• Korean Journal of Breeding Science
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• v.41 no.4
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• pp.468-473
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• 2009

Fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used for chromosome analysis of hybrids (2n=16) between onion (Allium cepa L., 2n=2X=16) and welsh onion (A. fistulosum L., 2n=2X=16). 5S rDNA, 45S rDNA, and tandemly repeated DNA (TSD) sequence were used as probes for FISH analysis. A. fistulosum specific DNA probe of telomeric repeats and A. fistulosum DNA were used for GISH analysis. In the analysis of meiotic chromosome GISH revealed that hybrids have 7 bivalants and 2 univalents chromosome and 2 univalents were derived from A. fistulosum chromosomes. In somatic chromosomes of hybrid each 8 chromosomes were derived from A. cepa and A. fistulosum, respectively. FISH signal of 45S rDNA probe in A. fistulosum was detected at secondary constriction of chromosomes, while FISH signal in A. cepa was observed in both secondary constriction and telomere of chromosomes. TDS signals in A. fistulosum chromosomes were detected at all subtelomeric of 8 chromosomes and also in 2 pericentromeric of the chromosomes, whereas TDS signals in A. cepa were observed only in subtelomeric in all chromosomes. The pattern of TDS signal in hybrid chromosomes was similar to those of A. fistulosum chromosomes.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.5
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• pp.603-609
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• 2011

Telomeres are special structures at the ends of eukaryotic chromosomes. Vertebrate telomeres consist of tandem repeats of conserved TTAGGG sequence and associated proteins. Birds are interesting models for molecular studies on aging and cellular senescence because of their slow aging rates and longer life spans for their body size. In this longitudinal study, we explored the possibility of using telomeres as an age-marker to predict age in Single Comb White Leghorn layer chickens. We quantified the relative amount of telomeric DNA in isolated peripheral blood lymphocytes by the Quantitative Fluorescence in situ Hybridization technique on interphase nuclei (IQ FISH) using telomere-specific DNA probes. We found that the amount of telomeric DNA (ATD) reduced significantly with an increase in chronological age of the chicken. Especially, the telomere shortening rates are greatly increased in growing individuals compared to laying and old-aged individuals. Therefore, using the ATD values obtained by IQ FISH we established the possibility of age prediction in chickens based on the telomere theory of aging. By regression analysis of the ATD values at each age interval, we formulated an equation to predict the age of chickens. In conclusion, the telomeric DNA values by IQ FISH analyses can be used as an effective age-marker in predicting the chronological age of chickens. The study has implications in the breeding and population genetics of poultry, especially the reproductive potential.

• The Korean Journal of Applied Statistics
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• v.24 no.5
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• pp.847-859
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• 2011

cDNA microarray-based comparative genomic hybridization(CGH) data includes low-intensity spots and thus a statistical strategy is needed to detect subtle differences between different cancer classes. In this study, genes displaying a high frequency of alteration in one of the different classes were selected among the pre-selected genes that show relatively large variations between genes compared to total variations. Utilizing copy-number changes of the selected genes, this study suggests a statistical approach to predict patients' classes with increased performance by pre-classifying patients with similar genetic alteration scores. Two-stage logistic regression model(TLRM) was suggested to pre-classify homogeneous patients and predict patients' classes for cancer prediction; a decision tree(DT) was combined with logistic regression on the set of informative genes. TLRM was constructed in cDNA microarray-based CGH data from the Cancer Metastasis Research Center(CMRC) at Yonsei University; it predicted the patients' clinical diagnoses with perfect matches (except for one patient among the high-risk and low-risk classified patients where the performance of predictions is critical due to the high sensitivity and specificity requirements for clinical treatments. Accuracy validated by leave-one-out cross-validation(LOOCV) was 83.3% while other classification methods of CART and DT performed as comparisons showed worse performances than TLRM.

• Korean Journal of Veterinary Service
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• v.37 no.1
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• pp.29-33
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• 2014

This study aimed at finding a fast, sensitive, and efficient protocol for molecular identification of intracellular protozoa Toxoplasma (T.) gondii. For molecular detection of T. gondii, we developed a polymerase chain reaction coupled with dot blot hybridization assay (PCR/DBH). For DBH analysis, the amplified DNA of T. gondii tachyzoite was labeled by incorporation of digoxigenin. The DBH assay alone was capable of detecting down to $1{\times}10^4$ pg of T. gondii genomic DNA. The PCR alone was capable of detecting down to $1{\times}10^3$ pg of T. gondii genomic DNA, whereas the PCR/DBH assay was capable of detecting down to $1{\times}10^2$ pg of T. gondii genomic DNA, indicating that sensitivity of the PCR/DBH method was approximately 10 to 100 times higher than PCR or DBH alone. Our PCR/DBH assay will be useful for confirming the presence of T. gondii on the samples and differentiating T. gondii infection from other intracellular protozoa infections.

• The Journal of Natural Sciences
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• v.5 no.1
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• pp.37-45
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• 1992

The gene coding for $\beta$-galactosidase of Neisseria lactamica 2118 was cloned into Escherichia coli MC 1061. The isolated 6.5 Kb EcoR I fragement and 7.2 Kb BamH I fragment of chromosomal DNA in Southern hybridization were ligated to a vector plasmid pBR322 and then transformed into Escherichia coli MC 1061 cells. Finally, I obtained three clones as $\beta$-galactosidase positive clone by colony hybridization and Southern hybridization($\beta$-galactosidase probe: lac Z gene of pMC1871). Three recombinant plasmids(pNL.13. 17 and 24) were found to contain the 7.2Kb BamH I fragment originated from Neisseria lactamica 2118 chromosomal DNA by Southern hybridization and pNL 24 was showed high homology to probe especially and also its physical map was constructed.

• Bulletin of the Korean Chemical Society
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• v.23 no.9
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• pp.1337-1339
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• 2002

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.19 no.10
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• pp.960-965
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• 2006

This research aims to develop the multiple channel electrochemical DNA chip using microfabrication technology. At first, we fabricated a high integration type DNA chip array by lithography technology. Several probe DNAs consisting of thiol group at their 5-end were immobilized on the gold electrodes. Then target DNAs were hybridized and reacted. Cyclic voltammetry showed a difference between target DNA and control DNA in the anodic peak current values. Therefore, it is able to detect a plural genes electrochemically after immobilization of a plural probe DNA and hybridization of non-labeling target DNA on the electrodes simultaneously. It suggested that this DNA chip could recognize the sequence specific genes.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2002.05a
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• pp.183-187
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• 2002

DNA microarray는 분자생물학 및 DNA 컴퓨팅 분야에 널리 사용되고 있는 실험 도구이다. DNA microarray를 이용하는 한 예는 알려진 유전자 집합을 바탕으로 하여 hybridization을 통해 새로운 DNA 서열을 분석하는 것이다. 이를 위한 가장 간단한 방법은 알려진 유전자의 모든 서열을 DNA microarray 상에 올려놓는 것이지만 이는 결과의 정확도 및 칩 제작비용 면에서 비효율적이다. 따라서 일반적으로는 유전자 서열 정보를 파악한 후 일련의 DNA 서열을 선택하는 probe 디자인 과정을 거친다. 그러나 현재 유전자 서열을 바탕으로 최적의 probe 집합을 찾는 결정적인 방법이 존재하고 있지 않다. 이에 본 논문은 oligo DNA microarray을 이용한 DNA 서열 분석 문제에 있어서 가능한 많은 유전자를 인식하면서 최소의 probe 개수를 갖는 집합을 찾는 방법을 제안한다. 제시된 방법은 가능한 probe 집합들로 해집합을 구성한 후, 유전알고리즘을 이용한 진화 과정을 통해 목적하는 probe 집합을 찾는다. 본 논문에서는 GenBank로부터 얻은 일련의 유전자 집합을 대상으로 실험하였으며 그 결과를 분석하였다.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2006.05a
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• pp.71-73
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• 2006

This research aims to develop a multiple channel electrochemical DNA chip using micro- fabrication technology. At first, we fabricated a high integrated type DNA chip array by lithography technology. Several probe DNAs consisting of thiol group at their 5-end were immobilized on the gold electrodes. Then target DNAs were hybridized by an electrical force. Redox peak of cyclic-voltammogram showed a difference between target DNA and mismatched DNA in the anodic peak current. Therefore. it is able to detect a various genes electrochemically after immobilization of a various probe DNA and hybridization of label-free DNA on the electrodes simultaneously. It suggested that this DNA chip could recognize the sequence specific genes.

• Korean Journal of Veterinary Research
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• v.35 no.3
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• pp.515-530
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• 1995

Coronaviridae에 속하는 transmissible gastroenteritis virus(TGEV)와 porcine epidemic diarrhea virus(PEDV)를 specific하게 detection할 수 있는 방법을 개발하고자 본 연구를 수행하였다. 두 바이러스 모두 RNA 바이러스이기 때문에 reverse transcription-polymerase chain reaction(RT-PCR)으로 nucleocapsid(N) protein gene의 cDNA를 증폭시켰다. SmaI으로 처리한 pTZ19R에 ligation시킨 후 염기서열을 밝히고자 sequencing하였다. 각각의 prototype virus와 비교하여 상동성을 밝혔다. 두 바이러스에 대한 cDNA probe를 제작하여 Southern blot hybridization을 실시하였다. TGEV의 경우 백신주인 P45와 병독주인 Miller strain을 사용하였다. cDNA를 증폭시키기 위해 N1/N1R과 N2/N2R 두 가지 primer를 이용한 결과, N1/N1R primer의 경우 586bp 크기의 PCR product를 얻을 수 있었고, N2/N2R primers로 582bp의 cDNA를 증폭시킬 수 있었다. PEDV 실험을 위하여 PED 임상 증상을 나타내는 분변을 이용하여 RT-PCR을 실시하였다. P2/P2R primer로 753bp의 PCR product를 얻을 수 있었다. TGEV의 두 가지 strain의 N protein gene을 sequencing하여 prototype인 Purdue strain과 염기서열 상동성을 조사한 결과, 97%이상의 높은 homology를 나타내었다. PED-V 역시 N protein gene을 sequencing하여 CV777과 염기서열 상동성을 조사한 결과 97%이상의 homology로 PEDV임을 알 수 있었다. TGEV와 PEDV의 염기서열을 비교한 결과 29%의 낮은 homology를 관찰할 수 있었다. 두 가지 바이러스의 N protein gene에 대한 cDNA probe를 제작하여 Southern blot hybridization을 한 결과, 각 바이러스에 매우 특이적 반응을 나타내었다.