生物学通路被广泛应用于基因功能学研究,但现有的生物学通路知识并不完善,仍需进一步扩充。生物信息学预测为通路扩充提供了一种有效且经济的途径。文章提出了一种融合蛋白质?蛋白质互作知识以及Gene Ontology(GO)数据库信息进行基因通...生物学通路被广泛应用于基因功能学研究,但现有的生物学通路知识并不完善,仍需进一步扩充。生物信息学预测为通路扩充提供了一种有效且经济的途径。文章提出了一种融合蛋白质?蛋白质互作知识以及Gene Ontology(GO)数据库信息进行基因通路预测的新方法。首先选取目标基因在蛋白质?蛋白质互作层面上的邻居所在的Kyoto Encyclopedia of Genes and Genomes(KEGG)通路为候选通路,然后通过检验候选通路中的基因是否在与目标基因关联的GO节点富集来判断目标基因的通路归属。分别利用Human Protein Reference Database(HPRD)和Biological General Repository for Interaction Datasets(BioGRID)数据库中的蛋白质?蛋白质互作信息进行预测。结果表明,在两套数据中,随着互作邻居个数的增加,预测的平均准确率(在所有目标基因注释的通路中被成功预测的比例)及相对准确率(在至少有一个注释通路被成功预测的基因集中,所有注释通路均被预测正确的基因所占的比例)均呈现上升趋势。当互作邻居个数达到22时,预测的平均准确率分别达到96.2%(HPRD)和96.3%(BioGRID),而相对准确率分别为93.3%(HPRD)和84.1%(BioGRID)。进一步利用新版数据库对旧版数据库中被更新的89个基因进行验证,至少有一个更新通路被预测正确的基因有50个,其中43个基因的更新通路被完全正确预测,相对准确率为86.0%。这些结果显示该方法是一种可靠且有效的通路扩充方法。展开更多
A rapid, ultrasensitive and convenient fluorescence measurement technology based on the enhancement of the fluorescence intensity resulting from the interaction of functionalized CdSe/CdS quantum dots （QDs） with bov...A rapid, ultrasensitive and convenient fluorescence measurement technology based on the enhancement of the fluorescence intensity resulting from the interaction of functionalized CdSe/CdS quantum dots （QDs） with bov/ne serum albumin （BSA） was proposed. The citrate-stabilized CdSe/CdS （QDs） were synthesized by using Se powder and Na2S as precursors instead of any pyrophoric organometallic precursors. The modified CdSe/CdS QDs are brighter and more stable against photobleaching in comparison with organic fluorophores. At pH 7.0, the fluorescence signal of CdSe/CdS is enhanced by increasing the concentration of BSA in the range of 0.1-10 μg/mL, and the low detection limit is 0.06 μg/mL. A linear relationship between the enhanced fluorescence peak intensity （△F） and BSA concentration （c） is established using equation △F=50.7c＋16.4 （R=0.996 36）. Results of determination for BSA in three synthetic samples are identical with the true values, and the recovery （98.9%-102.4%） and relative standard deviation （RSD, 1.8%-2.5%） are satisfactory.展开更多
Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators ha...Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators have reported specific interactions between linker histones and proteins involved in important cellular processes. The purpose of this review is to highlight evidence indicating an important alternative mode of action for H1, namely protein-protein interactions. We first review key aspects of the traditional view of linker histone action, including the importance of the H1 C-terminal domain. We then discuss the current state of knowledge of linker histone interactions with other proteins, and, where possible, highlight the mechanism of linker histone-mediated protein-protein interactions. Taken together, the data suggest a combinatorial role for the linker histones, functioning both as primary chromatin architectural proteins and simultaneously as recruitment hubs for proteins involved in accessing and modifying the chromatin fiber.展开更多
hPFTAIRE1 （PFTK1）, a Cdc2-related protein kinase, is highly expressed in human brain. It exhibits cytoplasmic distribution in Hela cells, although it contains two nuclear localization signals （NLSs） in its N-termi...hPFTAIRE1 （PFTK1）, a Cdc2-related protein kinase, is highly expressed in human brain. It exhibits cytoplasmic distribution in Hela cells, although it contains two nuclear localization signals （NLSs） in its N-terminus. To search for its substrates and regulatory components, we screened a two-hybrid library by using the full-length hPFTAIRE1 as a bait. Four 14-3-3 isoforms （β,ε,η,τ） were identified interacting with the hPFTAIRE1. We found a putative 14-3-3 binding consensus motif（RHSSPSS） in the hPFTAIRE 1, which overlapped with its second NLS. Deletion of the RHSSPSS motif or substitution of Ser^119 gwithAla in the conserved binding motif abolished the specific interaction between the hPFTAIRE 1 and the 14-3 -3 proteins. The mutant S 120A hPFTAIRE1 also showed a weak interaction to the 14-3-3 proteins. The results suggested that the Ser^119 is crucial for the interaction between hPFTAIREI and the 14-3-3 proteins. All the hPFTAIRE1 mutants distributed in cytoplasm of Hela cells and human neuroblastoma cells （SH-SY5Y） when fused to the C-terminus of a green fluorescent protein （GFP）, indicating that binding with the 14-3-3 proteins does not contribute to the subcellular localization of the hPFTAIRE1, although the binding may be involved in its signaling regulation.展开更多
AIM:To evaluate the potential of thioredoxin (TXN) and thioredoxin-interacting protein (TXNIP) expression as biomarkers for predicting gastric cancer recurrence. METHODS:TXN and TXNIP expression levels were acquired f...AIM:To evaluate the potential of thioredoxin (TXN) and thioredoxin-interacting protein (TXNIP) expression as biomarkers for predicting gastric cancer recurrence. METHODS:TXN and TXNIP expression levels were acquired from gene expression microarray data for 65 human gastric cancer tissues. We determined whether each gene expression level was associated with cancer recurrence and investigated the relationship between the two genes. For validation, the expression levels of TXN and TXNIP were measured by quantitative real- time reverse transcription polymerase chain reaction in 68 independent stage Ⅲ gastric cancer patients. The correlation between gene expression and cancer prognosis was evaluated. Immunohistochemical staining was performed to investigate the protein expression levels of TXN and TXNIP and to characterize the expression patterns of each protein. RESULTS:TXN was a prognosis-related gene (P = 0.009), whereas TXNIP, a TXN inhibitor, demonstrated a negative correlation with TXN in the gene expression microarray data. In the 68 stage Ⅲ patients, the expression levels of both TXN and TXNIP had a statistically significant effect on recurrence-free survival (RFS, P = 0.008 and P = 0.036, respectively). The low TXN and high TXNIP expression group exhibited a better prognosis than the other groups, and the high TXN and low TXNIP expression group exhibited a poorer prognosis (P < 0.001 for RFS and P = 0.001 for overall survival). More than half of the patients in the simulta-neously high TXN and low TXNIP expression group ex- perienced a recurrence within 1 year after curative surgery, and the 5-year survival rate of the patients in this group was 29%, compared with 89% in the low TXN and high TXNIP expression group. The TXN protein was overexpressed in 65% of the gastric cancer tissues, whereas the TXNIP protein was underexpressed in 85% of the cancer cells. In a correlation analysis, TXN and TXNIP were highly correlated with many oncogenes and tumor suppressors as well as with genes related to energy, protein synthesis and autophagy. CONCLUSION:TXN and TXNIP are promising prognostic markers for gastric cancer, and performing personalized adjuvant treatment based on TXN and TXNIP expression levels would be an effective practice in the treatment of gastric cancer.展开更多
A modified selectively infective phage (SIP) is developed to facilitate the selection of interacting antibody antigen pairs from a large single chain antibody (scFv) library in vivo. The system is constructed with a m...A modified selectively infective phage (SIP) is developed to facilitate the selection of interacting antibody antigen pairs from a large single chain antibody (scFv) library in vivo. The system is constructed with a modified helper phage M13KO7 and phagemid pCANTAB 5 E. The antigen fused to the C terminal of N1 N2 domain and the scFv to the N terminal of CT domain of the gIIIp of filamentous phage are encoded on the phage and phagemid vectors respectively. The phages produced by co transformants restore infectivity via interaction between antigen and antibody fusions in the cell periplasm. In a model system, the scFv fragment of the anti hemagglutinin 17/9 antibody and its corresponding antigen are detected in the presence of a 10 5 fold excess of a non interacting control pairs, which demonstrates this system to be very sensitive and facile to screen a large single chain antibody library.展开更多
Cells use various RNA （Ribonucleic Acid） regulatory mechanisms in order to temporally and coordinately influence the rate of protein synthesis. A deeper understanding of the dynamics of RNA regulation can ultimately...Cells use various RNA （Ribonucleic Acid） regulatory mechanisms in order to temporally and coordinately influence the rate of protein synthesis. A deeper understanding of the dynamics of RNA regulation can ultimately bridge the gap between transcriptional control and protein expression. The nonlinear process of RNA-Protein Interaction （RIP）, which can be viewed as the RNA analog of the better-known chromatin immunoprecipitation application （CHIP） plays a crucial role in post-transcriptional regulation of gene expression. While ChIP identifies DNA （Deoxyribonucleic Acid） targets of DNA-binding proteins in their cellular context, RIP can be used to identify specific RNA molecules associated with specific nuclear or cytoplasmic RNA-binding proteins. In this paper, a stochastic model in BioAmbients calculus for the protein synthesis and activation through RIP process is presemed.展开更多
Cells are crowded microenvironments filled with macromolecules undergoing constant phys- ical and chemical interactions. The physicochemical makeup of the cells aff）cts various cellular responses, determines cell-cel...Cells are crowded microenvironments filled with macromolecules undergoing constant phys- ical and chemical interactions. The physicochemical makeup of the cells aff）cts various cellular responses, determines cell-cell interactions and influences cell decisions. Chemical and physical properties diff）r between cells and within cells. Moreover, these properties are subject to dynamic changes in response to environmental signals, which often demand adjustments in the chemical or physical states of intracellular molecules. Indeed, cellular responses such as gene expression rely on the faithful relay of information from the outside to the inside of the cell, a process terrned signal transduction. The signal often traverses a complex path across subcellular spaces with variable physical chemistry, sometimes even influencing it. Understanding the molecular states of such signaling molecules and their intracellular environments is vital to our understanding of the cell. Exploring such intricate spaces is possible today largely because of experimental and theoretical tools. Here, we focus on one tool that is commonly used in chemical physics studies light. We summarize recent work which uses light to both visualize the cellular environment and also control intracel- lular processes along the axis of signal transduction. We highlight recent accomplishments in optical microscopy and optogenetics, an emerging experimental strategy which utilizes light to control the molecular processes in live cells. We believe that optogenetics lends un- precedented spatiotemporal precision to the manipulation of physicochemical properties in biological contexts. We hope to use this work to demonstrate new opportunities for chemical physicists who are interested in pursuing biological and biomedical questions.展开更多
文摘生物学通路被广泛应用于基因功能学研究,但现有的生物学通路知识并不完善,仍需进一步扩充。生物信息学预测为通路扩充提供了一种有效且经济的途径。文章提出了一种融合蛋白质?蛋白质互作知识以及Gene Ontology(GO)数据库信息进行基因通路预测的新方法。首先选取目标基因在蛋白质?蛋白质互作层面上的邻居所在的Kyoto Encyclopedia of Genes and Genomes(KEGG)通路为候选通路,然后通过检验候选通路中的基因是否在与目标基因关联的GO节点富集来判断目标基因的通路归属。分别利用Human Protein Reference Database(HPRD)和Biological General Repository for Interaction Datasets(BioGRID)数据库中的蛋白质?蛋白质互作信息进行预测。结果表明,在两套数据中,随着互作邻居个数的增加,预测的平均准确率(在所有目标基因注释的通路中被成功预测的比例)及相对准确率(在至少有一个注释通路被成功预测的基因集中,所有注释通路均被预测正确的基因所占的比例)均呈现上升趋势。当互作邻居个数达到22时,预测的平均准确率分别达到96.2%(HPRD)和96.3%(BioGRID),而相对准确率分别为93.3%(HPRD)和84.1%(BioGRID)。进一步利用新版数据库对旧版数据库中被更新的89个基因进行验证,至少有一个更新通路被预测正确的基因有50个,其中43个基因的更新通路被完全正确预测,相对准确率为86.0%。这些结果显示该方法是一种可靠且有效的通路扩充方法。
基金Project(50772133) supported by the National Natural Science Foundation of China
文摘A rapid, ultrasensitive and convenient fluorescence measurement technology based on the enhancement of the fluorescence intensity resulting from the interaction of functionalized CdSe/CdS quantum dots （QDs） with bov/ne serum albumin （BSA） was proposed. The citrate-stabilized CdSe/CdS （QDs） were synthesized by using Se powder and Na2S as precursors instead of any pyrophoric organometallic precursors. The modified CdSe/CdS QDs are brighter and more stable against photobleaching in comparison with organic fluorophores. At pH 7.0, the fluorescence signal of CdSe/CdS is enhanced by increasing the concentration of BSA in the range of 0.1-10 μg/mL, and the low detection limit is 0.06 μg/mL. A linear relationship between the enhanced fluorescence peak intensity （△F） and BSA concentration （c） is established using equation △F=50.7c＋16.4 （R=0.996 36）. Results of determination for BSA in three synthetic samples are identical with the true values, and the recovery （98.9%-102.4%） and relative standard deviation （RSD, 1.8%-2.5%） are satisfactory.
文摘Linker histones, e.g., H1, are best known for their ability to bind to nucleosomes and stabilize both nucleosome structure and condensed higher-order chromatin structures. However, over the years many investigators have reported specific interactions between linker histones and proteins involved in important cellular processes. The purpose of this review is to highlight evidence indicating an important alternative mode of action for H1, namely protein-protein interactions. We first review key aspects of the traditional view of linker histone action, including the importance of the H1 C-terminal domain. We then discuss the current state of knowledge of linker histone interactions with other proteins, and, where possible, highlight the mechanism of linker histone-mediated protein-protein interactions. Taken together, the data suggest a combinatorial role for the linker histones, functioning both as primary chromatin architectural proteins and simultaneously as recruitment hubs for proteins involved in accessing and modifying the chromatin fiber.
基金grants from National Natural Science Foundation of China （Nos. 30400073 ,30330010）.
文摘hPFTAIRE1 （PFTK1）, a Cdc2-related protein kinase, is highly expressed in human brain. It exhibits cytoplasmic distribution in Hela cells, although it contains two nuclear localization signals （NLSs） in its N-terminus. To search for its substrates and regulatory components, we screened a two-hybrid library by using the full-length hPFTAIRE1 as a bait. Four 14-3-3 isoforms （β,ε,η,τ） were identified interacting with the hPFTAIRE1. We found a putative 14-3-3 binding consensus motif（RHSSPSS） in the hPFTAIRE 1, which overlapped with its second NLS. Deletion of the RHSSPSS motif or substitution of Ser^119 gwithAla in the conserved binding motif abolished the specific interaction between the hPFTAIRE 1 and the 14-3 -3 proteins. The mutant S 120A hPFTAIRE1 also showed a weak interaction to the 14-3-3 proteins. The results suggested that the Ser^119 is crucial for the interaction between hPFTAIREI and the 14-3-3 proteins. All the hPFTAIRE1 mutants distributed in cytoplasm of Hela cells and human neuroblastoma cells （SH-SY5Y） when fused to the C-terminus of a green fluorescent protein （GFP）, indicating that binding with the 14-3-3 proteins does not contribute to the subcellular localization of the hPFTAIRE1, although the binding may be involved in its signaling regulation.
基金Supported by The Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology, No. 2010-0024248A Faculty Research Grant from Yonsei University College of Medicine for 2011, No. 6-2011-0113, 6-2011-0146
文摘AIM:To evaluate the potential of thioredoxin (TXN) and thioredoxin-interacting protein (TXNIP) expression as biomarkers for predicting gastric cancer recurrence. METHODS:TXN and TXNIP expression levels were acquired from gene expression microarray data for 65 human gastric cancer tissues. We determined whether each gene expression level was associated with cancer recurrence and investigated the relationship between the two genes. For validation, the expression levels of TXN and TXNIP were measured by quantitative real- time reverse transcription polymerase chain reaction in 68 independent stage Ⅲ gastric cancer patients. The correlation between gene expression and cancer prognosis was evaluated. Immunohistochemical staining was performed to investigate the protein expression levels of TXN and TXNIP and to characterize the expression patterns of each protein. RESULTS:TXN was a prognosis-related gene (P = 0.009), whereas TXNIP, a TXN inhibitor, demonstrated a negative correlation with TXN in the gene expression microarray data. In the 68 stage Ⅲ patients, the expression levels of both TXN and TXNIP had a statistically significant effect on recurrence-free survival (RFS, P = 0.008 and P = 0.036, respectively). The low TXN and high TXNIP expression group exhibited a better prognosis than the other groups, and the high TXN and low TXNIP expression group exhibited a poorer prognosis (P < 0.001 for RFS and P = 0.001 for overall survival). More than half of the patients in the simulta-neously high TXN and low TXNIP expression group ex- perienced a recurrence within 1 year after curative surgery, and the 5-year survival rate of the patients in this group was 29%, compared with 89% in the low TXN and high TXNIP expression group. The TXN protein was overexpressed in 65% of the gastric cancer tissues, whereas the TXNIP protein was underexpressed in 85% of the cancer cells. In a correlation analysis, TXN and TXNIP were highly correlated with many oncogenes and tumor suppressors as well as with genes related to energy, protein synthesis and autophagy. CONCLUSION:TXN and TXNIP are promising prognostic markers for gastric cancer, and performing personalized adjuvant treatment based on TXN and TXNIP expression levels would be an effective practice in the treatment of gastric cancer.
文摘A modified selectively infective phage (SIP) is developed to facilitate the selection of interacting antibody antigen pairs from a large single chain antibody (scFv) library in vivo. The system is constructed with a modified helper phage M13KO7 and phagemid pCANTAB 5 E. The antigen fused to the C terminal of N1 N2 domain and the scFv to the N terminal of CT domain of the gIIIp of filamentous phage are encoded on the phage and phagemid vectors respectively. The phages produced by co transformants restore infectivity via interaction between antigen and antibody fusions in the cell periplasm. In a model system, the scFv fragment of the anti hemagglutinin 17/9 antibody and its corresponding antigen are detected in the presence of a 10 5 fold excess of a non interacting control pairs, which demonstrates this system to be very sensitive and facile to screen a large single chain antibody library.
文摘Cells use various RNA （Ribonucleic Acid） regulatory mechanisms in order to temporally and coordinately influence the rate of protein synthesis. A deeper understanding of the dynamics of RNA regulation can ultimately bridge the gap between transcriptional control and protein expression. The nonlinear process of RNA-Protein Interaction （RIP）, which can be viewed as the RNA analog of the better-known chromatin immunoprecipitation application （CHIP） plays a crucial role in post-transcriptional regulation of gene expression. While ChIP identifies DNA （Deoxyribonucleic Acid） targets of DNA-binding proteins in their cellular context, RIP can be used to identify specific RNA molecules associated with specific nuclear or cytoplasmic RNA-binding proteins. In this paper, a stochastic model in BioAmbients calculus for the protein synthesis and activation through RIP process is presemed.
基金supported by the School of Molecular Cell Biology at the University of Illinois at Urbana-Champaign
文摘Cells are crowded microenvironments filled with macromolecules undergoing constant phys- ical and chemical interactions. The physicochemical makeup of the cells aff）cts various cellular responses, determines cell-cell interactions and influences cell decisions. Chemical and physical properties diff）r between cells and within cells. Moreover, these properties are subject to dynamic changes in response to environmental signals, which often demand adjustments in the chemical or physical states of intracellular molecules. Indeed, cellular responses such as gene expression rely on the faithful relay of information from the outside to the inside of the cell, a process terrned signal transduction. The signal often traverses a complex path across subcellular spaces with variable physical chemistry, sometimes even influencing it. Understanding the molecular states of such signaling molecules and their intracellular environments is vital to our understanding of the cell. Exploring such intricate spaces is possible today largely because of experimental and theoretical tools. Here, we focus on one tool that is commonly used in chemical physics studies light. We summarize recent work which uses light to both visualize the cellular environment and also control intracel- lular processes along the axis of signal transduction. We highlight recent accomplishments in optical microscopy and optogenetics, an emerging experimental strategy which utilizes light to control the molecular processes in live cells. We believe that optogenetics lends un- precedented spatiotemporal precision to the manipulation of physicochemical properties in biological contexts. We hope to use this work to demonstrate new opportunities for chemical physicists who are interested in pursuing biological and biomedical questions.
