• Restorative Dentistry and Endodontics
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• v.23 no.1
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• pp.328-338
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• 1998

Porphyromonas endodontalis, an anaerobic Gram negative cocobacillus which was known to be associated with the infected root canals and periapical lesions, is very difficult to culture and to detect by the traditional method in that it requires much time to induce the specific black pigmentation, and it is very sensitive to oxygen and the antibiotics added in the culture medium. In this study, the nucleotide sequences of the 'probe h' (0.73kb), one of the specific DNA probes top. endodontalis (ATCC 35406) which had been developed by our department, was determined and then a pair of primers for PCR amplification was fabricated to identify P. endodontalis. The plasmids containing 'probe h' were purified by $Wizard^{TM}$ Midipreps DNA Purification System (Promega Corp.), and the nucleotide sequences of the 'probe h' were determined by the dideoxy chain termination method using TaqTrack Sequencing System (Promega Corp.) and detected by fluorescent labelling method. The sense/antisense PCR primers were designed with computer software (Lasergene, DNASTAR Ind. PCR was done with a programmable GeneAmp PCR System 2400 (Perkin Elmer-Cetus Co.). Each sample containing the whole genomic DNA of P. endodontalis and other black-pigmented Bacteroides was itailly denatured at $94^{\circ}C$ for 5 min and then subjected to 30 cycles, each of them consisting of 60s at $94^{\circ}C$, 60s at $60^{\circ}C$, and 90s. at $72^{\circ}C$. The amplified DNA was resolved electrophoretically in a 1.0 % agarose gel in 1X TAE buffer, stained with EtBr, and photographed on a UV transilluminator. The results were as follows : 1. The nucleotide sequences of 'probe h' (743 base pairs) were obtained by dideoxy chain termination method, and from that results the specific primers to P. endodontalis (ATCC 35406), 'Primer H1/ Primer H2', were designed. 2. It has been found that 'Primer H1/H2' could detect P. endodontalis (ATCC 35406) using PCR. 3. The PCR system with this primers may be a powerful technique to amplify the specific sequences of 'probe h' of P. endodontalis (ATCC 35406) that produce distinct identification of it from other black-pigmented Bacteroides, and this could help us to determine the nature of periapical disease.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.28 no.8C
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• pp.803-810
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• 2003

This paper addresses an image processing technique for the human papillomavirus (HPV) DNA chip to discriminate whether the probes are hybridized with the target DNA. HPV DNA chip is designed to determine HPV gene-types by using DNA probes for 22 HPV types. In addition to the probes, the HPV DNA chip has markers that always react with the sample DNA. The positions of probe-dots in the final scanned image are fixed relative to the marker- dot locations with a small variation attributable to the accuracy of the dotter and the scanner. The probes are quadruplicated to enhance diagnostic fidelity. frier knowledge including the marker relative distance and the replication information of probes is integrated into the template matching technique with normalized covariance measure. It was demonstrated that the employment of both of the prior knowledges can be accomplished by simply averaging the template matching measures over the positions of the markers and probes. The resulting proposed scheme yields stable marker locating and probe classification.

• Proceedings of the Korean Society of Veterinary Service Conference
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• 1997.05a
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• pp.237.1-237
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• 1997

• Journal of The Korean Society of Grassland and Forage Science
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• v.17 no.4
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• pp.379-386
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• 1997

Recombinant plasmid, pBKH4, containing NPT II and P35S-BcHSP17.6 was constructed by ligation of Bum H I -digested pBKSl-l and BcHSP 17.6 (thermotolerance gene) 6om pBLH4. The tobacco leaf disc was cocultivated with transformed Agmbacterium tumefaciens bearing pBKH4 for 24 hours and transformed shoots were selected on MS-n/B medium containing $100\;{\mu\textrm{g}}/ml$ of kanamycin. Heat-killing temperature of Nicotima tabacum was $50^{\circ}$ for >15min, and transformed tobacco plants with BcHSP17.6 cDNA exhibited thermotolerance at the heat-killing temperature. The transgenic plants were analyzed by Southern blot hybridization with the probe of ${\alpha}^{_32}P$ labelled BcHSP17.6 cDNA. Transcription and expression level of BcHSP17.6 cDNA were also continued by Northern blot analysis and Ouchterlony double immunodiffusion assay. In this study, we suggest that the BcHSP17.6 cDNA introduced to tobacco plant is related to thenuoto-lerance and 17.6-kD LMW HSP acts as a protector from heat damage in plants.

• Korean Journal of Veterinary Research
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• v.39 no.1
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• pp.148-158
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• 1999

The purpose of this study was to establish a rapid, reliable diagnostic method detecting Encephalomyocarditis virus(EMCV) RNA in formalin-fixed, paraffin-embedded tissues of EMCV naturally infected pigs by cDNA probe of EMC $K_3$, the EMCV strain isolated from Korea. Using a biotin-labelled nick translated probe for the cDNA marker. We made up for some defects of radiolabeled method. In sits hybridization(ISH) technique, differently from the other nucleic acid hybridization methods, is able to detect the virus genome specifically in the state of the intact shapes of cells and/or tissues. We succeeded in performing the experiment to detect the EMCV within 1~2 hours using the $MicroProbe^{TM}$ capaillary action system. In this study, we observed highly specific positive signals of red color by staining the paraffin-embedded tissue sections of naturally EMCV-infected pig organs or tissues, including brain, heart, kidney and lacrimal gland with the Fast Red TR salt/Naphtol phosphate chromogen. The results suggested that this ISH method is considered as a highly sensitive and reliable tool for molecular biologic diagnosis of the EMC viral disease.

• Animal cells and systems
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• v.2 no.1
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• pp.113-116
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• 1998

A cDNA clone coding for ribosomal protein 46 (rp46) which is a component of 60S ribosomal large subunit has been identified from Drosophila melanogaster. A cDNA clone encoding S. cerevisiae rp46 was used as a probe to screen a Drosophila larvae cDNA library. The DNA sequence analysis revealed that the cDNA coding for Drosophils rp46 contains a complete reading frame of 153 nucleotides coding for 51 amino acids. The deduced amino acid sequence showed 71-75% homology with those of other eukaryotic organisms. Northern blot analysis showed that about 1-kb rp46 transcripts are abundant throughout fly development. Whole mount embryonic mRNA in situ hybridization also showed no preferential distribution of the transcripts to any specific region. The chromosomal in situ hybridization revealed that the identified gene is localized at position 60C on the right arm of the second polytene chromosome with a possibility of single copy.

• Korean Journal of Animal Reproduction
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• v.17 no.1
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• pp.43-48
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• 1993

These experiments were carried out to construct mouse testis cDNA library and to to seen H-Y Ag gene. Mouse testis was obtained from BALB/c inbreed mouse that was after-born 1 week. Isolation of mouse testis total RNA was carried out by guanidum/cesium choloride, poly(A+) mRNAs were purified by oligo d(T)-cellulose chromatography method. To investigate protein synthesis activity, in-vitro translation carried out by total RNA and poly(A+) mRNA. The products of in-vitro translation were identified in 12.5% PAGE. Single strand DNA and double strand DNA were synthesized from poly(A+) mRNA and purified using phenol/chloroform/isoamylalcohol. Synthesized cDNA was combined with cohesive Eco RI polylinker, its recombination efficiencies were identified by X-gal and IPTG. In the cDNA library, 1$\times$107 phagemids were screened with 32P labelled probe. Hybridization were carried on $65^{\circ}C$ for 16~20hours. And 1$\times$106 phagemids were screened with rabbit-anti-H-Y. In former, select 5 positive clones, and later, 1 positive clone. Its southern blot analysis showed various size of insert cDNA from 0.7kb to 3kb.

• Bulletin of the Korean Chemical Society
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• v.23 no.12
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• pp.1790-1800
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• 2002

The DNA nucleosides(dA, dC, dG, dT)bound to gold nanoparticles (~13 nm) in aqueous solution has been studied as a probe by the SERS and their coordination structures have been proposed on the basis of them. According to UV-Visible absorption of gold nanoparticles after modifying with DNA nucleosides, the rates of absorption of dA, dC, and dG were much faster than that of dT as monitored by the aggregation kinetics at 700 nm. These data indicated that the nucleosides dA, dC, and dG had a higher affinity for the gold nanoparticles surface than nucleoside dT. As the result of SERS spectra, the binding modes of each of the nucleosides on gold nanoparticles have been assigned. A dA binds to gold nanoparticles via a N(7) nitrogen atom of the imidazole ring, which the C(6)-$NH_2$ group also participates in the coordination process. In the case of dC, it binds to the gold surface via a N(3) nitrogen atom of the pyrimidine ring with a partial contribution from the oxygen of C(2)=O group. A coordination of dG to the gold surfaces is also proposed. Although the dG has the two different nitrogens of a pyrimidine ring and the amino group, the N(1) nitrogen atom of a pyrimidine ring has a higher affinity after the hydrogen migrates to the amino group. Conversely, dT binds via the oxygen of the C(4)=O group of the pyrimidine ring. Accordingly, these data suggest that the nitrogen atom of the imidazole or the pyrimidine ring in the DNA nucleosides will bind more fast to the gold nanoparticles surfaces than the oxygen atom of the carbonyl group.

• Journal of Life Science
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• v.8 no.3
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• pp.348-351
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• 1998

Common DNA fragments of the ${\beta}$-globin gene were observed from six races of the adult common carp: Hybrid-Yamato, Japanese wild type, Mirror, Suwa-Yamato, Scale German, and Saku-Yamato. Chromosomal DNAs isolated from the above six races were digested with restriction endonucleased EcoRI and PstI. The digested fragments were transferred onto nitrocellulose filter and hybridized with a probe of carp ${\beta}$-globin cDNA. Molecular sizes of the hybridized DNA fragments digested with EcoRI were 3.6Kb(Kilo base), 4.3Kb and 15Kb in Hybrid-Yamato, Japanese wild type, Mirror, Scale German and Saku-Yamato carp DNAs. In Scale German and Saku-Yamato carp DNAs, two and one more hybridized DNA fragments were observed, respectively. Molecular sizes of the hybridized DNA fragments digested with PstI were 2.2Kb, 6.5Kb, 7.8Kb and 9.2Kb in Hybrid-Yamato, 2.2Kb, 6.5Kb and 9.2Kb in Japanese wild type, 2.2Kb, 6.5Kb, 7.8Kb, and 13Kb in Mirror, 2,2Kb, 5,5Kb, 6.5Kb, 7.8Kb, 9.2Kb and13Kb in Scale German, and 2.2Kb, 5.5Kb, 6.5Kb, 9.2Kb and Saku-Yamato carp DNA. Therefore, depending on carps, three to six DNA fragments were hybridized with ${\beta}$-globin gene probe. Thus it indicated polymorphysm in the globin gene family of carp.

• Korean Journal of Microbiology
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• v.30 no.3
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• pp.232-238
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• 1992

Canz~~j~lohuc;tc.~jurn i werc studied for their heat shock responses at several elevated temperatures and their heat shock genes were detected by the technique of Southern hybridization. (.. ,jc\ulcorneruni sy~>thesized the major heat shock proteins of hsp90. hsphh. and hsphO at 48$^{\circ}$C . ant1 their w~u.ival rates were maintained as the same level at optimal temperature. '1-hc heat shock genes in chromosome of C ,jc:jutii werc determined to be homologous to the heat shock genes or E. t,oli. by showing strong signals in Southern hybridization analysis using clnaK and groESL- as DNA probe But the restriction sites for thc fragmcnts including heat shock genes were different betueen E. c,oli and C ,jtjuni.