• 한국생물공학회:학술대회논문집
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• 2000.04a
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• pp.600-603
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• 2000

DNA chip containing 207 E. coli genes related to important metabolisms such as (TCA cycle, glycolysis, fermentation and etc) were used to carry out a comprehensive investigation of the change in metabolism and physiology during high cell density culture of E. coli by fed-batch cultivation.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.442-445
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• 2014

In this work, we studied the interactions of the complexes of a DNA base inserted between graphene layers through density functional theory (DFT) calculations. We find that there exists the negligible energy barrier as well as robust and distinguishable electronic fingerprints during the translocation of the DNA bases. Our result shows that the bilayer graphene can be a possible candidate for the future-generation of DNA sequencing device platform.

• Macromolecular Research
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• v.15 no.6
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• pp.581-586
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• 2007

Cast DNA/polyethyleneimine (PEI) blend membranes containing different amounts of DNA were prepared using acid-base interaction and characterized with the aim of understanding the polymer electrolyte membrane properties. Two different molecular weights of PEI were used to provide the mechanical strength, while DNA, a polyelectrolyte, was used for the proton transport channel. Proton conductivity was observed for the DNA/PEI membrane and reached approximately $3.0{\times}10^{-3}S/cm$ for a DNA loading of 16 wt% at $80^{\circ}C$. The proton transport phenomena of the DNA/PEI complexes were investigated in terms of the complexation energy using the density functional theory method. In the case of DNA/PEI, a cisoid-type complex was more favorable for both the formation of the complex and the dissociation of hydrogen from the phosphate. Since the main requirement for proton transport in the polymer matrix is to dissociate the hydrogen from its ionic sites, this suggests the significant role played by the basicity of the matrix.

• Journal of Life Science
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• v.14 no.2
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• pp.255-262
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• 2004

We applied nuclear DNA content stained with 4'-6'-diamidino-2-phenylindole (DAPI) and total protein concentration to predict the existence of Cochlodinium polykrikoides before huge blooms occurred, based on a short-term survey at sites in the South Sea. Fluctuations in environmental conditions and nutrients (nitrate, nitrite, and phosphate) were of a similar range, regardless of sampling sites or early and middle field observations. However, C. polykrikoides abundance was significantly different depending on the station, with a higher cell density of 34, 62, and 57 cells L$^{-1}$ at Stn C2, C5, and C6, respectively than what was found in early August, 2000. In mid August, 2000, the highest cell density of 547 cells L$^{-1}$ at Stn C3 was observed. The relationship between C. polykrikoides abundance, DAPI-stained DNA content, and total protein concentration was a positive correlation coefficient, in particular a higher positive correlation was exposed to even a smaller abundance of C. polykrikoides. These results suggest that DNA stained by DAPI and total protein concentration could play an important index in easily predicting the presence of C. polykrikoides before blooms.

• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3719-3726
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• 2012

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

• Clinical and Experimental Reproductive Medicine
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• v.44 no.4
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• pp.201-206
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• 2017

Objective: The aim of this study was to compare the efficacy of swim-up and density gradient centrifugation (DGC) for reducing the amount of sperm with fragmented DNA, sex chromosome aneuploidy, and abnormal chromatin structure. Methods: Semen samples were obtained from 18 healthy male partners who attended infertility clinics for infertility investigations and were processed with swim-up and DGC. The percentages of sperm cells with fragmented DNA measured by the sperm chromatin dispersion test, normal sex chromosomes assessed by fluorescence in situ hybridization, and abnormal chromatin structure identified by toluidine blue staining were examined. Results: The percentage of sperm cells with fragmented DNA was significantly lower in the swim-up fraction (9.7%, p= 0.001) than in the unprocessed fraction (27.0%), but not in the DGC fraction (27.8%, p= 0.098). The percentage of sperm cells with normal X or Y chromosomes was comparable in the three fractions. The percentage of sperm cells with abnormal chromatin structure significantly decreased after DGC (from 15.7% to 10.3%, p= 0.002). The swim-up method also tended to reduce the percentage of sperm cells with abnormal chromatin structure, but the difference was not significant (from 15.7% to 11.6%, p= 0.316). Conclusion: The swim-up method is superior for enriching genetically competent sperm.

• Korean Journal of Ecology and Environment
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• v.56 no.1
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• pp.36-44
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• 2023

Environmental DNA (eDNA) can exist in both intracellular and extracellular forms in natural ecosystems. When targeting harmful cyanobacteria, extracellular eDNA indicates the presence of traces of cyanobacteria, while intracellular eDNA indicates the potential for cyanobacteria to occur. However, identifying the "actual" potential for harmful cyanobacteria to occur is difficult using the existing sediment eDNA analysis method, which uses silica beads and cannot distinguish between these two forms of eDNA. This study analyzes the applicability of a density gradient centrifugation method (Ludox method) that can selectively analyze intracellular eDNA in sediment to overcome the limitations of conventional sediment eDNA analysis. PCR was used to amplify the extracted eDNA based on the two different methods, and the relative amount of gene amplification was compared using electrophoresis and Image J application. While the conventional bead beating method uses sediment as it is to extract eDNA, it is unknown whether the mic gene amplified from eDNA exists in the cyanobacterial cell or only outside of the cell. However, since the Ludox method concentrates the intracellular eDNA of the sediment through filtration and density gradient, only the mic gene present in the cyanobacteria cells could be amplified. Furthermore, the bead beating method can analyze up to 1 g of sediment at a time, whereas the Ludox method can analyze 5 g to 30 g at a time. This gram of sediments makes it possible to search for even a small amount of mic gene that cannot be searched by conventional bead beating method. In this study, the Ludox method secured sufficient intracellular gene concentration and clearly distinguished intracellular and extracellular eDNA, enabling more accurate and detailed potential analysis. By using the Ludox method for environmental RNA expression and next-generation sequencing (NGS) of harmful cyanobacteria in the sediment, it will be possible to analyze the potential more realistically.

• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.845-848
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• 2001

For understanding physiology and metabolism under various culture conditions, combined analysis of transcriptome and proteome is attractable way. We have manufactured DNA microarray containing 2,850 genes including all functionally known and putative ones. In this study, we report analysis of transcriptome and proteome during the high cell density culture of E. coli by using DNA microarray and 2-DE. Fed-batch fermentation of E. coli was carried out by exponential feeding of nutrients until the maximum cell density reached 74 g dry cell weight/L (g DCW/L). Changes in transcriptome and proteome during the HCDC are analyzed qualitatively and quantitatively to provide their physiological and metabolic meanings.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 2003.10a
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• pp.173-173
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• 2003

With the introduction of DNA microarrays, a high throughput analysis of gene expression is now possible as a replacement to the traditional time-consuming Southern-blot analysis. This cDNA microarray should be ahighly favored technology in the area of molecular toxicology or analysis of environmental stresses.In this study, therefore, we developed a novel cDNA microarray for analyzing stress-specific responses in japanese Medaka fish. In the design and fabrication of this stress specific functional cDNA microarray, 123 different genes in Medaka fish were selected from eighteen different stress responsive groups and spotted on a 25${\times}$75 mm glass surface. After exposure of the fish to bisphenol A which is the one of the well-known endocrine disrupting chemicals (EDCs), over 1 or 10 days, the responses of the DNA chip were found to show distinct expression patterns according to the mode of toxic actions from environmental toxicants. As a results, they showed specific gene expression pattern to bisphenol A, additionally, the chemical spesific biomarkers could be suggested based on the chip analysis data. Therefore, this chip can be used to monitor stress responses of unknown and/or known toxic chemicals using Medaka fish and may be used for the further development of biomarkers by utilizing the gene expression patterns for known contaminants.

• Korean Journal of Poultry Science
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• v.41 no.2
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• pp.115-125
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• 2014

With Single Comb White Leghorn (WL) and Korean Native Chicken (KNC) breeds, we compared the stress response with chicken breeds that were subjected to a high stocking density. Stress response was analyzed by the quantity of telomeric DNA, the rate of DNA damage and the expression levels of heat shock proteins (HSPs) and hydroxyl-3-methyl-glutaryl coenzyme A reductase (HMGCR) genes on tissues and blood. The telomere length and telomere shortening rates were analyzed by quantitative fluorescence in situ hybridization on the nuclei of lymphocytes and tissues. The DNA damage rate of lymphocytes was quantified by the comet assay. The expression levels of HSP70, HSP90-${\alpha}$, HSP90-${\beta}$ and HMGCR genes were measured by quantitative real-time polymerase chain reaction in lymphocytes. There was no significant difference between KNC and WL in body weight, weight gain, telomere shortening rate and DNA damage rate. However, the growth rate significantly decreased in chickens raised under high stocking density conditions, as compared to the control group. The telomere-shortening rate, DNA damage and HSPs expression of the lymphocytes were significantly higher in the high stocking density group than the control. The stress condition and breeds had a significant effect on the expressions of HSP70, HSP90-${\alpha}$ and HSP90-${\beta}$ in lymphocytes, except HMGCR. The stress response of WL was higher than that of KNC, as analyzed to the expression of HSP70 and HSP90-${\alpha}$. Therefore, we concluded that the chickens which were exposed to a high stocking density had increased the individual physiological stress response regardless of breeds, and White Leghorns are more susceptible to stress condition than Korean Native Chickens.