• Title/Summary/Keyword: Modified n-gram

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High-Frequency Targeted Mutagenesis in Pseudomonas stutzeri Using a Vector-Free Allele-Exchange Protocol

  • Gomaa, Ahmed E.;Deng, Zhiping;Yang, Zhimin;Shang, Liguo;Zhan, Yuhua;Lu, Wei;Lin, Min;Yan, Yongliang
    • Journal of Microbiology and Biotechnology
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    • v.27 no.2
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    • pp.335-341
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    • 2017
  • The complexity of the bacterial recombination system is a barrier for the construction of bacterial mutants for the further functional investigation of specific genes. Several protocols have been developed to inactivate genes from the genus Pseudomonas. Those protocols are complicated and time-consuming and mostly do not enable easy construction of multiple knock-ins/outs. The current study describes a single and double crossover-recombination system using an optimized vector-free allele-exchange protocol for gene disruption and gene replacement in a single species of the family Pseudomonadaceae. The protocol is based on self-ligation (circularization) for the DNA cassette which has been obtained by overlapping polymerase chain reaction (Fusion-PCR), and carries an antibiotic resistance cassette flanked by homologous internal regions of the target locus. To establish the reproducibility of the approach, three different chromosomal genes (ncRNA31, rpoN, rpoS) were knocked-out from the root-associative bacterium Pseudomonas stutzeri A1501. The results showed that the P. stutzeri A1501 mutants, which are free of any plasmid backbone, could be obtained via a single or double crossover recombination. In order to optimize this protocol, three key factors that were found to have great effect on the efficiency of the homologous recombination were further investigated. Moreover, the modified protocol does not require further cloning steps, and it enables the construction of multiple gene knock-in/out mutants sequentially. This work provides a simple and rapid mutagenesis strategy for genome editing in P. stutzeri, which may also be applicable for other gram-negative bacteria.

A Study on Performance Evaluation of Hidden Markov Network Speech Recognition System (Hidden Markov Network 음성인식 시스템의 성능평가에 관한 연구)

  • 오세진;김광동;노덕규;위석오;송민규;정현열
    • Journal of the Institute of Convergence Signal Processing
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    • v.4 no.4
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    • pp.30-39
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    • 2003
  • In this paper, we carried out the performance evaluation of HM-Net(Hidden Markov Network) speech recognition system for Korean speech databases. We adopted to construct acoustic models using the HM-Nets modified by HMMs(Hidden Markov Models), which are widely used as the statistical modeling methods. HM-Nets are carried out the state splitting for contextual and temporal domain by PDT-SSS(Phonetic Decision Tree-based Successive State Splitting) algorithm, which is modified the original SSS algorithm. Especially it adopted the phonetic decision tree to effectively express the context information not appear in training speech data on contextual domain state splitting. In case of temporal domain state splitting, to effectively represent information of each phoneme maintenance in the state splitting is carried out, and then the optimal model network of triphone types are constructed by in the parameter. Speech recognition was performed using the one-pass Viterbi beam search algorithm with phone-pair/word-pair grammar for phoneme/word recognition, respectively and using the multi-pass search algorithm with n-gram language models for sentence recognition. The tree-structured lexicon was used in order to decrease the number of nodes by sharing the same prefixes among words. In this paper, the performance evaluation of HM-Net speech recognition system is carried out for various recognition conditions. Through the experiments, we verified that it has very superior recognition performance compared with the previous introduced recognition system.

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Sesquiterpenoids Bioconversion Analysis by Wood Rot Fungi

  • Lee, Su-Yeon;Ryu, Sun-Hwa;Choi, In-Gyu;Kim, Myungkil
    • 한국균학회소식:학술대회논문집
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    • 2016.05a
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    • pp.19-20
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    • 2016
  • Sesquiterpenoids are defined as $C_{15}$ compounds derived from farnesyl pyrophosphate (FPP), and their complex structures are found in the tissue of many diverse plants (Degenhardt et al. 2009). FPP's long chain length and additional double bond enables its conversion to a huge range of mono-, di-, and tri-cyclic structures. A number of cyclic sesquiterpenes with alcohol, aldehyde, and ketone derivatives have key biological and medicinal properties (Fraga 1999). Fungi, such as the wood-rotting Polyporus brumalis, are excellent sources of pharmaceutically interesting natural products such as sesquiterpenoids. In this study, we investigated the biosynthesis of P. brumalis sesquiterpenoids on modified medium. Fungal suspensions of 11 white rot species were inoculated in modified medium containing $C_6H_{12}O_6$, $C_4H_{12}N_2O_6$, $KH_2PO_4$, $MgSO_4$, and $CaCl_2$ for 20 days. Cultivation was stopped by solvent extraction via separation of the mycelium. The metabolites were identified as follows: propionic acid (1), mevalonic acid lactone (2), ${\beta}$-eudesmane (3), and ${\beta}$-eudesmol (4), respectively (Figure 1). The main peaks of ${\beta}$-eudesmane and ${\beta}$-eudesmol, which were indicative of sesquiterpene structures, were consistently detected for 5, 7, 12, and 15 days These results demonstrated the existence of terpene metabolism in the mycelium of P. brumalis. Polyporus spp. are known to generate flavor components such as methyl 2,4-dihydroxy-3,6-dimethyl benzoate; 2-hydroxy-4-methoxy-6-methyl benzoic acid; 3-hydroxy-5-methyl phenol; and 3-methoxy-2,5-dimethyl phenol in submerged cultures (Hoffmann and Esser 1978). Drimanes of sesquiterpenes were reported as metabolites from P. arcularius and shown to exhibit antimicrobial activity against Gram-positive bacteria such as Staphylococcus aureus (Fleck et al. 1996). The main metabolites of P. brumalis, ${\beta}$-Eudesmol and ${\beta}$-eudesmane, were categorized as eudesmane-type sesquiterpene structures. The eudesmane skeleton could be biosynthesized from FPP-derived IPP, and approximately 1,000 structures have been identified in plants as essential oils. The biosynthesis of eudesmol from P. brumalis may thus be an important tool for the production of useful natural compounds as presumed from its identified potent bioactivity in plants. Essential oils comprising eudesmane-type sesquiterpenoids have been previously and extensively researched (Wu et al. 2006). ${\beta}$-Eudesmol is a well-known and important eudesmane alcohol with an anticholinergic effect in the vascular endothelium (Tsuneki et al. 2005). Additionally, recent studies demonstrated that ${\beta}$-eudesmol acts as a channel blocker for nicotinic acetylcholine receptors at the neuromuscular junction, and it can inhibit angiogenesis in vitro and in vivo by blocking the mitogen-activated protein kinase (MAPK) signaling pathway (Seo et al. 2011). Variation of nutrients was conducted to determine an optimum condition for the biosynthesis of sesquiterpenes by P. brumalis. Genes encoding terpene synthases, which are crucial to the terpene synthesis pathway, generally respond to environmental factors such as pH, temperature, and available nutrients (Hoffmeister and Keller 2007, Yu and Keller 2005). Calvo et al. described the effect of major nutrients, carbon and nitrogen, on the synthesis of secondary metabolites (Calvo et al. 2002). P. brumalis did not prefer to synthesize sesquiterpenes under all growth conditions. Results of differences in metabolites observed in P. brumalis grown in PDB and modified medium highlighted the potential effect inorganic sources such as $C_4H_{12}N_2O_6$, $KH_2PO_4$, $MgSO_4$, and $CaCl_2$ on sesquiterpene synthesis. ${\beta}$-eudesmol was apparent during cultivation except for when P. brumalis was grown on $MgSO_4$-free medium. These results demonstrated that $MgSO_4$ can specifically control the biosynthesis of ${\beta}$-eudesmol. Magnesium has been reported as a cofactor that binds to sesquiterpene synthase (Agger et al. 2008). Specifically, the $Mg^{2+}$ ions bind to two conserved metal-binding motifs. These metal ions complex to the substrate pyrophosphate, thereby promoting the ionization of the leaving groups of FPP and resulting in the generation of a highly reactive allylic cation. Effect of magnesium source on the sesquiterpene biosynthesis was also identified via analysis of the concentration of total carbohydrates. Our current study offered further insight that fungal sesquiterpene biosynthesis can be controlled by nutrients. To profile the metabolites of P. brumalis, the cultures were extracted based on the growth curve. Despite metabolites produced during mycelia growth, there was difficulty in detecting significant changes in metabolite production, especially those at low concentrations. These compounds may be of interest in understanding their synthetic mechanisms in P. brumalis. The synthesis of terpene compounds began during the growth phase at day 9. Sesquiterpene synthesis occurred after growth was complete. At day 9, drimenol, farnesol, and mevalonic lactone (or mevalonic acid lactone) were identified. Mevalonic acid lactone is the precursor of the mevalonic pathway, and particularly, it is a precursor for a number of biologically important lipids, including cholesterol hormones (Buckley et al. 2002). Farnesol is the precursor of sesquiterpenoids. Drimenol compounds, bi-cyclic-sesquiterpene alcohols, can be synthesized from trans-trans farnesol via cyclization and rearrangement (Polovinka et al. 1994). They have also been identified in the basidiomycota Lentinus lepideus as secondary metabolites. After 12 days in the growth phase, ${\beta}$-elemene caryophyllene, ${\delta}$-cadiene, and eudesmane were detected with ${\beta}$-eudesmol. The data showed the synthesis of sesquiterpene hydrocarbons with bi-cyclic structures. These compounds can be synthesized from FPP by cyclization. Cyclic terpenoids are synthesized through the formation of a carbon skeleton from linear precursors by terpene cyclase, which is followed by chemical modification by oxidation, reduction, methylation, etc. Sesquiterpene cyclase is a key branch-point enzyme that catalyzes the complex intermolecular cyclization of the linear prenyl diphosphate into cyclic hydrocarbons (Toyomasu et al. 2007). After 20 days in stationary phase, the oxygenated structures eudesmol, elemol, and caryophyllene oxide were detected. Thus, after growth, sesquiterpenes were identified. Per these results, we showed that terpene metabolism in wood-rotting fungi occurs in the stationary phase. We also showed that such metabolism can be controlled by magnesium supplementation in the growth medium. In conclusion, we identified P. brumalis as a wood-rotting fungus that can produce sesquiterpenes. To mechanistically understand eudesmane-type sesquiterpene biosynthesis in P. brumalis, further research into the genes regulating the dynamics of such biosynthesis is warranted.

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Comparison of the Plant Characteristics and Nutritional Components between GM and Non-GM Chinese Cabbages Grown in the Central and Northern Parts of Korea (중·북부지역에서 재배된 GM 배추와 Non-GM 배추간의 식물체 특성 및 영양 성분 비교 분석)

  • Cho, Dong-Wook;Oh, Jin-Pyo;Park, Kuen-Woo;Lee, Dong-Jin;Chung, Kyu-Hwan
    • Horticultural Science & Technology
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    • v.28 no.5
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    • pp.836-844
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    • 2010
  • This study was carried out to investigate plant characteristics and nutritional components of the genetically modified (GM) Chinese cabbage and its control line grown in the central and northern parts of Korea in order to establish the evaluating protocol and standard assessment. The GM and non-GM Chinese cabbage was planted with normal and concentrated density at two locations in spring and fall of 2008 and 2009. From the statistic analysis on plant characteristics and nutritional components, there were not many significant differences between GM and non-GM Chinese cabbage. Only few differences in the plant characteristics were found between the dense and normal planting. In the dense planting, there was no significant difference between GM and non-GM Chinese cabbages except for three out of 18 plant traits, such as leaf shape, hairiness and midrib length. On the other hand, nine plant traits including leaf length, leaf width, leaf color, leaf shape, fresh weigh of ground part, number of leaf, midrib length, midrib width and root diameter were slightly different between GM and non-GM Chinese cabbage in the normal planting. In case of leaf length, midrib length, midrib width and fresh weigh of ground part, there were significantly differences not only between two lines, but also between two locations. From nutritional component analysis, only five fatty acids were identified in the Chinese cabbage: palmitic acid, oleic acid, stearic acid, linoleic acid and linolenic acid. Except linoleic acid, four fatty acids in one gram of dried sample from GM line were little higher than those from non-GM line. However, there were no significant differences in total contents of fatty acids not only between GM and non-GM Chinese cabbage line, but also between northern and central cultivating areas in the normal and dense planting. According to the composition of inorganic elements identified in the samples from both lines, there were six macro-elements, such as N, P, Ca, K, Mg and Na, and four micro-elements, Cu, Fe, Mn and Zn. Based on the result from PCA analysis, specific clusters were not found between GM Chinese cabbage and the control line, but found between two regions.

Enzymatic Characteristics of Water-Insoluble ${\alpha}-Amylase$ Immobilized on Dithiocarbamate Wool (Dithiocarbamate Wool에 고정(固定)된 불용성(不溶性) ${\alpha}-Amylase$의 특성(特性)에 대하여)

  • Lee, Kyung-Hee;Kim, Jong-Deog;Lee, Kang-Ho
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.14 no.2
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    • pp.164-170
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    • 1985
  • Yellowish modified wool, dithiocarbamate(DTC) wool, was synthesized by partial hydrolysis in 0.2 N-NaOH reacting with carbon disulfide to use as ${\alpha}-amylase$ immobilization matrix. ${\alpha}-amylase$ was immobilized reacting with sulfide group of DTC-wool by covalent binding within 1 hour. 0.5 gram of this preparation, $DTC-wool-{\alpha}-amylase$, contained 150 ug of enzyme protein and its specific activity was about 90% of the native one. General properties of $DTC-wool-{\alpha}-amylase$ were a little different from optimum temperature, optimum pH, heat stability, kinetic constants and activation energy. An apparent Michaelis constant and maximum velocity of $DTC-wool-{\alpha}-amylase$ were 5.56 mg/ml and 0.37 mg/ml. $min^{-1}$ respectively, while activation energy was 16.6 kcal/mole.

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