• Applied Biological Chemistry
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• v.50 no.4
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• pp.262-267
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• 2007

To access the natural product antibiotics produced by uncultured microorganisms, six cosmid libraries of DNA extracted directly from soil samples (environmental DNA, eDNA) were constructed and screened for the production of antibacterial active molecules. Of the approximately 60,000 clones screened, one antibacterial clone (YS92B) was detected. Ethyl acetate extracts of clone YS92B showed antibacterial activity against various pathogenic bacteria (Listeria monocytogenes, Bacillus subtilis, Pseudomonas syringae, Xanthomonas campestris pv. oryzae, Staphylococcus epidemis). Active constituents from cultures of YS92B were isolated and purified using a bioassay-guided fractionation against B. subtilis through a series of procedures (ethyl acetate extraction, Sephadex LH20 column chromatography, High Performance Liquid Chromatography). NMR (Nuclear Magnetic Resonance) spectral analysis of a major antibacterial active YS92B-VII indicated that it is a lauric acid linked to tyrosine. This report describes the characterization of antibacterially active long chain N-acyl derivatives of tyrosine that are produced by eDNA clones hosted in Escherichia coli from Korean soils.

• Journal of Soil and Groundwater Environment
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• v.17 no.6
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• pp.23-32
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• 2012

This study was conducted to monitor microbial species dynamics within the aquifer due to long term operation of geothermal heat pump system. The species were identified by molecular biological methods of 16S rDNA. Groundwater sample was collected from both open (S region) and closed geothermal recovery system (J region) along with the control. J measured and control as well as S measured found Ralstonia pickettii as dominant species at year 2010. In contrast, Rhodoferax ferrireducens was dominantly observed for the control of S. In 2011, Sediminibacterium sp. was universely identified as the dominant species regardless of the monitoring places and type of sample, i.e., measured or control. The difference in the dynamics between the measured and the control was not critically observed, but annual variation was more strikingly found. It reveals that possible environmental changes (e.g. ORP and DO) due to the operation of geothermal heat recovery system in aquifer could be more exceedingly preceded to differentiate annual variation of microbial species rather than positional differences.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.67.1-67
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• 2003

Phytophthora blight is a devastating disease of pepper and occurs almost anywhere peppers are grown. Phytophthora blight is caused by Phytophthora capsici and this pathogen can infect every part of the plant by moving inoculum in the soil, by infecting water on surface, by aerial dispersal to sporulating lesions. Management of Phytophthora blight currently relies on cultural practices, crop rotation, and use of selective fungicides. Since these treatments are a short-term management, a classical breeding for development of resistant pepper against the Phytophthora is an alternative. So far some of the resistant cultivars have been on the market, but those are limited regionally and commercially. Therefore, ultimately an elite line resistant against this disease should be developed, if possible, by biotechnology. We have set out a series of work recently in order to develop Phytophthora resistant pepper cultivar. For the first time, the cDNA microarray analysis was peformed using an EST chip that holds around 5000 pepper EST clones to identify genes responsive to Phytophthora infection. Total RNA samples were obtained from Capsicum annuum PI201234 after inoculating P. capsici to roots and soil and exposed to the chip. .Around 900 EST clones were up-regulated and down-regulated depending on the two RNA sample tissues, leaf and root. From those, we have found 55 transcription factors that may be involved in gene regulation of the disease defense mechanism. Further and in detail information will be provided in the poster.

• Journal of Crop Science and Biotechnology
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• v.11 no.2
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• pp.91-100
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• 2008

Melting curve analysis of fluorescently labeled DNA fragments is used extensively for genotyping single nucleotide polymorphism(SNP). Here, we evaluated a SNP genotyping method by melting curve analysis with the two probe chemistries in a 384-well plate format on a Roche LightCycler 480. The HybProbe chemistry is based on the fluorescence resonance energy transfer(FRET) and the SimpleProbe chemistry uses a terminal self-quenching fluorophore. We evaluated FRET HybProbes and SimpleProbes for two SNP sites closely linked to two quantitative trait loci(QTL) for southern root-knot nematode resistance. These probes were used to genotype the two parents and 94 $F_2$ plants from the cross of PI 96354$\times$Bossier. The SNP genotypes of all samples determined by the LightCycler software agreed with previously determined SSR genotypes and the SNP genotypes determined on a Luminex 100 flow cytometry instrument. Multiplexed HybProbes for the two SNPs showed a 98.4% success rate and 100% concordance between repeats two of the same 96 DNA samples. Also, we developed a HybProbe assay for the Rcs3 gene conditioning broad resistance to the frogeye leaf spot(FLS) disease. The LightCycler 480 provides rapid PCR on 384-well plate and allows simultaneous amplification and analysis in approximately 2 hours without any additional steps after amplification. This allowed for a reduction of the potential contamination of PCR products, simplicity, and enablement of a streamlined workflow. The melting curve analysis on the LightCycler 480 provided high-throughput and rapid SNP genotyping and appears highly effective for marker-assisted selection in soybean.

• Journal of Microbiology and Biotechnology
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• v.15 no.4
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• pp.734-739
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• 2005

Myxobacterium sp. HK1, isolated from Korean soil, degrades cellulose, differentiates to fruiting body, and its 16s rDNA has $95\%$ similarity to Polyangium sp. An anticancer molecule, CDMHK, was identified from culture broth of Myxobacterium sp. HK1, and purified by Diaion HP20, Silica gel, Sephadex LH-20 chromatography, and preparative HPLC using an YMC OSD-A C18 column. The molecular structure and formula were determined to be $C_{l2}H_{l9}N_3O_2$ (M.W 237) by MS spectrometry, 300 MHz $^{1}H\;and\;^{13}C$ NMR. The CDMHK was not active against Escherichia coli, Staphylococcus aureus, and Candida albicans. However, this molecule inhibited the growth of various cancer cell lines. The $ED_{50}$ values of CDMHK were determined to be 0.147, 0.086, 0.18, 0.166, and 0.142 $\mu$g/ml against A549, SK-OV-3, SK-MEL-2, VF498, and HCTl5 cancer cell lines, respectively. In addition, the CDMHK was able to induce apoptosis of the CCRF-CEM cancer cell line, evidenced by DNA fragmentation assay and DAPI staining.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.333-340
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• 2011

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P<0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

• Journal of Applied Biological Chemistry
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• v.59 no.1
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• pp.9-12
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• 2016

Strain AP01 was isolated for the biological cypermethrin degradation from soil and sediment in Busan. This strain was identified on the basis of phylogenetic analysis of the 16s rDNA sequence and assigned as Bacillus amyloliquefaciens AP01. AP01 could degrade about 45% of cypermethrin in the mineral medium at $30^{\circ}C$ and 180 rpm for 5 days. Furthermore when 2% glucose was added in the medium, the degradation rate of cypermethrin by strain AP01 was increased upto about 60%. Therefore, AP01 may serve as a promising strain in the bioremediation of soil polluted with cypermethrin.

• Microbiology and Biotechnology Letters
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• v.37 no.4
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• pp.316-321
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• 2009

We have isolated Chondromyces crocatus KYC2823 in pure culture and five other strains in mixed culture with companion bacteria from Korean soil samples. The strain KYC2823, which was isolated from the soil sample collected in Cheongdo-gun, Gyeongsangbuk-do, showed typical characteristics of C. crocatus, including the shape of fruiting bodies and production of a peculiar odor. In addition, the 16S rDNA sequence was 99.8% identical to that of the strain Cm c5, the proposed neotype strain of C. crocatus. Cloning and sequence analysis of the polyketide biosynthetic genes from KYC2823 by performing PCR have revealed that this strain has biosynthetic gene clusters for ajudazols (inhibitors of electron transport systems) and chondramides (substances affecting the function of the actin cytoskeleton), and biosynthetic genes for other polyketide compounds that have not been cloned yet.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.47-53
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• 2006

A streptomycete strain was isolated from the soil samples from Korea. The chemotaxonomy and 16S rDNA sequencing confirmed that the strain belonged to the genus Streptomyces and we named it Streptomyces sp. AO-0511. Two antibiotics, herbimycin A and dihydroherbimycin A produced by this strain were tested for their physico-chemical and biological characteristics. Both compounds were stable under acidic pH. Dihydroherbimycin A was more heat-stable and polar compared with herbimycin A. Only weak antibacterial activities were detected against Bacillus subtilus ATCC 6633 and Micrococcus luteus ATCC 9341. However, herbimycin A and dihydroherbimycin A showed strong inhibitory activities on lung cancer cells (A549 cells) and leukemia cells (HL-60). The cytotoxicity was determined using L5178Y and P388 cell lines. The results showed that herbimycin A and dihydroherbimycin A had lower toxic effects on the cells compared with the standard compounds, comptothecin and cyclosporin A. Therefore, both compounds could be good candidates for the development of new anticancer drugs.

• Journal of Plant Biotechnology
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• v.36 no.2
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• pp.124-129
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• 2009

In general, the root color of Codonopsis lanceolata is white, but red or blue-colored root is found at a low frequency in nature. Red or blue-colored roots have scarcity value, thus farmers wish to produce colored roots. The factors for determining the color of roots are unclear whether the color is controlled by genetically or simply by environmentally such as soil environment. Using in vitro culture system which is advantageous for setting of the same culture condition, we analyzed the physiological and morphological characteristics and genetic differences among red-, blue- and white lines of C. lanceolata. In the red colored roots, stems of in vitro cultured plantlet were colored in dark red pigment. Histological analysis revealed that the red pigment was accumulated in the outer cortex layer of the stem and determined as anthocyanin. Chlorophyll contents in red root lines were higher than those in white- and blue root lines. Plantlets from red roots were smaller in both shoot length and total leaf area than those from white- and blue roots. Genetic differences among the three different colored C. lanceolata were determined by RAPD (Randomly Amplified Polymorphic DNA) analysis. Each line of colored roots had clear DNA polymorphism. These results indicate that the occurrence of red- and blue colored roots in nature was determined by genetic factors rather than soil enviromental conditions.