• International Journal of Oral Biology
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• 제44권1호
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• pp.8-13
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• 2019

Recently, the importance of on-site detection of pathogens has drawn attention in the field of molecular diagnostics. Unlike in a laboratory environment, on-site detection of pathogens is performed under limited resources. In this study, we tried to optimize the experimental conditions for on-site detection of pathogens using a combination of ultra-fast convection polymerase chain reaction (cPCR), which does not require regular electricity, and nucleic acid lateral flow (NALF) immunoassay. Salmonella species was used as the model pathogen. DNA was amplified within 21 minutes (equivalent to 30 cycles of polymerase chain reaction) using ultra-fast cPCR, and the amplified DNA was detected within approximately 5 minutes using NALF immunoassay with nucleic acid detection (NAD) cassettes. In order to avoid false-positive results with NAD cassettes, we reduced the primer concentration or ultra-fast cPCR run time. For singleplex ultra-fast cPCR, the primer concentration needed to be lowered to $3{\mu}M$ or the run time needed to be reduced to 14 minutes. For duplex ultra-fast cPCR, $2{\mu}M$ of each primer set needed to be used or the run time needed to be reduced to 14 minutes. Under the conditions optimized in this study, the combination of ultra-fast cPCR and NALF immunoassay can be applied to on-site detection of pathogens. The combination can be easily applied to the detection of oral pathogens.

• BMB Reports
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• 제40권3호
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• pp.315-324
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• 2007

The novel $\alpha$-amylase purified from locally isolated strain, Bacillus sp. KR-8104, (KRA) (Enzyme Microb Technol; 2005; 36: 666-671) is active in a wide range of pH. The enzyme maximum activity is at pH 4.0 and it retains 90% of activity at pH 3.5. The irreversible thermoinactivation patterns of KRA and the enzyme activity are not changed in the presence and absence of $Ca^{2+}$ and EDTA. Therefore, KRA acts as a $Ca^{2+}$-independent enzyme. Based on circular dichroism (CD) data from thermal unfolding of the enzyme recorded at 222 nm, addition of $Ca^{2+}$ and EDTA similar to its irreversible thermoinactivation, does not influence the thermal denaturation of the enzyme and its Tm. The amino acid sequence of KRA was obtained from the nucleotide sequencing of PCR products of encoding gene. The deduced amino acid sequence of the enzyme revealed a very high sequence homology to Bacillus amyloliquefaciens (BAA) (85% identity, 90% similarity) and Bacillus licheniformis $\alpha$-amylases (BLA) (81% identity, 88% similarity). To elucidate and understand these characteristics of the $\alpha$-amylase, a model of 3D structure of KRA was constructed using the crystal structure of the mutant of BLA as the platform and refined with a molecular dynamics (MD) simulation program. Interestingly enough, there is only one amino acid substitution for KRA in comparison with BLA and BAA in the region involved in the calcium-binding sites. On the other hand, there are many amino acid differences between BLA and KRA at the interface of A and B domains and around the metal triad and active site area. These alterations could have a role in stabilizing the native structure of the loop in the active site cleft and maintenance and stabilization of the putative metal triad-binding site. The amino acid differences at the active site cleft and around the catalytic residues might affect their pKa values and consequently shift its pH profile. In addition, the intrinsic fluorescence intensity of the enzyme at 350 nm does not show considerable change at pH 3.5-7.0.

• Tribology and Lubricants
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• 제35권2호
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• pp.132-138
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• 2019

In this study, we demonstrate the effects of the acidic properties of montmorillonite (MMT), which is commonly used as a catalyst, on the conversion and selectivity of the dimer acid methyl ester (DAME) synthesis. We synthesize DAME by the dimerization of conjugated linoleic acid methyl ester (CLAME) and oleic acid methyl ester using MMT KSF. Incidentally, trimer acid methyl ester was formed as a by-product during the DAME synthesis. There is a necessity to adequately adjust the strength and quantity of the acid site to control the selectivity of DAME. Therefore, we vary the pH of the MMT acid by using various metal hydroxides. The purpose of this study is to increase the yield of monocyclic dimer acid methyl ester, which is a substance with adequate physical properties for industrial applications (e.g., lubricant and adhesive, etc.), using a heterogeneous catalyst. We report the dimerization of fatty acid methyl ester by using base treated-KSF, and apply it to conjugated soybean oil methyl ester. Then, we transmute the acid site properties of KSF, such as pH of 5 wt.% slurry KSF and various alkali metals (Li, Na, K, Ca). Characterization of base treated-KSF using a pH meter, x-ray diffraction, inductively coupled plasma-atomic emission spectrometer, Brunauer-Emmett-Teller surface analysis, and temperature-programmed desorption. We conduct an analysis of CLAME and DAME using nuclear magnetic resonance spectroscopy, gas chromatography, and gel permeation chromatography. Through these experiments, we demonstrate the effects of the acidic properties of KSF on the conversion and selectivity of the DAME synthesis, and evaluate its industrial potential by application to waste vegetable oil.

• Genomics & Informatics
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• 제21권1호
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• pp.9.1-9.13
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• 2023

Matrix metalloproteinase-9 (MMP-9) is a zinc and calcium-dependent proteolytic enzyme involved in extracellular matrix degradation. Overexpression of MMP-9 has been confirmed in several disorders, including cancers, Alzheimer's disease, autoimmune diseases, cardiovascular diseases, and dental caries. Therefore, MMP-9 inhibition is recommended as a therapeutic strategy for combating various diseases. Cinnamic acid derivatives have shown therapeutic effects in different cancers, Alzheimer's disease, cardiovascular diseases, and dental caries. A computational drug discovery approach was performed to evaluate the binding affinity of selected cinnamic acid derivatives to the MMP-9 active site. The stability of docked poses for top-ranked compounds was also examined. Twelve herbal cinnamic acid derivatives were tested for possible MMP-9 inhibition using the AutoDock 4.0 tool. The stability of the docked poses for the most potent MMP-9 inhibitors was assessed by molecular dynamics (MD) in 10 nanosecond simulations. Interactions between the best MMP-9 inhibitors in this study and residues incorporated in the MMP-9 active site were studied before and after MD simulations. Cynarin, chlorogenic acid, and rosmarinic acid revealed a considerable binding affinity to the MMP-9 catalytic domain (ΔG_binding < -10 kcal/ mol). The inhibition constant value for cynarin and chlorogenic acid were calculated at the picomolar scale and assigned as the most potent MMP-9 inhibitor from the cinnamic acid derivatives. The root-mean-square deviations for cynarin and chlorogenic acid were below 2 Å in the 10 ns simulation. Cynarin, chlorogenic acid, and rosmarinic acid might be considered drug candidates for MMP-9 inhibition.

• Journal of Photoscience
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• 제9권2호
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• pp.281-283
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• 2002

S-modulin in frog or its bovine homologue, recoverin, is a 26 kDa EF-hand $Ca^{2+}$-binding protein found in rod photoreceptors. The $Ca^{2+}$ -bound form of S-modulin binds to rhodopsin kinase (Rk) and inhibits its activity. Through this regulation, S-modulin is believed to modulate the light-sensitivity of a rod. In the present study, we tried to identify the interaction site of the $Ca^{2+}$ -bound form of S-modulin to Rk. First, we mapped roughly the interaction regions by using partial peptides of S-modulin. The result suggested that a specific region near the amino terminus is the interaction site of S- modulin. We then identified the essential amino acid residues in this region by using S-modulin mutant proteins: four amino acid residues were suggested to interact with Rk. These residues are located in a small closed pocket in the $Ca^{2+}$-free, inactive form of S-modulin, but exposed to the surface of the molecules in the $Ca^{2+}$ -bound, active form of S-modulin. Two additional amino acid residues were found to be crucial for the $Ca^{2+}$ -dependent conformational changes of S-modulin. The present study firstly identified the functional site of S-modulin, a member of a neuronal calcium sensor protein family.in family..

• 한국산림과학회지
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• 제96권5호
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• pp.503-509
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• 2007

The major objective of this study was to analyze the difference of the chemical characteristics of acid deposition in Quercus forests in Korea and Japan. The pH values of rainfall at the experimental forest of Kangwon National University (KS site) were higher than those at the Foresta Hills in Japan (JP site), and all chemical contents of throughfall and stemflow were much higher than those of rainfall in Quercus forest stands at the KS and JP site. The pH values, $Ca^{2+}$, $NO_3{^-}$ and $SO{_4}^{2-}$ concentration of throughfall and stemflow at the KS site showed seasonal variation. While at the JP site, the same pattern was shown in the pH values of throughfall and stemflow, however, did not show any difference among seasons. Also, the annual input of all nutrients in these two contrasting forests varied seasonally. These results can be used to predict the amounts of air pollutant that are washed off and leached by the rainfall and Yellow Sand (Asian dust), including NOx and SOx acid pollutants transported easterly from China in the spring. Therefore, it is necessary to quantify the inputs of dry and wet deposition throughout a full year to gain a more complete understanding of the effects of acid deposition on the nutrient cycles in these forest ecosystems.

• 청정기술
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• 제18권3호
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• pp.259-264
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• 2012

페롭스카이트형 산화물을 능금산법으로 합성하여 TG/DTA, XRD, XPS, TEM 및 $H_2$-TPR 등에 의해 특성분석을 하였고, 벤젠의 연소반응에서의 활성을 조사하였다. 대부분의 촉매들은 페롭스카이트 결정구조를 잘 가지고 있었으며 15에서 70 nm의 크기를 나타내었다. $LaMnO_3$ 촉매가 가장 높은 활성을 보여주었고 $350^{\circ}C$에서 거의 100%의 전환율을 나타내었다. 반응활성을 증가시키기 위해 페롭스카이트 산화물의 A-와 B-위치에 다른 금속이온의 치환을 행하였다. $LaMnO_3$ 촉매의 A-위치에 Sr을 일부분 치환시키면 벤젠의 전환율이 증가하였다. 또한, B-위치에 Co 및 Cu 이온의 치환 역시 촉매 활성을 증가시켰고, $LaMn_{1-x}B_xO_3$ (B = Co, Fe, Cu)형 페롭스카이트에서 촉매활성은 Co > Cu > Fe의 순서로 감소하였다.

• Journal of Microbiology
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• 제44권1호
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• pp.50-53
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• 2006

Cys-29 and Cys-251 of Streptomyces albus valine dehydrogenase(ValDH) were highly conserved in the corresponding region of $NAD(P)^+$-dependent amino acid dehydroganase sequences. To ascertain the functional role of these cysteine residues in S. albus ValDH, site-directed mutagenesis was performed to change each of the two residues to serine. Kinetic analyses of the enzymes mutated at Cys-29 and Cys-251 revealed that these residues are involved in catalysis. We also constructed mutant ValDH by substituting valine for leucine at 305 by site-directed mutagenesis. This residue was chosen, because it has been proposed to be important for substrate discrimination by phenylalanine dehydrogenase (PheDH) and leucine dehydrogenase (LeuDH). Kinetic analysis of the V305L mutant enzyme revealed that it is involved in the substrate binding site. However it displayed less activity than the wild type enzyme toward all aliphatic and aromatic amino acids tested.

• BMB Reports
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• 제33권1호
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• pp.43-48
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• 2000

4-Aminobutyrate aminotransferase is a key enzyme of the 4-aminobutyric acid shunt. It converts the neurotransmitter 4-aminobutyric acid to succinic semialdehyde. In order to study the structural and functional aspects of catalytically active Cys residues of pig brain 4-aminobutyrate aminotransferase, we purified the active form in E. coli by coproduction of thioredoxin. The structural arrangement for functional requirements of a dimeric protein using a bifunctional sultbydryl reagent was then characterized, and the spatial proximity between the essential SH groups and a cofactor (pyridoxal-5'-phosphate) binding site was determined. The bifunctional sultbydryl reagent DMDS reacted with the enzyme at the ratio of one molecule per enzyme dimer. This resulted in an approximately 50% loss of enzymatic activity. The spatial proximity of the distance between the essential SH groups and the cofactor-binding site was determined by the energy transfer measurement technique. The result (approximate 20 ${\AA}$) suggested that cross-linking of two sulfhydryl groups with DMDS is not near a PLP binding site.

• Environmental Sciences Bulletin of The Korean Environmental Sciences Society
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• 제4권2호
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• pp.95-102
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• 2000

Methane combustion over perovskite-type oxides prepared using the malic acid method was investigated. To enhance the catalytic activity, the perovskite oxides were modified by the substitution of metal into their A or B site. In addition, the reaction conditions, such as the temperature, space velocity, and partial pressure of the methane were varied to understand their effect on the catalytic performance. With the LaCoO3-type catalyst, the partial substitution of Sr or Ba into site A enhanced the catalytic activity in the methane combustion. With the LaBO3(B=Co, Fe, Mn, Cu)-type catalyst, the catalytic activities were exhibited in the order of Co>Fe Mn>Cu. Futhermore, the partial substitution of Co into site B enhanced the catalytic activity, whereas an excess amount of Co decreased the activity. The surface area and catalytic activity of the perovskite catalysts prepared using the malic acid method showed higher values than those prepared using the solid reaction method. The catalytic activity was enhanced with decreased methane concentration and with a decrease in the space velocity.