• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2008년도 International Meeting of the Microbiological Society of Korea
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• pp.106-106
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• 2008

• Journal of Microbiology and Biotechnology
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• 제15권5호
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• pp.1130-1134
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• 2005

To monitor the possibility of horizontal gene transfer between transgenic potato and bacteria in the environment, the gene flow from glufosinate-tolerant potato to bacteria in soils was investigated. The soil samples treated with the leaf tissue of either glufosinate-tolerant or glufosinate-sensitive potato were subjected to PCR and Southern hybridization to determine possible occurrence of glufosinate-resistant soil bacteria and to detect the bar (phosphinothricin acetyltransferase) gene, conferring tolerance to glufosinate. The bar gene was not detected from genomic DNAs extracted at different time intervals from the soil samples, which had been treated with the leaf tissue of either transgenic or non-transgenic potato for 2 to 8 weeks. In addition, the level of glufosinate-resistant bacteria isolated from the soil samples treated with the leaf tissue of transgenic potato was similar to that of the samples treated with non-transgenic potato after 4 months of incubation at $25^{\circ}C$. The bar gene was not detected in the genomic DNAs extracted from colonies growing on the plate containing glufosinate, indicating that the bacteria could acquire the resistant phenotype to glufosinate by another mechanism without the uptake of the bar gene from glufosinate-tolerant potato.

• Journal of Plant Biotechnology
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• 제48권3호
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• pp.139-147
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• 2021

Since whole-genome duplication (WGD) of diploid Chrysanthemum nankingense and de novo assembly whole-genome of C. seticuspe have been obtained, they have afforded to perceive the diversity evolution and gene discovery in the improved investigation of chrysanthemum breeding. The robust tools of high-throughput identification and analysis of gene function and expression produce their vast importance in chrysanthemum genomics. However, the gigantic genome size and heterozygosity are also mentioned as the major obstacles preventing the chrysanthemum breeding practices and functional genomics analysis. Nonetheless, some of technological contemporaries provide scientific efficient and promising solutions to diminish the drawbacks and investigate the high proficient methods for generous phenotyping data obtaining and system progress in future perspectives. This review provides valuable strategies for a broad overview about the high-throughput identification, and molecular analysis of gene function and expression in chrysanthemum. We also contribute the efficient proposition about specific protocols for considering chrysanthemum genes. In further perspective, the proper high-throughput identification will continue to advance rapidly and advertise the next generation in chrysanthemum breeding.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.53-55
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• 2000

Xenie is the JAVA application software that integrates and represents 'gene to function'information of human gene. Xenie extracts data from several heterogeneous molecular biology databases and provides integrated information in human readable and machine usable way. We defined 7 semantic frame classes (Gene, Transcript, Polypeptide, Protein_complex, Isotype, Functional_object, and Cell) as a common schema for storing and integrating gene to function information and relationship. Each of 7 semantic frame classes has data fields that are supposed to store biological data like gene symbol, disease information, cofactors, and inhibitors, etc. By using these semantic classes, Xenie can show how many transcripts and polypeptide has been known and what the function of gene products is in General. In detail, Xenie provides functional information of given human gene in the fields of semantic objects that are storing integrated data from several databases (Brenda, GDB, Genecards, HGMD, HUGO, LocusLink, OMIM, PIR, and SWISS-PROT). Although Xenie provide fully readable form of XML document for human researchers, the main goal of Xenie system is providing integrated data for other bioinformatic application softwares. Technically, Xenie provides two kinds of output format. One is JAVA persistent object, the other is XML document, both of them have been known as the most favorite solution for data exchange. Additionally, UML designs of Xenie and DTD for 7 semantic frame classes are available for easy data binding to other bioinformatic application systems. Hopefully, Xenie's output can provide more detailed and integrated information in several bioinformatic systems like Gene chip, 2D gel, biopathway related systems. Furthermore, through data integration, Xenie can also make a way for other bioiformatic systems to ask 'function based query'that was originally impossible to be answered because of separatly stored data in heterogeneous databases.

• Journal of Microbiology and Biotechnology
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• 제14권3호
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• pp.498-502
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• 2004

The current study was conducted to monitor the possibility of the gene transfer among soil bacteria, including the effect of drift due to rain and surface water, in relation to the release of genetically modified organisms into the environment. Four types of bacteria, each with a distinct antibiotic marker, kanamycin-resistant P. fluorescens, rifampicin-resistant P. putida, chloramphenicol-resistant B. subtilis, and spectinomycin-resistant B. subtilis, were plated using a small-scale soil-core device designed to track drifting microorganisms. After three weeks of culture in the device, no Pseudomonas colonies resistant to both kanamycin and rifampicin were found. Likewise, no Bacillus colonies resistant to both chloramphenicol and spectinomycin were found. The gene transfer from glyphosate-tolerant soybeans to soil bacteria, including Rhizobium spp. as a symbiotic bacteria, was examined by hybridization using the DNA extracted from soil taken from pots, in which glyphosate-tolerant soybeans had been growing for 6 months. The results showed that 35S, T-nos, and EPSPS were observed in the positive control, but not in the DNA extracted from the soilborne microorganisms. In addition, no transgenes, such as the 35S promoter, T-nos, and EPSPS introduced into the GMO soybeans were detected in soilborne bacteria, Rhizobium leguminosarum, thereby strongly rejecting the possibility of gene transfer from the GMO soybeans to the bacterium.

• BMB Reports
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• 제32권1호
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• pp.72-75
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• 1999

In an effort to understand the function of the eryBVII gene in the erythromycin biosynthetic gene cluster, we overexpressed the eryBVII gene in E. coli and TDP-6-deoxy-L-threo-D-glycero-4-hexulose was used as a substrate of the overexpressed EryBVII enzyme. The enzymatic reaction product was chemically modified by reduction and peracetylation. Structural analysis of the derivatized enzymatic products by GC-Mass Spectrophotometry indicated that TDP-6-deoxy-L-threo-D-glycero-4-hexulose could be converted into its epimer by EryBVII enzyme. Based on this result, TDP-6-deoxy-L-threo-D-glycero-4-hexulose was indeed the substrate of EryBVII enzyme and the function of the eryBVII gene was confirmed.

• Animal cells and systems
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• 제7권2호
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• pp.159-164
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• 2003

The RAD3 gene of Saccharomyces cerevisiae is required for excision repair and is essential for cell viability. The RAD3 encoded protein possesses a single stranded DNA-dependent ATPase and DNA and DNA-RNA helicase activities. To examine the extent of conservation of structure and function of a S. pombe RAD3 during eukaryotic evolution, the RAD3 homolog gene was isolated by screening of genomic DNA library. The isolated gene was designated as HRD3 (homolog of RAD3 gene). Southern blot analysis confirmed that S. pombe chromosome contains the same DNA as HRD3 gene and this gene exists as a single copy in S. pombe. The transcript of 2.8 kb was detected by Northern blot analysis, The level of transcripts increased by ultraviolet (UV) irradiation, indicating that HRD3 is one of the UV-inducible genes in S. pombe. Furthermore, the predicted partial sequence of HRD3 protein has 60％ identity to S. cerevisiae RAD3 gene. This homology was particularly striking in the regions identified as being conserved in a group of DNA helicases. Gene deletion experiments indicate that the HRD3 gene is essential for viability and DNA repair function. These observations suggest evolutionary conservation of other protein components with which HRD3 might interact in mediating its DNA repair and viability functions.

• Molecules and Cells
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• 제26권1호
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• pp.1-4
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• 2008

A gene's influence on an organism's Darwinian fitness ultimately determines whether it will be lost, maintained or modified by natural selection, yet biologists have few gene expression systems in which to measure whole-organism gene function. In the Department of Molecular Ecology at the Max Planck Institute for Chemical Ecology we are training "molecularly enabled field biologists" to use transformed plants silenced in the expression of environmentally regulated genes and the plant's native habitats as "laboratories." Research done in these natural laboratories will, we hope, increase our understanding of the function of genes at the level of the organism. Examples of the role of threonine deaminase and RNA-directed RNA polymerases illustrate the process.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.313-320
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• 2018

Rice is the staple food of more than 50% of the world population. Cultivated rice has the AA genome (diploid, 2n = 24) and small genome size of only 430 megabase (haploid genome). As the sequencing of rice genome was completed by the International Rice Genome Sequencing Project (IRGSP), many researchers in the world have been working to explore the gene function on rice genome. Insertional mutagenesis has been a powerful strategy for assessing gene function. In maize, well characterized transposable elements have traditionally been used to clone genes for which only phenotypic information is available. In rice endogenous mobile elements such as MITE and Tos have been used to generate gene-tagged populations. To date T-DNA and maize transposable element systems have been utilized as main insertional mutagens in rice. The Ac/Ds system offers the advantage of generating new mutants by secondary transposition from a single tagged gene. To enhance the efficiency of gene detection, advanced gene-tagging systems (i.e. activation, gene or enhancer trap) have been employed for functional genomic studies in rice. Internationally, there have been many projects to develop large scales of insertional mutagenized populations and databases of insertion sites has been established. Ultimate goals of these projects are to supply genetic materials and informations essential for functional analysis of rice genes and for breeding using agronomically important genes. In this report, we summarize the current status of Ac/Ds-mediated gene tagging systems that has been conducted by collaborative works in Korea.

• 전자공학회논문지CI
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• 제42권4호
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• pp.33-42
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• 2005

본 논문에서는 소속 함수와 신경망을 이용한 유전자 발현 정보의 분류 기법을 제안한다. 유전자 발현은 유전자가 mRNA와 생체의 기능을 일으키게 하는 단백질을 만들어내는 과정이다. 유전자 발현에 대한 정보는 유전자의 기능을 밝히고 유전자간의 상관 관계를 알아내는데 중요한 역할을 한다. 이러한 유전자 발현 연구를 위한 정보를 대량으로 신속하게 얻을 수 있는 도구가 DNA 칩이다. DNA 칩으로 얻은 수백$\~$수천개의 데이터는 그 데이터만으로는 의미를 갖지 못한다. 따라서 유전자 발현정도에 따라 수치적으로 획득된 데이터에서 의미적인 특성을 찾아내기 위해서는 클러스터링 방법이 필요하다. 본 논문에서는 수많은 유전자 데이터 중에서 주요 정보를 포함한 것으로 판단되는 유전자 데이터를 피셔 기준에 의하여 선택한다. 이때 선택된 데이터들이 클러스터링에 효과적인 데이터라고 보장할 수 없으므로, 클러스터링 성능을 저해하는 유전자 데이터의 영향력을 감소시키기 위해서 소속 함수를 이용하여 특징값을 계산하고, 계산된 특징값으로 얻은 특징 벡터들을 적용하여 역전파 신경망 학습을 수행한다. 본 논문에서 제안한 유전자 발현 정보의 분류 결과로 얻은 클러스터링의 성능은 기존의 연구 결과와 비교했을 때 다양한 유전자 데이터에 대하여 향상된 인식율을 보이는 것을 확인할 수 있었다.