• Asian-Australasian Journal of Animal Sciences
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• 제22권1호
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• pp.124-130
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• 2009

Estimating genetic interaction effects in animal genomics would be one of the most challenging studies because the phenotypic variation for economically important traits might be largely explained by interaction effects among multiple nucleotide sequence variants under various environmental exposures. Genetic improvement of economic animals would be expected by understanding multi-locus genetic interaction effects associated with economic traits. Most analyses in animal breeding and genetics, however, have excluded the possibility of genetic interaction effects in their analytical models. This review discusses a historical estimation of the genetic interaction and difficulties in analyzing the interaction effects. Furthermore, two recently developed methods for assessing genetic interactions are introduced to animal genomics. One is the restricted partition method, as a nonparametric grouping-based approach, that iteratively utilizes grouping of genotypes with the smallest difference into a new group, and the other is the Bayesian method that draws inferences about the genetic interaction effects based on their marginal posterior distributions and attains the marginalization of the joint posterior distribution through Gibbs sampling as a Markov chain Monte Carlo. Further developing appropriate and efficient methods for assessing genetic interactions would be urgent to achieve accurate understanding of genetic architecture for complex traits of economic animals.

• BMB Reports
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• 제48권1호
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• pp.6-12
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• 2015

Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future.

• 한국미생물·생명공학회지
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• 제24권3호
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• pp.371-375
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• 1996

TFD is a transcription factor database which consists of short functional DNA sequences called as signals and their references. SIGNAL SCAN, developed by Dan S. Prestridge, is used to determine what signals of TFD may exist in a DNA sequence. This program searches TFD database by using a simple algorithm for character string comparison. We developed TFSCAN that aims at searching for signals in an input DNA sequence more efficently than SIGNAL SCAN. Our algorithms consist of two parts, one constructs an automata by scanning sequences of rFD, the other searches for signals through this automata. Searching for signal-related references is radically improved in time by using an indexing method. Usage of TFSCAN is very simple and its output is obvious. We developed and installed a TFSCAN input form and a CGI program in GINet Web server, to use TFSCAN. The algorithm applying automata showed drastical results in improvement of computing time. This approach may apply to recognizing several biological patterns. We have been developing our algorithm to optimize the automata and to search more sensitively for signals.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2003년도 학술발표대회 발표논문초록집
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• pp.39-39
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• 2003

Methylation of DNA 5-cytosine in mammalian early embryo affects great deal in nuclear reprogramming and chromatin remodeling of developing embryo. Current efforts to clone and produce cloned animals including transgenic animals face various problems including low birth rate, irregular development, and so on. In this report, cDNA for the one of house keeping methyltransfcrase, Dnmt1 was cloned from bovine somatic tissues and was analyzed for its nucleotide sequences to investigate the structure and function of the gene in bovine early development. Nucleotide sequence of bovine Dnmt1 homologue showed 76.8% identity with that of human Dnmtl and 66.4% with mouse Dnmt1. Translated amino acid sequence showed 88.4% homology with human homologue and 75.8% homology with mouse counterpart. Three types of Dnmt1 are reported in mouse and human, and are likely present in bovine tissues. Understanding of role of Dnmt1 in bovine development may shed a light in the field of animal, especially bovine cloning.

• 한국경영과학회지
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• 제23권4호
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• pp.87-96
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• 1998

Using the concept of cellular manufacturing systems(CMS) in job shop manufacturing system is one of the most innovative approaches to improving plant productivity. However. several constraints in machine duplication cost, machining capability, cell space capacity, intercell moves and exceptional elements(EEs) are main problems that prevent achieving the goal of maintaining an ideal CMS environment. Minimizing intercell part traffics and EEs are the main objective of the cell formation problem because it is a critical point that improving production efficiency. Because the intercell moves could be changed according to the sequence of operation, it should be considered in assigning parts and machines to machine ceil. This paper presents a method that eliminates EEs under the constraints of machine duplication cost and ceil space capacity attaining two goals of minimizing machine duplications and minimizing intercell moves simultaneously. Developing an algorithm that calculates the machine duplications by cell-machine incidence matrix and part-machine Incidence matrix, and calculates the exact intercell moves considering the sequence of operation. Based on the number of machine duplications and exact intercell moves, the goal programming model which satisfying minimum machine duplications and minimum intercell moves is developed. A linear programming model is suggested that could calculates more effectively without damaging optimal solution. A numerical example is provided to illustrate these methods.

• Journal of Microbiology and Biotechnology
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• 제19권9호
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• pp.1051-1054
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• 2009

This cross-sectional study examined the distribution of HPV 58 sequence variation in Korean women for the first time. Among 1,750 Korean women, 53 women were positive for HPV 58 single infection, of whom 26 were without disease, 20 were with cervical intraepithelial neoplasia (CIN) 1, and 7 with CIN 2 or 3. Altogether, 36 different nucleotide sequence variations were identified with the L1, 20 within E2, 5 within E6, and 10 within E7. Further studies on variants of oncogenic HPVs are necessary, particularly for the purpose of developing more predictive HPV detection methods.

• 한국경영과학회:학술대회논문집
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• 한국경영과학회 1998년도 추계학술대회 논문집
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• pp.263-266
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• 1998

Several constraints in machine duplication cost, machining capability, cell space capacity, intercell moves and exceptional elements(EEs) are main problems that prevent achieving the goal of ideal Cellular Manufacturin System (CMS) environment. Minimizing intercell part traffics and EEs are the main objective of the cell formation problem as it's a critical point that improving production efficiency. Because the intercell moves could be changed according to the sequence of operation, it should be considered in assigning parts and machines to machine cells. This paper presents a method that eliminates EEs under the constraints of machine duplication cost and cell space capacity attaining two goals of minimizing machine duplications and minimizing intercell moves simultaneously. Developing an algorithm that calculates the machine duplications by cell-machine incidence matrix and part-machine incidence matrix, and calculates the exact intercell moves considering the sequence of operation. Based on the number of machine duplications and exact intercell moves, the goal programming model which satisfying minimum machine duplications and minimum intercell moves is developed. A linear programming model is suggested that could calculates more effectively without damaging optimal solution. A numerical example is provided to illustrate these methods.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.117-117
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• 2017

The onion (Allium cepa L.) is the most widely cultivated species of the genus Allium, especially it has been valued because of the pungent flavor and aroma. Allium species including onion has very large genome sizes ranging from approximately 10 to 20 Gbp, which have complicated genomic studies and precluded genome sequencing until recently. A population of 186 F2 individuals derived from a cross of 'Umjinara' ${\times}$ 'Sinsunhwang' and the two parental lines were used for this study. For the development of framework map, various types of markers including SSRs, RAPD, SNPs, and CAPS makers have been used for polymorphism test. Especially, a lot of SNP and CAPS loci were developed from the onion transcriptome sequence by RNASEQ of two parental lines. The GBS libraries have been constructed based on a modified protocol from Poland Lab using a two-enzyme system. We have been developing markers showing polymorphism between two parental lines, and genotyping for all F2 individuals were finished for a number of polymorphic markers. For the construction of GBS libraries, a set of 192 barcoded adapters were generated from complementary oligonucleotides with XhoI overhang sequence and unique barcodes of length 4-8 bp and they have been tested using two parental linesto determine the optimum conditions for GBS analysis.

• Journal of Plant Biotechnology
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• 제46권4호
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• pp.282-290
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• 2019

Cuphea viscosissima plants accumulate medium-chain fatty acids (MCFAs), i.e., those containing 8 ~ 14 carbons, in their seeds, in addition to the longer carbon chain fatty acids (≥16 carbons) found in a variety of plant species. Previous studies have reported the existence of three C. viscosissima MCFA-producing acyl-acyl carrier protein (ACP) thioesterases with different substrate specificities. In this study, CvFatB4, a novel cDNA clone encoding an acyl-ACP thioesterase (EC 3.1.2.14), was isolated from developing C. viscosissima seeds. Sequence alignment of the deduced amino acid sequence revealed that four catalytic residues for thioesterase activity are conserved and a putative N-terminal chloroplast transit peptide is present. Overexpression of CvFatB4 cDNA, which was under the control of the cauliflower mosaic virus 35S promoter, in Arabidopsis thaliana led to an increase in 16:0 fatty acid (palmitate) levels in the seed oil at the expense of 18:1 and other non-MCFAs.

• 한국정밀공학회:학술대회논문집
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• 한국정밀공학회 2000년도 춘계학술대회 논문집
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• pp.829-832
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• 2000

This paper describes a research work of developing a computer-aided design of product with bending and piercing for progressive working. An approach to the CAD system is based on the knowledge-based rules. Knowledge fur the CAD system is formulated from plasticity theories, experimental results and the empirical knowledge of field experts. The system has been written in AutoLISP on the AutoCAD with a personal computer and is composed of three main modules, which are input and shape treatment, flat pattern layout and strip layout module. Based on knowledge-based rules, the system is designed by considering several factors, such as radius and angle of bend, material and thickness of product, complexities of blank geometry and punch profile, bending sequence, and availability of press. Strip layout drawing automatically generated by piercing with punch profiles divided into for external area is simulated in 3-D graphic forms, including bending sequences for the product with piercing and bending. Results obtained using the modules enable the manufacturer of electronic products to be more efficient in this field.