation Technology
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• v.25 no.1
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• pp.68-77
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• 2021

In this paper, a GPS/MEMS IMU integrated navigation receiver module capable of operating in a high dynamic environment is designed and fabricated, and the results is confirmed. The designed module is composed of RF receiver unit, inertial measurement unit, signal processing unit, correlator, and navigation S/W. The RF receiver performs the functions of low noise amplification, frequency conversion, filtering, and automatic gain control. The inertial measurement unit collects measurement data from a MEMS class IMU applied with a 3-axis gyroscope, accelerometer, and geomagnetic sensor. In addition, it provides an interface to transmit to the navigation S/W. The signal processing unit and the correlator is implemented with FPGA logic to perform filtering and corrrelation value calculation. Navigation S/W is implemented using the internal CPU of the FPGA. The size of the manufactured module is 95.0×85.0×.12.5mm, the weight is 110g, and the navigation accuracy performance within the specification is confirmed in an environment of 1200m/s and acceleration of 10g.

• Korean Journal of Clinical Laboratory Science
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• v.53 no.2
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• pp.143-150
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• 2021

The recent spread of novel and highly variant pathogenic viruses, including the coronavirus (SARS-CoV-2), has increased the demand for diagnostic testing for rapid confirmation. This has resulted in investigating the functional capability of each space, and preparing facility guidelines to secure the safety of medical technologists. During viral evaluations, there is a requirement of negative pressure facilities along with thread separation, during pre-treatment of samples and before nucleic acid amplification. Space composition therefore needs to be planned by considering unidirectional air flow. This classification of safety management facilities is designated as biosafety level 2, and personal protective equipment is placed accordingly. In case of handling dangerous materials, they need to be carried out of the biosafety cabinet, and sterilizers are required for suitable disposal of infectious agents. A common feature of domestic laboratories is maintenance of the sample pre-treatment space at a negative pressure of -2.5 Pa or less, and arranging separate pre-treatment and reagent preparation spaces during the test process. We believe that the data generated in this study is meaningful, and offers an efficient direction and detailed flow for separation of the inspection process and space functions. Moreover, this study introduces construction of the laboratory by applying the safety management standards.

• Journal of Ecology and Environment
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• v.45 no.4
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• pp.203-217
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• 2021

Background: Sea turtles, which are globally endangered species, have been stranded and found as bycatch on the Korean shore recently. More studies on sea turtles in Korea are necessary to aid their conservation. To investigate the spatio-temporal occurrence patterns of sea turtles on the Korean shore, we recorded sampling locations and dates, identified species and sexes and measured sizes (maximum curved carapace length; CCL) of collected sea turtles from the year 2014 to 2020. For an analysis of diets through stomach contents, we identified the morphology of the remaining food and extracted DNA, followed by amplification, cloning, and sequencing. Results: A total of 62 stranded or bycaught sea turtle samples were collected from the Korean shores during the study period. There were 36 loggerhead turtles, which were the dominant species, followed by 19 green turtles, three hawksbill turtles, two olive ridley turtles, and two leatherback turtles. The highest numbers were collected in the year 2017 and during summer among the seasons. In terms of locations, most sea turtles were collected from the East Sea, especially from Pohang. Comparing the sizes of collected sea turtles according to species, the average CCL of loggerhead turtles was 79.8 cm, of green turtles was 73.5 cm, and of the relatively large leatherback turtle species was 126.2 cm. In most species, the proportion of females was higher than that of males and juveniles, and was more than 70% across all the species. Food remains were morphologically identified from 19 stomachs, mainly at class level. Seaweeds were abundant in stomachs of green turtles, and Bivalvia was the most detected food item in loggerhead turtles. Based on DNA analysis, food items from a total of 26 stomachs were identified to the species or genus level. The gulfweed, Sargassum thunbergii, and the kelp species, Saccharina japonica, were frequently detected from the stomachs of green turtles and the jellyfish, Cyanea nozakii, the swimming crab, Portunus trituberculatus, and kelps had high frequencies of occurrences in loggerhead turtles. Conclusions: Our findings support those of previous studies suggesting that sea turtles are steadily appearing in the Korean sea. In addition, we verified that fish and seaweed, which inhabit the Korean sea, are frequently detected in the stomach of sea turtles. Accordingly, there is a possibility that sea turtles use the Korean sea as feeding grounds and habitats. These results can serve as basic data for the conservation of globally endangered sea turtles.