• KSBB Journal
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• v.13 no.4
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• pp.383-390
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• 1998

Bacillus subtilis DT134 was resistant to 50-fold higher concentration of cadmium ions (Cd2+) than cadmium-sensitive B. subtilis BD224 in Luria Broth (LB) medium. Minimal inhibition concentration test in LB agar plates also showed similar results. The elevated cadmium resistance of B. subtilis DT134 strongly suggested a possible existence of cadmium resistance gene in it. Southern blot with Staphylococcus aureus cadA gene fragment (757 bp NlaIV-XmnI cadA DNA fragment) as probe was carried out to test the existence and similarity of the gene. In high stringency condition, there was no detectable signal, but in low stringency, a strong signal specific to the cadA probe could be detected. These results strongly suggested that there was some similarity between total DNA of B. subtilis DT134 and S. aureus pl258 in terms of cadmium resistance gene and the resistance mechanism might be an efflux mechanism. The subsequent efflux experiment showed that the cadmium resistance mechanism of B. subtilis DT134 was also due to the efflux of cadmium.

• Journal of Microbiology and Biotechnology
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• v.7 no.6
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• pp.373-377
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• 1997

The gene for isopenicillin N synthase (cyclase; IPNS) was cloned from Lysobacter lactamgenus using DNA probe amplified with primers based on the consensus sequences of isopenicillin N synthase genes of other ${\beta}$-lactam-producing microorganisms. The genomic library of L. lactamgenus using pUC18 plasmid cloned at the SacI site were screened with the PCR-generated DNA probe and three positive clones were isolated. Enzyme activities in E. coli clones were confirmed by bioassay and HPLC assay. Throughout the functional mapping, it was observed that the gene for isopenicillin N synthase is located at the 1.3-kb XhoI-BamHI fragment of insert of positive clones. Nucleotide sequencing at both ends of the XhoI-BamHI fragment revealed that IPNS of L. lactamgenus has the common amino acid sequences at amino- and carboxy-termini.

• Journal of KIISE:Software and Applications
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• v.34 no.12
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• pp.1056-1064
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• 2007

Biomolecular computing is a new computing paradigm that uses biomolecules such as DNA for information representation and processing. The huge number of molecules in a small volume and the innate massive parallelism inspired a novel computation method, and various computation models and molecular algorithms were developed for problem solving. In the meantime, the use of biomolecules for information processing supports the possibility of DNA computing as an application for biological problems. It has the potential as an analysis tool for biochemical information such as gene expression patterns. In this context, a DNA computing-based model of a biomolecular perceptron has been proposed and the result of its experimental implementation was presented previously. The weight encoding and weighted sum operation, which are the main components of a biomolecular perceptron, are based on the competitive hybridization reactions between the input molecules and weight-encoding probe molecules. However, thermodynamic symmetry in the competitive hybridizations is assumed, so there can be some error in the weight representation depending on the probe species in use. Here we suggest a generalized model of hybridization reactions considering the asymmetric thermodynamics in competitive hybridizations and present a weight encoding method for the reliable implementation of a biomolecular perceptron based on this model. We compare the accuracy of our weight encoding method with that of the previous one via computer simulations and present the condition of probe composition to satisfy the error limit.

• Proceedings of the Korea Society of Poultry Science Conference
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• 2004.11a
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• pp.13-15
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• 2004

Telomeres are the end of chromosomes and consist of a tandem repeat sequence of (TTAGGG)n and associated proteins. Telomeres are essential for chromosome stability and are related with cell senescence and apoptosis. This study was carried out to analyze the amount of telomeric DNA of chicken lymphocytes, which is to considered as bio-marker. The amount of telomeric DNA of lymphocytes in Korean Native Chicken and White Leghorn was analyzed by quantitative-fluorescence in situ hybridization (Q-FISH) technique using the chicken telomeric DNA probe. Telomere quantifies were compared among breeds, ages and sex, and the relationship between the amount of telomeres and their productive trait was also analyzed. Comparing the amount of telomeric DNA on lymphocytes during growing period, the amount of telomeres was gradually decreased as growing older. The telomere quantity was also significantly different in breeds and sex. Estimating correlation coefficient, the amount of telomeres was positively correlated to sexual maturity and body weight but negatively correlated to hen day egg production and egg weight. These results implicate the telomere quantity is considered as an individual bio-marker.

• Korean Journal of Plant Tissue Culture
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• v.24 no.2
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• pp.113-117
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• 1997

Simple sequence repeats (SSR) are widely dispersed throughout eukaryotic genomes, highly polymorphic, and easily typed using polymerase chain reaction (PCR). The objective of this study was to determine the polymorphism of different Chlamydomonas reinhartdtii strains and to determine the mode of inheritance of the SSR locus in Chlamydomonas. A genomic DNA library of C. reinhardtii was constructed and screened with a radiolabeled $(AC)_{11}$ probe for the selection of (CA/GT)n repeat clone. Selected clone was seqeuenced, and PCR primer set flanking (CA/GT)n sequence was constructed. PCR was used to specifically amplify the SSR locus from multiple isolates of C. reinhardtii. The locus was polymorphic in some of the C. reinhardtii isolates. However, the locus was amplified only 4 of 6 isolates of C. reinhardtii, not in other 2 isolates of C. reinhardtii, suggesting that this locus is not extensively conserved. A simple Mendelian inheritance pattern was found, which showed 2:2 segregation in the tetrads resulting from a cross between C. reinhardtii and C. smithii. Our results suggest that this simple sequence repeat DNA polymorphism will be useful for identity testing, population studies, linkage analysis, and genome mapping in Chlamydomonas.

• Microbiology and Biotechnology Letters
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• v.30 no.2
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• pp.116-122
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• 2002

The partial 165 rDNA sequences of 6 lactic acid bacterial strains isolated from Kimchi were determined. Two strains were Leuconostoc mesenteroides and the rest were incorrectly classified and turned out to be Lactobacillus. As the case of dairy lactic acid bacteria, the strains isolated from Kimchi also had cell-envelope proteinase (CEP) activity. As the result of partial CEP gene amplification with CEP-specific primers, the expected 1.2-kb amplificate was obtained not from Leu. mesenteroides but from Lactobacillus strains. The deduced amino acid sequence of PCR product amplified from the genomic DNA of Lactobacillus pentosus KFR1821 showed 95％ and 92％ homology with those of PrtPs from Lactococcus lactis subsp. cremoris and Lactobacillus paracasei subsp. paracasei, respectively. The PCR amplificate was used as a probe and the result of Southern hybridization illuminated the location of CEP gene in chromosomal DNA of Lb. pentosus KFR1821.

• Korean Journal of Veterinary Research
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• v.36 no.1
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• pp.195-207
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• 1996

To make the genomic DNA probe of Theileria sergenti, the merozoites were purified from erythrocytes of Korean cattle, The previous studies on the probe of T sergenti had resulted in two probes as KTS1 and KTS3 DNA fragment. Nucleotide sequence of both ends of the KTS1 and KST3 were determined in order to design primers for polymerase chain reaction. A pair of an uper primer(5'-CCTCTTGAAGTCATCCATGT-3'; nucleotide position 48) and a lower primer(5'-CACTGAGCTG GAAAGAGCTA-3'; nucleotide position 156) in pKTS1 were synthesized. The anticipated PCR product was 128bp in length. To examine the sensitivity of the PCR, KTS1 DNA and purified T sergenti DNA were serially diluted by tenfolds with distilled water. The primers were sensitive enough to detect 4ag of the authentic template DNA and 4fg of the purified T sergenti DNA by PCR. Furthermore, when the blood was serially diluted by two-folds with 0.9% saline, the pair could detect up to 0.00029%(about 164 parasites in $10{\mu}l$ of blood) of T sergenti infection in bovine erythrocytes by PCR. In a comparison of microscopic and PCR detection of T sergenti in the same samples from Chonbuk area, 47 and 51 out of 70 sample(67.1%) were positive by the former and by the latter method, respectively.

• Proceedings of the Korean Society of Fisheries Technology Conference
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• 2003.05a
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• pp.311-312
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• 2003

Microarray를 해석하는데 있어서 방해가 되는 요인에는 여러 가지가 있을 수 있다. 예를 들면 probe DNA의 농도, spotting 시의 습도, spot의 크기 및 모양, slide blocking 과정, lab리ing technique, hybri야zation 온도와 시간 그리고 background signal 등이 그것이다(Hegde et at., 2000). 본 연구에서는 전보에서 선정된 rhabdovirus의 96개 probe로 실제 oligonucleotide chip을 만들어 spot의 모양이나 크기에 관계되는 spotting 조건을 확립하고, slide blocking과 slide washing에 따른 background signal을 낮추기 위한 과정을 도입하였다. (중략)

• Biotechnology and Bioprocess Engineering:BBE
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• v.8 no.4
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• pp.263-267
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• 2003

Magnetic nanoparticles prepared from an alkaline solution of divalent and trivalent iron ions could covalently bind protein via the activation of Nethyl-N-(3-dimethylaminopropyl) carbodiimide (EDC). Trypsin and avidin were taken as the model proteins for the formation of protein-nanoparticle conjugates. The immobilized yield of protein increased with molar ratio of EDC/nanoparticie. Higher concentrations of added protein could yield higher immobilized protein densities on the particles. In contrast to EDC, the yields of protein immobilization via the a ctivation of cyanamide were relatively lower. Nanoparticles bound with avidin could attach a single-stranded DNA through the avidin-biotin interaction and hybridize with a DNA probe. The DNA hybridization was confirmed by fluorescence microscopy observations. Immobilized DNA on nanoparticles by this technique may have widespread applicability to the detection of specific nucleic acid sequence and targeting of DNA to particular cells.

• Microbiology and Biotechnology Letters
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• v.22 no.3
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• pp.246-251
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• 1994

Pseudomonas syringae pv. tabaci(Pa45) Tox$^{-}$ cells were infected with phage Ps90 strain isolated form the natural source, and the Ps90 lysogenized bacterial cells were then obtained. The lyxohenized cells produced tabtoxin and the phage induction occured when the cells treated with mitomycin C. The Southren hybridization alnalysis of the four EcoRI-treated plasmid fragments and the EcoRI-digested genomic DNA of Tox$^{+}$ and Tox$^{-}$ strains using phage DNA as a probe showed that only those DNA fragment of Tox$^{+}$ strain were related to the Ps90 phage DNA. Based on these results, the tabtoxin producing DNA fragments of the bacteris are presumed to have originated from the same phage DNA, and to be responsible for the pathogenecity of the bactrial strains.