• Journal of Microbiology and Biotechnology
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• v.32 no.10
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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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• v.39 no.4
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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.

• The Korean Journal of Malacology
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• v.30 no.4
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• pp.429-431
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• 2014

Since we reported a BLAST server for the mollusk in 2004, no work has reported the usability or modification of the server. To improve its usability, the BLAST server for the mollusk has been updated as version II (http://www.malacol.or.kr/blast) in the present study. The database was constructed by using the Intel server Platform ZSS130 dual Xeon 3.20 GHz CPU and Linux CentOS system and with NCBI WebBLAST package. We downloaded the mollusk nucleotide, amino acid, EST, GSS and mitochondrial genome sequences which can be opened through NCBI web BLAST and used them to build up the database. The updated database consists of 520,977 nucleotide sequences, 229,857 amino acid sequences, 586,498 EST sequences, 23,112 GSS and 565 mitochondrial genome sequences. Total database size is 1.2 GB. Furthermore, we have added repeat sequences, Escherichia coli sequences and vector sequences to facilitate data validation. The newly updated BLAST server for the mollusk will be useful for many malacological researchers as it will save time to identify and study various molluscan genes.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.7
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• pp.312-320
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• 2020

The objective of the study was to undertake a phylogenetic diversity census of ruminal archaea based on a meta-analysis of 16S rRNA gene sequences that were publicly available in the Ribosomal Database Project. A total of 8,416 sequences were retrieved from the Ribosomal Database Project (release 11, update 5) and included in the construction of a taxonomy tree. Species-level operational taxonomic units (OTUs) were analyzed at a 97% sequence similarity by using the QIIME program. Of the 8,416 sequences, 8,412 were classified into one of three phyla; however, the remaining four sequences could not be classified into a known phylum. The Euryarchaeota phylum was predominant and accounted for 99.8% of the archaeal sequences examined. Among the Euryarchaeota, 65.4% were assigned to Methanobrevibacter, followed by Methanosphaera (10.4%), Methanomassillicoccus (10.4%), Methanomicrobium (7.9%), Methanobacterium (1.9%), Methanimicrococcus (0.5%), Methanosarcina (0.1%), and Methanoculleus (0.1%). The 7,544 sequences that had been trimmed to the V2 and V3 regions clustered into 493 OTUs. Only 17 of those 493 OTUs were dominant groups and accounted for more than 1% of the 7,544 sequences. These results can help guide future research into the dominant ruminal methanogens that significantly contribute to methane emissions from ruminants, research that may lead to the development of anti-methanogenic compounds that inhibit these methanogens regardless of diet or animal species.

• Korean Journal of Plant Resources
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• v.35 no.2
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• pp.346-361
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• 2022

Food poisoning accidents caused by poisonous plants occur every year. As certain poisonous plants are mistaken for edible plants causing food poisoning, accurate species identification of poisonous plants is required. DNA barcodes suitable for species identification of poisonous plants and database that can be used for accurate species identification are necessary for their use in forensic cases. In this study, species identification of 19 poisonous plants native to Jeju Island using seven DNA barcodes (trnH-psbA, trnL-trnF, trnL intron, rbcL, matK, ITS1-ITS4, 18S rRNA) was performed to construct a database containing sequence information and DNA barcode universality. trnL-trnF barcode and ITS1-ITS4 barcode were the easiest markers for PCR amplification and sequence retrieval, and the combination of the two barcodes enabled single species identification in 18 out of 19 plants. Therefore, when an investigation of unknown poisonous plants is requested, combination of trnL-trnF and ITS1-ITS4 barcodes is considered as a primary marker for species identification. The database of recommended DNA barcodes for each poisonous plant presented in this study will be helpful in plants poisoning cases.

• Journal of Industrial Technology
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• v.21 no.A
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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.

• Journal of the Korean Society for Precision Engineering
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• v.15 no.10
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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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• v.42 no.2
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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.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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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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• v.16 no.9
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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.