• Genomics & Informatics
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• v.5 no.3
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• pp.124-128
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• 2007

Microarray technology enables us to measure the expression of tens of thousands of genes simultaneously under various experimental conditions. Clustering analysis is one of the most successful methods for analyzing microarray data using the assumption that co-expressed genes may be co-regulated. It is important to extract meaningful clusters from a long unordered list of clusters and to evaluate the functional homogeneity and heterogeneity of clusters. Many quality measures for clustering results have been suggested in different conditions. In the present study, we consider biological pathways as a collection of biological knowledge and used them as a reference for measuring the quality of clustering results and functional homogeneities. PathTalk visualizes and evaluates functional relationships between gene clusters and biological pathways.

• Molecules and Cells
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• v.23 no.3
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• pp.405-409
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• 2007

A putative type-I chalcone isomerase (CHI) cDNA clone EuNOD-CHI was previously isolated from the root nodule of Elaeagnus umbellata [Kim et al. (2003)]. To see if it encodes a functional CHI, we ectopically overexpressed it in the Arabidopsis (Arabidopsis thaliana) transparent testa 5 (tt5) mutant, which is defective in naringenin production and has yellow seeds due to proanthocyanidin deficiency. Ectopic overexpression of EuNOD-CHI resulted in recovery of normal seed coat color. Naringenin produced by CHI from naringenin chalcone was detected in the transgenic lines like in the wild-type, whereas it was absent from the tt5 mutant. We conclude that EuNOD-CHI encodes a functional type-I CHI. In situ hybridization revealed that EuNOD-CHI expression is localized to the infected cells of the fixation zone in root nodules.

• International Journal of Oral Biology
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• v.30 no.1
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• pp.31-37
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• 2005

Treponema maltophilum, a Group IV oral spirochete, is associated with periodontitis and endodontic infections. In this study we analyzed the functional role of the major surface protein of this organism (MspA) in human gingival fibroblasts (HGFs). The full-length gene encoding MspA was cloned and expressed in Escherichia coli by using the expression vector pQE-30. The recombinant protein (rMspA) was purified by affinity chromatography with nickel-nitrilotriacetic acid agarose and possible contamination of E. coli endotoxin in rMspA was removed by using polymyxin B-agarose. rMspA significantly induced the expression of pro inflammatory cytokines like IL-6 and IL-8 and intercellular adhesion molecule (ICAM)-1 in HGFs, when analyzed by reverse transcription-PCR, flow cytometry, and enzyme-linked immunosorbent assay. Our results indicate that MspA of T. maltophilum may play an important role in amplifying the local immune response by upregulating the expression of proinflammatory cytokines and ICAM-1.

• Interdisciplinary Bio Central
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• v.1 no.3
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• pp.11.1-11.5
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• 2009

One of the main issues of molecular evolution is to reveal the principles dictating protein evolutionary rates. A traditional hypothesis posits that protein evolutionary rates are mostly determined by the average functional importance of amino acids in a given protein. Thus the correlations of evolutionary rates with different variables such as PPI, gene essentiality and expression abundance have been studied to test the traditional hypothesis. Recently, mRNA expression abundance among the variables has drawn much attention, not only because it shows relatively strong correlation with protein evolutionary rates, but also because of the controversies surrounding an alternative hypothesis against the traditional one. Here, I will give an overview over the traditional hypothesis, and summarize the different variables that have been found to correlate with protein evolutionary rates. Then I will introduce pros and cons on the two different hypotheses.

• Journal of the Korean Society of Industry Convergence
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• v.5 no.4
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• pp.353-359
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• 2002

The focus of this study is that spacial, material, functional, cubical reasons are visually expressed on high-rise office Architecture in Korea according to the period of their completion. Office buildings are analyzed in three of exterior composition : Lower, Middle, Top part of the Building, Comparing the whole composition of the Building, forty-five types of compositions are extracted ; expression of formal, material, structural, functional Decoration which show the tendencies of Korean office buildings.

• The Journal of the Korea Contents Association
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• v.5 no.6
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• pp.163-171
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• 2005

Many food companies cooperate with the existing food until it reaches from the start of the 90s recently. which began to develop suitable new functional foods in the characteristic of each product So that consumers' consciousness may also get interested in the functional foods with which a as specific ingredient and as specific as possible are expected while the expectation for health and a long life becomes high. from which it consisted of and the propriety of functionality became the important point of a new-product-development strategy. A packing design also takes the advantage of development of such functional foods. therefore the seen research, with general consideration of such functional foods Who is going to investigate to the product communication-of-information method and differentiation strategy of more desirable functional foods by analyzing and seeing the functional characteristics which each product has to the fermented milk enjoyed and drunk, and these expression strategies.

• International Journal of Oral Biology
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• v.49 no.2
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• pp.48-52
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• 2024

This study explores the histological features and Bmp4 expression patterns in the replaced tooth germ of Xenopus laevis. Tooth germ formation starts from the dental placode through epithelial-mesenchymal interactions, involving various signaling pathways such as Fgf, Shh, Bmp, and Wnt. In mice, Bmp4 expression in the dental placode inhibits Pax9 expression in the dental mesenchyme. Although absent in the presumptive dental lamina of birds and toothless mammals, Bmp4 remains conserved in reptiles and fish owing to gene duplication. However, its expression in amphibian tooth germs is poorly understood. Three-month-old X. laevis were employed in this study. Initially, samples underwent paraffin embedding and were sectioned into 5 or 12 ㎛ ribbons for H&E staining and in situ hybridization, respectively. Results revealed teeth appearing in two maxillary rows: the labial side, with prefunctional and functional teeth, and the lingual side, with replaced tooth germs behind functional teeth. Enameloid was observed between the inner dental epithelium and dental mesenchyme at the cap or early bell stages, whereas enamel and dentin formed during the late bell or mineralization stages from the replaced tooth germ. Bmp4 expression was evident in the inner dental epithelium (ameloblasts), dental papilla (odontoblasts), stellate reticulum, and Hertwig's epithelial root sheath. Overall, these findings highlight the conservation of Bmp4 expression in X. laevis tooth development.

• Journal of Life Science
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• v.19 no.8
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• pp.1159-1163
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• 2009

It has been postulated that endoplasmic (ER) stress is involved in the development of several diseases. However, the detailed molecular mechanisms have not been fully understood. Therefore, we characterized a genetic network of genes induced by ER stress using cDNA microarray and gene set expression coherence analysis (GSECA), and identified gene function as well as several transcription regulators associated with ER stress. We analyzed time-dependent gene expression profiles in thapsigargin-treated Sk-Hep1 using an oligonucleotide expression chip, and then selected functional gene sets with significantly high expression coherence which was processed into functional clusters according to the expression similarities. The functions related to sugar binding, lysosome, ribosomal protein, ER lumen, and ER to golgi transport increased, whereas the functions with mRNA processing, DNA replication, DNA repair, cell cycle, electron transport chain and helicase activity decreased. Furthermore, functional clusters were investigated for the enrichment of regulatory motifs using GSECA, and several transcriptional regulators associated with regulation of ER-induced gene expression were found.

• BMB Reports
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• v.32 no.2
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• pp.181-188
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• 1999

4-Aminobutyrate aminotransferase plays an essential role in the 4-aminobutyric acid shunt, converting 4-aminobutyrate to succinic semialdehyde. Recombinant 4-aminobutyrate aminotransferases were overexpressed as their catalytically active forms in E. coli by coproduction with thioredoxin and their solubilities were also dramatically increased. In order to study the structural and functional aspects of the C-terminal domain of brain 4-aminobutyrate aminotransferase, we have constructed a C-terminal mutant of pig brain 4-aminobutyrate aminotransferase and analyzed the functional and structural roles of C-terminal amino acids residues on the enzyme. The deletion of five amino-acid residues from C-terminus did not interfere with the kinetic parameters and functional properties of the enzyme. Also, the deletion did not affect the dimeric structure of the protein aligned along the subunit interface at neutral pH. However, the deletion of the C-terminal region of the protein changed the stability of its dimeric structure at acidic pH. The dissociation of the enzyme acidic, facilitated by the deletion of five amino acids from C-terminus, abolished the catalytic activity.

• 한국인삼전략화협의회:학술대회논문집
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• v.2003 no.09
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• pp.54-63
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• 2003

"Korea ginseng (Panax ginseng C.A Meyer) is an important medicinal plant. Its root has been used as an herbal medicine that provides resistance to stress and disease, and prevents exhaustion since the ancient time. Ginsenosides, glycosylated triterpene (saponin), are considered to be the main active compounds of the ginseng root. Despite of considerable commercial interests of ginsenosides, very little is known about the genes and their biochemical pathways for ginsenoside biosynthesis. This work will focus on the identification of genes involved in ginsenoside biosynthesis and the dissection of ginsenoside biosynthetic pathway using a functional genomics tool. Expression sequence tags (ESTs) provide a valuable tool to discovery the genes in secondary metabolite biosynthesis. We generated over 21,155 ginseng ESTs that is now sufficient to facilitate discovering the genes involved in ginsenoside biosynthesis such as oxidosqualene cyclase(OSC), cytochrome P450 and glycosyltransferase. With ESTs information, microarray technology will be used for the analysis of gene expression, and the identification of genes including transcription factors expressed in tissues under given experimental condition. Heterogous system such as yeast and plants will allow us to do the functional analysis. And selected ginseng hairy root which show variation in ginsenoside production will be used as a material for functional analysis of candidate gene. Functional genomics approach will successfully accelerate gene discovery, and also provide promises of metabolic engineering for the ginsenoside production."