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Identification of Specific Gene Modules in Mouse Lung Tissue Exposed to Cigarette Smoke
Xing, Yong-Hua,Zhang, Jun-Ling,Lu, Lu,Li, De-Guan,Wang, Yue-Ying,Huang, Song,Li, Cheng-Cheng,Zhang, Zhu-Bo,Li, Jian-Guo,Xu, Guo-Shun,Meng, Ai-Min Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.10
Background: Exposure to cigarette may affect human health and increase risk of a wide range of diseases including pulmonary diseases, such as chronic obstructive pulmonary disease (COPD), asthma, lung fibrosis and lung cancer. However, the molecular mechanisms of pathogenesis induced by cigarettes still remain obscure even with extensive studies. With systemic view, we attempted to identify the specific gene modules that might relate to injury caused by cigarette smoke and identify hub genes for potential therapeutic targets or biomarkers from specific gene modules. Materials and Methods: The dataset GSE18344 was downloaded from the Gene Expression Omnibus (GEO) and divided into mouse cigarette smoke exposure and control groups. Subsequently, weighted gene co-expression network analysis (WGCNA) was used to construct a gene co-expression network for each group and detected specific gene modules of cigarette smoke exposure by comparison. Results: A total of ten specific gene modules were identified only in the cigarette smoke exposure group but not in the control group. Seven hub genes were identified as well, including Fip1l1, Anp32a, Acsl4, Evl, Sdc1, Arap3 and Cd52. Conclusions: Specific gene modules may provide better understanding of molecular mechanisms, and hub genes are potential candidates of therapeutic targets that may possible improve development of novel treatment approaches.
( Wan Xing Yong ),( Xu Cheng Fu ),( Lu Chao ),( Yu Wei Lai ),( Zhu Hua Tuo ),( Yu Chao Hui ),( Li You Ming ) 대한내과학회 2014 대한내과학회 추계학술대회 Vol.2014 No.1
Background: Serum uric acid is strongly associated with nonalcoholic fatty liver disease (NAFLD) and insulin resistance in patients. However, whether this association is causally or coincidentally with NAFLD and insulin resistance remains uncertain, neither the mechanisms behind this association are unclear so far. Methods: We first analyzed the impact of uric acid on development of hepatic steatosis in mice and two cell models (HepG2 and HL7702), and then explored the effect of uric acid on insulin signaling, including phosphorylation of insulin receptor substrate 1 (IRS1) and Akt in HepG2 and HL7702 cells. Further, we studied the role of NLRP3 inflammasome in regulation of hepatic steatosis and insulin signaling. Results: Uric acid directly induced hepatocyte fat accumulation both in vivo and in vitro. Further, uric acid treatment decreased insulin-induced phospho-Akt (ser437) and enhanced the phospho-IRS1(ser307) in HepG2 and HL7702 cells. Then, we found significant increases of NLRP3 inflammasome-related molecules, both mRNA and protein levels, including NLPR3, caspase-1, IL-1ß, and IL-18, in HepG2 and HL7702 cells stimulated with uric acid. We also found that uric acid induced significant elevations of IL-1ß and IL-18 levels in culture supernatants of HepG2 and HL7702 cells. Consistent with in vitro results, mice fed 8 weeks of hyperuricemia-inducing diet resulted in significant up-regulation of hepatic mRNA and protein expressions of NLPR3, caspase-1, IL-1ß and IL-18, and elevation of serum IL-1ß and IL-18 levels. Further experiments indicated that silencing NLRP3 expression significantly alleviated uric acid-induced fat accumulation in vitro. Moreover, inhibition of NLRP3 expression ameliorated uric acid induced insulin signaling impairing, confirmed by increased insulin- induced phospho-Akt (ser437) and reduced the phospho-IRS1(ser307) in vitro. Conclusions: Our results suggest that uric acid contributes to hepatic steatosis and impairs insulin signaling through the NLRP3 inflammasome dependent mechanism.
Proteomic Approach Analysis of Mammary Membrane Proteins Expression Profiles in Holstein Cows
Yang, Yong-xin,Cao, Sui-zhong,Zhang, Yong,Zhao, Xing-xu Asian Australasian Association of Animal Productio 2009 Animal Bioscience Vol.22 No.6
To investigate host defense mechanisms for protecting the mammary gland from mastitis infection, the membrane fraction of mammary tissues from Holstein cows was purified by differential velocity centrifugation, and then the sodium dodecyl sulfate-polyacrylamid gel electrophoresis (SDS-PAGE) separated proteins were identified by ion trap mass spectrometer equipped with a Surveyor high performance liquid chromatography (HPLC) system. A total of 183 proteins were identified. Bioinformatics software was applied to analyse physicochemical characteristics of the identified proteins and to predict biochemical function. These data may provide valuable information to investigate the mechanisms of mammary gland milk secretion and infectious disease, and enable a clear identification of proteins and potential protein targets for therapies.
Zhan, Yong-Hua,Huang, Xiao-Feng,Hu, Xing-Bin,An, Qun-Xing,Liu, Zhi-Xin,Zhang, Xian-Qing Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.3
Aims and Background: Prostate cancer is one of the most common malignant tumors in the male reproductive system, which causes the second most cancer deaths of males, and control of angiogenesis in prostate lesions is of obvious importance. This study assessed the effect of apogossypolone (ApoG2) on proliferation and apoptosis of human umbilical vein endothelial cells (HUVECs). Subjects and Methods: HUVECs were treated with different concentrations of ApoG2. The survival rate of HUVECs were determined by MTT assay. Utrastructural changes of HUVECs were assessed with transmission electron microscopy. Apoptosis in HUVECs was analyzed by flow cytometry and cell migration by Boyden chamber assay. Matrigel assays were used to quantify the development of tube-like networks. Results: ApoG2 significantly inhibited HUVEC growth even at 24 h (P<0.05). The inhibitory effect of ApoG2 is more obvious as the concentration and the culture time increased (P<0.05). These results indicate that ApoG2 inhibits the proliferation of HUVECs in a time- and concentration-dependent manner with increase of the apoptosis rate. Besides, ApoG2 reduced the formation of total pseudotubule length and network branches of HUVECs. Conclusions: The results suggest that ApoG2 inhibits angiogenesis of HUVECs by growth inhibition and apoptosis induction.
Xiong, Wei,Jiang, Yong-Xin,Ai, Yi-Qin,Liu, Shan,Wu, Xing-Rao,Cui, Jian-Guo,Qin, Ji-Yong,Liu, Yan,Xia, Yao-Xiong,Ju, Yun-He,He, Wen-Jie,Wang, Yong,Li, Yun-Fen,Hou, Yu,Wang, Li,Li, Wen-Hui Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.8
Background: Preoperative 5-fluorouracil (5-FU)-based chemoradiotherapy is a standard treatment for locally advanced colorectal cancer (CRC). However, CRC cells often develop chemoradiation resistance (CRR). Recent studies have shown that long non-coding RNA (lncRNA) plays critical roles in a myriad of biological processes and human diseases, as well as chemotherapy resistance. Since the roles of lncRNAs in 5-FU-based CRR in human CRC cells remain unknown, they were investigated in this study. Materials and Methods: A 5-FU-based concurrent CRR cell model was established using human CRC cell line HCT116. Microarray expression profiling of lncRNAs and mRNAs was undertaken in parental HCT116 and 5-FU-based CRR cell lines. Results: In total, 2,662 differentially expressed lncRNAs and 2,398 mRNAs were identified in 5-FU-based CRR HCT116 cells when compared with those in parental HCT116. Moreover, 6 lncRNAs and 6 mRNAs found to be differentially expressed were validated by quantitative real time PCR (qRT-PCR). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for the differentially expressed mRNAs indicated involvement of many, such as Jak-STAT, PI3K-Akt and NF-kappa B signaling pathways. To better understand the molecular basis of 5-FU-based CRR in CRC cells, correlated expression networks were constructed based on 8 intergenic lncRNAs and their nearby coding genes. Conclusions: Changes in lncRNA expression are involved in 5-FU-based CRR in CRC cells. These findings may provide novel insight for the prognosis and prediction of response to therapy in CRC patients.
A Mixed Co-clustering Algorithm Based on Information Bottleneck
Yongli Liu,Tianyi Duan,Xing Wan,Hao Chao 한국정보처리학회 2017 Journal of information processing systems Vol.13 No.6
Fuzzy co-clustering is sensitive to noise data. To overcome this noise sensitivity defect, possibilistic clusteringrelaxes the constraints in FCM-type fuzzy (co-)clustering. In this paper, we introduce a new possibilistic fuzzyco-clustering algorithm based on information bottleneck (ibPFCC). This algorithm combines fuzzy coclusteringand possibilistic clustering, and formulates an objective function which includes a distance functionthat employs information bottleneck theory to measure the distance between feature data point and featurecluster centroid. Many experiments were conducted on three datasets and one artificial dataset. Experimentalresults show that ibPFCC is better than such prominent fuzzy (co-)clustering algorithms as FCM, FCCM,RFCC and FCCI, in terms of accuracy and robustness.
Preparation of Chitooligosaccharides from Chitosan using Crude Enzyme of Bacillus cereus D-11
( Xing Ai Gao ),( Yong Feng Zhang ),( Ro Dong Park ),( Xiao Huang ),( Xin Ying Zhao ),( Jiao Xie ),( Rong De Jin ) 한국응용생명화학회 2012 Journal of Applied Biological Chemistry (J. Appl. Vol.55 No.1
In order to enzymatically produce chitooligosaccharide using the crude enzyme preparation from Bacillus cereus D-11, we first studied the optimal reaction conditions. It was found that the optimal temperature for hydrolysis of chitosan was 55oC. The ratio of enzyme/substrate should not be lower than 0.13 U/mg in the reaction mixture. The enzyme activity was stable below 50oC. The products of enzymatic reaction were analyzed by both thin layer chromatography and high performance liquid chromatography. Under the appropriate condition, chitosan was hydrolyzed using the enzyme preparation. The resulting chitooligosaccharides were purified and separated by Dowex (H+) ion exchange chromatography. From 4 g soluble chitosan, 0.95 g (GlcN)2, 1.43 g (GlcN)3, and 1.18 g (GlcN)4 were recovered.
Fabrication of Biodegradable Polyester Nanocomposites by Electrospinning for Tissue Engineering
Xing, Zhi-Cai,Han, Seung-Jin,Shin, Yong-Suk,Kang, Inn-Kyu Hindawi Publishing Corporation 2011 Journal of nanomaterials Vol.2011 No.-
<P>Recently, nanocomposites have emerged as an efficient strategy to upgrade the structural and functional properties of synthetic polymers. Polyesters have attracted wide attention because of their biodegradability and biocompatibility. A logic consequence has been the introduction of natural extracellular matrix (ECM) molecules, organic or inorganic nanostructures to biodegradable polymers to produce nanocomposites with enhanced properties. Consequently, the improvement of the interfacial adhesion between biodegradable polymers and natural ECM molecules or nanostructures has become the key technique in the fabrication of nanocomposites. Electrospinning has been employed extensively in the design and development of tissue engineering scaffolds to generate nanofibrous substrates of synthetic biodegradable polymers and to simulate the cellular microenvironment. In this paper, several types of biodegradable polyester nanocomposites were prepared by electrospinning, with the aim of being used as tissue engineering scaffolds. The combination of biodegradable nanofibrous polymers and natural ECM molecules or nanostructures opens new paradigms for tissue engineering applications.</P>