• Journal of Microbiology
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• v.43 no.2
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• pp.152-157
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• 2005

Strain Kw07$^T$, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from granules in an Up-flow Anaerobic Sludge Blanket (UASB) bioreactor used in the treatment of brewery waste­water. 16S rRNA gene sequence analysis revealed that strain Kw07T belongs to the a-4 subclass of the Proteobacteria, and the highest degree of sequence similarity was determined to be to Sphingopyxis macrogoltabida IFO 15033T (97.8%). Chemotaxonomic data revealed that strain Kw07T possesses a quinone system with the predominant compound Q-I0, the predominant fatty acid C,s:, OJ7c, and sphingolipids, aU of which corroborated our assignment ofthe strain to the Sphingopyxis genus. The results of DNA-DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Kw07T represents a distinct species. Based on these data, Kw07T (= KCTC 12209T = NBRC 100800T) should be classified as the type strain for a novel Sphingopyxis species, for which the name Sphingopyxis granuli sp. novo has been proposed.

• Korean Journal of Microbiology
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• v.35 no.3
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• pp.173-179
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• 1999

As a result of PCR-RFLP, the isolates used in this study were classified into five groups. Isolates 1 and 3 were included in AG-5 with 97% genetic similarity. Isolates 12 and 13 were included in AG-1 wilh 100% genetic similarily. Isolates 10 and AG-2-2 showed 97% similarity Isolates 7, 8, 11. 13, and 15 were included in AG-1. When isolates of 4, 5, 7 and 8 were restricted with Hae I. there was a single 700 bp fragment matched with AG-1. A 517 bp restriction fragment of isolate 9 was matched with AG-2-1. Based on the result of southem hybridization of genomic DNAs, all isolates restricted with Msp I showed more variable restriction differences than those restricted with Hae Ill. Isolates AG-2-1 and 9 showed 200 bp restriction fragment, and isolates 3 and AG-1 showed 1 kb restriction fragments.

• Microbiology and Biotechnology Letters
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• v.41 no.1
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• pp.8-16
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• 2013

An agar-hydrolyzing marine bacterium, strain GNUM08120, was isolated from Sargassum fulvellum collected from Yeongil bay of East Sea of Korea. The isolate was Gram-negative, aerobic, motile with single polar flagellum, and grew at 1-10% NaCl, pH 5.0-8.0, and $15-37^{\circ}C$. G+C content and the predominant respiratory quinone were 46.13 mol% and Q-8, respectively. The major cellular fatty acids were Summed feature 3 (24.5%), $C_{16:0}$ (21.7%), and $C_{18:1}{\omega}7c$ (12.5%). Based on 16S rRNA gene sequence similarity and DNA-DNA hybridization analyses, strain GNUM08120 was identified as a novel subspecies of Alteromonas macleodii, designated Alteromonas macleodii subsp. GNUM08120. Production of agarase by strain GNUM08120 was likely repressed by the effect of carbon catabolite repression caused by glucose. The crude agarase prepared from 12-h culture broth of strain GNUM08120 exhibited an optimum pH and temperature for agarase activity at 7.0 and $40^{\circ}C$, respectively. The crude enzyme produced (neo)agarobiose, (neo)agarotetraose, and (neo)agarohexaose as the hydrolyzed product of agarose.

• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2030-2035
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• 2016

Bacillus cereus causes food-borne illness through contaminated foods; therefore, its pathogenicity and genome sequences have been analyzed in several studies. We sequenced and analyzed B. cereus strain FORC_021 isolated from a sashimi restaurant. The genome sequence consists of 5,373,294 bp with 35.36% GC contents, 5,350 predicted CDSs, 42 rRNA genes, and 107 tRNA genes. Based on in silico DNA-DNA hybridization values, B. cereus ATCC $14579^T$ was closest to FORC_021 among the complete genome-sequenced strains. Three major enterotoxins were detected in FORC_021. Comparative genomic analysis of FORC_021 with ATCC $14579^T$ revealed that FORC_021 harbored an additional genomic region encoding virulence factors, such as putative ADP-ribosylating toxin, spore germination protein, internalin, and sortase. Furthermore, in vitro cytotoxicity testing showed that FORC_021 exhibited a high level of cytotoxicity toward INT-407 human epithelial cells. This genomic information of FORC_021 will help us to understand its pathogenesis and assist in managing food contamination.

• Journal of Microbiology and Biotechnology
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• v.28 no.7
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• pp.1133-1140
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• 2018

Pseudomonas fluorescens KLR101 was found to be capable of producing polyhydroxyalkanoate (PHA) using various sugars and fatty acids with carbon numbers ranging from 2 to 6. The PHA granules consisted mainly of a poly(3-hydroxybutyrate) homopolymer and/or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer. Genomic DNA of P. fluorescens was fractionated and cloned into a lambda library, in which a 5.8-kb fragment that hybridized to a heterologous phaC probe from Ralstonia eutropha was identified. In vivo expression in Klebsiella aerogenes KC2671 (pUMS), restriction mapping, Southern hybridization experiments, and sequencing data revealed that PHA biosynthesis by P. fluorescens relied upon a polypeptide encoded by a 1,683-bp non-operonal ORF, which was preceded by a possible -24/-12 promoter and highly similar to DNA sequences of a gene encoding PHA synthase in the genus Pseudomonas. In vivo expression of the putative PHA synthase gene ($phaC_{Pf}$) in a recombinant Escherichia coli strain was investigated by using glucose and decanoate as substrates. E. coli (${phaC_{Pf}}^+$, pUMS) grown in medium containing glucose accumulated PHA granules consisting mainly of 3-hydroxybutyrate, whereas only a trace amount of 3-hydroxydecanoate was detected from an E. coli fadR mutant (${phaC_{Pf}}^+$) grown in medium containing decanoate. In vitro enzymatic assessment experiments showed that 3-hydroxybutyryl-CoA was efficiently used as a substrate of purified $PhaC_{Pf}$, suggesting that the putative PHA synthase of P. fluorescens utilizes mainly short-chain-length PHA precursors as a substrate.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1993.11a
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• pp.17-20
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• 1993

As a step toward a more complete understanding of the molecular actions of TNF, we prepared a cDNA library from TNF-treated human FS-4 fibroblasts and used differential hybridization to identify cDNA clones corresponding to mRNAs enriched in TNF-treated eells. In Quiescent FS-4 cells n induces an increase in the level of some mRNAs within 20 to 30 min. Some of these immediate-early response mRNAs are elevated only transiently for about 30 to 120 min, e. g., c-fos and c-myc (Lin and Vilcek,1987) or the transcription factor IRF-1 (Fujita et al.1989). Such immediate-early gene products may be important for the activation of other genes, but their transient induction suggests that they are not the actual effector molecules responsible for the phenotypic changes induced by TNF. We chose a 3-h incubation with W because we were seeking cDNAs corresponding to messages that are more stably elevated after TNF treatment. Indeed, the results shown in Figure 8 and 9 indicate that all of the mRNAs corresponding to the eight TSG cDNAs isolated remained significantly elevated after 16h of continuous treatment with TNF, and their kinetics of induction were clearly different from those of the immediate-early response mRNAs such as c-fos, c-myc or IRF-1. Nevertheless, only the induction of TSG-21 (collagenase) and TSG-27 (stromelysin) nNAs was completely inhibited by cycloheximide and the induction of TSG-37 (metallothionein-II) was reduced in the presence of this inhibitor of protein synthesis. Induction of the other five TSG mRNAs by TNF was completelyresistant to cycloheximide, suggest ins that no protein intermediate is needed for the upregulation of these mRNAs.

• The Plant Pathology Journal
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• v.30 no.2
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• pp.208-214
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• 2014

Wild rice, Oryza grandiglumis shows hyper-resistance response to pathogen infection. In order to identify genes necessary for defense response in plants, we have carried out a subtractive hybridization coupled with a cDNA macroarray. An acidic PATHOGENESIS-RELATED1 (PR1) gene of the wild rice is highly identical to the acidic PR1 genes of different plant species. The OgPR1a cDNA has an apparent single open reading frame with a predicted molecular mass 40,621 Da and an isoelectic point of 5.14. Both in silico analysis and a transient expression assay in onion epidermal cells revealed that the OgPR1a protein could be localized in intercellular space in plants. The OgPR1a mRNA was strongly transcribed by the exogenous treatment with ethylene and jasmonic acid as well as protein phosphatase inhibitors. Additionally, ectopic expression of the OgPR1a conferred disease resistance on Arabidopsis to the bacterial and fungal infections.

• Korean Journal of Veterinary Research
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• v.39 no.2
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• pp.327-337
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• 1999

The transposon TnphoA was used to generate avirulent mutants from a type A Pasteurella multocida. A suicide vector plasmid pRT733 carrying TnphoA, having the kanamycin resistant gene and harbored in Escherichia coli K-12 strain SM10(${\lambda}pir$), was mated with streptomycin resistant P. multocida P-1059 strain as recipient. This resulted in the generation of two TnphoA insertion mutants (transconjugants, tc95-a and tc95-b) which were resistant both to kanamycin ($Km^{R}$) and streptomycin ($Sm^{R}$), secreted alkaline phosphatase, and were avirulent to turkeys. Southern blot hybridization using two probes derived from internal fragments of TnphoA, confirmed the insertion of TnphoA into 12.9kb or 13.7kb DNA fragment from the EcoRV digested genomic fragments of transconjugants. The two transconjugants, tc95-a and tc95-b, were distinguishable from their parent strains by differences in ribotypes, and outer membrane protein profiles. TnphoA insertion in both transconjugants also resulted in constitutive expression of a 33Kd iron regulated outer membrane protein (IROMP). The gene encoding $Sm^{R}$ was also located within the same 12.9kb EcoRV genomic fragment from both transconjugants. Furthermore, our finding that the recipient P. multocida P-1059 $Sm^{R}$ strain and both transconjugants were avirulent to turkeys suggest that the either 12.9kb or 13.7kb genomic DNA contains the virulence gene and speculate that the presence of $Sm^{R}$ gene or TnphoA insertion may be responsible for regulating and inactivating the gene(s) encoding virulence in P. multocida.

• Korean Journal of Microbiology
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• v.40 no.1
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• pp.1-6
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• 2004

Tetracycline resistant bacterial strains were isolated from 10 batches of Kimchi among 50 batches collected in Taegu restrict. The MIC of tetracycline ranged between 25 and> 100 ㎖/l. Total genomic DNA preparation from all 10 tetracycline resistant lactic acid bacterial isolates were subjected to PCR amplification with class-specific primers for tet(M) and tet(O). In only one isolate, HJ9, tet(M) was detected. By Southern blotting and hybridization with a tet(M)-specific probe, the tet(M) gene of HJ9 isolate could be localized on a plasmid. The partial nucleotide sequence and deduced amino acid sequence of tet(M) of HJ9 showed 90-99% and 94-100% homology to those of Gram positive bacteria, respectively. With sequencing of 16S rRNA, HJ9 isolate from Kimchi was identified as Lactobacillus sakei. From these results, Kimchi can be considered potential vehicle for the spread of antibiotic-resistant lactic acid bacteria along the food chain to the consumer.

• Korean Journal of Plant Taxonomy
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• v.48 no.4
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• pp.260-277
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• 2018

The evolution of chromosome numbers and the karyotype structure is a prominent feature of plant genomes contributing to or at least accompanying plant diversification and eventually leading to speciation. Polyploidy, the multiplication of whole chromosome sets, is widespread and ploidy-level variation is frequent at all taxonomic levels, including species and populations, in angiosperms. Analyses of chromosome numbers and ploidy levels of 252 taxa of Korean non-commelinid monocots indicated that diploids (ca. 44%) and tetraploids (ca. 14%) prevail, with fewer triploids (ca. 6%), pentaploids (ca. 2%), and hexaploids (ca. 4%) being found. The range of genome sizes of the analyzed taxa (0.3-44.5 pg/1C) falls well within that reported in the Plant DNA C-values database (0.061-152.33 pg/1C). Analyses of karyotype features in angiosperm often involve, in addition to chromosome numbers and genome sizes, mapping of selected repetitive DNAs in chromosomes. All of these data when interpreted in a phylogenetic context allow for the addressing of evolutionary questions concerning the large-scale evolution of the genomes as well as the evolution of individual repeat types, especially ribosomal DNAs (5S and 35S rDNAs), and other tandem and dispersed repeats that can be identified in any plant genome at a relatively low cost using next-generation sequencing technologies. The present work investigates chromosome numbers (n or 2n), base chromosome numbers (x), ploidy levels, rDNA loci numbers, and genome size data to gain insight into the incidence, evolution and significance of polyploidy in Korean monocots.