• 한국정보과학회논문지:소프트웨어및응용
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• 제35권8호
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• pp.501-511
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• 2008

프로브(probe) 디자인은 성공적인 DNA 마이크로어레이(DNA microarray) 실험을 위해서 필수적인 작업이다. 프로브가 만족시켜야 하는 조건은 마이크로어레이 실험의 목적이나 방법에 따라 다양하게 정의될 수 있는데, 대부분의 기존 연구에서는 각각의 조건에 대하여 각자 독립적으로 정해진 한계치(threshold) 값을 넘지 않는 프로브를 탐색하는 방법을 취하고 있다. 그러나, 본 연구에서는 프로브 디자인을 두가지 목적함수를 지닌 다중목적함수 최적화 문제(multiobjective optimization problem)로 정의하고, ${\epsilon}$-다중목적함수 진화 알고리즘(${\epsilon}$-multiobjective evolutionary algorithm)을 이용하여 해결하는 방법을 제시한다. 제시된 방법은 19종류의 고위험군 인유두종 바이러스(Human Papillomavirus) 유전자들에 대한 프로브 디자인과 52종류의 애기장대 칼모듈린 유전자군(Arabidopsis Calmodulin multigene family)에 대한 프로브 디자인에 각각 적용되었다. 제안한 방법론을 사용하여 기존의 공개 프로브 디자인 프로그램인 OligoArray 및 OligoWiz에 비해 목표유전사에 더 적합한 프로브를 찾을 수 있었다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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• pp.125-126
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• 2006

NimbleGen has developed strategies to use its high-density oligonucleotide microarray platform (385,000 probes per array) to map both promoter binding sites and copy number variation at very high-resolution in the human genome. Here we describe a genome-wide map of active promoters determined by experimentally locating the sites of transcription imitation complex binding throughout the human genome using microarrays combined with chromatin immunoprecipitation. This map defines 10,567 active promoters corresponding to 6,763 known genes and at least 1,196 un-annotated transcriptional units. Microarray-based comparative genomic hybridisation (CGH) is animportant research tool for investigating chromosomal aberrations frequently associated with complex diseases such as cancer, neuropsychiatric disorders, and congenital developmental disorders. NimbleGen array CGH is an ultra-high resolution (0.5-50 Kb) oligo array platform that can be used to detect amplifications and deletions and map the associated breakpoints on the whole-genome level or with custom fine-tiling arrays. For whole-genome array CGH, probes are tiled through genic and intergenic regions with a median probe spacing of 6 Kb, which provides a comprehensive, unbiased analysis of the genome.

• Molecules and Cells
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• 제24권3호
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• pp.394-408
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• 2007

Several genes/QTLs governing resistance/tolerance to abiotic and biotic stresses have been reported and mapped in rice. A QTL for submergence tolerance was found to be co-located with a major QTL for broad-spectrum bacterial leaf blight (bs-blb) resistance on the long arm of chromosome 5 in indica cultivars FR13A and IET8585. Using the Nipponbare (japonica) and 93-11 (indica) genome sequences, we identified, in silico, candidate genes in the chromosomal region [Kottapalli et al. (2006)]. Transcriptional profiling of FR13A and IET8585 using a rice 22K oligo array validated the above findings. Based on in silico analysis and arraying we observed that both cultivars respond to the above stresses through a common signaling system involving protein kinases, adenosine mono phosphate kinase, leucine rich repeat, PDZ/DHR/GLGF, and response regulator receiver protein. The combined approaches suggest that transcription factor EREBP on long arm of chromosome 5 regulates both submergence tolerance and blb resistance. Pyruvate decarboxylase and alcohol dehydrogenase, co-located in the same region, are candidate downstream genes for submergence tolerance at the seedling stage, and t-snare for bs-blb resistance. We also detected up-regulation of novel defense/stress-related genes including those encoding fumaryl aceto acetate (FAA) hydrolase, scramblase, and galactose oxidase, in response to the imposed stresses.

• 대한기계학회논문집B
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• 제35권12호
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• pp.1309-1316
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• 2011

본 논문에서는 올리고-dT 자성입자와 측면방향 자기영동 기술을 기반으로 하는 초고속 RNA 추출칩을 소개한다. 센자성 와이어에 유도된 고구배자장에 의해 RNA가 결합된 올리고-dT 자성입자를 분리함으로써 용해된 혈액으로부터 고속으로 RNA를 추출하였다. 유속이 20 ml/h까지 자성입자를 80% 이상의 효율로 분리할 수 있었으며, 분리시간은 총 1분 이내였다. 추출된 시료로부터 단백질에 대한 RNA 흡광비율(absorbance ratio of RNA to protein: A260/A280)이 1.7 이상임을 확인하였고, 따라서 추출된 RNA가 매우 순수함을 보였다. 추출된 RNA를 사용하여 cDNA 합성과 PCR을 수행하였으며, 이로부터 개발된 초고속 RNA 추출칩이 적은 양의 시료만으로 간편하며 빠르고 정교한 RT-PCR을 수행하는데 실용적임을 확인하였다.

• Asian Pacific Journal of Cancer Prevention
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• 제14권11호
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• pp.6281-6286
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• 2013

Background: To further investigate the molecular basis of lung cancer development, we utilize a microarray to identify differentially expressed genes associated with various TNM stages of adenocarcinoma, a subtype with increasing incidence in recent years in China. Methods: A 35K oligo gene array, covering about 25,100 genes, was used to screen differentially expressed genes among 90 tumor samples of lung adenocarcinoma in various TNM stages. To verify the gene array data, three genes (Zimp7, GINS2 and NAG-1) were confirmed by real-time RT-PCR in a different set of samples from the gene array. Results: First, we obtained 640 differentially expressed genes in lung adenocarcinomas compared to the surrounding normal lung tissues. Then, from the 640 candidates we identified 10 differentially expressed genes among different TNM stages (Stage I, II and IIIA), of which Zimp7, GINS2 and NAG-1 genes were first reported to be present at a high level in lung adenocarcinoma. The results of qRT-PCR for the three genes were consistent with those from the gene array. Conclusions: We identified 10 candidate genes associated with different TNM stages in lung adenocarcinoma in the Chinese population, which should provide new insights into the molecular basis underlying the development of lung adenocarcinoma and may offer new targets for the diagnosis, therapy and prognosis prediction.

• 한국미생물·생명공학회지
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• 제32권1호
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• pp.1-10
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• 2004

Many bacteria monitor their population density and control the expression of specialized gene sets in response to bacterial cell density based on a mechanism referred to as quorum sensing. In all cases, quorum sensing involves the production and detection of extracellular signaling molecules, auto inducers, as which Gram-negative and Gram-positive bacteria use most prevalently acylated homoserine lactones and processed oligo-peptides, respectively. Through quorum-sensing communication circuits, bacteria regulate a diverse array of physiological functions, including virulence, symbiosis, competence, conjugation, antibiotic production, motility, sporulation, and biofilm formation. Many pathogens have evolved quorum-sensing mechanisms to mount population-density-dependent attacks to over-whelm the defense responses of plants, animals, and humans. Since these AHL-mediated signaling mechanisms are widespread and highly conserved in many pathogenic bacteria, the disruption of quorum-sensing system might be an attractive target for novel anti-infective therapy. To control AHL-mediated pathogenicity, several promising strategies to disrupt bacterial quorum sensing have been reported, and several chemicals and enzymes have been also investigated for years. These studies indicate that anti-quorum sensing strategies could be developed as possible alternatives of antibiotics.

• 대한견주관절학회:학술대회논문집
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• 대한견주관절학회 2006년도 제14차 학술대회
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• pp.47-49
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• 2006

• 한국전자통신학회논문지
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• 제6권6호
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• pp.965-971
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• 2011

우리나라 암 발생빈도 중 간암은 위암에 이어 두 번째로 흔한 암으로서 조기에 발견될 경우는 치료성적이 우수하여 조기 발견이 대단히 중요시된다. 본 시스템은 간암의 조기발견을 위한 생체 정보 예측 시스템으로, 간암으로 확진된 환자 와 간암이외의 대조군의 혈청을 바이오칩에 반응시켜 압타머 단백질 바이오칩 프로파일을 기계학습을 통해 분류하는 시스템이다. 본 논문에서는 총 85샘플로 구성된 간암 확진환자와 310샘플로 구성된 간암이외의 대조군의 혈액시료를 1149의 서로 다른 올리고로 구성된 압타머 단백질 바이오칩에 반응시켜 획득한 데이터를 인공신경망을 통해 분석한 결과 95.38~97.95%의 분류 성능을 보였다.

• 동의생리병리학회지
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• 제17권2호
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• pp.529-541
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• 2003

Yukmijihwang-tang has been widely used as an and-aging herbal medicine for hundred years in Asian countries. Numerous studies show that Yukmijihwangtang has anti-oxidative effect both in vivo and in vitro. It has been reported that Moutan Cortex Radicis extract (MCR) was the most effective herb in Yukmijihwang-tang on undifferentiated PC12 cells upon oxidative-stressed with hydrogen peroxide. The purpose of this study is to; 1) evaluate the recovery of neuronal damage by assessing the anti-oxidant effect of MCR on PC12 cells differentiated with nerve growth factor (NGF), 2) identify candidate genes responsible for anti-oxidative effect on differentiated PC12 cells by oligonucleotide chip microarray. PC12 cells, which were differentiated by treating with NGF, were treated without or with hydrogen peroxide in the presence or absence of various concentration of MCR. Cell survival was determined by using MTS assay. Measurement of intracellular reactive oxygen species (ROS) generation was determined using the H2DCFDA assay The viability of cells treated with MCR was significantly recovered from stressed PC12 cell. In addition, wide rage of concentrations of MCR shows dose-dependent inhibitory effect on ROS production in oxidative-stressed cells. Total RNAs of cells without treatment(Control group), only treated with H₂O₂ (stressed group) and treated with both H₂O₂ and of MCR (MCR group) were isolated, and cDNAs was synthesized using oligoT7(dT) primer. The fragmented cRNAs, synthesized from cDNAs, were applied to Affymetrix GeneChip Rat Neurobiology U34 Array. mRNA of Calcium/calmodulin-dependent protein kinase II delta subunit(CaMKII), neuron glucose transporter (GLUT3) and myelin/oligodendrocyte glycoprotein(MOG) were downregulated in Stressed group comparing to Control group. P2X2-5 receptor (P2X2R-5), P2X2-4 receptor (P2X2R-4), c-fos, 25 kDa synaptosomal attachment protein(SNAP-25a) and GLUT3 were downregulated, whereas A2 adenosine receptor (A2AR), cathechol-O-methyltransferase(COMT), glucose transporter 1 (GLUT1), EST223333, heme oxygenase (HO), VGF, UI-R-CO-ja-a-07-0-Ul.s1 and macrophage migration inhibitory factor (MIF) were upregulated in MCA group comparing to Control group. Expression of Putative potassium channel subunit protein (ACK4), P2X2A-5, P2X2A-4, Interferon-gamma inducing factor isoform alpha precursor (IL-18α), EST199031, P2XR, P2X2 purinoceptor isoform e (P2X2R-e), Precursor interleukin 18 (IL-18) were downregulated, whereas MOO, EST223333, GLUT-1, MIF, Neuronatin alpha, UI-R-C0-ja-a-07-0-Ul.s1, A2. adenosine receptor, COMT, neuron-specific enolase (NSE), HO, VGF, A rat novel protein which is expressed with nerve injury (E12625) were upregulated in MCR group comparing to Stressed group. The results suggest that decreased viability and AOS production of PC12 cell by H₂O₂ may be, at lease, mediated by impaired glucose transporter expression. It is implicated that the MCR treatment protect PC12 cell from oxidative stress via following mechanisms; improving glucose transport into the cell, enhancing expression of anti-oxidative genes and protecting from dopamine cytotoxicity by increment of COMT and MIF expression. The list of differentially expressed genes may implicate further insight on the action and mechanism behind the anti-oxidative effects of herbal extract Moutan Cortex Radicis.