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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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A Eukaryotic Gene Structure Prediction Program Using Duration HMM
Tae, Hong-Seok ; Park, Gi-Jeong ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 207~215
Gene structure prediction, which is to predict protein coding regions in a given nucleotide sequence, is the most important process in annotating genes and greatly affects gene analysis and genome annotation. As eukaryotic genes have more complicated stuructures in DNA sequences than those of prokaryotic genes, analysis programs for eukaryotic gene structure prediction have more diverse and more complicated computational models. We have developed EGSP, a eukaryotic gene structure program, using duration hidden markov model. The program consists of two major processes, one of which is a training process to produce parameter values from training data sets and the other of which is to predict protein coding regions based on the parameter values. The program predicts multiple genes rather than a single gene from a DNA sequence. A few computational models were implemented to detect signal pattern and their scanning efficiency was tested. Prediction performance was calculated and was compared with those of a few commonly used programs, GenScan, GeneID and Morgan based on a few criteria. The results show that the program can be practically used as a stand-alone program and a module in a system. For gene prediction of eukaryotic microbial genomes, training and prediction analysis was done with Saccharomyces chromosomes and the result shows the program is currently practically applicable to real eukaryotic microbial genomes.l
High-level Expression of Human Procaspase-9 in Escherichia coli and Purification of its GST-tagged Recombinant Protein
Seong, Yeong-Mo ; Han, Cheol ; Choe, Ju-Yeon ; Park, Hyo-Jin ; Seong, Geun-Hye ; Nam, Min-Gyeong ; Kim, Sang-Su ; Kim, In-Gyeong ; Gang, Seong-Man ; Im, Hyang-Suk ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 216~222
Human caspase-9, an essential apoptosis initiator protease, was excessively degraded when expressed in Escherichia coli under the conventional induction condition. To optimize the conditions for induction and develop a rapid purification method for obtaining significant amounts of wild-type procaspase-9, we expressed procaspase-9 as GST fusion in E. coli. The addition of 0.01 mM IPTG as an inducer to the bacterial culture and decreasing the culture temperature to 25oC improved the production of procasapse-9 protein by circumventing proteolytic degradation in E. coli. The wild-type procaspae-9 was purified to approximately 70% purity with relatively high yields using the method developed in this study. In addition, we found that GST-caspase-9 is autocatalytically cleaved after aspartic acid 315, which is the same site for processing in mammalian cells, during expression in E. coli.
Characterization of NAD(P)H-nitroreductase Purified from the TNT-degrading Bacterium, Stenotrophomonas sp. OK-5
Ho, Eun-Mi ; Cheon, Jae-U ; Gang, Hyeong-Il ; O, Gye-Heon ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 223~229
The purpose of this work was to perform the characterization of NAD(P)H-nitroreductase isolated from Stenotrophomonas sp. OK-5 capable of degrading 2,4,6-trinitrotoluene (TNT). Initially, NADP(H)-nitroreductase by a series of purification processes including ammonium sulfate precipitation, DEAE-sepharose, andQ-sepharose was prepared. From samples harvested from fraction collector, three different fractions (I, II & III)having the enzyme activity of NAD(P)H-itroreductase were detected. Specific activities of three fractions I, II,and III of NAD(P)H-nitroreductase were determined to approximately 5.06 unit/mg, 4.95 unit/mg and 4.86 unit/mg, and concentrated to 10.5, 9.8, and 8.9-fold compared to crude extract, respectively. Among these three fractions,the fraction I of NAD(P)H-nitroreductase demonstrated the highest specific activity in this experiment. Several factors affecting on the enzyme activity of NAD(P)H-nitroreductase (fractions I, II & III) were investigated.The optimum temperature of all NAD(P)H-nitroreductase (fractions I, II & III) was 30oC, and the optimal pH was approximately 7.5. Metal ions such as Ag+, Cu2+, Hg2+ inhibited approximately 80% enzyme activity of all NAD(P)H-nitroreductase, and the enzyme activities were decreased about 30-40% inhibition in the presence of Mn2+ or Ca2+. However, Fe3+ showed stimulatory effect on the enzyme activity. The molecular weights of NAD(P)H-nitroreductase (fractions I, II & III) were measured about 27 kDa on the SDS-PAGE.
Characterization of Endopeptidase of Bacillus amyloliquefaciens S94 by Chemical Modificationtion
Kim, Jong-Il ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 230~234
An extracellular protease of Bacillus amyloliquefaciens S94 was purified to apparent homogeneity. The enzyme activity was strongly inhibited by general inhibitor for serine protease, PMSF, suggesting that the enzyme is a serine protease. The purified enzyme activity was inhibited by leucine peptidase inhibitor, bestatin, suggesting that the enzyme is a leucine endopeptidase. When the enzyme was chemically modified with PMSF, which specifically reacted with serine residue on the enzyme, the activity was eliminated. The endopeptidase activity was inhibited by the modifier which chemically modified carboxyl group of aspartate and glutamate. PLP, which would modify lysine residue, did not affect the endopepetidase activity to a greater extent. This demonstrates that serine and aspartate (or glutamate) residues of enzyme would participate in a important function of the endopeptidase activity.
Inhibition of HIV-1 Replication in CD4+ Peripheral Blood Lymphocytes by Intracellular Expression of RNA Aptamer
Lee, Seong-Uk ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 235~241
We have previously demonstrated that intracellular expression of an RNA aptamer termed RRE40, which was selected in vitro to bind HIV Rev 10-fold much tighter than wild-type RRE, efficiently protected human CD4+ T cell line, CEM, from HIV-1. In this study, to evaluate the efficacy of the RRE40 RNA in clinical settings, polyclonal CD4+ peripheral blood lymphocytes (PBLs) were transduced with retroviral vectors expressing RRE40 decoy RNA and then challenged with clinical isolates of HIV-1. In contrast to the control cells transduced with vectors expressing control tRNA, intracellular expression of RRE40 RNA more effectively inhibited HIV-1 replication in CD4+ PBLs. However, transient and diminished inhibition, rather than complete inhibition, of HIV-1 replication in PBLs expressing RRE40 decoys have been observed. These results suggest that RRE40 decoy RNA would be useful to inhibit HIV-1 replication in cells. However, development of more efficient gene transfer protocols and/or more effective decoy RNAs would be needed to apply RNA decoy to modulate HIV-1 patient.
Comparative Inactivation of Hepatitis A Virus and Murine Encephalomyocarditis Virus to Various Inactivation Processes
Kim, In-Seop ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 242~247
Murine encephalomyocarditis virus (EMCV) has been used as a surrogate for hepatitis A virus (HAV) for the validation of virus removal and/or inactivation during the manufacturing process of biopharmaceuticals. Recently international regulation for the validation of HAV safety has been reinforced because of the reported cases of HAV transmission to hemophiliac patients who had received ntihemophilic factors prepared from human plasma. The purpose of the present study was to compare the resistance of HAV and EMCV to various viral inactivation processes and then to standardize the HAV validation method. HAV was more resistant than EMCV to pasteurization (60oC heat treatment for 10 hr), low pH incubation (pH 3.9 at 25oC for 14 days), 0.1 M NaOH treatment, and lyophilization. EMCV was completely inactivated to undetectable levels within 2 hr of pasteurization, however, HAV was completely inactivated to undetectable levels after 5 hr treatment. EMCV was completely inactivated to undetectable levels within 15 min of 0.1 M NaOH treatment, however, residual infectivity of HAV still remained even after 120 min of treatment. The log reduction factors achieved during low pH incubation were 1.63 for HAV and 3.84 for EMCV. Also the log reduction factors achieved during a lyophilization process of antihemophilic factor VIII were 1.21 for HAV and 4.57 for EMCV. These results indicate that HAV rather than EMCV should be used for the virus validation study and the validation results obtained using EMCV should be precisely reviewed.
Isolation of Enterovirus Causing Aseptic Meningitis in Busan, 2000-2002 Years
Jo, Gyeong-Sun ; Jeong, Myeong-Ju ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 248~252
Enteroviruses isolation were attempted from samples obtained from aseptic meningitis-suspected patients in hospitals in Busan during 2000-2002. Enteroviruses were found in 2 of 292 cases in 2000, 4 of 371 cases in 2001, 83 of 703 cases in 2002. In 2000, the isolated viruses were found to be echovirus serotype 11 and coxsackievirus serotype B2. Coxsackievirus serotype B5 was isolated in 2001 and in 2002, echovirus serotypes 2, 3, 6, 7, 9, 13, 25, 30 were isolated in 70 cases while coxsackievirus serotypes B3 and B4 were isolated in 10 cases. Various specimens tended to emerge over the years. The occurrence in 2000 tended to be mostly focus during the cold months, December through January, while in 2001, it occurred in May. In 2002, occurrence was found to be distributed from April to November with the highest rate during June and July. The strains of Vero and HEp-2 of echovirus and coxsackievirus, respectively, are highly infectious. Electron micrograph of echovirus and coxsackievirus show that they are small nonenevolped, isometric-shaped viruses. Isolated RNA from strains of echovirus and coxsackievirus showing cytopathic effects were used to undergo nested PCR which resulted in a 436 bp single band in all the strains. The serotype was sent to the Department of Virology at the Korean National Institute of Health for identification.
Seasonal Monitoring of Airborne Microbial Concentrations in Kindergartens
Hwang, Gwang-Hwan ; Lee, A-Mi ; Sin, Hyeon-Jin ; Kim, Jong-Seol ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 253~259
To assess microbiological indoor air quality in kindergartens, concentrations of viable airborne microorganisms were seasonally determined at three kindergartens in Ulsan from April, 2002 to January, 2003. Sampling was performed with an impaction-type air sampler and three different media. The numbers of bacteria grown on Staphylococcus medium were between 84 and 4,150 MPN/m3 with an average of 827 MPN/m3, and those on standard method agar ranged from 50 to 2,636 MPN/m3 with an average of 580 MPN/m3. The bacterial concentrations were highest in summer, followed by fall, spring, and winter, and were significantly correlated with indoor temperature. Among the colonies, 45.6~61.0% were observed as Gram-positive cocci and 8.5~20.6% were Gramnegative rods. Micrococcus species were the dominant organisms. The numbers of fungi ranged from 0 to 1,888 MPN/m3(661 MPN/m3 average) based on colony counts with dichloran rose bengal chloramphenicol agar. On average, the fungal concentrations were highest in summer and lowest in winter. Penicillium species and Aspergillus species were identified from the colonies. The obtained data can be utilized as a step to set a guideline for bioaerosols in indoor environment of schools.
Evaluating the Impacts of Long-Term Use of Agricultural Chemicals on a Soil Ecosystem by Structural Analysis of Bacterial Community
Yun, Byeong-Jun ; Kim, Seong-Hyeon ; Lee, Dong-Heon ; O, Gye-Heon ; Gang, Hyeong-Il ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 260~266
In this study bacterial community was analyzed to evaluate the impacts of long-term use of agricultural chemicals on a soil ecosystem as well as to obtain fundamental data on the relationship. Sequences of 16S rRNA clones from a non-agricultural site and a tangerine orchard soil which has a history of long-term use of agricultural chemicals over 30 years were analyzed. This revealed that bacterial community containing 5 divisions and 18 genera was distributed in a tangerine orchard soil, while bacterial community containing 9 divisions and 44 genera was distributed. In a tangerine orchard soil site, the most abundant bacteria in subdivision level were placed into Proteobacteria γ group which occupied 56% of total clones. The other bacterial clones from the ocrhcard soil exposed to agricultural chemicals over 30 years were Acidobacteria group (25%), Fimicutes group (5%), Planctomycetes group (2%), Proteobacteria α (1%), δ group (1%), and Cyanobacteria group (1%). Whereas, the clones were from the non-agricultural site were distributed among the division or subdivision Acidobacteria group (14%), Planctomycetes group (13%), Proteobacteria α (10%), β (9%), δ (9%), Fimicutes group (8%), Verrucomicrobia group (8%), Actinobacteria group (6%), Proteobacteria γ group (3%), Bacteroidetes group (3%), Gemmatimonadetes group (3%), and Cyanobacteria group (1%). This finding suggests the possibility that long-term application of agricultural chemicals or fertilizers on a tangerine orchard might result in drastic reduction or alteration in the composition of the bacterial community in the contaminated soil site.
Degradation of Phenanthrene and Pyrene by Burkholderia sp. D5
Kim, Tae-Jeong ; Jo, Gyeong-Suk ; Ryu, Hui-Uk ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 267~271
Burkholderia sp. D5, a polyaromatic hydrocarbons(PAHs)-degrading bacterium, was isolated from oil-contaminated soil. The bacterium could utilize phenanthrene (Phe) as a sole carbon source but could not use pyrene (Pyr). However, the strain could degrade Pyr when a cosubstrate such as yeast extract (YE) was supplemented. The PAH degradation rate of the bacterium was enhanced by the addition of other organic materials such as YE, peptone and glucose. YE was a particularly effective additive in stimulating cell growth as well as PAH degradation. When 1 g-YE/L was supplemented into the basal salt medium (BSM) with 215 mg-Phe/L, the specific growth rate (0.28 h-1) and Phe-degrading rate (29.30 μmol/L/h) were enhanced approximately ten and two times more than those obtained in the BSM with 215 mg-Phe/L, respectively. Through kinetic analysis, the maximum specific growth rate (μmax) and PAH degrading rate (Vmax) for Phe were obtained as 0.34/h and 289
/L/h, respectively. Also, μmax and Vmax for Pyr were 0.27 h-1 and 50
/L/h, respectively. The degradation rates for each Phe (2.20 μmol/L/h) and Pyr (2.18 μmol/L/h) were lower in mixture substrates than in a single substrate (29.30
/L/h and 9.58
/L/h, respectively). Burkholderia sp. D5 can degrade Phe and Pyr contained in soil, and the PAH degradation rates in soil were 20.03
/L/h for Phe and 1.09
/L/h for Pyr.
Bacterial Diversity and its Phylogenetic Analysis in Lake Sapgyo
Kim, Myeong ; Jeon, Eun-Hyeong ; An, Tae-Yeong ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 272~276
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.
Isolation and Identification of the Bacteriophage P4 ost2, Suppressing sir Mutations of Bacteriophage P2
Kim, Gyeong-Jin ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 277~282
Bacteriophage P4 ost2 which is the P4 mutant suppressing sir mutations of Bacteriophage P2, was isolated as a plaque-former by plating P4 ash8 sid 71 kmr intS on the lawn of P2 sir3 lysogen. P4 ost2 turned out to be the P4 mutant suppressing sir mutations of P2 in one-step growth experiments.
Isolation and Identification of Bacteria from Air Conditioners and its Hygiene
Hong, Seong-Gap ; Jeong, Yong-Tae ; Cheon, Gyeong-Ho ; Baek, Sun-Yeong ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 283~287
This study was performed to identify the microorganisms from air conditioners and to investigate hygiene management on air conditioners. Eight species of bacteria were isolated and identified from twenty samples of coolers in air conditioners; Pantoea sp., Bacillus circulans, Bacillus pumilus, Corynebacterium, Flavimonas oryzihabitans, Ochrobacterum anthropi, Micrococcus sp., and non fermented bacilli (NFB). One thousand and three hundreds twenty-two persons who used air conditioners in their houses were investigated about the state of hygiene management in their air conditioners. One thousand and one hundred thirty eight persons (86%) of the total investigated persons ventilated their air conditioners and 1,128 persons (85%) of them cleaned their air conditioners. However, 864 persons (66%) of them did not clean filters and 1,089 persons (82%) did not clean the heat exchangers, both of which air conditioners could be easily contaminated by microorganisms. From these results, we could conclude that the contaminants, bacteria as mentioned the above, in air conditioners could cause human disease such as respiratory infections if the number of bacteria increase in air conditioners. Thus, the removal of contaminants and the improved hygiene of the air conditioners can prevent human diseases caused by the released bacteria during the use of air conditioners.
Isolation and Characterization of PAHs Degrading Sphingomonas sp. K-19
;Kim, Seong-Hwan;Son, Seung-Ryeol;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 288~292
We isolated a bacterium, K-19, which could degrade PAHs (polycyclic aromatic hydrocarbons) from a soil sample contaminated with PAHs. K-19 was cultured under the conditions where phenanthrene was a sole source of carbon and energy.
Antibiotic Resistance of Hemolytic Escherichia coli Isolated from Animals in Korea
Lee, Gye-Nam ; Park, Yong-Ho ; Jeong, Byeong-Yeol ; Lee, Yeon-Hui ;
The Korean Journal of Microbiology, volume 39, issue 4, 2003, Pages 293~295
Total 70 isolates of Escherichia coli obtained from pigs were studied. Forty four isolates had
-hemolytic activity which was heat labile. Minimum inhibitory concentration test indicated that 40 isolates (57.1%), 15 isolates (21.4%), 23 isolates (32.9%), and 5 isolates (7.1%) were resistant to ampicillin, cephalothin, gentamicin, and norfloxacin, respectively. None of them were extended spectrum
-lactamases (ESBLs) producer when the double disk synergy test (DDST) was performed.