• Molecules and Cells
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• 제25권1호
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• pp.78-85
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• 2008

In a search for new molecular pathways associated with asthma, we performed an mRNA differential display analysis using total RNA extracted from the tracheal tissues of ovalbumin (OVA)-challenged mice and sham controls. cDNAs corresponding to mRNAs for which expression levels were altered by OVA-challenge were isolate and sequenced. Twenty-eight genes differentially expressed in sham and OVA challenged mice were identified. A GenBank BLAST homology search revealed that they were related to cytoskeleton remodeling, transcription, protein synthesis and modification, energy production, and cell growth and differentiation. Two were selected for further characterization. Up-regulation of both the perinatal skeletal myosin heavy chain (skMHC) and fast skeletal muscle myosin light chain (skMLC) genes was confirmed by RT-PCR of trachea tissue from OVA challenged mice. Overexpression of skMLC protein was observed in the smooth muscle layers of OVA-challenged mice by immunohistochemistry, and the surface areas stained with skMLC antibody increased in the OVA-challenged mice. The overexpression of skMLC in murine asthma may be associated with the changes of bronchial smooth muscle.

• Journal of Crop Science and Biotechnology
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• 제10권4호
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• pp.231-236
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• 2007

Differentially expressed genes(DEG) were identified in a rice variety, Sathi, an indica type showing high allelopathic potential against barnyardgrass(Echinochloa crus-galli(L.) Beauv. var. frumentaceae). Rice plants were grown with and without barnyardgrass and total RNA was extracted from rice leaves at 45 days after seeding. DEG full-screening was performed by $GeneFishing^{TM}$ method. The differentially expressed bands were re-amplified and sequenced, then analyzed by Basic Local Alignment Search Tool(BLAST) searching for homology sequence identification. Gel electrophoresis showed nine possible genes associated with allelopathic potential in Sathi, six genes(namely DEG-1, 4, 5, 7, 8, and 9) showed higher expression, and three genes(DEG-2, 3 and 6) showed lower expression as compared to the control. cDNA sequence analysis showed that DEG-7 and DEG-9 had the same sequence. From RT PCR results, DEG-6 and DEG-7 were considered as true DEG, whereas DEG-1, 2, 3, 4, 5, and 8 were considered as putative DEG. Results from blast-n and blast-x search suggested that DEG-1 is homologous to a gene for S-adenosylmethionine synthetase, DEG-2 is homologous to a chloroplast gene for ribulose 1,5-bisphosphate carboxylase large subunit, DEG-8 is homologous to oxysterol-binding protein with an 85.7% sequence similarity, DEG-5 is homologous to histone 2B protein with a 47.9% sequence similarity, DEG-6 is homologous to nicotineamine aminotransferase with a 33.1% sequence similarity, DEG-3 has 98.8% similarity with nucleotides sequence that has 33.1% similarity with oxygen evolving complex protein in photosystem II, DEG-7 is homologous to nucleotides sequence that may relate with putative serin/threonine protein kinase and putative transposable element, and DEG-4 has 98.8% similarity with nucleotides sequence for an unknown protein.

• Journal of Microbiology and Biotechnology
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• 제25권4호
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• pp.511-520
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• 2015

Triclosan, the widely used biocide, specifically targets enoyl-acyl carrier protein reductase (ENR) in the bacterial fatty acid synthesis system. Although the fish pathogen Aeromonas salmonicida subsp. salmonicida exhibits triclosan resistance, the nature of this resistance has not been elucidated. Here, we aimed to characterize the triclosan resistance of A. salmonicida subsp. salmonicida causing furunculosis. The fosmid library of triclosan-resistant A. salmonicida subsp. salmonicida was constructed to select a fosmid clone showing triclosan resistance. With the fosmid clone showing triclosan resistance, a subsequent secondary library search resulted in the selection of subclone pTSR-1. DNA sequence analysis of pTSR-1 revealed the presence of a chromosomal-borne fabV-encoding ENR homolog. The ENR of A. salmonicida (FabVas) exhibited significant homology with previously known FabV, including the catalytic domain YX₍₈₎K. fabVas introduction into E. coli dramatically increased its resistance to triclosan. Heterologous expression of FabVas might functionally replace the triclosan-sensitive FabI in vivo to confer E. coli with triclosan resistance. A genome-wide search for fabVas homologs revealed the presence of an additional fabV gene (fabVas2) paralog in A. salmonicida strains and the fabVas orthologs from other gram-negative fish pathogens. Both of the potential FabV ENRs expressed similarly with or without triclosan supplement. This is the first report about the presence of two potential FabV ENRs in a single pathogenic bacterium. Our result suggests that triclosan-resistant ENRs are widely distributed in various bacteria in nature, and the wide use of this biocide can spread these triclosan-tolerant ENRs among fish pathogens and other pathogenic bacteria.

• Journal of Microbiology
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• 제44권5호
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• pp.572-576
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• 2006

To obtain primary idea on oral bacterium species that are generally present in periodotally healthy Koreans, the oral bacterial flora in the saliva of four periodontally healthy Koreans at different ages (5, 32, 35, 65) was investigated in this study. For this investigation, 16S rRNA gene clone libraries were generated from the saliva of the four healthy Koreans, and 50 clones were randomly selected from each saliva clone library and sequenced. Totally, 37 different kinds of bacterial 16S rRNA gene sequences were identified based on sequence homology search through GenBank database. The 37 kinds of saliva clone sequences were classified to 14 genera and 2 uncultured and 1 unidentified bacteria. Among the 14 identified genera, Streptococcus, Prevotella, and Veillollella were common genera, and Streptococcus was dominant genus that accounted for 7 different species. Among the seven Streptococcus species, S. salivarius appeared as the most common species. More numbers of species belonging to the genera Streptococcus and Prevotella was present in saliva from ages 32 and 35. While saliva from ages 5 and 65 showed more numbers of species belonging to the genera Rothia, including potential pathogenic species. Overall, saliva of a young child and a senior showed higher bacterial diversity than that of young adults.

• The Plant Pathology Journal
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• 제34권1호
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• pp.59-64
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• 2018

Bacteriophages of Acidovorax citrulli, the causal agent of bacterial fruit blotch, were isolated from 39 watermelon, pumpkin, and cucumber leaf samples collected from various regions of Korea and tested against 18 A. citrulli strains. Among the six phages isolated, ACP17 forms the largest plaque, and exhibits the morphology of phages in the Myoviridae family with a head diameter of $100{\pm}5nm$ and tail length of $150{\pm}5nm$. ACP17 has eclipse and latent periods of $25{\pm}5min$ and $50{\pm}5min$, respectively, and a burst size of 120. The genome of ACP17 is 156,281 base pairs with a G + C content of 58.7%, 263 open reading frames, and 4 transfer RNA genes. Blast search and phylogenetic analysis of the major capsid protein showed that ACP17 has limited homology to two Stentrophomonas phages, suggesting that ACP17 is a new type of Myoviridae isolated from A. citrulli.

• 한국해양바이오학회지
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• 제7권1호
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• pp.11-18
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• 2015

An extracellular alkaline ${\alpha}$-D-mannosidase produced by a strain named as MA-01 was produced and its preliminary enzyme activity was characterized. Upon determining the 16S rDNA sequence and its homology search, the strain was identified to be one of species of the Bacillus safensis. Localization of enzyme was elucidated that ${\alpha}$-D-mannosidase can be found in culture medium as an extracellular enzyme. In addition, partial enzyme activity of 63% compared with the extracellular enzyme activity was observed in membrane protein. The optimal pH and temperature of the ${\alpha}$-D-mannosidase were pH 7.5 and $37^{\circ}C$, respectively. The $K_m$ and $V_{max}$ values of the ${\alpha}$-D-mannosidase in crude enzyme toward p-nitrophenyl-${\alpha}$-D-mannopyranoside were determined to be $455.6{\mu}M$ and $10.8{\mu}mole/min/mg$ of protein, respectively. To the best of our knowledge, this is the first report described the alkaline ${\alpha}$-D-mannosidase from the family of B. safensis.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2001년도 추계학술발표대회
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• pp.625-628
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• 2001

토양으로부터 특이적인 광학 이성질체에 활성을 갖는 두 효소원을 선별한 후, 동정하여 Pseudomonas sp. S34와 B. stearothermophilus JY144로 명명하였고, genecloning과 sequencing을 통해 유전자의 특성 및 관련효소들과의 유연관계를 규명하였다. 규명된 정보의 분석과 비교를 통해 ketoprofen ethyl ester에 활성을 갖는 효소들의 구조적 특성을 추론할 수 있었고, 이를 바탕으로 발현시스템을 구축하였다. 대량생산된 효소를 활용한 반응의 결과 높은 수율과 순도를 갖는 각각의 광학이성질체를 경제적으로 생산할 수 있었다.

• Genomics & Informatics
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• 제2권3호
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• pp.142-146
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• 2004

Biological data and analysis tools are accumulated in distributed databases and web servers. For this reason, biologists who want to find information from the web should be aware of the various kinds of resources where it is located and how it is retrieved. Integrating the data from heterogeneous biological resources will enable biologists to discover new knowledge across the specific domain boundaries from sequences to expression, structure, and pathway. And inevitably biological databases contain noisy data. Therefore, consensus among databases will confirm the reliability of its contents. We have developed WeSAT that integrates distributed and heterogeneous biological databases and analysis tools, providing through Web Services protocols. In WeSAT, biologists are retrieved specific entries in SWISS-PROT/EMBL, PDB, and KEGG, which have annotated information about sequence, structure, and pathway. And further analysis is carried by integrated services for example homology search and multiple alignments. WeSAT makes it possible to retrieve real time updated data and analysis from the scattered databases in a single platform through Web Services.

• 한국식품위생안전성학회지
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• 제30권4호
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• pp.372-375
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• 2015

비피도박테리아 증식인자인 1,4-dihydroxy-2-naphthoic acid 생산 유산균주 LP2가 선행연구에서 자연치즈로부터 분리되었다. LP2 균주는16S rRNA 유전자 염기서열 분석에 의한 균주동정에서 Lactobacillus plantarum(99% 일치율)과 가장 높은 상동성을 나타내어 Lactobacillus plantarum LP2 균주로 명명하였다. LP2 균주의 배양 상등액은 Helicobacter pylori KCTC 12083 균주에 대하여 항균활성을 나타내었으며 이는 생산된 DHNA에 기인하는 것으로 추측되었다.

• Parasites, Hosts and Diseases
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• 제43권4호
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• pp.149-156
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• 2005

Four hundred and sixty five randomly selected clones from a cDNA library of Blattella germanica were partially sequenced and searched using BLAST as a means of analyzing the transcribed sequences of its genome. A total of 363 expressed sequence tags (ESTs) were generated from 465 clones after editing and trimming the vector and ambiguous sequences. About $42\%$ (154/363) of these clones showed significant homology with other data base registered genes. These new B. germanica genes constituted a broad range of transcripts distributed among ribosomal proteins, energy metabolism, allergens, proteases, protease inhibitors, enzymes, translation, cell signaling path-ways, and proteins of unknown function. Eighty clones were not well-matched by database searches, and these rep-resent new B. germanica-specific ESTs. Some genes which drew our attention are discussed. The information obtained increases our understanding of the B. germanica genome.