• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.5
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• pp.455-461
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• 2006

In this study, we have described a method for the fabrication of a protein chip on silicon substrate using hydrophobic thin film and microfluidic channels, for the simultaneous detection of multiple targets in samples. The use of hydrophobic thin film provides for a physical, chemical, and biological barrier for protein patterning. The microfluidic channels create four protein patterned strips on the silicon surfaces with a high signal-to-noise ratio. The feasibility of the protein chips was determined in order to discriminate between each protein interaction in a mixture sample that included biotin, ovalbumin, hepatitis B antigen, and hepatitis C antigen. In the fabrication of the multiplexed assay system, the utilization of the hydrophobic thin film and the microfluidic networks constitutes a more convenient method for the development of biosensors or biochips. This technique may be applicable to the simultaneous evaluation of multiple protein-protein interactions.

• Journal of the Korea Organic Resources Recycling Association
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• v.16 no.3
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• pp.75-82
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• 2008

Two UASB reactors were operated to investigate the effect of high concentration of sulfate on anaerobic digestion of propionate using an upflow anaerobic sludge blanket (UASB) reactor. An organic loading rate of $1.2kg\;COD/m^3{\cdot}d$ and a hydraulic retention time of 1.6 d were maintained during this study. In the absence of sulfate, the UASB reactor achieved about 95% removal of chemical oxygen demand whereas in the presence of $2,000\;SO_4^{2-}mg/L$, the COD removal rate decreased to 83% due probably to the inhibition of dissolved sulfide inhibition. Interactions between the methane producing bacteria (MPB) and sulfate reducing bacteria (SRB) were measured to investigate the competition between MPB and SRB. The MPB consumed average 58% of the available electron donors at $COD/SO_4^{2-}$ ratio of 1. Propionate was consumed mainly by SRB, converting sulfate into sulfide and suppressing the methane production. The specific methanogenic activity (SMA) using acetate and propionate increased as microorganism acclimated to the substrate.

• Journal of the Korean Vacuum Society
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• v.14 no.3
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• pp.143-146
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• 2005

A new method of x-ray photon correlation spectroscopy (XPCS) using coherent x-rays is developed recently for probing the dynamics of surface height fluctuations as a function of lateral length scale. This emerging technique applies the principles of dynamic light scattering in the x-ray regime. The short wavelength and slow time scales characteristic of XPCS extend the phase space accessible to scattering studies beyond some restrictions by light and neutron. In this paper, we demonstrate XPCS to study the dynamics of surface fluctuations in thin supported polymer films. We present experimental verification of the theoretical predictions for the wave vector and temperature dependence of the capillary wave relaxation times for the supported polymer films at melt for the film thicknesses thicker than 4 times of the radius of gyration of polymer. We observed a deviation from the conventional capillary wave predictions in thinner films. The analysis will be discussed in terms of surface tension, viscosity and effective interactions with the substrate.

• Molecules and Cells
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• v.38 no.5
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• pp.402-408
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• 2015

Protein O-GlcNAcylation, dictated by cellular UDP-N-acetylglucosamine (UDP-GlcNAc) levels, plays a crucial role in posttranslational modifications. The enzyme GlcNAc kinase (NAGK, E.C. 2.7.1.59) catalyzes the formation of GlcNAc-6-phosphate, which is a major substrate for the biosynthesis of UDP-GlcNAc. Recent studies have revealed the expression of NAGK in different types of cells especially in neuronal dendrites. Here, by immunocytochemistry (ICC) and immunonucleochemistry (INC) of cultured rat hippocampal neurons, HEK293T and GT1-7 cells, we have showed that NAGK immuno-reactive punctae being present in the nucleoplasm colocalized with small nuclear ribonucleoprotein-associated protein N (snRNPN) and p54NRB, which are speckle and paraspeckle markers, respectively. Furthermore, NAGK IR cluster was also found to be colocalized with GTF2H5 (general transcription factor IIH, polypeptide 5) immuno reactive punctae. In addition, relative localization to the ring of nuclear lamin matrix and to GlcNAc, which is highly enriched in nuclear pore complexes, showed that NAGK surrounds the nucleus at the cytoplasmic face of the nuclear outer membrane. By in situ proximity ligation assay (PLA) we confirmed the colocalization of NAGK with snRNPN in the nucleus and in dendrites, while we also verified the interactions of NAGK with p54NRB, and with GTF2H5 in the nucleus. These associations between NAGK with speckle, paraspeckle and general transcription factor suggest its regulatory roles in gene expression.

• Molecular & Cellular Toxicology
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• v.1 no.4
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• pp.237-247
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• 2005

Several features of the implant surface, such as roughness, topography, and composition play a relevant role in implant integration with bone. This study was conducted in order to determine the effects of various thin layer hydroxyapatite (HA) coatings on anodized Ti surfaces on the biological responses of a human osteoblast-like cell line (MG63). MG63 cells were cultured on A (100 nm HA coating on anodized surface), B (500-700 nm HA coating on anodized surface), C ($1{\mu}m$ HA coating on anodized surface), and control (non HA coating on anodized surface) Ti. The morphology of these cells was assessed by SEM. The cDNAs prepared from the total RNAs of the MG63 were hybridized into a human cDNA microarray (1,152 elements). The appearances of the surfaces observed by SEM were different on each of the four dental substrate types. MG63 cells cultured on A, C and control exhibited cell-matrix interactions. It was B surface showing cell-cell interaction. In the expression of several genes were up-, and down-regulated on the different surfaces. The attachment and expression of key osteogenic regulatory genes were enhanced by the surface morphology of the dental materials used.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.551-559
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• 2005

The recent rapid increase in genomic data related to many microorganisms and the development of computational tools to accurately analyze large amounts of data have enabled us to design several kinds of simulation approaches for the complex behaviors of cells. Among these approaches, dFBA (dynamic flux balance analysis), which utilizes FBA, differential equations, and regulatory events, has correctly predicted cellular behaviors under given environmental conditions. However, until now, dFBA has centered on substrate concentration, cell growth, and gene on/off, but a detailed hierarchical structure of a regulatory network has not been taken into account. The use of Boolean rules for regulatory events in dFBA has limited the representation of interactions between specific regulatory proteins and genes and the whole transcriptional regulation mechanism with environmental change. In this paper, we adopted the operon as the basic structure, constructed a hierarchical structure for a regulatory network with defined fundamental symbols, and introduced a weight between symbols in order to solve the above problems. Finally, the total control mechanism of regulatory elements (operons, genes, effectors, etc.) with time was simulated through the linkage of dFBA with regulatory network modeling. The lac operon, trp operon, and tna operon in the central metabolic network of E. coli were chosen as the basic models for control patterns. The suggested modeling method in this study can be adopted as a basic framework to describe other transcriptional regulations, and provide biologists and engineers with useful information on transcriptional regulation mechanisms under extracellular environmental change.

• Journal of Integrative Natural Science
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• v.4 no.4
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• pp.273-277
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• 2011

It's a threat for the public health that H1N1 (Influenza virus A) causes disease and transmits among humans. WHO (world health organization) declared that the infections caused by the new strain had reached pandemic proportions. The approved neuraminidase inhibitors (Zanamivir and Oseltamivir) and related investigative drug (BCX-1812) are potent, specific inhibitors of influenza A and B viruses. These drugs are highly effective to prevent influenza A and B infections. Early therapeutic use reduces illness duration and respiratory complications. Recently, we found one of the potent inhibitor of erystagallin A ($IC_{50}$ of 2.04 ${\mu}M$) for neuraminidase target, this inhibitor shows most similar structure to its natural substrate, sialic acid. Therefore, we chose 1l7f to get the receptor structure for docking study among many crystal structures. A docking study has been performed in Surflex-Dock module in SYBYL 8.1. In the present study, we attempt to compare the docking studies of pterocarpin and erystagallin A with neuraminidase receptor structure. In the previous report, the methoxy group of pterocarpin had H-bonding with Arg residues. The present docking results for erystagallin A showed the backbone of hydroxyl group shows significant H-bonding interactions with Arg152 and Arg292. The results showed that erystagallin A interacts more favorably with distinctive binding site rather than original active site. Therefore, we tried to reveal plausible binding mode and important amino acid for this inhibitor using docking and site id search calculations of Sybyl. The results obtained from this work may be utilized to design novel inhibitors for neuraminidase.

• Korean Journal of Materials Research
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• v.23 no.10
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• pp.580-585
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• 2013

To observe the formation of defects at the interface between an oxide semiconductor and $SiO_2$, ZnO was prepared on $SiO_2$ with various oxygen gas flow rates by RF magnetron sputtering deposition. The crystallinity of ZnO depends on the characteristic of the surface of the substrate. The crystallinity of ZnO on a Si wafer increased due to the activation of ionic interactions after an annealing process, whereas that of ZnO on $SiO_2$ changed due to the various types of defects which had formed as a result of the deposition conditions and the annealing process. To observe the chemical shift to understand of defect deformations at the interface between the ZnO and $SiO_2$, the O 1s electron spectra were convoluted into three sub-peaks by a Gaussian fitting. The O 1s electron spectra consisted of three peaks as metal oxygen (at 530.5 eV), $O^{2-}$ ions in an oxygen-deficient region (at 531.66 eV) and OH bonding (at 532.5 eV). In view of the crystallinity from the peak (103) in the XRD pattern, the metal oxygen increased with a decrease in the crystallinity. However, the low FWHM (full width at half maximum) at the (103) plane caused by the high crystallinity depended on the increment of the oxygen vacancies at 531.66 eV due to the generation of $O^{2-}$ ions in the oxygen-deficient region formed by thermal activation energy.

• Journal of Ginseng Research
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• v.42 no.3
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• pp.370-378
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• 2018

Background: Ginseng has been the subject of many experimental and clinical studies to uncover the diverse biological activities of its constituent compounds. It is a traditional medicine that has been used for its immunostimulatory, antithrombotic, antioxidative, anti-inflammatory, and anticancer effects. Ginseng may interact with concomitant medications and alter metabolism and/or drug transport, which may alter the known efficacy and safety of a drug; thus, the role of ginseng may be controversial when taken with other medications. Methods: We extensively assessed the effects of Korean Red Ginseng (KRG) in rats on the expression of enzymes responsible for drug metabolism [cytochrome p450 (CYP)] and transporters [multiple drug resistance (MDR) and organic anion transporter (OAT)] in vitro and on the pharmacokinetics of two probe drugs, midazolam and fexofenadine, after a 2-wk repeated administration of KRG at different doses. Results: The results showed that 30 mg/kg KRG significantly increased the expression level of CYP3A11 protein in the liver and 100 mg/kg KRG increased both the mRNA and protein expression of OAT1 in the kidney. Additionally, KRG significantly increased the mRNA and protein expression of OAT1, OAT3, and MDR1 in the liver. Although there were no significant changes in the metabolism of midazolam to its major metabolite, 1'-hydroxymidazolam, KRG significantly decreased the systemic exposure of fexofenadine in a dose-dependent manner. Conclusion: Because KRG is used as a health supplement, there is a risk of KRG overdose; thus, a clinical trial of high doses would be useful. The use of KRG in combination with P-glycoprotein substrate drugs should also be carefully monitored.

• Animal cells and systems
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• v.14 no.2
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• pp.99-114
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• 2010

With the consensus sequence information of the serum glucocorticoid-induced protein kinase-1 (SGK1) phosphorylation site {R-X-R-X-X-(S/T)$\Phi$; where $\Phi$ is any hydrophobic amino acid}, we noticed that the transient receptor potential vanilloid 4 (TRPV4) cation channel, a member of the TRP vanilloid subfamily, harbors the putative SGK1 phosphorylation site (on its Ser 824). We have demonstrated that TRPV4 is an SGK1 authentic substrate protein, with the phosphorylation on the Ser 824 of TRPV4 by SGK1. Further, using TRPV4 mutants (S824A and S824D), we noted that the modification of the Ser 824 activates its $Ca^{2+}$ entry, and sensitizes the TRPV4 channel to 4-$\alpha$-phorbol 12,13-didecanoate (4-${\alpha}PDD$) or heat, simultaneously enhancing its active state. Additionally, we determined that the modification of the Ser 824 controls both its plasma membrane localization and its protein interactions with calmodulin. Thus, we have proposed herein that phosphorylation on the Ser 824 of TRPV4 is one of the control points for the regulation of its functions.