• Journal of Life Science
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• v.23 no.10
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• pp.1295-1303
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• 2013

According to facts revealed up until the present, there are a total of 68 known phyla on earth, including 55 phyla of bacteria and 13 phyla of archaea. The human large intestine has 9 phyla of microorganisms, which is a relatively lower diversity compared to the general environments of soil or sea. The diversity of intestinal microorganisms is affected by the characteristics of the host (genetic background, sex, age, immune system, and gut motility), the diet (non-digestible carbohydrates, fat, prebiotics, probiotics), and the intake of antibiotics, which in turn have an effect on energy storage processes, gene expressions, and even metabolic diseases like obesity. Probiotics are referred to as living microorganisms that improve the intestinal microbiota and contribute to the health of the host; in addition, probiotics usually comprise lactic acid bacteria. Recently, bacteriotherapy using probiotics has been utilized to treat sicknesses like diarrhea and irritable bowel syndrome. Prebiotics are a food ingredient which can selectively adjust intestinal microorganisms and which comprise inulin, fructooligosaccharides, galactooligosaccharides, and lactulose. In recent days, attention has been paid to the use of dietary cellulose in the large intestine and the production of short chain fatty acids (short-chain fatty acids) in relation to obesity and anticancer. More research into microorganisms in the large intestine is necessary to identify specific microorganism species, which are adjusted by diverse non-digestible carbohydrates, prebiotics, and probiotics in the large intestine and to understand the connection between sicknesses and metabolites like short chain fatty acids produced by these microorganism species.

• Korean Journal of Plant Taxonomy
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• v.41 no.4
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• pp.299-314
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• 2011

The choice of molecular markers is the first step when selecting experimental plans in the field of population genetics. The popular molecular markers in population genetic studies are mainly allozyme, RAPD, RFLP, AFLP, microsatellite, SNP and ISSR. Among these, microsatellites are frequently found in nuclear, chloroplast and mitochondrial genome, showing a high level of polymorphism and nuclear microsatellites are codominant. Thus, it is a favorable molecular marker for population structure analyses and genetic diversity studies. Microsatellites are composed of tandem repeated 1~6 base pair nucleotide motifs and can be easily amplified by PCR reactions using locus specific primers. Because microsatellites have low cross-species transferability, however, they are only applicable between phylogenetically close species. In wild plants, the lack of genomic information and the high development cost of the microsatellite obstruct the wider use of microsatellites in plant population genetics research. In this review, we introduce the basis for microsatellite markers, the development process, and analytical methods as well as evolutionary models and their applications. In addition, possible genotyping errors which lead to erroneous conclusions are discussed.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.8
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• pp.535-542
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• 2013

Since case-based reasoning(CBR) has many advantages, it has been used for supporting decision making in various areas including medical checkup, production planning, customer classification, and so on. However, there are several factors to be set by heuristics when designing effective CBR systems. Among these factors, this study addresses the issue of selecting appropriate neighbors in case retrieval step. As the criterion for selecting appropriate neighbors, conventional studies have used the preset number of neighbors to combine(i.e. k of k-nearest neighbor), or the relative portion of the maximum similarity. However, this study proposes to use the absolute similarity threshold varying from 0 to 1, as the criterion for selecting appropriate neighbors to combine. In this case, too small similarity threshold value may make the model rarely produce the solution. To avoid this, we propose to adopt the coverage, which implies the ratio of the cases in which solutions are produced over the total number of the training cases, and to set it as the constraint when optimizing the similarity threshold. To validate the usefulness of the proposed model, we applied it to a real-world target marketing case of an online shopping mall in Korea. As a result, we found that the proposed model might significantly improve the performance of CBR.

• Journal of Life Science
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• v.16 no.7 s.80
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• pp.1235-1242
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• 2006

Sulforaphane, an isothiocyanate derived from hydrolysis of glucoraphanin in broccoli and other cruciferous vegetables, was shown to induce phase II detoxification enzymes and inhibit chemically induced mammary tumors in rodents. Recently, sulforaphane is known to induce cell cycle arrest and apoptosis in human canter cells, however its molecular mechanisms are poorly understood. In tile present study, we demonstrated that sulforaphane acted to inhibit proliferation and induce morphological changes of human hepatocarcinoma HepG2 cells. Treatment of HepG2 cells with $10{\mu}M\;or\;15{\mu}M$ sulforaphane resulted in significant G2/M cell cycle arrest as determined by DNA flow cytometry. Moreover, $20{\mu}M$ sulforaphane significantly induced the population of sub-G1 cells suggesting that sulforaphane induced apoptosis. This anti-proliferative effect of sulforaphane was accompanied by a marked inhibition of ryclin A, cyclin 31 and Cdc2 protein. However, the levels of tumor suppressor p53 and Cdk inhibitor p21 mRNA and protein expression were significantly increased by sulforaphane treatment in a concentration-dependent manner. Although further studies are needed, the present work suggests that sulforaphane may be a potential rhemoprevetiveichemotherapeucc agent for the treatment of human cancer cells.

• Korean Journal of Microbiology
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• v.44 no.4
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• pp.352-357
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• 2008

We evaluated cultivation methods to obtain pure cultures of previously uncultivated bacteria from soil. Soil bacteria (suspensions) were inoculated onto various oligotrophic media with one of the following additives: 1) soil extract; 2) anthraquinone disulfonate (humic acid analogue); 3) acyl homoserine lactones (quorum-signaling compounds); 4) catalase (for the protection of bacteria from exogenous peroxides). After the relatively long period (60 days) of incubation with elevated concentrations of $CO_2$ (5%, v/v), the media containing catalase showed the highest colony count. We purified 147 randomly selected colonies from the media and the isolates were subjected to the phylogenetic analyses of their 16S rRNA gene sequences. Phylogenetic analysis revealed that approximately 30% of the isolates might belong to novel species or novel family, suggesting that the media and incubation conditions used could be useful for the cultivation of as-yet-uncultured bacteria. Especially, bacteria belonging to the phylum Acidobacteria, ubiquitous bacterial taxon known as an uncultured bacterial group (at least difficult to culture from environmental samples), were successfully cultured in this study.

• Journal of Korea Water Resources Association
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• v.40 no.1 s.174
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• pp.89-99
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• 2007

Uncertainty analysis is used to eliminate the climatic variables of input nodes and construct the model of an optimal type from COMBINE-GRNNM-GA(Type-1), which have been developed in this issue(2007). The input variable which has the lowest smoothing factor during the training performance, is eliminated from the original COMBINE-GRNNM-GA (Type-1). And, the modified COMBINE-GRNNM-GA(Type-1) is retrained to find the new and lowest smoothing factor of the each climatic variable. The input variable which has the lowest smoothing factor, implies the least useful climatic variable for the model output. Furthermore, The sensitive and insensitive climatic variables are chosen from the uncertainty analysis of the input nodes. The optimal COMBINE-GRNNM-GA(Type-1) is developed to estimate and calculate the PE which is missed or ungaged and the $ET_r$ which is not measured with the least cost and endeavor Finally, the PE and $ET_r$. maps can be constructed to give the reference data for drought and irrigation and drainage networks system analysis using the optimal COMBINE-GRNNM-GA(Type-1) in South Korea.

• Korean Journal of Plant Tissue Culture
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• v.25 no.3
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• pp.207-217
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• 1998

Total of 78 strains were characterized based on the morphological characteristics of colonies isolated on Schroth, and New & Kerr's media for selection of hypervirulent wild-type Agrobacterium spp from galls, hairy root-like process and soil of Populus, Malus, Salix and Diopyros in Korea. Among them, 48 strains were able to induce tumors in carrot disc. Hypervirulent A. tumefaciens SP101 and SM042 were identified as biotype 1 and biotype 2, respectively, These strains formed fast growing, larger tumors as compared to those induced by other strains. The binary vector pGA643 with kanamycin resistant gene was mobilized from E. coli MC100 into A. tumefaciens strain SM042 isolated from soil, and/or disarmed vector PC2760 using a triparental mating method with E. coli HB101/pRK2013, and transconjugants, A. tumefaciens SM643 and PC643 were obtained in minimal media containing kanamycin and tetracycline. Tobacco tissues were cocultivated with conjugant Agrobacterium and then transferred to selective medium with 2,4-D and kanamycin to induce the transformants. Calli were formed more efficiently in cocultivation with A. tumefaciens SM643 than that with A. tumefaciens PC643. Most of calli transformed with A. tumefaciens PC643 were friable and regenerated into normal plantlets, while the calli transformed with A. tumefaciens SM643 were compact, hard, and mixed with friable calli. The friable calli formed normal shoots, while compact calli did not form shoots but only grew to typical compact tumor calli. When the shoots formed directly from tobacco stems without callus induction after transformation by A. tumefaciens SM643 with wild-type Ti-plasmid, normal transformed plants can be induced without using disarmed Ti-plasmid.

• Journal of Marine Bioscience and Biotechnology
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• v.1 no.2
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• pp.63-70
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• 2006

Natural product compounds are the source of numerous therapeutic agents. The marine environment produces natural products from a variety of structural classes exhibiting activity against numerous disease targets including anticancer agents. Among these, pectenotoxin-2 (PTX-2), which was first identified as a cytotoxic entity in marine sponges, which depolymerizes actin filaments, was found to be highly effective and more potent to activate an intrinsic pathway of apoptosis in p53-deficient tumor cells compared to those with functional p53 both in vitro and in vivo. However, the anti-proliferative mechanism of the compound at non-cytotoxic concentrations has not yet been explored. In the current study, we sought to investigate anti-proliferation and apoptosis of PTX-2 against U937 human leukemic cells and its underlying molecular mechanism. Exposure of U937 cells to PTX-2 resulted in growth inhibition and induction of apoptosis in dose- and time-dependent manner as measured by MTT assay, fluorescent microscopy and flow cytometric analysis. The anti-proliferative effect of PTX-2 was associated with a marked increase in the expression of cyclin-dependent kinase p21 (WAF1/CIP1) mRNA which was tumor suppressor p53-independent. The increase in apoptosis was connected with a time-dependent down-regulation of anti-apoptotic Bcl-XL and inhibitor of apoptosis proteins (IAPs) family such as XIAP and cIAP-2. Though additional studies are needed, these findings suggested that PTX-2-induced inhibition of U937 cells was associated with the induction of apoptotic cell death and the results provided important new insights into the possible molecular mechanisms of the anti-cancer activity of PTX-2.

• Journal of Life Science
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• v.23 no.2
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• pp.259-266
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• 2013

To isolate the fibrinolytic enzyme, 268 strains from 21 samples were morphologically isolated from Cheonggukjang collected from Korea and Japan. Among the 268 strains, protease-producing bacteria were isolated in nutrient agar medium including 1% skimmed milk. As a result of this, 22 strains were isolated. Apiweb site was used to identify these strains based on their biochemical properties. In addition, 16S rRNA sequencing was performed to identify the strain. Most of the identified strains were Bacillus subtilis and B. amyloliquefaciens. Fibrinolytic enzyme activity was measured with the fibrin plate method. Five strains were finally selected: A2-14, A2-20, C1-05, C1-09, and F2-01. Of those five strains, the A2-20 strain, which is close to B. amyloliquefaciens, showed the strongest fibrinolytic activity. The fibrinolytic enzyme produced by the A2-20 strain was partially purified from culture supernatant by gel filtration and ion exchange chromatography. The optimal pH and temperature values of the partially purified enzyme were 7.0 and $35^{\circ}C$, respectively. Purified protein analysis was carried out with SDS-PAGE and zymography. A genetic analysis was also conducted by PCR based on the consensus sequence of fibrinolytic enzyme. Corresponding genes with a partial sequence of the A2-20 strain were identified.

• The Korean Journal of Blood Transfusion
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• v.23 no.2
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• pp.152-161
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• 2012

Background: Since Jan. 2012, for performance evaluation of viral reagents, analysis of domestic samples has been recommended in order to obtain approval from the KFDA when they are first introduced to Korea. This regulation requires the standard domestic materials driven from locally infected samples. We tried manufacturing the plasma working standards of HBV, HCV, and HIV NAT using a mixed titer of viral loads. Methods: Forty three HBV DNA positive plasmas, 25 HCV RNA positive plasmas, and 26 HIV RNA positive plasmas were evaluated according to viral load and genotype. Several plasma units, which had high-titer viral loads and the common viral genotypes in Korea, were selected as the source materials for each viral standard. To adjust the appropriate concentration based on the detectable range of variable viral reagents, the source plasma was diluted to several concentrations, divided into small vials, and analyzed for quantification. Results: The 13 plasma working standards, which had variable viral loads for the mixed titer performance panel of HIV, HCV, and HBV NAT, were produced. Conclusion: These national standard materials were first produced in order to supply the mixed titer performance panel for the viral NAT reagent of the level IV transfusion related high-risk group in Korea.