• Journal of Periodontal and Implant Science
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• 제25권3호
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• pp.679-693
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• 1995

The present study has been performed to see the intrafamilial transmission of periodontopathic organism Actinobacillus actinomycetemcomitans in Koreans having various froms of periodontal diseases. 17 clinical isolates from 8 periodontal patients and 20m clinical isolates from their 8 family members were grown anaerobically for the serotyping and the extraction of genomic DNA. The DNA was digested with restriction endonucleases (EcoRI+HindIII) and plasmid pAA 2097(kindly provided by Dr. DiRienzo, Univ. of Pennsylvania) including 4.7kb-size randlomly clone probe for restriction length pleomorphism analysis(RFLP). RFLP patterns of reference serotypes a, b, c, d, and e were used as the genotypes A, B, C, D, and E, respectively for comparison of genotypes of clinical isolates. 28 out of total 37 clinical isoltes belonged to either one of 5 basic gentotypes and 9 remaining isolats did not fall into any types, and hence were designate as non-type(NT). Genotype C were the most frequently found one(35.1%) and genotype B has not isolated. Intrafamilial transmission of bacteria between spouses, brothers and sisters, and parents and their offsprings, resepctively could well be demonstrated by comparing RFLP patterns. There were not any specific genotypes which showed predominance over others in terms of transmission.

• 대한의생명과학회지
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• 제15권4호
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• pp.295-300
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• 2009

Tuberculosis caused by Mycobacterium tuberculosis (MTB) still remains to be the most dreadful infectious disease affecting almost every country. In the present study, we developed a simple and rapid but accurate and sensitive assay method for detecting MTB using microplate hybridization assay. For this, a selective region of the rpoB gene was used to design PCR primers, and MTB and Mycobacterium genus-specific probe molecules. The specificity of the assay was confirmed using fifteen different mycobacterial reference strains and twelve different non-mycobacterial reference strains, and the sensitivity was determined to be 100 fg using genomic DNA of MTB reference strain, H37Rv. Subsequently, a total of 62 sputum samples with diverse smear scores and culture positive results were used to evaluate the kit performance. In brief, the specificity and the sensitivity of the assay were 100% and 98.4%, respectively.

• BMB Reports
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• 제29권1호
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• pp.52-57
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• 1996

A specific DNA fragment from Korean radish (Raphanus sativus L.) was amplified by performing PCR with oligonucleotide primers which correspond to the highly conserved regions of plant peroxidases. The size of the PCR product was ca. 400 bp, as expected from the known plant peroxidase genes. Comparison of the nucleotide and deduced amino acid sequences of the PCR product to those of other plant peroxidase-encoding genes revealed that the amplified fragment corresponded to the highly conserved region I and III of plant peroxidases. By screening a genomic library of Korean radish using the amplified fragment as a probe, two positive clones, named prxK1 and prxK2, were isolated. Restriction mapping studies indicated that the 5.2 kb Sail fragment of the prxK1 clone and the 4.0 kb EcoRI fragment of the prxK2 clone encode separate isoperoxidase genes. Analyses of the promoter region of the prxK1 clone shows that putative CAAT box, CMT box, and TGA1b binding sequence (5' TGACGT) are present 718 bp upstream from the start codon.

• 식물조직배양학회지
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• 제28권1호
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• pp.47-52
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• 2001

구기자나무의 효과적인 재분화조건을 바탕으로 염류내성유 전자인 Bet A와 Bet B유전자의 도입을 시도하였다. 구기자나무의 절편체를 재료로 kinetin 1 mg/L, IBA 0.05 mg/L가 첨가된 MS배지에 2일간 전배양한 후 Agrobacterium과 공조배양 및 선발배지에서의 배양으로 kanamycin에 내성을 갖는 잠정적인 형질전환체를 유도하였다. 형질전환체는 PCR 기법 및 Southern blot분석으로 Bet A와 Bet B 유전자 전이를 확인하였고, 도입된 유전자의 발현은 RT-PCR 방법을 사용하여 확인하였다.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2003년도 추계학술발표회
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• pp.152-157
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• 2003

Diesel-contaminated soils were ozonated for different times (0 - 900 min) and incubated for 9 wk to monitor petroleum hydrocarbons (PH)-degradative potential of indigenous microorganisms in the soils. Increased ozonation time decreased not only concentration of PH but also number of microorganisms in the soils. Microorganisms in the ozonated soils increased during 9-wk incubation as monitored by culture- and nonculture-based methods. Higher (1-2 orders of magnitude) cell number was observed by quantitative analysis of soil DNA using probes detecting genes encoding 165 rRNA(rrn), naphthalene dioxygenase (nahA), toluene dioxygenase (todC), and alkane hydroxylase (alkB) than microbial abundance estimated by culture-based methods. Such PH-degraders were relatively a few or under detection limit in 900-min ozonated soil. Further PH-removal observed during the incubation period supported the presence of PH-degraders in ozonated soils. Highest reduction (25.4%) of total PH (TPH) was observed in 180-min ozonated soil white negligible reduction was shown in 900-min ozonated soil during the period, resulting in lowest TPH-concentration in 180-min ozonated soil among the ozonated soils. Microbial community composition in 9-wk incubated soils revealed slight difference between 900-min ozonated and unozonated soils as analyzed by whole cell hybridization using group-specific rRNA-targeted oligonucleotides. Results of this study suggest that appropriate ozonation and subsequent biodegradation by indigenous microorganisms may be a cost-effective and successful remediation strategy for PH-contaminated soils.

• 한국수의병리학회지
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• 제1권2호
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• pp.119-124
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• 1997

The objective of this study was to develop digoxigenin (DIG)-labeled in situ hybridization (ISH) test for diagnosis of Aujeszky's Disease(AD) in infected organs. Specific DNA with well conserved gene sequences encoding gp50 antigen in AD virus (ADV) was obtained by Polymerase Chain Reaction (PCR) method. A pair of oligonucleotide primers used in PCR allowed amplification of a 217 bp sequence from the gp50 ADV gene. The DNA was then labeled with DIG by primer labeling method for use as probe in ISH test to detect ADV nucleic acids in various tissue. Positive hybridization was demonstrated by dark pigmentation in nuclei and cytoplasm of ADV infected cells particularly in brain tonsillar crypt epithelium and pulmonary alveolar cells. This result suggests that ISH is a valuable sensitive and rapid diagnostic test for AD.

• Molecules and Cells
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• 제21권3호
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• pp.411-417
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• 2006

We have developed a polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) marker that can distinguish male-fertile (N) and male-sterile (S) cytoplasm in onions. The PCR-RFLP marker was located in a chloroplast psbA gene amplicon. Digesting the amplicons from different cytoplasm-containing varieties with the restriction enzyme MspI revealed that N-cytoplasm plants have a functional MspI site (CCGG), whereas the S-cytoplasm plants has a substitution in that site (CTGG), and thus no MspI target. The results obtained using this PCR-RFLP marker to distinguish between cytoplasmic male sterile factors in 35 onion varieties corresponded with those using a CMS-specific sequence-characterized amplified region (SCAR) marker. Moreover, the PCR-RFLP marker can identify N- ot S-cytoplasms in DNA sample mixtures in which they are in up to a 10-fold minority, indicating that use of the marker has high diagnostic precision. We also demonstrated the usefulness of the SNP detected in the psbA gene for high-throughput discrimination of CMS factors using Real-time PCR and a TaqMan probe assay.

• 대한수의학회지
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• 제34권2호
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• pp.327-333
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• 1994

The purpose of this study was to establish a rapid diagnostic method detecting Aujeszky's disease virus (ADV) DNA in the cultured cell monolayers (PK-15) and tissue sections of ADV(NYJ-1-87)-infected rats and pigs by in situ hybridization(ISH). Detection of specific ADV-DNA in infected cells was conducted by radiolabeled ISH method using $^{32}P-labeled $ DNA probe (BamH1 7 fragment) which contains a 6.3 Kb ADV-DNA insert. Where ADV-DNA was detected by radiolabeled ISH, the deposition of black photographic grains occurred in the nuclei and the cytoplasms of ADV-infected cells. Positive hybridization signal was often observed in the spinal trigerminal nucleus of the pons, the nucleus of the trigerminal ganglion neuron and the epithelial cells of tonsillar crypts. The results suggested that ISH is considered as a highly sensitive and reliable tool for confirmative diagnosis of this viral disease.

• 대한미생물학회지
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• 제35권4호
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• pp.283-288
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• 2000

The PCR primer set JW21-JW22 of Weiss et al. (19), which was reported to amplify a 139-bp fragment of the l6S rRNA gene of Helicobacter pylori, has been recently used for the detection of H. pylori in clinical specimens. However, when we applied JW21-JW22 PCR to other members of the genus Helicobacter and unrelated microorganisms, all of these bacteria produced a 139-bp PCR product. Therefore, we designed a novel primer set, HPU185-HPL826, which produced a 642-bp amplicon of the l6S rRNA gene of H. pylori. Then we further examined the specificity of the novel PCR assay using Southern blot hybridization with an internal probe, HPP225. The PCR assay described in this study was shown to be highly sensitive and specific only to the H. pylori 16S rRNA gene sequences.

• Genomics & Informatics
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• 제5권3호
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• pp.113-117
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• 2007

The development of microarray technology has facilitated the understanding of gene expression profiles. Despite its convenience, the cause of dye-bias that confounds data interpretation in dual-color DNA microarray experiments is not well known. In order to economize time and money, it is necessary to identify the cause of dye bias, since designing dye-swaps to reduce the dye-specific bias tends to be very expensive. Hence, we sought to determine the reliable cause of systematic dye bias after treating murine macrophage RAW 264.7 cells with 2-keto-3-deoxyoctonate (KDO), interferon-beta $(IFN-{\beta})$, and 8-bromoadenosine (8-BR). To find the cause of systematic dye bias from the point of view of fluorescence quenching, we examined the correlation between systematic dye bias and the proportion of each nucleotide in mRNA and oligonucleotide probe sequence. Cy3-dye bias was highly correlated with the proportion of adenines. Our results support the fact that systematic dye bias is affected by fluorescence quenching of each feature. In addition, we also found that the strength of fluorescence quenching is based on not only dye-dye interactions but also dye-nucleotide interactions as well.