• The Korean Journal of Food And Nutrition
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• v.17 no.3
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• pp.254-259
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• 2004

Rapid detection of foodbome pathogens is becoming increasingly important. The requirement for faster, more reliable tests has lead to the development of a wide range of rapid methods. Among these methods, the use of systems based on nucleic acid based detection has been increasing since they offer advantages of reduction in test time and more reliable detection or identification. Random Amplification Polymorphic DNA(RAPD) method has been used to fingerprint foodbome microorganisms; Listeria monocytogenes. In this study, 10-mer primer OPG-13(5'-CTCTCCGCCA-3') was used to generate RAPD-PCR for detection of pathogenic L. monocytogenes of Listeria spp. Among 20 primers tested, OPG-13 showed on acceptable result for the differentiation of a pathogenic Listeria from non-pathogenic microorganisms. Pathogenic Listeria, L. monocytogenes(ATCC 15313, 19111, 19112, 19113) showed two bands for 700 bp and 1,500 bp while non-pathogenic bacteria, L. ivanovii, L. grayi, L. murrayi, L. innocua, L. welshimeri, and L. seeligeri had only one band sizing from 2,000 to 2,300 bp. This RAPD method proved to be a valuable to gain important information on sources of pathogenic bacteria in food industry.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.377-382
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• 2013

The bacterial community structures of the marine sponge, Dactylospongia metachromia, collected from Chuuk of Micronesia on February 2012, were analyzed by denaturing gradient gel electrophoresis (DGGE). The DGGE fingerprints of two individuals of D. metachromia, CH607 and CH840 showed the same band patterns. The sequences derived from DGGE bands revealed 93~100% similarities with known bacterial species in the public database and high similarity with uncultured bacterial clones. The bacterial community structures of both D. metachromia sponges (CH607, CH840) were composed of 6 phyla, 8 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, Spirochaetes. DGGE fingerprint - based phylogenetic analysis revealed that the bacterial community profiles were identical in two individuals of the same sponge species collected from the same geographical location.

• YAKHAK HOEJI
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• v.57 no.2
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• pp.132-138
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• 2013

Acinetobacter baumannii is gram-negative bacilli that can be widely found in environments. Recently, A. baumannii emerged as a serious nosocomial infection. A total of 92 A. baumannii were isolated from hospitalized patients in Seoul, Korea, between December 2010 and April 2011. Antimicrobial susceptibility testing was investigated using CLSI agar dilution methods. Tigecycline non-susceptible A. baumannii isolates were investigated by repetitive extragenic palindromic sequence-based PCR (rep-PCR). Pulsed-field gel electrophoresis was performed to determine the epidemiological relationships. All clinical isolates showed high-level resistance to the most commonly used antibiotics: Ciprofloxacin (87.0%), Ampicillin/sulbactam (82.6%), Cefotaxime (81.5%), Ceftazidime (80.4%). Moreover, 50.0% of these isolates were non-susceptible to tigecycline. When evaluated by RAPD analysis, generated distinct band ranging in size from 1kb to 8k band varying from 4 to 10 bands. Stricter surveillance and more rapid detection are essential to prevent the spread of multi drug resistant A. baumannii.

• Proceedings of the Korean Society of Food Hygiene and Safety Conference
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• 1996.06a
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• pp.33-33
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• 1996

Interests in the field of rapid methods and automation in microbiology have been growing steadily on an international scale in recent years. International meetings concerned this problem have been held in elsewhere in the world countries since the past twenty years. But, unfortunately in the field of microbial examination in food hygiene, this problem have not yet been developed so much as in the field of clinical microbiology. Today, I would like to introduce you here present aspects of rapid and automation technologies, those which are manly carrying in milk and meats industries. My illustration will be given recent improved technologies using automatic apparatus and instruments along with process of microbial count procedure. Recent direct microbiological counting system (ChemeScan \ulcorner) as real time ultrasensitive analysis created by Cheminex Ltd., France is now most evolutional instrument to provide direct microbial counts, down to one cell, within 30 minutes. The results from these evaluations how a good correlation between the ChemScan system and the standard plate count method. This system will be successful application for not only in the field of pharmacology but also food microbiology. In addition, current identification of microbes by sophisticated instruments suitable for food microbiology, one of which Biology is manual system (BIOLOG\ulcorner), provides reference-level capability at a modes price. For the manual system, the color reactions in the microplate are read by eye and manually keyed into personal computer. Species identification appears on the computer screen within seconds, along with biotype patterns, a list of closely related species, and other useful statistics. In present this is useful application for microbial ecology and epidemiological survey. RiboPrinter system newly produced by DuPont is now focusing among microbiologists in the world, and is one of the biggest microbial characterization system using a DNA-based approach. The technology analyzer is bacterial culture for its genetic fingerprint or riboprint pattern. Finally Bio-cellTracer system for automatic measurement of fungal growth and Fukitori-Maseter, a Surface Hygiene Monitoring Kit by using swabe procedure in food processing environment are briefly illustrated in this presentation.

• Journal of Ecology and Environment
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• v.29 no.6
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• pp.551-558
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• 2006

Effects of Pb and $CO_2$ on soil microbial community associated with Pinus densiflora were investigated using community level physiological profiles (CLPP) and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) methods. Two-years pine trees were planted in Pb-contaminated soils and uncontaminated soils, and cultivated for 3 months in the growth chamber where $CO_2$ concentration was controlled at 380 or 760 ppmv. The structure of microbial community was analyzed in 6 kinds of soil samples (CA-0M : $CO_2$ 380 ppmv + Pb 0 mg/kg + initial, CB-0M : $CO_2$ 380 ppmv + Pb 500 mg/kg + initial, CA-3M : $CO_2$ 380 ppmv + Pb 0 mg/kg + after 3 months, CB-3M : $CO_2$ 380 ppmv + Pb 500 mglkg + after 3 months, EA-3M : $CO_2$ 760 ppmv + Pb 0 mg/kg + after 3 months, EB-3M : $CO_2$ 760 ppmv + Pb 500 mg/kg + after 3 months). After 3 months, the substrate utilization in the uncontaminated soil samples (CA-3M vs EA-3M) was not significantly influenced by $CO_2$ concentrations. However, the substrate utilization in the Pb-contaminated soil samples (CB-3M vs EB-3M) was enhanced by the elevated $CO_2$ concentrations. The results of principal component analysis based on substrate utilization activities showed that the structure of microbial community structure in each soil sample was grouped by Pb-contamination. The similarities of DGGE fingerprints were 56.3 % between the uncontaminated soil samples (CA-3M vs EA-3M), and 71.4% between the Pb-contaminated soil samples (CB-3M vs. EB-3M). The similarities between the soil samples under $CO_2$ 380 ppmv (CA-3M vs CB-3M) and $CO_2$, 760 ppmv (EA-3M vs EB-3M) were 53.3% and 35.8%, respectively. These results suggested that the structure of microbial community associated with Pinus densiflora were sensitively specialized by Pb-contamination rather than $CO_2$ concentration.

• Development and Reproduction
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• v.4 no.2
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• pp.147-152
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• 2000

Four clonal lines of ayu, Plecoglossus altivelis, were produced through gynogenesis, mixed before hatching and reared communally. After 10 months, a randomly taken sample was subjected to a standardized shallow water stressor. Hematocrit, hemoglobin, red blood cells count (RBC) and mean corpuscular volume (MCV) were obtained from stressed and non-stressed fish. DNA fingerprinting was used to confirm the clonal nature of the organisms and to identified the clonal line to which each fish belonged. 1 observed significant differences between clona] lines mostly in the hematocrit and MCV measured under no-stress conditions. Such differences are suggested to represent mainly genetic variance, on account of the common environment provided to all the experimental groups. The stress response ratio was lower than expected, mainly due to some unexpectedly high non-stress values. Heritability values (h$^2$) were medium to high for the no-stress measurements (mean 0.238) and very low or zero for the stressed groups'traits (excepting one high value of 0.484). 1 conclude that the use of communally reared clonal lines represents a good tool for the characterization of the physiological traits, thus allowing for their utilization as genetic selection criteria.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.21-22
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• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.

• Korean Journal of Microbiology
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• v.37 no.1
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• pp.72-79
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• 2001

The effect of phenol on the change of bacterial community in the effluent water from a wastewater treatment plant was analyzed by PCR and terminal restriction fragment length polymorphism (T-RFLP). The fragments of 16S rDNA were amplified by PCR with bacterial primers, where one of the primers was biotinylated at the 5'-end. After digestion with restriction enzymes, HaeIII and AluI, the biotinylated terminal restriction tragments (T-RFs) of the digested products were selectively isolated by using streptavidin paramagnetic particles. The single-stranded DNA of T-RFs was separated by electrophoresis on a polyacrylamide gel and detected by silver staining technique. When 10 standard strains were analyzed by our method, each strain had a unique T-RF which corresponded to the calculated size from the known sequences of RDP database. The T-RFLP fingerprint generated from the effluent water was very complex, and the predominant T-RFs corresponded to members of the genus Acinetobacter, Bacillus and Pseudomonas. In addition, the perturbation of bacterial community was observed when phenol was added to the sample at the final concentration of 250 $l^{-1}$. The number of T-RFs increased and the major bacterial population could be assigned to the genus Acinetobacter, Comamonas, Cytophaga and Pseudomonas. A intense band assigned to the putative genera of Acinetobacter and Cytophaga was eluted, amplified, and sequenced. The nucleotide sequence of the T-RF showed close relationship with the sequence of Acinetobacter junii.

• Journal of Korean Society of Forest Science
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• v.89 no.2
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• pp.167-172
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• 2000

Inter-simple sequence repeat (I-SSR) markers were analyzed from diploid genomes of 95 nutmeg trees (Torreya nucifera Siev. et Zucc.) in 5 populations. A total of 62 I-SSR amplicons were observed and 7 of them were monomorphic in 95 individuals. DNA fingerprint of each tree was verified by pooling the observed I-SSR amplicons. Most of the genetic diversity was allocated within population (90.65%) and all the populations revealed similar level of I-SSR amplicon diversity within population. Degree of population differentiation (${\phi}_{ST}=9.35%$) was moderate on the basis of criteria obtained from isozyme analysis. Based on the results of the cluster analysis of UPGMA, genetic relationships among 5 populations were not coincided with the pattern of geographic distribution. Non-significant confidence interval at each node also suggests that all the nutmeg populations are genetically not much differentiated.

• The Korean Journal of Mycology
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• v.42 no.1
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• pp.1-8
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• 2014

Twelve Universal fungal PCR fingerprint (UFPF) primers that were modified from Universal rice primer (URP) were used to assess genetic diversity of 64 Agaricus strains including 45 A. bisporus strains and other 19 strains of other Agaricus spp. Eight primers, UFPF1, UFPF2, UFPF3, UFPF7, UFPF9, UFPF10, UFPF11, and UFPF12 produced PCR polymorphic bands within and between the Agaricus species. Primer UFPF7 produced specific PCR polymorphic bands that are distinct Korean strain from different strains. Ninety five PCR polymorphic bands were inputted for UPGMA cluster analysis. Forty five strains of A. bisporus are genetically clustered into 8 groups, showing coefficient similarity from 0.75 to 0.9 among them. The varieties, Saea, Saedo, Saejeong and Saeyeon that have recently been developed in Korea were involved in the same group with close genetic relationship of coefficient similarity over 0.96, whereas, other Korean strains were genetically related to A. bisporus strains that were introduced from USA, Eroupe and Chinese.