• Journal of Microbiology and Biotechnology
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• 제32권10호
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• pp.1307-1314
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• 2022

In this study, we sought to investigate the various characteristics of Salmonella spp. isolated from raw chicken meats available in Korean markets. The data collected, such as food source of isolation, sampling information, serotype, virulence, and genetic profile including sequence type, were registered in the database for further comparative analysis of the strains isolated from the traceback investigation samples. To characterize serotype, virulence and gene sequences, we examined 113 domestically distributed chicken meat samples for contamination with Salmonella spp. Phylogenetic analysis was conducted on 24 strains (21.2%) of Salmonella isolated from 113 commercially available chicken meats and by-products, using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Serotyping of the isolated Salmonella spp. revealed S. Enteritidis in 11 strains (45.8%), S. Virchow in 6 strains (25%), S. Montevideo in 2 strains (8.3%), S. Bsilla in 2 strains (8.3%), S. Bareilly in 1 strain (4.2%), S. Dessau in 1 strain (4.2%), and S. Albany in 1 strain (4.2%). The genetic correlation indicated that 24 isolated strains were classified into 18 clusters with a genetic similarity of 64.4-100% between them. Eleven isolated S. Enteritidis strains were classified into 9 genotypes with a sequence identity of 74.4%, whereas the most distantly related S. Virchow was divided into five genotypes with 85.9% identity. Here, the MLST analysis indicated that the major Sequence Type (ST) of the Salmonella spp. isolated from domestic chicken sold in Chungcheong Province belongs to the ST 11 and 16, which differs from the genotype of Salmonella isolated from imported chicken. The differential sequence characteristics can be a genetic marker for identifying causative bacteria for epidemiological investigations of food poisoning.

• BMB Reports
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• 제39권4호
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• pp.441-447
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• 2006

Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and non-redundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain.

• 한국패류학회지
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• 제30권4호
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• pp.429-431
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• 2014

본 연구를 통하여 연체동물 전용 BLAST 서버 (Version II)가 웹주소 http://www.malacol.or.kr/blast에 구축되었다. 연체동물을 대상으로 하는 연구에 있어 필요한 정보를 매우 빠르게 얻을 수 있었다. 본 시스템을 사용하여 앞으로도 많은 연구가 진행되어지길 바라며, 아울러 많은 연체동물 연구자들에게 많은 도움이 되리라고 사료된다.

• 한국산학기술학회논문지
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• 제21권7호
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• pp.312-320
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• 2020

본 연구의 목적은 Ribosomal Database Project에서 공적으로 활용 가능한 16S rRNA 유전자 시퀀스들의 메타분석을 통해 반추위 고세균의 계통발생 다양성을 조사하는 것이다. 총 8,416개의 시퀀스가 Ribosomal Database Project(출시버전 11, 업데이트 5)로부터 회수되었고, taxonomy tree를 구축하는데 사용되었다. Species 수준의 OTUs가 97% sequence 유사성 기준으로 QIIME 프로그램을 사용하여 분석되었다. 총 8,416개의 시퀀스 중에서 8,412개의 시퀀스는 총 3개의 문으로 분류되었고, 나머지 4개의 시퀀스는 어떤 알려진 문으로 분류되지 못했다. Euryarchaeota는 가장 우점하는 문으로, 전체 고세균 시퀀스의 99.8%를 차지하였다. 이 중에서 차례로 Methanobrevibacter가 65.4%, Methanosphaera가 10.4%, Methanomassillicoccus가 10.4%, Methanomicrobium가 7.9%, Methanobacterium가 1.9%, Methanimicrococcus가 0.5%, Methanosarcina가 0.1%, Methanoculleus가 0.1%를 차지하였다. V2와 V3 영역으로 자른 7,544개의 시퀀스는 493개의 OTUs로 분류되었다. 총 493 OTUs 중에서 단지 17개만 우점하였고, 총 7,544 시퀀스 중 1% 이상을 차지하였다. 본 연구는 반추동물로 부터 메탄발생에 크게 기여하는 반추위 우점 메탄생성균 분석에 대한 향후 연구를 인도하는데 도움을 주고, 사료나 가축품종이 달라져도 이러한 메탄생성균을 억제하는 메탄저감제를 개발하는데 도움을 줄 것이다.

• 한국자원식물학회지
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• 제35권2호
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• pp.346-361
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• 2022

독성 식물로 인한 식중독 사고는 매년 발생하고 있으며, 일부 독성 식물은 식용 식물로 오인 섭취되어 식중독을 유발하기 때문에 독성 식물의 정확한 종 식별이 요구되고 있다. 이러한 요구에 따라 감정기관에서는 독성 식물의 종 식별에 적합한 DNA 바코드를 찾아 신속하고 정확한 종 식별에 활용할 수 있는 데이터베이스를 구축하는 것이 필요한 실정이다. 따라서 본 연구는 다양한 독성 식물에서 DNA 바코드 구간의 염기서열을 확보하고, 각각에 적합한 DNA 바코드를 확인하여 데이터베이스를 구축하고자 하였으며, 기초 연구로써 제주도에 자생하는 독성식물 19종을 선정하여 7개의 DNA 바코드 (trnH-psbA, trnL-trnF, trnL intron, rbcL, matK, ITS1-ITS4, 18S rRNA)를 이용한 종식별을 수행하였다. 종 식별 결과 trnL-trnF 바코드와 ITS1-ITS4 바코드가 PCR 증폭 및 염기서열 획득에 가장 용이하였으며, 두 개의 바코드를 조합하여 사용하면 19종 중 18종의 식물에서 단일 종 식별이 가능하였다. 따라서 미지의 독성 식물에 대한 감정이 의뢰되었을 때 trnL-trnF 바코드와 ITS1-ITS4 바코드를 조합하여 사용하면 신속한 종 식별에 도움이 될 것으로 사료된다. 본 연구에서 제시된 독성식물 19종의 염기서열 및 DNA 바코드 데이터베이스는 더욱 신속하고 정확한 독성 식물의 종 식별 감정에 도움이 될 것이다.

• 산업기술연구
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• 제21권A호
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• pp.155-166
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• 2001

This paper deals with the subsequence searching problem under time-warping. Our work is motivated by the observation that subsequence searches slow down quadratically as the average length of data sequences increases. To resolve this problem, the Segment-Based Approach for Subsequence Searches (SBASS) is proposed. The SBASS divides data and query sequences into a series of segments, and retrieves all data subsequences. Our segmentation scheme allows segments to have different lengths; thus we employ the time warping distance as a similarity measure for each segment pair. For efficient retrieval of similar subsequences, we extract feature vectors from all data segments exploiting their monotonically changing properties, and build a spatial index using feature vectors. The effectiveness of our approach is verified through extensive experiments.

• 한국정밀공학회지
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• 제15권10호
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• pp.51-57
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• 1998

In this paper, a computer aided process design technique, utilizing a forging simulator and a commercial CAD software, is presented together with its related design system for cold-former forging of ball joints. The forging sequence design is carried out through user-computer interaction by using design templates, design database, experience or knowledge-based rules and some basic laws found in the literature. The forging simulation technique is used to verify the process design. The detail designs including die set drawings and die manufacturing information are automatically generated. It has been shown that the engineer ing and design productivity is much improved by the presented approach in the practical standpoint of process design engineers.

• Journal of Applied Biological Chemistry
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• 제42권2호
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• pp.62-65
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• 1999

Iron regulatory proteins (IRPs) 1 and 2 bind with equally high affinity to specific RNA stem-loop sequences known as iron-responsive elements (IRE) which mediate the post-transcriptional regulation of many genes of iron metabolism. To study putative IRE-like sequences in RNA transcripts using the IRP-IRE interaction, Eight known genes from database were selected and the RNA binding activity of IRE-like sequences were compared to IRP-2. Among them, the IRE-like sequence in 3'-untranslational region (UTR) of divalent ration transporter-1 (DCT-1) shows a significant RNA binding affinity. This finding predicts that IRE consensus sequence present within 3'-UTR of DCT-1 might confer the regulation by IRP-2.

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2000년도 Proceedings of 2000 KSAM International Symposium and Spring Meeting
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• pp.135-141
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• 2000

Global Biodiversity is common interest of humans for better health and sustainable development of the society. To provide access and analysis on microbial diversity information, Bacteriology Insight Orienting System (BIOS) has been developed. BIOS contains 6402 species and subspecies names of bacteria and archaea, 2606 names of cyanobacteria by March 2000. BIOS of which web based analytical tool provides windows to compare the results of phylogenetic analysis based on 16S rDNA sequence and the results of cluster analysis on proteome profiling. The sequence data and 2 dimensional gel electrophoresis analysis data were accumulated in BIOS database content for cyanobacteria reclassification and taxonomy. (BIOS URL: http.://www-sp2000ao.nies.go.jp/bios/index.html).

• Journal of Microbiology and Biotechnology
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• 제16권9호
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• pp.1468-1471
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• 2006

The last step in L-carnitine biosynthesis in eukaryotic organisms is mediated by ${\gamma}$-butyrobetaine hydroxylase (EC1.14.11.1), a dioxygenase that converts ${\gamma}$-butyrobetaine to L-carnitine. This enzyme was previously identified from rat liver and humans, and the peptide sequence of human ${\gamma}$-butyrobetaine hydroxylase was used to search the Neurospora crassa genome database, which led to an identification of an open reading frame (ORF) consisting of 1,407 bp encoding a polypeptide of 468 amino acids. When this protein was expressed in Saccharomyces cerevisiae, the crude cell-free extract exhibited ${\gamma}$-butyrobetaine hydroxylase activity.