• Molecules and Cells
• /
• v.24 no.2
• /
• pp.200-209
• /
• 2007

We generated gene expression data from the tissues of 50 gastric cancer patients, and applied meta-analysis and gene set analysis to this data and three other stomach cancer gene expression data sets to define the gene expression changes in gastric tumors. By meta-analysis we identified genes consistently changed in gastric carcinomas, while gene set analysis revealed consistently changed biological themes. Genes and gene sets involved in digestion, fatty acid metabolism, and ion transport were consistently down-regulated in gastric carcinomas, while those involved in cellular proliferation, cell cycle, and DNA replication were consistently up-regulated. We also found significant differences between the genes and gene sets expressed in diffuse and intestinal type gastric carcinoma. By gene set analysis of cytogenetic bands, we identified many chromosomal regions with possible gross chromosomal changes (amplifications or deletions). Similar analysis of transcription factor binding sites (TFBSs), revealed transcription factors that may have caused the observed gene expression changes in gastric carcinomas, and we confirmed the overexpression of one of these, E2F1, in many gastric carcinomas by tissue array and immunohistochemistry. We have incorporated the results of our meta- and gene set analyses into a web accessible database (http://human-genome.kribb.re.kr/stomach/).

• Journal of Applied Biological Chemistry
• /
• v.56 no.1
• /
• pp.23-27
• /
• 2013

The roots of Brassica rapa ssp. were extracted with 95% aqueous ethanol and the concentrated extracts were partitioned using ethyl acetate (EtOAc), n-butyl alcohol and $H_2O$, successively. From the EtOAc fraction, five flavonoids were isolated through repeated silica gel and octadecyl silica gel (ODS) column chromatography (c.c.). Based on NMR, mass spectrometry (MS) and IR spectroscopic data, the chemical structures of the compounds were determined to be licochalcone A (1), 4,4'-dihydroxy-3'-methoxychalcone (2), liquirtigenin (3), liquiritin (4), and isoliquiritin (5). This is the first report of these compounds isolated from the root of this plant.

• Microbiology and Biotechnology Letters
• /
• v.45 no.1
• /
• pp.71-80
• /
• 2017

Tea is the most popular beverage in the world. The three main types are green, black, and post-fermented. Post-fermented teas are produced by the microbial fermentation of sun-dried green tea leaves (Camellia sinensis). In this study, the composition of the bacterial communities involved in the production of traditional oriental post-fermented teas (Korean algacha, dancha, and Chinese pu-erh) were investigated using 16S rRNA gene analysis. The dominant microorganisms present in the post-fermented teas included the ${\alpha}$-proteobacteria Rhodobacteraceae and Sphingomonas, and the ${\gamma}$-proteobacteria Pantoea. Cluster analysis confirmed that the microbial populations present in both Korean and Chinese post-fermented teas grouped into the same class. Interestingly, the dominant microorganism present in the Korean post-fermented teas was a bacterium, while for the Chinese post-fermented tea, it was a fungus.

• Journal of Plant Biotechnology
• /
• v.33 no.2
• /
• pp.93-97
• /
• 2006

The calmodulin as a Ca$^{2+}$-binding protein mediates cellular Ca$^{2+}$ signals in response to a wide array of stimuli in higher eukaryotes. Plants produce numerous calmodulin isoforms that exhibit differential gene expression patterns and sense different Ca$^{2+}$ signals. SCaM-5 is a soybean calmodulin that is involved in plant defense signaling. Here, we constructed a SCaM-5 CDNA under control of CaMV 35S promoter and transformed it into tomato (Lycopersicon esculentum). The constitutive over-expression of SCaM-5 in tomato plants exhibited a high levels of pathogenesis-related (PR) gene expression, and conferred an enhanced resistance to two fungal pathogen (Phytophthora capsici, Fusarium oxysporum), and a bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. Thus, this results collectively suggest that SCaM-5 plays an important role in plant defense of tomato.

• Journal of Life Science
• /
• v.16 no.4
• /
• pp.566-570
• /
• 2006

Pronuclear microinjection (PMI) is a primary method for producing transgenic mice and offers a powerful tool for investigating gene function in vivo. The method has several reported advantages and disadvantages. Here, we report another potential shortcoming. The survival rate of fertilized one cell-stage embryos was significantly reduced after PMI procedure (65.4% (1202/1838)). In addition, the proportion of embryos developing to full-term was also significantly lower than that of embryos not undergoing PMI (26.5% (319/1202) vs 41.9% (57/136)). Moreover, 3 out of 21 (14.3%) founder control mice which were non-transgene-carrying littermates of transgenic founders showed histopathological changes in their liver, which was comparable to that in of transgenic lineages (4 out of 27 (14.8%)). In conclusion, the mechanical damages in chromosomes occurring during PMI procedure may be a potential factor influencing phenotypes of transgenic mice.

• Journal of Life Science
• /
• v.20 no.5
• /
• pp.683-690
• /
• 2010

The yeast strains of Saccharomyces diastaticus produce one of three isozymes of an extracellular glucoamylase I, II or III, a type of exo-enzyme which can hydrolyse starch to generate glucose molecules from non-reducing ends. These enzymes are encoded by the STA1, STA2 and STA3 genes. Another gene, sporulation-specific glucoamylase (SGA), also exists in the genus Saccharomyces which is very homologous to the STA genes. The SGA has been known to be produced in the cytosol during sporulation. However, we hypothesized that the SGA is capable of being secreted to the extracellular region because of about 20 hydrophobic amino acid residues at the N-terminus which can function as a signal peptide. We expressed the cloned SGA gene in S. diastaticus YIY345. In order to compare the biochemical properties of the extracellular glucoamylase and the SGA, the SGA was purified from the culture supernatant through ammonium sulfate precipitation, DEAE-Sephadex A-50, CM-Sephadex C-50 and Sephadex G-200 chromatography. The molecular weight of the intact SGA was estimated to be about 130 kDa by gel filtration chromatography with high performance liquid chromatography (HPLC) column. Sodium dedecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed it was composed of two heterogeneous subunits, 63 kDa and 68 kDa. The deglycosylation of the SGA generated a new 59 kDa band on the SDS-PAGE analysis, indicating that two subunits are glycosylated but the extent of glycosylation is different between them. The optimum pH and temperature of the SGA were 5.5 and $45^{\circ}C$, respectively, whereas those for the extracellular glucoamylase were 5.0 and $50^{\circ}C$. The SGA were more sensitive to heat and SDS than the extracellular glucoamylase.

• Molecules and Cells
• /
• v.41 no.5
• /
• pp.413-422
• /
• 2018

Soybean transgenic plants with ectopically expressed AtABF3 were produced by Agrobacterium-mediated transformation and investigated the effects of AtABF3 expression on drought and salt tolerance. Stable Agrobacterium-mediated soybean transformation was carried based on the half-seed method (Paz et al. 2006). The integration of the transgene was confirmed from the genomic DNA of transformed soybean plants using PCR and the copy number of transgene was determined by Southern blotting using leaf samples from $T_2$ seedlings. In addition to genomic integration, the expression of the transgenes was analyzed by RT-PCR and most of the transgenic lines expressed the transgenes introduced. The chosen two transgenic lines (line #2 and #9) for further experiment showed the substantial drought stress tolerance by surviving even at the end of the 20-day of drought treatment. And the positive relationship between the levels of AtABF3 gene expression and drought-tolerance was confirmed by qRT-PCR and drought tolerance test. The stronger drought tolerance of transgenic lines seemed to be resulted from physiological changes. Transgenic lines #2 and #9 showed ion leakage at a significantly lower level (P < 0.01) than ${\underline{n}}on-{\underline{t}}ransgenic$ (NT) control. In addition, the chlorophyll contents of the leaves of transgenic lines were significantly higher (P < 0.01). The results indicated that their enhanced drought tolerance was due to the prevention of cell membrane damage and maintenance of chlorophyll content. Water loss by transpiration also slowly proceeded in transgenic plants. In microscopic observation, higher stomata closure was confirmed in transgenic lines. Especially, line #9 had 56% of completely closed stomata whereas only 16% were completely open. In subsequent salt tolerance test, the apparently enhanced salt tolerance of transgenic lines was measured in ion leakage rate and chlorophyll contents. Finally, the agronomic characteristics of ectopically expressed AtABF3 transgenic plants ($T_2$) compared to NT plants under regular watering (every 4 days) or low rate of watering condition (every 10 days) was investigated. When watered regularly, the plant height of drought-tolerant line (#9) was shorter than NT plants. However, under the drought condition, total seed weight of line #9 was significantly higher than in NT plants (P < 0.01). Moreover, the pods of NT plants showed severe withering, and most of the pods failed to set normal seeds. All the evidences in the study clearly suggested that overexpression of the AtABF3 gene conferred drought and salt tolerance in major crop soybean, especially under the growth condition of low watering.

• Biomolecules & Therapeutics
• /
• v.20 no.4
• /
• pp.425-430
• /
• 2012

Rumex acetosa is a perennial herb that is widely distributed across eastern Asia. Although the hot water extract of R. acetosa has been used to treat gastritis or gastric ulcers as a folk medicine, no scientific report exists for the use of this plant to treat gastric ulcers. Hence, the present study was undertaken to assess the anti-ulcer activity of water and 70% ethanol extracts obtained from R. acetosa, using an HCl/ethanol-induced gastric ulcer model in mice. Anti-inflammatory and free radical-scavenging activities of these two extracts were also evaluated and compared. As a result, the administration of R. acetosa extracts significantly reduced the occurrence of gastric ulcers. However, significant differences in protective activity against gastric ulcers were observed between the two samples. In the case of the group pretreated with an ethanol extract dosage of 100 mg/kg, the protective effect (90.9%) was higher than that of water extract (41.2%). Under histological evaluation, pretreatment with R. acetosa extracts reversed negative effects, such as inflammation, edema, moderate hemorrhaging and loss of epithelial cells, presented by HCl/ethanol-treated stomachs. Meanwhile, R. acetosa extracts showed potent DPPH radical-scavenging activity and decreased NO production in a murine macrophage cell line, RAW 264.7, in a dose-dependent manner without affecting cellular viability. The greater anti-ulcer and NO production inhibitory activities exhibited by ethanol extracts compared to water extracts could be ascribed to the higher emodin levels, a major anthraquinone component of this plant.

• Biomolecules & Therapeutics
• /
• v.27 no.5
• /
• pp.457-465
• /
• 2019

Patients with diabetes mellitus (DM) often suffer from diverse skin disorders, which might be attributable to skin barrier dysfunction. To explore the role of lipid alterations in the epidermis in DM skin disorders, we quantitated 49 lipids (34 ceramides, 14 free fatty acids (FFAs), and cholesterol) in the skin epidermis, liver, and kidneys of db/db mice, a Type 2 DM model, using UPLC-MS/MS. The expression of genes involved in lipid synthesis was also evaluated. With the full establishment of hyperglycemia at the age of 20 weeks, remarkable lipid enrichment was noted in the skin of the db/db mice, especially at the epidermis and subcutaneous fat bed. Prominent increases in the ceramides and FFAs (>3 fold) with short or medium chains ($LXR{\alpha}/{\beta}$ and $PPAR{\gamma}$, nuclear receptors promoting lipid synthesis, lipid synthesis enzymes such as elongases 1, 4, and 6, and fatty acid synthase and stearoyl-CoA desaturase were highly expressed in the skin and livers of the db/db mice. Collectively, our study demonstrates an extensive alteration in the skin and systemic lipid profiles of db/db mice, which could contribute to the development of skin disorders in DM.

• Journal of Life Science
• /
• v.29 no.2
• /
• pp.248-255
• /
• 2019

This research confirmed the diversity and characterization of gut microorganisms isolated from the intestinal organs of Muraenesox cinereus, collected on the Samcheonpo Coast and Seocheon Coast in South Korea. To isolate strains, Marine agar medium was basically used and cultivated at $37^{\circ}C$ and pH7 for several days aerobically. After single colony isolation, totally 49 pure single-colonies were isolated and phylogenetic analysis was carried out based on the result of 16S rRNA gene DNA sequencing, indicating that isolated strains were divided into 3 phyla, 13 families, 15 genera, 34 species and 49 strains. Proteobacteria phylum, the main phyletic group, comprised 83.7% with 8 families, 8 genera and 26 species of Aeromonadaceae, Pseudoalteromonadaceae, Shewanellaceae, Enterobacteriaceae, Morganellaceae, Moraxellaceae, Pseudomonadaceae, and Vibrionaceae. To confirm whether isolated strain can produce industrially useful enzyme or not, amylase, lipase, and protease enzyme assays were performed individually, showing that 39 strains possessed at least one enzyme activity. Especially the Aeromonas sp. strains showed all enzyme activity tested. This result indicated that isolated strains have shown the possibility of the industrial application. Therefore, this study has contributed for securing domestic genetic resources and the expansion of scientific knowledge of the gut microbial community in Muraenesox cinereus of South Korea.