• The Plant Pathology Journal
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• v.36 no.6
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• pp.618-627
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• 2020

Although limited progress have been made about pathogen system of Hibiscus rosa-sinensis and Hibiscus latent Fort Pierce virus (HLFPV), interaction between plant host and pathogen remain largely unknown, which led to deficiency of effective measures to control disease of hibiscus plants caused by HLFPV. In this study, infection of HLFPV in Hibiscus rosa-sinensis was firstly confirmed for the first time by traditional electron microscopy, modern reverse transcription polymerase chain reaction and RNA-seq methods in China (HLFPV-Ch). Sequence properties analyzing suggested that the full-length sequences (6,465 nt) of HLFPV-Ch had a high sequence identity and a similar genomic structure with other tobamoviruses. It includes a 5'-terminal untranslated region (UTR), followed by four open reading frames encoding for a 128.5-kDa replicase, a 186.5-kDa polymerase, a 31-kDa movement protein, 17.6-kDa coat protein, and the last a 3'-terminal UTR. Furthermore, HLFPV-Ch-derived virus-derived siRNAs (vsiRNAs) ant its putative target genes, reported also for the first time, were identified and characterized from disease Hibiscus rosa-sinensis through sRNA-seq and Patmatch server to investigate the interaction in this pathogen systems. HLFPV-Ch-derived vsiRNAs demonstrated several general and specific characteristics. Gene Ontology classification revealed predicted target genes by vsiRNAs are involved in abroad range of cellular component, molecular function and biological processes. Taken together, for first time, our results certified the HLFPV infection in China and provide an insight into interaction between HLFPV and Hibiscus rosa-sinensis.

• Molecules and Cells
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• v.37 no.3
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• pp.220-225
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• 2014

Suppression of bone morphogenetic protein (BMP) signaling induces neural induction in the ectoderm of developing embryos. BMP signaling inhibits neural induction via the expression of various neural suppressors. Previous research has demonstrated that the ectopic expression of dominant negative BMP receptors (DNBR) reduces the expression of target genes down-stream of BMP and leads to neural induction. Additionally, gain-of-function experiments have shown that BMP downstream target genes such as MSX1, GATA1b and Vent are involved in the suppression of neural induction. For example, the Vent1/2 genes are involved in the suppression of Geminin and Sox3 expression in the neural ectodermal region of embryos. In this paper, we investigated whether PV.1, a BMP downstream target gene, negatively regulates the expression of FoxD5b, which plays a role in maintaining a neural progenitor population. A promoter assay and a cyclohexamide experiment demonstrated that PV.1 negatively regulates FoxD5b expression.

• Journal of Ginseng Research
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• v.43 no.4
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• pp.625-634
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• 2019

Background: Ginsenoside Rg3, a derivative of steroidal saponins abundant in ginseng, has a range of effects on cancer cells, including anti-cell proliferation and anti-inflammation activity. Here, we investigate two long noncoding RNAs (lncRNAs), STXBP5-AS1 and RFX3-AS1, which are hypomethylated and hypermethylated in the promoter region by Rg3 in MCF-7 cancer cells. Methods: The lncRNAs epigenetically regulated by Rg3 were mined using methylation array analysis. The effect of the lncRNAs on the apoptosis and proliferation of MCF-7 cells was monitored in the presence of Rg3 or Korean Red Ginseng (KRG) extract after deregulating the lncRNAs. The expression of the lncRNAs and their target genes was examined using qPCR and Western blot analysis. The association between the expression of the target genes and the survival rate of breast cancer patients was analyzed using the Kaplan-Meier Plotter platform. Results: STXBP5-AS1 and RFX3-AS1 exhibited anti- and pro-proliferation effects, respectively, in the cancer cells, and the effects of Rg3 and KRG extract on apoptosis and cell proliferation were weakened after deregulating the lncRNAs. Of the genes located close to STXBP5-AS1 and RFX3-AS1 on the chromosome, STXBP5, GRM1, RFX3, and SLC1A1 were regulated by the lncRNAs on the RNA and protein level. Breast cancer patients that exhibited a higher expression of the target genes of the lncRNAs had a higher metastasis-free survival rate. Conclusion: The current study is the first to identify lncRNAs that are regulated by the presence of Rg3 and KRG extract and that subsequently contribute to inhibiting the proliferation of cancer cells.

• Molecules and Cells
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• v.42 no.1
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• pp.87-95
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• 2019

Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.

• Journal of Microbiology and Biotechnology
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• v.31 no.8
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• pp.1154-1162
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• 2021

The transcriptional capacities of target genes are strongly influenced by promoters, whereas few studies have focused on the development of robust, high-performance and cross-species promoters for wide application in different bacteria. In this work, four novel promoters (P_k.rtufB, P_k.r1, P_k.r2, and P_k.r3) were predicted from Ketogulonicigenium robustum and their inconsistency in the -10 and -35 region nucleotide sequences indicated they were different promoters. Their activities were evaluated by using green fluorescent protein (gfp) as a reporter in different species of bacteria, including K. vulgare SPU B805, Pseudomonas putida KT2440, Paracoccus denitrificans PD1222, Bacillus licheniformis and Raoultella ornithinolytica, due to their importance in metabolic engineering. Our results showed that the four promoters had different activities, with P_k.r1 showing the strongest activity in almost all of the experimental bacteria. By comparison with the commonly used promoters of E. coli (tufB, lac, lacUV5), K. vulgare (Psdh, Psndh) and P. putida KT2440 (JE111411), the four promoters showed significant differences due to only 12.62% nucleotide similarities, and relatively higher ability in regulating target gene expression. Further validation experiments confirmed their ability in initiating the target minCD cassette because of the shape changes under the promoter regulation. The overexpression of sorbose dehydrogenase and cytochrome c551 by P_k.r1 and P_k.r2 resulted in a 22.75% enhancement of 2-KGA yield, indicating their potential for practical application in metabolic engineering. This study demonstrates an example of applying bioinformatics to find new biological components for gene operation and provides four novel promoters with broad suitability, which enriches the usable range of promoters to realize accurate regulation in different genetic backgrounds.

• Management & Information Systems Review
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• v.34 no.1
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• pp.179-190
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• 2015

Local governments are commercializing natural environment, one of tourist commodities, to ensure that the proceeds from sale of tourist commodities are returned to local residents(Han Yeong-joo, Lee Moo-yong, 2001). In Songdo beach, Busan, cable car dismantled in 1980s due to the run-down state of the facility is poised for restoration in 26 years and can be said to be of great value as tourist commodity of the region and necessitates the demand forecast. To overcome limitations of demand forecast in existing studies, the analysis was made based on feasibility rate(Gruber index, self-confidence index), the realizable predictive value, for the willingness-to-visit rate when forecasting the demand of visitors. The results of demand forecast suggested that number of visitors would range from approximately 550,684 persons to 1,514,416 persons when the target region for demand forecast was confined to Busan Metropolitan City, and was in the range between 1,013,740 persons and 2,854,340 persons when the target region was expanded to cover Busan, Ulsan, and Gyeongnam. Based on the results of this study, estimation of visitors and demand forecast for Songdo offshore cable car restoration which reflect characteristics of Songdo beach of Busan would provide important basis for proceeding with tourism industry development project.

• Journal of Oral Medicine and Pain
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• v.30 no.4
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• pp.447-455
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• 2005

The purpose of this study was to examine the effect of Nd:YAG laser irradiation for sensory nerve conduction change. Nd:YAG laser was irradiated to mental region for 5 minutes with the parameters that 10 Hz and 20 Hz of 100 mJ/pulse. Target size of irradiation was 30 mm diameter of circle and target-tip distance was about 10 mm. Therefore, the power density were 212 $mW/cm^2$ and 424 $mW/cm^2$. Sensory nerve conduction was evaluated with $Neurometer^{\circled}$ CPT/C before and after Nd:YAG laser irradiation. As an outcomes, the current perception threshold(CPT) and pain tolerance threshold(PTT) were obtained. We made a comparison of these two values and the results were as follows. 1. There was no significant difference in CPT at 1W, 10 Hz and 2 W, 20 Hz Nd:YAG laser irradiation. 2. There was no significant difference in PTT at 10 Hz, 20 Hz of 100 mJ/pulse Nd:YAG laser. 3. There were no significant differences in CPT and PTT between 1 W, 10 Hz group and 2 W, 20 Hz group. Therefore, We can make a conclusion that Nd:YAG laser irradiation to mental region have no effect on mental nerve conduction in our study model.

• Journal of Navigation and Port Research
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• v.32 no.8
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• pp.637-643
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• 2008

When planning outfall system, the first target cif design is to maximize initial dilution of discharge effluent. To achieve the target effectively, the characteristics of mixing phenomenon between ambient and discharged water should be analyzed. Especially the analysis at the Near-Field-Region(NFR) as initial dilution zone should be preceded. Usually, the initial behavior of effluent through outfall system is rising toward the surface due to mixing with ambient water for heat discharge and sinking toward the bottom due to the difference of density for brine discharge. After mixed with eddies accompanied by the ambient water, the plumes are showing the same density and internal current pattern by advection and diffusion. Until recently, lots of studies are being carried out for the optimum design of outfall system. but it is difficult to find any studies of heat and brine discharge at the same time. Therefore, this study is hoped to provide some basic data for optimum design of outfall system.

• Journal of the Korean Society of Radiology
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• v.6 no.5
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• pp.403-408
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• 2012

Prompt gamma ray from the natural Indium sample was measured by using an assembly of BGO($Bi_4Ge_3O_{12}$) scintillation detectors in the neutron energy region from 1 to 300 eV. The assembly was composed of pieces of BGO. The spectrometer was composed geometrically as total energy absorption detector. 46-MeV electron linear accelerator which is located at Research Reactor Institute, Kyoto University used for neutron sources from photonuclear reaction. The measurement of the neutron capture resonances was performed to below neutron energy 1 keV, because of strong X-ray effect from photonuclear reaction in Ta target and short distance from the target to an assembly of detector. The distance of neutron flight path is $12.7{\pm}0.02m$. The large neutron capture resonances were measured from 1 to 400 eV. The energy in the capture resonance was compared with the evaluated values. The large resonances were seen in the present measurement. General agreement can be seen between the present measurement and the previous evaluated data in relevant energy region. In the present study, we measured the continues resonance structure above 1 keV neutron energy region. 91.49 eV new neutron capture resonance was found in present measurement.

• Journal of the Economic Geographical Society of Korea
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• v.6 no.2
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• pp.403-419
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• 2003

Busan Port, Korea, is a region that must take integrated measures against problems such as the excessive handling of cargo volume, the intensification of port congestion, and the construction of a new port to improve port competitive power. In particular, if a great deal of function in the existing area of Busan Port transfers to a new port, then the problems of port redevelopment will occur as shown in the cases of port developed countries explained hereafter. For Korean ports, port redevelopment in a port zone is implemented for improving the port productivity that targets a local area, but the entire and systematic port redevelopment is not accounted for. Focused on this point, the paper is to present the directions for full-scale port redevelopment of the existing zone of Busan Port. The findings are as follows: First, the region of Busan is divided according to a regional classification that is necessary for port redevelopment. Thereby, 4 zones, total 26 regions of redevelopment were selected. Second, overseas case studies were considered for port redevelopment. From these same studies, appropriate types of port development in Korea were extracted and presented. Third, the status and problems of the selected redevelopment regions were analyzed, and types of port redevelopment were assigned. This study was not applied to the strict evaluation technique by quantitative analysis, but the concept and directions for unprecedented port redevelopment were first defined and established. It is significant to select target areas for redevelopment by regional classification and present directions for developing each region by choosing Busan Port as a real case study. This initiation will greatly contribute to the succeeding study.