• Korean Journal of Microbiology
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• v.55 no.2
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• pp.123-130
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• 2019

Chelatase catalyzes the insertion of divalent metal into tetrapyrrole and plays a key role in the biosynthesis of metallated tetrapyrroles, such as cobalamin, siroheme, heme, and chlorophyll. SirB is a sirohydrochlorin (SHC) chelatase that generates cobalt-SHC or iron-SHC by inserting cobalt or iron into the center of sirohydrochlorin tetrapyrrole. To provide structural insights into the metal-binding and SHC-recognition mechanisms of SirB, we determined the crystal structure of SirB from Bacillus subtilis subsp. spizizenii (bssSirB) in complex with cobalt ions. bssSirB forms a monomeric ${\alpha}/{\beta}$ structure that consists of two domains, an N-terminal domain (NTD) and a C-terminal domain (CTD). The NTD and CTD of bssSirB adopt similar structures with a four-stranded ${\beta}-sheet$ that is decorated by ${\alpha}-helices$. bssSirB presents a highly conserved cavity that is generated between the NTD and CTD and interacts with a cobalt ion on top of the cavity using two histidine residues of the NTD. Moreover, our comparative structural analysis suggests that bssSirB would accommodate an SHC molecule into the interdomain cavity. Based on these structural findings, we propose that the cavity of bssSirB functions as the active site where cobalt insertion into SHC occurs.

• Applied Chemistry for Engineering
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• v.35 no.4
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• pp.335-340
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• 2024

In this paper, we synthesized organic and inorganic hybrid materials to introduce antibody functionality to UIO-66 and incorporated them into a surface plasmon resonance (SPR) assay to enhance the sensitivity of detecting small molecules such as oxytocin. A biological marker peptide called oxytocin may help in the diagnosis of heart failure, Alzheimer's disease, and cancer. To detect oxytocin at concentrations as low as a few femtomole (fM), we developed a surface sandwich assay utilizing a pair of oxytocin-specific antibodies for enhancing selectivity and one of metal organic frameworks [e.g., UiO-66-(COOH)₂] possessing high porosity and surface-area as a signal amplifier. Initially, real-time SPR assays were used to confirm that each selected oxytocin-specific antibody binds strongly to oxytocin and to different binding sites on oxytocin. One of these antibodies (e.g., anti-OXT[OTI5G4]) was immobilized on the surface of a thin gold chip. Upon sequential injecting of oxytocin and the other antibody (e.g., anti-OXT[4G11]) conjugated to UiO-66-(COOH)₂ onto the surface to form the surface sandwich complex of anti-OXT[OTI5G4]/oxytocin/UiO-66-(COOH)₂-anti-OXT[4G11]), SPR changes, which varied with oxytocin concentration, were then measured in real time. The results demonstrated that sensitivity was amplified by over a million-fold compared to assays without UiO-66-(COOH)₂, enabling oxytocin detection down to approximately 10 fM.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.13-13
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• 2015

Rice blast fungus, Magnaporthe oryzae, is the most destructive pathogen of rice in the world. This fungus has a biotrophic phase early in infection and switches to a necrotrophic lifestyle after host cell death. During the biotrophic phase, the fungus competes with host for nutrients and oxygen. Continuous uptake of oxygen is essential for successful establishment of blast disease of this pathogen. Here, we report transcriptional responses of the fungus to oxygen limitation. Transcriptome analysis using RNA-Seq identified 1,047 up-regulated genes in response to hypoxia. Those genes were involved in mycelial development, sterol biosynthesis, and metal ion transport based on hierarchical GO terms and well-conserved among three different fungal species. In addition, null mutants of three hypoxia-responsive genes were generated and tested for their roles on fungal development and pathogenicity. The mutants for a sterol regulatory element-binding protein gene, MoSRE1, and C4 methyl sterol oxidase gene, ERG25, exhibited increased sensitivity to hypoxia-mimetic agent, increased conidiation, and delayed invasive growth within host cells, suggesting important roles in fungal development. However, such defects did not cause any significant decrease in disease severity. The other null mutant for alcohol dehydrogenase gene, MoADH1, showed no defect in the hypoxia-mimic condition and fungal development. Taken together, this comprehensive transcriptional profiling in response to a hypoxia condition with experimental validations would provide new insights on fungal development and pathogenicity in plant pathogenic fungi.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.61-61
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• 2015

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most destructive diseases of rice worldwide. The rice - M. oryzae pathosystem has become a model in the study of plant - fungal interactions due to its economic importance and accumulating knowledge. During the evolutionary arms race with M. oryzae, rice plants evolved a repertoire of Resistance (R) genes to protect themselves from diseases in a gene-for-gene fashion. M. oryzae secretes a battery of small effector proteins to manipulate host functions for its successful infection, and some of them are recognized by host R proteins as avirulence effectors (AVR), which turns on strong immunity. Therefore, the analysis of interactions between AVRs and their cognate R proteins provide crucial insights into the molecular basis of plant - fungal interactions. Rice blast resistance genes Pik, Pia, Pii comprise pairs of protein-coding ORFs, Pik-1 and Pik-2, RGA4 and RGA5, Pii-1 and Pii-2, respectively. In all three cases, the paired genes are tightly linked and oriented to the opposite directions. In the AVR-Pik/Pik interaction, it has been unraveled that AVR-Pik binds to the N-terminal coiled-coil domain of Pik-1. RGA4 and RGA5 are necessary and sufficient to mediate Pia resistance and recognize the M. oryzae effectors AVR-Pia and AVR1-CO39. A domain at the C-terminus of RGA5 characterized by a heavy metal associated domain was identified as the AVR-binding domain of RGA5. Similarly, physical interactions among Pii-1, Pii-2 and AVR-Pii are being analyzed.

• Journal of Environmental Science International
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• v.24 no.5
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• pp.623-631
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• 2015

Microarray technology provides a unique tool for the determination of gene expression at the level of messenger RNA (mRNA). This study, the mRNA expression profiles provide insight into the mechanism of action of cadmium in Fleshy shrimp (Fenneropenaeus chinensis). The ability of genomic technologies was contributed decisively to development of new molecular biomarkers and to the determination of new possible gene targets. Also, it can be approach for monitoring of trace metal using oligo-chip microarray-based in potential model marine user level organisms. 15K oligo-chip for F. chinensis that include mostly unique sets of genes from cDNA sequences was developed. A total of 13,971 spots (1,181 mRNAs up- regulated and 996 down regulated) were identified to be significantly expressed on microarray by hierarchical clustering of genes after exposure to cadmium for different conditions (Cd24-5000 and Cd48-1000). Most of the changes of mRNA expression were observed at the long time and low concentration exposure of Cd48-1000. But, gene ontology analysis (GO annotation) were no significant different between experiments groups. It was observed that mRNA expression of main genes involved in metabolism, cell component, molecular binding and catalytic function. It was suggested that cadmium inhibited metabolism and growth of F. chinensis.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.7
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• pp.1024-1050
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• 2001

Avian spermatozoa are characterised by high concentrations of polyunsaturated fatty acids (PUFAs), in particular docosatetraenoic (DTA, 22:4n-6) and arachidonic (AA, 20:4n-6) acids. As a result they are vulnerable to lipid peroxidation, which is considered to be an important factor of male infertility. Antioxidant systems are expressed in spermatozoa and seminal plasma and build three major levels of antioxidant defense. The first level is based on the activity of superoxide dismutase (SOD) which is, in conjunction with glutathione peroxidase (GSH-Px), catalase and metal-binding proteins, responsible for prevention of free radical formation. The second level of defence is responsible for prevention and restriction of chain reaction propagation and includes chain-breaking antioxidants such as vitamin E, ascorbic acid, glutathione and some others. The third level of antioxidant defence deals with damaged molecules, repairing or removing them from the cell and includes specific enzymes such as lipases, proteases, DNA repair enzymes etc. In the review, profiles of PUFAs and the two first lines of antioxidant defence in avian spermatozoa are characterised. Dietary manipulation of the breeder's diet (PUFA, vitamin E and selenium) as an effective means of modulating fatty acid composition and antioxidant system is also considered. Antioxidant properties of seminal plasma and efficiencies of inclusion of antioxidants into semen diluents are also characterised.

• Journal of the Korean Ceramic Society
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• v.42 no.9 s.280
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• pp.624-630
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• 2005

To investigate the possibility of the $ZrO_2$ buffer layer as the insulator for the Metal-Ferroelectric-Insulator-semiconductor (MFIS) structure, $ZrO_2$ and $SrBi_2Ta_2O_9$ (SBT) thin films were deposited on the P-type Si(111) wafer by the R.F. magnetron-sputtering method. According to the process with and without the post-annealing of the $ZrO_2$ buffer layer and SBT thin film, the diffusion amount of Sr, Bi, Ta elements show slight difference through the Glow Discharge Spectrometer (GDS) analysis. From X-ray Photoelectron Spectroscopy (XPS) results, we could confirm that the post-annealing process affects the chemical binding condition of the interface between the $ZrO_2$ thin film and the Si substrate. Compared to the MFIS structure without the post-annealing of the $ZrO_2$ buffer layer, memory window value of MFlS structure with post-annealing of the $ZrO_2$ buffer layer were considerably improved. The window memory of the Pt/SBT (260 nm, $800^{\circ}C)/ZrO_2$ (20 nm) structure increases from 0.75 to 2.2 V under the applied voltage of 9 V after post-annealing.

• Journal of Microbiology and Biotechnology
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• v.11 no.1
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• pp.153-159
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• 2001

In order to clone the peptide synthetase gene form Lysobacter lactamgenus IFO 14,288, the gene fragments were amplified using primers for the adenylation domain and the thionylation domain of the peptide synthetase genes in other organisms by polymerase chain reaction (PCR). The resulting 0.5-kb fragment was cloned in a pGEM-T vector, and the nucleotide sequences were determined. Six different PCR products were obtained; three were identified to be a part of L-$\alpha$-aminoadipyl-L-cysteinyl-D-valine (ACV) synthetase and three to be other peptide synthetases. Using each of the two different classes of PCR products as mixed probes, a cosmid library of L. lactamgenus chromosomal DNA constructed in a pHC79 vector was screened by an in situ hybridization procedure, and one positive clone was selected which was bound by peptide synthetase gene fragments as well as ACV synthetase gene fragments. The partial sequence analysis formt he obtained pPTS-5 cosmid showed th presence of more than two open reading frames. These were for two putative membrane transporters, which were homologous with several integral membrane proteins including the ABC transporter ATP-binding protein of E. coli (YbjZ) and the metal ion uptake protein of Bacillus subtilis (YvrN). A 45% homology was also found between the two transporter proteins at the carboxy terminus. Through a hydropathy analysis and transmembrane analysis. 4-5 transmembrane domains were found in these two proteins. When the genes were expressed in Escherichia coli, the gene products inhibited the hose cell growth, probably due to the disturbance of the membrane transport system.

• Korean Journal of Materials Research
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• v.20 no.11
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• pp.623-627
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• 2010

Semiconducting metal oxides have been frequently used as gas sensing materials. While zinc oxide is a popular material for such applications, structures such as nanowires, nanorods and nanotubes, due to their large surface area, are natural candidates for use as gas sensors of higher sensitivity. The compound ZnO has been studied, due to its chemical and thermal stability, for use as an n-type semiconducting gas sensor. ZnO has a large exciton binding energy and a large bandgap energy at room temperature. Also, ZnO is sensitive to toxic and combustible gases. The NO gas properties of zinc oxide-single wall carbon nanotube (ZnO-SWCNT) composites were investigated. Fabrication includes the deposition of porous SWCNTs on thermally oxidized $SiO_2$ substrates followed by sputter deposition of Zn and thermal oxidation at $400^{\circ}C$ in oxygen. The Zn films were controlled to 50 nm thicknesses. The effects of microstructure and gas sensing properties were studied for process optimization through comparison of ZnO-SWCNT composites with ZnO film. The basic sensor response behavior to 10 ppm NO gas were checked at different operation temperatures in the range of $150-300^{\circ}C$. The highest sensor responses were observed at $300^{\circ}C$ in ZnO film and $250^{\circ}C$ in ZnO-SWCNT composites. The ZnO-SWCNT composite sensor showed a sensor response (~1300%) five times higher than that of pure ZnO thin film sensors at an operation temperature of $250^{\circ}C$.

• BMB Reports
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• v.33 no.2
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• pp.172-178
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• 2000

The lipoxygenase was purified 35 fold to homogeneity from the Korean red potato by an ammonium sulfate precipitation and DEAE-cellulose column chromatography. The simple purification method is useful for the preparation of pure lipoxygenase. The molecular weight of the enzyme was estimated to be 38,000 by SDS-polyacrylamide gel electrophoreses and Sepharose 6B column chromatography. The purified enzyme with 2 M $(NH_4)_2SO_4$ in a potassium phosphate buffer, pH 7.0, was very stable for 5 months at $-20^{\circ}C$. Because the purified lipoxygenase is very stable, it could be useful for the screening of a lipoxygenase inhibitor. The optimal pH and temperature for lipoxygenase purified from the red potato were found to be pH 9.0. and $30^{\circ}C$, respectively. The Km and Vmax values for linoleic acid of the lipoxygenase purified from the red potato were $48\;{\mu}M$ and $0.03\;{\mu}M$ per minute per milligram of protein, respectively. The enzyme was insensitive to the metal chelating agents tested (2 mM KCN, 1 and 10mM EDTA, and 1 mM $NaN_3$), but was inhibited by several divalent cations, such as $Cu^{++}$, $Co^{++}$ and $Ni^{++}$. The essential amino acids that were involved in the catalytic mechanism of the 5-lipoxygenase from the Korean red potato were determined by chemical modification studies. The catalytic activity of lipoxygenase from the red potato was seriously reduced after treatment with a diethylpyrocarbonate (DEPC) modifying histidine residue and Woodward's reagent (WRK) modifying aspartic/glutamic acid. The inactivation reaction of DEPC (WRK) processed in the form of pseudo-first-order kinetics. The double-logarithmic plot of the observed pseudo-first-order rate constant against the modifier concentration yielded a reaction order 2, indicating that two histidine residues (carboxylic acids) were essential for the lipoxygenase activity from the red potato. The linoleic acid protected the enzyme against inactivation by DEPC(WRK), revealing that histidine and carboxylic amino acids residues were present at the substrate binding site of the enzyme molecules.