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Sample records for analyzing protein interactome

  1. Building and analyzing protein interactome networks by cross-species comparisons

    Directory of Open Access Journals (Sweden)

    Blackman Barron

    2010-03-01

    Full Text Available Abstract Background A genomic catalogue of protein-protein interactions is a rich source of information, particularly for exploring the relationships between proteins. Numerous systems-wide and small-scale experiments have been conducted to identify interactions; however, our knowledge of all interactions for any one species is incomplete, and alternative means to expand these network maps is needed. We therefore took a comparative biology approach to predict protein-protein interactions across five species (human, mouse, fly, worm, and yeast and developed InterologFinder for research biologists to easily navigate this data. We also developed a confidence score for interactions based on available experimental evidence and conservation across species. Results The connectivity of the resultant networks was determined to have scale-free distribution, small-world properties, and increased local modularity, indicating that the added interactions do not disrupt our current understanding of protein network structures. We show examples of how these improved interactomes can be used to analyze a genome-scale dataset (RNAi screen and to assign new function to proteins. Predicted interactions within this dataset were tested by co-immunoprecipitation, resulting in a high rate of validation, suggesting the high quality of networks produced. Conclusions Protein-protein interactions were predicted in five species, based on orthology. An InteroScore, a score accounting for homology, number of orthologues with evidence of interactions, and number of unique observations of interactions, is given to each known and predicted interaction. Our website http://www.interologfinder.org provides research biologists intuitive access to this data.

  2. Virtual Interactomics of Proteins from Biochemical Standpoint

    Directory of Open Access Journals (Sweden)

    Jaroslav Kubrycht

    2012-01-01

    Full Text Available Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations.

  3. Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology.

    Science.gov (United States)

    Lin, Chung-Yen; Chin, Chia-Hao; Wu, Hsin-Hung; Chen, Shu-Hwa; Ho, Chin-Wen; Ko, Ming-Tat

    2008-07-01

    One major task in the post-genome era is to reconstruct proteomic and genomic interacting networks using high-throughput experiment data. To identify essential nodes/hubs in these interactomes is a way to decipher the critical keys inside biochemical pathways or complex networks. These essential nodes/hubs may serve as potential drug-targets for developing novel therapy of human diseases, such as cancer or infectious disease caused by emerging pathogens. Hub Objects Analyzer (Hubba) is a web-based service for exploring important nodes in an interactome network generated from specific small- or large-scale experimental methods based on graph theory. Two characteristic analysis algorithms, Maximum Neighborhood Component (MNC) and Density of Maximum Neighborhood Component (DMNC) are developed for exploring and identifying hubs/essential nodes from interactome networks. Users can submit their own interaction data in PSI format (Proteomics Standards Initiative, version 2.5 and 1.0), tab format and tab with weight values. User will get an email notification of the calculation complete in minutes or hours, depending on the size of submitted dataset. Hubba result includes a rank given by a composite index, a manifest graph of network to show the relationship amid these hubs, and links for retrieving output files. This proposed method (DMNC || MNC) can be applied to discover some unrecognized hubs from previous dataset. For example, most of the Hubba high-ranked hubs (80% in top 10 hub list, and >70% in top 40 hub list) from the yeast protein interactome data (Y2H experiment) are reported as essential proteins. Since the analysis methods of Hubba are based on topology, it can also be used on other kinds of networks to explore the essential nodes, like networks in yeast, rat, mouse and human. The website of Hubba is freely available at http://hub.iis.sinica.edu.tw/Hubba.

  4. PSIbase: a database of Protein Structural Interactome map (PSIMAP)

    OpenAIRE

    Gong, S.; Yoon, G.; Jang, I.; Bolser, D.; Panos, D.; Schroeder, M.; Choi, H.; Cho, Y.; Han, K.; Lee, S.; Choi, H.; Lappe, M.; Holm, L.; Kim, S.; Oh, D.

    2005-01-01

    Summary: Protein Structural Interactome map (PSIMAP) is a global interaction map that describes domain–domain and protein–protein interaction information for known Protein Data Bank structures. It calculates the Euclidean distance to determine interactions between possible pairs of structural domains in proteins. PSIbase is a database and file server for protein structural interaction information calculated by the PSIMAP algorithm. PSIbase also provides an easy-to-use protein domain assignmen...

  5. Virtual Interactomics of Proteins from Biochemical Standpoint

    Czech Academy of Sciences Publication Activity Database

    Kubrycht, J.; Sigler, Karel; Souček, P.

    2012-01-01

    Roč. 2012, AUG 2012 (2012), s. 976385 ISSN 2090-2182 Institutional support: RVO:61388971 Keywords : cell * protein * bioinformation Subject RIV: EE - Microbiology, Virology http://www.hindawi.com/journals/mbi/2012/976385/

  6. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

    Science.gov (United States)

    Brannan, Kristopher W; Jin, Wenhao; Huelga, Stephanie C; Banks, Charles A S; Gilmore, Joshua M; Florens, Laurence; Washburn, Michael P; Van Nostrand, Eric L; Pratt, Gabriel A; Schwinn, Marie K; Daniels, Danette L; Yeo, Gene W

    2016-10-20

    RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down of 12 nuclear and cytoplasmic RBPs followed by quantitative mass spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1,923 human, 489 fly, and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Interactome of invadopodia scaffold protein TKS5

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    Kropyvko S. V.

    2015-12-01

    Full Text Available TKS5 is a scaffold protein that takes part in invadopodia functioning and reactive oxygen species (ROS production. TKS5 is a critical component of invadopodia as its absence results in the loss of cancer cells ability to form these invasive structures. TKS5 is phosphorylated by SRC kinase and consequently interacts with the membrane phosphatidylinositol phosphates launching the invadopodia formation process. At later stages TKS5 regulates the actin cytoskeleton reorganization and extracellular matrix degradation. TKS5 also regulates the production of ROS, which are the important signal regulators of different cellular functions.

  8. In vitro nuclear interactome of the HIV-1 Tat protein.

    LENUS (Irish Health Repository)

    Gautier, Virginie W

    2009-01-01

    BACKGROUND: One facet of the complexity underlying the biology of HIV-1 resides not only in its limited number of viral proteins, but in the extensive repertoire of cellular proteins they interact with and their higher-order assembly. HIV-1 encodes the regulatory protein Tat (86-101aa), which is essential for HIV-1 replication and primarily orchestrates HIV-1 provirus transcriptional regulation. Previous studies have demonstrated that Tat function is highly dependent on specific interactions with a range of cellular proteins. However they can only partially account for the intricate molecular mechanisms underlying the dynamics of proviral gene expression. To obtain a comprehensive nuclear interaction map of Tat in T-cells, we have designed a proteomic strategy based on affinity chromatography coupled with mass spectrometry. RESULTS: Our approach resulted in the identification of a total of 183 candidates as Tat nuclear partners, 90% of which have not been previously characterised. Subsequently we applied in silico analysis, to validate and characterise our dataset which revealed that the Tat nuclear interactome exhibits unique signature(s). First, motif composition analysis highlighted that our dataset is enriched for domains mediating protein, RNA and DNA interactions, and helicase and ATPase activities. Secondly, functional classification and network reconstruction clearly depicted Tat as a polyvalent protein adaptor and positioned Tat at the nexus of a densely interconnected interaction network involved in a range of biological processes which included gene expression regulation, RNA biogenesis, chromatin structure, chromosome organisation, DNA replication and nuclear architecture. CONCLUSION: We have completed the in vitro Tat nuclear interactome and have highlighted its modular network properties and particularly those involved in the coordination of gene expression by Tat. Ultimately, the highly specialised set of molecular interactions identified will

  9. Identifying unexpected therapeutic targets via chemical-protein interactome.

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    Lun Yang

    Full Text Available Drug medications inevitably affect not only their intended protein targets but also other proteins as well. In this study we examined the hypothesis that drugs that share the same therapeutic effect also share a common therapeutic mechanism by targeting not only known drug targets, but also by interacting unexpectedly on the same cryptic targets. By constructing and mining an Alzheimer's disease (AD drug-oriented chemical-protein interactome (CPI using a matrix of 10 drug molecules known to treat AD towards 401 human protein pockets, we found that such cryptic targets exist. We recovered from CPI the only validated therapeutic target of AD, acetylcholinesterase (ACHE, and highlighted several other putative targets. For example, we discovered that estrogen receptor (ER and histone deacetylase (HDAC, which have recently been identified as two new therapeutic targets of AD, might already have been targeted by the marketed AD drugs. We further established that the CPI profile of a drug can reflect its interacting character towards multi-protein sets, and that drugs with the same therapeutic attribute will share a similar interacting profile. These findings indicate that the CPI could represent the landscape of chemical-protein interactions and uncover "behind-the-scenes" aspects of the therapeutic mechanisms of existing drugs, providing testable hypotheses of the key nodes for network pharmacology or brand new drug targets for one-target pharmacology paradigm.

  10. A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize.

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    Matt eGeisler

    2015-06-01

    Full Text Available Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6,004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize.

  11. RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

    KAUST Repository

    Köster, Tino

    2017-04-13

    RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

  12. Dissection of protein interactomics highlights microRNA synergy.

    Science.gov (United States)

    Zhu, Wenliang; Zhao, Yilei; Xu, Yingqi; Sun, Yong; Wang, Zhe; Yuan, Wei; Du, Zhimin

    2013-01-01

    Despite a large amount of microRNAs (miRNAs) have been validated to play crucial roles in human biology and disease, there is little systematic insight into the nature and scale of the potential synergistic interactions executed by miRNAs themselves. Here we established an integrated parameter synergy score to determine miRNA synergy, by combining the two mechanisms for miRNA-miRNA interactions, miRNA-mediated gene co-regulation and functional association between target gene products, into one single parameter. Receiver operating characteristic (ROC) analysis indicated that synergy score accurately identified the gene ontology-defined miRNA synergy (AUC = 0.9415, psynergy, implying poor expectancy of widespread synergy. However, targeting more key genes made two miRNAs more likely to act synergistically. Compared to other miRNAs, miR-21 was a highly exceptional case due to frequent appearance in the top synergistic miRNA pairs. This result highlighted its essential role in coordinating or strengthening physiological and pathological functions of other miRNAs. The synergistic effect of miR-21 and miR-1 were functionally validated for their significant influences on myocardial apoptosis, cardiac hypertrophy and fibrosis. The novel approach established in this study enables easy and effective identification of condition-restricted potent miRNA synergy simply by concentrating the available protein interactomics and miRNA-target interaction data into a single parameter synergy score. Our results may be important for understanding synergistic gene regulation by miRNAs and may have significant implications for miRNA combination therapy of cardiovascular disease.

  13. Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC).

    Science.gov (United States)

    Hubner, Nina C; Mann, Matthias

    2011-04-01

    Large-scale proteomic screens are increasingly employed for placing genes into specific pathways. Therefore generic methods providing a physiological context for protein-protein interaction studies are of great interest. In recent years many protein-protein interactions have been determined by affinity purification followed by mass spectrometry (AP-MS). Among many different AP-MS approaches, the recently developed Quantitative BAC InteraCtomics (QUBIC) approach is particularly attractive as it uses tagged, full-length baits that are expressed under endogenous control. For QUBIC large cell line collections expressing tagged proteins from BAC transgenes or gene trap loci have been developed and are freely available. Here we describe detailed workflows on how to obtain specific protein binding partners with high confidence under physiological conditions. The methods are based on fast, streamlined and generic purification procedures followed by single run liquid chromatography-mass spectrometric analysis. Quantification is achieved either by the stable isotope labeling of amino acids in cell culture (SILAC) method or by a 'label-free' procedure. In either case data analysis is performed by using the freely available MaxQuant environment. The QUBIC approach enables biologists with access to high resolution mass spectrometry to perform small and large-scale protein interactome mappings. Copyright © 2010 Elsevier Inc. All rights reserved.

  14. Mining protein interactomes to improve their reliability and support the advancement of network medicine

    KAUST Repository

    Alanis Lobato, Gregorio

    2015-09-23

    High-throughput detection of protein interactions has had a major impact in our understanding of the intricate molecular machinery underlying the living cell, and has permitted the construction of very large protein interactomes. The protein networks that are currently available are incomplete and a significant percentage of their interactions are false positives. Fortunately, the structural properties observed in good quality social or technological networks are also present in biological systems. This has encouraged the development of tools, to improve the reliability of protein networks and predict new interactions based merely on the topological characteristics of their components. Since diseases are rarely caused by the malfunction of a single protein, having a more complete and reliable interactome is crucial in order to identify groups of inter-related proteins involved in disease etiology. These system components can then be targeted with minimal collateral damage. In this article, an important number of network mining tools is reviewed, together with resources from which reliable protein interactomes can be constructed. In addition to the review, a few representative examples of how molecular and clinical data can be integrated to deepen our understanding of pathogenesis are discussed.

  15. Next Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstock Research

    Energy Technology Data Exchange (ETDEWEB)

    Ecker, Joseph Robert [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Trigg, Shelly [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Univ. of California, San Diego, CA (United States). Biological Sciences Dept.; Garza, Renee [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Song, Haili [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; MacWilliams, Andrew [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Nery, Joseph [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Reina, Joaquin [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Bartlett, Anna [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Castanon, Rosa [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Goubil, Adeline [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Feeney, Joseph [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; O' Malley, Ronan [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Huang, Shao-shan Carol [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Zhang, Zhuzhu [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.; Galli, Mary [The Salk Inst. for Biological Studies, La Jolla, CA (United States). Genome Analysis and Plant Biology Lab.

    2016-11-30

    Biofuel crop cultivation is a necessary step in heading towards a sustainable future, making their genomic studies a priority. While technology platforms that currently exist for studying non-model crop species, like switch-grass or sorghum, have yielded large quantities of genomic and expression data, still a large gap exists between molecular mechanism and phenotype. The aspect of molecular activity at the level of protein-protein interactions has recently begun to bridge this gap, providing a more global perspective. Interactome analysis has defined more specific functional roles of proteins based on their interaction partners, neighborhoods, and other network features, making it possible to distinguish unique modules of immune response to different plant pathogens(Jiang, Dong, and Zhang 2016). As we work towards cultivating heartier biofuel crops, interactome data will lead to uncovering crop-specific defense and development networks. However, the collection of protein interaction data has been limited to expensive, time-consuming, hard-to-scale assays that mostly require cloned ORF collections. For these reasons, we have successfully developed a highly scalable, economical, and sensitive yeast two-hybrid assay, ProCREate, that can be universally applied to generate proteome-wide primary interactome data. ProCREate enables en masse pooling and massively paralleled sequencing for the identification of interacting proteins by exploiting Cre-lox recombination. ProCREate can be used to screen ORF/cDNA libraries from feedstock plant tissues. The interactome data generated will yield deeper insight into many molecular processes and pathways that can be used to guide improvement of feedstock productivity and sustainability.

  16. Expanding the substantial interactome of NEMO using protein microarrays.

    LENUS (Irish Health Repository)

    Fenner, Beau J

    2010-01-01

    Signal transduction by the NF-kappaB pathway is a key regulator of a host of cellular responses to extracellular and intracellular messages. The NEMO adaptor protein lies at the top of this pathway and serves as a molecular conduit, connecting signals transmitted from upstream sensors to the downstream NF-kappaB transcription factor and subsequent gene activation. The position of NEMO within this pathway makes it an attractive target from which to search for new proteins that link NF-kappaB signaling to additional pathways and upstream effectors. In this work, we have used protein microarrays to identify novel NEMO interactors. A total of 112 protein interactors were identified, with the most statistically significant hit being the canonical NEMO interactor IKKbeta, with IKKalpha also being identified. Of the novel interactors, more than 30% were kinases, while at least 25% were involved in signal transduction. Binding of NEMO to several interactors, including CALB1, CDK2, SAG, SENP2 and SYT1, was confirmed using GST pulldown assays and coimmunoprecipitation, validating the initial screening approach. Overexpression of CALB1, CDK2 and SAG was found to stimulate transcriptional activation by NF-kappaB, while SYT1 overexpression repressed TNFalpha-dependent NF-kappaB transcriptional activation in human embryonic kidney cells. Corresponding with this finding, RNA silencing of CDK2, SAG and SENP2 reduced NF-kappaB transcriptional activation, supporting a positive role for these proteins in the NF-kappaB pathway. The identification of a host of new NEMO interactors opens up new research opportunities to improve understanding of this essential cell signaling pathway.

  17. Characterization of the Translationally Controlled Tumor Protein (TCTP) Interactome Reveals Novel Binding Partners in Human Cancer Cells.

    Science.gov (United States)

    Li, Siting; Chen, Minghai; Xiong, Qian; Zhang, Jia; Cui, Zongqiang; Ge, Feng

    2016-10-07

    Translationally controlled tumor protein (TCTP) is a highly conserved housekeeping protein present in eukaryotic organisms. It is involved in regulating many fundamental processes and plays a critical role in tumor reversion and tumorigenesis. Increasing evidence suggests that TCTP plays a role in the regulation of cell fate determination and is a promising therapeutic target for cancer. To decipher the exact mechanisms by which TCTP functions and how all these functions are integrated, we analyzed the interactome of TCTP in HeLa cells by coimmunoprecipitation (IP) and mass spectrometry (MS). A total of 98 proteins were identified. We confirmed the in vitro and in vivo association of TCTP with six of the identified binding proteins using reciprocal IP and bimolecular fluorescence complementation (BiFC) analysis, respectively. Moreover, TCTP interacted with Y-box-binding protein 1 (YBX1), and their interaction was localized to the N-terminal region of TCTP and the 1-129 amino acid (aa) residues of YBX1. The YBX1 protein plays an important role in cell proliferation, RNA splicing, DNA repair, drug resistance, and stress response to extracellular signals. These data suggest that the interaction of TCTP with YBX1 might cooperate or coordinate their functions in the control of diverse regulatory pathways in cancer cells. Taken together, our results not only reveal a large number of TCTP-associated proteins that possess pleiotropic functions, but also provide novel insights into the molecular mechanisms of TCTP in tumorigenesis.

  18. The L1TD1 Protein Interactome Reveals the Importance of Post-transcriptional Regulation in Human Pluripotency

    Directory of Open Access Journals (Sweden)

    Maheswara Reddy Emani

    2015-03-01

    Full Text Available The RNA-binding protein L1TD1 is one of the most specific and abundant proteins in pluripotent stem cells and is essential for the maintenance of pluripotency in human cells. Here, we identify the protein interaction network of L1TD1 in human embryonic stem cells (hESCs and provide insights into the interactome network constructed in human pluripotent cells. Our data reveal that L1TD1 has an important role in RNA splicing, translation, protein traffic, and degradation. L1TD1 interacts with multiple stem-cell-specific proteins, many of which are still uncharacterized in the context of development. Further, we show that L1TD1 is a part of the pluripotency interactome network of OCT4, SOX2, and NANOG, bridging nuclear and cytoplasmic regulation and highlighting the importance of RNA biology in pluripotency.

  19. Searching for cellular partners of hantaviral nonstructural protein NSs: Y2H screening of mouse cDNA library and analysis of cellular interactome.

    Directory of Open Access Journals (Sweden)

    Tuomas Rönnberg

    Full Text Available Hantaviruses (Bunyaviridae are negative-strand RNA viruses with a tripartite genome. The small (S segment encodes the nucleocapsid protein and, in some hantaviruses, also the nonstructural protein (NSs. The aim of this study was to find potential cellular partners for the hantaviral NSs protein. Toward this aim, yeast two-hybrid (Y2H screening of mouse cDNA library was performed followed by a search for potential NSs protein counterparts via analyzing a cellular interactome. The resulting interaction network was shown to form logical, clustered structures. Furthermore, several potential binding partners for the NSs protein, for instance ACBD3, were identified and, to prove the principle, interaction between NSs and ACBD3 proteins was demonstrated biochemically.

  20. Protein-mRNA interactome capture: cartography of the mRNP landscape.

    Science.gov (United States)

    Ryder, Sean P

    2016-01-01

    RNA-binding proteins play a variety of roles in cellular physiology. Some regulate mRNA processing, mRNA abundance, and translation efficiency. Some fight off invader RNA through small RNA-driven silencing pathways. Others sense foreign sequences in the form of double-stranded RNA and activate the innate immune response. Yet others, for example cytoplasmic aconitase, act as bi-functional proteins, processing metabolites in one conformation and regulating metabolic gene expression in another. Not all are involved in gene regulation. Some play structural roles, for example, connecting the translational machinery to the endoplasmic reticulum outer membrane. Despite their pervasive role and relative importance, it has remained difficult to identify new RNA-binding proteins in a systematic, unbiased way. A recent body of literature from several independent labs has defined robust, easily adaptable protocols for mRNA interactome discovery. In this review, I summarize the methods and review some of the intriguing findings from their application to a wide variety of biological systems.

  1. Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef.

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    Mahdi Sarmady

    Full Text Available Virus proteins alter protein pathways of the host toward the synthesis of viral particles by breaking and making edges via binding to host proteins. In this study, we developed a computational approach to predict viral sequence hotspots for binding to host proteins based on sequences of viral and host proteins and literature-curated virus-host protein interactome data. We use a motif discovery algorithm repeatedly on collections of sequences of viral proteins and immediate binding partners of their host targets and choose only those motifs that are conserved on viral sequences and highly statistically enriched among binding partners of virus protein targeted host proteins. Our results match experimental data on binding sites of Nef to host proteins such as MAPK1, VAV1, LCK, HCK, HLA-A, CD4, FYN, and GNB2L1 with high statistical significance but is a poor predictor of Nef binding sites on highly flexible, hoop-like regions. Predicted hotspots recapture CD8 cell epitopes of HIV Nef highlighting their importance in modulating virus-host interactions. Host proteins potentially targeted or outcompeted by Nef appear crowding the T cell receptor, natural killer cell mediated cytotoxicity, and neurotrophin signaling pathways. Scanning of HIV Nef motifs on multiple alignments of hepatitis C protein NS5A produces results consistent with literature, indicating the potential value of the hotspot discovery in advancing our understanding of virus-host crosstalk.

  2. Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome.

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    Donglei Du

    Full Text Available Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A What is the general difference between signal emitting and receiving in a protein interactome? B Which proteins are among the top ranked in directional ranking? C Are high ranked proteins more evolutionarily conserved than low ranked ones? D Do proteins with similar ranking tend to have similar subcellular locations? In this study, we address these questions using the forward, reverse, and non-directional PageRank approaches to rank an information-directional network of human proteins and study their evolutionary conservation. The forward ranking gives credit to information receivers, reverse ranking to information emitters, and non-directional ranking mainly to the number of interactions. The protein lists generated by the forward and non-directional rankings are highly correlated, but those by the reverse and non-directional rankings are not. The results suggest that the signal emitting/receiving system is characterized by key-emittings and relatively even receivings in the human protein interactome. Signaling pathway proteins are frequent in top ranked ones. Eight proteins are both informational top emitters and top receivers. Top ranked proteins, except a few species-related novel-function ones, are evolutionarily well conserved. Protein-subunit ranking position reflects subunit function. These results demonstrate the usefulness of different PageRank approaches in characterizing protein networks and provide insights to protein interaction in the cell.

  3. Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome.

    Science.gov (United States)

    Du, Donglei; Lee, Connie F; Li, Xiu-Qing

    2012-01-01

    Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A) What is the general difference between signal emitting and receiving in a protein interactome? B) Which proteins are among the top ranked in directional ranking? C) Are high ranked proteins more evolutionarily conserved than low ranked ones? D) Do proteins with similar ranking tend to have similar subcellular locations? In this study, we address these questions using the forward, reverse, and non-directional PageRank approaches to rank an information-directional network of human proteins and study their evolutionary conservation. The forward ranking gives credit to information receivers, reverse ranking to information emitters, and non-directional ranking mainly to the number of interactions. The protein lists generated by the forward and non-directional rankings are highly correlated, but those by the reverse and non-directional rankings are not. The results suggest that the signal emitting/receiving system is characterized by key-emittings and relatively even receivings in the human protein interactome. Signaling pathway proteins are frequent in top ranked ones. Eight proteins are both informational top emitters and top receivers. Top ranked proteins, except a few species-related novel-function ones, are evolutionarily well conserved. Protein-subunit ranking position reflects subunit function. These results demonstrate the usefulness of different PageRank approaches in characterizing protein networks and provide insights to protein interaction in the cell.

  4. Construction and application of a protein and genetic interaction network (yeast interactome).

    Science.gov (United States)

    Stuart, Gregory R; Copeland, William C; Strand, Micheline K

    2009-04-01

    Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data. To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (www.yeastgenome.org) and the database of yeast transcription factors at YEASTRACT (www.yeastract.com). These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome.

  5. High-quality binary interactome mapping.

    Science.gov (United States)

    Dreze, Matija; Monachello, Dario; Lurin, Claire; Cusick, Michael E; Hill, David E; Vidal, Marc; Braun, Pascal

    2010-01-01

    Physical interactions mediated by proteins are critical for most cellular functions and altogether form a complex macromolecular "interactome" network. Systematic mapping of protein-protein, protein-DNA, protein-RNA, and protein-metabolite interactions at the scale of the whole proteome can advance understanding of interactome networks with applications ranging from single protein functional characterization to discoveries on local and global systems properties. Since the early efforts at mapping protein-protein interactome networks a decade ago, the field has progressed rapidly giving rise to a growing number of interactome maps produced using high-throughput implementations of either binary protein-protein interaction assays or co-complex protein association methods. Although high-throughput methods are often thought to necessarily produce lower quality information than low-throughput experiments, we have recently demonstrated that proteome-scale interactome datasets can be produced with equal or superior quality than that observed in literature-curated datasets derived from large numbers of small-scale experiments. In addition to performing all experimental steps thoroughly and including all necessary controls and quality standards, careful verification of all interacting pairs and validation tests using independent, orthogonal assays are crucial to ensure the release of interactome maps of the highest possible quality. This chapter describes a high-quality, high-throughput binary protein-protein interactome mapping pipeline that includes these features. Copyright © 2010 Elsevier Inc. All rights reserved.

  6. Viruses and interactomes in translation.

    Science.gov (United States)

    Meyniel-Schicklin, Laurène; de Chassey, Benoît; André, Patrice; Lotteau, Vincent

    2012-07-01

    A decade of high-throughput screenings for intraviral and virus-host protein-protein interactions led to the accumulation of data and to the development of theories on laws governing interactome organization for many viruses. We present here a computational analysis of intraviral protein networks (EBV, FLUAV, HCV, HSV-1, KSHV, SARS-CoV, VACV, and VZV) and virus-host protein networks (DENV, EBV, FLUAV, HCV, and VACV) from up-to-date interaction data, using various mathematical approaches. If intraviral networks seem to behave similarly, they are clearly different from the human interactome. Viral proteins target highly central human proteins, which are precisely the Achilles' heel of the human interactome. The intrinsic structural disorder is a distinctive feature of viral hubs in virus-host interactomes. Overlaps between virus-host data sets identify a core of human proteins involved in the cellular response to viral infection and in the viral capacity to hijack the cell machinery for viral replication. Host proteins that are strongly targeted by a virus seem to be particularly attractive for other viruses. Such protein-protein interaction networks and their analysis represent a powerful resource from a therapeutic perspective.

  7. An Interactome-Centered Protein Discovery Approach Reveals Novel Components Involved in Mitosome Function and Homeostasis in Giardia lamblia.

    Directory of Open Access Journals (Sweden)

    Samuel Rout

    2016-12-01

    Full Text Available Protozoan parasites of the genus Giardia are highly prevalent globally, and infect a wide range of vertebrate hosts including humans, with proliferation and pathology restricted to the small intestine. This narrow ecological specialization entailed extensive structural and functional adaptations during host-parasite co-evolution. An example is the streamlined mitosomal proteome with iron-sulphur protein maturation as the only biochemical pathway clearly associated with this organelle. Here, we applied techniques in microscopy and protein biochemistry to investigate the mitosomal membrane proteome in association to mitosome homeostasis. Live cell imaging revealed a highly immobilized array of 30-40 physically distinct mitosome organelles in trophozoites. We provide direct evidence for the single giardial dynamin-related protein as a contributor to mitosomal morphogenesis and homeostasis. To overcome inherent limitations that have hitherto severely hampered the characterization of these unique organelles we applied a novel interaction-based proteome discovery strategy using forward and reverse protein co-immunoprecipitation. This allowed generation of organelle proteome data strictly in a protein-protein interaction context. We built an initial Tom40-centered outer membrane interactome by co-immunoprecipitation experiments, identifying small GTPases, factors with dual mitosome and endoplasmic reticulum (ER distribution, as well as novel matrix proteins. Through iterative expansion of this protein-protein interaction network, we were able to i significantly extend this interaction-based mitosomal proteome to include other membrane-associated proteins with possible roles in mitosome morphogenesis and connection to other subcellular compartments, and ii identify novel matrix proteins which may shed light on mitosome-associated metabolic functions other than Fe-S cluster biogenesis. Functional analysis also revealed conceptual conservation of protein

  8. An Interactome-Centered Protein Discovery Approach Reveals Novel Components Involved in Mitosome Function and Homeostasis in Giardia lamblia.

    Science.gov (United States)

    Rout, Samuel; Zumthor, Jon Paulin; Schraner, Elisabeth M; Faso, Carmen; Hehl, Adrian B

    2016-12-01

    Protozoan parasites of the genus Giardia are highly prevalent globally, and infect a wide range of vertebrate hosts including humans, with proliferation and pathology restricted to the small intestine. This narrow ecological specialization entailed extensive structural and functional adaptations during host-parasite co-evolution. An example is the streamlined mitosomal proteome with iron-sulphur protein maturation as the only biochemical pathway clearly associated with this organelle. Here, we applied techniques in microscopy and protein biochemistry to investigate the mitosomal membrane proteome in association to mitosome homeostasis. Live cell imaging revealed a highly immobilized array of 30-40 physically distinct mitosome organelles in trophozoites. We provide direct evidence for the single giardial dynamin-related protein as a contributor to mitosomal morphogenesis and homeostasis. To overcome inherent limitations that have hitherto severely hampered the characterization of these unique organelles we applied a novel interaction-based proteome discovery strategy using forward and reverse protein co-immunoprecipitation. This allowed generation of organelle proteome data strictly in a protein-protein interaction context. We built an initial Tom40-centered outer membrane interactome by co-immunoprecipitation experiments, identifying small GTPases, factors with dual mitosome and endoplasmic reticulum (ER) distribution, as well as novel matrix proteins. Through iterative expansion of this protein-protein interaction network, we were able to i) significantly extend this interaction-based mitosomal proteome to include other membrane-associated proteins with possible roles in mitosome morphogenesis and connection to other subcellular compartments, and ii) identify novel matrix proteins which may shed light on mitosome-associated metabolic functions other than Fe-S cluster biogenesis. Functional analysis also revealed conceptual conservation of protein translocation

  9. Oncoprotein AEG-1 is an Endoplasmic Reticulum RNA Binding Protein Whose Interactome is Enriched In Organelle Resident Protein-Encoding mRNAs.

    Science.gov (United States)

    Hsu, Jack C-C; Reid, David W; Hoffman, Alyson M; Sarkar, Devanand; Nicchitta, Christopher V

    2018-02-07

    Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs. Cluster mapping of the AEG-1/RNA interaction sites demonstrated a normalized rank order interaction of coding sequence > 5' untranslated region, with 3' untranslated region interactions only weakly represented. Intriguingly, AEG-1/membrane protein mRNA interaction sites clustered downstream of encoded transmembrane domains, suggestive of a role in membrane protein biogenesis. Secretory and cytosolic protein-encoding mRNAs were also represented in the AEG-1 RNA interactome, with the latter category notably enriched in genes functioning in mRNA localization, translational regulation, and RNA quality control. Bioinformatic analyses of RNA binding motifs and predicted secondary structure characteristics indicate that AEG-1 lacks established RNA binding sites though shares the property of high intrinsic disorder commonly seen in RBPs. These data implicate AEG-1 in the localization and regulation of secretory and membrane protein-encoding mRNAs and provide a framework for understanding AEG-1 function in health and disease. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  10. Interactome of the hepatitis C virus: Literature mining with ANDSystem.

    Science.gov (United States)

    Saik, Olga V; Ivanisenko, Timofey V; Demenkov, Pavel S; Ivanisenko, Vladimir A

    2016-06-15

    A study of the molecular genetics mechanisms of host-pathogen interactions is of paramount importance in developing drugs against viral diseases. Currently, the literature contains a huge amount of information that describes interactions between HCV and human proteins. In addition, there are many factual databases that contain experimentally verified data on HCV-host interactions. The sources of such data are the original data along with the data manually extracted from the literature. However, the manual analysis of scientific publications is time consuming and, because of this, databases created with such an approach often do not have complete information. One of the most promising methods to provide actualisation and completeness of information is text mining. Here, with the use of a previously developed method by the authors using ANDSystem, an automated extraction of information on the interactions between HCV and human proteins was conducted. As a data source for the text mining approach, PubMed abstracts and full text articles were used. Additionally, external factual databases were analyzed. On the basis of this analysis, a special version of ANDSystem, extended with the HCV interactome, was created. The HCV interactome contains information about the interactions between 969 human and 11 HCV proteins. Among the 969 proteins, 153 'new' proteins were found not previously referred to in any external databases of protein-protein interactions for HCV-host interactions. Thus, the extended ANDSystem possesses a more comprehensive detailing of HCV-host interactions versus other existing databases. It was interesting that HCV proteins more preferably interact with human proteins that were already involved in a large number of protein-protein interactions as well as those associated with many diseases. Among human proteins of the HCV interactome, there were a large number of proteins regulated by microRNAs. It turned out that the results obtained for protein-protein

  11. Alzheimer disease: An interactome of many diseases

    Directory of Open Access Journals (Sweden)

    Balaji S Rao

    2014-01-01

    Full Text Available Alzheimer Disease (AD is an outcome as well as source of many diseases. Alzheimer is linked with many other diseases like Diabetes type 2, cholesterolemia, hypertension and many more. But how each of these diseases affecting other is still unknown to scientific community. Signaling Pathways of one disease is interlinked with other disease. But to what extent healthy brain is affected when any signaling in human body is disturbed is the question that matters. There is a need of Pathway analysis, Protein-Protein interaction (PPI and the conserved interactome study in AD and linked diseases. It will be helpful in finding the potent drug or vaccine target in conscious manner. In the present research the Protein-Protein interaction of all the proteins involved in Alzheimer Disease is analyzed using ViSANT and osprey tools and pathway analysis further reveals the significant genes/proteins linking AD with other diseases.

  12. A comprehensive protein-protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1.

    Science.gov (United States)

    DeMille, Desiree; Bikman, Benjamin T; Mathis, Andrew D; Prince, John T; Mackay, Jordan T; Sowa, Steven W; Hall, Tacie D; Grose, Julianne H

    2014-07-15

    Per-Arnt-Sim (PAS) kinase is a sensory protein kinase required for glucose homeostasis in yeast, mice, and humans, yet little is known about the molecular mechanisms of its function. Using both yeast two-hybrid and copurification approaches, we identified the protein-protein interactome for yeast PAS kinase 1 (Psk1), revealing 93 novel putative protein binding partners. Several of the Psk1 binding partners expand the role of PAS kinase in glucose homeostasis, including new pathways involved in mitochondrial metabolism. In addition, the interactome suggests novel roles for PAS kinase in cell growth (gene/protein expression, replication/cell division, and protein modification and degradation), vacuole function, and stress tolerance. In vitro kinase studies using a subset of 25 of these binding partners identified Mot3, Zds1, Utr1, and Cbf1 as substrates. Further evidence is provided for the in vivo phosphorylation of Cbf1 at T211/T212 and for the subsequent inhibition of respiration. This respiratory role of PAS kinase is consistent with the reported hypermetabolism of PAS kinase-deficient mice, identifying a possible molecular mechanism and solidifying the evolutionary importance of PAS kinase in the regulation of glucose homeostasis. © 2014 DeMille et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  13. Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity.

    Directory of Open Access Journals (Sweden)

    Andrey Alexeyenko

    2010-05-01

    Full Text Available In order to generate hypotheses regarding the mechanisms by which 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin causes toxicity, we analyzed global gene expression changes in developing zebrafish embryos exposed to this potent toxicant in the context of a dynamic gene network. For this purpose, we also computationally inferred a zebrafish (Danio rerio interactome based on orthologs and interaction data from other eukaryotes.Using novel computational tools to analyze this interactome, we distinguished between dioxin-dependent and dioxin-independent interactions between proteins, and tracked the temporal propagation of dioxin-dependent transcriptional changes from a few genes that were altered initially, to large groups of biologically coherent genes at later times. The most notable processes altered at later developmental stages were calcium and iron metabolism, embryonic morphogenesis including neuronal and retinal development, a variety of mitochondria-related functions, and generalized stress response (not including induction of antioxidant genes. Within the interactome, many of these responses were connected to cytochrome P4501A (cyp1a as well as other genes that were dioxin-regulated one day after exposure. This suggests that cyp1a may play a key role initiating the toxic dysregulation of those processes, rather than serving simply as a passive marker of dioxin exposure, as suggested by earlier research.Thus, a powerful microarray experiment coupled with a flexible interactome and multi-pronged interactome tools (which are now made publicly available for microarray analysis and related work suggest the hypothesis that dioxin, best known in fish as a potent cardioteratogen, has many other targets. Many of these types of toxicity have been observed in mammalian species and are potentially caused by alterations to cyp1a.

  14. POINeT: protein interactome with sub-network analysis and hub prioritization

    Directory of Open Access Journals (Sweden)

    Lai Jin-Mei

    2009-04-01

    Full Text Available Abstract Background Protein-protein interactions (PPIs are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal consideration. Moreover, the reliability of available PPI resources, which consist of low- and high-throughput data, for network construction remains a significant challenge. Even though a number of software tools are available to facilitate PPI network analysis, an integrated tool is crucial to alleviate the burden on querying across multiple web servers and software tools. Results We have constructed an integrated web service, POINeT, to simplify the process of PPI searching, analysis, and visualization. POINeT merges PPI and tissue-specific expression data from multiple resources. The tissue-specific PPIs and the numbers of research papers supporting the PPIs can be filtered with user-adjustable threshold values and are dynamically updated in the viewer. The network constructed in POINeT can be readily analyzed with, for example, the built-in centrality calculation module and an integrated network viewer. Nodes in global networks can also be ranked and filtered using various network analysis formulas, i.e., centralities. To prioritize the sub-network, we developed a ranking filtered method (S3 to uncover potential novel mediators in the midbody network. Several examples are provided to illustrate the functionality of POINeT. The network constructed from four schizophrenia risk markers suggests that EXOC4 might be a novel marker for this disease. Finally, a liver-specific PPI network has been filtered with adult and fetal liver expression profiles. Conclusion The functionalities provided by POINeT are highly improved compared to previous version of POINT. POINeT enables the identification and ranking of potential novel genes involved in a sub-network. Combining with tissue-specific gene expression profiles, PPIs specific to

  15. The Binary Protein Interactome of Treponema pallidum – The Syphilis Spirochete

    Science.gov (United States)

    Goll, Johannes; Häuser, Roman; McKevitt, Matthew T.; Palzkill, Timothy; Uetz, Peter

    2008-01-01

    Protein interaction networks shed light on the global organization of proteomes but can also place individual proteins into a functional context. If we know the function of bacterial proteins we will be able to understand how these species have adapted to diverse environments including many extreme habitats. Here we present the protein interaction network for the syphilis spirochete Treponema pallidum which encodes 1,039 proteins, 726 (or 70%) of which interact via 3,649 interactions as revealed by systematic yeast two-hybrid screens. A high-confidence subset of 991 interactions links 576 proteins. To derive further biological insights from our data, we constructed an integrated network of proteins involved in DNA metabolism. Combining our data with additional evidences, we provide improved annotations for at least 18 proteins (including TP0004, TP0050, and TP0183 which are suggested to be involved in DNA metabolism). We estimate that this “minimal” bacterium contains on the order of 3,000 protein interactions. Profiles of functional interconnections indicate that bacterial proteins interact more promiscuously than eukaryotic proteins, reflecting the non-compartmentalized structure of the bacterial cell. Using our high-confidence interactions, we also predict 417,329 homologous interactions (“interologs”) for 372 completely sequenced genomes and provide evidence that at least one third of them can be experimentally confirmed. PMID:18509523

  16. Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology

    Directory of Open Access Journals (Sweden)

    Lin Chieh-Hua

    2006-12-01

    Full Text Available Abstract Background Proteins control and mediate many biological activities of cells by interacting with other protein partners. This work presents a statistical model to predict protein interaction networks of Drosophila melanogaster based on insight into domain interactions. Results Three high-throughput yeast two-hybrid experiments and the collection in FlyBase were used as our starting datasets. The co-occurrences of domains in these interactive events are converted into a probability score of domain-domain interaction. These scores are used to infer putative interaction among all available open reading frames (ORFs of fruit fly. Additionally, the likelihood function is used to estimate all potential protein-protein interactions. All parameters are successfully iterated and MLE is obtained for each pair of domains. Additionally, the maximized likelihood reaches its converged criteria and maintains the probability stable. The hybrid model achieves a high specificity with a loss of sensitivity, suggesting that the model may possess major features of protein-protein interactions. Several putative interactions predicted by the proposed hybrid model are supported by literatures, while experimental data with a low probability score indicate an uncertain reliability and require further proof of interaction. Fly-DPI is the online database used to present this work. It is an integrated proteomics tool with comprehensive protein annotation information from major databases as well as an effective means of predicting protein-protein interactions. As a novel search strategy, the ping-pong search is a naïve path map between two chosen proteins based on pre-computed shortest paths. Adopting effective filtering strategies will facilitate researchers in depicting the bird's eye view of the network of interest. Fly-DPI can be accessed at http://flydpi.nhri.org.tw. Conclusion This work provides two reference systems, statistical and biological, to evaluate

  17. An extracellular interactome of Immunoglobulin and LRR proteins reveals receptor-ligand networks

    Science.gov (United States)

    Özkan, Engin; Carrillo, Robert A.; Eastman, Catharine L.; Weiszmann, Richard; Waghray, Deepa; Johnson, Karl G.; Zinn, Kai; Celniker, Susan E.; Garcia, K. Christopher

    2013-01-01

    Extracellular domains of cell-surface receptors and ligands mediate cell-cell communication, adhesion, and initiation of signaling events, but most existing protein-protein “interactome” datasets lack information for extracellular interactions. We probed interactions between receptor extracellular domains, focusing on the Immunoglobulin Superfamily (IgSF), Fibronectin type-III (FnIII) and Leucine-rich repeat (LRR) families of Drosophila, a set of 202 proteins, many of which are known to be important in neuronal and developmental functions. Out of 20503 candidate protein pairs tested, we observed 106 interactions, 83 of which were previously unknown. We ‘deorphanized’ the 20-member subfamily of defective in proboscis IgSF proteins, showing that they selectively interact with an 11-member subfamily of previously uncharacterized IgSF proteins. Both subfamilies interact with a single common ‘orphan’ LRR protein. We also observed new interactions between Hedgehog and EGFR pathway components. Several of these interactions could be visualized in live-dissected embryos, demonstrating that this approach can identify physiologically relevant receptor-ligand pairs. PMID:23827685

  18. Mitochondrial protein interactome elucidated by chemical cross-linking mass spectrometry.

    Science.gov (United States)

    Schweppe, Devin K; Chavez, Juan D; Lee, Chi Fung; Caudal, Arianne; Kruse, Shane E; Stuppard, Rudy; Marcinek, David J; Shadel, Gerald S; Tian, Rong; Bruce, James E

    2017-02-14

    Mitochondrial protein interactions and complexes facilitate mitochondrial function. These complexes range from simple dimers to the respirasome supercomplex consisting of oxidative phosphorylation complexes I, III, and IV. To improve understanding of mitochondrial function, we used chemical cross-linking mass spectrometry to identify 2,427 cross-linked peptide pairs from 327 mitochondrial proteins in whole, respiring murine mitochondria. In situ interactions were observed in proteins throughout the electron transport chain membrane complexes, ATP synthase, and the mitochondrial contact site and cristae organizing system (MICOS) complex. Cross-linked sites showed excellent agreement with empirical protein structures and delivered complementary constraints for in silico protein docking. These data established direct physical evidence of the assembly of the complex I-III respirasome and enabled prediction of in situ interfacial regions of the complexes. Finally, we established a database and tools to harness the cross-linked interactions we observed as molecular probes, allowing quantification of conformation-dependent protein interfaces and dynamic protein complex assembly.

  19. Conserved salt-bridge competition triggered by phosphorylation regulates the protein interactome

    KAUST Repository

    Skinner, John J.

    2017-12-05

    Phosphorylation is a major regulator of protein interactions; however, the mechanisms by which regulation occurs are not well understood. Here we identify a salt-bridge competition or “theft” mechanism that enables a phospho-triggered swap of protein partners by Raf Kinase Inhibitory Protein (RKIP). RKIP transitions from inhibiting Raf-1 to inhibiting G-protein–coupled receptor kinase 2 upon phosphorylation, thereby bridging MAP kinase and G-Protein–Coupled Receptor signaling. NMR and crystallography indicate that a phosphoserine, but not a phosphomimetic, competes for a lysine from a preexisting salt bridge, initiating a partial unfolding event and promoting new protein interactions. Structural elements underlying the theft occurred early in evolution and are found in 10% of homo-oligomers and 30% of hetero-oligomers including Bax, Troponin C, and Early Endosome Antigen 1. In contrast to a direct recognition of phosphorylated residues by binding partners, the salt-bridge theft mechanism represents a facile strategy for promoting or disrupting protein interactions using solvent-accessible residues, and it can provide additional specificity at protein interfaces through local unfolding or conformational change.

  20. A human phenome-interactome network of protein complexes implicated in genetic disorders

    DEFF Research Database (Denmark)

    Hansen, Kasper Lage; Karlberg, Erik, Olof, Linnart; Størling, Zenia, Marian

    2007-01-01

    the known disease-causing protein as the top candidate, and in 870 intervals with no identified disease-causing gene, provides novel candidates implicated in disorders such as retinitis pigmentosa, epithelial ovarian cancer, inflammatory bowel disease, amyotrophic lateral sclerosis, Alzheimer disease, type...

  1. The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome

    Science.gov (United States)

    Niepel, Mario; Molloy, Kelly R.; Williams, Rosemary; Farr, Julia C.; Meinema, Anne C.; Vecchietti, Nicholas; Cristea, Ileana M.; Chait, Brian T.; Rout, Michael P.; Strambio-De-Castillia, Caterina

    2013-01-01

    The basket of the nuclear pore complex (NPC) is generally depicted as a discrete structure of eight protein filaments that protrude into the nucleoplasm and converge in a ring distal to the NPC. We show that the yeast proteins Mlp1p and Mlp2p are necessary components of the nuclear basket and that they also embed the NPC within a dynamic protein network, whose extended interactome includes the spindle organizer, silencing factors, the proteasome, and key components of messenger ribonucleoproteins (mRNPs). Ultrastructural observations indicate that the basket reduces chromatin crowding around the central transporter of the NPC and might function as a docking site for mRNP during nuclear export. In addition, we show that the Mlps contribute to NPC positioning, nuclear stability, and nuclear envelope morphology. Our results suggest that the Mlps are multifunctional proteins linking the nuclear transport channel to multiple macromolecular complexes involved in the regulation of gene expression and chromatin maintenance. PMID:24152732

  2. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.

    Directory of Open Access Journals (Sweden)

    Raffi Tonikian

    2009-10-01

    Full Text Available SH3 domains are peptide recognition modules that mediate the assembly of diverse biological complexes. We scanned billions of phage-displayed peptides to map the binding specificities of the SH3 domain family in the budding yeast, Saccharomyces cerevisiae. Although most of the SH3 domains fall into the canonical classes I and II, each domain utilizes distinct features of its cognate ligands to achieve binding selectivity. Furthermore, we uncovered several SH3 domains with specificity profiles that clearly deviate from the two canonical classes. In conjunction with phage display, we used yeast two-hybrid and peptide array screening to independently identify SH3 domain binding partners. The results from the three complementary techniques were integrated using a Bayesian algorithm to generate a high-confidence yeast SH3 domain interaction map. The interaction map was enriched for proteins involved in endocytosis, revealing a set of SH3-mediated interactions that underlie formation of protein complexes essential to this biological pathway. We used the SH3 domain interaction network to predict the dynamic localization of several previously uncharacterized endocytic proteins, and our analysis suggests a novel role for the SH3 domains of Lsb3p and Lsb4p as hubs that recruit and assemble several endocytic complexes.

  3. Characterization of protein interactomes of DNA damages: application to oxidation injuries

    International Nuclear Information System (INIS)

    Pietras-Barbier, Ewa

    2013-01-01

    Cyclo-nucleosides are complex DNA damages implying both bases and sugar residues. They are generated by free radicals, in particular by the effect of ionizing radiations, and are not easily covered by cellular mechanisms. Using a protein trapping technique on probes containing these injuries, the negative influence of cyclo-nucleosides on the recognition of its target sequence by a DREF transcription factor and on the interactions of PARP1 with DNA have been identified. Interactions between Fpg bacterial glycosylase and cyclo-nucleosides have been analysed and it has been found that this enzyme has an affinity for them, without excision activity. Finally, a Thermococcus gammatolerans radiation resistant archae has been studied: the formation of simple and complex oxidation injuries at strong radiation doses has been measured and the action mechanism of two new glycosylases has been explained. (author) [fr

  4. Analyzing Protein Dynamics Using Dimensionality Reduction

    OpenAIRE

    Eryol, Atahan

    2015-01-01

    This thesis investigates dimensionality reduction for analyzing the dynamics ofprotein simulations, particularly disordered proteins which do not fold into a xedshape but are thought to perform their functions through their movements. Ratherthan analyze the movement of the proteins in 3D space, we use dimensionalityreduction to project the molecular structure of the proteins into a target space inwhich each structure is represented as a point. All that is needed to do this arethe pairwise dis...

  5. Diffusion of information throughout the host interactome reveals gene expression variations in network proximity to target proteins of hepatitis C virus.

    Directory of Open Access Journals (Sweden)

    Ettore Mosca

    Full Text Available Hepatitis C virus infection is one of the most common and chronic in the world, and hepatitis associated with HCV infection is a major risk factor for the development of cirrhosis and hepatocellular carcinoma (HCC. The rapidly growing number of viral-host and host protein-protein interactions is enabling more and more reliable network-based analyses of viral infection supported by omics data. The study of molecular interaction networks helps to elucidate the mechanistic pathways linking HCV molecular activities and the host response that modulates the stepwise hepatocarcinogenic process from preneoplastic lesions (cirrhosis and dysplasia to HCC. Simulating the impact of HCV-host molecular interactions throughout the host protein-protein interaction (PPI network, we ranked the host proteins in relation to their network proximity to viral targets. We observed that the set of proteins in the neighborhood of HCV targets in the host interactome is enriched in key players of the host response to HCV infection. In opposition to HCV targets, subnetworks of proteins in network proximity to HCV targets are significantly enriched in proteins reported as differentially expressed in preneoplastic and neoplastic liver samples by two independent studies. Using multi-objective optimization, we extracted subnetworks that are simultaneously "guilt-by-association" with HCV proteins and enriched in proteins differentially expressed. These subnetworks contain established, recently proposed and novel candidate proteins for the regulation of the mechanisms of liver cells response to chronic HCV infection.

  6. Information flow analysis of interactome networks.

    Directory of Open Access Journals (Sweden)

    Patrycja Vasilyev Missiuro

    2009-04-01

    Full Text Available Recent studies of cellular networks have revealed modular organizations of genes and proteins. For example, in interactome networks, a module refers to a group of interacting proteins that form molecular complexes and/or biochemical pathways and together mediate a biological process. However, it is still poorly understood how biological information is transmitted between different modules. We have developed information flow analysis, a new computational approach that identifies proteins central to the transmission of biological information throughout the network. In the information flow analysis, we represent an interactome network as an electrical circuit, where interactions are modeled as resistors and proteins as interconnecting junctions. Construing the propagation of biological signals as flow of electrical current, our method calculates an information flow score for every protein. Unlike previous metrics of network centrality such as degree or betweenness that only consider topological features, our approach incorporates confidence scores of protein-protein interactions and automatically considers all possible paths in a network when evaluating the importance of each protein. We apply our method to the interactome networks of Saccharomyces cerevisiae and Caenorhabditis elegans. We find that the likelihood of observing lethality and pleiotropy when a protein is eliminated is positively correlated with the protein's information flow score. Even among proteins of low degree or low betweenness, high information scores serve as a strong predictor of loss-of-function lethality or pleiotropy. The correlation between information flow scores and phenotypes supports our hypothesis that the proteins of high information flow reside in central positions in interactome networks. We also show that the ranks of information flow scores are more consistent than that of betweenness when a large amount of noisy data is added to an interactome. Finally, we

  7. PSAIA – Protein Structure and Interaction Analyzer

    Directory of Open Access Journals (Sweden)

    Vlahoviček Kristian

    2008-04-01

    Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

  8. 3D structure prediction of histone acetyltransferase (HAC proteins of the p300/CBP family and their interactome in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Amar Cemanovic

    2014-09-01

    Full Text Available Histone acetylation is an important posttranslational modification correlated with gene activation. In Arabidopsis thaliana the histone acetyltransferase (HAC proteins of the CBP family are homologous to animal p300/CREB (cAMP-responsive element-binding proteins, which are important histone acetyltransferases participating in many physiological processes, including proliferation, differentiation, and apoptosis. In this study the 3-D structure of all HAC protein subunits in Arabidopsis thaliana: HAC1, HAC2, HAC4, HAC5 and HAC12 is predicted by homology modeling and confirmed by Ramachandran plot analysis. The amino acid sequences HAC family members are highly similar to the sequences of the homologous human p300/CREB protein. Conservation of p300/CBP domains among the HAC proteins was examined further by sequence alignment and pattern search. The domains of p300/CBP required for the HAC function, such as PHD, TAZ and ZZ domains, are conserved in all HAC proteins. Interactome analysis revealed that HAC1, HAC5 and HAC12 proteins interact with S-adenosylmethionine-dependent methyltransferase domaincontaining protein that shows methyltransferase activity, suggesting an additional function of the HAC proteins. Additionally, HAC5 has a strong interaction value for the putative c-myb-like transcription factor MYB3R-4, which suggests that it also may have a function in regulation of DNA replication.

  9. Interactome analysis reveals ZNF804A, a schizophrenia risk gene, as a novel component of protein translational machinery critical for embryonic neurodevelopment.

    Science.gov (United States)

    Zhou, Y; Dong, F; Lanz, T A; Reinhart, V; Li, M; Liu, L; Zou, J; Xi, H S; Mao, Y

    2018-04-01

    Recent genome-wide association studies identified over 100 genetic loci that significantly associate with schizophrenia (SZ). A top candidate gene, ZNF804A, was robustly replicated in different populations. However, its neural functions are largely unknown. Here we show in mouse that ZFP804A, the homolog of ZNF804A, is required for normal progenitor proliferation and neuronal migration. Using a yeast two-hybrid genome-wide screen, we identified novel interacting proteins of ZNF804A. Rather than transcriptional factors, genes involved in mRNA translation are highly represented in our interactome result. ZNF804A co-fractionates with translational machinery and modulates the translational efficiency as well as the mTOR pathway. The ribosomal protein RPSA interacts with ZNF804A and rescues the migration and translational defects caused by ZNF804A knockdown. RNA immunoprecipitation-RNAseq (RIP-Seq) identified transcripts bound to ZFP804A. Consistently, ZFP804A associates with many short transcripts involved in translational and mitochondrial regulation. Moreover, among the transcripts associated with ZFP804A, a SZ risk gene, neurogranin (NRGN), is one of ZFP804A targets. Interestingly, downregulation of ZFP804A decreases NRGN expression and overexpression of NRGN can ameliorate ZFP804A-mediated migration defect. To verify the downstream targets of ZNF804A, a Duolink in situ interaction assay confirmed genes from our RIP-Seq data as the ZNF804A targets. Thus, our work uncovered a novel mechanistic link of a SZ risk gene to neurodevelopment and translational control. The interactome-driven approach here is an effective way for translating genome-wide association findings into novel biological insights of human diseases.

  10. The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti

    Directory of Open Access Journals (Sweden)

    Rodriguez-Llorente Ignacio

    2009-06-01

    Full Text Available Abstract Background Rhizobium-Legume symbiosis is an attractive biological process that has been studied for decades because of its importance in agriculture. However, this system has undergone extensive study and although many of the major factors underpinning the process have been discovered using traditional methods, much remains to be discovered. Results Here we present an analysis of the 'Symbiosis Interactome' using novel computational methods in order to address the complex dynamic interactions between proteins involved in the symbiosis of the model bacteria Sinorhizobium meliloti with its plant hosts. Our study constitutes the first large-scale analysis attempting to reconstruct this complex biological process, and to identify novel proteins involved in establishing symbiosis. We identified 263 novel proteins potentially associated with the Symbiosis Interactome. The topology of the Symbiosis Interactome was used to guide experimental techniques attempting to validate novel proteins involved in different stages of symbiosis. The contribution of a set of novel proteins was tested analyzing the symbiotic properties of several S. meliloti mutants. We found mutants with altered symbiotic phenotypes suggesting novel proteins that provide key complementary roles for symbiosis. Conclusion Our 'systems-based model' represents a novel framework for studying host-microbe interactions, provides a theoretical basis for further experimental validations, and can also be applied to the study of other complex processes such as diseases.

  11. Data set of interactomes and metabolic pathways of proteins differentially expressed in brains with Alzheimer׳s disease

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    Benito Minjarez

    2016-06-01

    Full Text Available Alzheimer׳s disease is one of the main causes of dementia in the elderly and its frequency is on the rise worldwide. It is considered the result of complex interactions between genetic and environmental factors, being many of them unknown. Therefore, there is a dire necessity for the identification of novel molecular players for the understanding of this disease. In this data article we determined the protein expression profiles of whole protein extracts from cortex regions of brains from patients with Alzheimer׳s disease in comparison to a normal brain. We identified 721 iTRAQ-labeled polypeptides with more than 95% in confidence. We analyzed all proteins that changed in their expression level and located them in the KEGG metabolic pathways, as well as in the mitochondrial complexes of the electron transport chain and ATP synthase. In addition, we analyzed the over- and sub-expressed polypeptides through IPA software, specifically Core I and Biomarkers I modules. Data in this article is related to the research article “Identification of proteins that are differentially expressed in brains with Alzheimer’s disease using iTRAQ labeling and tandem mass spectrometry” (Minjarez et al., 2016 [1].

  12. "Fuzziness" in the celular interactome: a historical perspective.

    Science.gov (United States)

    Welch, G Rickey

    2012-01-01

    Some historical background is given for appreciating the impact of the empirical construct known as the cellular protein-protein interactome, which is a seemingly de novo entity that has arisen of late within the context of postgenomic systems biology. The approach here builds on a generalized principle of "fuzziness" in protein behavior, proposed by Tompa and Fuxreiter.(1) Recent controversies in the analysis and interpretation of the interactome studies are rationalized historically under the auspices of this concept. There is an extensive literature on protein-protein interactions, dating to the mid-1900s, which may help clarify the "fuzziness" in the interactome picture and, also, provide a basis for understanding the physiological importance of protein-protein interactions in vivo.

  13. The Topology of the Growing Human Interactome Data

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    Janjić Vuk

    2014-06-01

    Full Text Available We have long moved past the one-gene-one-function concept originally proposed by Beadle and Tatum back in 1941; but the full understanding of genotype-phenotype relations still largely relies on the analysis of static, snapshot-like, interaction data sets. Here, we look at what global patterns can be uncovered if we simply trace back the human interactome network over the last decade of protein-protein interaction (PPI screening. We take a purely topological approach and find that as the human interactome is getting denser, it is not only gaining in structure (in terms of now being better fit by structured network models than before, but also there are patterns in the way in which it is growing: (a newly added proteins tend to get linked to existing proteins in the interactome that are not know to interact; and (b new proteins tend to link to already well connected proteins. Moreover, the alignment between human and yeast interactomes spanning over 40% of yeast’s proteins - that are involved in regulation of transcription, RNA splicing and other cellcycle- related processes-suggests the existence of a part of the interactome which remains topologically and functionally unaffected through evolution. Furthermore, we find a small sub-network, specific to the “core” of the human interactome and involved in regulation of transcription and cancer development, whose wiring has not changed within the human interactome over the last 10 years of interacome data acquisition. Finally, we introduce a generalisation of the clustering coefficient of a network as a new measure called the cycle coefficient, and use it to show that PPI networks of human and model organisms are wired in a tight way which forbids the occurrence large cycles.

  14. sCLIP-an integrated platform to study RNA-protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs.

    Science.gov (United States)

    Kargapolova, Yulia; Levin, Michal; Lackner, Karl; Danckwardt, Sven

    2017-06-02

    RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing. sCLIP exploits linear amplification of the immunoprecipitated RNA improving the complexity of the sequencing-library despite significantly reducing the amount of input material and omitting several purification steps. Additionally, it permits a radiolabel-free visualization of immunoprecipitated RNA. In a proof of concept, we identify that CSTF2tau binds many previously not recognized RNAs including histone, snoRNA and snRNAs. CSTF2tau-binding is associated with internal oligoadenylation resulting in shortened snRNA isoforms subjected to rapid degradation. We provide evidence for a new mechanism whereby CSTF2tau controls the abundance of snRNAs resulting in alternative splicing of several RNAs including ANK2 with critical roles in tumorigenesis and cardiac function. Combined with a bioinformatic pipeline sCLIP thus uncovers new functions for established RBPs and fosters the illumination of RBP-protein interaction landscapes in health and disease. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Interactome Screening Identifies the ER Luminal Chaperone Hsp47 as a Regulator of the Unfolded Protein Response Transducer IRE1α.

    Science.gov (United States)

    Sepulveda, Denisse; Rojas-Rivera, Diego; Rodríguez, Diego A; Groenendyk, Jody; Köhler, Andres; Lebeaupin, Cynthia; Ito, Shinya; Urra, Hery; Carreras-Sureda, Amado; Hazari, Younis; Vasseur-Cognet, Mireille; Ali, Maruf M U; Chevet, Eric; Campos, Gisela; Godoy, Patricio; Vaisar, Tomas; Bailly-Maitre, Béatrice; Nagata, Kazuhiro; Michalak, Marek; Sierralta, Jimena; Hetz, Claudio

    2018-01-18

    Maintenance of endoplasmic reticulum (ER) proteostasis is controlled by a dynamic signaling network known as the unfolded protein response (UPR). IRE1α is a major UPR transducer, determining cell fate under ER stress. We used an interactome screening to unveil several regulators of the UPR, highlighting the ER chaperone Hsp47 as the major hit. Cellular and biochemical analysis indicated that Hsp47 instigates IRE1α signaling through a physical interaction. Hsp47 directly binds to the ER luminal domain of IRE1α with high affinity, displacing the negative regulator BiP from the complex to facilitate IRE1α oligomerization. The regulation of IRE1α signaling by Hsp47 is evolutionarily conserved as validated using fly and mouse models of ER stress. Hsp47 deficiency sensitized cells and animals to experimental ER stress, revealing the significance of Hsp47 to global proteostasis maintenance. We conclude that Hsp47 adjusts IRE1α signaling by fine-tuning the threshold to engage an adaptive UPR. Copyright © 2018 Elsevier Inc. All rights reserved.

  16. Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

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    Kirouac Daniel C

    2012-05-01

    Full Text Available Abstract Background Understanding the information-processing capabilities of signal transduction networks, how those networks are disrupted in disease, and rationally designing therapies to manipulate diseased states require systematic and accurate reconstruction of network topology. Data on networks central to human physiology, such as the inflammatory signalling networks analyzed here, are found in a multiplicity of on-line resources of pathway and interactome databases (Cancer CellMap, GeneGo, KEGG, NCI-Pathway Interactome Database (NCI-PID, PANTHER, Reactome, I2D, and STRING. We sought to determine whether these databases contain overlapping information and whether they can be used to construct high reliability prior knowledge networks for subsequent modeling of experimental data. Results We have assembled an ensemble network from multiple on-line sources representing a significant portion of all machine-readable and reconcilable human knowledge on proteins and protein interactions involved in inflammation. This ensemble network has many features expected of complex signalling networks assembled from high-throughput data: a power law distribution of both node degree and edge annotations, and topological features of a “bow tie” architecture in which diverse pathways converge on a highly conserved set of enzymatic cascades focused around PI3K/AKT, MAPK/ERK, JAK/STAT, NFκB, and apoptotic signaling. Individual pathways exhibit “fuzzy” modularity that is statistically significant but still involving a majority of “cross-talk” interactions. However, we find that the most widely used pathway databases are highly inconsistent with respect to the actual constituents and interactions in this network. Using a set of growth factor signalling networks as examples (epidermal growth factor, transforming growth factor-beta, tumor necrosis factor, and wingless, we find a multiplicity of network topologies in which receptors couple to downstream

  17. A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).

    Science.gov (United States)

    Stacey, R Greg; Skinnider, Michael A; Scott, Nichollas E; Foster, Leonard J

    2017-10-23

    -to-use data analysis pipeline that predicts interactomes and protein complexes from co-elution data. PrInCE allows researchers without bioinformatics expertise to analyze high-throughput co-elution datasets.

  18. Uncovering Arabidopsis membrane protein interactome enriched in transporters using mating-based split ubiquitin assays and classification models

    Directory of Open Access Journals (Sweden)

    Jin eChen

    2012-06-01

    Full Text Available High-throughput data are a double-edged sword; for the benefit of large amount of data, there is an associated cost of noise. To increase reliability and scalability of high-throughput protein interaction data generation, we tested the efficacy of classification to enrich potential protein-protein interactions (pPPIs. We applied this method to identify interactions among Arabidopsis membrane proteins enriched in transporters. We validated our method with multiple retests. Classification improved the quality of the ensuing interaction network and was effective in reducing the search space and increasing true positive rate. The final network of 541 interactions among 239 proteins (of which 179 are transporters is the first protein interaction network enriched in membrane transporters reported for any organism. This network has similar topological attributes to other published protein interaction networks. It also extends and fills gaps in currently available biological networks in plants and allows building a number of hypotheses about processes and mechanisms involving signal-transduction and transport systems.

  19. Proteomic Profiling and the Predicted Interactome of Host Proteins in Compatible and Incompatible Interactions Between Soybean and Fusarium virguliforme.

    Science.gov (United States)

    Iqbal, M Javed; Majeed, Maryam; Humayun, Maheen; Lightfoot, David A; Afzal, Ahmed J

    2016-12-01

    Sudden death syndrome (SDS) is a complex of two diseases of soybean (Glycine max), caused by the soil borne pathogenic fungus Fusarium virguliforme. The root rot and leaf scorch diseases both result in significant yield losses worldwide. Partial SDS resistance has been demonstrated in multiple soybean cultivars. This study aimed to highlight proteomic changes in soybean roots by identifying proteins which are differentially expressed in near isogenic lines (NILs) contrasting at the Rhg1/Rfs2 locus for partial resistance or susceptibility to SDS. Two-dimensional gel electrophoresis resolved approximately 1000 spots on each gel; 12 spots with a significant (P disease resistance, stress tolerance, and metabolism. This is the first report which identifies proteins whose abundances are altered in response to fungal infection leading to SDS. The results provide valuable information about SDS resistance in soybean plants, and plant partial resistance responses in general. More importantly, several of the identified proteins could be good candidates for the development of SDS-resistant soybean plants.

  20. PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes

    Directory of Open Access Journals (Sweden)

    Gopal Balasubramanian

    2010-09-01

    Full Text Available Abstract Background Signal transduction events often involve transient, yet specific, interactions between structurally conserved protein domains and polypeptide sequences in target proteins. The identification and validation of these associating domains is crucial to understand signal transduction pathways that modulate different cellular or developmental processes. Bioinformatics strategies to extract and integrate information from diverse sources have been shown to facilitate the experimental design to understand complex biological events. These methods, primarily based on information from high-throughput experiments, have also led to the identification of new connections thus providing hypothetical models for cellular events. Such models, in turn, provide a framework for directing experimental efforts for validating the predicted molecular rationale for complex cellular processes. In this context, it is envisaged that the rational design of peptides for protein-peptide binding studies could substantially facilitate the experimental strategies to evaluate a predicted interaction. This rational design procedure involves the integration of protein-protein interaction data, gene ontology, physico-chemical calculations, domain-domain interaction data and information on functional sites or critical residues. Results Here we describe an integrated approach called "PeptideMine" for the identification of peptides based on specific functional patterns present in the sequence of an interacting protein. This approach based on sequence searches in the interacting sequence space has been developed into a webserver, which can be used for the identification and analysis of peptides, peptide homologues or functional patterns from the interacting sequence space of a protein. To further facilitate experimental validation, the PeptideMine webserver also provides a list of physico-chemical parameters corresponding to the peptide to determine the feasibility of

  1. IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools.

    Science.gov (United States)

    Carazzolle, Marcelo Falsarella; de Carvalho, Lucas Miguel; Slepicka, Hugo Henrique; Vidal, Ramon Oliveira; Pereira, Gonçalo Amarante Guimarães; Kobarg, Jörg; Meirelles, Gabriela Vaz

    2014-01-01

    High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two

  2. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions*

    Science.gov (United States)

    Shatsky, Maxim; Dong, Ming; Liu, Haichuan; Yang, Lee Lisheng; Choi, Megan; Singer, Mary E.; Geller, Jil T.; Fisher, Susan J.; Hall, Steven C.; Hazen, Terry C.; Brenner, Steven E.; Butland, Gareth; Jin, Jian; Witkowska, H. Ewa; Chandonia, John-Marc; Biggin, Mark D.

    2016-01-01

    Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification of endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR. PMID:27099342

  3. Cell Interactomics and Carcinogenetic Mechanisms

    CERN Document Server

    Baianu, IC; Report to the Institute of Genomics

    2004-01-01

    Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quant...

  4. A critical and Integrated View of the Yeast Interactome

    Directory of Open Access Journals (Sweden)

    Stephen G. Oliver

    2006-04-01

    Full Text Available Global studies of protein–protein interactions are crucial to both elucidating gene function and producing an integrated view of the workings of living cells. High-throughput studies of the yeast interactome have been performed using both genetic and biochemical screens. Despite their size, the overlap between these experimental datasets is very limited. This could be due to each approach sampling only a small fraction of the total interactome. Alternatively, a large proportion of the data from these screens may represent false-positive interactions. We have used the Genome Information Management System (GIMS to integrate interactome datasets with transcriptome and protein annotation data and have found significant evidence that the proportion of false-positive results is high. Not all high-throughput datasets are similarly contaminated, and the tandem affinity purification (TAP approach appears to yield a high proportion of reliable interactions for which corroborating evidence is available. From our integrative analyses, we have generated a set of verified interactome data for yeast.

  5. Functional interactome of Aquaporin 1 sub-family reveals new physiological functions in Arabidopsis Thaliana

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    Mohamed Ragab Abdel Gawwad

    2013-09-01

    Full Text Available Aquaporins are channel proteins found in plasma membranes and intercellular membranes of different cellular compartments, facilitate the water flux, solutes and gases across the cellular plasma membranes. The present study highlights the sub-family plasma membrane intrinsic protein (PIP predicting the 3-D structure and analyzing the functional interactome of it homologs. PIP1 homologs integrate with many proteins with different plant physiological roles in Arabidopsis thaliana including; PIP1A and PIP1B: facilitate the transport of water, diffusion of amino acids and/or peptides from the vacuolar compartment to the cytoplasm, play a role in the control of cell turgor and cell expansion and involved in root water uptake respectively. In addition we found that PIP1B plays a defensive role against Pseudomonas syringae infection through the interaction with the plasma membrane Rps2 protein. Another substantial function of PIP1C via the interaction with PIP2E is the response to nematode infection. Generally, PIP1 sub-family interactome controlling many physiological processes in plant cell like; osmoregulation in plants under high osmotic stress such as under a high salt, response to nematode, facilitate the transport of water across cell membrane and regulation of floral initiation in Arabidopsis thaliana.

  6. A Map of the Arenavirus Nucleoprotein-Host Protein Interactome Reveals that Junín Virus Selectively Impairs the Antiviral Activity of Double-Stranded RNA-Activated Protein Kinase (PKR).

    Science.gov (United States)

    King, Benjamin R; Hershkowitz, Dylan; Eisenhauer, Philip L; Weir, Marion E; Ziegler, Christopher M; Russo, Joanne; Bruce, Emily A; Ballif, Bryan A; Botten, Jason

    2017-08-01

    on an increased basic understanding of these viruses and, in particular, their interactions with the host cell machinery. Identifying host proteins critical for the viral life cycle and/or pathogenesis represents a useful strategy to uncover new drug targets. This study reveals, for the first time, the extensive human protein interactome of arenavirus nucleoproteins and uncovers a potent antiviral host protein that is neutralized during Junín virus infection. In so doing, it shows further insight into the interplay between the virus and the host innate immune response and provides an important data set for the field. Copyright © 2017 American Society for Microbiology.

  7. PMD: A Resource for Archiving and Analyzing Protein Microarray data.

    Science.gov (United States)

    Xu, Zhaowei; Huang, Likun; Zhang, Hainan; Li, Yang; Guo, Shujuan; Wang, Nan; Wang, Shi-Hua; Chen, Ziqing; Wang, Jingfang; Tao, Sheng-Ce

    2016-01-27

    Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn.

  8. From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization.

    Directory of Open Access Journals (Sweden)

    Jimin Song

    Full Text Available Numerous studies have suggested that hub proteins in the S. cerevisiae physical interaction network are more likely to be essential than other proteins. The proposed reasons underlying this observed relationship between topology and functioning have been subject to some controversy, with recent work suggesting that it arises due to the participation of hub proteins in essential complexes and processes. However, do these essential modules themselves have distinct network characteristics, and how do their essential proteins differ in their topological properties from their non-essential proteins? We aimed to advance our understanding of protein essentiality by analyzing proteins, complexes and processes within their broader functional context and by considering physical interactions both within and across complexes and biological processes. In agreement with the view that essentiality is a modular property, we found that the number of intracomplex or intraprocess interactions that a protein has is a better indicator of its essentiality than its overall number of interactions. Moreover, we found that within an essential complex, its essential proteins have on average more interactions, especially intracomplex interactions, than its non-essential proteins. Finally, we built a module-level interaction network and found that essential complexes and processes tend to have higher interaction degrees in this network than non-essential complexes and processes; that is, they exhibit a larger amount of functional cross-talk than their non-essential counterparts.

  9. Organization of physical interactomes as uncovered by network schemas.

    Science.gov (United States)

    Banks, Eric; Nabieva, Elena; Chazelle, Bernard; Singh, Mona

    2008-10-01

    Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning. We introduce network schemas to elucidate shared mechanisms within interactomes. Network schemas specify descriptions of proteins and the topology of interactions among them. We develop algorithms for systematically uncovering recurring, over-represented schemas in physical interaction networks. We apply our methods to the S. cerevisiae interactome, focusing on schemas consisting of proteins described via sequence motifs and molecular function annotations and interacting with one another in one of four basic network topologies. We identify hundreds of recurring and over-represented network schemas of various complexity, and demonstrate via graph-theoretic representations how more complex schemas are organized in terms of their lower-order constituents. The uncovered schemas span a wide range of cellular activities, with many signaling and transport related higher-order schemas. We establish the functional importance of the schemas by showing that they correspond to functionally cohesive sets of proteins, are enriched in the frequency with which they have instances in the H. sapiens interactome, and are useful for predicting protein function. Our findings suggest that network schemas are a powerful paradigm for organizing, interrogating, and annotating cellular networks.

  10. The human interactome knowledge base (hint-kb): An integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique

    KAUST Repository

    Theofilatos, Konstantinos A.

    2013-07-12

    Proteins are the functional components of many cellular processes and the identification of their physical protein–protein interactions (PPIs) is an area of mature academic research. Various databases have been developed containing information about experimentally and computationally detected human PPIs as well as their corresponding annotation data. However, these databases contain many false positive interactions, are partial and only a few of them incorporate data from various sources. To overcome these limitations, we have developed HINT-KB (http://biotools.ceid.upatras.gr/hint-kb/), a knowledge base that integrates data from various sources, provides a user-friendly interface for their retrieval, cal-culatesasetoffeaturesofinterest and computesaconfidence score for every candidate protein interaction. This confidence score is essential for filtering the false positive interactions which are present in existing databases, predicting new protein interactions and measuring the frequency of each true protein interaction. For this reason, a novel machine learning hybrid methodology, called (Evolutionary Kalman Mathematical Modelling—EvoKalMaModel), was used to achieve an accurate and interpretable scoring methodology. The experimental results indicated that the proposed scoring scheme outperforms existing computational methods for the prediction of PPIs.

  11. Intrinsic disorder in the BK channel and its interactome.

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    Zhenling Peng

    Full Text Available The large-conductance Ca2+-activated K+ (BK channel is broadly expressed in various mammalian cells and tissues such as neurons, skeletal and smooth muscles, exocrine cells, and sensory cells of the inner ear. Previous studies suggest that BK channels are promiscuous binders involved in a multitude of protein-protein interactions. To gain a better understanding of the potential mechanisms underlying BK interactions, we analyzed the abundance, distribution, and potential mechanisms of intrinsic disorder in 27 BK channel variants from mouse cochlea, 104 previously reported BK-associated proteins (BKAPS from cytoplasmic and membrane/cytoskeletal regions, plus BK β- and γ-subunits. Disorder was evaluated using the MFDp algorithm, which is a consensus-based predictor that provides a strong and competitive predictive quality and PONDR, which can determine long intrinsically disordered regions (IDRs. Disorder-based binding sites or molecular recognition features (MoRFs were found using MoRFpred and ANCHOR. BKAP functions were categorized based on Gene Ontology (GO terms. The analyses revealed that the BK variants contain a number of IDRs. Intrinsic disorder is also common in BKAPs, of which ∼ 5% are completely disordered. However, intrinsic disorder is very differently distributed within BK and its partners. Approximately 65% of the disordered segments in BK channels are long (IDRs (>50 residues, whereas >60% of the disordered segments in BKAPs are short IDRs that range in length from 4 to 30 residues. Both α and γ subunits showed various amounts of disorder as did hub proteins of the BK interactome. Our analyses suggest that intrinsic disorder is important for the function of BK and its BKAPs. Long IDRs in BK are engaged in protein-protein and protein-ligand interactions, contain multiple post-translational modification sites, and are subjected to alternative splicing. The disordered structure of BK and its BKAPs suggests one of the underlying

  12. Dissecting and analyzing key residues in protein-DNA complexes.

    Science.gov (United States)

    Kulandaisamy, A; Srivastava, Ambuj; Nagarajan, R; Gromiha, M Michael

    2018-04-01

    Protein-DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein-DNA complexes, the integrative study of binding and stabilizing residues is important. In the present study, we have identified key residues that play a dual role in both binding and stability from a nonredundant dataset of 319 protein-DNA complexes. We observed that key residues are identified in very less number of complexes (29%) and only about 4% of stabilizing/binding residues are identified as key residues. Specifically, stabilizing residues have higher preference to be key residues than binding residues. These key residues include polar, nonpolar, aliphatic, aromatic, and charged amino acids. Moreover, we have analyzed and discussed the key residues in different protein-DNA complexes, which are classified based on protein structural class, function, DNA strand, and their conformations. Especially, Ser, Thr, Tyr, Arg, and Lys residues are commonly found in most of the subclasses of protein-DNA complexes. Further, we analyzed atomic contacts, which show that polar-nonpolar is more enriched than other types of contacts. In addition, the charged contacts are highly preferred in protein-DNA complexes compared with protein-protein and protein-RNA complexes. Finally, we have discussed the sequence and structural features of key residues such as conservation score, surrounding hydrophobicity, solvent accessibility, secondary structure, and long-range order. This study will be helpful to understand the recognition mechanism and structural and functional aspects of protein-DNA complexes. Copyright © 2017 John Wiley & Sons, Ltd.

  13. Mapping the Small Molecule Interactome by Mass Spectrometry.

    Science.gov (United States)

    Flaxman, Hope A; Woo, Christina M

    2018-01-16

    Mapping small molecule interactions throughout the proteome provides the critical structural basis for functional analysis of their impact on biochemistry. However, translation of mass spectrometry-based proteomics methods to directly profile the interaction between a small molecule and the whole proteome is challenging because of the substoichiometric nature of many interactions, the diversity of covalent and noncovalent interactions involved, and the subsequent computational complexity associated with their spectral assignment. Recent advances in chemical proteomics have begun fill this gap to provide a structural basis for the breadth of small molecule-protein interactions in the whole proteome. Innovations enabling direct characterization of the small molecule interactome include faster, more sensitive instrumentation coupled to chemical conjugation, enrichment, and labeling methods that facilitate detection and assignment. These methods have started to measure molecular interaction hotspots due to inherent differences in local amino acid reactivity and binding affinity throughout the proteome. Measurement of the small molecule interactome is producing structural insights and methods for probing and engineering protein biochemistry. Direct structural characterization of the small molecule interactome is a rapidly emerging area pushing new frontiers in biochemistry at the interface of small molecules and the proteome.

  14. A DIseAse MOdule Detection (DIAMOnD algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome.

    Directory of Open Access Journals (Sweden)

    Susan Dina Ghiassian

    2015-04-01

    Full Text Available The observation that disease associated proteins often interact with each other has fueled the development of network-based approaches to elucidate the molecular mechanisms of human disease. Such approaches build on the assumption that protein interaction networks can be viewed as maps in which diseases can be identified with localized perturbation within a certain neighborhood. The identification of these neighborhoods, or disease modules, is therefore a prerequisite of a detailed investigation of a particular pathophenotype. While numerous heuristic methods exist that successfully pinpoint disease associated modules, the basic underlying connectivity patterns remain largely unexplored. In this work we aim to fill this gap by analyzing the network properties of a comprehensive corpus of 70 complex diseases. We find that disease associated proteins do not reside within locally dense communities and instead identify connectivity significance as the most predictive quantity. This quantity inspires the design of a novel Disease Module Detection (DIAMOnD algorithm to identify the full disease module around a set of known disease proteins. We study the performance of the algorithm using well-controlled synthetic data and systematically validate the identified neighborhoods for a large corpus of diseases.

  15. Defining a modular signalling network from the fly interactome.

    Science.gov (United States)

    Baudot, Anaïs; Angelelli, Jean-Baptiste; Guénoche, Alain; Jacq, Bernard; Brun, Christine

    2008-05-19

    Signalling pathways relay information by transmitting signals from cell surface receptors to intracellular effectors that eventually activate the transcription of target genes. Since signalling pathways involve several types of molecular interactions including protein-protein interactions, we postulated that investigating their organization in the context of the global protein-protein interaction network could provide a new integrated view of signalling mechanisms. Using a graph-theory based method to analyse the fly protein-protein interaction network, we found that each signalling pathway is organized in two to three different signalling modules. These modules contain canonical proteins of the signalling pathways, known regulators as well as other proteins thereby predicted to participate to the signalling mechanisms. Connections between the signalling modules are prominent as compared to the other network's modules and interactions within and between signalling modules are among the more central routes of the interaction network. Altogether, these modules form an interactome sub-network devoted to signalling with particular topological properties: modularity, density and centrality. This finding reflects the integration of the signalling system into cell functioning and its important role connecting and coordinating different biological processes at the level of the interactome.

  16. Defining a Modular Signalling Network from the Fly Interactome

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    Jacq Bernard

    2008-05-01

    Full Text Available Abstract Background Signalling pathways relay information by transmitting signals from cell surface receptors to intracellular effectors that eventually activate the transcription of target genes. Since signalling pathways involve several types of molecular interactions including protein-protein interactions, we postulated that investigating their organization in the context of the global protein-protein interaction network could provide a new integrated view of signalling mechanisms. Results Using a graph-theory based method to analyse the fly protein-protein interaction network, we found that each signalling pathway is organized in two to three different signalling modules. These modules contain canonical proteins of the signalling pathways, known regulators as well as other proteins thereby predicted to participate to the signalling mechanisms. Connections between the signalling modules are prominent as compared to the other network's modules and interactions within and between signalling modules are among the more central routes of the interaction network. Conclusion Altogether, these modules form an interactome sub-network devoted to signalling with particular topological properties: modularity, density and centrality. This finding reflects the integration of the signalling system into cell functioning and its important role connecting and coordinating different biological processes at the level of the interactome.

  17. Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell

    Directory of Open Access Journals (Sweden)

    Marín Ignacio

    2009-07-01

    Full Text Available Abstract Background The characterization of the global functional structure of a cell is a major goal in bioinformatics and systems biology. Gene Ontology (GO and the protein-protein interaction network offer alternative views of that structure. Results This study presents a comparison of the global structures of the Gene Ontology and the interactome of Saccharomyces cerevisiae. Sensitive, unsupervised methods of clustering applied to a large fraction of the proteome led to establish a GO-interactome correlation value of +0.47 for a general dataset that contains both high and low-confidence interactions and +0.58 for a smaller, high-confidence dataset. Conclusion The structures of the yeast cell deduced from GO and interactome are substantially congruent. However, some significant differences were also detected, which may contribute to a better understanding of cell function and also to a refinement of the current ontologies.

  18. Identification of Human Disease Genes from Interactome Network Using Graphlet Interaction

    Science.gov (United States)

    Yang, Lun; Wei, Dong-Qing; Qi, Ying-Xin; Jiang, Zong-Lai

    2014-01-01

    Identifying genes related to human diseases, such as cancer and cardiovascular disease, etc., is an important task in biomedical research because of its applications in disease diagnosis and treatment. Interactome networks, especially protein-protein interaction networks, had been used to disease genes identification based on the hypothesis that strong candidate genes tend to closely relate to each other in some kinds of measure on the network. We proposed a new measure to analyze the relationship between network nodes which was called graphlet interaction. The graphlet interaction contained 28 different isomers. The results showed that the numbers of the graphlet interaction isomers between disease genes in interactome networks were significantly larger than random picked genes, while graphlet signatures were not. Then, we designed a new type of score, based on the network properties, to identify disease genes using graphlet interaction. The genes with higher scores were more likely to be disease genes, and all candidate genes were ranked according to their scores. Then the approach was evaluated by leave-one-out cross-validation. The precision of the current approach achieved 90% at about 10% recall, which was apparently higher than the previous three predominant algorithms, random walk, Endeavour and neighborhood based method. Finally, the approach was applied to predict new disease genes related to 4 common diseases, most of which were identified by other independent experimental researches. In conclusion, we demonstrate that the graphlet interaction is an effective tool to analyze the network properties of disease genes, and the scores calculated by graphlet interaction is more precise in identifying disease genes. PMID:24465923

  19. Identification of human disease genes from interactome network using graphlet interaction.

    Directory of Open Access Journals (Sweden)

    Xiao-Dong Wang

    Full Text Available Identifying genes related to human diseases, such as cancer and cardiovascular disease, etc., is an important task in biomedical research because of its applications in disease diagnosis and treatment. Interactome networks, especially protein-protein interaction networks, had been used to disease genes identification based on the hypothesis that strong candidate genes tend to closely relate to each other in some kinds of measure on the network. We proposed a new measure to analyze the relationship between network nodes which was called graphlet interaction. The graphlet interaction contained 28 different isomers. The results showed that the numbers of the graphlet interaction isomers between disease genes in interactome networks were significantly larger than random picked genes, while graphlet signatures were not. Then, we designed a new type of score, based on the network properties, to identify disease genes using graphlet interaction. The genes with higher scores were more likely to be disease genes, and all candidate genes were ranked according to their scores. Then the approach was evaluated by leave-one-out cross-validation. The precision of the current approach achieved 90% at about 10% recall, which was apparently higher than the previous three predominant algorithms, random walk, Endeavour and neighborhood based method. Finally, the approach was applied to predict new disease genes related to 4 common diseases, most of which were identified by other independent experimental researches. In conclusion, we demonstrate that the graphlet interaction is an effective tool to analyze the network properties of disease genes, and the scores calculated by graphlet interaction is more precise in identifying disease genes.

  20. The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication.

    Science.gov (United States)

    de Chassey, Benoît; Aublin-Gex, Anne; Ruggieri, Alessia; Meyniel-Schicklin, Laurène; Pradezynski, Fabrine; Davoust, Nathalie; Chantier, Thibault; Tafforeau, Lionel; Mangeot, Philippe-Emmanuel; Ciancia, Claire; Perrin-Cocon, Laure; Bartenschlager, Ralf; André, Patrice; Lotteau, Vincent

    2013-01-01

    Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1) appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution.

  1. The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication.

    Directory of Open Access Journals (Sweden)

    Benoît de Chassey

    Full Text Available Influenza A NS1 and NS2 proteins are encoded by the RNA segment 8 of the viral genome. NS1 is a multifunctional protein and a virulence factor while NS2 is involved in nuclear export of viral ribonucleoprotein complexes. A yeast two-hybrid screening strategy was used to identify host factors supporting NS1 and NS2 functions. More than 560 interactions between 79 cellular proteins and NS1 and NS2 proteins from 9 different influenza virus strains have been identified. These interacting proteins are potentially involved in each step of the infectious process and their contribution to viral replication was tested by RNA interference. Validation of the relevance of these host cell proteins for the viral replication cycle revealed that 7 of the 79 NS1 and/or NS2-interacting proteins positively or negatively controlled virus replication. One of the main factors targeted by NS1 of all virus strains was double-stranded RNA binding domain protein family. In particular, adenosine deaminase acting on RNA 1 (ADAR1 appeared as a pro-viral host factor whose expression is necessary for optimal viral protein synthesis and replication. Surprisingly, ADAR1 also appeared as a pro-viral host factor for dengue virus replication and directly interacted with the viral NS3 protein. ADAR1 editing activity was enhanced by both viruses through dengue virus NS3 and influenza virus NS1 proteins, suggesting a similar virus-host co-evolution.

  2. Label-Free Protein-RNA Interactome Analysis Identifies Khsrp Signaling Downstream of the p38/Mk2 Kinase Complex as a Critical Modulator of Cell Cycle Progression.

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    Jorge Boucas

    Full Text Available Growing evidence suggests a key role for RNA binding proteins (RBPs in genome stability programs. Additionally, recent developments in RNA sequencing technologies, as well as mass-spectrometry techniques, have greatly expanded our knowledge on protein-RNA interactions. We here use full transcriptome sequencing and label-free LC/MS/MS to identify global changes in protein-RNA interactions in response to etoposide-induced genotoxic stress. We show that RBPs have distinct binding patterns in response to genotoxic stress and that inactivation of the RBP regulator module, p38/MK2, can affect the entire spectrum of protein-RNA interactions that take place in response to stress. In addition to validating the role of known RBPs like Srsf1, Srsf2, Elavl1 in the genotoxic stress response, we add a new collection of RBPs to the DNA damage response. We identify Khsrp as a highly regulated RBP in response to genotoxic stress and further validate its role as a driver of the G(1/S transition through the suppression of Cdkn1a(P21 transcripts. Finally, we identify KHSRP as an indicator of overall survival, as well as disease free survival in glioblastoma multiforme.

  3. Analyzing the effect of homogeneous frustration in protein folding.

    Science.gov (United States)

    Contessoto, Vinícius G; Lima, Debora T; Oliveira, Ronaldo J; Bruni, Aline T; Chahine, Jorge; Leite, Vitor B P

    2013-10-01

    The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy landscape of protein folding is funneled toward the native state, a conformational state that is consistent with the principle of minimal frustration. It has been accepted that real proteins are selected through natural evolution, satisfying the minimum frustration criterion. However, there is evidence that a low degree of frustration accelerates folding. We examined the interplay between topological and energetic protein frustration. We employed a Cα structure-based model for simulations with a controlled nonspecific energetic frustration added to the potential energy function. Thermodynamics and kinetics of a group of 19 proteins are completely characterized as a function of increasing level of energetic frustration. We observed two well-separated groups of proteins: one group where a little frustration enhances folding rates to an optimal value and another where any energetic frustration slows down folding. Protein energetic frustration regimes and their mechanisms are explained by the role of non-native contact interactions in different folding scenarios. These findings strongly correlate with the protein free-energy folding barrier and the absolute contact order parameters. These computational results are corroborated by principal component analysis and partial least square techniques. One simple theoretical model is proposed as a useful tool for experimentalists to predict the limits of improvements in real proteins. Copyright © 2013 Wiley Periodicals, Inc.

  4. Chemical approaches to detect and analyze protein sulfenic acids

    Science.gov (United States)

    Furdui, Cristina M.; Poole, Leslie B.

    2013-01-01

    Orchestration of many processes relying on intracellular signal transduction is recognized to require the generation of hydrogen peroxide as a second messenger, yet relatively few molecular details of how this oxidant acts to regulate protein function are currently understood. This review describes emerging chemical tools and approaches that can be applied to study protein oxidation in biological systems, with a particular emphasis on a key player in protein redox regulation, cysteine sulfenic acid. While sulfenic acids (within purified proteins or simple mixtures) are detectable by physical approaches like X-ray crystallography, nuclear magnetic resonance and mass spectrometry, the propensity of these moieties to undergo further modification in complex biological systems has necessitated the development of chemical probes, reporter groups and analytical approaches to allow for their selective detection and quantification. Provided is an overview of techniques that are currently available for the study of sulfenic acids, and some of the biologically meaningful data that have been collected using such approaches. PMID:24105931

  5. ProteinAC: a frequency domain technique for analyzing protein dynamics

    Science.gov (United States)

    Bozkurt Varolgunes, Yasemin; Demir, Alper

    2018-03-01

    It is widely believed that the interactions of proteins with ligands and other proteins are determined by their dynamic characteristics as opposed to only static, time-invariant processes. We propose a novel computational technique, called ProteinAC (PAC), that can be used to analyze small scale functional protein motions as well as interactions with ligands directly in the frequency domain. PAC was inspired by a frequency domain analysis technique that is widely used in electronic circuit design, and can be applied to both coarse-grained and all-atom models. It can be considered as a generalization of previously proposed static perturbation-response methods, where the frequency of the perturbation becomes the key. We discuss the precise relationship of PAC to static perturbation-response schemes. We show that the frequency of the perturbation may be an important factor in protein dynamics. Perturbations at different frequencies may result in completely different response behavior while magnitude and direction are kept constant. Furthermore, we introduce several novel frequency dependent metrics that can be computed via PAC in order to characterize response behavior. We present results for the ferric binding protein that demonstrate the potential utility of the proposed techniques.

  6. Disruption of intraflagellar protein transport in photoreceptor cilia causes Leber congenital amaurosis in humans and mice

    NARCIS (Netherlands)

    Boldt, K.; Mans, D.A.; Won, J.; Reeuwijk, J. van; Vogt, A.; Kinkl, N.; Letteboer, S.J.F.; Hicks, W.L.; Hurd, R.E.; Naggert, J.K.; Texier, Y.; Hollander, A.I. den; Koenekoop, R.K.; Bennett, J.; Cremers, F.P.M.; Gloeckner, C.J.; Nishina, P.M.; Roepman, R.; Ueffing, M.

    2011-01-01

    The mutations that cause Leber congenital amaurosis (LCA) lead to photoreceptor cell death at an early age, causing childhood blindness. To unravel the molecular basis of LCA, we analyzed how mutations in LCA5 affect the connectivity of the encoded protein lebercilin at the interactome level. In

  7. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara Elizabeth

    2016-05-11

    Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  8. Molecular characterization and interactome analysis of Trypanosoma cruzi tryparedoxin II.

    Science.gov (United States)

    Arias, Diego G; Piñeyro, María Dolores; Iglesias, Alberto A; Guerrero, Sergio A; Robello, Carlos

    2015-04-29

    Trypanosoma cruzi, the causative agent of Chagas disease, possesses two tryparedoxins (TcTXNI and TcTXNII), belonging to the thioredoxin superfamily. TXNs are oxidoreductases which mediate electron transfer between trypanothione and peroxiredoxins. This constitutes a difference with the host cells, in which these activities are mediated by thioredoxins. These differences make TXNs an attractive target for drug development. In a previous work we characterized TcTXNI, including the redox interactome. In this work we extend the study to TcTXNII. We demonstrate that TcTXNII is a transmembrane protein anchored to the surface of the mitochondria and endoplasmic reticulum, with a cytoplasmatic orientation of the redox domain. It would be expressed during the metacyclogenesis process. In order to continue with the characterization of the redox interactome of T. cruzi, we designed an active site mutant TcTXNII lacking the resolving cysteine, and through the expression of this mutant protein and incubation with T. cruzi proteins, heterodisulfide complexes were isolated by affinity chromatography and identified by mass spectrometry. This allowed us to identify sixteen TcTXNII interacting proteins, which are involved in a wide range of cellular processes, indicating the relevance of TcTXNII, and contributing to our understanding of the redox interactome of T. cruzi. T. cruzi, the causative agent of Chagas disease, constitutes a major sanitary problem in Latin America. The number of estimated infected persons is ca. 8 million, 28 million people are at risk of infection and ~20,000 deaths occur per year in endemic regions. No vaccines are available at present, and most drugs currently in use were developed decades ago and show variable efficacy with undesirable side effects. The parasite is able to live and prolipherate inside macrophage phagosomes, where it is exposed to cytotoxic reactive oxygen and nitrogen species, derived from macrophage activation. Therefore, T. cruzi

  9. The Breast Cancer DNA Interactome

    Science.gov (United States)

    2013-10-01

    RG . Demonstration of receptors for insulin-like growth factor binding protein-3 on Hs578T human breast cancer cells. J Biol Chem. 1993;268:26045-8...Interaction Profiles in Breast Cancer Reveal Altered Chromatin Architecture Michael J. Zeitz1*, Ferhat Ay2, Julia D. Heidmann1, Paula L. Lerner1...Illumina sequencing data have been submitted to the GEO database accession number: GSE49521. Mapping and Filtering of 4C Reads We first de -multiplexed the

  10. Poplar Interactome: Project Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Jaiswal, Pankaj [Oregon State Univ., Corvallis, OR (United States)

    2018-03-21

    The feedstock plant Poplar has many advantages over traditional crop plants. Not only Poplar needs low energy input and off season storage as compared to feedstocks such as corn, in the winter season Poplar biomass is stored on the stem/trunk, and Poplar plantations serve as large carbon sink. A key constraint to the expansion of cellulosic bioenergy sources such as in Poplar however, is the negative consequence of converting land use from food crops to energy crops. Therefore in order for Poplar to become a viable energy crop it needs to be grown mostly on marginal land unsuitable agricultural crops. For this we need a better understanding of abiotic stress and adaptation response in poplar. In the process we expected to find new and existing poplar genes and their function that respond to sustain abiotic stress. We carried out an extensive gene expression study on the control untreated and stress (drought, salinity, cold and heat) treated poplar plants. The samples were collected from the stem, leaf and root tissues. The RNA of protein coding genes and regulatory smallRNA genes were sequenced generating more than a billion reads. This is the first such known study in Poplar plants. These were used for quantification and genomic analysis to identify stress responsive genes in poplar. Based on the quantification and genomic analysis, a select set of genes were studied for gene-gene interactions to find their association to stress response. The data was also used to find novel stress responsive genes in poplar that were previously not identified in the Poplar reference genome. The data is made available to the public through the national and international genomic data archives.

  11. Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs

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    Jianhua Cao

    2014-11-01

    Full Text Available The regulatory relationship and connectivity among genes involved in myogenesis and hypertrophy of skeletal muscle in pigs still remain large challenges. Presentation of gene interactions is a potential way to understand the mechanisms of developmental events in skeletal muscle. In this study, genome-wide transcripts and miRNA profiling was determined for Landrace pigs at four time points using microarray chips. A comprehensive method integrating gene ontology annotation and interactome network mapping was conducted to analyze the biological patterns and interaction modules of muscle development events based on differentially expressed genes and miRNAs. Our results showed that in total 484 genes and 34 miRNAs were detected for the duration from embryonic stage to adult in pigs, which composed two linear expression patterns with consensus changes. Moreover, the gene ontology analysis also disclosed that there were three typical biological events i.e., microstructure assembly of sarcomere at early embryonic stage, myofibril formation at later embryonic stage and function establishments of myoblast cells at postnatal stage. The interactome mappings of different time points also found the down-regulated trend of gene expression existed across the whole duration, which brought a possibility to introduce the myogenesis related miRNAs into the interactome regulatory networks of skeletal muscle in pigs.

  12. Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations

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    Guimarães Katia S

    2006-04-01

    Full Text Available Abstract Background Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient associations and are part of several complexes at different stages of a cellular process. A better understanding of this higher-order organization of proteins into overlapping complexes is an important step towards unveiling functional and evolutionary mechanisms behind biological networks. Results We propose a new method for identifying and representing overlapping protein complexes (or larger units called functional groups within a protein interaction network. We develop a graph-theoretical framework that enables automatic construction of such representation. We illustrate the effectiveness of our method by applying it to TNFα/NF-κB and pheromone signaling pathways. Conclusion The proposed representation helps in understanding the transitions between functional groups and allows for tracking a protein's path through a cascade of functional groups. Therefore, depending on the nature of the network, our representation is capable of elucidating temporal relations between functional groups. Our results show that the proposed method opens a new avenue for the analysis of protein interaction networks.

  13. Investigation of PARP-1, PARP-2, and PARG interactomes by affinity-purification mass spectrometry

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    Isabelle Maxim

    2010-04-01

    Full Text Available Abstract Background Poly(ADP-ribose polymerases (PARPs catalyze the formation of poly(ADP-ribose (pADPr, a post-translational modification involved in several important biological processes, namely surveillance of genome integrity, cell cycle progression, initiation of the DNA damage response, apoptosis, and regulation of transcription. Poly(ADP-ribose glycohydrolase (PARG, on the other hand, catabolizes pADPr and thereby accounts for the transient nature of poly(ADP-ribosylation. Our investigation of the interactomes of PARP-1, PARP-2, and PARG by affinity-purification mass spectrometry (AP-MS aimed, on the one hand, to confirm current knowledge on these interactomes and, on the other hand, to discover new protein partners which could offer insights into PARPs and PARG functions. Results PARP-1, PARP-2, and PARG were immunoprecipitated from human cells, and pulled-down proteins were separated by gel electrophoresis prior to in-gel trypsin digestion. Peptides were identified by tandem mass spectrometry. Our AP-MS experiments resulted in the identifications of 179 interactions, 139 of which are novel interactions. Gene Ontology analysis of the identified protein interactors points to five biological processes in which PARP-1, PARP-2 and PARG may be involved: RNA metabolism for PARP-1, PARP-2 and PARG; DNA repair and apoptosis for PARP-1 and PARP-2; and glycolysis and cell cycle for PARP-1. Conclusions This study reveals several novel protein partners for PARP-1, PARP-2 and PARG. It provides a global view of the interactomes of these proteins as well as a roadmap to establish the systems biology of poly(ADP-ribose metabolism.

  14. Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs.

    Science.gov (United States)

    Gao, Jinxu; Mfuh, Adelphe; Amako, Yuka; Woo, Christina M

    2018-03-15

    Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment and isotope-recoding of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, we identified the NSAID interactome consisting of over 1000 significantly enriched proteins and directly characterized nearly 200 conjugated peptides representing direct binding sites of the photo-NSAIDs with proteins from Jurkat and K562 cells. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κB) and novel interactions (e.g., AP-2, proteasome). The conjugated peptides revealed direct NSAID binding sites from the cell surface to the nucleus and a specific binding site hotspot for the three photo-NSAIDs on histones H2A and H2B. NSAID binding stabilized COX-2 and histone H2A by cellular thermal shift assay. Since small molecule stabilization of protein complexes is a gain of function regulatory mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-PAL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest.

  15. PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.

    Science.gov (United States)

    Li, Fei; Li, Peng; Xu, Wenjian; Peng, Yuxing; Bo, Xiaochen; Wang, Shengqi

    2010-01-15

    The propagation of perturbations in protein concentration through a protein interaction network (PIN) can shed light on network dynamics and function. In order to facilitate this type of study, PerturbationAnalyzer, which is an open source plugin for Cytoscape, has been developed. PerturbationAnalyzer can be used in manual mode for simulating user-defined perturbations, as well as in batch mode for evaluating network robustness and identifying significant proteins that cause large propagation effects in the PINs when their concentrations are perturbed. Results from PerturbationAnalyzer can be represented in an intuitive and customizable way and can also be exported for further exploration. PerturbationAnalyzer has great potential in mining the design principles of protein networks, and may be a useful tool for identifying drug targets. PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer. Supplementary data are available at Bioinformatics online.

  16. BIS2Analyzer: a server for co-evolution analysis of conserved protein families.

    Science.gov (United States)

    Oteri, Francesco; Nadalin, Francesca; Champeimont, Raphaël; Carbone, Alessandra

    2017-07-03

    Along protein sequences, co-evolution analysis identifies residue pairs demonstrating either a specific co-adaptation, where changes in one of the residues are compensated by changes in the other during evolution or a less specific external force that affects the evolutionary rates of both residues in a similar magnitude. In both cases, independently of the underlying cause, co-evolutionary signatures within or between proteins serve as markers of physical interactions and/or functional relationships. Depending on the type of protein under study, the set of available homologous sequences may greatly differ in size and amino acid variability. BIS2Analyzer, openly accessible at http://www.lcqb.upmc.fr/BIS2Analyzer/, is a web server providing the online analysis of co-evolving amino-acid pairs in protein alignments, especially designed for vertebrate and viral protein families, which typically display a small number of highly similar sequences. It is based on BIS2, a re-implemented fast version of the co-evolution analysis tool Blocks in Sequences (BIS). BIS2Analyzer provides a rich and interactive graphical interface to ease biological interpretation of the results. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis

    Science.gov (United States)

    Rohira, Harsha; Bhat, Ashwini G.; Passi, Anurag; Mukherjee, Keya; Choudhary, Kumari Sonal; Kumar, Vikas; Arora, Anshula; Munusamy, Prabhakaran; Subramanian, Ahalyaa; Venkatachalam, Aparna; S, Gayathri; Raj, Sweety; Chitra, Vijaya; Verma, Kaveri; Zaheer, Salman; J, Balaganesh; Gurusamy, Malarvizhi; Razeeth, Mohammed; Raja, Ilamathi; Thandapani, Madhumohan; Mevada, Vishal; Soni, Raviraj; Rana, Shruti; Ramanna, Girish Muthagadhalli; Raghavan, Swetha; Subramanya, Sunil N.; Kholia, Trupti; Patel, Rajesh; Bhavnani, Varsha; Chiranjeevi, Lakavath; Sengupta, Soumi; Singh, Pankaj Kumar; Atray, Naresh; Gandhi, Swati; Avasthi, Tiruvayipati Suma; Nisthar, Shefin; Anurag, Meenakshi; Sharma, Pratibha; Hasija, Yasha; Dash, Debasis; Sharma, Arun; Scaria, Vinod; Thomas, Zakir; Chandra, Nagasuma; Brahmachari, Samir K.; Bhardwaj, Anshu

    2012-01-01

    A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative ‘Connect to Decode’ (C2D) to generate the first and largest manually curated interactome of Mtb termed ‘interactome pathway’ (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach. PMID:22808064

  18. Quantum Interactomics and Cancer Molecular Mechanisms: I. Report Outline

    CERN Document Server

    Baianu, I C

    2004-01-01

    Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quant...

  19. Evaluation of Colorimetric Assays for Analyzing Reductively Methylated Proteins: Biases and Mechanistic Insights

    Science.gov (United States)

    Brady, Pamlea N.; Macnaughtan, Megan A.

    2015-01-01

    Colorimetric protein assays, such as the Coomassie blue G-250 dye-binding (Bradford) and bicinchoninic acid (BCA) assays, are commonly used to quantify protein concentration. The accuracy of these assays depends on the amino acid composition. Because of the extensive use of reductive methylation in the study of proteins and the importance of biological methylation, it is necessary to evaluate the impact of lysyl methylation on the Bradford and BCA assays. Unmodified and reductively methylated proteins were analyzed using the absorbance at 280 nm to standardize the concentrations. Using model compounds, we demonstrate that the dimethylation of lysyl ε-amines does not affect the proteins’ molar extinction coefficients at 280 nm. For the Bradford assay, the response (absorbance per unit concentration) of the unmodified and reductively methylated proteins were similar with a slight decrease in the response upon methylation. For the BCA assay, the responses of the reductively methylated proteins were consistently higher, overestimating the concentrations of the methylated proteins. The enhanced color-formation in the BCA assay may be due to the lower acid dissociation constants of the lysyl ε-dimethylamines, compared to the unmodified ε-amine, favoring Cu(II) binding in biuret-like complexes. The implications for the analysis of biologically methylated samples are discussed. PMID:26342307

  20. Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs.

    Science.gov (United States)

    Chang, Xiao; Xu, Tao; Li, Yun; Wang, Kai

    2013-01-01

    The protein-protein interaction (PPI) networks are dynamically organized as modules, and are typically described by hub dichotomy: 'party' hubs act as intramodule hubs and are coexpressed with their partners, yet 'date' hubs act as coordinators among modules and are incoherently expressed with their partners. However, there remains skepticism about the existence of hub dichotomy. Since different algorithms and data sets were used in previous studies to test the model of hub classification, the conclusions may be largely influenced by the potential inherent biases. In this study, we evaluated two data sets of yeast interactome, and systematically investigated the behavior of hubs from multiple perspectives including co-expression patterns, topological roles and functional classifications. Our results revealed consistency between the two data sets, confirming the presence of hub dichotomy. Furthermore, we analyzed a human interactome data set, and demonstrated that the modular architecture of the PPI networks was more complicated than hub dichotomy.

  1. Analyzing import intermediates of mitochondrial proteins by blue native gel electrophoresis.

    Science.gov (United States)

    Waizenegger, Thomas; Rapaport, Doron

    2007-01-01

    Blue native gel electrophoresis (BNGE) is a powerful tool for analyzing native protein complexes from biological membranes as well as water-soluble proteins. It can be used for determining relative molecular masses of protein complexes and their subunit composition and for the detection of subcomplexes. We describe the analysis by BNGE of in vitro import reactions composed of radiolabeled precursor proteins and isolated mitochondria. Such an analysis is a powerful tool to follow import intermediates and to study assembly of protein complexes. Analysis of import reactions by BNGE provides information on the molecular mass of the complex with which the imported precursor is associated. In addition, components of such a complex can be identified by incubating the mitochondrial lysate with either soluble antibodies or antibodies coupled to protein A matrix. The binding of soluble antibodies to specific complexes results in an observed shift in their apparent molecular mass (antibody shift). Alternatively, addition of matrix-bound antibodies followed by removal of the matrix from the mixture will result in depletion of the specific complex from the mitochondrial lysate (antibody depletion). The experimental details of these techniques are described.

  2. STUDY OF THE VISCOSITY OF PROTEIN SOLUTIONS THROUGH THE RAPID VISCOSITY ANALYZER (RVA

    Directory of Open Access Journals (Sweden)

    Maura P. Alves

    2014-05-01

    Full Text Available This study aimed to determine viscosity curves prepared from whey protein concentrates (WPCs by the rapid viscosity analyzer (RVA and determine the optimal heat treatment time in order to obtain the maximum viscosity solutions at this stage. The WPCs produced from whey samples initially subjected to thermal treatment and microfiltration presented composition compatible with the international standards, with a significant difference (p<0.05 for fat concentration. Viscographic profiles indicated that WPCs produced from microfiltered whey had higher viscosities than those subjected to heat treatment. In addition, 10 min was determined to be the optimal length of time for heat treatment in order to maximise WPCs viscosity. These results indicate that WPC production can be designed for different food applications. Finally, a rapid viscosity analyzer was demonstrated to be an appropriate tool to study the application of whey proteins in food systems.

  3. A rapid and cost-effective fluorescence detection in tube (FDIT method to analyze protein phosphorylation

    Directory of Open Access Journals (Sweden)

    Xiao Jin

    2016-11-01

    Full Text Available Abstract Background Protein phosphorylation is one of the most important post-translational modifications catalyzed by protein kinases in living organisms. The advance of genome sequencing provided the information of protein kinase families in many organisms, including both model and non-model plants. The development of proteomics technologies also enabled scientists to efficiently reveal a large number of protein phosphorylations of an organism. However, kinases and phosphorylation targets are still to be connected to illustrate the complicated network in life. Results Here we adapted Pro-Q® Diamond (Pro-Q® Diamond Phosphoprotein Gel Stain, a widely used phosphoprotein gel-staining fluorescence dye, to establish a rapid, economical and non-radioactive fluorescence detection in tube (FDIT method to analyze phosphorylated proteins. Taking advantages of high sensitivity and specificity of Pro-Q® diamond, the FDIT method is also demonstrated to be rapid and reliable, with a suitable linear range for in vitro protein phosphorylation. A significant and satisfactory protein kinase reaction was detected as fast as 15 min from Wheat Kinase START 1.1 (WKS1.1 on a thylakoid ascorbate peroxidase (tAPX, an established phosphorylation target in our earlier study. Conclusion The FDIT method saves up to 95% of the dye consumed in a gel staining method. The FDIT method is remarkably quick, highly reproducible, unambiguous and capable to be scaled up to dozens of samples. The FDIT method could serve as a simple and sensitive alternative procedure to determine protein kinase reactions with zero radiation exposure, as a supplementation to other widely used radioactive and in-gel assays.

  4. Striatal Transcriptome and Interactome Analysis of Shank3-overexpressing Mice Reveals the Connectivity between Shank3 and mTORC1 Signaling

    Directory of Open Access Journals (Sweden)

    Yeunkum Lee

    2017-06-01

    Full Text Available Mania causes symptoms of hyperactivity, impulsivity, elevated mood, reduced anxiety and decreased need for sleep, which suggests that the dysfunction of the striatum, a critical component of the brain motor and reward system, can be causally associated with mania. However, detailed molecular pathophysiology underlying the striatal dysfunction in mania remains largely unknown. In this study, we aimed to identify the molecular pathways showing alterations in the striatum of SH3 and multiple ankyrin repeat domains 3 (Shank3-overexpressing transgenic (TG mice that display manic-like behaviors. The results of transcriptome analysis suggested that mammalian target of rapamycin complex 1 (mTORC1 signaling may be the primary molecular signature altered in the Shank3 TG striatum. Indeed, we found that striatal mTORC1 activity, as measured by mTOR S2448 phosphorylation, was significantly decreased in the Shank3 TG mice compared to wild-type (WT mice. To elucidate the potential underlying mechanism, we re-analyzed previously reported protein interactomes, and detected a high connectivity between Shank3 and several upstream regulators of mTORC1, such as tuberous sclerosis 1 (TSC1, TSC2 and Ras homolog enriched in striatum (Rhes, via 94 common interactors that we denominated “Shank3-mTORC1 interactome”. We noticed that, among the 94 common interactors, 11 proteins were related to actin filaments, the level of which was increased in the dorsal striatum of Shank3 TG mice. Furthermore, we could co-immunoprecipitate Shank3, Rhes and Wiskott-Aldrich syndrome protein family verprolin-homologous protein 1 (WAVE1 proteins from the striatal lysate of Shank3 TG mice. By comparing with the gene sets of psychiatric disorders, we also observed that the 94 proteins of Shank3-mTORC1 interactome were significantly associated with bipolar disorder (BD. Altogether, our results suggest a protein interaction-mediated connectivity between Shank3 and certain upstream

  5. Evaluation of the synergistic effects of milk proteins in a rapid viscosity analyzer.

    Science.gov (United States)

    Stephani, Rodrigo; Borges de Souza, Alisson; Leal de Oliveira, Marcone Augusto; Perrone, Ítalo Tuler; Fernandes de Carvalho, Antônio; Cappa de Oliveira, Luiz Fernando

    2015-12-01

    Protein systems (PS) are routinely used by companies from Brazil and around the globe to improve the texture, yield, and palatability of processed foods. Understanding the synergistic behavior among the different protein structures of these systems during thermal treatment under the influence of pH can help to better define optimum conditions for products and processes. The interpretation of the reactions and interactions that occur simultaneously among the protein constituents of these systems as dispersions during thermal processing is still a major challenge. Here, using a rapid viscosity analyzer, we observed the rheological changes in the startup viscosities of 5 PS obtained by combining varying proportions of milk protein concentrate and whey protein concentrate under different conditions of pH (5.0, 6.5, and 7.0) and heat processing (85°C/15min and 95°C/5min). The solutions were standardized to 25% of total solids and 17% of protein. Ten analytical parameters were used to characterize each of the startup-viscosity ramps for 35 experiments conducted in a 2×3 × 5 mixed planning matrix, using principal component analysis to interpret behavioral similarities. The study showed the clear influence of pH 5.5 in the elevation of the initial temperature of the PS startup viscosity by at least 5°C, as well as the effect of different milk protein concentrate:whey protein concentrate ratios above 15:85 at pH 7.0 on the viscographic profile curves. These results suggested that the primary agent driving the changes was the synergism among the reactions and interactions of casein with whey proteins during processing. This study reinforces the importance of the rapid viscosity analyzer as an analytical tool for the simulation of industrial processes involving PS, and the use of the startup viscosity ramp as a means of interpreting the interactions of system components with respect to changes related to the treatment temperature. Copyright © 2015 American Dairy Science

  6. Ovarian Cancer Differential Interactome and Network Entropy Analysis Reveal New Candidate Biomarkers.

    Science.gov (United States)

    Ayyildiz, Dilara; Gov, Esra; Sinha, Raghu; Arga, Kazim Yalcin

    2017-05-01

    Ovarian cancer is one of the most common cancers and has a high mortality rate due to insidious symptoms and lack of robust diagnostics. A hitherto understudied concept in cancer pathogenesis may offer new avenues for innovation in ovarian cancer biomarker development. Cancer cells are characterized by an increase in network entropy, and several studies have exploited this concept to identify disease-associated gene and protein modules. We report in this study the changes in protein-protein interactions (PPIs) in ovarian cancer within a differential network (interactome) analysis framework utilizing the entropy concept and gene expression data. A compendium of six transcriptome datasets that included 140 samples from laser microdissected epithelial cells of ovarian cancer patients and 51 samples from healthy population was obtained from Gene Expression Omnibus, and the high confidence human protein interactome (31,465 interactions among 10,681 proteins) was used. The uncertainties of the up- or downregulation of PPIs in ovarian cancer were estimated through an entropy formulation utilizing combined expression levels of genes, and the interacting protein pairs with minimum uncertainty were identified. We identified 105 proteins with differential PPI patterns scattered in 11 modules, each indicating significantly affected biological pathways in ovarian cancer such as DNA repair, cell proliferation-related mechanisms, nucleoplasmic translocation of estrogen receptor, extracellular matrix degradation, and inflammation response. In conclusion, we suggest several PPIs as biomarker candidates for ovarian cancer and discuss their future biological implications as potential molecular targets for pharmaceutical development as well. In addition, network entropy analysis is a concept that deserves greater research attention for diagnostic innovation in oncology and tumor pathogenesis.

  7. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells

    Science.gov (United States)

    Giurato, Giorgio; Nassa, Giovanni; Salvati, Annamaria; Alexandrova, Elena; Rizzo, Francesca; Nyman, Tuula A.; Weisz, Alessandro; Tarallo, Roberta

    2018-03-01

    The nuclear receptor estrogen receptor 2 (ESR2, ERβ) modulates cancer cell proliferation and tumor growth, exerting an oncosuppressive role in breast cancer (BC). Interaction proteomics by tandem affinity purification coupled to mass spectrometry was previously applied in BC cells to identify proteins acting in concert with ERβ to control key cellular functions, including gene transcription, RNA splicing and post-transcriptional mRNA regulation. These studies revealed an involvement of RNA in ERβ interactome assembly and functions. By applying native protein complex purification followed by nano LC-MS/MS before and after in vitro RNA removal, we generated a large dataset of newly identified nuclear ERβ interactors, including a subset associating with the receptor via RNA bridging. These datasets will be useful to investigate further the role of ERβ, nuclear RNAs and the other proteins identified here in BC and other cell types.

  8. Analyzing Forced Unfolding of Protein Tandems by Ordered Variates, 1: Independent Unfolding Times

    Science.gov (United States)

    Bura, E.; Klimov, D. K.; Barsegov, V.

    2007-01-01

    Most of the mechanically active proteins are organized into tandems of identical repeats, (D)N, or heterogeneous tandems, D1–D2–…–DN. In current atomic force microscopy experiments, conformational transitions of protein tandems can be accessed by employing constant stretching force f (force-clamp) and by analyzing the recorded unfolding times of individual domains. Analysis of unfolding data for homogeneous tandems relies on the assumption that unfolding times are independent and identically distributed, and involves inference of the (parent) probability density of unfolding times from the histogram of the combined unfolding times. This procedure cannot be used to describe tandems characterized by interdomain interactions, or heteregoneous tandems. In this article, we introduce an alternative approach that is based on recognizing that the observed data are ordered, i.e., first, second, third, etc., unfolding times. The approach is exemplified through the analysis of unfolding times for a computer model of the homogeneous and heterogeneous tandems, subjected to constant force. We show that, in the experimentally accessible range of stretching forces, the independent and identically distributed assumption may not hold. Specifically, the uncorrelated unfolding transitions of individual domains at lower force may become correlated (dependent) at elevated force levels. The proposed formalism can be used in atomic force microscopy experiments to infer the unfolding time distributions of individual domains from experimental histograms of ordered unfolding times, and it can be extended to analyzing protein tandems that exhibit interdomain interactions. PMID:17496033

  9. Data management of protein interaction networks

    CERN Document Server

    Cannataro, Mario

    2012-01-01

    Interactomics: a complete survey from data generation to knowledge extraction With the increasing use of high-throughput experimental assays, more and more protein interaction databases are becoming available. As a result, computational analysis of protein-to-protein interaction (PPI) data and networks, now known as interactomics, has become an essential tool to determine functionally associated proteins. From wet lab technologies to data management to knowledge extraction, this timely book guides readers through the new science of interactomics, giving them the tools needed to: Generate

  10. Effects of protein and phosphate buffer concentrations on thermal denaturation of lysozyme analyzed by isoconversional method.

    Science.gov (United States)

    Cao, X M; Tian, Y; Wang, Z Y; Liu, Y W; Wang, C X

    2016-07-03

    Thermal denaturation of lysozymes was studied as a function of protein concentration, phosphate buffer concentration, and scan rate using differential scanning calorimetry (DSC), which was then analyzed by the isoconversional method. The results showed that lysozyme thermal denaturation was only slightly affected by the protein concentration and scan rate. When the protein concentration and scan rate increased, the denaturation temperature (Tm) also increased accordingly. On the contrary, the Tm decreased with the increase of phosphate buffer concentration. The denaturation process of lysozymes was accelatated and the thermal stability was reduced with the increase of phosphate concentration. One part of degeneration process was not reversible where the aggregation occurred. The other part was reversible. The apparent activation energy (Ea) was computed by the isoconversional method. It decreased with the increase of the conversion ratio (α). The observed denaturation process could not be described by a simple reaction mechanism. It was not a process involving 2 standard reversible states, but a multi-step process. The new opportunities for investigating the kinetics process of protein denaturation can be supplied by this novel isoconversional method.

  11. When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks.

    Science.gov (United States)

    Iván, Gábor; Grolmusz, Vince

    2011-02-01

    Enormous and constantly increasing quantity of biological information is represented in metabolic and in protein interaction network databases. Most of these data are freely accessible through large public depositories. The robust analysis of these resources needs novel technologies, being developed today. Here we demonstrate a technique, originating from the PageRank computation for the World Wide Web, for analyzing large interaction networks. The method is fast, scalable and robust, and its capabilities are demonstrated on metabolic network data of the tuberculosis bacterium and the proteomics analysis of the blood of melanoma patients. The Perl script for computing the personalized PageRank in protein networks is available for non-profit research applications (together with sample input files) at the address: http://uratim.com/pp.zip.

  12. Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of ‘date' and ‘party' hubs

    Science.gov (United States)

    Chang, Xiao; Xu, Tao; Li, Yun; Wang, Kai

    2013-01-01

    The protein-protein interaction (PPI) networks are dynamically organized as modules, and are typically described by hub dichotomy: ‘party' hubs act as intramodule hubs and are coexpressed with their partners, yet ‘date' hubs act as coordinators among modules and are incoherently expressed with their partners. However, there remains skepticism about the existence of hub dichotomy. Since different algorithms and data sets were used in previous studies to test the model of hub classification, the conclusions may be largely influenced by the potential inherent biases. In this study, we evaluated two data sets of yeast interactome, and systematically investigated the behavior of hubs from multiple perspectives including co-expression patterns, topological roles and functional classifications. Our results revealed consistency between the two data sets, confirming the presence of hub dichotomy. Furthermore, we analyzed a human interactome data set, and demonstrated that the modular architecture of the PPI networks was more complicated than hub dichotomy. PMID:23603706

  13. Analytical performances of Hemoclot Protein C Reagent on ACL TOP analyzer.

    Science.gov (United States)

    Calmette, Leyla; Charpentier, Nicole; Tircot, Caroline; Bigot, Delphine; Dunois, Claire; Amiral, Jean; Tetegan, Marcelle; Sep Hieng, Sonnthida; Peltier, Jean-Yves

    2016-12-01

    Our study aimed to evaluate and validate according to standard NF EN ISO 15189 the original protocol ajustement of Hemoclot Protein C (PC) (Hyphen BioMed), clotting-based assay of PC on ACL TOP analyzer (Werfen/Instrumentation Laboratory). We evaluated the performance in terms of imprecision and we validate additional parameters in range B required by the SH GTA 04 (COFRAC): repeatability, reproducibility, detection and quantification limits, limits of linearity, stability, inter-samples and inter-reagents contamination, inaccuracy, evaluation of interferences (hemolysis, bilirubinemia and chyles). A comparison with Hemoclot PC on STA Compact analyzer (Stago) was performed. Coefficients of variation were lower than 5 %. Detection and quantification limits were respectively 8.3 % and 9.3 %. Superior limit of linearity was 140 %. The test didn't diplay any inter-samples and inter-reagents contamination. Reagent after reconstitution was stable 6 hours on ACL TOP. No interferences were observed for hemoglobin lower than 500 mg/dL, for bilirubin lower than and for chyles lower than 300 mg/dL. Comparison with Hemoclot PC on STA analyzer (Stago) was satisfactory. Hemoclot PC adjusted on ACL TOP analyzer showed satisfactory analytical performances with criteria chosen in our study. These data allow a better knowledge of the performances of this test and were useful to make a validation file in range B as recommended by SH GTA 04.

  14. A Versatile Platform to Analyze Low-Affinity and Transient Protein-Protein Interactions in Living Cells in Real Time

    Directory of Open Access Journals (Sweden)

    Yao-Cheng Li

    2014-12-01

    Full Text Available Summary: Protein-protein interactions (PPIs play central roles in orchestrating biological processes. While some PPIs are stable, many important ones are transient and hard to detect with conventional approaches. We developed ReBiL, a recombinase enhanced bimolecular luciferase complementation platform, to enable detection of weak PPIs in living cells. ReBiL readily identified challenging transient interactions between an E3 ubiquitin ligase and an E2 ubiquitin-conjugating enzyme. ReBiL’s ability to rapidly interrogate PPIs in diverse conditions revealed that some stapled α-helical peptides, a class of PPI antagonists, induce target-independent cytosolic leakage and cytotoxicity that is antagonized by serum. These results explain the requirement for serum-free conditions to detect stapled peptide activity, and define a required parameter to evaluate for peptide antagonist approaches. ReBiL’s ability to expedite PPI analysis, assess target specificity and cell permeability, and reveal off-target effects of PPI modifiers should facilitate the development of effective, cell-permeable PPI therapeutics and the elaboration of diverse biological mechanisms. : Li et al. developed a recombinase-enhanced bimolecular luciferase complementation platform, termed ReBiL, to evaluate low-affinity protein-protein interactions (PPIs that are not detectable by other methods and to analyze PPI antagonists in living cells. ReBiL showed that small-molecule p53-Mdm2 antagonists disrupt their intended targets effectively in cells, whereas stapled peptides did not. Stapled peptides unexpectedly induced cell membrane disruption resulting in p53-independent death associated with cytoplasmic leakage. ReBiL is also valuable for high-throughput screening and for deciphering signaling mechanisms mediated by protein interactions.

  15. Duchenne Muscular Dystrophy (DMD) Protein-Protein Interaction Mapping.

    Science.gov (United States)

    Rezaei Tavirani, Mostafa; OkHOVATIAN, Farshad; Zamanian Azodi, Mona; Rezaei Tavirani, Majid

    2017-01-01

    Duchenne muscular dystrophy (DMD) is one of the mortal diseases, subjected to study in terms of molecular investigation. In this study, the protein interaction map of this muscle-wasting condition was generated to gain a better knowledge of interactome profile of DMD. Applying Cytoscape and String Database, the protein-protein interaction network was constructed and the gene ontology of the constructed network was analyzed for biological process, molecular function, and cellular component annotations. Among 100 proteins related to DMD, dystrophin, utrophin, caveolin 3, and myogenic differentiation 1 play key roles in DMD network. In addition, the gene ontology analysis showed that regulation processes, kinase activity, and sarcoplasmic reticulum were the highlighted biological processes, molecular function, and cell component enrichments respectively for the proteins related to DMD. The central proteins and the enriched ontologies can be suggested as possible prominent agents in DMD; however, the validation studies may be required.

  16. Quantitative interactome analysis reveals a chemoresistant edgotype.

    Science.gov (United States)

    Chavez, Juan D; Schweppe, Devin K; Eng, Jimmy K; Zheng, Chunxiang; Taipale, Alex; Zhang, Yiyi; Takara, Kohji; Bruce, James E

    2015-08-03

    Chemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for 'edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype.

  17. Efficient Prediction of Progesterone Receptor Interactome Using a Support Vector Machine Model

    Directory of Open Access Journals (Sweden)

    Ji-Long Liu

    2015-03-01

    Full Text Available Protein-protein interaction (PPI is essential for almost all cellular processes and identification of PPI is a crucial task for biomedical researchers. So far, most computational studies of PPI are intended for pair-wise prediction. Theoretically, predicting protein partners for a single protein is likely a simpler problem. Given enough data for a particular protein, the results can be more accurate than general PPI predictors. In the present study, we assessed the potential of using the support vector machine (SVM model with selected features centered on a particular protein for PPI prediction. As a proof-of-concept study, we applied this method to identify the interactome of progesterone receptor (PR, a protein which is essential for coordinating female reproduction in mammals by mediating the actions of ovarian progesterone. We achieved an accuracy of 91.9%, sensitivity of 92.8% and specificity of 91.2%. Our method is generally applicable to any other proteins and therefore may be of help in guiding biomedical experiments.

  18. Interactomes to Biological Phase Space: a call to begin thinking at a new level in computational biology.

    Energy Technology Data Exchange (ETDEWEB)

    Davidson, George S.; Brown, William Michael

    2007-09-01

    Techniques for high throughput determinations of interactomes, together with high resolution protein collocalizations maps within organelles and through membranes will soon create a vast resource. With these data, biological descriptions, akin to the high dimensional phase spaces familiar to physicists, will become possible. These descriptions will capture sufficient information to make possible realistic, system-level models of cells. The descriptions and the computational models they enable will require powerful computing techniques. This report is offered as a call to the computational biology community to begin thinking at this scale and as a challenge to develop the required algorithms and codes to make use of the new data.3

  19. Toxoplasmosis and Polygenic Disease Susceptibility Genes: Extensive Toxoplasma gondii Host/Pathogen Interactome Enrichment in Nine Psychiatric or Neurological Disorders

    Directory of Open Access Journals (Sweden)

    C. J. Carter

    2013-01-01

    Full Text Available Toxoplasma gondii is not only implicated in schizophrenia and related disorders, but also in Alzheimer's or Parkinson's disease, cancer, cardiac myopathies, and autoimmune disorders. During its life cycle, the pathogen interacts with ~3000 host genes or proteins. Susceptibility genes for multiple sclerosis, Alzheimer's disease, schizophrenia, bipolar disorder, depression, childhood obesity, Parkinson's disease, attention deficit hyperactivity disorder (multiple sclerosis, and autism (, but not anorexia or chronic fatigue are highly enriched in the human arm of this interactome and 18 (ADHD to 33% (MS of the susceptibility genes relate to it. The signalling pathways involved in the susceptibility gene/interactome overlaps are relatively specific and relevant to each disease suggesting a means whereby susceptibility genes could orient the attentions of a single pathogen towards disruption of the specific pathways that together contribute (positively or negatively to the endophenotypes of different diseases. Conditional protein knockdown, orchestrated by T. gondii proteins or antibodies binding to those of the host (pathogen derived autoimmunity and metabolite exchange, may contribute to this disruption. Susceptibility genes may thus be related to the causes and influencers of disease, rather than (and as well as to the disease itself.

  20. A computational interactome for prioritizing genes associated with complex agronomic traits in rice (Oryza sativa).

    Science.gov (United States)

    Liu, Shiwei; Liu, Yihui; Zhao, Jiawei; Cai, Shitao; Qian, Hongmei; Zuo, Kaijing; Zhao, Lingxia; Zhang, Lida

    2017-04-01

    Rice (Oryza sativa) is one of the most important staple foods for more than half of the global population. Many rice traits are quantitative, complex and controlled by multiple interacting genes. Thus, a full understanding of genetic relationships will be critical to systematically identify genes controlling agronomic traits. We developed a genome-wide rice protein-protein interaction network (RicePPINet, http://netbio.sjtu.edu.cn/riceppinet) using machine learning with structural relationship and functional information. RicePPINet contained 708 819 predicted interactions for 16 895 non-transposable element related proteins. The power of the network for discovering novel protein interactions was demonstrated through comparison with other publicly available protein-protein interaction (PPI) prediction methods, and by experimentally determined PPI data sets. Furthermore, global analysis of domain-mediated interactions revealed RicePPINet accurately reflects PPIs at the domain level. Our studies showed the efficiency of the RicePPINet-based method in prioritizing candidate genes involved in complex agronomic traits, such as disease resistance and drought tolerance, was approximately 2-11 times better than random prediction. RicePPINet provides an expanded landscape of computational interactome for the genetic dissection of agronomically important traits in rice. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  1. Hydrogen bond rotations as a uniform structural tool for analyzing protein architecture

    Science.gov (United States)

    Penner, Robert C.; Andersen, Ebbe S.; Jensen, Jens L.; Kantcheva, Adriana K.; Bublitz, Maike; Nissen, Poul; Rasmussen, Anton M. H.; Svane, Katrine L.; Hammer, Bjørk; Rezazadegan, Reza; Nielsen, Niels Chr.; Nielsen, Jakob T.; Andersen, Jørgen E.

    2014-12-01

    Proteins fold into three-dimensional structures, which determine their diverse functions. The conformation of the backbone of each structure is locally at each Cα effectively described by conformational angles resulting in Ramachandran plots. These, however, do not describe the conformations around hydrogen bonds, which can be non-local along the backbone and are of major importance for protein structure. Here, we introduce the spatial rotation between hydrogen bonded peptide planes as a new descriptor for protein structure locally around a hydrogen bond. Strikingly, this rotational descriptor sampled over high-quality structures from the protein data base (PDB) concentrates into 30 localized clusters, some of which correlate to the common secondary structures and others to more special motifs, yet generally providing a unifying systematic classification of local structure around protein hydrogen bonds. It further provides a uniform vocabulary for comparison of protein structure near hydrogen bonds even between bonds in different proteins without alignment.

  2. A simple guide to biochemical approaches for analyzing protein-lipid interactions.

    Science.gov (United States)

    Zhao, Hongxia; Lappalainen, Pekka

    2012-08-01

    Eukaryotic cells contain many different membrane compartments with characteristic shapes, lipid compositions, and dynamics. A large fraction of cytoplasmic proteins associate with these membrane compartments. Such protein-lipid interactions, which regulate the subcellular localizations and activities of peripheral membrane proteins, are fundamentally important for a variety of cell biological processes ranging from cytoskeletal dynamics and membrane trafficking to intracellular signaling. Reciprocally, many membrane-associated proteins can modulate the shape, lipid composition, and dynamics of cellular membranes. Determining the exact mechanisms by which these proteins interact with membranes will be essential to understanding their biological functions. In this Technical Perspective, we provide a brief introduction to selected biochemical methods that can be applied to study protein-lipid interactions. We also discuss how important it is to choose proper lipid composition, type of model membrane, and biochemical assay to obtain reliable and informative data from the lipid-interaction mechanism of a protein of interest.

  3. Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus.

    Science.gov (United States)

    Shea, Patrick R; Virtaneva, Kimmo; Kupko, John J; Porcella, Stephen F; Barry, William T; Wright, Fred A; Kobayashi, Scott D; Carmody, Aaron; Ireland, Robin M; Sturdevant, Daniel E; Ricklefs, Stacy M; Babar, Imran; Johnson, Claire A; Graham, Morag R; Gardner, Donald J; Bailey, John R; Parnell, Michael J; Deleo, Frank R; Musser, James M

    2010-03-09

    Relatively little is understood about the dynamics of global host-pathogen transcriptome changes that occur during bacterial infection of mucosal surfaces. To test the hypothesis that group A Streptococcus (GAS) infection of the oropharynx provokes a distinct host transcriptome response, we performed genome-wide transcriptome analysis using a nonhuman primate model of experimental pharyngitis. We also identified host and pathogen biological processes and individual host and pathogen gene pairs with correlated patterns of expression, suggesting interaction. For this study, 509 host genes and seven biological pathways were differentially expressed throughout the entire 32-day infection cycle. GAS infection produced an initial widespread significant decrease in expression of many host genes, including those involved in cytokine production, vesicle formation, metabolism, and signal transduction. This repression lasted until day 4, at which time a large increase in expression of host genes was observed, including those involved in protein translation, antigen presentation, and GTP-mediated signaling. The interactome analysis identified 73 host and pathogen gene pairs with correlated expression levels. We discovered significant correlations between transcripts of GAS genes involved in hyaluronic capsule production and host endocytic vesicle formation, GAS GTPases and host fibrinolytic genes, and GAS response to interaction with neutrophils. We also identified a strong signal, suggesting interaction between host gammadelta T cells and genes in the GAS mevalonic acid synthesis pathway responsible for production of isopentenyl-pyrophosphate, a short-chain phospholipid that stimulates these T cells. Taken together, our results are unique in providing a comprehensive understanding of the host-pathogen interactome during mucosal infection by a bacterial pathogen.

  4. Interactome analysis of transcriptional coactivator multiprotein bridging factor 1 unveils a yeast AP-1-like transcription factor involved in oxidation tolerance of mycopathogen Beauveria bassiana.

    Science.gov (United States)

    Chu, Xin-Ling; Dong, Wei-Xia; Ding, Jin-Li; Feng, Ming-Guang; Ying, Sheng-Hua

    2018-02-01

    Oxidation tolerance is an important determinant to predict the virulence and biocontrol potential of Beauveria bassiana, a well-known entomopathogenic fungus. As a transcriptional coactivator, multiprotein bridging factor 1 mediates the activity of transcription factor in diverse physiological processes, and its homolog in B. bassiana (BbMBF1) contributes to fungal oxidation tolerance. In this study, the BbMBF1-interactomes under oxidative stress and normal growth condition were deciphered by mass spectrometry integrated with the immunoprecipitation. BbMBF1p factor has a broad interaction with proteins that are involved in various cellular processes, and this interaction is dynamically regulated by oxidative stress. Importantly, a B. bassiana homolog of yeast AP-1-like transcription factor (BbAP-1) was specifically associated with the BbMBF1-interactome under oxidation and significantly contributed to fungal oxidation tolerance. In addition, qPCR analysis revealed that several antioxidant genes are jointly controlled by BbAP-1 and BbMBF1. Conclusively, it is proposed that BbMBF1p protein mediates BbAP-1p factor to transcribe the downstream antioxidant genes in B. bassiana under oxidative stress. This study demonstrates for the first time a proteomic view of the MBF1-interactome in fungi, and presents an initial framework to probe the transcriptional mechanism involved in fungal response to oxidation, which will provide a new strategy to improve the biocontrol efficacy of B. bassiana.

  5. Analyzing the roles of multi-functional proteins in cells: The case of arrestins and GRKs.

    Science.gov (United States)

    Gurevich, Vsevolod V; Gurevich, Eugenia V

    2015-01-01

    Most proteins have multiple functions. Obviously, conventional methods of manipulating the level of the protein of interest in the cell, such as over-expression, knockout or knockdown, affect all of its functions simultaneously. The key advantage of these methods is that over-expression, knockout or knockdown does not require any knowledge of the molecular mechanisms of the function(s) of the protein of interest. The disadvantage is that these approaches are inadequate to elucidate the role of an individual function of the protein in a particular cellular process. An alternative is the use of re-engineered proteins, in which a single function is eliminated or enhanced. The use of mono-functional elements of a multi-functional protein can also yield cleaner answers. This approach requires detailed knowledge of the structural basis of each function of the protein in question. Thus, a lot of preliminary structure-function work is necessary to make it possible. However, when this information is available, replacing the protein of interest with a mutant in which individual functions are modified can shed light on the biological role of those particular functions. Here, we illustrate this point using the example of protein kinases, most of which have additional non-enzymatic functions, as well as arrestins, known multi-functional signaling regulators in the cell.

  6. Correlation between centromere protein-F autoantibodies and cancer analyzed by enzyme-linked immunosorbent assay

    DEFF Research Database (Denmark)

    Welner, Simon; Trier, Nicole Hartwig; Morten Frisch, Morten

    2013-01-01

    Centromere protein-F (CENP-F) is a large nuclear protein of 367 kDa, which is involved in multiple mitosis-related events such as proper assembly of the kinetochores, stabilization of heterochromatin, chromosome alignment and mitotic checkpoint signaling. Several studies have shown a correlation...

  7. Oligomeric state of membrane transport proteins analyzed with blue native electrophoresis and analytical ultracentrifugation

    NARCIS (Netherlands)

    Heuberger, E.H M L; Veenhoff, L.M.; Duurkens, R.H.T.; Friesen, R.H.E.; Poolman, B.

    2002-01-01

    Blue native electrophoresis is used widely for the analysis of non-dissociated protein complexes with respect to composition, oligomeric state and molecular mass. However, the effects of detergent or dye binding on the mass and stability of the integral membrane proteins have not been studied. By

  8. The Porphyromonas gingivalis/Host Interactome Shows Enrichment in GWASdb Genes Related to Alzheimer's Disease, Diabetes and Cardiovascular Diseases

    Directory of Open Access Journals (Sweden)

    Chris J. Carter

    2017-12-01

    Full Text Available Periodontal disease is of established etiology in which polymicrobial synergistic ecology has become dysbiotic under the influence of Porphyromonas gingivalis. Following breakdown of the host's protective oral tissue barriers, P. gingivalis migrates to developing inflammatory pathologies that associate with Alzheimer's disease (AD. Periodontal disease is a risk factor for cardiovascular disorders (CVD, type II diabetes mellitus (T2DM, AD and other chronic diseases, whilst T2DM exacerbates periodontitis. This study analyzed the relationship between the P. gingivalis/host interactome and the genes identified in genome-wide association studies (GWAS for the aforementioned conditions using data from GWASdb (P < 1E-03 and, in some cases, from the NCBI/EBI GWAS database (P < 1E-05. Gene expression data from periodontitis or P. gingivalis microarray was compared to microarray datasets from the AD hippocampus and/or from carotid artery plaques. The results demonstrated that the host genes of the P. gingivalis interactome were significantly enriched in genes deposited in GWASdb genes related to cognitive disorders, AD and dementia, and its co-morbid conditions T2DM, obesity, and CVD. The P. gingivalis/host interactome was also enriched in GWAS genes from the more stringent NCBI-EBI database for AD, atherosclerosis and T2DM. The misregulated genes in periodontitis tissue or P. gingivalis infected macrophages also matched those in the AD hippocampus or atherosclerotic plaques. Together, these data suggest important gene/environment interactions between P. gingivalis and susceptibility genes or gene expression changes in conditions where periodontal disease is a contributory factor.

  9. [Interactions between proteins and cation exchange adsorbents analyzed by NMR and hydrogen/deuterium exchange technique].

    Science.gov (United States)

    Wang, Kang; Hao, Dongxia; Qi, Shuting; Ma, Guanghui

    2014-09-01

    In silico acquirement of the accurate residue details of protein on chromatographic media is a bottleneck in protein chromatography separation and purification. Here we developed a novel approach by coupling with H/D exchange and nuclear magnetic resonance to observe hen egg white lysozyme (HEWL) unfolding behavior adsorbed on cation exchange media (SP Sepharose FF). Analysis of 1D 1H-NMR shows that protein unfolding accelerated H/D exchange rate, leading to more loss of signal of amide hydrogen owing to exposure of residues and the more unfolding of protein. Analysis of two-dimensional hydrogen-hydrogen total correlation spectroscopy shows that lysozyme lost more signals and experienced great unfolding during its adsorption on media surface. However, for several distinct fragments, the protection degrees varied, the adsorbed lysozyme lost more signal intensity and was less protected at disorder structures (coil, bend, and turn), but was comparatively more protected against exchange at secondary structure domains (α-helix, β-sheet). Finally, the binding site was determined by electrostatic calculations using computer simulation methods in conjunction with hydrogen deuterium labeled protein and NMR. This study would help deeply understand the microscopic mechanism of protein chromatography and guide the purposely design of chromatographic process and media. Moreover, it also provide an effective tool to study the protein and biomaterials interaction in other applications.

  10. An Overview of MYC and Its Interactome

    Science.gov (United States)

    Conacci-Sorrell, Maralice; McFerrin, Lisa; Eisenman, Robert N.

    2014-01-01

    This review is intended to provide a broad outline of the biological and molecular functions of MYC as well as of the larger protein network within which MYC operates. We present a view of MYC as a sensor that integrates multiple cellular signals to mediate a broad transcriptional response controlling many aspects of cell behavior. We also describe the larger transcriptional network linked to MYC with emphasis on the MXD family of MYC antagonists. Last, we discuss evidence that the network has evolved for millions of years, dating back to the emergence of animals. PMID:24384812

  11. Analyzing modifiers of protein aggregation in C. elegans by native agarose gel electrophoresis

    NARCIS (Netherlands)

    Holmberg, Mats; Nollen, Ellen A A; Hatters, Danny M.; Hannan, Anthony J.

    2013-01-01

    The accumulation of specific aggregation-prone proteins during aging is thought to be involved in several diseases, most notably Alzheimer's and Parkinson's disease as well as polyglutamine expansion disorders such as Huntington's disease. Caenorhabditis elegans disease models with transgenic

  12. A new theoretical approach to analyze complex processes in cytoskeleton proteins.

    Science.gov (United States)

    Li, Xin; Kolomeisky, Anatoly B

    2014-03-20

    Cytoskeleton proteins are filament structures that support a large number of important biological processes. These dynamic biopolymers exist in nonequilibrium conditions stimulated by hydrolysis chemical reactions in their monomers. Current theoretical methods provide a comprehensive picture of biochemical and biophysical processes in cytoskeleton proteins. However, the description is only qualitative under biologically relevant conditions because utilized theoretical mean-field models neglect correlations. We develop a new theoretical method to describe dynamic processes in cytoskeleton proteins that takes into account spatial correlations in the chemical composition of these biopolymers. Our approach is based on analysis of probabilities of different clusters of subunits. It allows us to obtain exact analytical expressions for a variety of dynamic properties of cytoskeleton filaments. By comparing theoretical predictions with Monte Carlo computer simulations, it is shown that our method provides a fully quantitative description of complex dynamic phenomena in cytoskeleton proteins under all conditions.

  13. A draft of the human septin interactome.

    Directory of Open Access Journals (Sweden)

    Marcel Nakahira

    Full Text Available BACKGROUND: Septins belong to the GTPase superclass of proteins and have been functionally implicated in cytokinesis and the maintenance of cellular morphology. They are found in all eukaryotes, except in plants. In mammals, 14 septins have been described that can be divided into four groups. It has been shown that mammalian septins can engage in homo- and heterooligomeric assemblies, in the form of filaments, which have as a basic unit a hetero-trimeric core. In addition, it has been speculated that the septin filaments may serve as scaffolds for the recruitment of additional proteins. METHODOLOGY/PRINCIPAL FINDINGS: Here, we performed yeast two-hybrid screens with human septins 1-10, which include representatives of all four septin groups. Among the interactors detected, we found predominantly other septins, confirming the tendency of septins to engage in the formation of homo- and heteropolymeric filaments. CONCLUSIONS/SIGNIFICANCE: If we take as reference the reported arrangement of the septins 2, 6 and 7 within the heterofilament, (7-6-2-2-6-7, we note that the majority of the observed interactions respect the "group rule", i.e. members of the same group (e.g. 6, 8, 10 and 11 can replace each other in the specific position along the heterofilament. Septins of the SEPT6 group preferentially interacted with septins of the SEPT2 group (p<0.001, SEPT3 group (p<0.001 and SEPT7 group (p<0.001. SEPT2 type septins preferentially interacted with septins of the SEPT6 group (p<0.001 aside from being the only septin group which interacted with members of its own group. Finally, septins of the SEPT3 group interacted preferentially with septins of the SEPT7 group (p<0.001. Furthermore, we found non-septin interactors which can be functionally attributed to a variety of different cellular activities, including: ubiquitin/sumoylation cycles, microtubular transport and motor activities, cell division and the cell cycle, cell motility, protein

  14. StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data.

    Science.gov (United States)

    Nurminen, Anssi; Hytönen, Vesa P; Valencia, Alfonso

    2018-02-14

    StructureMapper is a high-throughput algorithm for automated mapping of protein primary amino sequence locations to existing three-dimensional protein structures. The algorithm is intended for facilitating easy and efficient utilization of structural information in protein characterization and proteomics. StructureMapper provides an analysis of the identified structural locations that includes surface accessibility, flexibility, protein-protein interfacing, intrinsic disorder prediction, secondary structure assignment, biological assembly information, and sequence identity percentages, among other metrics. We have showcased the use of the algorithm by estimating the coverage of structural information of the human proteome, identifying critical interface residues in DNA polymerase γ, profiling structurally protease cleavage sites and post-translational modification sites, and by identifying putative, novel phosphoswitches. The StructureMapper algorithm is available as an online service and standalone implementation at http://structuremapper.uta.fi. vesa.hytonen@uta.fi. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

  15. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

    Science.gov (United States)

    Haney, P. J.; Badger, J. H.; Buldak, G. L.; Reich, C. I.; Woese, C. R.; Olsen, G. J.

    1999-01-01

    The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs from mesophilic Methanococcus species. Although the growth temperatures of the mesophiles are about 50 degrees C below that of M. jannaschii, their genomic G+C contents are nearly identical. The properties most correlated with the proteins of the thermophile include higher residue volume, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and fewer uncharged polar residues (Ser, Thr, Asn, and Gln). These are recurring themes, with all trends applying to 83-92% of the proteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature change are the same relatively conservative changes observed in all proteins, but in the case of the mesophile/thermophile comparison there is a directional bias. We identify 26 specific pairs of amino acids with a statistically significant (P < 0.01) preferred direction of replacement.

  16. Analyzing Forced Unfolding of Protein Tandems by Ordered Variates, 2: Dependent Unfolding Times

    Science.gov (United States)

    Bura, E.; Klimov, D. K.; Barsegov, V.

    2008-01-01

    Statistical analyses of forced unfolding data for protein tandems, i.e., unfolding forces (force-ramp) and unfolding times (force-clamp), used in single-molecule dynamic force spectroscopy rely on the assumption that the unfolding transitions of individual protein domains are independent (uncorrelated) and characterized, respectively, by identically distributed unfolding forces and unfolding times. In our previous work, we showed that in the experimentally accessible piconewton force range, this assumption, which holds at a lower constant force, may break at an elevated force level, i.e., the unfolding transitions may become correlated when force is increased. In this work, we develop much needed statistical tests for assessing the independence of the unobserved forced unfolding times for individual protein domains in the tandem and equality of their parent distributions, which are based solely on the observed ordered unfolding times. The use and performance of these tests are illustrated through the analysis of unfolding times for computer models of protein tandems. The proposed tests can be used in force-clamp atomic force microscopy experiments to obtain accurate information on protein forced unfolding and to probe data on the presence of interdomain interactions. The order statistics-based formalism is extended to cover the analysis of correlated unfolding transitions. The use of order statistics leads naturally to the development of new kinetic models, which describe the probabilities of ordered unfolding transitions rather than the populations of chemical species. PMID:18065466

  17. Adipocyte size and cellular expression of caveolar proteins analyzed by confocal microscopy

    DEFF Research Database (Denmark)

    Hulstrøm, Veronica; Prats Gavalda, Clara; Vinten, Jørgen

    2013-01-01

    Caveolae are abundant in adipocytes and are involved in the regulation of lipid accumulation, which is the main volume determinant of these cells. We have developed and applied a confocal microscopic technique for measuring individual cellular expression of the caveolar proteins cavin-1 and caveo......Caveolae are abundant in adipocytes and are involved in the regulation of lipid accumulation, which is the main volume determinant of these cells. We have developed and applied a confocal microscopic technique for measuring individual cellular expression of the caveolar proteins cavin-1...... and caveolin-1 along with the size of individual adipocytes. The technique was applied on collagenase isolated adipocytes from ad libitum fed Sprague-Dawley rats of different age (4-26 wk) and weight (103-629 g). We found that cellular expression of caveolar proteins was variable (SD of log expression...... in the range from 0.25 to 0.65). Regression analysis of protein expression on adipocyte size revealed that the expression of the caveolar proteins cavin-1 and caveolin-1 on adipocytes from individual rats was tightly related to adipocyte cell surface area (mean coefficient of regression was 0.83 for cavin...

  18. Lamina Associated Polypeptide 1 (LAP1 Interactome and Its Functional Features

    Directory of Open Access Journals (Sweden)

    Joana B. Serrano

    2016-01-01

    Full Text Available Lamina-associated polypeptide 1 (LAP1 is a type II transmembrane protein of the inner nuclear membrane encoded by the human gene TOR1AIP1. LAP1 is involved in maintaining the nuclear envelope structure and appears be involved in the positioning of lamins and chromatin. To date, LAP1’s precise function has not been fully elucidated but analysis of its interacting proteins will permit unraveling putative associations to specific cellular pathways and cellular processes. By assessing public databases it was possible to identify the LAP1 interactome, and this was curated. In total, 41 interactions were identified. Several functionally relevant proteins, such as TRF2, TERF2IP, RIF1, ATM, MAD2L1 and MAD2L1BP were identified and these support the putative functions proposed for LAP1. Furthermore, by making use of the Ingenuity Pathways Analysis tool and submitting the LAP1 interactors, the top two canonical pathways were “Telomerase signalling” and “Telomere Extension by Telomerase” and the top functions “Cell Morphology”, “Cellular Assembly and Organization” and “DNA Replication, Recombination, and Repair”. Once again, putative LAP1 functions are reinforced but novel functions are emerging.

  19. Intrinsic Disorder in PTEN and its Interactome Confers Structural Plasticity and Functional Versatility

    Science.gov (United States)

    Malaney, Prerna; Pathak, Ravi Ramesh; Xue, Bin; Uversky, Vladimir N.; Davé, Vrushank

    2013-01-01

    IDPs, while structurally poor, are functionally rich by virtue of their flexibility and modularity. However, how mutations in IDPs elicit diseases, remain elusive. Herein, we have identified tumor suppressor PTEN as an intrinsically disordered protein (IDP) and elucidated the molecular principles by which its intrinsically disordered region (IDR) at the carboxyl-terminus (C-tail) executes its functions. Post-translational modifications, conserved eukaryotic linear motifs and molecular recognition features present in the C-tail IDR enhance PTEN's protein-protein interactions that are required for its myriad cellular functions. PTEN primary and secondary interactomes are also enriched in IDPs, most being cancer related, revealing that PTEN functions emanate from and are nucleated by the C-tail IDR, which form pliable network-hubs. Together, PTEN higher order functional networks operate via multiple IDP-IDP interactions facilitated by its C-tail IDR. Targeting PTEN IDR and its interaction hubs emerges as a new paradigm for treatment of PTEN related pathologies. PMID:23783762

  20. Statistical applications in nutrigenomics : analyzing multiple genes and proteins in relation to complex diseases in humans

    NARCIS (Netherlands)

    Heidema, A.G.

    2008-01-01

    Background The recent advances in technology provide the possibility to obtain large genomic datasets that contain information on large numbers of variables, while the sample sizes are moderate to small. This has lead to statistical challenges in the analysis of multiple genes and proteins in

  1. Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ.

    NARCIS (Netherlands)

    Vischer, N.O.; Verheul, J.; Postma, M.; van den Berg van Saparoea, H.B.; Galli, E.; Natale, P.; Gerdes, K.; Luirink, J.; Vollmer, W.; Vicente, M.; den Blaauwen, T.

    2015-01-01

    The rod-shaped Gram-negative bacterium Escherichia coli multiplies by elongation followed by binary fission. Longitudinal growth of the cell envelope and synthesis of the new poles are organized by two protein complexes called elongasome and divisome, respectively. We have analyzed the

  2. Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ

    NARCIS (Netherlands)

    Vischer, N.O.E.; Verheul, J.; Postma, M.; van den Berg van Saparoea, B.; Galli, E.; Natale, P.; Gerdes, K.; Luirink, J.; Vollmer, W.; Vicente, M; den Blaauwen, T.

    2015-01-01

    The rod-shaped Gram-negative bacterium Escherichia coli multiplies by elongation followed by binary fission. Longitudinal growth of the cell envelope and synthesis of the new poles are organized by two protein complexes called elongasome and divisome, respectively. We have analyzed the

  3. Protein characterization of pasteurized milk, cheese whey and their mixtures by using the CEM SprintTM analyzer

    Directory of Open Access Journals (Sweden)

    Igor Moura Paiva

    2016-06-01

    Full Text Available In this work, the protein analyzer SprintTM was assessed regarding its capacity of predicting addition of whey in milk. This type of practice is relatively common in dairy plants, since whey, as it is a protein component, may be added with little loss of milk protein content. Besides,its incorrect elimination contributes to environmental pollution. Mixtures of milk and whey were prepared in different levels of addition and two methods of milk partition were tested. The results indicated that the concentration of trichloroacetic acid (TCA from the selected method was not suitable for the present purpose while the chosen method using glacial acetic acid (GAA has presented a satisfactory separation of the soluble and insoluble milk components. Even though the concentration of whey protein and casein are the essential parameters for determining whey addition in milk, the use of measurements from total protein was important in order to improve the linearity of the method due to the fact that the rates whey protein/total protein and casein/total protein presented the best results concerning fraud prediction capacity. Therefore, as the equipment is a rapid, safe and efficient platform, it can be used as an alternative to be implemented in laboratories of food quality control which perform or plan to perform assays to verify the whey addition in fluid milk.

  4. Analysis of the robustness of network-based disease-gene prioritization methods reveals redundancy in the human interactome and functional diversity of disease-genes.

    Directory of Open Access Journals (Sweden)

    Emre Guney

    Full Text Available Complex biological systems usually pose a trade-off between robustness and fragility where a small number of perturbations can substantially disrupt the system. Although biological systems are robust against changes in many external and internal conditions, even a single mutation can perturb the system substantially, giving rise to a pathophenotype. Recent advances in identifying and analyzing the sequential variations beneath human disorders help to comprehend a systemic view of the mechanisms underlying various disease phenotypes. Network-based disease-gene prioritization methods rank the relevance of genes in a disease under the hypothesis that genes whose proteins interact with each other tend to exhibit similar phenotypes. In this study, we have tested the robustness of several network-based disease-gene prioritization methods with respect to the perturbations of the system using various disease phenotypes from the Online Mendelian Inheritance in Man database. These perturbations have been introduced either in the protein-protein interaction network or in the set of known disease-gene associations. As the network-based disease-gene prioritization methods are based on the connectivity between known disease-gene associations, we have further used these methods to categorize the pathophenotypes with respect to the recoverability of hidden disease-genes. Our results have suggested that, in general, disease-genes are connected through multiple paths in the human interactome. Moreover, even when these paths are disturbed, network-based prioritization can reveal hidden disease-gene associations in some pathophenotypes such as breast cancer, cardiomyopathy, diabetes, leukemia, parkinson disease and obesity to a greater extend compared to the rest of the pathophenotypes tested in this study. Gene Ontology (GO analysis highlighted the role of functional diversity for such diseases.

  5. Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ

    Directory of Open Access Journals (Sweden)

    Norbert O.E. Vischer

    2015-06-01

    Full Text Available The rod-shaped Gram-negative bacterium Escherichia coli multiplies by elongation followed by binary fission. Longitudinal growth of the cell envelope and synthesis of the new poles are organized by two protein complexes called elongasome and divisome, respectively. We have analyzed the spatio-temporal localization patterns of many of these morphogenetic proteins by immunolabeling the wild type strain MC4100 grown to steady state in minimal glucose medium at 28°C. This allowed the direct comparison of morphogenetic protein localization patterns as a function of cell age as imaged by phase contrast and fluorescence wide field microscopy. Under steady state conditions the age distribution of the cells is constant and is directly correlated to cell length. To quantify cell size and protein localization parameters in thousands of labeled cells, we developed 'Coli-Inspector', which is a project running under ImageJ with the plugin 'ObjectJ'. ObjectJ organizes image-analysis tasks using an integrated approach with the flexibility to produce different output formats from existing markers such as intensity data and geometrical parameters. ObjectJ supports the combination of automatic and interactive methods giving the user complete control over the method of image analysis and data collection, with visual inspection tools for quick elimination of artifacts. Coli-inspector was used to sort the cells according to division cycle cell age and to analyze the spatio-temporal localization pattern of each protein. A unique dataset has been created on the concentration and position of the proteins during the cell cycle. We show for the first time that a subset of morphogenetic proteins have a constant cellular concentration during the cell division cycle whereas another set exhibits a cell division cycle dependent concentration variation. Using the number of proteins present at midcell, the stoichiometry of the divisome is discussed.

  6. Deciphering peculiar protein-protein interacting modules in Deinococcus radiodurans

    Directory of Open Access Journals (Sweden)

    Barkallah Insaf

    2009-04-01

    Full Text Available Abstract Interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (IRRB might be a part of the answer to the question as to how IRRB, particularly Deinococcus radiodurans R1 (Deira, resist ionizing radiation. Here, using the Database of Interacting Proteins (DIP and the Protein Structural Interactome (PSI-base server for PSI map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in Deira and other IRRB, but which are absent in IRSB. Among these, 18 domains and their interactomes have been identified in DNA checkpoint and repair; kinases pathways; energy and nucleotide metabolisms were the important biological processes that were found to be involved. This finding provides new clues to the cellular pathways that can to be important for ionizing-radiation resistance in Deira.

  7. An affinity pull-down approach to identify the plant cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara Elizabeth

    2013-09-03

    Cyclic nucleotides (CNs) are intracellular second messengers that play an important role in mediating physiological responses to environmental and developmental signals, in species ranging from bacteria to humans. In response to these signals, CNs are synthesized by nucleotidyl cyclases and then act by binding to and altering the activity of downstream target proteins known as cyclic nucleotide-binding proteins (CNBPs). A number of CNBPs have been identified across kingdoms including transcription factors, protein kinases, phosphodiesterases, and channels, all of which harbor conserved CN-binding domains. In plants however, few CNBPs have been identified as homology searches fail to return plant sequences with significant matches to known CNBPs. Recently, affinity pull-down techniques have been successfully used to identify CNBPs in animals and have provided new insights into CN signaling. The application of these techniques to plants has not yet been extensively explored and offers an alternative approach toward the unbiased discovery of novel CNBP candidates in plants. Here, an affinity pull-down technique for the identification of the plant CN interactome is presented. In summary, the method involves an extraction of plant proteins which is incubated with a CN-bait, followed by a series of increasingly stringent elutions that eliminates proteins in a sequential manner according to their affinity to the bait. The eluted and bait-bound proteins are separated by one-dimensional gel electrophoresis, excised, and digested with trypsin after which the resultant peptides are identified by mass spectrometry - techniques that are commonplace in proteomics experiments. The discovery of plant CNBPs promises to provide valuable insight into the mechanism of CN signal transduction in plants. © Springer Science+Business Media New York 2013.

  8. Analyzing the pathways enriched in genes associated with nicotine dependence in the context of human protein-protein interaction network.

    Science.gov (United States)

    Hu, Ying; Fang, Zhonghai; Yang, Yichen; Fan, Ting; Wang, Ju

    2018-03-16

    Nicotine dependence is the primary addictive stage of cigarette smoking. Although a lot of studies have been performed to explore the molecular mechanism underlying nicotine dependence, our understanding on this disorder is still far from complete. Over the past decades, an increasing number of candidate genes involved in nicotine dependence have been identified by different technical approaches, including the genetic association analysis. In this study, we performed a comprehensive collection of candidate genes reported to be genetically associated with nicotine dependence. Then, the biochemical pathways enriched in these genes were identified by considering the gene's propensity to be related to nicotine dependence. One of the most widely used pathway enrichment analysis approach, over-representation analysis, ignores the function non-equivalence of genes in candidate gene set and may have low discriminative power in identifying some dysfunctional pathways. To overcome such drawbacks, we constructed a comprehensive human protein-protein interaction network, and then assigned a function weighting score to each candidate gene based on their network topological features. Evaluation indicated the function weighting score scheme was consistent with available evidence. Finally, the function weighting scores of the candidate genes were incorporated into pathway analysis to identify the dysfunctional pathways involved in nicotine dependence, and the interactions between pathways was detected by pathway crosstalk analysis. Compared to conventional over-representation based pathway analysis tool, the modified method exhibited improved discriminative power and detected some novel pathways potentially underlying nicotine dependence. In summary, we conducted a comprehensive collection of genes associated with nicotine dependence and then detected the biochemical pathways enriched in these genes using a modified pathway enrichment analysis approach with function weighting

  9. Characterization of the Cardiac Overexpression of HSPB2 Reveals Mitochondrial and Myogenic Roles Supported by a Cardiac HspB2 Interactome.

    Directory of Open Access Journals (Sweden)

    Julianne H Grose

    Full Text Available Small Heat Shock Proteins (sHSPs are molecular chaperones that transiently interact with other proteins, thereby assisting with quality control of proper protein folding and/or degradation. They are also recruited to protect cells from a variety of stresses in response to extreme heat, heavy metals, and oxidative-reductive stress. Although ten human sHSPs have been identified, their likely diverse biological functions remain an enigma in health and disease, and much less is known about non-redundant roles in selective cells and tissues. Herein, we set out to comprehensively characterize the cardiac-restricted Heat Shock Protein B-2 (HspB2, which exhibited ischemic cardioprotection in transgenic overexpressing mice including reduced infarct size and maintenance of ATP levels. Global yeast two-hybrid analysis using HspB2 (bait and a human cardiac library (prey coupled with co-immunoprecipitation studies for mitochondrial target validation revealed the first HspB2 "cardiac interactome" to contain many myofibril and mitochondrial-binding partners consistent with the overexpression phenotype. This interactome has been submitted to the Biological General Repository for Interaction Datasets (BioGRID. A related sHSP chaperone HspB5 had only partially overlapping binding partners, supporting specificity of the interactome as well as non-redundant roles reported for these sHSPs. Evidence that the cardiac yeast two-hybrid HspB2 interactome targets resident mitochondrial client proteins is consistent with the role of HspB2 in maintaining ATP levels and suggests new chaperone-dependent functions for metabolic homeostasis. One of the HspB2 targets, glyceraldehyde 3-phosphate dehydrogenase (GAPDH, has reported roles in HspB2 associated phenotypes including cardiac ATP production, mitochondrial function, and apoptosis, and was validated as a potential client protein of HspB2 through chaperone assays. From the clientele and phenotypes identified herein, it is

  10. Factors affecting interactome-based prediction of human genes associated with clinical signs.

    Science.gov (United States)

    González-Pérez, Sara; Pazos, Florencio; Chagoyen, Mónica

    2017-07-17

    Clinical signs are a fundamental aspect of human pathologies. While disease diagnosis is problematic or impossible in many cases, signs are easier to perceive and categorize. Clinical signs are increasingly used, together with molecular networks, to prioritize detected variants in clinical genomics pipelines, even if the patient is still undiagnosed. Here we analyze the ability of these network-based methods to predict genes that underlie clinical signs from the human interactome. Our analysis reveals that these approaches can locate genes associated with clinical signs with variable performance that depends on the sign and associated disease. We analyzed several clinical and biological factors that explain these variable results, including number of genes involved (mono- vs. oligogenic diseases), mode of inheritance, type of clinical sign and gene product function. Our results indicate that the characteristics of the clinical signs and their related diseases should be considered for interpreting the results of network-prediction methods, such as those aimed at discovering disease-related genes and variants. These results are important due the increasing use of clinical signs as an alternative to diseases for studying the molecular basis of human pathologies.

  11. Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6mb00701e Click here for additional data file. Click here for additional data file.

    Science.gov (United States)

    Sailem, Heba Z.; Kümper, Sandra; Tape, Christopher J.; McCully, Ryan R.; Paul, Angela; Anjomani-Virmouni, Sara; Jørgensen, Claus; Poulogiannis, George; Marshall, Christopher J.

    2017-01-01

    Localisation and protein function are intimately linked in eukaryotes, as proteins are localised to specific compartments where they come into proximity of other functionally relevant proteins. Significant co-localisation of two proteins can therefore be indicative of their functional association. We here present COLA, a proteomics based strategy coupled with a bioinformatics framework to detect protein–protein co-localisations on a global scale. COLA reveals functional interactions by matching proteins with significant similarity in their subcellular localisation signatures. The rapid nature of COLA allows mapping of interactome dynamics across different conditions or treatments with high precision. PMID:27824369

  12. Weighted Protein Interaction Network Analysis of Frontotemporal Dementia.

    Science.gov (United States)

    Ferrari, Raffaele; Lovering, Ruth C; Hardy, John; Lewis, Patrick A; Manzoni, Claudia

    2017-02-03

    The genetic analysis of complex disorders has undoubtedly led to the identification of a wealth of associations between genes and specific traits. However, moving from genetics to biochemistry one gene at a time has, to date, rather proved inefficient and under-powered to comprehensively explain the molecular basis of phenotypes. Here we present a novel approach, weighted protein-protein interaction network analysis (W-PPI-NA), to highlight key functional players within relevant biological processes associated with a given trait. This is exemplified in the current study by applying W-PPI-NA to frontotemporal dementia (FTD): We first built the state of the art FTD protein network (FTD-PN) and then analyzed both its topological and functional features. The FTD-PN resulted from the sum of the individual interactomes built around FTD-spectrum genes, leading to a total of 4198 nodes. Twenty nine of 4198 nodes, called inter-interactome hubs (IIHs), represented those interactors able to bridge over 60% of the individual interactomes. Functional annotation analysis not only reiterated and reinforced previous findings from single genes and gene-coexpression analyses but also indicated a number of novel potential disease related mechanisms, including DNA damage response, gene expression regulation, and cell waste disposal and potential biomarkers or therapeutic targets including EP300. These processes and targets likely represent the functional core impacted in FTD, reflecting the underlying genetic architecture contributing to disease. The approach presented in this study can be applied to other complex traits for which risk-causative genes are known as it provides a promising tool for setting the foundations for collating genomics and wet laboratory data in a bidirectional manner. This is and will be critical to accelerate molecular target prioritization and drug discovery.

  13. Predicting interactome network perturbations in human cancer: application to gene fusions in acute lymphoblastic leukemia

    Science.gov (United States)

    Hajingabo, Leon Juvenal; Daakour, Sarah; Martin, Maud; Grausenburger, Reinhard; Panzer-Grümayer, Renate; Dequiedt, Franck; Simonis, Nicolas; Twizere, Jean-Claude

    2014-01-01

    Genomic variations such as point mutations and gene fusions are directly or indirectly associated with human diseases. They are recognized as diagnostic, prognostic markers and therapeutic targets. However, predicting the functional effect of these genetic alterations beyond affected genes and their products is challenging because diseased phenotypes are likely dependent of complex molecular interaction networks. Using as models three different chromosomal translocations—ETV6-RUNX1 (TEL-AML1), BCR-ABL1, and TCF3-PBX1 (E2A-PBX1)—frequently found in precursor-B-cell acute lymphoblastic leukemia (preB-ALL), we develop an approach to extract perturbed molecular interactions from gene expression changes. We show that the MYC and JunD transcriptional circuits are specifically deregulated after ETV6-RUNX1 and TCF3-PBX1 gene fusions, respectively. We also identified the bulk mRNA NXF1-dependent machinery as a direct target for the TCF3-PBX1 fusion protein. Through a novel approach combining gene expression and interactome data analysis, we provide new insight into TCF3-PBX1 and ETV6-RUNX1 acute lymphoblastic leukemia. PMID:25273558

  14. Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

    Directory of Open Access Journals (Sweden)

    Kevin M. Harlen

    2016-06-01

    Full Text Available Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II C-terminal domain (CTD and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7, we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3′ end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3′ splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes.

  15. Exploitation of complex network topology for link prediction in biological interactomes

    KAUST Repository

    Alanis Lobato, Gregorio

    2014-06-01

    The network representation of the interactions between proteins and genes allows for a holistic perspective of the complex machinery underlying the living cell. However, the large number of interacting entities within the cell makes network construction a daunting and arduous task, prone to errors and missing information. Fortunately, the structure of biological networks is not different from that of other complex systems, such as social networks, the world-wide web or power grids, for which growth models have been proposed to better understand their structure and function. This means that we can design tools based on these models in order to exploit the topology of biological interactomes with the aim to construct more complete and reliable maps of the cell. In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable and biologically meaningful information that enriches the datasets to which we have access today.

  16. Structure homology and interaction redundancy for discovering virus–host protein interactions

    Science.gov (United States)

    de Chassey, Benoît; Meyniel-Schicklin, Laurène; Aublin-Gex, Anne; Navratil, Vincent; Chantier, Thibaut; André, Patrice; Lotteau, Vincent

    2013-01-01

    Virus–host interactomes are instrumental to understand global perturbations of cellular functions induced by infection and discover new therapies. The construction of such interactomes is, however, technically challenging and time consuming. Here we describe an original method for the prediction of high-confidence interactions between viral and human proteins through a combination of structure and high-quality interactome data. Validation was performed for the NS1 protein of the influenza virus, which led to the identification of new host factors that control viral replication. PMID:24008843

  17. Structure homology and interaction redundancy for discovering virus-host protein interactions.

    Science.gov (United States)

    de Chassey, Benoît; Meyniel-Schicklin, Laurène; Aublin-Gex, Anne; Navratil, Vincent; Chantier, Thibaut; André, Patrice; Lotteau, Vincent

    2013-10-01

    Virus-host interactomes are instrumental to understand global perturbations of cellular functions induced by infection and discover new therapies. The construction of such interactomes is, however, technically challenging and time consuming. Here we describe an original method for the prediction of high-confidence interactions between viral and human proteins through a combination of structure and high-quality interactome data. Validation was performed for the NS1 protein of the influenza virus, which led to the identification of new host factors that control viral replication.

  18. Characterization of clinical signs in the human interactome.

    Science.gov (United States)

    Chagoyen, Monica; Pazos, Florencio

    2016-06-15

    Many diseases are related by shared associated molecules and pathways, exhibiting comorbidities and common phenotypes, an indication of the continuous nature of the human pathological landscape. Although it is continuous, this landscape is always partitioned into discrete diseases when studied at the molecular level. Clinical signs are also important phenotypic descriptors that can reveal the molecular mechanisms that underlie pathological states, but have seldom been the subject of systemic research. Here, we quantify the modular nature of the clinical signs associated with genetic diseases in the human interactome. We found that clinical signs are reflected as modules at the molecular network level, to at least to the same extent as diseases. They can thus serve as a valid complementary partition of the human pathological landscape, with implications for etiology research, diagnosis and treatment. monica.chagoyen@cnb.csic.es Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development.

    Science.gov (United States)

    Kunz, Meik; Liang, Chunguang; Nilla, Santosh; Cecil, Alexander; Dandekar, Thomas

    2016-01-01

    The drug-minded protein interaction database (DrumPID) has been designed to provide fast, tailored information on drugs and their protein networks including indications, protein targets and side-targets. Starting queries include compound, target and protein interactions and organism-specific protein families. Furthermore, drug name, chemical structures and their SMILES notation, affected proteins (potential drug targets), organisms as well as diseases can be queried including various combinations and refinement of searches. Drugs and protein interactions are analyzed in detail with reference to protein structures and catalytic domains, related compound structures as well as potential targets in other organisms. DrumPID considers drug functionality, compound similarity, target structure, interactome analysis and organismic range for a compound, useful for drug development, predicting drug side-effects and structure-activity relationships.Database URL:http://drumpid.bioapps.biozentrum.uni-wuerzburg.de. © The Author(s) 2016. Published by Oxford University Press.

  20. Disease networks. Uncovering disease-disease relationships through the incomplete interactome.

    Science.gov (United States)

    Menche, Jörg; Sharma, Amitabh; Kitsak, Maksim; Ghiassian, Susan Dina; Vidal, Marc; Loscalzo, Joseph; Barabási, Albert-László

    2015-02-20

    According to the disease module hypothesis, the cellular components associated with a disease segregate in the same neighborhood of the human interactome, the map of biologically relevant molecular interactions. Yet, given the incompleteness of the interactome and the limited knowledge of disease-associated genes, it is not obvious if the available data have sufficient coverage to map out modules associated with each disease. Here we derive mathematical conditions for the identifiability of disease modules and show that the network-based location of each disease module determines its pathobiological relationship to other diseases. For example, diseases with overlapping network modules show significant coexpression patterns, symptom similarity, and comorbidity, whereas diseases residing in separated network neighborhoods are phenotypically distinct. These tools represent an interactome-based platform to predict molecular commonalities between phenotypically related diseases, even if they do not share primary disease genes. Copyright © 2015, American Association for the Advancement of Science.

  1. System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of soybean (Glycine max.

    Directory of Open Access Journals (Sweden)

    Yungang Xu

    Full Text Available Cellular interactome, in which genes and/or their products interact on several levels, forming transcriptional regulatory-, protein interaction-, metabolic-, signal transduction networks, etc., has attracted decades of research focuses. However, such a specific type of network alone can hardly explain the various interactive activities among genes. These networks characterize different interaction relationships, implying their unique intrinsic properties and defects, and covering different slices of biological information. Functional gene network (FGN, a consolidated interaction network that models fuzzy and more generalized notion of gene-gene relations, have been proposed to combine heterogeneous networks with the goal of identifying functional modules supported by multiple interaction types. There are yet no successful precedents of FGNs on sparsely studied non-model organisms, such as soybean (Glycine max, due to the absence of sufficient heterogeneous interaction data. We present an alternative solution for inferring the FGNs of soybean (SoyFGNs, in a pioneering study on the soybean interactome, which is also applicable to other organisms. SoyFGNs exhibit the typical characteristics of biological networks: scale-free, small-world architecture and modularization. Verified by co-expression and KEGG pathways, SoyFGNs are more extensive and accurate than an orthology network derived from Arabidopsis. As a case study, network-guided disease-resistance gene discovery indicates that SoyFGNs can provide system-level studies on gene functions and interactions. This work suggests that inferring and modelling the interactome of a non-model plant are feasible. It will speed up the discovery and definition of the functions and interactions of other genes that control important functions, such as nitrogen fixation and protein or lipid synthesis. The efforts of the study are the basis of our further comprehensive studies on the soybean functional

  2. Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme

    Directory of Open Access Journals (Sweden)

    Moschopoulos Charalampos

    2011-06-01

    Full Text Available Abstract Background Recent technological advances applied to biology such as yeast-two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of protein interaction networks. These interaction networks represent a rich, yet noisy, source of data that could be used to extract meaningful information, such as protein complexes. Several interaction network weighting schemes have been proposed so far in the literature in order to eliminate the noise inherent in interactome data. In this paper, we propose a novel weighting scheme and apply it to the S. cerevisiae interactome. Complex prediction rates are improved by up to 39%, depending on the clustering algorithm applied. Results We adopt a two step procedure. During the first step, by applying both novel and well established protein-protein interaction (PPI weighting methods, weights are introduced to the original interactome graph based on the confidence level that a given interaction is a true-positive one. The second step applies clustering using established algorithms in the field of graph theory, as well as two variations of Spectral clustering. The clustered interactome networks are also cross-validated against the confirmed protein complexes present in the MIPS database. Conclusions The results of our experimental work demonstrate that interactome graph weighting methods clearly improve the clustering results of several clustering algorithms. Moreover, our proposed weighting scheme outperforms other approaches of PPI graph weighting.

  3. MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria.

    Directory of Open Access Journals (Sweden)

    Jiabin Wang

    Full Text Available Mitochondrion plays a central role in diverse biological processes in most eukaryotes, and its dysfunctions are critically involved in a large number of diseases and the aging process. A systematic identification of mitochondrial proteomes and characterization of functional linkages among mitochondrial proteins are fundamental in understanding the mechanisms underlying biological functions and human diseases associated with mitochondria. Here we present a database MitProNet which provides a comprehensive knowledgebase for mitochondrial proteome, interactome and human diseases. First an inventory of mammalian mitochondrial proteins was compiled by widely collecting proteomic datasets, and the proteins were classified by machine learning to achieve a high-confidence list of mitochondrial proteins. The current version of MitProNet covers 1124 high-confidence proteins, and the remainders were further classified as middle- or low-confidence. An organelle-specific network of functional linkages among mitochondrial proteins was then generated by integrating genomic features encoded by a wide range of datasets including genomic context, gene expression profiles, protein-protein interactions, functional similarity and metabolic pathways. The functional-linkage network should be a valuable resource for the study of biological functions of mitochondrial proteins and human mitochondrial diseases. Furthermore, we utilized the network to predict candidate genes for mitochondrial diseases using prioritization algorithms. All proteins, functional linkages and disease candidate genes in MitProNet were annotated according to the information collected from their original sources including GO, GEO, OMIM, KEGG, MIPS, HPRD and so on. MitProNet features a user-friendly graphic visualization interface to present functional analysis of linkage networks. As an up-to-date database and analysis platform, MitProNet should be particularly helpful in comprehensive studies of

  4. The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine.

    Science.gov (United States)

    Cortese-Krott, Miriam M; Koning, Anne; Kuhnle, Gunter G C; Nagy, Peter; Bianco, Christopher L; Pasch, Andreas; Wink, David A; Fukuto, Jon M; Jackson, Alan A; van Goor, Harry; Olson, Kenneth R; Feelisch, Martin

    2017-10-01

    Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 00, 000-000.

  5. Protein complexes in the archaeon Methanothermobacter thermautotrophicus analyzed by blue native/SDS-PAGE and mass spectrometry.

    NARCIS (Netherlands)

    Farhoud, M.H.; Wessels, H.C.T.; Steenbakkers, P.J.M.; Mattijssen, S.; Wevers, R.A.; Engelen, B.G.M. van; Jetten, M.S.M.; Smeitink, J.A.M.; Heuvel, L.P.W.J. van den; Keltjens, J.T.M.

    2005-01-01

    Methanothermobacter thermautotrophicus is a thermophilic archaeon that produces methane as the end product of its primary metabolism. The biochemistry of methane formation has been extensively studied and is catalyzed by individual enzymes and proteins that are organized in protein complexes.

  6. Analyzing Protein Micro-Heterogeneity in Chicken Ovalbumin by High-Resolution Native Mass Spectrometry Exposes Qualitatively and Semi-Quantitatively 59 Proteoforms

    NARCIS (Netherlands)

    Yang, Y.; Barendregt, A.; Kamerling, J.P.; Heck, A.J.R.

    2013-01-01

    Taking chicken Ovalbumin as a prototypical example of a eukaryotic protein we use high-resolution native electrospray ionization mass spectrometry on a modified Exactive Orbitrap mass analyzer to qualitatively and semiquantitatively dissect 59 proteoforms in the natural protein. This variety is

  7. Protein function prediction involved on radio-resistant bacteria

    International Nuclear Information System (INIS)

    Mezhoud, Karim; Mankai, Houda; Sghaier, Haitham; Barkallah, Insaf

    2009-01-01

    Previously, we identified 58 proteins under positive selection in ionizing-radiation-resistant bacteria (IRRB) but absent in all ionizing-radiation-sensitive bacteria (IRSB). These are good reasons to believe these 58 proteins with their interactions with other proteins (interactomes) are a part of the answer to the question as to how IRRB resist to radiation, because our knowledge of interactomes of positively selected orphan proteins in IRRB might allow us to define cellular pathways important to ionizing-radiation resistance. Using the Database of Interacting Proteins and the PSIbase, we have predicted interactions of orthologs of the 58 proteins under positive selection in IRRB but absent in all IRSB. We used integrate experimental data sets with molecular interaction networks and protein structure prediction from databases. Among these, 18 proteins with their interactomes were identified in Deinococcus radiodurans R1. DNA checkpoint and repair, kinases pathways, energetic and nucleotide metabolisms were the important biological process that found. We predicted the interactomes of 58 proteins under positive selection in IRRB. It is hoped our data will provide new clues as to the cellular pathways that are important for ionizing-radiation resistance. We have identified news proteins involved on DNA management which were not previously mentioned. It is an important input in addition to protein that studied. It does still work to deepen our study on these new proteins

  8. Building protein-protein interaction networks for Leishmania species through protein structural information.

    Science.gov (United States)

    Dos Santos Vasconcelos, Crhisllane Rafaele; de Lima Campos, Túlio; Rezende, Antonio Mauro

    2018-03-06

    Systematic analysis of a parasite interactome is a key approach to understand different biological processes. It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum. These parasites cause Leishmaniasis, a worldwide distributed and neglected disease, with limited treatment options using currently available drugs. The predicted interactions were obtained from a meta-approach, applying rigid body docking tests and template-based docking on protein structures predicted by different comparative modeling techniques. In addition, we trained a machine-learning algorithm (Gradient Boosting) using docking information performed on a curated set of positive and negative protein interaction data. Our final model obtained an AUC = 0.88, with recall = 0.69, specificity = 0.88 and precision = 0.83. Using this approach, it was possible to confidently predict 681 protein structures and 6198 protein interactions for L. braziliensis, and 708 protein structures and 7391 protein interactions for L. infantum. The predicted networks were integrated to protein interaction data already available, analyzed using several topological features and used to classify proteins as essential for network stability. The present study allowed to demonstrate the importance of integrating different methodologies of interaction prediction to increase the coverage of the protein interaction of the studied protocols, besides it made available protein structures and interactions not previously reported.

  9. Defining a Modular Signalling Network from the Fly Interactome

    OpenAIRE

    Jacq Bernard; Guénoche Alain; Angelelli Jean-Baptiste; Baudot Anaïs; Brun Christine

    2008-01-01

    Abstract Background Signalling pathways relay information by transmitting signals from cell surface receptors to intracellular effectors that eventually activate the transcription of target genes. Since signalling pathways involve several types of molecular interactions including protein-protein interactions, we postulated that investigating their organization in the context of the global protein-protein interaction network could provide a new integrated view of signalling mechanisms. Results...

  10. MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

    KAUST Repository

    Abdel-Azeim, Safwat

    2014-05-06

    Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

  11. Analyzing bean extracts using time-dependent SDS trapping to quantify the kinetic stability of phaseolin proteins.

    Science.gov (United States)

    Thibeault, Jane; Church, Jennifer; Ortiz-Perez, Brian; Addo, Samuel; Hill, Shakeema; Khalil, Areeg; Young, Malaney; Xia, Ke; Colón, Wilfredo

    2017-09-30

    In common beans and lima bean, the storage protein phaseolin is difficult to degrade and SDS-resistant, a sign of kinetic stability. Kinetically stable proteins (KSPs) are characterized by having a high-energy barrier between the native and denatured states that results in very slow unfolding. Such proteins are resistant to proteolytic degradation and detergents, such as SDS. Here the method SDS-Trapping of Proteins (S-TraP) is applied directly on bean extracts to quantify the kinetic stability of phaseolin in lima bean and several common beans, including black bean, navy bean, and small red bean. The bean extracts were incubated in SDS at various temperatures (60-75 °C) for different time periods, followed by SDS-PAGE analysis at room temperature, and subsequent band quantification to determine the kinetics of phaseolin unfolding. Eyring plot analysis showed that the phaseolin from each bean has high kinetic stability, with an SDS-trapping (i.e. unfolding) half-life ranging from about 20-100 years at 24 °C and 2-7 years at 37 °C. The remarkably high kinetic stability of these phaseolin proteins is consistent with the low digestibility of common beans and lima bean, as well as their relatively high germination temperatures. From a practical perspective, this work exemplifies that S-TraP is a useful and cost-effective method for quantifying the kinetic stability of proteins in biological extracts or lysates. Depending on the protein to be studied and its abundance, S-TraP may be performed directly on the extract without need for protein purification. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Differentially regulated proteins in Prevotella intermedia after oxidative stress analyzed by 2D electrophoresis and mass spectrometry.

    Science.gov (United States)

    Santos, Simone G; Diniz, Cláudio G; Silva, Vânia L; Lima, Francisca L; Andrade, Hélida M; Chapeaurouge, Donat A; Perales, Jonas; Serufo, José Carlos; Carvalho, Maria Auxiliadora R; Farias, Luiz M

    2012-02-01

    Prevotella intermedia is a rod-shaped, Gram-negative anaerobic bacterium found in human indigenous microbiota that plays an important role in opportunistic infections. The successful colonization depends on the ability of anaerobes to respond to oxidative stress (OS) in oxygenated tissues as well as to resist oxidative events from the host immune system until anaerobic conditions are present at the infection site. As knowledge of the mechanisms of protection against OS in Prevotella is limited, studies are needed to clarify aspects of molecular biology, physiology and ecology of this bacterium. The aim of this study was to access the proteins differentially regulated in P. intermedia after exposure to molecular oxygen by using two-dimensional gel electrophoresis (2DE) associated with the approach of MALDI-TOF/TOF Tandem Mass Spectrometry. The identity of the protein was evaluated by database search for homologous genomic sequences of P. intermedia strain 17 (TIGR). Twenty five out of 72 proteins found were identified as up-regulated (17) or down-regulated (9). These proteins were related to a variety of metabolic process, some of which could be associated to antioxidant and redox regulatory roles. Our data indicate that OS may stimulate an adaptive response in P. intermedia whose effect on its biology may be evidenced by the increase in aerotolerance and changes in protein abundance in the oxygen adapted cells. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Supplementary Material for: The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara

    2016-01-01

    Abstract Background Cyclic nucleotides have been shown to play important signaling roles in many physiological processes in plants including photosynthesis and defence. Despite this, little is known about cyclic nucleotide-dependent signaling mechanisms in plants since the downstream target proteins remain unknown. This is largely due to the fact that bioinformatics searches fail to identify plant homologs of protein kinases and phosphodiesterases that are the main targets of cyclic nucleotides in animals. Methods An affinity purification technique was used to identify cyclic nucleotide binding proteins in Arabidopsis thaliana. The identified proteins were subjected to a computational analysis that included a sequence, transcriptional co-expression and functional annotation analysis in order to assess their potential role in plant cyclic nucleotide signaling. Results A total of twelve cyclic nucleotide binding proteins were identified experimentally including key enzymes in the Calvin cycle and photorespiration pathway. Importantly, eight of the twelve proteins were shown to contain putative cyclic nucleotide binding domains. Moreover, the identified proteins are post-translationally modified by nitric oxide, transcriptionally co-expressed and annotated to function in hydrogen peroxide signaling and the defence response. The activity of one of these proteins, GLYGOLATE OXIDASE 1, a photorespiratory enzyme that produces hydrogen peroxide in response to Pseudomonas, was shown to be repressed by a combination of cGMP and nitric oxide treatment. Conclusions We propose that the identified proteins function together as points of cross-talk between cyclic nucleotide, nitric oxide and reactive oxygen species signaling during the defence response.

  14. Updating the Cornell Net Carbohydrate and Protein System feed library and analyzing model sensitivity to feed inputs.

    Science.gov (United States)

    Higgs, R J; Chase, L E; Ross, D A; Van Amburgh, M E

    2015-09-01

    The Cornell Net Carbohydrate and Protein System (CNCPS) is a nutritional model that evaluates the environmental and nutritional resources available in an animal production system and enables the formulation of diets that closely match the predicted animal requirements. The model includes a library of approximately 800 different ingredients that provide the platform for describing the chemical composition of the diet to be formulated. Each feed in the feed library was evaluated against data from 2 commercial laboratories and updated when required to enable more precise predictions of dietary energy and protein supply. A multistep approach was developed to predict uncertain values using linear regression, matrix regression, and optimization. The approach provided an efficient and repeatable way of evaluating and refining the composition of a large number of different feeds against commercially generated data similar to that used by CNCPS users on a daily basis. The protein A fraction in the CNCPS, formerly classified as nonprotein nitrogen, was reclassified to ammonia for ease and availability of analysis and to provide a better prediction of the contribution of metabolizable protein from free AA and small peptides. Amino acid profiles were updated using contemporary data sets and now represent the profile of AA in the whole feed rather than the insoluble residue. Model sensitivity to variation in feed library inputs was investigated using Monte Carlo simulation. Results showed the prediction of metabolizable energy was most sensitive to variation in feed chemistry and fractionation, whereas predictions of metabolizable protein were most sensitive to variation in digestion rates. Regular laboratory analysis of samples taken on-farm remains the recommended approach to characterizing the chemical components of feeds in a ration. However, updates to the CNCPS feed library provide a database of ingredients that are consistent with current feed chemistry information and

  15. Investigation of the HIV-1 matrix interactome during virus replication.

    Science.gov (United States)

    Li, Yan; Frederick, Kristin M; Haverland, Nicole A; Ciborowski, Pawel; Belshan, Michael

    2016-02-01

    Like all viruses, human immunodeficiency virus type 1 (HIV-1) requires host cellular factors for productive replication. Identification of these factors may lead to the development of novel cell-based inhibitors. A Strep-tag was inserted into the C-terminus of the matrix (MA) region of the HIV-1 gag gene. The resultant virus was replication competent and used to infect Jurkat T-cells. MA complexes were affinity purified with Strep-Tactin agarose. Protein quantification was performed using sequential window acquisition of all theoretical fragment ion spectra (SWATH) MS, data were log2 -transformed, and Student t-tests with Bonferroni correction used to determine statistical significance. Several candidate proteins were validated by immunoblot and investigated for their role in virus infection by siRNA knockdown assays. A total of 17 proteins were found to be statistically different between the infected versus uninfected and untagged control samples. X-ray repair cross-complementing protein 6 (Ku70), X-ray repair cross-complementing protein 5 (Ku80), and Y-box binding protein 1 (YB-1) were confirmed to interact with MA by immunoblot. Knockdown of two candidates, EZRIN and Y-box binding protein 1, enhanced HIV infection in vitro. The Strep-tag allowed for the capture of viral protein complexes in the context of virus replication. Several previously described factors were identified and at least two candidate proteins were found to play a role in HIV-1 infection. These data further increase our understanding of HIV host -cell interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. HINT-KB: The human interactome knowledge base

    KAUST Repository

    Theofilatos, Konstantinos A.

    2012-01-01

    Proteins and their interactions are considered to play a significant role in many cellular processes. The identification of Protein-Protein interactions (PPIs) in human is an open research area. Many Databases, which contain information about experimentally and computationally detected human PPIs as well as their corresponding annotation data, have been developed. However, these databases contain many false positive interactions, are partial and only a few of them incorporate data from various sources. To overcome these limitations, we have developed HINT-KB (http://150.140.142.24:84/Default.aspx) which is a knowledge base that integrates data from various sources, provides a user-friendly interface for their retrieval, estimates a set of features of interest and computes a confidence score for every candidate protein interaction using a modern computational hybrid methodology. © 2012 IFIP International Federation for Information Processing.

  17. Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction.

    Science.gov (United States)

    Silva, Joana Vieira; Yoon, Sooyeon; Domingues, Sara; Guimarães, Sofia; Goltsev, Alexander V; da Cruz E Silva, Edgar Figueiredo; Mendes, José Fernando F; da Cruz E Silva, Odete Abreu Beirão; Fardilha, Margarida

    2015-01-16

    Amyloid precursor protein (APP) is widely recognized for playing a central role in Alzheimer's disease pathogenesis. Although APP is expressed in several tissues outside the human central nervous system, the functions of APP and its family members in other tissues are still poorly understood. APP is involved in several biological functions which might be potentially important for male fertility, such as cell adhesion, cell motility, signaling, and apoptosis. Furthermore, APP superfamily members are known to be associated with fertility. Knowledge on the protein networks of APP in human testis and spermatozoa will shed light on the function of APP in the male reproductive system. We performed a Yeast Two-Hybrid screen and a database search to study the interaction network of APP in human testis and sperm. To gain insights into the role of APP superfamily members in fertility, the study was extended to APP-like protein 2 (APLP2). We analyzed several topological properties of the APP interaction network and the biological and physiological properties of the proteins in the APP interaction network were also specified by gene ontologyand pathways analyses. We classified significant features related to the human male reproduction for the APP interacting proteins and identified modules of proteins with similar functional roles which may show cooperative behavior for male fertility. The present work provides the first report on the APP interactome in human testis. Our approach allowed the identification of novel interactions and recognition of key APP interacting proteins for male reproduction, particularly in sperm-oocyte interaction.

  18. An "on-matrix" digestion procedure for AP-MS experiments dissects the interplay between complex-conserved and serotype-specific reactivities in Dengue virus-human plasma interactome.

    Science.gov (United States)

    Ramos, Yassel; Huerta, Vivian; Martín, Dayron; Palomares, Sucel; Yero, Alexis; Pupo, Dianne; Gallien, Sebastien; Martín, Alejandro M; Pérez-Riverol, Yasset; Sarría, Mónica; Guirola, Osmany; Chinea, Glay; Domon, Bruno; González, Luis Javier

    2017-07-13

    The interactions between the four Dengue virus (DENV) serotypes and plasma proteins are crucial in the initial steps of viral infection to humans. Affinity purification combined with quantitative mass spectrometry analysis, has become one of the most powerful tools for the investigation on novel protein-protein interactions. Using this approach, we report here that a significant number of bait-interacting proteins do not dissociate under standard elution conditions, i.e. acid pH and chaotropic agents, and that this problem can be circumvented by using the "on-matrix" digestion procedure described here. This procedure enabled the identification of 16 human plasma proteins interacting with domain III from the envelope protein of DENV serotypes 1, 3 and 4 that would have not been detected otherwise and increased the known DIIIE interactors in human plasma to 59 proteins. Selected Reaction Monitoring analysis evidenced DENV interactome in human plasma is rather conserved although significant differences on the reactivity of viral serotypes with specific proteins do exist. A comparison between the serotype-dependent profile of reactivity and the conservation pattern of amino acid residues suggests an evolutionary selection of highly conserved interactions with the host and other interactions mediated for surface regions of higher variability. False negative results on the identification of interacting proteins in pull-down experiments compromise the subsequent interpretation of results and the formulation of a working hypothesis for the derived future work. In this study we demonstrate the presence of bait-interacting proteins reluctant to dissociate under elution conditions of acid pH and presence of chaotropics. We propose the direct proteolytic digestion of proteins while still bound to the affinity matrix ("on-matrix" digestion) and evaluate the impact of this methodology in the comparative study of the interactome of the four serotypes of Dengue virus mediated by

  19. Proteomic, cellular, and network analyses reveal new DUSP3 interactions with nucleolar proteins in HeLa cells.

    Science.gov (United States)

    Panico, Karine; Forti, Fabio Luis

    2013-12-06

    DUSP3 (or Vaccinia virus phosphatase VH1-related; VHR) is a small dual-specificity phosphatase known to dephosphorylate c-Jun N-terminal kinases and extracellular signal-regulated kinases. In human cervical cancer cells, DUSP3 is overexpressed, localizes preferentially to the nucleus, and plays a key role in cellular proliferation and senescence triggering. Other DUSP3 functions are still unknown, as illustrated by recent and unpublished results from our group showing that this enzyme mediates DNA damage response or repair processes. In this study, we sought to identify new interactions between DUSP3 and proteins directly or indirectly involved in or correlated with its biological roles in HeLa cells exposed to gamma or UV radiation. By using GST-DUSP as bait, we pulled down interacting proteins and identified them by LC-MS/MS. Of the 46 proteins obtained, six hits were extensively validated by immune techniques; the proteins Nucleophosmin, HnRNP C1/C2, and Nucleolin were the most promising targets found to directly interact with DUSP3. We then analyzed the DUSP3 interactomes using physical protein-protein interaction networks using our hits as the seed list. The validated hits as well as unvalidated hits fluctuated on the DUSP3 interactomes of HeLa cells, independent of the time post radiation, which confirmed our proteomic and experimental data and clearly showed the proximity of DUSP3 to proteins involved in processes intimately related to DNA repair and senescence, such as Ku70 and Tert, via interactions with nucleolar proteins, which were identified in this study, that regulate DNA/RNA structure and functions.

  20. A shift in plant proteome profile for a Bromodomain containing RNA binding Protein (BRP1) in plants infected with Cucumber mosaic virus and its satellite RNA.

    Science.gov (United States)

    Chaturvedi, Sonali; Rao, A L N

    2016-01-10

    Host proteins are the integral part of a successful infection caused by a given RNA virus pathogenic to plants. Therefore, identification of crucial host proteins playing an important role in establishing the infection process is likely to help in devising approaches to curbing disease spread. Cucumber mosaic virus (Q-CMV) and its satellite RNA (QsatRNA) are important pathogens of many economically important crop plants worldwide. In a previous study, we demonstrated the biological significance of a Bromodomain containing RNA-binding Protein (BRP1) in the infection cycle of QsatRNA, making BRP1 an important host protein to study. To further shed a light on the mechanistic role of BRP1 in the replication of Q-CMV and QsatRNA, we analyzed the Nicotiana benthamiana host protein interactomes either for BRP1 alone or in the presence of Q-CMV or QsatRNA. Co-immunoprecipitation, followed by LC-MS/MS analysis of BRP1-FLAG on challenging with Q-CMV or QsatRNA has led us to observe a shift in the host protein interactome of BRP1. We discuss the significance of these results in relation to Q-CMV and its QsatRNA infection cycle. Host proteins play an important role in replication and infection of eukaryotic cells by a wide-range of RNA viruses pathogenic to humans, animals and plants. Since a given eukaryotic cell typically contains ~30,000 different proteins, recent advances made in proteomics and bioinformatics approaches allowed the identification of host proteins critical for viral replication and pathogenesis. Although Cucumber mosaic virus (CMV) and its satRNA are well characterized at molecular level, information concerning the network of host factors involved in their replication and pathogenesis is still on its infancy. We have recently observed that a Bromodomain containing host protein (BRP1) is obligatory to transport satRNA to the nucleus. Consequently, it is imperative to apply proteomics and bioinformatics approaches in deciphering how host interactome network

  1. Gel-forming mucin interactome drives mucus viscoelasticity.

    Science.gov (United States)

    Demouveaux, Bastien; Gouyer, Valérie; Gottrand, Frédéric; Narita, Tetsuharu; Desseyn, Jean-Luc

    2018-02-01

    Mucus is a hydrogel that constitutes the first innate defense in all mammals. The main organic component of mucus, gel-forming mucins, forms a complex network through both reversible and irreversible interactions that drive mucus gel formation. Significant advances in the understanding of irreversible gel-forming mucins assembly have been made using recombinant protein approaches. However, little is known about the reversible interactions that may finely modulate mucus viscoelasticity, which can be characterized using rheology. This approach can be used to investigate both the nature of gel-forming mucins interactions and factors that influence hydrogel formation. This knowledge is directly relevant to the development of new drugs to modulate mucus viscoelasticity and to restore normal mucus functions in diseases such as in cystic fibrosis. The aim of the present review is to summarize the current knowledge about the relationship between the mucus protein matrix and its functions, with emphasis on mucus viscoelasticity. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Application of an improved biuret method to the determination of total protein in urine and cerebrospinal fluid without concentration step by use of Hitachi 7170 auto-analyzer.

    Science.gov (United States)

    Guobing, X; Lili, J; Lihua, Z; Tiean, X

    2001-01-01

    A biuret automated colorimetric assay for total protein in urine and cerebrospinal fluids was established. The procedures were as follows. Acidify all urine sample before analysis. Add precipitant Na(2)WO(4) to urine samples. After 10 min, centrifuge, decant the supernatant fluid, drain the inverted tubes on absorbent tissue, dissolve the precipitation with 0.1 mol/L NaOH, and finally adapt the reconstituted urine to the Hitachi 7170 analyzer. A cell-free cerebrospinal fluid sample produced by centrifugation can be inserted in an auto-analyzer for protein measurement directly. The program: mix 35 microl sample (CSF or reconstituted urine) and standard with 0.2 mol/L NaOH; incurable at 37 degrees C for 5 min, and real A1. Add concentrated biuret reagent, and 10 min later measure absorbance A2 at 546 nm vs. reagent blank. Secondary wavelength was 700 nm. The test results were calculated against a one-point standard. This biuret colorimetric method was relatively simple, fast, and accurate for the determination of protein in urine and cerebrospinal fluid, with a wide linearity extending from 0.125 g/L up to 6 g/L, had a good correlation with Benzethonium chloride turbidimetry technique, and was a practical routine method. Copyright 2001 Wiley-Liss, Inc.

  3. Comparative study of NBT reduction method for estimation of glycated protein (serum fructoseamine) with glycated HbA1c estimated on DCA 2000+Analyzer (immunoagglutination inhibition).

    Science.gov (United States)

    Sahu, Ashok; Sarkar, Purnima Dey

    2008-01-01

    Glycated protein estimation is a diagnostic tool, used for the long term and short term monitoring of the glycemic status of diabetic patients. The present study is designed to compare and correlate modified NBT reduction method for the estimation of Glycated protein (serum fructosamine) with HbAlc estimated on DCA+2000 Analyzer. Glycated protein (serum fructosamine) reduces Nitro Blue Tetrazolium (NBT) reagent in alkaline medium to tetrazinolyl radical NBT+ which forms a highly colored monoformazen compound, absorbance of which is directly proportional to the concentration of glycated protein (serum fructosamine) present in the sample and is recorded as delta A/min. The results of modified NBT were then compared with HbA1c estimated by immunoagglutination inhibition method. Correlation coefficient between HbAlc with serum fructosamine was found to be r = 0.739 using Schimadzu CL-750 spectrophotometer and r = 0.731 using colorimeter. Results of this study were found to be statistically significant P < 0.001. Hence this method could be used for routine monitoring of blood glucose control in diabetics as HbA1c estimation.

  4. Transient analyzer

    International Nuclear Information System (INIS)

    Muir, M.D.

    1975-01-01

    The design and design philosophy of a high performance, extremely versatile transient analyzer is described. This sub-system was designed to be controlled through the data acquisition computer system which allows hands off operation. Thus it may be placed on the experiment side of the high voltage safety break between the experimental device and the control room. This analyzer provides control features which are extremely useful for data acquisition from PPPL diagnostics. These include dynamic sample rate changing, which may be intermixed with multiple post trigger operations with variable length blocks using normal, peak to peak or integrate modes. Included in the discussion are general remarks on the advantages of adding intelligence to transient analyzers, a detailed description of the characteristics of the PPPL transient analyzer, a description of the hardware, firmware, control language and operation of the PPPL transient analyzer, and general remarks on future trends in this type of instrumentation both at PPPL and in general

  5. Revealing missing parts of the interactome via link prediction.

    Directory of Open Access Journals (Sweden)

    Yuriy Hulovatyy

    Full Text Available Protein interaction networks (PINs are often used to "learn" new biological function from their topology. Since current PINs are noisy, their computational de-noising via link prediction (LP could improve the learning accuracy. LP uses the existing PIN topology to predict missing and spurious links. Many of existing LP methods rely on shared immediate neighborhoods of the nodes to be linked. As such, they have limitations. Thus, in order to comprehensively study what are the topological properties of nodes in PINs that dictate whether the nodes should be linked, we introduce novel sensitive LP measures that are expected to overcome the limitations of the existing methods. We systematically evaluate the new and existing LP measures by introducing "synthetic" noise into PINs and measuring how accurate the measures are in reconstructing the original PINs. Also, we use the LP measures to de-noise the original PINs, and we measure biological correctness of the de-noised PINs with respect to functional enrichment of the predicted interactions. Our main findings are: 1 LP measures that favor nodes which are both "topologically similar" and have large shared extended neighborhoods are superior; 2 using more network topology often though not always improves LP accuracy; and 3 LP improves biological correctness of the PINs, plus we validate a significant portion of the predicted interactions in independent, external PIN data sources. Ultimately, we are less focused on identifying a superior method but more on showing that LP improves biological correctness of PINs, which is its ultimate goal in computational biology. But we note that our new methods outperform each of the existing ones with respect to at least one evaluation criterion. Alarmingly, we find that the different criteria often disagree in identifying the best method(s, which has important implications for LP communities in any domain, including social networks.

  6. Antibody tagged gold nanoparticles as scattering probes for the pico molar detection of the proteins in blood serum using nanoparticle tracking analyzer.

    Science.gov (United States)

    Kashid, Sahebrao Balaso; Tak, Rajesh D; Raut, Rajesh Warluji

    2015-09-01

    We report a rapid one-step immunoassay to detect protein using antibody conjugated gold nanoparticles (AbGNPs) where the targeted protein concentration was determined by analyzing the gold nanoparticle aggregation caused by antibody-antigen interactions using nanoparticles tracking analysis (NTA) technique. The sandwich structure constituting the binding of the targeted human IgG to the gold nanoparticle conjugates with goat anti human monoclonal IgG (AbGNPs) was confirmed by transmission electron microscopy. The binding of human IgG (antigen, mentioned hence forth as AT) induce AbGNPs to form dimers or trimers through a typical antibody-antigen-antibody sandwich structure that can be analyzed for the sensitive determination on the basis of change in hydrodynamic diameter of AbGNPs. By this method the minimum detectable concentration of AT is found to be below 2pg/ml. We expect that a significant change in the hydrodynamic diameter of AbGNP could form the basis for the rapid one-step immunoassay development. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Major proteins in normal human lymphocyte subpopulations separated by fluorescence-activated cell sorting and analyzed by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Madsen, P S; Hokland, M; Ellegaard, J

    1988-01-01

    We have compared the overall patterns of protein synthesis of normal human lymphocyte subpopulations taken from five volunteers using high resolution two-dimensional gel electrophoresis. The lymphocytes were isolated using density gradient centrifugation, labeled with subtype-specific Mo......Abs, and separated to a high degree of homogeneity by FACS into CD4+ helper T cells, CD8+ suppressor T cells, CD20+ B cells, and N901 (NHK-1)+ NK cells. The four lymphocyte subpopulations were labeled with [35S]methionine for 14 hr, solubilized in lysis buffer, and analyzed by two-dimensional gel electrophoresis...... (IEF). Of about 1000 proteins resolved in each case, most were found to be common to all subpopulations. However, eight putative markers for B1+ (proteins 5525, Mr = 63,700; 5621, Mr = 63,700; 8311, Mr = 36,900; 2202, Mr = 36,300; 6121, Mr = 30,300; 106, Mr = 29,300; 5009, Mr = 23,000; 8012, Mr = 11...

  8. Influenza A virus encoding secreted Gaussia luciferase as useful tool to analyze viral replication and its inhibition by antiviral compounds and cellular proteins.

    Directory of Open Access Journals (Sweden)

    Nadine Eckert

    Full Text Available Reporter genes inserted into viral genomes enable the easy and rapid quantification of virus replication, which is instrumental to efficient in vitro screening of antiviral compounds or in vivo analysis of viral spread and pathogenesis. Based on a published design, we have generated several replication competent influenza A viruses carrying either fluorescent proteins or Gaussia luciferase. Reporter activity could be readily quantified in infected cultures, but the virus encoding Gaussia luciferase was more stable than viruses bearing fluorescent proteins and was therefore analyzed in detail. Quantification of Gaussia luciferase activity in the supernatants of infected culture allowed the convenient and highly sensitive detection of viral spread, and enzymatic activity correlated with the number of infectious particles released from infected cells. Furthermore, the Gaussia luciferase encoding virus allowed the sensitive quantification of the antiviral activity of the neuraminidase inhibitor (NAI zanamivir and the host cell interferon-inducible transmembrane (IFITM proteins 1-3, which are known to inhibit influenza virus entry. Finally, the virus was used to demonstrate that influenza A virus infection is sensitive to a modulator of endosomal cholesterol, in keeping with the concept that IFITMs inhibit viral entry by altering cholesterol levels in the endosomal membrane. In sum, we report the characterization of a novel influenza A reporter virus, which allows fast and sensitive detection of viral spread and its inhibition, and we show that influenza A virus entry is sensitive to alterations of endosomal cholesterol levels.

  9. Differential occurrence of interactions and interaction domains in proteins containing homopolymeric amino acid repeats

    Directory of Open Access Journals (Sweden)

    Ilaria ePelassa

    2015-12-01

    Full Text Available Homopolymeric amino acids repeats (AARs, which are widespread in proteomes, have often been viewed simply as spacers between protein domains, or even as ‘junk’ sequences with no obvious function but with a potential to cause harm upon expansion as in genetic diseases associated with polyglutamine or polyalanine expansions, including Huntington disease and cleidocranial dysplasia. A growing body of evidence indicates however that at least some AARs can form organized, functional protein structures and can regulate protein function. In particular, certain AARs can mediate protein-protein interactions, either through homotypic AAR-AAR contacts or through heterotypic contacts with other protein domains. It is still unclear however, whether AARs may have a generalized, proteome-wide role in shaping protein-protein interaction networks. Therefore, we have undertaken here a bioinformatics screening of the human proteome and interactome in search of quantitative evidence of such a role. We first identified the sets of proteins that contain repeats of any one of the 20 amino acids, as well as control sets of proteins chosen at random in the proteome. We then analyzed the connectivity between the proteins of the AAR-containing protein sets and we compared it with that observed in the corresponding control networks. We find evidence for different degrees of connectivity in the different AAR-containing protein networks. Indeed, networks of proteins containing polyglutamine, polyglutamate, polyproline and other AARs show significantly increased levels of connectivity, whereas networks containing polyleucine and other hydrophobic repeats show lower degrees of connectivity. Furthermore, we observed that numerous protein-protein, -nucleic acid and -lipid interaction domains are significantly enriched in specific AAR protein groups. These findings support the notion of a generalized, combinatorial role of AARs, together with conventional protein interaction

  10. Klinefelter syndrome comorbidities linked to increased X chromosome gene dosage and altered protein interactome activity

    DEFF Research Database (Denmark)

    Belling, Kirstine González-Izarzugaza; Russo, Francesco; Jensen, Anders Boeck

    2017-01-01

    Klinefelter syndrome (KS) (47,XXY) is the most common male sex chromosome aneuploidy. Diagnosis and clinical supervision remain a challenge due to varying phenotypic presentation and insufficient characterization of the syndrome. Here we combine health data-driven epidemiology and molecular level...

  11. The interactomic analysis reveals pathogenic protein networks in Phomopsis longicolla underlying seed decay of soybean

    Science.gov (United States)

    Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease causes poor seed quality and is one of the most economically important diseases in soybean. The objectives of this study were to perform ...

  12. Novel Technology for Protein-Protein Interaction-based Targeted Drug Discovery

    Directory of Open Access Journals (Sweden)

    Jung Me Hwang

    2011-12-01

    Full Text Available We have developed a simple but highly efficient in-cell protein-protein interaction (PPI discovery system based on the translocation properties of protein kinase C- and its C1a domain in live cells. This system allows the visual detection of trimeric and dimeric protein interactions including cytosolic, nuclear, and/or membrane proteins with their cognate ligands. In addition, this system can be used to identify pharmacological small compounds that inhibit specific PPIs. These properties make this PPI system an attractive tool for screening drug candidates and mapping the protein interactome.

  13. Intranuclear interactomic inhibition of NF-κB suppresses LPS-induced severe sepsis

    Energy Technology Data Exchange (ETDEWEB)

    Park, Sung-Dong [Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Cheon, So Yeong [Department of Anesthesiology and Pain Medicine, Anesthesia and Pain Research Institute, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Park, Tae-Yoon; Shin, Bo-Young [Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Oh, Hyunju; Ghosh, Sankar [Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032 (United States); Koo, Bon-Nyeo, E-mail: koobn@yuhs.ac [Department of Anesthesiology and Pain Medicine, Anesthesia and Pain Research Institute, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Lee, Sang-Kyou, E-mail: sjrlee@yonsei.ac.kr [Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2015-08-28

    Suppression of nuclear factor-κB (NF-κB) activation, which is best known as a major regulator of innate and adaptive immune responses, is a potent strategy for the treatment of endotoxic sepsis. To inhibit NF-κB functions, we designed the intra-nuclear transducible form of transcription modulation domain (TMD) of RelA (p65), called nt-p65-TMD, which can be delivered effectively into the nucleus without influencing the cell viability, and work as interactomic inhibitors via disruption of the endogenous p65-mediated transcription complex. nt-p65-TMD effectively inhibited the secretion of pro-inflammatory cytokines, including TNF-α, IL-1β, or IL-6 from BV2 microglia cells stimulated by lipopolysaccharide (LPS). nt-p65-TMD did not inhibit tyrosine phosphorylation of signaling mediators such as ZAP-70, p38, JNK, or ERK involved in T cell activation, but was capable of suppressing the transcriptional activity of NF-κB without the functional effect on that of NFAT upon T-cell receptor (TCR) stimulation. The transduced nt-p65-TMD in T cell did not affect the expression of CD69, however significantly inhibited the secretion of T cell-specific cytokines such as IL-2, IFN-γ, IL-4, IL-17A, or IL-10. Systemic administration of nt-p65-TMD showed a significant therapeutic effect on LPS-induced sepsis model by inhibiting pro-inflammatory cytokines secretion. Therefore, nt-p65-TMD can be a novel therapeutics for the treatment of various inflammatory diseases, including sepsis, where a transcription factor has a key role in pathogenesis, and further allows us to discover new functions of p65 under normal physiological condition without genetic alteration. - Highlights: • The nt-p65-TMD is intra-nuclear interactomic inhibitor of endogenous p65. • The nt-p65-TMD effectively inhibited the secretion of pro-inflammatory cytokines. • The excellent therapeutic potential of nt-p65-TMD was confirmed in sepsis model.

  14. Intranuclear interactomic inhibition of NF-κB suppresses LPS-induced severe sepsis

    International Nuclear Information System (INIS)

    Park, Sung-Dong; Cheon, So Yeong; Park, Tae-Yoon; Shin, Bo-Young; Oh, Hyunju; Ghosh, Sankar; Koo, Bon-Nyeo; Lee, Sang-Kyou

    2015-01-01

    Suppression of nuclear factor-κB (NF-κB) activation, which is best known as a major regulator of innate and adaptive immune responses, is a potent strategy for the treatment of endotoxic sepsis. To inhibit NF-κB functions, we designed the intra-nuclear transducible form of transcription modulation domain (TMD) of RelA (p65), called nt-p65-TMD, which can be delivered effectively into the nucleus without influencing the cell viability, and work as interactomic inhibitors via disruption of the endogenous p65-mediated transcription complex. nt-p65-TMD effectively inhibited the secretion of pro-inflammatory cytokines, including TNF-α, IL-1β, or IL-6 from BV2 microglia cells stimulated by lipopolysaccharide (LPS). nt-p65-TMD did not inhibit tyrosine phosphorylation of signaling mediators such as ZAP-70, p38, JNK, or ERK involved in T cell activation, but was capable of suppressing the transcriptional activity of NF-κB without the functional effect on that of NFAT upon T-cell receptor (TCR) stimulation. The transduced nt-p65-TMD in T cell did not affect the expression of CD69, however significantly inhibited the secretion of T cell-specific cytokines such as IL-2, IFN-γ, IL-4, IL-17A, or IL-10. Systemic administration of nt-p65-TMD showed a significant therapeutic effect on LPS-induced sepsis model by inhibiting pro-inflammatory cytokines secretion. Therefore, nt-p65-TMD can be a novel therapeutics for the treatment of various inflammatory diseases, including sepsis, where a transcription factor has a key role in pathogenesis, and further allows us to discover new functions of p65 under normal physiological condition without genetic alteration. - Highlights: • The nt-p65-TMD is intra-nuclear interactomic inhibitor of endogenous p65. • The nt-p65-TMD effectively inhibited the secretion of pro-inflammatory cytokines. • The excellent therapeutic potential of nt-p65-TMD was confirmed in sepsis model

  15. Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design.

    Science.gov (United States)

    Antal, Miklós A; Böde, Csaba; Csermely, Peter

    2009-04-01

    The network paradigm is increasingly used to describe the dynamics of complex systems. Here we review the current results and propose future development areas in the assessment of perturbation waves, i.e. propagating structural changes in amino acid networks building individual protein molecules and in protein-protein interaction networks (interactomes). We assess the possibilities and critically review the initial attempts for the application of game theory to the often rather complicated process, when two protein molecules approach each other, mutually adjust their conformations via multiple communication steps and finally, bind to each other. We also summarize available data on the application of percolation theory for the prediction of amino acid network- and interactome-dynamics. Furthermore, we give an overview of the dissection of signals and noise in the cellular context of various perturbations. Finally, we propose possible applications of the reviewed methodologies in drug design.

  16. Analyzing pepsin degradation assay conditions used for allergenicity assessments to ensure that pepsin susceptible and pepsin resistant dietary proteins are distinguishable.

    Directory of Open Access Journals (Sweden)

    Rong Wang

    Full Text Available The susceptibility of a dietary protein to proteolytic degradation by digestive enzymes, such as gastric pepsin, provides information on the likelihood of systemic exposure to a structurally intact and biologically active macromolecule, thus informing on the safety of proteins for human and animal consumption. Therefore, the purpose of standardized in vitro degradation studies that are performed during protein safety assessments is to distinguish whether proteins of interest are susceptible or resistant to pepsin degradation via a study design that enables study-to-study comparison. Attempting to assess pepsin degradation under a wide-range of possible physiological conditions poses a problem because of the lack of robust and consistent data collected under a large-range of sub-optimal conditions, which undermines the needs to harmonize in vitro degradation conditions. This report systematically compares the effects of pH, incubation time, and pepsin-to-substrate protein ratio on the relative degradation of five dietary proteins: three pepsin susceptible proteins [ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco, horseradish peroxidase (HRP, hemoglobin (Hb], and two pepsin resistant proteins [lipid transfer protein (LTP and soybean trypsin inhibitor (STI]. The results indicate that proteins susceptible to pepsin degradation are readily distinguishable from pepsin-resistant proteins when the reaction conditions are within the well-characterized optima for pepsin. The current standardized in vitro pepsin resistant assay with low pH and high pepsin-to-substrate ratio fits this purpose. Using non-optimal pH and/or pepsin-to-substrate protein ratios resulted in susceptible proteins no longer being reliably degraded by this stomach enzyme, which compromises the ability of this in vitro assay to distinguish between resistant and susceptible proteins and, therefore, no longer providing useful data to an overall weight-of-evidence approach to

  17. Interactome of Radiation-Induced microRNA-Predicted Target Genes

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    Tenzin W. Lhakhang

    2012-01-01

    Full Text Available The microRNAs (miRNAs function as global negative regulators of gene expression and have been associated with a multitude of biological processes. The dysfunction of the microRNAome has been linked to various diseases including cancer. Our laboratory recently reported modulation in the expression of miRNA in a variety of cell types exposed to ionizing radiation (IR. To further understand miRNA role in IR-induced stress pathways, we catalogued a set of common miRNAs modulated in various irradiated cell lines and generated a list of predicted target genes. Using advanced bioinformatics tools we identified cellular pathways where miRNA predicted target genes function. The miRNA-targeted genes were found to play key roles in previously identified IR stress pathways such as cell cycle, p53 pathway, TGF-beta pathway, ubiquitin-mediated proteolysis, focal adhesion pathway, MAPK signaling, thyroid cancer pathway, adherens junction, insulin signaling pathway, oocyte meiosis, regulation of actin cytoskeleton, and renal cell carcinoma pathway. Interestingly, we were able to identify novel targeted pathways that have not been identified in cellular radiation response, such as aldosterone-regulated sodium reabsorption, long-term potentiation, and neutrotrophin signaling pathways. Our analysis indicates that the miRNA interactome in irradiated cells provides a platform for comprehensive modeling of the cellular stress response to IR exposure.

  18. Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E.

    Science.gov (United States)

    Waters, Shafagh A; McAteer, Sean P; Kudla, Grzegorz; Pang, Ignatius; Deshpande, Nandan P; Amos, Timothy G; Leong, Kai Wen; Wilkins, Marc R; Strugnell, Richard; Gally, David L; Tollervey, David; Tree, Jai J

    2017-02-01

    RNA sequencing studies have identified hundreds of non-coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high-throughput analysis of RNA-RNA interactions in bacteria. Here we demonstrate that in vivo sRNA-mRNA duplexes can be recovered using UV-crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base-paired sRNA-mRNA duplexes in association with RNase E, allowing proximity-dependent ligation and sequencing of cognate sRNA-mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA-mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co-regulated target mRNAs. We identified multiple mRNA targets for the pathotype-specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli Numerous sRNA interactions were also identified with non-coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome. © 2016 The Authors. Published under the terms of the CC BY 4.0 license.

  19. Reversible oxidation of phosphatase and tensin homolog (PTEN) alters its interactions with signaling and regulatory proteins.

    Science.gov (United States)

    Verrastro, Ivan; Tveen-Jensen, Karina; Woscholski, Rudiger; Spickett, Corinne M; Pitt, Andrew R

    2016-01-01

    Phosphatase and tensin homolog (PTEN) is involved in a number of different cellular processes including metabolism, apoptosis, cell proliferation and survival. It is a redox-sensitive dual-specificity protein phosphatase that acts as a tumor suppressor by negatively regulating the PI3K/Akt pathway. While direct evidence of redox regulation of PTEN downstream signaling has been reported, the effect of PTEN redox status on its protein-protein interactions is poorly understood. PTEN-GST in its reduced and a DTT-reversible H2O2-oxidized form was immobilized on a glutathione-sepharose support and incubated with cell lysate to capture interacting proteins. Captured proteins were analyzed by LC-MSMS and comparatively quantified using label-free methods. 97 Potential protein interactors were identified, including a significant number that are novel. The abundance of fourteen interactors was found to vary significantly with the redox status of PTEN. Altered binding to PTEN was confirmed by affinity pull-down and Western blotting for Prdx1, Trx, and Anxa2, while DDB1 was validated as a novel interactor with unaltered binding. These results suggest that the redox status of PTEN causes a functional variation in the PTEN interactome. The resin capture method developed had distinct advantages in that the redox status of PTEN could be directly controlled and measured. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Cell fusion assay by expression of respiratory syncytial virus (RSV) fusion protein to analyze the mutation of palivizumab-resistant strains.

    Science.gov (United States)

    Yasui, Yosuke; Yamaji, Yoshiaki; Sawada, Akihito; Ito, Takashi; Nakayama, Tetsuo

    2016-05-01

    Respiratory syncytial virus (RSV) consists of fusion (F), glyco (G), and small hydrophobic (SH) proteins as envelope proteins, and infects through cell fusion. F protein is expressed on the surface of infected cells, and induces cell fusion. In the present report, expression plasmids of the F, G and SH proteins were constructed and cell fusion activity was investigated under T7 RNA polymerase. F protein alone induced cell fusion at a lower concentration than previously reported, and co-expression of F and SH proteins induced cell fusion more efficiently than F protein alone. Palivizumab is the only prophylactic agent against RSV infection. Palivizumab-resistant strains having mutations of the F protein of K272E and S275F were reported. These mutations were introduced into an F-expression plasmid, and exhibited no inhibition of cell fusion with palivizumab. Among the RSV F protein mutants, N276S has been reported to have partial resistance against palivizumab, but the F expression plasmid with the N276S mutation showed a reduction in cell fusion in the presence of palivizumab, showing no resistance to palivizumab. The present expression system was useful for investigating the mechanisms of RSV cell fusion. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Hypothesis: NDL Proteins Function in Stress Responses by Regulating Microtubule Organization

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    Nisha eKhatri

    2015-10-01

    Full Text Available N-MYC DOWNREGULATED-LIKE proteins (NDL, members of the alpha/beta hydrolase superfamily were recently rediscovered as interactors of G-protein signaling in Arabidopsis thaliana. Although the precise molecular function of NDL proteins is still elusive, in animals these proteins play protective role in hypoxia and expression is induced by hypoxia and nickel, indicating role in stress. Homology of NDL1 with animal counterpart NDRG suggests similar functions in animals and plants. It is well established that stress responses leads to the microtubule depolymerization and reorganization which is crucial for stress tolerance. NDRG is a microtubule-associated protein (MAP which mediates the microtubule organization in animals by causing acetylation and increases the stability of α-tubulin. As NDL1 is highly homologous to NDRG, involvement of NDL1 in the microtubule organization during plant stress can also be expected. Discovery of interaction of NDL with protein kinesin light chain- related 1, enodomembrane family protein 70, syntaxin-23, tubulin alpha-2 chain, as a part of G protein interactome initiative encourages us to postulate microtubule stabilizing functions for NDL family in plants. Our search for NDL interactors in G protein interactome also predicts the role of NDL proteins in abiotic stress tolerance management. Based on published report in animals and predicted interacting partners for NDL in G protein interactome lead us to hypothesize involvement of NDL in the microtubule organization during abiotic stress management in plants.

  2. Major proteins in normal human lymphocyte subpopulations separated by fluorescence-activated cell sorting and analyzed by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Madsen, P S; Hokland, M; Ellegaard, J

    1988-01-01

    We have compared the overall patterns of protein synthesis of normal human lymphocyte subpopulations taken from five volunteers using high resolution two-dimensional gel electrophoresis. The lymphocytes were isolated using density gradient centrifugation, labeled with subtype-specific MoAbs, and ......We have compared the overall patterns of protein synthesis of normal human lymphocyte subpopulations taken from five volunteers using high resolution two-dimensional gel electrophoresis. The lymphocytes were isolated using density gradient centrifugation, labeled with subtype-specific Mo...... markers were observed in all cell types. All the putative protein markers have been identified in the protein database of human peripheral blood mononuclear cells (PBMCs) (see accompanying article by Celis et al.). Comparison of the overall patterns of protein synthesis of the unsorted PBMCs with those...

  3. Genetically encoded releasable photo-cross-linking strategies for studying protein-protein interactions in living cells.

    Science.gov (United States)

    Yang, Yi; Song, Haiping; He, Dan; Zhang, Shuai; Dai, Shizhong; Xie, Xiao; Lin, Shixian; Hao, Ziyang; Zheng, Huangtao; Chen, Peng R

    2017-10-01

    Although protein-protein interactions (PPIs) have crucial roles in virtually all cellular processes, the identification of more transient interactions in their biological context remains challenging. Conventional photo-cross-linking strategies can be used to identify transient interactions, but these approaches often suffer from high background due to the cross-linked bait proteins. To solve the problem, we have developed membrane-permeable releasable photo-cross-linkers that allow for prey-bait separation after protein complex isolation and can be installed in proteins of interest (POIs) as unnatural amino acids. Here we describe the procedures for using two releasable photo-cross-linkers, DiZSeK and DiZHSeC, in both living Escherichia coli and mammalian cells. A cleavage after protein photo-cross-linking (CAPP ) strategy based on the photo-cross-linker DiZSeK is described, in which the prey protein pool is released from a POI after affinity purification. Prey proteins are analyzed using mass spectrometry or 2D gel electrophoresis for global comparison of interactomes from different experimental conditions. An in situ cleavage and mass spectrometry (MS)-label transfer after protein photo-cross-linking (IMAPP) strategy based on the photo-cross-linker DiZHSeC is also described. This strategy can be used for the identification of cross-linking sites to allow detailed characterization of PPI interfaces. The procedures for photo-cross-linker incorporation, photo-cross-linking of interaction partners and affinity purification of cross-linked complexes are similar for the two photo-cross-linkers. The final section of the protocol describes prey-bait separation (for CAPP) and MS-label transfer and identification (for IMAPP). After plasmid construction, the CAPP and IMAPP strategies can be completed within 6 and 7 d, respectively.

  4. Comparing Enterovirus 71 with Coxsackievirus A16 by analyzing nucleotide sequences and antigenicity of recombinant proteins of VP1s and VP4s

    Directory of Open Access Journals (Sweden)

    Sun Yu

    2011-11-01

    Full Text Available Abstract Background Enterovirus 71 (EV71 and Coxsackievirus A16 (CA16 are two major etiological agents of Hand, Foot and Mouth Disease (HFMD. EV71 is associated with severe cases but not CA16. The mechanisms contributed to the different pathogenesis of these two viruses are unknown. VP1 and VP4 are two major structural proteins of these viruses, and should be paid close attention to. Results The sequences of vp1s from 14 EV71 and 14 CA16, and vp4s from 10 EV71 and 1 CA16 isolated in this study during 2007 to 2009 HFMD seasons were analyzed together with the corresponding sequences available in GenBank using DNAStar and MEGA 4.0. Phylogenetic analysis of complete vp1s or vp4s showed that EV71 isolated in Beijing belonged to C4 and CA16 belonged to lineage B2 (lineage C. VP1s and VP4s from 4 strains of viruses expressed in E. coli BL21 cells were used to detect IgM and IgG in human sera by Western Blot. The detection of IgM against VP1s of EV71 and CA16 showed consistent results with current infection, while none of the sera were positive against VP4s of EV71 and CA16. There was significant difference in the positive rates between EV71 VP1 and CA16 VP1 (χ2 = 5.02, P 2 = 15.30, P 2 = 26.47, P 2 = 16.78, P Conclusions EV71 and CA16 were highly diverse in the nucleotide sequences of vp1s and vp4s. The sera positive rates of VP1 and VP4 of EV71 were lower than those of CA16 respectively, which suggested a less exposure rate to EV71 than CA16 in Beijing population. Human serum antibodies detected by Western blot using VP1s and VP4s as antigen indicated that the immunological reaction to VP1 and VP4 of both EV71 and CA16 was different.

  5. Evidence That a Psychopathology Interactome Has Diagnostic Value, Predicting Clinical Needs: An Experience Sampling Study

    Science.gov (United States)

    van Os, Jim; Lataster, Tineke; Delespaul, Philippe; Wichers, Marieke; Myin-Germeys, Inez

    2014-01-01

    measures of psychopathology, similarly moderated by momentary interactions with emotions and context. Conclusion The results suggest that psychopathology, represented as an interactome at the momentary level of temporal resolution, is informative in diagnosing clinical needs, over and above traditional symptom measures. PMID:24466189

  6. Study of the stress proteins secreted by Leishmania donovani after treatment with edelfosine, mitelfosine and ilmofosine, and morphological alterations analyzed by electronic microscopy

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    Azzouz S.

    2009-09-01

    Full Text Available We studied the stress proteins induced in protozoa Leishmania donovani after treatment with edelfosine, miltefosine and ilmofosine. We studied the morphological and structural modifications caused in the promastigote forms of the parasite after treatment with the three alkyl-lysophospholipids (ALPs. A resistant strain of L. donovani to miltefosine was obtained and the morphological modifications were observed. The stress proteins induction was studied in promastigote forms and also in amastigote-like forms obtained in vitro. The proteins synthesized with the three alkyl-lysophospholipids were compared to those obtained by heat shock. The axenic amastigote forms synthesized a pattern of different proteins for those observed in the promastigote forms. The morphological alterations were observed under electronic microscopy. The membrane and mitochondria were the organs most affected by the three ALPs. We noted an apparition of vacuoles and vesicles in the treated promastigotes. In the resistant strain, we noted myelin bodies in the treated and untreated parasites.

  7. Neuroplasticity pathways and protein-interaction networks are modulated by vortioxetine in rodents

    DEFF Research Database (Denmark)

    Waller, Jessica A.; Nygaard, Sara Holm; Li, Yan

    2017-01-01

    and rat in response to distinct treatment regimens and in different brain regions. Furthermore, analysis of complexes of physically-interacting proteins reveal that biomarkers involved in transcriptional regulation, neurodevelopment, neuroplasticity, and endocytosis are modulated by vortioxetine....... A subsequent qPCR study examining the expression of targets in the protein-protein interactome space in response to chronic vortioxetine treatment over a range of doses provides further biological validation that vortioxetine engages neuroplasticity networks. Thus, the same biology is regulated in different...

  8. Specificity and commonality of the phosphoinositide-binding proteome analyzed by quantitative mass spectrometry

    DEFF Research Database (Denmark)

    Jungmichel, Stephanie; Sylvestersen, Kathrine B; Choudhary, Chuna Ram

    2014-01-01

    than the total number of phospho- or ubiquitin-binding domains. Translocation and inhibitor assays of identified PIP-binding proteins confirmed that our methodology targets direct interactors. The PIP interactome encompasses proteins from diverse cellular compartments, prominently including the nucleus......Phosphoinositides (PIPs) play key roles in signaling and disease. Using high-resolution quantitative mass spectrometry, we identified PIP-interacting proteins and profiled their binding specificities toward all seven PIP variants. This analysis revealed 405 PIP-binding proteins, which is greater......, this dual specificity is explained by a decreased number of positively charged residues in the L1 subdomain compared with DOCK1. The presented PIP-binding proteome and its specificity toward individual PIPs should be a valuable resource for the community....

  9. Towards Inferring Protein Interactions: Challenges and Solutions

    Directory of Open Access Journals (Sweden)

    Ji Xiang

    2006-01-01

    Full Text Available Discovering interacting proteins has been an essential part of functional genomics. However, existing experimental techniques only uncover a small portion of any interactome. Furthermore, these data often have a very high false rate. By conceptualizing the interactions at domain level, we provide a more abstract representation of interactome, which also facilitates the discovery of unobserved protein-protein interactions. Although several domain-based approaches have been proposed to predict protein-protein interactions, they usually assume that domain interactions are independent on each other for the convenience of computational modeling. A new framework to predict protein interactions is proposed in this paper, where no assumption is made about domain interactions. Protein interactions may be the result of multiple domain interactions which are dependent on each other. A conjunctive norm form representation is used to capture the relationships between protein interactions and domain interactions. The problem of interaction inference is then modeled as a constraint satisfiability problem and solved via linear programing. Experimental results on a combined yeast data set have demonstrated the robustness and the accuracy of the proposed algorithm. Moreover, we also map some predicted interacting domains to three-dimensional structures of protein complexes to show the validity of our predictions.

  10. Hepatitis C virus infection protein network.

    Science.gov (United States)

    de Chassey, B; Navratil, V; Tafforeau, L; Hiet, M S; Aublin-Gex, A; Agaugué, S; Meiffren, G; Pradezynski, F; Faria, B F; Chantier, T; Le Breton, M; Pellet, J; Davoust, N; Mangeot, P E; Chaboud, A; Penin, F; Jacob, Y; Vidalain, P O; Vidal, M; André, P; Rabourdin-Combe, C; Lotteau, V

    2008-01-01

    A proteome-wide mapping of interactions between hepatitis C virus (HCV) and human proteins was performed to provide a comprehensive view of the cellular infection. A total of 314 protein-protein interactions between HCV and human proteins was identified by yeast two-hybrid and 170 by literature mining. Integration of this data set into a reconstructed human interactome showed that cellular proteins interacting with HCV are enriched in highly central and interconnected proteins. A global analysis on the basis of functional annotation highlighted the enrichment of cellular pathways targeted by HCV. A network of proteins associated with frequent clinical disorders of chronically infected patients was constructed by connecting the insulin, Jak/STAT and TGFbeta pathways with cellular proteins targeted by HCV. CORE protein appeared as a major perturbator of this network. Focal adhesion was identified as a new function affected by HCV, mainly by NS3 and NS5A proteins.

  11. ZCURVE_CoV: a new system to recognize protein coding genes in coronavirus genomes, and its applications in analyzing SARS-CoV genomes.

    Science.gov (United States)

    Chen, Ling-Ling; Ou, Hong-Yu; Zhang, Ren; Zhang, Chun-Ting

    2003-07-25

    A new system to recognize protein coding genes in the coronavirus genomes, specially suitable for the SARS-CoV genomes, has been proposed in this paper. Compared with some existing systems, the new program package has the merits of simplicity, high accuracy, reliability, and quickness. The system ZCURVE_CoV has been run for each of the 11 newly sequenced SARS-CoV genomes. Consequently, six genomes not annotated previously have been annotated, and some problems of previous annotations in the remaining five genomes have been pointed out and discussed. In addition to the polyprotein chain ORFs 1a and 1b and the four genes coding for the major structural proteins, spike (S), small envelop (E), membrane (M), and nuleocaspid (N), respectively, ZCURVE_CoV also predicts 5-6 putative proteins in length between 39 and 274 amino acids with unknown functions. Some single nucleotide mutations within these putative coding sequences have been detected and their biological implications are discussed. A web service is provided, by which a user can obtain the annotated result immediately by pasting the SARS-CoV genome sequences into the input window on the web site (http://tubic.tju.edu.cn/sars/). The software ZCURVE_CoV can also be downloaded freely from the web address mentioned above and run in computers under the platforms of Windows or Linux.

  12. Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin

    Directory of Open Access Journals (Sweden)

    Li Weijun

    2011-01-01

    Full Text Available Abstract Background Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS to characterize potential protein-protein interactions in membrane fractions. Results Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins, which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane

  13. Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guérin.

    Science.gov (United States)

    Zheng, Jianhua; Wei, Candong; Zhao, Lina; Liu, Liguo; Leng, Wenchuan; Li, Weijun; Jin, Qi

    2011-01-18

    Tuberculosis is an infectious bacterial disease in humans caused primarily by Mycobacterium tuberculosis, and infects one-third of the world's total population. Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been widely used to prevent tuberculosis worldwide since 1921. Membrane proteins play important roles in various cellular processes, and the protein-protein interactions involved in these processes may provide further information about molecular organization and cellular pathways. However, membrane proteins are notoriously under-represented by traditional two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and little is known about mycobacterial membrane and membrane-associated protein complexes. Here we investigated M. bovis BCG by an alternative proteomic strategy coupling blue native PAGE to liquid chromatography tandem mass spectrometry (LC-MS/MS) to characterize potential protein-protein interactions in membrane fractions. Using this approach, we analyzed native molecular composition of protein complexes in BCG membrane fractions. As a result, 40 proteins (including 12 integral membrane proteins), which were organized in 9 different gel bands, were unambiguous identified. The proteins identified have been experimentally confirmed using 2-D SDS PAGE. We identified MmpL8 and four neighboring proteins that were involved in lipid transport complexes, and all subunits of ATP synthase complex in their monomeric states. Two phenolpthiocerol synthases and three arabinosyltransferases belonging to individual operons were obtained in different gel bands. Furthermore, two giant multifunctional enzymes, Pks7 and Pks8, and four mycobacterial Hsp family members were determined. Additionally, seven ribosomal proteins involved in polyribosome complex and two subunits of the succinate dehydrogenase complex were also found. Notablely, some proteins with high hydrophobicity or multiple transmembrane helixes were identified well in our work. In this

  14. Immunolocalization of NuMA and phosphorylated proteins during the cell cycle in human breast and prostate cancer cells as analyzed by immunofluorescence and postembedding immunoelectron microscopy.

    Science.gov (United States)

    Gobert, G N; Hueser, C N; Curran, E M; Sun, Q Y; Glinsky, V V; Welshons, W V; Eisenstark, A; Schatten, H

    2001-05-01

    The formation of mitotic centrosomes is a complex process in which a number of cellular proteins translocate to mitotic poles and play a critical role in the organization of the mitotic apparatus. The 238-kDa nuclear mitotic apparatus protein NuMA is one of the important proteins that plays a significant role in this process. NuMA resides in the nucleus during interphase and becomes transiently associated with mitotic centrosomes after multiple steps of phosphorylations. The role of NuMA in the interphase nucleus is not well known but it is clear that NuMA responds to external signals (such as hormones) that induce cell division, or heat shock that induces apoptosis. In order to determine the function of NuMA it is important to study its localization. Here we report on nuclear organization of NuMA during the cell cycle in estrogen responsive MCF-7 breast cancer cells and in androgen responsive LNCaP prostate cancer cells using immunoelectron microscopy, and on correlation to MPM-2 monoclonal phosphoprotein antibody. These results show that NuMA is present in speckled and punctate form associated with distinct material corresponding to a speckled or punctate immunofluorescence appearance in the nucleus while MPM-2 is uniformly dispersed in the nucleus. At prophase NuMA disperses in the cytoplasm and associates with microtubules while MPM-2 is uniformly distributed in the cytoplasm. During metaphase or anaphase anti-NuMA labeling is associated with spindle fibers. During telophase NuMA relocates to electron-dense areas around chromatin and finally to the reconstituted nuclei. These results demonstrate NuMA organization in MCF-7 and LNCaP cells in the log phase of cell culture growth.

  15. Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: matching high information content with high throughput.

    Science.gov (United States)

    Holdgate, Geoff A; Anderson, Malcolm; Edfeldt, Fredrik; Geschwindner, Stefan

    2010-10-01

    Affinity-based technologies have become impactful tools to detect, monitor and characterize molecular interactions using recombinant target proteins. This can aid the understanding of biological function by revealing mechanistic details, and even more importantly, enables the identification of new improved ligands that can modulate the biological activity of those targets in a desired fashion. The selection of the appropriate technology is a key step in that process, as each one of the currently available technologies offers a characteristic type of biophysical information about the ligand-binding event. Alongside the indisputable advantages of each of those technologies they naturally display diverse restrictions that are quite frequently related to the target system to be studied but also to the affinity, solubility and molecular size of the ligands. This paper discusses some of the theoretical and experimental aspects of the most common affinity-based methods, what type of information can be gained from each one of those approaches, and what requirements as well as limitations are expected from working with recombinant proteins on those platforms and how those can be optimally addressed.

  16. Lentiviral Gag assembly analyzed through the functional characterization of chimeric simian immunodeficiency viruses expressing different domains of the feline immunodeficiency virus capsid protein.

    Directory of Open Access Journals (Sweden)

    María J Esteva

    Full Text Available To gain insight into the functional relationship between the capsid (CA domains of the Gag polyproteins of simian and feline immunodeficiency viruses (SIV and FIV, respectively, we constructed chimeric SIVs in which the CA-coding region was partially or totally replaced by the equivalent region of the FIV CA. The phenotypic characterization of the chimeras allowed us to group them into three categories: the chimeric viruses that, while being assembly-competent, exhibit a virion-associated unstable FIV CA; a second group represented only by the chimeric SIV carrying the N-terminal domain (NTD of the FIV CA which proved to be assembly-defective; and a third group constituted by the chimeric viruses that produce virions exhibiting a mature and stable FIV CA protein, and which incorporate the envelope glycoprotein and contain wild-type levels of viral genome RNA and reverse transcriptase. Further analysis of the latter group of chimeric SIVs demonstrated that they are non-infectious due to a post-entry impairment, such as uncoating of the viral core, reverse transcription or nuclear import of the preintegration complex. Furthermore, we show here that the carboxyl-terminus domain (CTD of the FIV CA has an intrinsic ability to dimerize in vitro and form high-molecular-weight oligomers, which, together with our finding that the FIV CA-CTD is sufficient to confer assembly competence to the resulting chimeric SIV Gag polyprotein, provides evidence that the CA-CTD exhibits more functional plasticity than the CA-NTD. Taken together, our results provide relevant information on the biological relationship between the CA proteins of primate and nonprimate lentiviruses.

  17. Use of the REVERT®total protein stain as a loading control demonstrates significant benefits over the use of housekeeping proteins when analyzing brain homogenates by Western blot: An analysis of samples representing different gonadal hormone states.

    Science.gov (United States)

    Kirshner, Z Z; Gibbs, R B

    2018-01-30

    Western blot is routinely used to quantify differences in the levels of target proteins in tissues. Standard methods typically use measurements of housekeeping proteins to control for variations in loading and protein transfer. This is problematic, however, when housekeeping proteins also are affected by experimental conditions such as injury, disease, and/or gonadal hormone manipulations. Our goal was to evaluate an alternative and perhaps superior method for conducting Western blot analysis of brain tissue homogenates from rats with distinct physiologically relevant gonadal hormone states. Tissues were collected from the hippocampus, frontal cortex, and striatum of young adult female rats that either were ovariectomized to model surgical menopause, or were treated with the ovatotoxin 4-vinylcyclohexene diepoxide (VCD) to model transitional menopause. Tissues also were collected from rats with a normal estrous cycle killed at proestrus when estradiol levels are high, and at diestrus when estradiol levels are low. Western blot detection of α-tubulin, β-actin, and GAPDH was performed and were compared for sensitivity and reliability with a fluorescent total protein stain (REVERT ® ). Results show that the total protein stain was much less variable across samples and had a greater linear range than α-tubulin, β-actin, or GAPDH. The stain was stable and easy to use, and did not interfere with the immunodetection or multiplexed detection of the housekeeping proteins. In addition, we show that normalization of our data to total protein, but not to GAPDH, revealed significant differences in α-tubulin expression in the hippocampus as a function of treatment, and that gel-to-gel consistency in measuring differences between paired samples run on multiple gels was significantly better when data were normalized to total protein than when normalized to GAPDH. These results demonstrate that the REVERT ® total protein stain can be used in Western blot analysis of brain

  18. MADS interactomics : towards understanding the molecular mechanisms of plant MADS-domain transcription factor function

    NARCIS (Netherlands)

    Smaczniak, C.D.

    2013-01-01

    Protein-protein and protein-DNA interactions are essential for the molecular action of transcription factors. By combinatorial binding to target gene promoters, transcription factors are able to up- or down-regulate the expression of these genes. MADS-domain proteins comprise a large family of

  19. Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions.

    Science.gov (United States)

    Hubner, Nina C; Bird, Alexander W; Cox, Jürgen; Splettstoesser, Bianca; Bandilla, Peter; Poser, Ina; Hyman, Anthony; Mann, Matthias

    2010-05-17

    Protein interactions are involved in all cellular processes. Their efficient and reliable characterization is therefore essential for understanding biological mechanisms. In this study, we show that combining bacterial artificial chromosome (BAC) TransgeneOmics with quantitative interaction proteomics, which we call quantitative BAC-green fluorescent protein interactomics (QUBIC), allows specific and highly sensitive detection of interactions using rapid, generic, and quantitative procedures with minimal material. We applied this approach to identify known and novel components of well-studied complexes such as the anaphase-promoting complex. Furthermore, we demonstrate second generation interaction proteomics by incorporating directed mutational transgene modification and drug perturbation into QUBIC. These methods identified domain/isoform-specific interactors of pericentrin- and phosphorylation-specific interactors of TACC3, which are necessary for its recruitment to mitotic spindles. The scalability, simplicity, cost effectiveness, and sensitivity of this method provide a basis for its general use in small-scale experiments and in mapping the human protein interactome.

  20. Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference

    Directory of Open Access Journals (Sweden)

    Tingting Zheng

    2017-09-01

    Full Text Available Background: A range of computational methods that rely on the analysis of genome-wide expression datasets have been developed and successfully used for drug repositioning. The success of these methods is based on the hypothesis that introducing a factor (in this case, a drug molecule that could reverse the disease gene expression signature will lead to a therapeutic effect. However, it has also been shown that globally reversing the disease expression signature is not a prerequisite for drug activity. On the other hand, the basic idea of significant anti-correlation in expression profiles could have great value for establishing diet-disease associations and could provide new insights into the role of dietary interventions in disease.Methods: We performed an integrated analysis of publicly available gene expression profiles for foods, diseases and drugs, by calculating pairwise similarity scores for diet and disease gene expression signatures and characterizing their topological features in protein-protein interaction networks.Results: We identified 485 diet-disease pairs where diet could positively influence disease development and 472 pairs where specific diets should be avoided in a disease state. Multiple evidence suggests that orange, whey and coconut fat could be beneficial for psoriasis, lung adenocarcinoma and macular degeneration, respectively. On the other hand, fructose-rich diet should be restricted in patients with chronic intermittent hypoxia and ovarian cancer. Since humans normally do not consume foods in isolation, we also applied different algorithms to predict synergism; as a result, 58 food pairs were predicted. Interestingly, the diets identified as anti-correlated with diseases showed a topological proximity to the disease proteins similar to that of the corresponding drugs.Conclusions: In conclusion, we provide a computational framework for establishing diet-disease associations and additional information on the role of

  1. Analyzing Protein Changes in Guinea Pig Tissue Lysates Using Non-guinea Pig Specific Antibodies: Procedures for Western Blotting and Examples Using 16 Individual Antibodies for Common CNS Proteins

    National Research Council Canada - National Science Library

    Johnson, Erik A; Daugherty, Kelly S

    2006-01-01

    .... Common Western blotting techniques were used to compare immunostaining patterns of tissue lysates between a known species, rat, and the guinea pig using antibodies to several common CNS proteins...

  2. Characterization of the Saccharomyces cerevisiae ATP-Interactome using the iTRAQ-SPROX Technique

    Science.gov (United States)

    Geer, M. Ariel; Fitzgerald, Michael C.

    2016-02-01

    The stability of proteins from rates of oxidation (SPROX) technique was used in combination with an isobaric mass tagging strategy to identify adenosine triphosphate (ATP) interacting proteins in the Saccharomyces cerevisiae proteome. The SPROX methodology utilized in this work enabled 373 proteins in a yeast cell lysate to be assayed for ATP interactions (both direct and indirect) using the non-hydrolyzable ATP analog, adenylyl imidodiphosphate (AMP-PNP). A total of 28 proteins were identified with AMP-PNP-induced thermodynamic stability changes. These protein hits included 14 proteins that were previously annotated as ATP-binding proteins in the Saccharomyces Genome Database (SGD). The 14 non-annotated ATP-binding proteins included nine proteins that were previously found to be ATP-sensitive in an earlier SPROX study using a stable isotope labeling with amino acids in cell culture (SILAC)-based approach. A bioinformatics analysis of the protein hits identified here and in the earlier SILAC-SPROX experiments revealed that many of the previously annotated ATP-binding protein hits were kinases, ligases, and chaperones. In contrast, many of the newly discovered ATP-sensitive proteins were not from these protein classes, but rather were hydrolases, oxidoreductases, and nucleic acid-binding proteins.

  3. Predicted protein interactions of IFITMs may shed light on mechanisms of Zika virus-induced microcephaly and host invasion [version 2; referees: 2 approved, 1 approved with reservations, 1 not approved

    Directory of Open Access Journals (Sweden)

    Madhavi K. Ganapathiraju

    2017-11-01

    Full Text Available After the first reported case of Zika virus (ZIKV in Brazil, in 2015, a significant increase in the reported cases of microcephaly was observed. Microcephaly is a neurological condition in which the infant’s head is significantly smaller with complications in brain development. Recently, two small membrane-associated interferon-inducible transmembrane proteins (IFITM1 and IFITM3 have been shown to repress members of the flaviviridae family which includes ZIKV. However, the exact mechanisms leading to the inhibition of the virus are yet unknown. Here, we assembled an interactome of IFITM1 and IFITM3 with known protein-protein interactions (PPIs collected from publicly available databases and novel PPIs predicted using the High-confidence Protein-Protein Interaction Prediction (HiPPIP model. We analyzed the functional and pathway associations of the interacting proteins, and found that there are several immunity pathways (toll-like receptor signaling, cd28 signaling in T-helper cells, crosstalk between dendritic cells and natural killer cells, neuronal pathways (axonal guidance signaling, neural tube closure and actin cytoskeleton signaling and developmental pathways (neural tube closure, embryonic skeletal system development that are associated with these interactors. Our novel PPIs associate cilia dysfunction in ependymal cells to microcephaly, and may also shed light on potential targets of ZIKV for host invasion by immunosuppression and cytoskeletal rearrangements. These results could help direct future research in elucidating the mechanisms underlying host defense to ZIKV and other flaviviruses.

  4. Triangle network motifs predict complexes by complementing high-error interactomes with structural information

    Directory of Open Access Journals (Sweden)

    Labudde Dirk

    2009-06-01

    Full Text Available Abstract Background A lot of high-throughput studies produce protein-protein interaction networks (PPINs with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs representing binding evidence on proteins, forming PPI-SDDI-PPI triangles. Results We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from Munich Information center for Protein Sequences (MIPS. PPI-SDDI-PPI triangles have ~20 times higher overlap with MIPS complexes than using second-level neighbors in PPINs without SDDIs. The biological interpretation for triangles is that a SDDI causes two proteins to be observed with common interaction partners in high-throughput experiments. The relatively few SDDIs overlapping with PPINs are part of highly connected SDDI components, and are more likely to be detected in experimental studies. We demonstrate the utility of PPI-SDDI-PPI triangles by reconstructing myosin-actin processes in the nucleus, cytoplasm, and cytoskeleton, which were not obvious in the original PPIN. Using other complementary datatypes in place of SDDIs to form triangles, such as PubMed co-occurrences or threading information, results in a similar ability to find protein complexes. Conclusion Given high-error PPINs with missing information, triangles of mixed datatypes are a promising direction for finding protein complexes. Integrating PPINs with SDDIs improves finding complexes. Structural SDDIs partially explain the high functional similarity of second-level neighbors in PPINs. We estimate that

  5. An interactomics overview of the human and bovine milk proteome over lactation

    NARCIS (Netherlands)

    Zhang, Lina; Dijk, van Aalt-Jan; Hettinga, Kasper

    2017-01-01

    Background: Milk is the most important food for growth and development of the neonate, because of its nutrient composition and presence of many bioactive proteins. Differences between human and bovine milk in low abundant proteins have not been extensively studied. To better understand the

  6. From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks.

    KAUST Repository

    Cannistraci, C.V.

    2013-04-08

    Growth and remodelling impact the network topology of complex systems, yet a general theory explaining how new links arise between existing nodes has been lacking, and little is known about the topological properties that facilitate link-prediction. Here we investigate the extent to which the connectivity evolution of a network might be predicted by mere topological features. We show how a link/community-based strategy triggers substantial prediction improvements because it accounts for the singular topology of several real networks organised in multiple local communities - a tendency here named local-community-paradigm (LCP). We observe that LCP networks are mainly formed by weak interactions and characterise heterogeneous and dynamic systems that use self-organisation as a major adaptation strategy. These systems seem designed for global delivery of information and processing via multiple local modules. Conversely, non-LCP networks have steady architectures formed by strong interactions, and seem designed for systems in which information/energy storage is crucial.

  7. Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome.

    Science.gov (United States)

    Luisi, Pierre; Alvarez-Ponce, David; Pybus, Marc; Fares, Mario A; Bertranpetit, Jaume; Laayouni, Hafid

    2015-04-02

    Genes vary in their likelihood to undergo adaptive evolution. The genomic factors that determine adaptability, however, remain poorly understood. Genes function in the context of molecular networks, with some occupying more important positions than others and thus being likely to be under stronger selective pressures. However, how positive selection distributes across the different parts of molecular networks is still not fully understood. Here, we inferred positive selection using comparative genomics and population genetics approaches through the comparison of 10 mammalian and 270 human genomes, respectively. In agreement with previous results, we found that genes with lower network centralities are more likely to evolve under positive selection (as inferred from divergence data). Surprisingly, polymorphism data yield results in the opposite direction than divergence data: Genes with higher centralities are more likely to have been targeted by recent positive selection during recent human evolution. Our results indicate that the relationship between centrality and the impact of adaptive evolution highly depends on the mode of positive selection and/or the evolutionary time-scale. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation.

    Science.gov (United States)

    Aw, Jong Ghut Ashley; Shen, Yang; Wilm, Andreas; Sun, Miao; Lim, Xin Ni; Boon, Kum-Loong; Tapsin, Sidika; Chan, Yun-Shen; Tan, Cheng-Peow; Sim, Adelene Y L; Zhang, Tong; Susanto, Teodorus Theo; Fu, Zhiyan; Nagarajan, Niranjan; Wan, Yue

    2016-05-19

    Identifying pairwise RNA-RNA interactions is key to understanding how RNAs fold and interact with other RNAs inside the cell. We present a high-throughput approach, sequencing of psoralen crosslinked, ligated, and selected hybrids (SPLASH), that maps pairwise RNA interactions in vivo with high sensitivity and specificity, genome-wide. Applying SPLASH to human and yeast transcriptomes revealed the diversity and dynamics of thousands of long-range intra- and intermolecular RNA-RNA interactions. Our analysis highlighted key structural features of RNA classes, including the modular organization of mRNAs, its impact on translation and decay, and the enrichment of long-range interactions in noncoding RNAs. Additionally, intermolecular mRNA interactions were organized into network clusters and were remodeled during cellular differentiation. We also identified hundreds of known and new snoRNA-rRNA binding sites, expanding our knowledge of rRNA biogenesis. These results highlight the underexplored complexity of RNA interactomes and pave the way to better understanding how RNA organization impacts biology. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Modeling complexes of modeled proteins.

    Science.gov (United States)

    Anishchenko, Ivan; Kundrotas, Petras J; Vakser, Ilya A

    2017-03-01

    Structural characterization of proteins is essential for understanding life processes at the molecular level. However, only a fraction of known proteins have experimentally determined structures. This fraction is even smaller for protein-protein complexes. Thus, structural modeling of protein-protein interactions (docking) primarily has to rely on modeled structures of the individual proteins, which typically are less accurate than the experimentally determined ones. Such "double" modeling is the Grand Challenge of structural reconstruction of the interactome. Yet it remains so far largely untested in a systematic way. We present a comprehensive validation of template-based and free docking on a set of 165 complexes, where each protein model has six levels of structural accuracy, from 1 to 6 Å C α RMSD. Many template-based docking predictions fall into acceptable quality category, according to the CAPRI criteria, even for highly inaccurate proteins (5-6 Å RMSD), although the number of such models (and, consequently, the docking success rate) drops significantly for models with RMSD > 4 Å. The results show that the existing docking methodologies can be successfully applied to protein models with a broad range of structural accuracy, and the template-based docking is much less sensitive to inaccuracies of protein models than the free docking. Proteins 2017; 85:470-478. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  10. PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440

    OpenAIRE

    Park, Seong-Jin; Choi, Jong-Soon; Kim, Byoung-Chul; Jho, Seong-Woong; Ryu, Jea-Woon; Park, Daeui; Lee, Kyung-A; Bhak, Jong; Kim, Seung Il

    2009-01-01

    Abstract Background Pseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organism for genetic and physiological studies and for the development of biotechnological applications. In order to provide a more systematic application of the organism, we have constructed a protein-protein interaction (PPI) network analysis system of P. putida KT2440....

  11. Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

    Directory of Open Access Journals (Sweden)

    Liang-Hui Chu

    Full Text Available Angiogenesis involves stimulation of endothelial cells (EC by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome" could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A. We used the Short Time-series Expression Miner (STEM to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC and human microvascular EC (MEC. The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

  12. Protein-protein interactions and cancer: targeting the central dogma.

    Science.gov (United States)

    Garner, Amanda L; Janda, Kim D

    2011-01-01

    Between 40,000 and 200,000 protein-protein interactions have been predicted to exist within the human interactome. As these interactions are of a critical nature in many important cellular functions and their dysregulation is causal of disease, the modulation of these binding events has emerged as a leading, yet difficult therapeutic arena. In particular, the targeting of protein-protein interactions relevant to cancer is of fundamental importance as the tumor-promoting function of several aberrantly expressed proteins in the cancerous state is directly resultant of its ability to interact with a protein-binding partner. Of significance, these protein complexes play a crucial role in each of the steps of the central dogma of molecular biology, the fundamental processes of genetic transmission. With the many important discoveries being made regarding the mechanisms of these genetic process, the identification of new chemical probes are needed to better understand and validate the druggability of protein-protein interactions related to the central dogma. In this review, we provide an overview of current small molecule-based protein-protein interaction inhibitors for each stage of the central dogma: transcription, mRNA splicing and translation. Importantly, through our analysis we have uncovered a lack of necessary probes targeting mRNA splicing and translation, thus, opening up the possibility for expansion of these fields.

  13. Characterization of the CLASP2 Protein Interaction Network Identifies SOGA1 as a Microtubule-Associated Protein

    DEFF Research Database (Denmark)

    Sørensen, Rikke Kruse; Krantz, James; Barker, Natalie

    2017-01-01

    and built a CLASP2 protein network in 3T3-L1 adipocytes. Using two different commercially available antibodies for CLASP2 and an antibody for epitope-tagged, overexpressed CLASP2, we performed multiple affinity purification coupled with mass spectrometry (AP-MS) experiments in combination with label-free......, glycogen synthase, and glycogenin. Investigating the SOGA1 interactome confirmed SOGA1 can reciprocal co-IP both CLASP2 and MARK2 as well as glycogen synthase and glycogenin. SOGA1 was confirmed to colocalize with CLASP2 and also with tubulin, which identifies SOGA1 as a new microtubule-associated protein...

  14. Proteomic-coupled-network analysis of T877A-androgen receptor interactomes can predict clinical prostate cancer outcomes between White (non-Hispanic and African-American groups.

    Directory of Open Access Journals (Sweden)

    Naif Zaman

    Full Text Available The androgen receptor (AR remains an important contributor to the neoplastic evolution of prostate cancer (CaP. CaP progression is linked to several somatic AR mutational changes that endow upon the AR dramatic gain-of-function properties. One of the most common somatic mutations identified is Thr877-to-Ala (T877A, located in the ligand-binding domain, that results in a receptor capable of promiscuous binding and activation by a variety of steroid hormones and ligands including estrogens, progestins, glucocorticoids, and several anti-androgens. In an attempt to further define somatic mutated AR gain-of-function properties, as a consequence of its promiscuous ligand binding, we undertook a proteomic/network analysis approach to characterize the protein interactome of the mutant T877A-AR in LNCaP cells under eight different ligand-specific treatments (dihydrotestosterone, mibolerone, R1881, testosterone, estradiol, progesterone, dexamethasone, and cyproterone acetate. In extending the analysis of our multi-ligand complexes of the mutant T877A-AR we observed significant enrichment of specific complexes between normal and primary prostatic tumors, which were furthermore correlated with known clinical outcomes. Further analysis of certain mutant T877A-AR complexes showed specific population preferences distinguishing primary prostatic disease between white (non-Hispanic vs. African-American males. Moreover, these cancer-related AR-protein complexes demonstrated predictive survival outcomes specific to CaP, and not for breast, lung, lymphoma or medulloblastoma cancers. Our study, by coupling data generated by our proteomics to network analysis of clinical samples, has helped to define real and novel biological pathways in complicated gain-of-function AR complex systems.

  15. Are protein hubs faster folders? Exploration based on Escherichia coli proteome.

    Science.gov (United States)

    Xu, Hong-Rui; Cheng, Jun-Feng; Hu, Xiao-Pan; Chu, Ying-Ying; Ma, Bin-Guang

    2016-12-01

    Protein hubs in protein-protein interaction network are especially important due to their central roles in the entire network. Despite of their importance, the folding kinetics of hub proteins in comparison with non-hubs is still unknown. In this work, the folding rates for protein hubs and non-hubs were predicted and compared for the interactome of Escherichia coli K12, and the results showed that hub proteins fold faster than non-hub proteins. A possible explanation might be that protein hubs have more and fast-folding structural conformations than non-hubs, which leads to the notion of "hub of hubs" in the protein conformation space. It was found that the sequence and structure features relevant to protein folding rates are also different between hub and non-hub proteins. Moreover, the interacting proteins tend to have similar folding rates. These results gave insightful implications for understanding the interplay between the mechanisms of protein folding and interaction.

  16. Proteins interacting with cloning scars: a source of false positive protein-protein interactions.

    Science.gov (United States)

    Banks, Charles A S; Boanca, Gina; Lee, Zachary T; Florens, Laurence; Washburn, Michael P

    2015-02-23

    A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine "cloning scar" present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected.

  17. Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH).

    Science.gov (United States)

    Helwak, Aleksandra; Tollervey, David

    2014-03-01

    RNA-RNA interactions have critical roles in many cellular processes, but studying them is difficult and laborious. Here we describe an experimental procedure, termed cross-linking ligation and sequencing of hybrids (CLASH), which allows high-throughput identification of sites of RNA-RNA interaction. During CLASH, a tagged bait protein is UV-cross-linked in cell cultures to stabilize RNA interactions, and it is purified under denaturing conditions. RNAs associated with the bait protein are partially truncated, and the ends of RNA duplexes are ligated together. After linker addition, cDNA library preparation and high-throughput sequencing, the ligated duplexes give rise to chimeric cDNAs, which unambiguously identify RNA-RNA interaction sites independent of bioinformatic predictions. This protocol is optimized for studying miRNA targets bound by Argonaute (AGO) proteins, but it should be easily adapted for other RNA-binding proteins and classes of RNA. The protocol requires ∼5 d to complete, excluding the time required for high-throughput sequencing and bioinformatic analyses.

  18. A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2

    Directory of Open Access Journals (Sweden)

    Sylvie Lalonde

    2010-09-01

    Full Text Available Interactions between membrane proteins and the soluble fraction are essential for signal transduction and for regulating nutrient transport. To gain insights into the membrane-based interactome, 3,852 open reading frames (ORFs out of a target list of 8,383 representing membrane and signaling proteins from Arabidopsis thaliana were cloned into a Gateway compatible vector. The mating-based split-ubiquitin system was used to screen for potential protein-protein interactions (pPPIs among 490 Arabidopsis ORFs. A binary robotic screen between 142 receptor-like kinases, 72 transporters, 57 soluble protein kinases and phosphatases, 40 glycosyltransferases, 95 proteins of various functions and 89 proteins with unknown function detected 387 out of 90,370 possible PPIs. A secondary screen confirmed 343 (of 387 pPPIs between 179 proteins, yielding a scale-free network (r2=0.863. Eighty of 142 transmembrane receptor-like kinases (RLK tested positive, identifying three homomers, 63 heteromers and 80 pPPIs with other proteins. Thirty-one out of 142 RLK interactors (including RLKs had previously been found to be phosphorylated; thus interactors may be substrates for respective RLKs. None of the pPPIs described here had been reported in the major interactome databases, including potential interactors of G protein-coupled receptors, phospholipase C, and AMT ammonium transporters. Two RLKs found as putative interactors of AMT1;1 were independently confirmed using a split luciferase assay in Arabidopsis protoplasts. These RLKs may be involved in ammonium-dependent phosphorylation of the C-terminus and regulation of ammonium uptake activity. The robotic screening method established here will enable a systematic analysis of membrane protein interactions in fungi, plants and metazoa.

  19. The chemical interactome space between the human host and the genetically defined gut metabotypes

    DEFF Research Database (Denmark)

    Jacobsen, Ulrik Plesner; Nielsen, Henrik Bjørn; Hildebrand, Falk

    2013-01-01

    symbiosis in the gut of mammals, mechanistic understanding of the contributions of the gut microbiome and how variations in the metabotypes are linked to the host health are obscure. Here, we mapped the entire metabolic potential of the gut microiome based solely on metagenomics sequencing data derived from...... of the Prevotella genera is a key factor indicating a low metabolic potential. These metagenome-based metabolic signatures were used to study the interaction networks between bacteria-specific metabolites and human proteins. We found that thirty-three such metabolites interact with disease-relevant protein...... complexes several of which are highly expressed in cells and tissues involved in the signaling and shaping of the adaptive immune system and associated with squamous cell carcinoma and bladder cancer. From this set of metabolites, eighteen are present in DrugBank providing evidence that we carry a natural...

  20. IQGAP1 Interactome Analysis by In Vitro Reconstitution and Live Cell 3-Color FRET Microscopy

    Science.gov (United States)

    Wallrabe, Horst; Cai, Ying; Sun, Yuansheng; Periasamy, A.; Luzes, R.; Fang, Xiaolan; Kan, Ho-Man; Cameron, L. C.; Schafer, Dorothy A.; Bloom, George S.

    2014-01-01

    IQGAP1 stimulates branched actin filament nucleation by activating N-WASP, which then activates the Arp2/3 complex. N-WASP can be activated by other factors, including GTP-bound Cdc42 or Rac1, which also bind IQGAP1. Here we report the use of purified proteins for in vitro binding and actin polymerization assays, and Förster (or fluorescence) resonance energy transfer (FRET) microscopy of cultured cells to illuminate functional interactions among IQGAP1, N-WASP, actin, and either Cdc42 or Rac1. In pyrene-actin assembly assays containing N-WASP and Arp2/3 complex, IQGAP1 plus either small G protein cooperatively stimulated actin filament nucleation by reducing the lag time before 50% maximum actin polymerization was reached. Similarly, Cdc42 and Rac1 modulated the binding of IQGAP1 to N-WASP in a dose-dependent manner, with Cdc42 enhancing the interaction and Rac1 reducing the interaction. These in vitro reconstitution results suggested that IQGAP1 interacts by similar, yet distinct mechanisms with Cdc42 versus Rac1 to regulate actin filament assembly through N-WASP in vivo. The physiological relevance of these multi-protein interactions was substantiated by 3-color FRET microscopy of live MDCK cells expressing various combinations of fluorescent N-WASP, IQGAP1, Cdc42, Rac1 and actin. This study also establishes 3-color FRET microscopy as a powerful tool for studying dynamic intermolecular interactions in live cells. PMID:24124181

  1. Chromatin Affinity Purification and Quantitative Mass Spectrometry Defining the Interactome of Histone Modification Patterns*

    Science.gov (United States)

    Nikolov, Miroslav; Stützer, Alexandra; Mosch, Kerstin; Krasauskas, Andrius; Soeroes, Szabolcs; Stark, Holger; Urlaub, Henning; Fischle, Wolfgang

    2011-01-01

    DNA and histone modifications direct the functional state of chromatin and thereby the readout of the genome. Candidate approaches and histone peptide affinity purification experiments have identified several proteins that bind to chromatin marks. However, the complement of factors that is recruited by individual and combinations of DNA and histone modifications has not yet been defined. Here, we present a strategy based on recombinant, uniformly modified chromatin templates used in affinity purification experiments in conjunction with SILAC-based quantitative mass spectrometry for this purpose. On the prototypic H3K4me3 and H3K9me3 histone modification marks we compare our method with a histone N-terminal peptide affinity purification approach. Our analysis shows that only some factors associate with both, chromatin and peptide matrices but that a surprisingly large number of proteins differ in their association with these templates. Global analysis of the proteins identified implies specific domains mediating recruitment to the chromatin marks. Our proof-of-principle studies show that chromatin templates with defined modification patterns can be used to decipher how the histone code is read and translated. PMID:21836164

  2. Synthetic Oligosaccharide Libraries and Microarray Technology: A Powerful Combination for the Success of Current Glycosaminoglycan Interactomics.

    Science.gov (United States)

    Pomin, Vitor H; Wang, Xu

    2017-11-20

    Glycosaminoglycans (GAGs) are extracellular matrix and/or cell-surface sulfated glycans crucial to the regulation of various signaling proteins, the functions of which are essential in many pathophysiological systems. Because structural heterogeneity is high in GAG chains and purification is difficult, the use of structurally defined GAG oligosaccharides from natural sources as molecular models in both biophysical and pharmacological assays is limited. To overcome this obstacle, GAG-like oligosaccharides of well-defined structures are currently being synthesized by chemical and/or enzymatic means in many research groups around the world. These synthetic GAG oligosaccharides serve as useful molecular tools in studies of GAG-protein interactions. In this review, besides discussing the commonest routes used for the synthesis of GAG oligosaccharides, we also survey some libraries of these synthetic models currently available for research and discuss their activities in interaction studies with functional proteins, especially through the microarray approach. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Analyzing Peace Pedagogies

    Science.gov (United States)

    Haavelsrud, Magnus; Stenberg, Oddbjorn

    2012-01-01

    Eleven articles on peace education published in the first volume of the Journal of Peace Education are analyzed. This selection comprises peace education programs that have been planned or carried out in different contexts. In analyzing peace pedagogies as proposed in the 11 contributions, we have chosen network analysis as our method--enabling…

  4. The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors.

    Directory of Open Access Journals (Sweden)

    Susanne Pfefferle

    2011-10-01

    Full Text Available Coronaviruses (CoVs are important human and animal pathogens that induce fatal respiratory, gastrointestinal and neurological disease. The outbreak of the severe acute respiratory syndrome (SARS in 2002/2003 has demonstrated human vulnerability to (Coronavirus CoV epidemics. Neither vaccines nor therapeutics are available against human and animal CoVs. Knowledge of host cell proteins that take part in pivotal virus-host interactions could define broad-spectrum antiviral targets. In this study, we used a systems biology approach employing a genome-wide yeast-two hybrid interaction screen to identify immunopilins (PPIA, PPIB, PPIH, PPIG, FKBP1A, FKBP1B as interaction partners of the CoV non-structural protein 1 (Nsp1. These molecules modulate the Calcineurin/NFAT pathway that plays an important role in immune cell activation. Overexpression of NSP1 and infection with live SARS-CoV strongly increased signalling through the Calcineurin/NFAT pathway and enhanced the induction of interleukin 2, compatible with late-stage immunopathogenicity and long-term cytokine dysregulation as observed in severe SARS cases. Conversely, inhibition of cyclophilins by cyclosporine A (CspA blocked the replication of CoVs of all genera, including SARS-CoV, human CoV-229E and -NL-63, feline CoV, as well as avian infectious bronchitis virus. Non-immunosuppressive derivatives of CspA might serve as broad-range CoV inhibitors applicable against emerging CoVs as well as ubiquitous pathogens of humans and livestock.

  5. Miniature mass analyzer

    CERN Document Server

    Cuna, C; Lupsa, N; Cuna, S; Tuzson, B

    2003-01-01

    The paper presents the concept of different mass analyzers that were specifically designed as small dimension instruments able to detect with great sensitivity and accuracy the main environmental pollutants. The mass spectrometers are very suited instrument for chemical and isotopic analysis, needed in environmental surveillance. Usually, this is done by sampling the soil, air or water followed by laboratory analysis. To avoid drawbacks caused by sample alteration during the sampling process and transport, the 'in situ' analysis is preferred. Theoretically, any type of mass analyzer can be miniaturized, but some are more appropriate than others. Quadrupole mass filter and trap, magnetic sector, time-of-flight and ion cyclotron mass analyzers can be successfully shrunk, for each of them some performances being sacrificed but we must know which parameters are necessary to be kept unchanged. To satisfy the miniaturization criteria of the analyzer, it is necessary to use asymmetrical geometries, with ion beam obl...

  6. Analog multivariate counting analyzers

    CERN Document Server

    Nikitin, A V; Armstrong, T P

    2003-01-01

    Characterizing rates of occurrence of various features of a signal is of great importance in numerous types of physical measurements. Such signal features can be defined as certain discrete coincidence events, e.g. crossings of a signal with a given threshold, or occurrence of extrema of a certain amplitude. We describe measuring rates of such events by means of analog multivariate counting analyzers. Given a continuous scalar or multicomponent (vector) input signal, an analog counting analyzer outputs a continuous signal with the instantaneous magnitude equal to the rate of occurrence of certain coincidence events. The analog nature of the proposed analyzers allows us to reformulate many problems of the traditional counting measurements, and cast them in a form which is readily addressed by methods of differential calculus rather than by algebraic or logical means of digital signal processing. Analog counting analyzers can be easily implemented in discrete or integrated electronic circuits, do not suffer fro...

  7. Hypothesis review: are clathrin-mediated endocytosis and clathrin-dependent membrane and protein trafficking core pathophysiological processes in schizophrenia and bipolar disorder?

    LENUS (Irish Health Repository)

    2012-02-01

    Clathrin-mediated endocytosis (CME) is the best-characterized mechanism governing cellular membrane and protein trafficking. In this hypothesis review, we integrate recent evidence implicating CME and related cellular trafficking mechanisms in the pathophysiology of psychotic disorders such as schizophrenia and bipolar disorder. The evidence includes proteomic and genomic findings implicating proteins and genes of the clathrin interactome. Additionally, several important candidate genes for schizophrenia, such as dysbindin, are involved in processes closely linked to CME and membrane trafficking. We discuss that key aspects of psychosis neuropathology such as synaptic dysfunction, white matter changes and aberrant neurodevelopment are all influenced by clathrin-dependent processes, and that other cellular trafficking mechanisms previously linked to psychoses interact with the clathrin interactome in important ways. Furthermore, many antipsychotic drugs have been shown to affect clathrin-interacting proteins. We propose that the targeted pharmacological manipulation of the clathrin interactome may offer fruitful opportunities for novel treatments of schizophrenia.Molecular Psychiatry advance online publication, 11 October 2011; doi:10.1038\\/mp.2011.123.

  8. Structures and short linear motif of disordered transcription factor regions provide clues to the interactome of the cellular hub radical-induced cell death1

    DEFF Research Database (Denmark)

    O'Shea, Charlotte; Staby, Lasse; Bendsen, Sidsel Krogh

    2017-01-01

    Intrinsically disordered protein regions (IDRs) lack a well-defined three-dimensional structure, but often facilitate key protein functions. Some interactions between IDRs and folded protein domains rely on short linear motifs (SLiMs). These motifs are challenging to identify, but once found can...... point to larger networks of interactions, such as with proteins that serve as hubs for essential cellular functions. The stress-associated plant protein Radical-Induced Cell Death1 (RCD1) is one such hub, interacting with many transcription factors via their flexible IDRs. To identify the SLiM bound...... by RCD1, we analyzed the IDRs in three protein partners - DREB2A, ANAC013, and ANAC046 - considering parameters such as disorder, context, charges, and pI. Using a combined bioinformatics and experimental approach, we have identified the bipartite RCD1-binding SLiM as [DE]-x(1,2)-[YF]-x(1,4)-[DE...

  9. Analyzing Stereotypes in Media.

    Science.gov (United States)

    Baker, Jackie

    1996-01-01

    A high school film teacher studied how students recognized messages in film, examining how film education could help students identify and analyze racial and gender stereotypes. Comparison of students' attitudes before and after the film course found that the course was successful in raising students' consciousness. (SM)

  10. Centrifugal analyzer development

    International Nuclear Information System (INIS)

    Burtis, C.A.; Bauer, M.L.; Bostick, W.D.

    1976-01-01

    The development of the centrifuge fast analyzer (CFA) is reviewed. The development of a miniature CFA with computer data analysis is reported and applications for automated diagnostic chemical and hematological assays are discussed. A portable CFA system with microprocessor was adapted for field assays of air and water samples for environmental pollutants, including ammonia, nitrates, nitrites, phosphates, sulfates, and silica. 83 references

  11. Americal options analyzed differently

    NARCIS (Netherlands)

    Nieuwenhuis, J.W.

    2003-01-01

    In this note we analyze in a discrete-time context and with a finite outcome space American options starting with the idea that every tradable should be a martingale under a certain measure. We believe that in this way American options become more understandable to people with a good working

  12. Evolution of protein-protein interaction networks in yeast.

    Directory of Open Access Journals (Sweden)

    Andrew Schoenrock

    Full Text Available Interest in the evolution of protein-protein and genetic interaction networks has been rising in recent years, but the lack of large-scale high quality comparative datasets has acted as a barrier. Here, we carried out a comparative analysis of computationally predicted protein-protein interaction (PPI networks from five closely related yeast species. We used the Protein-protein Interaction Prediction Engine (PIPE, which uses a database of known interactions to make sequence-based PPI predictions, to generate high quality predicted interactomes. Simulated proteomes and corresponding PPI networks were used to provide null expectations for the extent and nature of PPI network evolution. We found strong evidence for conservation of PPIs, with lower than expected levels of change in PPIs for about a quarter of the proteome. Furthermore, we found that changes in predicted PPI networks are poorly predicted by sequence divergence. Our analyses identified a number of functional classes experiencing fewer PPI changes than expected, suggestive of purifying selection on PPIs. Our results demonstrate the added benefit of considering predicted PPI networks when studying the evolution of closely related organisms.

  13. Distinctive Behaviors of Druggable Proteins in Cellular Networks.

    Directory of Open Access Journals (Sweden)

    Costas Mitsopoulos

    2015-12-01

    Full Text Available The interaction environment of a protein in a cellular network is important in defining the role that the protein plays in the system as a whole, and thus its potential suitability as a drug target. Despite the importance of the network environment, it is neglected during target selection for drug discovery. Here, we present the first systematic, comprehensive computational analysis of topological, community and graphical network parameters of the human interactome and identify discriminatory network patterns that strongly distinguish drug targets from the interactome as a whole. Importantly, we identify striking differences in the network behavior of targets of cancer drugs versus targets from other therapeutic areas and explore how they may relate to successful drug combinations to overcome acquired resistance to cancer drugs. We develop, computationally validate and provide the first public domain predictive algorithm for identifying druggable neighborhoods based on network parameters. We also make available full predictions for 13,345 proteins to aid target selection for drug discovery. All target predictions are available through canSAR.icr.ac.uk. Underlying data and tools are available at https://cansar.icr.ac.uk/cansar/publications/druggable_network_neighbourhoods/.

  14. Distinctive Behaviors of Druggable Proteins in Cellular Networks.

    Science.gov (United States)

    Mitsopoulos, Costas; Schierz, Amanda C; Workman, Paul; Al-Lazikani, Bissan

    2015-12-01

    The interaction environment of a protein in a cellular network is important in defining the role that the protein plays in the system as a whole, and thus its potential suitability as a drug target. Despite the importance of the network environment, it is neglected during target selection for drug discovery. Here, we present the first systematic, comprehensive computational analysis of topological, community and graphical network parameters of the human interactome and identify discriminatory network patterns that strongly distinguish drug targets from the interactome as a whole. Importantly, we identify striking differences in the network behavior of targets of cancer drugs versus targets from other therapeutic areas and explore how they may relate to successful drug combinations to overcome acquired resistance to cancer drugs. We develop, computationally validate and provide the first public domain predictive algorithm for identifying druggable neighborhoods based on network parameters. We also make available full predictions for 13,345 proteins to aid target selection for drug discovery. All target predictions are available through canSAR.icr.ac.uk. Underlying data and tools are available at https://cansar.icr.ac.uk/cansar/publications/druggable_network_neighbourhoods/.

  15. Analyzed Using Statistical Moments

    International Nuclear Information System (INIS)

    Oltulu, O.

    2004-01-01

    Diffraction enhanced imaging (DEl) technique is a new x-ray imaging method derived from radiography. The method uses a monorheumetten x-ray beam and introduces an analyzer crystal between an object and a detector Narrow angular acceptance of the analyzer crystal generates an improved contrast over the evaluation radiography. While standart radiography can produce an 'absorption image', DEl produces 'apparent absorption' and 'apparent refraction' images with superior quality. Objects with similar absorption properties may not be distinguished with conventional techniques due to close absorption coefficients. This problem becomes more dominant when an object has scattering properties. A simple approach is introduced to utilize scattered radiation to obtain 'pure absorption' and 'pure refraction' images

  16. Charged particle analyzer PLAZMAG

    International Nuclear Information System (INIS)

    Apathy, Istvan; Endroeczy, Gabor; Szemerey, Istvan; Szendroe, Sandor

    1985-01-01

    The scientific task of the charged particle analyzer PLAZMAG, a part of the VEGA space probe, and the physical background of the measurements are described. The sensor of the device face the Sun and the comet Halley measuring the energy and mass spectrum of ion and electron components of energies lower than 25 keV. The tasks of the individual electronic parts, the design aspects and the modes of operation in different phases of the flight are dealt with. (author)

  17. Fractional channel multichannel analyzer

    Science.gov (United States)

    Brackenbush, L.W.; Anderson, G.A.

    1994-08-23

    A multichannel analyzer incorporating the features of the present invention obtains the effect of fractional channels thus greatly reducing the number of actual channels necessary to record complex line spectra. This is accomplished by using an analog-to-digital converter in the asynchronous mode, i.e., the gate pulse from the pulse height-to-pulse width converter is not synchronized with the signal from a clock oscillator. This saves power and reduces the number of components required on the board to achieve the effect of radically expanding the number of channels without changing the circuit board. 9 figs.

  18. Plutonium solution analyzer

    International Nuclear Information System (INIS)

    Burns, D.A.

    1994-09-01

    A fully automated analyzer has been developed for plutonium solutions. It was assembled from several commercially available modules, is based upon segmented flow analysis, and exhibits precision about an order of magnitude better than commercial units (0.5%-O.05% RSD). The system was designed to accept unmeasured, untreated liquid samples in the concentration range 40-240 g/L and produce a report with sample identification, sample concentrations, and an abundance of statistics. Optional hydraulics can accommodate samples in the concentration range 0.4-4.0 g/L. Operating at a typical rate of 30 to 40 samples per hour, it consumes only 0.074 mL of each sample and standard, and generates waste at the rate of about 1.5 mL per minute. No radioactive material passes through its multichannel peristaltic pump (which remains outside the glovebox, uncontaminated) but rather is handled by a 6-port, 2-position chromatography-type loop valve. An accompanying computer is programmed in QuickBASIC 4.5 to provide both instrument control and data reduction. The program is truly user-friendly and communication between operator and instrument is via computer screen displays and keyboard. Two important issues which have been addressed are waste minimization and operator safety (the analyzer can run in the absence of an operator, once its autosampler has been loaded)

  19. Ring Image Analyzer

    Science.gov (United States)

    Strekalov, Dmitry V.

    2012-01-01

    Ring Image Analyzer software analyzes images to recognize elliptical patterns. It determines the ellipse parameters (axes ratio, centroid coordinate, tilt angle). The program attempts to recognize elliptical fringes (e.g., Newton Rings) on a photograph and determine their centroid position, the short-to-long-axis ratio, and the angle of rotation of the long axis relative to the horizontal direction on the photograph. These capabilities are important in interferometric imaging and control of surfaces. In particular, this program has been developed and applied for determining the rim shape of precision-machined optical whispering gallery mode resonators. The program relies on a unique image recognition algorithm aimed at recognizing elliptical shapes, but can be easily adapted to other geometric shapes. It is robust against non-elliptical details of the image and against noise. Interferometric analysis of precision-machined surfaces remains an important technological instrument in hardware development and quality analysis. This software automates and increases the accuracy of this technique. The software has been developed for the needs of an R&TD-funded project and has become an important asset for the future research proposal to NASA as well as other agencies.

  20. Plutonium solution analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Burns, D.A.

    1994-09-01

    A fully automated analyzer has been developed for plutonium solutions. It was assembled from several commercially available modules, is based upon segmented flow analysis, and exhibits precision about an order of magnitude better than commercial units (0.5%-O.05% RSD). The system was designed to accept unmeasured, untreated liquid samples in the concentration range 40-240 g/L and produce a report with sample identification, sample concentrations, and an abundance of statistics. Optional hydraulics can accommodate samples in the concentration range 0.4-4.0 g/L. Operating at a typical rate of 30 to 40 samples per hour, it consumes only 0.074 mL of each sample and standard, and generates waste at the rate of about 1.5 mL per minute. No radioactive material passes through its multichannel peristaltic pump (which remains outside the glovebox, uncontaminated) but rather is handled by a 6-port, 2-position chromatography-type loop valve. An accompanying computer is programmed in QuickBASIC 4.5 to provide both instrument control and data reduction. The program is truly user-friendly and communication between operator and instrument is via computer screen displays and keyboard. Two important issues which have been addressed are waste minimization and operator safety (the analyzer can run in the absence of an operator, once its autosampler has been loaded).

  1. Analyzing Water's Optical Absorption

    Science.gov (United States)

    2002-01-01

    A cooperative agreement between World Precision Instruments (WPI), Inc., and Stennis Space Center has led the UltraPath(TM) device, which provides a more efficient method for analyzing the optical absorption of water samples at sea. UltraPath is a unique, high-performance absorbance spectrophotometer with user-selectable light path lengths. It is an ideal tool for any study requiring precise and highly sensitive spectroscopic determination of analytes, either in the laboratory or the field. As a low-cost, rugged, and portable system capable of high- sensitivity measurements in widely divergent waters, UltraPath will help scientists examine the role that coastal ocean environments play in the global carbon cycle. UltraPath(TM) is a trademark of World Precision Instruments, Inc. LWCC(TM) is a trademark of World Precision Instruments, Inc.

  2. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  3. PREFACE: Physics approaches to protein interactions and gene regulation Physics approaches to protein interactions and gene regulation

    Science.gov (United States)

    Nussinov, Ruth; Panchenko, Anna R.; Przytycka, Teresa

    2011-06-01

    Physics approaches focus on uncovering, modeling and quantitating the general principles governing the micro and macro universe. This has always been an important component of biological research, however recent advances in experimental techniques and the accumulation of unprecedented genome-scale experimental data produced by these novel technologies now allow for addressing fundamental questions on a large scale. These relate to molecular interactions, principles of bimolecular recognition, and mechanisms of signal propagation. The functioning of a cell requires a variety of intermolecular interactions including protein-protein, protein-DNA, protein-RNA, hormones, peptides, small molecules, lipids and more. Biomolecules work together to provide specific functions and perturbations in intermolecular communication channels often lead to cellular malfunction and disease. A full understanding of the interactome requires an in-depth grasp of the biophysical principles underlying individual interactions as well as their organization in cellular networks. Phenomena can be described at different levels of abstraction. Computational and systems biology strive to model cellular processes by integrating and analyzing complex data from multiple experimental sources using interdisciplinary tools. As a result, both the causal relationships between the variables and the general features of the system can be discovered, which even without knowing the details of the underlying mechanisms allow for putting forth hypotheses and predicting the behavior of the systems in response to perturbation. And here lies the strength of in silico models which provide control and predictive power. At the same time, the complexity of individual elements and molecules can be addressed by the fields of molecular biophysics, physical biology and structural biology, which focus on the underlying physico-chemical principles and may explain the molecular mechanisms of cellular function. In this issue

  4. Downhole Fluid Analyzer Development

    Energy Technology Data Exchange (ETDEWEB)

    Bill Turner

    2006-11-28

    A novel fiber optic downhole fluid analyzer has been developed for operation in production wells. This device will allow real-time determination of the oil, gas and water fractions of fluids from different zones in a multizone or multilateral completion environment. The device uses near infrared spectroscopy and induced fluorescence measurement to unambiguously determine the oil, water and gas concentrations at all but the highest water cuts. The only downhole components of the system are the fiber optic cable and windows. All of the active components--light sources, sensors, detection electronics and software--will be located at the surface, and will be able to operate multiple downhole probes. Laboratory testing has demonstrated that the sensor can accurately determine oil, water and gas fractions with a less than 5 percent standard error. Once installed in an intelligent completion, this sensor will give the operating company timely information about the fluids arising from various zones or multilaterals in a complex completion pattern, allowing informed decisions to be made on controlling production. The research and development tasks are discussed along with a market analysis.

  5. PULSE HEIGHT ANALYZER

    Science.gov (United States)

    Johnstone, C.W.

    1958-01-21

    An anticoincidence device is described for a pair of adjacent channels of a multi-channel pulse height analyzer for preventing the lower channel from generating a count pulse in response to an input pulse when the input pulse has sufficient magnitude to reach the upper level channel. The anticoincidence circuit comprises a window amplifier, upper and lower level discriminators, and a biased-off amplifier. The output of the window amplifier is coupled to the inputs of the discriminators, the output of the upper level discriminator is connected to the resistance end of a series R-C network, the output of the lower level discriminator is coupled to the capacitance end of the R-C network, and the grid of the biased-off amplifier is coupled to the junction of the R-C network. In operation each discriminator produces a negative pulse output when the input pulse traverses its voltage setting. As a result of the connections to the R-C network, a trigger pulse will be sent to the biased-off amplifier when the incoming pulse level is sufficient to trigger only the lower level discriminator.

  6. Analyzing Spacecraft Telecommunication Systems

    Science.gov (United States)

    Kordon, Mark; Hanks, David; Gladden, Roy; Wood, Eric

    2004-01-01

    Multi-Mission Telecom Analysis Tool (MMTAT) is a C-language computer program for analyzing proposed spacecraft telecommunication systems. MMTAT utilizes parameterized input and computational models that can be run on standard desktop computers to perform fast and accurate analyses of telecommunication links. MMTAT is easy to use and can easily be integrated with other software applications and run as part of almost any computational simulation. It is distributed as either a stand-alone application program with a graphical user interface or a linkable library with a well-defined set of application programming interface (API) calls. As a stand-alone program, MMTAT provides both textual and graphical output. The graphs make it possible to understand, quickly and easily, how telecommunication performance varies with variations in input parameters. A delimited text file that can be read by any spreadsheet program is generated at the end of each run. The API in the linkable-library form of MMTAT enables the user to control simulation software and to change parameters during a simulation run. Results can be retrieved either at the end of a run or by use of a function call at any time step.

  7. Soft Decision Analyzer

    Science.gov (United States)

    Steele, Glen; Lansdowne, Chatwin; Zucha, Joan; Schlensinger, Adam

    2013-01-01

    The Soft Decision Analyzer (SDA) is an instrument that combines hardware, firmware, and software to perform realtime closed-loop end-to-end statistical analysis of single- or dual- channel serial digital RF communications systems operating in very low signal-to-noise conditions. As an innovation, the unique SDA capabilities allow it to perform analysis of situations where the receiving communication system slips bits due to low signal-to-noise conditions or experiences constellation rotations resulting in channel polarity in versions or channel assignment swaps. SDA s closed-loop detection allows it to instrument a live system and correlate observations with frame, codeword, and packet losses, as well as Quality of Service (QoS) and Quality of Experience (QoE) events. The SDA s abilities are not confined to performing analysis in low signal-to-noise conditions. Its analysis provides in-depth insight of a communication system s receiver performance in a variety of operating conditions. The SDA incorporates two techniques for identifying slips. The first is an examination of content of the received data stream s relation to the transmitted data content and the second is a direct examination of the receiver s recovered clock signals relative to a reference. Both techniques provide benefits in different ways and allow the communication engineer evaluating test results increased confidence and understanding of receiver performance. Direct examination of data contents is performed by two different data techniques, power correlation or a modified Massey correlation, and can be applied to soft decision data widths 1 to 12 bits wide over a correlation depth ranging from 16 to 512 samples. The SDA detects receiver bit slips within a 4 bits window and can handle systems with up to four quadrants (QPSK, SQPSK, and BPSK systems). The SDA continuously monitors correlation results to characterize slips and quadrant change and is capable of performing analysis even when the

  8. Label-free LC-MSe in tissue and serum reveals protein networks underlying differences between benign and malignant serous ovarian tumors.

    Directory of Open Access Journals (Sweden)

    Wouter Wegdam

    Full Text Available PURPOSE: To identify proteins and (molecular/biological pathways associated with differences between benign and malignant epithelial ovarian tumors. EXPERIMENTAL PROCEDURES: Serum of six patients with a serous adenocarcinoma of the ovary was collected before treatment, with a control group consisting of six matched patients with a serous cystadenoma. In addition to the serum, homogeneous regions of cells exhibiting uniform histology were isolated from benign and cancerous tissue by laser microdissection. We subsequently employed label-free liquid chromatography tandem mass spectrometry (LC-MSe to identify proteins in these serum and tissues samples. Analyses of differential expression between samples were performed using Bioconductor packages and in-house scripts in the statistical software package R. Hierarchical clustering and pathway enrichment analyses were performed, as well as network enrichment and interactome analysis using MetaCore. RESULTS: In total, we identified 20 and 71 proteins that were significantly differentially expressed between benign and malignant serum and tissue samples, respectively. The differentially expressed protein sets in serum and tissue largely differed with only 2 proteins in common. MetaCore network analysis, however inferred GCR-alpha and Sp1 as common transcriptional regulators. Interactome analysis highlighted 14-3-3 zeta/delta, 14-3-3 beta/alpha, Alpha-actinin 4, HSP60, and PCBP1 as critical proteins in the tumor proteome signature based on their relative overconnectivity. The data have been deposited to the ProteomeXchange with identifier PXD001084. DISCUSSION: Our analysis identified proteins with both novel and previously known associations to ovarian cancer biology. Despite the small overlap between differentially expressed protein sets in serum and tissue, APOA1 and Serotransferrin were significantly lower expressed in both serum and cancer tissue samples, suggesting a tissue-derived effect in serum

  9. InSilico Proteomics System: Integration and Application of Protein and Protein-Protein Interaction Data using Microsoft .NET

    Directory of Open Access Journals (Sweden)

    Straßer Wolfgang

    2006-12-01

    Full Text Available In the last decades, biological databases became the major knowledge resource for researchers in the field of molecular biology. The distribution of information among these databases is one of the major problems. An overview about the subject area of data access and representation of protein and protein-protein interaction data within public biological databases is described. For a comprehensive and consistent way of searching and analysing integrated protein and protein-protein interaction data, the InSilico Proteomics (ISP project has been initiated. Its three main objectives are (1 to provide an integrated knowledge pool for data investigation and global network analysis functions for a better understanding of a cell’s interactome, (2 employment of public data for plausibility analysis and validation of in-house experimental data and (3 testing the applicability of Microsoft’s .NET architecture for bioinformatics applications. Data integrated into the ISP database can be queried through the Web portal PRIMOS (PRotein Interaction and MOlecule Search which is freely available at http://biomis.fh-hagenberg.at/isp/primos.

  10. Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization.

    Science.gov (United States)

    Wang, Hua; Huang, Heng; Ding, Chris; Nie, Feiping

    2013-04-01

    Protein interactions are central to all the biological processes and structural scaffolds in living organisms, because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Several high-throughput methods, for example, yeast two-hybrid system and mass spectrometry method, can help determine protein interactions, which, however, suffer from high false-positive rates. Moreover, many protein interactions predicted by one method are not supported by another. Therefore, computational methods are necessary and crucial to complete the interactome expeditiously. In this work, we formulate the problem of predicting protein interactions from a new mathematical perspective--sparse matrix completion, and propose a novel nonnegative matrix factorization (NMF)-based matrix completion approach to predict new protein interactions from existing protein interaction networks. Through using manifold regularization, we further develop our method to integrate different biological data sources, such as protein sequences, gene expressions, protein structure information, etc. Extensive experimental results on four species, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, and Caenorhabditis elegans, have shown that our new methods outperform related state-of-the-art protein interaction prediction methods.

  11. Nanodisc-solubilized membrane protein library reflects the membrane proteome.

    Science.gov (United States)

    Marty, Michael T; Wilcox, Kyle C; Klein, William L; Sligar, Stephen G

    2013-05-01

    The isolation and identification of unknown membrane proteins offers the prospect of discovering new pharmaceutical targets and identifying key biochemical receptors. However, interactions between membrane protein targets and soluble ligands are difficult to study in vitro due to the insolubility of membrane proteins in non-detergent systems. Nanodiscs, nanoscale discoidal lipid bilayers encircled by a membrane scaffold protein belt, have proven to be an effective platform to solubilize membrane proteins and have been used to study a wide variety of purified membrane proteins. This report details the incorporation of an unbiased population of membrane proteins from Escherichia coli membranes into Nanodiscs. This solubilized membrane protein library (SMPL) forms a soluble in vitro model of the membrane proteome. Since Nanodiscs contain isolated proteins or small complexes, the SMPL is an ideal platform for interactomics studies and pull-down assays of membrane proteins. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the protein population before and after formation of the Nanodisc library indicates that a large percentage of the proteins are incorporated into the library. Proteomic identification of several prominent bands demonstrates the successful incorporation of outer and inner membrane proteins into the Nanodisc library.

  12. A Human XPC Protein Interactome—A Resource

    Directory of Open Access Journals (Sweden)

    Abigail Lubin

    2013-12-01

    Full Text Available Global genome nucleotide excision repair (GG-NER is responsible for identifying and removing bulky adducts from non-transcribed DNA that result from damaging agents such as UV radiation and cisplatin. Xeroderma pigmentosum complementation group C (XPC is one of the essential damage recognition proteins of the GG-NER pathway and its dysfunction results in xeroderma pigmentosum (XP, a disorder involving photosensitivity and a predisposition to cancer. To better understand the identification of DNA damage by XPC in the context of chromatin and the role of XPC in the pathogenesis of XP, we characterized the interactome of XPC using a high throughput yeast two-hybrid screening. Our screening showed 49 novel interactors of XPC involved in DNA repair and replication, proteolysis and post-translational modifications, transcription regulation, signal transduction, and metabolism. Importantly, we validated the XPC-OTUD4 interaction by co-IP and provided evidence that OTUD4 knockdown in human cells indeed affects the levels of ubiquitinated XPC, supporting a hypothesis that the OTUD4 deubiquitinase is involved in XPC recycling by cleaving the ubiquitin moiety. This high-throughput characterization of the XPC interactome provides a resource for future exploration and suggests that XPC may have many uncharacterized cellular functions.

  13. SCOWLP classification: Structural comparison and analysis of protein binding regions

    Directory of Open Access Journals (Sweden)

    Anders Gerd

    2008-01-01

    Full Text Available Abstract Background Detailed information about protein interactions is critical for our understanding of the principles governing protein recognition mechanisms. The structures of many proteins have been experimentally determined in complex with different ligands bound either in the same or different binding regions. Thus, the structural interactome requires the development of tools to classify protein binding regions. A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering protein interaction networks, understanding protein function, rational engineering and design. Description Protein binding regions (PBRs might be ideally described as well-defined separated regions that share no interacting residues one another. However, PBRs are often irregular, discontinuous and can share a wide range of interacting residues among them. The criteria to define an individual binding region can be often arbitrary and may differ from other binding regions within a protein family. Therefore, the rational behind protein interface classification should aim to fulfil the requirements of the analysis to be performed. We extract detailed interaction information of protein domains, peptides and interfacial solvent from the SCOWLP database and we classify the PBRs of each domain family. For this purpose, we define a similarity index based on the overlapping of interacting residues mapped in pair-wise structural alignments. We perform our classification with agglomerative hierarchical clustering using the complete-linkage method. Our classification is calculated at different similarity cut-offs to allow flexibility in the analysis of PBRs, feature especially interesting for those protein families with conflictive binding regions

  14. Role of Bacterioferritin & Ferritin in M. tuberculosis Pathogenesis and Drug Resistance: A Future Perspective by Interactomic Approach

    Directory of Open Access Journals (Sweden)

    Divakar Sharma

    2017-06-01

    Full Text Available Tuberculosis is caused by Mycobacterium tuberculosis, one of the most successful and deadliest human pathogen. Aminoglycosides resistance leads to emergence of extremely drug resistant strains of M. tuberculosis. Iron is crucial for the biological functions of the cells. Iron assimilation, storage and their utilization is not only involved in pathogenesis but also in emergence of drug resistance strains. We previously reported that iron storing proteins (bacterioferritin and ferritin were found to be overexpressed in aminoglycosides resistant isolates. In this study we performed the STRING analysis of bacterioferritin & ferritin proteins and predicted their interactive partners [ferrochelatase (hemH, Rv1877 (hypothetical protein/probable conserved integral membrane protein, uroporphyrinogen decarboxylase (hemE trigger factor (tig, transcriptional regulatory protein (MT3948, hypothetical protein (MT1928, glnA3 (glutamine synthetase, molecular chaperone GroEL (groEL1 & hsp65, and hypothetical protein (MT3947]. We suggested that interactive partners of bacterioferritin and ferritin are directly or indirectly involved in M. tuberculosis growth, homeostasis, iron assimilation, virulence, resistance, and stresses.

  15. Proteomic analyses of the SMYD family interactomes identify HSP90 as a novel target for SMYD2.

    Science.gov (United States)

    Abu-Farha, Mohamed; Lanouette, Sylvain; Elisma, Fred; Tremblay, Véronique; Butson, Jeffery; Figeys, Daniel; Couture, Jean-François

    2011-10-01

    The SMYD (SET and MYND domain) family of lysine methyltransferases (KMTs) plays pivotal roles in various cellular processes, including gene expression regulation and DNA damage response. Initially identified as genuine histone methyltransferases, specific members of this family have recently been shown to methylate non-histone proteins such as p53, VEGFR, and the retinoblastoma tumor suppressor (pRb). To gain further functional insights into this family of KMTs, we generated the protein interaction network for three different human SMYD proteins (SMYD2, SMYD3, and SMYD5). Characterization of each SMYD protein network revealed that they associate with both shared and unique sets of proteins. Among those, we found that HSP90 and several of its co-chaperones interact specifically with the tetratrico peptide repeat (TPR)-containing SMYD2 and SMYD3. Moreover, using proteomic and biochemical techniques, we provide evidence that SMYD2 methylates K209 and K615 on HSP90 nucleotide-binding and dimerization domains, respectively. In addition, we found that each methylation site displays unique reactivity in regard to the presence of HSP90 co-chaperones, pH, and demethylation by the lysine amine oxidase LSD1, suggesting that alternative mechanisms control HSP90 methylation by SMYD2. Altogether, this study highlights the ability of SMYD proteins to form unique protein complexes that may underlie their various biological functions and the SMYD2-mediated methylation of the key molecular chaperone HSP90.

  16. The Type 1 Diabetes - HLA Susceptibility Interactome - Identification of HLA Genotype-Specific Disease Genes for Type 1 Diabetes

    DEFF Research Database (Denmark)

    Brorsson, C.; Hansen, Niclas Tue; Bergholdt, R.

    2010-01-01

    Background: The individual contribution of genes in the HLA region to the risk of developing type 1 diabetes (T1D) is confounded by the high linkage disequilibrium (LD) in this region. Using a novel approach we have combined genetic association data with information on functional protein......-protein interactions to elucidate risk independent of LD and to place the genetic association into a functional context. Methodology/Principal Findings: Genetic association data from 2300 single nucleotide polymorphisms (SNPs) in the HLA region was analysed in 2200 T1D family trios divided into six risk groups based...... on HLA-DRB1 genotypes. The best SNP signal in each gene was mapped to proteins in a human protein interaction network and their significance of clustering in functional network modules was evaluated. The significant network modules identified through this approach differed between the six HLA risk groups...

  17. Multichannel analyzer development in CAMAC

    International Nuclear Information System (INIS)

    Nagy, J.Z.; Zarandy, A.

    1988-01-01

    The data acquisition in TOKAMAK experiments some CAMAC modules have been developed. The modules are the following: 64 K analyzer memory, 32 K analyzer memory, 6-channel pulse peak analyzer memory which contains the 32 K analyzer memory and eight AD-converters

  18. Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale

    Science.gov (United States)

    Kuzu, Guray; Gursoy, Attila; Nussinov, Ruth; Keskin, Ozlem

    2013-01-01

    Cellular functions are performed through protein-protein interactions; therefore, identification of these interactions is crucial for understanding biological processes. Recent studies suggest that knowledge-based approaches are more useful than ‘blind’ docking for modeling at large scales. However, a caveat of knowledge-based approaches is that they treat molecules as rigid structures. The Protein Data Bank (PDB) offers a wealth of conformations. Here, we exploited ensemble of the conformations in predictions by a knowledge-based method, PRISM. We tested ‘difficult’ cases in a docking-benchmark dataset, where the unbound and bound protein forms are structurally different. Considering alternative conformations for each protein, the percentage of successfully predicted interactions increased from ~26% to 66%, and 57% of the interactions were successfully predicted in an ‘unbiased’ scenario, in which data related to the bound forms were not utilized. If the appropriate conformation, or relevant template interface, is unavailable in the PDB, PRISM could not predict the interaction successfully. The pace of the growth of the PDB promises a rapid increase of ensemble conformations emphasizing the merit of such knowledge-based ensemble strategies for higher success rates in protein-protein interaction predictions on an interactome-scale. We constructed the structural network of ERK interacting proteins as a case study. PMID:23590674

  19. Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Sandip Chakraborty

    2016-01-01

    Full Text Available Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins are expected to be “seen” by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes’ adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another.

  20. Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks.

    Science.gov (United States)

    Chakraborty, Sandip; Alvarez-Ponce, David

    2016-01-01

    Proteins within a molecular network are expected to be subject to different selective pressures depending on their relative hierarchical positions. However, it is not obvious what genes within a network should be more likely to evolve under positive selection. On one hand, only mutations at genes with a relatively high degree of control over adaptive phenotypes (such as those encoding highly connected proteins) are expected to be "seen" by natural selection. On the other hand, a high degree of pleiotropy at these genes is expected to hinder adaptation. Previous analyses of the human protein-protein interaction network have shown that genes under long-term, recurrent positive selection (as inferred from interspecific comparisons) tend to act at the periphery of the network. It is unknown, however, whether these trends apply to other organisms. Here, we show that long-term positive selection has preferentially targeted the periphery of the yeast interactome. Conversely, in flies, genes under positive selection encode significantly more connected and central proteins. These observations are not due to covariation of genes' adaptability and centrality with confounding factors. Therefore, the distribution of proteins encoded by genes under recurrent positive selection across protein-protein interaction networks varies from one species to another.

  1. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein.

    Science.gov (United States)

    Khamina, Kseniya; Lercher, Alexander; Caldera, Michael; Schliehe, Christopher; Vilagos, Bojan; Sahin, Mehmet; Kosack, Lindsay; Bhattacharya, Anannya; Májek, Peter; Stukalov, Alexey; Sacco, Roberto; James, Leo C; Pinschewer, Daniel D; Bennett, Keiryn L; Menche, Jörg; Bergthaler, Andreas

    2017-12-01

    RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/- mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host.

  2. Comparison of high-sensitivity C-reactive protein serum assay results obtained using Dade-Behring BNII nephelometer and Ortho Vitros FS 5.1 clinical analyzer in respect of CRP-related risk assessment of chronic metabolic diseases.

    Science.gov (United States)

    Kusnierz-Cabala, Beata; Gernand, Wojciech; Zabek-Adamska, Anna; Tokarz, Aleksandra; Naskalski, Jerzy W

    2008-01-01

    Serum concentration of high sensitive C-reactive protein (hsCRP) can predict the risk of chronic metabolic and cardiovascular diseases but it is unclear whether turbidimetric high sensitive assays of CRP are adequate. Concentrations of serum CRP in 126 samples of serum were measured with high-sensitivity methods using nephelometry (BN II Nephelometer) and turbidimetry (Ortho Vitros FS 5.1). For CRP concentrations measured by nephelometry and turbidimetry intra-assay CVs were 3.2 and 0.9% at mean CRP concentrations of 1.4 and 2.1 mg/l, inter-assay CVs for commercial controls were 3.1% and 3.6% at mean concentrations of 1.3 and 1.7 mg/l, and mean biases were 7.62% and 2.26%, respectively. Measurements were strongly, linearly correlated (r = 0.99; CRP vitros = 0.03 +1.03 CRP (BN II)). When disease risk was assessed by nephelometry and turbidimetry, results were similar. If the risk of disease was classified as moderate (1.0 3.0 mg/l), the frequency of misclassified cases was only 2.3 and 2.1%, respectively. The classification agreement weighted kappa coefficient was 0.94 (95% C.I.: 0.89-0.98). turbidimetric high sensitive CRP assays can properly classify CRP-related prediction of chronic metabolic diseases with special consideration on cardiovascular risk.

  3. Frequency of Interferon-Resistance Conferring Substitutions in Amino Acid Positions 70 and 91 of Core Protein of the Russian HCV 1b Isolates Analyzed in the T-Cell Epitopic Context

    Directory of Open Access Journals (Sweden)

    V. S. Kichatova

    2018-01-01

    Full Text Available Amino acid substitutions R70Q/H and L91M in HCV subtype 1b core protein can affect the response to interferon and are associated with the development of hepatocellular carcinoma. We found that the rate of R70Q/H in HCV 1b from Russia was 31.2%, similar to that in HCV strains from Asia (34.0%, higher than that in the European (18.0%, p=0.0010, but lower than that in the US HCV 1b strains (62.8%, p<0.0001. Substitution L91M was found in 80.4% of the Russian HCV 1b isolates, higher than in Asian isolates (43.8%, p<0.0001. Thus, a significant proportion of Russian HCV 1b isolates carry the unfavorable R70Q/H and/or L91M substitution. In silico analysis of the epitopic structure of the regions of substitutions revealed that both harbor clusters of T-cell epitopes. Peptides encompassing these regions were predicted to bind to a panel of HLA class I molecules, with substitutions impairing peptide recognition by HLA I molecules of the alleles prevalent in Russia. This indicates that HCV 1b with R70Q/H and L91M substitutions may have evolved as the immune escape variants. Impairment of T-cell recognition may play a part in the negative effect of these substitutions on the response to IFN treatment.

  4. The Interactome of the Glucocorticoid Receptor and Its Influence on the Actions of Glucocorticoids in Combatting Inflammatory and Infectious Diseases

    Science.gov (United States)

    Petta, Ioanna; Dejager, Lien; Ballegeer, Marlies; Lievens, Sam; Tavernier, Jan; Libert, Claude

    2016-01-01

    SUMMARY Glucocorticoids (GCs) have been widely used for decades as a first-line treatment for inflammatory and autoimmune diseases. However, their use is often hampered by the onset of adverse effects or resistance. GCs mediate their effects via binding to glucocorticoid receptor (GR), a transcription factor belonging to the family of nuclear receptors. An important aspect of GR's actions, including its anti-inflammatory capacity, involves its interactions with various proteins, such as transcription factors, cofactors, and modifying enzymes, which codetermine receptor functionality. In this review, we provide a state-of-the-art overview of the protein-protein interactions (PPIs) of GR that positively or negatively affect its anti-inflammatory properties, along with mechanistic insights, if known. Emphasis is placed on the interactions that affect its anti-inflammatory effects in the presence of inflammatory and microbial diseases. PMID:27169854

  5. Quantitative Interaction Proteomics of Neurodegenerative Disease Proteins

    Directory of Open Access Journals (Sweden)

    Fabian Hosp

    2015-05-01

    Full Text Available Several proteins have been linked to neurodegenerative disorders (NDDs, but their molecular function is not completely understood. Here, we used quantitative interaction proteomics to identify binding partners of Amyloid beta precursor protein (APP and Presenilin-1 (PSEN1 for Alzheimer’s disease (AD, Huntingtin (HTT for Huntington’s disease, Parkin (PARK2 for Parkinson’s disease, and Ataxin-1 (ATXN1 for spinocerebellar ataxia type 1. Our network reveals common signatures of protein degradation and misfolding and recapitulates known biology. Toxicity modifier screens and comparison to genome-wide association studies show that interaction partners are significantly linked to disease phenotypes in vivo. Direct comparison of wild-type proteins and disease-associated variants identified binders involved in pathogenesis, highlighting the value of differential interactome mapping. Finally, we show that the mitochondrial protein LRPPRC interacts preferentially with an early-onset AD variant of APP. This interaction appears to induce mitochondrial dysfunction, which is an early phenotype of AD.

  6. A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations.

    Science.gov (United States)

    Huang, Sing-Han; Lo, Yu-Shu; Luo, Yong-Chun; Tseng, Yu-Yao; Yang, Jinn-Moon

    2018-03-19

    One of the crucial steps toward understanding the associations among molecular interactions, pathways, and diseases in a cell is to investigate detailed atomic protein-protein interactions (PPIs) in the structural interactome. Despite the availability of large-scale methods for analyzing PPI networks, these methods often focused on PPI networks using genome-scale data and/or known experimental PPIs. However, these methods are unable to provide structurally resolved interaction residues and their conservations in PPI networks. Here, we reconstructed a human three-dimensional (3D) structural PPI network (hDiSNet) with the detailed atomic binding models and disease-associated mutations by enhancing our PPI families and 3D-domain interologs from 60,618 structural complexes and complete genome database with 6,352,363 protein sequences across 2274 species. hDiSNet is a scale-free network (γ = 2.05), which consists of 5177 proteins and 19,239 PPIs with 5843 mutations. These 19,239 structurally resolved PPIs not only expanded the number of PPIs compared to present structural PPI network, but also achieved higher agreement with gene ontology similarities and higher co-expression correlation than the ones of 181,868 experimental PPIs recorded in public databases. Among 5843 mutations, 1653 and 790 mutations involved in interacting domains and contacting residues, respectively, are highly related to diseases. Our hDiSNet can provide detailed atomic interactions of human disease and their associated proteins with mutations. Our results show that the disease-related mutations are often located at the contacting residues forming the hydrogen bonds or conserved in the PPI family. In addition, hDiSNet provides the insights of the FGFR (EGFR)-MAPK pathway for interpreting the mechanisms of breast cancer and ErbB signaling pathway in brain cancer. Our results demonstrate that hDiSNet can explore structural-based interactions insights for understanding the mechanisms of disease

  7. Protein-protein interaction network and subcellular localization of the Arabidopsis thaliana ESCRT machinery

    Directory of Open Access Journals (Sweden)

    Lynn eRichardson

    2011-06-01

    Full Text Available The Endosomal Sorting Complex Required for Transport (ESCRT consists of several multi-protein subcomplexes which assemble sequentially at the endosomal surface and function in multivesicular body (MVB biogenesis. While ESCRT has been relatively well characterized in yeasts and mammals, comparably little is known about ESCRT in plants. Here we explored the yeast two-hybrid protein interaction network and subcellular localization of the Arabidopsis thaliana ESCRT machinery. We show that Arabidopsis ESCRT interactome possess a number of protein-protein interactions that are either conserved in yeasts and mammals or distinct to plants. We show also that most of the Arabidopsis ESCRT proteins examined at least partially localize to MVBs in plant cells when ectopically expressed on their own or co-expressed with other interacting ESCRT proteins, and some also induce abnormal MVB phenotypes, consistent with their proposed functional roles in MVB biogenesis. Overall, our results help define the plant ESCRT machinery by highlighting both conserved and unique features when compared to ESCRT in other evolutionarily diverse organisms, providing a foundation for further exploration of ESCRT in plants.

  8. PM 3655 PHILIPS Logic analyzer

    CERN Multimedia

    A logic analyzer is an electronic instrument that captures and displays multiple signals from a digital system or digital circuit. A logic analyzer may convert the captured data into timing diagrams, protocol decodes, state machine traces, assembly language, or may correlate assembly with source-level software. Logic Analyzers have advanced triggering capabilities, and are useful when a user needs to see the timing relationships between many signals in a digital system.

  9. Digital Multi Channel Analyzer Enhancement

    International Nuclear Information System (INIS)

    Gonen, E.; Marcus, E.; Wengrowicz, U.; Beck, A.; Nir, J.; Sheinfeld, M.; Broide, A.; Tirosh, D.

    2002-01-01

    A cement analyzing system based on radiation spectroscopy had been developed [1], using novel digital approach for real-time, high-throughput and low-cost Multi Channel Analyzer. The performance of the developed system had a severe problem: the resulted spectrum suffered from lack of smoothness, it was very noisy and full of spikes and surges, therefore it was impossible to use this spectrum for analyzing the cement substance. This paper describes the work carried out to improve the system performance

  10. Identification of new protein-protein and protein-DNA interactions linked with wood formation in Populus trichocarpa.

    Science.gov (United States)

    Petzold, H Earl; Rigoulot, Stephen B; Zhao, Chengsong; Chanda, Bidisha; Sheng, Xiaoyan; Zhao, Mingzhe; Jia, Xiaoyan; Dickerman, Allan W; Beers, Eric P; Brunner, Amy M

    2018-03-01

    Cellular processes, such as signal transduction and cell wall deposition, are organized by macromolecule interactions. Experimentally determined protein-protein interactions (PPIs) and protein-DNA interactions (PDIs) relevant to woody plant development are sparse. To begin to develop a Populus trichocarpa Torr. & A. Gray wood interactome, we applied the yeast-two-hybrid (Y2H) assay in different ways to enable the discovery of novel PPIs and connected networks. We first cloned open reading frames (ORFs) for 361 genes markedly upregulated in secondary xylem compared with secondary phloem and performed a binary Y2H screen with these proteins. By screening a xylem cDNA library for interactors of a subset of these proteins and then recapitulating the process by using a subset of the interactors as baits, we ultimately identified 165 PPIs involving 162 different ORFs. Thirty-eight transcription factors (TFs) included in our collection of P. trichocarpa wood ORFs were used in a Y1H screen for binding to promoter regions of three genes involved in lignin biosynthesis resulting in 40 PDIs involving 20 different TFs. The network incorporating both the PPIs and PDIs included 14 connected subnetworks, with the largest having 132 members. Protein-protein interactions and PDIs validated previous reports and also identified new candidate wood formation proteins and modules through their interactions with proteins and promoters known to be involved in secondary cell wall synthesis. Selected examples are discussed including a PPI between Mps one binder (MOB1) and a mitogen-activated protein kinase kinase kinase kinase (M4K) that was further characterized by assays confirming the PPI as well as its effect on subcellular localization. Mapping of published transcriptomic data showing developmentally detailed expression patterns across a secondary stem onto the network supported that the PPIs and PDIs are relevant to wood formation, and also illustrated that wood

  11. Multichannel analyzer type CMA-3

    International Nuclear Information System (INIS)

    Czermak, A.; Jablonski, J.; Ostrowicz, A.

    1978-01-01

    Multichannel analyzer CMA-3 is designed for two-parametric analysis with operator controlled logical windows. It is implemented in CAMAC standard. A single crate contains all required modules and is controlled by the PDP-11/10 minicomputer. Configuration of CMA-3 is shown. CMA-3 is the next version of the multichannel analyzer described in report No 958/E-8. (author)

  12. Comparison of fiber length analyzers

    Science.gov (United States)

    Don Guay; Nancy Ross Sutherland; Walter Rantanen; Nicole Malandri; Aimee Stephens; Kathleen Mattingly; Matt Schneider

    2005-01-01

    In recent years, several fiber new fiber length analyzers have been developed and brought to market. The new instruments provide faster measurements and the capability of both laboratory and on-line analysis. Do the various fiber analyzers provide the same length, coarseness, width, and fines measurements for a given fiber sample? This paper provides a comparison of...

  13. The Clavibacter michiganensis subsp. michiganensis-tomato interactome reveals the perception of pathogen by the host and suggests mechanisms of infection

    Energy Technology Data Exchange (ETDEWEB)

    Savidor, Alon [Tel Aviv University; Teper, [Tel Aviv University; Gartemann, KH [Tel Aviv University; Eichenlaub, R [Tel Aviv University; Chalupowicz, L [Tel Aviv University; Manulis-Sasson, S [Tel Aviv University; Barash, I [Tel Aviv University; Tews, H [Tel Aviv University; Mayer, K [Tel Aviv University; Giannone, Richard J [ORNL; Hettich, Robert {Bob} L [ORNL; Sessa, G [Tel Aviv University

    2012-01-01

    The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) causes wilt and canker disease of tomato (Solanum lycopersicum). Mechanisms of Cmm pathogenicity and tomato response to Cmm infection are not well understood. To explore the interaction between Cmm and tomato, multidimensional protein identification technology (MudPIT) and tandem mass spectrometry were used to analyze in vitro and in planta generated samples. The results show that during infection Cmm senses the plant environment, transmits signals, induces, and then secretes multiple hydrolytic enzymes, including serine proteases of the Pat-1, Ppa, and Sbt familes, the CelA, XysA, and NagA glycosyl hydrolases, and other cell wall-degrading enzymes. Tomato induction of pathogenesis-related (PR) proteins, LOX1, and other defense-related proteins during infection indicates that the plant senses the invading bacterium and mounts a basal defense response, although partial with some suppressed components including class III peroxidases and a secreted serine peptidase. The tomato ethylene-synthesizing enzyme ACC-oxidase was induced during infection with the wild-type Cmm but not during infection with an endophytic Cmm strain, identifying Cmm-triggered host synthesis of ethylene as an important factor in disease symptom development. The proteomic data were also used to improve Cmm genome annotation, and thousands of Cmm gene models were confirmed or expanded.

  14. Visualization of protein interaction networks: problems and solutions

    Science.gov (United States)

    2013-01-01

    Background Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI) are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN) and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins) and edges (interactions), the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology) that enriches the PINs with semantic information, but complicates their visualization. Methods In these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i) technology, i.e. availability/license of the software and supported OS (Operating System) platforms; (ii) interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii) visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv) analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the possibility to

  15. Nuclear fuel microsphere gamma analyzer

    International Nuclear Information System (INIS)

    Valentine, K.H.; Long, E.L. Jr.; Willey, M.G.

    1977-01-01

    A gamma analyzer system is provided for the analysis of nuclear fuel microspheres and other radioactive particles. The system consists of an analysis turntable with means for loading, in sequence, a plurality of stations within the turntable; a gamma ray detector for determining the spectrum of a sample in one section; means for analyzing the spectrum; and a receiver turntable to collect the analyzed material in stations according to the spectrum analysis. Accordingly, particles may be sorted according to their quality; e.g., fuel particles with fractured coatings may be separated from those that are not fractured, or according to other properties. 4 claims, 3 figures

  16. Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Furuya Toshio

    2011-02-01

    Full Text Available Abstract Background The amount of data on protein-protein interactions (PPIs available in public databases and in the literature has rapidly expanded in recent years. PPI data can provide useful information for researchers in pharmacology and medicine as well as those in interactome studies. There is urgent need for a novel methodology or software allowing the efficient utilization of PPI data in pharmacology and medicine. Results To address this need, we have developed the 'Druggable Protein-protein Interaction Assessment System' (Dr. PIAS. Dr. PIAS has a meta-database that stores various types of information (tertiary structures, drugs/chemicals, and biological functions associated with PPIs retrieved from public sources. By integrating this information, Dr. PIAS assesses whether a PPI is druggable as a target for small chemical ligands by using a supervised machine-learning method, support vector machine (SVM. Dr. PIAS holds not only known druggable PPIs but also all PPIs of human, mouse, rat, and human immunodeficiency virus (HIV proteins identified to date. Conclusions The design concept of Dr. PIAS is distinct from other published PPI databases in that it focuses on selecting the PPIs most likely to make good drug targets, rather than merely collecting PPI data.

  17. Emerging putative associations between non-coding RNAs and protein-coding genes in Neuropathic Pain. Added value from re-using microarray data.

    Directory of Open Access Journals (Sweden)

    Enrico Capobianco

    2016-10-01

    Full Text Available Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs. This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve injury, and studied in a rat model, using two neuronal tissues, namely dorsal root ganglion (DRG and sciatic nerve (SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes, and re-purposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parent genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to neuropathic pain. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN, and 8 in DRG, antisense RNA (31 asRNA in SN, and 12 in DRG and pseudogenes (456 in SN, 56 in DRG. In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly

  18. Market study: Whole blood analyzer

    Science.gov (United States)

    1977-01-01

    A market survey was conducted to develop findings relative to the commercialization potential and key market factors of the whole blood analyzer which is being developed in conjunction with NASA's Space Shuttle Medical System.

  19. JGromacs: a Java package for analyzing protein simulations.

    Science.gov (United States)

    Münz, Márton; Biggin, Philip C

    2012-01-23

    In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .

  20. JGromacs: A Java Package for Analyzing Protein Simulations

    Science.gov (United States)

    2011-01-01

    In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. Availability: JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license. PMID:22191855

  1. CSTT Update: Fuel Quality Analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Brosha, Eric L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lujan, Roger W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mukundan, Rangachary [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rockward, Tommy [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Romero, Christopher J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Williams, Stefan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wilson, Mahlon S. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2018-02-06

    These are slides from a presentation. The following topics are covered: project background (scope and approach), developing the prototype (timeline), update on intellectual property, analyzer comparisons (improving humidification, stabilizing the baseline, applying clean-up strategy, impact of ionomer content and improving clean-up), proposed operating mode, considerations for testing in real-world conditions (Gen 1 analyzer electronics development, testing partner identified, field trial planning), summary, and future work.

  2. Compact analyzer: an interactive simulator

    International Nuclear Information System (INIS)

    Ipakchi, A.; Khadem, M.; Colley, R.W.

    1985-01-01

    Compact Analyzer is a computer system that combines dynamic simulation models with interactive and color graphics user interface functions to provide a cost-effective simulator for dynamic analysis and evaluation of power plant operation, with engineering and training applications. Most dynamic simulation packages such as RETRAN and TRAC are designed for a batch-mode operation. With advancements in computer technology and man/machine interface capabilities, it is possible to integrate such codes with interactive and graphic functions into advanced simulators. The US Nuclear Regulatory Commission has sponsored development of plant analyzers with such characteristics. The Compact Analyzer is an Electric Power Research Institute (EPRI)-sponsored project, which currently utilizes the EPRI modular modeling system (MMS) for process simulation, and uses an adaptable color graphic package for dynamic display of the simulation results

  3. On-Demand Urine Analyzer

    Science.gov (United States)

    Farquharson, Stuart; Inscore, Frank; Shende, Chetan

    2010-01-01

    A lab-on-a-chip was developed that is capable of extracting biochemical indicators from urine samples and generating their surface-enhanced Raman spectra (SERS) so that the indicators can be quantified and identified. The development was motivated by the need to monitor and assess the effects of extended weightlessness, which include space motion sickness and loss of bone and muscle mass. The results may lead to developments of effective exercise programs and drug regimes that would maintain astronaut health. The analyzer containing the lab-on-a- chip includes materials to extract 3- methylhistidine (a muscle-loss indicator) and Risedronate (a bone-loss indicator) from the urine sample and detect them at the required concentrations using a Raman analyzer. The lab-on- a-chip has both an extractive material and a SERS-active material. The analyzer could be used to monitor the onset of diseases, such as osteoporosis.

  4. Multichannel analyzer embedded in FPGA

    International Nuclear Information System (INIS)

    Garcia D, A.; Hernandez D, V. M.; Vega C, H. R.; Ordaz G, O. O.; Bravo M, I.

    2017-10-01

    Ionizing radiation has different applications, so it is a very significant and useful tool, which in turn can be dangerous for living beings if they are exposed to uncontrolled doses. However, due to its characteristics, it cannot be perceived by any of the senses of the human being, so that in order to know the presence of it, radiation detectors and additional devices are required to quantify and classify it. A multichannel analyzer is responsible for separating the different pulse heights that are generated in the detectors, in a certain number of channels; according to the number of bits of the analog to digital converter. The objective of the work was to design and implement a multichannel analyzer and its associated virtual instrument, for nuclear spectrometry. The components of the multichannel analyzer were created in VHDL hardware description language and packaged in the Xilinx Vivado design suite, making use of resources such as the ARM processing core that the System on Chip Zynq contains and the virtual instrument was developed on the LabView programming graphics platform. The first phase was to design the hardware architecture to be embedded in the FPGA and for the internal control of the multichannel analyzer the application was generated for the ARM processor in C language. For the second phase, the virtual instrument was developed for the management, control and visualization of the results. The data obtained as a result of the development of the system were observed graphically in a histogram showing the spectrum measured. The design of the multichannel analyzer embedded in FPGA was tested with two different radiation detection systems (hyper-pure germanium and scintillation) which allowed determining that the spectra obtained are similar in comparison with the commercial multichannel analyzers. (Author)

  5. Analyzing Generation Y Workforce Motivation

    Science.gov (United States)

    2011-03-01

    Analyzing Generation Y Workforce Motivation Ian N. Barford n Patrick T. Hester R Defense AT&L: Special Edition: March –April 2011 36 Report...REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE Analyzing Generation Y Workforce Motivation 5a. CONTRACT NUMBER 5b...between 1965 and 1979), and Generation Y (born between 1980 and 2000). 37 Defense AT&L: Special Edition: March –April 2011 Defense AT&L: Special

  6. The security analyzer: A security analyzer program written in Prolog

    International Nuclear Information System (INIS)

    Zimmerman, B.D.; Densley, P.J.

    1986-09-01

    The Security Analyzer is a software tool capable of analyzing the effectiveness of a facility's security system. It is written in the Prolog logic programming computer language, using entity-relationship data modeling techniques. The program performs the following functions: (1) provides descriptive, locational and operational status information about intrusion detectors and assessment devices (i.e., ''sensors'' and ''cameras'') upon request; (2) provides for storage and retrieval of maintenance history information for various components of the security system (including intrusion detectors), and allows for changing that information as desired; (3) provides a ''search'' mode, wherein all paths are found from any specified physical location to another specified location which satisfy user chosen ''intruder detection'' probability and elapsed time criteria (i.e., the program finds the ''weakest paths'' from a security point of view). The first two of these functions can be provided fairly easily with a conventional database program; the third function could be provided using Fortran or some similar language, though with substantial difficulty. In the Security Analyzer program, all these functions are provided in a simple and straight-forward manner. This simplicity is possible because the program is written in the symbolic (as opposed to numeric) processing language Prolog, and because the knowledge base is structured according to entity-relationship modeling principles. Also, the use of Prolog and the entity-relationship modeling technique allows the capabilities of the Security analyzer program, both for knowledge base interrogation and for searching-type operations, to be easily expanded in ways that would be very difficult for a numeric and more algorithmically deterministic language such as Fortran to duplicate. 4 refs

  7. Historical Thinking: Analyzing Student and Teacher Ability to Analyze Sources

    OpenAIRE

    Cowgill II, Daniel Armond; Waring, Scott M.

    2017-01-01

    The purpose of this study was to partially replicate the Historical Problem Solving: A Study of the Cognitive Process Using Historical Evidence study conducted by Sam Wineburg in 1991. The Historical Problem Solving study conducted by Wineburg (1991) sought to compare the ability of historians and top level students, as they analyzed pictures and written documents centered on the Battle of Lexington Green. In this version of the study, rather than compare historians and students, we sought ...

  8. The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.

    Science.gov (United States)

    Yip, Kevin Y; Yu, Haiyuan; Kim, Philip M; Schultz, Martin; Gerstein, Mark

    2006-12-01

    Biological processes involve complex networks of interactions between molecules. Various large-scale experiments and curation efforts have led to preliminary versions of complete cellular networks for a number of organisms. To grapple with these networks, we developed TopNet-like Yale Network Analyzer (tYNA), a Web system for managing, comparing and mining multiple networks, both directed and undirected. tYNA efficiently implements methods that have proven useful in network analysis, including identifying defective cliques, finding small network motifs (such as feed-forward loops), calculating global statistics (such as the clustering coefficient and eccentricity), and identifying hubs and bottlenecks. It also allows one to manage a large number of private and public networks using a flexible tagging system, to filter them based on a variety of criteria, and to visualize them through an interactive graphical interface. A number of commonly used biological datasets have been pre-loaded into tYNA, standardized and grouped into different categories. The tYNA system can be accessed at http://networks.gersteinlab.org/tyna. The source code, JavaDoc API and WSDL can also be downloaded from the website. tYNA can also be accessed from the Cytoscape software using a plugin.

  9. Pollution Analyzing and Monitoring Instruments.

    Science.gov (United States)

    1972

    Compiled in this book is basic, technical information useful in a systems approach to pollution control. Descriptions and specifications are given of what is available in ready made, on-the-line commercial equipment for sampling, monitoring, measuring and continuously analyzing the multitudinous types of pollutants found in the air, water, soil,…

  10. Methods of analyzing crude oil

    Energy Technology Data Exchange (ETDEWEB)

    Cooks, Robert Graham; Jjunju, Fred Paul Mark; Li, Anyin; Rogan, Iman S.

    2017-08-15

    The invention generally relates to methods of analyzing crude oil. In certain embodiments, methods of the invention involve obtaining a crude oil sample, and subjecting the crude oil sample to mass spectrometry analysis. In certain embodiments, the method is performed without any sample pre-purification steps.

  11. Analyzing Software Piracy in Education.

    Science.gov (United States)

    Lesisko, Lee James

    This study analyzes the controversy of software piracy in education. It begins with a real world scenario that presents the setting and context of the problem. The legalities and background of software piracy are explained and true court cases are briefly examined. Discussion then focuses on explaining why individuals and organizations pirate…

  12. The Convertible Arbitrage Strategy Analyzed

    NARCIS (Netherlands)

    Loncarski, I.; Ter Horst, J.R.; Veld, C.H.

    2006-01-01

    This paper analyzes convertible bond arbitrage on the Canadian market for the period 1998 to 2004.Convertible bond arbitrage is the combination of a long position in convertible bonds and a short position in the underlying stocks. Convertible arbitrage has been one of the most successful strategies

  13. Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes

    Science.gov (United States)

    2013-01-01

    Background MicroRNAs (miRNAs) are important post-transcriptional regulators that have been demonstrated to play an important role in human diseases. Elucidating the associations between miRNAs and diseases at the systematic level will deepen our understanding of the molecular mechanisms of diseases. However, miRNA-disease associations identified by previous computational methods are far from completeness and more effort is needed. Results We developed a computational framework to identify miRNA-disease associations by performing random walk analysis, and focused on the functional link between miRNA targets and disease genes in protein-protein interaction (PPI) networks. Furthermore, a bipartite miRNA-disease network was constructed, from which several miRNA-disease co-regulated modules were identified by hierarchical clustering analysis. Our approach achieved satisfactory performance in identifying known cancer-related miRNAs for nine human cancers with an area under the ROC curve (AUC) ranging from 71.3% to 91.3%. By systematically analyzing the global properties of the miRNA-disease network, we found that only a small number of miRNAs regulated genes involved in various diseases, genes associated with neurological diseases were preferentially regulated by miRNAs and some immunological diseases were associated with several specific miRNAs. We also observed that most diseases in the same co-regulated module tended to belong to the same disease category, indicating that these diseases might share similar miRNA regulatory mechanisms. Conclusions In this study, we present a computational framework to identify miRNA-disease associations, and further construct a bipartite miRNA-disease network for systematically analyzing the global properties of miRNA regulation of disease genes. Our findings provide a broad perspective on the relationships between miRNAs and diseases and could potentially aid future research efforts concerning miRNA involvement in disease pathogenesis

  14. Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Sarbottam ePiya

    2014-12-01

    Full Text Available The phytohormone auxin regulates nearly all aspects of plant growth and development. Based on the current model in Arabidopsis thaliana, Auxin/indole-3-acetic acid (Aux/IAA proteins repress auxin-inducible genes by inhibiting auxin response transcription factors (ARFs. Experimental evidence suggests that heterodimerization between Aux/IAA and ARF proteins are related to their unique biological functions. The objective of this study was to generate the Aux/IAA-ARF protein-protein interaction map using full length sequences and locate the interacting protein pairs to specific gene co-expression networks in order to define tissue-specific responses of the Aux/IAA-ARF interactome. Pairwise interactions between 19 ARFs and 29 Aux/IAAs resulted in the identification of 213 specific interactions of which 79 interactions were previously unknown. The incorporation of co-expression profiles with protein-protein interaction data revealed a strong correlation of gene co-expression for 70% of the ARF-Aux/IAA interacting pairs in at least one tissue/organ, indicative of the biological significance of these interactions. Importantly, ARF4-8 and 19, which were found to interact with almost all Aux-Aux/IAA showed broad co-expression relationships with Aux/IAA genes, thus, formed the central hubs of the co-expression network. Our analyses provide new insights into the biological significance of ARF-Aux/IAA associations in the morphogenesis and development of various plant tissues and organs.

  15. Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis.

    Science.gov (United States)

    Piya, Sarbottam; Shrestha, Sandesh K; Binder, Brad; Stewart, C Neal; Hewezi, Tarek

    2014-01-01

    The phytohormone auxin regulates nearly all aspects of plant growth and development. Based on the current model in Arabidopsis thaliana, Auxin/indole-3-acetic acid (Aux/IAA) proteins repress auxin-inducible genes by inhibiting auxin response transcription factors (ARFs). Experimental evidence suggests that heterodimerization between Aux/IAA and ARF proteins are related to their unique biological functions. The objective of this study was to generate the Aux/IAA-ARF protein-protein interaction map using full length sequences and locate the interacting protein pairs to specific gene co-expression networks in order to define tissue-specific responses of the Aux/IAA-ARF interactome. Pairwise interactions between 19 ARFs and 29 Aux/IAAs resulted in the identification of 213 specific interactions of which 79 interactions were previously unknown. The incorporation of co-expression profiles with protein-protein interaction data revealed a strong correlation of gene co-expression for 70% of the ARF-Aux/IAA interacting pairs in at least one tissue/organ, indicative of the biological significance of these interactions. Importantly, ARF4-8 and 19, which were found to interact with almost all Aux-Aux/IAA showed broad co-expression relationships with Aux/IAA genes, thus, formed the central hubs of the co-expression network. Our analyses provide new insights into the biological significance of ARF-Aux/IAA associations in the morphogenesis and development of various plant tissues and organs.

  16. Bio::Homology::InterologWalk--a Perl module to build putative protein-protein interaction networks through interolog mapping.

    Science.gov (United States)

    Gallone, Giuseppe; Simpson, T Ian; Armstrong, J Douglas; Jarman, Andrew P

    2011-07-18

    Protein-protein interaction (PPI) data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction. We introduce Bio::Homology::InterologWalk, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, Drosophila melanogaster. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation. Our interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy to customise the results by post-processing, allowing the

  17. Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping

    Directory of Open Access Journals (Sweden)

    Armstrong J Douglas

    2011-07-01

    Full Text Available Abstract Background Protein-protein interaction (PPI data are widely used to generate network models that aim to describe the relationships between proteins in biological systems. The fidelity and completeness of such networks is primarily limited by the paucity of protein interaction information and by the restriction of most of these data to just a few widely studied experimental organisms. In order to extend the utility of existing PPIs, computational methods can be used that exploit functional conservation between orthologous proteins across taxa to predict putative PPIs or 'interologs'. To date most interolog prediction efforts have been restricted to specific biological domains with fixed underlying data sources and there are no software tools available that provide a generalised framework for 'on-the-fly' interolog prediction. Results We introduce Bio::Homology::InterologWalk, a Perl module to retrieve, prioritise and visualise putative protein-protein interactions through an orthology-walk method. The module uses orthology and experimental interaction data to generate putative PPIs and optionally collates meta-data into an Interaction Prioritisation Index that can be used to help prioritise interologs for further analysis. We show the application of our interolog prediction method to the genomic interactome of the fruit fly, Drosophila melanogaster. We analyse the resulting interaction networks and show that the method proposes new interactome members and interactions that are candidates for future experimental investigation. Conclusions Our interolog prediction tool employs the Ensembl Perl API and PSICQUIC enabled protein interaction data sources to generate up to date interologs 'on-the-fly'. This represents a significant advance on previous methods for interolog prediction as it allows the use of the latest orthology and protein interaction data for all of the genomes in Ensembl. The module outputs simple text files, making it easy

  18. Mango: combining and analyzing heterogeneous biological networks.

    Science.gov (United States)

    Chang, Jennifer; Cho, Hyejin; Chou, Hui-Hsien

    2016-01-01

    Heterogeneous biological data such as sequence matches, gene expression correlations, protein-protein interactions, and biochemical pathways can be merged and analyzed via graphs, or networks. Existing software for network analysis has limited scalability to large data sets or is only accessible to software developers as libraries. In addition, the polymorphic nature of the data sets requires a more standardized method for integration and exploration. Mango facilitates large network analyses with its Graph Exploration Language, automatic graph attribute handling, and real-time 3-dimensional visualization. On a personal computer Mango can load, merge, and analyze networks with millions of links and can connect to online databases to fetch and merge biological pathways. Mango is written in C++ and runs on Mac OS, Windows, and Linux. The stand-alone distributions, including the Graph Exploration Language integrated development environment, are freely available for download from http://www.complex.iastate.edu/download/Mango. The Mango User Guide listing all features can be found at http://www.gitbook.com/book/j23414/mango-user-guide.

  19. Analyzer for gamma cameras diagnostic

    International Nuclear Information System (INIS)

    Oramas Polo, I.; Osorio Deliz, J. F.; Diaz Garcia, A.

    2013-01-01

    This research work was carried out to develop an analyzer for gamma cameras diagnostic. It is composed of an electronic system that includes hardware and software capabilities, and operates from the acquisition of the 4 head position signals of a gamma camera detector. The result is the spectrum of the energy delivered by nuclear radiation coming from the camera detector head. This system includes analog processing of position signals from the camera, digitization and the subsequent processing of the energy signal in a multichannel analyzer, sending data to a computer via a standard USB port and processing of data in a personal computer to obtain the final histogram. The circuits are composed of an analog processing board and a universal kit with micro controller and programmable gate array. (Author)

  20. New approach to analyzing vulnerability

    International Nuclear Information System (INIS)

    O'Callaghan, P.B.; Carlson, R.L.; Riedeman, G.W.

    1986-01-01

    The Westinghouse Hanford Company (WHC) has recently completed construction of the Fuel Cycle Plant (FCP) at Richland, Washington. At start-up the facility will fabricate driver fuel for the Fast Flux Test Facility in the Secure Automated Fabrication line. After construction completion, but before facility certification, the Department of Energy (DOE) Richland Operation Office requested that a vulnerability analysis be performed which assumed multiple insiders as a threat to the security system. A unique method of analyzing facility vulnerabilities was developed at the Security Applications Center (SAC), which is managed by WHC for DOE. The method that was developed verifies a previous vulnerability assessment, as well as introducing a modeling technique which analyzes security alarms in relation to delaying factors and possible insider activities. With this information it is possible to assess the relative strength or weakness of various possible routes to and from a target within a facility

  1. Methods for Analyzing Social Media

    DEFF Research Database (Denmark)

    Jensen, Jakob Linaa

    2013-01-01

    Social media is becoming increasingly attractive for users. It is a fast way to communicate ideas and a key source of information. It is therefore one of the most influential mediums of communication of our time and an important area for audience research. The growth of social media invites many...... new questions such as: How can we analyze social media? Can we use traditional audience research methods and apply them to online content? Which new research strategies have been developed? Which ethical research issues and controversies do we have to pay attention to? This book focuses on research...... strategies and methods for analyzing social media and will be of interest to researchers and practitioners using social media, as well as those wanting to keep up to date with the subject....

  2. Portable Tandem Mass Spectrometer Analyzer

    Science.gov (United States)

    1991-07-01

    FILE : MHCI TUNE TABLE 84 (SCANNING with PARENT) SCAN RANGE 10.9 TO 700.0 TUNE MASS 355.0 (AUTO) >LENS 1-3 -13. 88 0. 2: POFF - 1. 2 9: COFF - 4. 1 3...and 500 ng of caffeine in I uL of chloroform by GC/A?:,,MS using negative ions. Also analyzed were barbiturates, extracted from urine, in the 3-5 Mg

  3. Remote Laser Diffraction PSD Analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Batcheller, Thomas Aquinas; Huestis, Gary Michael; Bolton, Steven Michael

    2000-06-01

    Particle size distribution (PSD) analysis of radioactive slurry samples were obtained using a modified "off-the-shelf" classical laser light scattering particle size analyzer. A Horiba Instruments Inc. Model La-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a "hot cell" (gamma radiation) environment. The general details of the modifications to this analyzer are presented in this paper. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not achievable - making this technology far superior than the traditional methods used previously. Remote deployment and utilization of this technology is in an exploratory stage. The risk of malfunction in this radiation environment is countered by gaining of this tremendously useful fundamental engineering data. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives.

  4. Remote Laser Diffraction PSD Analyzer

    International Nuclear Information System (INIS)

    Batcheller, Thomas Aquinas; Huestis, Gary Michael; Bolton, Steven Michael

    2000-01-01

    Particle size distribution (PSD) analysis of radioactive slurry samples were obtained using a modified ''off-the-shelf'' classical laser light scattering particle size analyzer. A Horiba Instruments Inc. Model La-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a ''hot cell'' (gamma radiation) environment. The general details of the modifications to this analyzer are presented in this paper. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not achievable--making this technology far superior than the traditional methods used previously. Remote deployment and utilization of this technology is in an exploratory stage. The risk of malfunction in this radiation environment is countered by gaining of this tremendously useful fundamental engineering data. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives

  5. Sulfur Dioxide Analyzer Instrument Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Springston, Stephen R. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-05-01

    The Sulfur Dioxide Analyzer measures sulfur dioxide based on absorbance of UV light at one wavelength by SO2 molecules which then decay to a lower energy state by emitting UV light at a longer wavelength. Specifically, SO2 + hυ1 →SO2 *→SO2 + hυ2 The emitted light is proportional to the concentration of SO2 in the optical cell. External communication with the analyzer is available through an Ethernet port configured through the instrument network of the AOS systems. The Model 43i-TLE is part of the i-series of Thermo Scientific instruments. The i-series instruments are designed to interface with external computers through the proprietary Thermo Scientific iPort Software. However, this software is somewhat cumbersome and inflexible. Brookhaven National Laboratory (BNL) has written an interface program in National Instruments LabView that both controls the Model 43i-TLE Analyzer AND queries the unit for all measurement and housekeeping data. The LabView vi (the software program written by BNL) ingests all raw data from the instrument and outputs raw data files in a uniform data format similar to other instruments in the AOS and described more fully in Section 6.0 below.

  6. Remote Laser Diffraction PSD Analyzer

    International Nuclear Information System (INIS)

    Batcheller, T.A.; Huestis, G.M.; Bolton, S.M.

    2000-01-01

    Particle size distribution (PSD) analysis of radioactive slurry samples were obtained using a modified off-the-shelf classical laser light scattering particle size analyzer. A Horiba Instruments Inc. Model La-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a hot cell (gamma radiation) environment. The general details of the modifications to this analyzer are presented in this paper. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not achievable - making this technology far superior than the traditional methods used previously. Remote deployment and utilization of this technology is in an exploratory stage. The risk of malfunction in this radiation environment is countered by gaining of this tremendously useful fundamental engineering data. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives

  7. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach.

    Science.gov (United States)

    Cheung, Mike W-L; Jak, Suzanne

    2016-01-01

    Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists-and probably the most crucial one-is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study.

  8. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach

    Science.gov (United States)

    Cheung, Mike W.-L.; Jak, Suzanne

    2016-01-01

    Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists—and probably the most crucial one—is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study. PMID:27242639

  9. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach

    Directory of Open Access Journals (Sweden)

    Mike W.-L. Cheung

    2016-05-01

    Full Text Available Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists – and probably the most crucial one – is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study.

  10. A Multiplex Enzymatic Machinery for Cellular Protein S-nitrosylation.

    Science.gov (United States)

    Seth, Divya; Hess, Douglas T; Hausladen, Alfred; Wang, Liwen; Wang, Ya-Juan; Stamler, Jonathan S

    2018-02-01

    S-nitrosylation, the oxidative modification of Cys residues by nitric oxide (NO) to form S-nitrosothiols (SNOs), modifies all main classes of proteins and provides a fundamental redox-based cellular signaling mechanism. However, in contrast to other post-translational protein modifications, S-nitrosylation is generally considered to be non-enzymatic, involving multiple chemical routes. We report here that endogenous protein S-nitrosylation in the model organism E. coli depends principally upon the enzymatic activity of the hybrid cluster protein Hcp, employing NO produced by nitrate reductase. Anaerobiosis on nitrate induces both Hcp and nitrate reductase, thereby resulting in the S-nitrosylation-dependent assembly of a large interactome including enzymes that generate NO (NO synthase), synthesize SNO-proteins (SNO synthase), and propagate SNO-based signaling (trans-nitrosylases) to regulate cell motility and metabolism. Thus, protein S-nitrosylation by NO in E. coli is essentially enzymatic, and the potential generality of the multiplex enzymatic mechanism that we describe may support a re-conceptualization of NO-based cellular signaling. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Dissecting spatio-temporal protein networks driving human heart development and related disorders

    DEFF Research Database (Denmark)

    Hansen, Kasper Lage; Mølgård, Kjeld; Greenway, Steven

    2010-01-01

    development, we combined detailed phenotype information from deleterious mutations in 255 genes with high-confidence experimental interactome data, and coupled the results to thorough experimental validation. Hereby, we made the first systematic analysis of spatio-temporal protein networks driving many stages......Aberrant organ development is associated with a wide spectrum of disorders, from schizophrenia to congenital heart disease, but systems-level insight into the underlying processes is very limited. Using heart morphogenesis as general model for dissecting the functional architecture of organ...... of a developing organ identifying several novel signaling modules. Our results show that organ development relies on surprisingly few, extensively recycled, protein modules that integrate into complex higher-order networks. This design allows the formation of a complicated organ using simple building blocks...

  12. Charged particle mobility refrigerant analyzer

    Science.gov (United States)

    Allman, S.L.; Chunghsuan Chen; Chen, F.C.

    1993-02-02

    A method for analyzing a gaseous electronegative species comprises the steps of providing an analysis chamber; providing an electric field of known potential within the analysis chamber; admitting into the analysis chamber a gaseous sample containing the gaseous electronegative species; providing a pulse of free electrons within the electric field so that the pulse of free electrons interacts with the gaseous electronegative species so that a swarm of electrically charged particles is produced within the electric field; and, measuring the mobility of the electrically charged particles within the electric field.

  13. Fuel analyzer; Analisador de combustiveis

    Energy Technology Data Exchange (ETDEWEB)

    Cozzolino, Roberval [RS Motors, Indaiatuba, SP (Brazil)

    2008-07-01

    The current technology 'COMBUSTIMETRO' aims to examine the fuel through performance of the engine, as the role of the fuel is to produce energy for the combustion engine in the form of which is directly proportional to the quality and type of fuel. The 'COMBUSTIMETRO' has an engine that always keeps the same entry of air, fuel and fixed point of ignition. His operation is monitored by sensors (Sonda Lambda, RPM and Gases Analyzer) connected to a processor that performs calculations and records the information, generate reports and graphs. (author)

  14. Liver plasma membranes: an effective method to analyze membrane proteome.

    Science.gov (United States)

    Cao, Rui; Liang, Songping

    2012-01-01

    Plasma membrane proteins are critical for the maintenance of biological systems and represent important targets for the treatment of disease. The hydrophobicity and low abundance of plasma membrane proteins make them difficult to analyze. The protocols given here are the efficient isolation/digestion procedures for liver plasma membrane proteomic analysis. Both protocol for the isolation of plasma membranes and protocol for the in-gel digestion of gel-embedded plasma membrane proteins are presented. The later method allows the use of a high detergent concentration to achieve efficient solubilization of hydrophobic plasma membrane proteins while avoiding interference with the subsequent LC-MS/MS analysis.

  15. In silico structure-based approaches to discover protein-protein interaction-targeting drugs.

    Science.gov (United States)

    Shin, Woong-Hee; Christoffer, Charles W; Kihara, Daisuke

    2017-12-01

    A core concept behind modern drug discovery is finding a small molecule that modulates a function of a target protein. This concept has been successfully applied since the mid-1970s. However, the efficiency of drug discovery is decreasing because the druggable target space in the human proteome is limited. Recently, protein-protein interaction (PPI) has been identified asan emerging target space for drug discovery. PPI plays a pivotal role in biological pathways including diseases. Current human interactome research suggests that the number of PPIs is between 130,000 and 650,000, and only a small number of them have been targeted as drug targets. For traditional drug targets, in silico structure-based methods have been successful in many cases. However, their performance suffers on PPI interfaces because PPI interfaces are different in five major aspects: From a geometric standpoint, they have relatively large interface regions, flat geometry, and the interface surface shape tends to fluctuate upon binding. Also, their interactions are dominated by hydrophobic atoms, which is different from traditional binding-pocket-targeted drugs. Finally, PPI targets usually lack natural molecules that bind to the target PPI interface. Here, we first summarize characteristics of PPI interfaces and their known binders. Then, we will review existing in silico structure-based approaches for discovering small molecules that bind to PPI interfaces. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Historical Thinking: Analyzing Student and Teacher Ability to Analyze Sources

    Directory of Open Access Journals (Sweden)

    Daniel Armond Cowgill II

    2017-05-01

    Full Text Available The purpose of this study was to partially replicate the Historical Problem Solving: A Study of the Cognitive Process Using Historical Evidence study conducted by Sam Wineburg in 1991. The Historical Problem Solving study conducted by Wineburg (1991 sought to compare the ability of historians and top level students, as they analyzed pictures and written documents centered on the Battle of Lexington Green. In this version of the study, rather than compare historians and students, we sought out to compare the analytical skills of teachers and students. The main findings relate to the fact that the participants lacked the ability to engage in the very complex activities associated with historical inquiry and the utilization of primary sources in learning about the past. This lack of ability should be used to improve teacher professional development programs and help them develop the skills needed to not only engage in historical evaluation themselves but to also develop skills that will allow them to instruct students to do the same.

  17. Analysis of damaged DNA / proteins interactions: Methodological optimizations and applications to DNA lesions induced by platinum anticancer drugs

    International Nuclear Information System (INIS)

    Bounaix Morand du Puch, Ch

    2010-10-01

    DNA lesions contribute to the alteration of DNA structure, thereby inhibiting essential cellular processes. Such alterations may be beneficial for chemotherapies, for example in the case of platinum anticancer agents. They generate bulky adducts that, if not repaired, ultimately cause apoptosis. A better understanding of the biological response to such molecules can be obtained through the study of proteins that directly interact with the damages. These proteins constitute the DNA lesions interactome. This thesis presents the development of tools aiming at increasing the list of platinum adduct-associated proteins. Firstly, we designed a ligand fishing system made of damaged plasmids immobilized onto magnetic beads. Three platinum drugs were selected for our study: cisplatin, oxali-platin and satra-platin. Following exposure of the trap to nuclear extracts from HeLa cancer cells and identification of retained proteins by proteomics, we obtained already known candidates (HMGB1, hUBF, FACT complex) but also 29 new members of the platinated-DNA interactome. Among them, we noted the presence of PNUTS, TOX4 and WDR82, which associate to form the recently-discovered PTW/PP complex. Their capture was then confirmed with a second model, namely breast cancer cell line MDA MB 231, and the biological consequences of such an interaction now need to be elucidated. Secondly, we adapted a SPRi bio-chip to the study of platinum-damaged DNA/proteins interactions. Affinity of HMGB1 and newly characterized TOX4 for adducts generated by our three platinum drugs could be validated thanks to the bio-chip. Finally, we used our tools, as well as analytical chemistry and biochemistry methods, to evaluate the role of DDB2 (a factor involved in the recognition of UV-induced lesions) in the repair of cisplatin adducts. Our experiments using MDA MB 231 cells differentially expressing DDB2 showed that this protein is not responsible for the repair of platinum damages. Instead, it appears to act

  18. Compact Microwave Fourier Spectrum Analyzer

    Science.gov (United States)

    Savchenkov, Anatoliy; Matsko, Andrey; Strekalov, Dmitry

    2009-01-01

    A compact photonic microwave Fourier spectrum analyzer [a Fourier-transform microwave spectrometer, (FTMWS)] with no moving parts has been proposed for use in remote sensing of weak, natural microwave emissions from the surfaces and atmospheres of planets to enable remote analysis and determination of chemical composition and abundances of critical molecular constituents in space. The instrument is based on a Bessel beam (light modes with non-zero angular momenta) fiber-optic elements. It features low power consumption, low mass, and high resolution, without a need for any cryogenics, beyond what is achievable by the current state-of-the-art in space instruments. The instrument can also be used in a wide-band scatterometer mode in active radar systems.

  19. The RNA-binding protein repertoire of Arabidopsis thaliana

    KAUST Repository

    Marondedze, Claudius

    2016-07-11

    RNA-binding proteins (RBPs) have essential roles in determining the fate of RNA from synthesis to decay and have been studied on a protein-by-protein basis, or computationally based on a number of well-characterised RNA-binding domains. Recently, high-throughput methods enabled the capture of mammalian RNA-binding proteomes. To gain insight into the role of Arabidopsis thaliana RBPs at the systems level, we have employed interactome capture techniques using cells from different ecotypes grown in cultures and leaves. In vivo UV-crosslinking of RNA to RBPs, oligo(dT) capture and mass spectrometry yielded 1,145 different proteins including 550 RBPs that either belong to the functional category ‘RNA-binding’, have known RNA-binding domains or have orthologs identified in mammals, C. elegans, or S. cerevisiae in addition to 595 novel candidate RBPs. We noted specific subsets of RBPs in cultured cells and leaves and a comparison of Arabidopsis, mammalian, C. elegans, and S. cerevisiae RBPs reveals a common set of proteins with a role in intermediate metabolism, as well as distinct differences suggesting that RBPs are also species and tissue specific. This study provides a foundation for studies that will advance our understanding of the biological significance of RBPs in plant developmental and stimulus specific responses.

  20. Curating the innate immunity interactome.

    LENUS (Irish Health Repository)

    Lynn, David J

    2010-01-01

    The innate immune response is the first line of defence against invading pathogens and is regulated by complex signalling and transcriptional networks. Systems biology approaches promise to shed new light on the regulation of innate immunity through the analysis and modelling of these networks. A key initial step in this process is the contextual cataloguing of the components of this system and the molecular interactions that comprise these networks. InnateDB (http:\\/\\/www.innatedb.com) is a molecular interaction and pathway database developed to facilitate systems-level analyses of innate immunity.

  1. The Breast Cancer DNA Interactome

    Science.gov (United States)

    2014-12-01

    CADPS2 are present in autism spectrum disorders and intellectual disability patients. EMBOMol Med 2014;6 [Epub ahead of print].[50] Kopsida E, Mikaelsson...JaenischR.Global loss of imprinting leads to widespread tumorigenesis in adult mice. Cancer Cell 2005;8(4):275 85. [53] Soejima H, Higashimoto K

  2. BioPlex Display: An Interactive Suite for Large-Scale AP-MS Protein-Protein Interaction Data.

    Science.gov (United States)

    Schweppe, Devin K; Huttlin, Edward L; Harper, J Wade; Gygi, Steven P

    2018-01-05

    The development of large-scale data sets requires a new means to display and disseminate research studies to large audiences. Knowledge of protein-protein interaction (PPI) networks has become a principle interest of many groups within the field of proteomics. At the confluence of technologies, such as cross-linking mass spectrometry, yeast two-hybrid, protein cofractionation, and affinity purification mass spectrometry (AP-MS), detection of PPIs can uncover novel biological inferences at a high-throughput. Thus new platforms to provide community access to large data sets are necessary. To this end, we have developed a web application that enables exploration and dissemination of the growing BioPlex interaction network. BioPlex is a large-scale interactome data set based on AP-MS of baits from the human ORFeome. The latest BioPlex data set release (BioPlex 2.0) contains 56 553 interactions from 5891 AP-MS experiments. To improve community access to this vast compendium of interactions, we developed BioPlex Display, which integrates individual protein querying, access to empirical data, and on-the-fly annotation of networks within an easy-to-use and mobile web application. BioPlex Display enables rapid acquisition of data from BioPlex and development of hypotheses based on protein interactions.

  3. Radiation energy detector and analyzer

    International Nuclear Information System (INIS)

    Roberts, T.G.

    1981-01-01

    A radiation detector array and a method for measuring the spectral content of radiation. The radiation sensor or detector is an array or stack of thin solid-electrolyte batteries. The batteries, arranged in a stack, may be composed of independent battery cells or may be arranged so that adjacent cells share a common terminal surface. This common surface is possible since the polarity of the batteries with respect to an adjacent battery is unrestricted, allowing a reduction in component parts of the assembly and reducing the overall stack length. Additionally, a test jig or chamber for allowing rapid measurement of the voltage across each battery is disclosed. A multichannel recorder and display may be used to indicate the voltage gradient change across the cells, or a small computer may be used for rapidly converting these voltage readings to a graph of radiation intensity versus wavelength or energy. The behavior of the batteries when used as a radiation detector and analyzer are such that the voltage measurements can be made at leisure after the detector array has been exposed to the radiation, and it is not necessary to make rapid measurements as is now done

  4. Thomson parabola ion energy analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Cobble, James A [Los Alamos National Laboratory; Flippo, Kirk A [Los Alamos National Laboratory; Letzring, Samuel A [Los Alamos National Laboratory; Lopez, Frank E [Los Alamos National Laboratory; Offermann, Dustin T [Los Alamos National Laboratory; Oertel, John A [Los Alamos National Laboratory; Mastrosimone, Dino [UNIV OF ROCHESTER

    2010-01-01

    A new, versatile Thomson parabola ion energy (TPIE) analyzer has been designed and constructed for use at the OMEGA-EP facility. Multi-MeV ions from EP targets are transmitted through a W pinhole into a (5- or 8-kG) magnetic field and subsequently through a parallel electric field of up to 30 kV/cm. The ion drift region may have a user-selected length of 10, 50, or 80 cm. With the highest fields, 500-Me V C{sup 6+} and C{sup 5+} may be resolved. TPIE is TIM-mounted at OMEGA-EP and is qualified in all existing TIMs. The instrument runs on pressure-interlocked 15-VDC power available in EP TIM carts. It may be inserted to within several inches of the target to attain sufficient flux for a measurement. For additional flux control, the user may select a square-aperture W pinhole of 0.004-inch or 0.010-inch. The detector consists of CR-39 backed by an image plate. The fully relativistic design code and design features are discussed. Ion spectral results from first use at OMEGA-EP are expected.

  5. Nuclear plant analyzer desktop workstation

    International Nuclear Information System (INIS)

    Beelman, R.J.

    1990-01-01

    In 1983 the U.S. Nuclear Regulatory Commission (USNRC) commissioned the Idaho National Engineering Laboratory (INEL) to develop a Nuclear Plant Analyzer (NPA). The NPA was envisioned as a graphical aid to assist reactor safety analysts in comprehending the results of thermal-hydraulic code calculations. The development was to proceed in three distinct phases culminating in a desktop reactor safety workstation. The desktop NPA is now complete. The desktop NPA is a microcomputer based reactor transient simulation, visualization and analysis tool developed at INEL to assist an analyst in evaluating the transient behavior of nuclear power plants by means of graphic displays. The NPA desktop workstation integrates advanced reactor simulation codes with online computer graphics allowing reactor plant transient simulation and graphical presentation of results. The graphics software, written exclusively in ANSI standard C and FORTRAN 77 and implemented over the UNIX/X-windows operating environment, is modular and is designed to interface to the NRC's suite of advanced thermal-hydraulic codes to the extent allowed by that code. Currently, full, interactive, desktop NPA capabilities are realized only with RELAP5

  6. Analyzing endocrine system conservation and evolution.

    Science.gov (United States)

    Bonett, Ronald M

    2016-08-01

    Analyzing variation in rates of evolution can provide important insights into the factors that constrain trait evolution, as well as those that promote diversification. Metazoan endocrine systems exhibit apparent variation in evolutionary rates of their constituent components at multiple levels, yet relatively few studies have quantified these patterns and analyzed them in a phylogenetic context. This may be in part due to historical and current data limitations for many endocrine components and taxonomic groups. However, recent technological advancements such as high-throughput sequencing provide the opportunity to collect large-scale comparative data sets for even non-model species. Such ventures will produce a fertile data landscape for evolutionary analyses of nucleic acid and amino acid based endocrine components. Here I summarize evolutionary rate analyses that can be applied to categorical and continuous endocrine traits, and also those for nucleic acid and protein-based components. I emphasize analyses that could be used to test whether other variables (e.g., ecology, ontogenetic timing of expression, etc.) are related to patterns of rate variation and endocrine component diversification. The application of phylogenetic-based rate analyses to comparative endocrine data will greatly enhance our understanding of the factors that have shaped endocrine system evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Evidence for the robustness of protein complexes to inter-species hybridization.

    Directory of Open Access Journals (Sweden)

    Jean-Baptiste Leducq

    Full Text Available Despite the tremendous efforts devoted to the identification of genetic incompatibilities underlying hybrid sterility and inviability, little is known about the effect of inter-species hybridization at the protein interactome level. Here, we develop a screening platform for the comparison of protein-protein interactions (PPIs among closely related species and their hybrids. We examine in vivo the architecture of protein complexes in two yeast species (Saccharomyces cerevisiae and Saccharomyces kudriavzevii that diverged 5-20 million years ago and in their F1 hybrids. We focus on 24 proteins of two large complexes: the RNA polymerase II and the nuclear pore complex (NPC, which show contrasting patterns of molecular evolution. We found that, with the exception of one PPI in the NPC sub-complex, PPIs were highly conserved between species, regardless of protein divergence. Unexpectedly, we found that the architecture of the complexes in F1 hybrids could not be distinguished from that of the parental species. Our results suggest that the conservation of PPIs in hybrids likely results from the slow evolution taking place on the very few protein residues involved in the interaction or that protein complexes are inherently robust and may accommodate protein divergence up to the level that is observed among closely related species.

  8. Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer.

    Science.gov (United States)

    Latysheva, Natasha S; Oates, Matt E; Maddox, Louis; Flock, Tilman; Gough, Julian; Buljan, Marija; Weatheritt, Robert J; Babu, M Madan

    2016-08-18

    Gene fusions are common cancer-causing mutations, but the molecular principles by which fusion protein products affect interaction networks and cause disease are not well understood. Here, we perform an integrative analysis of the structural, interactomic, and regulatory properties of thousands of putative fusion proteins. We demonstrate that genes that form fusions (i.e., parent genes) tend to be highly connected hub genes, whose protein products are enriched in structured and disordered interaction-mediating features. Fusion often results in the loss of these parental features and the depletion of regulatory sites such as post-translational modifications. Fusion products disproportionately connect proteins that did not previously interact in the protein interaction network. In this manner, fusion products can escape cellular regulation and constitutively rewire protein interaction networks. We suggest that the deregulation of central, interaction-prone proteins may represent a widespread mechanism by which fusion proteins alter the topology of cellular signaling pathways and promote cancer. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins.

    Science.gov (United States)

    Zanzoni, Andreas; Spinelli, Lionel; Braham, Shérazade; Brun, Christine

    2017-08-10

    Fusobacterium nucleatum is a gram-negative anaerobic species residing in the oral cavity and implicated in several inflammatory processes in the human body. Although F. nucleatum abundance is increased in inflammatory bowel disease subjects and is prevalent in colorectal cancer patients, the causal role of the bacterium in gastrointestinal disorders and the mechanistic details of host cell functions subversion are not fully understood. We devised a computational strategy to identify putative secreted F. nucleatum proteins (FusoSecretome) and to infer their interactions with human proteins based on the presence of host molecular mimicry elements. FusoSecretome proteins share similar features with known bacterial virulence factors thereby highlighting their pathogenic potential. We show that they interact with human proteins that participate in infection-related cellular processes and localize in established cellular districts of the host-pathogen interface. Our network-based analysis identified 31 functional modules in the human interactome preferentially targeted by 138 FusoSecretome proteins, among which we selected 26 as main candidate virulence proteins, representing both putative and known virulence proteins. Finally, six of the preferentially targeted functional modules are implicated in the onset and progression of inflammatory bowel diseases and colorectal cancer. Overall, our computational analysis identified candidate virulence proteins potentially involved in the F. nucleatum-human cross-talk in the context of gastrointestinal diseases.

  10. Dynamic protein interaction modules in human hepatocellular carcinoma progression.

    Science.gov (United States)

    Yu, Hui; Lin, Chen-Ching; Li, Yuan-Yuan; Zhao, Zhongming

    2013-01-01

    Gene expression profiles have been frequently integrated with the human protein interactome to uncover functional modules under specific conditions like disease state. Beyond traditional differential expression analysis, differential co-expression analysis has emerged as a robust approach to reveal condition-specific network modules, with successful applications in a few human disease studies. Hepatocellular carcinoma (HCC), which is often interrelated with the Hepatitis C virus, typically develops through multiple stages. A comprehensive investigation of HCC progression-specific differential co-expression modules may advance our understanding of HCC's pathophysiological mechanisms. Compared with differentially expressed genes, differentially co-expressed genes were found more likely enriched with Hepatitis C virus binding proteins and cancer-mutated genes, and they were clustered more densely in the human reference protein interaction network. These observations indicated that a differential co-expression approach could outperform the standard differential expression network analysis in searching for disease-related modules. We then proposed a differential co-expression network approach to uncover network modules involved in HCC development. Specifically, we discovered subnetworks that enriched differentially co-expressed gene pairs in each HCC transition stage, and further resolved modules with coherent co-expression change patterns over all HCC developmental stages. Our identified network modules were enriched with HCC-related genes and implicated in cancer-related biological functions. In particular, APC and YWHAZ were highlighted as two most remarkable genes in the network modules, and their dynamic interaction partnership was resolved in HCC development. We demonstrated that integration of differential co-expression with the protein interactome could outperform the traditional differential expression approach in discovering network modules of human diseases

  11. Computational probing protein-protein interactions targeting small molecules.

    Science.gov (United States)

    Wang, Yong-Cui; Chen, Shi-Long; Deng, Nai-Yang; Wang, Yong

    2016-01-15

    With the booming of interactome studies, a lot of interactions can be measured in a high throughput way and large scale datasets are available. It is becoming apparent that many different types of interactions can be potential drug targets. Compared with inhibition of a single protein, inhibition of protein-protein interaction (PPI) is promising to improve the specificity with fewer adverse side-effects. Also it greatly broadens the drug target search space, which makes the drug target discovery difficult. Computational methods are highly desired to efficiently provide candidates for further experiments and hold the promise to greatly accelerate the discovery of novel drug targets. Here, we propose a machine learning method to predict PPI targets in a genomic-wide scale. Specifically, we develop a computational method, named as PrePPItar, to Predict PPIs as drug targets by uncovering the potential associations between drugs and PPIs. First, we survey the databases and manually construct a gold-standard positive dataset for drug and PPI interactions. This effort leads to a dataset with 227 associations among 63 PPIs and 113 FDA-approved drugs and allows us to build models to learn the association rules from the data. Second, we characterize drugs by profiling in chemical structure, drug ATC-code annotation, and side-effect space and represent PPI similarity by a symmetrical S-kernel based on protein amino acid sequence. Then the drugs and PPIs are correlated by Kronecker product kernel. Finally, a support vector machine (SVM), is trained to predict novel associations between drugs and PPIs. We validate our PrePPItar method on the well-established gold-standard dataset by cross-validation. We find that all chemical structure, drug ATC-code, and side-effect information are predictive for PPI target. Moreover, we can increase the PPI target prediction coverage by integrating multiple data sources. Follow-up database search and pathway analysis indicate that our new

  12. Systematic Identification of Proteins Binding to Chromatin-Embedded Ubiquitylated H2B Reveals Recruitment of SWI/SNF to Regulate Transcription

    Directory of Open Access Journals (Sweden)

    Efrat Shema-Yaacoby

    2013-08-01

    Full Text Available Chromatin posttranslational modifications (PTMs, including monoubiquitylation of histone H2B on lysine 120 (H2Bub1, play a major role in regulating genome functions. To elucidate the molecular mechanisms of H2Bub1 activity, a chromatin template uniformly containing H2Bub1 was used as an affinity matrix to identify preferentially interacting human proteins. Over 90 such factors were found, including proteins and protein complexes associated with transcription, RNA posttranscriptional modifications, and DNA replication and repair. Notably, we found that the SWI/SNF chromatin remodeling complex associates preferentially with H2Bub1-rich chromatin. Moreover, SWI/SNF is required for optimal transcription of a subset of genes that are selectively dependent on H2Bub1. Our findings substantially expand the known H2Bub1 interactome and provide insights into the functions of this PTM in mammalian gene regulation.

  13. Proximity Utilizing Biotinylation of Nuclear Proteins in vivo

    Directory of Open Access Journals (Sweden)

    Arman Kulyyassov

    2015-06-01

    Full Text Available Introduction. The human genome consists of roughly 30,000 genes coding for over 500,000 different proteins, of which more than 10,000 proteins can be produced by the cell at any given time (the cellular “proteome”. It has been estimated that over 80% of proteins do not operate alone, but in complexes. These protein-protein interactions (PPI are regulated by several mechanisms. For example, post-translational modifications (methylation, acetylation, phosphorylation, or ubiquitination or metal-binding can lead to conformational changes that alter the affinity and kinetic parameters of the interaction. Many PPIs are part of larger cellular networks of interactions or interactomes. Indeed, these interactions are at the core of the entire interactomics system of any living cell, and so, aberrant PPIs are the basis of multiple diseases, such as neurodegenerative diseases and cancer. The objective of this study was to develop a method of monitoring protein-protein interactions and proximity dependence in vivo.Methods. The biotin ligase BirA was fused to the protein of interest, and the Biotin Acceptor Peptide (BAP was fused to an interacting partner to make the detection of its biotinylation possible by western blot or mass spectrometry.Results. Using several experimental systems (BirA.A + BAP.B, we showed that the biotinylation is interaction/proximity dependent. Here, A and B are the next nuclear proteins used in the experiments – 3 paralogues of heterochromatin protein HP1a (CBX5, HP1b (CBX1, HP1g (CBX3, wild type and transcription mutant factor Kap1, translesion DNA polymerase PolH and E3, ubiquitin ligase RAD18, Proliferative Cell Nuclear Antigen (PCNA, ubiquitin Ub, SUMO-2/3, different types and isoforms of histones H2A, H2Az, H3.1, H3.3, CenpA, H2A.BBD, and macroH2A. The variant of this approach is termed PUB-NChIP (Proximity Utilizing Biotinylation with Native Chromatin Immuno-precipitation and is designed to purify and study the protein

  14. The SOX2-interactome in brain cancer cells identifies the requirement of MSI2 and USP9X for the growth of brain tumor cells.

    Directory of Open Access Journals (Sweden)

    Jesse L Cox

    Full Text Available Medulloblastomas and glioblastomas, the most common primary brain tumors in children and adults, respectively, are extremely difficult to treat. Efforts to identify novel proteins essential for the growth of these tumors may help to further our understanding of the biology of these tumors, as well as, identify targets for future therapies. The recent identification of multiple transcription factor-centric protein interaction landscapes in embryonic stem cells has identified numerous understudied proteins that are essential for the self-renewal of these stem cells. To identify novel proteins essential for the fate of brain tumor cells, we examined the protein interaction network of the transcription factor, SOX2, in medulloblastoma cells. For this purpose, Multidimensional Protein Identification Technology (MudPIT identified >280 SOX2-associated proteins in the medulloblastoma cell line DAOY. To begin to understand the roles of SOX2-associated proteins in brain cancer, we focused on two SOX2-associated proteins, Musashi 2 (MSI2 and Ubiquitin Specific Protease 9x (USP9X. Recent studies have implicated MSI2, a putative RNA binding protein, and USP9X, a deubiquitinating enzyme, in several cancers, but not brain tumors. We demonstrate that knockdown of MSI2 significantly reduces the growth of DAOY cells as well as U87 and U118 glioblastoma cells. We also demonstrate that the knockdown of USP9X in DAOY, U87 and U118 brain tumor cells strongly reduces their growth. Together, our studies identify a large set of SOX2-associated proteins in DAOY medulloblastoma cells and identify two proteins, MSI2 and USP9X, that warrant further investigation to determine whether they are potential therapeutic targets for brain cancer.

  15. Analysis of Dermal Papilla Cell Interactome Using STRING Database to Profile the ex Vivo Hair Growth Inhibition Effect of a Vinca Alkaloid Drug, Colchicine

    Directory of Open Access Journals (Sweden)

    Ching-Wu Hsia

    2015-02-01

    Full Text Available Dermal papillae (DPs control the formation of hair shafts. In clinical settings, colchicine (CLC induces patients’ hair shedding. Compared to the control, the ex vivo hair fiber elongation of organ cultured vibrissa hair follicles (HFs declined significantly after seven days of CLC treatment. The cultured DP cells (DPCs were used as the experimental model to study the influence of CLC on the protein dynamics of DPs. CLC could alter the morphology and down-regulate the expression of alkaline phosphatase (ALP, the marker of DPC activity, and induce IκBα phosphorylation of DPCs. The proteomic results showed that CLC modulated the expression patterns (fold > 2 of 24 identified proteins, seven down-regulated and 17 up-regulated. Most of these proteins were presumably associated with protein turnover, metabolism, structure and signal transduction. Protein-protein interactions (PPI among these proteins, established by Search Tool for the Retrieval of Interacting Genes/Proteins (STRING database, revealed that they participate in protein metabolic process, translation, and energy production. Furthermore, ubiquitin C (UbC was predicted to be the controlling hub, suggesting the involvement of ubiquitin-proteasome system in modulating the pathogenic effect of CLC on DPC.

  16. The Kub5-Hera/RPRD1B interactome: a novel role in preserving genetic stability by regulating DNA mismatch repair

    Science.gov (United States)

    Patidar, Praveen L.; Motea, Edward A.; Fattah, Farjana J.; Zhou, Yunyun; Morales, Julio C.; Xie, Yang; Garner, Harold R.; Boothman, David A.

    2016-01-01

    Ku70-binding protein 5 (Kub5)-Hera (K-H)/RPRD1B maintains genetic integrity by concomitantly minimizing persistent R-loops and promoting repair of DNA double strand breaks (DSBs). We used tandem affinity purification-mass spectrometry, co-immunoprecipitation and gel-filtration chromatography to define higher-order protein complexes containing K-H scaffolding protein to gain insight into its cellular functions. We confirmed known protein partners (Ku70, RNA Pol II, p15RS) and discovered several novel associated proteins that function in RNA metabolism (Topoisomerase 1 and RNA helicases), DNA repair/replication processes (PARP1, MSH2, Ku, DNA-PKcs, MCM proteins, PCNA and DNA Pol δ) and in protein metabolic processes, including translation. Notably, this approach directed us to investigate an unpredicted involvement of K-H in DNA mismatch repair (MMR) where K-H depletion led to concomitant MMR deficiency and compromised global microsatellite stability. Mechanistically, MMR deficiency in K-H-depleted cells was a consequence of reduced stability of the core MMR proteins (MLH1 and PMS2) caused by elevated basal caspase-dependent proteolysis. Pan-caspase inhibitor treatment restored MMR protein loss. These findings represent a novel mechanism to acquire MMR deficiency/microsatellite alterations. A significant proportion of colon, endometrial and ovarian cancers exhibit k-h expression/copy number loss and may have severe mutator phenotypes with enhanced malignancies that are currently overlooked based on sporadic MSI+ screening. PMID:26819409

  17. WD40-repeat proteins in plant cell wall formation: current evidence and research prospects

    Directory of Open Access Journals (Sweden)

    Gea eGuerriero

    2015-12-01

    Full Text Available The metabolic complexity of living organisms relies on supramolecular protein structures which ensure vital processes, such as signal transduction, transcription, translation and cell wall synthesis. In eukaryotes WD40-repeat (WDR proteins often function as molecular hubs mediating supramolecular interactions. WDR proteins may display a variety of interacting partners and participate in the assembly of complexes involved in distinct cellular functions. In plants, the formation of lignocellulosic biomass involves extensive synthesis of cell wall polysaccharides, a process that requires the assembly of large transmembrane enzyme complexes, intensive vesicle trafficking, interactions with the cytoskeleton, and coordinated gene expression. Because of their function as supramolecular hubs, WDR proteins could participate in each or any of these steps, although to date only few WDR proteins have been linked to the cell wall by experimental evidence. Nevertheless, several potential cell wall-related WDR proteins were recently identified using in silico aproaches, such as analyses of co-expression, interactome and conserved gene neighbourhood. Notably, some WDR genes are frequently genomic neighbours of genes coding for GT2-family polysaccharide synthases in eukaryotes, and this WDR-GT2 collinear microsynteny is detected in diverse taxa. In angiosperms, two WDR genes are collinear to cellulose synthase genes, CESAs, whereas in ascomycetous fungi several WDR genes are adjacent to chitin synthase genes, chs. In this Perspective we summarize and discuss experimental and in silico studies on the possible involvement of WDR proteins in plant cell wall formation. The prospects of biotechnological engineering for enhanced biomass production are discussed.

  18. Merging in-silico and in vitro salivary protein complex partners using the STRING database: A tutorial.

    Science.gov (United States)

    Crosara, Karla Tonelli Bicalho; Moffa, Eduardo Buozi; Xiao, Yizhi; Siqueira, Walter Luiz

    2018-01-16

    Protein-protein interaction is a common physiological mechanism for protection and actions of proteins in an organism. The identification and characterization of protein-protein interactions in different organisms is necessary to better understand their physiology and to determine their efficacy. In a previous in vitro study using mass spectrometry, we identified 43 proteins that interact with histatin 1. Six previously documented interactors were confirmed and 37 novel partners were identified. In this tutorial, we aimed to demonstrate the usefulness of the STRING database for studying protein-protein interactions. We used an in-silico approach along with the STRING database (http://string-db.org/) and successfully performed a fast simulation of a novel constructed histatin 1 protein-protein network, including both the previously known and the predicted interactors, along with our newly identified interactors. Our study highlights the advantages and importance of applying bioinformatics tools to merge in-silico tactics with experimental in vitro findings for rapid advancement of our knowledge about protein-protein interactions. Our findings also indicate that bioinformatics tools such as the STRING protein network database can help predict potential interactions between proteins and thus serve as a guide for future steps in our exploration of the Human Interactome. Our study highlights the usefulness of the STRING protein database for studying protein-protein interactions. The STRING database can collect and integrate data about known and predicted protein-protein associations from many organisms, including both direct (physical) and indirect (functional) interactions, in an easy-to-use interface. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Complex Systems Analysis of Cell Cycling Models in Carcinogenesis:II. Cell Genome and Interactome, Neoplastic Non-random Transformation Models in Topoi with Lukasiewicz-Logic and MV Algebras

    CERN Document Server

    Baianu, I C

    2004-01-01

    Quantitative Biology, abstract q-bio.OT/0406045 From: I.C. Baianu Dr. [view email] Date (v1): Thu, 24 Jun 2004 02:45:13 GMT (164kb) Date (revised v2): Fri, 2 Jul 2004 00:58:06 GMT (160kb) Complex Systems Analysis of Cell Cycling Models in Carcinogenesis: II. Authors: I.C. Baianu Comments: 23 pages, 1 Figure Report-no: CC04 Subj-class: Other Carcinogenesis is a complex process that involves dynamically inter-connected modular sub-networks that evolve under the influence of micro-environmentally induced perturbations, in non-random, pseudo-Markov chain processes. An appropriate n-stage model of carcinogenesis involves therefore n-valued Logic treatments of nonlinear dynamic transformations of complex functional genomes and cell interactomes. Lukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous, Boolean or "fuzzy", logic models of genetic activities in vivo....

  20. Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.

    Science.gov (United States)

    Jin, Guangxu; Zhang, Shihua; Zhang, Xiang-Sun; Chen, Luonan

    2007-11-21

    It has been recognized that modular organization pervades biological complexity. Based on network analysis, 'party hubs' and 'date hubs' were proposed to understand the basic principle of module organization of biomolecular networks. However, recent study on hubs has suggested that there is no clear evidence for coexistence of 'party hubs' and 'date hubs'. Thus, an open question has been raised as to whether or not 'party hubs' and 'date hubs' truly exist in yeast interactome. In contrast to previous studies focusing on the partners of a hub or the individual proteins around the hub, our work aims to study the network motifs of a hub or interactions among individual proteins including the hub and its neighbors. Depending on the relationship between a hub's network motifs and protein complexes, we define two new types of hubs, 'motif party hubs' and 'motif date hubs', which have the same characteristics as the original 'party hubs' and 'date hubs' respectively. The network motifs of these two types of hubs display significantly different features in spatial distribution (or cellular localizations), co-expression in microarray data, controlling topological structure of network, and organizing modularity. By virtue of network motifs, we basically solved the open question about 'party hubs' and 'date hubs' which was raised by previous studies. Specifically, at the level of network motifs instead of individual proteins, we found two types of hubs, motif party hubs (mPHs) and motif date hubs (mDHs), whose network motifs display distinct characteristics on biological functions. In addition, in this paper we studied network motifs from a different viewpoint. That is, we show that a network motif should not be merely considered as an interaction pattern but be considered as an essential function unit in organizing modules of networks.

  1. 7 CFR 801.7 - Reference methods and tolerances for near-infrared spectroscopy (NIRS) analyzers.

    Science.gov (United States)

    2010-01-01

    ... Association Method A-20, Analysis for Starch in Corn, Second revision, April 15, 1986, Standard Analytical... Method 992.23. (3) NIRS corn oil, protein, and starch analyzers. The maintenance tolerances for the NIRS... Starch method, Corn Refiners Association Method A-20. (4) NIRS barley protein analyzers. The maintenance...

  2. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

  3. Portable Programmable Multifunction Body Fluids Analyzer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Liquid Logic proposes to develop a very capable analyzer based on its digital microfluidic technology. Such an analyzer would be:  Capable of both...

  4. Riboproteomics: A versatile approach for the identification of host protein interaction network in plant pathogenic noncoding RNAs.

    Directory of Open Access Journals (Sweden)

    Sonali Chaturvedi

    Full Text Available Pathogenic or non-pathogenic small (17 to 30 nt and long (>200 nt non-coding RNAs (ncRNAs have been implicated in the regulation of gene expression at transcriptional, post-transcriptional and epigenetic level by interacting with host proteins. However, lack of suitable experimental system precludes the identification and evaluation of the functional significance of host proteins interacting with ncRNAs. In this study, we present a first report on the application of riboproteomics to identify host proteins interacting with small, highly pathogenic, noncoding satellite RNA (sat-RNA associated with Cucumber mosaic virus, the helper virus (HV. RNA affinity beads containing sat-RNA transcripts of (+ or (--sense covalently coupled to cyanogen bromide activated sepharose beads were incubated with total protein extracts from either healthy or HV-infected Nicotiana benthamiana leaves. RNA-protein complexes bound to the beads were eluted and subjected to MudPIT analysis. Bioinformatics programs PANTHER classification and WoLF-PSORT were used to further classify the identified host proteins in each case based on their functionality and subcellular distribution. Finally, we observed that the host protein network interacting with plus and minus-strand transcripts of sat-RNA, in the presence or absence of HV is distinct, and the global interactome of host proteins interacting with satRNA in either of the orientations is very different.

  5. Elucidation of epithelial-mesenchymal transition-related pathways in a triple-negative breast cancer cell line model by multi-omics interactome analysis

    DEFF Research Database (Denmark)

    Pauling, Josch K; Christensen, Anne G; Batra, Richa

    2014-01-01

    exhibiting epithelial-like and mesenchymal-like morphology, respectively. Here we identified altered protein signaling activity in a complex biologically relevant network, related to focal adhesion and migration of breast cancer cells. We found dysregulated functional network modules revealing altered...... obtained from a triple-negative breast cancer cell line model, combining data sets of gene and protein expression as well as protein phosphorylation. We focus on alterations associated with the phenotypical differences arising from epithelial-mesenchymal transition in two breast cancer cell lines...... with generation of biological networks. This allows identification of intrinsic patterns in the data and their linkage to a specific context such as cellular compartments, diseases or functions. Identification of aberrant pathways by traditional approaches is often limited to biological networks based on either...

  6. Analyzing Influenza Virus Sequences using Binary Encoding Approach

    Directory of Open Access Journals (Sweden)

    Ham Ching Lam

    2012-01-01

    Full Text Available Capturing mutation patterns of each individual influenza virus sequence is often challenging; in this paper, we demonstrated that using a binary encoding scheme coupled with dimension reduction technique, we were able to capture the intrinsic mutation pattern of the virus. Our approach looks at the variance between sequences instead of the commonly used p-distance or Hamming distance. We first convert the influenza genetic sequences to a binary strings and form a binary sequence alignment matrix and then apply Principal Component Analysis (PCA to this matrix. PCA also provides identification power to identify reassortant virus by using data projection technique. Due to the sparsity of the binary string, we were able to analyze large volume of influenza sequence data in a very short time. For protein sequences, our scheme also allows the incorporation of biophysical properties of each amino acid. Here, we present various encouraging results from analyzing influenza nucleotide, protein and genome sequences using the proposed approach.

  7. ALS Associated Mutations in Matrin 3 Alter Protein-Protein Interactions and Impede mRNA Nuclear Export.

    Science.gov (United States)

    Boehringer, Ashley; Garcia-Mansfield, Krystine; Singh, Gurkaran; Bakkar, Nadine; Pirrotte, Patrick; Bowser, Robert

    2017-11-06

    Mutations in Matrin 3 have recently been linked to ALS, though the mechanism that induces disease in these patients is unknown. To define the protein interactome of wild-type and ALS-linked MATR3 mutations, we performed immunoprecipitation followed by mass spectrometry using NSC-34 cells expressing human wild-type or mutant Matrin 3. Gene ontology analysis identified a novel role for Matrin 3 in mRNA transport centered on proteins in the TRanscription and EXport (TREX) complex, known to function in mRNA biogenesis and nuclear export. ALS-linked mutations in Matrin 3 led to its re-distribution within the nucleus, decreased co-localization with endogenous Matrin 3 and increased co-localization with specific TREX components. Expression of disease-causing Matrin 3 mutations led to nuclear mRNA export defects of both global mRNA and more specifically the mRNA of TDP-43 and FUS. Our findings identify a potential pathogenic mechanism attributable to MATR3 mutations and further link cellular transport defects to ALS.

  8. Comparing human-Salmonella with plant-Salmonella protein-protein interaction predictions

    Directory of Open Access Journals (Sweden)

    Sylvia eSchleker

    2015-01-01

    Full Text Available Salmonellosis is the most frequent food-borne disease world-wide and can be transmitted to humans by a variety of routes, especially via animal and plant products. Salmonella bacteria are believed to use not only animal and human but also plant hosts despite their evolutionary distance. This raises the question if Salmonella employs similar mechanisms in infection of these diverse hosts. Given that most of our understanding comes from its interaction with human hosts, we investigate here to what degree knowledge of Salmonella-human interactions can be transferred to the Salmonella-plant system. Reviewed are recent publications on analysis and prediction of Salmonella-host interactomes. Putative protein-protein interactions (PPIs between Salmonella and its human and Arabidopsis hosts were retrieved utilizing purely interolog-based approaches in which predictions were inferred based on available sequence and domain information of known PPIs, and machine learning approaches that integrate a larger set of useful information from different sources. Transfer learning is an especially suitable machine learning technique to predict plant host targets from the knowledge of human host targets. A comparison of the prediction results with transcriptomic data shows a clear overlap between the host proteins predicted to be targeted by PPIs and their gene ontology enrichment in both host species and regulation of gene expression. In particular, the cellular processes Salmonella interferes with in plants and humans are catabolic processes. The details of how these processes are targeted, however, are quite different between the two organisms, as expected based on their evolutionary and habitat differences. Possible implications of this observation on evolution of host-pathogen communication are discussed.

  9. Ontological visualization of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Hill David P

    2005-02-01

    Full Text Available Abstract Background Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and regulation of individual proteins. The Gene Ontology (GO is used by model organism databases and other bioinformatics resources to provide functional annotation of proteins. The annotation process provides a mechanism to document the binding of one protein with another. We have constructed protein interaction networks for mouse proteins utilizing the information encoded in the GO annotations. The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions. Results GO annotation at Mouse Genome Informatics (MGI captures 1318 curated, documented interactions. These include 129 binary interactions and 125 interaction involving three or more gene products. Three networks involve over 30 partners, the largest involving 109 proteins. Several tools are available at MGI to visualize and analyze these data. Conclusions Curators at the MGI database annotate protein-protein interaction data from experimental reports from the literature. Integration of these data with the other types of data curated at MGI places protein binding data into the larger context of mouse biology and facilitates the generation of new biological hypotheses based on physical interactions among gene products.

  10. Using expert systems to analyze ATE data

    Science.gov (United States)

    Harrington, Jim

    1994-01-01

    The proliferation of automatic test equipment (ATE) is resulting in the generation of large amounts of component data. Some of this component data is not accurate due to the presence of noise. Analyzing this data requires the use of new techniques. This paper describes the process of developing an expert system to analyze ATE data and provides an example rule in the CLIPS language for analyzing trip thresholds for high gain/high speed comparators.

  11. Electrical spectrum & network analyzers a practical approach

    CERN Document Server

    Helfrick, Albert D

    1991-01-01

    This book presents fundamentals and the latest techniques of electrical spectrum analysis. It focuses on instruments and techniques used on spectrum and network analysis, rather than theory. The book covers the use of spectrum analyzers, tracking generators, and network analyzers. Filled with practical examples, the book presents techniques that are widely used in signal processing and communications applications, yet are difficult to find in most literature.Key Features* Presents numerous practical examples, including actual spectrum analyzer circuits* Instruction on how to us

  12. ADAM: Analyzer for Dialectal Arabic Morphology

    Directory of Open Access Journals (Sweden)

    Wael Salloum

    2014-12-01

    Full Text Available While Modern Standard Arabic (MSA has many resources, Arabic Dialects, the primarily spoken local varieties of Arabic, are quite impoverished in this regard. In this article, we present ADAM (Analyzer for Dialectal Arabic Morphology. ADAM is a poor man’s solution to quickly develop morphological analyzers for dialectal Arabic. ADAM has roughly half the out-of-vocabulary rate of a state-of-the-art MSA analyzer and is comparable in its recall performance to an Egyptian dialectal morphological analyzer that took years and expensive resources to build.

  13. Docosohaexanoic acid-supplemented PACA44 cell lines and over-activation of Krebs cycle: an integrated proteomic, metabolomic and interactomic overview.

    Science.gov (United States)

    D'Alessandro, Angelo; D'Amici, Gian Maria; Timperio, Anna Maria; Merendino, Nicolò; Zolla, Lello

    2011-09-06

    Recent investigations have pointed out the ability of fatty acids, in particular of docosohaexanoic acid (DHA), to induce growth inhibition and apoptosis in the human PaCa-44 pancreatic cancer cell line through a series of mechanisms which has been hypothesized to mimic apoptosis. While preliminary evidences indicated the involvement of lipid-targeting oxidative stress in DHA-induced apoptotic processes, mainly through the alteration of the glutathione (GSH) homeostasis and oxidized-glutathione (GSSG) turn-over through their extra-cellular extrusion, no further molecular data have been hitherto accumulated. To this end, we hereby propose simultaneous protein-targeting and metabolite-oriented analyses, which have been integrated through the auxilium of in silico elaboration of those protein-protein interaction pathways and enrichment of biological/molecular functions. To determine the most suitable time window for the early onset of the DHA-triggered apoptosis phenomena we performed flow cytometry-based apoptotic assessment at 24, 48 and 72 h. Results indicated that the focus of apoptosis onset ranged from 48 to 72 h. From these analyses it emerges that the metabolism of control human PaCa-44 pancreatic cancer cell line mainly leans on glycolytic pathways, while it is promptly switched to Kreb's cycle activation (overexpression of Kreb's cycle enzymes in DHA-treated cells against controls) and modulation of the GSH homeostasis through an increased production of GSSG-reducing NADPH coenzyme via the shift of the glycolytic energy flux towards the pentose phosphate pathway. Interestingly, it also emerges a role for structural protein alteration in DHA-treated cells, which might be linked to cytoskeletal alterations occurring during apoptosis. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. A new tessera into the interactome of the isc operon:A novel interaction between HscB and IscS

    Directory of Open Access Journals (Sweden)

    Annalisa Pastore

    2016-09-01

    Full Text Available Iron sulfur clusters are essential universal prosthetic groups which can be formed inorganically but, in biology, are bound to proteins and produced enzymatically. Most of the components of the machine that produces the clusters are conserved throughout evolution. In bacteria, they are encoded in the isc operon. Previous reports provide information on the role of specific components but a clear picture of how the whole machine works is still missing. We have carried out a study of the effects of the co-chaperone HscB from the model system E. coli. We document a previously undetected weak interaction between the chaperone HscB and the desulfurase IscS, one of the two main players of the machine. The binding site involves a region of HscB in the longer stem of the approximately L-shaped molecules, whereas the interacting surface of IscS overlaps with the surface previously involved in binding other proteins, such as ferredoxin and frataxin. Our findings provide an entirely new perspective to our comprehension of the role of HscB and propose this protein as a component of the IscS complex.

  15. A New Tessera into the Interactome of theiscOperon: A Novel Interaction between HscB and IscS.

    Science.gov (United States)

    Puglisi, Rita; Yan, Robert; Adinolfi, Salvatore; Pastore, Annalisa

    2016-01-01

    Iron sulfur clusters are essential universal prosthetic groups which can be formed inorganically but, in biology, are bound to proteins and produced enzymatically. Most of the components of the machine that produces the clusters are conserved throughout evolution. In bacteria, they are encoded in the isc operon. Previous reports provide information on the role of specific components but a clear picture of how the whole machine works is still missing. We have carried out a study of the effects of the co-chaperone HscB from the model system E. coli . We document a previously undetected weak interaction between the chaperone HscB and the desulfurase IscS, one of the two main players of the machine. The binding site involves a region of HscB in the longer stem of the approximately L-shaped molecule, whereas the interacting surface of IscS overlaps with the surface previously involved in binding other proteins, such as ferredoxin and frataxin. Our findings provide an entirely new perspective to our comprehension of the role of HscB and propose this protein as a component of the IscS complex.

  16. A two-hybrid assay to study protein interactions within the secretory pathway.

    Directory of Open Access Journals (Sweden)

    Danielle H Dube

    Full Text Available Interactions of transcriptional activators are difficult to study using transcription-based two-hybrid assays due to potent activation resulting in false positives. Here we report the development of the Golgi two-hybrid (G2H, a method that interrogates protein interactions within the Golgi, where transcriptional activators can be assayed with negligible background. The G2H relies on cell surface glycosylation to report extracellularly on protein-protein interactions occurring within the secretory pathway. In the G2H, protein pairs are fused to modular domains of the reporter glycosyltransferase, Och1p, and proper cell wall formation due to Och1p activity is observed only when a pair of proteins interacts. Cells containing interacting protein pairs are identified by selectable phenotypes associated with Och1p activity and proper cell wall formation: cells that have interacting proteins grow under selective conditions and display weak wheat germ agglutinin (WGA binding by flow cytometry, whereas cells that lack interacting proteins display stunted growth and strong WGA binding. Using this assay, we detected the interaction between transcription factor MyoD and its binding partner Id2. Interfering mutations along the MyoD:Id2 interaction interface ablated signal in the G2H assay. Furthermore, we used the G2H to detect interactions of the activation domain of Gal4p with a variety of binding partners. Finally, selective conditions were used to enrich for cells encoding interacting partners. The G2H detects protein-protein interactions that cannot be identified via traditional two-hybrid methods and should be broadly useful for probing previously inaccessible subsets of the interactome, including transcriptional activators and proteins that traffic through the secretory pathway.

  17. Analyzing metabolomics-based challenge test

    NARCIS (Netherlands)

    Vis, D.J.; Westerhuis, J.A.; Jacobs, D.M.; van Duynhoven, J.P.M.; Wopereis, S.; van Ommen, B.; Hendriks, M.M.W.B.; Smilde, A.K.

    2015-01-01

    Challenge tests are used to assess the resilience of human beings to perturbations by analyzing responses to detect functional abnormalities. Well known examples are allergy tests and glucose tolerance tests. Increasingly, metabolomics analysis of blood or serum samples is used to analyze the

  18. The C-terminal domain of the bacterial SSB protein acts as a DNA maintenance hub at active chromosome replication forks.

    Directory of Open Access Journals (Sweden)

    Audrey Costes

    2010-12-01

    Full Text Available We have investigated in vivo the role of the carboxy-terminal domain of the Bacillus subtilis Single-Stranded DNA Binding protein (SSB(Cter as a recruitment platform at active chromosomal forks for many proteins of the genome maintenance machineries. We probed this SSB(Cter interactome using GFP fusions and by Tap-tag and biochemical analysis. It includes at least 12 proteins. The interactome was previously shown to include PriA, RecG, and RecQ and extended in this study by addition of DnaE, SbcC, RarA, RecJ, RecO, XseA, Ung, YpbB, and YrrC. Targeting of YpbB to active forks appears to depend on RecS, a RecQ paralogue, with which it forms a stable complex. Most of these SSB partners are conserved in bacteria, while others, such as the essential DNA polymerase DnaE, YrrC, and the YpbB/RecS complex, appear to be specific to B. subtilis. SSB(Cter deletion has a moderate impact on B. subtilis cell growth. However, it markedly affects the efficiency of repair of damaged genomic DNA and arrested replication forks. ssbΔCter mutant cells appear deficient in RecA loading on ssDNA, explaining their inefficiency in triggering the SOS response upon exposure to genotoxic agents. Together, our findings show that the bacterial SSB(Cter acts as a DNA maintenance hub at active chromosomal forks that secures their propagation along the genome.

  19. Bam35 tectivirus intraviral interaction map unveils new function and localization of phage ORFan proteins.

    Science.gov (United States)

    Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter; Salas, Margarita; Redrejo-Rodríguez, Modesto

    2017-07-26

    Tectiviridae comprises a group of tail-less, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria.In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing the knowledge of the viral proteome, we carried out a comprehensive yeast two-hybrid analysis among all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprises 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggested that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, being the latter also supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving non-structural proteins, such as the DNA binding protein P1 and the genome terminal protein (P4), which was confirmed by co-immunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tail-less viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown

  20. Introducing the hypothome

    DEFF Research Database (Denmark)

    Madsen, Claus Desler; Zambach, Sine; Suravajhala, Prashanth

    2014-01-01

    An interactome is defined as a network of protein-protein interactions built from experimentally verified interactions. Basic science as well as application-based research of potential new drugs can be promoted by including proteins that are only predicted into interactomes. The disadvantage...... of doing so is the risk of devaluing the definition of interactomes. By adding proteins that have only been predicted, an interactome can no longer be classified as experimentally verified and the integrity of the interactome will be endured. Therefore, we propose the term 'hypothome' (collection...... of hypothetical interactions of predicted proteins). The purpose of such a term is to provide a denotation to the interactome concept allowing the interaction of predicted proteins without devaluing the integrity of the interactome. We define a rule-set for a hypothome and have integrated the predicted protein...

  1. Proteomic analysis reveals new cardiac-specific dystrophin-associated proteins.

    Directory of Open Access Journals (Sweden)

    Eric K Johnson

    Full Text Available Mutations affecting the expression of dystrophin result in progressive loss of skeletal muscle function and cardiomyopathy leading to early mortality. Interestingly, clinical studies revealed no correlation in disease severity or age of onset between cardiac and skeletal muscles, suggesting that dystrophin may play overlapping yet different roles in these two striated muscles. Since dystrophin serves as a structural and signaling scaffold, functional differences likely arise from tissue-specific protein interactions. To test this, we optimized a proteomics-based approach to purify, identify and compare the interactome of dystrophin between cardiac and skeletal muscles from as little as 50 mg of starting material. We found selective tissue-specific differences in the protein associations of cardiac and skeletal muscle full length dystrophin to syntrophins and dystrobrevins that couple dystrophin to signaling pathways. Importantly, we identified novel cardiac-specific interactions of dystrophin with proteins known to regulate cardiac contraction and to be involved in cardiac disease. Our approach overcomes a major challenge in the muscular dystrophy field of rapidly and consistently identifying bona fide dystrophin-interacting proteins in tissues. In addition, our findings support the existence of cardiac-specific functions of dystrophin and may guide studies into early triggers of cardiac disease in Duchenne and Becker muscular dystrophies.

  2. Proteomic Analysis Reveals New Cardiac-Specific Dystrophin-Associated Proteins

    Science.gov (United States)

    Johnson, Eric K.; Zhang, Liwen; Adams, Marvin E.; Phillips, Alistair; Freitas, Michael A.; Froehner, Stanley C.; Green-Church, Kari B.; Montanaro, Federica

    2012-01-01

    Mutations affecting the expression of dystrophin result in progressive loss of skeletal muscle function and cardiomyopathy leading to early mortality. Interestingly, clinical studies revealed no correlation in disease severity or age of onset between cardiac and skeletal muscles, suggesting that dystrophin may play overlapping yet different roles in these two striated muscles. Since dystrophin serves as a structural and signaling scaffold, functional differences likely arise from tissue-specific protein interactions. To test this, we optimized a proteomics-based approach to purify, identify and compare the interactome of dystrophin between cardiac and skeletal muscles from as little as 50 mg of starting material. We found selective tissue-specific differences in the protein associations of cardiac and skeletal muscle full length dystrophin to syntrophins and dystrobrevins that couple dystrophin to signaling pathways. Importantly, we identified novel cardiac-specific interactions of dystrophin with proteins known to regulate cardiac contraction and to be involved in cardiac disease. Our approach overcomes a major challenge in the muscular dystrophy field of rapidly and consistently identifying bona fide dystrophin-interacting proteins in tissues. In addition, our findings support the existence of cardiac-specific functions of dystrophin and may guide studies into early triggers of cardiac disease in Duchenne and Becker muscular dystrophies. PMID:22937058

  3. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers......, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods....

  4. Multiplex Assay for Live-Cell Monitoring of Cellular Fates of Amyloid-β Precursor Protein (APP)

    Science.gov (United States)

    Nykänen, Niko-Petteri; Yan, Xu; Sakha, Prasanna; Huttunen, Henri J.

    2014-01-01

    Amyloid-β precursor protein (APP) plays a central role in pathogenesis of Alzheimer's disease. APP has a short half-life and undergoes complex proteolytic processing that is highly responsive to various stimuli such as changes in cellular lipid or energy homeostasis. Cellular trafficking of APP is controlled by its large protein interactome, including dozens of cytosolic adaptor proteins, and also by interactions with lipids. Currently, cellular regulation of APP is mostly studied based on appearance of APP-derived proteolytic fragments to conditioned media and cellular extracts. Here, we have developed a novel live-cell assay system based on several indirect measures that reflect altered APP trafficking and processing in cells. Protein-fragment complementation assay technology for detection of APP-BACE1 protein-protein interaction forms the core of the new assay. In a multiplex form, the assay can measure four endpoints: total cellular APP level, total secreted sAPP level in media, APP-BACE1 interaction in cells and in exosomes released by the cells. Functional validation of the assay with pharmacological and genetic tools revealed distinct patterns of cellular fates of APP, with immediate mechanistic implications. This new technology will facilitate functional genomics studies of late-onset Alzheimer's disease, drug discovery efforts targeting APP and characterization of the physiological functions of APP and its proteolytic fragments. PMID:24932508

  5. Time-delay analyzer with continuous discretization

    International Nuclear Information System (INIS)

    Bayatyan, G.L.; Darbinyan, K.T.; Mkrtchyan, K.K.; Stepanyan, S.S.

    1988-01-01

    A time-delay analyzer is described which when triggered by a start pulse of adjustable duration performs continuous discretization of the analyzed signal within nearly 22 ns time intervals, the recording in a memory unit with following slow read-out of the information to the computer and its processing. The time-delay analyzer consists of four CAMAC-VECTOR systems of unit width. With its help one can separate comparatively short, small-amplitude rare signals against the background of quasistationary noise processes. 4 refs.; 3 figs

  6. Systems Analyze Water Quality in Real Time

    Science.gov (United States)

    2010-01-01

    A water analyzer developed under Small Business Innovation Research (SBIR) contracts with Kennedy Space Center now monitors treatment processes at water and wastewater facilities around the world. Originally designed to provide real-time detection of nutrient levels in hydroponic solutions for growing plants in space, the ChemScan analyzer, produced by ASA Analytics Inc., of Waukesha, Wisconsin, utilizes spectrometry and chemometric algorithms to automatically analyze multiple parameters in the water treatment process with little need for maintenance, calibration, or operator intervention. The company has experienced a compound annual growth rate of 40 percent over its 15-year history as a direct result of the technology's success.

  7. Low Gravity Drug Stability Analyzer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this proposed program through Phase III is to build a space-worthy Drug Stability Analyzer that can determine the extent of drug degradation. It will be...

  8. On-Demand Urine Analyzer, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The overall goal of this program (through Phase III) is to develop an analyzer that can be integrated into International Space Station (ISS) toilets to measure key...

  9. Low Gravity Drug Stability Analyzer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The overall goal of this proposed program (through Phase III) is to build a space-worthy Drug Stability Analyzer that can determine the extent of drug degradation....

  10. Analyzing the economic impacts of transportation projects.

    Science.gov (United States)

    2013-09-01

    The main goal of the study is to explore methods, approaches and : analytical software tools for analyzing economic activity that results from largescale : transportation investments in Connecticut. The primary conclusion is that the : transportation...

  11. Low Gravity Drug Stability Analyzer, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The overall goal of this proposed program (through Phase III) is to build a space-worthy Drug Stability Analyzer that can determine the extent of drug degradation....

  12. Guide to analyzing investment options using TWIGS.

    Science.gov (United States)

    Charles R Blinn; Dietmar W. Rose; Monique L. Belli

    1988-01-01

    Describes methods for analyzing economic return of simulated stand management alternatives in TWIGS. Defines and discusses net present value, equivalent annual income, soil expectation value, and real vs. nominal analyses. Discusses risk and sensitivity analysis when comparing alternatives.

  13. Ultrasensitive Atmospheric Analyzer for Miniature UAVs Project

    Data.gov (United States)

    National Aeronautics and Space Administration — In this SBIR Phase I effort, Los Gatos Research (LGR) proposes to develop a highly-accurate, lightweight, low-power gas analyzer for quantification of water vapor...

  14. Digital dynamic amplitude-frequency spectra analyzer

    International Nuclear Information System (INIS)

    Kalinnikov, V.A.; )

    2006-01-01

    The spectra analyzer is intended for the dynamic spectral analysis of signals physical installations and noise filtering. The recurrence Fourier transformation algorithm is used in the digital dynamic analyzer. It is realized on the basis of the fast logic FPGA matrix and the special signal ADSP microprocessor. The discretization frequency is 2 kHz-10 MHz. The number of calculated spectral coefficients is not less 512. The functional fast-action is 20 ns [ru

  15. CooVar: Co-occurring variant analyzer

    Directory of Open Access Journals (Sweden)

    Vergara Ismael A

    2012-11-01

    Full Text Available Abstract Background Evaluating the impact of genomic variations (GV on protein-coding transcripts is an important step in identifying variants of functional significance. Currently available programs for variant annotation depend on external databases or annotate multiple variants affecting the same transcript independently, which limits program use to organisms available in these databases or results in potentially incorrect or incomplete annotations. Findings We have developed CooVar (Co-occurring Variant Analyzer, a database-independent program for assessing the impact of GVs on protein-coding transcripts. CooVar takes GVs, reference genome sequence, and protein-coding exons as input and provides annotated GVs and transcripts as output. Other than similar programs, CooVar considers the combined impact of all GVs affecting the same transcript, generating biologically more accurate annotations. CooVar is operated from the command-line and supports standard file formats VCF, GFF/GTF, and GVF, which makes it easy to integrate into existing computational pipelines. We have extensively tested CooVar on worm and human data sets and demonstrate that it generates correct annotations in only a short amount of time. Conclusions CooVar is an easy-to-use and lightweight variant annotation tool that considers the combined impact of GVs on protein-coding transcripts. CooVar is freely available at http://genome.sfu.ca/projects/coovar/.

  16. A glimpse into the regulation of the Wilson disease protein, ATP7B, sheds light on the complexity of mammalian apical trafficking pathways.

    Science.gov (United States)

    Gupta, Arnab; Das, Santanu; Ray, Kunal

    2018-03-01

    Wilson disease (WD), a Mendelian disorder of copper metabolism caused by mutations in the ATP7B gene, manifests a large spectrum of phenotypic variability. This phenomenon of extensive symptom variation is not frequently associated with a monogenic disorder. We hypothesize that the phenotypic variability in WD is primarily driven by the variations in interacting proteins that regulate the ATP7B function and localization in the cell. Based on existing literature, we delineated a potential molecular mechanism for ATP7B mediated copper transport in the milieu of its interactome, its dysfunction in WD and the resulting variability in the phenotypic manifestation. Understanding the copper-induced apical trafficking of ATP7B also significantly contributes to the appreciation of the complexities of the ligand-induced transport pathway. We believe that this holistic view of WD will pave the way for a better opportunity for rational drug design and therapeutics.

  17. Chromatin immunoprecipitation to analyze DNA binding sites of HMGA2.

    Directory of Open Access Journals (Sweden)

    Nina Winter

    Full Text Available BACKGROUND: HMGA2 is an architectonic transcription factor abundantly expressed during embryonic and fetal development and it is associated with the progression of malignant tumors. The protein harbours three basically charged DNA binding domains and an acidic protein binding C-terminal domain. DNA binding induces changes of DNA conformation and hence results in global overall change of gene expression patterns. Recently, using a PCR-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment procedure two consensus sequences for HMGA2 binding have been identified. METHODOLOGY/PRINCIPAL FINDINGS: In this investigation chromatin immunoprecipitation (ChIP experiments and bioinformatic methods were used to analyze if these binding sequences can be verified on chromatin of living cells as well. CONCLUSION: After quantification of HMGA2 protein in different cell lines the colon cancer derived cell line HCT116 was chosen for further ChIP experiments because of its 3.4-fold higher HMGA2 protein level. 49 DNA fragments were obtained by ChIP. These fragments containing HMGA2 binding sites have been analyzed for their AT-content, location in the human genome and similarities to sequences generated by a SELEX study. The sequences show a significantly higher AT-content than the average of the human genome. The artificially generated SELEX sequences and short BLAST alignments (11 and 12 bp of the ChIP fragments from living cells show similarities in their organization. The flanking regions are AT-rich, whereas a lower conservation is present in the center of the sequences.

  18. Systems and methods for modeling and analyzing networks

    Science.gov (United States)

    Hill, Colin C; Church, Bruce W; McDonagh, Paul D; Khalil, Iya G; Neyarapally, Thomas A; Pitluk, Zachary W

    2013-10-29

    The systems and methods described herein utilize a probabilistic modeling framework for reverse engineering an ensemble of causal models, from data and then forward simulating the ensemble of models to analyze and predict the behavior of the network. In certain embodiments, the systems and methods described herein include data-driven techniques for developing causal models for biological networks. Causal network models include computational representations of the causal relationships between independent variables such as a compound of interest and dependent variables such as measured DNA alterations, changes in mRNA, protein, and metabolites to phenotypic readouts of efficacy and toxicity.

  19. Analyzing Log Files using Data-Mining

    Directory of Open Access Journals (Sweden)

    Marius Mihut

    2008-01-01

    Full Text Available Information systems (i.e. servers, applications and communication devices create a large amount of monitoring data that are saved as log files. For analyzing them, a data-mining approach is helpful. This article presents the steps which are necessary for creating an ‘analyzing instrument’, based on an open source software called Waikato Environment for Knowledge Analysis (Weka [1]. For exemplification, a system log file created by a Windows-based operating system, is used as input file.

  20. A Novel Architecture For Multichannel Analyzer

    International Nuclear Information System (INIS)

    Marcus, E.; Elhanani, I.; Nir, J.; Ellenbogen, M.; Kadmon, Y.; Tirosh, D.

    1999-01-01

    A novel digital approach to real-time, high-throughput, low-cost Multichannel Analyzer (MCA) for radiation spectroscopy is being presented. The MCA input is a shaped nuclear pulse sampled at a high rate, using an Analog-to-Digital Converter (ADC) chip. The digital samples are analyzed by a state-of-the-art Field Programmable Gate Away (FPGA). A customized algorithm is utilized to estimate the peak of the pulse, to reject pile-up and to eliminate processing dead time. The valid pulses estimated peaks are transferred to a micro controller system that creates the histogram and controls the Human Machine Interface (HMI)

  1. Advances on CT analyzing urolithiasis constituents

    International Nuclear Information System (INIS)

    Feng Qiang; Ma Zhijun

    2009-01-01

    Urolithiasis is common and frequently-occurring diseases of urology. The treatment of lithiasis is not only relevant with the size, location, brittle and infection of calculi, but also affected by urolithiasis constituents. Knowing the urolithiasis constituents in advance is no doubt to guide treatment. But so far an reliable inspection method was not found to analyze accurately urolithiasis constituents in vivo. CT judge precisely the size, location of calculi and analyze roughly the urolithiasis constituents in vivo, especially the appear of dual soure CT, which provide a new method for studying urolithiasis constituents. It may be helpful to find the cause, prevention and therapy of calculi. (authors)

  2. Empirical mode decomposition for analyzing acoustical signals

    Science.gov (United States)

    Huang, Norden E. (Inventor)

    2005-01-01

    The present invention discloses a computer implemented signal analysis method through the Hilbert-Huang Transformation (HHT) for analyzing acoustical signals, which are assumed to be nonlinear and nonstationary. The Empirical Decomposition Method (EMD) and the Hilbert Spectral Analysis (HSA) are used to obtain the HHT. Essentially, the acoustical signal will be decomposed into the Intrinsic Mode Function Components (IMFs). Once the invention decomposes the acoustic signal into its constituting components, all operations such as analyzing, identifying, and removing unwanted signals can be performed on these components. Upon transforming the IMFs into Hilbert spectrum, the acoustical signal may be compared with other acoustical signals.

  3. Electrical aerosol analyzer: calibration and performance

    Energy Technology Data Exchange (ETDEWEB)

    Pui, D.Y.H.; Liu, B.Y.H.

    1976-01-01

    The Electrical Aerosol Analyzer (EAA) was calibrated by means of monodisperse aerosols generated by two independent techniques. In the 0.02 to 1 ..mu..m diameter range, the aerosol was generated by electrostatic classification. In the range between 0.007 and 0.03 ..mu..m, the aerosols were generated by the photo-oxidation of SO/sub 2/ in a smog chamber. Calibration data are presented showing the performance of the EAA as an aerosol detector and as a size distribution analyzer.

  4. BWR plant analyzer development at BNL

    International Nuclear Information System (INIS)

    Cheng, H.S.; Wulff, W.; Mallen, A.N.; Lekach, S.V.; Stritar, A.; Cerbone, R.J.

    1985-01-01

    Advanced technology for high-speed interactive nuclear power plant simulations is of great value for timely resolution of safety issues, for plant monitoring, and for computer-aided emergency responses to an accident. Presented is the methodology employed at BNL to develop a BWR plant analyzer capable of simulating severe plant transients at much faster than real-time process speeds. Five modeling principles are established and a criterion is given for selecting numerical procedures and efficient computers to achieve the very high simulation speeds. Typical results are shown to demonstrate the modeling fidelity of the BWR plant analyzer

  5. High throughput assays for analyzing transcription factors.

    Science.gov (United States)

    Li, Xianqiang; Jiang, Xin; Yaoi, Takuro

    2006-06-01

    Transcription factors are a group of proteins that modulate the expression of genes involved in many biological processes, such as cell growth and differentiation. Alterations in transcription factor function are associated with many human diseases, and therefore these proteins are attractive potential drug targets. A key issue in the development of such therapeutics is the generation of effective tools that can be used for high throughput discovery of the critical transcription factors involved in human diseases, and the measurement of their activities in a variety of disease or compound-treated samples. Here, a number of innovative arrays and 96-well format assays for profiling and measuring the activities of transcription factors will be discussed.

  6. Bacterial co-expression of human Tau protein with protein kinase A and 14-3-3 for studies of 14-3-3/phospho-Tau interaction.

    Directory of Open Access Journals (Sweden)

    Kristina V Tugaeva

    Full Text Available Abundant regulatory 14-3-3 proteins have an extremely wide interactome and coordinate multiple cellular events via interaction with specifically phosphorylated partner proteins. Notwithstanding the key role of 14-3-3/phosphotarget interactions in many physiological and pathological processes, they are dramatically underexplored. Here, we focused on the 14-3-3 interaction with human Tau protein associated with the development of several neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Among many known phosphorylation sites within Tau, protein kinase A (PKA phosphorylates several key residues of Tau and induces its tight interaction with 14-3-3 proteins. However, the stoichiometry and mechanism of 14-3-3 interaction with phosphorylated Tau (pTau are not clearly elucidated. In this work, we describe a simple bacterial co-expression system aimed to facilitate biochemical and structural studies on the 14-3-3/pTau interaction. We show that dual co-expression of human fetal Tau with PKA in Escherichia coli results in multisite Tau phosphorylation including also naturally occurring sites which were not previously considered in the context of 14-3-3 binding. Tau protein co-expressed with PKA displays tight functional interaction with 14-3-3 isoforms of a different type. Upon triple co-expression with 14-3-3 and PKA, Tau protein could be co-purified with 14-3-3 and demonstrates complex which is similar to that formed in vitro between individual 14-3-3 and pTau obtained from dual co-expression. Although used in this study for the specific case of the previously known 14-3-3/pTau interaction, our co-expression system may be useful to study of other selected 14-3-3/phosphotarget interactions and for validations of 14-3-3 complexes identified by other methods.

  7. FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation.

    Science.gov (United States)

    Popow, Johannes; Alleaume, Anne-Marie; Curk, Tomaz; Schwarzl, Thomas; Sauer, Sven; Hentze, Matthias W

    2015-11-01

    Mitochondrial RNA processing is an essential step for the synthesis of the components of the electron transport chain in all eukaryotic organisms, yet several aspects of mitochondrial RNA biogenesis and regulation are not sufficiently understood. RNA interactome capture identified several disease-relevant RNA-binding proteins (RBPs) with noncanonical RNA-binding architectures, including all six members of the FASTK (FAS-activated serine/threonine kinase) family of proteins. A mutation within one of these newly assigned FASTK RBPs, FASTKD2, causes a rare form of Mendelian mitochondrial encephalomyopathy. To investigate whether RNA binding of FASTKD2 contributes to the disease phenotype, we identified the RNA targets of FASTKD2 by iCLIP. FASTKD2 interacts with a defined set of mitochondrial transcripts including 16S ribosomal RNA (RNR2) and NADH dehydrogenase subunit 6 (ND6) messenger RNA. CRISPR-mediated deletion of FASTKD2 leads to aberrant processing and expression of RNR2 and ND6 mRNA that encodes a subunit of the respiratory complex I. Metabolic phenotyping of FASTKD2-deficient cells reveals impaired cellular respiration with reduced activities of all respiratory complexes. This work identifies key aspects of the molecular network of a previously uncharacterized, disease-relevant RNA-binding protein, FASTKD2, by a combination of genomic, molecular, and metabolic analyses. © 2015 Popow et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. The pepATTRACT web server for blind, large-scale peptide-protein docking.

    Science.gov (United States)

    de Vries, Sjoerd J; Rey, Julien; Schindler, Christina E M; Zacharias, Martin; Tuffery, Pierre

    2017-07-03

    Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets. Its performance is similar or better than state-of-the-art local docking protocols that do require binding site information. Here we present a novel web server that carries out the rigid-body stage of pepATTRACT. On the peptiDB benchmark, the web server generates a correct model in the top 50 in 34% of the cases. Compared to the full pepATTRACT protocol, this leads to some loss of performance, but the computation time is reduced from ∼18 h to ∼10 min. Combined with the fact that it is fully blind, this makes the web server well-suited for large-scale in silico protein-peptide docking experiments. The rigid-body pepATTRACT server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Environmental applications of the centrifugal fast analyzer

    International Nuclear Information System (INIS)

    Goldstein, G.; Strain, J.E.; Bowling, J.L.

    1975-12-01

    The centrifugal fast analyzer (GeMSAEC Fast Analyzer) was applied to the analysis of pollutants in air and water. Since data acquisition and processing are computer controlled, considerable effort went into devising appropriate software. A modified version of the standard FOCAL interpreter was developed which includes special machine language functions for data timing, acquisition, and storage, and also permits chaining together of programs stored on a disk. Programs were written and experimental procedures developed to implement spectrophotometric, turbidimetric, kinetic (including initial-rate, fixed-time, and variable-time techniques), and chemiluminescence methods of analysis. Analytical methods were developed for the following elements and compounds: SO 2 , O 3 , Ca, Cr, Cu, Fe, Mg, Se(IV), Zn, Cl - , I - , NO 2 - , PO 4 -3 , S -2 , and SO 4 -2 . In many cases, standard methods could be adapted to the centrifugal analyzer, in others new methods were employed. In general, analyses performed with the centrifugal fast analyzer were faster, more precise, and more accurate than with conventional instrumentation

  10. Fluidization quality analyzer for fluidized beds

    Science.gov (United States)

    Daw, C.S.; Hawk, J.A.

    1995-07-25

    A control loop and fluidization quality analyzer for a fluidized bed utilizes time varying pressure drop measurements. A fast-response pressure transducer measures the overall bed pressure drop, or over some segment of the bed, and the pressure drop signal is processed to produce an output voltage which changes with the degree of fluidization turbulence. 9 figs.

  11. How to Analyze Company Using Social Network?

    Science.gov (United States)

    Palus, Sebastian; Bródka, Piotr; Kazienko, Przemysław

    Every single company or institution wants to utilize its resources in the most efficient way. In order to do so they have to be have good structure. The new way to analyze company structure by utilizing existing within company natural social network and example of its usage on Enron company are presented in this paper.

  12. Analyzing Vessel Behavior Using Process Mining

    NARCIS (Netherlands)

    Maggi, F.M.; Mooij, A.J.; Aalst, W.M.P. van der

    2013-01-01

    In the maritime domain, electronic sensors such as AIS receivers and radars collect large amounts of data about the vessels in a certain geographical area. We investigate the use of process mining techniques for analyzing the behavior of the vessels based on these data. In the context of maritime

  13. Images & Issues: How to Analyze Election Rhetoric.

    Science.gov (United States)

    Rank, Hugh

    Although it is impossible to know in advance the credibility of political messages, such persuasive discourse can be analyzed in a non-partisan, common sense way using predictable patterns in content and form. The content of a candidate's message can be summarized as "I am competent and trustworthy; from me, you'll get 'more good' and 'less…

  14. Thermal and Evolved-Gas Analyzer Illustration

    Science.gov (United States)

    2008-01-01

    This is a computer-aided drawing of the Thermal and Evolved-Gas Analyzer, or TEGA, on NASA's Phoenix Mars Lander. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  15. Statistical network analysis for analyzing policy networks

    DEFF Research Database (Denmark)

    Robins, Garry; Lewis, Jenny; Wang, Peng

    2012-01-01

    and policy network methodology is the development of statistical modeling approaches that can accommodate such dependent data. In this article, we review three network statistical methods commonly used in the current literature: quadratic assignment procedures, exponential random graph models (ERGMs...... has much to offer in analyzing the policy process....

  16. Consideration Regarding Diagnosis Analyze of Corporate Management

    Directory of Open Access Journals (Sweden)

    Mihaela Ciopi OPREA

    2009-01-01

    Full Text Available Diagnosis management aims to identify critical situations and positive aspectsof corporate management. An effective diagnosis made by a team with thestatus of independence from the organization’s management is for managers auseful feedback necessary to improve performance. The work presented focuseson the methodology to achieve effective diagnosis, considering multitudecriteria and variables to be analyzed.

  17. Analyzing and Interpreting Research in Health Education ...

    African Journals Online (AJOL)

    While qualitative research is used when little or nothing is known about the subject, quantitative research is required when there are quantifiable variables to be measured. By implication, health education research is based on phenomenological, ethnographical and/or grounded theoretical approaches that are analyzable ...

  18. Analyzing Languages for Specific Purposes Discourse

    Science.gov (United States)

    Bowles, Hugo

    2012-01-01

    In the last 20 years, technological advancement and increased multidisciplinarity has expanded the range of data regarded as within the scope of languages for specific purposes (LSP) research and the means by which they can be analyzed. As a result, the analytical work of LSP researchers has developed from a narrow focus on specialist terminology…

  19. Automatic radioxenon analyzer for CTBT monitoring

    International Nuclear Information System (INIS)

    Bowyer, T.W.; Abel, K.H.; Hensley, W.K.

    1996-12-01

    Over the past 3 years, with support from US DOE's NN-20 Comprehensive Test Ban Treaty (CTBT) R ampersand D program, PNNL has developed and demonstrated a fully automatic analyzer for collecting and measuring the four Xe radionuclides, 131m Xe(11.9 d), 133m Xe(2.19 d), 133 Xe (5.24 d), and 135 Xe(9.10 h), in the atmosphere. These radionuclides are important signatures in monitoring for compliance to a CTBT. Activity ratios permit discriminating radioxenon from nuclear detonation and that from nuclear reactor operations, nuclear fuel reprocessing, or medical isotope production and usage. In the analyzer, Xe is continuously and automatically separated from the atmosphere at flow rates of about 7 m 3 /h on sorption bed. Aliquots collected for 6-12 h are automatically analyzed by electron-photon coincidence spectrometry to produce sensitivities in the range of 20-100 μBq/m 3 of air, about 100-fold better than with reported laboratory-based procedures for short time collection intervals. Spectral data are automatically analyzed and the calculated radioxenon concentrations and raw gamma- ray spectra automatically transmitted to data centers

  20. Performance optimization of spectroscopic process analyzers

    NARCIS (Netherlands)

    Boelens, Hans F. M.; Kok, Wim Th; de Noord, Onno E.; Smilde, Age K.

    2004-01-01

    To increase the power and the robustness of spectroscopic process analyzers, methods are needed that suppress the spectral variation that is not related to the property of interest in the process stream. An approach for the selection of a suitable method is presented. The approach uses the net

  1. Identification of Novel Proteins Co-Purifying with Cockayne Syndrome Group B (CSB Reveals Potential Roles for CSB in RNA Metabolism and Chromatin Dynamics.

    Directory of Open Access Journals (Sweden)

    Serena Nicolai

    Full Text Available The CSB protein, a member of the SWI/SNF ATP dependent chromatin remodeling family of proteins, plays a role in a sub-pathway of nucleotide excision repair (NER known as transcription coupled repair (TCR. CSB is frequently mutated in Cockayne syndrome group B, a segmental progeroid human autosomal recessive disease characterized by growth failure and degeneration of multiple organs. Though initially classified as a DNA repair protein, recent studies have demonstrated that the loss of CSB results in pleiotropic effects. Identification of novel proteins belonging to the CSB interactome may be useful not only for predicting the molecular basis for diverse pathological symptoms of CS-B patients but also for unraveling the functions of CSB in addition to its authentic role in DNA repair. In this study, we performed tandem affinity purification (TAP technology coupled with mass spectrometry and co-immunoprecipitation studies to identify and characterize the proteins that potentially interact with CSB-TAP. Our approach revealed 33 proteins that were not previously known to interact with CSB. These newly identified proteins indicate potential roles for CSB in RNA metabolism involving repression and activation of transcription process and in the maintenance of chromatin dynamics and integrity.

  2. ITK and ANALYZE: a synergistic integration

    Science.gov (United States)

    Augustine, Kurt E.; Holmes, David R., III; Robb, Richard A.

    2004-05-01

    The Insight Toolkit (ITK) is a C++ open-source software toolkit developed under sponsorship of the National Library of Medicine. It provides advanced algorithms for performing image registration and segmentation, but does not provide support for visualization and analysis, nor does it offer any graphical user interface (GUI). The purpose of this integration project is to make ITK readily accessible to end-users with little or no programming skills, and provide interactive processing, visualization and measurement capabilities. This is achieved through the integration of ITK with ANALYZE, a multi-dimension image visualization/analysis application installed in over 300 institutions around the world, with a user-base in excess of 4000. This integration is carried out at both the software foundation and GUI levels. The foundation technology upon which ANALYZE is built is a comprehensive C-function library called AVW. A new set of AVW-ITK functions have been developed and integrated into the AVW library, and four new ITK modules have been added to the ANALYZE interface. Since ITK is a software developer"s toolkit, the only way to access its intrinsic power is to write programs that incorporate it. Integrating ITK with ANALYZE opens the ITK algorithms to end-users who otherwise might never be able to take advantage of the toolkit"s advanced functionality. In addition, this integration provides end-to-end interactive problem solving capabilities which allow all users, including programmers, an integrated system to readily display and quantitatively evaluate the results from the segmentation and registration routines in ITK, regardless of the type or format of input images, which are comprehensively supported in ANALYZE.

  3. Identification of New Protein Interactions between Dengue Fever Virus and Its Hosts, Human and Mosquito

    Science.gov (United States)

    Mairiang, Dumrong; Zhang, Huamei; Sodja, Ann; Murali, Thilakam; Suriyaphol, Prapat; Malasit, Prida; Limjindaporn, Thawornchai; Finley, Russell L.

    2013-01-01

    The four divergent serotypes of dengue virus are the causative agents of dengue fever, dengue hemorrhagic fever and dengue shock syndrome. About two-fifths of the world's population live in areas where dengue is prevalent, and thousands of deaths are caused by the viruses every year. Dengue virus is transmitted from one person to another primarily by the yellow fever mosquito, Aedes aegypti. Recent studies have begun to define how the dengue viral proteins interact with host proteins to mediate viral replication and pathogenesis. A combined analysis of these studies, however, suggests that many virus-host protein interactions remain to be identified, especially for the mosquito host. In this study, we used high-throughput yeast two-hybrid screening to identify mosquito and human proteins that physically interact with dengue proteins. We tested each identified host protein against the proteins from all four serotypes of dengue to identify interactions that are conserved across serotypes. We further confirmed many of the interactions using co-affinity purification assays. As in other large-scale screens, we identified some previously detected interactions and many new ones, moving us closer to a complete host – dengue protein interactome. To help summarize and prioritize the data for further study, we combined our interactions with other published data and identified a subset of the host-dengue interactions that are now supported by multiple forms of evidence. These data should be useful for understanding the interplay between dengue and its hosts and may provide candidates for drug targets and vector control strategies. PMID:23326450

  4. Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data.

    Science.gov (United States)

    You, Zhu-Hong; Lei, Ying-Ke; Gui, Jie; Huang, De-Shuang; Zhou, Xiaobo

    2010-11-01

    High-throughput protein interaction data, with ever-increasing volume, are becoming the foundation of many biological discoveries, and thus high-quality protein-protein interaction (PPI) maps are critical for a deeper understanding of cellular processes. However, the unreliability and paucity of current available PPI data are key obstacles to the subsequent quantitative studies. It is therefore highly desirable to develop an approach to deal with these issues from the computational perspective. Most previous works for assessing and predicting protein interactions either need supporting evidences from multiple information resources or are severely impacted by the sparseness of PPI networks. We developed a robust manifold embedding technique for assessing the reliability of interactions and predicting new interactions, which purely utilizes the topological information of PPI networks and can work on a sparse input protein interactome without requiring additional information types. After transforming a given PPI network into a low-dimensional metric space using manifold embedding based on isometric feature mapping (ISOMAP), the problem of assessing and predicting protein interactions is recasted into the form of measuring similarity between points of its metric space. Then a reliability index, a likelihood indicating the interaction of two proteins, is assigned to each protein pair in the PPI networks based on the similarity between the points in the embedded space. Validation of the proposed method is performed with extensive experiments on densely connected and sparse PPI network of yeast, respectively. Results demonstrate that the interactions ranked top by our method have high-functional homogeneity and localization coherence, especially our method is very efficient for large sparse PPI network with which the traditional algorithms fail. Therefore, the proposed algorithm is a much more promising method to detect both false positive and false negative interactions

  5. Codon Bias Patterns of E. coli's Interacting Proteins.

    Directory of Open Access Journals (Sweden)

    Maddalena Dilucca

    Full Text Available Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, CompAI, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for E.coli, comparing CompAI with other widely used indices: tAI, CAI, and Nc. We show that CompAI and tAI capture similar information by being positively correlated with gene conservation, measured by the Evolutionary Retention Index (ERI, and essentiality, whereas, CAI and Nc appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of tAI and CompAI with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs. We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in E.coli. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by CompAI and tAI. Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, CompAI turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation. Notably, CompAI may potentially correlate with translation speed measurements, by accounting for the specific delay induced by wobble-pairing between codons and anticodons.

  6. Methodology for analyzing risk at nuclear facilities

    International Nuclear Information System (INIS)

    Yoo, Hosik; Lee, Nayoung; Ham, Taekyu; Seo, Janghoon

    2015-01-01

    Highlights: • A new methodology for evaluating the risk at nuclear facilities was developed. • Five measures reflecting all factors that should be concerned to assess risk were developed. • The attributes on NMAC and nuclear security culture are included as attributes for analyzing. • The newly developed methodology can be used to evaluate risk of both existing facility and future nuclear system. - Abstract: A methodology for evaluating risks at nuclear facilities is developed in this work. A series of measures is drawn from the analysis of factors that determine risks. Five measures are created to evaluate risks at nuclear facilities. These include the legal and institutional framework, material control, physical protection system effectiveness, human resources, and consequences. Evaluation attributes are developed for each measure and specific values are given in order to calculate the risk value quantitatively. Questionnaires are drawn up on whether or not a state has properly established a legal and regulatory framework (based on international standards). These questionnaires can be a useful measure for comparing the status of the physical protection regime between two countries. Analyzing an insider threat is not an easy task and no methodology has been developed for this purpose. In this study, attributes that could quantitatively evaluate an insider threat, in the case of an unauthorized removal of nuclear materials, are developed by adopting the Nuclear Material Accounting & Control (NMAC) system. The effectiveness of a physical protection system, P(E), could be analyzed by calculating the probability of interruption, P(I), and the probability of neutralization, P(N). In this study, the Tool for Evaluating Security System (TESS) code developed by KINAC is used to calculate P(I) and P(N). Consequence is an important measure used to analyze risks at nuclear facilities. This measure comprises radiological, economic, and social damage. Social and

  7. Comparison of chemistry analytes between 2 portable, commercially available analyzers and a conventional laboratory analyzer in reptiles.

    Science.gov (United States)

    McCain, Stephanie L; Flatland, Bente; Schumacher, Juergen P; Clarke Iii, Elsburgh O; Fry, Michael M

    2010-12-01

    Advantages of handheld and small bench-top biochemical analyzers include requirements for smaller sample volume and practicality for use in the field or in practices, but little has been published on the performance of these instruments compared with standard reference methods in analysis of reptilian blood. The aim of this study was to compare reptilian blood biochemical values obtained using the Abaxis VetScan Classic bench-top analyzer and a Heska i-STAT handheld analyzer with values obtained using a Roche Hitachi 911 chemical analyzer. Reptiles, including 14 bearded dragons (Pogona vitticeps), 4 blue-tongued skinks (Tiliqua gigas), 8 Burmese star tortoises (Geochelone platynota), 10 Indian star tortoises (Geochelone elegans), 5 red-tailed boas (Boa constrictor), and 5 Northern pine snakes (Pituophis melanoleucus melanoleucus), were manually restrained, and a single blood sample was obtained and divided for analysis. Results for concentrations of albumin, bile acids, calcium, glucose, phosphates, potassium, sodium, total protein, and uric acid and activities of aspartate aminotransferase and creatine kinase obtained from the VetScan Classic and Hitachi 911 were compared. Results for concentrations of chloride, glucose, potassium, and sodium obtained from the i-STAT and Hitachi 911 were compared. Compared with results from the Hitachi 911, those from the VetScan Classic and i-STAT had variable correlations, and constant or proportional bias was found for many analytes. Bile acid data could not be evaluated because results for 44 of 45 samples fell below the lower linearity limit of the VetScan Classic. Although the 2 portable instruments might provide measurements with clinical utility, there were significant differences compared with the reference analyzer, and development of analyzer-specific reference intervals is recommended. ©2010 American Society for Veterinary Clinical Pathology.

  8. Modeling extreme ultraviolet suppression of electrostatic analyzers

    International Nuclear Information System (INIS)

    Gershman, Daniel J.; Zurbuchen, Thomas H.

    2010-01-01

    In addition to analyzing energy-per-charge ratios of incident ions, electrostatic analyzers (ESAs) for spaceborne time-of-flight mass spectrometers must also protect detectors from extreme ultraviolet (EUV) photons from the Sun. The required suppression rate often exceeds 1:10 7 and is generally established in tests upon instrument design and integration. This paper describes a novel technique to model the EUV suppression of ESAs using photon ray tracing integrated into SIMION, the most commonly used ion optics design software for such instruments. The paper compares simulation results with measurements taken from the ESA of the Mass instrument flying onboard the Wind spacecraft. This novel technique enables an active inclusion of EUV suppression requirements in the ESA design process. Furthermore, the simulation results also motivate design rules for such instruments.

  9. Real-time airborne particle analyzer

    Science.gov (United States)

    Reilly, Peter T.A.

    2012-10-16

    An aerosol particle analyzer includes a laser ablation chamber, a gas-filled conduit, and a mass spectrometer. The laser ablation chamber can be operated at a low pressure, which can be from 0.1 mTorr to 30 mTorr. The ablated ions are transferred into a gas-filled conduit. The gas-filled conduit reduces the electrical charge and the speed of ablated ions as they collide and mix with buffer gases in the gas-filled conduit. Preferably, the gas filled-conduit includes an electromagnetic multipole structure that collimates the nascent ions into a beam, which is guided into the mass spectrometer. Because the gas-filled conduit allows storage of vast quantities of the ions from the ablated particles, the ions from a single ablated particle can be analyzed multiple times and by a variety of techniques to supply statistically meaningful analysis of composition and isotope ratios.

  10. Analyzing Technique of Power Systems Under Deregulation

    Science.gov (United States)

    Miyauchi, Hajime; Kita, Hiroyuki; Ishigame, Atsushi

    Deregulation of the electric utilities has been progressing. Even under the deregulation, the reliability should be the most important problem of power systems. However, according to the deregulation, operation and scheduling of power systems are changing and new techniques to analyze power systems are introducing. To evaluate reliability of power systems, adequacy and security are well employed recently. This paper presents the new analyzing technique which will be realized in near future from the viewpoint of adequacy and security. First, simulation tool to evaluate adequacy is described. As an example of this tool, MARS and other methods are mentioned. Next, to evaluate the security, security constrained unit commitment (SCUC) and security constrained optimal power flow (SCOPF) are mentioned. Finally, some topics concerning ancillary service are described.

  11. Development of a nuclear plant analyzer (NPA)

    International Nuclear Information System (INIS)

    De Vlaminck, M.; Mampaey, L.; Vanhoenacker, L.; Bastenaire, F.

    1990-01-01

    A Nuclear Plant Analyzer has been developed by TRACTABEL. Three distinct functional units make up the Nuclear Plant Analyser, a model builder, a run time unit and an analysis unit. The model builder is intended to build simulation models which describe on the one hand the geometric structure and initial conditions of a given plant and on the other hand command control logics and reactor protection systems. The run time unit carries out dialog between the user and the thermal-hydraulic code. The analysis unit is aimed at deep analyzing of the transient results. The model builder is being tested in the framework of the International Standard Problem ISP-26, which is the simulation of a LOCA on the Japanese ROSA facility

  12. Computer-based radionuclide analyzer system

    International Nuclear Information System (INIS)

    Ohba, Kengo; Ishizuka, Akira; Kobayashi, Akira; Ohhashi, Hideaki; Tsuruoka, Kimitoshi.

    1978-01-01

    The radionuclide analysis in nuclear power plants, practiced for the purpose of monitoring the quality of the primary loop water, the confirmation of the performance of reactor cleanup system and monitoring the radioactive waste effluent, is an important job. Important as it is, it requires considerable labor of experts, because the samples to be analyzed are multifarious and very large in number, and in addition, this job depends much on manual work. With a view of saving the labor, simplifying and standardizing the work, reducing radiation exposure, and automatizing the work of analysis, the computerized analyzer system has been worked out. The results of its performance test at the operating power plant have proved that the development has fairly accomplished the objects and that the system is well useful. The developmental work was carried out by the cooperation between The Tokyo Electric Power Co. and Toshiba in about 4 years from 1974 to this year. (auth.)

  13. Analyzing the Existing Undergraduate Engineering Leadership Skills

    OpenAIRE

    Hamed M. Almalki; Luis Rabelo; Charles Davis; Hammad Usmani; Debra Hollister; Alfonso Sarmiento

    2016-01-01

    Purpose: Studying and analyzing the undergraduate engineering students' leadership skills to discover their potential leadership strengths and weaknesses. This study will unveil potential ways to enhance the ways we teach engineering leadership. The research has great insights that might assist engineering programs to improve curricula for the purpose of better engineering preparation to meet industry's demands. Methodology and Findings: 441 undergraduate engineering students have been s...

  14. Analyzing negative ties in social networks

    Directory of Open Access Journals (Sweden)

    Mankirat Kaur

    2016-03-01

    Full Text Available Online social networks are a source of sharing information and maintaining personal contacts with other people through social interactions and thus forming virtual communities online. Social networks are crowded with positive and negative relations. Positive relations are formed by support, endorsement and friendship and thus, create a network of well-connected users whereas negative relations are a result of opposition, distrust and avoidance creating disconnected networks. Due to increase in illegal activities such as masquerading, conspiring and creating fake profiles on online social networks, exploring and analyzing these negative activities becomes the need of hour. Usually negative ties are treated in same way as positive ties in many theories such as balance theory and blockmodeling analysis. But the standard concepts of social network analysis do not yield same results in respect of each tie. This paper presents a survey on analyzing negative ties in social networks through various types of network analysis techniques that are used for examining ties such as status, centrality and power measures. Due to the difference in characteristics of flow in positive and negative tie networks some of these measures are not applicable on negative ties. This paper also discusses new methods that have been developed specifically for analyzing negative ties such as negative degree, and h∗ measure along with the measures based on mixture of positive and negative ties. The different types of social network analysis approaches have been reviewed and compared to determine the best approach that can appropriately identify the negative ties in online networks. It has been analyzed that only few measures such as Degree and PN centrality are applicable for identifying outsiders in network. For applicability in online networks, the performance of PN measure needs to be verified and further, new measures should be developed based upon negative clique concept.

  15. Analyzing Architecture of Mithraism Rock Temples

    OpenAIRE

    Zohre AliJabbari

    2017-01-01

    This analyzes the architecture of rock temples of West and Northwest of Iran, as well as factors influencing their formation. The creation of rock architecture in this area of Iran is influenced by the religious, geographical and political atmosphere of their time. Most of these structures are formed by dominated empires in the first millennium BC. And in some works we are observing their continuity in later periods and change in their functions. One of the reasons that have attracted man to ...

  16. General methods for analyzing bounded proportion data

    OpenAIRE

    Hossain, Abu

    2017-01-01

    This thesis introduces two general classes of models for analyzing proportion response variable when the response variable Y can take values between zero and one, inclusive of zero and/or one. The models are inflated GAMLSS model and generalized Tobit GAMLSS model. The inflated GAMLSS model extends the flexibility of beta inflated models by allowing the distribution on (0,1) of the continuous component of the dependent variable to come from any explicit or transformed (i.e. logit or truncated...

  17. Development of a Portable Water Quality Analyzer

    OpenAIRE

    Germán COMINA; Martin NISSFOLK; José Luís SOLÍS

    2010-01-01

    A portable water analyzer based on a voltammetric electronic tongue has been developed. The system uses an electrochemical cell with two working electrodes as sensors, a computer controlled potentiostat, and software based on multivariate data analysis for pattern recognition. The system is suitable to differentiate laboratory made and real in-situ river water samples contaminated with different amounts of Escherichia coli. This bacteria is not only one of the main indicators for water qualit...

  18. Moving Block Bootstrap for Analyzing Longitudinal Data.

    Science.gov (United States)

    Ju, Hyunsu

    In a longitudinal study subjects are followed over time. I focus on a case where the number of replications over time is large relative to the number of subjects in the study. I investigate the use of moving block bootstrap methods for analyzing such data. Asymptotic properties of the bootstrap methods in this setting are derived. The effectiveness of these resampling methods is also demonstrated through a simulation study.

  19. A chemical analyzer for charged ultrafine particles

    OpenAIRE

    S. G. Gonser; A. Held

    2013-01-01

    New particle formation is a frequent phenomenon in the atmosphere and of major significance for the earth's climate and human health. To date the mechanisms leading to the nucleation of particles as well as to aerosol growth are not completely understood. A lack of appropriate measurement equipment for online analysis of the chemical composition of freshly nucleated particles is one major limitation. We have developed a Chemical Analyzer for Charged Ultrafine Particles (CAChUP) capable...

  20. A chemical analyzer for charged ultrafine particles

    OpenAIRE

    S. G. Gonser; A. Held

    2013-01-01

    New particle formation is a frequent phenomenon in the atmosphere and of major significance for the Earth's climate and human health. To date the mechanisms leading to the nucleation of particles as well as to aerosol growth are not completely understood. A lack of appropriate measurement equipment for online analysis of the chemical composition of freshly nucleated particles is one major limitation. We have developed a Chemical Analyzer for Charged Ultrafine Particles (CAChUP) capable of ana...

  1. A seal analyzer for testing container integrity

    International Nuclear Information System (INIS)

    McDaniel, P.; Jenkins, C.

    1988-01-01

    This paper reports on the development of laboratory and production seal analyzer that offers a rapid, nondestructive method of assuring the seal integrity of virtually any type of single or double sealed container. The system can test a broad range of metal cans, drums and trays, membrane-lidded vessels, flexible pouches, aerosol containers, and glass or metal containers with twist-top lids that are used in the chemical/pesticide (hazardous materials/waste), beverage, food, medical and pharmaceutical industries

  2. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  3. Neutral Particle Analyzer Diagnostic on NSTX

    Energy Technology Data Exchange (ETDEWEB)

    S.S. Medley; A.L. Roquemore

    2004-03-16

    The Neutral Particle Analyzer (NPA) diagnostic on the National Spherical Torus Experiment (NSTX) utilizes a PPPL-designed E||B spectrometer that measures the energy spectra of minority hydrogen and bulk deuterium species simultaneously with 39 energy channels per mass specie and a time resolution of 1 ms. The calibrated energy range is E = 0.5-150 keV and the energy resolution varies from AE/E = 3-7% over the surface of the microchannel plate detector.

  4. Neutral Particle Analyzer Diagnostic on NSTX

    International Nuclear Information System (INIS)

    Medley, S.S.; Roquemore, A.L.

    2004-01-01

    The Neutral Particle Analyzer (NPA) diagnostic on the National Spherical Torus Experiment (NSTX) utilizes a PPPL-designed E||B spectrometer that measures the energy spectra of minority hydrogen and bulk deuterium species simultaneously with 39 energy channels per mass specie and a time resolution of 1 ms. The calibrated energy range is E = 0.5-150 keV and the energy resolution varies from AE/E = 3-7% over the surface of the microchannel plate detector

  5. A Raman-Based Portable Fuel Analyzer

    Science.gov (United States)

    Farquharson, Stuart

    2010-08-01

    Fuel is the single most import supply during war. Consider that the US Military is employing over 25,000 vehicles in Iraq and Afghanistan. Most fuel is obtained locally, and must be characterized to ensure proper operation of these vehicles. Fuel properties are currently determined using a deployed chemical laboratory. Unfortunately, each sample requires in excess of 6 hours to characterize. To overcome this limitation, we have developed a portable fuel analyzer capable of determine 7 fuel properties that allow determining fuel usage. The analyzer uses Raman spectroscopy to measure the fuel samples without preparation in 2 minutes. The challenge, however, is that as distilled fractions of crude oil, all fuels are composed of hundreds of hydrocarbon components that boil at similar temperatures, and performance properties can not be simply correlated to a single component, and certainly not to specific Raman peaks. To meet this challenge, we measured over 800 diesel and jet fuels from around the world and used chemometrics to correlate the Raman spectra to fuel properties. Critical to the success of this approach is laser excitation at 1064 nm to avoid fluorescence interference (many fuels fluoresce) and a rugged interferometer that provides 0.1 cm-1 wavenumber (x-axis) accuracy to guarantee accurate correlations. Here we describe the portable fuel analyzer, the chemometric models, and the successful determination of these 7 fuel properties for over 100 unknown samples provided by the US Marine Corps, US Navy, and US Army.

  6. Thermo Scientific Sulfur Dioxide Analyzer Instrument Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Springston, S. R. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-03-01

    The Sulfur Dioxide Analyzer measures sulfur dioxide based on absorbance of UV light at one wavelength by SO2 molecules which then decay to a lower energy state by emitting UV light at a longer wavelength. Specifically, SO2 + hυ1 →SO2 *→SO2 + hυ2 The emitted light is proportional to the concentration of SO2 in the optical cell. External communication with the analyzer is available through an Ethernet port configured through the instrument network of the AOS systems. The Model 43i-TLE is part of the i-series of Thermo Scientific instruments. The i-series instruments are designed to interface with external computers through the proprietary Thermo Scientific iPort Software. However, this software is somewhat cumbersome and inflexible. BNL has written an interface program in National Instruments LabView that both controls the Model 43i-TLE Analyzer AND queries the unit for all measurement and housekeeping data. The LabView vi (the software program written by BNL) ingests all raw data from the instrument and outputs raw data files in a uniform data format similar to other instruments in the AOS and described more fully in Section 6.0 below.

  7. Visual analyzer as anticipatory system (functional organization)

    Science.gov (United States)

    Kirvelis, Dobilas

    2000-05-01

    Hypothetical functional organization of the visual analyzer is presented. The interpretation of visual perception, anatomic and morphological structure of visual systems of animals, neuro-physiological, psychological and psycho-physiological data in the light of a number of the theoretical solutions of image recognition and visual processes simulation enable active information processing. The activities in special areas of cortex are as follows: focused attention, prediction with analysis of visual scenes and synthesis, predictive mental images. In the projection zone of visual cortex Area Streata or V1 a "sensory" screen (SS) and "reconstruction" screen (RS) are supposed to exist. The functional structure of visual analyzer consist of: analysis of visual scenes projected onto SS; "tracing" of images; preliminary recognition; reversive image reconstruction onto RS; comparison of images projected onto SS with images reconstructed onto RS; and "correction" of preliminary recognition. Special attention is paid to the quasiholographical principles of the neuronal organization within the brain, of the image "tracing," and of reverse image reconstruction. Tachistoscopic experiments revealed that the duration of one such hypothesis-testing cycle of the human visual analyzers is about 8-10 milliseconds.

  8. IRISpy: Analyzing IRIS Data in Python

    Science.gov (United States)

    Ryan, Daniel; Christe, Steven; Mumford, Stuart; Baruah, Ankit; Timothy, Shelbe; Pereira, Tiago; De Pontieu, Bart

    2017-08-01

    IRISpy is a new community-developed open-source software library for analysing IRIS level 2 data. It is written in Python, a free, cross-platform, general-purpose, high-level programming language. A wide array of scientific computing software packages have already been developed in Python, from numerical computation (NumPy, SciPy, etc.), to visualization and plotting (matplotlib), to solar-physics-specific data analysis (SunPy). IRISpy is currently under development as a SunPy-affiliated package which means it depends on the SunPy library, follows similar standards and conventions, and is developed with the support of of the SunPy development team. IRISpy’s has two primary data objects, one for analyzing slit-jaw imager data and another for analyzing spectrograph data. Both objects contain basic slicing, indexing, plotting, and animating functionality to allow users to easily inspect, reduce and analyze the data. As part of this functionality the objects can output SunPy Maps, TimeSeries, Spectra, etc. of relevant data slices for easier inspection and analysis. Work is also ongoing to provide additional data analysis functionality including derivation of systematic measurement errors (e.g. readout noise), exposure time correction, residual wavelength calibration, radiometric calibration, and fine scale pointing corrections. IRISpy’s code base is publicly available through github.com and can be contributed to by anyone. In this poster we demonstrate IRISpy’s functionality and future goals of the project. We also encourage interested users to become involved in further developing IRISpy.

  9. Air sampling unit for breath analyzers

    Science.gov (United States)

    Szabra, Dariusz; Prokopiuk, Artur; Mikołajczyk, Janusz; Ligor, Tomasz; Buszewski, Bogusław; Bielecki, Zbigniew

    2017-11-01

    The paper presents a portable breath sampling unit (BSU) for human breath analyzers. The developed unit can be used to probe air from the upper airway and alveolar for clinical and science studies. The BSU is able to operate as a patient interface device for most types of breath analyzers. Its main task is to separate and to collect the selected phases of the exhaled air. To monitor the so-called I, II, or III phase and to identify the airflow from the upper and lower parts of the human respiratory system, the unit performs measurements of the exhaled CO2 (ECO2) in the concentration range of 0%-20% (0-150 mm Hg). It can work in both on-line and off-line modes according to American Thoracic Society/European Respiratory Society standards. A Tedlar bag with a volume of 5 dm3 is mounted as a BSU sample container. This volume allows us to collect ca. 1-25 selected breath phases. At the user panel, each step of the unit operation is visualized by LED indicators. This helps us to regulate the natural breathing cycle of the patient. There is also an operator's panel to ensure monitoring and configuration setup of the unit parameters. The operation of the breath sampling unit was preliminarily verified using the gas chromatography/mass spectrometry (GC/MS) laboratory setup. At this setup, volatile organic compounds were extracted by solid phase microextraction. The tests were performed by the comparison of GC/MS signals from both exhaled nitric oxide and isoprene analyses for three breath phases. The functionality of the unit was proven because there was an observed increase in the signal level in the case of the III phase (approximately 40%). The described work made it possible to construct a prototype of a very efficient breath sampling unit dedicated to breath sample analyzers.

  10. A chemical analyzer for charged ultrafine particles

    Science.gov (United States)

    Gonser, S. G.; Held, A.

    2013-09-01

    New particle formation is a frequent phenomenon in the atmosphere and of major significance for the Earth's climate and human health. To date the mechanisms leading to the nucleation of particles as well as to aerosol growth are not completely understood. A lack of appropriate measurement equipment for online analysis of the chemical composition of freshly nucleated particles is one major limitation. We have developed a Chemical Analyzer for Charged Ultrafine Particles (CAChUP) capable of analyzing particles with diameters below 30 nm. A bulk of size-separated particles is collected electrostatically on a metal filament, resistively desorbed and subsequently analyzed for its molecular composition in a time of flight mass spectrometer. We report on technical details as well as characterization experiments performed with the CAChUP. Our instrument was tested in the laboratory for its detection performance as well as for its collection and desorption capabilities. The manual application of defined masses of camphene (C10H16) to the desorption filament resulted in a detection limit between 0.5 and 5 ng, and showed a linear response of the mass spectrometer. Flow tube experiments of 25 nm diameter secondary organic aerosol from ozonolysis of alpha-pinene also showed a linear relation between collection time and the mass spectrometer's signal intensity. The resulting mass spectra from the collection experiments are in good agreement with published work on particles generated by the ozonolysis of alpha-pinene. A sensitivity study shows that the current setup of CAChUP is ready for laboratory measurements and for the observation of new particle formation events in the field.

  11. A computer program for analyzing channel geometry

    Science.gov (United States)

    Regan, R.S.; Schaffranek, R.W.

    1985-01-01

    The Channel Geometry Analysis Program (CGAP) provides the capability to process, analyze, and format cross-sectional data for input to flow/transport simulation models or other computational programs. CGAP allows for a variety of cross-sectional data input formats through use of variable format specification. The program accepts data from various computer media and provides for modification of machine-stored parameter values. CGAP has been devised to provide a rapid and efficient means of computing and analyzing the physical properties of an open-channel reach defined by a sequence of cross sections. CGAP 's 16 options provide a wide range of methods by which to analyze and depict a channel reach and its individual cross-sectional properties. The primary function of the program is to compute the area, width, wetted perimeter, and hydraulic radius of cross sections at successive increments of water surface elevation (stage) from data that consist of coordinate pairs of cross-channel distances and land surface or channel bottom elevations. Longitudinal rates-of-change of cross-sectional properties are also computed, as are the mean properties of a channel reach. Output products include tabular lists of cross-sectional area, channel width, wetted perimeter, hydraulic radius, average depth, and cross-sectional symmetry computed as functions of stage; plots of cross sections; plots of cross-sectional area and (or) channel width as functions of stage; tabular lists of cross-sectional area and channel width computed as functions of stage for subdivisions of a cross section; plots of cross sections in isometric projection; and plots of cross-sectional area at a fixed stage as a function of longitudinal distance along an open-channel reach. A Command Procedure Language program and Job Control Language procedure exist to facilitate program execution on the U.S. Geological Survey Prime and Amdahl computer systems respectively. (Lantz-PTT)

  12. Remote Laser Diffraction Particle Size Distribution Analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Batcheller, Thomas Aquinas; Huestis, Gary Michael; Bolton, Steven Michael

    2001-03-01

    In support of a radioactive slurry sampling and physical characterization task, an “off-the-shelf” laser diffraction (classical light scattering) particle size analyzer was utilized for remote particle size distribution (PSD) analysis. Spent nuclear fuel was previously reprocessed at the Idaho Nuclear Technology and Engineering Center (INTEC—formerly recognized as the Idaho Chemical Processing Plant) which is on DOE’s INEEL site. The acidic, radioactive aqueous raffinate streams from these processes were transferred to 300,000 gallon stainless steel storage vessels located in the INTEC Tank Farm area. Due to the transfer piping configuration in these vessels, complete removal of the liquid can not be achieved. Consequently, a “heel” slurry remains at the bottom of an “emptied” vessel. Particle size distribution characterization of the settled solids in this remaining heel slurry, as well as suspended solids in the tank liquid, is the goal of this remote PSD analyzer task. A Horiba Instruments Inc. Model LA-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a “hot cell” (gamma radiation) environment. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not previously achievable—making this technology far superior than the traditional methods used. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives.

  13. Analyzing Argumentation In Rich, Natural Contexts

    Directory of Open Access Journals (Sweden)

    Anita Reznitskaya

    2008-02-01

    Full Text Available The paper presents the theoretical and methodological aspects of research on the development of argument- ation in elementary school children. It presents a theoretical framework detailing psychological mechanisms responsible for the acquisition and transfer of argumentative discourse and demonstrates several applications of the framework, described in sufficient detail to guide future empirical investigations of oral, written, individual, or group argumentation performance. Software programs capable of facilitating data analysis are identified and their uses illustrated. The analytic schemes can be used to analyze large amounts of verbal data with reasonable precision and efficiency. The conclusion addresses more generally the challenges for and possibilities of empirical study of the development of argumentation.

  14. Thermo Scientific Ozone Analyzer Instrument Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Springston, S. R. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-03-01

    The primary measurement output from the Thermo Scientific Ozone Analyzer is the concentration of the analyte (O3) reported at 1-s resolution in units of ppbv in ambient air. Note that because of internal pneumatic switching limitations the instrument only makes an independent measurement every 4 seconds. Thus, the same concentration number is repeated roughly 4 times at the uniform, monotonic 1-s time base used in the AOS systems. Accompanying instrument outputs include sample temperatures, flows, chamber pressure, lamp intensities and a multiplicity of housekeeping information. There is also a field for operator comments made at any time while data is being collected.

  15. Grid and Data Analyzing and Security

    Directory of Open Access Journals (Sweden)

    Fatemeh SHOKRI

    2012-12-01

    Full Text Available This paper examines the importance of secure structures in the process of analyzing and distributing information with aid of Grid-based technologies. The advent of distributed network has provided many practical opportunities for detecting and recording the time of events, and made efforts to identify the events and solve problems of storing information such as being up-to-date and documented. In this regard, the data distribution systems in a network environment should be accurate. As a consequence, a series of continuous and updated data must be at hand. In this case, Grid is the best answer to use data and resource of organizations by common processing.

  16. Development of a Portable Water Quality Analyzer

    Directory of Open Access Journals (Sweden)

    Germán COMINA

    2010-08-01

    Full Text Available A portable water analyzer based on a voltammetric electronic tongue has been developed. The system uses an electrochemical cell with two working electrodes as sensors, a computer controlled potentiostat, and software based on multivariate data analysis for pattern recognition. The system is suitable to differentiate laboratory made and real in-situ river water samples contaminated with different amounts of Escherichia coli. This bacteria is not only one of the main indicators for water quality, but also a main concern for public health, affecting especially people living in high-burden, resource-limiting settings.

  17. Light-weight analyzer for odor recognition

    Energy Technology Data Exchange (ETDEWEB)

    Vass, Arpad A; Wise, Marcus B

    2014-05-20

    The invention provides a light weight analyzer, e.g., detector, capable of locating clandestine graves. The detector utilizes the very specific and unique chemicals identified in the database of human decompositional odor. This detector, based on specific chemical compounds found relevant to human decomposition, is the next step forward in clandestine grave detection and will take the guess-work out of current methods using canines and ground-penetrating radar, which have historically been unreliable. The detector is self contained, portable and built for field use. Both visual and auditory cues are provided to the operator.

  18. Nonlinear single-spin spectrum analyzer.

    Science.gov (United States)

    Kotler, Shlomi; Akerman, Nitzan; Glickman, Yinnon; Ozeri, Roee

    2013-03-15

    Qubits have been used as linear spectrum analyzers of their environments. Here we solve the problem of nonlinear spectral analysis, required for discrete noise induced by a strongly coupled environment. Our nonperturbative analytical model shows a nonlinear signal dependence on noise power, resulting in a spectral resolution beyond the Fourier limit as well as frequency mixing. We develop a noise characterization scheme adapted to this nonlinearity. We then apply it using a single trapped ion as a sensitive probe of strong, non-Gaussian, discrete magnetic field noise. Finally, we experimentally compared the performance of equidistant vs Uhrig modulation schemes for spectral analysis.

  19. Protein stability: a crystallographer’s perspective

    International Nuclear Information System (INIS)

    Deller, Marc C.; Kong, Leopold; Rupp, Bernhard

    2016-01-01

    An understanding of protein stability is essential for optimizing the expression, purification and crystallization of proteins. In this review, discussion will focus on factors affecting protein stability on a somewhat practical level, particularly from the view of a protein crystallographer. Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed

  20. Analyzing delay causes in Egyptian construction projects.

    Science.gov (United States)

    Marzouk, Mohamed M; El-Rasas, Tarek I

    2014-01-01

    Construction delays are common problems in civil engineering projects in Egypt. These problems occur frequently during project life-time leading to disputes and litigation. Therefore, it is essential to study and analyze causes of construction delays. This research presents a list of construction delay causes retrieved from literature. The feedback of construction experts was obtained through interviews. Subsequently, a questionnaire survey was prepared. The questionnaire survey was distributed to thirty-three construction experts who represent owners, consultants, and contractor's organizations. Frequency Index, Severity Index, and Importance Index are calculated and according to the highest values of them the top ten delay causes of construction projects in Egypt are determined. A case study is analyzed and compared to the most important delay causes in the research. Statistical analysis is carried out using analysis of variance ANOVA method to test delay causes, obtained from the survey. The test results reveal good correlation between groups while there is significant difference between them for some delay causes and finally roadmap for prioritizing delay causes groups is presented.

  1. Plutonium solution analyzer. Revised February 1995

    International Nuclear Information System (INIS)

    Burns, D.A.

    1995-02-01

    A fully automated analyzer has been developed for plutonium solutions. It was assembled from several commercially available modules, is based upon segmented flow analysis, and exhibits precision about an order of magnitude better than commercial units (0.5%--0.05% RSD). The system was designed to accept unmeasured, untreated liquid samples in the concentration range 40--240 g/l: and produce a report with sample identification, sample concentrations, and an abundance of statistics. Optional hydraulics can accommodate samples in the concentration range 0.4--4.0 g/y. Operating at a typical rate of 30 to 40 samples per hour, it consumes only 0.074 ml of each sample and standard, and generates waste at the rate of about 1.5 ml per minute. No radioactive material passes through its multichannel peristaltic pump (which remains outside the glovebox, uncontaminated) but rather is handled by a 6-port, 2-position chromatography-type loop valve. An accompanying computer is programmed in QuickBASIC 4.5 to provide both instrument control and data reduction. The program is truly user-friendly and communication between operator and instrument is via computer screen displays and keyboard. Two important issues which have been addressed are waste minimization and operator safety (the analyzer can run in the absence of an operator, once its autosampler has been loaded)

  2. Analyzing block placement errors in SADP patterning

    Science.gov (United States)

    Kobayashi, Shinji; Okada, Soichiro; Shimura, Satoru; Nafus, Kathleen; Fonseca, Carlos; Demand, Marc; Biesemans, Serge; Versluijs, Janko; Ercken, Monique; Foubert, Philippe; Miyazaki, Shinobu

    2016-03-01

    We discuss edge placement errors (EPE) for multi-patterning of Mx critical layers using ArF lithography. Specific focus is placed on the block formation part of the process. While plenty of literature characterization data exist on spacer formation, only limited published data is available on block processes. We analyze the accuracy of placing blocks relative to narrow spacers. Many publications calculate EPE assuming Gaussian distributions for key process variations contributing to EPE. For practical reasons, each contributor is measured on dedicated test structures. In this work, we complement such analysis and directly measure the EPE in product. We perform high density sampling of blocks using CDSEM images and analyze all feature edges of interest. We find that block placement errors can be very different depending on their local design context. Specifically we report on 2 block populations (further called block A and B) which have a 4x different standard deviation. We attribute this to differences in local topography (spacer shape) and interaction with the plasma-etch process design. Block A (on top of the `core space' S1) has excellent EPE uniformity of ~1 nm while block B (on top of `gap space' S2) has degraded EPE control of ~4 nm. Finally, we suggest that the SOC etch process is at the origin on positioning blocks accurately on slim spacers, helping the manufacturability of spacer-based patterning techniques, and helping its extension toward the 5nm node.

  3. Analyzing rare diseases terms in biomedical terminologies

    Directory of Open Access Journals (Sweden)

    Erika Pasceri

    2012-03-01

    Full Text Available Rare disease patients too often face common problems, including the lack of access to correct diagnosis, lack of quality information on the disease, lack of scientific knowledge of the disease, inequities and difficulties in access to treatment and care. These things could be changed by implementing a comprehensive approach to rare diseases, increasing international cooperation in scientific research, by gaining and sharing scientific knowledge about and by developing tools for extracting and sharing knowledge. A significant aspect to analyze is the organization of knowledge in the biomedical field for the proper management and recovery of health information. For these purposes, the sources needed have been acquired from the Office of Rare Diseases Research, the National Organization of Rare Disorders and Orphanet, organizations that provide information to patients and physicians and facilitate the exchange of information among different actors involved in this field. The present paper shows the representation of rare diseases terms in biomedical terminologies such as MeSH, ICD-10, SNOMED CT and OMIM, leveraging the fact that these terminologies are integrated in the UMLS. At the first level, it was analyzed the overlap among sources and at a second level, the presence of rare diseases terms in target sources included in UMLS, working at the term and concept level. We found that MeSH has the best representation of rare diseases terms.

  4. CALIBRATION OF ONLINE ANALYZERS USING NEURAL NETWORKS

    Energy Technology Data Exchange (ETDEWEB)

    Rajive Ganguli; Daniel E. Walsh; Shaohai Yu

    2003-12-05

    Neural networks were used to calibrate an online ash analyzer at the Usibelli Coal Mine, Healy, Alaska, by relating the Americium and Cesium counts to the ash content. A total of 104 samples were collected from the mine, with 47 being from screened coal, and the rest being from unscreened coal. Each sample corresponded to 20 seconds of coal on the running conveyor belt. Neural network modeling used the quick stop training procedure. Therefore, the samples were split into training, calibration and prediction subsets. Special techniques, using genetic algorithms, were developed to representatively split the sample into the three subsets. Two separate approaches were tried. In one approach, the screened and unscreened coal was modeled separately. In another, a single model was developed for the entire dataset. No advantage was seen from modeling the two subsets separately. The neural network method performed very well on average but not individually, i.e. though each prediction was unreliable, the average of a few predictions was close to the true average. Thus, the method demonstrated that the analyzers were accurate at 2-3 minutes intervals (average of 6-9 samples), but not at 20 seconds (each prediction).

  5. Analyzing Virtual Physics Simulations with Tracker

    Science.gov (United States)

    Claessens, Tom

    2017-12-01

    In the physics teaching community, Tracker is well known as a user-friendly open source video analysis software, authored by Douglas Brown. With this tool, the user can trace markers indicated on a video or on stroboscopic photos and perform kinematic analyses. Tracker also includes a data modeling tool that allows one to fit some theoretical equations of motion onto experimentally obtained data. In the field of particle mechanics, Tracker has been effectively used for learning and teaching about projectile motion, "toss up" and free-fall vertical motion, and to explain the principle of mechanical energy conservation. Also, Tracker has been successfully used in rigid body mechanics to interpret the results of experiments with rolling/slipping cylinders and moving rods. In this work, I propose an original method in which Tracker is used to analyze virtual computer simulations created with a physics-based motion solver, instead of analyzing video recording or stroboscopic photos. This could be an interesting approach to study kinematics and dynamics problems in physics education, in particular when there is no or limited access to physical labs. I demonstrate the working method with a typical (but quite challenging) problem in classical mechanics: a slipping/rolling cylinder on a rough surface.

  6. Calibration of the portable wear metal analyzer

    Science.gov (United States)

    Quinn, Michael J.

    1987-12-01

    The Portable Wear Metal Analyzer (PWMA), a graphite furnace atomic absorption (AA) spectrometer, developed under a contract for this laboratory, was evaluated using powdered metal particles suspended in oil. The PWMA is a microprocessor controlled automatic sequential multielement AA spectrometer designed to support the deployed aircraft requirement for spectrometric oil analysis. The PWMA will analyze for nine elements (Ni, Fe, Cu, Cr, Ag, Mg, Si, Ti, Al) at a rate of 4 min per sample. The graphite tube and modified sample introduction system increase the detection of particles in oil when compared to the currently used techniques of flame AA or spark atomic emission (AE) spectroscopy. The PWMA shows good-to-excellent response for particles in sizes of 0 to 5 and 5 to 10 micrometers and fair response to particles of 10 to 20 and 20 to 30 micrometers. All trends in statistical variations are easily explained by system considerations. Correction factors to the calibration curves are necessary to correlate the analytical capability of the PWMA to the performance of existing spectrometric oil analysis (SOA) instruments.

  7. Solar Probe ANalyzer for Ions - Laboratory Performance

    Science.gov (United States)

    Livi, R.; Larson, D. E.; Kasper, J. C.; Korreck, K. E.; Whittlesey, P. L.

    2017-12-01

    The Parker Solar Probe (PSP) mission is a heliospheric satellite that will orbit the Sun closer than any prior mission to date with a perihelion of 35 solar radii (RS) and an aphelion of 10 RS. PSP includes the Solar Wind Electrons Alphas and Protons (SWEAP) instrument suite, which in turn consists of four instruments: the Solar Probe Cup (SPC) and three Solar Probe ANalyzers (SPAN) for ions and electrons. Together, this suite will take local measurements of particles and electromagnetic fields within the Sun's corona. SPAN-Ai has completed flight calibration and spacecraft integration and is set to be launched in July of 2018. The main mode of operation consists of an electrostatic analyzer (ESA) at its aperture followed by a Time-of-Flight section to measure the energy and mass per charge (m/q) of the ambient ions. SPAN-Ai's main objective is to measure solar wind ions within an energy range of 5 eV - 20 keV, a mass/q between 1-60 [amu/q] and a field of view of 2400x1200. Here we will show flight calibration results and performance.

  8. Optoacoustic 13C-breath test analyzer

    Science.gov (United States)

    Harde, Hermann; Helmrich, Günther; Wolff, Marcus

    2010-02-01

    The composition and concentration of exhaled volatile gases reflects the physical ability of a patient. Therefore, a breath analysis allows to recognize an infectious disease in an organ or even to identify a tumor. One of the most prominent breath tests is the 13C-urea-breath test, applied to ascertain the presence of the bacterium helicobacter pylori in the stomach wall as an indication of a gastric ulcer. In this contribution we present a new optical analyzer that employs a compact and simple set-up based on photoacoustic spectroscopy. It consists of two identical photoacoustic cells containing two breath samples, one taken before and one after capturing an isotope-marked substrate, where the most common isotope 12C is replaced to a large extent by 13C. The analyzer measures simultaneously the relative CO2 isotopologue concentrations in both samples by exciting the molecules on specially selected absorption lines with a semiconductor laser operating at a wavelength of 2.744 μm. For a reliable diagnosis changes of the 13CO2 concentration of 1% in the exhaled breath have to be detected at a concentration level of this isotope in the breath of about 500 ppm.

  9. Analyzing surface coatings in situ: High-temperature surface film analyzer developed

    International Nuclear Information System (INIS)

    Anon.

    1991-01-01

    Scientists at Argonne National Laboratory (ANL) have devised a new instrument that can analyze surface coatings under operating conditions. The High-Temperature Surface Film Analyzer is the first such instrument to analyze the molecular composition and structure of surface coatings on metals and solids under conditions of high temperature and pressure in liquid environments. Corrosion layers, oxide coatings, polymers or paint films, or adsorbed molecules are examples of conditions that can be analyzed using this instrument. Film thicknesses may vary from a few molecular layers to several microns or thicker. The instrument was originally developed to study metal corrosion in aqueous solutions similar to the cooling water systems of light-water nuclear reactors. The instrument may have use for the nuclear power industry where coolant pipes degrade due to stress corrosion cracking, which often leads to plant shutdown. Key determinants in the occurrence of stress corrosion cracking are the properties and composition of corrosion scales that form inside pipes. The High-Temperature Surface Analyzer can analyze these coatings under laboratory conditions that simulate the same hostile environment of high temperature, pressure, and solution that exist during plant operations. The ability to analyze these scales in hostile liquid environments is unique to the instrument. Other applications include analyzing paint composition, corrosion of materials in geothermal power systems, integrity of canisters for radioactive waste storage, corrosion inhibitor films on piping and drilling systems, and surface scales on condenser tubes in industrial hot water heat exchangers. The device is not patented

  10. Automated Root Tracking with "Root System Analyzer"

    Science.gov (United States)

    Schnepf, Andrea; Jin, Meina; Ockert, Charlotte; Bol, Roland; Leitner, Daniel

    2015-04-01

    Crucial factors for plant development are water and nutrient availability in soils. Thus, root architecture is a main aspect of plant productivity and needs to be accurately considered when describing root processes. Images of root architecture contain a huge amount of information, and image analysis helps to recover parameters describing certain root architectural and morphological traits. The majority of imaging systems for root systems are designed for two-dimensional images, such as RootReader2, GiA Roots, SmartRoot, EZ-Rhizo, and Growscreen, but most of them are semi-automated and involve mouse-clicks in each root by the user. "Root System Analyzer" is a new, fully automated approach for recovering root architectural parameters from two-dimensional images of root systems. Individual roots can still be corrected manually in a user interface if required. The algorithm starts with a sequence of segmented two-dimensional images showing the dynamic development of a root system. For each image, morphological operators are used for skeletonization. Based on this, a graph representation of the root system is created. A dynamic root architecture model helps to determine which edges of the graph belong to an individual root. The algorithm elongates each root at the root tip and simulates growth confined within the already existing graph representation. The increment of root elongation is calculated assuming constant growth. For each root, the algorithm finds all possible paths and elongates the root in the direction of the optimal path. In this way, each edge of the graph is assigned to one or more coherent roots. Image sequences of root systems are handled in such a way that the previous image is used as a starting point for the current image. The algorithm is implemented in a set of Matlab m-files. Output of Root System Analyzer is a data structure that includes for each root an identification number, the branching order, the time of emergence, the parent

  11. Analyzing and forecasting the European social climate

    Directory of Open Access Journals (Sweden)

    Liliana DUGULEANĂ

    2015-06-01

    Full Text Available The paper uses the results of the sample survey Eurobarometer, which has been requested by the European Commission. The social climate index is used to measure the level of perceptions of population by taking into account their personal situation and their perspective at national level. The paper makes an analysis of the evolution of social climate indices for the countries of European Union and offers information about the expectations of population of analyzed countries. The obtained results can be compared with the forecasting of Eurobarometer, on short term of one year and medium term of five years. Modelling the social climate index and its influence factors offers useful information about the efficiency of social protection and inclusion policies.

  12. Analyzer of neutron flux in real time

    International Nuclear Information System (INIS)

    Rojas S, A.S.; Carrillo M, R.A.; Balderas, E.G.

    1999-01-01

    With base in the study of the real signals of neutron flux of instability events occurred in the Laguna Verde nuclear power plant where the nucleus oscillation phenomena of the reactor are in the 0 to 2.5 Hz range, it has been seen the possibility about the development a surveillance and diagnostic equipment capable to analyze in real time the behavior of nucleus in this frequencies range. An important method for surveillance the stability of the reactor nucleus is the use of the Power spectral density which allows to determine the frequencies and amplitudes contained in the signals. It is used an instrument carried out by LabVIEW graphic programming with a data acquisition card of 16 channels which works at Windows 95/98 environment. (Author)

  13. Analyzing the Control Structure of PEPA

    DEFF Research Database (Denmark)

    Yang, Fan; Nielson, Hanne Riis

    expressed in PEPA. The analysis technique we adopted is Data Flow Analysis. We begin the analysis by defining an appropriate transfer function, then with the classical worklist algorithm we construct a finite automaton that captures all possible interactions among processes. By annotating labels and layers...... to PEPA programs, the approximating result is very precise. Based on the analysis, we also develop algorithms for validating the deadlock property of PEPA programs. The techniques have been implemented in a tool which is able to analyze processes with a control structure that more than one thousand states.......The Performance Evaluation Process Algebra, PEPA, is introduced by Jane Hillston as a stochastic process algebra for modelling distributed systems and especially suitable for performance evaluation. We present a static analysis that very precisely approximates the control structure of processes...

  14. Buccal microbiology analyzed by infrared spectroscopy

    Science.gov (United States)

    de Abreu, Geraldo Magno Alves; da Silva, Gislene Rodrigues; Khouri, Sônia; Favero, Priscila Pereira; Raniero, Leandro; Martin, Airton Abrahão

    2012-01-01

    Rapid microbiological identification and characterization are very important in dentistry and medicine. In addition to dental diseases, pathogens are directly linked to cases of endocarditis, premature delivery, low birth weight, and loss of organ transplants. Fourier Transform Infrared Spectroscopy (FTIR) was used to analyze oral pathogens Aggregatibacter actinomycetemcomitans ATCC 29523, Aggregatibacter actinomycetemcomitans-JP2, and Aggregatibacter actinomycetemcomitans which was clinically isolated from the human blood-CI. Significant spectra differences were found among each organism allowing the identification and characterization of each bacterial species. Vibrational modes in the regions of 3500-2800 cm-1, the 1484-1420 cm-1, and 1000-750 cm-1 were used in this differentiation. The identification and classification of each strain were performed by cluster analysis achieving 100% separation of strains. This study demonstrated that FTIR can be used to decrease the identification time, compared to the traditional methods, of fastidious buccal microorganisms associated with the etiology of the manifestation of periodontitis.

  15. Nuclear Plant Analyzer: Installation manual. Volume 1

    International Nuclear Information System (INIS)

    Snider, D.M.; Wagner, K.L.; Grush, W.H.; Jones, K.R.

    1995-01-01

    This report contains the installation instructions for the Nuclear Plant Analyzer (NPA) System. The NPA System consists of the Computer Visual System (CVS) program, the NPA libraries, the associated utility programs. The NPA was developed at the Idaho National Engineering Laboratory under the sponsorship of the US Nuclear Regulatory Commission to provide a highly flexible graphical user interface for displaying the results of these analysis codes. The NPA also provides the user with a convenient means of interactively controlling the host program through user-defined pop-up menus. The NPA was designed to serve primarily as an analysis tool. After a brief introduction to the Computer Visual System and the NPA, an analyst can quickly create a simple picture or set of pictures to aide in the study of a particular phenomenon. These pictures can range from simple collections of square boxes and straight lines to complex representations of emergency response information displays

  16. Using wavelet features for analyzing gamma lines

    International Nuclear Information System (INIS)

    Medhat, M.E.; Abdel-hafiez, A.; Hassan, M.F.; Ali, M.A.; Uzhinskii, V.V.

    2004-01-01

    Data processing methods for analyzing gamma ray spectra with symmetric bell-shaped peaks form are considered. In many cases the peak form is symmetrical bell shaped in particular a Gaussian case is the most often used due to many physical reasons. The problem is how to evaluate parameters of such peaks, i.e. their positions, amplitudes and also their half-widths, that is for a single peak and overlapped peaks. Through wavelet features by using Marr wavelet (Mexican Hat) as a correlation method, it could be to estimate the optimal wavelet parameters and to locate peaks in the spectrum. The performance of the proposed method and others shows a better quality of wavelet transform method

  17. Coke from small-diameter tubes analyzed

    International Nuclear Information System (INIS)

    Albright, L.F.

    1988-01-01

    The mechanism for coke deposit formation and the nature of the coke itself can vary with the design of the ethylene furnace tube bank. In this article, coke deposits from furnaces with small-diameter pyrolysis tubes are examined. The samples were taken from four furnaces of identical design (Plant B). As in both the first and second installments of the series, the coke deposits were examined using a scanning electron microscope (SEM) and an energy dispersive X-ray analyzer (EDAX). The deposits from the small-diameter tubes are compared with the coke deposits from the furnace discussed in earlier articles. Analysis of the coke in both sets of samples are then used to offer recommendations for improved decoking procedures, operating procedures, better feed selection, and better selection of the metallurgy used in furnace tubes, to extend the operating time of the furnace tubes by reducing the amount and type of coke build up

  18. Analyzing Options for Airborne Emergency Wireless Communications

    Energy Technology Data Exchange (ETDEWEB)

    Michael Schmitt; Juan Deaton; Curt Papke; Shane Cherry

    2008-03-01

    In the event of large-scale natural or manmade catastrophic events, access to reliable and enduring commercial communication systems is critical. Hurricane Katrina provided a recent example of the need to ensure communications during a national emergency. To ensure that communication demands are met during these critical times, Idaho National Laboratory (INL) under the guidance of United States Strategic Command has studied infrastructure issues, concerns, and vulnerabilities associated with an airborne wireless communications capability. Such a capability could provide emergency wireless communications until public/commercial nodes can be systematically restored. This report focuses on the airborne cellular restoration concept; analyzing basic infrastructure requirements; identifying related infrastructure issues, concerns, and vulnerabilities and offers recommended solutions.

  19. Sensors and Automated Analyzers for Radionuclides

    International Nuclear Information System (INIS)

    Grate, Jay W.; Egorov, Oleg B.

    2003-01-01

    The production of nuclear weapons materials has generated large quantities of nuclear waste and significant environmental contamination. We have developed new, rapid, automated methods for determination of radionuclides using sequential injection methodologies to automate extraction chromatographic separations, with on-line flow-through scintillation counting for real time detection. This work has progressed in two main areas: radionuclide sensors for water monitoring and automated radiochemical analyzers for monitoring nuclear waste processing operations. Radionuclide sensors have been developed that collect and concentrate radionuclides in preconcentrating minicolumns with dual functionality: chemical selectivity for radionuclide capture and scintillation for signal output. These sensors can detect pertechnetate to below regulatory levels and have been engineered into a prototype for field testing. A fully automated process monitor has been developed for total technetium in nuclear waste streams. This instrument performs sample acidification, speciation adjustment, separation and detection in fifteen minutes or less

  20. Analyzing, Modelling, and Designing Software Ecosystems

    DEFF Research Database (Denmark)

    Manikas, Konstantinos

    the development, implementation, and use of telemedicine services. We initially expand the theory of software ecosystems by contributing to the definition and understanding of software ecosystems, providing means of analyzing existing and designing new ecosystems, and defining and measuring the qualities...... of software ecosystems. We use these contributions to design a software ecosystem in the telemedicine services of Denmark with (i) a common platform that supports and promotes development from different actors, (ii) high software interaction, (iii) strong social network of actors, (iv) robust business....... This thesis documents the groundwork towards addressing the challenges faced by telemedical technologies today and establishing telemedicine as a means of patient diagnosis and treatment. Furthermore, it serves as an empirical example of designing a software ecosystem....

  1. Analyzing Strategic Business Rules through Simulation Modeling

    Science.gov (United States)

    Orta, Elena; Ruiz, Mercedes; Toro, Miguel

    Service Oriented Architecture (SOA) holds promise for business agility since it allows business process to change to meet new customer demands or market needs without causing a cascade effect of changes in the underlying IT systems. Business rules are the instrument chosen to help business and IT to collaborate. In this paper, we propose the utilization of simulation models to model and simulate strategic business rules that are then disaggregated at different levels of an SOA architecture. Our proposal is aimed to help find a good configuration for strategic business objectives and IT parameters. The paper includes a case study where a simulation model is built to help business decision-making in a context where finding a good configuration for different business parameters and performance is too complex to analyze by trial and error.

  2. Method and apparatus for analyzing ionizable materials

    International Nuclear Information System (INIS)

    Ehrlich, B.J.; Hall, R.C.; Thiede, P.W.

    1979-01-01

    An apparatus and method are described for analyzing a solution of ionizable compounds in a liquid. The solution is irradiated with electromagnetic radiation to ionize the compounds and the electrical conductivity of the solution is measured. The radiation may be X-rays, ultra-violet, infra-red or microwaves. The solution may be split into two streams, only one of which is irradiated, the other being used as a reference by comparing conductivities of the two streams. The liquid must be nonionizable and is preferably a polar solvent. The invention provides an analysis technique useful in liquid chromatography and in gas chromatography after dissolving the eluted gases in a suitable solvent. Electrical conductivity measurements performed on the irradiated eluent provide a quantitative indication of the ionizable materials existing within the eluent stream and a qualitative indication of the purity of the eluent stream. (author)

  3. Analyzing, Modelling, and Designing Software Ecosystems

    DEFF Research Database (Denmark)

    Manikas, Konstantinos

    as the software development and distribution by a set of actors dependent on each other and the ecosystem. We commence on the hypothesis that the establishment of a software ecosystem on the telemedicine services of Denmark would address these issues and investigate how a software ecosystem can foster...... the development, implementation, and use of telemedicine services. We initially expand the theory of software ecosystems by contributing to the definition and understanding of software ecosystems, providing means of analyzing existing and designing new ecosystems, and defining and measuring the qualities...... of software ecosystems. We use these contributions to design a software ecosystem in the telemedicine services of Denmark with (i) a common platform that supports and promotes development from different actors, (ii) high software interaction, (iii) strong social network of actors, (iv) robust business...

  4. Stackable differential mobility analyzer for aerosol measurement

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Meng-Dawn [Oak Ridge, TN; Chen, Da-Ren [Creve Coeur, MO

    2007-05-08

    A multi-stage differential mobility analyzer (MDMA) for aerosol measurements includes a first electrode or grid including at least one inlet or injection slit for receiving an aerosol including charged particles for analysis. A second electrode or grid is spaced apart from the first electrode. The second electrode has at least one sampling outlet disposed at a plurality different distances along its length. A volume between the first and the second electrode or grid between the inlet or injection slit and a distal one of the plurality of sampling outlets forms a classifying region, the first and second electrodes for charging to suitable potentials to create an electric field within the classifying region. At least one inlet or injection slit in the second electrode receives a sheath gas flow into an upstream end of the classifying region, wherein each sampling outlet functions as an independent DMA stage and classifies different size ranges of charged particles based on electric mobility simultaneously.

  5. Analyzing use cases for knowledge acquisition

    Science.gov (United States)

    Kelsey, Robert L.; Webster, Robert B.

    2000-03-01

    The analysis of use cases describing construction of simulation configuration files in a data/information management system can lead to the acquisition of new information and knowledge. In this application, a user creates a use case with an eXtensible Markup Language (XML) description representing a configuration file for simulation of a physical system. INtelligent agents analyze separate versions of the XML descriptions of a user and additionally, make comparisons of the descriptions with examples form a library of use cases. The agents can then make recommendations to a user on how to proceed or if tutoring is necessary. In a proof-of-concept test, new information is acquired and a user learns from the agent-facilitated tutoring.

  6. Spectroscopic methods to analyze drug metabolites.

    Science.gov (United States)

    Yi, Jong-Jae; Park, Kyeongsoon; Kim, Won-Je; Rhee, Jin-Kyu; Son, Woo Sung

    2018-03-09

    Drug metabolites have been monitored with various types of newly developed techniques and/or combination of common analytical methods, which could provide a great deal of information on metabolite profiling. Because it is not easy to analyze whole drug metabolites qualitatively and quantitatively, a single solution of analytical techniques is combined in a multilateral manner to cover the widest range of drug metabolites. Mass-based spectroscopic analysis of drug metabolites has been expanded with the help of other parameter-based methods. The current development of metabolism studies through contemporary pharmaceutical research are reviewed with an overview on conventionally used spectroscopic methods. Several technical approaches for conducting drug metabolic profiling through spectroscopic methods are discussed in depth.

  7. Analyzing petabytes of data with Hadoop

    CERN Multimedia

    CERN. Geneva

    2009-01-01

    Abstract The open source Apache Hadoop project provides a powerful suite of tools for storing and analyzing petabytes of data using commodity hardware. After several years of production use inside of web companies like Yahoo! and Facebook and nearly a year of commercial support and development by Cloudera, the technology is spreading rapidly through other disciplines, from financial services and government to life sciences and high energy physics. The talk will motivate the design of Hadoop and discuss some key implementation details in depth. It will also cover the major subprojects in the Hadoop ecosystem, go over some example applications, highlight best practices for deploying Hadoop in your environment, discuss plans for the future of the technology, and provide pointers to the many resources available for learning more. In addition to providing more information about the Hadoop platform, a major goal of this talk is to begin a dialogue with the ATLAS research team on how the tools commonly used in t...

  8. Orthopedic surgical analyzer for percutaneous vertebroplasty

    Science.gov (United States)

    Tack, Gye Rae; Choi, Hyung Guen; Lim, Do H.; Lee, Sung J.

    2001-05-01

    Since the spine is one of the most complex joint structures in the human body, its surgical treatment requires careful planning and high degree of precision to avoid any unwanted neurological compromises. In addition, comprehensive biomechanical analysis can be very helpful because the spine is subject to a variety of load. In case for the osteoporotic spine in which the structural integrity has been compromised, it brings out the double challenges for a surgeon both clinically and biomechanically. Thus, we have been developing an integrated medical image system that is capable of doing the both. This system is called orthopedic surgical analyzer and it combines the clinical results from image-guided examination and the biomechanical data from finite element analysis. In order to demonstrate its feasibility, this system was applied to percutaneous vertebroplasty. Percutaneous vertebroplasty is a surgical procedure that has been recently introduced for the treatment of compression fracture of the osteoporotic vertebrae. It involves puncturing vertebrae and filling with polymethylmethacrylate (PMMA). Recent studies have shown that the procedure could provide structural reinforcement for the osteoporotic vertebrae while being minimally invasive and safe with immediate pain relief. However, treatment failures due to excessive PMMA volume injection have been reported as one of complications. It is believed that control of PMMA volume is one of the most critical factors that can reduce the incidence of complications. Since the degree of the osteoporosis can influence the porosity of the cancellous bone in the vertebral body, the injection volume can be different from patient to patient. In this study, the optimal volume of PMMA injection for vertebroplasty was predicted based on the image analysis of a given patient. In addition, biomechanical effects due to the changes in PMMA volume and bone mineral density (BMD) level were investigated by constructing clinically

  9. Interfacial Protein-Protein Associations

    OpenAIRE

    Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2013-01-01

    While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for ...

  10. Protein complex interactor analysis and differential activity of KDM3 subfamily members towards H3K9 methylation.

    Directory of Open Access Journals (Sweden)

    Michael Brauchle

    Full Text Available Histone modifications play an important role in chromatin organization and gene regulation, and their interpretation is referred to as epigenetic control. The methylation levels of several lysine residues in histone tails are tightly controlled, and JmjC domain-containing proteins are one class of broadly expressed enzymes catalyzing methyl group removal. However, several JmjC proteins remain uncharacterized, gaps persist in understanding substrate recognition, and the integration of JmjC proteins into signaling pathways is just emerging. The KDM3 subfamily is an evolutionarily conserved group of histone demethylase proteins, thought to share lysine substrate specificity. Here we use a systematic approach to compare KDM3 subfamily members. We show that full-length KDM3A and KDM3B are H3K9me1/2 histone demethylases whereas we fail to observe histone demethylase activity for JMJD1C using immunocytochemical and biochemical approaches. Structure-function analyses revealed the importance of a single amino acid in KDM3A implicated in the catalytic activity towards H3K9me1/2 that is not conserved in JMJD1C. Moreover, we use quantitative proteomic analyses to identify subsets of the interactomes of the 3 proteins. Specific interactor candidates were identified for each of the three KDM3 subfamily members. Importantly, we find that SCAI, a known transcriptional repressor, interacts specifically with KDM3B. Taken together, we identify substantial differences in the biology of KDM3 histone demethylases, namely enzymatic activity and protein-protein interactions. Such comparative approaches pave the way to a better understanding of histone demethylase specificity and protein function at a systems level and are instrumental in identifying the more subtle differences between closely related proteins.

  11. PROTEIN - WHICH IS BEST?

    Directory of Open Access Journals (Sweden)

    Michael J. Falvo

    2004-09-01

    Full Text Available Protein intake that exceeds the recommended daily allowance is widely accepted for both endurance and power athletes. However, considering the variety of proteins that are available much less is known concerning the benefits of consuming one protein versus another. The purpose of this paper is to identify and analyze key factors in order to make responsible recommendations to both the general and athletic populations. Evaluation of a protein is fundamental in determining its appropriateness in the human diet. Proteins that are of inferior content and digestibility are important to recognize and restrict or limit in the diet. Similarly, such knowledge will provide an ability to identify proteins that provide the greatest benefit and should be consumed. The various techniques utilized to rate protein will be discussed. Traditionally, sources of dietary protein are seen as either being of animal or vegetable origin. Animal sources provide a complete source of protein (i.e. containing all essential amino acids, whereas vegetable sources generally lack one or more of the essential amino acids. Animal sources of dietary protein, despite providing a complete protein and numerous vitamins and minerals, have some health professionals concerned about the amount of saturated fat common in these foods compared to vegetable sources. The advent of processing techniques has shifted some of this attention and ignited the sports supplement marketplace with derivative products such as whey, casein and soy. Individually, these products vary in quality and applicability to certain populations. The benefits that these particular proteins possess are discussed. In addition, the impact that elevated protein consumption has on health and safety issues (i.e. bone health, renal function are also reviewed

  12. Sound of proteins

    DEFF Research Database (Denmark)

    2007-01-01

    In my group we work with Molecular Dynamics to model several different proteins and protein systems. We submit our modelled molecules to changes in temperature, changes in solvent composition and even external pulling forces. To analyze our simulation results we have so far used visual inspection...... and statistical analysis of the resulting molecular trajectories (as everybody else!). However, recently I started assigning a particular sound frequency to each amino acid in the protein, and by setting the amplitude of each frequency according to the movement amplitude we can "hear" whenever two aminoacids...

  13. Semantics based approach for analyzing disease-target associations.

    Science.gov (United States)

    Kaalia, Rama; Ghosh, Indira

    2016-08-01

    A complex disease is caused by heterogeneous biological interactions between genes and their products along with the influence of environmental factors. There have been many attempts for understanding the cause of these diseases using experimental, statistical and computational methods. In the present work the objective is to address the challenge of representation and integration of information from heterogeneous biomedical aspects of a complex disease using semantics based approach. Semantic web technology is used to design Disease Association Ontology (DAO-db) for representation and integration of disease associated information with diabetes as the case study. The functional associations of disease genes are integrated using RDF graphs of DAO-db. Three semantic web based scoring algorithms (PageRank, HITS (Hyperlink Induced Topic Search) and HITS with semantic weights) are used to score the gene nodes on the basis of their functional interactions in the graph. Disease Association Ontology for Diabetes (DAO-db) provides a standard ontology-driven platform for describing genes, proteins, pathways involved in diabetes and for integrating functional associations from various interaction levels (gene-disease, gene-pathway, gene-function, gene-cellular component and protein-protein interactions). An automatic instance loader module is also developed in present work that helps in adding instances to DAO-db on a large scale. Our ontology provides a framework for querying and analyzing the disease associated information in the form of RDF graphs. The above developed methodology is used to predict novel potential targets involved in diabetes disease from the long list of loose (statistically associated) gene-disease associations. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. A framework to analyze emissions implications of ...

    Science.gov (United States)

    Future year emissions depend highly on the evolution of the economy, technology and current and future regulatory drivers. A scenario framework was adopted to analyze various technology development pathways and societal change while considering existing regulations and future uncertainty in regulations and evaluate resulting emissions growth patterns. The framework integrates EPA’s energy systems model with an economic Input-Output (I/O) Life Cycle Assessment model. The EPAUS9r MARKAL database is assembled from a set of technologies to represent the U.S. energy system within MARKAL bottom-up technology rich energy modeling framework. The general state of the economy and consequent demands for goods and services from these sectors are taken exogenously in MARKAL. It is important to characterize exogenous inputs about the economy to appropriately represent the industrial sector outlook for each of the scenarios and case studies evaluated. An economic input-output (I/O) model of the US economy is constructed to link up with MARKAL. The I/O model enables user to change input requirements (e.g. energy intensity) for different sectors or the share of consumer income expended on a given good. This gives end-users a mechanism for modeling change in the two dimensions of technological progress and consumer preferences that define the future scenarios. The framework will then be extended to include environmental I/O framework to track life cycle emissions associated

  15. Analyzing Music Services Positioning Through Qualitative Research

    Directory of Open Access Journals (Sweden)

    Manuel Cuadrado

    2015-12-01

    Full Text Available Information technologies have produced new ways of distributing and consuming music, mainly by youth, in relation to both goods and services. In the case of goods, there has been a dramatic shift from traditional ways of buying and listening to music to new digital platforms. There has also been an evolution in relation to music services. In this sense, live music concerts have been losing their audiences over the past few years, as have music radio stations, in favor of streaming platforms. Curious about this phenomenon, we conducted an exploratory research in order to analyze how all these services, both traditional and new ones were perceived. Specifically, we aimed to study youth´s assessment of the three most relevant music service categories: music radio stations, digital streaming platforms, and pop-rock music festivals. To do so, we used the projective technique of image association to gather information. The population of the study consisted of individuals between 18 and 25 years of age. Our results, after using content analysis, were poor due to spontaneous recall. Therefore, we duplicated the study, but in a more focus-oriented way. Information gathered this time allowed us not only to better know how all these organizations are positioned but also to obtain a list of descriptors to be used in a subsequent descriptive research study.

  16. Analyzing Architecture of Mithraism Rock Temples

    Directory of Open Access Journals (Sweden)

    Zohre AliJabbari

    2017-06-01

    Full Text Available This analyzes the architecture of rock temples of West and Northwest of Iran, as well as factors influencing their formation. The creation of rock architecture in this area of Iran is influenced by the religious, geographical and political atmosphere of their time. Most of these structures are formed by dominated empires in the first millennium BC. And in some works we are observing their continuity in later periods and change in their functions. One of the reasons that have attracted man to mountain and rock in different schools was the religious structure of community. According to the sanctity of mountains and rocks in the ancient religions, especially in Mithraism, valuable temples and places of worship have emerged in the mountains. Their obvious characteristic is circular dome-shaped spaces; simplicity, arrangement of spaces and the way of creating light that correspond with the tradition of Mithraism in Iran. Mehr Temple in Maragheh, Dashkasan in Zanjan, and Qadamgah Temple in Azarshahr are the rock temples in northwest of Iran that signs and symbols on them indicate the performance of Mithraism duties in these temples. In the West of Iran, Cogan cave in Lorestan, considering the characteristics of Mithraism temples, in a period had function as a temple for the worship of Mithra. This research investigates architectural futures of these temples.

  17. Analyzing the Existing Undergraduate Engineering Leadership Skills

    Directory of Open Access Journals (Sweden)

    Hamed M. Almalki

    2016-12-01

    Full Text Available Purpose: Studying and analyzing the undergraduate engineering students' leadership skills to discover their potential leadership strengths and weaknesses. This study will unveil potential ways to enhance the ways we teach engineering leadership. The research has great insights that might assist engineering programs to improve curricula for the purpose of better engineering preparation to meet industry's demands. Methodology and Findings: 441 undergraduate engineering students have been surveyed in two undergraduate engineering programs to discover their leadership skills. The results in both programs were revealing that undergraduate engineering students are lacking behind in the visionary leadership skills compared to directing, including and cultivating leadership styles. Recommendation: A practical framework has been proposed to enhance the lacking leadership skills by utilizing the Matrix of Change (MOC, and the Balanced Scorecard BSC to capture the best leadership scenarios to design virtual simulation environment as per the lacking leadership skills which is the visionary leadership skills in this case. After that, the virtual simulation will be used to provide an experiential learning by replacing human beings with avatars that can be managed or dramatized by real people to enable the creation of live, practical, measurable, and customizable leadership development programs.

  18. Analyzing human errors in flight mission operations

    Science.gov (United States)

    Bruno, Kristin J.; Welz, Linda L.; Barnes, G. Michael; Sherif, Josef

    1993-01-01

    A long-term program is in progress at JPL to reduce cost and risk of flight mission operations through a defect prevention/error management program. The main thrust of this program is to create an environment in which the performance of the total system, both the human operator and the computer system, is optimized. To this end, 1580 Incident Surprise Anomaly reports (ISA's) from 1977-1991 were analyzed from the Voyager and Magellan projects. A Pareto analysis revealed that 38 percent of the errors were classified as human errors. A preliminary cluster analysis based on the Magellan human errors (204 ISA's) is presented here. The resulting clusters described the underlying relationships among the ISA's. Initial models of human error in flight mission operations are presented. Next, the Voyager ISA's will be scored and included in the analysis. Eventually, these relationships will be used to derive a theoretically motivated and empirically validated model of human error in flight mission operations. Ultimately, this analysis will be used to make continuous process improvements continuous process improvements to end-user applications and training requirements. This Total Quality Management approach will enable the management and prevention of errors in the future.

  19. Complete denture analyzed by optical coherence tomography

    Science.gov (United States)

    Negrutiu, Meda L.; Sinescu, Cosmin; Todea, Carmen; Podoleanu, Adrian G.

    2008-02-01

    The complete dentures are currently made using different technologies. In order to avoid deficiencies of the prostheses made using the classical technique, several alternative systems and procedures were imagined, directly related to the material used and also to the manufacturing technology. Thus, at the present time, there are several injecting systems and technologies on the market, that use chemoplastic materials, which are heat cured (90-100°C), in dry or wet environment, or cold cured (below 60°C). There are also technologies that plasticize a hard cured material by thermoplastic processing (without any chemical changes) and then inject it into a mold. The purpose of this study was to analyze the existence of possible defects in several dental prostheses using a non invasive method, before their insertion in the mouth. Different dental prostheses, fabricated from various materials were investigated using en-face optical coherence tomography. In order to discover the defects, the scanning was made in three planes, obtaining images at different depths, from 0,01 μm to 2 mm. In several of the investigated prostheses we f