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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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The Korean Journal of Microbiology
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Journal DOI :
The Microbiological Society of Korea
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Volume & Issues
Volume 39, Issue 3 - Sep 2003
Volume 39, Issue 2 - Jun 2003
Volume 39, Issue 1 - Mar 2003
Volume 39, Issue 4 - Jan 2003
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NOGSEC: A NOnparametric method for Genome SEquence Clustering
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 67~75
One large topic in comparative genomics is to predict functional annotation by classifying protein sequences. Computational approaches for function prediction include protein structure prediction, sequence alignment and domain prediction or binding site prediction. This paper is on another computational approach searching for sets of homologous sequences from sequence similarity graph. Methods based on similarity graph do not need previous knowledges about sequences, but largely depend on the researcher's subjective threshold settings. In this paper, we propose a genome sequence clustering method of iterative testing and graph decomposition, and a simple method to calculate a strict threshold having biochemical meaning. Proposed method was applied to known bacterial genome sequences and the result was shown with the BAG algorithm's. Result clusters are lacking some completeness, but the confidence level is very high and the method does not need user-defined thresholds.
Enhancement of PHB depolymerase Activity from Alcaligenes faecalis T1 by DNA Shuffling
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 76~82
To prepare evolved PHB depolymerase with increased activity for PHB or P(3HB-co-3HV) compared to the activity of the original PHB depolymerase from Alcaligenes faecalis T1, random mutation of the cloned PHB depolymerase gene was performed by using a DNA shuffling method. A library of mutated PHB depolymerase genes from A. faecalis T1 was fused to the ice nucleation protein (INP) gene from Pseudomonas syringae in pJHCl 1 and approximately 7,000 transformants were isolated. Using M9 minimal medium containing PHB or P(3HB-co-3HV) as the carbon source, mutants showing alteration in PHB depolymerase activity were selected from the transformants. The PHB depolymease activity of the transformants was confirmed by the formation of halo around colony and the turbidity decrease tests using culture supermatants. The catalytic activity of PHB depolymerase of the best mutant II-4 for PHB or P(3HB-co-13 mol% 3HV) was approximately 1.8-fold and 3.2-fold, respectively, higher than that of the original PHB depolymerase. DNA sequence analysis revealed that three amino acid residues (Ala209Val, Leu258Phe, and Asp263Thr) were substituted in II-4. From the mutational analysis, it was presumed that the substitution of amino acids near catalytic triad to more hydrophobic amino acids enhance the catalytic activity of PHB depolymerase from A. faecalis T1.
Expression Pattern of Acetyl Xylan Esterase of Streptomyces coelicolor A3(2) in Escherichia coli
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 83~88
We cloned a gene encoding acetyl xylan esterase(axeA) of Streptomyces coelicolor A3(2) and studied its expression pattern in Escherichia coli. The full sequence of axeA was amplified by PCR. Sequence analysis of the PCR product revealed an open reading frame of 1,008 nucleotides encoding a protein consisted of 335 amino acid residues, with a calculated molecular mass of about 38 kDa. The base sequence showed 98% homology to the same gene of Streptomyces lividans. Two different kinds of acetyl xylan esterases were produced in Escherichia coli(pLacI) by IPTG induction; their molecular weights were 38 kDa and 34 kDa, respectively. Of these, 38 kDa protein seemed to be a total protein holding N-terminal signal peptide region, whereas 34 kDa protein seemed to be a matured protein without signal peptide which was produced by peptide bond cleavage between two amino acid residues of alanine 41 and alanine 42.
Isolation and Identification of Influenza Viruses from Busan, during 2000-2001
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 89~94
Respiratory viruses were isolated from patients with acute respiratory infections in Busan during 2000-2001 and characterized for their antigenic properties. In 2000, 39 out of 43 isolated viruses were identified as influenza viruses and the others were adenoviruses. Among the isolated influenza viruses,23 were type A influenza viruses and 16 were type B influenza viruses. As a result of antigenic characterization, the influenza viruses were determined to A/Sydney/05/97(H3N2)-like, A/Beijing/262/95(H1N1)-like, and B/Harbin07/94-like viruses and serotypes of the isolated adenoviruses were type 1, 2, and 5. In 2001, 56 viruses were isolated and all of the viruses were identified as influenza viruses. They were A/panama/253/99(H3N2)-like and A/Newcaledonia/2007/99(H1Nl)-like viruses when determined by their antigenic properties. The sex distribution of the patients is as follows, 14 males (32.56%),23 females (67.44％) in 2000, and 23 males (41.07%), 33 females (58.93%) in 2001. Occurrence rate was found to be higher in female patients in both years. Age distribution of patients, in 2000, 48.84％ of infection occurred in 0 to 1 year old while in 2002, 33.93% occurred among 11-20 year olds. In 2000, occurrence rate was found to be high in January and again in April and various types of viruses were isolated. These results may be useful for vaccine development and establishment of reliable epidemic data.
Effects of Environmental Factors on the Bacterial Community in Eutrophic Masan Reservoir
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 95~101
The total bacterial numbers, Eubacterial community structures and environmental factors which affect bacterial community were estimated monthly using DAPI and fluorescent in situ hybridization monthly, from June to November 2000 to evaluate the correlation between the bacterial community and environmental factors in eutrophic agricultural Masan reservoir in Asan. Average water temperatures varied from 12.3 to
, pH 7.5 to 9.0, DO 7. I~12.8 mg/L, COD 6.4~13.0 mg/L, chlorophyll a 30.5~99.0 mg/㎥, SS 7.S~25.7 mg/L, TN 1.748~3.543 mg/L., and TP 0.104~0.581 mg/L, respectively. Total bacterial numbers showed high ranges from 0.4 to 9.6
cells/ml, and these indicated the mesotrophic or eutrophic state. The ratio of Eubacteria to total bacteria was 67.6-88.0%, which was higher than that in other reservoir. The relationships of total bacteria and Eubacteria community were more significant with organic nitrogen (Org-N), and organic phosphorus (Org-P) than with water temperature. Proteobacteria groups showed strongly significant relationships with Org-P and Org-N and significant relationships with water temperature, conductivity, COD, and inorganic nitrogen. C-F group was the most significant with Org-N, and HGC group with water temperature. However, relationships of Chl-a, pH, DO and SS showed no significance with any bacterial community. These results were different from other studies, because of the specific characteristics of Masan reservoir such as old, shallow and eutrophic states. The seasonal variation of bacterial community in Masan reservoir does not seem to depend on phytoplankton dynamics but on storm event and organic materials from watershed and the sediment of reservoir.
Isolation and Characterization of Diesel Oil Degrading Bacterium, Pseudomonas sp. GENECO 1 Isolated from Oil Contaminated Soil
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 102~107
With the enrichment culture technique, bacterial strains which degrade diesel oil were isolated from soil contaminated with diesel oil. One of the isolates named GENECO 1 showed the highest activity for emulsification of diesel oil as well as the highest growth rate. This strain, GENECO 1, was identified as a Pseudomonas sp. based on its biochemical, physiological characteristics and 16S rDNA sequences. The optimal cultural conditions for cell growth and oil emulsifying activity of its culture were as follow;
for temperature, 7.0 for pH. Diesel oil degradation was analysed by the gas chromatography. More than 95% of 1% treated diesel oil were converted into a form no longer extractable by mixed organic solvents after 96 hours incubation.
Characterization of Diesel Oil-Degrading Bacteria
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 108~113
Diesel oil-degrading bacterial strains were isolated from diesel oil contaminated soil and called HS series (HS1, HS2 and HS3). These strains were identified as Acinetobacter sp. (HS1) and Pseudomonas sp. (HS2 and HS3) based on Biolog test, cellular fatty acid composition, and 16S rDNA sequence analysis. These strains were coltivated in liquid minimal media containing 2% diesel oil, and diesel oil-degrading activity was measured. As result, all strains degraded over 70% of total diesel oil. But PAH (polycyclic aromatic hydrocarbon)- and pris- tane-degrading rate of these strain was below 20％ of total PAH and pristane. The HS 1 strain showed highest hydrophobicity and low emulsifying activity among the experimental strains and high diesel oil-degrading activity. From the above-mentioned result, microcosm experiment was performed with the HS1 strain. The HS1 strain showed a degrading activity of over 80% of total diesel oil in microcosm test. And microbial activity was correlated to diesel oil-degrading activity. Therefore, it is suggested that the HS1 strains could be effectively used for the bioremediation for diesel oil.
Development of a Method for Rapid Analysis of DNA Hybridization
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 114~117
In molecular biology, it is necessary to develop an easy and rapid method to identify a specific DNA sequence. Though Southern and Northern blot techniques have been used widely for the analysis of gene structure and function, those methods are inconvenient in the points that we need to control incubation temperature, time, and other parameters to get the final result. In this study, we report a new method for the rapid analysis of specific DNA sequence with the modification of an immunochromatographic method. The lateral flow DNA analysis strip is composed of a sample pad, a nitrocellulose membrane for the separation and propagation of analytes, and an absorption pad for the generation of capillary action. Capture DNA was immobilized on the membrane by UV cross-linking and target DNA was labeled with Cy-5 for signaling. The samples containing target DNA were applied onto the sample pad, incubated for 15 min for separation, and scanned with a GSI fluorescence scanner. Though the hybridization reaction occurs in a short time without any washing steps, there appears to be little cross hybridization between the different sequences. The result showed a possibility that the new method can be used for the rapid identification of specific DNA sequence among the samples.
Construction of New P4-Derived Vector Plasmid Containing Tetracyclin Resistance Marker for the Bacteriophage P2-P4 System
Kim, Kyoung-Jin ;
The Korean Journal of Microbiology, volume 39, issue 2, 2003, Pages 118~122
To develop vector plasmid for the bacteriophage P2-P4 system which is a useful experimental tool for the study of viral capsid assembly, we constructed a new P4-derived vector plasmid starting from P4 ash8 sid71 With recombinant DNA technology, a portion of P4 genome was deleted and tetracyclin resistance gene (terR) was introduced into P4 genome to give P4 selectivity. Resulting P4 ash8(sid71) terR was 12.09 kb long and could be converted to a viable bacteriophage with P2 infection. The burst size of induced bacteriophage form of P4 ash8(sid71) terR was determined. The CsCl buoyant equilibrium density gradient experiment of new P4 derivative suggested the upper limit of packaging capacity in P2-size head.