• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.219-237
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• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• Molecules and Cells
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• v.23 no.2
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• pp.220-227
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• 2007

The development of suitable genetic markers would be useful for defining species and delineating the species boundaries of morphologically indistinguishable sponges. In this study, genetic variation in the sequences of nuclear rDNA and the mitochondrial cytochrome c oxidase subunit 1 and 3 (CO1 and CO3) regions were compared in morphologically indistinguishable Korean Halichondriidae sponges in order to determine the most suitable species-specific molecular marker region. The maximal congeneric nucleotide divergences of Halichondriidae sponges in CO1 and CO3 are similar to those found among anthozoan cnidarians, but they are 2- to 8-fold lower than those found among genera of other triploblastic metazoans. Ribosomal internal transcribed spacer regions (ITS: ITS1 + ITS2) showed higher congeneric variation (17.28% in ITS1 and 10.29% in ITS2) than those of CO1 and CO3. Use of the guidelines for species thresholds suggested in the recent literature indicates that the mtDNA regions are not appropriate for use as species-specific DNA markers for the Halichondriidae sponges, whereas the rDNA ITS regions are suitable because ITS exhibits a low level of intraspecific variation and a relatively high level of interspecific variation. In addition, to test the reliability of the ITS regions for identifying Halichondriidae sponges by PCR, a species-specific multiplex PCR primer set was developed.

• Journal of Life Science
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• v.14 no.4
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• pp.614-619
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• 2004

This study was undertaken to investigate the different responses of cultured plant cells to paraquat treatment and nucleus-DNA damage in relation to enzyme activity of superoxide dismutase (SOD). Furthermore, this study was also carried out to understand the antioxidative mechanism of plant cells to environmental stress. We selected two different species of plant cultured cells, Ipomoea batatas as high-SOD species and Lonicera japonica as low-SOD species. The total activity and specific activity of SOD in a chlorophyllous cell of I. batatas were 3,736 unit/gㆍfresh weight and 547 unit/mgㆍprotein, respectively, and those in L. japonica were 23 unit/gㆍfresh weight and 13 unit/mgㆍprotein, respectively SOD activity in chlorophyllous I. batatas cells reached its maximum level at 10 to 15 days after subculture, whereas that in L. japonica remained at a very low SOD level during the whole period of subculture. In comparison to L. japonica, I. batatas, a high-SOD species, showed high tolerance to paraquat 10 and 50 mg/l treatment in terms of cell viability and electrolyte leakage. Based on the result of comet assay, the nucleus-DNA damage of two species by paraquat 50 mg/l treatment was not significantly different. However, I. batatas cells repaired their damaged DNA more effectively than the cells of the low-SOD species, L. japonica.

• The Journal of the Korea Contents Association
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• v.13 no.8
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• pp.466-473
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• 2013

Gene expression is regulated by a wide range of mechanisms at the DNA sequence level. In addition, gene expression is also regulated by epigenetic mechanisms through DNA methylation, histone modification, and ncRNA. To understand the regulation of gene expression at the epigenetic level, we constructed aging related gene database and analyzed epigenetic properties that are focused on DNA methylation. The DNA methylation of promoter or upstream region of the genes induces to repress the gene expression. We compared and analyzed distribution between whole human genes and aging related genes in the epigenetic properties such as CGI distribution, methylation motif pattern, and TFBS (transcription factor binding site) distribution. In contrast to methylation motif pattern, CGI and TFBS distributions are positively correlated with epigenetic regulation of aging related gene expression. In this study, the epigenetic data about DNA methylation of the aging genes will provide us to understand phenomena of the aging and epigenetic mechanism for regulation of aging related genes.

• The Korean Journal of Zoology
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• v.33 no.3
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• pp.365-372
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• 1990

For the effort to produce transgenic amphibians, a plasmid DNA sequence (cytoplasmic actin promoter-linked bacterial $\beta$-galactosidase gene) was microinjected into fertilized Xenopus eggs. It appeared that the injection of 20 nl solution containing 1-2 ng of DNA was not toxic, but over 4 ng was toxic to embryonic development. The translational product of $\beta$-gal gene ($\beta$-galactosidase) had enzyme activity in all three germ layers of the embryo. Expression of the injected $\beta$-gal genes was first detected at mid-gastrula stage, and the activity persisted up to stage 43 (feeding tadpole) with decreased level of retention. However, the level of the expression was various among the injected individuals as well as each experiment. That is, $\beta$-galactosidase activities did not appear in all cells, instead a localized distribution pattern. Although other possibilities could not be omitted, this mosaic distribution of gene expression seemed to arise from unequal partition of the injected DNA into each blastomere during early cleavage.

• Molecules and Cells
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• v.46 no.4
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• pp.200-205
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• 2023

DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a member of the phosphatidylinositol 3-kinase-related kinase family is a well-known player in repairing DNA double-strand break through non-homologous end joining pathway. This mechanism has allowed us to understand its critical role in T and B cell development through V(D)J recombination and class switch recombination, respectively. We have also learned that the defects in these mechanisms lead to the severely combined immunodeficiency (SCID). Here we highlight some of the latest evidence where DNA-PKcs has been shown to localize not only in the nucleus but also in the cytoplasm, phosphorylating various proteins involved in cellular metabolism and cytokine production. While it is an exciting time to unveil novel functions of DNA-PKcs, one should carefully choose experimental models to study DNA-PKcs as the experimental evidence has been shown to differ between cells of defective DNA-PKcs and those of DNA-PKcs knockout. Moreover, while there are several DNA-PK inhibitors currently being evaluated in the clinical trials in an attempt to increase the efficacy of radiotherapy or chemotherapy, multiple functions and subcellular localization of DNA-PKcs in various types of cells may further complicate the effects at the cellular and organismal level.

• 제어로봇시스템학회:학술대회논문집
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• 2004.08a
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• pp.190-195
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• 2004

We propose a pattern classification algorithm using self-nonself discrimination principle of immune cells and apply it to DNA pattern classification problem. Pattern classification problem in bioinformatics is very important and frequent one. In this paper, we propose a classification algorithm based on the negative selection of the immune system to classify DNA patterns. The negative selection is the process to determine an antigenic receptor that recognize antigens, nonself cells. The immune cells use this antigen receptor to judge whether a self or not. If one composes ${\eta}$ groups of antigenic receptor for ${\eta}$ different patterns, these receptor groups can classify into ${\eta}$ patterns. We propose a pattern classification algorithm based on the negative selection in nucleotide base level and amino acid level. Also to show the validity of our algorithm, experimental results of RNA group classification are presented.

• KSBB Journal
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• v.6 no.4
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• pp.385-388
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• 1991

Embryogenic cell suspension cultures of B. striata were established as transferred selected embryogenic callus into liquid medium. Protoplasts isolated from embryogenic cell suspensions were electroporated in buffered solutions containing plasmid DNA of pBI121. Transient GUS (beta-glucuronidase) activity measurement and selection for kanamycin resistent showed that expression of foreign genes and stable transformation were achieved. GUS transient gene expression was increased by increasing DNA concentration of pBI121 plasmid and affected by the level of the applied voltage. An optimal level of GUS activity was obtained after electroporation with a pulse of 200-300 voltage/1180 uF. Protoplast viability was up to the 80% at the optimal voltage.

• BMB Reports
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• v.31 no.3
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• pp.249-253
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• 1998

The developmental regulation of Caenorhabditis elegans DNA topoisomerase I expression was examined using synchronized Caenorhabditis elegans cultures. Variations of the relative mRNA and protein levels of the enzyme during their development were measured by Northern and Western analyses, respectively. The mRNA level was the highest at the embryonic stage, decreasing rapidly to the one tenth level at the L1 stage, and then increasing by a few fold at the L4 and young adult stages. The protein level was the highest at the L1 stage, with gradual decreasing at the following stages until it showed a slight increase at the young adult stage. Based on our results of the expressional regulation, the possible roles of DNA topoisomerase I in the development of C. elegans are discussed.

• Microbiology and Biotechnology Letters
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• v.18 no.4
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• pp.406-410
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• 1990

The influence of glucose concentration on cell growth rate and on the expression level of the strong promoter obtained from alkali-tolerant Bacillus sp. YA-14 chromosomal DNA was studied. In fed-batch culture, the promoter activity could be maximized by maintaining a very low level of glucose concentration in the broth and glucose consumption rate below 1.08g/g cell-h. The induction of the promoter was possible by addition of sporulation medium after the cell was grown in growth medium with only low level of CAT activity.