• Microbiology and Biotechnology Letters
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• v.34 no.2
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• pp.101-108
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• 2006

YNB54 strain which shows inhibitory activities specific to the plant pathogenic Phytophthora sp. on potato dextrose agar medium was screened among lots of strains isolated from Korean soils. To identify taxonomy of the Phytophthora specific antagonistic bacteria YNB54, 165 rDNA sequence, MIDI fatty acid composition, DNA-DNA hybridization, GC content, and commercial multitest systems such as API 20E and Biolog GN were performed. Results of commercial kits including lots of biochemical and physiological reactions showed that this strain was closely related to taxa including Enterobacter cloacae and Enterobacter cancerogenus species than other genera(Citerobacter Klebsiella, Leclercia). Also, analysis of its MIDI, G+C contents, and DNA-DNA hybridization suggests that this strain was more similiar to the Genus Enterobacter than other genera (Citerobacter Klebsiella, Leclercia). This strain was potentially identified as Enterobacter sp. by these results. But our 16S ribosomal DNA sequences (rDNA) analysis confirmed that it was more closely related to the cluster of Citerobacter freundii ATCC 29935 than any other Enterobacter species. In the absence of defined phylogenetic critia for delineating genera, the results observed with Citrobacter and Enterobacter species suggest that further studies are needed to clarify their relationships. This investigation demonstrates that YNB54 strain is genetically diverse and potentially more taxonomically complex than hitherto realized. Further study is necessary to confirm their taxonomic positions.

• Journal of Life Science
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• v.13 no.1
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• pp.99-104
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• 2003

Aromatic compounds are of major concern among environmental pollutants due to their toxicity and persistence. To monitor aromatic compounds in a real time with a better sensitivity, a new method of SPR (surface plasmon resonance) based on DNA chip (Biacore 3000) was developed here. It is thought that CapR regulatory protein as a complex with phenol, could bind to their corresponding promoter, Po. Biotinylated DNA oligomers for the promoter was synthesized by PCR and coupled onto streptoavidin-linked CM5-chip. CapR regulatory proteins were purified after cloning their genes in pET21a (+) vector and expressing proteins. The interaction was assessed by the system where the regulatory proteins flowed with or without phenol through the cells of DNA chip. CapR regulatory protein even in the presence of phenol had no response to its promoter, Po, suggesting that other factor(s) might be required for the activation of Po promoter. The present work reveals a promising possibility of the SPR-based DNA chip in monitoring specific environmental pollutants in a real time.

• Korean Journal of Microbiology
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• v.48 no.4
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• pp.275-283
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• 2012

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Asteropus simplex collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and MA media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 94% similarities compared with known bacterial species, and the isolates belonged to five phyla, Alphaproteobacteria, Gammaproteobacteria Actinobacteria, Bacteroidetes, and Firmicutes, of which Gammaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge-derived total gDNA showed 12 DGGE bands, and their sequences showed more than 90% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven phyla, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Actinobacteira, Chloroflexi, and Nitrospira. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with A. simplex by both RFLP and DGGE methods, however, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture-independent method than in culture-dependent method.

• Journal of Life Science
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• v.9 no.1
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• pp.14-16
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• 1999

Genetic variability was monitored by random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) in dicofol-susceptible (S), dicofol-resistant (R) and its reverse-selected (RS) strains of two-spotted spider mite, of Tetranychus urticae. Before the reverse-selection, RS strain, selected reversely from R strain, was 23-fold resistance ratio at {TEX}$LC_{50}${/TEX} to S strain. The resistance was started to in incline slowly to the resistance level of S strain after one year, and the resistance ratio was 4-fold in the 7 years after then. PCR-amplification of T. urticae DNA showed polymorphism in the amplifications with 12 primers in 100 kinds of arbitrary DNA sequences. RAPD amplification with primer OPR-12 (5`-ACAGGTGCGT-3`) showed amplified bands at 1,000 base pair in the S-and RS-strain, and at 350 base pair in R-strain. The results of polymorphism are genetic variabilities derived from development and selection of resistance in each strain. The peculiarly amplified fragments were guessed to participate in dicofol resistance. From the analysis of genetic similarity, it is inferred the gene composition of S-and RS-strain is much closer than that of R-strain.

• Ocean and Polar Research
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• v.28 no.2
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• pp.107-117
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• 2006

Freshwater algal studies in North polar environments are relatively few. This study presented the algal-flora, -biomass and genetic features of dominant cells collected from temporary ponds around the Polar Research Station (PRS), Norway. Water samples were collected from 4 stations around PRS, and analyzed for their environmental and biological variables. Water temperature, salinity and conductivity ranged from 5 to $10^{\circ}C$, 0.1 to $0.3%_{\circ}$ and 0.21 to $0.36{\mu}S/cm$, respectively. Chlorophyll a concentration ranged from 1.8 to $11.1{\mu}g/l$, and that of the size-fractionated cells was recorded from 0.7 to $1.1{\mu}g/l$ in picoplankton 0.3 to $6.5{\mu}g/l$ in nanoplankton, and 0.4 to $3.9{\mu}g/l$ in microplankton respectively. Algal flora in the present study was recorded as 10 genera, in which Chlamydomonas, particularly, was dominant in all studied sites. By comparison of Chlamydomonas 18S rDNA sequences, including two isolates from PRS, they formed a distinct clade against others: sequence similarity was significantly low (<97.2%) with C. noctigama, being the highest score by BLAST search in GenBank. This study was valuable for basic knowledge regarding the freshwater algae around PRS and their genetic information.

• Journal of the korean society of oceanography
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• v.35 no.3
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• pp.158-160
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• 2000

The relativity of four isolates of C. polykrikoides was determined by comparative sequence analysis based on direct sequencing of PCR amplified ribosomal DNA (the internal transcribed spacer region and the 5.8S rDNA). Sequence comparisons indicated that four isolates had the same nucleotide sites in the ITS regions, as well as a total of 585 nucleotide length and 100% homology. The molecular data revealed that C. polykrikoides in Korean coastal waters show no genetical difference.

• Microbiology and Biotechnology Letters
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• v.32 no.1
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• pp.16-21
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• 2004

Six bacterial strains which formed large halo on chitosan-containing agar plate were isolated from beach mud and crabs at South coast of Korean peninsula. They were designated as Bacillus cereus KNUC51, B. cereus KNUC52, B. cereus KNUC53, B. cereus KNUC54, B. cereus KNUC55, and Paenibacillus favisporus KNUC56 by analysing their morphologies and 16S rDNA sequences. Chitosanase activities of all isolates were similar to that of B. subtilis 168. To enhance the activity of chitosanase, a powerful mutagen, MNNG was treated for P favisporus KNUC56. Three mutants showed higher activity of chitosanase than that of the original strain. The DNA fragments containing chitosanase gene from B. cereus sources were cloned, sequenced, and their deduced amino acid sequence analysis showed over 93% homologies with that of the known B. cereus ATCC14579. Extracellular sample from the isolates was incubated in proper reaction mixture including chitosan for 5 minutes at $37^{\circ}C$ to produce 3-10 chitosan oligomers which has been known to be active for clinical agents and agronomical agents.

• Animal cells and systems
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• v.16 no.5
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• pp.415-424
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• 2012

Four species of ophichthid leptocephali were identified using 12S rDNA sequences, and their morphological descriptions were first provided based on six individuals (S1-S3,M1, and E1-E2) collected from the East Sea and the Korea Strait between September 2008 and October 2010. Mitochondrial 12S rDNA 859-861 base pairs of ophichthid leptocephali were compared with those of 16 ophichthids adult and 2 outgroups (Anguilla japonica and Conger myriaster). Leptocephali of S1 and E1 were very closely clustered with adult of Scolecenchelys borealis (D=0.002) and Echelus uropterus (D=0.000), respectively. However, leptocephali of S2-S3 andM1 were slightly far clustered with leptocephalus of S1 (D=0.006) and adult of Muraenichthys gymnopterus (0.034), respectively. We believe that S1 and E1 are S. borealis and E. uropterus, respectively, in which the former is unrecorded species in Korea. However, S2-S3 and M1 may be undescribed species belonging to genus Scolecenchelys and Muraenichthys, respectively, because total numbers of myomeres for S2-S3 (148-158) and M1 (151) were not consistent with total numbers of vertebrae or distribution for any adult of Scolecenchelys spp. and Muraenichthys spp. in the world. We propose the new Korean name 'Dong-hae-mul-baem' for S. borealis.

• Korean Journal of Veterinary Research
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• v.32 no.3
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• pp.389-398
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• 1992

Molecular cloning was carried out on the Danish strain of bovine viral diarrhea virus(BVDV) to construct strategy for the diagnostic tools and effective vaccine of BVD afterwards. A recombinant DNA clone(No. 29) was established successfully from cDNA for viral RNA tailed with adenine homopolymer at 3'-end. $^{32}P$-labeled DNA probes of 300~1,800bp fragments, originating from the clone 29, directed specific DNA-RNA hybridization results with BVDV RNA. Recombinant DNA of the clone 29 was about 5,200bp representing 41.6% of the full length of Danish strain's RNA, and restriction sites were recognized for EcoR I, Sst I, Hin d III and Pst I restriction enzymes in the DNA fragment.

• Korean Journal of Microbiology
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• v.39 no.4
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• pp.272-276
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• 2003

Sapgyo Lake is an artificial freshwater reservoir which is located to the midwest of Korea and is the main water reservoir for industry and agriculture of the region. In this study we investigated environmental factors and the change of bacterial community with the influence of surrounding inflow water and the seasonal variation using the molecular ecological approach. Water samples were collected at front of the dike in May and August, 2001. Bacterial genomic DNAs were extracted directly and purified for the amplification of bacterial 16S rDNA. Clone libraries of the 16S rDNA were constructed using pGEM-T easy vector and RFLP analysis was performed to make a group as OTUs with 4 base recognizing enzymes (MspI and HaeIII). The estimated values of richness in August sample was higher than in May. Thirty-three of 153 clones in May and thirty-eight of 131 clones in August were sequenced from forward region of bacterial 16S rDNA for about 600~800 bp. Proteobacteria, Cytophaga, gram positive bacteria and Verrucomicrobia were observed both months. Especially, Planctomyces, cyanobacteria and chloroplast appeared in August when algal bloom occurred. On the whole investigation, Sapgyo lake showed a typical community structure of estuarine and was influenced by heterochthonous organic matters from the surrounding stream.