• Korean Journal of Microbiology
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• v.44 no.4
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• pp.333-338
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• 2008

Computational analysis of partial rpoB gene sequence (777 bp) was done in this study to identify B. anthracis and its closely related species B. cereus and B. thuringiensis. Sequence data including 17 B. anthracis strains, 9 B. cereus strains, and 7 B. thuringiensis strains were obtained by searching databases. Those sequences were aligned and used for other computational analysis. B. anthracis strains were identificated by in silico restriction enzyme digestion. B. cereus and B. thuringiensis were not segregated by this method. Those sequencing and BLAST search were required to distinguish the two. In actual identification tests, B. anthracis strains could be identified by PCR-RFLP, and B. cereus and B. thuringiensis strains were distinguished by BLAST search with reliable e-value. In this study fast and accurate method for identifying three Bacillus species, and flow chart of identification were developed.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.1
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• pp.53-58
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• 2006

This study was conducted to investigate the crossability, seed dormancy and overwintering ability of rice plant in GM (glufosinate ammonium-resistant lines. Iksan 483 and Milyang 204) and non-GM (their parents) or red rice (Andongaengmi). Seed-setting rate was not significantly different between GM and non-GM rice varieties. Iksan 483 and Milyang 204 showed the similar level of seed germination rate from 30 to 50 days after heading as compared to non-GM rice varieties. After overwintering in paddy field, seed germination rate of GM and non-GM rice varieties ranged from 14.3 % to 57.6 % in dry soil condition, but there was no germination in wet-soil except red rice. The result in wet-soil condition may help to set up a strategy for reducing the risk of gene flow of transgene via dispersal of seeds of GM plants. The crossability, seed dormancy and seed overwintering of Iksan 483 and Milyang 204, herbicide resistant GM rice varieties, were not significantly different compared to non-GM rice varieties. The results might be helpful to reduce the risk of transgene dispersal from GM crop via seeds and pollens.

• Animal cells and systems
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• v.16 no.3
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• pp.224-229
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• 2012

The Korean shiner (Coreoleuciscus splendidus, Gobioninae), a small freshwater fish native to Korea Peninsula, widely inhabits in most of the major drainages in South Korea. Here we describe the development of 14 novel and polymorphic microsatellites for this species and its effective utilization in estimation of genetic diversity using 72 individuals from three sampling sites in different drainages. Loci were isolated from a microsatellite enrichment procedure using probe-labeled magnetic beads. A total of 242 alleles were detected across all loci with an average of 17.3 alleles per locus ranging 4 32. The loci varied levels of polymorphism as evident from its expecte heterozygosity ranging from 0.111 to 0.957. The average pairwise $F_{ST}$ between two populations examined shows significant differentiation ($F_{ST}$ = 0.215, p<0.05). The 14 microsatellite loci developed here will also be useful to explain for the genetic structures among geographically isolated populations and gene flow dynamics within drainages in this species as well as the closely related species.

• Nuclear Engineering and Technology
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• v.41 no.9
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• pp.1171-1180
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• 2009

The internal core baffle structure of a French Pressurized Water Reactor (PWR) consists of a collection of baffles and formers that are attached to the barrel. The connections are done thanks to a large number of bolts (about 1500). After inspection, some of the bolts have been found cracked. This has been attributed to the Irradiation Assisted Stress Corrosion Cracking (IASCC). The $Electricit\acute{e}$ De France (EDF) has set up a research program to gain better knowledge of the temperature distribution, which may affect the bolts and the whole structure. The temperature distribution in the structure was calculated thanks to the thermal code SYRTHES that used a finite element approach. The heat transfer between the by-pass flow inside the cavities of the core baffle and the structure was accounted for thanks to a strong thermal coupling between the thermal code SYRTHES and the CFD code named Code_Saturne. The results for the CP0 plant design show that both the high temperature and strong temperature gradients could potentially induce mechanical stresses. The CPY design, where each bolt is individually cooled, had led to a reduction of temperatures inside the structures. A new parallel version of SYRTHES, for calculations on very large meshes and based on MPI, has been developed. A demonstration test on the complete structure that has led to about 1.1 billion linear tetraedra has been calculated on 2048 processors of the EDF Blue Gene computer.

• Genomics & Informatics
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• v.19 no.2
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• pp.14.1-14.6
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• 2021

Coronavirus disease 2019 (COVID-19) is an on-going pandemic disease infecting millions of people across the globe. Recent reports of reduction in antibody levels and the re-emergence of the disease in recovered patients necessitated the understanding of the pandemic at the core level. The cases of multiple organ failures emphasized the consideration of different organ systems while managing the disease. The present study employed RNA sequencing data to determine the disease associated differentially regulated genes and their related protein interactions in several organ systems. It signified the importance of early diagnosis and treatment of the disease. A map of protein interactions of multiple organ systems was built and uncovered CAV1 and CTNNB1 as the top degree nodes. A core interactions sub-network was analyzed to identify different modules of functional significance. AR, CTNNB1, CAV1, and PIK3R1 proteins were unfolded as bridging nodes interconnecting different modules for the information flow across several pathways. The present study also highlighted some of the druggable targets to analyze in drug re-purposing strategies against the COVID-19 pandemic. Therefore, the protein interactions map and the modular interactions of the differentially regulated genes in the multiple organ systems would incline the scientists and researchers to investigate in novel therapeutics for the COVID-19 pandemic expeditiously.

• Journal of Gastric Cancer
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• v.19 no.3
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• pp.254-277
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• 2019

Inflammation can be a causative factor for carcinogenesis or can result from a consequence of cancer progression. Moreover, cancer therapeutic interventions can also induce an inflammatory response. Various inflammatory parameters are used to assess the inflammatory status during cancer treatment. It is important to select the most optimal biomarker among these parameters. Additionally, suitable biomarkers must be examined if there are no known parameters. We briefly reviewed the published literature for the use of inflammatory parameters in the treatment of patients with cancer. Most studies on inflammation evaluated the correlation between host characteristics, effect of interventions, and clinical outcomes. Additionally, the levels of C-reactive protein, albumin, lymphocytes, and platelets were the most commonly used laboratory parameters, either independently or in combination with other laboratory parameters and clinical characteristics. Furthermore, the immune parameters are classically examined using flow cytometry, immunohistochemical staining, and enzyme-linked immunosorbent assay techniques. However, gene expression profiling can aid in assessing the overall peri-interventional immune status. The checklists of guidelines, such as STAndards for Reporting of Diagnostic accuracy and REporting recommendations for tumor MARKer prognostic studies should be considered when designing studies to investigate the inflammatory parameters. Finally, the data should be interpreted after adjusting for clinically important variables, such as age and cancer stage.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.59 no.3
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• pp.253-262
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• 2023

To identify sand crab Ovalipes punctatus populations and establish management units for each population, mtDNA COI regions were analyzed. As a result, the clade of O. punctatus in Korea were separated by two with a genetic distance of 0.17-2.08%, and there was no significant difference in the result of pairwise FST values representing genetic differentiation by sampling areas (p > 0.05). Also, no geographical separation found in the distribution of haplotypes and the results of the haplotype network. This result suggests that O. punctatus larvae were dispersed for a long time by the ocean current by suffering meroplanktonic period for 1 month, and increased the gene flow due to the development of the swimming legs for the increase in mobility. Therefore, in the results of mtDNA COI region analysis of O. punctatus in the East Sea, Yellow Sea, South Sea and East China Sea (Ieodo) of Korea, no clear intra-species differentiation was found.

• Journal of Environmental Science International
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• v.33 no.4
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• pp.235-247
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• 2024

A total of 64 individuals of Acanthogobius flavimanus, which inhabit the coast of Korea, were collected from 8 regions from July to August 2023. A haplotype network and a phylogenetic tree were created. The genomic DNA of the target fish species was compared and analyzed with the genomic DNA of four regions in Japan downloaded from the National Center for Biotechnology Information (NCBI). In the haplotype network of Acanthogoboius flavimanus, Eocheong-do (EC) and Goseong (MAJ) exhibited low genetic similarity with other regions in Korea and Japan. The Phylogenetic tree showed that the population of MAJ exhibited differences in genetic structure compared to populations in other regions of Korea and Japan, indicating a distant relationship. Most marine organisms are known to migrate and spread via ocean currents, which is the most crucial factor promoting gene flow through larvae between populations. The haplotype of Acanthogobius flavimanus in MAJ differs from the haplotypes in Korea and Japan. The population in MAJ is believed to have limited genetic exchange due to the North Korea Cold Currents. We identified haplotype patterns based on the geographical distribution of Acanthogobius flavimanus off the coast of Korea and inferred that ocean currents have some influence on genetic distances.

• Oncology Letters
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• v.17 no.1
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• pp.379-387
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• 2019

Lymphocyte antigen 6 family member K (LY6K) is upregulated in a number of types of cancer and promotes tumor cell proliferation and metastasis. In addition, LY6K is involved in tamoxifen resistance in breast cancer. However, the in vivo molecular mechanism of LY6K has not yet been investigated. In the present study, transgenic mice overexpressing human LY6K (hLY6K) were generated using the pMAMneo vector, and the effect of LY6K upregulation in vivo was investigated. A total of 4 transgenic mice were generated, and the gene copy number was examined using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). RT-qPCR demonstrated that mRNA of hLY6K was overexpressed in the thymus and spleen of the transgenic mice compared with wild-type mice. Flow cytometric analysis demonstrated that the proportions of B and T cells in the spleen were similar in wild-type and transgenic mice; however, the proportion of thymic mature T cells decreased in the transgenic mice, while there was an increase in the proportion of naïve T cells. These findings suggest that the overexpression of LY6K suppresses T cell development, and that LY6K is a potential therapeutic target for cancer.

• Journal of Life Science
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• v.17 no.5 s.85
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• pp.678-686
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• 2007

Human mesenchymal stem cells(hMSC), that have been reported to be present in bone marrow, adipose tissues, dermis, muscles and peripheral blood, have the potential to differentiate along different lineages including those forming bone, cartilage, fat, muscle and neuron. Therefore, hMSC are attractive candidates for cell and gene therapy. The optimal conditions for hMSC expansion require medium supplemented with fetal bovine serum(FBS). Some forms of cell therapy will involve multiple doses, raising a concern over immunological reactions caused by medium-derived FBS proteins. Previously, we have shown that hADSC can be cultured in human serum(HS) during their isolation and expansion, and that they maintain their proliferative capacity and ability for multilineage differentiation and promote engraftment of peripheral blood-derived CD34 cells mobilized from bone marrow in NOD/SCID mice. In this study we determined whether hADSC grown in HS maintain surface markers expression similar with cells grown in FBS during culture expansion and compared gene expression profile by Affymetrix microarray. Flow cytometry analysis showed that HLA-DR, CD117, CD29 and CD44 expression in HS-cultured hADSC during culture expansion were similar with that in FBS-cultured cells. However, the gene expression profile in HS-cultured hADSC was significantly different from that in FBS-cultured cells. Therefore, these data indicated that HS-cultured hADSC should be used in vivo animal study of hADSC transplantation for direct extrapolation of preclinical data into clinical application.