• The Plant Pathology Journal
• /
• v.16 no.5
• /
• pp.252-256
• /
• 2000

The 16S-23S rRNA intergenic spacer regions (ISRs) were sequenced and analyzed to design specific primer for identification of Pectobacterium chrysanthemi. Two types ISRs, large and small ISRs, were identified from three strains (ATCC 11663, KACC 10163 and KACC 10165) of P. chrysanthemi and Pectobacterium carotovorum subsp. carotovorum ATCC 15713.Large ISRs contained transfer RNA-Ile(tRNA$^{Ile}$)and tRNA$^{Ala}$, and small ISRs contained tRNA$^{Glu}$. Size of the small ISRs of P. chrysanthemi ranged on 354-356 bp, while it was 451 bp in small ISR of P. carotovorum subsp. carotovorum ATCC 15713. From hypervariable region of small ISRs, species-specific primer for P. chrysanthemi with 20 bp length (CHPG) was designed from hypervariable region of small ISRs, which was used as forward promer to detect P. chrysanthemi strains with R23-1R produced PCR product of about 260bp size (CHSF) only from P. chrysanthemi strains, not from other Pectobacterium spp. and Erwinia spp. Direct PCR from bacterial cell without extracting DNA successfully amplified a specific fragment, CHSF, from P. chrysanthemi ATCC 11663. The limit of PCR detection was 1${\pm}10^2$ cfu/ml.

• Korean Journal of Microbiology
• /
• v.23 no.4
• /
• pp.282-290
• /
• 1985

Small size antibiotic resistance plasmids having molecular weights less than 10 Mdal were isolated and characterized from ten clinically isolated multiple resistant Staphylococcus aureus. Agarose gel electrophoresis profiles and antibiotic resistance patterns divided these strains into four groups. Strain 2-23-6, the representative strain of a group of five strains conferred two plasmids of molecular weights $1.6{\times}10^6\;dal\;and\;2.0{\times}10^6$ dal. The small plasmid (pSBK 112) specified macrolides, lincosamides and streptogramin type B (MLS) resistance gene which are expressed constitutively. Lage plasmid (pSBK 125) specified chloramphenicol resistance gene which is inducible. Strain 10-5 conferred a $3.0{\times}10^6$ dal plasmid (pSBK 141) which carry an inducible ampicillin resistance gene and strain P-H-2 conferred and $1.6{\times}10^6$ dal plasmid (pSBK 190) which carry a constitutive MLS resistance gene. Strain D-H-1 conferred four plasmids of molecular weights $0.8{\times}10^6$ dal (pSBK 201), $1.6{\times}10^6$ dal (pSBK 202), $2.5{\times}10^6$ dal (pSBK 203), and $1.2{\times}10^7$ dal (pDBK 204), respectively. Among those four plasmids, only pSBK 203 specified chloramphenicol resistance gene. Curing of constitutive MLS resistance using acriding orange or ethidium bromide in 2-23-6 and P-H-2 strains produced 'inducible' MLS resistance strains which are less resistant to MLS than the wild type strains, suggesting that there are two resistance genes in both strains; one is constitutive and the other is inducible.

• ALGAE
• /
• v.38 no.4
• /
• pp.241-252
• /
• 2023

The genera Carolibrandtia and Chlorella have been described as small green algae with spherical cell shapes that inhabit various environments. Species of these genera are often difficult to identify because of their simple morphology and high phenotypic plasticity. We investigated two small coccoid strains from Antarctica based on morphology, molecular phylogeny by two alignment methods which have been applied to previous phylogenetic studies of the genus Chlorella, and comparison of the secondary structures of nuclear small subunit (SSU) and internal transcribed spacer (ITS) rDNA sequences. Light microscopy of two strains revealed spherical cells containing chloroplasts with pyrenoids, and the morphological characteristics of the strains were nearly identical to those of other Chlorella species. However, based on the phylogenetic analyses of nuclear SSU and ITS rDNA sequences, it was determined that the Antarctic microalgal strains belonged to two genera, as the Chlorella and Carolibrandtia. In addition, the secondary structures of the SSU and ITS2 sequences were analyzed to detect compensatory base changes (CBCs) that were used to identify and describe the two strains. A unique CBC in the SSU rDNA gene was decisive for distinguishing strain CCAP 211/45. The ITS2 rDNA sequences for each strain were compared to those obtained previously from other closely related species. Following the comparison of morphological and molecular characteristics, we propose KSF0092 as a new species, Chlorella terrestris sp. nov., and the reassignment of the strain Chlorella antarctica CCAP 211/45 into Carolibrandtia antarctica comb. nov.

• Research in Plant Disease
• /
• v.12 no.2
• /
• pp.129-133
• /
• 2006

A bacterial disease of small red bean (Phaseolus angularis) was observed on field-grown plants in Suwon in year 2003. Leaf symptoms initially appeared as water-soaked spots that gradually enlarged, became flaccid and necrotic and were often bordered by a small zone of lemon yellow tissue. In the case of severe infection, dead leaves were defoliated. Pod symptoms consisted of the lesions that were generally circular, slightly sunken and dark reddish brown. Isolation made from diseased leaves on yeast extract dextrose calcium carbonate agar yielded nearly pure cultures of a yellow-pigmented bacterium typical of a xanthomonad. Three bacterial strains were purified and used for further tests. Pathogenicity of strains was confirmed on 3-week-old small red bean plants sprayed with bacterial suspensions containing $10^8 cfu/ml$ of phosphate buffered saline. The representative Xanthomonas strains isolated from small red bean were compared with X. axonopodis pv. phaseoli and X. axonopodis pv. phaseoli var. fuscans type strains for fatty acid profiles, biochemical tests and metabolic fingerprints using Biolog GN2 microplate, showing that all outcomes were indistinguishable between our isolates and reference strains. Two of three strains produced a melanin-like brown pigment extracellularly on King's medium B agar. These results suggest that this new small red bean disease observed in Suwon is bacterial fuscous blight caused by X. axonopodis pv. phaseoli and X. axonopodis pv. phaseoli var. fuscans.

• ALGAE
• /
• v.24 no.4
• /
• pp.205-212
• /
• 2009

Molecular genetic tools are widely used to learn more about the identical characterization of obscure microalgal strains. At the Korea Marine Microalgae Culture Center (KMMCC), the authors deduced the genetic relationship of 41 strains of the genus Tetraselmis by analysing a small subunit ribosomal DNA (18S rDNA) sequences. Forty-one strains were seperated into five groups, which showed over a 98-99% similarity to Tetraselmis striata or Tetraselmis sp. Tsbre. Also, 13 strains among them had an identical genotype to Tetraselmis striata while 5 strains had with Tetraselmis sp. Tsbre, respectively. The mean size of each strain generally showed the tendency of different variation according to the groups.

• Journal of Microbiology
• /
• v.35 no.4
• /
• pp.259-263
• /
• 1997

To study the phylogenetic relationships of species of Trichaptum and to infer intraspecific dibergence of T. abietinum, partial mitochondrial small subunit rDNA sequences were determined. Six strains of T. abietinum, two of T. biforme, and one of T. fusco-violaceum were examined. Parsimony and distance analyses showed that each Trichaptum species forms a distinct group and that T. abietinum consists of two or more subgroups. Strains from North America were distantly related to one another but the European strain formed an independent group with three Korean strains, suggesting the possibility that Korean taxa may be phylogenetically closer to European taxa than to North American taxa.

• Parasites, Hosts and Diseases
• /
• v.51 no.4
• /
• pp.401-412
• /
• 2013

Because of an increased number of Acanthamoeba keratitis (AK) along with associated disease burdens, medical professionals have become more aware of this pathogen in recent years. In this study, by analyzing both the nuclear 18S small subunit ribosomal RNA (18S rRNA) and mitochondrial 16S rRNA gene loci, 27 clinical Acanthamoeba strains that caused AK in Japan were classified into 3 genotypes, T3 (3 strains), T4 (23 strains), and T5 (one strain). Most haplotypes were identical to the reference haplotypes reported from all over the world, and thus no specificity of the haplotype distribution in Japan was found. The T4 sub-genotype analysis using the 16S rRNA gene locus also revealed a clear subconformation within the T4 cluster, and lead to the recognition of a new sub-genotype T4i, in addition to the previously reported sub-genotypes T4a-T4h. Furthermore, 9 out of 23 strains in the T4 genotype were identified to a specific haplotype (AF479533), which seems to be a causal haplotype of AK. While heterozygous nuclear haplotypes were observed from 2 strains, the mitochondrial haplotypes were homozygous as T4 genotype in the both strains, and suggested a possibility of nuclear hybridization (mating reproduction) between different strains in Acanthamoeba. The nuclear 18S rRNA gene and mitochondrial 16S rRNA gene loci of Acanthamoeba spp. possess different unique characteristics usable for the genotyping analyses, and those specific features could contribute to the establishment of molecular taxonomy for the species complex of Acanthamoeba.

• Structural Engineering and Mechanics
• /
• v.18 no.1
• /
• pp.59-78
• /
• 2004

This paper is devoted to illustrate some numerical procedures to solve the boundary equilibrium problems of three-dimensional solids that are subjected to thermal strains. The constitutive equations take into account the bounded tensile strength of the material and they are presented in the framework of non-linear elasticity and small strains. The associated equilibrium problem is solved numerically by means of the finite element method and the numerical techniques, i.e. the Newton-Raphson method and the secant method, are revised in order to assure the solution convergence of the discretized problem. Some numerical examples are illustrated.

• Microbiology and Biotechnology Letters
• /
• v.24 no.2
• /
• pp.166-172
• /
• 1996

It is well known that actinomycetes would be useful for screening of biologically active compounds. Not only to isolate diverse actinomycete strains but to ferment those strains effectively would be important. Seven hundred and forty six strains were isolated from Cheju province, 216 strains were from Chungnam province, 158 strains were from the natural caves at Chungbuk and Kangwon provinces and 202 strains were from Chungwon area at Chungbuk province. All of these 1,322 strains were fermented on a small scale using two different media and tested for their antimicrobial activities against four bacterial strains and one yeast strain. As the result, 12.3% of those isolates were active against Staphylococcus aureus KCTC 1916, 7.6% were Staphylococcus aureus KCTC 1928, 3.9% were Escherichia coli KCTC 1924, 3.0% were Candida albicans KCTC 1940, and 2.2% were Salmonella typhimurium KCTC 1926. About 40% of those isolates showed antimicrobial activities at both two media but the others showed at either one. According to the genus of isolated strains, Streptomyces and Micromonospora showed activities with higher frequencies than others.

• Asian-Australasian Journal of Animal Sciences
• /
• v.16 no.12
• /
• pp.1816-1821
• /
• 2003

Reliable PCR based identification of lactobacilli has been described utilizing the sequence of 16S-23S rRNA intergenic spacer region. Those sequence comparisons showed a high degree of difference in homology among the strains of L. rhamnosus, L. casei, L. acidophilus and L. helveticus whose 16S-23S rRNA intergenic small SR's sizes were 222 bp, 222 bp, 206 bp and 216 bp respectively. The sequence of 16S-23S rRNA intergenic spacer region of L. rhamnosus ATCC 53103 revealed the close relatedness to those of L. casei strains by the homology ranges from 95.4% to 97.2%. 16S-23S rRNA intergenic spacer region nucleotide sequence of L. acidophilus showed some distant relatedness with L. rhamnosus ATCC 53103 with the homology ranges from 40.3% to 41.8% and that with L. helveticus was shown to be 30% of homology, which exists at the most distant phylogenetic relatedness. The identification of species and strain of lactobacilli was possible on the basis of these results. The common sequences among the 17 strains were CTAAGGAA located in the initiating position of the DNA and some discrepancies were found between the same strains based on these results.