• Genomics & Informatics
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• v.6 no.2
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• pp.64-67
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• 2008

The Korean Rice Ds-tagging lines Database (KRDD) is designed to provide information about Ac/Ds insertion lines and activation tagging lines using japonica rice. This database has provided information on 18,158 Ds lines, which includes the ID, description, photo image, sequence information, and gene characteristics. The KRDD is visualized using a web-based graphical view, and anonymous users can query and browse the data using the search function. It has four major menus of web pages: (i) a Blast Search menu of a mutant line; Blast from rice Ds-tagging mutant lines; (ii) a primer design tool to identify genotypes of Ds insertion lines; (iii) a Phenotype menu for Ds lines, searching by identification name and phenotype characteristics; and (iv) a Management menu for Ds lines.

• Proceedings of the Korean Society of Medical Physics Conference
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• 2002.09a
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• pp.360-362
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• 2002

Myocardial tagging technique such as spatial modulation of magnetization (SPAMM) allows the study of myocardial motion with high accuracy. Tagging contrast of such a tagging images can affect to the accuracy of the estimation of tag intersection in order to analyze the myocardial motion. Tagging contrast can be affected by tagline spacing. The aim of this study was to investigate the relationship between tagline spacing of SPAMM image and tagging contrast-to-noise ratio (CNR) experimentally. One healthy volunteer was undergone electrocardiographically triggered MR imaging with SPAMM-based tagging pulse sequence at a 1.5T MR scanner (Gyroscan Intera, Philips Medical System, Netherland). Horizontally modulated stripe patterns were imposed with a range from 3.6mm to 9.6mm of tagline spacing. Images of the left ventricle (LV) wall were acquired at the mid-ventricle level during cardiac cycle with FEEPI (TR/TE/FA=5.8/2.2/10). Tagging CNR for each image was calculated with a software which developed in our group. During contraction, tagging CNR was more rapidly decreased in case of short tagline spacing than in case of long tagline spacing. In the same heart phase, CNR was increased corresponding with tag line spacing. Especially, at the fully contracted heart phase, CNR was more rapidly increased than the other heart phases as a function of tagline spacing.

• Proceedings of the Botanical Society of Korea Conference
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• 2002.04a
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• pp.110-110
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• 2002

• Journal of Plant Biotechnology
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• v.34 no.4
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• pp.285-291
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• 2007

This study describes conditions for the mass production of activation-tagged mutant hairy root lines of ginseng by cocultivation with Agrobacterium rhizogenes. Because it is not currently possible to produce progeny from transgenic ginseng, a loss-of-function approach for functional genomics cannot be appliable to this species. A gain-of-function approach is alternatively the choice and hairy root production by cocultivation of A. rhizogenes would be most practical to obtain a large number of mutants. Various sources of explants were subjected to genetic transformation with various strains of A. rhizogenes harboring the activation-tagging vector pKH01 to determine optimum conditions for the highest frequency of hairy root formation on explants. Petiole explants cocultivated with A. rhizogenes R1000 produced hairy roots at a frequency of 85.9% after 4 weeks of culture. Conditions for maximum growth or branching rate of hairy roots were also investigated by using various culture media. Petiole explants cultured on half strength Schenk and Hildebrandt medium produced vigorously growing branched roots at a rate of 2.6 after 4 weeks of culture. A total of 1,989 lines of hairy root mutants were established in this study. These hairy root lines will be useful to determine functions of genes for biosynthesis of ginsenosides.

• Journal of Internet Computing and Services
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• v.12 no.5
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• pp.29-37
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• 2011

Recently, many user-participating web services have been used widely as the evolution of internet web technology has rapidly been developed. Users share various content and opinion on line using a site like ‘Social bookmarking.’ Users can share others’ bookmarking history and create tags while bookmarking web sites; we call it collaborative tagging. In this paper, we studied empirical analysis for widely used social bookmarking and collaborative tagging which the result shows minority of users is actively using the bookmarking and a few sites and tags are used by majority of the users. 24% users tagged 80%, 75% sites and 81% tags were tagged below than 3 times. Types of bookmarking activities were found different by users and early appointed tags get more frequency by majority. We also identified relative proportions of tags on certain sites are becoming convergence gradually. We expect the result of this paper will give opportunities to help further developing social bookmarking system.

• Korean Journal of Environmental Agriculture
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• v.25 no.4
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• pp.371-381
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• 2006

New proteomic techniques have been pioneered extensively in recent years, enabling the high-throughput and systematic analyses of cellular proteins in combination with bioinformatic tools. Furthermore, the development of such novel proteomic techniques facilitates the elucidation of the functions of proteins under stress or disease conditions, resulting in the discovery of biomarkers for responses to environmental stimuli. The ultimate objective of proteomics is targeted toward the entire proteome of life, subcellular localization biochemical activities, and the regulation thereof. Comprehensive analysis strategies of proteomics can be classified into three categories: (i) protein separation via 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification via either Edman sequencing or mass spectrometry (MS), and (iii) proteome quantitation. Currently, MS-based proteomics techniques have shifted from qualitative proteome analysis via 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, toward quantitative proteome analysis. In vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes. protein-labeling tagging with isotope-coded affinity tags, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope-labeled amino acids can be in vivo labeled into live culture cells via metabolic incorporation. MS-based proteomics techniques extend to the detection of the phosphopeptide mapping of biologically crucial proteins, which ale associated with post-translational modification. These complementary proteomic techniques contribute to our current understanding of the manner in which life responds to differing environment.

• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.196-204
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• 2010

With the completion of genome sequencing of several organisms, attention has been focused to determine the function and functional network of proteins by proteome analysis. The recent techniques of proteomics have been advanced quickly so that the high-throughput and systematic analyses of cellular proteins are enabled in combination with bioinformatics tools. Furthermore, the development of proteomic techniques helps to elucidate the functions of proteins under stress or diseased condition, resulting in the discovery of biomarkers responsible for the biological stimuli. Ultimate goal of proteomics orients toward the entire proteome of life, subcellular localization, biochemical activities, and their regulation. Comprehensive analysis strategies of proteomics can be classified as three categories: (i) protein separation by 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification by either Edman sequencing or mass spectrometry (MS), and (iii) quanitation of proteome. Currently MS-based proteomics turns shiftly from qualitative proteome analysis by 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, to quantitative proteome analysis. Some new techniques which include top-down mass spectrometry and tandem affinity purification have emerged. The in vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes, protein-labeling tagging with isotope-coded affinity tag, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope labeled amino acid can be in vivo labeled into live culture cells through metabolic incorporation. MS-based proteomics extends to detect the phosphopeptide mapping of biologically crucial protein known as one of post-translational modification. These complementary proteomic techniques contribute to not only the understanding of basic biological function but also the application to the applied sciences for industry.

• Proceedings of the Botanical Society of Korea Conference
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• 1999.07a
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• pp.11-15
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• 1999

In order to evlauate feasibility of the gene tagging by the maize transposable element Ac in heterologous plant systems, we have investigated physical distances and directions of transposition of the element in Arabidopsis thaliana and tobacco cultured cell line BY-2. We prepared a T-DNA construct that carried a non-autonomous derivative of Ac with a site for cleavage by endonuclease I-Scel (designated dAc-I-RS element). Another cleavage site was also introduced into the T-DNA region outside dAc-I-RS. A number of transgenic Arabidopsis plants were generated, each of which had a single copy of the T-DNA at a different chromosomal location. To examine the pattern of transposition, three out of these transgenic plants were crossed with the Arabidopsis plant that carried the gene for Ac transposase and progeny in which dAc-I-RS had been transposed were isolated. After digestion of the genomic DNA of these progeny with I-SceI, sizes of segment of DNA were determined byd pulse-field gel electrophoresis. We also performed linkage analysis for the transposed elements and sites of mutations near the elements. Our results with three transgenic lines showed that 50% of all transposition events had occurred within 1,700 kilo-base pairs (kb) on the same chromosome, with 35% within 200 kb, and that the elements transposed in both directions on the chromosome with roughly equal probability. The data thus indicate that the Ac-Ds system is most useful for tagging of genes that are present within 200 kb of the chromosomal site of Ac in Arabidopsis. In addition, determination of the precise localization of the transposed dAc-I-RS element should definitely assist in map-based cloning of genes around insertion sites. In the present paper, we report typical examples of such gene isolation studies.

• Proceedings of the Botanical Society of Korea Conference
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• 1985.08b
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• pp.51-57
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• 1985

In order to evlauate feasibility of the gene tagging by the maize transposable element Ac in heterologous plant systems, we have investigated physical distances and directions of transposition of the element in Arabidopsis thaliana and tobacco cultured cell line BY-2. We prepared a T-DNA construct that carried a non-autonomous derivative of Ac with a site for cleavage by endonuclease I-Scel (designated dAc-I-RS element). Another cleavage site was also introduced into the T-DNA region outside dAc-I-RS. A number of transgenic Arabidopsis plants were generated, each of which had a single copy of the T-DNA at a different chromosomal location. To examine the pattern of transposition, three out of these transgenic plants were crossed with the Arabidopsis plant that carried the gene for Ac transposase and progeny in which dAc-I-RS had been transposed were isolated. After digestion of the genomic DNA of these progeny with I-SceI, sizes of segment of DNA were determined byd pulse-field gel electrophoresis. We also performed linkage analysis for the transposed elements and sites of mutations near the elements. Our results with three transgenic lines showed that 50% of all transposition events had occurred within 1, 700 kilo-base pairs (kb) on the same chromosome, with 35% within 200 kb, and that the elements transposed in both directions on the chromosome with roughly equal probability. The data thus indicate that the Ac-Ds system is most useful for tagging of genes that are present within 200 kb of the chromosomal site of Ac in Arabidopsis. In addition, determination of the precise localization of the transposed dAc-I-RS element should definitely assist in map-based cloning of genes around insertion sites. In the present paper, we report typical examples of such gene isolation studies.

• Korean Journal of Plant Resources
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• v.24 no.5
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• pp.514-520
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• 2011

This study describes conditions for the mass production of mutant hairy root lines by co-cultivation with A. rhizogenes harboring the activation tagging vector pHC7. Various sources of explants were subjected to genetic transformation with A. rhizogenes to determine optimum conditions and cultivar for the highest frequency of hairy root formation on explants. Hairy root formation also were investigated in transformed hairy roots grown in various culture media. Finally, a total of approximately 2,500 lines of hairy root mutants were produced in this study. A managing system for metabolomics in hairy root lines also were established. These hairy root lines will be useful to determine functions of genes relating biosynthesis pathway of secondary metabolites.