• Proceedings of the Microbiological Society of Korea Conference
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• 2001.11a
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• pp.46-53
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• 2001

A commensal thermophile, Symbiobacterium toebii, isolated from hay compost (toebii) in Korea commensally interacted with a thermophilic Geobacillus toebii sp. nov., which was a new species within the genus Geobacillus on the basis of the phenotypic traits and molecular systematic data. S. toebii required the crude extracts and/or culture supernatant of the Geobacillus toebii for axenic growth and could grow on the temperature between 45 and $70^{\circ}C$ (optimum: $60^{\circ}C$; 2.4 h doubling time) and pH 6.0 and 9.0 (optimum: pH 7.5). The G+C content of the genomic DNA was $65 mol\%$, and the major quinones were MK-6 and MK-7. A phylogenetic analysis of its 16S rDNA sequence indicated that Symbiobacterium toebii was closely related with solely reported Symbiobacterium thermophilum. The presence of the commensal thermophile 16S rDNA and accumulation of indole in all the enriched cultures indicate that Symbiobacterium toebii is widely distributed in the various soils. The genome of S. toebii constituted a circular chromosome of 3,280,275 base pairs and there was not an extra-chromosomal element (ECE). It contained about 4,107 predicted coding sequences. Of these protein coding genes, about $45.6\%$ was encoded well-known proteins and annotated the functional assignment of 1,874 open reading frames (ORFs), and the rest predicted to have unknown functions. The genes encoding thermostable tyrosine phenol-lyase and tryptophan indole-lyase were cloned from the genomic DNA of S. toebii and the enzymatic production of L-tyrosine and L-tryptophan was carried out with two thermostable enzymes overexpressed in recombinant E. coli.

• The Korean Journal of Mycology
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• v.39 no.1
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• pp.22-30
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• 2011

Weonhyeong is one of important commercial strains. It has good characteristics of bundle formation, grey colored pilei and high productivity. We previously reported grouping of 70 strains of Pleurotus ostreatus in which one group contained 35 strains including Weonhyeong. Four strains in that group showed same profiles implicating no variety distinction for mushroom cultivation. Now we developed a specific marker for identification of Weonhyeong. Sequence Characterized Amplified Region (SCAR) marker was developed from the RAPD amplicon. SCAR marker 'S-OPO5' produced only one band specific to 2183, 2240, 2595 and 2725 strains showing similar banding patterns to Weonhyeong in RAPD-PCR results. The sequence of 'S-OPO5' marker was unknown when compared with the data in the Genbank using BLASTN. BLASTX results indicated that the marker showed significant alignment with the protein sequences in Tricholoma bakamatsutake reverse transcriptase. The results indicate that this new SCAR marker ('S-OPO5') will be valuable to distinguish the Weonhyeong similar strains from Pleurotus spp.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.12 no.8
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• pp.3541-3546
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• 2011

Autophagy is an evolutionarily conserved lysosomal pathway for degrading cytoplasmic proteins, macromolecules, and organelles in addition to recycling protein and ATP synthesis. Although autophagy is very important during embryogenesis, the mechanism underlying the dynamic development during this process remains largely unknown. In order to obtain insights into autophagy in early embryo development, we analyzed gene expression levels of autophagy-related genes (ATGs) in mouse embryos developing in vitro. Using real time RT-PCR technique, ATGs including Atg2a, Atg3, Atg4b, Atg5, Atg6, Atg7, Atg9a, and Wipi3, as maternal transcripts, were only up-regulated in 1-cell embryo stage before zygotic genomic activation (ZGA), and then expression decreased from 2-cell to blastocyst embryo stage. ATGs including Dram and Atg9b were expressed abundantly in 1-cell embryo state and in blastocyst embryo stage, athough Atg8 and Ulk1 were constantly expressed during preimplantation stage. However, Atg4d were only up-expressed from 4-cell to blastocyst stage. These results suggest that autophagy is related in mouse embryo, which possibly gives an important role for early development.

• Biomolecules & Therapeutics
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• v.22 no.2
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• pp.129-135
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• 2014

Previously, we reported that lysophosphatidylethanolamine (LPE), a lyso-type metabolite of phosphatidylethanolamine, can increase intracellular $Ca^{2+}$ ($[Ca^{2+}]_i$) via type 1 lysophosphatidic acid (LPA) receptor ($LPA_1$) and CD97, an adhesion G-protein-coupled receptor (GPCR), in MDA-MB-231 breast cancer cells. Furthermore, LPE signaling was suggested as like $LPA_1/CD97-G_{i/o}$ proteins-phospholipase $C-IP_3-Ca^{2+}$ increase in these cells. In the present study, we further investigated actions of LPE not only in the $[Ca^{2+}]_i$ increasing effect but also in cell proliferation and migration in MDA-MB-231 breast cancer cells. We utilized chemically different LPEs and a specific inhibitor of $LPA_1$, AM-095 in comparison with responses in SK-OV3 ovarian cancer cells. It was found that LPE-induced $Ca^{2+}$ response in MDA-MB-231 cells was evoked in a different manner to that in SK-OV3 cells in terms of structural requirements. AM-095 inhibited LPE-induced $Ca^{2+}$ response and cell proliferation in MDA-MB-231 cells, but not in SK-OV3 cells, supporting $LPA_1$ involvement only in MDA-MB-231 cells. LPA had significant effects on cell proliferation and migration in MDA-MB-231 cells, whereas LPE had less or no significant effect. However, LPE modulations of MAPKs (ERK1/2, JNK and p38 MAPK) was not different to those by LPA in the cells. These data support the involvement of LPA1 in LPE-induced $Ca^{2+}$ response and cell proliferation in breast MDA-MB-231 cells but unknown GPCRs (not $LPA_1$) in LPE-induced responses in SK-OV3 cells. Furthermore, although LPE and LPA utilized $LPA_1$, LPA utilized more signaling cascades than LPE, resulting in stronger responses by LPA in proliferation and migration than LPE in MDA-MB-231 cells.

• Journal of Physiology & Pathology in Korean Medicine
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• v.27 no.6
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• pp.782-788
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• 2013

Chrysanthemum zawadskii Herbich var. latilobum Kitamura (Compositae), colloquially known "Gujulcho" in Korea, has been used in traditional medicine for the treatment of various diseases, including cough, common cold, bladder-related disorders, gastroenteric disorders, hypertension, and inflammatory diseases, such as pneumonia, bronchitis, pharyngitis, and rheumatoid arthritis (RA) However, the effect of Chrysanthemum zawadskii var. latilobum on breast cancer invasion is unknown. In this study, we investigated the inhibitory effect of Chrysanthemum zawadskii var. latilobum extract (CZE) on 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced matrix metalloproteinase-9 (MMP-9) expression and cell invasion, as well as the molecular mechanisms involved in MCF-7 cells. CZE were not cytotoxic up to 100 ${\mu}g/ml$ concentration in the MCF-7 cell line. CZE decreased MMP-9 expression. TPA substantially increased NF-${\kappa}B$ DNA binding activity. Pre-treatment with CZE inhibited TPA-stimulated NF-${\kappa}B$ binding activity and NF-${\kappa}B$ related protein expression. To identify invasion ability of MCF-7 cells decreased by CZE, we used martrigel invasion assay. As a result, it is significantly decreased cell invasion. These results indicate that CZE-mediated inhibition of TPA-induced MMP-9 expression and cell invasion involves the suppression of the NF-${\kappa}B$ pathway in MCF-7 cells. Chrysanthemum zawadskii var. latilobum may have potential value in restricting breast cancer metastasis.

• Applied Biological Chemistry
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• v.18 no.3
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• pp.167-176
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• 1975

As a study on the ATP-inhibited ribonuclease of Bacillus subtilis the screening work for obtaining the ATP-inhibited ribonuclease negative mutant were carried out. And mutant strain was selected by the treatment of N-methyl-N'-nitro-N-nitrosoguanidine (NTG). For the selected strain the enzyme purification and some physiological properties were examined and the results obtained were as follows. 1. Among tested 1817 strains with the treatment of NTG, 101 strain was selected as a mutant strain. 2. ATP-inhibited ribonuclease was tentatively purified by several independent column chromatography. The results with Sephadex G-75 column were 30 times purification, 99% recovery, and 20 times purification, 98% recovery, respectively. 3. ATP-inhibited ribonuclease was purified by 60 times through acid treatment, ammonium fractionation, and two successive chromatography. 4. The purified ribonuclease were shown to be effectively concentrated in robonnclease content and to have reduced numbers of protein band on Disc electrophoresis. 5. This enzyme degraded single-stranded RNA to 2',3'-cyclic AMP, 2',3'-cyclic CMP, 2',3,-cyclic GMP, 2',3'-cyclic UMP and some unknown intermediates. The enzyme could not split double-stranded RNA.

• Journal of Nutrition and Health
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• v.25 no.6
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• pp.429-449
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• 1992

The consumption of foods rich in TDF should not be associated with impaired mineral absorp-tion and long-term mineral status. In surveys of populations consuming high amounts of TDF e.g Third World populations and vegetarinas gross deficiencies in mineral nutrition have not been noted. If mineral status is low among these groups it is most likely caused by the inadequacy or imbalance of the diet and not by the TDF. The key word is interaction which should be inte-rpreted in dietary imbalances that produce nut-rient deficiencies. There are no strong data to support the concept that TDF inhibits mineral absorption through a binding chelation mechanism. Limited data sug-gest that positively charged groups on polymers such as chitosan and cholestyramine will decrease iron absorption in humans and animals. Because TDF does not contain positively charged groups future research should be directed at the possible role of protein consumed along with TDF and the combination of effects on mineral nutrition Phytic acid is acknowledged as a potent chela-tor of zinc. However its association with zinc and its propensity to lower Zn bioavaiability may enhance the absorption of other elements notably copper and iron. The importance of interactions among nutrients including TDF will gain addi-tional attention in the scientific community. Soluble and insoluble dietary fiber function di-fferently in the intestine. Insoluble fibers accele-rate movement through the intestine. Soluble die-tary fibers appear to regulated blood concentra-tions of glucose and cholesterol albeit by some unknown mechanism. In creased viscosity produ-ced by the SDF in the intestine may provide an explanation of how this class of polymers affects plasma glucose cholesterol and other nutrients. Employing a double-perfusion technique in the rat we demonstrated that viscosity produced by SDF will delay transfer of zinc into the circulatory system. This delayed absorption should not be interpreted as decreased utilization. A great deal of additional research is required to prove the importance of luminaly viscosity produced by SDF on slowing nutrient absorption or regulating bllod nutrient homeostasis. Increased intake of TDF in the total human diet appears desirable. A dietary intake of 35g/day should not be considered to have a negative effect on mineral absorption. It is important to educate people that an intake of more than 35g TDF/day may cause an imbalance in the diet that can adve-rsely affect mineral utilization. Acknowledgments. Appreciation is given to Dr. George V. Vahouny(deceased) who was intense a great competitor in and out of science and who gave the author inspiration Portions of this work were supported by the University of Missouri Ag-ricultural Station and by a grant from the Univer-rch Support Grant RR 07053 from the National Institutes of Health. Contribution of the Missouri Agriculatural Experiments Station Journal Series No. 10747.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.7
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• pp.962-970
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• 2012

This study aimed to investigate the effects of ruminal infusion of garlic oil (GO) on fermentation dynamics, fatty acid (FA) profile, and abundance of bacteria involved in biohydrogenation in the rumen. Six wethers fitted with ruminal fistula were assigned to two groups for cross-over design with a 14-d interval. Each 30-d experimental period consisted of a 27-d adaptation and a 3-d sample collection. Goats were fed a basal diet without (control) or with GO ruminal infusion (0.8 g/d). Ruminal contents collected before (0 h) and at 2, 4, 6, 8, and 10 h after morning feeding were used for fermentation analysis, and 0 h samples were further used for FA determination and DNA extraction. Garlic oil had no influence on dry matter intakes of concentrate and hay. During ruminal fermentation, GO had no effects on total VFA concentration and individual VFA molar proportions, whereas GO increased the concentrations of ammonia nitrogen and microbial crude protein (p<0.05). Compared with control, GO group took a longer time for total VFA concentration and propionate molar proportion to reach their respective maxima after morning feeding. The ratio of acetate to propionate in control reduced sharply after morning feeding, whereas it remained relatively stable in GO group. Fatty acid analysis showed that GO reduced saturated FA proportion (p<0.05), while increasing the proportions of C18, t11-18:1 (TVA), c9,t11-conjugated linoleic acid (c9,t11-CLA), t10,c12-CLA, and polyunsaturated FA (p<0.05). The values of TVA/(c9,t11-CLA+TVA) and C18:0/(TVA+C18:0) were reduced by GO (p<0.05). Real-time PCR showed that GO tended to reduce Butyrivibrio proteoclasticus abundance (p = 0.058), whereas GO had no effect on total abundance of the Butyrivibrio group bacteria. A low correlation was found between B. proteoclasticus abundance and C18:0/(TVA+C18:0) (p = 0.910). The changes of fermentation over time suggested a role of GO in delaying the fermentation process and maintaining a relatively modest change of ruminal environment. The inhibitory effects of GO on the final step of biohydrogenation may be related to its antibacterial activity against B. proteoclasticus and other unknown bacteria involved.

• Clinical and Experimental Pediatrics
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• v.52 no.2
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• pp.256-260
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• 2009

Idiopathic pulmonary hemosiderosis (IPH) is a rare disease affecting mostly children. This disorder is characterized by recurrent episodes of hemoptysis, bilateral diffuse pulmonary infiltrates, and iron-deficiency anemia. An acute fulminant alveolar hemorrhage can be fatal due to respiratory failure, while chronic hemorrhage leads to hemosiderin-laden macrophages and pulmonary fibrosis. Genetic, autoimmune, allergic, environmental, and metabolic mechanisms of pathogenesis have been suggested, but the etiology of IPH remains unknown. We report on a 9-year-old girl with idiopathic pulmonary hemosiderosis who showed seasonal recurrences without cause.

• KIISE Transactions on Computing Practices
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• v.20 no.9
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• pp.513-518
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• 2014

It has become possible for small scale laboratories to interpret large scale genomic DNA, thanks to the reduction of the sequencing cost by the development of next generation sequencing (NGS). De novo assembly is a method which creates a putative original sequence by reconstructing reads without using a reference sequence. There have been various study results on de novo assembly, however, it is still difficult to get the desired results even by using the same assembly procedures and the analysis tools which were suggested in the studies reported. This is mainly because there are no specific guidelines for the assembly procedures or know-hows for the use of such analysis tools. In this study, to resolve these problems, we introduce steps to finding whole genome of an unknown DNA via NGS technology and de novo assembly, while providing the pros and cons of the various analysis tools used in each step. We used 350Mbp of Toxocara canis DNA as an application case for the detailed explanations of each stated step. We also extend our works for prediction of protein-coding genes and their functions from the draft genome sequence by comparing its homology with reference sequences of other nematodes.