• Korean Journal of Poultry Science
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• v.37 no.3
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• pp.275-282
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• 2010

Chicken is an important livestock as a valuable biomedical model as well as food for human, and there is a strong rationale for improving our understanding on metabolism and physiology of this organism. The first draft of chicken genome assembly was released in 2004, which enables elaboration on the linkage between genetic and metabolic traits of chicken. The objectives of this study were thus to reconstruct metabolic pathway of the chicken genome and to construct a chicken specific pathway genome database (PGDB). We developed a comprehensive genome database for chicken by integrating all the known annotations for chicken genes and proteins using a pipeline written in Perl. Based on the comprehensive genome annotations, metabolic pathways of the chicken genome were reconstructed using the PathoLogic algorithm in Pathway Tools software. We identified a total of 212 metabolic pathways, 2,709 enzymes, 71 transporters, 1,698 enzymatic reactions, 8 transport reactions, and 1,360 compounds in the current chicken genome build, Gallus_gallus-2.1. Comparative metabolic analysis with the human, mouse and cattle genomes revealed that core metabolic pathways are highly conserved in the chicken genome. It was indicated the quality of assembly and annotations of the chicken genome need to be improved and more researches are required for improving our understanding on function of genes and metabolic pathways of avian species. We conclude that the chicken PGDB is useful for studies on avian and chicken metabolism and provides a platform for comparative genomic and metabolic analysis of animal biology and biomedicine.

• Horticultural Science & Technology
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• v.33 no.2
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• pp.242-250
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• 2015

Insertional mutagenesis induced by T-DNA or transposon tagging offers possibilities for analysis of gene function. However, its potential remains limited unless good methods for detecting the target locus are developed. We describe a PCR technique for efficient identification of DNA sequences adjacent to the inserted T-DNA in a higher plant, Chinese cabbage (Brassica rapa ssp. pekinensis). This strategy, which we named variable argument thermal asymmetric interlaced PCR (VA-TAIL PCR), was designed by modifying a single-step annealing-extension PCR by including a touch-up PCR protocol and using long gene-specific primers. Amplification efficiency of this PCR program was significantly increased by employing an autosegment extension method and linked sequence strategy in nested long gene-specific primers. For this technique, arbitrary degenerate (AD) primers specific to B. rapa were designed by analyzing the Integr8 proteome database. These primers showed higher accuracy and utility in the identification of flanking DNA sequences from individual transgenic Chinese cabbages in a large T-DNA inserted population. The VA-TAIL PCR method described in this study allows the identification of DNA regions flanking known DNA fragments. This method has potential biotechnological applications, being highly suitable for identification of target genomic loci in insertional mutagenesis screens.

• Journal of Life Science
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• v.30 no.8
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• pp.672-679
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• 2020

Distal myopathy is a clinically and genetically heterogeneous group of degenerative diseases of the distal muscle. Glycogen storage disease type IXD (GSD9D) is a metabolic distal myopathy characterized by muscle deficiency of phosphorylase kinase, a key regulatory enzyme in glycogen metabolism. Affected individuals may develop muscle weakness, degeneration, and cramps, as well as abnormal muscle pain and stiffness after exercise. It has been reported that mutations in the PHKA1 gene which encodes the alpha subunit of muscle phosphorylase kinase cause GSD9D. In this study, we examined a Korean GSD9D family with a c.3314T>C (p.I1105T) mutation in the PHKA1 gene. This mutation has not been previously reported in any mutation database nor was it found in 500 healthy controls. The mutation region is well conserved in various other species, and in silico analysis predicts that it is likely to be pathogenic. To date, only seven mutations in the PHKA1 gene have been documented, and this is the first report of Korean GSD9D patients. This study also describes and compares the clinical symptoms and pathological conditions of previously reported cases and these Korean patients. We believe that our findings will be useful for the molecular diagnosis of GSD9D.

• Horticultural Science & Technology
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• v.31 no.3
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• pp.344-351
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• 2013

Microsatellite is one of the most suitable marker for cultivar identification as it has great discrimination power for cultivars with narrow genetic variation. The polymorphism level between 358 microsatellite primer pairs and 11 commercial cucumber cultivars was investigated. Thirty-one primer pairs showed high polymorphism within cucumber cultivars with different fruit types. These markers were applied for the constructing DNA profile data base of 110 commercial cucumber cultivars through multiplex PCR and fluorescence based automatic detection system. A total of 139 polymorphic amplified fragments were obtained by using 31 microsatellite markers. The average of PIC value was 0.610 ranging from 0.253 to 0.873. One hundred and thirty nine microsatellite loci were used to calculate Jaccard's distance coefficients for UPGMA cluster analysis. A clustering group of varieties, based on the results of microsatellite analysis, were categorized into plant shape and fruit type. Almost the cultivars were discriminated by marker genotypes. This information may be useful to compare through genetic relationship analysis between existing variety and candidate varieties in distinctive tests and protection of plant breeders' intellectual property rights through variety identification.

• Korean Journal of Clinical Laboratory Science
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• v.52 no.3
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• pp.202-213
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• 2020

Although technological advances have allowed the efficient collection of large amounts of microbiome data for microbiological studies, proper analysis tools for such big data are still lacking. Additionally, analyses of microbial communities using poor databases can lead to misleading results. Hence, this study aimed to design an appropriate method for the analysis of big microbial databases. Bacteria were collected from the fingertips and personal belongings (mobile phones and laptop keyboards) of individuals. The genomic DNA was extracted from these bacteria and subjected to next-generation sequencing by targeting the 16S rRNA gene. The accuracy of the bacterial matching percentage between the fingertips and personal belongings was verified using a formula and an environment-related and human-related database. To design appropriate analysis, the bacterial matching accuracy was calculated based on the following three categories: comparison between qualitative and quantitative analysis, comparisons within same-gender participants as well as all participants regardless of gender, and comparison between the use of a human-related bacterial database (hDB) and environment-related bacterial database (eDB). The results showed that qualitative analysis, comparisons within same-gender participants, and the use of hDB provided relatively accurate results. This study provides an analytical method to obtain accurate results when conducting studies involving big microbiological data using human-derived microorganisms.

• Horticultural Science & Technology
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• v.31 no.5
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• pp.580-589
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• 2013

This study was carried out to evaluate the suitability of microsatellite markers for varietal identification and genetic relationship of 170 commercial pepper cultivars. The relationship between marker genotypes and 11 pepper cultivars with different morphological traits was also analyzed. Of the 302 pairs of microsatellite primers screened against 11 pepper cultivars, 24 pairs were highly polymorphic in terms of number of alleles. These markers were applied for the construction of DNA profile data base for 170 commercial pepper cultivars. A total of 164 polymorphic amplified fragments were obtained from 24 microsatellite primers. The average polymorphism information content was 0.673 ranging from 0.324 to 0.824. One hundred and sixty four microsatellite alleles were used to calculate Jaccard's distance coefficients using unweighted pair group method. A clustering group of varieties, based on the results of microsatellite analysis, were categorized into 3 major groups corresponding to morphological traits. The phenogram discriminated all varieties by markers genotypes. These microsatellite markers will be useful as a tool for protection of plant breeders' intellectual property rights through variety identification in distinctness, uniformity and stability test.

• Korean Management Science Review
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• v.18 no.1
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• pp.135-145
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• 2001

In recent environment of dynamic management, there is growing recognition that information and knowledge management systems are essential for efficient/effective decision making by CEO. To cope with this situation, we suggest the Data-Miming scheme as a key component of integrated information and knowledge management system. The proposed system measures business performance by considering both VA(Value-Added), which represents stakeholder’s point of view and EVA (Economic Value-Added), which represents shareholder’s point of view. To mine the new information & Knowledge discovery, we applied the improved genetic algorithms that consider predictability, understandability (lucidity) and reasonability factors simultaneously, we use a linear combination model for GAs learning structure. Although this model’s predictability will be more decreased than non-linear model, this model can increase the knowledge’s understandability that is meaning of induced values. Moreover, we introduce a random variable scheme based on normal distribution for initial chromosomes in GAs, so we can expect to increase the knowledge’s reasonability that is degree of expert’s acceptability. the random variable scheme based on normal distribution uses statistical correlation/determination coefficient that is calculated with training data. To demonstrate the performance of the system, we conducted a case study using financial data of Korean automobile industry over 16 years from 1981 to 1996, which is taken from database of KISFAS (Korea Investors Services Financial Analysis System).

• Proceedings of the Korea Contents Association Conference
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• 2015.05a
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• pp.231-232
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• 2015

최근 유전체학, NGS(Next Generation Sequencing) 기술, IT/NT 장비의 발전 등에 따라 방대한 양의 바이오-메디컬 데이터가 생산되고, 이에 따라 빅데이터를 활용한 헬스케어 산업이 급속히 발달하고 있으며, 이와 관련된 빅데이터 기술은 국민의 건강 증대와 건강한 고령 삶을 제공하는 핵심 기술로 급부상하고 있다. 패스웨이는 단백질, 유전자, 세포 등의 생체적 요소 간의 역학관계 혹은 상호작용 등을 네트워크 형식으로 표현한 생물학적 심층지식으로, 바이오-메디컬 빅데이터 분석에 있어서 널리 활용되고 있다. 하지만 패스웨이는 매우 다양한 형태를 갖고 용량이 매우 큰 빅데이터로 이를 분석하는데 많은 시간이 소요된다. 그래서 본 논문에서는 세계적으로 가장 우수하고 방대한 양의 패스웨이를 제공하는 KEGG 패스웨이 데이터베이스로부터 사용자가 관심 갖는 패스웨이만을 자동 수집하고 패스웨이 간 계층구조를 기반으로 네트워크를 구성 후, 해당 패스웨이 네트워크에 대한 클러스터링과 핵심 패스웨이 선정을 통해 패스웨이 간의 역학관계 또는 상호작용을 직관적으로 분석할 수 시스템을 제안했다.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2000.10a
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• pp.328-332
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• 2000

As DNA sequences have been known through the Genome project the techniques for dealing with molecule-level gene information are being made researches briskly. It is also urgent to develop new computer algorithms for making databases and analyzing it efficiently considering the vastness of the information for known sequences. In this respect, this paper studies the association rule search algorithms for finding out the characteristics shown by means of the association between promoter sequences and genes, which is one of the important research areas in molecular biology. This paper treat biological data, while previous search algorithms used transaction data. So, we design a transformed association nile algorithm that covers data types and biological properties. These research results will contribute to reducing the time and the cost for biological experiments by minimizing their candidates.

• Proceedings of the Korean Operations and Management Science Society Conference
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• 2006.05a
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• pp.1702-1706
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• 2006

In the field of rice research, insertional mutants have become a valuable resource for studies of gene function. However, a well-designed database yet in the area of rice functional genomics. The relevant data are widely distributed and independently managed by the individual research groups. Heterogeneous data format in the distributed database systems causes many problems related to redundancy and compatibility. In this research, integration of the distributed databases using agent technology is pursued. In particular, a data integration agent, an ontology agent, a comparison agent, and resource agents are designed, whereby the integrated database is maintained. Moreover a framework for the web-based information system, which provides information to biologists and permits biologists to add new data to the database, is proposed. To establish an interoperable data format, an XML-based data model is also developed adopting ontology concept.