• Journal of KIISE:Databases
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• v.33 no.1
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• pp.12-31
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• 2006

The n-gram inverted index has two major advantages: language-neutral and error-tolerant. Due to these advantages, it has been widely used in information retrieval or in similar sequence matching for DNA and Protein databases. Nevertheless, the n-gram inverted index also has drawbacks: the size tends to be very large, and the performance of queries tends to be bad. In this paper, we propose the two-level n-gram inverted index (simply, the n-gram/2L index) that significantly reduces the size and improves the query performance while preserving the advantages of the n-gram inverted index. The proposed index eliminates the redundancy of the position information that exists in the n-gram inverted index. The proposed index is constructed in two steps: 1) extracting subsequences of length m from documents and 2) extracting n-grams from those subsequences. We formally prove that this two-step construction is identical to the relational normalization process that removes the redundancy caused by a non-trivial multivalued dependency. The n-gram/2L index has excellent properties: 1) it significantly reduces the size and improves the Performance compared with the n-gram inverted index with these improvements becoming more marked as the database size gets larger; 2) the query processing time increases only very slightly as the query length gets longer. Experimental results using databases of 1 GBytes show that the size of the n-gram/2L index is reduced by up to 1.9${\~}$2.7 times and, at the same time, the query performance is improved by up to 13.1 times compared with those of the n-gram inverted index.

• Microbiology and Biotechnology Letters
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• v.6 no.4
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• pp.187-196
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• 1978

Antimetabolite N-2292 substance, an antagonist of L-aspartic acid and L-glutamic acid was isolated from the fermentation broth of Streptomyces. Taxonomical study on the producing strain made it a related species of Streptomyces albulus judged by cultural characteristics and carbon utilization. N-2292 substance was isolated as amorphous white powder with melting point at 185$^{\circ}C$. From the physicochemical characteristics of the substance, it was peptide like substance. It was active against Gram positive and Gram negative bacteria but negative against yeast and mold in its biological properties. It was reversed by L-Asp and L-Glu on the synthetic medium.

• Journal of Environmental Health Sciences
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• v.37 no.2
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• pp.133-140
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• 2011

Antimicrobial activity and bactericidal activity of Caesalpinia sappan L. extracts were investigated against five food-borne pathogens, E. coli, S. aureus, S. typhimurium, B. cereus and L. monocytogenes. Methanol extract of Caesalpinia sappan L. revealed antimicrobial activities against five pathogens. In particular, by paper disc diffusion the highest activity was shown against L. monocytogenes. Antimicrobial activities of methanol extracts showed the most potent activities, but hexane fraction had no activity. Fractions of ethyl acetate and butanol turned out to have higher antimicrobial activities against Gram(+) bacteria than Gram(-) bacteria. The minimum inhibitory concentration against five food-borne pathogens was 1.563 mg/ml on Gram(+) bacteria and 3.125 mg/ml on Gram(-) bacteria. The result of antimicrobial activity in a shaking flask method showed that bacterial growth rate fell by more than 99.999% at 3.125 mg/ml of methanol extract. The highest rate of viable reduction (99.998%) was shown at 0.781 mg/ml of methanol extract against L. monocytogenes. After five minutes of reaction between test strains and methanol extracts, the growth rates of five kinds of bacteria were reduced by more than 99.999% at a concentration of 100 mg/ml. Therefore, it is suggested that methanol extracts of Caesalpinia sappan L. can be developed as a natural sanitizer or disinfectant.

• KSBB Journal
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• v.17 no.2
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• pp.162-168
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• 2002

Human ferritin H- and L-chain genes(hfH and hfL) were cloned into the yeast shuttle vector YEp352 with various promoters, and the vectors constructed were used to transform Saccharomyces cerevisiae 2805. Three different promoters fused to hfH and hfL were used: galactokinase 1 (GAL1) promoter, glyceraldehyde-3-phosphate dehydrogenase(GPD) promoter and alcohol dehydrogenase 1(ADH1 ) promoter. SDS-polyacrylamide gel electrophoresis and Western blotting analyses displayed expression of the introduced hfH and hfL. In the production of both ferritin H and L subunits GAL1 promoter was more effective than GPD promoter or ADH1 promoter. Ferritin H and L subunits produced in S. cerevisiae were spontaneously assembled into its holoproteins as proven on native polyacrylamide gels. Both recombinant H and L-chain ferritins were catalytically active in forming iron core. When the cells were cultured in the medium containing 10 mM ferric citrate, the cell-associated concentration of iron was 174.9 $\mu\textrm{g}$ Per gram(dry cell weight) for the recombinant yeast YG-L and 148.8 $\mu\textrm{g}$ Per gram(dry cell weight) for the recombinant yeast YG-L but was 49.4 $\mu\textrm{g}$ Per gram(dry cell weight) in the wild type, indicating that the iron contents of yeast is improved by heterologous expression of human ferritin H-chain or L-chain genes.

• Korean Journal of Microbiology
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• v.27 no.4
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• pp.404-414
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• 1989

Attempts were made to isolate and identify Gram-positive or lactic acid bacteria in Kimchi fermentation. Species diversity depended on isolation media and temperatures, and diversity tended to be reduced with decrease of temperature. MRS and KM (natural medium prepared from Kimchi materials) were suitable respectively for isolation and present number of species. Identification of isolates was performed by dichotomous identification schemes arranged on the basis of Bergey's manual of Systematic Bacteriology (1986). Gram-positive bacteria isolated at different temperatures (5, 15, $25^{\circ}C$) were 5 species of Leuconostoc, 4 species of Streptococcus, 3 species of Pediococcus, 2 species of Bacillus and 18 species of Lactobacillus. Species with high frequency of appearance were Lactobacillus plantarum, Streptococcus raffinolactis, Leuconostoc mesenteroides subsp. mesenteroides at $25^{\circ}C$, L. plantarum, Lactobacillus fructosus, L. mesenteroides subsp. mesenteroides at $15^{\circ}C$ and L. mesenteroides subsp. mesenteroides, Leuconosotoc paramesenteroides, Lactobacillus maltaromicus at $15^{\circ}C$. In general, Kimchi fermentation was achieved by Lactobacillus spp. (59.7% frequency) at $25^{\circ}C$ and Leuconostoc spp. (65.2% frequency) at $5^{\circ}C$. Pediococcus cerevisiae and Streptococcus faecalis which have been so far known as bacteria of Kimchi fermentation were not isolated.

• Korean journal of food and cookery science
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• v.26 no.2
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• pp.206-213
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• 2010

In this study, the antibacterial activities of essential oil from Zanthoxylum schinifolium against four Gram-positive bacteria and six Gram-negative bacteria were investigated. The antibacterial activity of the oils was determined using the agar-well diffusion assay, MIC (minimum inhibitory concentration) and MBC (minimum bactericidal concentration). In particular, essential oil from Z. schinifolium showed higher antibacterial activity against Gram-positive bacteria than against Gram-negative bacteria. Essential oil from Z. schinifolium displayed large inhibition zones especially against Bacillus cereus (31 mm). At concentrations between 0 and $20\;{\mu}g/mL$ the oils showed an antibacterial effect against both Gram-negative and Gram-positive bacteria. The minimum inhibitory concentration (MIC) values against nine bacteria ranged from 1.25 to $5\;{\mu}g/mL$. The minimum bactericidal concentration (MBC) values against eight bacterial ranged from 2.5 to $20\;{\mu}g/mL$, except Shigella sonnei. Furthermore, our finding on the antibacterial activities of essential oils from Zanthoxylum schinifolium validated the use of this plant for medical purposes.

• Preventive Nutrition and Food Science
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• v.12 no.3
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• pp.135-140
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• 2007

Antibacterial activities of the major phenolic components from Camellia sinensis L. were investigated against several pathogenic microorganisms including Gram-positive strains like Staphylococcus aureus ATCC 29213 and Streptococcus pyogens 308A; and Gram-negative strains like Escherichia coli ATCC 25922, Escherichia coli 078, Pseudomonas aeruginosa 9027, and Enterobacter cloacae 1321E. The MIC values demonstrate that both (-)-epicatechin and (-)-epigallocatechin were more considerably toxic against Staphylococcus aureus ATCC 29213 than the other two catechins like (-)-epicatechingallate and (-)-epigallocatechin-3-gallate. (-)-Epicatechingallate and (-)-epigallocatechin-3-gallate were most inhibitory against Escherichia coli ATCC 25922. As a result, (-)-epicatechin showed predominant antibacterial activities among tea varieties. The contents of major polyphenolic components such as four catechins, theaflavin, and quercetin were different according to fermentation processes. The total contents of four catechins were ranged from 13.81 to 1.33%, with (-)-epigallocatechin-3-gallate being dominant among tea varieties; theaflavin was found the characteristic pigment in fully-fermented black tea.

• Microbiology and Biotechnology Letters
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• v.38 no.1
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• pp.105-111
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• 2010

Caesalpinia sappan L. has long been commonly used in oriental folk medicines to treat diseases. To investigate the antibacterial effects from C. sappan L. heart wood, the MeOH soluble extract was successively fractionated by using hexane, $CHC1_3$, EtOAc, BuOH, MeOH, and $H_2O$. Among of these extracts, the EtOAc fraction which partitioned to 3.94% of the highest yields was to be the most active against all human pathogenic bacteria in this experiment. In addition, the antibacterial activities of the EtOAc fraction were more effective against Gram (+) bacteria compared to those against Gram (-) bacteria, which showed difference of the antibacterial activities against Gram (-) bacteria. To confirm the identity of the active substances, the EtOAc fraction was further separated by silica gel adsorption column, high performance liquid chromatography, and 98.48% purity of brazilin (1.67 mg)/EtOAc (10 mg) fraction was obtained from 300 g of C. sappan L. heart wood. The isolated active substance was a single compound of yellow crystalline, and was identified as brazilin ($C_{16}H_{14}O_5$) by MS, and $^lH$-NMR and $^{13}C$-NMR. These results suggest that the brazilin in the EtOAc fraction from MeOH extract of C. sappan L. has a potential as a natural therapeutic agent against human pathogenic Gram (+) bacteria such as Staphylococcus aureus.

• Journal of Microbiology and Biotechnology
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• v.15 no.2
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• pp.330-336
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• 2005

Lactococcus lactis A164 is a nisin Z-producing strain isolated from kimchi. Its antimicrobial spectrum has been found to be active against most Gram-positive bacteria tested, yet inactive against Gram-negative bacteria [3]. Accordingly, to overcome this drawback, the current study attempted to express human $\beta$-defensin-l (hBD-l), which kills both Gram-positive and Gram-negative bacteria in L. lactis AI64. When the hBD-l cDNA was introduced using a nisin Z-controlled expression cassette, the L. lactis A164 transformants grew very poorly, due to the bactericidal effect of the expressed hBD-l against the transformants. Therefore, a gene fusion system was designed to reduce the toxicity of the expressed heterologous protein against the host cells. As such, the hBD-l gene was fused to the DsbC- Tag of pET -40b(+), then introduced to L. lactis A 164. The transformants expressed an intracellular 35.6-kDa DsbC-hBD-l fusion protein that exhibited slight activity against the host cells, yet not enough to strongly inhibit the cell growth. To obtain the recombinant hBD-l, the DsbC-hBD-l fusion protein was purified by nickel-affinity column chromatography, and the DsbC-Tag removed by cleaving with enterokinase. The cleaved mature hBD-l exhibited strong bactericidal activity against E. coli JM109, indicating that the recombinant L. lactis A 164 produced a biologically active hBD-I. In addition, the recombinant L. lactis A 164 was also found to produce the same level of nisin Z as the wild-type.

• Journal of Pharmacopuncture
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• v.16 no.2
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• pp.15-22
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• 2013

Objective: Evaluations of the in-vitro anti-bacterial activities of aqueous extracts of Acacia catechu (L.F.)Willd, Castanea sativa, Ephedra sinica stapf and Shilajita mumiyo against gram-positive bacteria (Staphylococcus aureus, Streptococcus pneumonia) and gram-negative bacteria (Escherichia coli, klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa) are reasonable since these ethnomedicinal plants have been used in Persian folk medicine for treating skin diseases, venereal diseases, respiratory problems and nervous disorders for ages. Methods: The well diffusion method (KB testing) with a concentration of $250{\mu}g/disc$ was used for evaluating the minimal inhibitory concentrations (MIC). Maximum synergistic effects of different combinations of components were also observed. Results: A particular combination of Acacia catechu (L.F.) Willd, Castanea sativa, Ephedra sinica stapf and shilajita mumiyo extracts possesses an outstanding anti-bacterial activity. It's inhibiting effect on microorganisms is significant when compared to the control group (P<0.05). Staphylococcus aureus was the most sensitive microorganism. The highest anti-bacterial activity against gram-positive bacteria (Staphylococcus aureus, Streptococcus pneumonia) or gram-negative bacteria (Escherichia coli, Klebsiella pneumonia, Proteus mirabilis, and Pseudomonas aeruginosa) was exerted by formula number 2 (table 1). Conclusion: The results reveal the presence of anti-bacterial activities of Acacia catechu, Castanea sativa husk, Ephedra sp. and Mumiyo against gram-positive and gram-negative bacteria. Synergistic effects in a combined formula, especially in formula number 2 (ASLAN$^{(R)}$) can lead to potential sources of new antiseptic agents for treatment of acute or chronic skin ulcers. These results considering the significant anti-bacterial effect of the present formulation, support ethnopharmacological uses against diarrheal and venereal diseases and demonstrate use of these plants to treat infectious diseases.