• Bulletin of the Korean Chemical Society
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• v.14 no.4
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• pp.491-496
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• 1993

A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

• Bulletin of the Korean Chemical Society
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• v.20 no.10
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• pp.1159-1164
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• 1999

The study investigated the effect of carrier composition (ionic strength and pH) on the retention of various proteins in flow field-flow fractionation (Flow FFF) as well as the conformational change of Bovine Serum Albumin (BSA) with urea concentration, storage time and temperature. The study found that the retention of protein in Flow FFF increased with the ionic strength of the carrier liquid. Most proteins were well solubilized at pH = 7-8. The hydrodynamic diameters obtained from Flow FFF retention data agree well with theoretical values. The retention increased and the peak shape became distorted at extreme pH conditions of the carrier solution. The selected carrier composition for comparison between the literature value of proteins was 0.05 M tris buffer solution with a pH of 8. Storing BSA at 4 ±2℃ over a period of three months resulted in slow dimerization. Also, in case of the storage of BSA at 37 ±5℃ for one week, the retention of both BSA monomer and dimer increased with the urea concentration. Finally, the structural composition of specific enzymes: malonyl-CoA decarboxylase (MCDC) and malonyl-CoA synthesis (MCS) was determined by using Flow FFF at specific carrier solutions. The molecular weight of the natural MCDC was determined to be 208 kDa, which means it is a homotetramer, while that of the MCS was determined to be 47 kDa, which means it is a monomer.

• The Korean Journal of Oral and Maxillofacial Pathology
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• v.41 no.1
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• pp.9-16
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• 2017

Porphyromonas gingivalis is a gram-negative bacteria of rod shape, and grown in an anerobic condition. It colonizes in subgingival crevice and is known as a major pathogen causing chronic periodontitis. It possesses an invasive property and replicative potential within various cell types, presumably playing an important role in modulating biological behaviors of oral cancer. However, the pathophysiology of P. gingivalis in the malignant transformation of oral cancer has not been fully understood. In this study, we aimed to investigate molecular changes of oral squamous cell carcinoma cells induced by repetitive P. gingivalis infection that clinically resembles chronic periodontitis.

• Molecules and Cells
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• v.42 no.7
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• pp.530-545
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• 2019

Tumor cells can vary epigenetically during ionizing irradiation (IR) treatment. These epigenetic variegations can influence IR response and shape tumor aggressiveness. However, epigenetic disturbance of histones after IR, implicating in IR responsiveness, has been elusive. Here, we investigate whether altered histone modification after IR can influence radiation responsiveness. The oncogenic CXCL12 mRNA and protein were more highly expressed in residual cancer cells from a hepatoma heterotopic murine tumor microenvironment and coculture of human hepatoma Huh7 and normal IMR90 cells after radiation. H3K4 methylation was also enriched and H3K9 methylation was decreased at its promoter region. Accordingly, invasiveness and the subpopulation of aggressive $CD133^+/CD24^-$ cells increased after IR. Histone demethylase inhibitor IOX1 attenuated CXCL12 expression and the malignant subpopulation, suggesting that responses to IR can be partially mediated via histone modifications. Taken together, radiation-induced histone alterations at the CXCL12 promoter in hepatoma cells are linked to CXCL12 upregulation and increased aggressiveness in the tumor microenvironment.

• The Korean Journal of Mycology
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• v.47 no.2
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• pp.125-130
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• 2019

A fungal isolate, designated KNU-JJ-1824, was isolated from a soil sample collected from a field on Jeju, Korea. Colonies of the isolates cultured on PDA, MEA and CMAD for 14 days grew to diameters of 49~51 mm, 60~63 mm, and 47~50 mm, respectively. The colonies of this fungal isolate were dark green in color on both sides, and had irregular margins on the PDA media. Mycelia submerged and exhibited clear lines from the center to the edge on MEA media. On CMAD media, they were dark brown to greenish-brown, with narrow white margins. The shape of the conidia was guttulate, fusiform or clavate, and $1.9{\sim}3.4{\times}6.5{\sim}10.2{\mu}m$ in size. A molecular phylogenetic tree was constructed using dataset from small subunit (SSU) rDNA and the internal transcribed spacer (ITS) regions, and the isolate was found to cluster with Scleroconidioma sphagnicola UAMH 9731. Based on the results of the phylogenetic tree analysis and the cultural and morphological characteristics, the isolate was identified as Scleroconidioma sphagnicola. We report S. sphagnicola for the first time in Korea.

• Parasites, Hosts and Diseases
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• v.59 no.3
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• pp.311-317
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• 2021

The present study reports a rare case of Taenia saginata infection, which was initially diagnosed as acute cholecystitis in a Tibetan patient at the Qinghai-Tibetan Plateau pastoral area, China. A 45-year-old female was initially diagnosed with acute cholecystitis at a hospital in China. She had a slight fever, weight loss and constipation and complained of pain in the upper abdomen and left back areas. Increase of monocyte, eosinophil and basophil levels were shown. Taenia sp. eggs were detected in a fecal examination. An adult tapeworm approximately 146 cm in length, whitish-yellow color, was collected from the patient after treatment with traditional Chinese medicine. The adult tapeworm had a scolex and proglottids with genital pores. The scolex was rectangular shape with 4 suckers and rostellum without hooklet. The cox1 gene sequence shared 99.5-99.8% homology with that of T. saginata from other regions in China. The patient was diagnosed finally infected with T. saginata by morphological and molecular charateristics.

• Geomechanics and Engineering
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• v.27 no.6
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• pp.615-626
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• 2021

The main objective of this study is to present a fast and reliable approach to predict the swelling potential of clay-bearing rocks. Investigations showed that there is a good correlation between the swelling potential of a rock and its desire to absorb water due to its clay content which could be measured using the "Contact Angle" test as one of the most common ways to determine the wettability. In this test, the angle between a water drop and the flat rock surface on which it rests is measured. The present method is very fast and returns repeatable results and requires minimal sample preparation. Only having a saw-cut surface of a sample with any shape is all one needs to perform this test. The logic behind this approach is that the swelling potential of a rock is a function of its mineral content and molecular structure, which are not only distributed in the bulk of the sample but also reflected on its surface. Therefore, to evaluate swelling behavior, it is not necessary to wait for a sample to get wet all the way to its "internal structure" (which, due to the low permeability of clay-bearing rocks, is very slow and time-consuming). Instead, one can have a good sense of swelling potential by studying its surface. Parametric studies on the effect of moisture content, porosity, and surface roughness on the contact angle measurements showed that using a saw-cut oven-dried sample is a convenient way to evaluate the swelling potential by this method.

• Korean Journal of Plant Taxonomy
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• v.53 no.3
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• pp.201-212
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• 2023

Parasenecio pentaphylla, a new species of the genus Parasenecio from Mt. Ilwol-san, Ilwol-myeon, Yeongyang-gun, Gyeongsangbuk-do, Korea, is described and illustrated here. In Korea, this species has been recognized as P. adenostyloides, known to be a Japanese endemic species. However, it is clearly distinguished from P. adenostyloides by its involucre shape, the number of phyllaries, the number of florets per capitulum, and the ratio of the tube length to the throat length. A molecular phylogenetic analysis using the Internal Transcribed Spacer region also clearly indicated that P. pentaphyllaria was genetically distinct from P. adenostyloides. Therefore, it is recognized as an independent species, different from P. adenostyloides. The specific epithet "pentaphyllaria" was given based on its characteristic of having five phyllaries.

• BMB Reports
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• v.56 no.7
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• pp.392-397
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• 2023

In this study, recombinant Fc-fused Prostate acid phosphatase (PAP) proteins were produced in transgenic plants. PAP was fused to immunoglobulin (Ig) A and M Fc domain (PAP-IgA Fc and PAP-IgM Fc), which were tagged to the ER retention sequence KDEL to generate PAP-IgA FcK and PAP-IgM FcK. Agrobacterium-mediated transformation was performed to produce transgenic tobacco plants expressing four recombinant proteins. Genomic PCR and RT-PCR analyses confirmed the transgene insertion and mRNA transcription of PAP-IgA Fc, PAP-IgM Fc, PAP-IgA FcK, and PAP-IgM FcK in tobacco plant leaves. Western blot confirmed the expression of PAP-IgA Fc, PAP-IgM Fc, PAP-IgA FcK, and PAP-IgM FcK proteins. SEC-HPLC and Bio-TEM analyses were performed to confirm the size and shape of the plant-derived recombinant PAP-Fc fusion proteins. In mice experiments, the plant-derived IgA and IgM Fc fused proteins induced production of total IgGs including IgG1 against PAP. This result suggests that IgA and IgM Fc fusion can be applied to produce recombinant PAP proteins as a prostate cancer vaccine in plant expression system.

• Journal of The Korean Astronomical Society
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• v.56 no.2
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• pp.149-157
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• 2023

The propagation speed of a circumstellar pattern revealed in the plane of the sky is often assumed to represent the expansion speed of the wind matter ejected from a post-main-sequence star at the center. We point out that the often-adopted isotropic wind assumption and the binary hypothesis as the underlying origin for the circumstellar pattern in the shape of multilayered shells are, however, mutually incompatible. We revisit the hydrodynamic models for spiral-shell patterns induced by the orbital motion of a hypothesized binary, of which one star is losing mass at a high rate. The distributions of transverse wind velocities as a function of position angle in the plane of the sky are explored along viewing directions. The variation of the transverse wind velocity is as large as half the average wind velocity over the entire three dimensional domain in the simulated models investigated in this work. The directional dependence of the wind velocity is indicative of the overall morphology of the circumstellar material, implying that kinematic information is an important ingredient in modeling the snapshot monitoring (often in the optical and near-infrared) or the spectral imaging observations for molecular line emissions.