• 생명과학회지
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• 제26권8호
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• pp.904-910
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• 2016

가축의 경제형질은 대부분 복합형질 상태이며, 많은 유전자와 생물대사회로에 의해 조절된다. 시스템 생물학은 생명현상을 하나의 복합체로 가정하고, 형질에 관여하는 유전자들에 대한 기능적 관계를 분석하는 학문이다. 유전자 네트워크는 시스템 생물학의 하나의 연구분야로써, 유전자 기능의 상관관계를 지도화하여 오믹스 데이터를 통합 분석하여 해석한다. 유전자 네트워크는 단백질-단백질 상호작용, 공발현, 조절인자, 유전자형 기반으로 다양한 유전자의 기능적 상호작용을 표현할 수 있다. 또한, 네트워크를 구성하기 위해서는 유전자 간 연결 정도에 가중치를 두거나, 인접한 유전자 수 계산 등의 네트워크 토폴로지 알고리즘이 적용된다. 가축에서는 이러한 연구가 단형질에 대한 유전자 발현, 단백질 상호작용 등에 국한되어 있는 실정이다. 본 논문에서는 유전자 공발현 네트워크와 단백질-단백질 상호작용 네트워크 분석법을 확립하고 소의 102개 경제형질에 대하여 유전자 네트워크 분석 결과에 대한 데이터베이스를 구축하였다. 102개의 경제형질은 Animal Trait Ontology (ATO) 명명법에 의하여 분류하여 제공하였다. 각 형질에 포함된 유전자 리스트는 Animal QTL database에서 제공하는 양적유전형질좌위의 물리적 위치에 존재하는 유전자군을 추출하였다. 유전자 공발현 네트워크는 R의 WGCNA 패키지를 활용하였으며, 단백질-단백질 상호작용 네트워크는 Human Protein Reference Database에서 사람과 소의 orthologous group에 포함된 유전자를 대상으로 단백질 상호작용 관계를 규명하였다. 네트워크 분석 결과는 관계형 테이블로 구축하였으며, 구축한 데이터베이스를 관련 연구진에게 공유하기 위하여 웹 기반의 유전자 네트워크 가시화 시스템을 구현하였다(http://www.nabc.go.kr/cg). 웹 데이터베이스 구현을 위하여 Ontle 프로그램을 활용하여 다양한 방식으로 유전자 네트워크 가시화 작업을 수행하였다. 이 시스템을 통하여 사용자는 관련 형질의 후보 유전자군 탐색, 유전자 네트워크 분석 결과, 유전자 사이의 기능적 연결관계를 손쉽게 살펴볼 수 있게 될 것이다.

• Genomics & Informatics
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• 제19권1호
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• pp.4.1-4.9
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• 2021

Lip and oral cavity cancer, which can occur in any part of the mouth, is the 11th most common type of cancer worldwide. The major obstacles to patients' survival are the poor prognosis, lack of specific biomarkers, and expensive therapeutic alternatives. This study aimed to identify the main genes and pathways associated with lip and oral cavity carcinoma using network analysis and to analyze its molecular mechanism and prognostic significance further. In this study, 472 genes causing lip and oral cavity carcinoma were retrieved from the DisGeNET database. A protein-protein interaction network was developed for network analysis using the STRING database. VEGFA, IL6, MAPK3, INS, TNF, MAPK8, MMP9, CXCL8, EGF, and PTGS2 were recognized as network hub genes using the maximum clique centrality algorithm available in cytoHubba, and nine potential drug candidates (ranibizumab, siltuximab, sulindac, pomalidomide, dexrazoxane, endostatin, pamidronic acid, cetuximab, and apricoxib) for lip and oral cavity cancer were identified from the DGIdb database. Gene enrichment analysis was also performed to identify the gene ontology categorization of cellular components, biological processes, molecular functions, and biological pathways. The genes identified in this study could furnish a new understanding of the underlying molecular mechanisms of carcinogenesis and provide more reliable biomarkers for early diagnosis, prognostication, and treatment of lip and oral cavity cancer.

• Genomics & Informatics
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• 제19권2호
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• pp.16.1-16.14
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• 2021

Even in the current age of advanced medicine, the prognosis of malignant peritoneal mesothelioma (MPM) remains abysmal. Molecular mechanisms responsible for the initiation and progression of MPM are still largely not understood. Adopting an integrated bioinformatics approach, this study aims to identify the key genes and pathways responsible for MPM. Genes that are differentially expressed in MPM in comparison with the peritoneum of healthy controls have been identified by analyzing a microarray gene expression dataset. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of these differentially expressed genes (DEG) were conducted to gain a better insight. A protein-protein interaction (PPI) network of the proteins encoded by the DEGs was constructed using STRING and hub genes were detected analyzing this network. Next, the transcription factors and miRNAs that have possible regulatory roles on the hub genes were detected. Finally, survival analyses based on the hub genes were conducted using the GEPIA2 web server. Six hundred six genes were found to be differentially expressed in MPM; 133 are upregulated and 473 are downregulated. Analyzing the STRING generated PPI network, six dense modules and 12 hub genes were identified. Fifteen transcription factors and 10 miRNAs were identified to have the most extensive regulatory functions on the DEGs. Through bioinformatics analyses, this work provides an insight into the potential genes and pathways involved in MPM.

• Biotechnology and Bioprocess Engineering:BBE
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• 제6권5호
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• pp.326-331
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• 2001

With the aim of developing of pH-sensitive controlled drug release system, a poly(Llysine) (PLL) based cationic semi-interpenetrating polymer network (semi-IPN) has been synthesized. This cationic hydrogel was designed to swell at lower pH and de-swell at higher pH and therefore be applicable for achieving regulated drug release at a specific pH range. In addition to the pH sensitivity, this hydrogel was anticipated to interact with an ionic drug, providing another means to regulate the release rate of ionic drugs. This semi-IPN hydrogel was prepared using a free-radical polymerization method and by crosslinking of the polyethylene glycol (PEG)-methacrylate polymer through the PLL network. The two polymers were penetrated with each other via interpolymer complexation to yield the semi-IPN structures. The PLL hydrogel thus prepared showed dynamic swelling/de-swelling behavior in response to pH change, and such a behavior was influenced by both the concentrations of PLL and PEG-methacrylate. Drug release from this semi-IPN hydrogel was also investigated using a model protein drug, streptokinase. Streptokinase release was found to be dependent on its ionic interaction with the PLL backbones as well as on the swelling of the semi-IPN hydrogel. These results suggest that a PLL semi-IPN hydrogel could potentially be used as a drug delivery platform to modulate drug release by pH-sensitivity and ionic interaction.

• Genomics & Informatics
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• 제19권4호
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• pp.42.1-42.17
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• 2021

Salivary gland carcinoma (SGC) is rare cancer, constituting 6% of neoplasms in the head and neck area. The most responsible genes and pathways involved in the pathology of this disorder have not been fully understood. We aimed to identify differentially expressed genes (DEGs), the most critical hub genes, transcription factors, signaling pathways, and biological processes (BPs) associated with the pathogenesis of primary SGC. The mRNA dataset GSE153283 in the Gene Expression Omnibus database was re-analyzed for determining DEGs in cancer tissue of patients with primary SGC compared to the adjacent normal tissue (adjusted p-value < 0.001; |Log2 fold change| > 1). A protein interaction map (PIM) was built, and the main modules within the network were identified and focused on the different pathways and BP analyses. The hub genes of PIM were discovered, and their associated gene regulatory network was built to determine the master regulators involved in the pathogenesis of primary SGC. A total of 137 genes were found to be differentially expressed in primary SGC. The most significant pathways and BPs that were deregulated in the primary disease condition were associated with the cell cycle and fibroblast proliferation procedures. TP53, EGF, FN1, NOTCH1, EZH2, COL1A1, SPP1, CDKN2A, WNT5A, PDGFRB, CCNB1, and H2AFX were demonstrated to be the most critical genes linked with the primary SGC. SPIB, FOXM1, and POLR2A significantly regulate all the hub genes. This study illustrated several hub genes and their master regulators that might be appropriate targets for the therapeutic aims of primary SGC.

• The Korean Journal of Physiology and Pharmacology
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• 제28권1호
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• pp.59-72
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• 2024

To investigate the mechanism of Wenshen Xuanbi Decoction (WSXB) in treating osteoarthritis (OA) via network pharmacology, bioinformatics analysis, and experimental verification. The active components and prediction targets of WSXB were obtained from the TCMSP database and Swiss Target Prediction website, respectively. OA-related genes were retrieved from GeneCards and OMIM databases. Protein-protein interaction and functional enrichment analyses were performed, resulting in the construction of the Herb-Component-Target network. In addition, differential genes of OA were obtained from the GEO database to verify the potential mechanism of WSXB in OA treatment. Subsequently, potential active components were subjected to molecular verification with the hub targets. Finally, we selected the most crucial hub targets and pathways for experimental verification in vitro. The active components in the study included quercetin, linolenic acid, methyl linoleate, isobergapten, and beta-sitosterol. AKT1, tumor necrosis factor (TNF), interleukin (IL)-6, GAPDH, and CTNNB1 were identified as the most crucial hub targets. Molecular docking revealed that the active components and hub targets exhibited strong binding energy. Experimental verification demonstrated that the mRNA and protein expression levels of IL-6, IL-17, and TNF in the WSXB group were lower than those in the KOA group (p < 0.05). WSXB exhibits a chondroprotective effect on OA and delays disease progression. The mechanism is potentially related to the suppression of IL-17 and TNF signaling pathways and the down-regulation of IL-6.

• IMMUNE NETWORK
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• 제3권1호
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• pp.23-28
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• 2003

Background: Intracellular antibody specific to hepatitis B virus X protein (HBx) might be useful for studying the role of HBx in hepatocellular carcinogenesis and HBV replication. Methods: With variable region genes for H7 monoclonal anti-HBx Ab, we constructed a vector for bacterial expression of single chain Ab (scFv) and a vector for eukaryotic cell expression of it. The expression of H7 scFv and its binding activity against HBx was examined by immunoblotting and immunofluorescence microscopy. Results: H7 scFv expressed in bacterial cells retained reactivity to HBx. We demonstrated its intracytoplasmic expression in CosM6 eukaryotic cells. Conclusion: This is the first study showing the expression of intracellular anti-HBx Ab in eukaryotic cells. H7 scFv may be a good tool to study the function of HBx in HBV infection.

• Preventive Nutrition and Food Science
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• 제2권4호
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• pp.281-284
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• 1997

Heat-induced gelation is an important functional property of whey proteins. Preheating of calcium reduced whey was reported to increase gel strength. 5% whey-protein solutions were preheated at pH7 and at various temperatures(60~8$0^{\circ}C$) for 15 minutes. The amount of soluble aggregates and denaturation enthalpy of preheated whey proteins were measured. Preheating temperature was negatively correlated with denaturation enthalpy($R^2$=0.857, P=0.08) and positive with the amount of soluble aggregates($R^2$=0.921, P=0.002). Denaturation enthalpy was negatively correlated with gel strength($R^2$=0.93, P=0.002). Soluble aggregates and gel strength were positively correlated($R^2$=0.972, P=0.0003). The formation of three dimensional gel network requires controlled protein denaturation and aggregation. Since preheating leads to the partial denaturation of proteins and the formation of soluble aggregates, preheated whey proteins have a higher gel strength than non-preheated one.

• IMMUNE NETWORK
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• 제14권5호
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• pp.241-248
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• 2014

It is debatable whether AMP-activated protein kinase (AMPK) activation is involved in anti-apoptotic or pro-apoptotic signaling. AICAR treatment increases AMPK-${\alpha}1$ phosphorylation, decreases intracellular reactive oxygen species (ROS) levels, and significantly increases Annexin V-positive cells, DNA laddering, and caspase activity in human myeloid cell. AMPK activation is therefore implicated in apoptosis. However, AMPK-${\alpha}1$-knockdown THP-1 cells are more sensitive to apoptosis than control THP-1 cells are, suggesting that the apoptosis is AMPK-independent. Low doses of AICAR induce cell proliferation, whereas high doses of AICAR suppress cell proliferation. Moreover, these effects are significantly correlated with the downregulation of intracellular ROS, strongly suggesting that AICAR-induced apoptosis is critically associated with the inhibition of NADPH oxidase by AICAR. Collectively, our results demonstrate that in AICAR-induced apoptosis, intracellular ROS levels are far more relevant than AMPK activation.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2006년도 한국컴퓨터종합학술대회 논문집 Vol.33 No.1 (A)
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• pp.7-9
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• 2006

단백질 상호작용 관계들은 고 성능 실험 기법을 이용한 생물학적 실험에 의해서 대규모로 추출되고, 동시에 이들을 구성하는 단백질 데이터 역시 공공 데이터베이스에 빈번하게 갱신되고 있다. 이 갱신으로 인하여 인터넷을 통해 공개되는 공공 데이터베이스와 PPI(Protein-Protein interaction) 네트워크에 포함된 단백질 데이터가 서로 일치하지 않게 된다. 본 논문에서는 PPI 네트워크에 존재하는 단백질을 래퍼(Wrapper)를 이용하여 빈번하게 갱신되는 공공 데이터베이스의 단백질로 식별하고, 이 식별을 통해 PPI 네트워크에 존재하는 데이터들을 항상 최신 데이터로 동기화함으로써 데이터의 실시간성을 제공하고 데이터에 대한 신뢰도를 보장할 수 있도록 하였다.