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( Xiao Fen Jin ),( Bo Zhu ),( Ri He Peng ),( Hai Hua Jiang ),( Jian Min Chen ),( Jing Zhuang ),( Jian Zhang ),( Quan Hong Yao ),( Ai Sheng Xiong ) 생화학분자생물학회 (구 한국생화학분자생물학회) 2010 BMB Reports Vol.43 No.8
In this study, we cloned the ERF-B3 subfamily transcription factor gene BnaERF-B3-hy15 from Brassica napus L. Huyou15. This 600 bp gene encodes a 199 amino acid classic ethylene responsive factor (ERF), which shown no binding or very weak binding GCC box-binding activity by the yeast one-hybrid assay. We used gene shuffling and the yeast one-hybrid system to obtain three mutated sequences that can bind to the GCC box. Sequence analysis indicated that two residues, Gly156 in the AP2 domain and Phe62 at the N-terminal domain were mutated to arginine and serine, respectively. Changes of Gly156 to arginine and Phe62 to serine increased the GCC- binding activity of BnaERF-B3-hy15 and the alter of Gly156 to arginine changed the AP2-domain structure of BnaERF-B3- hy15. [BMB reports 2010; 43(8): 567-572]
( Tangliu ),( Jianpeng ),( Xiao-fen Wang ),( Jin Yang ),( Bing Guo ) 한국인터넷정보학회 2012 KSII Transactions on Internet and Information Syst Vol.6 No.9
Based on the current solutions to the problem of energy hole, this paper proposed a nonuniform node distribution clustering algorithm, NNDC. Firstly, we divide the network into rings, and then have an analysis and calculation on nodes` energy consumption in each ring of the network when clustering algorithm is applied to collect data. We also put forward a scheme of nonuniform node distribution on the basis of the proportion of nodes` energy consumption in each ring, and change nodes` active/hibernating states under density control mechanism when network coverage is guaranteed. Simulation shows NNDC algorithm can satisfyingly balance nodes` energy consumption and effectively avoid the problem of energy hole.
Du, Ze-Peng,Wu, Bing-Li,Wang, Shao-Hong,Shen, Jin-Hui,Lin, Xuan-Hao,Zheng, Chun-Peng,Wu, Zhi-Yong,Qiu, Xiao-Yang,Zhan, Xiao-Fen,Xu, Li-Yan,Li, En-Min Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.16
NGAL (neutrophil gelatinase-associated lipocalin) is a novel cancer-related protein involves multiple functions in many cancers and other diseases. We previously overexpressed NGAL to analyze its role in esophageal squamous cell carcinoma (ESCC). In this study, a protein-protein interaction (PPI) was constructed and the shortest paths from NGAL to transcription factors in the network were analyzed. We found 28 shortest paths from NGAL to RELA, most of them obeying the principle of extracellular to cytoplasm, then nucleus. These shortest paths were also prioritized according to their normalized intensity from the microarray by the order of interaction cascades. A systems approach was developed in this study by linking differentially expressed genes with publicly available PPI data, Gene Ontology and subcellular localizaton for the integrated analyses. These shortest paths from NGAL to DEG transcription factors or other transcription factors in the PPI network provide important clues for future experimental identification of new pathways.
Du, Ze-Peng,Wu, Bing-Li,Xie, Jian-Jun,Lin, Xuan-Hao,Qiu, Xiao-Yang,Zhan, Xiao-Fen,Wang, Shao-Hong,Shen, Jin-Hui,Li, En-Min,Xu, Li-Yan Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.13
Fascin-1 (FSCN1) is an actin-bundling protein that induces cell membrane protrusions, increases cell motility, and is overexpressed in various human epithelial cancers, including esophageal squamous cell carcinoma (ESCC). We analyzed various protein-protein interactions (PPI) of differentially-expressed genes (DEGs), in fascin knockdown ESCC cells, to explore the role of fascin overexpression. The node-degree distributions indicated these PPI sub-networks to be characterized as scale-free. Subcellular localization analysis revealed DEGs to interact with other proteins directly or indirectly, distributed in multiple layers of extracellular membrane-cytoskeleton/ cytoplasm-nucleus. The functional annotation map revealed hundreds of significant gene ontology (GO) terms, especially those associated with cytoskeleton organization of FSCN1. The Random Walk with Restart algorithm was applied to identify the prioritizations of these DEGs when considering their relationship with FSCN1. These analyses based on PPI network have greatly expanded our comprehension of the mRNA expression profile following fascin knockdown to future examine the roles and mechanisms of fascin action.
Li, Xin,Wang, Yang,Li, Xing-Wang,Liu, Bao-Cheng,Zhao, Qing-Zhu,Li, Wei-Dong,Chen, Shi-Qing,Huang, Xiao-Ye,Yang, Feng-Ping,Wang, Quan,Wang, Jin-Fen,Xiao, Yan-Zeng,Xu, Yi-Feng,Feng, Guo-Yin,Peng, Zhi-Ha Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.5
Colorectal cancer (CRC), now the third most common cancer across the world, is known to aggregate in families. USP7 is a very important protein with an important role in regulating the p53 pathway, which is critical for genomic stability and tumor suppression. We here genotyped eight SNPs within the USP7 gene and conducted a case-control study in 312 CRC patients and 270 healthy subjects in the Chinese Han population. No significant associations were found for any single SNP and CRC risk. Our data eliminate USP7 as a potential candidate gene towards for CRC in the Han Chinese population.