• Proceedings of the Korean Information Science Society Conference
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• 2003.04c
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• pp.407-409
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• 2003

최근 바이오인포메틱스 분야는 IT의 발전과 더불어 급속한 발전을 이루어 왔다. 또한 기존의 분자생물학분야의 연구들을 컴퓨터의 첨단 기술을 이용하여 자동화, 전산화하는 것으로 생명정보의 데이터베이스 구축을 시작으로 서열정보의 주석처리 둥이 발전되어 왔다. 또한 분자생물학의 오랜 연구결과들 중 수많은 문헌들을 토대로 한 분석인 텍스트마이닝, 정보추출은 전산학의 방법으로 데이터를 추출, 수집하여 분자생물학 데이터의 양적 팽창을 더욱 가속화하고 있다. 본 논문에서는 수집된 biological Pathway 정보의 효율적인 저장, 재사용 그리고 활용을 위해 바이오 온톨로지 기반의 XML DB를 설계하고자 한다. XML 스키마를 이용해 표현한 온톨로지를 기반으로 다양한 포맷의 생물학 데이터를 수집하고 수집된 데이터들로 XML DB를 구축한 후 Biological Pathway 정보 표현과 재사용. 나아가 생명정보학 응용분야에 활용하려 한다.

• Archives of Pharmacal Research
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• v.29 no.8
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• pp.666-676
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• 2006

Gangliosides are widely distributed in mammalian cells and play important roles in various functions such as cell differentiation and growth control. In addition, diabetes and obesity cause abnormal development of reproductive processes in a variety of species. However, the mechanisms underlying these effects, and how they are related, are not fully understood. This study examined whether the differential expression of gangliosides is implicated in the abnormal follicular development and uterine architecture of streptozotocin (STZ)-induced and db/db diabetic mice. Based upon the mobility on high-performance thin-layer chromatography, mouse ovary consisted of at least five different ganglioside components, mainly gangliosides GM3, GM1, GD1a and GT1b, and diabetic ovary exhibited a significant reduction in ganglioside expression with apparent changes in the major gangliosides. A prominent immunofluorescence microscopy showed a dramatic loss of ganglioside GD1a expression in the primary, secondary and Graafian follicles of STZ-induced and db/db diabetic mice. A significant decrease in ganglioside GD3 expression was also observed in the ovary of db/db mice. In the uterus of STZ-induced diabetic mice, expression of gangliosides GD1a and GT1b was obviously reduced, but gangliosides GM1, GM2 and GD3 expression was increased. In contrast, the uterus of db/db mice showed a significant increase in gangliosides GM1, GD1a and GD3 expression. Taken together, a complex pattern of ganglioside expression was seen in the ovary and uterus of normoglycemic ICR and $db/^+$ mice, and the correspoding tissues in diabetic mice are characterized by appreciable changes of the major ganglioside expression. These results suggest that alterations in ganglioside expression caused by diabetes mellitus may be implicated in abnormal ovarian development and uterine structure.

• Journal of Korean Society of Environmental Engineers
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• v.28 no.10
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• pp.1082-1089
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• 2006

This study describes a methodology to develop a environmental and geographical information system for managing a national scale which is supports the environmental fate modeling. This system was developed via the integration of environmental and geographical information database(DB) and the DB usage software. For the sound environmental management, the DB were constructed by extracting the geometrical figures-such as points, polylines, and/or polygons-based on the geographical information previously developed in Korea. Then it was connected with the environmental information. Based on the Visual Basic Complier, the software can be a useful tool for visualizing the DB, for searching the environmental & geographical information, and supporting the environmental fate modeling.

• Journal of Life Science
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• v.16 no.3 s.76
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• pp.472-476
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• 2006

We have built a database server called HorseDB which contains the genome annotation information and biological information for horse from public database entries. The aims of HorseDB are the integration of biological information and horse genome data on genome scale using bioinformatic methods. To facilitate the extraction of useful information among collected horse genome and biological data, we developed a user-friendly interface system, HorseDB; an Integrated Horse Resource and web Service. The database is categorized by the general horse information data, a sequence annotation data, and a world-wide web analysis program interface. The database also provides an easy access for user to find out the useful information within horse genomes and support analyzed information, such as sequence alignment and gene annotation results. HorseDB can be accessed at http://www.primate.or.kr./horse.

• The Korean Journal of Malacology
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• v.31 no.3
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• pp.243-247
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• 2015

A stand-alone BLAST server is available that provides a convenient and amenable platform for the analysis of molluscan sequence information especially the EST sequences generated by traditional sequencing methods. However, it is found that the server has limitations in the annotation of molluscan sequences generated using next-generation sequencing (NGS) platforms due to inconsistencies in molluscan sequence available at NCBI. We constructed a web-based interface for a new stand-alone BLAST, called PANM-DB (Protostome DB) for the analysis of molluscan NGS data. The PANM-DB includes the amino acid sequences from the protostome groups-Arthropoda, Nematoda, and Mollusca downloaded from GenBank with the NCBI taxonomy Browser. The sequences were translated into multi-FASTA format and stored in the database by using the formatdb program at NCBI. PANM-DB contains 6% of NCBInr database sequences (as of 24-06-2015), and for an input of 10,000 RNA-seq sequences the processing speed was 15 times faster by using PANM-DB when compared with NCBInr DB. It was also noted that PANM-DB show two times more significant hits with diverse annotation profiles as compared with Mollusks DB. Hence, the construction of PANM-DB is a significant step in the annotation of molluscan sequence information obtained from NGS platforms. The PANM-DB is freely downloadable from the web-based interface (Malacological Society of Korea, http://malacol.or/kr/blast) as compressed file system and can run on any compatible operating system.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.1-4
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• 1999

Beijing White Chickens laying larger eggs and smaller eggs were respectively used as parental individuals for mating to produce the F1 progeny and then the F1 progeny individuals mated to produce 125 individuals of the F2 progeny. Three bands associated with the egg weight performance were identified from DNA fingerprints of the 125 individuals generated with a bovine minisatellite probe BM6.5B. The simple linear correlation analysis showed that the coefficients of correlation between frequencies of the three bands (DB1, DB2 and DB3) and egg weights were -0.6, -0.6 and 0.9, respectively.

• Genomics & Informatics
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• v.9 no.4
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• pp.197-199
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• 2011

The biological interpretation of two-dimensional (2D) gel electrophoresis experiments is a key step toward understanding the functions of biological systems. We here present a web-based integrated database, called 2DSpotDB, for the management of proteome data derived from several pathogens. The 2DSpotDB was established as a part of the management of a pathogen proteome project at the Korea National Institute of Health. The goals of the 2DSpotDB implementation are to store and define important pathogen genes, retrieve information obtained by 2D polyacrylamide gel electrophoresis and mass spectrometry, and create an integrated system to provide pathogen proteome information for biological scientists. This database currently contains 14 gels and information on 387 protein spots, among which 329 proteins were identified and annotated.

• The Korean Journal of Food And Nutrition
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• v.25 no.1
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• pp.99-104
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• 2012

The goal of this study was to examine the ameliorative effects of black ginseng(BG) in male obese diabetic C57BLKS/ J-db/db mice. Ten-week-old male db/db mice were administrated 300 mg/kg of F-BG daily for 6 weeks, The db/db mice where corresponded to the normal group and db/db mice which were the diabetic positive group were not provided BG treatment. The supressive effects of treatment were examined on serum lipids levels, which included total cholesterol, triglyceride, LDL-cholesterol and nonesterified fatty acid. Also, weight changes and the relative weight of liver and kidney, organ pathological investigation were measured. The effects of treatment were assessed by comparing the results of the db/db mice that received BG for 6 weeks with that of the diabetic positive group. Significant differences in several biological parameters such as HDL level(p<0.05), TG level(p<0.05) and NEFA level(p<0.05) were observed for the BG group. BG treatment increased the HDL level and decreased the NEFA level, which could ameliorate hyperlipidemia or blood circulation.

• Genomics & Informatics
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• v.7 no.4
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• pp.212-216
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• 2009

WebChemDB is an integrated chemical database retrieval system that provides access to over 8 million publicly available chemical structures, including related information on their biological activities and direct links to other public chemical resources, such as PubChem, ChEBI, and DrugBank. The data are publicly available over the web, using two-dimensional (2D) and three-dimensional (3D) structure retrieval systems with various filters and molecular descriptors. The web services API also provides researchers with functionalities to programmatically manipulate, search, and analyze the data.

• Journal of Applied Biological Chemistry
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• v.53 no.2
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• pp.91-98
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• 2010

This study was aimed to investigate the contents of flavonoids and the biological activity of fermented beverage of medical plants, DeulBit (DB). 50 g of Cassia semen (Cassia tora L.), 50 g of Omija (Schisandra chinensis Baillon.), 50 g of Gugija (Lycium chinense Mill), 50g of Menthae herba, 75 g of Chrysanthemum indicum Linne, 25 g of Dioscorea batatas, 5 g of Lindera obtusiloba Blume, 150 g of Polygonatum odoratum, 25 g of Glycyrrhiza uralensis, 25 g of Acanthopanacis cortex, 100 g of green tea (Camellia sinensis), and 100 g of Laminaria japonica was fermented with sucrose ($50.0{\sim}60.0^{\circ}Brix$.) and 0.5% of deep sea water in 10 L of distilled water for six months at room temperature. Total flavonoids contents of DB was calculated to $3.4{\pm}0.5\;{\mu}g/g$ and antioxidative activity of DB was measured by using DPPH radical scavenging and SOD-like activity. DPPH radical scavenging and SOD-like activity of DB was 96% and 29% at 100% of DB, respectively. In addition, DB indicated about 88% and 66% of the xanthine oxidase and angiotensin converting enzyme inhibitory activities at 1% and 10% of DB, respectively and showed fibrinolytic activity. Nitric oxide (NO) synthesis was increased to 15 times by addition of DB. In addition, NO productions of the macrophages RAW264.7 cells stimulated with lipopolysaccharide (LPS) were reduced to 40.4% by addition of DB. These results suggested that DB is significant role for antioxidative and fibrinolytic activity, and have the strong xanthine oxidase and angiotensin converting enzyme inhibitory activities.