• The Journal of the Korea Contents Association
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• v.10 no.6
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• pp.49-54
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• 2010

As information on gene sequences is not only diverse but also extremely huge in volume, high-performance computer and information technology techniques are required to build and analyze gene sequence databases. This has given rise to the discipline of bioinformatics, a field of research where computers are utilized to collect, to manage, to save, to evaluate, and to analyze biological data. In line with such continued development in bioinformatics, the Korea Institute of Science and Technology Information (KISTI) has built an infrastructure for the biological information, based on the information technology, and provided the information for researchers of bioscience. This paper analyzes the reference fields of Genbank, the most frequently used gene database by the global researchers among the life information databases, and proposes the interface method to NDSL which is the science and technology information integrated service provided by KISTI. For these, after collecting Genbank data from NCBI FTP site, we rebuilt the database by separating Genbank text files into the basic gene data and the reference data. So new tables are generated through extracting the paper and patent information from Genbank reference fields. Then we suggest the method of connection with the paper DB and the patent DB operated by KISTI.

• Proceedings of the Korea Information Processing Society Conference
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• 2008.11a
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• pp.603-606
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• 2008

최근 들어 분자생물학의 급속한 발전과 2001년 인간유전체사업의 완료로 인해 전세계적으로 엄청난 양의 유전정보가 공개되었다. 유전자 서열정보는 그 양이 방대하고 다양하기에 데이터베이스 구축 및 분석을 위하여 고성능 컴퓨터 및 정보기술 기법이 필요하다. 그래서 컴퓨터를 활용하여 생물학적 데이터를 수집, 관리, 저장, 평가, 분석하는 연구분야인 생명정보학(바이오인포매틱스)이라는 학문이 지속적으로 발전하고 있다. 이런 생명정보학 발전에 발맞추어 한국과학기술정보연구원(KISTI)에서는 정보기술을 기반으로 한 생명정보 인프라를 구축하여 생명과학 연구자들에게 제공하고 있다. 본 논문에서는 생명정보 데이터베이스중에서 연구자들이 가장 많이 이용하는 유전자 데이터베이스인 Genbank를 활용 및 분석하여 KISTI에서 운영하는 학술논문 제공 사이트인 NDSL(http://scholar.ndsl.kr)과 연계 가능한 서비스 모델을 개발하기 위하여 1) NCBI FTP 사이트에서 Genbank 데이터를 수집하고, 2) Genbank 텍스트 파일을 유전자 기본정보와 참고 데이터베이스로 재구축하며, 3) Genbank refrence 필드에서 논문 및 특허 정보 추출을 통한 새로운 테이블을 생성하여 NDSL과 연계 가능한 서비스 모델을 제안하였다.

• Korean Journal of Organic Agriculture
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• v.22 no.4
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• pp.801-813
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• 2014

A study was conducted to improve the biological activity of two medicinal plants, Eucommia ulmoides Oliv. and Glycyrrhiza uralensis, by fermentation. The biological activity was assessed by determining antibacterial, antioxidant and antimethanogenic properties. Fermentation was achieved by adding the plant materials in MRS broth at 10% (w/v) and different starter cultures at 1% (v/v). Condition for fermentation were incubation temperature of $30^{\circ}C$ and agitation at 150 rpm for 48 h. Six starter cultures, Weissella confusa NJ28 (Genbank accession number KJ914897), Weissella cibaria NJ33 (Genbank accession number KJ914898), Lactobacillus curvatus NJ40 (Genbank accession number KJ914899), Lactobacillus brevis NJ42 (Genbank accession number KJ914900), Lactobacillus plantarum NJ45 (Genbank accession number KJ914901) and Lactobacillus sakei NJ48 (Genbank accession number KJ914902) were used. Antibacterial activity was observed in L. curvatus NJ40 and L. plantarum NJ45 only as opposed to other treatments, including the non-fermented groups, which showed no antibacterial activity. Both plants showed antioxidant activity, although E. ulmoides Oliv. had lower activity than G. uralensis. However, fermentation by all strains significantly improved (p<0.05), antioxidant activity in both plants compared to non-fermented treatment. Six treatments were based on antibacterial activity results, selected for in vitro rumen fermentation; 1) non-fermented E. ulmoides, 2) fermented E. ulmoides NJ40, 3) fermented E. ulmoides NJ45, 4) non-fermented G. uralensis, 5) fermented G. uralensis NJ40, 6) fermented G. uralensis NJ45. A negative control was also added, making a total of 7 treatments for the in vitro experiment. Medicinal plant-based treatments significantly improved (p<0.05) total volatile fatty acid (VFA) concentration. Significant methane reduction per mol of VFA were observed in G. uralensis (p<0.05). Based on the present study, fermentation improves the biological activity of E. ulmoides Oliv. and G. uralensis. Fermented G. uralensis could also be applied as an enteric methane mitigating agent in ruminant animals.

• Proceedings of the Korean Information Science Society Conference
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• 2003.04a
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• pp.638-640
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• 2003

최근 바이오인포매틱스 분야의 발전에 따라 방대한 양의 유전체 데이터에 대한 연구가 진행되고 있으며, 이러한 데이터를 효율적으로 다루기 위해 다양한 형태의 파일과 데이터베이스들이 사용되고 있다. 하지만 표준화의 미비로 인하여 데이터의 관리와 변환에 어려움이 많다. 본 논문에서는 이러한 문제점을 해결하기 위하여 바이오인포매틱스 데이터를 다루기 위한 표준으로 다양한 XML 포맷들 중에서 BSML(Bioinformatic Sequence Markup Language)을 채택하고, Genbank 파일을 변환하여 관계형 데이터베이스에 저장하는 모듈을 개발한다. 또한 관계형 데이터베이스 형태의 유전체 데이터를 BSML 형태로, Genbank 파일 형태를 BSML 형태로 그리고 AGAVE(Architecture for Genomic Annotation)파일 형태를 BSML 형태로 변환하는 변환기롤 개발하고자 한다.

• Journal of Life Science
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• v.27 no.1
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• pp.89-94
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• 2017

DNA sequences of the intergenic spacer 1 and intergenic spacer 2 of the nineteen plants belonging Vitis genus were collected from the Genbank. DNA sequences of the same regions of Vitis thunbergii var. sinuata and Ampelopsis brevipedunculata var. heterophylla, both common plants in Korea, were not available in Genbank. Those two plants were collected, their genomic DNA encoding 18S rRNA, intergenic spacer 1, 5.8S rRNA, intergenic spacer 2 and part of 28S rRNA amplified and DNA sequence determined. DNA sequences of twenty-one plants including two Korean plants were aligned by the Multiple sequence comparison by log-expectation(MUSCLE) algorithm and the alignment was used to calculate neighbor-joining tree and pairwise distance. The results indicate DNA sequences of the two Korean plants are highly homologous with each other, but they are quite distantly related to the other Vitis plants. Distant relationship of the two Korean plants with the other Vitis plants might be due to independent evolution of those two plants in geographically isolated environment. Those two Korean plants are classified in different genera based on the morphology, one in Vitis genus and the other in Ampelopsis genus, providing another example of discrepancy between morphological and genetic classification.

• Korean Journal of Microbiology
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• v.33 no.2
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• pp.149-156
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• 1997

We have employed comparative RFL,P(Restriction Fragment Ixngth Pol~iniorphism) analysis and molecular phylogenetic techniques to investigate the diversity of uncultured microorganisms associated with the anaerobic PCP degradation in PCP-adapted enrichment cultures inoculated by samples from anaerobic cewage sludgc(Jangrim, Pusan) and leachate of landfill site(Kimhae). 16s rDNA cloncs were obtairted by PCR amplification of mixed population DNAs extracted directly from the nonactive and active stage ol each PCP-adapted culture. After three rounds of comparative RFLP analyses. two RFLP types. designated as Ala and Hld, were found prevalent and common in both active stage samples. Thc analysis of phylogenctic diversity bawd on the 5'-terminal 180 nt of sequences from whole clones of the Ala and Bld RFLP types showed close similarity among themselves. In case of Bld clones, 7XQ of them shared identical sequences. Thcse resuliq suggest that the clones of both RFLP types wcre originated from highly affiliated microorganisms which are e~iriched as a result of metabolic activity to PCP. The full-length 16s rRNA sequence of each representative clone from both RFLP types was determined. and an Ala clone w i n found to he related to Clo.strrdiurn ulfutzac~(Genk~ank No. Z69203) and a Bld clone to Thermobacteroides proteolyticus(Genbank No. X09335), with sequence similarities of 89%' and 97%. respectively.

• Journal of the Korean Applied Science and Technology
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• v.40 no.4
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• pp.881-889
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• 2023

The genus Hymenobacter, type genus of the family Hymenobacteraceae and a member of the phylum Bacteroidota includes gram-negative and red-pigmented rods. Those bacteria have been isolated from various environments of the earth. I isolated a red-pigmented, gram-negative rod from a pond in the campus of the Changwon University, Changwon, Kyeongnam and designated this bacterium as strain B2. Strain B2 was further analyzed phylogenetically and biochemically, and concluded as a member of genus Hymenobacter. BLAST search of the 16S rRNA gene sequence of strain B2 showed its homology lower than 98.7% with those sequences of the other bacteria whose 16S rRNA gene sequences have been reported. Fatty acid composition of the strain B2 was analyzed and its major fatty acids are summed feature 3(C_16:1 ω7c and/or C_16:1 ω6c, 22.8%), iso-C_15:0 (16.2%), anteiso-C_15:0(12.9%), C_16:1ω5c(12.4%) and summed feature 4 (iso-C_17:1 I/anteiso-C_17:1)(9.5%) showing significant differences in fatty acid compositions between strain B2 and the other known Hymenobacter species. DNA sequence of 16S rRNA gene of strain B2 was deposited in genbank under accession number OQ318247.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2002.11a
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• pp.116.1-116
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• 2002

• Journal of Marine Bioscience and Biotechnology
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• v.2 no.2
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• pp.120-122
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• 2007

A $Q_{10}$-producing photosynthetic bacterium was isolated from the silt at Nakdong river. The isolate had 1.55 mg of $Q_{10}$ per gram of dry cell. By the 16s-rDNA sequence analysis, the isolate was found to be Rhodobacter sphaeroids with 100% similarity (Genbank Accession No.=AM696701).

• Journal of Species Research
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• v.5 no.2
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• pp.220-222
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• 2016

An Uraniidae moth, Lyssa zampa (Butler, 1869) is newly discovered from southern Korea. One male specimen was collected at a valley of south aspect of Mt. Hallasan, Jejudo in July, 2014. This species is briefly described and illustrated here. DNA barcoding sequence (Genbank KU160388) for the species was provided for species identification.