• 대한전기학회논문지:전기물성ㆍ응용부문C
• /
• 제51권6호
• /
• pp.265-270
• /
• 2002

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and application area. So, the improvement of DNA hybridization detection method is very important for the determination of this hybridization reaction. Several molecular biological techniques require accurate predictions of matched versus mismatched hybridization thermodynamics, such as PCR, sequencing by hybridization, gene diagnostics and antisense oligonucleotide probes. In addition, recent developments of oligonucleotide chip arrays as means for biochemical assays and DNA sequencing requires accurate knowledge of hybridization thermodynamics and population ratios at matched and mismatched target sites. In this study, we report the characteristics of the probe and matched, mismatched target oligonucleotide hybridization reaction using thermodynamic method. Thermodynamic of 5 oligonucleotides with central and terminal mismatch sequences were obtained by measured UV-absorbance as a function of temperature. The data show that the nearest-neighbor base-pair model is adequate for predicting thermodynamics of oligonucleotides with average deviations for $\Delta$H$^{0}$ , $\Delta$S$^{0}$ , $\Delta$G$_{37}$ $^{0}$ and T$_{m}$, respectively.>$^{0}$ and T$_{m}$, respectively.

• Journal of Information Processing Systems
• /
• 제8권3호
• /
• pp.459-470
• /
• 2012

Recently, high-throughput technologies such as the two-hybrid system, protein chip, Mass Spectrometry, and the phage display have furnished a lot of data on protein-protein interactions (PPIs), but the data has not been accurate so far and the quantity has also been limited. In this respect, computational techniques for the prediction and validation of PPIs have been developed. However, existing computational methods do not take into account the fact that a PPI is actually originated from the interactions of domains that each protein contains. So, in this work, the information on domain modules of individual proteins has been employed in order to find out the protein interaction relationship. The system developed here, WASPI (Web-based Assistant System for Protein-protein interaction Inference), has been implemented to provide many functional insights into the protein interactions and their domains. To achieve those objectives, several preprocessing steps have been taken. First, the domain module information of interacting proteins was extracted by taking advantage of the InterPro database, which includes protein families, domains, and functional sites. The InterProScan program was used in this preprocess. Second, the homology comparison with the GO (Gene Ontology) and COG (Clusters of Orthologous Groups) with an E-value of $10^{-5}$, $10^{-3}$ respectively, was employed to obtain the information on the function and annotation of each interacting protein of a secondary PPI database in the WASPI. The BLAST program was utilized for the homology comparison.

• Genomics & Informatics
• /
• 제19권1호
• /
• pp.2.1-2.10
• /
• 2021

BRAF inhibitors (e.g., vemurafenib) are widely used to treat metastatic melanoma with the BRAF V600E mutation. The initial response is often dramatic, but treatment resistance leads to disease progression in the majority of cases. Although secondary mutations in the mitogen-activated protein kinase signaling pathway are known to be responsible for this phenomenon, the molecular mechanisms governing acquired resistance are not known in more than half of patients. Here we report a genome- and transcriptome-wide study investigating the molecular mechanisms of acquired resistance to BRAF inhibitors. A microfluidic chip with a concentration gradient of vemurafenib was utilized to rapidly obtain therapy-resistant clones from two melanoma cell lines with the BRAF V600E mutation (A375 and SK-MEL-28). Exome and transcriptome data were produced from 13 resistant clones and analyzed to identify secondary mutations and gene expression changes. Various mechanisms, including phenotype switching and metabolic reprogramming, have been determined to contribute to resistance development differently for each clone. The roles of microphthalmia-associated transcription factor, the master transcription factor in melanocyte differentiation/dedifferentiation, were highlighted in terms of phenotype switching. Our study provides an omics-based comprehensive overview of the molecular mechanisms governing acquired resistance to BRAF inhibitor therapy.

• Clinical and Experimental Reproductive Medicine
• /
• 제34권1호
• /
• pp.19-31
• /
• 2007

목 적: 자궁내막증은 자궁내부에 존재하여야 할 자금내막조직이 자궁 외에 존재하는 질환으로 그 발생기전은 아직 명확하게 밝혀져 있지 않다. 이에 저자들은 자궁내막증 환자와 정상 대조군의 자궁내막조직 간의 유전자 발현의 차이가 자궁내막증의 발병과 관련이 있을 것이라는 가정 하에 DNA microarray 기술을 도입하여 연구를 시행하였다. 연구방법: 2002년 1월부터 2002년 12월까지의 기간 동안 본원 산부인과에서 자궁내막증 환자와 자궁내막증 이외의 다른 부인과적 질환으로 수술을 시행한 환자들을 대상으로 채취한 자궁내막 조직으로 KNU 4.8K cDNA chip을 이용하여 유전자 발현을 비교 연구하였다. 유전자칩으로 자궁내막증 조직에서 발현의 증감을 보였던 유전자 중에서 8종의 유전자를 대상으르 RT-PCR이나 real time RT-PCR 법을 통하여 그 발현 양상을 검증하였다. 결 과: 자궁내막증에 이환된 여성의 자궁내막조직에서 대조군에 비하여 높게 발현되고 있는 것으로 나타난 유전자들은 ATP synthase H transporting F1 (ATP5B), eukaryotic translation elongation factor 1, isocitrate dehydrogenase 1 (NADP+), mitochondrial ribosomal protein L3, ATP synthase H+ trarsporting (ATP5C1), LPS induced TNF-$\alpha$ factor 등으로 세포의 에너지 생성과 대사과정 및 신호전달에 관여하는 유전자들이었다. 한편 자궁내막중 환자의 자궁내막조직에서 대조군에 비하여 낮게 발현된 유전자들은 insulin like growth factor II associated protein, EGF-containing fibulin-like EMP1, matrix Gla protein, TGF beta-induced, TGF beta receptor 1(activin A receptor type II-like kinase), cystallin alpha B, fibulin 5, tissue inhibitor of metalloproteinase 3, collage type XII, alpha 1, tissue inhibitor of metalloproteinase 1, decorin 등으로 세포외기질의 구성 및 기능에 관련이 있었다. 결 론: 이상의 DNA mirroarry 및 RT-PCR을 통해 얻어진 결과에서 자궁내막증의 자궁내막조직에서 대조군에 비하여 유전자들의 발현에 차이가 있음을 확인하였다.

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

• Asian-Australasian Journal of Animal Sciences
• /
• 제31권6호
• /
• pp.784-790
• /
• 2018

Objective: The genetic effects of an individual on the phenotypes of its social partners, such as its pen mates, are known as social genetic effects. This study aims to identify the candidate genes for social (pen-mates') average daily gain (ADG) in pigs by using the genome-wide association approach. Methods: Social ADG (sADG) was the average ADG of unrelated pen-mates (strangers). We used the phenotype data (16,802 records) after correcting for batch (week), sex, pen, number of strangers (1 to 7 pigs) in the pen, full-sib rate (0% to 80%) within pen, and age at the end of the test. A total of 1,041 pigs from Landrace breeds were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel, which comprised 61,565 single nucleotide polymorphism (SNP) markers. After quality control, 909 individuals and 39,837 markers remained for sADG in genome-wide association study. Results: We detected five new SNPs, all on chromosome 6, which have not been associated with social ADG or other growth traits to date. One SNP was inside the prostaglandin $F2{\alpha}$ receptor (PTGFR) gene, another SNP was located 22 kb upstream of gene interferon-induced protein 44 (IFI44), and the last three SNPs were between 161 kb and 191 kb upstream of the EGF latrophilin and seven transmembrane domain-containing protein 1 (ELTD1) gene. PTGFR, IFI44, and ELTD1 were never associated with social interaction and social genetic effects in any of the previous studies. Conclusion: The identification of several genomic regions, and candidate genes associated with social genetic effects reported here, could contribute to a better understanding of the genetic basis of interaction traits for ADG. In conclusion, we suggest that the PTGFR, IFI44, and ELTD1 may be used as a molecular marker for sADG, although their functional effect was not defined yet. Thus, it will be of interest to execute association studies in those genes.

• 한국생물정보학회:학술대회논문집
• /
• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
• /
• pp.66-72
• /
• 2003

Toxicogenomics is now emerging as one of the most important genomics application because the toxicity test based on gene expression profiles is expected more precise and efficient than current histopathological approach in pre-clinical phase. One of the challenging points in Toxicogenomics is the construction of intelligent database management system which can deal with very heterogeneous and complex data from many different experimental and information sources. Here we present a new Toxicogenomics database developed as a part of 'Toxicogenomics for Efficient Safety Test (TEST) project'. The TEST database is especially focused on the connectivity of heterogeneous data and intelligent query system which enables users to get inspiration from the complex data sets. The database deals with four kinds of information; compound information, histopathological information, gene expression information, and annotation information. Currently, TEST database has Toxicogenomics information fer 12 molecules with 4 efficacy classes; anti cancer, antibiotic, hypotension, and gastric ulcer. Users can easily access all kinds of detailed information about there compounds and simultaneously, users can also check the confidence of retrieved information by browsing the quality of experimental data and toxicity grade of gene generated from our toxicology annotation system. Intelligent query system is designed for multiple comparisons of experimental data because the comparison of experimental data according to histopathological toxicity, compounds, efficacy, and individual variation is crucial to find common genetic characteristics .Our presented system can be a good information source for the study of toxicology mechanism in the genome-wide level and also can be utilized fur the design of toxicity test chip.

• 한국정보과학회논문지:시스템및이론
• /
• 제31권9호
• /
• pp.514-526
• /
• 2004

최근 마이크로어레이 실험기술의 개발로 인해서 생물학자들은 한꺼번에 수천 혹은 수만 개의 유전자 발현실험이 가능하게 되었다. 마이크로어레이를 이용한 유전자 발현 패턴 분석에 필요한 이미지의 분석 작업은 사용자의 많은 수작업이 필요하며, 올바른 결과를 얻기 위해서 많은 주의가 필요하다. 그러므로 사용자의 수작업을 최소화하고 정확한 발현결과를 얻기 위해서 마이크로어레이 이미지의 자동 분석 방법이 필요하다. 일반적으로 마이크로어레이 데이타는 반점(spot) 위치의 변동이나 모양, 크기가 고르지 않는 것과 같은 다양한 문제로 인하여 자동 분석이 어렵다. 특히 블록과 반점의 주소를 결정하는 것은 마이크로어레이 분석 중 어려운 단계이며, 대부분 상용 프로그램에서는 수작업을 통해서 해결하거나, 수작업이 필요한 반자동시스템을 이용하고 있다. 본 논문에서는 균일 격자(regular grid) 구조 탐색을 이용하여 새로운 블록과 반점의 주소를 결정하는 알고리즘을 소개한다. 본 알고리즘에서는 입력된 반점들의 중심점을 이용하여, 균등 일직선 서열(equally spaced and collinear sequence)을 생성하고 이를 통하여 이미지의 기울기와 단위길이를 계산한다. 계산되어진 기울기와 단위길이를 이용하여 가상점을 허용한 균등 일직선서열을 다시 생성하고, 이를 이용하여 마이크로어레이의 주소를 결정한다. 실험 결과 다양한 실험 데이터에 대하여 매우 안정적이며, 신뢰성이 높은 결과를 얻을 수 있었다. 본 알고리즘에 대한 자세한 정보는 http://jade.cs.pusan.ac.kr/~autogrid에 정리되어 있다.

• The Korean Journal of Physiology and Pharmacology
• /
• 제12권2호
• /
• pp.83-87
• /
• 2008

The fyn-related kinase (FRK) belongs to the tyrosine kinase family of protein kinases. Recent studies have shown that Frk affects pancreatic beta cell number during embryogenesis and promotes beta cell cytotoxic signals in response to streptozotocin. To investigate the genetic association between FRK polymorphisms and the risk of obesity in Korean population, single nucleotide polymorphisms (SNPs) in the FRK gene region were selected and analyzed. The body mass index (BMI) was calculated, and biochemical data (systolic blood pressure, diastolic blood pressure, hemoglobin A1C, triglyceride, total cholesterol, high density lipoprotein, and low density lipoprotein) of blood sample from each subject were also measured. One hundred fifty five healthy control and 204 overweight/obesity subjects were recruited. Genotype frequencies of six SNPs [rs6568920 (+8391G>A), rs3756772 (+56780A>G), rs3798234 (+75687C>T), rs9384970 (+68506G>A), rs1933739 (+72978G>A), and rs9400883 (+75809A>G)] in the FRK gene were determined by Affymetrix Targeted Genotyping Chip data. According to the classification of Korean Society for the Study of Obesity, control (BMI 18 to < 23) and overweight/obesity (BMI$\geq$23) subjects were recruited. For the analysis of genetic data, EM algorithm, SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs were used. Multiple logistic regression analysis (codominant, dominant, and recessive models) was performed. Age and gender as covariates were adjusted. For biochemical data, Student's t test was used. The mean value of BMI in the control and overweigh/obesity groups was 21.1${\pm}$1.2 (mean${\pm}$SD) and 25.6${\pm}$2.0, respectively. All biochemical data of the overweight/obesity group were statistically significance, compared with the control group. Among six SNPs, two linkage disequilibrium (LD) blocks were discovered. One block consisted of rs1933739 and rs9400883, and the other comprised rs3756772 and rs3798234. One SNP (rs9384970, +68506G>A) showed an association with overweight/obesity in the codominant model (p=0.03). Interestingly, the AA genotype distribution in the overweight/obesity group (n=7, 3.5%) was higher than those in the control group (n=1, 0.6%), which is not found in either Japanese or Chinese subjects. Therefore, the AA genotype of rs9384970 may be a risk factor for development of obesity in Korean population. The results suggest that FRK may be associated with overweight/obesity in Korean population.

• IMMUNE NETWORK
• /
• 제5권4호
• /
• pp.205-214
• /
• 2005

Background: We examined global gene expression profiles of peripheral blood mononuclear cells (PBMCs) in patients with ulcerative colitis (DC), and tested whether the identified genes with the altered expression might be associated with susceptibility to UC. Methods: PBMCs from 8 UC and 8 normal healthy (NH) volunteers were collected, and total RNAs were subjected to the human 8.0K cDNA chip for the micro array analysis. Real time-PCR (RT-PCR) was performed to verify the results of micro array. One hundred forty UC patients and 300 NH controls were recruited for single nucleotide polymorphism (SNP) analysis. Results: Twenty-five immune function-related genes with over 2-fold expression were identified. Of these genes, two chemokines, namely, CXCL1 and CCL20, were selected because of their potential importance in the evocation of host innate and adaptive immunity. Four SNPs were identified in the promoter and coding regions of CXCL1, while there was no significant difference between all patients with UC and controls in their polymorphisms, except minor association at g.57A>G (rs2071425, p=0.02). On the other hand, among three novel and one known SNPs identified in the promoter region of CCL20, g. -1,706 G>A (p=0.000000055), g. -1,458 G>A (p=0.0048), and g. -962C>A (p=0.0006) were found to be significantly associated with the susceptibility of Uc. Conclusion: Altered gene expression in mononuclear cells may contribute to IBD pathogenesis. Although the findings need to be confirmed in other populations with larger numbers of patients, the current results demonstrated that polymorphisms in the promoter region of CCL20 are positively associated with the development of Uc.