WorldWideScience

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. Mapping the human protein interactome

    Institute of Scientific and Technical Information of China (English)

    Daniel Figeys

    2008-01-01

    Interactions are the essence of all biomolecules because they cannot fulfill their roles without interacting with other molecules. Hence, mapping the interactions of biomolecules can be useful for understanding their roles and functions. Furthermore, the development of molecular based systems biology requires an understanding of the biomolecular interactions. In recent years, the mapping of protein-protein interactions in different species has been reported, but few reports have focused on the large-scale mapping of protein-protein interactions in human. Here, we review the developments in protein interaction mapping and we discuss issues and strategies for the mapping of the human protein interactome.

  3. Inferring modules from human protein interactome classes

    Directory of Open Access Journals (Sweden)

    Chaurasia Gautam

    2010-07-01

    Full Text Available Abstract Background The integration of protein-protein interaction networks derived from high-throughput screening approaches and complementary sources is a key topic in systems biology. Although integration of protein interaction data is conventionally performed, the effects of this procedure on the result of network analyses has not been examined yet. In particular, in order to optimize the fusion of heterogeneous interaction datasets, it is crucial to consider not only their degree of coverage and accuracy, but also their mutual dependencies and additional salient features. Results We examined this issue based on the analysis of modules detected by network clustering methods applied to both integrated and individual (disaggregated data sources, which we call interactome classes. Due to class diversity, we deal with variable dependencies of data features arising from structural specificities and biases, but also from possible overlaps. Since highly connected regions of the human interactome may point to potential protein complexes, we have focused on the concept of modularity, and elucidated the detection power of module extraction algorithms by independent validations based on GO, MIPS and KEGG. From the combination of protein interactions with gene expressions, a confidence scoring scheme has been proposed before proceeding via GO with further classification in permanent and transient modules. Conclusions Disaggregated interactomes are shown to be informative for inferring modularity, thus contributing to perform an effective integrative analysis. Validation of the extracted modules by multiple annotation allows for the assessment of confidence measures assigned to the modules in a protein pathway context. Notably, the proposed multilayer confidence scheme can be used for network calibration by enabling a transition from unweighted to weighted interactomes based on biological evidence.

  4. Introducing the hypothome: A way to integrate predicted proteins in interactomes

    DEFF Research Database (Denmark)

    Desler, Claus; Zambach, Sine; Suravajhala, Prashanth;

    2014-01-01

    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...

  5. Interactome Data and Databases: Different Types of Protein Interaction

    Directory of Open Access Journals (Sweden)

    Alberto de Luis

    2006-04-01

    Full Text Available In recent years, the biomolecular sciences have been driven forward by overwhelming advances in new biotechnological high-throughput experimental methods and bioinformatic genome-wide computational methods. Such breakthroughs are producing huge amounts of new data that need to be carefully analysed to obtain correct and useful scientific knowledge. One of the fields where this advance has become more intense is the study of the network of ‘protein–protein interactions’, i.e. the ‘interactome’. In this short review we comment on the main data and databases produced in this field in last 5 years. We also present a rationalized scheme of biological definitions that will be useful for a better understanding and interpretation of ‘what a protein–protein interaction is’ and ‘which types of protein–protein interactions are found in a living cell’. Finally, we comment on some assignments of interactome data to defined types of protein interaction and we present a new bioinformatic tool called APIN (Agile Protein Interaction Network browser, which is in development and will be applied to browsing protein interaction databases.

  6. 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

  7. Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

    Science.gov (United States)

    Simonis, Nicolas; Rual, Jean-François; Carvunis, Anne-Ruxandra; Tasan, Murat; Lemmens, Irma; Hirozane-Kishikawa, Tomoko; Hao, Tong; Sahalie, Julie M; Venkatesan, Kavitha; Gebreab, Fana; Cevik, Sebiha; Klitgord, Niels; Fan, Changyu; Braun, Pascal; Li, Ning; Ayivi-Guedehoussou, Nono; Dann, Elizabeth; Bertin, Nicolas; Szeto, David; Dricot, Amélie; Yildirim, Muhammed A; Lin, Chenwei; de Smet, Anne-Sophie; Kao, Huey-Ling; Simon, Christophe; Smolyar, Alex; Ahn, Jin Sook; Tewari, Muneesh; Boxem, Mike; Milstein, Stuart; Yu, Haiyuan; Dreze, Matija; Vandenhaute, Jean; Gunsalus, Kristin C; Cusick, Michael E; Hill, David E; Tavernier, Jan; Roth, Frederick P; Vidal, Marc

    2009-01-01

    To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards.We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of approximately 10,000 x approximately 10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new empirical quality control framework, we show that the resulting data set (Worm Interactome 2007, or WI-2007) was similar in quality to low-throughput data curated from the literature. We filtered previous interaction data sets and integrated them with WI-2007 to generate a high-confidence consolidated map (Worm Interactome version 8, or WI8). This work allowed us to estimate the size of the worm interactome at approximately 116,000 interactions. Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins PMID:19123269

  8. FUNCTIONAL INTERACTOMICS: DETERMINING THE ROLES PLAYED BY MEMBERS OF THE POPULAR BIOMASS PROTEIN-PROTEIN INTERACTOME

    Energy Technology Data Exchange (ETDEWEB)

    Beers, Eric; Brunner, Amy; Helm, Richard

    2015-07-31

    Proteins are molecular machines that are required for nearly all biological functions based on interactions with other molecules such as carbohydrates, lipids, other low molecular weight molecules, nucleic acids and other proteins. Here we map protein-protein interactions relevant to biomass production by focusing on proteins coexpressed in poplar xylem, the site of the majority of lignocellulose synthesis and hence biomass accumulation in poplar. Work proposed here will yield novel biological and bioinformatic resources that can benefit a variety of ongoing and future projects focusing on plant biomass/cell wall biology. The protein-protein interaction map that results from these studies will comprise an advanced view of protein-protein interactions in a model biomass tissue. Results will be made available to the biomass research community to serve as tools for developing new strategies for altering biomass quality and quantity.

  9. Inferring the Brassica rapa interactome using protein-protein interaction data from Arabidopsis thaliana

    OpenAIRE

    Jianhua eYang; Kim eOsman; Mudassar eIqbal; Stekel, Dov J; Zewei eLuo; Armstrong, Susan J; Franklin, F. Chris H.

    2013-01-01

    Following successful completion of the Brassica rapa sequencing project, the next step is to investigate functions of individual genes/proteins. For Arabidopsis thaliana, large amounts of protein-protein interaction (PPI) data are available from the major PPI databases. It is known that Brassica crop species are closely related to A. thaliana. This provides an opportunity to infer the B. rapa interactome using PPI data available from A. thaliana. In this paper, we present an inferred B. rapa ...

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

    Directory of Open Access Journals (Sweden)

    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. Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana.

    Science.gov (United States)

    Yang, Jianhua; Osman, Kim; Iqbal, Mudassar; Stekel, Dov J; Luo, Zewei; Armstrong, Susan J; Franklin, F Chris H

    2012-01-01

    Following successful completion of the Brassica rapa sequencing project, the next step is to investigate functions of individual genes/proteins. For Arabidopsis thaliana, large amounts of protein-protein interaction (PPI) data are available from the major PPI databases (DBs). It is known that Brassica crop species are closely related to A. thaliana. This provides an opportunity to infer the B. rapa interactome using PPI data available from A. thaliana. In this paper, we present an inferred B. rapa interactome that is based on the A. thaliana PPI data from two resources: (i) A. thaliana PPI data from three major DBs, BioGRID, IntAct, and TAIR. (ii) ortholog-based A. thaliana PPI predictions. Linking between B. rapa and A. thaliana was accomplished in three complementary ways: (i) ortholog predictions, (ii) identification of gene duplication based on synteny and collinearity, and (iii) BLAST sequence similarity search. A complementary approach was also applied, which used known/predicted domain-domain interaction data. Specifically, since the two species are closely related, we used PPI data from A. thaliana to predict interacting domains that might be conserved between the two species. The predicted interactome was investigated for the component that contains known A. thaliana meiotic proteins to demonstrate its usability. PMID:23293649

  12. Inferring the Brassica rapa interactome using protein-protein interaction data from Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Jianhua eYang

    2013-01-01

    Full Text Available Following successful completion of the Brassica rapa sequencing project, the next step is to investigate functions of individual genes/proteins. For Arabidopsis thaliana, large amounts of protein-protein interaction (PPI data are available from the major PPI databases. It is known that Brassica crop species are closely related to A. thaliana. This provides an opportunity to infer the B. rapa interactome using PPI data available from A. thaliana. In this paper, we present an inferred B. rapa interactome that is based on the A. thaliana PPI data from two resources: (i A. thaliana PPI data from three major databases, BioGRID, IntAct and TAIR. (ii ortholog-based A. thaliana PPI predictions. Linking between B. rapa and A. thaliana was accomplished in three complementary ways: (i ortholog predictions, (ii identification of gene duplication based on synteny and collinearity, and (iii BLAST sequence similarity search. A complementary approach was also applied, which used known/predicted domain-domain interaction data. Specifically, since the two species are closely related, we used PPI data from A. thaliana to predict interacting domains that might be conserved between the two species. The predicted interactome was investigated for the component that contains known A. thaliana meiotic proteins to demonstrate its usability.

  13. Mapping the Protein-Protein Interactome Networks Using Yeast Two-Hybrid Screens.

    Science.gov (United States)

    Rajagopala, Seesandra Venkatappa

    2015-01-01

    The yeast two-hybrid system (Y2H) is a powerful method to identify binary protein-protein interactions in vivo. Here we describe Y2H screening strategies that use defined libraries of open reading frames (ORFs) and cDNA libraries. The array-based Y2H system is well suited for interactome studies of small genomes with an existing ORFeome clones preferentially in a recombination based cloning system. For large genomes, pooled library screening followed by Y2H pairwise retests may be more efficient in terms of time and resources, but multiple sampling is necessary to ensure comprehensive screening. While the Y2H false positives can be efficiently reduced by using built-in controls, retesting, and evaluation of background activation; implementing the multiple variants of the Y2H vector systems is essential to reduce the false negatives and ensure comprehensive coverage of an interactome. PMID:26621469

  14. 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

    We performed a systematic, large-scale analysis of human protein complexes comprising gene products implicated in many different categories of human disease to create a phenome-interactome network. This was done by integrating quality-controlled interactions of human proteins with a validated, co...

  15. Protein-protein interaction databases: keeping up with growing interactomes

    OpenAIRE

    Lehne Benjamin; Schlitt Thomas

    2009-01-01

    Abstract Over the past few years, the number of known protein-protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein-protein interaction data. Protein-protein interactions have been retrieved from six major databases, integrated and the results compared. The six databases (the Biological General Repository for Interaction Datasets [BioGRID], the Molecular INTeraction ...

  16. Protein-protein interaction databases: keeping up with growing interactomes

    Directory of Open Access Journals (Sweden)

    Lehne Benjamin

    2009-04-01

    Full Text Available Abstract Over the past few years, the number of known protein-protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein-protein interaction data. Protein-protein interactions have been retrieved from six major databases, integrated and the results compared. The six databases (the Biological General Repository for Interaction Datasets [BioGRID], the Molecular INTeraction database [MINT], the Biomolecular Interaction Network Database [BIND], the Database of Interacting Proteins [DIP], the IntAct molecular interaction database [IntAct] and the Human Protein Reference Database [HPRD] differ in scope and content; integration of all datasets is non-trivial owing to differences in data annotation. With respect to human protein-protein interaction data, HPRD seems to be the most comprehensive. To obtain a complete dataset, however, interactions from all six databases have to be combined. To overcome this limitation, meta-databases such as the Agile Protein Interaction Database (APID offer access to integrated protein-protein interaction datasets, although these also currently have certain restrictions.

  17. 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.

  18. Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana

    OpenAIRE

    Yang, Jianhua; Osman, Kim; Iqbal, Mudassar; Stekel, Dov J; Luo, Zewei; Armstrong, Susan J; Franklin, F. Chris H.

    2013-01-01

    Following successful completion of the Brassica rapa sequencing project, the next step is to investigate functions of individual genes/proteins. For Arabidopsis thaliana, large amounts of protein–protein interaction (PPI) data are available from the major PPI databases (DBs). It is known that Brassica crop species are closely related to A. thaliana. This provides an opportunity to infer the B. rapa interactome using PPI data available from A. thaliana. In this paper, we present an inferred B....

  19. A Highly Efficient Approach to Protein Interactome Mapping Based on Collaborative Filtering Framework

    OpenAIRE

    Luo, Xin; You, Zhuhong; Zhou, Mengchu; Li, Shuai; Leung, Hareton; Xia, Yunni; Zhu, Qingsheng

    2015-01-01

    The comprehensive mapping of protein-protein interactions (PPIs) is highly desired for one to gain deep insights into both fundamental cell biology processes and the pathology of diseases. Finely-set small-scale experiments are not only very expensive but also inefficient to identify numerous interactomes despite their high accuracy. High-throughput screening techniques enable efficient identification of PPIs; yet the desire to further extract useful knowledge from these data leads to the pro...

  20. Integration of multiple biological features yields high confidence human protein interactome.

    Science.gov (United States)

    Karagoz, Kubra; Sevimoglu, Tuba; Arga, Kazim Yalcin

    2016-08-21

    The biological function of a protein is usually determined by its physical interaction with other proteins. Protein-protein interactions (PPIs) are identified through various experimental methods and are stored in curated databases. The noisiness of the existing PPI data is evident, and it is essential that a more reliable data is generated. Furthermore, the selection of a set of PPIs at different confidence levels might be necessary for many studies. Although different methodologies were introduced to evaluate the confidence scores for binary interactions, a highly reliable, almost complete PPI network of Homo sapiens is not proposed yet. The quality and coverage of human protein interactome need to be improved to be used in various disciplines, especially in biomedicine. In the present work, we propose an unsupervised statistical approach to assign confidence scores to PPIs of H. sapiens. To achieve this goal PPI data from six different databases were collected and a total of 295,288 non-redundant interactions between 15,950 proteins were acquired. The present scoring system included the context information that was assigned to PPIs derived from eight biological attributes. A high confidence network, which included 147,923 binary interactions between 13,213 proteins, had scores greater than the cutoff value of 0.80, for which sensitivity, specificity, and coverage were 94.5%, 80.9%, and 82.8%, respectively. We compared the present scoring method with others for evaluation. Reducing the noise inherent in experimental PPIs via our scoring scheme increased the accuracy significantly. As it was demonstrated through the assessment of process and cancer subnetworks, this study allows researchers to construct and analyze context-specific networks via valid PPI sets and one can easily achieve subnetworks around proteins of interest at a specified confidence level. PMID:27196966

  1. Targeted Interactomics in Plants Through Protein Complex Isolation

    Institute of Scientific and Technical Information of China (English)

    Geert De Jaeger

    2012-01-01

    TAPtag technology is the most widely applied tool to pick up in situ protein interactions in a proteome wide setting.Our research team has developed a versatile TAP technology platform for protein complex isolation from plants.We isolated complexes for hundreds of proteins and extensively demonstrated the power of our technology for protein discovery,functional analysis of proteins and protein complexes,and the modelling of protein networks.Complexes are purified from Arabidopsis cell suspension cultures or seedlings and we are currently translating the technology towards crop plants to bring complex purification in a developmental context.Besides protein complexes,we are deriving protocol variations to isolate chromatin complexes.

  2. Recent advances in large-scale protein interactome mapping

    OpenAIRE

    Virja Mehta; Laura Trinkle-Mulcahy

    2016-01-01

    Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other ‘omics’ data to gain a better understanding of functional pathways and networks) and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past f...

  3. Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins.

    Science.gov (United States)

    Maeda, Kenji; Anand, Kanchan; Chiapparino, Antonella; Kumar, Arun; Poletto, Mattia; Kaksonen, Marko; Gavin, Anne-Claude

    2013-09-12

    The internal organization of eukaryotic cells into functionally specialized, membrane-delimited organelles of unique composition implies a need for active, regulated lipid transport. Phosphatidylserine (PS), for example, is synthesized in the endoplasmic reticulum and then preferentially associates--through mechanisms not fully elucidated--with the inner leaflet of the plasma membrane. Lipids can travel via transport vesicles. Alternatively, several protein families known as lipid-transfer proteins (LTPs) can extract a variety of specific lipids from biological membranes and transport them, within a hydrophobic pocket, through aqueous phases. Here we report the development of an integrated approach that combines protein fractionation and lipidomics to characterize the LTP-lipid complexes formed in vivo. We applied the procedure to 13 LTPs in the yeast Saccharomyces cerevisiae: the six Sec14 homology (Sfh) proteins and the seven oxysterol-binding homology (Osh) proteins. We found that Osh6 and Osh7 have an unexpected specificity for PS. In vivo, they participate in PS homeostasis and the transport of this lipid to the plasma membrane. The structure of Osh6 bound to PS reveals unique features that are conserved among other metazoan oxysterol-binding proteins (OSBPs) and are required for PS recognition. Our findings represent the first direct evidence, to our knowledge, for the non-vesicular transfer of PS from its site of biosynthesis (the endoplasmic reticulum) to its site of biological activity (the plasma membrane). We describe a new subfamily of OSBPs, including human ORP5 and ORP10, that transfer PS and propose new mechanisms of action for a protein family that is involved in several human pathologies such as cancer, dyslipidaemia and metabolic syndrome. PMID:23934110

  4. Recent advances in large-scale protein interactome mapping.

    Science.gov (United States)

    Mehta, Virja; Trinkle-Mulcahy, Laura

    2016-01-01

    Protein-protein interactions (PPIs) underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other 'omics' data to gain a better understanding of functional pathways and networks) and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past few years. They include improvements in the computation prediction of PPIs and the literature curation of low-throughput studies of specific protein complexes, but also an increase in the deposition of high-quality data from non-biased high-throughput experimental PPI mapping strategies into publicly available databases. PMID:27158474

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

    Directory of Open Access Journals (Sweden)

    Beau J Fenner

    Full Text Available 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.

  6. 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.

  7. Improving the yeast two-hybrid system with permutated fusions proteins: the Varicella Zoster Virus interactome

    Directory of Open Access Journals (Sweden)

    Haas Jürgen

    2010-02-01

    Full Text Available Abstract Background Yeast two-hybrid (Y2H screens have been among the most powerful methods to detect and analyze protein-protein interactions. However, they suffer from a significant degree of false negatives, i.e. true interactions that are not detected, and to a certain degree from false positives, i.e. interactions that appear to take place only in the context of the Y2H assay. While the fraction of false positives remains difficult to estimate, the fraction of false negatives in typical Y2H screens is on the order of 70-90%. Here we present novel Y2H vectors that significantly decrease the number of false negatives and help to mitigate the false positive problem. Results We have constructed two new vectors (pGBKCg and pGADCg that allow us to make both C-terminal fusion proteins of DNA-binding and activation domains. Both vectors can be combined with existing vectors for N-terminal fusions and thus allow four different bait-prey combinations: NN, CC, NC, and CN. We have tested all ~4,900 pairwise combinations of the 70 Varicella-Zoster-Virus (VZV proteins for interactions, using all possible combinations. About ~20,000 individual Y2H tests resulted in 182 NN, 89 NC, 149 CN, and 144 CC interactions. Overlap between screens ranged from 17% (NC-CN to 43% (CN-CC. Performing four screens (i.e. permutations instead of one resulted in about twice as many interactions and thus much fewer false negatives. In addition, interactions that are found in multiple combinations confirm each other and thus provide a quality score. This study is the first systematic analysis of such N- and C-terminal Y2H vectors. Conclusions Permutations of C- and N-terminal Y2H vectors dramatically increase the coverage of interactome studies and thus significantly reduce the number of false negatives. We suggest that future interaction screens should use such vector combinations on a routine basis, not the least because they provide a built-in quality score for Y2H

  8. Global De Novo Protein-Protein Interactome Elucidates Interactions of Drought-Responsive Proteins in Horse Gram (Macrotyloma uniflorum).

    Science.gov (United States)

    Bhardwaj, Jyoti; Gangwar, Indu; Panzade, Ganesh; Shankar, Ravi; Yadav, Sudesh Kumar

    2016-06-01

    Inspired by the availability of de novo transcriptome of horse gram (Macrotyloma uniflorum) and recent developments in systems biology studies, the first ever global protein-protein interactome (PPI) map was constructed for this highly drought-tolerant legume. Large-scale studies of PPIs and the constructed database would provide rationale behind the interplay at cascading translational levels for drought stress-adaptive mechanisms in horse gram. Using a bidirectional approach (interolog and domain-based), a high-confidence interactome map and database for horse gram was constructed. Available transcriptomic information for shoot and root tissues of a sensitive (M-191; genotype 1) and a drought-tolerant (M-249; genotype 2) genotype of horse gram was utilized to draw comparative PPI subnetworks under drought stress. High-confidence 6804 interactions were predicted among 1812 proteins covering about one-fourth of the horse gram proteome. The highest number of interactions (33.86%) in horse gram interactome matched with Arabidopsis PPI data. The top five hub nodes mostly included ubiquitin and heat-shock-related proteins. Higher numbers of PPIs were found to be responsive in shoot tissue (416) and root tissue (2228) of genotype 2 compared with shoot tissue (136) and root tissue (579) of genotype 1. Characterization of PPIs using gene ontology analysis revealed that kinase and transferase activities involved in signal transduction, cellular processes, nucleocytoplasmic transport, protein ubiquitination, and localization of molecules were most responsive to drought stress. Hence, these could be framed in stress adaptive mechanisms of horse gram. Being the first legume global PPI map, it would provide new insights into gene and protein regulatory networks for drought stress tolerance mechanisms in horse gram. Information compiled in the form of database (MauPIR) will provide the much needed high-confidence systems biology information for horse gram genes, proteins, and

  9. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins

    Directory of Open Access Journals (Sweden)

    Rebecca Bish

    2015-07-01

    Full Text Available DDX6 (p54/RCK is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58 of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2 and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2. We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6’s multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6’s interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions

  10. Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins.

    Science.gov (United States)

    Bish, Rebecca; Cuevas-Polo, Nerea; Cheng, Zhe; Hambardzumyan, Dolores; Munschauer, Mathias; Landthaler, Markus; Vogel, Christine

    2015-01-01

    DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6's multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6's interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions-many of which are likely

  11. 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.

  12. 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.

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

    Science.gov (United States)

    Rönnberg, Tuomas; Jääskeläinen, Kirsi; Blot, Guillaume; Parviainen, Ville; Vaheri, Antti; Renkonen, Risto; Bouloy, Michele; Plyusnin, Alexander

    2012-01-01

    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.

  14. The membrane- and soluble-protein helix-helix interactome: similar geometry via different interactions.

    Science.gov (United States)

    Zhang, Shao-Qing; Kulp, Daniel W; Schramm, Chaim A; Mravic, Marco; Samish, Ilan; DeGrado, William F

    2015-03-01

    α Helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of similar folds with various interhelical distances. The composition of the residues that pack at the interface between corresponding motifs shows that hydrophobic residues tend to be more enriched in the water-soluble class of structures and small residues in the transmembrane class. The latter group facilitates packing via sidechain- and backbone-mediated hydrogen bonds within the low-dielectric membrane milieu. The helix-helix interactome space, with its associated sequence preferences and accompanying hydrogen-bonding patterns, should be useful for engineering, prediction, and design of protein structure. PMID:25703378

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

    Directory of Open Access Journals (Sweden)

    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.

  16. Harvesting candidate genes responsible for serious adverse drug reactions from a chemical-protein interactome.

    Directory of Open Access Journals (Sweden)

    Lun Yang

    2009-07-01

    Full Text Available Identifying genetic factors responsible for serious adverse drug reaction (SADR is of critical importance to personalized medicine. However, genome-wide association studies are hampered due to the lack of case-control samples, and the selection of candidate genes is limited by the lack of understanding of the underlying mechanisms of SADRs. We hypothesize that drugs causing the same type of SADR might share a common mechanism by targeting unexpectedly the same SADR-mediating protein. Hence we propose an approach of identifying the common SADR-targets through constructing and mining an in silico chemical-protein interactome (CPI, a matrix of binding strengths among 162 drug molecules known to cause at least one type of SADR and 845 proteins. Drugs sharing the same SADR outcome were also found to possess similarities in their CPI profiles towards this 845 protein set. This methodology identified the candidate gene of sulfonamide-induced toxic epidermal necrolysis (TEN: all nine sulfonamides that cause TEN were found to bind strongly to MHC I (Cw*4, whereas none of the 17 control drugs that do not cause TEN were found to bind to it. Through an insight into the CPI, we found the Y116S substitution of MHC I (B*5703 enhances the unexpected binding of abacavir to its antigen presentation groove, which explains why B*5701, not B*5703, is the risk allele of abacavir-induced hypersensitivity. In conclusion, SADR targets and the patient-specific off-targets could be identified through a systematic investigation of the CPI, generating important hypotheses for prospective experimental validation of the candidate genes.

  17. Exploring a structural protein-drug interactome for new therapeutics in lung cancer.

    Science.gov (United States)

    Peng, Xiaodong; Wang, Fang; Li, Liwei; Bum-Erdene, Khuchtumur; Xu, David; Wang, Bo; Sinn, Anthony A; Pollok, Karen E; Sandusky, George E; Li, Lang; Turchi, John J; Jalal, Shadia I; Meroueh, Samy O

    2014-03-01

    The pharmacology of drugs is often defined by more than one protein target. This property can be exploited to use approved drugs to uncover new targets and signaling pathways in cancer. Towards enabling a rational approach to uncover new targets, we expand a structural protein-ligand interactome () by scoring the interaction among 1000 FDA-approved drugs docked to 2500 pockets on protein structures of the human genome. This afforded a drug-target network whose properties compared favorably with previous networks constructed using experimental data. Among drugs with the highest degree and betweenness two are cancer drugs and one is currently used for treatment of lung cancer. Comparison of predicted cancer and non-cancer targets reveals that the most cancer-specific compounds were also the most selective compounds. Analysis of compound flexibility, hydrophobicity, and size showed that the most selective compounds were low molecular weight fragment-like heterocycles. We use a previously-developed screening approach using the cancer drug erlotinib as a template to screen other approved drugs that mimic its properties. Among the top 12 ranking candidates, four are cancer drugs, two of them kinase inhibitors (like erlotinib). Cellular studies using non-small cell lung cancer (NSCLC) cells revealed that several drugs inhibited lung cancer cell proliferation. We mined patient records at the Regenstrief Medical Record System to explore the possible association of exposure to three of these drugs with occurrence of lung cancer. Preliminary in vivo studies using the non-small cell lung cancer (NCLSC) xenograft model showed that losartan- and astemizole-treated mice had tumors that weighed 50 (p < 0.01) and 15 (p < 0.01) percent less than the treated controls. These results set the stage for further exploration of these drugs and to uncover new drugs for lung cancer therapy. PMID:24402119

  18. Identification of the interactome between fish plasma proteins and Edwardsiella tarda reveals tissue-specific strategies against bacterial infection.

    Science.gov (United States)

    Li, Hui; Huang, Xiaoyan; Zeng, Zaohai; Peng, Xuan-Xian; Peng, Bo

    2016-09-01

    Elucidating the complex pathogen-host interaction is essential for a comprehensive understanding of how these remarkable agents invade their hosts and how the hosts defend against these invaders. During the infection, pathogens interact intensively with host to enable their survival, which can be revealed through their interactome. Edwardsiella tarda is a Gram-negative bacterial pathogen causing huge economic loss in aquaculture and a spectrum of intestinal and extraintestinal diseases in humans. E. tarda is an ideal model for host-pathogen investigation as it infects fish in three distinct steps: entering the host, circulating through the blood and establishing infection. We adopted a previous established proteomic approach that inactivated E. tarda cells and covalent crosslink fish plasma proteins were used to capture plasma proteins and bacterial outer membrane proteins, respectively. By the combinatorial use of proteomic and biochemical approaches, six plasma proteins and seven outer membrane proteins (OMPs) were identified. Interactions among these proteins were validated with protein-array, far-Western blotting and co-immunoprecipitation. At last, seventeen plasma protein-bacteria protein-protein interaction were confirmed to be involved in the interaction network, forming a complex interactome. Compared to our previous results, different host proteins were detected, whereas some of the bacterial proteins were similar, which indicates that hosts adopt tissue-specific strategies to cope with the same pathogen during infection. Thus, our results provide a robust demonstration of both bacterial initiators and host receptors or interacting proteins to further explore infection and anti-infective mechanisms between hosts and microbes. PMID:27458055

  19. Protein interactome mining defines melatonin MT1 receptors as integral component of presynaptic protein complexes of neurons.

    Science.gov (United States)

    Benleulmi-Chaachoua, Abla; Chen, Lina; Sokolina, Kate; Wong, Victoria; Jurisica, Igor; Emerit, Michel Boris; Darmon, Michèle; Espin, Almudena; Stagljar, Igor; Tafelmeyer, Petra; Zamponi, Gerald W; Delagrange, Philippe; Maurice, Pascal; Jockers, Ralf

    2016-01-01

    In mammals, the hormone melatonin is mainly produced by the pineal gland with nocturnal peak levels. Its peripheral and central actions rely either on its intrinsic antioxidant properties or on binding to melatonin MT1 and MT2 receptors, belonging to the G protein-coupled receptor (GPCR) super-family. Melatonin has been reported to be involved in many functions of the central nervous system such as circadian rhythm regulation, neurotransmission, synaptic plasticity, memory, sleep, and also in Alzheimer's disease and depression. However, little is known about the subcellular localization of melatonin receptors and the molecular aspects involved in neuronal functions of melatonin. Identification of protein complexes associated with GPCRs has been shown to be a valid approach to improve our understanding of their function. By combining proteomic and genomic approaches we built an interactome of MT1 and MT2 receptors, which comprises 378 individual proteins. Among the proteins interacting with MT1 , but not with MT2 , we identified several presynaptic proteins, suggesting a potential role of MT1 in neurotransmission. Presynaptic localization of MT1 receptors in the hypothalamus, striatum, and cortex was confirmed by subcellular fractionation experiments and immunofluorescence microscopy. MT1 physically interacts with the voltage-gated calcium channel Cav 2.2 and inhibits Cav 2.2-promoted Ca(2+) entry in an agonist-independent manner. In conclusion, we show that MT1 is part of the presynaptic protein network and negatively regulates Cav 2.2 activity, providing a first hint for potential synaptic functions of MT1. PMID:26514267

  20. Affinity purification-mass spectrometry analysis of bcl-2 interactome identified SLIRP as a novel interacting protein.

    Science.gov (United States)

    Trisciuoglio, D; Desideri, M; Farini, V; De Luca, T; Di Martile, M; Tupone, M G; Urbani, A; D'Aguanno, S; Del Bufalo, D

    2016-01-01

    Members of the bcl-2 protein family share regions of sequence similarity, the bcl-2 homology (BH) domains. Bcl-2, the most studied member of this family, has four BH domains, BH1-4, and has a critical role in resistance to antineoplastic drugs by regulating the mitochondrial apoptotic pathway. Moreover, it is also involved in other relevant cellular processes such as tumor progression, angiogenesis and autophagy. Deciphering the network of bcl-2-interacting factors should provide a critical advance in understanding the different functions of bcl-2. Here, we characterized bcl-2 interactome by mass spectrometry in human lung adenocarcinoma cells. In silico functional analysis associated most part of the identified proteins to mitochondrial functions. Among them we identified SRA stem-loop interacting RNA-binding protein, SLIRP, a mitochondrial protein with a relevant role in regulating mitochondrial messenger RNA (mRNA) homeostasis. We validated bcl-2/SLIRP interaction by immunoprecipitation and immunofluorescence experiments in cancer cell lines from different histotypes. We showed that, although SLIRP is not involved in mediating bcl-2 ability to protect from apoptosis and oxidative damage, bcl-2 binds and stabilizes SLIRP protein and regulates mitochondrial mRNA levels. Moreover, we demonstrated that the BH4 domain of bcl-2 has a role in maintaining this binding. PMID:26866271

  1. The interactome challenge.

    Science.gov (United States)

    Aitchison, John D; Rout, Michael P

    2015-11-23

    The properties of living cells are mediated by a huge number of ever-changing interactions of their component macromolecules forming living machines; collectively, these are termed the interactome. Pathogenic alterations in interactomes mechanistically underlie diseases. Therefore, there exists an essential need for much better tools to reveal and dissect interactomes. This need is only now beginning to be met. PMID:26572620

  2. 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

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

    Directory of Open Access Journals (Sweden)

    Andrey Alexeyenko

    Full Text Available BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

  4. Charting the NF-κB pathway interactome map.

    Directory of Open Access Journals (Sweden)

    Paolo Tieri

    Full Text Available Inflammation is part of a complex physiological response to harmful stimuli and pathogenic stress. The five components of the Nuclear Factor κB (NF-κB family are prominent mediators of inflammation, acting as key transcriptional regulators of hundreds of genes. Several signaling pathways activated by diverse stimuli converge on NF-κB activation, resulting in a regulatory system characterized by high complexity. It is increasingly recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be higher than those taken into consideration from canonical pathway representations. Scope of the present analysis is to provide a wider, systemic picture of the NF-κB signaling system. Data from different sources such as literature, functional enrichment web resources, protein-protein interaction and pathway databases have been gathered, curated, integrated and analyzed in order to reconstruct a single, comprehensive picture of the proteins that interact with, and participate to the NF-κB activation system. Such a reconstruction shows that the NF-κB interactome is substantially different in quantity and quality of components with respect to canonical representations. The analysis highlights that several neglected but topologically central proteins may play a role in the activation of NF-κB mediated responses. Moreover the interactome structure fits with the characteristics of a bow tie architecture. This interactome is intended as an open network resource available for further development, refinement and analysis.

  5. 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

  6. The binary protein interactome of Treponema pallidum--the syphilis spirochete.

    Directory of Open Access Journals (Sweden)

    Björn Titz

    Full Text Available 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.

  7. The Membrane- and Soluble-Protein Helix-Helix Interactome: Similar Geometry via Different Interactions

    OpenAIRE

    Zhang, Shao-Qing; Kulp, Daniel W.; Schramm, Chaim A.; Mravic, Marco; Samish, Ilan; DeGrado, William F

    2015-01-01

    Alpha-helices are a basic unit of protein secondary structure and therefore the interaction between helices is crucial to understanding tertiary and higher-order folds. Comparing subtle variations in the structural and sequence motifs between membrane and soluble proteins sheds light on the different constraints faced by each environment and elucidates the complex puzzle of membrane protein folding. Here, we demonstrate that membrane and water-soluble helix pairs share a small number of simil...

  8. 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

  9. The comprehensive native interactome of a fully functional tagged prion protein.

    Directory of Open Access Journals (Sweden)

    Dorothea Rutishauser

    Full Text Available The enumeration of the interaction partners of the cellular prion protein, PrP(C, may help clarifying its elusive molecular function. Here we added a carboxy proximal myc epitope tag to PrP(C. When expressed in transgenic mice, PrP(myc carried a GPI anchor, was targeted to lipid rafts, and was glycosylated similarly to PrP(C. PrP(myc antagonized the toxicity of truncated PrP, restored prion infectibility of PrP(C-deficient mice, and was physically incorporated into PrP(Sc aggregates, indicating that it possessed all functional characteristics of genuine PrP(C. We then immunopurified myc epitope-containing protein complexes from PrP(myc transgenic mouse brains. Gentle differential elution with epitope-mimetic decapeptides, or a scrambled version thereof, yielded 96 specifically released proteins. Quantitative mass spectrometry with isotope-coded tags identified seven proteins which co-eluted equimolarly with PrP(C and may represent component of a multiprotein complex. Selected PrP(C interactors were validated using independent methods. Several of these proteins appear to exert functions in axomyelinic maintenance.

  10. Recent advances in large-scale protein interactome mapping [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Virja Mehta

    2016-04-01

    Full Text Available Protein-protein interactions (PPIs underlie most, if not all, cellular functions. The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other ‘omics’ data to gain a better understanding of functional pathways and networks and for focused biological studies. Despite the significant challenges of such an undertaking, major strides have been made over the past few years. They include improvements in the computation prediction of PPIs and the literature curation of low-throughput studies of specific protein complexes, but also an increase in the deposition of high-quality data from non-biased high-throughput experimental PPI mapping strategies into publicly available databases.

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

    International Nuclear Information System (INIS)

    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)

  12. The HTLV-1 Tax interactome

    Directory of Open Access Journals (Sweden)

    Kettmann Richard

    2008-08-01

    Full Text Available Abstract The Tax1 oncoprotein encoded by Human T-lymphotropic virus type I is a major determinant of viral persistence and pathogenesis. Tax1 affects a wide variety of cellular signalling pathways leading to transcriptional activation, proliferation and ultimately transformation. To carry out these functions, Tax1 interacts with and modulates activity of a number of cellular proteins. In this review, we summarize the present knowledge of the Tax1 interactome and propose a rationale for the broad range of cellular proteins identified so far.

  13. 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.

  14. 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.

  15. Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling.

    Science.gov (United States)

    Larance, Mark; Kirkwood, Kathryn J; Tinti, Michele; Brenes Murillo, Alejandro; Ferguson, Michael A J; Lamond, Angus I

    2016-07-01

    We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754).

  16. Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling*

    Science.gov (United States)

    Larance, Mark; Kirkwood, Kathryn J.; Tinti, Michele; Brenes Murillo, Alejandro; Ferguson, Michael A. J.; Lamond, Angus I.

    2016-01-01

    We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754). PMID:27114452

  17. PTIR: Predicted Tomato Interactome Resource.

    Science.gov (United States)

    Yue, Junyang; Xu, Wei; Ban, Rongjun; Huang, Shengxiong; Miao, Min; Tang, Xiaofeng; Liu, Guoqing; Liu, Yongsheng

    2016-01-01

    Protein-protein interactions (PPIs) are involved in almost all biological processes and form the basis of the entire interactomics systems of living organisms. Identification and characterization of these interactions are fundamental to elucidating the molecular mechanisms of signal transduction and metabolic pathways at both the cellular and systemic levels. Although a number of experimental and computational studies have been performed on model organisms, the studies exploring and investigating PPIs in tomatoes remain lacking. Here, we developed a Predicted Tomato Interactome Resource (PTIR), based on experimentally determined orthologous interactions in six model organisms. The reliability of individual PPIs was also evaluated by shared gene ontology (GO) terms, co-evolution, co-expression, co-localization and available domain-domain interactions (DDIs). Currently, the PTIR covers 357,946 non-redundant PPIs among 10,626 proteins, including 12,291 high-confidence, 226,553 medium-confidence, and 119,102 low-confidence interactions. These interactions are expected to cover 30.6% of the entire tomato proteome and possess a reasonable distribution. In addition, ten randomly selected PPIs were verified using yeast two-hybrid (Y2H) screening or a bimolecular fluorescence complementation (BiFC) assay. The PTIR was constructed and implemented as a dedicated database and is available at http://bdg.hfut.edu.cn/ptir/index.html without registration. PMID:27121261

  18. Dengue-2 Structural Proteins Associate with Human Proteins to Produce a Coagulation and Innate Immune Response Biased Interactome

    Directory of Open Access Journals (Sweden)

    Soares Luis RB

    2011-01-01

    Full Text Available Abstract Background Dengue virus infection is a public health threat to hundreds of millions of individuals in the tropical regions of the globe. Although Dengue infection usually manifests itself in its mildest, though often debilitating clinical form, dengue fever, life-threatening complications commonly arise in the form of hemorrhagic shock and encephalitis. The etiological basis for the virus-induced pathology in general, and the different clinical manifestations in particular, are not well understood. We reasoned that a detailed knowledge of the global biological processes affected by virus entry into a cell might help shed new light on this long-standing problem. Methods A bacterial two-hybrid screen using DENV2 structural proteins as bait was performed, and the results were used to feed a manually curated, global dengue-human protein interaction network. Gene ontology and pathway enrichment, along with network topology and microarray meta-analysis, were used to generate hypothesis regarding dengue disease biology. Results Combining bioinformatic tools with two-hybrid technology, we screened human cDNA libraries to catalogue proteins physically interacting with the DENV2 virus structural proteins, Env, cap and PrM. We identified 31 interacting human proteins representing distinct biological processes that are closely related to the major clinical diagnostic feature of dengue infection: haemostatic imbalance. In addition, we found dengue-binding human proteins involved with additional key aspects, previously described as fundamental for virus entry into cells and the innate immune response to infection. Construction of a DENV2-human global protein interaction network revealed interesting biological properties suggested by simple network topology analysis. Conclusions Our experimental strategy revealed that dengue structural proteins interact with human protein targets involved in the maintenance of blood coagulation and innate anti

  19. Mapping the functional yeast ABC transporter interactome

    OpenAIRE

    Snider, Jamie; Hanif, Asad; Lee, Mid Eum; Jin, Ke; Yu, Analyn R.; Graham, Chris; Chuk, Matthew; Damjanovic, Dunja; Wierzbicka, Marta; Tang, Priscilla; Balderes, Dina; Wong, Victoria; Jessulat, Matthew; Darowski, Katelyn D.; Luis, Bryan-Joseph San

    2013-01-01

    ABC transporters are a ubiquitous class of integral membrane proteins of immense clinical interest because of their strong association with human disease and pharmacology. To improve our understanding of these proteins, we used Membrane Yeast Two-Hybrid (MYTH) technology to map the protein interactome of all non-mitochondrial ABC transporters in the model organism Saccharomy cescerevisiae, and combined this data with previously reported yeast ABC transporter interactions in the BioGRID databa...

  20. Mapping the functional yeast ABC transporter interactome.

    Science.gov (United States)

    Snider, Jamie; Hanif, Asad; Lee, Mid Eum; Jin, Ke; Yu, Analyn R; Graham, Chris; Chuk, Matthew; Damjanovic, Dunja; Wierzbicka, Marta; Tang, Priscilla; Balderes, Dina; Wong, Victoria; Jessulat, Matthew; Darowski, Katelyn D; San Luis, Bryan-Joseph; Shevelev, Igor; Sturley, Stephen L; Boone, Charles; Greenblatt, Jack F; Zhang, Zhaolei; Paumi, Christian M; Babu, Mohan; Park, Hay-Oak; Michaelis, Susan; Stagljar, Igor

    2013-09-01

    ATP-binding cassette (ABC) transporters are a ubiquitous class of integral membrane proteins of immense clinical interest because of their strong association with human disease and pharmacology. To improve our understanding of these proteins, we used membrane yeast two-hybrid technology to map the protein interactome of all of the nonmitochondrial ABC transporters in the model organism Saccharomyces cerevisiae and combined this data with previously reported yeast ABC transporter interactions in the BioGRID database to generate a comprehensive, integrated 'interactome'. We show that ABC transporters physically associate with proteins involved in an unexpectedly diverse range of functions. We specifically examine the importance of the physical interactions of ABC transporters in both the regulation of one another and in the modulation of proteins involved in zinc homeostasis. The interaction network presented here will be a powerful resource for increasing our fundamental understanding of the cellular role and regulation of ABC transporters. PMID:23831759

  1. Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome--clozapine-induced agranulocytosis as a case study.

    Directory of Open Access Journals (Sweden)

    Lun Yang

    2011-03-01

    Full Text Available In the era of personalized medical practice, understanding the genetic basis of patient-specific adverse drug reaction (ADR is a major challenge. Clozapine provides effective treatments for schizophrenia but its usage is limited because of life-threatening agranulocytosis. A recent high impact study showed the necessity of moving clozapine to a first line drug, thus identifying the biomarkers for drug-induced agranulocytosis has become important. Here we report a methodology termed as antithesis chemical-protein interactome (CPI, which utilizes the docking method to mimic the differences in the drug-protein interactions across a panel of human proteins. Using this method, we identified HSPA1A, a known susceptibility gene for CIA, to be the off-target of clozapine. Furthermore, the mRNA expression of HSPA1A-related genes (off-target associated systems was also found to be differentially expressed in clozapine treated leukemia cell line. Apart from identifying the CIA causal genes we identified several novel candidate genes which could be responsible for agranulocytosis. Proteins related to reactive oxygen clearance system, such as oxidoreductases and glutathione metabolite enzymes, were significantly enriched in the antithesis CPI. This methodology conducted a multi-dimensional analysis of drugs' perturbation to the biological system, investigating both the off-targets and the associated off-systems to explore the molecular basis of an adverse event or the new uses for old drugs.

  2. SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome.

    Science.gov (United States)

    Yang, Lun; Luo, Heng; Chen, Jian; Xing, Qinghe; He, Lin

    2009-07-01

    Serious adverse drug reactions (SADRs) are caused by unexpected drug-human protein interactions, and some polymorphisms within binding pockets make the population carrying these polymorphisms susceptible to SADR. Predicting which populations are likely to be susceptible to SADR will not only strengthen drug safety, but will also assist enterprises to adjust R&D and marketing strategies. Making such predictions has recently been facilitated by the introduction of a web server named SePreSA. The server has a comprehensive collection of the structural models of nearly all the well known SADR targets. Once a drug molecule is submitted, the scale of its potential interaction with multi-SADR targets is calculated using the DOCK program. The server utilizes a 2-directional Z-transformation scoring algorithm, which computes the relative drug-protein interaction strength based on the docking-score matrix of a chemical-protein interactome, thus achieve greater accuracy in prioritizing SADR targets than simply using dock scoring functions. The server also suggests the binding pattern of the lowest docking score through 3D visualization, by highlighting and visualizing amino acid residues involved in the binding on the customer's browser. Polymorphism information for different populations for each of the interactive residues will be displayed, helping users to deduce the population-specific susceptibility of their drug molecule. The server is freely available at http://SePreSA.Bio-X.cn/. PMID:19417066

  3. MaxiK channel interactome reveals its interaction with GABA transporter 3 and heat shock protein 60 in the mammalian brain.

    Science.gov (United States)

    Singh, H; Li, M; Hall, L; Chen, S; Sukur, S; Lu, R; Caputo, A; Meredith, A L; Stefani, E; Toro, L

    2016-03-11

    Large conductance voltage and calcium-activated potassium (MaxiK) channels are activated by membrane depolarization and elevated cytosolic Ca(2+). In the brain, they localize to neurons and astrocytes, where they play roles such as resetting the membrane potential during an action potential, neurotransmitter release, and neurovascular coupling. MaxiK channels are known to associate with several modulatory proteins and accessory subunits, and each of these interactions can have distinct physiological consequences. To uncover new players in MaxiK channel brain physiology, we applied a directed proteomic approach and obtained MaxiK channel pore-forming α subunit brain interactome using specific antibodies. Controls included immunoprecipitations with rabbit immunoglobulin G (IgG) and with anti-MaxiK antibodies in wild type and MaxiK channel knockout mice (Kcnma1(-/-)), respectively. We have found known and unreported interactive partners that localize to the plasma membrane, extracellular space, cytosol and intracellular organelles including mitochondria, nucleus, endoplasmic reticulum and Golgi apparatus. Localization of MaxiK channel to mitochondria was further confirmed using purified brain mitochondria colabeled with MitoTracker. Independent proof of MaxiK channel interaction with previously unidentified partners is given for GABA transporter 3 (GAT3) and heat shock protein 60 (HSP60). In human embryonic kidney 293 cells containing SV40 T-antigen (HEK293T) cells, both GAT3 and HSP60 coimmunoprecipitated and colocalized with MaxiK channel; colabeling was observed mainly at the cell periphery with GAT3 and intracellularly with HSP60 with protein proximity indices of ∼ 0.6 and ∼ 0.4, respectively. In rat primary hippocampal neurons, colocalization index was identical for GAT3 (∼ 0.6) and slightly higher for HSP60 (∼ 0.5) association with MaxiK channel. The results of this study provide a complete interactome of MaxiK channel the mouse brain, further establish

  4. MaxiK channel interactome reveals its interaction with GABA transporter 3 and heat shock protein 60 in the mammalian brain.

    Science.gov (United States)

    Singh, H; Li, M; Hall, L; Chen, S; Sukur, S; Lu, R; Caputo, A; Meredith, A L; Stefani, E; Toro, L

    2016-03-11

    Large conductance voltage and calcium-activated potassium (MaxiK) channels are activated by membrane depolarization and elevated cytosolic Ca(2+). In the brain, they localize to neurons and astrocytes, where they play roles such as resetting the membrane potential during an action potential, neurotransmitter release, and neurovascular coupling. MaxiK channels are known to associate with several modulatory proteins and accessory subunits, and each of these interactions can have distinct physiological consequences. To uncover new players in MaxiK channel brain physiology, we applied a directed proteomic approach and obtained MaxiK channel pore-forming α subunit brain interactome using specific antibodies. Controls included immunoprecipitations with rabbit immunoglobulin G (IgG) and with anti-MaxiK antibodies in wild type and MaxiK channel knockout mice (Kcnma1(-/-)), respectively. We have found known and unreported interactive partners that localize to the plasma membrane, extracellular space, cytosol and intracellular organelles including mitochondria, nucleus, endoplasmic reticulum and Golgi apparatus. Localization of MaxiK channel to mitochondria was further confirmed using purified brain mitochondria colabeled with MitoTracker. Independent proof of MaxiK channel interaction with previously unidentified partners is given for GABA transporter 3 (GAT3) and heat shock protein 60 (HSP60). In human embryonic kidney 293 cells containing SV40 T-antigen (HEK293T) cells, both GAT3 and HSP60 coimmunoprecipitated and colocalized with MaxiK channel; colabeling was observed mainly at the cell periphery with GAT3 and intracellularly with HSP60 with protein proximity indices of ∼ 0.6 and ∼ 0.4, respectively. In rat primary hippocampal neurons, colocalization index was identical for GAT3 (∼ 0.6) and slightly higher for HSP60 (∼ 0.5) association with MaxiK channel. The results of this study provide a complete interactome of MaxiK channel the mouse brain, further establish

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

    Science.gov (United States)

    Minjarez, Benito; Calderón-González, Karla Grisel; Valero Rustarazo, Ma Luz; Herrera-Aguirre, María Esther; Labra-Barrios, María Luisa; Rincon-Limas, Diego E; Sánchez Del Pino, Manuel M; Mena, Raul; Luna-Arias, Juan Pedro

    2016-06-01

    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]. PMID:27257613

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

    Directory of Open Access Journals (Sweden)

    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].

  7. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells.

    Science.gov (United States)

    Whisenant, Thomas C; Peralta, Eigen R; Aarreberg, Lauren D; Gao, Nina J; Head, Steven R; Ordoukhanian, Phillip; Williamson, Jamie R; Salomon, Daniel R

    2015-01-01

    Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. We immunoprecipitated U2AF2 to identify what mRNA transcripts were bound as a function of activation by TCR crosslinking and costimulation. In parallel, mass spectrometry revealed the proteins incorporated into the U2AF2-centered RNA/protein interactome. Molecules that retained interaction with the U2AF2 complex after RNAse treatment were designated as "central" interactome members (CIMs). Mass spectrometry also identified a second class of activation-induced proteins, "peripheral" interactome members (PIMs), that bound to the same transcripts but were not in physical association with U2AF2 or its partners. siRNA knockdown of two CIMs and two PIMs caused changes in activation marker expression, cytokine secretion, and gene expression that were unique to each protein and mapped to pathways associated with key aspects of T cell activation. While knocking down the PIM, SYNCRIP, impacts a limited but immunologically important set of U2AF2-bound transcripts, knockdown of U2AF1 significantly impairs assembly of the majority of protein and mRNA components in the activation-induced interactome. These results demonstrated that CIMs and PIMs, either directly or indirectly through RNA, assembled into activation-induced U2AF2 complexes and play roles in post-transcriptional regulation of genes related to cytokine secretion. These data suggest an additional layer of regulation mediated by the activation-induced assembly of RNA

  8. Interactome Analysis of the NS1 Protein Encoded by Influenza A H1N1 Virus Reveals a Positive Regulatory Role of Host Protein PRP19 in Viral Replication.

    Science.gov (United States)

    Kuo, Rei-Lin; Li, Zong-Hua; Li, Li-Hsin; Lee, Kuo-Ming; Tam, Ee-Hong; Liu, Helene M; Liu, Hao-Ping; Shih, Shin-Ru; Wu, Chih-Ching

    2016-05-01

    Influenza A virus, which can cause severe respiratory illnesses in infected individuals, is responsible for worldwide human pandemics. The NS1 protein encoded by this virus plays a crucial role in regulating the host antiviral response through various mechanisms. In addition, it has been reported that NS1 can modulate cellular pre-mRNA splicing events. To investigate the biological processes potentially affected by the NS1 protein in host cells, NS1-associated protein complexes in human cells were identified using coimmunoprecipitation combined with GeLC-MS/MS. By employing software to build biological process and protein-protein interaction networks, NS1-interacting cellular proteins were found to be related to RNA splicing/processing, cell cycle, and protein folding/targeting cellular processes. By monitoring spliced and unspliced RNAs of a reporter plasmid, we further validated that NS1 can interfere with cellular pre-mRNA splicing. One of the identified proteins, pre-mRNA-processing factor 19 (PRP19), was confirmed to interact with the NS1 protein in influenza A virus-infected cells. Importantly, depletion of PRP19 in host cells reduced replication of influenza A virus. In summary, the interactome of influenza A virus NS1 in host cells was comprehensively profiled, and our findings reveal a novel regulatory role for PRP19 in viral replication. PMID:27096427

  9. A proteome-scale map of the human interactome network.

    Science.gov (United States)

    Rolland, Thomas; Taşan, Murat; Charloteaux, Benoit; Pevzner, Samuel J; Zhong, Quan; Sahni, Nidhi; Yi, Song; Lemmens, Irma; Fontanillo, Celia; Mosca, Roberto; Kamburov, Atanas; Ghiassian, Susan D; Yang, Xinping; Ghamsari, Lila; Balcha, Dawit; Begg, Bridget E; Braun, Pascal; Brehme, Marc; Broly, Martin P; Carvunis, Anne-Ruxandra; Convery-Zupan, Dan; Corominas, Roser; Coulombe-Huntington, Jasmin; Dann, Elizabeth; Dreze, Matija; Dricot, Amélie; Fan, Changyu; Franzosa, Eric; Gebreab, Fana; Gutierrez, Bryan J; Hardy, Madeleine F; Jin, Mike; Kang, Shuli; Kiros, Ruth; Lin, Guan Ning; Luck, Katja; MacWilliams, Andrew; Menche, Jörg; Murray, Ryan R; Palagi, Alexandre; Poulin, Matthew M; Rambout, Xavier; Rasla, John; Reichert, Patrick; Romero, Viviana; Ruyssinck, Elien; Sahalie, Julie M; Scholz, Annemarie; Shah, Akash A; Sharma, Amitabh; Shen, Yun; Spirohn, Kerstin; Tam, Stanley; Tejeda, Alexander O; Trigg, Shelly A; Twizere, Jean-Claude; Vega, Kerwin; Walsh, Jennifer; Cusick, Michael E; Xia, Yu; Barabási, Albert-László; Iakoucheva, Lilia M; Aloy, Patrick; De Las Rivas, Javier; Tavernier, Jan; Calderwood, Michael A; Hill, David E; Hao, Tong; Roth, Frederick P; Vidal, Marc

    2014-11-20

    Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ?14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ?30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a "broader" human interactome network than currently appreciated. The map also uncovers significant interconnectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high-quality interactome models will help "connect the dots" of the genomic revolution.

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

    Directory of Open Access Journals (Sweden)

    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

  11. Biochemical Methods to Analyze Wnt Protein Secretion.

    Science.gov (United States)

    Glaeser, Kathrin; Boutros, Michael; Gross, Julia Christina

    2016-01-01

    Wnt proteins act as potent morphogens in various aspects of embryonic development and adult tissue homeostasis. However, in addition to its physiological importance, aberrant Wnt signaling has been linked to the onset and progression of different types of cancer. On the cellular level, the secretion of Wnt proteins involves trafficking of lipid-modified Wnts from the endoplasmic reticulum (ER) to Golgi and further compartments via the Wnt cargo receptor evenness interrupted. Others and we have recently shown that Wnt proteins are secreted on extracellular vesicles (EVs) such as microvesicles and exosomes. Although more details about specific regulation of Wnt secretion steps are emerging, it remains largely unknown how Wnt proteins are channeled into different release pathways such as lipoprotein particles, EVs and cytonemes. Here, we describe protocols to purify and quantify Wnts from the supernatant of cells by either assessing total Wnt proteins in the supernatant or monitoring Wnt proteins on EVs. Purified Wnts from the supernatant as well as total cellular protein content can be investigated by immunoblotting. Additionally, the relative activity of canonical Wnts in the supernatant can be assessed by a dual-luciferase Wnt reporter assay. Quantifying the amount of secreted Wnt proteins and their activity in the supernatant of cells allows the investigation of intracellular trafficking events that regulate Wnt secretion and the role of extracellular modulators of Wnt spreading. PMID:27590148

  12. 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.

  13. Toward functional analysis of protein interactome using "in vitro virus": in silico analyses of Fos/Jun interactors.

    Science.gov (United States)

    Miyamoto-Sato, Etsuko; Yanagawa, Hiroshi

    2006-01-01

    Our high-throughput in vitro virus (IVV) method for selection of protein-protein interactions (PPI) and complexes, based on a simple cell-free co-translation and selection followed by computational sequence data analysis, was previously used to identify 31 Fos and Jun interactors. Here, in silico analyses of biological function, localization and phenotype of these AP-1 (Fos/Jun) interactors were performed. The results suggest that Fos and Jun do not necessarily work together, but also interact separately with novel interactors, including products of disease-related genes. Fos showed transcription-related activities, while Jun interacted with motor-related and structural proteins. The reliability of the IVV selection for the Fos interactors was further confirmed by means of in vitro reciprocal prey and bait protein experiments and co-immunoprecipitation. Further study of these novel interactors may provide clues to new pathways or mechanisms of biological functions and diseases.

  14. Proteomics: an efficient tool to analyze nematode proteins

    Science.gov (United States)

    Proteomic technologies have been successfully used to analyze proteins structure and characterization in plants, animals, microbes and humans. We used proteomics methodologies to separate and characterize soybean cyst nematode (SCN) proteins. Optimizing the quantity of proteins required to separat...

  15. Essential and non-essential interactions in interactome networks: the Escherichia coli division proteins FtsQ-FtsN interaction.

    Science.gov (United States)

    Grenga, L; Rizzo, A; Paolozzi, L; Ghelardini, P

    2013-12-01

    The Escherichia coli division protein FtsQ, which plays a central role in the septosome assembly, interacts with several protein partners of the division machinery. Its interaction with FtsB and FtsL allows the formation of the trimeric complex connecting the early cytoplasmic cell division proteins with the late, essentially periplasmic, ones. Little is known about the interactions that FtsQ contracts with other divisome components, besides the fact that all are localized in its periplasmic domain. In this domain, two independent subdomains, both involved in FtsQ, FtsI and FtsN interactions, were also identified. The study of FtsQ interaction-defective mutants constituted a basis to investigate the biological significance of its interactions. However, in the case of interactions where two independent sites are involved, mutation(s) in one domain can be suppressed by the presence of the still-functional second interaction region. To ascertain the biological role of these interactions, it is therefore necessary to select double mutants, where both sites are impaired. This paper describes the behaviour of FtsQ double mutants that have lost the ability to interact with FtsN, which is the last component in the hierarchy of divisome assembly, and is necessary to guarantee its stability and function. PMID:23782448

  16. 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

  17. 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...

  18. 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.

  19. 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

  20. Electron transfer interactome of cytochrome C.

    Directory of Open Access Journals (Sweden)

    Alexander N Volkov

    Full Text Available Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes - necessary for a comprehensive understanding of the cellular signaling and metabolism - is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc. Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1 reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2 indicates that the ET can take place from more than one protein-protein orientation, and 3 suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility.

  1. Network Organization of the Huntingtin Proteomic Interactome in Mammalian Brain

    OpenAIRE

    Shirasaki, Dyna I; Greiner, Erin R.; Al-Ramahi, Ismael; Gray, Michelle; Boontheung, Pinmanee; Geschwind, Daniel H.; Botas, Juan; Coppola, Giovanni; Horvath, Steve; Loo, Joseph A.; Yang, X. William

    2012-01-01

    We used affinity-purification mass spectrometry to identify 747 candidate proteins that are complexed with Huntingtin (Htt) in distinct brain regions and ages in Huntington’s disease (HD) and wildtype mouse brains. To gain a systems-level view of the Htt interactome, we applied Weighted Gene Correlation Network Analysis (WGCNA) to the entire proteomic dataset to unveil a verifiable rank of Htt-correlated proteins and a network of Htt-interacting protein modules, with each module highlighting ...

  2. Computational analysis of the LRRK2 interactome

    Directory of Open Access Journals (Sweden)

    Claudia Manzoni

    2015-02-01

    Full Text Available LRRK2 was identified in 2004 as the causative protein product of the Parkinson’s disease locus designated PARK8. In the decade since then, genetic studies have revealed at least 6 dominant mutations in LRRK2 linked to Parkinson’s disease, alongside one associated with cancer. It is now well established that coding changes in LRRK2 are one of the most common causes of Parkinson’s. Genome-wide association studies (GWAs have, more recently, reported single nucleotide polymorphisms (SNPs around the LRRK2 locus to be associated with risk of developing sporadic Parkinson’s disease and inflammatory bowel disorder. The functional research that has followed these genetic breakthroughs has generated an extensive literature regarding LRRK2 pathophysiology; however, there is still no consensus as to the biological function of LRRK2. To provide insight into the aspects of cell biology that are consistently related to LRRK2 activity, we analysed the plethora of candidate LRRK2 interactors available through the BioGRID and IntAct data repositories. We then performed GO terms enrichment for the LRRK2 interactome. We found that, in two different enrichment portals, the LRRK2 interactome was associated with terms referring to transport, cellular organization, vesicles and the cytoskeleton. We also verified that 21 of the LRRK2 interactors are genetically linked to risk for Parkinson’s disease or inflammatory bowel disorder. The implications of these findings are discussed, with particular regard to potential novel areas of investigation.

  3. Computational analysis of the LRRK2 interactome.

    Science.gov (United States)

    Manzoni, Claudia; Denny, Paul; Lovering, Ruth C; Lewis, Patrick A

    2015-01-01

    LRRK2 was identified in 2004 as the causative protein product of the Parkinson's disease locus designated PARK8. In the decade since then, genetic studies have revealed at least 6 dominant mutations in LRRK2 linked to Parkinson's disease, alongside one associated with cancer. It is now well established that coding changes in LRRK2 are one of the most common causes of Parkinson's. Genome-wide association studies (GWAs) have, more recently, reported single nucleotide polymorphisms (SNPs) around the LRRK2 locus to be associated with risk of developing sporadic Parkinson's disease and inflammatory bowel disorder. The functional research that has followed these genetic breakthroughs has generated an extensive literature regarding LRRK2 pathophysiology; however, there is still no consensus as to the biological function of LRRK2. To provide insight into the aspects of cell biology that are consistently related to LRRK2 activity, we analysed the plethora of candidate LRRK2 interactors available through the BioGRID and IntAct data repositories. We then performed GO terms enrichment for the LRRK2 interactome. We found that, in two different enrichment portals, the LRRK2 interactome was associated with terms referring to transport, cellular organization, vesicles and the cytoskeleton. We also verified that 21 of the LRRK2 interactors are genetically linked to risk for Parkinson's disease or inflammatory bowel disorder. The implications of these findings are discussed, with particular regard to potential novel areas of investigation. PMID:25737818

  4. Competing endogenous RNA and interactome bioinformatic analyses on human telomerase.

    Science.gov (United States)

    Arancio, Walter; Pizzolanti, Giuseppe; Genovese, Swonild Ilenia; Baiamonte, Concetta; Giordano, Carla

    2014-04-01

    We present a classic interactome bioinformatic analysis and a study on competing endogenous (ce) RNAs for hTERT. The hTERT gene codes for the catalytic subunit and limiting component of the human telomerase complex. Human telomerase reverse transcriptase (hTERT) is essential for the integrity of telomeres. Telomere dysfunctions have been widely reported to be involved in aging, cancer, and cellular senescence. The hTERT gene network has been analyzed using the BioGRID interaction database (http://thebiogrid.org/) and related analysis tools such as Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index) and GeneMANIA (http://genemania.org/). The network of interaction of hTERT transcripts has been further analyzed following the competing endogenous (ce) RNA hypotheses (messenger [m] RNAs cross-talk via micro [mi] RNAs) using the miRWalk database and tools (www.ma.uni-heidelberg.de/apps/zmf/mirwalk/). These analyses suggest a role for Akt, nuclear factor-κB (NF-κB), heat shock protein 90 (HSP90), p70/p80 autoantigen, 14-3-3 proteins, and dynein in telomere functions. Roles for histone acetylation/deacetylation and proteoglycan metabolism are also proposed. PMID:24713059

  5. 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.

    Directory of Open Access Journals (Sweden)

    Marcelo Falsarella Carazzolle

    Full Text Available 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

  6. 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.

  7. Defining a Modular Signalling Network from the Fly Interactome

    Directory of Open Access Journals (Sweden)

    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.

  8. Quantum Interactomics and Cancer Molecular Mechanisms

    OpenAIRE

    Baianu, Dr. I.C.

    1987-01-01

    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...

  9. 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.

  10. Nuclear Functions of Nucleolin through Global Proteomics and Interactomic Approaches.

    Science.gov (United States)

    Salvetti, Anna; Couté, Yohann; Epstein, Alberto; Arata, Loredana; Kraut, Alexandra; Navratil, Vincent; Bouvet, Philippe; Greco, Anna

    2016-05-01

    Nucleolin (NCL) is a major component of the cell nucleolus, which has the ability to rapidly shuttle to several other cells' compartments. NCL plays important roles in a variety of essential functions, among which are ribosome biogenesis, gene expression, and cell growth. However, the precise mechanisms underlying NCL functions are still unclear. Our study aimed to provide new information on NCL functions via the identification of its nuclear interacting partners. Using an interactomics approach, we identified 140 proteins co-purified with NCL, among which 100 of them were specifically found to be associated with NCL after RNase digestion. The functional classification of these proteins confirmed the prominent role of NCL in ribosome biogenesis and additionally revealed the possible involvement of nuclear NCL in several pre-mRNA processing pathways through its interaction with RNA helicases and proteins participating in pre-mRNA splicing, transport, or stability. NCL knockdown experiments revealed that NCL regulates the localization of EXOSC10 and the amount of ZC3HAV1, two components of the RNA exosome, further suggesting its involvement in the control of mRNA stability. Altogether, this study describes the first nuclear interactome of human NCL and provides the basis for further understanding the mechanisms underlying the essential functions of this nucleolar protein. PMID:27049334

  11. HIV-host interactome revealed directly from infected cells.

    Science.gov (United States)

    Luo, Yang; Jacobs, Erica Y; Greco, Todd M; Mohammed, Kevin D; Tong, Tommy; Keegan, Sarah; Binley, James M; Cristea, Ileana M; Fenyö, David; Rout, Michael P; Chait, Brian T; Muesing, Mark A

    2016-01-01

    Although genetically compact, HIV-1 commandeers vast arrays of cellular machinery to sustain and protect it during cycles of viral outgrowth. Transposon-mediated saturation linker scanning mutagenesis was used to isolate fully replication-competent viruses harbouring a potent foreign epitope tag. Using these viral isolates, we performed differential isotopic labelling and affinity-capture mass spectrometric analyses on samples obtained from cultures of human lymphocytes to classify the vicinal interactomes of the viral Env and Vif proteins as they occur during natural infection. Importantly, interacting proteins were recovered without bias, regardless of their potential for positive, negative or neutral impact on viral replication. We identified specific host associations made with trimerized Env during its biosynthesis, at virological synapses, with innate immune effectors (such as HLA-E) and with certain cellular signalling pathways (for example, Notch1). We also defined Vif associations with host proteins involved in the control of nuclear transcription and nucleoside biosynthesis as well as those interacting stably or transiently with the cytoplasmic protein degradation apparatus. Our approach is broadly applicable to elucidating pathogen-host interactomes, providing high-certainty identification of interactors by their direct access during cycling infection. Understanding the pathophysiological consequences of these associations is likely to provide strategic targets for antiviral intervention. PMID:27572969

  12. A viral-human interactome based on structural motif-domain interactions captures the human infectome.

    Directory of Open Access Journals (Sweden)

    Aldo Segura-Cabrera

    Full Text Available Protein interactions between a pathogen and its host are fundamental in the establishment of the pathogen and underline the infection mechanism. In the present work, we developed a single predictive model for building a host-viral interactome based on the identification of structural descriptors from motif-domain interactions of protein complexes deposited in the Protein Data Bank (PDB. The structural descriptors were used for searching, in a database of protein sequences of human and five clinically important viruses; therefore, viral and human proteins sharing a descriptor were predicted as interacting proteins. The analysis of the host-viral interactome allowed to identify a set of new interactions that further explain molecular mechanism associated with viral infections and showed that it was able to capture human proteins already associated to viral infections (human infectome and non-infectious diseases (human diseasome. The analysis of human proteins targeted by viral proteins in the context of a human interactome showed that their neighbors are enriched in proteins reported with differential expression under infection and disease conditions. It is expected that the findings of this work will contribute to the development of systems biology for infectious diseases, and help guide the rational identification and prioritization of novel drug targets.

  13. Evaluation of a rapid protein analyzer for determination of protein in milk and cream.

    Science.gov (United States)

    Amamcharla, J K; Metzger, L E

    2010-08-01

    Accurate and rapid measurement of the protein content of milk is important from both a product quality and an economic standpoint. The Sprint rapid protein analyzer (CEM Corporation, Matthews, NC) is a commercial system based on a dye-binding technique and can be used for rapid measurement of protein in foods. The objective of the present study was to compare the Sprint method with the reference method (Kjeldahl method). Milk and cream samples were analyzed in duplicate for true protein and crude protein (CP) using the reference method as well as the rapid method. Method comparison statistics (regression analysis, graphical representation, standard deviation of residuals, repeatability, and so on) were used to evaluate the agreement between the 2 methods. Regression coefficients and the intercepts were not significantly different from 1 and zero for CP measurement in milk and cream, respectively. The average coefficient of variance between the duplicate CP measurements for the Sprint method was found to be 0.40, 0.49, and 0.76 for milk, light cream, and heavy cream, respectively. True protein measurement in milk and cream also followed a similar trend. Overall, there exists a sufficient level of agreement between the Sprint rapid protein analyzer and Kjeldahl method for true protein and CP measurement of milk and cream samples.

  14. ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis.

    Science.gov (United States)

    Pankow, Sandra; Bamberger, Casimir; Calzolari, Diego; Martínez-Bartolomé, Salvador; Lavallée-Adam, Mathieu; Balch, William E; Yates, John R

    2015-12-24

    Deletion of phenylalanine 508 of the cystic fibrosis transmembrane conductance regulator (∆F508 CFTR) is the major cause of cystic fibrosis, one of the most common inherited childhood diseases. The mutated CFTR anion channel is not fully glycosylated and shows minimal activity in bronchial epithelial cells of patients with cystic fibrosis. Low temperature or inhibition of histone deacetylases can partly rescue ∆F508 CFTR cellular processing defects and function. A favourable change of ∆F508 CFTR protein-protein interactions was proposed as a mechanism of rescue; however, CFTR interactome dynamics during temperature shift and inhibition of histone deacetylases are unknown. Here we report the first comprehensive analysis of the CFTR and ∆F508 CFTR interactome and its dynamics during temperature shift and inhibition of histone deacetylases. By using a novel deep proteomic analysis method, we identify 638 individual high-confidence CFTR interactors and discover a ∆F508 deletion-specific interactome, which is extensively remodelled upon rescue. Detailed analysis of the interactome remodelling identifies key novel interactors, whose loss promote ∆F508 CFTR channel function in primary cystic fibrosis epithelia or which are critical for CFTR biogenesis. Our results demonstrate that global remodelling of ∆F508 CFTR interactions is crucial for rescue, and provide comprehensive insight into the molecular disease mechanisms of cystic fibrosis caused by deletion of F508.

  15. Chemical approaches to detect and analyze protein sulfenic acids.

    Science.gov (United States)

    Furdui, Cristina M; Poole, Leslie B

    2014-01-01

    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.

  16. A "candidate-interactome" aggregate analysis of genome-wide association data in multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    Rosella Mechelli

    Full Text Available Though difficult, the study of gene-environment interactions in multifactorial diseases is crucial for interpreting the relevance of non-heritable factors and prevents from overlooking genetic associations with small but measurable effects. We propose a "candidate interactome" (i.e. a group of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated. The P values of all single nucleotide polymorphism mapping to a given interactome were obtained from the last genome-wide association study of the International Multiple Sclerosis Genetics Consortium & the Wellcome Trust Case Control Consortium, 2. The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology. However, in line with recent data on the coexistence of common and unique strategies used by viruses to perturb the human molecular system, also other viruses have a similar potential, though probably less relevant in epidemiological terms.

  17. Analyzing models for interactions of aptamers to proteins

    Science.gov (United States)

    Silva, Dilson; Missailidis, Sotiris

    2014-10-01

    We have devised an experimental and theoretical model, based on fluorescent spectroscopy and molecular modelling, to describe the interaction of aptamer (selected against various protein targets) with proteins and albumins in particular. This model, described in this work, has allowed us to decipher the nature of the interactions between aptamers and albumins, the binding site of the aptamers to albumins, the potential role of primer binding to the albumin and expand to the ability of albumin to carry aptamers in the bloodstream, providing data to better understand the level of free aptamer for target binding. We are presenting the study of a variety of aptamers, including those against the MUC1 tumour marker, heparanase and human kallikrein 6 with bovine and human serum albumins and the effect these interactions may have on the bioavailability of the aptamer for target-specific binding and therapeutic activity.

  18. Intracellular interactome of secreted antibody Fab fragment in Pichia pastoris reveals its routes of secretion and degradation.

    Science.gov (United States)

    Pfeffer, Martin; Maurer, Michael; Stadlmann, Johannes; Grass, Josephine; Delic, Marizela; Altmann, Friedrich; Mattanovich, Diethard

    2012-03-01

    Protein translation, translocation, folding, processing, and secretion in eukaryotic cells are complex and not always straightforward processes, e.g., different routes of secretion and degradation exist. Formation of malfolded proteins in the endoplasmic reticulum (ER) can be one of the major bottlenecks for recombinant protein production. In this regard, an in-depth analysis of the interactions of a secreted protein during its pathway through the cell may be beneficial, as realized in this study for the methylotrophic yeast Pichia pastoris. The antibody fragment Fab3H6 used here is the anti-idiotype to the HIV neutralizing antibody 2F5 and is known to be intracellularly degraded in significant amounts when expressed in P. pastoris. The interactome of Fab3H6 was analyzed by using a pull-down mass spectrometry approach, and 23 proteins were found to bind specifically to the antibody fragment. Those allowed concluding that Fab3H6 is post-translationally translocated into the ER and degraded via the proteasome as well as the vacuole. In line with this, the expression of Fab3H6 increased the proteasomal activities by over 20%. Partial inhibition of the proteasome resulted in a significant increase of extracellular Fab3H6. Thus, it seems that ER quality control overshoots its requirements for the recombinant protein expressed and that more than just terminally malfolded protein is degraded by ER-associated degradation. This work will further facilitate our understanding how recombinant proteins behave in the secretory pathway. PMID:22350260

  19. InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research.

    Science.gov (United States)

    Poglayen, Daniel; Marín-López, Manuel Alejandro; Bonet, Jaume; Fornes, Oriol; Garcia-Garcia, Javier; Planas-Iglesias, Joan; Segura, Joan; Oliva, Baldo; Fernandez-Fuentes, Narcis

    2016-06-15

    Virtually all the biological processes that occur inside or outside cells are mediated by protein-protein interactions (PPIs). Hence, the charting and description of the PPI network, initially in organisms, the interactome, but more recently in specific tissues, is essential to fully understand cellular processes both in health and disease. The study of PPIs is also at the heart of renewed efforts in the medical and biotechnological arena in the quest of new therapeutic targets and drugs. Here, we present a mini review of 11 computational tools and resources tools developed by us to address different aspects of PPIs: from interactome level to their atomic 3D structural details. We provided details on each specific resource, aims and purpose and compare with equivalent tools in the literature. All the tools are presented in a centralized, one-stop, web site: InteractoMIX (http://interactomix.com). PMID:27284060

  20. The arabidopsis cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara

    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.

  1. Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service

    Directory of Open Access Journals (Sweden)

    Yoon Kyong-Oh

    2008-01-01

    Full Text Available Abstract Background Protein-protein interactions (PPIs play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysaccharides production, toxins release, iron acquisition, and effector proteins secretion. Many such mechanisms involve some kind of protein-protein interaction in hosts. Our first aim was to predict the whole protein interaction pairs (interactome of Xanthomonas oryzae pathovar oryzae (Xoo that is an important pathogenic bacterium that causes bacterial blight (BB in rice. We developed a detection protocol to find possibly interacting proteins in its host using whole genome PPI prediction algorithms. The second aim was to build a DB server and a bioinformatic procedure for finding target proteins in Xoo for developing pesticides that block host-pathogen protein interactions within critical biochemical pathways. Description A PPI network in Xoo proteome was predicted by bioinformatics algorithms: PSIMAP, PEIMAP, and iPfam. We present the resultant species specific interaction network and host-pathogen interaction, XooNET. It is a comprehensive predicted initial PPI data for Xoo. XooNET can be used by experimentalists to pick up protein targets for blocking pathological interactions. XooNET uses most of the major types of PPI algorithms. They are: 1 Protein Structural Interactome MAP (PSIMAP, a method using structural domain of SCOP, 2 Protein Experimental Interactome MAP (PEIMAP, a common method using public resources of experimental protein interaction information such as HPRD, BIND, DIP, MINT, IntAct, and BioGrid, and 3 Domain-domain interactions, a method using Pfam domains such as iPfam. Additionally, XooNET provides information on network properties of the Xoo interactome. Conclusion XooNET is an open and free public

  2. Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases.

    Directory of Open Access Journals (Sweden)

    Ruth Barshir

    2014-06-01

    Full Text Available An open question in human genetics is what underlies the tissue-specific manifestation of hereditary diseases, which are caused by genomic aberrations that are present in cells across the human body. Here we analyzed this phenomenon for over 300 hereditary diseases by using comparative network analysis. We created an extensive resource of protein expression and interactions in 16 main human tissues, by integrating recent data of gene and protein expression across tissues with data of protein-protein interactions (PPIs. The resulting tissue interaction networks (interactomes shared a large fraction of their proteins and PPIs, and only a small fraction of them were tissue-specific. Applying this resource to hereditary diseases, we first show that most of the disease-causing genes are widely expressed across tissues, yet, enigmatically, cause disease phenotypes in few tissues only. Upon testing for factors that could lead to tissue-specific vulnerability, we find that disease-causing genes tend to have elevated transcript levels and increased number of tissue-specific PPIs in their disease tissues compared to unaffected tissues. We demonstrate through several examples that these tissue-specific PPIs can highlight disease mechanisms, and thus, owing to their small number, provide a powerful filter for interrogating disease etiologies. As two thirds of the hereditary diseases are associated with these factors, comparative tissue analysis offers a meaningful and efficient framework for enhancing the understanding of the molecular basis of hereditary diseases.

  3. Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases.

    Science.gov (United States)

    Barshir, Ruth; Shwartz, Omer; Smoly, Ilan Y; Yeger-Lotem, Esti

    2014-06-01

    An open question in human genetics is what underlies the tissue-specific manifestation of hereditary diseases, which are caused by genomic aberrations that are present in cells across the human body. Here we analyzed this phenomenon for over 300 hereditary diseases by using comparative network analysis. We created an extensive resource of protein expression and interactions in 16 main human tissues, by integrating recent data of gene and protein expression across tissues with data of protein-protein interactions (PPIs). The resulting tissue interaction networks (interactomes) shared a large fraction of their proteins and PPIs, and only a small fraction of them were tissue-specific. Applying this resource to hereditary diseases, we first show that most of the disease-causing genes are widely expressed across tissues, yet, enigmatically, cause disease phenotypes in few tissues only. Upon testing for factors that could lead to tissue-specific vulnerability, we find that disease-causing genes tend to have elevated transcript levels and increased number of tissue-specific PPIs in their disease tissues compared to unaffected tissues. We demonstrate through several examples that these tissue-specific PPIs can highlight disease mechanisms, and thus, owing to their small number, provide a powerful filter for interrogating disease etiologies. As two thirds of the hereditary diseases are associated with these factors, comparative tissue analysis offers a meaningful and efficient framework for enhancing the understanding of the molecular basis of hereditary diseases. PMID:24921629

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line.

    Directory of Open Access Journals (Sweden)

    Xiuzhi Jia

    Full Text Available Human uveitis is a type of T cell-mediated autoimmune disease that often shows relapse-remitting courses affecting multiple biological processes. As a cytoplasmic process, autophagy has been seen as an adaptive response to cell death and survival, yet the link between autophagy and T cell-mediated autoimmunity is not certain. In this study, based on the differentially expressed genes (GSE19652 between the recurrent versus monophasic T cell lines, whose adoptive transfer to susceptible animals may result in respective recurrent or monophasic uveitis, we proposed grouping annotations on a subcellular layered interactome framework to analyze the specific bioprocesses that are linked to the recurrence of T cell autoimmunity. That is, the subcellular layered interactome was established by the Cytoscape and Cerebral plugin based on differential expression, global interactome, and subcellular localization information. Then, the layered interactomes were grouping annotated by the ClueGO plugin based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. The analysis showed that significant bioprocesses with autophagy were orchestrated in the cytoplasmic layered interactome and that mTOR may have a regulatory role in it. Furthermore, by setting up recurrent and monophasic uveitis in Lewis rats, we confirmed by transmission electron microscopy that, in comparison to the monophasic disease, recurrent uveitis in vivo showed significantly increased autophagy activity and extended lymphocyte infiltration to the affected retina. In summary, our framework methodology is a useful tool to disclose specific bioprocesses and molecular targets that can be attributed to a certain disease. Our results indicated that targeted inhibition of autophagy pathways may perturb the recurrence of uveitis.

  8. Charting the interactome of PDE3A in human cells using an IBMX based chemical proteomics approach

    DEFF Research Database (Denmark)

    Corradini, Eleonora; Klaasse, Gruson; Leurs, Ulrike;

    2015-01-01

    proteomics characterization of this resin in HeLa cell lysates led to the capture of several different PDEs. Combining the IBMX-resin with in-solution competition with the available more selective PDE inhibitors, cilostamide and papaverine, allowed us to selectively probe the interactome of PDE3A in He...... processes inspiring the quest for and synthesis of selective PDE inhibitors, that unfortunately have led to very mixed successes in clinical trials. This may be partially caused by their pharmacological action. Accumulating data suggests that small differences between different PDE isoforms may already...... comprehensive way. Affinity based chemical proteomics is a relatively new tool to identify specific protein-protein interactions. Here, to study the interactome of PDEs, we synthesized a broad spectrum PDE-capturing resin based on the non-selective PDE inhibitor 3-isobutyl-1-methylxanthine (IBMX). Chemical...

  9. Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Rohit Vashisht

    Full Text Available 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.

  10. 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...

  11. Evaluation of colorimetric assays for analyzing reductively methylated proteins: Biases and mechanistic insights.

    Science.gov (United States)

    Brady, Pamlea N; Macnaughtan, Megan A

    2015-12-15

    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 responses (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 with the unmodified ε-amine, favoring Cu(II) binding in biuret-like complexes. The implications for the analysis of biologically methylated samples are discussed.

  12. Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex.

    Science.gov (United States)

    Obado, Samson O; Brillantes, Marc; Uryu, Kunihiro; Zhang, Wenzhu; Ketaren, Natalia E; Chait, Brian T; Field, Mark C; Rout, Michael P

    2016-02-01

    The nuclear pore complex (NPC) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression. The components of NPCs from several eukaryotic lineages have been determined, but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary level. Significantly, recent evidence indicates that compositional similarity does not necessarily correspond to homologous architecture between NPCs from different taxa. To address this, we describe the interactome of the trypanosome NPC, a representative, highly divergent eukaryote. We identify numerous new NPC components and report an exhaustive interactome, allowing assignment of trypanosome nucleoporins to discrete NPC substructures. Remarkably, despite retaining similar protein composition, there are exceptional architectural dissimilarities between opisthokont (yeast and vertebrates) and excavate (trypanosomes) NPCs. Whilst elements of the inner core are conserved, numerous peripheral structures are highly divergent, perhaps reflecting requirements to interface with divergent nuclear and cytoplasmic functions. Moreover, the trypanosome NPC has almost complete nucleocytoplasmic symmetry, in contrast to the opisthokont NPC; this may reflect divergence in RNA export processes at the NPC cytoplasmic face, as we find evidence supporting Ran-dependent mRNA export in trypanosomes, similar to protein transport. We propose a model of stepwise acquisition of nucleocytoplasmic mechanistic complexity and demonstrate that detailed dissection of macromolecular complexes provides fuller understanding of evolutionary processes. PMID:26891179

  13. Analyzing the functions and structure of the human lipodystrophy protein seipin.

    Science.gov (United States)

    Sim, M F Michelle; Talukder, Mesbah Uddin; Dennis, Rowena J; Edwardson, J Michael; Rochford, Justin J

    2014-01-01

    Disruption of the gene BSCL2, which encodes the protein seipin, causes severe generalized lipodystrophy in humans with a near complete absence of adipose tissue. Moreover, cell culture studies have demonstrated that seipin plays a critical cell-autonomous role in adipocyte differentiation. These observations reveal seipin as a critical regulator of human adipose tissue development; however, until recently very little has been known about the potential molecular functions of this intriguing protein. Despite significant recent interest in the function of seipin, our understanding of its molecular role(s) remains limited. The topology of seipin and lack of evidence for any enzymatic domains or activity indicate that it may act principally as a scaffold for other proteins or play a structural role in altering membrane curvature and/or budding. Work in this area has been hampered by several factors, including the lack of homology that might imply testable functions, the poor availability of antibodies to the endogenous protein and the observation that this hydrophobic ER membrane-resident protein is difficult to analyze by standard Western blotting techniques. Here we summarize some of the techniques we have applied to investigate the association of seipin with a recently identified binding partner, lipin 1. In addition, we describe the use of atomic force microscopy (AFM) to image oligomers of the seipin protein. We believe that AFM will offer a valuable tool to examine the association of candidate binding proteins with the seipin oligomer.

  14. A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories

    Directory of Open Access Journals (Sweden)

    Ucar Duygu

    2007-04-01

    Full Text Available Abstract Understanding the protein folding mechanism remains a grand challenge in structural biology. In the past several years, computational theories in molecular dynamics have been employed to shed light on the folding process. Coupled with high computing power and large scale storage, researchers now can computationally simulate the protein folding process in atomistic details at femtosecond temporal resolution. Such simulation often produces a large number of folding trajectories, each consisting of a series of 3D conformations of the protein under study. As a result, effectively managing and analyzing such trajectories is becoming increasingly important. In this article, we present a spatio-temporal mining approach to analyze protein folding trajectories. It exploits the simplicity of contact maps, while also integrating 3D structural information in the analysis. It characterizes the dynamic folding process by first identifying spatio-temporal association patterns in contact maps, then studying how such patterns evolve along a folding trajectory. We demonstrate that such patterns can be leveraged to summarize folding trajectories, and to facilitate the detection and ordering of important folding events along a folding path. We also show that such patterns can be used to identify a consensus partial folding pathway across multiple folding trajectories. Furthermore, we argue that such patterns can capture both local and global structural topology in a 3D protein conformation, thereby facilitating effective structural comparison amongst conformations. We apply this approach to analyze the folding trajectories of two small synthetic proteins-BBA5 and GSGS (or Beta3S. We show that this approach is promising towards addressing the above issues, namely, folding trajectory summarization, folding events detection and ordering, and consensus partial folding pathway identification across trajectories.

  15. 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.

  16. Amaltheys: A fluorescence-based analyzer to assess cheese milk denatured whey proteins.

    Science.gov (United States)

    Lacotte, Pierre; Gomez, Franck; Bardeau, Floriane; Muller, Sabine; Acharid, Abdelhaq; Quervel, Xavier; Trossat, Philippe; Birlouez-Aragon, Inès

    2015-10-01

    The cheese industry faces many challenges to optimize cheese yield and quality. A very precise standardization of the cheese milk is needed, which is achieved by a fine control of the process and milk composition. Thorough analysis of protein composition is important to determine the amount of protein that will be retained in the curd or lost in the whey. The fluorescence-based Amaltheys analyzer (Spectralys Innovation, Romainville, France) was developed to assess pH 4.6-soluble heat-sensitive whey proteins (sWP*) in 5 min. These proteins are those that can be denatured upon heat-treatment and further retained in the curd after coagulation. Monitoring of sWP* in milk and subsequent adaptation of the process is a reliable solution to achieve stable cheese yield and quality. Performance of the method was evaluated by an accredited laboratory on a 0 to 7 g/L range. Accuracy compared with the reference Kjeldahl method is also provided with a standard error of 0.25 g/L. Finally, a 4-mo industrial trial in a cheese plant is described, where Amaltheys was used as a process analytical technology to monitor sWP* content in ingredients and final cheese milk. Calibration models over quality parameters of final cheese were also built from near-infrared and fluorescence spectroscopic data. The Amaltheys analyzer was found to be a rapid, compact, and accurate device to help implementation of standardization procedures in the dairy industry.

  17. A core of kinase-regulated interactomes defines the neoplastic MDSC lineage.

    Science.gov (United States)

    Gato-Cañas, Maria; Martinez de Morentin, Xabier; Blanco-Luquin, Idoia; Fernandez-Irigoyen, Joaquin; Zudaire, Isabel; Liechtenstein, Therese; Arasanz, Hugo; Lozano, Teresa; Casares, Noelia; Chaikuad, Apirat; Knapp, Stefan; Guerrero-Setas, David; Escors, David; Kochan, Grazyna; Santamaría, Enrique

    2015-09-29

    Myeloid-derived suppressor cells (MDSCs) differentiate from bone marrow precursors, expand in cancer-bearing hosts and accelerate tumor progression. MDSCs have become attractive therapeutic targets, as their elimination strongly enhances anti-neoplastic treatments. Here, immature myeloid dendritic cells (DCs), MDSCs modeling tumor-infiltrating subsets or modeling non-cancerous (NC)-MDSCs were compared by in-depth quantitative proteomics. We found that neoplastic MDSCs differentially expressed a core of kinases which controlled lineage-specific (PI3K-AKT and SRC kinases) and cancer-induced (ERK and PKC kinases) protein interaction networks (interactomes). These kinases contributed to some extent to myeloid differentiation. However, only AKT and ERK specifically drove MDSC differentiation from myeloid precursors. Interfering with AKT and ERK with selective small molecule inhibitors or shRNAs selectively hampered MDSC differentiation and viability. Thus, we provide compelling evidence that MDSCs constitute a distinct myeloid lineage distinguished by a "kinase signature" and well-defined interactomes. Our results define new opportunities for the development of anti-cancer treatments targeting these tumor-promoting immune cells. PMID:26320174

  18. Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

    Science.gov (United States)

    Nguyen, Tri C.; Cao, Xiaoyi; Yu, Pengfei; Xiao, Shu; Lu, Jia; Biase, Fernando H.; Sridhar, Bharat; Huang, Norman; Zhang, Kang; Zhong, Sheng

    2016-01-01

    The pervasive transcription of our genome presents a possibility of revealing new genomic functions by investigating RNA interactions. Current methods for mapping RNA–RNA interactions have to rely on an ‘anchor' protein or RNA and often require molecular perturbations. Here we present the MARIO (Mapping RNA interactome in vivo) technology to massively reveal RNA–RNA interactions from unperturbed cells. We mapped tens of thousands of endogenous RNA–RNA interactions from mouse embryonic stem cells and brain. We validated seven interactions by RNA antisense purification and one interaction using single-molecule RNA–FISH. The experimentally derived RNA interactome is a scale-free network, which is not expected from currently perceived promiscuity in RNA–RNA interactions. Base pairing is observed at the interacting regions between long RNAs, including transposon transcripts, suggesting a class of regulatory sequences acting in trans. In addition, MARIO data reveal thousands of intra-molecule interactions, providing in vivo data on high-order RNA structures. PMID:27338251

  19. 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. PMID:26409966

  20. ChIP-Seq to Analyze the Binding of Replication Proteins to Chromatin.

    Science.gov (United States)

    Ostrow, A Zachary; Viggiani, Christopher J; Aparicio, Jennifer G; Aparicio, Oscar M

    2015-01-01

    Chromatin immunoprecipitation (ChIP) is a widely used method to study interactions between proteins and discrete chromosomal loci in vivo. ChIP was originally developed for in vivo analysis of protein associations with candidate DNA sequences known or suspected to bind the protein of interest. The advent of DNA microarrays enabled the unbiased, genome-scale identification of all DNA sequences enriched by ChIP, providing a genomic map of a protein's chromatin binding. This method, termed ChIP-chip, is broadly applicable and has been particularly valuable in DNA replication studies to map potential replication origins in Saccharomyces cerevisiae and other organisms based on the specific association of certain replication proteins with these chromosomal elements, which are distributed throughout the genome. More recently, high-throughput sequencing (HTS) technologies have replaced microarrays as the preferred method for genomic analysis of ChIP experiments, and this combination is termed ChIP-Seq. We present a detailed ChIP-Seq protocol for S. cerevisiae that can be adapted for different HTS platforms and for different organisms. We also outline general schemes for data analysis; however, HTS data analyses usually must be tailored specifically for individual studies, depending on the experimental design, data characteristics, and the genome being analyzed.

  1. 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

  2. Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution.

    Science.gov (United States)

    Urban, Michael; Vor der Brüggen, Marc; Tampé, Robert

    2016-01-01

    Membrane protein transport on the single protein level still evades detailed analysis, if the substrate translocated is non-electrogenic. Considerable efforts have been made in this field, but techniques enabling automated high-throughput transport analysis in combination with solvent-free lipid bilayer techniques required for the analysis of membrane transporters are rare. This class of transporters however is crucial in cell homeostasis and therefore a key target in drug development and methodologies to gain new insights desperately needed. The here presented manuscript describes the establishment and handling of a novel biochip for the analysis of membrane protein mediated transport processes at single transporter resolution. The biochip is composed of microcavities enclosed by nanopores that is highly parallel in its design and can be produced in industrial grade and quantity. Protein-harboring liposomes can directly be applied to the chip surface forming self-assembled pore-spanning lipid bilayers using SSM-techniques (solid supported lipid membranes). Pore-spanning parts of the membrane are freestanding, providing the interface for substrate translocation into or out of the cavity space, which can be followed by multi-spectral fluorescent readout in real-time. The establishment of standard operating procedures (SOPs) allows the straightforward establishment of protein-harboring lipid bilayers on the chip surface of virtually every membrane protein that can be reconstituted functionally. The sole prerequisite is the establishment of a fluorescent read-out system for non-electrogenic transport substrates. High-content screening applications are accomplishable by the use of automated inverted fluorescent microscopes recording multiple chips in parallel. Large data sets can be analyzed using the freely available custom-designed analysis software. Three-color multi spectral fluorescent read-out furthermore allows for unbiased data discrimination into different

  3. A novel approach to analyze membrane proteins by laser mass spectrometry: from protein subunits to the integral complex.

    Science.gov (United States)

    Morgner, Nina; Kleinschroth, Thomas; Barth, Hans-Dieter; Ludwig, Bernd; Brutschy, Bernhard

    2007-08-01

    A novel laser-based mass spectrometry method termed LILBID (laser-induced liquid bead ion desorption) is applied to analyze large integral membrane protein complexes and their subunits. In this method the ions are IR-laser desorbed from aqueous microdroplets containing the hydrophobic protein complexes solubilized by detergent. The method is highly sensitive, very efficient in sample handling, relatively tolerant to various buffers, and detects the ions in narrow, mainly low-charge state distributions. The crucial experimental parameter determining whether the integral complex or its subunits are observed is the laser intensity: At very low intensity level corresponding to an ultrasoft desorption, the intact complexes, together with few detergent molecules, are transferred into vacuum. Under these conditions the oligomerization state of the complex (i.e., its quaternary structure) may be analyzed. At higher laser intensity, complexes are thermolyzed into subunits, with any residual detergent being stripped off to yield the true mass of the polypeptides. The model complexes studied are derived from the respiratory chain of the soil bacterium Paracoccus denitrificans and include complexes III (cytochrome bc(1) complex) and IV (cytochrome c oxidase). These are well characterized multi-subunit membrane proteins, with the individual hydrophobic subunits being composed of up to 12 transmembrane helices. PMID:17544294

  4. A Computational Protein Phenotype Prediction Approach to Analyze the Deleterious Mutations of Human MED12 Gene.

    Science.gov (United States)

    Banaganapalli, Babajan; Mohammed, Kaleemuddin; Khan, Imran Ali; Al-Aama, Jumana Y; Elango, Ramu; Shaik, Noor Ahmad

    2016-09-01

    Genetic mutations in MED12, a subunit of Mediator complex are seen in a broad spectrum of human diseases. However, the underlying basis of how these pathogenic mutations elicit protein phenotype changes in terms of 3D structure, stability and protein binding sites remains unknown. Therefore, we aimed to investigate the structural and functional impacts of MED12 mutations, using computational methods as an alternate to traditional in vivo and in vitro approaches. The MED12 gene mutations details and their corresponding clinical associations were collected from different databases and by text-mining. Initially, diverse computational approaches were applied to categorize the different classes of mutations based on their deleterious impact to MED12. Then, protein structures for wild and mutant types built by integrative modeling were analyzed for structural divergence, solvent accessibility, stability, and functional interaction deformities. Finally, this study was able to identify that genetic mutations mapped to exon-2 region, highly conserved LCEWAV and Catenin domains induce biochemically severe amino acid changes which alters the protein phenotype as well as the stability of MED12-CYCC interactions. To better understand the deleterious nature of FS-IDs and Indels, this study asserts the utility of computational screening based on their propensity towards non-sense mediated decay. Current study findings may help to narrow down the number of MED12 mutations to be screened for mediator complex dysfunction associated genetic diseases. This study supports computational methods as a primary filter to verify the plausible impact of pathogenic mutations based on the perspective of evolution, expression and phenotype of proteins. J. Cell. Biochem. 117: 2023-2035, 2016. © 2016 Wiley Periodicals, Inc. PMID:26813965

  5. Characterization of the Drosophila Atlastin Interactome Reveals VCP as a Functionally Related Interactor

    Institute of Scientific and Technical Information of China (English)

    Niamh C.O'Sullivan; Nina Dr(a)ger; Cahir J.O'Kane

    2013-01-01

    At least 25 genes,many involved in trafficking,localisation or shaping of membrane organelles,have been identified as causative genes for the neurodegenerative disorder hereditary spastic paraplegia (HSP).One of the most commonly mutated HSP genes,atlastin-1,encodes a dynamin-like GTPase that mediates homotypic fusion of endoplasmic reticulum (ER) membranes.However,the molecular mechanisms of atlastin-l-related membrane fusion and axonopathy remain unclear.To better understand its mode of action,we used affinity purification coupled with mass spectrometry to identify protein interactors of atlastin in Drosophila.Analysis of 72 identified proteins revealed that the atlastin interactome contains many proteins involved in protein processing and transport,in addition to proteins with roles in mRNA binding,metabolism and mitochondrial proteins.The highest confidence interactor from mass spectrometry analysis,the ubiquitin-selective AAA-ATPase valosin-containing protein (VCP),was validated as an atlastin-interacting protein,and VCP and atlastin showed overlapping subcellular distributions.Furthermore,VCP acted as a genetic modifier of atlastin:loss of VCP partially suppressed an eye phenotype caused by atlastin overexpression,whereas overexpression of VCP enhanced this phenotype.These interactions between atlastin and VCP suggest a functional relationship between these two proteins,and point to potential shared mechanisms between HSP and other forms of neurodegeneration.

  6. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells

    OpenAIRE

    Whisenant, Thomas C.; Peralta, Eigen R.; Aarreberg, Lauren D.; Gao, Nina J.; Head, Steven R; Phillip Ordoukhanian; Jamie R Williamson; Salomon, Daniel R.

    2015-01-01

    Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing act...

  7. 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.

  8. 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

  9. Long-term potentiation modulates synaptic phosphorylation networks and reshapes the structure of the postsynaptic interactome.

    Science.gov (United States)

    Li, Jing; Wilkinson, Brent; Clementel, Veronica A; Hou, Junjie; O'Dell, Thomas J; Coba, Marcelo P

    2016-01-01

    The postsynaptic site of neurons is composed of more than 1500 proteins arranged in protein-protein interaction complexes, the composition of which is modulated by protein phosphorylation through the actions of complex signaling networks. Components of these networks function as key regulators of synaptic plasticity, in particular hippocampal long-term potentiation (LTP). The postsynaptic density (PSD) is a complex multicomponent structure that includes receptors, enzymes, scaffold proteins, and structural proteins. We triggered LTP in the mouse hippocampus CA1 region and then performed large-scale analyses to identify phosphorylation-mediated events in the PSD and changes in the protein-protein interactome of the PSD that were associated with LTP induction. Our data indicated LTP-induced reorganization of the PSD. The dynamic reorganization of the PSD links glutamate receptor signaling to kinases (writers) and phosphatases (erasers), as well as the target proteins that are modulated by protein phosphorylation and the proteins that recognize the phosphorylation status of their binding partners (readers). Protein phosphorylation and protein interaction networks converged at highly connected nodes within the PSD network. Furthermore, the LTP-regulated phosphoproteins, which included the scaffold proteins Shank3, Syngap1, Dlgap1, and Dlg4, represented the "PSD risk" for schizophrenia and autism spectrum disorder, such that without these proteins in the analysis, the association with the PSD and these two psychiatric diseases was not present. These data are a rich resource for future studies of LTP and suggest that the PSD holds the keys to understanding the molecular events that contribute to complex neurological disorders that affect synaptic plasticity. PMID:27507650

  10. Searching for the Holy Grail; protein–protein interaction analysis and modulation

    OpenAIRE

    Morelli, Xavier; Hupp, Ted

    2012-01-01

    The EMBO workshop on ‘Protein–Protein Interaction Analysis & Modulation' covered protein network analysis, the modulation of protein–protein interactions, and the daunting challenge of integrating interactomes in systems biology and in the modelling of signalling networks.

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

    OpenAIRE

    Igor Moura Paiva; Virgílio de Carvalho dos Anjos; Maria José Valenzuela Bell; Marco Antônio Moreira Furtado

    2016-01-01

    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 ...

  12. Computational analysis of the LRRK2 interactome

    OpenAIRE

    Manzoni, Claudia; Denny, Paul; Lovering, Ruth C.; Lewis, Patrick A.

    2015-01-01

    LRRK2 was identified in 2004 as the causative protein product of the Parkinson’s disease locus designated PARK8. In the decade since then, genetic studies have revealed at least 6 dominant mutations in LRRK2 linked to Parkinson’s disease, alongside one associated with cancer. It is now well established that coding changes in LRRK2 are one of the most common causes of Parkinson’s. Genome-wide association studies (GWAs) have, more recently, reported single nucleotide polymorphisms (SNPs) around...

  13. Computational analysis of the LRRK2 interactome.

    OpenAIRE

    C. Manzoni; Denny, P; Lovering, R.C.; Lewis, P. A.

    2015-01-01

    LRRK2 was identified in 2004 as the causative protein product of the Parkinson’s disease locus designated PARK8. In the decade since then, genetic studies have revealed at least 6 dominant mutations in LRRK2 linked to Parkinson’s disease, alongside one associated with cancer. It is now well established that coding changes in LRRK2 are one of the most common causes of Parkinson’s. Genome-wide association studies (GWAs) have, more recently, reported single nucleotide polymorphisms (SNPs) around...

  14. 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

    gene expression, protein expression or post-translational modifications. To overcome single omics analysis, we developed a set of computational methods that allow a combined analysis of data collections from multiple omics fields utilizing hybrid interactome networks. We apply these methods to data...... 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...

  15. 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

  16. ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome

    Science.gov (United States)

    Tinti, Michele; Madeira, Fábio; Murugesan, Gavuthami; Hoxhaj, Gerta; Toth, Rachel; MacKintosh, Carol

    2014-01-01

    The dimeric 14-3-3 proteins dock onto pairs of phosphorylated Ser and Thr residues on hundreds of proteins, and thereby regulate many events in mammalian cells. To facilitate global analyses of these interactions, we developed a web resource named ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome, which integrates multiple data sets on 14-3-3-binding phosphoproteins. ANIA also pinpoints candidate 14-3-3-binding phosphosites using predictor algorithms, assisted by our recent discovery that the human 14-3-3-interactome is highly enriched in 2R-ohnologues. 2R-ohnologues are proteins in families of two to four, generated by two rounds of whole genome duplication at the origin of the vertebrate animals. ANIA identifies candidate ‘lynchpins’, which are 14-3-3-binding phosphosites that are conserved across members of a given 2R-ohnologue protein family. Other features of ANIA include a link to the catalogue of somatic mutations in cancer database to find cancer polymorphisms that map to 14-3-3-binding phosphosites, which would be expected to interfere with 14-3-3 interactions. We used ANIA to map known and candidate 14-3-3-binding enzymes within the 2R-ohnologue complement of the human kinome. Our projections indicate that 14-3-3s dock onto many more human kinases than has been realized. Guided by ANIA, PAK4, 6 and 7 (p21-activated kinases 4, 6 and 7) were experimentally validated as a 2R-ohnologue family of 14-3-3-binding phosphoproteins. PAK4 binding to 14-3-3 is stimulated by phorbol ester, and involves the ‘lynchpin’ site phosphoSer99 and a major contribution from Ser181. In contrast, PAK6 and PAK7 display strong phorbol ester-independent binding to 14-3-3, with Ser113 critical for the interaction with PAK6. These data point to differential 14-3-3 regulation of PAKs in control of cell morphology. Database URL: https://ania-1433.lifesci.dundee.ac.uk/prediction/webserver/index.py PMID:24501395

  17. ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome.

    Science.gov (United States)

    Tinti, Michele; Madeira, Fábio; Murugesan, Gavuthami; Hoxhaj, Gerta; Toth, Rachel; Mackintosh, Carol

    2014-01-01

    The dimeric 14-3-3 proteins dock onto pairs of phosphorylated Ser and Thr residues on hundreds of proteins, and thereby regulate many events in mammalian cells. To facilitate global analyses of these interactions, we developed a web resource named ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome, which integrates multiple data sets on 14-3-3-binding phosphoproteins. ANIA also pinpoints candidate 14-3-3-binding phosphosites using predictor algorithms, assisted by our recent discovery that the human 14-3-3-interactome is highly enriched in 2R-ohnologues. 2R-ohnologues are proteins in families of two to four, generated by two rounds of whole genome duplication at the origin of the vertebrate animals. ANIA identifies candidate 'lynchpins', which are 14-3-3-binding phosphosites that are conserved across members of a given 2R-ohnologue protein family. Other features of ANIA include a link to the catalogue of somatic mutations in cancer database to find cancer polymorphisms that map to 14-3-3-binding phosphosites, which would be expected to interfere with 14-3-3 interactions. We used ANIA to map known and candidate 14-3-3-binding enzymes within the 2R-ohnologue complement of the human kinome. Our projections indicate that 14-3-3s dock onto many more human kinases than has been realized. Guided by ANIA, PAK4, 6 and 7 (p21-activated kinases 4, 6 and 7) were experimentally validated as a 2R-ohnologue family of 14-3-3-binding phosphoproteins. PAK4 binding to 14-3-3 is stimulated by phorbol ester, and involves the 'lynchpin' site phosphoSer99 and a major contribution from Ser181. In contrast, PAK6 and PAK7 display strong phorbol ester-independent binding to 14-3-3, with Ser113 critical for the interaction with PAK6. These data point to differential 14-3-3 regulation of PAKs in control of cell morphology. Database URL: https://ania-1433.lifesci.dundee.ac.uk/prediction/webserver/index.py.

  18. 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...

  19. High throughput methods for analyzing transition metals in proteins on a microgram scale.

    Science.gov (United States)

    Atanassova, Anelia; Högbom, Martin; Zamble, Deborah B

    2008-01-01

    Transition metals are among the most common ligands that contribute to the biochemical and physiological properties of proteins. In the course of structural proteomic projects, the detection of transition metal cofactors prior to the determination of a high-resolution structure is extremely beneficial. This information can be used to select tractable targets from the proteomic pipeline because the presence of a metal often improves protein stability and can be used to help solve the phasing problem in x-ray crystallography. Recombinant proteins are often purified with substoichiometric amounts of metal loaded, so additional metal may be needed to obtain the homogeneous protein solution crucial for structural analysis. Furthermore, identifying a metal cofactor provides a clue about the nature of the biological role of an unclassified protein and can be applied with structural data in the assignation of a putative function. Many of the existing methods for transition metal analysis of purified proteins have limitations, which include a requirement for a large quantity of protein or a reliance on equipment with a prohibitive cost.The authors have developed two simple high throughput methods for identifying metalloproteins on a microgram scale. Each of the techniques has distinct advantages and can be applied to address divergent experimental goals. The first method, based on simple luminescence and colorimetric reactions, is fast, cheap, and semiquantitative. The second method, which employs HPLC separation, is accurate and affords unambiguous metal identification. PMID:18542873

  20. Layers: A molecular surface peeling algorithm and its applications to analyze protein structures

    Science.gov (United States)

    Karampudi, Naga Bhushana Rao; Bahadur, Ranjit Prasad

    2015-11-01

    We present an algorithm ‘Layers’ to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest classifier to predict the RTP of a given polypeptide sequence. Layers is a standalone application; however, it can be merged with other applications to reduce the computational load when working with large datasets of protein structures. Layers is available freely at http://www.csb.iitkgp.ernet.in/applications/mol_layers/main.

  1. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures

    OpenAIRE

    Fördös Gergely; Biro Jan C

    2005-01-01

    Abstract Background The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid...

  2. 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 relat

  3. 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...

  4. 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.

  5. 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.

  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. 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

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

    Science.gov (United States)

    Grose, Julianne H; Langston, Kelsey; Wang, Xiaohui; Squires, Shayne; Mustafi, Soumyajit Banerjee; Hayes, Whitney; Neubert, Jonathan; Fischer, Susan K; Fasano, Matthew; Saunders, Gina Moore; Dai, Qiang; Christians, Elisabeth; Lewandowski, E Douglas; Ping, Peipei; Benjamin, Ivor J

    2015-01-01

    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 tempting to

  9. 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 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.

  10. A Novel MALDI Matrix for Analyzing Peptides and Proteins: Paraffin Wax Immobilized Matrix

    Institute of Scientific and Technical Information of China (English)

    WEI Yuanlong; MEI Yuan; XU Zhe; WANG Cuihong; GUO Yinlong; DU Yiping; ZHANG Weibing

    2009-01-01

    A new kind of MALDI matrix, termed paraffin wax immobilized matrix, was used to study peptide mixtures and proteins. During the preparation process, the paraffin wax was heated and coated on the stainless-steel target plate, and then 2,5-dihydrobenzoic acid (DHB) was deposited on the paraffin layer and stainless-steel target plate to obtain different kinds of matrix spots. The morphology of matrices on different supports and peptide-matrix co-crystallization were observed by a high resolution digital-video microscopy system. Peptide mixtures and bovine serum albumin (BSA) digests were used to investigate the performance of the immobilized matrices on the paraffin target. The MALDI-FTMS analysis results also showed that the detection sensitivity of matrices immobilized in the paraffin sample support was better than that on other sample supports.

  11. Analyzing Plasmodium falciparum erythrocyte membrane protein 1 gene expression by a next generation sequencing based method

    DEFF Research Database (Denmark)

    Jespersen, Jakob S.; Petersen, Bent; Seguin-Orlando, Andaine;

    2013-01-01

    Plasmodium falciparum is responsible for most cases of severe malaria and causes >1 million deaths every year. The particular virulence of this Plasmodium species is highly associated with the expression of certain members of the Plasmodium falciparum erythrocyte membrane protein 1(PfEMP1) family......, encoded by ~60 highly variable 'var' genes per haploid genome. PfEMP1 is exported to the surface of infected erythrocytes and is thought to be fundamental to immune evasion by adhesion to host and parasite factors. The highly variable nature has constituted a roadblock in var expression studies aimed...... at identifying PfEMP1 features associated with high virulence. Here we present the first effective method for sequence analysis of var genes expressed in field samples: a sequential PCR and next generation sequencing based technique applied on expressed var sequence tags and subsequently on long range PCR...

  12. 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.

  13. 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.

  14. The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages.

    Science.gov (United States)

    Mariano, Rachelle; Wuchty, Stefan; Vizoso-Pinto, Maria G; Häuser, Roman; Uetz, Peter

    2016-04-22

    Although an abundance of bacteriophages exists, little is known about interactions between their proteins and those of their bacterial hosts. Here, we experimentally determined the phage-host interactomes of the phages Dp-1 and Cp-1 and their underlying protein interaction network in the host Streptococcus pneumoniae. We compared our results to the interaction patterns of E. coli phages lambda and T7. Dp-1 and Cp-1 target highly connected host proteins, occupy central network positions, and reach many protein clusters through the interactions of their targets. In turn, lambda and T7 targets cluster to conserved and essential proteins in E. coli, while such patterns were largely absent in S. pneumoniae. Furthermore, targets in E. coli were mutually strongly intertwined, while targets of Dp-1 and Cp-1 were strongly connected through essential and orthologous proteins in their immediate network vicinity. In both phage-host systems, the impact of phages on their protein targets appears to extend from their network neighbors, since proteins that interact with phage targets were located in central network positions, have a strong topologically disruptive effect and touch complexes with high functional heterogeneity. Such observations suggest that the phages, biological impact is accomplished through a surprisingly limited topological reach of their targets.

  15. Network analysis identifies protein clusters of functional importance in juvenile idiopathic arthritis

    OpenAIRE

    Stevens, Adam; Meyer, Stefan; Hanson, Daniel; Clayton, Peter; Donn, Rachelle

    2014-01-01

    Introduction Our objective was to utilise network analysis to identify protein clusters of greatest potential functional relevance in the pathogenesis of oligoarticular and rheumatoid factor negative (RF-ve) polyarticular juvenile idiopathic arthritis (JIA). Methods JIA genetic association data were used to build an interactome network model in BioGRID 3.2.99. The top 10% of this protein:protein JIA Interactome was used to generate a minimal essential network (MEN). Reactome FI Cytoscape 2.83...

  16. Hepatitis B Virus Protein X Induces Degradation of Talin-1

    Science.gov (United States)

    van de Klundert, Maarten A. A.; van den Biggelaar, Maartje; Kootstra, Neeltje A.; Zaaijer, Hans L.

    2016-01-01

    In the infected human hepatocyte, expression of the hepatitis B virus (HBV) accessory protein X (HBx) is essential to maintain viral replication in vivo. HBx critically interacts with the host damaged DNA binding protein 1 (DDB1) and the associated ubiquitin ligase machinery, suggesting that HBx functions by inducing the degradation of host proteins. To identify such host proteins, we systematically analyzed the HBx interactome. One HBx interacting protein, talin-1 (TLN1), was proteasomally degraded upon HBx expression. Further analysis showed that TLN1 levels indeed modulate HBV transcriptional activity in an HBx-dependent manner. This indicates that HBx-mediated TLN1 degradation is essential and sufficient to stimulate HBV replication. Our data show that TLN1 can act as a viral restriction factor that suppresses HBV replication, and suggest that the HBx relieves this restriction by inducing TLN1 degradation. PMID:27775586

  17. Analyzing swine sera for functional antibody titers against influenza A neuraminidase proteins using an enzyme-linked lectin assay (ELLA).

    Science.gov (United States)

    Sandbulte, Matthew R; Eichelberger, Maryna C

    2014-01-01

    Neuraminidase (NA) is an envelope glycoprotein of influenza viruses, including swine-lineage influenza A viruses. NA possesses sialidase activity, which is functionally important at multiple points in viral replication, counter-balancing the sialic acid receptor binding activity of the hemagglutinin (HA), the other major envelope glycoprotein. The NA proteins of influenza A viruses have been classified into nine serological subtypes, and they undergo antigenic drift variation similar to that of HA. Antibodies to NA are analyzed much less often than antibodies to HA. The conventional assay for NA inhibition (NI) antibody titration, established decades ago, is widely considered unwieldy and inefficient for routine use. In recent years, a few new formats have been developed which still measure inhibition of NA enzymatic function, but more efficiently and with less chemical waste produced. Described here is the enzyme-linked lectin assay (ELLA), which is performed in 96-well plates and analyzed on a spectrophotometric plate reader. An important factor in adoption of the ELLA technique for animal studies, such as swine, is the choice of NA antigen, which may be purified protein or whole virus containing an antigenically irrelevant HA protein. This NI assay, in conjunction with the hemagglutination inhibiting (HI) antibody assay, offers a practical way to characterize viral isolates more fully and to quantify antibodies induced by infection or vaccination.

  18. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures

    Directory of Open Access Journals (Sweden)

    Fördös Gergely

    2005-07-01

    Full Text Available Abstract Background The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user a. selects a structure from PDB; b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s c. defines a distance from these atoms (3–15 Å. The SeqX tool detects every residue that is located within the defined distances from the defined "backbone" atom(s; provides a DotPlot-like visualization (Residues Contact Map, and calculates the frequency of every possible residue pairs (Residue Contact Table in the observed structure. It is possible to exclude +/- 1 to 10 neighbor residues in the same polymeric chain from detection, which greatly improves the specificity of detections (up to 60% when tested on dsDNA. Results obtained on protein structures showed highly significant correlations with results obtained from literature (p Conclusion The tool is simple and easy to use and provides a quick and reliable visualization and analyses of residue co-locations in protein and nucleic acid structures. Availability and requirements http://janbiro.com/Downloads.html SeqX, Java J2SE Runtime Environment 5.0 (available from [see Additional file 1] http://www.sun.com and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors. Additional File 1 SeqX_1.041_05601.jar. see this article Click here for file

  19. Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase.

    Science.gov (United States)

    López, Abraham; Vilaseca, Marta; Madurga, Sergio; Varese, Monica; Tarragó, Teresa; Giralt, Ernest

    2016-07-01

    Ion mobility mass spectrometry (IMMS) is a biophysical technique that allows the separation of isobaric species on the basis of their size and shape. The high separation capacity, sensitivity and relatively fast time scale measurements confer IMMS great potential for the study of proteins in slow (µs-ms) conformational equilibrium in solution. However, the use of this technique for examining dynamic proteins is still not generalized. One of the major limitations is the instability of protein ions in the gas phase, which raises the question as to what extent the structures detected reflect those in solution. Here, we addressed this issue by analyzing the conformational landscape of prolyl oligopeptidase (POP) - a model of a large dynamic enzyme in the µs-ms range - by native IMMS and compared the results obtained in the gas phase with those obtained in solution. In order to interpret the experimental results, we used theoretical simulations. In addition, the stability of POP gaseous ions was explored by charge reduction and collision-induced unfolding experiments. Our experiments disclosed two species of POP in the gas phase, which correlated well with the open and closed conformations in equilibrium in solution; moreover, a gas-phase collapsed form of POP was also detected. Therefore, our findings not only support the potential of IMMS for the study of multiple co-existing conformations of large proteins in slow dynamic equilibrium in solution but also stress the need for careful data analysis to avoid artifacts. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27434808

  20. 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

  1. Evaluation of clustering algorithms for protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    van Helden Jacques

    2006-11-01

    Full Text Available Abstract Background Protein interactions are crucial components of all cellular processes. Recently, high-throughput methods have been developed to obtain a global description of the interactome (the whole network of protein interactions for a given organism. In 2002, the yeast interactome was estimated to contain up to 80,000 potential interactions. This estimate is based on the integration of data sets obtained by various methods (mass spectrometry, two-hybrid methods, genetic studies. High-throughput methods are known, however, to yield a non-negligible rate of false positives, and to miss a fraction of existing interactions. The interactome can be represented as a graph where nodes correspond with proteins and edges with pairwise interactions. In recent years clustering methods have been developed and applied in order to extract relevant modules from such graphs. These algorithms require the specification of parameters that may drastically affect the results. In this paper we present a comparative assessment of four algorithms: Markov Clustering (MCL, Restricted Neighborhood Search Clustering (RNSC, Super Paramagnetic Clustering (SPC, and Molecular Complex Detection (MCODE. Results A test graph was built on the basis of 220 complexes annotated in the MIPS database. To evaluate the robustness to false positives and false negatives, we derived 41 altered graphs by randomly removing edges from or adding edges to the test graph in various proportions. Each clustering algorithm was applied to these graphs with various parameter settings, and the clusters were compared with the annotated complexes. We analyzed the sensitivity of the algorithms to the parameters and determined their optimal parameter values. We also evaluated their robustness to alterations of the test graph. We then applied the four algorithms to six graphs obtained from high-throughput experiments and compared the resulting clusters with the annotated complexes. Conclusion This

  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. Analyzing the Expression Level and Cellular Location of the Tip-1 Protein in Oral Cancer Cell Lines

    Directory of Open Access Journals (Sweden)

    N Mansoursamaei

    2005-10-01

    Full Text Available Oral squamous cell carcinoma (OSCC is the sixth most common cancer in the world and accounts for approximately 4% of all cancers and 2% of all cancer death.The single most important factor in the prevention of the disease is early detection although, due to increased risk of secondary malignancy, survival remains poor with only a 25% 5 years survival. Both hereditary and environmental factors have been shown to have a productive role in this disease. For example, although chronic exposure of oral epithelium to tobacco smoke and alcohol are amongst the most important aetiological factors, it is now becoming realized that infection with high risk types of human papilloma virus (HPV are also involved as causative agent in a subset of this disease. All of these OSCC associated factors are known to promote genetic instability in the target oral epithelial cells. Work in our laboratories has indicated that the Tax interacting protein 1 (Tip-1 is also a target for the HPV 16 E6 protein may play an important role in controlling genetic instability during the oncogenic process (Hampson L., et al unpublished. So far 14 oral cancer cell lines have been grown in cell culture and RNA extracted from these. Tip-1 transcript levels were analyzed in this material by Northern blotting and competitive template quantitative PCR, which showed that Tip-1 levels were higher in some, cell lines than others (4 high, 6 moderate, 4 low level. Cell ploidy was determined by FACS analysis of propidium iodide stained cells, which showed that out of all the OSCC cell lines tested the cell line (BICR 68 had the greatest numbers of polyploid cells and also had the highest expression of Tip-1 RNA.

  5. Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity

    OpenAIRE

    Tan Kai; Kim Jongkwang

    2010-01-01

    Abstract Background Recent advances in proteomic technologies have enabled us to create detailed protein-protein interaction maps in multiple species and in both normal and diseased cells. As the size of the interaction dataset increases, powerful computational methods are required in order to effectively distil network models from large-scale interactome data. Results We present an algorithm, miPALM (Module Inference by Parametric Local Modularity), to infer protein complexes in a protein-pr...

  6. Identifying drug-target proteins based on network features

    Institute of Scientific and Technical Information of China (English)

    ZHU MingZhu; GAO Lei; LI Xia; LIU ZhiCheng

    2009-01-01

    Proteins rarely function in isolation Inside and outside cells, but operate as part of a highly Intercon-nected cellular network called the interaction network. Therefore, the analysis of the properties of drug-target proteins in the biological network is especially helpful for understanding the mechanism of drug action In terms of informatice. At present, no detailed characterization and description of the topological features of drug-target proteins have been available in the human protein-protein interac-tion network. In this work, by mapping the drug-targets in DrugBank onto the interaction network of human proteins, five topological indices of drug-targets were analyzed and compared with those of the whole protein interactome set and the non-drug-target set. The experimental results showed that drug-target proteins have higher connectivity and quicker communication with each other in the PPI network. Based on these features, all proteins In the interaction network were ranked. The results showed that, of the top 100 proteins, 48 are covered by DrugBank; of the remaining 52 proteins, 9 are drug-target proteins covered by the TTD, Matador and other databases, while others have been dem-onstrated to be drug-target proteins in the literature.

  7. Identifying drug-target proteins based on network features

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Proteins rarely function in isolation inside and outside cells, but operate as part of a highly intercon- nected cellular network called the interaction network. Therefore, the analysis of the properties of drug-target proteins in the biological network is especially helpful for understanding the mechanism of drug action in terms of informatics. At present, no detailed characterization and description of the topological features of drug-target proteins have been available in the human protein-protein interac- tion network. In this work, by mapping the drug-targets in DrugBank onto the interaction network of human proteins, five topological indices of drug-targets were analyzed and compared with those of the whole protein interactome set and the non-drug-target set. The experimental results showed that drug-target proteins have higher connectivity and quicker communication with each other in the PPI network. Based on these features, all proteins in the interaction network were ranked. The results showed that, of the top 100 proteins, 48 are covered by DrugBank; of the remaining 52 proteins, 9 are drug-target proteins covered by the TTD, Matador and other databases, while others have been dem- onstrated to be drug-target proteins in the literature.

  8. MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts.

    Science.gov (United States)

    Basha, Omer; Flom, Dvir; Barshir, Ruth; Smoly, Ilan; Tirman, Shoval; Yeger-Lotem, Esti

    2015-07-01

    The identification of the molecular pathways active in specific contexts, such as disease states or drug responses, often requires an extensive view of the potential interactions between a subset of proteins. This view is not easily obtained: it requires the integration of context-specific protein list or expression data with up-to-date data of protein interactions that are typically spread across multiple databases. The MyProteinNet web server allows users to easily create such context-sensitive protein interaction networks. Users can automatically gather and consolidate data from up to 11 different databases to create a generic protein interaction network (interactome). They can score the interactions based on reliability and filter them by user-defined contexts including molecular expression and protein annotation. The output of MyProteinNet includes the generic and filtered interactome files, together with a summary of their network attributes. MyProteinNet is particularly geared toward building human tissue interactomes, by maintaining tissue expression profiles from multiple resources. The ability of MyProteinNet to facilitate the construction of up-to-date, context-specific interactomes and its applicability to 11 different organisms and to tens of human tissues, make it a powerful tool in meaningful analysis of protein networks. MyProteinNet is available at http://netbio.bgu.ac.il/myproteinnet.

  9. An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis.

    Directory of Open Access Journals (Sweden)

    Shikha Vashisht

    Full Text Available Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.

  10. “Stop Ne(c)king around”: How interactomics contributes to functionally characterize Nek family kinases

    Institute of Scientific and Technical Information of China (English)

    Gabriela; Vaz; Meirelles; Arina; Marina; Perez; Edmárcia; Elisa; de; Souza; Ferna; Luisa; Basei; Priscila; Ferreira; Papa; Talita; Diniz; Melo; Hanchuk; Vanessa; Bomfim; Cardoso; Jrg; Kobarg

    2014-01-01

    Aside from Polo and Aurora, a third but less studied kinase family involved in mitosis regulation is the never in mitosis-gene A(NIMA)-related kinases(Neks). The founding member of this family is the sole member NIMA of Aspergillus nidulans, which is crucial for the initiation of mitosis in that organism. All 11 human Neks have been functionally assigned to one of the three core functions established for this family in mammals:(1) centrioles/mitosis;(2) primary ciliary function/ciliopathies; and(3) DNA damage response(DDR). Recent findings, especially on Nek 1 and 8, showed however, that several Neks participate in parallel in at least two of these contexts: primary ciliary function and DDR. In the core section of this in-depth review, we report the current detailed functional knowledge on each of the 11 Neks. In the discussion, we return to the cross-connections among Neks and point out how our and other groups’ functional and interactomics studies revealed that most Neks interact with protein partners associated with two if not all three of the functional contexts. We then raise the hypothesis that Neks may be the connecting regulatory elements that allow the cell to fine tune and synchronize the cellular events associated with these three core functions. The new and exciting findings on the Nek family open new perspectives and should allow the Neks to finally claim the attention they deserve in the field of kinases and cell cycle biology.

  11. 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.

  12. Analyzing the basic principles of tissue microarray data measuring the cooperative phenomena of marker proteins in invasive breast cancer

    OpenAIRE

    Korsching, Eberhard; Buerger, Horst; Boecker, Florian; Packeisen, Jens; Agelopoulos, Konstantin; Poos, Kathrin; Nadler, Walter

    2013-01-01

    Background: The analysis of a protein-expression pattern from tissue microarray (TMA) data will not immediately give an answer on synergistic or antagonistic effects between the observed proteins. But contrary to apparent first impression, it is possible to reveal those cooperative phenomena from TMA data. The data is (1) preserving a lot of the original physiological information content and (2) because of minor variances between the tumor samples, contains several related slightly different ...

  13. Identification of canine platelet proteins separated by differential detergent fractionation for nonelectrophoretic proteomics analyzed by Gene Ontology and pathways analysis

    Directory of Open Access Journals (Sweden)

    Trichler SA

    2014-01-01

    Full Text Available Shauna A Trichler,1,* Sandra C Bulla,1,* Nandita Mahajan,1 Kari V Lunsford,2 Ken Pendarvis,3 Bindu Nanduri,4,5 Fiona M McCarthy,3 Camilo Bulla1 1Department of Pathobiology and Population Medicine, 2Department of Clinical Sciences and Animal Health Center, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 3Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ, 4Department of Biological Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 5Institute for Genomics, Biocomputing and Biotechnology, Starkville, MS, USA *These authors contributed equally to this work Abstract: During platelet development, proteins necessary for the many functional roles of the platelet are stored within cytoplasmic granules. Platelets have also been shown to take up and store many plasma proteins into granules. This makes the platelet a potential novel source of biomarkers for many disease states. Approaches to sample preparation for proteomic studies for biomarkers search vary. Compared with traditional two-dimensional polyacrylamide gel electrophoresis systems, nonelectrophoretic proteomics methods that employ offline protein fractionation methods such as the differential detergent fractionation method have clear advantages. Here we report a proteomic survey of the canine platelet proteome using differential detergent fractionation coupled with mass spectrometry and functional modeling of the canine platelet proteins identified. A total of 5,974 unique proteins were identified from platelets, of which only 298 (5% had previous experimental evidence of in vivo expression. The use of offline prefractionation of canine proteins by differential detergent fractionation resulted in greater proteome coverage as compared with previous reports. This initial study contributes to a broader understanding of canine platelet biology and aids functional research

  14. Application of various statistical methods to analyze genetic diversity of Austrian (Pinus nigra Arn. and Scots pine (Pinus sylvestris L. based on protein markers

    Directory of Open Access Journals (Sweden)

    Lučić Aleksandar

    2011-01-01

    Full Text Available This paper presents the results of studies on protein polymorphism in seeds of Scots pine (Pinus sylvestris L. and Austrian pine (Pinus nigra Arn. as the most important economic species of the genus Pinus in Serbia. Polymorphism of protein markers was determined in selected genotypes originating from seven populations (Scots pine and six populations (Austrian pine. Analysis of protein markers was performed using two statistical methods, NTSYS and correspondence analysis. Both methods give the same arrangement of the analyzed populations, whereby, because of a different view of genetic distances, they can and should be combined, enabling easier and more precise understanding of mutual relationships of the observation units.

  15. Protein extraction and gel-based separation methods to analyze responses to pathogens in carnation (Dianthus caryophyllus L).

    Science.gov (United States)

    Ardila, Harold Duban; Fernández, Raquel González; Higuera, Blanca Ligia; Redondo, Inmaculada; Martínez, Sixta Tulia

    2014-01-01

    We are currently using a 2-DE-based proteomics approach to study plant responses to pathogenic fungi by using the carnation (Dianthus caryophyllus L)-Fusarium oxysporum f. sp. dianthi pathosystem. It is clear that the protocols for the first stages of a standard proteomics workflow must be optimized to each biological system and objectives of the research. The optimization procedure for the extraction and separation of proteins by 1-DE and 2-DE in the indicated system is reported. This strategy can be extrapolated to other plant-pathogen interaction systems in order to perform an evaluation of the changes in the host protein profile caused by the pathogen and to identify proteins which, at early stages, are involved or implicated in the plant defense response.

  16. A Simple Spreadsheet Program to Simulate and Analyze the Far-UV Circular Dichroism Spectra of Proteins

    Science.gov (United States)

    Abriata, Luciano A.

    2011-01-01

    A simple algorithm was implemented in a spreadsheet program to simulate the circular dichroism spectra of proteins from their secondary structure content and to fit [alpha]-helix, [beta]-sheet, and random coil contents from experimental far-UV circular dichroism spectra. The physical basis of the method is briefly reviewed within the context of…

  17. 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.

  18. 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

  19. Evaluation of high sensitivity C-reactive protein assay in cerebrospinal fluid on the Dimension RxL analyzer

    Directory of Open Access Journals (Sweden)

    Jozo Ćorić

    2012-04-01

    Full Text Available Introduction: Low sensitivity and specificity in traditional laboratory tests became insufficient for accurate diagnostics and initiation of proper treatment of patients infected with bacterial meningitis. High sensitivity C reactive protein (hsCRP may be an appropriate supplement for rapid diagnosis of bacterial meningitis. The subject of our investigation was the determination of C- reactive protein in cerebrospinal fluid (CSF duringacute bacterial meningitis.Methods: HsCRP was analysed by a sensitive immunoturbidimetric assay using the Dimension RxL analyser (Siemens. Cerebrospinal fluid concentrations of C-reactive protein have been measured in 20 patients(age range,1 to 50 years presenting with acute bacterial meningitis and also in a non-infected, non-inflamed control group (n=25.Results: The accuracy and precision of the method proved to be satisfactory. Repeatability of serial sampling for hsCRP described by coefficient of variation were CV=2.1-4.5%. This assay hsCRP in cerebrospinal fluid demonstrates adequate performance characteristics for routine clinical use. Elevated levels of CRP were found in 95% patients with bacterial meningitis. The mean CRP value in 25 uninfected control group was 0.25 mg/L (range 0.10-0.55. The mean CRP for patients with bacterial meningitis was 21.4 mg/L (range 0.40-100.Conclusions: A sensitive assay for CRP in CSF would be an useful adjunct to conventional investigation of acute infective meningitis.

  20. Comparison of measurements of canine plasma creatinine, glucose, proteins, urea, alanine aminotransferase, and alkaline phosphatase obtained with Spotchem SP 4430 and Vitros 250 analyzers.

    Science.gov (United States)

    Trumel, C; Diquélou, A; Germain, C; Palanché, F; Braun, J P

    2005-12-01

    The suitability of the Spotchem 4430 benchtop biochemistry analyzer for canine blood samples was tested for creatinine, glucose, proteins, urea, alkaline phosphatases and alanine aminotransferase. Results obtained from whole blood and corresponding heparin plasma were identical except for proteins which were higher in plasma (n=10). Between series imprecision (n=10) was 0.93). The slopes of the Passing-Bablock's regression ranged from 0.90 to 1.20 and intercepts were low. The mean biases were low, except for creatinine for which the results obtained by Spotchem (Jaffe reaction) were about 20 micromol/L higher than with the Vitros (enzymatic reaction). The results of this study show that the Spotchem analyzer is suitable for use in canine whole blood or plasma when small numbers of tests are to be performed and large analyzers are not available. PMID:16054888

  1. A quantitative approach to analyzing genome reductive evolution using protein-protein interaction networks: A case study ofMycobacterium leprae

    Directory of Open Access Journals (Sweden)

    Richard O Akinola

    2016-03-01

    Full Text Available The advance in high-throughput sequencing technologies has yielded complete genome sequences of several organisms, including complete bacterial genomes. The growing number of these available sequenced genomes has enabled analyses of their dynamics, as well as the molecular and evolutionary processes which these organisms are under. Comparative genomics of different bacterial genomes have highlighted their genome size and gene content in association with lifestyles and adaptation to various environments and have contributed to enhancing our understanding of the mechanisms of their evolution. Protein-protein functional interactions mediate many essential processes for maintaining the stability of the biological systems under changing environmental conditions. Thus, these interactions play crucial roles in the evolutionary processes of different organisms, especially for obligate intracellular bacteria, proven to generally have reduced genome sizes compared to their nearest free-living relatives. In this study, we used the approach based on the Renormalization Group (RG analysis technique and the Maximum-Excluded-Mass-Burning (MEMB model to investigate the evolutionary process of genome reduction in relation to the organization of functional networks of two organisms. Using a Mycobacterium leprae (MLP network in comparison with a Mycobacterium tuberculosis (MTB network as a case study, we show that reductive evolution in MLP was as a result of removal of important proteins from neighbours of corresponding orthologous MTB proteins. While each orthologous MTB protein had an increase in number of interacting partners in most instances, the corresponding MLP protein had lost some of them. This work provides a quantitative model for mapping reductive evolution and protein-protein functional interaction network organization in terms of roles played by different proteins in the network structure.

  2. Conservation and divergence within the clathrin interactome of Trypanosoma cruzi.

    Science.gov (United States)

    Kalb, Ligia Cristina; Frederico, Yohana Camila A; Boehm, Cordula; Moreira, Claudia Maria do Nascimento; Soares, Maurilio José; Field, Mark C

    2016-01-01

    Trypanosomatids are parasitic protozoa with a significant burden on human health. African and American trypanosomes are causative agents of Nagana and Chagas disease respectively, and speciated about 300 million years ago. These parasites have highly distinct life cycles, pathologies, transmission strategies and surface proteomes, being dominated by the variant surface glycoprotein (African) or mucins (American) respectively. In African trypanosomes clathrin-mediated trafficking is responsible for endocytosis and post-Golgi transport, with several mechanistic aspects distinct from higher organisms. Using clathrin light chain (TcCLC) and EpsinR (TcEpsinR) as affinity handles, we identified candidate clathrin-associated proteins (CAPs) in Trypanosoma cruzi; the cohort includes orthologs of many proteins known to mediate vesicle trafficking, but significantly not the AP-2 adaptor complex. Several trypanosome-specific proteins common with African trypanosomes, were also identified. Fluorescence microscopy revealed localisations for TcEpsinR, TcCLC and TcCHC at the posterior region of trypomastigote cells, coincident with the flagellar pocket and Golgi apparatus. These data provide the first systematic analysis of clathrin-mediated trafficking in T. cruzi, allowing comparison between protein cohorts and other trypanosomes and also suggest that clathrin trafficking in at least some life stages of T. cruzi may be AP-2-independent. PMID:27502971

  3. Ocean plankton. Determinants of community structure in the global plankton interactome.

    Science.gov (United States)

    Lima-Mendez, Gipsi; Faust, Karoline; Henry, Nicolas; Decelle, Johan; Colin, Sébastien; Carcillo, Fabrizio; Chaffron, Samuel; Ignacio-Espinosa, J Cesar; Roux, Simon; Vincent, Flora; Bittner, Lucie; Darzi, Youssef; Wang, Jun; Audic, Stéphane; Berline, Léo; Bontempi, Gianluca; Cabello, Ana M; Coppola, Laurent; Cornejo-Castillo, Francisco M; d'Ovidio, Francesco; De Meester, Luc; Ferrera, Isabel; Garet-Delmas, Marie-José; Guidi, Lionel; Lara, Elena; Pesant, Stéphane; Royo-Llonch, Marta; Salazar, Guillem; Sánchez, Pablo; Sebastian, Marta; Souffreau, Caroline; Dimier, Céline; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Gorsky, Gabriel; Not, Fabrice; Ogata, Hiroyuki; Speich, Sabrina; Stemmann, Lars; Weissenbach, Jean; Wincker, Patrick; Acinas, Silvia G; Sunagawa, Shinichi; Bork, Peer; Sullivan, Matthew B; Karsenti, Eric; Bowler, Chris; de Vargas, Colomban; Raes, Jeroen

    2015-05-22

    Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.

  4. Systematic Determination of Human Cyclin Dependent Kinase (CDK)-9 Interactome Identifies Novel Functions in RNA Splicing Mediated by the DEAD Box (DDX)-5/17 RNA Helicases.

    Science.gov (United States)

    Yang, Jun; Zhao, Yingxin; Kalita, Mridul; Li, Xueling; Jamaluddin, Mohammad; Tian, Bing; Edeh, Chukwudi B; Wiktorowicz, John E; Kudlicki, Andrzej; Brasier, Allan R

    2015-10-01

    Inducible transcriptional elongation is a rapid, stereotypic mechanism for activating immediate early immune defense genes by the epithelium in response to viral pathogens. Here, the recruitment of a multifunctional complex containing the cyclin dependent kinase 9 (CDK9) triggers the process of transcriptional elongation activating resting RNA polymerase engaged with innate immune response (IIR) genes. To identify additional functional activity of the CDK9 complex, we conducted immunoprecipitation (IP) enrichment-stable isotope labeling LC-MS/MS of the CDK9 complex in unstimulated cells and from cells activated by a synthetic dsRNA, polyinosinic/polycytidylic acid [poly (I:C)]. 245 CDK9 interacting proteins were identified with high confidence in the basal state and 20 proteins in four functional classes were validated by IP-SRM-MS. These data identified that CDK9 interacts with DDX 5/17, a family of ATP-dependent RNA helicases, important in alternative RNA splicing of NFAT5, and mH2A1 mRNA two proteins controlling redox signaling. A direct comparison of the basal versus activated state was performed using stable isotope labeling and validated by IP-SRM-MS. Recruited into the CDK9 interactome in response to poly(I:C) stimulation are HSPB1, DNA dependent kinases, and cytoskeletal myosin proteins that exchange with 60S ribosomal structural proteins. An integrated human CDK9 interactome map was developed containing all known human CDK9- interacting proteins. These data were used to develop a probabilistic global map of CDK9-dependent target genes that predicted two functional states controlling distinct cellular functions, one important in immune and stress responses. The CDK9-DDX5/17 complex was shown to be functionally important by shRNA-mediated knockdown, where differential accumulation of alternatively spliced NFAT5 and mH2A1 transcripts and alterations in downstream redox signaling were seen. The requirement of CDK9 for DDX5 recruitment to NFAT5 and mH2A1

  5. The Claudin Megatrachea Protein Complex*

    Science.gov (United States)

    Jaspers, Martin H. J.; Nolde, Kai; Behr, Matthias; Joo, Seol-hee; Plessmann, Uwe; Nikolov, Miroslav; Urlaub, Henning; Schuh, Reinhard

    2012-01-01

    Claudins are integral transmembrane components of the tight junctions forming trans-epithelial barriers in many organs, such as the nervous system, lung, and epidermis. In Drosophila three claudins have been identified that are required for forming the tight junctions analogous structure, the septate junctions (SJs). The lack of claudins results in a disruption of SJ integrity leading to a breakdown of the trans-epithelial barrier and to disturbed epithelial morphogenesis. However, little is known about claudin partners for transport mechanisms and membrane organization. Here we present a comprehensive analysis of the claudin proteome in Drosophila by combining biochemical and physiological approaches. Using specific antibodies against the claudin Megatrachea for immunoprecipitation and mass spectrometry, we identified 142 proteins associated with Megatrachea in embryos. The Megatrachea interacting proteins were analyzed in vivo by tissue-specific knockdown of the corresponding genes using RNA interference. We identified known and novel putative SJ components, such as the gene product of CG3921. Furthermore, our data suggest that the control of secretion processes specific to SJs and dependent on Sec61p may involve Megatrachea interaction with Sec61 subunits. Also, our findings suggest that clathrin-coated vesicles may regulate Megatrachea turnover at the plasma membrane similar to human claudins. As claudins are conserved both in structure and function, our findings offer novel candidate proteins involved in the claudin interactome of vertebrates and invertebrates. PMID:22930751

  6. 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

    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...... 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...

  7. Predicting Protein-Protein Interactions Using BiGGER: Case Studies

    OpenAIRE

    Almeida, Rui M; Simone Dell’Acqua; Ludwig Krippahl; Moura, José J. G.; Pauleta, Sofia R.

    2016-01-01

    The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate ...

  8. Analyzing the Effects of Climate Factors on Soybean Protein, Oil Contents, and Composition by Extensive and High-Density Sampling in China.

    Science.gov (United States)

    Song, Wenwen; Yang, Ruping; Wu, Tingting; Wu, Cunxiang; Sun, Shi; Zhang, Shouwei; Jiang, Bingjun; Tian, Shiyan; Liu, Xiaobing; Han, Tianfu

    2016-05-25

    From 2010 to 2013, 763 soybean samples were collected from an extensive area of China. The correlations between seed compositions and climate data were analyzed. The contents of crude protein and water-soluble protein, total amount of protein plus oil, and most of the amino acids were positively correlated with an accumulated temperature ≥15 °C (AT15) and the mean daily temperature (MDT) but were negatively correlated with hours of sunshine (HS) and diurnal temperature range (DTR). The correlations of crude oil and most fatty acids with climate factors were opposite to those of crude protein. Crude oil content had a quadratic regression relationship with MDT, and a positive correlation between oil content and MDT was found when the daily temperature was soybean protein and oil contents. The study illustrated the effects of climate factors on soybean protein and oil contents and proposed agronomic practices for improving soybean quality in different regions of China. The results provide a foundation for the regionalization of high-quality soybean production in China and similar regions in the world.

  9. targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

    Directory of Open Access Journals (Sweden)

    Chandra Nagasuma

    2008-12-01

    Full Text Available Abstract Background Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion The pipeline developed provides

  10. A second-generation protein-protein interaction network of Helicobacter pylori.

    Science.gov (United States)

    Häuser, Roman; Ceol, Arnaud; Rajagopala, Seesandra V; Mosca, Roberto; Siszler, Gabriella; Wermke, Nadja; Sikorski, Patricia; Schwarz, Frank; Schick, Matthias; Wuchty, Stefan; Aloy, Patrick; Uetz, Peter

    2014-05-01

    Helicobacter pylori infections cause gastric ulcers and play a major role in the development of gastric cancer. In 2001, the first protein interactome was published for this species, revealing over 1500 binary protein interactions resulting from 261 yeast two-hybrid screens. Here we roughly double the number of previously published interactions using an ORFeome-based, proteome-wide yeast two-hybrid screening strategy. We identified a total of 1515 protein-protein interactions, of which 1461 are new. The integration of all the interactions reported in H. pylori results in 3004 unique interactions that connect about 70% of its proteome. Excluding interactions of promiscuous proteins we derived from our new data a core network consisting of 908 interactions. We compared our data set to several other bacterial interactomes and experimentally benchmarked the conservation of interactions using 365 protein pairs (interologs) of E. coli of which one third turned out to be conserved in both species.

  11. Portable Analyzer for Rapid Analysis of Total Protein, Fat and Lactose Contents in Raw Milk Measured by Non-dispersive Short-wave Near-infrared Spectrometry

    Institute of Scientific and Technical Information of China (English)

    FENG Xu-dong; SU Rui; XU Nan; WANG Xing-hua; YU Ai-min; ZHANG Han-qi; CAO Yan-bo

    2013-01-01

    A novel portable analyzer for raw milk quality control during the material purchase at dairy plants was developed,by which the percentages(mass fraction) of main components including total protein,fat,and lactose of an unhomogenized milk sample could be determinated in 1 min with the help of non-dispersive short-wave near-infrared (NDSWNIR) spectrometry in a wavelength range from 600 nm to 1100 nm and multivariate calibration.The analyzer was designed with a single-beam optical system,which comprised a temperature control module,a multi-channel narrow-band light source(16 wavelengths),a glass absorption cell with 15 mm sample thickness,a silicon photodiode detector,several compound lenses and a recorder module.A total of 80 raw milk samples were collected at a dairy farm twice a month for 4 months.The samples were scanned with a common UV-Vis-NIR spectrometer and analyzed according to China GB standard methods.The uninformative variables elimination(UVE) method was carried out on the spectrum data and the percentages of main components of all the samples to choose the peak emitting wavelength of each channel of the light source.Another 90 raw milk samples were collected from the same dairy farm thrice a month for 3 months.The samples were analyzed according to China GB standard methods and with the proposed analyzer.The percentages of the main components and the NDSWNIR absorption data of the samples were used for the construction and validation of the multivariate calibration model with partial least squares(PLS) method.The root-mean-square errors of prediction(RMSEP) of total protein,fat and lactose were 0.201,0.172 and 0.247 and the coefficients of correlation(R) were 0.932,0.981 and 0.933,respectively.

  12. Domain-Domain Interactions Underlying Herpesvirus-Human Protein-Protein Interaction Networks

    OpenAIRE

    Zohar Itzhaki

    2011-01-01

    Protein-domains play an important role in mediating protein-protein interactions. Furthermore, the same domain-pairs mediate different interactions in different contexts and in various organisms, and therefore domain-pairs are considered as the building blocks of interactome networks. Here we extend these principles to the host-virus interface and find the domain-pairs that potentially mediate human-herpesvirus interactions. Notably, we find that the same domain-pairs used by other organisms ...

  13. Construction of multiple recombinant SLA-I proteins by linking heavy chains and light chains in vitro and analyzing their secondary and 3-dimensional structures.

    Science.gov (United States)

    Gao, Feng-shan; Bai, Jing; Zhang, Qiang; Xu, Chong-bo; Li, Yanmin

    2012-07-10

    Six breeds of swine were used to study the structure of swine leukocyte antigen class I (SLA-I). SLA-I complexes were produced by linking SLA-2 genes and β(2)m genes via a linker encoding a 15 amino acid glycine-rich sequence, (G4S)3, using splicing overlap extension (SOE)-PCR in vitro. The six recombinant SLA-2-linker-β(2)m genes were each inserted into p2X vectors and their expression induced in Escherichia coli TB1. The expressed proteins were detected by SDS-PAGE and western blotting. The maltose binding protein (MBP)-SLA-I fusion proteins were purified by amylose affinity chromatography followed by cleavage with factor Xa and separation of the SLA-I protein monomers from the MBP using a DEAE Ceramic Hyper D F column. The purified SLA-I monomers were detected by circular dichroism (CD) spectroscopy and the 3-dimensional (3D) structure of the constructed single-chain SLA-I molecules were analyzed by homology modeling. Recombinant SLA-2-Linker-β(2)m was successfully amplified from all six breeds of swine by SOE-PCR and expressed as fusion proteins of 84.1 kDa in pMAL-p2X, followed by confirmation by western blotting. After purification and cleavage of the MBP-SLA-I fusion proteins, SLA-I monomeric proteins of 41.6 kDa were separated. CD spectroscopy demonstrated that the SLA-I monomers had an α-helical structure, and the average α-helix, β-sheet, turn and random coil contents were 21.6%, 37.9%, 15.0% and 25.5%, respectively. Homology modeling of recombinant single-chain SLA-I molecules showed that the heavy chain and light chain constituted SLA-I complex with an open antigenic peptide-binding groove. It was concluded that the expressed SLA-I proteins in pMAL-p2X folded correctly and could be used to bind and screen nonameric peptides in vitro.

  14. HIV protein sequence hotspots for crosstalk with host hub proteins.

    Directory of Open Access Journals (Sweden)

    Mahdi Sarmady

    Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

  15. Lukasiewicz-Topos Models of Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models

    CERN Document Server

    Baianu, I C

    2004-01-01

    A categorical and Lukasiewicz-Topos framework for Lukasiewicz Algebraic Logic models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes is proposed. 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 logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Lukasiewicz Topos with an n-valued Lukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.

  16. 蛋白质快速检测仪测定乳及乳制品中蛋白质%Fast Determination of Protein in Milk and Dairy Products Using Protein Fast Analyzer

    Institute of Scientific and Technical Information of China (English)

    冯旭东; 安卫东; 丁毅; 于爱民; 刘静; 高德江; 王智宏; 于永

    2011-01-01

    A rapid analyzer for the determination of protein were developed. The effects of experimental parameters, including temperature, time, and foreign substances were investigated. Several milk and dairy products were analyzed using the protein fast analyzer. The experimental results showed that protein reagent can react with protein within 1 min at room temperature. The whole process of protein determination in dairy products only takes 5 - 10 min. The protein fast analyzer was applied to the determination of protein in dairy products, the relative error is lower 5% compared to Kjeldahl method and standard amount method of protein in milk power. The relative standard deviation is lower 1%. The determination results of protein were not affected by foreign substances, such as melamine, urea, glycine, ammonium nitrate and so on.%采用研制的蛋白质快速检测仪,系统地考察了温度、时间和干扰物质等因素对蛋白质测定的影响及检测仪的重复性,并将检测仪应用于新鲜乳、纯牛奶、牛奶饮料(核桃、燕麦、红枣)、牛初乳、奶粉、豆奶粉、豆浆粉和鸡蛋等样品中蛋白质的定量测定.实验结果表明,在17~40℃条件下,蛋白质试剂与蛋白质在1 min内即可完成反应,整个蛋白质含量测定过程仅需5~10 min,测定结果的精密度(RSD)小于1%,与凯式定氮法测定结果和标准物质比较,测定结果的相对误差均小于5%,且不受三聚氰胺、尿素、甘氨酸和硝酸铵等非蛋白氮的干扰,表明此仪器具有较好的准确度和重复性,可应用于乳及乳制品中蛋白质的快速定量测定.

  17. A Transporter Interactome Is Essential for the Acquisition of Antimicrobial Resistance to Antibiotics

    Science.gov (United States)

    Shuster, Yonatan; Steiner-Mordoch, Sonia; Alon Cudkowicz, Noemie; Schuldiner, Shimon

    2016-01-01

    Awareness of the problem of antimicrobial resistance (AMR) has escalated and drug-resistant infections are named among the most urgent problems facing clinicians today. Our experiments here identify a transporter interactome and portray its essential function in acquisition of antimicrobial resistance. By exposing E. coli cells to consecutive increasing concentrations of the fluoroquinolone norfloxacin we generated in the laboratory highly resistant strains that carry multiple mutations, most of them identical to those identified in clinical isolates. With this experimental paradigm, we show that the MDTs function in a coordinated mode to provide an essential first-line defense mechanism, preventing the drug reaching lethal concentrations, until a number of stable efficient alterations occur that allow survival. Single-component efflux transporters remove the toxic compounds from the cytoplasm to the periplasmic space where TolC-dependent transporters expel them from the cell. We postulate a close interaction between the two types of transporters to prevent rapid leak of the hydrophobic substrates back into the cell. The findings change the prevalent concept that in Gram-negative bacteria a single multidrug transporter, AcrAB-TolC type, is responsible for the resistance. The concept of a functional interactome, the process of identification of its members, the elucidation of the nature of the interactions and its role in cell physiology will change the existing paradigms in the field. We anticipate that our work will have an impact on the present strategy searching for inhibitors of AcrAB-TolC as adjuvants of existing antibiotics and provide novel targets for this urgent undertaking. PMID:27050393

  18. 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. PMID:26111897

  19. 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.

  20. Oxygen analyzer

    Science.gov (United States)

    Benner, William H.

    1986-01-01

    An oxygen analyzer which identifies and classifies microgram quantities of oxygen in ambient particulate matter and for quantitating organic oxygen in solvent extracts of ambient particulate matter. A sample is pyrolyzed in oxygen-free nitrogen gas (N.sub.2), and the resulting oxygen quantitatively converted to carbon monoxide (CO) by contact with hot granular carbon (C). Two analysis modes are made possible: (1) rapid determination of total pyrolyzable oxygen obtained by decomposing the sample at 1135.degree. C., or (2) temperature-programmed oxygen thermal analysis obtained by heating the sample from room temperature to 1135.degree. C. as a function of time. The analyzer basically comprises a pyrolysis tube containing a bed of granular carbon under N.sub.2, ovens used to heat the carbon and/or decompose the sample, and a non-dispersive infrared CO detector coupled to a mini-computer to quantitate oxygen in the decomposition products and control oven heating.

  1. Next challenges in protein–protein docking: from proteome to interactome and beyond

    NARCIS (Netherlands)

    Melquiond, A.S.J.; Karaca, E.; Kastritis, P.; Bonvin, A.M.J.J.

    2012-01-01

    Advances in biophysics and biochemistry have pushed back the limits for the structural characterization of biomolecular assemblies. Large efforts have been devoted to increase both resolution and accuracy of the methods, probe into the smallest biomolecules as well as the largest macromolecular mach

  2. Exhaustive search of the SNP-SNP interactome identifies epistatic effects on brain volume in two cohorts

    OpenAIRE

    Hibar, Derrek P.; Stein, Jason L.; Jahanshad, Neda; Kohannim, Omid; Toga, Arthur W.; McMahon, Katie L.; de Zubicaray, Greig I; Montgomery, Grant W; Martin, Nicholas G.; Wright, Margaret J.; Weiner, Michael W.; Thompson, Paul M.

    2013-01-01

    The SNP-SNP interactome has rarely been explored in the context of neuroimaging genetics mainly due to the complexity of conducting ∼1011 pairwise statistical tests. However, recent advances in machine learning, specifically the iterative sure independence screening (SIS) method, have enabled the analysis of datasets where the number of predictors is much larger than the number of observations. Using an implementation of the SIS algorithm (called EPISIS), we used exhaustive search of the geno...

  3. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

    OpenAIRE

    Hosur, R.; Peng, J.; A Vinayagam; Stelzl, U.; Xu, J.; Perrimon, N; Bienkowska, J.; Berger, B.

    2012-01-01

    Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-positive and false-negative rates. Coev2Net is easily applied to thousands of binary protein interactions and has superior predictive performance over existing methods. We experim...

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

    International Nuclear Information System (INIS)

    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

  5. 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.

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    CERN Document Server

    Antal, Miklos A; Csermely, Peter

    2008-01-01

    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.

  9. Coev2Net: a computational framework for boosting confidence in high-throughput protein-protein interaction datasets

    OpenAIRE

    Hosur, Raghavendra; Peng, Jian; Vinayagam, Arunachalam; Stelzl, Ulrich; Xu, Jinbo; Perrimon, Norbert; Bienkowska, Jadwiga R.; Berger, Bonnie

    2012-01-01

    Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-positive and false-negative rates. Coev2Net is easily applied to thousands of binary protein interactions and has superior predictive performance over existing methods. We experim...

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

    Directory of Open Access Journals (Sweden)

    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.

  11. 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.

  12. Field Deployable DNA analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Wheeler, E; Christian, A; Marion, J; Sorensen, K; Arroyo, E; Vrankovich, G; Hara, C; Nguyen, C

    2005-02-09

    This report details the feasibility of a field deployable DNA analyzer. Steps for swabbing cells from surfaces and extracting DNA in an automatable way are presented. Since enzymatic amplification reactions are highly sensitive to environmental contamination, sample preparation is a crucial step to make an autonomous deployable instrument. We perform sample clean up and concentration in a flow through packed bed. For small initial samples, whole genome amplification is performed in the packed bed resulting in enough product for subsequent PCR amplification. In addition to DNA, which can be used to identify a subject, protein is also left behind, the analysis of which can be used to determine exposure to certain substances, such as radionuclides. Our preparative step for DNA analysis left behind the protein complement as a waste stream; we determined to learn if the proteins themselves could be analyzed in a fieldable device. We successfully developed a two-step lateral flow assay for protein analysis and demonstrate a proof of principle assay.

  13. Searching for the Holy Grail; protein–protein interaction analysis and modulation

    Science.gov (United States)

    Morelli, Xavier; Hupp, Ted

    2012-01-01

    The first EMBO workshop on ‘Protein–Protein Interaction Analysis & Modulation' took place in June 2012 in Roscoff, France. It brought together researchers to discuss the growing field of protein network analysis and the modulation of protein–protein interactions, as well as outstanding related issues including the daunting challenge of integrating interactomes in systems biology and in the modelling of signalling networks. PMID:22986552

  14. Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases.

    OpenAIRE

    Ruth Barshir; Omer Shwartz; Smoly, Ilan Y.; Esti Yeger-Lotem

    2014-01-01

    An open question in human genetics is what underlies the tissue-specific manifestation of hereditary diseases, which are caused by genomic aberrations that are present in cells across the human body. Here we analyzed this phenomenon for over 300 hereditary diseases by using comparative network analysis. We created an extensive resource of protein expression and interactions in 16 main human tissues, by integrating recent data of gene and protein expression across tissues with data of protein-...

  15. Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases

    OpenAIRE

    Barshir, Ruth; Shwartz, Omer; Smoly, Ilan Y.; Yeger-Lotem, Esti

    2014-01-01

    An open question in human genetics is what underlies the tissue-specific manifestation of hereditary diseases, which are caused by genomic aberrations that are present in cells across the human body. Here we analyzed this phenomenon for over 300 hereditary diseases by using comparative network analysis. We created an extensive resource of protein expression and interactions in 16 main human tissues, by integrating recent data of gene and protein expression across tissues with data of protein-...

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

    Directory of Open Access Journals (Sweden)

    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.

  17. Lipid Vesicle-mediated Affinity Chromatography using Magnetic Activated Cell Sorting (LIMACS): a Novel Method to Analyze Protein-lipid Interaction

    OpenAIRE

    Bieberich, Erhard

    2011-01-01

    The analysis of lipid protein interaction is difficult because lipids are embedded in cell membranes and therefore, inaccessible to most purification procedures. As an alternative, lipids can be coated on flat surfaces as used for lipid ELISA and Plasmon resonance spectroscopy. However, surface coating lipids do not form microdomain structures, which may be important for the lipid binding properties. Further, these methods do not allow for the purification of larger amounts of proteins bindin...

  18. Molecular Architecture of Spinal Cord Injury Protein Interaction Network.

    Directory of Open Access Journals (Sweden)

    Ali Alawieh

    Full Text Available Spinal cord injury (SCI is associated with complex pathophysiological processes that follow the primary traumatic event and determine the extent of secondary damage and functional recovery. Numerous reports have used global and hypothesis-driven approaches to identify protein changes that contribute to the overall pathology of SCI in an effort to identify potential therapeutic interventions. In this study, we use a semi-automatic annotation approach to detect terms referring to genes or proteins dysregulated in the SCI literature and develop a curated SCI interactome. Network analysis of the SCI interactome revealed the presence of a rich-club organization corresponding to a "powerhouse" of highly interacting hub-proteins. Studying the modular organization of the network have shown that rich-club proteins cluster into modules that are specifically enriched for biological processes that fall under the categories of cell death, inflammation, injury recognition and systems development. Pathway analysis of the interactome and the rich-club revealed high similarity indicating the role of the rich-club proteins as hubs of the most prominent pathways in disease pathophysiology and illustrating the centrality of pro-and anti-survival signal competition in the pathology of SCI. In addition, evaluation of centrality measures of single nodes within the rich-club have revealed that neuronal growth factor (NGF, caspase 3, and H-Ras are the most central nodes and potentially an interesting targets for therapy. Our integrative approach uncovers the molecular architecture of SCI interactome, and provide an essential resource for evaluating significant therapeutic candidates.

  19. Model-free methods of analyzing domain motions in proteins from simulation : A comparison of normal mode analysis and molecular dynamics simulation of lysozyme

    NARCIS (Netherlands)

    Hayward, S; Kitao, A; Berendsen, HJC

    1997-01-01

    Model-free methods are introduced to determine quantities pertaining to protein domain motions from normal mode analyses and molecular dynamics simulations, For the normal mode analysis, the methods are based on the assumption that in low frequency modes, domain motions can be well approximated by m

  20. Reproducibility of Protein Identification of Selected Cell Types in Barrett's Esophagus Analyzed by Combining Laser-Capture Microdissection and Mass Spectrometry

    NARCIS (Netherlands)

    C. Stingl; F.G.I. van Vilsteren; C. Guzel; F.J.W. ten Kate; M. Visser; K.K. Krishnadath; J.J. Bergman; T.M. Luider

    2011-01-01

    Barrett's esophagus (BE) is associated with increased risk of esophageal adenocarcinoma (EAC) and characterized by replacement of normal esophageal squamous epithelium by columnar epithelium. These alterations are also reflected in changes in the protein-expression profiles of the cell types involve

  1. 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.

  2. 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

  3. VirusMentha: a new resource for virus-host protein interactions

    OpenAIRE

    Calderone, Alberto; Licata, Luana; Cesareni, Gianni

    2014-01-01

    Viral infections often cause diseases by perturbing several cellular processes in the infected host. Viral proteins target host proteins and either form new complexes or modulate the formation of functional host complexes. Describing and understanding the perturbation of the host interactome following viral infection is essential for basic virology and for the development of antiviral therapies. In order to provide a general overview of such interactions, a few years ago we developed VirusMIN...

  4. Understanding Protein-Protein Interactions Using Local Structural Features

    DEFF Research Database (Denmark)

    Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier;

    2013-01-01

    Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... interacting and non-interacting protein pairs to classify the structural features that sustain the binding (or non-binding) behavior. Our study indicates that not only the interacting region but also the rest of the protein surface are important for the interaction fate. The interpretation of this...... classification suggests that the balance between favoring and disfavoring structural features determines if a pair of proteins interacts or not. Our results are in agreement with previous works and support the funnel-like intermolecular energy landscape theory that explains PPIs. We have used these features to...

  5. 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 trans

  6. Protein Complex Purification by Affinity Capture.

    Science.gov (United States)

    LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P

    2016-01-01

    Affinity capture has become a powerful technique for consistently purifying endogenous protein complexes, facilitating biochemical and biophysical assays on otherwise inaccessible biological assemblies, and enabling broader interactomic exploration. For this procedure, cells are broken and their contents separated and extracted into a solvent, permitting access to target macromolecular complexes thus released in solution. The complexes are specifically enriched from the extract onto a solid medium coupled with an affinity reagent-usually an antibody-that recognizes the target either directly or through an appended affinity tag, allowing subsequent characterization of the complex. Here, we discuss approaches and considerations for purifying endogenous yeast protein complexes by affinity capture. PMID:27371601

  7. Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family

    Directory of Open Access Journals (Sweden)

    Eskandari Sepehr

    2007-10-01

    Full Text Available Abstract Background Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent technological advances, structural coverage of membrane integral proteins continues to be sparse. ConSequently, sequence-based methods represent an important alternative to illuminate functional roles. In this report, we critically examine the ability of several computational methods to provide functional insight within two specific areas. First, can phylogenomic methods accurately describe the functional diversity across a membrane integral protein family? And second, can sequence-based strategies accurately predict key functional sites? Due to the presence of a recently solved structure and a vast amount of experimental mutagenesis data, the neurotransmitter/Na+ symporter (NSS family is an ideal model system to assess the quality of our predictions. Results The raw NSS sequence dataset contains 181 sequences, which have been aligned by various methods. The resultant phylogenetic trees always contain six major subfamilies are consistent with the functional diversity across the family. Moreover, in well-represented subfamilies, phylogenetic clustering recapitulates several nuanced functional distinctions. Functional sites are predicted using six different methods (phylogenetic motifs, two methods that identify subfamily-specific positions, and three different conservation scores. A canonical set of 34 functional sites identified by Yamashita et al. within the recently solved LeuTAa structure is used to assess the quality of the predictions, most of which are predicted by the bioinformatic methods. Remarkably, the importance of these sites is largely confirmed by experimental mutagenesis. Furthermore, the collective set of functional site predictions qualitatively clusters along the proposed transport pathway, further

  8. Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service

    OpenAIRE

    Yoon Kyong-Oh; Kim Ki-Bong; Park Hyunseok; Cho Hee; Park Young-Jin; Kim Yeong; Kim Byoung-Chul; Cho Seong-Woong; Park Daeui; Kim Jeong-Gu; Park Soo-Jun; Lee Byoung-Moo; Bhak Jong

    2008-01-01

    Abstract Background Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. Phytopathogenic bacteria infect hosts through attachment to host tissue, enzyme secretion, exopolysaccharides production, toxins release, iron acquisition, and effector proteins secretion. Many such mechanisms involve some kind of protein-protein interaction in hosts....

  9. 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.

  10. Dynamic modularity in protein interaction networks predicts breast cancer outcome

    DEFF Research Database (Denmark)

    Taylor, Ian W; Linding, Rune; Warde-Farley, David;

    2009-01-01

    in biochemical structure were observed between the two types of hubs. Signaling domains were found more often in intermodular hub proteins, which were also more frequently associated with oncogenesis. Analysis of two breast cancer patient cohorts revealed that altered modularity of the human interactome may...... to predict patient outcome. An analysis of hub proteins identified intermodular hub proteins that are co-expressed with their interacting partners in a tissue-restricted manner and intramodular hub proteins that are co-expressed with their interacting partners in all or most tissues. Substantial differences...... be useful as an indicator of breast cancer prognosis....

  11. Stabilizing mutation of CTNNB1/beta-catenin and protein accumulation analyzed in a large series of parathyroid tumors of Swedish patients

    Directory of Open Access Journals (Sweden)

    Åkerström Göran

    2008-06-01

    Full Text Available Abstract Background Aberrant accumulation of β-catenin plays an important role in a variety of human neoplasms. We recently reported accumulation of β-catenin in parathyroid adenomas from patients with primary hyperparathyroidism (pHPT. In CTNNB1 exon 3, we detected a stabilizing mutation (S37A in 3 out of 20 analyzed adenomas. The aim of the present study was to determine the frequency and zygosity of mutations in CTNNB1 exon 3, and β-catenin accumulation in a large series of parathyroid adenomas of Swedish patients. Results The mutation S37A (TCT > GCT was detected by direct DNA sequencing of PCR fragments in 6 out of 104 sporadic parathyroid adenomas (5.8%. Taking our previous study into account, a total of 9 out of 124 (7.3% adenomas displayed the same mutation. The mutations were homozygous by DNA sequencing, restriction enzyme cleavage, and gene copy number determination using the GeneChip 500 K Mapping Array Set. All tumors analyzed by immunohistochemistry, including those with mutation, displayed aberrant β-catenin accumulation. Western blotting revealed a slightly higher expression level of β-catenin and nonphosphorylated active β-catenin in tumors with mutation compared to those without. Presence of the mutation was not related to distinct clinical characteristics. Conclusion Aberrant accumulation of β-catenin is very common in parathyroid tumors, and is caused by stabilizing homozygous mutation in 7.3% of Swedish pHPT patients.

  12. 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.

  13. Evolutionarily conserved herpesviral protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Even Fossum

    2009-09-01

    Full Text Available Herpesviruses constitute a family of large DNA viruses widely spread in vertebrates and causing a variety of different diseases. They possess dsDNA genomes ranging from 120 to 240 kbp encoding between 70 to 170 open reading frames. We previously reported the protein interaction networks of two herpesviruses, varicella-zoster virus (VZV and Kaposi's sarcoma-associated herpesvirus (KSHV. In this study, we systematically tested three additional herpesvirus species, herpes simplex virus 1 (HSV-1, murine cytomegalovirus and Epstein-Barr virus, for protein interactions in order to be able to perform a comparative analysis of all three herpesvirus subfamilies. We identified 735 interactions by genome-wide yeast-two-hybrid screens (Y2H, and, together with the interactomes of VZV and KSHV, included a total of 1,007 intraviral protein interactions in the analysis. Whereas a large number of interactions have not been reported previously, we were able to identify a core set of highly conserved protein interactions, like the interaction between HSV-1 UL33 with the nuclear egress proteins UL31/UL34. Interactions were conserved between orthologous proteins despite generally low sequence similarity, suggesting that function may be more conserved than sequence. By combining interactomes of different species we were able to systematically address the low coverage of the Y2H system and to extract biologically relevant interactions which were not evident from single species.

  14. Insights into the polerovirus-plant interactome revealed by co-immunoprecipitation and mass spectrometry

    Science.gov (United States)

    The identification of host proteins that interact with virus proteins is a major challenge for the field of virology. Phloem-limited viruses pose extraordinary challenges for in vivo protein interaction experiments because these viruses are localized in very few and highly specialized host cells. ...

  15. Struct2Net: a web service to predict protein–protein interactions using a structure-based approach

    OpenAIRE

    Singh, Rohit; Park, Daniel; Xu, Jinbo; Hosur, Raghavendra; Berger, Bonnie

    2010-01-01

    Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein–protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of the PPI interactome remains inadequate. We believe that Struct2Net is the first community-wide resource to provide structure-based PPI predictions that go beyond homology modeling...

  16. Identifying components of the hair-cell interactome involved in cochlear amplification

    Directory of Open Access Journals (Sweden)

    Cheatham MaryAnn

    2009-03-01

    Full Text Available Abstract Background Although outer hair cells (OHCs play a key role in cochlear amplification, it is not fully understood how they amplify sound signals by more than 100 fold. Two competing or possibly complementary mechanisms, stereocilia-based and somatic electromotility-based amplification, have been considered. Lacking knowledge about the exceptionally rich protein networks in the OHC plasma membrane, as well as related protein-protein interactions, limits our understanding of cochlear function. Therefore, we focused on finding protein partners for two important membrane proteins: Cadherin 23 (cdh23 and prestin. Cdh23 is one of the tip-link proteins involved in transducer function, a key component of mechanoelectrical transduction and stereocilia-based amplification. Prestin is a basolateral membrane protein responsible for OHC somatic electromotility. Results Using the membrane-based yeast two-hybrid system to screen a newly built cDNA library made predominantly from OHCs, we identified two completely different groups of potential protein partners using prestin and cdh23 as bait. These include both membrane bound and cytoplasmic proteins with 12 being de novo gene products with unknown function(s. In addition, some of these genes are closely associated with deafness loci, implying a potentially important role in hearing. The most abundant prey for prestin (38% is composed of a group of proteins involved in electron transport, which may play a role in OHC survival. The most abundant group of cdh23 prey (55% contains calcium-binding domains. Since calcium performs an important role in hair cell mechanoelectrical transduction and amplification, understanding the interactions between cdh23 and calcium-binding proteins should increase our knowledge of hair cell function at the molecular level. Conclusion The results of this study shed light on some protein networks in cochlear hair cells. Not only was a group of de novo genes closely associated

  17. Digital Microfluidics Sample Analyzer

    Science.gov (United States)

    Pollack, Michael G.; Srinivasan, Vijay; Eckhardt, Allen; Paik, Philip Y.; Sudarsan, Arjun; Shenderov, Alex; Hua, Zhishan; Pamula, Vamsee K.

    2010-01-01

    Three innovations address the needs of the medical world with regard to microfluidic manipulation and testing of physiological samples in ways that can benefit point-of-care needs for patients such as premature infants, for which drawing of blood for continuous tests can be life-threatening in their own right, and for expedited results. A chip with sample injection elements, reservoirs (and waste), droplet formation structures, fluidic pathways, mixing areas, and optical detection sites, was fabricated to test the various components of the microfluidic platform, both individually and in integrated fashion. The droplet control system permits a user to control droplet microactuator system functions, such as droplet operations and detector operations. Also, the programming system allows a user to develop software routines for controlling droplet microactuator system functions, such as droplet operations and detector operations. A chip is incorporated into the system with a controller, a detector, input and output devices, and software. A novel filler fluid formulation is used for the transport of droplets with high protein concentrations. Novel assemblies for detection of photons from an on-chip droplet are present, as well as novel systems for conducting various assays, such as immunoassays and PCR (polymerase chain reaction). The lab-on-a-chip (a.k.a., lab-on-a-printed-circuit board) processes physiological samples and comprises a system for automated, multi-analyte measurements using sub-microliter samples of human serum. The invention also relates to a diagnostic chip and system including the chip that performs many of the routine operations of a central labbased chemistry analyzer, integrating, for example, colorimetric assays (e.g., for proteins), chemiluminescence/fluorescence assays (e.g., for enzymes, electrolytes, and gases), and/or conductometric assays (e.g., for hematocrit on plasma and whole blood) on a single chip platform.

  18. 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.

  19. Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses

    Directory of Open Access Journals (Sweden)

    Simonis Nicolas

    2012-03-01

    Full Text Available Abstract Background Human T-cell leukemia virus type 1 (HTLV-1 and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL, whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in a dynamic struggle of activating and antagonistic interactions with host cells. Investigations focused on one or a few genes have identified several human factors interacting with HTLV viral proteins. Most of the available interaction data concern the highly investigated HTLV-1 Tax protein. Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression. Results We employ a scalable methodology for the systematic mapping and comparison of pathogen-host protein interactions that includes stringent yeast two-hybrid screening and systematic retest, as well as two independent validations through an additional protein interaction detection method and a functional transactivation assay. The final data set contained 166 interactions between 10 viral proteins and 122 human proteins. Among the 166 interactions identified, 87 and 79 involved HTLV-1 and HTLV-2 -encoded proteins, respectively. Targets for HTLV-1 and HTLV-2 proteins implicate a diverse set of cellular processes including the ubiquitin-proteasome system, the apoptosis, different cancer pathways and the Notch signaling pathway. Conclusions This study constitutes a first pass, with homogeneous data, at comparative analysis of host targets for HTLV-1 and -2 retroviruses, complements currently existing data for formulation of systems biology models of retroviral induced diseases and presents new insights on biological pathways involved in retroviral infection.

  20. In Cell Interactome of Oleocanthal, an Extra Virgin Olive Oil Bioactive Component.

    Science.gov (United States)

    Cassiano, Chiara; Casapullo, Agostino; Tosco, Alessandra; Monti, Maria Chiara; Riccio, Raffaele

    2015-06-01

    A copper-(I)-catalyzed variation of the Huisgen 1,3-dipolar cycloaddition has been applied to lead the in living-cell mass-spectrometry based identification of protein targets of oleocanthal, a natural metabolite daily ingested by millions of people. Chemical proteomics revealed heat-shock proteins, HSP70 and HSP90, as main oleocanthal interactors in living systems. These two proteins are involved in cancer development and, thus, our findings could have important outcomes for a deep evaluation of the bio-pharmacological significance of oleocanthal. PMID:26197539

  1. A protein-protein interaction map of the Trypanosoma brucei paraflagellar rod.

    Directory of Open Access Journals (Sweden)

    Sylvain Lacomble

    Full Text Available We have conducted a protein interaction study of components within a specific sub-compartment of a eukaryotic flagellum. The trypanosome flagellum contains a para-crystalline extra-axonemal structure termed the paraflagellar rod (PFR with around forty identified components. We have used a Gateway cloning approach coupled with yeast two-hybrid, RNAi and 2D DiGE to define a protein-protein interaction network taking place in this structure. We define two clusters of interactions; the first being characterised by two proteins with a shared domain which is not sufficient for maintaining the interaction. The other cohort is populated by eight proteins, a number of which possess a PFR domain and sub-populations of this network exhibit dependency relationships. Finally, we provide clues as to the structural organisation of the PFR at the molecular level. This multi-strand approach shows that protein interactome data can be generated for insoluble protein complexes.

  2. 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.

  3. 应用于自动生化分析仪的尿总蛋白试剂的评价%Evaluation on Urinary Total Protein Reagent Used in Automatic Biochemical Analyzer

    Institute of Scientific and Technical Information of China (English)

    何健; 陈秀英

    2014-01-01

    Objective The main aim is to evaluate the reagent for quantitative colorimetric analysis of urinary total protein used in automatic biochemical analyzer. Methods Urinary total protein reagent was evaluated for precision and linearity using Hitachi 7170A automatic biochemical analyzer, and the results were compared with those by manual method. Results The results indicated nice intra-batch and inter-batch reproducibility, and the linear range was 4.2g/L, which was close to the linear range labeled in the instruction provided in the kit. While in the comparison manual tests, r =0.998 and the regression equation was Y=0.9496X+0.1791, P>0.05, which indicate no significant differences between the two methods. Conclusion The urinary total protein used in automatic biochemical analyzer is rapid, precise, convenient and cost-efficient, so it could be used widely as a manual alternative method for determination of urinary proteins.%目的:对应用于全自动生化分析仪的定量比色分析尿总蛋白试剂进行评价。方法使用日立7170A全自动生化分析仪对尿总蛋白试剂进行精密度、线性及与手工法进行对比试验的评价。结果批内及批间重复性皆较好,线性范围为4.2g/L接近试剂盒说明书标明的线性范围,与手工法对比试验中,r=0.998,回归方程Y=0.9496X+0.1791,P>0.05,两方法之间无显著性差异。结论使用于全自动生化分析仪的尿总蛋白试剂,具有快速、准确、简便、成本低等优点,可代替手工法测定尿蛋白,易于广泛应用。

  4. Proteomic-Coupled-Network Analysis of T877A-Androgen Receptor Interactomes Can Predict Clinical Prostate Cancer Outcomes between White (Non-Hispanic) and African-American Groups

    Science.gov (United States)

    Zaman, Naif; Giannopoulos, Paresa N.; Chowdhury, Shafinaz; Bonneil, Eric; Thibault, Pierre; Wang, Edwin; Trifiro, Mark; Paliouras, Miltiadis

    2014-01-01

    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. PMID:25409505

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

    Science.gov (United States)

    Zaman, Naif; Giannopoulos, Paresa N; Chowdhury, Shafinaz; Bonneil, Eric; Thibault, Pierre; Wang, Edwin; Trifiro, Mark; Paliouras, Miltiadis

    2014-01-01

    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.

  6. 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.

  7. Interactome of Two Diverse RNA Granules Links mRNA Localization to Translational Repression in Neurons

    Directory of Open Access Journals (Sweden)

    Renate Fritzsche

    2013-12-01

    Full Text Available Transport of RNAs to dendrites occurs in neuronal RNA granules, which allows local synthesis of specific proteins at active synapses on demand, thereby contributing to learning and memory. To gain insight into the machinery controlling dendritic mRNA localization and translation, we established a stringent protocol to biochemically purify RNA granules from rat brain. Here, we identified a specific set of interactors for two RNA-binding proteins that are known components of neuronal RNA granules, Barentsz and Staufen2. First, neuronal RNA granules are much more heterogeneous than previously anticipated, sharing only a third of the identified proteins. Second, dendritically localized mRNAs, e.g., Arc and CaMKIIα, associate selectively with distinct RNA granules. Third, our work identifies a series of factors with known roles in RNA localization, translational control, and RNA quality control that are likely to keep localized transcripts in a translationally repressed state, often in distinct types of RNPs.

  8. A more appropriate Protein Classification using Data Mining

    CERN Document Server

    Rahman, Muhammad Mahbubur; Abdullah-Al-Mamun,; Mursalin, Tamnun E

    2011-01-01

    Research in bioinformatics is a complex phenomenon as it overlaps two knowledge domains, namely, biological and computer sciences. This paper has tried to introduce an efficient data mining approach for classifying proteins into some useful groups by representing them in hierarchy tree structure. There are several techniques used to classify proteins but most of them had few drawbacks on their grouping. Among them the most efficient grouping technique is used by PSIMAP. Even though PSIMAP (Protein Structural Interactome Map) technique was successful to incorporate most of the protein but it fails to classify the scale free property proteins. Our technique overcomes this drawback and successfully maps all the protein in different groups, including the scale free property proteins failed to group by PSIMAP. Our approach selects the six major attributes of protein: a) Structure comparison b) Sequence Comparison c) Connectivity d) Cluster Index e) Interactivity f) Taxonomic to group the protein from the databank ...

  9. Interactome for Auxiliary Splicing Factor U2AF65 Suggests Diverse Roles

    OpenAIRE

    Justin R Prigge; Iverson, Sonya V.; Siders, Ashley M.; Schmidt, Edward E.

    2009-01-01

    U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) is an essential component of the splicing machinery that is composed of two protein subunits, the 35 kD U2AF35 (U2AF1) and the 65 kD U2AF65 (U2AF2). U2AF interacts with various splicing factors within this machinery. Here we expand the list of mammalian splicing factors that are known to interact with U2AF65 as well as the list of nuclear proteins not known to participate in splicing that interact with U2AF65. Using a yeast two-hybrid...

  10. Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis

    DEFF Research Database (Denmark)

    Berchtold, Lukas Adrian; Størling, Zenia Marian; Ortis, Fernanda;

    2011-01-01

    Type 1 diabetes (T1D) is a complex disease characterized by the loss of insulin-secreting ß-cells. Although the disease has a strong genetic component, and several loci are known to increase T1D susceptibility risk, only few causal genes have currently been identified. To identify disease-causing...... genes in T1D, we performed an in silico "phenome-interactome analysis" on a genome-wide linkage scan dataset. This method prioritizes candidates according to their physical interactions at the protein level with other proteins involved in diabetes. A total of 11 genes were predicted to be likely disease...

  11. Analysis of the Bile Salt Export Pump (ABCB11) Interactome Employing Complementary Approaches.

    Science.gov (United States)

    Przybylla, Susanne; Stindt, Jan; Kleinschrodt, Diana; Schulte Am Esch, Jan; Häussinger, Dieter; Keitel, Verena; Smits, Sander H; Schmitt, Lutz

    2016-01-01

    The bile salt export pump (BSEP, ABCB11) plays an essential role in the formation of bile. In hepatocytes, BSEP is localized within the apical (canalicular) membrane and a deficiency of canalicular BSEP function is associated with severe forms of cholestasis. Regulation of correct trafficking to the canalicular membrane and of activity is essential to ensure BSEP functionality and thus normal bile flow. However, little is known about the identity of interaction partners regulating function and localization of BSEP. In our study, interaction partners of BSEP were identified in a complementary approach: Firstly, BSEP interaction partners were co-immunoprecipitated from human liver samples and identified by mass spectrometry (MS). Secondly, a membrane yeast two-hybrid (MYTH) assay was used to determine protein interaction partners using a human liver cDNA library. A selection of interaction partners identified both by MYTH and MS were verified by in vitro interaction studies using purified proteins. By these complementary approaches, a set of ten novel BSEP interaction partners was identified. With the exception of radixin, all other interaction partners were integral or membrane-associated proteins including proteins of the early secretory pathway and the bile acyl-CoA synthetase, the second to last, ER-associated enzyme of bile salt synthesis. PMID:27472061

  12. Direct and heterologous approaches to identify the LET-756/FGF interactome

    Directory of Open Access Journals (Sweden)

    Birnbaum Daniel

    2006-05-01

    Full Text Available Abstract Background Fibroblast growth factors (FGFs are multifunctional proteins that play important roles in cell communication, proliferation and differentiation. However, many aspects of their activities are not well defined. LET-756, one of the two C. elegans FGFs, is expressed throughout development and is essential for worm development. It is both expressed in the nucleus and secreted. Results To identify nuclear factors associated with LET-756, we used three approaches. First, we screened a two-hybrid cDNA library derived from mixed stages worms and from a normalized library, using LET-756 as bait. This direct approach allowed the identification of several binding partners that play various roles in the nucleus/nucleolus, such as PAL-1, a transcription regulator, or RPS-16, a component of the small ribosomal subunit. The interactions were validated by co-immunoprecipitation and determination of their site of occurrence in mammalian cells. Second, because patterns of protein interactions may be conserved throughout species, we searched for orthologs of known mammalian interactors and measured binary interaction with these predicted candidates. We found KIN-3 and KIN-10, the orthologs of CK2α and CK2β, as new partners of LET-756. Third, following the assumption that recognition motifs mediating protein interaction may be conserved between species, we screened a two-hybrid cDNA human library using LET-756 as bait. Among the few FGF partners detected was 14-3-3β. In support of this interaction we showed that the two 14-3-3β orthologous proteins, FTT-1 and FTT-2/PAR-5, interacted with LET-756. Conclusion We have conducted the first extensive search for LET-756 interactors using a multi-directional approach and established the first interaction map of LET-756/FGF with other FGF binding proteins from other species. The interactors identified play various roles in developmental process or basic biochemical events such as ribosome biogenesis.

  13. 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

    2015-01-01

    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.

  14. 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.

  15. 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.

  16. The Intermodulation Lockin Analyzer

    CERN Document Server

    Tholen, Erik A; Forchheimer, Daniel; Schuler, Vivien; Tholen, Mats O; Hutter, Carsten; Haviland, David B

    2011-01-01

    Nonlinear systems can be probed by driving them with two or more pure tones while measuring the intermodulation products of the drive tones in the response. We describe a digital lock-in analyzer which is designed explicitly for this purpose. The analyzer is implemented on a field-programmable gate array, providing speed in analysis, real-time feedback and stability in operation. The use of the analyzer is demonstrated for Intermodulation Atomic Force Microscopy. A generalization of the intermodulation spectral technique to arbitrary drive waveforms is discussed.

  17. 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...

  18. Analyzing in the present

    DEFF Research Database (Denmark)

    Revsbæk, Line; Tanggaard, Lene

    2015-01-01

    the interdependency between researcher and researched. On this basis, we advocate an explicit “open-state-of mind” listening as a key aspect of analyzing qualitative material, often described only as a matter of reading transcribed empirical materials, reading theory, and writing. The article contributes......The article presents a notion of “analyzing in the present” as a source of inspiration in analyzing qualitative research materials. The term emerged from extensive listening to interview recordings during everyday commuting to university campus. Paying attention to the way different parts...... of various interviews conveyed diverse significance to the listening researcher at different times became a method of continuously opening up the empirical material in a reflexive, breakdown-oriented process of analysis. We argue that situating analysis in the present of analyzing emphasizes and acknowledges...

  19. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  20. Software Design Analyzer System

    Science.gov (United States)

    Tausworthe, R. C.

    1985-01-01

    CRISP80 software design analyzer system a set of programs that supports top-down, hierarchic, modular structured design, and programing methodologies. CRISP80 allows for expression of design as picture of program.

  1. Total organic carbon analyzer

    Science.gov (United States)

    Godec, Richard G.; Kosenka, Paul P.; Smith, Brian D.; Hutte, Richard S.; Webb, Johanna V.; Sauer, Richard L.

    1991-01-01

    The development and testing of a breadboard version of a highly sensitive total-organic-carbon (TOC) analyzer are reported. Attention is given to the system components including the CO2 sensor, oxidation reactor, acidification module, and the sample-inlet system. Research is reported for an experimental reagentless oxidation reactor, and good results are reported for linearity, sensitivity, and selectivity in the CO2 sensor. The TOC analyzer is developed with gravity-independent components and is designed for minimal additions of chemical reagents. The reagentless oxidation reactor is based on electrolysis and UV photolysis and is shown to be potentially useful. The stability of the breadboard instrument is shown to be good on a day-to-day basis, and the analyzer is capable of 5 sample analyses per day for a period of about 80 days. The instrument can provide accurate TOC and TIC measurements over a concentration range of 20 ppb to 50 ppm C.

  2. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  3. 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.

  4. Analyzing Workforce Education. Monograph.

    Science.gov (United States)

    Texas Community & Technical Coll. Workforce Education Consortium.

    This monograph examines the issue of task analysis as used in workplace literacy programs, debating the need for it and how to perform it in a rapidly changing environment. Based on experiences of community colleges in Texas, the report analyzes ways that task analysis can be done and how to implement work force education programs more quickly.…

  5. List mode multichannel analyzer

    Science.gov (United States)

    Archer, Daniel E.; Luke, S. John; Mauger, G. Joseph; Riot, Vincent J.; Knapp, David A.

    2007-08-07

    A digital list mode multichannel analyzer (MCA) built around a programmable FPGA device for onboard data analysis and on-the-fly modification of system detection/operating parameters, and capable of collecting and processing data in very small time bins (<1 millisecond) when used in histogramming mode, or in list mode as a list mode MCA.

  6. Centrifugal analyzer development

    International Nuclear Information System (INIS)

    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

  7. Analyzing business models

    DEFF Research Database (Denmark)

    Nielsen, Christian

    2014-01-01

    , because the costs of processing and analyzing it exceed the benefits indicating bounded rationality. Hutton (2002) concludes that the analyst community’s inability to raise important questions on quality of management and the viability of its business model inevitably led to the Enron debacle. There seems...

  8. Analyzing Pseudophosphatase Function.

    Science.gov (United States)

    Hinton, Shantá D

    2016-01-01

    Pseudophosphatases regulate signal transduction cascades, but their mechanisms of action remain enigmatic. Reflecting this mystery, the prototypical pseudophosphatase STYX (phospho-serine-threonine/tyrosine-binding protein) was named with allusion to the river of the dead in Greek mythology to emphasize that these molecules are "dead" phosphatases. Although proteins with STYX domains do not catalyze dephosphorylation, this in no way precludes their having other functions as integral elements of signaling networks. Thus, understanding their roles in signaling pathways may mark them as potential novel drug targets. This chapter outlines common strategies used to characterize the functions of pseudophosphatases, using as an example MK-STYX [mitogen-activated protein kinase (MAPK) phospho-serine-threonine/tyrosine binding], which has been linked to tumorigenesis, apoptosis, and neuronal differentiation. We start with the importance of "restoring" (when possible) phosphatase activity in a pseudophosphatase so that the active mutant may be used as a comparison control throughout immunoprecipitation and mass spectrometry analyses. To this end, we provide protocols for site-directed mutagenesis, mammalian cell transfection, co-immunoprecipitation, phosphatase activity assays, and immunoblotting that we have used to investigate MK-STYX and the active mutant MK-STYXactive. We also highlight the importance of utilizing RNA interference (RNAi) "knockdown" technology to determine a cellular phenotype in various cell lines. Therefore, we outline our protocols for introducing short hairpin RNA (shRNA) expression plasmids into mammalians cells and quantifying knockdown of gene expression with real-time quantitative PCR (qPCR). A combination of cellular, molecular, biochemical, and proteomic techniques has served as powerful tools in identifying novel functions of the pseudophosphatase MK-STYX. Likewise, the information provided here should be a helpful guide to elucidating the

  9. Analyzing Pseudophosphatase Function.

    Science.gov (United States)

    Hinton, Shantá D

    2016-01-01

    Pseudophosphatases regulate signal transduction cascades, but their mechanisms of action remain enigmatic. Reflecting this mystery, the prototypical pseudophosphatase STYX (phospho-serine-threonine/tyrosine-binding protein) was named with allusion to the river of the dead in Greek mythology to emphasize that these molecules are "dead" phosphatases. Although proteins with STYX domains do not catalyze dephosphorylation, this in no way precludes their having other functions as integral elements of signaling networks. Thus, understanding their roles in signaling pathways may mark them as potential novel drug targets. This chapter outlines common strategies used to characterize the functions of pseudophosphatases, using as an example MK-STYX [mitogen-activated protein kinase (MAPK) phospho-serine-threonine/tyrosine binding], which has been linked to tumorigenesis, apoptosis, and neuronal differentiation. We start with the importance of "restoring" (when possible) phosphatase activity in a pseudophosphatase so that the active mutant may be used as a comparison control throughout immunoprecipitation and mass spectrometry analyses. To this end, we provide protocols for site-directed mutagenesis, mammalian cell transfection, co-immunoprecipitation, phosphatase activity assays, and immunoblotting that we have used to investigate MK-STYX and the active mutant MK-STYXactive. We also highlight the importance of utilizing RNA interference (RNAi) "knockdown" technology to determine a cellular phenotype in various cell lines. Therefore, we outline our protocols for introducing short hairpin RNA (shRNA) expression plasmids into mammalians cells and quantifying knockdown of gene expression with real-time quantitative PCR (qPCR). A combination of cellular, molecular, biochemical, and proteomic techniques has served as powerful tools in identifying novel functions of the pseudophosphatase MK-STYX. Likewise, the information provided here should be a helpful guide to elucidating the

  10. Lear CAN analyzer

    OpenAIRE

    Peiró Ibañez, Felipe

    2013-01-01

    Since it was introduced in the automotive industry, the protocol CAN (Controller Area Network) has been widely used for its benefits. This has led many companies to offer several hardware and software solutions in order to monitor the communications that gives this protocol. The current master thesis presents the Lear CAN Analyzer as a software tool developed within the company LEAR Corporation. It is designed to be used in the automobile industry as a complement or substitute for other co...

  11. Analyzing business process management

    OpenAIRE

    Skjæveland, Børge

    2013-01-01

    Within the Oil & Gas Industry, the market is constantly growing more competitive, forcing companies to continually adapt to changes. Companies need to cut costs and improve the business efficiency. One way of successfully managing these challenges is to implement business process management in the organization. This thesis will analyze how Oceaneering Asset Integrity AS handled the implementation of a Business Process Management System and the effects it had on the employees. The main goal...

  12. Radioisotope analyzer of barium

    International Nuclear Information System (INIS)

    Principle of operation and construction of radioisotope barium sulphate analyzer type MZB-2 for fast determination of barium sulphate content in barite ores and enrichment products are described. The gauge equipped with Am-241 and a scintillation detector enables measurement of barium sulphate content in prepared samples of barite ores in the range 60% - 100% with the accuracy of 1%. The gauge is used in laboratories of barite mine and ore processing plant. 2 refs., 2 figs., 1 tab. (author)

  13. IPv6 Protocol Analyzer

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    With the emerging of next generation Intemet protocol (IPv6), it is expected to replace the current version of Internet protocol (IPv4) that will be exhausted in the near future. Besides providing adequate address space, some other new features are included into the new 128 bits of IP such as IP auto configuration, quality of service, simple routing capability, security, mobility and multicasting. The current protocol analyzer will not be able to handle IPv6 packets. This paper will focus on developing protocol analyzer that decodes IPv6 packet. IPv6 protocol analyzer is an application module,which is able to decode the IPv6 packet and provide detail breakdown of the construction of the packet. It has to understand the detail construction of the IPv6, and provide a high level abstraction of bits and bytes of the IPv6 packet.Thus it increases network administrators' understanding of a network protocol,helps he/she in solving protocol related problem in a IPv6 network environment.

  14. 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

    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...... 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...

  15. Fluorescence analyzer for lignin

    Science.gov (United States)

    Berthold, John W.; Malito, Michael L.; Jeffers, Larry

    1993-01-01

    A method and apparatus for measuring lignin concentration in a sample of wood pulp or black liquor comprises a light emitting arrangement for emitting an excitation light through optical fiber bundles into a probe which has an undiluted sensing end facing the sample. The excitation light causes the lignin concentration to produce fluorescent emission light which is then conveyed through the probe to analyzing equipment which measures the intensity of the emission light. Measures a This invention was made with Government support under Contract Number DOE: DE-FC05-90CE40905 awarded by the Department of Energy (DOE). The Government has certain rights in this invention.

  16. Analyzing Chinese Financial Reporting

    Institute of Scientific and Technical Information of China (English)

    SABRINA; ZHANG

    2008-01-01

    If the world’s capital markets could use a harmonized accounting framework it would not be necessary for a comparison between two or more sets of accounting standards. However,there is much to do before this becomes reality.This article aims to pres- ent a general overview of China’s General Accepted Accounting Principles(GAAP), U.S.General Accepted Accounting Principles and International Financial Reporting Standards(IFRS),and to analyze the differ- ences among IFRS,U.S.GAAP and China GAAP using fixed assets as an example.

  17. The Identification of Novel Protein-Protein Interactions in Liver that Affect Glucagon Receptor Activity.

    Directory of Open Access Journals (Sweden)

    Junfeng Han

    Full Text Available Glucagon regulates glucose homeostasis by controlling glycogenolysis and gluconeogenesis in the liver. Exaggerated and dysregulated glucagon secretion can exacerbate hyperglycemia contributing to type 2 diabetes (T2D. Thus, it is important to understand how glucagon receptor (GCGR activity and signaling is controlled in hepatocytes. To better understand this, we sought to identify proteins that interact with the GCGR to affect ligand-dependent receptor activation. A Flag-tagged human GCGR was recombinantly expressed in Chinese hamster ovary (CHO cells, and GCGR complexes were isolated by affinity purification (AP. Complexes were then analyzed by mass spectrometry (MS, and protein-GCGR interactions were validated by co-immunoprecipitation (Co-IP and Western blot. This was followed by studies in primary hepatocytes to assess the effects of each interactor on glucagon-dependent glucose production and intracellular cAMP accumulation, and then in immortalized CHO and liver cell lines to further examine cell signaling. Thirty-three unique interactors were identified from the AP-MS screening of GCGR expressing CHO cells in both glucagon liganded and unliganded states. These studies revealed a particularly robust interaction between GCGR and 5 proteins, further validated by Co-IP, Western blot and qPCR. Overexpression of selected interactors in mouse hepatocytes indicated that two interactors, LDLR and TMED2, significantly enhanced glucagon-stimulated glucose production, while YWHAB inhibited glucose production. This was mirrored with glucagon-stimulated cAMP production, with LDLR and TMED2 enhancing and YWHAB inhibiting cAMP accumulation. To further link these interactors to glucose production, key gluconeogenic genes were assessed. Both LDLR and TMED2 stimulated while YWHAB inhibited PEPCK and G6Pase gene expression. In the present study, we have probed the GCGR interactome and found three novel GCGR interactors that control glucagon

  18. 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.

  19. WD40 proteins propel cellular networks.

    Science.gov (United States)

    Stirnimann, Christian U; Petsalaki, Evangelia; Russell, Robert B; Müller, Christoph W

    2010-10-01

    Recent findings indicate that WD40 domains play central roles in biological processes by acting as hubs in cellular networks; however, they have been studied less intensely than other common domains, such as the kinase, PDZ or SH3 domains. As suggested by various interactome studies, they are among the most promiscuous interactors. Structural studies suggest that this property stems from their ability, as scaffolds, to interact with diverse proteins, peptides or nucleic acids using multiple surfaces or modes of interaction. A general scaffolding role is supported by the fact that no WD40 domain has been found with intrinsic enzymatic activity despite often being part of large molecular machines. We discuss the WD40 domain distributions in protein networks and structures of WD40-containing assemblies to demonstrate their versatility in mediating critical cellular functions.

  20. Residual gas analyzer calibration

    Science.gov (United States)

    Lilienkamp, R. H.

    1972-01-01

    A technique which employs known gas mixtures to calibrate the residual gas analyzer (RGA) is described. The mass spectra from the RGA are recorded for each gas mixture. This mass spectra data and the mixture composition data each form a matrix. From the two matrices the calibration matrix may be computed. The matrix mathematics requires the number of calibration gas mixtures be equal to or greater than the number of gases included in the calibration. This technique was evaluated using a mathematical model of an RGA to generate the mass spectra. This model included shot noise errors in the mass spectra. Errors in the gas concentrations were also included in the valuation. The effects of these errors was studied by varying their magnitudes and comparing the resulting calibrations. Several methods of evaluating an actual calibration are presented. The effects of the number of gases in then, the composition of the calibration mixture, and the number of mixtures used are discussed.

  1. Analyzing architecture articles

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In the present study, we express the quality, function, and characteristics of architecture to help people comprehensively understand what architecture is. We also reveal the problems and conflict found in population, land, water resources, pollution, energy, and the organization systems in construction. China’s economy is transforming. We should focus on the cities, architectural environment, energy conservation, emission-reduction, and low-carbon output that will result in successful green development. We should macroscopically and microscopically analyze the development, from the natural environment to the artificial environment; from the relationship between human beings and nature to the combination of social ecology in cities, and farmlands. We must learn to develop and control them harmoniously and scientifically to provide a foundation for the methods used in architecture research.

  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. 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. PMID:27540857

  4. A novel immuno-competitive capture mass spectrometry strategy for protein-protein interaction profiling reveals that LATS kinases regulate HCV replication through NS5A phosphorylation.

    Science.gov (United States)

    Meistermann, Hélène; Gao, Junjun; Golling, Sabrina; Lamerz, Jens; Le Pogam, Sophie; Tzouros, Manuel; Sankabathula, Sailaja; Gruenbaum, Lore; Nájera, Isabel; Langen, Hanno; Klumpp, Klaus; Augustin, Angélique

    2014-11-01

    Mapping protein-protein interactions is essential to fully characterize the biological function of a protein and improve our understanding of diseases. Affinity purification coupled to mass spectrometry (AP-MS) using selective antibodies against a target protein has been commonly applied to study protein complexes. However, one major limitation is a lack of specificity as a substantial part of the proposed binders is due to nonspecific interactions. Here, we describe an innovative immuno-competitive capture mass spectrometry (ICC-MS) method to allow systematic investigation of protein-protein interactions. ICC-MS markedly increases the specificity of classical immunoprecipitation (IP) by introducing a competition step between free and capturing antibody prior to IP. Instead of comparing only one experimental sample with a control, the methodology generates a 12-concentration antibody competition profile. Label-free quantitation followed by a robust statistical analysis of the data is then used to extract the cellular interactome of a protein of interest and to filter out background proteins. We applied this new approach to specifically map the interactome of hepatitis C virus (HCV) nonstructural protein 5A (NS5A) in a cellular HCV replication system and uncovered eight new NS5A-interacting protein candidates along with two previously validated binding partners. Follow-up biological validation experiments revealed that large tumor suppressor homolog 1 and 2 (LATS1 and LATS2, respectively), two closely related human protein kinases, are novel host kinases responsible for NS5A phosphorylation at a highly conserved position required for optimal HCV genome replication. These results are the first illustration of the value of ICC-MS for the analysis of endogenous protein complexes to identify biologically relevant protein-protein interactions with high specificity.

  5. Pseudostupidity and analyzability.

    Science.gov (United States)

    Cohn, L S

    1989-01-01

    This paper seeks to heighten awareness of pseudostupidity and the potential analyzability of patients who manifest it by defining and explicating it, reviewing the literature, and presenting in detail the psychoanalytic treatment of a pseudostupid patient. Pseudostupidity is caused by an inhibition of the integration and synthesis of thoughts resulting in a discrepancy between intellectual capacity and apparent intellect. The patient's pseudostupidity was determined in part by his need to prevent his being more successful than father, i.e., defeating his oedipal rival. Knowing and learning were instinctualized. The patient libidinally and defensively identified with father's passive, masochistic position. He needed to frustrate the analyst as he had felt excited and frustrated by his parents' nudity and thwarted by his inhibitions. He wanted to cause the analyst to feel as helpless as he, the patient, felt. Countertransference frustration was relevant and clinically useful in the analysis. Interpretation of evolving relevant issues led to more anxiety and guilt, less pseudostupidity, a heightened alliance, and eventual working through. Negative therapeutic reactions followed the resolution of pseudostupidity. PMID:2708771

  6. 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.

  7. 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.

  8. Crew Activity Analyzer

    Science.gov (United States)

    Murray, James; Kirillov, Alexander

    2008-01-01

    The crew activity analyzer (CAA) is a system of electronic hardware and software for automatically identifying patterns of group activity among crew members working together in an office, cockpit, workshop, laboratory, or other enclosed space. The CAA synchronously records multiple streams of data from digital video cameras, wireless microphones, and position sensors, then plays back and processes the data to identify activity patterns specified by human analysts. The processing greatly reduces the amount of time that the analysts must spend in examining large amounts of data, enabling the analysts to concentrate on subsets of data that represent activities of interest. The CAA has potential for use in a variety of governmental and commercial applications, including planning for crews for future long space flights, designing facilities wherein humans must work in proximity for long times, improving crew training and measuring crew performance in military settings, human-factors and safety assessment, development of team procedures, and behavioral and ethnographic research. The data-acquisition hardware of the CAA (see figure) includes two video cameras: an overhead one aimed upward at a paraboloidal mirror on the ceiling and one mounted on a wall aimed in a downward slant toward the crew area. As many as four wireless microphones can be worn by crew members. The audio signals received from the microphones are digitized, then compressed in preparation for storage. Approximate locations of as many as four crew members are measured by use of a Cricket indoor location system. [The Cricket indoor location system includes ultrasonic/radio beacon and listener units. A Cricket beacon (in this case, worn by a crew member) simultaneously transmits a pulse of ultrasound and a radio signal that contains identifying information. Each Cricket listener unit measures the difference between the times of reception of the ultrasound and radio signals from an identified beacon

  9. 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

  10. Characterization of amyloid-β precursor protein intracellular domain-associated transcriptional complexes in SH-SY5Y neurocytes

    Institute of Scientific and Technical Information of China (English)

    Wulin Yang; Amy Yong Chen Lau; Shuizhong Luo; Qian Zhu3; Li Lu

    2012-01-01

    [Objective] Alzheimer's disease (AD) is one of the major disorders worldwide.Recent research suggests that the amyloid-β precursor protein intracellular domain (AICD) is a potential contributor to AD development and progression.The small AICD is rapidly degraded after processing from the full-length protein.The present study aimed to apply a highly efficient biotinylation approach in vitro to study AICD-associated complexes in neurocytes.[Methods] By coexpressing Escherichia coli biotin ligase with biotinyl-tagged AICD in the SH-SY5Y neuronal cell line,the effects of AICD overexpression on cell proliferation and apoptosis were analyzed.Besides,AICD-associated nuclear transcriptional complexes were purified and then examined by mass spectrometry.[Results] Our data showed that AICD overexpression not only affected cell proliferation but also led to apoptosis in differentiated SH-SY5Y cells.Moreover,biotinylation allowed single-step purification of biotinylated AICD-associated complexes from total nuclear extract via high-affinity biotin-streptavidin binding.Following this by mass spectrometry,we identified physically associated proteins,some reported previously and other novel binding partners,CUX1 and SPT5.[Conclusion]Based on these [Results],a map of theAICD-associated nuclear interactome was depicted.Specifically,AICD can activate CUXI transcriptional activity,which may be associated with AICD-dependent neuronal cell death.This work helps to understand the AICD-associated biologicalevents in AD progression and provides novel insights into the development of AD.

  11. Relationships between predicted moonlighting proteins, human diseases and comorbidities from a network perspective.

    Directory of Open Access Journals (Sweden)

    Andreas eZanzoni

    2015-06-01

    Full Text Available Moonlighting proteins are a subset of multifunctional proteins characterized by their multiple, independent and unrelated biological functions. We recently set up a large-scale identification of moonlighting proteins using a protein-protein interaction network approach. We established that 3% of the current human interactome is composed of predicted moonlighting proteins. We found that disease-related genes are over-represented among those candidates. Here, by comparing moonlighting candidates to non-candidates as groups, we further show that (i they are significantly involved in more than one disease, (ii they contribute to complex rather than monogenic diseases, (iii the diseases in which they are involved are phenotypically different according to their annotations, finally, (iv they are enriched for diseases pairs showing statistically significant comorbidity patterns based on Medicare records. Altogether, our results suggest that some observed comorbidities between phenotypically different diseases could be due to a shared protein involved in unrelated biological processes.

  12. InterMitoBase: An annotated database and analysis platform of protein-protein interactions for human mitochondria

    Directory of Open Access Journals (Sweden)

    Zhang Chenyu

    2011-06-01

    Full Text Available Abstract Background The mitochondrion is an essential organelle which plays important roles in diverse biological processes, such as metabolism, apoptosis, signal transduction and cell cycle. Characterizing protein-protein interactions (PPIs that execute mitochondrial functions is fundamental in understanding the mechanisms underlying biological functions and diseases associated with mitochondria. Investigations examining mitochondria are expanding to the system level because of the accumulation of mitochondrial proteomes and human interactome. Consequently, the development of a database that provides the entire protein interaction map of the human mitochondrion is urgently required. Results InterMitoBase provides a comprehensive interactome of human mitochondria. It contains the PPIs in biological pathways mediated by mitochondrial proteins, the PPIs between mitochondrial proteins and non-mitochondrial proteins as well as the PPIs between mitochondrial proteins. The current version of InterMitoBase covers 5,883 non-redundant PPIs of 2,813 proteins integrated from a wide range of resources including PubMed, KEGG, BioGRID, HPRD, DIP and IntAct. Comprehensive curations have been made on the interactions derived from PubMed. All the interactions in InterMitoBase are annotated according to the information collected from their original sources, GenBank and GO. Additionally, InterMitoBase features a user-friendly graphic visualization platform to present functional and topological analysis of PPI networks identified. This should aid researchers in the study of underlying biological properties. Conclusions InterMitoBase is designed as an integrated PPI database which provides the most up-to-date PPI information for human mitochondria. It also works as a platform by integrating several on-line tools for the PPI analysis. As an analysis platform and as a PPI database, InterMitoBase will be an important database for the study of mitochondria biochemistry

  13. Predicting protein-protein interactions in the post synaptic density.

    Science.gov (United States)

    Bar-shira, Ossnat; Chechik, Gal

    2013-09-01

    The post synaptic density (PSD) is a specialization of the cytoskeleton at the synaptic junction, composed of hundreds of different proteins. Characterizing the protein components of the PSD and their interactions can help elucidate the mechanism of long-term changes in synaptic plasticity, which underlie learning and memory. Unfortunately, our knowledge of the proteome and interactome of the PSD is still partial and noisy. In this study we describe a computational framework to improve the reconstruction of the PSD network. The approach is based on learning the characteristics of PSD protein interactions from a set of trusted interactions, expanding this set with data collected from large scale repositories, and then predicting novel interaction with proteins that are suspected to reside in the PSD. Using this method we obtained thirty predicted interactions, with more than half of which having supporting evidence in the literature. We discuss in details two of these new interactions, Lrrtm1 with PSD-95 and Src with Capg. The first may take part in a mechanism underlying glutamatergic dysfunction in schizophrenia. The second suggests an alternative mechanism to regulate dendritic spines maturation.

  14. 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

  15. 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

  16. High-throughput proteomic characterization of plasma rich in growth factors (PRGF-Endoret)-derived fibrin clot interactome.

    Science.gov (United States)

    Anitua, Eduardo; Prado, Roberto; Azkargorta, Mikel; Rodriguez-Suárez, Eva; Iloro, Ibon; Casado-Vela, Juan; Elortza, Felix; Orive, Gorka

    2015-11-01

    Plasma rich in growth factors (PRGF®-Endoret®) is an autologous technology that contains a set of proteins specifically addressed to wound healing and tissue regeneration. The scaffold formed by using this technology is a clot mainly composed of fibrin protein, forming a three-dimensional (3D) macroscopic network. This biomaterial is easily obtained by biotechnological means from blood and can be used in a range of situations to help wound healing and tissue regeneration. Although the main constituent of this clot is the fibrin scaffold, little is known about other proteins interacting in this clot that may act as adjuvants in the healing process. The aim of this study was to characterize the proteins enclosed by PRGF-Endoret scaffold, using a double-proteomic approach that combines 1D-SDS-PAGE approach followed by LC-MS/MS, and 2-DE followed by MALDI-TOF/TOF. The results presented here provide a description of the catalogue of key proteins in close contact with the fibrin scaffold. The obtained lists of proteins were grouped into families and networks according to gene ontology. Taken together, an enrichment of both proteins and protein families specifically involved in tissue regeneration and wound healing has been found.

  17. 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.

  18. 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...

  19. 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

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

    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 SMYDS).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.%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

  1. Adding protein context to the human protein-protein interaction network to reveal meaningful interactions.

    Directory of Open Access Journals (Sweden)

    Martin H Schaefer

    Full Text Available Interactions of proteins regulate signaling, catalysis, gene expression and many other cellular functions. Therefore, characterizing the entire human interactome is a key effort in current proteomics research. This challenge is complicated by the dynamic nature of protein-protein interactions (PPIs, which are conditional on the cellular context: both interacting proteins must be expressed in the same cell and localized in the same organelle to meet. Additionally, interactions underlie a delicate control of signaling pathways, e.g. by post-translational modifications of the protein partners - hence, many diseases are caused by the perturbation of these mechanisms. Despite the high degree of cell-state specificity of PPIs, many interactions are measured under artificial conditions (e.g. yeast cells are transfected with human genes in yeast two-hybrid assays or even if detected in a physiological context, this information is missing from the common PPI databases. To overcome these problems, we developed a method that assigns context information to PPIs inferred from various attributes of the interacting proteins: gene expression, functional and disease annotations, and inferred pathways. We demonstrate that context consistency correlates with the experimental reliability of PPIs, which allows us to generate high-confidence tissue- and function-specific subnetworks. We illustrate how these context-filtered networks are enriched in bona fide pathways and disease proteins to prove the ability of context-filters to highlight meaningful interactions with respect to various biological questions. We use this approach to study the lung-specific pathways used by the influenza virus, pointing to IRAK1, BHLHE40 and TOLLIP as potential regulators of influenza virus pathogenicity, and to study the signalling pathways that play a role in Alzheimer's disease, identifying a pathway involving the altered phosphorylation of the Tau protein. Finally, we provide the

  2. 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.

  3. 斜带石斑鱼三丁基锡结合蛋白基因的克隆与分析%Molecular cloning and analyzing of tributyltin-binding protein in orange-spotted grouper(Epinephelus coioides)

    Institute of Scientific and Technical Information of China (English)

    李锦光; 梁旭方; 郁颖; 李观贵; 李光照

    2010-01-01

    采用RT-PCR和RACE方法获得了斜带石斑鱼(Epinephelus coioides)三丁基锡结合蛋白(tributyltin-binding protein,TBT-bp)肝脏基因的cDNA全长序列.TBT-bp基因cDNA序列全长836 bp,含696 bp的开放阅读框,编码231个氨基酸.虽然编码蛋白序列与牙鲆(Paralichthys olivaceus)和底鳉(Fundulus heteroclitus)TBT-bp2序列同源性不高(分别为52%、20%),但是保守的信号肽序列结构与二级结构分析提示它们属于同一蛋白家族.系统树分析表明,此次克隆得到的斜带石斑鱼三丁基锡结合蛋白基因cDNA序列属于2型三丁基锡结合蛋白(tributyltin-binding protein type2,TBT-bp2).斜带石斑鱼TBT-bp基因cDNA全序列的获得为海水养殖鱼类中三丁基锡的去毒代谢相关分子机理研究奠定了基础,对今后进一步进行种苗育苗的研发,并以此为依据提高其人工育苗及仔鱼成活率有重要意义.

  4. Analyzing the H19- and T65-epitopes in 38 kd phosphorylated protein of Marek's disease viruses and comparing chicken immunological reactions to viruses point-mutated in the epitopes

    Institute of Scientific and Technical Information of China (English)

    CUI Zhizhong; ZHANG Zhi; QIN Aijian; Lee Lucy F

    2004-01-01

    DNA sequencing analysis in 38 kd phosphorylated protein (pp38) ORF of Marek's disease viruses (MDV) indicated that all tested 10 virulent strains with different pathotypes had 'A' at base #320 and glutamine at aa#107 while reacted with monoclonal antibody (Mab) H19 in indirect fluorescence antibody test (IFA). However, vaccine strain CVI988 had 'G' at base#320 and arginine at aa#107 instead, when it was negative in IFA with Mab H19. Some strains were also reactive with Mab T65 in IFA while there was 'G' at base #326 and glycine at aa#109, but the other strains, which had 'A' at base #326 and glutamic acid at aa#109, did not react with Mab T65. By comparison of CVI988 to its point mutants CVI/rpp38(AG) and CVI/rpp38(AA) with 1 or 2 base(s) changes at bases #320 and /or #326 of pp38 gene for their reactivity with Mab H19 and T65, it was confirmed that the glutamine at aa#107 and glycine at aa#109 were critical to epitopes H19 and T65 respectively. Immuno-reactions to MDV were compared in SPF chickens inoculated with cloned CVI988 and its mutant CVI/rpp38(AG). It was found that antibody responses to MDV in chickens inoculated with CVI/rpp38(AG) were delayed and significantly lower than that in chickens inoculated with the native CVI988. By differential comparison of antibody titers to different antigens, a third epitope specific to CVI988 and dependent on arginine at aa#107 was suggested to be responsible for the big difference in antibody responses induced by native CVI988 and its mutant.

  5. Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

    Directory of Open Access Journals (Sweden)

    Vandepoele Klaas

    2009-06-01

    Full Text Available Abstract Background Large-scale identification of the interrelationships between different components of the cell, such as the interactions between proteins, has recently gained great interest. However, unraveling large-scale protein-protein interaction maps is laborious and expensive. Moreover, assessing the reliability of the interactions can be cumbersome. Results In this study, we have developed a computational method that exploits the existing knowledge on protein-protein interactions in diverse species through orthologous relations on the one hand, and functional association data on the other hand to predict and filter protein-protein interactions in Arabidopsis thaliana. A highly reliable set of protein-protein interactions is predicted through this integrative approach making use of existing protein-protein interaction data from yeast, human, C. elegans and D. melanogaster. Localization, biological process, and co-expression data are used as powerful indicators for protein-protein interactions. The functional repertoire of the identified interactome reveals interactions between proteins functioning in well-conserved as well as plant-specific biological processes. We observe that although common mechanisms (e.g. actin polymerization and components (e.g. ARPs, actin-related proteins exist between different lineages, they are active in specific processes such as growth, cancer metastasis and trichome development in yeast, human and Arabidopsis, respectively. Conclusion We conclude that the integration of orthology with functional association data is adequate to predict protein-protein interactions. Through this approach, a high number of novel protein-protein interactions with diverse biological roles is discovered. Overall, we have predicted a reliable set of protein-protein interactions suitable for further computational as well as experimental analyses.

  6. Analyzing Valuation Practices through Contracts

    DEFF Research Database (Denmark)

    Tesnière, Germain; Labatut, Julie; Boxenbaum, Eva

    This paper seeks to analyze the most recent changes in how societies value animals. We analyze this topic through the prism of contracts between breeding companies and farmers. Focusing on new valuation practices and qualification of breeding animals, we question the evaluation of difficult...... commensurable entities (animal, embryo, mating) and the impacts of these valuation and qualifications on government of living entities....

  7. Analyzing data files in SWAN

    CERN Document Server

    Gajam, Niharika

    2016-01-01

    Traditionally analyzing data happens via batch-processing and interactive work on the terminal. The project aims to provide another way of analyzing data files: A cloud-based approach. It aims to make it a productive and interactive environment through the combination of FCC and SWAN software.

  8. Role of Intrinsic Protein Disorder in the Function and Interactions of the Transcriptional Coactivators CREB-binding Protein (CBP) and p300.

    Science.gov (United States)

    Dyson, H Jane; Wright, Peter E

    2016-03-25

    The transcriptional coactivators CREB-binding protein (CBP) and p300 undergo a particularly rich set of interactions with disordered and partly ordered partners, as a part of their ubiquitous role in facilitating transcription of genes. CBP and p300 contain a number of small structured domains that provide scaffolds for the interaction of disordered transactivation domains from a wide variety of partners, including p53, hypoxia-inducible factor 1α (HIF-1α), NF-κB, and STAT proteins, and are the targets for the interactions of disordered viral proteins that compete with cellular factors to disrupt signaling and subvert the cell cycle. The functional diversity of the CBP/p300 interactome provides an excellent example of the power of intrinsic disorder to facilitate the complexity of living systems.

  9. 焦磷酸测序法分析中国荷斯坦牛、娟姗牛及水牛的乳蛋白基因多态性%Genetic polymorphisms of milk protein in Chinese Holstein cattle, Jersey cattle and water buffalo analyzed by pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    任大喜; 陈有亮; 刘建新; 李玲; 林波; 曾庆坤

    2014-01-01

    ObjectiveTo analyze and compare the genetic polymorphisms of milk protein in Chinese Holstein cattle, Jersey cattle and water buffalo.MethodsThe primers were designed according to the milk protein polymorphic sites of Holstein, and the genetic polymorphisms were analyzed by pyrosequencing and confirmed by RP-HPLC.ResultsGenetic polymorphisms of milk protein genes (β-casein,κ-casein andβ-lactoglobulin) were detected in Chinese Holstein cattle and Jersey cattle. However, no polymorphism was found in water buffalo exceptκ-casein, and the polymorphic site was different with Holstein and Jersey. ConclusionMilk protein polymorphism was found in Chinese Holstein, Jersey and buffalo, and pyrose-quencing was a high-throughput and fast method for milk protein genotyping.%目的:本研究旨在分析和比较中国荷斯坦牛、娟姗牛和水牛的乳蛋白基因多态性。方法根据奶牛多态位点设计引物,采用焦磷酸测序法分析乳蛋白基因多态性,并采用高效液相色谱法进行验证。结果荷斯坦牛和娟姗牛的乳蛋白(β-casein,κ-casein和β-lactoglobulin)均存在基因多态性,而水牛仅在κ-casein上存在多态性且多态位点与另两种奶牛不同。结论中国荷斯坦牛、娟姗牛和水牛的乳蛋白基因均存在多态性,焦磷酸测序法能高通量、快速测定乳蛋白基因多态性。

  10. 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.

  11. Nuclear fuel microsphere gamma analyzer

    Science.gov (United States)

    Valentine, Kenneth H.; Long, Jr., Ernest L.; Willey, Melvin 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.

  12. Visualization of protein interaction networks: problems and solutions

    Directory of Open Access Journals (Sweden)

    Agapito Giuseppe

    2013-01-01

    Full Text Available Abstract 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

  13. 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.

  14. Screening for Host Factors Directly Interacting with RSV Protein: Microfluidics.

    Science.gov (United States)

    Kipper, Sarit; Avrahami, Dorit; Bajorek, Monika; Gerber, Doron

    2016-01-01

    We present a high-throughput microfluidics platform to identify novel host cell binding partners of respiratory syncytial virus (RSV) matrix (M) protein. The device consists of thousands of reaction chambers controlled by micro-mechanical valves. The microfluidic device is mated to a microarray-printed custom-made gene library. These genes are then transcribed and translated on-chip, resulting in a protein array ready for binding to RSV M protein.Even small viral proteome, such as that of RSV, presents a challenge due to the fact that viral proteins are usually multifunctional and thus their interaction with the host is complex. Protein microarrays technology allows the interrogation of protein-protein interactions, which could possibly overcome obstacles by using conventional high throughput methods. Using microfluidics platform we have identified new host interactors of M involved in various cellular pathways. A number of microfluidics based assays have already provided novel insights into the virus-host interactome, and the results have important implications for future antiviral strategies aimed at targets of viral protein interactions with the host. PMID:27464694

  15. Loviisa nuclear power plant analyzer

    International Nuclear Information System (INIS)

    The APROS Simulation Environment has been developed since 1986 by Imatran Voima Oy (IVO) and the Technical Research Centre of Finland (VTT). It provides tools, solution algorithms and process components for use in different simulation systems for design, analysis and training purposes. One of its main nuclear applications is the Loviisa Nuclear Power Plant Analyzer (LPA). The Loviisa Plant Analyzer includes all the important plant components both in the primary and in the secondary circuits. In addition, all the main control systems, the protection system and the high voltage electrical systems are included. (orig.)

  16. Analyzing the Grammar of English

    CERN Document Server

    Teschner, Richard V

    2007-01-01

    Analyzing the Grammar of English offers a descriptive analysis of the indispensable elements of English grammar. Designed to be covered in one semester, this textbook starts from scratch and takes nothing for granted beyond a reading and speaking knowledge of English. Extensively revised to function better in skills-building classes, it includes more interspersed exercises that promptly test what is taught, simplified and clarified explanations, greatly expanded and more diverse activities, and a new glossary of over 200 technical terms.Analyzing the Grammar of English is the only English gram

  17. 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

  18. Software-Design-Analyzer System

    Science.gov (United States)

    Tausworthe, Robert C.

    1991-01-01

    CRISP-90 software-design-analyzer system, update of CRISP-80, is set of computer programs constituting software tool for design and documentation of other software and supporting top-down, hierarchical, modular, structured methodologies for design and programming. Written in Microsoft QuickBasic.

  19. FORTRAN Static Source Code Analyzer

    Science.gov (United States)

    Merwarth, P.

    1984-01-01

    FORTRAN Static Source Code Analyzer program, SAP (DEC VAX version), automatically gathers statistics on occurrences of statements and structures within FORTRAN program and provides reports of those statistics. Provisions made for weighting each statistic and provide an overall figure of complexity.

  20. The stromal cell-surface protease fibroblast activation protein-α localizes to lipid rafts and is recruited to invadopodia.

    Science.gov (United States)

    Knopf, Julia D; Tholen, Stefan; Koczorowska, Maria M; De Wever, Olivier; Biniossek, Martin L; Schilling, Oliver

    2015-10-01

    Fibroblast activation protein alpha (FAPα) is a cell surface protease expressed by cancer-associated fibroblasts in the microenvironment of most solid tumors. As there is increasing evidence for proteases having non-catalytic functions, we determined the FAPα interactome in cancer-associated fibroblasts using the quantitative immunoprecipitation combined with knockdown (QUICK) method. Complex formation with adenosin deaminase, erlin-2, stomatin, prohibitin, Thy-1 membrane glycoprotein, and caveolin-1 was further validated by immunoblotting. Co-immunoprecipitation (co-IP) of the known stoichiometric FAPα binding partner dipeptidyl-peptidase IV (DPPIV) corroborated the proteomic strategy. Reverse co-IPs validated the FAPα interaction with caveolin-1, erlin-2, and stomatin while co-IP upon RNA-interference mediated knock-down of DPPIV excluded adenosin deaminase as a direct FAPα interaction partner. Many newly identified FAPα interaction partners localize to lipid rafts, including caveolin-1, a widely-used marker for lipid raft localization. We hypothesized that this indicates a recruitment of FAPα to lipid raft structures. In density gradient centrifugation, FAPα co-fractionates with caveolin-1. Immunofluorescence optical sectioning microscopy of FAPα and lipid raft markers further corroborates recruitment of FAPα to lipid rafts and invadopodia. FAPα is therefore an integral component of stromal lipid rafts in solid tumors. In essence, we provide one of the first interactome analyses of a cell surface protease and translate these results into novel biological aspects of a marker protein for cancer-associated fibroblasts.

  1. Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data

    Science.gov (United States)

    Raju, Hemalatha B.; Tsinoremas, Nicholas F.; Capobianco, Enrico

    2016-01-01

    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 (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes and repurposing 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 parental 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 NP. 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 and 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 identified in protein–protein

  2. 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....

  3. Introduction: why analyze single cells?

    Science.gov (United States)

    Di Carlo, Dino; Tse, Henry Tat Kwong; Gossett, Daniel R

    2012-01-01

    Powerful methods in molecular biology are abundant; however, in many fields including hematology, stem cell biology, tissue engineering, and cancer biology, data from tools and assays that analyze the average signals from many cells may not yield the desired result because the cells of interest may be in the minority-their behavior masked by the majority-or because the dynamics of the populations of interest are offset in time. Accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. In this chapter, we discuss the rationale for performing analyses on individual cells in more depth, cover the fields of study in which single-cell behavior is yielding new insights into biological and clinical questions, and speculate on how single-cell analysis will be critical in the future.

  4. The Statistical Loop Analyzer (SLA)

    Science.gov (United States)

    Lindsey, W. C.

    1985-01-01

    The statistical loop analyzer (SLA) is designed to automatically measure the acquisition, tracking and frequency stability performance characteristics of symbol synchronizers, code synchronizers, carrier tracking loops, and coherent transponders. Automated phase lock and system level tests can also be made using the SLA. Standard baseband, carrier and spread spectrum modulation techniques can be accomodated. Through the SLA's phase error jitter and cycle slip measurements the acquisition and tracking thresholds of the unit under test are determined; any false phase and frequency lock events are statistically analyzed and reported in the SLA output in probabilistic terms. Automated signal drop out tests can be performed in order to trouble shoot algorithms and evaluate the reacquisition statistics of the unit under test. Cycle slip rates and cycle slip probabilities can be measured using the SLA. These measurements, combined with bit error probability measurements, are all that are needed to fully characterize the acquisition and tracking performance of a digital communication system.

  5. Predicting Protein-Protein Interactions Using BiGGER: Case Studies.

    Science.gov (United States)

    Almeida, Rui M; Dell'Acqua, Simone; Krippahl, Ludwig; Moura, José J G; Pauleta, Sofia R

    2016-01-01

    The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three Case Studies: (Case Study A) in which no specific contact data is available; (Case Study B) when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling) on one of the partners is available; and (Case Study C) when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields. PMID:27517887

  6. Predicting Protein-Protein Interactions Using BiGGER: Case Studies

    Directory of Open Access Journals (Sweden)

    Rui M. Almeida

    2016-08-01

    Full Text Available The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three Case Studies: (Case Study A in which no specific contact data is available; (Case Study B when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling on one of the partners is available; and (Case Study C when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields.

  7. Satellite-based interference analyzer

    Science.gov (United States)

    Varice, H.; Johannsen, K.; Sabaroff, S.

    1977-01-01

    System identifies terrestrial sources of radiofrequency interference and measures their frequency spectra and amplitudes. Designed to protect satellite communication networks, system measures entire noise spectrum over selected frequency band and can raster-scan geographical region to locate noise sources. Once interference is analyzed, realistic interference protection ratios are determined and mathematical models for predicting ratio-frequency noise spectra are established. This enhances signal-detection and locates optimum geographical positions and frequency bands for communication equipment.

  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.

  9. 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

  10. 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.

  11. 磷酸化蛋白质组学鉴定 PTPLAD1调控的结肠癌细胞酪氨酸磷酸化蛋白质%Phosphoproteomics to analyze PTPLAD1-regulated tyrosine-phosphoryla-ted proteins in colon cancer cells

    Institute of Scientific and Technical Information of China (English)

    胡阳; 杨杰; 余汝媛; 汪洋

    2015-01-01

    目的:用磷酸化蛋白质组学的方法鉴定并分析结肠癌细胞中含蛋白酪氨酸磷酸酶样A结构域蛋白1( PTPLAD1)调控的酪氨酸磷酸化蛋白。方法:运用siRNA技术沉默PTPLAD1的表达,于细胞培养条件下运用氨基酸稳定同位素标记技术( stable lsotope labeling with amino acids in cell culture, SILAC)标记细胞,用酪氨酸磷酸化抗体免疫沉淀富集酪氨酸磷酸化蛋白,用LTQ-OrbitrapXL质谱鉴定因敲低PTPLAD1所出现的差异表达的酪氨酸磷酸化蛋白,进一步利用Ingenuity Pathway Analysis ( IPA)软件对这些差异蛋白进行生物信息学分析。结果:用real-time PCR筛选得到有效的siRNA干扰片段,Western blot验证其干扰效果及有效干扰时间。质谱鉴定PTPLAD1调控的差异酪氨酸磷酸化蛋白共20个,其中显著上调的8个,显著下调的10个,主要为转录因子及肿瘤标志物相关蛋白。 IPA软件的结果表明PTPLAD1调控的差异酪氨酸磷酸化蛋白的功能主要与器官发育分化、维持组织分化类型及细胞凋亡、增殖相关。结论:成功鉴定出PTPLAD1调控的差异酪氨酸磷酸化蛋白,可以为后续研究PTP-LAD1在结肠癌的发生发展中的作用及机理提供基础。%AIM:To identify and analyze tyrosine-phosphorylated proteins regulated by protein tyrosine phos-phatase-like A domain containing protein 1 ( PTPLAD1) in colon cancer cells by phosphoproteomics.METHODS: The expression of PTPLAD1 in colon cancer cell line HCT-116 was knocked down by small interfering RNAs, and the differenti-al expression of tyrosine-phosphorylated proteins in response to the konckdown of PTPLAD1 in HCT-116 cells was identified by stable isotope labeling with amino acid in cell culture ( SILAC) , coupled with the tyrosine phosphorylation antibody im-munoprecipitation and LC-MS/MS analysis.The Ingenuity Pathway Analysis ( IPA) software was employed for bioinformat-ics analysis on the

  12. The Aqueduct Global Flood Analyzer

    Science.gov (United States)

    Iceland, Charles

    2015-04-01

    As population growth and economic growth take place, and as climate change accelerates, many regions across the globe are finding themselves increasingly vulnerable to flooding. A recent OECD study of the exposure of the world's large port cities to coastal flooding found that 40 million people were exposed to a 1 in 100 year coastal flood event in 2005, and the total value of exposed assets was about US 3,000 billion, or 5% of global GDP. By the 2070s, those numbers were estimated to increase to 150 million people and US 35,000 billion, or roughly 9% of projected global GDP. Impoverished people in developing countries are particularly at risk because they often live in flood-prone areas and lack the resources to respond. WRI and its Dutch partners - Deltares, IVM-VU University Amsterdam, Utrecht University, and PBL Netherlands Environmental Assessment Agency - are in the initial stages of developing a robust set of river flood and coastal storm surge risk measures that show the extent of flooding under a variety of scenarios (both current and future), together with the projected human and economic impacts of these flood scenarios. These flood risk data and information will be accessible via an online, easy-to-use Aqueduct Global Flood Analyzer. We will also investigate the viability, benefits, and costs of a wide array of flood risk reduction measures that could be implemented in a variety of geographic and socio-economic settings. Together, the activities we propose have the potential for saving hundreds of thousands of lives and strengthening the resiliency and security of many millions more, especially those who are most vulnerable. Mr. Iceland will present Version 1.0 of the Aqueduct Global Flood Analyzer and provide a preview of additional elements of the Analyzer to be released in the coming years.

  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. [Examination of the olfactory analyzer].

    Science.gov (United States)

    Domrachev, A A; Afon'kin, V Iu

    2002-01-01

    A method of threshold olfactometry is proposed consisting in the use of three olfactive substances (tincture of valerian, acetic acid, liquid ammonia) in selected concentrations. This allows to investigate the thresholds of certain modality. Each concentration of the olfactive substance is placed into a glass bottle (100 ml) and stored at the temperature 18-20 degrees C. The examination of the state of the olfactory analyzer within a 24-h working day showed stability of threshold olfactometry when the organism is tired. Utilization of threshold olfactometry in some diagnostic areas is shown. PMID:12056163

  15. Managing healthcare information: analyzing trust.

    Science.gov (United States)

    Söderström, Eva; Eriksson, Nomie; Åhlfeldt, Rose-Mharie

    2016-08-01

    Purpose - The purpose of this paper is to analyze two case studies with a trust matrix tool, to identify trust issues related to electronic health records. Design/methodology/approach - A qualitative research approach is applied using two case studies. The data analysis of these studies generated a problem list, which was mapped to a trust matrix. Findings - Results demonstrate flaws in current practices and point to achieving balance between organizational, person and technology trust perspectives. The analysis revealed three challenge areas, to: achieve higher trust in patient-focussed healthcare; improve communication between patients and healthcare professionals; and establish clear terminology. By taking trust into account, a more holistic perspective on healthcare can be achieved, where trust can be obtained and optimized. Research limitations/implications - A trust matrix is tested and shown to identify trust problems on different levels and relating to trusting beliefs. Future research should elaborate and more fully address issues within three identified challenge areas. Practical implications - The trust matrix's usefulness as a tool for organizations to analyze trust problems and issues is demonstrated. Originality/value - Healthcare trust issues are captured to a greater extent and from previously unchartered perspectives. PMID:27477934

  16. COBSTRAN - COMPOSITE BLADE STRUCTURAL ANALYZER

    Science.gov (United States)

    Aiello, R. A.

    1994-01-01

    The COBSTRAN (COmposite Blade STRuctural ANalyzer) program is a pre- and post-processor that facilitates the design and analysis of composite turbofan and turboprop blades, as well as composite wind turbine blades. COBSTRAN combines composite mechanics and laminate theory with a data base of fiber and matrix properties. As a preprocessor for NASTRAN or another Finite Element Method (FEM) program, COBSTRAN generates an FEM model with anisotropic homogeneous material properties. Stress output from the FEM program is provided as input to the COBSTRAN postprocessor. The postprocessor then uses the composite mechanics and laminate theory routines to calculate individual ply stresses, strains, interply stresses, thru-the-thickness stresses and failure margins. COBSTRAN is designed to carry out the many linear analyses required to efficiently model and analyze blade-like structural components made of multilayered angle-plied fiber composites. Components made from isotropic or anisotropic homogeneous materials can also be modeled as a special case of COBSTRAN. NASTRAN MAT1 or MAT2 material cards are generated according to user supplied properties. COBSTRAN is written in FORTRAN 77 and was implemented on a CRAY X-MP with a UNICOS 5.0.12 operating system. The program requires either COSMIC NASTRAN or MSC NASTRAN as a structural analysis package. COBSTRAN was developed in 1989, and has a memory requirement of 262,066 64 bit words.

  17. ProtNet: a tool for stochastic simulations of protein interaction networks dynamics

    Science.gov (United States)

    Bernaschi, Massimo; Castiglione, Filippo; Ferranti, Alessandra; Gavrila, Caius; Tinti, Michele; Cesareni, Gianni

    2007-01-01

    Background Protein interactions support cell organization and mediate its response to any specific stimulus. Recent technological advances have produced large data-sets that aim at describing the cell interactome. These data are usually presented as graphs where proteins (nodes) are linked by edges to their experimentally determined partners. This representation reveals that protein-protein interaction (PPI) networks, like other kinds of complex networks, are not randomly organized and display properties that are typical of "hierarchical" networks, combining modularity and local clustering to scale free topology. However informative, this representation is static and provides no clue about the dynamic nature of protein interactions inside the cell. Results To fill this methodological gap, we designed and implemented a computer model that captures the discrete and stochastic nature of protein interactions. In ProtNet, our simplified model, the intracellular space is mapped onto either a two-dimensional or a three-dimensional lattice with each lattice site having a linear size (5 nm) comparable to the diameter of an average globular protein. The protein filled lattice has an occupancy (e.g. 20%) compatible with the estimated crowding of proteins in the cell cytoplasm. Proteins or protein complexes are free to translate and rotate on the lattice that represents a sort of naïve unstructured cell (devoid of compartments). At each time step, molecular entities (proteins or complexes) that happen to be in neighboring cells may interact and form larger complexes or dissociate depending on the interaction rules defined in an experimental protein interaction network. This whole procedure can be seen as a sort of "discrete molecular dynamics" applied to interacting proteins in a cell. We have tested our model by performing different simulations using as interaction rules those derived from an experimental interactome of Saccharomyces cerevisiae (1378 nodes, 2491 edges) and

  18. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

    Science.gov (United States)

    Corominas, Roser; Yang, Xinping; Lin, Guan Ning; Kang, Shuli; Shen, Yun; Ghamsari, Lila; Broly, Martin; Rodriguez, Maria; Tam, Stanley; Trigg, Shelly A; Fan, Changyu; Yi, Song; Tasan, Murat; Lemmens, Irma; Kuang, Xingyan; Zhao, Nan; Malhotra, Dheeraj; Michaelson, Jacob J; Vacic, Vladimir; Calderwood, Michael A; Roth, Frederick P; Tavernier, Jan; Horvath, Steve; Salehi-Ashtiani, Kourosh; Korkin, Dmitry; Sebat, Jonathan; Hill, David E; Hao, Tong; Vidal, Marc; Iakoucheva, Lilia M

    2014-04-11

    Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases.

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

    International Nuclear Information System (INIS)

    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

  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. 应用PPIN分析肝移植临床耐受患者PBMC基因表达特点%Apply protein-protein interaction network to analyze characteristics of the gene expression in PBMC of operational tolerant liver transplant recipients

    Institute of Scientific and Technical Information of China (English)

    徐洪来; 肖敏; 杨超; 高义; 雒真龙; 周鸿敏; 陈忠华

    2013-01-01

    应用生物信息学方法分析肝移植临床耐受患者PBMC基因表达特征,筛选临床耐受关键基因.从GEO数据库获取19个肝移植临床耐受病例及22个非临床耐受病例基因表达谱数据.应用DAVID网络软件进行差异基因功能注释与聚类分析;通过Cytoscape软件的MiMI插件构建蛋白质相互作用网络(PPIN)筛选肝移植临床耐受关键基因.差异基因涉及蛋白质及RNA代谢、免疫应答、膜结构调节等复杂生物过程.PPIN网络分析获得10个临床耐受核心基因.我们的研究表明:肝移植临床耐受涉及外周血免疫细胞复杂的基因表达调控机制及蛋白质间相互作用;RNA的转录后加工及蛋白质降解在免疫耐受的形成中发挥了重要作用;RBM8A、DHX9、CBL、IKBKB、CSNK2A1、HSPA8等核心基因发挥重要的免疫调节功能.%In this paper we use methods of bioinformatics to explore the characteristics of the gene expression and screen key genes in PBMCs of operational tolerant patients receiving liver transplantation using bio-informatics.A data-set of gene expression profiles of 19 operational tolerant samples of liver transplantation and 22 non-tolerant was downloaded from database GEO.We applied DAVID network software to annotate and functionally classified the differential genes.The MiMI plug-in for cytoscape was used to screen key genes related to operational tolerance by protein-protein interaction network(PPIN)analysis.Differential genes were involved in complicated and diversified biological processes such as metabolism of protein and RNA,immune response,membrane organization and so on.10 core genes highly related to operational tolerance were obtained by PPIN analysis.Our results indicate that the immune mechanism of operational tolerance of liver grafts involves sophisticated regulation mechanism of gene expression and extensive protein-protein interaction in PBMCs; RNA post-transcriptional processing and proteins degradation

  2. 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.

  3. Analyzing and modeling heterogeneous behavior

    Science.gov (United States)

    Lin, Zhiting; Wu, Xiaoqing; He, Dongyue; Zhu, Qiang; Ni, Jixiang

    2016-05-01

    Recently, it was pointed out that the non-Poisson statistics with heavy tail existed in many scenarios of human behaviors. But most of these studies claimed that power-law characterized diverse aspects of human mobility patterns. In this paper, we suggest that human behavior may not be driven by identical mechanisms and can be modeled as a Semi-Markov Modulated Process. To verify our suggestion and model, we analyzed a total of 1,619,934 records of library visitations (including undergraduate and graduate students). It is found that the distribution of visitation intervals is well fitted with three sections of lines instead of the traditional power law distribution in log-log scale. The results confirm that some human behaviors cannot be simply expressed as power law or any other simple functions. At the same time, we divided the data into groups and extracted period bursty events. Through careful analysis in different groups, we drew a conclusion that aggregate behavior might be composed of heterogeneous behaviors, and even the behaviors of the same type tended to be different in different period. The aggregate behavior is supposed to be formed by "heterogeneous groups". We performed a series of experiments. Simulation results showed that we just needed to set up two states Semi-Markov Modulated Process to construct proper representation of heterogeneous behavior.

  4. 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.

  5. Reverse PCA, a systematic approach for identifying genes important for the physical interaction between protein pairs.

    Directory of Open Access Journals (Sweden)

    Ifat Lev

    Full Text Available Protein-protein interactions (PPIs are of central importance for many areas of biological research. Several complementary high-throughput technologies have been developed to study PPIs. The wealth of information that emerged from these technologies led to the first maps of the protein interactomes of several model organisms. Many changes can occur in protein complexes as a result of genetic and biochemical perturbations. In the absence of a suitable assay, such changes are difficult to identify, and thus have been poorly characterized. In this study, we present a novel genetic approach (termed "reverse PCA" that allows the identification of genes whose products are required for the physical interaction between two given proteins. Our assay starts with a yeast strain in which the interaction between two proteins of interest can be detected by resistance to the drug, methotrexate, in the context of the protein-fragment complementation assay (PCA. Using synthetic genetic array (SGA technology, we can systematically screen mutant libraries of the yeast Saccharomyces cerevisiae to identify those mutations that disrupt the physical interaction of interest. We were able to successfully validate this novel approach by identifying mutants that dissociate the conserved interaction between Cia2 and Mms19, two proteins involved in Iron-Sulfur protein biogenesis and genome stability. This method will facilitate the study of protein structure-function relationships, and may help in elucidating the mechanisms that regulate PPIs.

  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.

  7. Interactome analysis of the EV71 5' untranslated region in differentiated neuronal cells SH-SY5Y and regulatory role of FBP3 in viral replication.

    Science.gov (United States)

    Huang, Hsing-I; Chang, Ying-Ying; Lin, Jhao-Yin; Kuo, Rei-Lin; Liu, Hao-Ping; Shih, Shin-Ru; Wu, Chih-Ching

    2016-09-01

    Enterovirus 71 (EV71), a single-stranded RNA virus, is one of the most serious neurotropic pathogens in the Asia-Pacific region. Through interactions with host proteins, the 5' untranslated region (5'UTR) of EV71 is important for viral replication. To gain a protein profile that interact with the EV71 5'UTR in neuronal cells, we performed a biotinylated RNA-protein pull-down assay in conjunction with LC-MS/MS analysis. A total of 109 proteins were detected and subjected to Database for Annotation, Visualization and Integrated Discovery (DAVID) analyses. These proteins were found to be highly correlated with biological processes including RNA processing/splicing, epidermal cell differentiation, and protein folding. A protein-protein interaction network was constructed using the STRING online database to illustrate the interactions of those proteins that are mainly involved in RNA processing/splicing or protein folding. Moreover, we confirmed that the far-upstream element binding protein 3 (FBP3) was able to bind to the EV71 5'UTR. The redistribution of FBP3 in subcellular compartments was observed after EV71 infection, and the decreased expression of FBP3 in host neuronal cells markedly inhibited viral replication. Our results reveal various host proteins that potentially interact with the EV71 5'UTR in neuronal cells, and we found that FBP3 could serve as a positive regulator in host cells. PMID:27291656

  8. Interactome analysis of the EV71 5' untranslated region in differentiated neuronal cells SH-SY5Y and regulatory role of FBP3 in viral replication.

    Science.gov (United States)

    Huang, Hsing-I; Chang, Ying-Ying; Lin, Jhao-Yin; Kuo, Rei-Lin; Liu, Hao-Ping; Shih, Shin-Ru; Wu, Chih-Ching

    2016-09-01

    Enterovirus 71 (EV71), a single-stranded RNA virus, is one of the most serious neurotropic pathogens in the Asia-Pacific region. Through interactions with host proteins, the 5' untranslated region (5'UTR) of EV71 is important for viral replication. To gain a protein profile that interact with the EV71 5'UTR in neuronal cells, we performed a biotinylated RNA-protein pull-down assay in conjunction with LC-MS/MS analysis. A total of 109 proteins were detected and subjected to Database for Annotation, Visualization and Integrated Discovery (DAVID) analyses. These proteins were found to be highly correlated with biological processes including RNA processing/splicing, epidermal cell differentiation, and protein folding. A protein-protein interaction network was constructed using the STRING online database to illustrate the interactions of those proteins that are mainly involved in RNA processing/splicing or protein folding. Moreover, we confirmed that the far-upstream element binding protein 3 (FBP3) was able to bind to the EV71 5'UTR. The redistribution of FBP3 in subcellular compartments was observed after EV71 infection, and the decreased expression of FBP3 in host neuronal cells markedly inhibited viral replication. Our results reveal various host proteins that potentially interact with the EV71 5'UTR in neuronal cells, and we found that FBP3 could serve as a positive regulator in host cells.

  9. Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.

    Directory of Open Access Journals (Sweden)

    Arthur Brady

    Full Text Available As increasing amounts of high-throughput data for the yeast interactome become available, more system-wide properties are uncovered. One interesting question concerns the fault tolerance of protein interaction networks: whether there exist alternative pathways that can perform some required function if a gene essential to the main mechanism is defective, absent or suppressed. A signature pattern for redundant pathways is the BPM (between-pathway model motif, introduced by Kelley and Ideker. Past methods proposed to search the yeast interactome for BPM motifs have had several important limitations. First, they have been driven heuristically by local greedy searches, which can lead to the inclusion of extra genes that may not belong in the motif; second, they have been validated solely by functional coherence of the putative pathways using GO enrichment, making it difficult to evaluate putative BPMs in the absence of already known biological annotation. We introduce stable bipartite subgraphs, and show they form a clean and efficient way of generating meaningful BPMs which naturally discard extra genes included by local greedy methods. We show by GO enrichment measures that our BPM set outperforms previous work, covering more known complexes and functional pathways. Perhaps most importantly, since our BPMs are initially generated by examining the genetic-interaction network only, the location of edges in the protein-protein physical interaction network can then be used to statistically validate each candidate BPM, even with sparse GO annotation (or none at all. We uncover some interesting biological examples of previously unknown putative redundant pathways in such areas as vesicle-mediated transport and DNA repair.

  10. 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.

  11. InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.

    Science.gov (United States)

    Yu, Jinchao; Vavrusa, Marek; Andreani, Jessica; Rey, Julien; Tufféry, Pierre; Guerois, Raphaël

    2016-07-01

    The structural modeling of protein-protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/.

  12. 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.

  13. The Amyloid Precursor Protein Controls PIKfyve Function.

    Science.gov (United States)

    Balklava, Zita; Niehage, Christian; Currinn, Heather; Mellor, Laura; Guscott, Benjamin; Poulin, Gino; Hoflack, Bernard; Wassmer, Thomas

    2015-01-01

    While the Amyloid Precursor Protein (APP) plays a central role in Alzheimer's disease, its cellular function still remains largely unclear. It was our goal to establish APP function which will provide insights into APP's implication in Alzheimer's disease. Using our recently developed proteo-liposome assay we established the interactome of APP's intracellular domain (known as AICD), thereby identifying novel APP interactors that provide mechanistic insights into APP function. By combining biochemical, cell biological and genetic approaches we validated the functional significance of one of these novel interactors. Here we show that APP binds the PIKfyve complex, an essential kinase for the synthesis of the endosomal phosphoinositide phosphatidylinositol-3,5-bisphosphate. This signalling lipid plays a crucial role in endosomal homeostasis and receptor sorting. Loss of PIKfyve function by mutation causes profound neurodegeneration in mammals. Using C. elegans genetics we demonstrate that APP functionally cooperates with PIKfyve in vivo. This regulation is required for maintaining endosomal and neuronal function. Our findings establish an unexpected role for APP in the regulation of endosomal phosphoinositide metabolism with dramatic consequences for endosomal biology and important implications for our understanding of Alzheimer's disease. PMID:26125944

  14. The Amyloid Precursor Protein Controls PIKfyve Function.

    Directory of Open Access Journals (Sweden)

    Zita Balklava

    Full Text Available While the Amyloid Precursor Protein (APP plays a central role in Alzheimer's disease, its cellular function still remains largely unclear. It was our goal to establish APP function which will provide insights into APP's implication in Alzheimer's disease. Using our recently developed proteo-liposome assay we established the interactome of APP's intracellular domain (known as AICD, thereby identifying novel APP interactors that provide mechanistic insights into APP function. By combining biochemical, cell biological and genetic approaches we validated the functional significance of one of these novel interactors. Here we show that APP binds the PIKfyve complex, an essential kinase for the synthesis of the endosomal phosphoinositide phosphatidylinositol-3,5-bisphosphate. This signalling lipid plays a crucial role in endosomal homeostasis and receptor sorting. Loss of PIKfyve function by mutation causes profound neurodegeneration in mammals. Using C. elegans genetics we demonstrate that APP functionally cooperates with PIKfyve in vivo. This regulation is required for maintaining endosomal and neuronal function. Our findings establish an unexpected role for APP in the regulation of endosomal phosphoinositide metabolism with dramatic consequences for endosomal biology and important implications for our understanding of Alzheimer's disease.

  15. 磺基水杨酸检测尿液和脑脊液蛋白自动比浊法的建立%Establishment of a method for detecting urine and cerebro-spinal fluid proteins by sulfosalicylic acid turbidimetry using automatic biochemical analyzer

    Institute of Scientific and Technical Information of China (English)

    肖春海; 黄敏洁; 吴娟芳; 赵忆凡; 沈玉萍

    2012-01-01

    Objective To evaluate and improve the method for detecting urine and cerebro-spinal fluid proteins by sulfosalicylic acid turbidimetry using automatic biochemical analyzer. Methods The improved sulfosalicylic acid turbidimetry using automatic biochemical analyzer(I-SS assay) and its parameters were established. The precision, linear range and recovery rate were evaluated and compared with the traditional sulfosalicylic acid turbidimetry ( T-SS assay). Results The within-run and between-rum coefficients of variation (CV) were 1. 2%-l. 5% and 2. L%-3. 5%. The linear range was 0. 037-2. 38 g/L. The recovery rate was 85. 6%-109. 2%. The correlation with the T-SS assay was Y I-ss - 0.980 AX T-ss +0.010 8, and the correlation coefficient (r) was 0.982. Conclusions The I-SS assay is sensitive and accurate, and it is suitable to automatic biochemical analyzer.%目的 对磺基水杨酸比浊法进行改良,并对其测定尿液和脑脊液蛋白的自动化分析进行评价.方法 应用改良磺基水杨酸仪器比浊法(简称仪器法),在全自动生化分析仪上建立测定参数,评价其方法的精密度、线性范围、回收率,并与手工磺基水杨酸比浊法(简称手工法)进行比较.结果 批内和批间变异系数(CV)分别为1.2% ~1.5%和2.1% ~3.5%.线性范围为0.037 ~ 2.38 g/L.回收率为85.6% ~ 109.2%.与手工法比较,Y仪器=0.980 4X手工 +0.010 8,相关系数(r)=0.982.结论 改良的磺基水杨酸比浊法测定微量总蛋白具有较高的精密度和准确度,适合于全自动生化分析仪.

  16. VORFFIP-driven dock: V-D2OCK, a fast and accurate protein docking strategy.

    Directory of Open Access Journals (Sweden)

    Joan Segura

    Full Text Available The experimental determination of the structure of protein complexes cannot keep pace with the generation of interactomic data, hence resulting in an ever-expanding gap. As the structural details of protein complexes are central to a full understanding of the function and dynamics of the cell machinery, alternative strategies are needed to circumvent the bottleneck in structure determination. Computational protein docking is a valid and valuable approach to model the structure of protein complexes. In this work, we describe a novel computational strategy to predict the structure of protein complexes based on data-driven docking: VORFFIP-driven dock (V-D2OCK. This new approach makes use of our newly described method to predict functional sites in protein structures, VORFFIP, to define the region to be sampled during docking and structural clustering to reduce the number of models to be examined by users. V-D2OCK has been benchmarked using a validated and diverse set of protein complexes and compared to a state-of-art docking method. The speed and accuracy compared to contemporary tools justifies the potential use of VD2OCK for high-throughput, genome-wide, protein docking. Finally, we have developed a web interface that allows users to browser and visualize V-D2OCK predictions from the convenience of their web-browsers.

  17. Novel Interactome of Saccharomyces cerevisiae Myosin Type II Identified by a Modified Integrated Membrane Yeast Two-Hybrid (iMYTH Screen

    Directory of Open Access Journals (Sweden)

    Ednalise Santiago

    2016-05-01

    Full Text Available Nonmuscle myosin type II (Myo1p is required for cytokinesis in the budding yeast Saccharomyces cerevisiae. Loss of Myo1p activity has been associated with growth abnormalities and enhanced sensitivity to osmotic stress, making it an appealing antifungal therapeutic target. The Myo1p tail-only domain was previously reported to have functional activity equivalent to the full-length Myo1p whereas the head-only domain did not. Since Myo1p tail-only constructs are biologically active, the tail domain must have additional functions beyond its previously described role in myosin dimerization or trimerization. The identification of new Myo1p-interacting proteins may shed light on the other functions of the Myo1p tail domain. To identify novel Myo1p-interacting proteins, and determine if Myo1p can serve as a scaffold to recruit proteins to the bud neck during cytokinesis, we used the integrated split-ubiquitin membrane yeast two-hybrid (iMYTH system. Myo1p was iMYTH-tagged at its C-terminus, and screened against both cDNA and genomic prey libraries to identify interacting proteins. Control experiments showed that the Myo1p-bait construct was appropriately expressed, and that the protein colocalized to the yeast bud neck. Thirty novel Myo1p-interacting proteins were identified by iMYTH. Eight proteins were confirmed by coprecipitation (Ape2, Bzz1, Fba1, Pdi1, Rpl5, Tah11, and Trx2 or mass spectrometry (AP-MS (Abp1. The novel Myo1p-interacting proteins identified come from a range of different processes, including cellular organization and protein synthesis. Actin assembly/disassembly factors such as the SH3 domain protein Bzz1 and the actin-binding protein Abp1 represent likely Myo1p interactions during cytokinesis.

  18. 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

  19. Setting up a Bioluminescence Resonance Energy Transfer high throughput screening assay to search for protein/protein interaction inhibitors in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Cyril eCouturier

    2012-09-01

    Full Text Available Each step of the cell life and its response or adaptation to its environment are mediated by a network of protein/protein interactions termed interactome. Our knowledge of this network keeps growing due to the development of sensitive techniques devoted to study these interactions. The bioluminescence resonance energy transfer (BRET technique was primarily developed to allow the dynamic monitoring of protein-protein interactions in living cells, and has widely been used to study receptor activation by intra- or extra-molecular conformational changes within receptors and activated complexes in mammal cells. Some interactions are described as crucial in human pathological processes, and a new class of drugs targeting them has recently emerged. The BRET method is well suited to identify inhibitors of protein-protein interactions and here is described why and how to set up and optimize a High Throughput Screening assay based on BRET to search for such inhibitory compounds. The different parameters to take into account when developing such BRET assays in mammal cells are reviewed to give general guidelines: considerations on the targeted interaction, choice of BRET version, inducibility of the interaction, kinetic of the monitored interaction, and of the BRET reading, influence substrate concentration, number of cells and medium composition used on the Z’ factor, and expected interferences for colored or fluorescent compounds.

  20. Analysis of damaged DNA / proteins interactions: Methodological optimizations and applications to DNA lesions induced by platinum anticancer drugs; Analyse des interactions ADN lese / proteines: Optimisations methodologiques et applications aux dommages de l'ADN engendres par les derives du platine

    Energy Technology Data Exchange (ETDEWEB)

    Bounaix Morand du Puch, Ch

    2010-10-15

    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

  1. 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....

  2. 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.

  3. Protein-tyrosine phosphorylation in Bacillus subtilis: a 10-year retrospective

    Directory of Open Access Journals (Sweden)

    Josef eDeutscher

    2015-01-01

    Full Text Available The discovery of tyrosine-phosphorylated proteins in Bacillus subtilis in the year 2003 was followed by a decade of intensive research activity. Here we provide an overview of the lessons learned in that period. While the number of characterized kinases and phosphatases involved in reversible protein-tyrosine phosphorylation in B. subtilis has remained essentially unchanged, the number of proteins known to be targeted by this post-translational modification has increased dramatically. This is mainly due to phosphoproteomics and interactomics studies, which were instrumental in identifying new tyrosine-phosphorylated proteins. Despite their structural similarity, the two B. subtilis protein-tyrosine kinases (BY-kinases, PtkA and PtkB (EpsB, seem to accomplish different functions in the cell. The PtkB is encoded by a large operon involved in exopolysaccharide production, and its main role appears to be the control of this process. The PtkA seems to have a more complex role; it phosphorylates and regulates a large number of proteins involved in the DNA, fatty acid and carbon metabolism and engages in physical interaction with other types of kinases (Ser/Thr kinases, leading to mutual phosphorylation. PtkA also seems to respond to several activator proteins, which direct its activity towards different substrates. In that respect PtkA seems to function as a highly connected signal integration device.

  4. 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...

  5. The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions.

    Science.gov (United States)

    Beckmann, Benedikt M; Castello, Alfredo; Medenbach, Jan

    2016-06-01

    Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism.

  6. The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions.

    Science.gov (United States)

    Beckmann, Benedikt M; Castello, Alfredo; Medenbach, Jan

    2016-06-01

    Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism. PMID:27165283

  7. Discovery and targeted LC-MS/MS of purified polerovirus reveals differences in the virus-host interactome associated with altered aphid transmission.

    Directory of Open Access Journals (Sweden)

    Michelle Cilia

    Full Text Available Circulative transmission of viruses in the Luteoviridae, such as cereal yellow dwarf virus (CYDV, requires a series of precisely orchestrated interactions between virus, plant, and aphid proteins. Natural selection has favored these viruses to be retained in the phloem to facilitate acquisition and transmission by aphids. We show that treatment of infected oat tissue homogenate with sodium sulfite reduces transmission of the purified virus by aphids. Transmission electron microscopy data indicated no gross change in virion morphology due to treatments. However, treated virions were not acquired by aphids through the hindgut epithelial cells and were not transmitted when injected directly into the hemocoel. Analysis of virus preparations using nanoflow liquid chromatography coupled to tandem mass spectrometry revealed a number of host plant proteins co-purifying with viruses, some of which were lost following sodium sulfite treatment. Using targeted mass spectrometry, we show data suggesting that several of the virus-associated host plant proteins accumulated to higher levels in aphids that were fed on CYDV-infected plants compared to healthy plants. We propose two hypotheses to explain these observations, and these are not mutually exclusive: (a that sodium sulfite treatment disrupts critical virion-host protein interactions required for aphid transmission, or (b that host infection with CYDV modulates phloem protein expression in a way that is favorable for virus uptake by aphids. Importantly, the genes coding for the plant proteins associated with virus may be examined as targets in breeding cereal crops for new modes of virus resistance that disrupt phloem-virus or aphid-virus interactions.

  8. Discovery and targeted LC-MS/MS of purified polerovirus reveals differences in the virus-host interactome associated with altered aphid transmission.

    Science.gov (United States)

    Cilia, Michelle; Peter, Kari A; Bereman, Michael S; Howe, Kevin; Fish, Tara; Smith, Dawn; Gildow, Fredrick; MacCoss, Michael J; Thannhauser, Theodore W; Gray, Stewart M

    2012-01-01

    Circulative transmission of viruses in the Luteoviridae, such as cereal yellow dwarf virus (CYDV), requires a series of precisely orchestrated interactions between virus, plant, and aphid proteins. Natural selection has favored these viruses to be retained in the phloem to facilitate acquisition and transmission by aphids. We show that treatment of infected oat tissue homogenate with sodium sulfite reduces transmission of the purified virus by aphids. Transmission electron microscopy data indicated no gross change in virion morphology due to treatments. However, treated virions were not acquired by aphids through the hindgut epithelial cells and were not transmitted when injected directly into the hemocoel. Analysis of virus preparations using nanoflow liquid chromatography coupled to tandem mass spectrometry revealed a number of host plant proteins co-purifying with viruses, some of which were lost following sodium sulfite treatment. Using targeted mass spectrometry, we show data suggesting that several of the virus-associated host plant proteins accumulated to higher levels in aphids that were fed on CYDV-infected plants compared to healthy plants. We propose two hypotheses to explain these observations, and these are not mutually exclusive: (a) that sodium sulfite treatment disrupts critical virion-host protein interactions required for aphid transmission, or (b) that host infection with CYDV modulates phloem protein expression in a way that is favorable for virus uptake by aphids. Importantly, the genes coding for the plant proteins associated with virus may be examined as targets in breeding cereal crops for new modes of virus resistance that disrupt phloem-virus or aphid-virus interactions. PMID:23118947

  9. 46 CFR 154.1360 - Oxygen analyzer.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 5 2010-10-01 2010-10-01 false Oxygen analyzer. 154.1360 Section 154.1360 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS CARGOES SAFETY STANDARDS... Instrumentation § 154.1360 Oxygen analyzer. The vessel must have a portable analyzer that measures oxygen...

  10. Role of protein phosphorylation in the regulation of cell cycle and DNA-related processes in bacteria

    Directory of Open Access Journals (Sweden)

    Transito eGarcia-Garcia

    2016-02-01

    Full Text Available In all living organisms, the phosphorylation of proteins modulates various aspects of their functionalities. In eukaryotes, protein phosphorylation plays a key role in cell signaling, gene expression, and differentiation. Protein phosphorylation is also involved in the global control of DNA replication during the cell cycle, as well as in the mechanisms that cope with stress-induced replication blocks. Similar to eukaryotes, bacteria use Hanks-type kinases and phosphatases for signal transduction, and protein phosphorylation is involved in numerous cellular processes. However, it remains unclear whether protein phosphorylation in bacteria can also regulate the activity of proteins involved in DNA-mediated processes such as DNA replication or repair. Accumulating evidence supported by functional and biochemical studies suggests that phospho-regulatory mechanisms also take place during the bacterial cell cycle. Recent phosphoproteomics and interactomics studies identified numerous phosphoproteins involved in various aspect of DNA metabolism strongly supporting the existence of such level of regulation in bacteria. Similar to eukaryotes, bacterial scaffolding-like proteins emerged as platforms for kinase activation and signaling. This review reports the current knowledge on the phosphorylation of proteins involved in the maintenance of genome integrity and the regulation of cell cycle in bacteria that reveals surprising similarities to eukaryotes.

  11. Role of Protein Phosphorylation in the Regulation of Cell Cycle and DNA-Related Processes in Bacteria.

    Science.gov (United States)

    Garcia-Garcia, Transito; Poncet, Sandrine; Derouiche, Abderahmane; Shi, Lei; Mijakovic, Ivan; Noirot-Gros, Marie-Françoise

    2016-01-01

    In all living organisms, the phosphorylation of proteins modulates various aspects of their functionalities. In eukaryotes, protein phosphorylation plays a key role in cell signaling, gene expression, and differentiation. Protein phosphorylation is also involved in the global control of DNA replication during the cell cycle, as well as in the mechanisms that cope with stress-induced replication blocks. Similar to eukaryotes, bacteria use Hanks-type kinases and phosphatases for signal transduction, and protein phosphorylation is involved in numerous cellular processes. However, it remains unclear whether protein phosphorylation in bacteria can also regulate the activity of proteins involved in DNA-mediated processes such as DNA replication or repair. Accumulating evidence supported by functional and biochemical studies suggests that phospho-regulatory mechanisms also take place during the bacterial cell cycle. Recent phosphoproteomics and interactomics studies identified numerous phosphoproteins involved in various aspect of DNA metabolism strongly supporting the existence of such level of regulation in bacteria. Similar to eukaryotes, bacterial scaffolding-like proteins emerged as platforms for kinase activation and signaling. This review reports the current knowledge on the phosphorylation of proteins involved in the maintenance of genome integrity and the regulation of cell cycle in bacteria that reveals surprising similarities to eukaryotes. PMID:26909079

  12. Graphical Features of Functional Genes in Human Protein Interaction Network.

    Science.gov (United States)

    Wang, Pei; Chen, Yao; Lu, Jinhu; Wang, Qingyun; Yu, Xinghuo

    2016-06-01

    With the completion of the human genome project, it is feasible to investigate large-scale human protein interaction network (HPIN) with complex networks theory. Proteins are encoded by genes. Essential, viable, disease, conserved, housekeeping (HK) and tissue-enriched (TE) genes are functional genes, which are organized and functioned via interaction networks. Based on up-to-date data from various databases or literature, two large-scale HPINs and six subnetworks are constructed. We illustrate that the HPINs and most of the subnetworks are sparse, small-world, scale-free, disassortative and with hierarchical modularity. Among the six subnetworks, essential, disease and HK subnetworks are more densely connected than the others. Statistical analysis on the topological structures of the HPIN reveals that the lethal, the conserved, the HK and the TE genes are with hallmark graphical features. Receiver operating characteristic (ROC) curves indicate that the essential genes can be distinguished from the viable ones with accuracy as high as almost 70%. Closeness, semi-local and eigenvector centralities can distinguish the HK genes from the TE ones with accuracy around 82%. Furthermore, the Venn diagram, cluster dendgrams and classifications of disease genes reveal that some classes of disease genes are with hallmark graphical features, especially for cancer genes, HK disease genes and TE disease genes. The findings facilitate the identification of some functional genes via topological structures. The investigations shed some light on the characteristics of the compete interactome, which have potential implications in networked medicine and biological network control. PMID:26841412

  13. Analyzing shotgun proteomic data with PatternLab for proteomics

    OpenAIRE

    Carvalho, Paulo C; Yates, John R.; Barbosa, Valmir C

    2010-01-01

    PatternLab for proteomics is a one-stop-shop computational environment for analyzing shotgun proteomic data. Its modules provide means to pinpoint proteins / peptides that are differentially expressed, those that are unique to a state, and can also cluster the ones that share similar expression profiles in time-course experiments as well as help in interpreting results according to Gene Ontology. PatternLab is user-friendly, simple, and provides a graphical user interface.

  14. 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.

  15. 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

    2011-09-01

    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.

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

    OpenAIRE

    Ching-Wu Hsia; Ming-Yi Ho; Hao-Ai Shui; Chong-Bin Tsai; Min-Jen Tseng

    2015-01-01

    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 alkal...

  17. 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

  18. iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.

    Science.gov (United States)

    Turner, Brian; Razick, Sabry; Turinsky, Andrei L; Vlasblom, James; Crowdy, Edgard K; Cho, Emerson; Morrison, Kyle; Donaldson, Ian M; Wodak, Shoshana J

    2010-01-01

    We present iRefWeb, a web interface to protein interaction data consolidated from 10 public databases: BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MINT, MPact, MPPI and OPHID. iRefWeb enables users to examine aggregated interactions for a protein of interest, and presents various statistical summaries of the data across databases, such as the number of organism-specific interactions, proteins and cited publications. Through links to source databases and supporting evidence, researchers may gauge the reliability of an interaction using simple criteria, such as the detection methods, the scale of the study (high- or low-throughput) or the number of cited publications. Furthermore, iRefWeb compares the information extracted from the same publication by different databases, and offers means to follow-up possible inconsistencies. We provide an overview of the consolidated protein-protein interaction landscape and show how it can be automatically cropped to aid the generation of meaningful organism-specific interactomes. iRefWeb can be accessed at: http://wodaklab.org/iRefWeb. Database URL: http://wodaklab.org/iRefWeb/ PMID:20940177

  19. Arabidopsis 14-3-3 proteins: fascinating and less fascinating aspects

    Directory of Open Access Journals (Sweden)

    Nina eJaspert

    2011-12-01

    Full Text Available 14-3-3 dimers are well known to interact with diverse target proteins throughout eukaryotes. Most notably, association of 14-3-3s commonly requires phosphorylation of a serine or threonine residue within a specific sequence motif of the client protein. Studies with a focus on individual target proteins have unequivocally demonstrated 14-3-3s to be the crucial factors modifying the client’s activity state upon phosphorylation and, thus, finishing the job initiated by a kinase. In this respect, a recent in-depth analysis of the rice transcription factor FLOWERING LOCUS D1 (OsFD1 revealed 14-3-3s to be essential players in floral induction. However, such fascinating discoveries can often be ascribed to the random identification of 14-3-3 as an interaction partner of the favorite protein. In contrast, our understanding of 14-3-3 function in higher organisms is frustratingly limited, mainly due to an overwhelming spectrum of putative targets in combination with the existence of a multigene 14-3-3 family. In this review we will discuss our current understanding of the function of plant 14-3-3 proteins, taking into account surveys of the Arabidopsis 14-3-3 interactome.

  20. 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.

  1. Designing of Acousto-optic Spectrum Analyzer

    Institute of Scientific and Technical Information of China (English)

    WANG Dan-zhi; SHAO Ding-rong; LI Shu-jian

    2004-01-01

    The structure of the acousto-optic spectrum analyzer was investigated including the RF amplifying circuit, the optical structures and the postprocessing circuit, and the design idea of the module was applied to design the spectrum analyzer. The modularization spectrum analyzer takes on the performance stabilization and higher reliability, and according to different demands, the different modules can be used. The spectrum analyzer had such performances as the detecting frequency error of 0.58MHz,detecting responsivity of 90 dBm and bandwidth of 50 Mhz.

  2. A novel genetic system based on zinc finger nucleases for the identification of interactions between proteins in vivo.

    Directory of Open Access Journals (Sweden)

    Ling Wang

    Full Text Available Yeast two-hybrid (Y2H methods are powerful tools for detecting protein-protein interactions. The traditional Y2H method has been widely applied to screen novel protein interactions since it was established two decades ago. The high false-positive rate of the traditional method drove the development of modified Y2H systems. Here, we describe a novel Y2H system using zinc-finger nucleases (ZFNs. ZFNs contain two functional domains, a zinc-finger DNA-binding domain (ZFP and a non-specific nuclease domain (FokI. In this system, the bait is expressed as a fusion protein with a specific ZFP, and the prey is fused to the FokI. A reporter vector is designed such that the ZFN target site disrupts the Gal4 open reading frame. By transforming the three plasmids into a yeast strain (AH109, the interaction between the bait and prey proteins reconstitutes ZFN function and generates the double-strand break (DSB on its target site. The DNA DSB repair restores Gal4 function, which activates the expression of the four reporter genes. We used p53-SV40LT interacting proteins to prove the concept. In addition, 80% positive rate was observed in a cDNA screening test against WDSV orfA protein. Our results strongly suggested that this Y2H system could increase screening reliability and reproducibility, and provide a novel approach for interactomics research.

  3. Performance evaluation of PL-11 platelet analyzer

    Institute of Scientific and Technical Information of China (English)

    张有涛

    2013-01-01

    Objective To evaluate and report the performance of PL-11 platelet analyzer. Methods Intravenous blood sam-ples anticoagulated with EDTA-K2 and sodium citrate were tested by the PL-11 platelet analyzer to evaluate the intra-assay and interassay coefficient of variation(CV),

  4. 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

    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.

  5. The C-terminal domain of the bacterial SSB protein acts as a DNA maintenance hub at active chromosome replication forks.

    Science.gov (United States)

    Costes, Audrey; Lecointe, François; McGovern, Stephen; Quevillon-Cheruel, Sophie; Polard, Patrice

    2010-01-01

    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. PMID:21170359

  6. 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.

  7. 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.

  8. Differential Gene Expression and Protein Phosphorylation as Factors Regulating the State of the Arabidopsis SNX1 Protein Complexes in Response to Environmental Stimuli

    Science.gov (United States)

    Brumbarova, Tzvetina; Ivanov, Rumen

    2016-01-01

    Endosomal recycling of plasma membrane proteins contributes significantly to the regulation of cellular transport and signaling processes. Members of the Arabidopsis (Arabidopsis thaliana) SORTING NEXIN (SNX) protein family were shown to mediate the endosomal retrieval of transporter proteins in response to external challenges. Our aim is to understand the possible ways through which external stimuli influence the activity of SNX1 in the root. Several proteins are known to contribute to the function of SNX1 through direct protein–protein interaction. We, therefore, compiled a list of all Arabidopsis proteins known to physically interact with SNX1 and employed available gene expression and proteomic data for a comprehensive analysis of the transcriptional and post-transcriptional regulation of this interactome. The genes encoding SNX1-interaction partners showed distinct expression patterns with some, like FAB1A, being uniformly expressed, while others, like MC9 and BLOS1, were expressed in specific root zones and cell types. Under stress conditions known to induce SNX1-dependent responses, two genes encoding SNX1-interacting proteins, MC9 and NHX6, showed major gene-expression variations. We could also observe zone-specific transcriptional changes of SNX1 under iron deficiency, which are consistent with the described role of the SNX1 protein. This suggests that the composition of potential SNX1-containing protein complexes in roots is cell-specific and may be readjusted in response to external stimuli. On the level of post-transcriptional modifications, we observed stress-dependent changes in the phosphorylation status of SNX1, FAB1A, and CLASP. Interestingly, the phosphorylation events affecting SNX1 interactors occur in a pattern which is largely complementary to transcriptional regulation. Our analysis shows that transcriptional and post-transcriptional regulation play distinct roles in SNX1-mediated endosomal recycling under external stress. PMID:27725825

  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. On-Demand Urine Analyzer Project

    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...

  11. 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...

  12. 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...

  13. Analyzing IS User Requirements using Organizational Semiotics

    Directory of Open Access Journals (Sweden)

    Kamyar Raissifar

    2014-09-01

    Full Text Available In recent years, lack of appropriate understanding of IS user requirements, has been one of the most important causes of IS development failure. Therefore, many methods were introduced for better analyzing user requirements; some of them were philosophically different. Organizational semiotics (OS is one of these methods, which with phenomenological and action-oriented view, tries to get better system requirement analysis. In this research, first, organizational semiotics and SSADM was compared, with focus on their ability to elicit and analyze IS user requirements, and then, OS was applied in analyzing an IS requirement analysis case. Research findings show that OS in many dimensions is superior to SSADM; although SSADM has superiority in few dimensions too. Therefore using OS can help analyzing IS user requirements more appropriately.

  14. Analyzing Log Files using Data-Mining

    OpenAIRE

    Marius Mihut

    2008-01-01

    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.

  15. Network analysis using organizational risk analyzer

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The tool system of the organizational risk analyzer (ORA) to study the network of East Turkistan terrorists is selected. The model of the relationships among its personnel, knowledge, resources and task entities is represented by the meta-matrix in ORA, with which to analyze the risks and vulnerabilities of organizational structure quantitatively, and obtain the last vulnerabilities and risks of the organization. Case study in this system shows that it should be a shortcut to destroy effectively the network...

  16. The Information Flow Analyzing Based on CPC

    Institute of Scientific and Technical Information of China (English)

    ZHANG Zhang; LI Hui

    2005-01-01

    The information flow chart within product life cycle is given out based on collaborative production commerce (CPC) thoughts. In this chart, the separated information systems are integrated by means of enterprise knowledge assets that are promoted by CPC from production knowledge. The information flow in R&D process is analyzed in the environment of virtual R&D group and distributed PDM. In addition, the information flow throughout the manufacturing and marketing process is analyzed in CPC environment.

  17. QUBIT DATA STRUCTURES FOR ANALYZING COMPUTING SYSTEMS

    Directory of Open Access Journals (Sweden)

    Vladimir Hahanov

    2014-11-01

    Full Text Available Qubit models and methods for improving the performance of software and hardware for analyzing digital devices through increasing the dimension of the data structures and memory are proposed. The basic concepts, terminology and definitions necessary for the implementation of quantum computing when analyzing virtual computers are introduced. The investigation results concerning design and modeling computer systems in a cyberspace based on the use of two-component structure are presented.

  18. 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.

  19. A systematic study of nuclear interactome of C-terminal domain small phosphatase-like 2 using inducible expression system and shotgun proteomics.

    Science.gov (United States)

    Kang, NaNa; Koo, JaeHyung; Wang, Sen; Hur, Sun Jin; Bahk, Young Yil

    2016-06-01

    RNA polymerase II C-terminal domain phosphatases are newly emerging family of phosphatases that contain FCPH domain with Mg+2-binding DXDX(T/V) signature motif. Its subfamily includes small CTD phosphatases (SCPs). Recently, we identified several interacting partners of human SCP1 with appearance of dephosphorylation and O-GlcNAcylation. In this study, using an established cell line with inducible CTDSPL2 protein (a member of the new phosphatase family), proteomic screening was conducted to identify binding partners of CTDSPL2 in nuclear extract through immunoprecipitation of CTDSPL2 with its associated. This approach led to the identification of several interacting partners of CTDSPL2. This will provide a better understanding on CTDSPL2. [BMB Reports 2016; 49(6): 319-324]. PMID:26674342

  20. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... the vegetarian proteins, whether they have carbohydrate. Best Protein Choices The best choices are: Plant-based proteins ...

  1. 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.

  2. Detecting influenza outbreaks by analyzing Twitter messages

    CERN Document Server

    Culotta, Aron

    2010-01-01

    We analyze over 500 million Twitter messages from an eight month period and find that tracking a small number of flu-related keywords allows us to forecast future influenza rates with high accuracy, obtaining a 95% correlation with national health statistics. We then analyze the robustness of this approach to spurious keyword matches, and we propose a document classification component to filter these misleading messages. We find that this document classifier can reduce error rates by over half in simulated false alarm experiments, though more research is needed to develop methods that are robust in cases of extremely high noise.

  3. Progresses in analyzing 26Al with SMCAMS

    International Nuclear Information System (INIS)

    Shanghai Mini-Cyclotron based Accelerator Mass Spectrometer (SMCAMS) was especially designed for analyzing 14C. In order to accelerate and analyze 26Al the accelerated orbit and beam optics in injection system were calculated and harmonic number and acceleration turns was optimized. Preliminary experiment was carried out. In which a beam current of 1.15 x 10-9A for 27Al- and 0.038 CPS background for 26Al were measured. The limited sensitivity of 26Al/27Al is 5.25 x 10-12. (authors)

  4. 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.

  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. PMID:16834538

  6. Analyzing the Information Economy: Tools and Techniques.

    Science.gov (United States)

    Robinson, Sherman

    1986-01-01

    Examines methodologies underlying studies which measure the information economy and considers their applicability and limitations for analyzing policy issues concerning libraries and library networks. Two studies provide major focus for discussion: Porat's "The Information Economy: Definition and Measurement" and Machlup's "Production and…

  7. 40 CFR 92.109 - Analyzer specifications.

    Science.gov (United States)

    2010-07-01

    ... comparable results to an HFID not using this procedure. These data must be submitted to the Administrator for... consistent with the general requirements of 40 CFR part 1065, subpart I, for sampling and analysis of... NO2 to NO converter. (ii) For high vacuum CL analyzers with heated capillary modules, supplying...

  8. Portable peltier-cooled X RF analyzer

    International Nuclear Information System (INIS)

    Full text: Recent development of semiconductor detectors has made it possible to design portable battery operated XRF-analyzers. Energy resolution and good peak to background ratio are close to liquid nitrogen cooled detector values. Application examples are given and a comparison of the new device between old ones is made. (author)

  9. 40 CFR 90.313 - Analyzers required.

    Science.gov (United States)

    2010-07-01

    ... ionization (HFID) type. For constant volume sampling, the hydrocarbon analyzer may be of the flame ionization (FID) type or of the heated flame ionization (HFID) type. (ii) For the HFID system, if the temperature... drying. Chemical dryers are not an acceptable method of removing water from the sample. Water removal...

  10. 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 sa

  11. Miniature retarding grid ion energy analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, G.W.; Sawin, H.H.

    1992-12-01

    A retarding grid analyzer intended for use as a high-density ({approximately}10{sup 12}/cc) plasma diagnostic has been designed, built and tested. The analyzer`s external dimensions are 0.125 inch x0.125 inch x0.050 inch which are smaller than macroscopic plasma scale lengths, thus allowing it to be stalk mounted and moved throughout the plasma. The grids are 2000 line/inch nickel mesh so that the linear dimension of grid open area is less than the debye length for plasmas with 10 eV electrons and 10{sup 12}/cc densities. Successive grids are separated by 0.01 inch in order to avoid space charge effects between grids and thus allow unprecedented energy resolution. Also, because the linear dimension normal to the grid is small compared to the ion mean free path in high pressure (>100 mTorr) discharges, it can be used without the differential pumping required of larger GEA`s in such discharges. The analyzer has been tested on a plasma beam source (a modified ASTeX Compact ECR source) and on an ASTeX S1500ECR source, and has been used as an edge diagnostic on the VERSATOR tokamak at M.I.T. Ion energy distribution functions as narrow as 5 eV have been measured.

  12. 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.

  13. Analyzing computer system performance with Perl

    CERN Document Server

    Gunther, Neil J

    2011-01-01

    This expanded second edition of Analyzing Computer System Performance with Perl::PDQ, builds on the success of the first edition. It contains new chapters on queues, tools and virtualization, and new Perl listing format to aid readability of PDQ models.

  14. Analyzing volatile compounds in dairy products

    Science.gov (United States)

    Volatile compounds give the first indication of the flavor in a dairy product. Volatiles are isolated from the sample matrix and then analyzed by chromatography, sensory methods, or an electronic nose. Isolation may be performed by solvent extraction or headspace analysis, and gas chromatography i...

  15. Strengthening 4-H by Analyzing Enrollment Data

    Science.gov (United States)

    Hamilton, Stephen F.; Northern, Angela; Neff, Robert

    2014-01-01

    The study reported here used data from the ACCESS 4-H Enrollment System to gain insight into strengthening New York State's 4-H programming. Member enrollment lists from 2009 to 2012 were analyzed using Microsoft Excel to determine trends and dropout rates. The descriptive data indicate declining 4-H enrollment in recent years and peak…

  16. 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…

  17. Imaging thermal plasma mass and velocity analyzer

    Science.gov (United States)

    Yau, Andrew W.; Howarth, Andrew

    2016-07-01

    We present the design and principle of operation of the imaging ion mass and velocity analyzer on the Enhanced Polar Outflow Probe (e-POP), which measures low-energy (1-90 eV/e) ion mass composition (1-40 AMU/e) and velocity distributions using a hemispherical electrostatic analyzer (HEA), a time-of-flight (TOF) gate, and a pair of toroidal electrostatic deflectors (TED). The HEA and TOF gate measure the energy-per-charge and azimuth of each detected ion and the ion transit time inside the analyzer, respectively, providing the 2-D velocity distribution of each major ionospheric ion species and resolving the minor ion species under favorable conditions. The TED are in front of the TOF gate and optionally sample ions at different elevation angles up to ±60°, for measurement of 3-D velocity distribution. We present examples of observation data to illustrate the measurement capability of the analyzer, and show the occurrence of enhanced densities of heavy "minor" O++, N+, and molecular ions and intermittent, high-velocity (a few km/s) upward and downward flowing H+ ions in localized regions of the quiet time topside high-latitude ionosphere.

  18. Quantum Key Distribution with Screening and Analyzing

    CERN Document Server

    Kye, W H

    2006-01-01

    We propose a quantum key distribution scheme by using screening angles and analyzing detectors which enable to notice the presence of Eve who eavesdrops the quantum channel. We show the security of the proposed quantum key distribution against impersonation, photon number splitting, Trojan Horse, and composite attacks.

  19. Quantum Key Distribution with Screening and Analyzing

    OpenAIRE

    Kye, Won-Ho

    2006-01-01

    We propose a quantum key distribution scheme by using screening angles and analyzing detectors which enable to notice the presence of Eve who eavesdrops the quantum channel, as the revised protocol of the recent quantum key distribution [Phys. Rev. Lett. 95, 040501 (2005)]. We discuss the security of the proposed quantum key distribution against various attacks including impersonation attack and Trojan Horse attack.

  20. 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.

  1. Graphic method for analyzing common path interferometers

    DEFF Research Database (Denmark)

    Glückstad, J.

    1998-01-01

    Common path interferometers are widely used for visualizing phase disturbances and fluid flows. They are attractive because of the inherent simplicity and robustness in the setup. A graphic method will be presented for analyzing and optimizing filter parameters in common path interferometers....

  2. Analysis of correlations between protein complex and protein-protein interaction and mRNA expression

    Institute of Scientific and Technical Information of China (English)

    CAI Lun; XUE Hong; LU Hongchao; ZHAO Yi; ZHU Xiaopeng; BU Dongbo; LING Lunjiang; CHEN Runsheng

    2003-01-01

    Protein-protein interaction is a physical interaction of two proteins in living cells. In budding yeast Saccharomyces cerevisiae, large-scale protein-protein interaction data have been obtained through high-throughput yeast two-hybrid systems (Y2H) and protein complex purification techniques based on mass-spectrometry. Here, we collect 11855 interactions between total 2617 proteins. Through seriate genome-wide mRNA expression data, similarity between two genes could be measured. Protein complex data can also be obtained publicly and can be translated to pair relationship that any two proteins can only exist in the same complex or not. Analysis of protein complex data, protein-protein interaction data and mRNA expression data can elucidate correlations between them. The results show that proteins that have interactions or similar expression patterns have a higher possibility to be in the same protein complex than randomized selected proteins, and proteins which have interactions and similar expression patterns are even more possible to exist in the same protein complex. The work indicates that comprehensive integration and analysis of public large-scale bioinformatical data, such as protein complex data, protein-protein interaction data and mRNA expression data, may help to uncover their relationships and common biological information underlying these data. The strategies described here may help to integrate and analyze other functional genomic and proteomic data, such as gene expression profiling, protein-localization mapping and large-scale phenotypic data, both in yeast and in other organisms.

  3. Methodology for analyzing risk at nuclear facilities

    International Nuclear Information System (INIS)

    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

  4. 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.

  5. An improved prism energy analyzer for neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Schulz, J., E-mail: jennifer.schulz@helmholtz-berlin.de [Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin (Germany); Ott, F. [Laboratoire Leon Brillouin, Bât 563 CEA Saclay, 91191 Gif sur Yvette Cedex (France); Krist, Th. [Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, 14109 Berlin (Germany)

    2014-04-21

    The effects of two improvements of an existing neutron energy analyzer consisting of stacked silicon prism rows are presented. First we tested the effect of coating the back of the prism rows with an absorbing layer to suppress neutron scattering by total reflection and by refraction at small angles. Experiments at HZB showed that this works perfectly. Second the prism rows were bent to shift the transmitted wavelength band to larger wavelengths. At HZB we showed that bending increased the transmission of neutrons with a wavelength of 4.9 Å. Experiments with a white beam at the EROS reflectometer at LLB showed that bending of the energy analyzing device to a radius of 7.9 m allows to shift the transmitted wavelength band from 0 to 9 Å to 2 to 16 Å.

  6. The EPOS Automated Selective Chemistry Analyzer evaluated.

    Science.gov (United States)

    Moses, G C; Lightle, G O; Tuckerman, J F; Henderson, A R

    1986-01-01

    We evaluated the analytical performance of the EPOS (Eppendorf Patient Oriented System) Automated Selective Chemistry Analyzer, using the following tests for serum analytes: alanine and aspartate aminotransferases, lactate dehydrogenase, creatine kinase, gamma-glutamyltransferase, alkaline phosphatase, and glucose. Results from the EPOS correlated well with those from comparison instruments (r greater than or equal to 0.990). Precision and linearity limits were excellent for all tests; linearity of the optical and pipetting systems was satisfactory. Reagent carryover was negligible. Sample-to-sample carryover was less than 1% for all tests, but only lactate dehydrogenase was less than the manufacturer's specified 0.5%. Volumes aspirated and dispensed by the sample and reagent II pipetting systems differed significantly from preset values, especially at lower settings; the reagent I system was satisfactory at all volumes tested. Minimal daily maintenance and an external data-reduction system make the EPOS a practical alternative to other bench-top chemistry analyzers.

  7. Simulation of a Hyperbolic Field Energy Analyzer

    CERN Document Server

    Gonzalez-Lizardo, Angel

    2016-01-01

    Energy analyzers are important plasma diagnostic tools with applications in a broad range of disciplines including molecular spectroscopy, electron microscopy, basic plasma physics, plasma etching, plasma processing, and ion sputtering technology. The Hyperbolic Field Energy Analyzer (HFEA) is a novel device able to determine ion and electron energy spectra and temperatures. The HFEA is well suited for ion temperature and density diagnostics at those situations where ions are scarce. A simulation of the capacities of the HFEA to discriminate particles of a particular energy level, as well as to determine temperature and density is performed in this work. The electric field due the combination of the conical elements, collimator lens, and Faraday cup applied voltage was computed in a well suited three-dimensional grid. The field is later used to compute the trajectory of a set of particles with a predetermined energy distribution. The results include the observation of the particle trajectories inside the sens...

  8. An improved prism energy analyzer for neutrons

    International Nuclear Information System (INIS)

    The effects of two improvements of an existing neutron energy analyzer consisting of stacked silicon prism rows are presented. First we tested the effect of coating the back of the prism rows with an absorbing layer to suppress neutron scattering by total reflection and by refraction at small angles. Experiments at HZB showed that this works perfectly. Second the prism rows were bent to shift the transmitted wavelength band to larger wavelengths. At HZB we showed that bending increased the transmission of neutrons with a wavelength of 4.9 Å. Experiments with a white beam at the EROS reflectometer at LLB showed that bending of the energy analyzing device to a radius of 7.9 m allows to shift the transmitted wavelength band from 0 to 9 Å to 2 to 16 Å

  9. 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.

  10. SACO: Static analyzer for concurrent objects

    OpenAIRE

    Albert Albiol, Elvira; Arenas Sánchez, Purificación; Flores Montoya, A.; Genaim, Samir; Gómez-Zamalloa Gil, Miguel; Martín Martín, Enrique; Puebla, G.; Román Díez, Guillermo

    2014-01-01

    We present the main concepts, usage and implementation of SACO, a static analyzer for concurrent objects. Interestingly, SACO is able to infer both liveness(namely termination and resource boundedness) and safety properties (namely deadlock freedom) of programs based on concurrent objects. The system integrates auxiliary analyses such as points-to and may-happen-in-parallel, which are essential for increasing the accuracy of the aforementioned more complex properties. SACO provides accurate ...

  11. LEGAL-EASE:Analyzing Chinese Financial Statements

    Institute of Scientific and Technical Information of China (English)

    EDWARD; MA

    2008-01-01

    In this article,we will focus on under- standing and analyzing the typical accounts of Chinese financial statements,including the balance sheet and income statement. Accounts are generally incorrectly prepared. This can be due to several factors,incom- petence,as well as more serious cases of deliberate attempts to deceive.Regardless, accounts can be understood and errors or specific acts of misrepresentation uncovered. We will conduct some simple analysis to demonstrate how these can be spotted.

  12. Organization theory. Analyzing health care organizations.

    Science.gov (United States)

    Cors, W K

    1997-02-01

    Organization theory (OT) is a tool that can be applied to analyze and understand health care organizations. Transaction cost theory is used to explain, in a unifying fashion, the myriad changes being undertaken by different groups of constituencies in health care. Agency theory is applied to aligning economic incentives needed to ensure Integrated Delivery System (IDS) success. By using tools such as OT, a clearer understanding of organizational changes is possible. PMID:10164970

  13. A gas filter correlation analyzer for methane

    Science.gov (United States)

    Sebacher, D. I.

    1978-01-01

    A fast-response instrument for monitoring CH4 was designed and tested using a modified nondispersive infrared technique. An analysis of the single-beam rotating-cell system is presented along with the signal processing circuit. A calibration of the instrument shows that the technique can be used to measure CH4 concentrations as small as 5 ppm-m and the effects of interfering gases are analyzed.

  14. Information Theory for Analyzing Neural Networks

    OpenAIRE

    Sørngård, Bård

    2014-01-01

    The goal of this thesis was to investigate how information theory could be used to analyze artificial neural networks. For this purpose, two problems, a classification problem and a controller problem were considered. The classification problem was solved with a feedforward neural network trained with backpropagation, the controller problem was solved with a continuous-time recurrent neural network optimized with evolution.Results from the classification problem shows that mutual information ...

  15. Firms’ Innovation Strategies Analyzed and Explained

    OpenAIRE

    Tavassoli, Sam; Karlsson, Charlie

    2015-01-01

    This paper analyzes various innovation strategies of firms. Using five waves of the Community Innovation Survey in Sweden, we have traced the innovative behavior of firms over a ten-year period, i.e. between 2002 and 2012. We distinguish between sixteen innovation strategies, which compose of Schumpeterian four types of innovations (process, product, marketing, and organizational) plus various combinations of these four types. First, we find that firms are not homogenous in choosing innovatio...

  16. The analyzing of Dove marketing strategy

    Institute of Scientific and Technical Information of China (English)

    Guo; Yaohui

    2015-01-01

    <正>1.Introduction In this report,I try to analyze the related information about DOVE chocolate.Firstly,I would like to introduce this product.Dove chocolate is one of a series of products launched by the world’s largest pet food and snack food manufacturers,U.S.multinational food company Mars(Mars).Entered China in 1989,It becomes China’s leading brand of chocolate in

  17. Coordinating, Scheduling, Processing and Analyzing IYA09

    Science.gov (United States)

    Gipson, John; Behrend, Dirk; Gordon, David; Himwich, Ed; MacMillan, Dan; Titus, Mike; Corey, Brian

    2010-01-01

    The IVS scheduled a special astrometric VLBI session for the International Year of Astronomy 2009 (IYA09) commemorating 400 years of optical astronomy and 40 years of VLBI. The IYA09 session is the most ambitious geodetic session to date in terms of network size, number of sources, and number of observations. We describe the process of designing, coordinating, scheduling, pre-session station checkout, correlating, and analyzing this session.

  18. Modular Construction of Shape-Numeric Analyzers

    Directory of Open Access Journals (Sweden)

    Bor-Yuh Evan Chang

    2013-09-01

    Full Text Available The aim of static analysis is to infer invariants about programs that are precise enough to establish semantic properties, such as the absence of run-time errors. Broadly speaking, there are two major branches of static analysis for imperative programs. Pointer and shape analyses focus on inferring properties of pointers, dynamically-allocated memory, and recursive data structures, while numeric analyses seek to derive invariants on numeric values. Although simultaneous inference of shape-numeric invariants is often needed, this case is especially challenging and is not particularly well explored. Notably, simultaneous shape-numeric inference raises complex issues in the design of the static analyzer itself. In this paper, we study the construction of such shape-numeric, static analyzers. We set up an abstract interpretation framework that allows us to reason about simultaneous shape-numeric properties by combining shape and numeric abstractions into a modular, expressive abstract domain. Such a modular structure is highly desirable to make its formalization and implementation easier to do and get correct. To achieve this, we choose a concrete semantics that can be abstracted step-by-step, while preserving a high level of expressiveness. The structure of abstract operations (i.e., transfer, join, and comparison follows the structure of this semantics. The advantage of this construction is to divide the analyzer in modules and functors that implement abstractions of distinct features.

  19. 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.

  20. Analyzing Malware Based on Volatile Memory

    Directory of Open Access Journals (Sweden)

    Liang Hu

    2013-11-01

    Full Text Available To explain the necessity of comprehensive and automatically analysis process for volatile memory, this paper summarized ordinarily analyzing methods and their common points especially for concerned data source. Then, a memory analysis framework Volatiltiy-2.2 and statistical output file size are recommended. In addition, to address the limitation of plug-ins classification in analyzing procedure, a user perspective classify is necessary and proposed. Furthermore, according to target data source differences on the base of result data set volume and employed relational method is introduced for comprehensive analysis guideline procedure. Finally, a test demo including DLLs loading order list analyzing is recommend, in which DLL load list is regard as different kind of characteristics typical data source with process and convert into process behavior fingerprint. The clustering for the fingerprint is employed string similar degree algorithm model in the demo, which has a wide range applications in traditional malware behavior analysis, and it is proposed that these methods also can be applied for volatile memory

  1. Aliasing Errours in Parallel Signature Analyzers

    Institute of Scientific and Technical Information of China (English)

    闵应骅; YashwantK.Malaiya

    1990-01-01

    A Linear Feedback Shift Register(LFSR)can be used to compress test response data as a Signature Analyzer(SA).Parallel Signature Analyzers(PSAs)implemented as multiple input LFSRs are faster and require less hardware overhead than Serial Signature Analyzers(SSAs) for compacting test response data for Built-In Self-Test(BIST)in IC of boare-testing environments.However,the SAs are prone to aliasing errors because of some specific types of error patterns.An alias is a faulty output signature that is identical to the fault-free signature.A penetrating analysis of detecting capability of SAs depends strongly on mathematical manipulations,instead of being aware of some special cases of examples.In addition,the analysis should not be restricted to a particular structure of LFSR,but be appropriate for various structures of LFSRs.This paper presents necessary and sufficient conditions for aliasing errors based on a complete mathematical description of various types of SAs.An LFSR reconfiguration scheme is suggested which will prevent any aliasing double errors.Such a prevention cannot be obtained by any extension of an LFSR.

  2. Method of stabilizing single channel analyzers

    International Nuclear Information System (INIS)

    A method and the apparatus to reduce the drift of single channel analyzers are described. Essentially, this invention employs a time-sharing or multiplexing technique to insure that the outputs from two single channel analyzers (SCAS) maintain the same count ratio regardless of variations in the threshold voltage source or voltage changes, the multiplexing technique is accomplished when a flip flop, actuated by a clock, changes state to switch the output from the individual SCAS before these outputs are sent to a ratio counting scalar. In the particular system embodiment disclosed that illustrates this invention, the sulfur content of coal is determined by subjecting the coal to radiation from a neutron producing source. A photomultiplier and detector system equates the transmitted gamma radiation to an analog voltage signal and sends the same signal after amplification, to a SCA system that contains the invention. Therein, at least two single channel analyzers scan the analog signal over different parts of a spectral region. The two outputs may then be sent to a digital multiplexer so that the output from the multiplexer contains counts falling within two distinct segments of the region. By dividing the counts from the multiplexer by each other, the percentage of sulfur within the coal sample under observation may be determined. (U.S.)

  3. Analyzing Intracellular Binding and Diffusion with Continuous Fluorescence Photobleaching

    Science.gov (United States)

    Wachsmuth, Malte; Weidemann, Thomas; Müller, Gabriele; Hoffmann-Rohrer, Urs W.; Knoch, Tobias A.; Waldeck, Waldemar; Langowski, Jörg

    2003-01-01

    Transport and binding of molecules to specific sites are necessary for the assembly and function of ordered supramolecular structures in cells. For analyzing these processes in vivo, we have developed a confocal fluorescence fluctuation microscope that allows both imaging of the spatial distribution of fluorescent molecules with confocal laser scanning microscopy and probing their mobility at specific positions in the cell with fluorescence correlation spectroscopy and continuous fluorescence photobleaching (CP). Because fluorescence correlation spectroscopy is restricted to rapidly diffusing particles and CP to slower processes, these two methods complement each other. For the analysis of binding-related contributions to mobility we have derived analytical expressions for the temporal behavior of CP curves from which the bound fraction and/or the dissociation rate or residence time at binding sites, respectively, can be obtained. In experiments, we investigated HeLa cells expressing different fluorescent proteins: Although enhanced green fluorescent protein (EGFP) shows high mobility, fusions of histone H2B with the yellow fluorescent protein are incorporated into chromatin, and these nuclei exhibit the presence of a stably bound and a freely diffusing species. Nonpermanent binding was found for mTTF-I, a transcription termination factor for RNA polymerase I, fused with EGFP. The cells show fluorescent nucleoli, and binding is transient. CP yields residence times for mTTF-I-EGFP of ∼13 s. PMID:12719264

  4. Evaluation of strategy for analyzing mouse liver plasma membrane proteome

    Institute of Scientific and Technical Information of China (English)

    CHEN; Ping; ZHANG; LiJun; LI; XuanWen; WANG; XiE; CAO; Rui; LIU; Zhen; XIONG; JiXian; PENG; Xia; WEI; YingJuan; YING; XingFeng; WANG; XianChun; LIANG; SongPing

    2007-01-01

    Plasma membrane (PM) proteome is one of the major subproteomes present in the cell,and is very important in liver function. In the present work, C57 mouse liver PM was purified by density-gradient centrifugation. The purified PM was verified by electron microscope analysis and Western blotting. The results showed that the PM was enriched by more than 20-fold and the contamination of mitochondria was reduced by 2-fold compared with the homogenization fraction. Proteins were separated by 2DE and 1DE, trypsin-digested and submitted to ESI-Q-TOF and MALDI-TOF-TOF mass spectrometry or directly digested in solution and analyzed by LC-ESI ion trap mass spectrometry. In all, 547 non-redundant mouse liver PM proteins were identified, of which 34% contributed to plasma membrane or plasma membrane-related proteins. This study optimized and evaluated the HLPP plasma membrane proteome analysis method and made a systematic analysis on PM proteome.

  5. Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito.

    Directory of Open Access Journals (Sweden)

    Dumrong Mairiang

    Full Text Available 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.

  6. Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

    OpenAIRE

    Selvaraj S; Jayaram B; Saranya N; Gromiha M; Fukui Kazuhiko

    2011-01-01

    Abstract Background Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology. Methods We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such...

  7. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    . The biophysical and structural investigations of PPIs consequently demand hybrid approaches, implementing orthogonal methods and strategies for global data analysis. Currently, impressive developments in hardware and software within several methodologies define a new era for the biostructural community. Data can......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...

  8. A chemical analyzer for charged ultrafine particles

    Directory of Open Access Journals (Sweden)

    S. G. Gonser

    2013-04-01

    Full Text Available 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 consequently analyzed for its molecular composition in a time of flight mass spectrometer. We report of 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 known 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.

  9. 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)

  10. 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.

  11. FOMA: A Fast Optical Multichannel Analyzer

    Science.gov (United States)

    Haskovec, J. S.; Bramson, G.; Brooks, N. H.; Perry, M.

    1989-12-01

    A Fast Optical Multichannel Analyzer (FOMA) was built for spectroscopic measurements with fast time resolution on the DIII-D tokamak. The FOMA utilizes a linear photodiode array (RETICON RL 1024 SA) as the detector sensor. An external recharge switch and ultrafast operational amplifiers permit a readout time per pixel of 300 ns. In conjunction with standard CAMAC digitizer and timing modules, a readout time of 500 microns is achieved for the full 1024-element array. Data acquired in bench tests and in actual spectroscopic measurements on the DIII-D tokamak is presented to illustrate the camera's capability.

  12. Spectrum Analyzers Incorporating Tunable WGM Resonators

    Science.gov (United States)

    Savchenkov, Anatoliy; Matsko, Andrey; Strekalov, Dmitry; Maleki, Lute

    2009-01-01

    A photonic instrument is proposed to boost the resolution for ultraviolet/ optical/infrared spectral analysis and spectral imaging allowing the detection of narrow (0.00007-to-0.07-picometer wavelength resolution range) optical spectral signatures of chemical elements in space and planetary atmospheres. The idea underlying the proposal is to exploit the advantageous spectral characteristics of whispering-gallery-mode (WGM) resonators to obtain spectral resolutions at least three orders of magnitude greater than those of optical spectrum analyzers now in use. Such high resolutions would enable measurement of spectral features that could not be resolved by prior instruments.

  13. APPLICATION OF IMAGE MANIPULATION FOR CAVITATION ANALYZING

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A new method, which is called image manipulation,is introduced to analyze the cavitation of flow field for the first time. As the complexity of the cavitation development must be considering,only the method of image manipulation can calculate the strength of the cavitation more accurately. This method based on wavelet transform is used to eliminate the noise. The area of the cavitations is deduced to serve as the strength of cavitation. The method is applied in an example of inducer's rotating cavitation. The results show that using image manipulation can get the accurate date of cavitation with ease,and the reason of the inducer shaft's vibration is uncovered clearly.

  14. Analyzing the Biology on the System Level

    Institute of Scientific and Technical Information of China (English)

    Wei Tong

    2004-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology, and summarizes the analysis methods, experimental technologies, research developments, and so on in the four key fields of systems biology-systemic structures, dynamics, control methods, and design principles.

  15. Analyzing Ever Growing Datasets in PHENIX

    Energy Technology Data Exchange (ETDEWEB)

    Pinkenburg, C.; PHENIX Collaboration

    2010-10-18

    After 10 years of running, the PHENIX experiment has by now accumulated more than 700 TB of reconstructed data which are directly used for analysis. Analyzing these amounts of data efficiently requires a coordinated approach. Beginning in 2005 we started to develop a system for the RHIC Atlas Computing Facility (RACF) which allows the efficient analysis of these large data sets. The Analysis Taxi is now the tool which allows any collaborator to process any data set taken since 2003 in weekly passes with turnaround times of typically three to four days.

  16. CRISP90 - SOFTWARE DESIGN ANALYZER SYSTEM

    Science.gov (United States)

    Tausworthe, R. C.

    1994-01-01

    The CRISP90 Software Design Analyzer System, an update of CRISP-80, is a set of programs forming a software design and documentation tool which supports top-down, hierarchic, modular, structured design and programming methodologies. The quality of a computer program can often be significantly influenced by the design medium in which the program is developed. The medium must foster the expression of the programmer's ideas easily and quickly, and it must permit flexible and facile alterations, additions, and deletions to these ideas as the design evolves. The CRISP90 software design analyzer system was developed to provide the PDL (Programmer Design Language) programmer with such a design medium. A program design using CRISP90 consists of short, English-like textual descriptions of data, interfaces, and procedures that are imbedded in a simple, structured, modular syntax. The display is formatted into two-dimensional, flowchart-like segments for a graphic presentation of the design. Together with a good interactive full-screen editor or word processor, the CRISP90 design analyzer becomes a powerful tool for the programmer. In addition to being a text formatter, the CRISP90 system prepares material that would be tedious and error prone to extract manually, such as a table of contents, module directory, structure (tier) chart, cross-references, and a statistics report on the characteristics of the design. Referenced modules are marked by schematic logic symbols to show conditional, iterative, and/or concurrent invocation in the program. A keyword usage profile can be generated automatically and glossary definitions inserted into the output documentation. Another feature is the capability to detect changes that were made between versions. Thus, "change-bars" can be placed in the output document along with a list of changed pages and a version history report. Also, items may be marked as "to be determined" and each will appear on a special table until the item is

  17. Analyzing PICL trace data with MEDEA

    Energy Technology Data Exchange (ETDEWEB)

    Merlo, A.P. [Pavia Univ. (Italy). Dipt di Informatica e Sistemistica; Worley, P.H. [Oak Ridge National Lab., TN (United States)

    1993-11-01

    Execution traces and performance statistics can be collected for parallel applications on a variety of multiprocessor platforms by using the Portable Instrumented Communication Library (PICL). The static and dynamic performance characteristics of performance data can be analyzed easily and effectively with the facilities provided within the MEasurements Description Evaluation and Analysis tool (MEDEA). This report describes the integration of the PICL trace file format into MEDEA. A case study is then outlined that uses PICL and MEDEA to characterize the performance of a parallel benchmark code executed on different hardware platforms and using different parallel algorithms and communication protocols.

  18. Using SCR methods to analyze requirements documentation

    Science.gov (United States)

    Callahan, John; Morrison, Jeffery

    1995-01-01

    Software Cost Reduction (SCR) methods are being utilized to analyze and verify selected parts of NASA's EOS-DIS Core System (ECS) requirements documentation. SCR is being used as a spot-inspection tool. Through this formal and systematic approach of the SCR requirements methods, insights as to whether the requirements are internally inconsistent or incomplete as the scenarios of intended usage evolve in the OC (Operations Concept) documentation. Thus, by modelling the scenarios and requirements as mode charts using the SCR methods, we have been able to identify problems within and between the documents.

  19. On the analysis of membrane protein circular dichroism spectra

    OpenAIRE

    Sreerama, Narasimha; Woody, Robert W.

    2004-01-01

    Analysis of circular dichroism spectra of proteins provides information about protein secondary structure. Analytical methods developed for such an analysis use structures and spectra of a set of reference proteins. The reference protein sets currently in use include soluble proteins with a wide range of secondary structures, and perform quite well in analyzing CD spectra of soluble proteins. The utility of soluble protein reference sets in analyzing membrane protein CD spectra, however, has ...

  20. Evaluation of the Konelab 20XT clinical chemistry analyzer.

    Science.gov (United States)

    Stojanović, Natasa; Rogić, Dunja; Stavljenić-Rukavina, Ana

    2005-01-01

    The Konelab 20XT (Thermo Electron Oy, Finland) is a clinical chemistry analyzer for colorimetric, immunoturbidimetric and ion-selective electrode measurements. The aim of our work was to evaluate the analytical performances of the Konelab 20XT according to the European Clinical Chemistry Laboratory Standards Guidelines. A total of 30 analytes including substrates, enzymes, electrolytes and specific proteins were tested. Investigation results showed low imprecision (within-run coefficient of variation was below 3.5% and between-day coefficient of variation was less than 2.5% for most analytes at all three levels studied) and acceptable accuracy of the analyzer. No significant sample- or reagent-related carry-over was found. It was demonstrated that the analytical system operates within the claimed linearity ranges. The results compared well with those obtained by instruments routinely used in our laboratory (Olympus AU2700, Behring Nephelometer II). In general, the data on interference by hemoglobin, hyperbilirubinemia and turbidity are in accordance with known facts. However, slight hemolysis was found to interfere with the alkaline phosphatase (ALP) assay and mild lipemia affected the glucose assay. The Konelab 20XT is an easy-to-use analyzer that is suitable for routine and emergency analyses in small laboratories.

  1. The BRCA1-binding protein BRAP2 can act as a cytoplasmic retention factor for nuclear and nuclear envelope-localizing testicular proteins.

    Science.gov (United States)

    Davies, Rebecca G; Wagstaff, Kylie M; McLaughlin, Eileen A; Loveland, Kate L; Jans, David A

    2013-12-01

    Regulation of nuclear protein import is central to many cellular processes such as development, with a key mechanism being factors that retain cargoes in the cytoplasm that normally localize in the nucleus. The breast cancer antigen BRCA1-binding protein BRAP2 has been reported as a novel negative regulator of nuclear import of various nuclear localization signal (NLS)-containing viral and cellular proteins, but although implicated in differentiation pathways and highly expressed in tissues including testis, the gamut of targets for BRAP2 action in a developmental context is unknown. As a first step towards defining the BRAP2 interactome, we performed a yeast-2-hybrid screen to identify binding partners of BRAP2 in human testis. Here we report characterization for the first time of three of these: the high mobility group (HMG)-box-domain-containing chromatin component HMG20A, nuclear mitotic apparatus protein NuMA1 and synaptic nuclear envelope protein SYNE2. Co-immunoprecipitation experiments indicate association of BRAP2 with HMG20A, NuMA1, and SYNE2 in testis, underlining the physiological relevance of the interactions, with immunohistochemistry showing that where BRAP2 is co-expressed with HMG20A and NuMA1, both are present in the cytoplasm, in contrast to their nuclear localization in other testicular cell types. Importantly, quantitative confocal microscopic analysis of cultured cells indicates that ectopic expression of BRAP2 inhibits nuclear localization of HMG20A and NuMA1, and prevents nuclear envelope accumulation of SYNE2, the first report of BRAP2 altering localization of a non-nuclear protein. These results imply for the first time that BRAP2 may have an important role in modulating subcellular localization during testicular development. PMID:23707952

  2. Analyzing and Mining Ordered Information Tables

    Institute of Scientific and Technical Information of China (English)

    SAI Ying (赛英); Y. Y. Yao

    2003-01-01

    Work in inductive learning has mostly been concentrated on classifying. However,there are many applications in which it is desirable to order rather than to classify instances. For modelling ordering problems, we generalize the notion of information tables to ordered information tables by adding order relations in attribute values. Then we propose a data analysis model by analyzing the dependency of attributes to describe the properties of ordered information tables.The problem of mining ordering rules is formulated as finding association between orderings of attribute values and the overall ordering of objects. An ordering rules may state that "if the value of an object x on an attribute a is ordered ahead of the value of another object y on the same attribute, then x is ordered ahead of y". For mining ordering rules, we first transform an ordered information table into a binary information table, and then apply any standard machine learning and data mining algorithms. As an illustration, we analyze in detail Maclean's universities ranking for the year 2000.

  3. 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.

  4. Analyzing Network Coding Gossip Made Easy

    CERN Document Server

    Haeupler, Bernhard

    2010-01-01

    We give a new technique to analyze the stopping time of gossip protocols that are based on random linear network coding (RLNC). Our analysis drastically simplifies, extends and strengthens previous results. We analyze RLNC gossip in a general framework for network and communication models that encompasses and unifies the models used previously in this context. We show, in most settings for the first time, that it converges with high probability in the information-theoretically optimal time. Most stopping times are of the form O(k + T) where k is the number of messages to be distributed and T is the time it takes to disseminate one message. This means RLNC gossip achieves "perfect pipelining". Our analysis directly extends to highly dynamic networks in which the topology can change completely at any time. This remains true even if the network dynamics are controlled by a fully adaptive adversary that knows the complete network state. Virtually nothing besides simple O(kT) sequential flooding protocols was prev...

  5. Atmospheric Aerosol Chemistry Analyzer: Demonstration of feasibility

    Energy Technology Data Exchange (ETDEWEB)

    Mroz, E.J.; Olivares, J.; Kok, G.

    1996-04-01

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The project objective was to demonstrate the technical feasibility of an Atmospheric Aerosol Chemistry Analyzer (AACA) that will provide a continuous, real-time analysis of the elemental (major, minor and trace) composition of atmospheric aerosols. The AACA concept is based on sampling the atmospheric aerosol through a wet cyclone scrubber that produces an aqueous suspension of the particles. This suspension can then be analyzed for elemental composition by ICP/MS or collected for subsequent analysis by other methods. The key technical challenge was to develop a wet cyclone aerosol sampler suitable for respirable particles found in ambient aerosols. We adapted an ultrasonic nebulizer to a conventional, commercially available, cyclone aerosol sampler and completed collection efficiency tests for the unit, which was shown to efficiently collect particles as small as 0.2 microns. We have completed the necessary basic research and have demonstrated the feasibility of the AACA concept.

  6. Analyzing Interoperability of Protocols Using Model Checking

    Institute of Scientific and Technical Information of China (English)

    WUPeng

    2005-01-01

    In practical terms, protocol interoperability testing is still laborious and error-prone with little effect, even for those products that have passed conformance testing. Deadlock and unsymmetrical data communication are familiar in interoperability testing, and it is always very hard to trace their causes. The previous work has not provided a coherent way to analyze why the interoperability was broken among protocol implementations under test. In this paper, an alternative approach is presented to analyzing these problems from a viewpoint of implementation structures. Sequential and concurrent structures are both representative implementation structures, especially in event-driven development model. Our research mainly discusses the influence of sequential and concurrent structures on interoperability, with two instructive conclusions: (a) a sequential structure may lead to deadlock; (b) a concurrent structure may lead to unsymmetrical data communication. Therefore, implementation structures carry weight on interoperability, which may not gain much attention before. To some extent, they are decisive on the result of interoperability testing. Moreover, a concurrent structure with a sound task-scheduling strategy may contribute to the interoperability of a protocol implementation. Herein model checking technique is introduced into interoperability analysis for the first time. As the paper shows, it is an effective way to validate developers' selections on implementation structures or strategies.

  7. Analyzing delay causes in Egyptian construction projects

    Directory of Open Access Journals (Sweden)

    Mohamed M. Marzouk

    2014-01-01

    Full Text Available 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.

  8. The Solar Wind Ion Analyzer for MAVEN

    Science.gov (United States)

    Halekas, J. S.; Taylor, E. R.; Dalton, G.; Johnson, G.; Curtis, D. W.; McFadden, J. P.; Mitchell, D. L.; Lin, R. P.; Jakosky, B. M.

    2015-12-01

    The Solar Wind Ion Analyzer (SWIA) on the MAVEN mission will measure the solar wind ion flows around Mars, both in the upstream solar wind and in the magneto-sheath and tail regions inside the bow shock. The solar wind flux provides one of the key energy inputs that can drive atmospheric escape from the Martian system, as well as in part controlling the structure of the magnetosphere through which non-thermal ion escape must take place. SWIA measurements contribute to the top level MAVEN goals of characterizing the upper atmosphere and the processes that operate there, and parameterizing the escape of atmospheric gases to extrapolate the total loss to space throughout Mars' history. To accomplish these goals, SWIA utilizes a toroidal energy analyzer with electrostatic deflectors to provide a broad 360∘×90∘ field of view on a 3-axis spacecraft, with a mechanical attenuator to enable a very high dynamic range. SWIA provides high cadence measurements of ion velocity distributions with high energy resolution (14.5 %) and angular resolution (3.75∘×4.5∘ in the sunward direction, 22.5∘×22.5∘ elsewhere), and a broad energy range of 5 eV to 25 keV. Onboard computation of bulk moments and energy spectra enable measurements of the basic properties of the solar wind at 0.25 Hz.

  9. Sentiment Analyzer for Arabic Comments System

    Directory of Open Access Journals (Sweden)

    Alaa El-Dine Ali Hamouda

    2013-04-01

    Full Text Available Today, the number of users of social network is increasing. Millions of users share opinions on different aspects of life every day. Therefore social network are rich sources of data for opinion mining and sentiment analysis. Also users have become more interested in following news pages on Facebook. Several posts; political for example, have thousands of users’ comments that agree/disagree with the post content. Such comments can be a good indicator for the community opinion about the post content. For politicians, marketers, decision makers …, it is required to make sentiment analysis to know the percentage of users agree, disagree and neutral respect to a post. This raised the need to analyze theusers’ comments in Facebook. We focused on Arabic Facebook news pages for the task of sentiment analysis. We developed a corpus for sentiment analysis and opinion mining purposes. Then, we used different machine learning algorithms – decision tree, support vector machines, and naive bayes - to develop sentiment analyzer. The performance of the system using each technique was evaluated and compared with others.

  10. 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.

  11. Statistical network analysis for analyzing policy networks

    DEFF Research Database (Denmark)

    Robins, Garry; Lewis, Jenny; Wang, Peng

    2012-01-01

    To analyze social network data using standard statistical approaches is to risk incorrect inference. The dependencies among observations implied in a network conceptualization undermine standard assumptions of the usual general linear models. One of the most quickly expanding areas of social......), and stochastic actor-oriented models. We focus most attention on ERGMs by providing an illustrative example of a model for a strategic information network within a local government. We draw inferences about the structural role played by individuals recognized as key innovators and conclude that such an approach...... 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...

  12. 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...... structures, supporting actor involvement in the ecosystem, and (v) proper orchestration and governance of the ecosystem to promote and support the changes and the health of the ecosystem. Our work contributes to Net4Care, a platform to serve as the common platform in the software ecosystem under...... establishment. In addition, it contributes by providing input and guidelines on the role and activity of 4S organization, an organization to serve as an orchestrator in the ecosystem with the aim of managing the platform, supporting actor and software interactions, and promoting the ecosystem health...

  13. Fully Analyzing an Algebraic Polya Urn Model

    CERN Document Server

    Morcrette, Basile

    2012-01-01

    This paper introduces and analyzes a particular class of Polya urns: balls are of two colors, can only be added (the urns are said to be additive) and at every step the same constant number of balls is added, thus only the color compositions varies (the urns are said to be balanced). These properties make this class of urns ideally suited for analysis from an "analytic combinatorics" point-of-view, following in the footsteps of Flajolet-Dumas-Puyhaubert, 2006. Through an algebraic generating function to which we apply a multiple coalescing saddle-point method, we are able to give precise asymptotic results for the probability distribution of the composition of the urn, as well as local limit law and large deviation bounds.

  14. 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.

  15. Analyzing petabytes of data with Hadoop

    CERN Document Server

    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...

  16. 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.

  17. Complex networks theory for analyzing metabolic networks

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jing; YU Hong; LUO Jianhua; CAO Z.W.; LI Yixue

    2006-01-01

    One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of the organism,while networks are appropriate abstract description of all kinds of interactions. In the past few years, great achievement has been made in developing theory of complex networks for revealing the organizing principles that govern the formation and evolution of various complex biological, technological and social networks. This paper reviews the accomplishments in constructing genome-based metabolic networks and describes how the theory of complex networks is applied to analyze metabolic networks.

  18. 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.

  19. Composite blade structural analyzer (COBSTRAN) user's manual

    Science.gov (United States)

    Aiello, Robert A.

    1989-01-01

    The installation and use of a computer code, COBSTRAN (COmposite Blade STRuctrual ANalyzer), developed for the design and analysis of composite turbofan and turboprop blades and also for composite wind turbine blades was described. This code combines composite mechanics and laminate theory with an internal data base of fiber and matrix properties. Inputs to the code are constituent fiber and matrix material properties, factors reflecting the fabrication process, composite geometry and blade geometry. COBSTRAN performs the micromechanics, macromechanics and laminate analyses of these fiber composites. COBSTRAN generates a NASTRAN model with equivalent anisotropic homogeneous material properties. Stress output from NASTRAN is used to calculate individual ply stresses, strains, interply stresses, thru-the-thickness stresses and failure margins. Curved panel structures may be modeled providing the curvature of a cross-section is defined by a single value function. COBSTRAN is written in FORTRAN 77.

  20. Composite Blade Structural Analyzer (COBSTRAN) demonstration manual

    Science.gov (United States)

    Aiello, Robert A.

    1989-01-01

    The input deck setup is described for a computer code, composite blade structural analyzer (COBSTRAN) which was developed for the design and analysis of composite turbofan and turboprop blades and also for composite wind turbine blades. This manual is intended for use in conjunction with the COBSTRAN user's manual. Seven demonstration problems are described with pre- and postprocessing input decks. Modeling of blades which are solid thru-the-thickness and also aircraft wing airfoils with internal spars is shown. Corresponding NASTRAN and databank input decks are also shown. Detail descriptions of each line of the pre- and post-processing decks is provided with reference to the Card Groups defined in the user's manual. A dictionary of all program variables and terms used in this manual may be found in Section 6 of the user's manual.

  1. Three Practical Methods for Analyzing Slope Stability

    Institute of Scientific and Technical Information of China (English)

    XU Shiguang; ZHANG Shitao; ZHU Chuanbing; YIN Ying

    2008-01-01

    Since the environmental capacity and the arable as well as the inhabitant lands have actually reached a full balance, the slopes are becoming the more and more important options for various engineering constructions. Because of the geological complexity of the slope, the design and thedecision-making of a slope-based engineering is still not ractical to rely solely on the theoretical analysis and numerical calculation, but mainly on the experience of the experts. Therefore, it hasimportant practical significance to turn some successful experience into mathematic equations. Basedupon the abundant typical slope engineering construction cases in Yunnan, Southwestern China, 3methods for yzing the slope stability have been developed in this paper. First of all, the corresponded analogous mathematic equation for analyzing slope stability has been established through case studies. Then, artificial neural network and multivariate regression analysis have alsobeen set up when 7 main influencing factors are adopted

  2. A calibration free vector network analyzer

    Science.gov (United States)

    Kothari, Arpit

    Recently, two novel single-port, phase-shifter based vector network analyzer (VNA) systems were developed and tested at X-band (8.2--12.4 GHz) and Ka-band (26.4--40 GHz), respectively. These systems operate based on electronically moving the standing wave pattern, set up in a waveguide, over a Schottky detector and sample the standing wave voltage for several phase shift values. Once this system is fully characterized, all parameters in the system become known and hence theoretically, no other correction (or calibration) should be required to obtain the reflection coefficient, (Gamma), of an unknown load. This makes this type of VNA "calibration free" which is a significant advantage over other types of VNAs. To this end, a VNA system, based on this design methodology, was developed at X-band using several design improvements (compared to the previous designs) with the aim of demonstrating this "calibration-free" feature. It was found that when a commercial VNA (HP8510C) is used as the source and the detector, the system works as expected. However, when a detector is used (Schottky diode, log detector, etc.), obtaining correct Gamma still requires the customary three-load calibration. With the aim of exploring the cause, a detailed sensitivity analysis of prominent error sources was performed. Extensive measurements were done with different detection techniques including use of a spectrum analyzer as power detector. The system was tested even for electromagnetic compatibility (EMC) which may have contributed to this issue. Although desired results could not be obtained using the proposed standing-wave-power measuring devices like the Schottky diode but the principle of "calibration-free VNA" was shown to be true.

  3. Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.

    Science.gov (United States)

    Rozenblatt-Rosen, Orit; Deo, Rahul C; Padi, Megha; Adelmant, Guillaume; Calderwood, Michael A; Rolland, Thomas; Grace, Miranda; Dricot, Amélie; Askenazi, Manor; Tavares, Maria; Pevzner, Samuel J; Abderazzaq, Fieda; Byrdsong, Danielle; Carvunis, Anne-Ruxandra; Chen, Alyce A; Cheng, Jingwei; Correll, Mick; Duarte, Melissa; Fan, Changyu; Feltkamp, Mariet C; Ficarro, Scott B; Franchi, Rachel; Garg, Brijesh K; Gulbahce, Natali; Hao, Tong; Holthaus, Amy M; James, Robert; Korkhin, Anna; Litovchick, Larisa; Mar, Jessica C; Pak, Theodore R; Rabello, Sabrina; Rubio, Renee; Shen, Yun; Singh, Saurav; Spangle, Jennifer M; Tasan, Murat; Wanamaker, Shelly; Webber, James T; Roecklein-Canfield, Jennifer; Johannsen, Eric; Barabási, Albert-László; Beroukhim, Rameen; Kieff, Elliott; Cusick, Michael E; Hill, David E; Münger, Karl; Marto, Jarrod A; Quackenbush, John; Roth, Frederick P; DeCaprio, James A; Vidal, Marc

    2012-07-26

    Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations. Genome sequencing efforts have identified numerous germline mutations, and large numbers of somatic genomic alterations, associated with a predisposition to cancer. However, it remains difficult to distinguish background, or 'passenger', cancer mutations from causal, or 'driver', mutations in these data sets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations. Here we test the hypothesis that genomic variations and tumour viruses may cause cancer through related mechanisms, by systematically examining host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways, such as Notch signalling and apoptosis, that go awry in cancer. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on a par with their identification through functional genomics and large-scale cataloguing of tumour mutations. Together, these complementary approaches increase the specificity of cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate the prioritization of cancer-causing driver genes to advance the understanding of the genetic basis of human cancer. PMID:22810586

  4. Interpreting cancer genomes using systematic host perturbations by tumour virus proteins

    Science.gov (United States)

    Rozenblatt-Rosen, Orit; Deo, Rahul C.; Padi, Megha; Adelmant, Guillaume; Calderwood, Michael A.; Rolland, Thomas; Grace, Miranda; Dricot, Amélie; Askenazi, Manor; Tavares, Maria; Pevzner, Sam; Abderazzaq, Fieda; Byrdsong, Danielle; Carvunis, Anne-Ruxandra; Chen, Alyce A.; Cheng, Jingwei; Correll, Mick; Duarte, Melissa; Fan, Changyu; Feltkamp, Mariet C.; Ficarro, Scott B.; Franchi, Rachel; Garg, Brijesh K.; Gulbahce, Natali; Hao, Tong; Holthaus, Amy M.; James, Robert; Korkhin, Anna; Litovchick, Larisa; Mar, Jessica C.; Pak, Theodore R.; Rabello, Sabrina; Rubio, Renee; Shen, Yun; Singh, Saurav; Spangle, Jennifer M.; Tasan, Murat; Wanamaker, Shelly; Webber, James T.; Roecklein-Canfield, Jennifer; Johannsen, Eric; Barabási, Albert-László; Beroukhim, Rameen; Kieff, Elliott; Cusick, Michael E.; Hill, David E.; Münger, Karl; Marto, Jarrod A.; Quackenbush, John; Roth, Frederick P.; DeCaprio, James A.; Vidal, Marc

    2012-01-01

    Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype-phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations1. Genome sequencing efforts have identified numerous germline mutations associated with cancer predisposition and large numbers of somatic genomic alterations2. However, it remains challenging to distinguish between background, or “passenger” and causal, or “driver” cancer mutations in these datasets. Human viruses intrinsically depend on their host cell during the course of infection and can elicit pathological phenotypes similar to those arising from mutations3. To test the hypothesis that genomic variations and tumour viruses may cause cancer via related mechanisms, we systematically examined host interactome and transcriptome network perturbations caused by DNA tumour virus proteins. The resulting integrated viral perturbation data reflects rewiring of the host cell networks, and highlights pathways that go awry in cancer, such as Notch signalling and apoptosis. We show that systematic analyses of host targets of viral proteins can identify cancer genes with a success rate on par with their identification through functional genomics and large-scale cataloguing of tumour mutations. Together, these complementary approaches result in increased specificity for cancer gene identification. Combining systems-level studies of pathogen-encoded gene products with genomic approaches will facilitate prioritization of cancer-causing driver genes so as to advance understanding of the genetic basis of human cancer. PMID:22810586

  5. An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client.

    Science.gov (United States)

    Bigenzahn, Johannes W; Fauster, Astrid; Rebsamen, Manuele; Kandasamy, Richard K; Scorzoni, Stefania; Vladimer, Gregory I; Müller, André C; Gstaiger, Matthias; Zuber, Johannes; Bennett, Keiryn L; Superti-Furga, Giulio

    2016-03-01

    Tandem affinity purification-mass spectrometry (TAP-MS) is a popular strategy for the identification of protein-protein interactions, characterization of protein complexes, and entire networks. Its employment in cellular settings best fitting the relevant physiology is limited by convenient expression vector systems. We developed an easy-to-handle, inducible, dually selectable retroviral expression vector allowing dose- and time-dependent control of bait proteins bearing the efficient streptavidin-hemagglutinin (SH)-tag at their N- or C termini. Concomitant expression of a reporter fluorophore allows to monitor bait-expressing cells by flow cytometry or microscopy and enables high-throughput phenotypic assays. We used the system to successfully characterize the interactome of the neuroblastoma RAS viral oncogene homolog (NRAS) Gly12Asp (G12D) mutant and exploited the advantage of reporter fluorophore expression by tracking cytokine-independent cell growth using flow cytometry. Moreover, we tested the feasibility of studying cytotoxicity-mediating proteins with the vector system on the cell death-inducing mixed lineage kinase domain-like protein (MLKL) Ser358Asp (S358D) mutant. Interaction proteomics analysis of MLKL Ser358Asp (S358D) identified heat shock protein 90 (HSP90) as a high-confidence interacting protein. Further phenotypic characterization established MLKL as a novel HSP90 client. In summary, this novel inducible expression system enables SH-tag-based interaction studies in the cell line proficient for the respective phenotypic or signaling context and constitutes a valuable tool for experimental approaches requiring inducible or traceable protein expression.

  6. Protein - Which is Best?

    Science.gov (United States)

    Hoffman, Jay R; Falvo, Michael J

    2004-09-01

    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. Key PointsHigher protein needs are seen in athletic populations.Animal proteins is an important source of protein, however potential health concerns do exist from a diet of protein

  7. Comparison of two dry chemistry analyzers and a wet chemistry analyzer using canine serum.

    Science.gov (United States)

    Lanevschi, Anne; Kramer, John W.

    1996-01-01

    Canine serum was used to compare seven chemistry analytes on two tabletop clinical dry chemistry analyzers, Boehringer's Reflotron and Kodak's Ektachem. Results were compared to those obtained on a wet chemistry reference analyzer, Roche Diagnostic's Cobas Mira. Analytes measured were urea nitrogen (BUN), creatinine, glucose, aspartate aminotransferase (AST), alanine aminotransferase (ALT), cholesterol and bilirubin. Nine to 12 canine sera with values in the low, normal, and high range were evaluated. The correlations were acceptable for all comparisons with correlation coefficients greater than 0.98 for all analytes. Regression analysis resulted in significant differences for both tabletop analyzers when compared to the reference analyzer for cholesterol and bilirubin, and for glucose and AST on the Kodak Ektachem. Differences appeared to result from proportional systematic error occurring at high analyte concentrations.

  8. Analysis of Phosphorylation-dependent Protein Interactions of Adhesion and Degranulation Promoting Adaptor Protein (ADAP) Reveals Novel Interaction Partners Required for Chemokine-directed T cell Migration.

    Science.gov (United States)

    Kuropka, Benno; Witte, Amelie; Sticht, Jana; Waldt, Natalie; Majkut, Paul; Hackenberger, Christian P R; Schraven, Burkhart; Krause, Eberhard; Kliche, Stefanie; Freund, Christian

    2015-11-01

    Stimulation of T cells leads to distinct changes of their adhesive and migratory properties. Signal propagation from activated receptors to integrins depends on scaffolding proteins such as the adhesion and degranulation promoting adaptor protein (ADAP)(1). Here we have comprehensively investigated the phosphotyrosine interactome of ADAP in T cells and define known and novel interaction partners of functional relevance. While most phosphosites reside in unstructured regions of the protein, thereby defining classical SH2 domain interaction sites for master regulators of T cell signaling such as SLP76, Fyn-kinase, and NCK, other binding events depend on structural context. Interaction proteomics using different ADAP constructs comprising most of the known phosphotyrosine motifs as well as the structured domains confirm that a distinct set of proteins is attracted by pY571 of ADAP, including the ζ-chain-associated protein kinase of 70 kDa (ZAP70). The interaction of ADAP and ZAP70 is inducible upon stimulation either of the T cell receptor (TCR) or by chemokine. NMR spectroscopy reveals that the N-terminal SH2 domains within a ZAP70-tandem-SH2 construct is the major site of interaction with phosphorylated ADAP-hSH3(N) and microscale thermophoresis (MST) indicates an intermediate binding affinity (Kd = 2.3 μm). Interestingly, although T cell receptor dependent events such as T cell/antigen presenting cell (APC) conjugate formation and adhesion are not affected by mutation of Y571, migration of T cells along a chemokine gradient is compromised. Thus, although most phospho-sites in ADAP are linked to T cell receptor related functions we have identified a unique phosphotyrosine that is solely required for chemokine induced T cell behavior.

  9. Toward Integrated μNetwork Analyzer

    Science.gov (United States)

    Kmec, M.; Helbig, M.; Herrmann, R.; Rauschenbach, P.; Sachs, J.; Schilling, K.

    The article deals with recent development steps toward monolithically integrated micro-Network Analyzer (μNA). The device will deploy M-Sequence-based single-chip transceivers with a built-in ultra-wideband wave separation unit in the receiver chains. The introduced on-chip wideband wave separation is realized using an optimized resistive directional coupler combined with a customized differential LNA as detector. The wave separation works almost down to DC, and its upper frequency limit is determined by the performance of the implemented technology (i.e., bridge resistors, transistors, etc.), the selected circuit topology, and the wirings of particular coupler components but also by the IC packaging itself. Even though the upper limit is designed to be compatible with the analog input bandwidth of the receiver circuit [which is about 18 GHz for naked die (Kmec et al., M-Sequence based single chip UWB-radar sensor. ANTEM/AMEREM 2010 Conference, Ottawa, 2010)], the packaged IC is intended for use up to 8 GHz. Finally, the discussed transceiver is a further development of the mother SiGe System-on-Chip (SoC) presented in the work cited above.

  10. 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.

  11. The model JSR-12 neutron coincidence analyzer

    International Nuclear Information System (INIS)

    This paper reports that one of the ways in which non-destructive assays for nuclear materials is made involved counting the neutron signatures which result from spontaneous or induced fissions in fissile materials. A major problem in determining the number of fission neutrons is trying to separate them from the background of neutrons arising from alpha particle interactions with lighter nuclei in the matrix materials of the samples being assayed. The JSR-12 neutron coincidence analyzer operates on the principle that fission neutrons occur in multiples of two or more, whereas background neutrons occur randomly as single events. By exploiting this time correlation difference, the JSR-12 can determine the fission neutron signal. This instrument represents a considerable upgrade from the industry standard JSR-11, by doubling the response speed and adding complete computer control of all functions, as well as employing non-volatile memory for data storage. Operation has been simplified for field use by using an LCD display to guide the operator in setting up assay parameters, and by time-date tagging all assays for later retrieval

  12. Analyzing Design Heating Loads in Superinsulated Buildings

    Energy Technology Data Exchange (ETDEWEB)

    Arena, Lois [Consortium for Advanced Residential Buildings, Norwalk, CT (United States)

    2015-06-16

    The U.S. Department of Energy’s Building America research team Consortium for Advanced Residential Buildings (CARB) worked with the EcoVillage cohousing community in Ithaca, New York, on the Third Residential EcoVillage Experience neighborhood. This communityscale project consists of 40 housing units—15 apartments and 25 single-family residences. Units range in size from 450 ft2 to 1,664 ft2 and cost from $80,000 for a studio apartment to $235,000 for a three- or four-bedroom single-family home. For the research component of this project, CARB analyzed current heating system sizing methods for superinsulated homes in cold climates to determine if changes in building load calculation methodology should be recommended. Actual heating energy use was monitored and compared to results from the Air Conditioning Contractors of America’s Manual J8 (MJ8) and the Passive House Planning Package software. Results from that research indicate that MJ8 significantly oversizes heating systems for superinsulated homes and that thermal inertia and internal gains should be considered for more accurate load calculations.

  13. NRC plant-analyzer development at BNL

    International Nuclear Information System (INIS)

    The objective of this program is to develop an LWR engineering plant analyzer capable of performing realistic and accurate simulations of plant transients and Small-Break Loss of Coolant Accidents at real-time and faster than real-time computing speeds and at low costs for preparing, executing and evaluating such simulations. The program is directed toward facilitating reactor safety analyses, on-line plant monitoring, on-line accident diagnosis and mitigation and toward improving reactor operator training. The AD10 of Applied Dynamics International, Ann Arbor, MI, a special-purpose peripheral processor for high-speed systems simulation, is programmed through a PDP-11/34 minicomputer and carries out digital simulations with analog hardware in the input/output loop (up to 256 channels). Analog signals from a control panel are being used now to activate or to disable valves and to trip pump drive motors or regulators without interrupting the simulation. An IBM personal computer with multicolor graphics capabilities and a CRT monitor are used to produce on-line labelled diagrams of selected plant parameters as functions of time

  14. Qualitative Methodology in Analyzing Educational Phenomena

    Directory of Open Access Journals (Sweden)

    Antonio SANDU

    2010-12-01

    Full Text Available Semiological analysis of educational phenomena allow researchers access to a multidimensional universe of meanings that is represented by the school, not so much seen as an institution, but as a vector of social action through educational strategies. We consider education as a multidimensional phenomenon since its analysis allows the researcher to explore a variety of research hypotheses of different paradigmatic perspectives that converge in an educational finality. According to the author Simona Branc one of the most appropriate methods used in qualitative data analysis is Grounded Theory; this one assumes a systematic process of generating concepts and theories based on the data collected. Specialised literature defines Grounded Theory as an inductive approach that starts with general observations and during the analytical process creates conceptual categories that explain the theme explored. Research insist on the role of the sociologic theory of managing the research data and for providing ways of conceptualizing the descriptions and explanations.Qualitative content analysis is based on the constructivist paradigm (constructionist in the restricted sense that we used previously. It aims to create an “understanding of the latent meanings of the analyzed messages”. Quantitative content analysis involves a process of encoding and statistical analysis of data extracted from the content of the paper in the form of extractions like: frequencies, contingency analysis, etc

  15. Analyzing Spatiotemporal Anomalies through Interactive Visualization

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    2014-06-01

    Full Text Available As we move into the big data era, data grows not just in size, but also in complexity, containing a rich set of attributes, including location and time information, such as data from mobile devices (e.g., smart phones, natural disasters (e.g., earthquake and hurricane, epidemic spread, etc. We are motivated by the rising challenge and build a visualization tool for exploring generic spatiotemporal data, i.e., records containing time location information and numeric attribute values. Since the values often evolve over time and across geographic regions, we are particularly interested in detecting and analyzing the anomalous changes over time/space. Our analytic tool is based on geographic information system and is combined with spatiotemporal data mining algorithms, as well as various data visualization techniques, such as anomaly grids and anomaly bars superimposed on the map. We study how effective the tool may guide users to find potential anomalies through demonstrating and evaluating over publicly available spatiotemporal datasets. The tool for spatiotemporal anomaly analysis and visualization is useful in many domains, such as security investigation and monitoring, situation awareness, etc.

  16. Signal processing and analyzing works of art

    Science.gov (United States)

    Johnson, Don H.; Johnson, C. Richard, Jr.; Hendriks, Ella

    2010-08-01

    In examining paintings, art historians use a wide variety of physico-chemical methods to determine, for example, the paints, the ground (canvas primer) and any underdrawing the artist used. However, the art world has been little touched by signal processing algorithms. Our work develops algorithms to examine x-ray images of paintings, not to analyze the artist's brushstrokes but to characterize the weave of the canvas that supports the painting. The physics of radiography indicates that linear processing of the x-rays is most appropriate. Our spectral analysis algorithms have an accuracy superior to human spot-measurements and have the advantage that, through "short-space" Fourier analysis, they can be readily applied to entire x-rays. We have found that variations in the manufacturing process create a unique pattern of horizontal and vertical thread density variations in the bolts of canvas produced. In addition, we measure the thread angles, providing a way to determine the presence of cusping and to infer the location of the tacks used to stretch the canvas on a frame during the priming process. We have developed weave matching software that employs a new correlation measure to find paintings that share canvas weave characteristics. Using a corpus of over 290 paintings attributed to Vincent van Gogh, we have found several weave match cliques that we believe will refine the art historical record and provide more insight into the artist's creative processes.

  17. Analyzing modified unimodular gravity via Lagrange multipliers

    Science.gov (United States)

    Sáez-Gómez, Diego

    2016-06-01

    The so-called unimodular version of general relativity is revisited. Unimodular gravity is constructed by fixing the determinant of the metric, which leads to the trace-free part of the equations instead of the usual Einstein field equations. Then a cosmological constant naturally arises as an integration constant. While unimodular gravity turns out to be equivalent to general relativity (GR) at the classical level, it provides important differences at the quantum level. Here we extend the unimodular constraint to some extensions of general relativity that have drawn a lot of attention over the last years—f (R ) gravity (or its scalar-tensor picture) and Gauss-Bonnet gravity. The corresponding unimodular version of such theories is constructed as well as the conformal transformation that relates the Einstein and Jordan frames for these nonminimally coupled theories. From the classical point of view, the unimodular versions of such extensions are completely equivalent to their originals, but an effective cosmological constant arises naturally, which may provide a richer description of the evolution of the Universe. Here we analyze the case of Starobisnky inflation and compare it with the original one.

  18. 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 found defects which may cause their fracture. These defects are totally included in the prostheses material and can not be vizualised with other imagistic methods. In conclusion, en-face OCT is an important investigative tool for the dental practice.

  19. Analyzing Contents of a Computer Cache

    Science.gov (United States)

    Beahan, John; Khanoyan, Garen; Some, Raphael; Callum, Leslie

    2004-01-01

    The Cache Contents Estimator (CCE) is a computer program that provides information on the contents of level-1 cache of a PowerPC computer. The CCE is configurable to enable simulation of any processor in the PowerPC family. The need for CCE arises because the contents of level-1 caches are not available to either hardware or software readout mechanisms, yet information on the contents is crucial in the development of fault-tolerant or highly available computing systems and for realistic modeling and prediction of computing- system performance. The CCE comprises two independent subprograms: (1) the Dynamic Application Address eXtractor (DAAX), which extracts the stream of address references from an application program undergoing execution and (2) the Cache Simulator (CacheSim), which models the level-1 cache of the processor to be analyzed, by mimicking what the cache controller would do, in response to the address stream from DAAX. CacheSim generates a running estimate of the contents of the data and the instruction subcaches of the level-1 cache, hit/miss ratios, the percentage of cache that contains valid or active data, and time-stamped histograms of the cache content.

  20. Analyzing Consumer Behavior Towards Contemporary Food Retailers

    Directory of Open Access Journals (Sweden)

    E.Dursun

    2008-01-01

    Full Text Available The objective of this research is analyzing consumer behaviors towards to contemporary food retailers. Food retailing has been changing during recent years in Turkey. Foreign investors captivated with this market potential of food retailing. Retailer‟s format has been changed and featuring large-scale, extended product variety and full service retailers spreading rapidly through the nation-wide. Consumers‟ tend to shop their household needs from contemporary retailers due mainly to urbanism, increasing women workforce and income growth. In this research, original data collected through face-to-face interview from 385 respondents which are located in Istanbul. Different Socio-Economic Status (SES groups‟ ratio for Istanbul was forming sampling distribution. Consumers prefer closest food retailers which are mainly purchasing food products. Consumers purchase more than their planned what their needs; especially C SES group average comes first for the spending money for unplanned shopping. Chain stores and hypermarkets are the most preferred retailers in food purchasing. Moreover, consumer responses to judgments related to retailing are being investigating with factor analysis.