• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.215-220
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• 2005

Generally, enzymes in the starch biosynthesis pathway exist in many isoforms, contributing to the difficulties in the dissection of their specific roles in controlling starch properties. In this study, we present an algorithm as an alternative method to classify isoforms of starch biosynthesis enzymes based on their conserved secondary structures. Analysis of the predicted secondary structure of plant soluble starch synthase I (SSI) and soluble starch synthase II (SSII) demonstrates that these two classes of isoform can be reclassified into three subsets, SS-A, SS-B and SS-C, according to the differences in the secondary structure of the protein at C-terminus. SS-A reveals unique structural features that are conserved only in cereal plants, while those of SS-B are found in all plants and SS-C is restricted to barley. These findings enable us to increase the accuracy in the estimation of evolutionary distance between isoforms of starch synthases. Moreover, it facilitates the elucidation of correlations between the functions of each enzyme isoforms and the properties of starches. Our secondary structure analysis tool can be applicable to study the functions of other plant enzyme isoforms of economical importance.

• Journal of Microbiology and Biotechnology
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• v.20 no.8
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• pp.1196-1203
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• 2010

In the present work, methanethiol and dimethyldisulfide were investigated as sulfur sources for methionine synthesis in Corynebacterium glutamicum. In silico pathway analysis predicted a high methionine yield for these reduced compounds, provided that they could be utilized. Wild-type cells were able to grow on both methanethiol and dimethyldisulfide as sole sulfur sources. Isotope labeling studies with mutant strains, exhibiting targeted modification of methionine biosynthesis, gave detailed insight into the underlying pathways involved in the assimilation of methanethiol and dimethyldisulfide. Both sulfur compounds are incorporated as an entire molecule, adding the terminal S-$CH_3$ group to O-acetylhomoserine. In this reaction, methionine is directly formed. MetY (O-acetylhomoserine sulfhydrylase) was identified as the enzyme catalyzing the reaction. The deletion of metY resulted in methionine auxotrophic strains grown on methanethiol or dimethyldisulfide as sole sulfur sources. Plasmid-based overexpression of metY in the ${\Delta}$metY background restored the capacity to grow on methanethiol or dimethyldisulfide as sole sulfur sources. In vitro studies with the C. glutamicum wild type revealed a relatively low activity of MetY for methanethiol (63 mU/mg) and dimethyldisulfide (61 mU/mg). Overexpression of metY increased the in vitro activity to 1,780 mU/mg and was beneficial for methionine production, since the intracellular methionine pool was increased 2-fold in the engineered strain. This positive effect was limited by a depletion of the metY substrate O-acetylhomoserine, suggesting a need for further metabolic engineering targets towards competitive production strains.

• 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 Marine Life Science
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• v.7 no.2
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• pp.94-101
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• 2022

In this study, the marine medaka Oryzias javanicus was exposed to two concentrations of non-toxin-producing red tide dinoflagellate C. polykrikoides (1,000 and 2,000 cells ml^-1) for 96 h, and the time-course biochemical responses of antioxidant and immunity parameters were analyzed in the liver tissue. Significant ichthyotoxicity with increasing cell concentrations of C. polykrikoides and exposure period was observed for 96 h. Opercular respiratory rate was lowered in marine medaka exposed to 2,000 cells ml^-1 of C. polykrikoides. Intracellular malondialdehyde (MDA) content significantly elevated in response to both cell concentrations. In the case of glutathione (GSH) content, the levels were significantly elevated by 1,000 cells ml^-1 of C. polykrikoides, but the contents significantly depleted upon exposure to 2,000 cells ml^-1 of C. polykrikoides. Similarly, enzymatic activities of catalase (CAT) and superoxide dismutase (SOD) were increased by 1,000 cells ml^-1 of C. polykrikoides, whereas their activities were lowered by 2,000 cells ml^-1 of C. polykrikoides. Analysis of the two immunity parameters, alternative complement pathway and lysozyme, showed significantly lowered activities in 2,000 cells ml^-1 of C. polykrikoides-exposed liver tissue. These biochemical effects of C. polykrikoides on marine medaka would be helpful for understanding its acute effects in marine fish.

• The Korea Journal of Herbology
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• v.32 no.4
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• pp.9-15
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• 2017

Objectives : In this study, the inhibitory activities of Korean Medicine against pancreatic lipase in vitro and biochemical analyses in vivo were measured to determine its possibility as a well-matched sauce material with chicken. Methods : The inhibitory activity on pancreatic lipase enzyme of 11 samples were evaluated in vitro and then 5 samples were selected. The activity of pancreatic lipase was investigated using orlistat as a positive control. Animals were divided into eight groups (n=7). The experimental groups except for normal group were fed 60% high-fat diet for 7 days. 5 samples were orally administered at a dose of 200 mg/kg body weight and orlistat were orally administrated at a dose of 60 mg/kg body weight for 7 days. Biochemical anaylses of 5 samples were executed based on lipid parameters analysis. Results : Korean Medicines with an $IC_{50}$ of below 1 mg/kg were Scutellariae Radix, Gardeniae Fructus, Theae Folium Coptidis Radix, and Mori Cortex Radicis. Body weight change of Mori Cortex Radicis reduced significantly, however fecal triglyceride couldn't regulate effectively. The most excellent inhibitory effect of pancreatic lipase showed in Scutellariae Radix treatment and also regulated significantly serum triglyceride and total cholesterol. Moreover, the supplementation of Coptidis Radix excreted meaningfully triglyceride to fece. Conclusions : In conclusion, Coptidis Radix may exert anti-obesity effect by directly inhibiting pancreatic lipase, which would prevent the absorption of lipid from the small intestine. Besides, Mori Cortex Radicis may led to the decrease of the body weight via the different pathway.

• Journal of Marine Life Science
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• v.8 no.2
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• pp.190-195
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• 2023

In this research, the marine medaka Oryzias javanicus underwent a 96 h exposure to two concentrations of the red tide dinoflagellate Karenia mikimotoi (1,000 and 5,000 cells mL^-1), and the temporal variations in biochemical responses related to antioxidant and immunity parameters were assessed in the liver tissue. The study revealed a significant increase in ichthyotoxicity with elevated cell concentrations of K. mikimotoi, especially evident at 96 h in marine medaka exposed to 5,000 cells mL^-1. At 1,000 cells mL^-1 of K. mikimotoi, the opercular respiratory rate showed a significant increase, whereas exposure to 5,000 cells mL^-1 resulted in a lowered rate. The intracellular malondialdehyde content was significantly elevated in response to both cell concentrations at 96 h. Regarding glutathione content, levels were significantly increased by exposure to both cell concentrations. Catalase and superoxide dismutase enzymatic activities experienced an increase at 1,000 cells mL^-1 of K. mikimotoi, while their activities were reduced at 5,000 cells mL^-1 at 96 h. The analysis of two immunity parameters, alternative complement pathway and lysozyme, demonstrated significantly reduced activities in the liver tissue exposed to 5,000 cells mL^-1 of K. mikimotoi. These findings aim to enhance the understanding of K. mikimotoi toxicity in marine fish by offering insights into biochemical responses associated with harmful algal blooms.

• Journal of KIISE:Software and Applications
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• v.31 no.3
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• pp.343-352
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• 2004

Recently, the information processing of ever increasing bio-related data is becoming a very important issue. One of the main sources of these bio-data comes with the form of biopathways, which includes molecular transactions and processes that are part of biochemical systems. The information represented by biopathways includes various organic relations among its components. However, most of the current systems to represent biopathways have been initially developed without computer processing in mind, and hence suffer from inconsistencies and ambiguities. In this paper, we propose an improved notation, called UniPath, for clear and systematic representation of biopathways. The proposed system is designed to provide a unified representation of metabolic and regulatory pathways. We also designed and implemented a graphic editor for UniPath to draw biopathwavs map according to the proposed notation. The graphic editor is designed so that biopathway data can be easily transformed into XML format.

• Journal of Physiology & Pathology in Korean Medicine
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• v.22 no.4
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• pp.841-848
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• 2008

Archyranthes radix has had extensive therapeutic application, and there has been increasing interest in its biological effects. However, the biochemical effects of Archyranthes radix on chondrocyte oxidative stress have never been systematically investigated. Therefore, we investigated the effects of Acyranthes radix on role of MAPK signal transduction pathway on oxidative stress induced by hydrogen peroxide in rat articular chondrocytes. The statistically significant inhibitory action of Archyranthes radix on cell proliferation was observed at above $5{\mu}g/m{\ell}$. Next, we examined the time-dependent effect of $5{\mu}g/m{\ell}$ Archyranthes radix on cell proliferaion. Archyranthes radix significantly inhibited cell proliferation from 12 hr after treatment (P<0.05). $H_2O_2$, resulted in a time- and dose-dependent cell proliferation, which was largely attributed to oxidative damage. Acyranthes radix and $H_2O_2$ treatment caused marked sustained activation of phosphorylation of ERK1/2. Moreover, the synergistic phosphorylation of p44/42 MAPK by $H_2O_2$ and Archyranthes radix was selectively inhibited by PD 98059, a p44/42 MAPK inhibitor. In conclusion, these results are consistent with the hypothesis that under conditions of oxidative stress, the $H_2O_2$-induced inhibition of cell proliferation in the rat chondrocyte is mediated through a modulation of the Archyranthes radix signaling pathway, promoting further phosphorylation of p44/42 MAPK, indicating a potentially important role in cartilage repair and in the treatment of osteoarthritic cartilage.

• Journal of Microbiology and Biotechnology
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• v.29 no.11
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• pp.1830-1840
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• 2019

Loliolide is one of the most ubiquitous monoterpenoid compounds found in algae, and its potential therapeutic effect on various dermatological conditions via agent-induced biological functions, including anti-oxidative and anti-apoptotic properties, was demonstrated. Here, we investigated the effects of loliolide on hair growth in dermal papilla (DP) cells, the main components regulating hair growth and loss conditions. For this purpose, we used a three-dimensional (3D) DP spheroid model that mimics the in vivo hair follicle system. Biochemical assays showed that low doses of loliolide increased the viability and size of 3D DP spheroids in a dose-dependent manner. This result correlated with increases in expression levels of hair growth-related autocrine factors including VEGF, IGF-1, and KGF. Immunoblotting and luciferase-reporter assays further revealed that loliolide induced AKT phosphorylation, and this effect led to stabilization of β-catenin, which plays a crucial role in the hair-inductive properties of DP cells. Further experiments showed that loliolide increased the expression levels of the DP signature genes, ALP, BMP2, VCAN, and HEY1. Furthermore, conditioned media from loliolide-treated DP spheroids significantly enhanced proliferation and the expression of hair growth regulatory genes in keratinocytes. These results suggested that loliolide could function in the hair growth inductivity of DP cells via the AKT/β-catenin signaling pathway.

• Journal of Ginseng Research
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• v.33 no.3
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• pp.212-218
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• 2009

Triterpenoid saponins were synthesized in Panax ginseng C.A. Meyer via the isoprenoid pathway by cyclization of 2,3-oxidosqualene to give primarily oleanane (beta-amyrin) or dammarane triterpenoid skeletons. The triterpenoids are backbone and undergoes various modifications (oxidation, substitution and glycosylation), mediated by cytochrome P450 (CYP)-dependent monooxygenases, glycosyltransferase and other enzymes. This is likely to be due in part to the complexity of the molecules and the lack of pathway intermediates for biochemical studies. A cDNA clone encoding a putative CYP gene was isolated from flower bud of ginseng and transformed into the plant(Nicotiana tabacum cv. Xanthi) and confirmed by PCR analysis. The CYP gene (PgCYP) contained an open reading frame(ORF) encoding mature protein of 500 amino acids. The expression of PgCYP were investigated in transgenic tobacco by reverse transcriptase-polymerase chain reaction (RT-PCR).