• Journal of Microbiology and Biotechnology
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• v.30 no.12
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• pp.1905-1911
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• 2020

Homoserine dehydrogenase (HSD) catalyzes the reversible conversion of ʟ-aspartate-4-semialdehyde to ʟ-homoserine in the aspartate pathway for the biosynthesis of lysine, methionine, threonine, and isoleucine. HSD has attracted great attention for medical and industrial purposes due to its recognized application in the development of pesticides and is being utilized in the large scale production of ʟ-lysine. In this study, HSD from Bacillus subtilis (BsHSD) was overexpressed in Escherichia coli and purified to homogeneity for biochemical characterization. We examined the enzymatic activity of BsHSD for ʟ-homoserine oxidation and found that BsHSD exclusively prefers NADP+ to NAD+ and that its activity was maximal at pH 9.0 and in the presence of 0.4 M NaCl. By kinetic analysis, Km values for ʟ-homoserine and NADP+ were found to be 35.08 ± 2.91 mM and 0.39 ± 0.05 mM, respectively, and the Vmax values were 2.72 ± 0.06 μmol/min-1 mg-1 and 2.79 ± 0.11 μmol/min-1 mg-1, respectively. The apparent molecular mass determined with size-exclusion chromatography indicated that BsHSD forms a tetramer, in contrast to the previously reported dimeric HSDs from other organisms. This novel oligomeric assembly can be attributed to the additional C-terminal ACT domain of BsHSD. Thermal denaturation monitoring by circular dichroism spectroscopy was used to determine its melting temperature, which was 54.8℃. The molecular and biochemical features of BsHSD revealed in this study may lay the foundation for future studies on amino acid metabolism and its application for industrial and medical purposes.

• Journal of Korean Elementary Science Education
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• v.17 no.2
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• pp.55-65
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• 1998

This study was intended to suggest the desirable direction in the 7th national curriculum revision through the analysis of the elementary science textbooks in the 6th national curriculum. The analysis system was composed of three categories, (1)knowledge (2)inquiry process and (3)attitude. And knowledge was divided into fact, concept and rule. And inquiry process was divided into thirteen subcategories such as manipulating experimental apparatus, observing, measuring, recording data, classifying, interpreting/ predicting, determining relationship/ causal explanation, extrapolating/ interpolating, drawing conclusions/ formulating a generalization or model, evaluating, formulating a problem, generating a hypothesis and designing an experiment/ controlling variables. Each sentence in the textbooks was considered as an analyzing unit. The frequency and percentage of each category were counted and the ratios were calculated. The findings could be summarized as follows: 1. The content of the elementary science textbooks was composed of knowledge 10.3%, inquiry process 88.8%, attitude 0.8% respectively. 2. As increasing the grades, the ratio of knowledge showed high frequency, but that of attitude showed low frequency. 3. In All the grades, the ratio of observing was the highest in inquiry process. 4. In the domain of physics and chemistry, the manipulating experimental apparatus showed high frequency. In the domain of biology and earth science, the role of observing was emphasized.

• Journal of Microbiology and Biotechnology
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• v.13 no.5
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• pp.823-827
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• 2003

Streptomyces venezuelae ATCC 15439 is notable in its ability to produce two distinct groups of macrolactones. It has been reported that the generation of two macrolactone structures results from alternative expression of pikromycin (Pik) polyketide synthase (PKS). It was previously reported that the hybrid pikromycin-tylosin PKS can also produce two different macrolactones but its mechanistic basis remains unclear. In order to address this question, a series of site-directed mutagenesis of tentative alternative ribosome binding site and translation start codons in tylGV were performed. The results suggest that macrolactone ring size is not determined by the alternative expression of TylGV but through other mechanism(s) involving direct interaction between the PikAIII and TE domain or skipping of the final chain elongation step. This provides new insight into the mechanism of macrolactone ring size determination in hybrid PKS as well as an opportunity to develop novel termination activities for combinatorial biosynthesis.

• BMB Reports
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• v.29 no.1
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• pp.58-62
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• 1996

The structural changes in the electron donor side of the PSII reaction center have been monitored since heat treatment ($45^{\circ}C$ for 5 min) of thylakoids is known to decrease the oxygen evolving activity. In heat-treated spinach chloroplast thylakoids, the inhibitory effect of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) on the electron transport activity of the PSII reaction center from diphenyl carbazide to dichlorophenolindophenol became reduced approximately 3.8 times and [$^{14}C$]-labeled DCMU binding on the D1 polypeptide decreased to 25~30% that of intact thylakoid membranes, implying that the conformational changes of the DCMU binding pocket, residing on the D1 polypeptide, occur by heat treatment. The accessibility of trypsin to the $NH_2$-terminus of the cytochrome b-559 ${\alpha}$-subunit, assayed with Western blot using an antibody generated against the synthetic peptide (Arg-68 to Arg-80) of the COOH-terminal domain, was also increased, indicating that heat-treatment caused changes in the structural environments near the stromal side of the cytochrome b-559 ${\alpha}$-subunit, allowing trypsin more easily to cleave the $NH_2$-terminal domain. Therefore, the structural changes in the electron donor side of the PSII reaction center complexes could be one of the reasons why the oxygen evolving activity of the heat-treated thylakoid membranes decreased.

• BMB Reports
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• v.39 no.5
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• pp.578-585
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• 2006

The cDNA of a firefly luciferase from lantern mRNA of Lampyroidea maculata has been cloned, sequenced and functionally expressed. The cDNA has an open reading frame of 1647 bp and codes for a 548-residue-long polypeptide. Noteworthy, sequence comparison as well as homology modeling showed the highest degree of similarity with H. unmunsana and L. mingrelica luciferases, suggesting a close phylogenetic relationship despite the geographical distance separation. The deduced amino acid sequence of the luciferase gene of firefly L. maculata showed 93% identity to H. unmunsana. Superposition of the three-dimensional model of L. maculata luciferase (generated by homology modeling) and three dimensional structure of Photinus pyralis luciferase revealed that the spatial arrangements of Luciferin and ATP-binding residues are very similar. Putative signature of AMP-binding domain among the various firefly species and Lampyroidea maculata was compared and a striking similarity was found. Different motifs and sites have been identified in Lampyroidea maculata by sequence analysis. Expression and purification of luciferase from Lampyroidea maculata was carried out using Ni-NTA Sepharose. Bioluminescence emission spectrum was similar to Photinus pyralis luciferase.

• Proceedings of the Korean Society for Language and Information Conference
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• 2007.11a
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• pp.105-114
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• 2007

This paper addresses a method for customizing an English-to-Korean machine translation system from general domain to patent domain. The customizing method consists of following steps: 1) linguistically studying about characteristics of patent documents, 2) extracting unknown words from large patent documents and constructing large bilingual terminology, 3) extracting and constructing the patent-specific translation patterns 4) customizing the translation engine modules of the existing general MT system according to linguistic study about characteristics of patent documents, and 5) evaluating the accuracy of translation modules and the translation quality. This research was performed under the auspices of the MIC (Ministry of Information and Communication) of Korean government during 2005-2006. The translation accuracy of the customized English-Korean patent translation system is 82.43% on the average in 5 patent fields (machinery, electronics, chemistry, medicine and computer) according to the evaluation of 7 professional human translators. In 2006, the patent MT system started an on-line patent MT service in IPAC (International Patent Assistance Center) under MOCIE (Ministry of Commerce, Industry and Energy) in Korea. In 2007, KIPO (Korean Intellectual Property Office) tries to launch an English-Korean patent MT service.

• Atmosphere
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• v.25 no.4
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• pp.639-657
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• 2015

There is an increasing need to improve the air quality over South Korea to protect public health from local and remote anthropogenic pollutant emissions that are in an increasing trend. Here, we evaluate the performance of the WRF-Chem (Weather Research and Forecasting-Chemistry) model in simulating near-surface air quality of major Korean cities, and investigate the impacts of time-varying chemical initial and lateral boundary conditions (IC/BCs) on the air quality simulation using a chemical downscaling technique. The model domain was configured over the East Asian region and anthropogenic MICS-Asia 2010 emissions and biogenic MEGAN-2 emissions were applied with RACM gaseous chemistry and MADE/SORGAM aerosol mechanism. Two simulations were conducted for a 30-days period on April 2010 with chemical IC/BCs from the WRF-Chem default chemical species profiles ('WRF experiment') and the MOZART-4 (Model for OZone And Related chemical Tracers version 4) ('WRF_MOZART experiment'), respectively. The WRF_MOZART experiment has showed a better performance to predict near-surface CO, $NO_2$, $SO_2$, and $O_3$ mixing ratios at 7 major Korean cities than the WRF experiment, showing lower mean bias error (MBE) and higher index of agreement (IOA). The quantitative impacts of the chemical IC/BCs have depended on atmospheric residence time of the pollutants as well as the relative difference of chemical mixing ratios between the WRF and WRF_MOZART experiments at the lateral boundaries. Specifically, the WRF_MOZART experiment has reduced MBE in CO and O3 mixing ratios by 60~80 ppb and 5~10 ppb over South Korea than those in the WRF-Chem default simulation, while it has a marginal impact on $NO_2$ and $SO_2$ mixing ratios. Without using MOZART-4 chemical IC, the WRF simulation has required approximately 6-days chemical spin-up time for the East Asian model domain. Overall, the results indicate that realistic chemical IC/BCs are prerequisite in the WRF-Chem simulation to improve a forecast skill of local air quality over South Korea, even in case the model domain is sufficiently large to represent anthropogenic emissions from China, Japan, and South Korea.

• BMB Reports
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• v.30 no.5
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• pp.362-369
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• 1997

Multiple phosphorylation of the carboxy-terminal domain (CTD) of the largest subunit in RNA polymerase II (RNAP II) is thought to play an important role in the transcription cycle. The preinitiation complex in a partially purified complete transcription system suggested that RNA polymerase IIA containing unphosphorylated CTD is involved in complex assembly, whereas RNA polymerase IIO containing Ser and Thr phosphorylated CTD is not involved in preinitiation complex assembly. Recently a minimal transcription system was developed which requires chemically defined minimal components for its transcription: TBP, TFIIB, TFIIF, RNAP II and a supercoiled adenovirus-2 major late promoter (Ad-2 MLP). It would be using interesting to determine the consequence of CTD phosphorylation on preinitiation complex formation using the minimal transcription system. Contrary to the results from the partially purified complete transcription system, both RNA polymerase IIA and IIO are equally recruited in the preinitiation complex formation. The discrepancy may result from the two different assays used to determine complex formation, the use of chemically undefined complete and defined minimal transcription systems. This implicates that some factors in the complete transcription system are involved in the distinction between RNAP IIA and IIO in complex assembly. In addition multiple tyrosine phosphorylation of the CTD of RNAP II was prepared with c-Abl kinase and its recruiting ability in the preinitiation complex was examined. Compare with Ser and Thr phosphorylated RNAP IIO, Tyr phosphorylated RNAP IlOy forms a stable preinitiation complex in both the minimal and complete transcription systems. Based on these results, it seems that tyrosine phosphorylation of the CTD is important in the transcription cycle on the special subset of class-II promoter or has a different role in the transcription process.

• Interdisciplinary Bio Central
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• v.1 no.2
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• pp.8.1-8.6
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• 2009

Introduction: It is a challenge to design a protein score function which stabilizes the native structures of many proteins simultaneously. The coarse-grained description of proteins to construct the pairwise-contact score function usually ignores the backbone directionality of protein structures. We propose a new two-body score function which stabilizes all native states of 1,006 proteins simultaneously. This two-body score function differs from the usual pairwise-contact functions in that it considers two adjacent amino acids at two ends of each peptide bond with the backbone directionality from the N-terminal to the C-terminal. The score is a corresponding propensity for a directional alignment of two adjacent amino acids with their local environments. Results and Discussion: We show that the construction of a directional adjacency-score function was achieved using 1,006 training proteins with the sequence homology less than 30%, which include all representatives of different protein classes. After parameterizing the local environments of amino acids into 9 categories depending on three secondary structures and three kinds of hydrophobicity of amino acids, the 32,400 adjacency-scores of amino acids could be determined by the perceptron learning and the protein threading. These could stabilize simultaneously all native folds of 1,006 training proteins. When these parameters are tested on the new distinct 382 proteins with the sequence homology less than 90%, 371 (97.1%) proteins could recognize their native folds. We also showed using these parameters that the retro sequence of the SH3 domain, the B domain of Staphylococcal protein A, and the B1 domain of Streptococcal protein G could not be stabilized to fold, which agrees with the experimental evidence.

• Journal of Life Science
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• v.30 no.1
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• pp.88-95
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• 2020

Using a random arbitrarily primed polymerase chain reaction, messenger RNA expression levels were assessed after exposure to 10% (v/v) toluene for 8 hr in solvent-tolerant Pseudomonas sp. BCNU 106. Among the 100 up-expressed products, 50 complementary DNA fragments were confirmed to express repeatedly; these were cloned and then sequenced. Blast analysis revealed that toluene stimulated an adaptive increase in the gene expression level in association with transcriptions such as LysR family of transcriptional regulators and RNA polymerase factor sigma-32. The expression of catalase and Mn2+/Fe2+ transporter genes functionally associated with inorganic ion transport and metabolism increased, and the increased expression of type IV pilus assembly PilZ and multi-sensor signal transduction histidine kinase genes, functionally categorized into signal transduction and mechanisms, was also demonstrated under toluene stress. The gene expression level of beta-hexosaminidase in association with carbohydrate transport and metabolism increased, and those of DNA polymerase III subunit epsilon, DNA-3-methyladenine glycosylase II, DEAD/DEAH box helicase domain-containing protein, and ABC transporter also increased after exposure to toluene in DNA replication, recombination, and repair, and even in defense mechanism. In particular, the RNAs corresponding to the ABC transporter, Mn2+/Fe2+ transporter, and the β-hexosaminidase gene were confirmed to be markedly induced in the presence of 10% toluene. Thus, defense mechanism, cellular ion homeostasis, and biofilm formation were shown as essential for toluene tolerance in Pseudomonas sp. BCNU 106.