The elements of network profile are proposed.Based on the network traffic distribution model,the network profile includes the application request rate,the branch transfer probability,the ratio of application requests,...The elements of network profile are proposed.Based on the network traffic distribution model,the network profile includes the application request rate,the branch transfer probability,the ratio of application requests,and the probability distribution of the requested objects.Based on the evaluation method of network performance reliability,four simulation cases are constructed in OPNET software,and the results show the four elements of profile have impacts on the network reliability.展开更多
This paper describes a simple method of generating concentration gradients with linear and parabolic profiles by using a Christmas tree-shaped microfluidic network.The microfluidic gradient generator consists of two p...This paper describes a simple method of generating concentration gradients with linear and parabolic profiles by using a Christmas tree-shaped microfluidic network.The microfluidic gradient generator consists of two parts：a Christmas tree-shaped network for gradient generation and a broad microchannel for detection.A two-dimensional model was built to analyze the flow field and the mass transfer in the microfluidic network.The simulating results show that a series of linear and parabolic gradient profiles were generated via adjusting relative flow rate ratios of the two source solutions（R_L^2≥0.995 and _PR^2≥0.999）,which could match well with the experimental results（R_L^2≥0.987 and _PR^2≥0.996）.The proposed method is promising for the generation of linear and parabolic concentration gradient profiles,with the potential in chemical and biological applications such as combinatorial chemistry synthesis,stem cell differentiation or cytotoxicity assays.展开更多
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated dat...Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene（s） of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.展开更多
A major focus of systems biology is to characterize interactions between cellular compo- nents, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protei...A major focus of systems biology is to characterize interactions between cellular compo- nents, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flex- ible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to recon- struct biological networks including protein-DNA interactions, posttranslational protein modifica- tions （PTMs）, lectin glycan recognition, pathogen-host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological sys- tems. We will also discuss emerging applications and future directions of protein microarray tech- nology in the global frontier.展开更多
Cellular functions, either under the normal or pathological conditions or under different stresses, are the results of the coordinated action of multiple proteins interacting in macromolecular complexes or assemblies....Cellular functions, either under the normal or pathological conditions or under different stresses, are the results of the coordinated action of multiple proteins interacting in macromolecular complexes or assemblies. The precise determination of the specific composition of protein complexes, especially using scalable and high-throughput methods, represents a systematic approach toward revealing particular cellular biological functions. In this regard, the direct profiling protein-protein interactions (PPIs) represent an efficient way to dissect functional pathways for revealing novel protein functions. In this review, we illustrate the technological evolution for the large-scale and precise identification of PPIs toward higher physiologically relevant accuracy. These techniques aim at improving the efficiency of complex pull-down, the signal specificity and accuracy in distinguishing specific PPIs, and the accuracy of identifying physiological relevant PPIs. A newly developed streamline proteomic approach for mapping the binary relationship of PPIs in a protein complex is introduced.展开更多
文摘The elements of network profile are proposed.Based on the network traffic distribution model,the network profile includes the application request rate,the branch transfer probability,the ratio of application requests,and the probability distribution of the requested objects.Based on the evaluation method of network performance reliability,four simulation cases are constructed in OPNET software,and the results show the four elements of profile have impacts on the network reliability.
基金Supported by the National Natural Science Foundation of China(81372358,81527801,51303140,and 81602489)the Natural Science Foundation of Hubei Province(2014CFA029)+1 种基金the Colleges of Hubei Province Outstanding Youth Science and Technology Innovation Team(T201305)the Applied Foundational Research Program of Wuhan Municipal Science and Technology Bureau(2015060101010056)
文摘This paper describes a simple method of generating concentration gradients with linear and parabolic profiles by using a Christmas tree-shaped microfluidic network.The microfluidic gradient generator consists of two parts：a Christmas tree-shaped network for gradient generation and a broad microchannel for detection.A two-dimensional model was built to analyze the flow field and the mass transfer in the microfluidic network.The simulating results show that a series of linear and parabolic gradient profiles were generated via adjusting relative flow rate ratios of the two source solutions（R_L^2≥0.995 and _PR^2≥0.999）,which could match well with the experimental results（R_L^2≥0.987 and _PR^2≥0.996）.The proposed method is promising for the generation of linear and parabolic concentration gradient profiles,with the potential in chemical and biological applications such as combinatorial chemistry synthesis,stem cell differentiation or cytotoxicity assays.
基金supported by grants from Strategic Priority Research Program of the Chinese Academy of Sciences(No. XDA08020102 to Z.Z.and S.H.)International Partnership Program of the Chinese Academy of Sciences(No.153F11KYSB20160008)+3 种基金National Programs for High Technology Research and Development (863 ProgramNo.2015AA020108 to Z.Z.)National Natural Science Foundation of China(No.31100915 to LH.)the 100-Talent Program of Chinese Academy of Sciences(awarded to Z.Z.)
文摘Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene（s） of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.
基金the Grants awarded to HZ (Grant No. RR020839, DK082840,RO1GM076102, CA125807, CA160036 and HG006434)an F31 NRSA Predoctoral Fellowship to IU (Grant No.5F31GM096716)
文摘A major focus of systems biology is to characterize interactions between cellular compo- nents, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flex- ible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to recon- struct biological networks including protein-DNA interactions, posttranslational protein modifica- tions （PTMs）, lectin glycan recognition, pathogen-host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological sys- tems. We will also discuss emerging applications and future directions of protein microarray tech- nology in the global frontier.
基金support from the Shanghai Science and Technology Development Program (Grant Nos. 03DZ14024 & 07ZR14010)the 863 High Technology Foundation of China (Grant No. 2006AA02A310)+1 种基金US NIH 1R01AI064806-01A2, 5R21DK082706U.S. Department of Energy, the Office of Science (BER) (Grant No. DE-FG02- 07ER64422)
文摘Cellular functions, either under the normal or pathological conditions or under different stresses, are the results of the coordinated action of multiple proteins interacting in macromolecular complexes or assemblies. The precise determination of the specific composition of protein complexes, especially using scalable and high-throughput methods, represents a systematic approach toward revealing particular cellular biological functions. In this regard, the direct profiling protein-protein interactions (PPIs) represent an efficient way to dissect functional pathways for revealing novel protein functions. In this review, we illustrate the technological evolution for the large-scale and precise identification of PPIs toward higher physiologically relevant accuracy. These techniques aim at improving the efficiency of complex pull-down, the signal specificity and accuracy in distinguishing specific PPIs, and the accuracy of identifying physiological relevant PPIs. A newly developed streamline proteomic approach for mapping the binary relationship of PPIs in a protein complex is introduced.
