• BMB Reports
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• v.44 no.11
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• pp.725-729
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• 2011

We report a novel mechanism of a CDH1 splicing mutation in a patient with signet ring cell carcinoma of the stomach. A 27-year-old man complaining of aggravated dyspepsia was diagnosed with signet ring cell carcinoma. Both his father and uncle had died of stomach cancer at a young age. DNA sequencing analysis of the CDH1 gene revealed a splice site mutation (c.833-2A>G). By RNA/cDNA sequencing analysis, CDH1 c.833-2A>G generated a new acceptor site within intron 6, causing the insertion of a 79-bp intronic sequence between exon 6 and 7 (r.833-79_833-1ins), and resulting in a frame shift. E-cadherin immunohistochemical staining revealed a loss of CDH1 expression. This study reveals the disease-causing mechanism of this splicing mutation, and emphasizes the need for functional studies using RNA samples for the accurate interpretation of detected splicing variant. This is the first reported case of a CDH1 mutation in a Korean patient.

• Journal of Physiology & Pathology in Korean Medicine
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• v.19 no.3
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• pp.618-622
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• 2005

Articular cartilage is an important target for studying the arthritic diseases. To verify the therapeutic effects of bee venom herb-acupuncture in vivo, 3${\mu}$l of diluted solution of bee venom for herb-acupuncture were injected into articular cavity once a day during 3 months after making full-thickness defects in rat articular cartilage. Histological examination and immunohistochemistry indicated that the chondrocyte-like tissue was formed during the repair process of cartilage injury, and the expression of a cartilage-specific protein, collagen type II, were significantly activated. It means that the expression of the gene encoding type I collagen was down-regulated, whereas those of collagen type II were up-regulated. Histological examination by hematoxylin-eosin staining indicated that the cells regained their original round morphology. In addition, a homogeneous distribution of articular cartilage extracellular matrices was detected around the cells. These results suggested that bee venom herb-acupuncture was very effective on the recovery of articular chondrocyte phenotype.

• Journal of Mushroom
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• v.11 no.4
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• pp.187-193
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• 2013

A galactose fermentation bacterium producing lactose from red seaweed, which was known well to compromise the galactose as main reducing sugar, was isolated from button mushroom bed in Buyeo-Gun, Chungchugnamdo province. The lactic acid bacteria MONGB-2 was identified as Lactobacillus paracasei subsp. tolerans by analysis of 16S rRNA gene sequence. When the production of lactic acid and acetic acid by L. paracasei MONGB-2 was investigated by HPLC analysis with various carbohydrates, the strain MONGB-2 efficiently convert the glucose and galactose to lactic acid with the yield of 18.86 g/L and 18.23 g/L, respectively and the ratio of lactic acid to total organic acids was 1.0 and 0.91 g/g for both substrates. However, in the case of acetic acid fermentation, other carbohydrates besides galactose and red seaweed hydrolysate could not be totally utilized as carbon sources for acetic acid production by the strain. The lactic acid production from glucose and galactose in the fermentation time courses was gradually enhanced upto 60 h fermentation and the maximal concentration reached to be 16-18 g/L from both substrates after 48 h of fermentation. The initial concentration of glucose and galactose were completely consumed within 36 h of fermentation, of which the growth of cell also was maximum level. In addition, the bioconversion of lactic acid from the red seaweed hydrolysate by L. paracasei MONGB-2 appeared to be about 20% levels of the initial substrates concentration and this results were entirely lower than those of galactose and glucose showed about 60% of conversion. The apparent results showed that L. paracasei MONGB-2 could produce the lactic acid with glucose as well as galactose by the homofermentation through EMP pathway.

• Mass Spectrometry Letters
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• v.3 no.4
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• pp.93-100
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• 2012

Cellular processes such as proliferation, differentiation, and adaptation to environmental changes are regulated by protein phosphorylation. In order to enhance the understanding of molecular dynamics for biological process in detail, it is necessary to develop sensitive and comprehensive analytical methods for the determination of protein phosphorylation. Neural stem cells hold great promise for neural repair following an injury or disease. In this study, we made differentiated oligodendrocytes from human neural stem cells using over-expression of olig2 gene. We confirmed using quantitative phosphoproteome analysis approach that combines stable isotope labeling by amino acids in cell culture (SILAC) and $TiO_2$ micro-column for phosphopeptide enrichment with $MS^2$ and $MS^3$ mass spectrometry. We detected 275 phosphopeptides which were modulated at least 2-fold between human neural stem cells and oligodendrocytes. Among them, 23 phosphoproteins were up-regulated in oligodendrocytes and 79 phosphoproteins were up-regulated in F3 cells.

• Journal of Microbiology and Biotechnology
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• v.15 no.3
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• pp.551-559
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• 2005

The recent rapid increase in genomic data related to many microorganisms and the development of computational tools to accurately analyze large amounts of data have enabled us to design several kinds of simulation approaches for the complex behaviors of cells. Among these approaches, dFBA (dynamic flux balance analysis), which utilizes FBA, differential equations, and regulatory events, has correctly predicted cellular behaviors under given environmental conditions. However, until now, dFBA has centered on substrate concentration, cell growth, and gene on/off, but a detailed hierarchical structure of a regulatory network has not been taken into account. The use of Boolean rules for regulatory events in dFBA has limited the representation of interactions between specific regulatory proteins and genes and the whole transcriptional regulation mechanism with environmental change. In this paper, we adopted the operon as the basic structure, constructed a hierarchical structure for a regulatory network with defined fundamental symbols, and introduced a weight between symbols in order to solve the above problems. Finally, the total control mechanism of regulatory elements (operons, genes, effectors, etc.) with time was simulated through the linkage of dFBA with regulatory network modeling. The lac operon, trp operon, and tna operon in the central metabolic network of E. coli were chosen as the basic models for control patterns. The suggested modeling method in this study can be adopted as a basic framework to describe other transcriptional regulations, and provide biologists and engineers with useful information on transcriptional regulation mechanisms under extracellular environmental change.

• Journal of Life Science
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• v.20 no.6
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• pp.819-824
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• 2010

Genus Phyllostachys is a long-lived woody species primarily distributed throughout South East Asia. Many species of this genus has been regarded as medically and ecologically important in the world. We evaluated representative samples of the four taxa with RAPD to estimate genetic relationships within the genus Phyllostachys. The percentages of polymorphic loci were 8.9-33.3% at the species level. P. bambusoides was found to show lower genetic diversity (H=0.018) than other species. Total genetic diversity ($H_T$) was 0.315, genetic diversity within populations ($H_S$) was 0.043, the proportion of total genetic diversity partitioned among populations ($G_{ST}$) was 0.659 and the gene flow (Nm) was 0.0263. As some Korean populations were isolated and patchily distributed, they exhibited low levels of genetic diversity. The four taxa of the genus Phyllostachys analyzed were distinctly related to a monophyletic. P. nigra var. henonis. Stapf was found to be more closely related to P. pubescens than to P. nigra. P. bambusoides was quite distinct from the remaining species.

• Korean Journal of Agricultural Science
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• v.39 no.2
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• pp.255-261
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• 2012

A bacterium AB-55, isolated from waste mushroom bed of Agaricus bisporus in Sukseong-myeon, Buyeo-gun, Chungcheongnam-do, Korea, was screened onto xylan agar congo-red plate by the xylanolysis method and was used to produce an xylanase in shaker buffle flask cultures containing oat spelt xylans. The phylogenetic analysis using 16S rRNA gene sequence data showed that the strain AB-55 had the highest homology (99.0%) with Bacillus subtilis and it was named as Bacillus subtilis AB-55. A xylanase was purified by ammonium sulfate precipitation (50~80%), gel filtration on sephacryl S-300, and ion exchange chromatography on DEAE sepharose FF. The molecular weight of the xylanase was estimated as 44 kDa by SDS-PAGE. Optimal pH and temperature for the xylanase activity was pH 7 and $50^{\circ}C$, respectively. N-terminal amino acid sequence of the enzyme was identified as Ser-Ala-Val-Lys-His-Gly-Ala-Ile-Val-Phe. The substrate specificity of the enzyme exhibited that it hydrolyzed efficiently oat spelt xylan as well as beechwood xylan, but showed no activity against Avicel and carboxymethyl clellulose (CMC). The enzyme activity was enhanced by $Fe^{2+}$ and $Mn^{2+}$ whereas was entirely inhibited by $Hg^+$.

• Journal of Life Science
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• v.19 no.11
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• pp.1666-1671
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• 2009

In Brassica, S locus glycoprotein (SLG) and S locus receptor kinase (SRK) genes function together for self-recognition in the self-incompatibility response. In addition, a water channel called aquaporins (MOD) is required for the self-incompatibility response. In this study, we isolated the SC-SLG, SC-SRK, and SC-MOD genes from a self-compatible line of B. oleracea. In the self-compatible line, the SC-SLG, SC-SRK, and SC-MOD genes showed the highest degree of sequence similarity with published data and to normal expression by RT-PCR. Therefore, it can be concluded that the SCR/SP11 gene of the B. oleracea pollen may not function and/or that mutations may occur in genes for self-incompatibility that are not linked to the S locus region.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2010.10a
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• pp.17-17
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• 2010

Rhizobacteria are a diverse group of free-living soil bacteria that live in plant rhizosphere and colonized the root system. Plant growth-promoting rhizobacteria (PGPR) possessing ACC deaminase (ACCD) can reduce ACC and ethylene in plant tissue and mediated the growth of plants under various stresses including salt stress. ACCD decrease ethylene levels in plant tissue that produce high levels of ethylene in tissue via elevated levels of ACC under salt stress. We selected strains of Pseudomonas sp. possessing ACCD activity for their ability to promote plant growth under salt stress from soil sample collected at Byeonsan, Jeonbuk, South Korea. The Pseudomonas strains possessing ACCD increased the rate of the seedling and growth of chinese cabbage seeds under salt stress. We cloned ACCD gene from P.fluorescens and expressed recombinant protein in Escherichia coli. The active form of recombinant ACCD converted ACC to a-ketobutyrate. The in vivo treatment of recombinant ACCD itself increase the rate of the seedling and growth of Chinese cabbage seeds under salt stress. The polyclonal P.fluorescens anti-ACCD antibody specifically reacted with ACCD originated from Pseudomonas. This indicates that the antibody might act as an important indicator for ACCD driven from Pseudomonas exhibiting plant growth-promoting activity. This study will be useful for identification of newly isolated PGPR containing ACCD and exploioting the ACCD activity from PGPR against various biotic and abiotic stresses.

• Journal of Periodontal and Implant Science
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• v.43 no.4
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• pp.168-176
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• 2013

Purpose: The purpose of the current study was to examine the effect of dexamethasone (Dex) at various concentrations on the apoptosis and mineralization of human periodontal ligament (hPDL) cells. Methods: hPDL cells were obtained from the mid-third of premolars extracted for orthodontic reasons, and a primary culture of hPDL cells was prepared using an explant technique. Groups of cells were divided according to the concentration of Dex (0, 1, 10, 100, and 1,000 nM). A 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay was performed for evaluation of cellular viability, and alkaline phosphatase activity was examined for osteogenic differentiation of hPDL cells. Alizarin Red S staining was performed for observation of mineralization, and real-time polymerase chain reaction was performed for the evaluation of related genes. Results: Increasing the Dex concentration was found to reduce cellular viability, with an increase in alkaline phosphatase activity and mineralization. Within the range of Dex concentrations tested in this study, 100 nM of Dex was found to promote the most vigorous differentiation and mineralization of hPDL cells. Dex-induced osteogenic differentiation and mineralization was accompanied by an increase in the level of osteogenic and apoptosis-related genes and a reduction in the level of antiapoptotic genes. The decrease in hPDL cellular viability by glucocorticoid may be explained in part by the increased prevalence of cell apoptosis, as demonstrated by BAX expression and decreased expression of the antiapoptotic gene, Bcl-2. Conclusions: An increase in hPDL cell differentiation rather than cellular viability at an early stage is likely to be a key factor in glucocorticoid induced mineralization. In addition, apoptosis might play an important role in Dex-induced tissue regeneration; however, further study is needed for investigation of the precise mechanism.