• Journal of Microbiology and Biotechnology
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• v.25 no.10
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• pp.1614-1620
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• 2015

Plasmid-cured derivative strains of Bacillus anthracis are frequently used in laboratory studies. Plasmid incompatibility, which does not increase the risk of chromosomal mutation, is a useful method for plasmid curing. However, in bacteria containing multiple plasmids, it often requires the sequential introduction of multiple, specific incompatibility plasmids. This lengthy process renders the traditional plasmid incompatibility method inefficient and mutation-prone. In this study, we successfully cured plasmids pXO1 and pXO2 from B. anthracis A16 simultaneously using only one recombinant incompatible plasmid, pKORT, to obtain a plasmid-free strain, designated A16DD. This method may also be useful for the simultaneous, one-step curing of multiple plasmids from other bacteria, including Bacillus thuringiensis and Yersinia pestis.

• Korean Journal of Microbiology
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• v.43 no.4
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• pp.317-320
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• 2007

In this paper, we have developed base-calling error detection program and algorithm which show the list of the genes or sequences that are suspected to contain base-calling errors. Those programs detect dubious bases in a few aspects in the process of microbial genome project. The first module detects base-calling error from the Phrap file by using contig assembly information. The second module analyzes frame shift mutation if it is originated from real mutation or artifact. Finally, in the case that there is control microbial genome annotation information, the third module extracts and shows the candidate base-calling error list by comparative genome analysis method.

• Journal of the Institute of Convergence Signal Processing
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• v.3 no.2
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• pp.71-75
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• 2002

We propose a new method to deal with the optimized auto-tuning for the PID controller which is used to the process-control in various fields. First of all, in this method, 1st order delay system with dead time which is modelled from the unit step response of the system is Pade-approximated, then initial values are determined by the Ziegler-Nichols method and deciding binary strings of parents generation using by the fitness values of genetic algorithms, we perform selection, crossover and mutation to generate the descendant generation. The advantage of this method is better than the Ziegler-Nickels method in characteristic of output, and has extent of applying without limit of K, L, T parameters.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.8 no.7
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• pp.1553-1557
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• 2004

A real-time processing system for embedded hardware genetic algorithm is suggested. In order to operate basic module of genetic algorithm in parallel, such as selection, crossover, mutation and evaluation, dual processors based architecture is implemented. The system consists of two Xscale processors and two FPGA with evolvable hardware, which enables to process genetic algorithm efficiently by distributing the computational load of hardware genetic algorithm to each processors equally. The hardware genetic algorithm runs on Linux OS and the resulted chromosome is executed on evolvable hardware in FPGA. Furthermore, the suggested architecture can be extended easily for a couple of connected processors in serial, making it accelerate to compute a real-time hardware genetic algorithm. To investigate the effect of proposed approach, performance comparisons is experimented for an typical computation of genetic algorithm.

• Computers and Concrete
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• v.11 no.6
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• pp.541-569
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• 2013

There is a wide variety of existing Genetic Algorithms (GA) operators and parameters in the literature. However, there is no unique technique that shows the best performance for different classes of optimization problems. Hence, the evaluation of these operators and parameters, which influence the effectiveness of the search process, must be carried out on a problem basis. This paper presents a comparison for the influence of GA operators and parameters on the performance of the damage identification problem using the finite element model updating method (FEMU). The damage is defined as reduction in bending rigidity of the finite elements of a reinforced concrete beam. A certain damage scenario is adopted and identified using different GA operators by minimizing the differences between experimental and analytical modal parameters. In this study, different selection, crossover and mutation operators are compared with each other based on the reliability, accuracy and efficiency criteria. The exploration and exploitation capabilities of different operators are evaluated. Also a comparison is carried out for the parallel and sequential GAs with different population sizes and the effect of the multiple use of some crossover operators is investigated. The results show that the roulettewheel selection technique together with real valued encoding gives the best results. It is also apparent that the Non-uniform Mutation as well as Parent Centric Normal Crossover can be confidently used in the damage identification problem. Nevertheless the parallel GAs increases both computation speed and the efficiency of the method.

• Journal of Korean Society of Industrial and Systems Engineering
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• v.28 no.3
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• pp.149-155
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• 2005

In this paper, we optimize simulation model of a manufacturing system using the real-coded genetic algorithm. Because the manufacturing system expressed by simulation model has stochastic process, the objective functions such as the throughput of a manufacturing system or the resource utilization are not optimized by simulation itself. So, in order to solve it, we apply optimization methods such as a genetic algorithm to simulation method. Especially, the genetic algorithm is known to more effective method than other methods to find global optimum, because the genetic algorithm uses entity pools to find the optimum. In this study, therefore, we apply the real-coded genetic algorithm to simulation optimization of a manufacturing system, which is known to more effective method than the binary-coded genetic algorithm when we optimize the constraint problems. We use the reproduction operator of the applied real-coded genetic algorithm as technique of the remainder stochastic sample with replacement and the crossover operator as the technique of simple crossover. Also, we use the mutation operator as the technique of the dynamic mutation that configures the searching area with generations.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.426-433
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• 2018

Plant tissue culture is a technique that has invariably been used for various purposes such as obtaining transgenic plants for crop improvement or functional analysis of genes. However, this process can be associated with a variety of genetic and epigenetic instabilities in regenerated plants, termed as somaclonal variation. In this study, we investigated mutation spectrum, chromosomal distributions of nucleotide substitution types of single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) by whole genome re-sequencing between Dongjin and Nipponbare along with regenerated plants of Dongjin from different induction periods. Results indicated that molecular spectrum of mutations in regenerated rice against Dongjin genome ranged from $9.14{\times}10^{-5}$ to $1.37{\times}10^{-4}$ during one- to three-month callus inductions, while natural mutation rate between Dongjin and Nipponbare genomes was $6.97{\times}10^{-4}$. Non-random chromosome distribution of SNP and InDel was observed in both regenerants and Dongjin genomes, with the highest densities on chromosome 11. The transition to transversion ratio was 2.25 in common SNPs of regenerants against Dongjin genome with the highest C/T transition frequency, which was similar to that of Dongjin against Nipponbare genome.

• Journal of Microbiology and Biotechnology
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• v.29 no.3
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• pp.419-428
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• 2019

Phytases are enzymes that can hydrolyze phytate and its salts into inositol and phosphoric acid, and have been utilized to increase the availability of nutrients in animal feed and mitigate environmental pollution. However, the enzymes' low thermostability has limited their application during the feed palletization process. In this study, a combination of B-value calculation and protein surface engineering was applied to rationally evolve the heat stability of Escherichia coli phytase. After systematic alignment and mining for homologs of the original phytase from the histidine acid phosphatase family, the two models 1DKL and 1DKQ were chosen and used to identify the B-values and spatial distribution of key amino acid residues. Consequently, thirteen potential amino acid mutation sites were obtained and categorized into six domains to construct mutant libraries. After five rounds of iterative mutation screening, the thermophilic phytase mutant P56214 was finally yielded. Compared with the wild-type, the residual enzyme activity of the mutant increased from 20% to 75% after incubation at $90^{\circ}C$ for 5 min. Compared with traditional methods, the rational engineering approach used in this study reduces the screening workload and provides a reference for future applications of phytases as green catalysts.

• Proceedings of the Korean Society of Applied Pharmacology
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• 2006.11a
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• pp.127-130
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• 2006

Coenzyme Q10(CoQ10) is a biological quinine compound that is widely found in living organisms including yeast, plants, and animals. CoQ10 has two major physiological activities:(a)mitochondrial electron-transport activity and (b )antioxidant activity. Various clinical applications are also available: Parkinson's disease, Heart disease, diabetes. Because of its various application filed, the market size of CoQ10 is continuously expanding all over the world. A Japanese company, Nisshin Pharma Inc. is the first industrial producer of CoQ10(1974). CoQ10 can be produced by fermentation and chemical synthesis. In several companies, these two methods are used for the production of CoQ10:chemical synthesis - Yungjin, Daewoong, Nishin Parma; fermentation - Kaneka, Kyowa, Yungjin, etc. Researchs in microbial production of CoQ10 have several steps: screening of producing microorganisms, strain development, fermentation process, purification process, scale-up process, plant production. Several strategies are available for the strain development : Random mutation and screening, directed metabolic engineering. For the optimization of fermentation process, various conditions (nutrient, aeration, temperature, culture type, etc.) are considered. Purification is one of the most important step because the quality of final products entirely depends on its purity. The production cost will be reduced and the quality of the CoQ10 will be impoved by continuous researches in strain development, fermentation process, purification process.

• 한국약용작물학회:학술대회논문집
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• 2006.11a
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• pp.127-130
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• 2006

Coenzyme Q10(CoQ10) is a biological quinine compound that is widely found in living organisms including yeast, plants, and animals. CoQ10 has two major physiological activities:(a)mitochondrial electron-transport activity and (b)antioxidant activity. Various clinical applications are also available : Parkinson's disease, Heart disease, diabetes. Because of its various application filed, the market size of CoQ 10 is continuously expanding all over the world. A Japanese company, Nisshin Pharma Inc. is the first industrial producer of CoQ10(1974). CoQ10 can be produced by fermentation and chemical synthesis. In several companies, these two methods are used for the production of CoQ10:chemical synthesis - Yungjin, Daewoong, Nishin Parma; fermentation - Kaneka, Kyowa, Yungjin, etc. Researchs in microbial production of CoQ10 have several steps: screening of producing microorganisms, strain development, fermentation process, purification process, scale-up process, plant production. Several strategies are available for the strain development : Random mutation and screening, directed metabolic engineering. For the optimization of fermentation process, various conditions (nutrient, aeration, temperature, culture type, etc.) are considered. Purification is one of the most important step because the quality of final products entirely depends on its purity. The production cost will be reduced and the quality of the CoQ10 will be impoved by continuous researches in strain development, fermentation process, purification process.