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Sample records for interaction analysis involving

  1. Weak interactions involving organic fluorine: analysis of structural motifs in Flunazirine and Haloperidol

    Science.gov (United States)

    Prasanna, M. D.; Row, T. N. Guru

    2001-05-01

    The crystal structure of Flunazirine, an anticonvulsant drug, is analyzed in terms of intermolecular interactions involving fluorine. The structure displays motifs formed by only weak interactions C-H⋯F and C-H⋯π. The motifs thus generated show cavities, which could serve as hosts for complexation. The structure of Flunazirine displays cavities formed by C-H⋯F and C-H⋯π interactions. Haloperidol, an antipsychotic drug, shows F⋯F interactions in the crystalline lattice in lieu of Cl⋯Cl interactions. However, strong O-H⋯N interactions dominate packing. The salient features of the two structures in terms of intermolecular interactions reveal, even though organic fluorine has lower tendency to engage in hydrogen bonding and F⋯F interactions, these interactions could play a significant role in the design of molecular assemblies via crystal engineering.

  2. Modelization of nanospace interaction involving a ferromagnetic atom: a spin polarization effect study by thermogravimetric analysis.

    Science.gov (United States)

    Santhanam, K S V; Chen, Xu; Gupta, S

    2014-04-01

    Ab initio studies of ferromagnetic atom interacting with carbon nanotubes have been reported in the literature that predict when the interaction is strong, a higher hybridization with confinement effect will result in spin polarization in the ferromagnetic atom. The spin polarization effect on the thermal oxidation to form its oxide is modeled here for the ferromagnetic atom and its alloy, as the above studies predict the 4s electrons are polarized in the atom. The four models developed here provide a pathway for distinguishing the type of interaction that exists in the real system. The extent of spin polarization in the ferromagnetic atom has been examined by varying the amount of carbon nanotubes in the composites in the thermogravimetric experiments. In this study we report the experimental results on the CoNi alloy which appears to show selective spin polarization. The products of the thermal oxidation has been analyzed by Fourier Transform Infrared Spectroscopy.

  3. Structural analysis of pyridine-imino boronic esters involving secondary interactions on solid state

    Science.gov (United States)

    Sánchez-Portillo, Paola; Arenaza-Corona, Antonino; Hernández-Ahuactzi, Irán F.; Barba, Victor

    2017-04-01

    Twelve boronic esters (1a-1l) synthesized from 4-halo- substituted arylboronic acids (halo = F, Cl, Br, I and CF3) with 2-amino-2- alkyl (H, Me) -1,3-propanediol in presence of (3- or 4)-pyridine carboxaldehyde are described. A solvent mixture toluene/methanol 1:4 ratio was used. All compounds include both donor/acceptor functional groups, which are the necessary elements to self-assembly of the molecular species. Several secondary interactions as I⋯N, Br⋯Br, Br⋯B, F⋯B, Csbnd H⋯N, Csbnd H⋯O, Br⋯π and Csbnd H⋯π support the 1D and 2D polymeric frameworks in solid state. The coordination of the nitrogen atom from the pyridine moiety with the boron atom was not observed in either solution or solid state.

  4. Analysis of the RelA:CBP/p300 interaction reveals its involvement in NF-κB-driven transcription.

    Science.gov (United States)

    Mukherjee, Sulakshana P; Behar, Marcelo; Birnbaum, Harry A; Hoffmann, Alexander; Wright, Peter E; Ghosh, Gourisankar

    2013-09-01

    NF-κB plays a vital role in cellular immune and inflammatory response, survival, and proliferation by regulating the transcription of various genes involved in these processes. To activate transcription, RelA (a prominent NF-κB family member) interacts with transcriptional co-activators like CREB-binding protein (CBP) and its paralog p300 in addition to its cognate κB sites on the promoter/enhancer regions of DNA. The RelA:CBP/p300 complex is comprised of two components--first, DNA binding domain of RelA interacts with the KIX domain of CBP/p300, and second, the transcriptional activation domain (TAD) of RelA binds to the TAZ1 domain of CBP/p300. A phosphorylation event of a well-conserved RelA(Ser276) is prerequisite for the former interaction to occur and is considered a decisive factor for the overall RelA:CBP/p300 interaction. The role of the latter interaction in the transcription of RelA-activated genes remains unclear. Here we provide the solution structure of the latter component of the RelA:CBP complex by NMR spectroscopy. The structure reveals the folding of RelA-TA2 (a section of TAD) upon binding to TAZ1 through its well-conserved hydrophobic sites in a series of grooves on the TAZ1 surface. The structural analysis coupled with the mechanistic studies by mutational and isothermal calorimetric analyses allowed the design of RelA-mutants that selectively abrogated the two distinct components of the RelA:CBP/p300 interaction. Detailed studies of these RelA mutants using cell-based techniques, mathematical modeling, and genome-wide gene expression analysis showed that a major set of the RelA-activated genes, larger than previously believed, is affected by this interaction. We further show how the RelA:CBP/p300 interaction controls the nuclear response of NF-κB through the negative feedback loop of NF-κB pathway. Additionally, chromatin analyses of RelA target gene promoters showed constitutive recruitment of CBP/p300, thus indicating a possible role of

  5. Analysis of the RelA:CBP/p300 interaction reveals its involvement in NF-κB-driven transcription.

    Directory of Open Access Journals (Sweden)

    Sulakshana P Mukherjee

    2013-09-01

    Full Text Available NF-κB plays a vital role in cellular immune and inflammatory response, survival, and proliferation by regulating the transcription of various genes involved in these processes. To activate transcription, RelA (a prominent NF-κB family member interacts with transcriptional co-activators like CREB-binding protein (CBP and its paralog p300 in addition to its cognate κB sites on the promoter/enhancer regions of DNA. The RelA:CBP/p300 complex is comprised of two components--first, DNA binding domain of RelA interacts with the KIX domain of CBP/p300, and second, the transcriptional activation domain (TAD of RelA binds to the TAZ1 domain of CBP/p300. A phosphorylation event of a well-conserved RelA(Ser276 is prerequisite for the former interaction to occur and is considered a decisive factor for the overall RelA:CBP/p300 interaction. The role of the latter interaction in the transcription of RelA-activated genes remains unclear. Here we provide the solution structure of the latter component of the RelA:CBP complex by NMR spectroscopy. The structure reveals the folding of RelA-TA2 (a section of TAD upon binding to TAZ1 through its well-conserved hydrophobic sites in a series of grooves on the TAZ1 surface. The structural analysis coupled with the mechanistic studies by mutational and isothermal calorimetric analyses allowed the design of RelA-mutants that selectively abrogated the two distinct components of the RelA:CBP/p300 interaction. Detailed studies of these RelA mutants using cell-based techniques, mathematical modeling, and genome-wide gene expression analysis showed that a major set of the RelA-activated genes, larger than previously believed, is affected by this interaction. We further show how the RelA:CBP/p300 interaction controls the nuclear response of NF-κB through the negative feedback loop of NF-κB pathway. Additionally, chromatin analyses of RelA target gene promoters showed constitutive recruitment of CBP/p300, thus indicating a

  6. Comparative genomic analysis reveals a diverse repertoire of genes involved in prokaryote-eukaryote interactions within the Pseudovibrio genus.

    Directory of Open Access Journals (Sweden)

    Stefano eRomano

    2016-03-01

    Full Text Available Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage.Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus.Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche

  7. Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus.

    Science.gov (United States)

    Romano, Stefano; Fernàndez-Guerra, Antonio; Reen, F Jerry; Glöckner, Frank O; Crowley, Susan P; O'Sullivan, Orla; Cotter, Paul D; Adams, Claire; Dobson, Alan D W; O'Gara, Fergal

    2016-01-01

    Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its

  8. Structural Analysis of the 14-3-3ζ/Chibby Interaction Involved in Wnt/β-Catenin Signaling.

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    Ryan C Killoran

    Full Text Available The partially disordered Chibby (Cby is a conserved nuclear protein that antagonizes the Wnt/β-catenin signaling pathway. By competing with the Tcf/Lef family proteins for binding to β-catenin, Cby abrogates the β-catenin-mediated transcription of Wnt signaling genes. Additionally, upon phosphorylation on S20 by the kinase Akt, Cby forms a complex with 14-3-3 to facilitate the nuclear export of β-catenin, which represents another crucial mechanism for the regulation of Wnt signaling. To obtain a mechanistic understanding of the 14-3-3/Cby interaction, we have extensively characterized the complex using X-ray crystallography, nuclear magnetic resonance (NMR spectroscopy, and isothermal titration calorimetry (ITC. The crystal structure of the human 14-3-3ζ/Cby protein-peptide complex reveals a canonical binding mode; however the residue at the +2 position from the phosphorylated serine is shown to be uniquely oriented relative to other solved structures of 14-3-3 complexes. Our ITC results illustrate that although the phosphorylation of S20 is essential for Cby to recognize 14-3-3, residues flanking the phosphorylation site also contribute to the binding affinity. However, as is commonly observed in other 14-3-3/phosphopeptide crystal structures, residues of Cby flanking the 14-3-3 binding motif lack observable electron density. To obtain a more detailed binding interface, we have completed the backbone NMR resonance assignment of 14-3-3ζ. NMR titration experiments reveal that residues outside of the 14-3-3 conserved binding cleft, namely a flexible loop consisting of residues 203-210, are also involved in binding Cby. By using a combined X-ray and NMR approach, we have dissected the molecular basis of the 14-3-3/Cby interaction.

  9. Proteomic analysis of cPKCβII-interacting proteins involved in HPC-induced neuroprotection against cerebral ischemia of mice.

    Science.gov (United States)

    Bu, Xiangning; Zhang, Nan; Yang, Xuan; Liu, Yanyan; Du, Jianli; Liang, Jing; Xu, Qunyuan; Li, Junfa

    2011-04-01

    Hypoxic preconditioning (HPC) initiates intracellular signaling pathway to provide protection against subsequent cerebral ischemic injuries, and its mechanism may provide molecular targets for therapy in stroke. According to our study of conventional protein kinase C βII (cPKCβII) activation in HPC, the role of cPKCβII in HPC-induced neuroprotection and its interacting proteins were determined in this study. The autohypoxia-induced HPC and middle cerebral artery occlusion (MCAO)-induced cerebral ischemia mouse models were prepared as reported. We found that HPC reduced 6 h MCAO-induced neurological deficits, infarct volume, edema ratio and cell apoptosis in peri-infarct region (penumbra), but cPKCβII inhibitors Go6983 and LY333531 blocked HPC-induced neuroprotection. Proteomic analysis revealed that the expression of four proteins in cytosol and eight proteins in particulate fraction changed significantly among 49 identified cPKCβII-interacting proteins in cortex of HPC mice. In addition, HPC could inhibit the decrease of phosphorylated collapsin response mediator protein-2 (CRMP-2) level and increase of CRMP-2 breakdown product. TAT-CRMP-2 peptide, which prevents the cleavage of endogenous CRMP-2, could inhibit CRMP-2 dephosphorylation and proteolysis as well as the infarct volume of 6 h MCAO mice. This study is the first to report multiple cPKCβII-interacting proteins in HPC mouse brain and the role of cPKCβII-CRMP-2 in HPC-induced neuroprotection against early stages of ischemic injuries in mice.

  10. Analysis of Cl…Cl and C-H…Cl intermolecular interactions involving chlorine in substituted 2-chloroquinoline derivatives

    Indian Academy of Sciences (India)

    Venkatesha R Hathwar; S Mohana Roopan; R Subashini; F Nawaz Khan; T N Guru Row

    2010-09-01

    Six crystal structures of substituted 2-chloroquinoline derivatives have been analysed to evaluate the role of Cl atom as a self recognizing unit resulting in the formation of Cl…Cl and C-H…Cl interactions to generate supramolecular assembly in the solid state. The features of Type I and Type II geometries associated with Cl…Cl interactions have been analysed to show directional preferences leading to differences in the packing motifs in these crystal structures. C-H…Cl interactions are generated exclusively in structures depicting Type II Cl…Cl interaction have been observed in these structures.

  11. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.;

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were...

  12. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were t...

  13. Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication.

    Directory of Open Access Journals (Sweden)

    Ji'an Pan

    Full Text Available Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12 provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins.

  14. Managing stakeholder involvement in decision-making : A comparative analysis of six interactive processes in The Netherlands

    NARCIS (Netherlands)

    J. Edelenbos (Jurian); E-H. Klijn (Erik-Hans)

    2006-01-01

    textabstractInitiatives to encourage and stimulate the involvement of citizens but also various societal organisations in decision-making can be seen in a wide variety of European countries. Citizens panels, citizens charters, new forms of participation and other forms are being used to increase the

  15. Managing stakeholder involvement in decision-making : A comparative analysis of six interactive processes in The Netherlands

    NARCIS (Netherlands)

    J. Edelenbos (Jurian); E-H. Klijn (Erik-Hans)

    2006-01-01

    textabstractInitiatives to encourage and stimulate the involvement of citizens but also various societal organisations in decision-making can be seen in a wide variety of European countries. Citizens panels, citizens charters, new forms of participation and other forms are being used to increase the

  16. Interaction Network among Escherichia coli Membrane Proteins Involved in Cell Division as Revealed by Bacterial Two-Hybrid Analysis

    OpenAIRE

    Karimova, Gouzel; Dautin, Nathalie; Ladant, Daniel

    2005-01-01

    Formation of the Escherichia coli division septum is catalyzed by a number of essential proteins (named Fts) that assemble into a ring-like structure at the future division site. Several of these Fts proteins are intrinsic transmembrane proteins whose functions are largely unknown. Although these proteins appear to be recruited to the division site in a hierarchical order, the molecular interactions underlying the assembly of the cell division machinery remain mostly unspecified. In the prese...

  17. Functional analysis of Abp1p-interacting proteins involved in endocytosis of the MCC component in Aspergillus oryzae.

    Science.gov (United States)

    Matsuo, Kento; Higuchi, Yujiro; Kikuma, Takashi; Arioka, Manabu; Kitamoto, Katsuhiko

    2013-07-01

    We have investigated the functions of three endocytosis-related proteins in the filamentous fungus Aspergillus oryzae. Yeast two-hybrid screening using the endocytic marker protein AoAbp1 (A.oryzae homolog of Saccharomyces cerevisiae Abp1p) as a bait identified four interacting proteins named Aip (AoAbp1 interacting proteins). In mature hyphae, EGFP (enhanced green fluorescent protein) fused to Aips colocalized with AoAbp1 at the hyphal tip region and the plasma membrane, suggesting that Aips function in endocytosis. aipA is a putative AAA ATPase and its function has been dissected (Higuchi et al., 2011). aipB, the homolog of A. nidulans myoA, encodes an essential class I myosin and its conditional mutant showed a germination defect. aipC and aipD do not contain any recognizable domains except some proline-rich regions which may interact with two SH3 (Src homology 3) domains of AoAbp1. Neither aipC nor aipD disruptants showed any defects in their growth, but the aipC disruptant formed less conidia compared with the control strain. In addition, the aipC disruptant was resistant to the triazole antifungal drugs that inhibit ergosterol biosynthesis. Although no aip disruptants showed any defects in the uptake of the fluorescent dye FM4-64, the endocytosis of the arginine permease AoCan1, one of the MCC (membrane compartment of Can1p) components, was delayed in both aipC and aipD disruptants. In A. oryzae, AoCan1 localized mainly at the plasma membrane in the basal region of hyphae, suggesting that different endocytic mechanisms exist in apical and basal regions of highly polarized cells.

  18. Learning models of activities involving interacting objects

    DEFF Research Database (Denmark)

    Manfredotti, Cristina; Pedersen, Kim Steenstrup; Hamilton, Howard J.;

    2013-01-01

    We propose the LEMAIO multi-layer framework, which makes use of hierarchical abstraction to learn models for activities involving multiple interacting objects from time sequences of data concerning the individual objects. Experiments in the sea navigation domain yielded learned models that were...... then successfully applied to activity recognition, activity simulation and multi-target tracking. Our method compares favourably with respect to previously reported results using Hidden Markov Models and Relational Particle Filtering....

  19. Proteomic analysis of ACTN4-interacting proteins reveals it's a putative involvement in mRNA metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Khotin, Mikhail, E-mail: h_mg@mail.ru [Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av., 4, 194064 St. Petersburg (Russian Federation); Turoverova, Lidia [Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av., 4, 194064 St. Petersburg (Russian Federation); Aksenova, Vasilisa [Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av., 4, 194064 St. Petersburg (Russian Federation); Department of Genetics, St. Petersburg State University, Universitetskaya nab., 7/9, 199034 St. Petersburg (Russian Federation); Barlev, Nikolai [Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av., 4, 194064 St. Petersburg (Russian Federation); Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN (United Kingdom); Borutinskaite, Veronika Viktorija [Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linkoeping University, SE-581 85 Linkoeping (Sweden); Department of Developmental Biology, Institute of Biochemistry, LT-08662 Vilnius (Lithuania); Vener, Alexander [Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linkoeping University, SE-581 85 Linkoeping (Sweden); Bajenova, Olga [Department of Genetics, St. Petersburg State University, Universitetskaya nab., 7/9, 199034 St. Petersburg (Russian Federation); Magnusson, Karl-Eric [Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linkoeping University, SE-581 85 Linkoeping (Sweden); Pinaev, George P. [Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av., 4, 194064 St. Petersburg (Russian Federation); Tentler, Dmitri, E-mail: dtentler@mail.cytspb.rssi.ru [Department of Cell Cultures, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky av., 4, 194064 St. Petersburg (Russian Federation)

    2010-06-25

    Alpha-actinin 4 (ACTN4) is an actin-binding protein. In the cytoplasm, ACTN4 participates in structural organisation of the cytoskeleton via cross-linking of actin filaments. Nuclear localisation of ACTN4 has also been reported, but no clear role in the nucleus has been established. In this report, we describe the identification of proteins associated with ACTN4 in the nucleus. A combination of two-dimensional gel electrophoresis (2D-GE) and MALDI-TOF mass-spectrometry revealed a large number of ACTN4-bound proteins that are involved in various aspects of mRNA processing and transport. The association of ACTN4 with different ribonucleoproteins suggests that a major function of nuclear ACTN4 may be regulation of mRNA metabolism and signaling.

  20. Single-cell Transcriptional Analysis Reveals Novel Neuronal Phenotypes and Interaction Networks involved In the Central Circadian Clock

    Directory of Open Access Journals (Sweden)

    James Park

    2016-10-01

    Full Text Available Single-cell heterogeneity confounds efforts to understand how a population of cells organizes into cellular networks that underlie tissue-level function. This complexity is prominent in the mammalian suprachiasmatic nucleus (SCN. Here, individual neurons exhibit a remarkable amount of asynchronous behavior and transcriptional heterogeneity. However, SCN neurons are able to generate precisely coordinated synaptic and molecular outputs that synchronize the body to a common circadian cycle by organizing into cellular networks. To understand this emergent cellular network property, it is important to reconcile single-neuron heterogeneity with network organization. In light of recent studies suggesting that transcriptionally heterogeneous cells organize into distinct cellular phenotypes, we characterized the transcriptional, spatial, and functional organization of 352 SCN neurons from mice experiencing phase-shifts in their circadian cycle. Using the community structure detection method and multivariate analytical techniques, we identified previously undescribed neuronal phenotypes that are likely to participate in regulatory networks with known SCN cell types. Based on the newly discovered neuronal phenotypes, we developed a data-driven neuronal network structure in which multiple cell types interact through known synaptic and paracrine signaling mechanisms. These results provide a basis from which to interpret the functional variability of SCN neurons and describe methodologies towards understanding how a population of heterogeneous single cells organizes into cellular networks that underlie tissue-level function.

  1. Coevolution of hosts and microorganisms: an analysis of the involvment of cytokines in host-parasite interactions

    Directory of Open Access Journals (Sweden)

    Owen Williams

    1992-01-01

    Full Text Available Parasites may employ particular strategies of eluding an immune response by taking advantage of those mechanisms that normally guarantee immunological self-tolerance. Much in the way as it occurs during the establishment of self-tolerance, live pathogens may induce clonal deletion, functional inactivation(anergy and immunosupression. At this latter level, it appears that certain pathogens produce immunosupresive cytokine-like mediators or provoke like host the secrete cytokines that will compromise the anti-parasite immune response. It appears that immune responses that preferentially involve T helper l cells (secretors of interleukin-2-and interferon-y tend to be protective, whereas T helper 2 cells (secretors of IL-4, IL5, IL-6, and IL-10, a population that antagonizes T helper cells, mediate disease susceptibility and are immunopathological reactions. Cytokines produced by T helper 2 cells mediate many symptoms of infection, including eosinophilia, mastocytosis, hyperimmunoglobulinemia, and elevated IgE levels. Administration of IL-2 and IFN-y has beneficial effects in many infections mediated by viruses, bacteria, and protozoa. The use of live vaccinia virus might be an avenue for the treatment of or vaccination against infection. We have found that a vaccinia virus expressing the gene for human IL-2, though attenuated, precipitates autoimmune disease in immunodeficient athymic mice. Thus, although T helper l cytokines may have desired immunostimulatory properties, they also may lead to unwarranted autoaggressive responses.

  2. Comparative Transcriptome Analysis of Adipose Tissues Reveals that ECM-Receptor Interaction Is Involved in the Depot-Specific Adipogenesis in Cattle.

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    Hyun-Jeong Lee

    Full Text Available Adipocytes mainly function as energy storage and endocrine cells. Adipose tissues showed the biological and genetic difference based on their depots. The difference of adipocytes between depots might be influenced by the inherent genetic programing for adipogenesis. We used RNA-seq technique to investigate the transcriptomes in 3 adipose tissues of omental (O, subcutaneous (S and intramuscular (I fats in cattle. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the bovine genome using Tophat2. Differentially expressed genes (DEG between adipose tissues were detected by EdgeR. We identified 5797, 2156, and 5455 DEGs in the comparison between OI, OS, and IS respectively and also found 5657 DEGs in the comparison between the intramuscular and the combined omental and subcutaneous fats (C (FDR<0.01. Depot specifically up- and down- regulated DEGs were 853 in S, 48 in I, and 979 in O. The numbers of DEGs and functional annotation studies suggested that I had the different genetic profile compared to other two adipose tissues. In I, DEGs involved in the developmental process (eg. EGR2, FAS, and KLF7 were up-regulated and those in the immune system process were down-regulated. Many DEGs from the adipose tissues were enriched in the various GO terms of developmental process and KEGG pathway analysis showed that the ECM-receptor interaction was one of commonly enriched pathways in all of the 3 adipose tissues and also functioned as a sub-pathway of other enriched pathways. However, genes involved in the ECM-receptor interaction were differentially regulated depending on the depots. Collagens, main ECM constituents, were significantly up-regulated in S and integrins, transmembrane receptors, were up-regulated in I. Different laminins were up-regulated in the different depots. This comparative transcriptome analysis of three adipose tissues suggested that the interactions between ECM components and transmembrane receptors of fat cells

  3. Interactive methods to involve users into workspace design process

    DEFF Research Database (Denmark)

    Souza da Conceição, Carolina; Broberg, Ole; Banke, Palle

    2013-01-01

    This paper addresses the question of whether the use of a combination of interactive methods involving workers can lead to a useful input to the (re)design of their workspace. The workbook and the layout design game methods were tested, and a comparison between their use and the ergonomic analysis...

  4. Proteomic analysis of wild-type and mutant huntingtin-associated proteins in mouse brains identifies unique interactions and involvement in protein synthesis.

    Science.gov (United States)

    Culver, Brady P; Savas, Jeffrey N; Park, Sung K; Choi, Jeong H; Zheng, Shuqiu; Zeitlin, Scott O; Yates, John R; Tanese, Naoko

    2012-06-22

    Huntington disease is a neurodegenerative disorder caused by a CAG repeat amplification in the gene huntingtin (HTT) that is reflected by a polyglutamine expansion in the Htt protein. Nearly 20 years of research have uncovered roles for Htt in a wide range of cellular processes, and many of these discoveries stemmed from the identification of Htt-interacting proteins. However, no study has employed an impartial and comprehensive strategy to identify proteins that differentially associate with full-length wild-type and mutant Htt in brain tissue, the most relevant sample source to the disease condition. We analyzed Htt affinity-purified complexes from wild-type and HTT mutant juvenile mouse brain from two different biochemical fractions by tandem mass spectrometry. We compared variations in protein spectral counts relative to Htt to identify those proteins that are the most significantly contrasted between wild-type and mutant Htt purifications. Previously unreported Htt interactions with Myo5a, Prkra (PACT), Gnb2l1 (RACK1), Rps6, and Syt2 were confirmed by Western blot analysis. Gene Ontology analysis of these and other Htt-associated proteins revealed a statistically significant enrichment for proteins involved in translation among other categories. Furthermore, Htt co-sedimentation with polysomes in cytoplasmic mouse brain extracts is dependent upon the presence of intact ribosomes. Finally, wild-type or mutant Htt overexpression inhibits cap-dependent translation of a reporter mRNA in an in vitro system. Cumulatively, these data support a new role for Htt in translation and provide impetus for further study into the link between protein synthesis and Huntington disease pathogenesis.

  5. Quantifying Engagement: Measuring Player Involvement in Human-Avatar Interactions.

    Science.gov (United States)

    Norris, Anne E; Weger, Harry; Bullinger, Cory; Bowers, Alyssa

    2014-05-01

    This research investigated the merits of using an established system for rating behavioral cues of involvement in human dyadic interactions (i.e., face-to-face conversation) to measure involvement in human-avatar interactions. Gameplay audio-video and self-report data from a Feasibility Trial and Free Choice study of an effective peer resistance skill building simulation game (DRAMA-RAMA™) were used to evaluate reliability and validity of the rating system when applied to human-avatar interactions. The Free Choice study used a revised game prototype that was altered to be more engaging. Both studies involved girls enrolled in a public middle school in Central Florida that served a predominately Hispanic (greater than 80%), low-income student population. Audio-video data were coded by two raters, trained in the rating system. Self-report data were generated using measures of perceived realism, predictability and flow administered immediately after game play. Hypotheses for reliability and validity were supported: Reliability values mirrored those found in the human dyadic interaction literature. Validity was supported by factor analysis, significantly higher levels of involvement in Free Choice as compared to Feasibility Trial players, and correlations between involvement dimension sub scores and self-report measures. Results have implications for the science of both skill-training intervention research and game design.

  6. A Scoping Analysis Of The Impact Of SiC Cladding On Late-Phase Accident Progression Involving Core–Concrete Interaction

    Energy Technology Data Exchange (ETDEWEB)

    Farmer, M. T. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-11-01

    The overall objective of the current work is to carry out a scoping analysis to determine the impact of ATF on late phase accident progression; in particular, the molten core-concrete interaction portion of the sequence that occurs after the core debris fails the reactor vessel and relocates into containment. This additional study augments previous work by including kinetic effects that govern chemical reaction rates during core-concrete interaction. The specific ATF considered as part of this study is SiC-clad UO2.

  7. Proteomic analysis of Fasciola hepatica excretory and secretory products (FhESPs) involved in interacting with host PBMCs and cytokines by shotgun LC-MS/MS.

    Science.gov (United States)

    Liu, Qing; Huang, Si-Yang; Yue, Dong-Mei; Wang, Jin-Lei; Wang, Yujian; Li, Xiangrui; Zhu, Xing-Quan

    2017-02-01

    Fasciola hepatica is a helminth parasite with a worldwide distribution, which can cause chronic liver disease, fasciolosis, leading to economic losses in the livestock and public health in many countries. Control is mostly reliant on the use of drugs, and as a result, drug resistance has now emerged. The identification of F. hepatica genes involved in interaction between the parasite and host immune system is utmost important to elucidate the evasion mechanisms of the parasite and develop more effective strategies against fasciolosis. In this study, we aimed to identify molecules in F. hepatica excretory and secretory products (FhESPs) interacting with the host peripheral blood mononuclear cells (PBMCs), Th1-like cytokines (IL2 and IFN-γ), and Th17-like cytokines (IL17) by Co-IP combined with tandem mass spectrometry. The results showed that 14, 16, and 9 proteins in FhESPs could bind with IL2, IL17, and IFN-γ, respectively, which indicated that adult F. hepatica may evade the host immune responses through directly interplaying with cytokines. In addition, nine proteins in FhESPs could adhere to PBMCs. Our findings provided potential targets as immuno-regulators, and will be helpful to elucidate the molecular basis of host-parasite interactions and search for new potential proteins as vaccine and drug target candidates.

  8. Interaction Involvement: A Fundamental Dimension of Interpersonal Communication Competence.

    Science.gov (United States)

    Cegala, Donald J.

    E. Husserl's concept of intentionality provides a conceptual perspective of interpersonal communication that suggests a notion of face-to-face communication called "interaction involvement." Structured along dimensions of awareness and responsiveness, interaction involvement explains interpersonal communication as a transactional relationship…

  9. Involving Collaborative Interaction in EFL Classroom from Sociocultural Perspective

    Institute of Scientific and Technical Information of China (English)

    李艺

    2016-01-01

    According to Vygotsky's theory of sociocultural theory (SCT), language use, classroom activity, and classroom structure are the primary means of mediation. In English as a Foreign Language (EFL) classroom, SCT provides a framework for teachers to involve collaborative interaction and constructive classroom approaches to support students ' development. By involving collaborative interaction, language teachers use it as a tool to reform the teaching mode, stimulating students ' potential ability, and assessing the improvement in students' learning experience.

  10. Analysis of protein-protein interactions involved in the activation of the Shc/Grb-2 pathway by the ErbB-2 kinase.

    Science.gov (United States)

    Ricci, A; Lanfrancone, L; Chiari, R; Belardo, G; Pertica, C; Natali, P G; Pelicci, P G; Segatto, O

    1995-10-19

    In murine fibroblasts activation of the Shc/Grb-2 pathway by the ErbB-2 kinase involves tyrosine phosphorylation of Shc products and the formation of Shc/ErbB-2, Shc/Grb-2 and Grb-2/ErbB-2 complexes. Tyr 1139 of ErbB-2 bound to the Grb-2 SH2 domain in vitro as well as in intact cells. Tyr 1221 and 1248 are binding sites of gp185ErbB-2 for Shc SH2 domain in vitro whereas Tyr 1196 and 1248 are major binding sites of ErbB-2 for Shc PTB domain. Inhibition of Shc/ErbB-2 complex formation in intact cells was obtained by simultaneous mutational inactivation of Shc SH2 and Shc PTB binding sites of gp185ErbB-2. Shc/ErbB-2 complexes are formed upon activation of the ErbB-2 kinase and tyrosine phosphorylation of Shc proteins; they are located in both cytosol and cellular membranes. ErbB-2 activation induces also translocation of Grb-2 from cytosol to membranes. This network of protein-protein interactions may reflect the ability of the Shc/Grb-2 pathway to act as a molecular switch controlling different cellular functions regulated by RTK activation. In fact the Ras GDP exchanger mSOS was recruited in Grb-2/ErbB-2 complexes; furthermore besides mSOS, other polypeptides present in either cytosolic or membrane preparations were able to complex in vitro with Grb-2 SH3 domains.

  11. SM2PH-db: an interactive system for the integrated analysis of phenotypic consequences of missense mutations in proteins involved in human genetic diseases.

    Science.gov (United States)

    Friedrich, Anne; Garnier, Nicolas; Gagnière, Nicolas; Nguyen, Hoan; Albou, Laurent-Philippe; Biancalana, Valérie; Bettler, Emmanuel; Deléage, Gilbert; Lecompte, Odile; Muller, Jean; Moras, Dino; Mandel, Jean-Louis; Toursel, Thierry; Moulinier, Luc; Poch, Olivier

    2010-02-01

    Understanding how genetic alterations affect gene products at the molecular level represents a first step in the elucidation of the complex relationships between genotypic and phenotypic variations, and is thus a major challenge in the postgenomic era. Here, we present SM2PH-db (http://decrypthon.igbmc.fr/sm2ph), a new database designed to investigate structural and functional impacts of missense mutations and their phenotypic effects in the context of human genetic diseases. A wealth of up-to-date interconnected information is provided for each of the 2,249 disease-related entry proteins (August 2009), including data retrieved from biological databases and data generated from a Sequence-Structure-Evolution Inference in Systems-based approach, such as multiple alignments, three-dimensional structural models, and multidimensional (physicochemical, functional, structural, and evolutionary) characterizations of mutations. SM2PH-db provides a robust infrastructure associated with interactive analysis tools supporting in-depth study and interpretation of the molecular consequences of mutations, with the more long-term goal of elucidating the chain of events leading from a molecular defect to its pathology. The entire content of SM2PH-db is regularly and automatically updated thanks to a computational grid data federation facilities provided in the context of the Decrypthon program.

  12. Involving Collaborative Interaction in EFL Classroom from Sociocultural Perspective

    Institute of Scientific and Technical Information of China (English)

    李艺

    2016-01-01

    According to Vygotsky's theory of sociocultural theory(SCT),language use,classroom activity,and classroom structure are the primary means of mediation.In English as a Foreign Language(EFL)classroom,SCT provides a framework for teachers to involve collaborative interaction and constructive classroom approaches to support students'development.By involving collaborative interaction,language teachers use it as a tool to reform the teaching mode,stimulating students'potential ability,and assessing the improvement in students'learning experience.

  13. Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions.

    Science.gov (United States)

    Mangiola, Stefano; Young, Neil D; Sternberg, Paul W; Strube, Christina; Korhonen, Pasi K; Mitreva, Makedonka; Scheerlinck, Jean-Pierre; Hofmann, Andreas; Jex, Aaron R; Gasser, Robin B

    2014-03-01

    Parasitic nematodes cause diseases of major economic importance in animals. Key representatives are species of Dictyocaulus (=lungworms), which cause bronchitis (=dictyocaulosis, commonly known as "husk") and have a major adverse impact on the health of livestock. In spite of their economic importance, very little is known about the immunomolecular biology of these parasites. Here, we conducted a comprehensive investigation of the adult transcriptome of Dictyocaulus filaria of small ruminants and compared it with that of Dictyocaulus viviparus of bovids. We then identified a subset of highly transcribed molecules inferred to be linked to host-parasite interactions, including cathepsin B peptidases, fatty-acid and/or retinol-binding proteins, β-galactoside-binding galectins, secreted protein 6 precursors, macrophage migration inhibitory factors, glutathione peroxidases, a transthyretin-like protein and a type 2-like cystatin. We then studied homologues of D. filaria type 2-like cystatin encoded in D. viviparus and 24 other nematodes representing seven distinct taxonomic orders, with a particular focus on their proposed role in immunomodulation and/or metabolism. Taken together, the present study provides new insights into nematode-host interactions. The findings lay the foundation for future experimental studies and could have implications for designing new interventions against lungworms and other parasitic nematodes. The future characterisation of the genomes of Dictyocaulus spp. should underpin these endeavours.

  14. Modeling supercritical fluid extraction process involving solute-solid interaction

    Energy Technology Data Exchange (ETDEWEB)

    Goto, M.; Roy, B. Kodama, A.; Hirose, T. [Kumamoto Univ., Kumamoto (Japan)

    1998-04-01

    Extraction or leaching of solute from natural solid material is a mass transfer process involving dissolution or release of solutes from a solid matrix. Interaction between the solute and solid matrix often influences the supercritical fluid extraction process. A model accounting for the solute-solid interaction as well as mass transfer is developed. The BET equation is used to incorporate the interaction and the solubility of solutes into the local equilibrium in the model. Experimental data for the supercritical extraction of essential oil and cuticular wax from peppermint leaves are successfully analyzed by the model. The effects of parameters on the extraction behavior are demonstrated to illustrate the concept of the model. 18 refs., 5 figs., 1 tab.

  15. The role of father involvement and dyadic interactions in the development of family interactive abilities: a multilevel approach.

    Directory of Open Access Journals (Sweden)

    Alessandra Simonelli

    2016-11-01

    Full Text Available The present study aims to investigate, using multilevel analysis, the development of family interactions from pregnancy to preschool age, in a longitudinal perspective. Moreover, it intends to explore the impact of couple relationship and father involvement in childcare on the developmental trend of the quality of mother-father-child interactions.103 primiparous families were assessed at 7th month of pregnancy, 4th, 9th, 18th months of child’s life and during preschool age (36-48th, using the observational procedure named Lausanne Trilogue Play. Parents’ perception of marital satisfaction was assessed with the Dyadic Adjustment Scale at each point of measure; moreover, in the postnatal assessment parents completed the Father Involvement Questionnaire. Results showed that family interactions increase over time. Second, a decrease of marital adjustment is associated to an improvement of the quality of family interactions. Moreover, father involvement predicts the quality of family interactions from the earliest stages of child’s life.In a longitudinal perspective, family interactions and marital quality show opposite developmental trends and father’s involvement represents a particularly important feature of the family.

  16. INCA- INTERACTIVE CONTROLS ANALYSIS

    Science.gov (United States)

    Bauer, F. H.

    1994-01-01

    The Interactive Controls Analysis (INCA) program was developed to provide a user friendly environment for the design and analysis of linear control systems, primarily feedback control systems. INCA is designed for use with both small and large order systems. Using the interactive graphics capability, the INCA user can quickly plot a root locus, frequency response, or time response of either a continuous time system or a sampled data system. The system configuration and parameters can be easily changed, allowing the INCA user to design compensation networks and perform sensitivity analysis in a very convenient manner. A journal file capability is included. This stores an entire sequence of commands, generated during an INCA session into a file which can be accessed later. Also included in INCA are a context-sensitive help library, a screen editor, and plot windows. INCA is robust to VAX-specific overflow problems. The transfer function is the basic unit of INCA. Transfer functions are automatically saved and are available to the INCA user at any time. A powerful, user friendly transfer function manipulation and editing capability is built into the INCA program. The user can do all transfer function manipulations and plotting without leaving INCA, although provisions are made to input transfer functions from data files. By using a small set of commands, the user may compute and edit transfer functions, and then examine these functions by using the ROOT_LOCUS, FREQUENCY_RESPONSE, and TIME_RESPONSE capabilities. Basic input data, including gains, are handled as single-input single-output transfer functions. These functions can be developed using the function editor or by using FORTRAN- like arithmetic expressions. In addition to the arithmetic functions, special functions are available to 1) compute step, ramp, and sinusoid functions, 2) compute closed loop transfer functions, 3) convert from S plane to Z plane with optional advanced Z transform, and 4) convert from Z

  17. INCA- INTERACTIVE CONTROLS ANALYSIS

    Science.gov (United States)

    Bauer, F. H.

    1994-01-01

    The Interactive Controls Analysis (INCA) program was developed to provide a user friendly environment for the design and analysis of linear control systems, primarily feedback control systems. INCA is designed for use with both small and large order systems. Using the interactive graphics capability, the INCA user can quickly plot a root locus, frequency response, or time response of either a continuous time system or a sampled data system. The system configuration and parameters can be easily changed, allowing the INCA user to design compensation networks and perform sensitivity analysis in a very convenient manner. A journal file capability is included. This stores an entire sequence of commands, generated during an INCA session into a file which can be accessed later. Also included in INCA are a context-sensitive help library, a screen editor, and plot windows. INCA is robust to VAX-specific overflow problems. The transfer function is the basic unit of INCA. Transfer functions are automatically saved and are available to the INCA user at any time. A powerful, user friendly transfer function manipulation and editing capability is built into the INCA program. The user can do all transfer function manipulations and plotting without leaving INCA, although provisions are made to input transfer functions from data files. By using a small set of commands, the user may compute and edit transfer functions, and then examine these functions by using the ROOT_LOCUS, FREQUENCY_RESPONSE, and TIME_RESPONSE capabilities. Basic input data, including gains, are handled as single-input single-output transfer functions. These functions can be developed using the function editor or by using FORTRAN- like arithmetic expressions. In addition to the arithmetic functions, special functions are available to 1) compute step, ramp, and sinusoid functions, 2) compute closed loop transfer functions, 3) convert from S plane to Z plane with optional advanced Z transform, and 4) convert from Z

  18. An analysis of aircraft accidents involving fires

    Science.gov (United States)

    Lucha, G. V.; Robertson, M. A.; Schooley, F. A.

    1975-01-01

    All U. S. Air Carrier accidents between 1963 and 1974 were studied to assess the extent of total personnel and aircraft damage which occurred in accidents and in accidents involving fire. Published accident reports and NTSB investigators' factual backup files were the primary sources of data. Although it was frequently not possible to assess the relative extent of fire-caused damage versus impact damage using the available data, the study established upper and lower bounds for deaths and damage due specifically to fire. In 12 years there were 122 accidents which involved airframe fires. Eighty-seven percent of the fires occurred after impact, and fuel leakage from ruptured tanks or severed lines was the most frequently cited cause. A cost analysis was performed for 300 serious accidents, including 92 serious accidents which involved fire. Personal injury costs were outside the scope of the cost analysis, but data on personnel injury judgements as well as settlements received from the CAB are included for reference.

  19. Interactive Controls Analysis (INCA)

    Science.gov (United States)

    Bauer, Frank H.

    1989-01-01

    Version 3.12 of INCA provides user-friendly environment for design and analysis of linear control systems. System configuration and parameters easily adjusted, enabling INCA user to create compensation networks and perform sensitivity analysis in convenient manner. Full complement of graphical routines makes output easy to understand. Written in Pascal and FORTRAN.

  20. Interactive Controls Analysis (INCA)

    Science.gov (United States)

    Bauer, Frank H.

    1989-01-01

    Version 3.12 of INCA provides user-friendly environment for design and analysis of linear control systems. System configuration and parameters easily adjusted, enabling INCA user to create compensation networks and perform sensitivity analysis in convenient manner. Full complement of graphical routines makes output easy to understand. Written in Pascal and FORTRAN.

  1. Identification of genetic components involved in Lotus-endophyte interactions

    DEFF Research Database (Denmark)

    Zgadzaj, Rafal Lukasz

    colonisation of below-ground plant organs. It focused on bacterial endophyte, Rhizobium KAW12, colonisation of spontaneously formed nodules in snf1 mutants and symbiotic signalling mutants in a snf1 background. Additionally, participation of genes required for rhizobial accomodation during endophytic invasion...... was tested by coinoculation experiments with Rhizobium KAW12 and nodule inducing strains or their symbiotically deficient mutants. Such approaches allowed to identify genes possibly involved in host-endophyte recognition. Additionally, bacterial mutants used in these screenings pointed towards...... populations depending on their genotype. Additionally, analysis of Lotus defence response genes was performed after inoculation with epiphytic and endophytic strains of Rhizobium, indicating only minimal differences in their perception by the host....

  2. Spectroscopic studies of interactions involving horseradish peroxidase and Tb3+.

    Science.gov (United States)

    Guo, Shaofen; Zhou, Qing; Lu, Tianhong; Ding, Xiaolan; Huang, Xiaohua

    2008-09-01

    The spectroscopic properties of interactions involving horseradish peroxidase (HRP) and Tb3+ in the simulated physiological solution was investigated with some electrochemical and spectroscopic methods, such as cyclic voltammetry (CV), circular dichroism (CD), X-ray photoelectron spectroscopy (XPS) and synchronous fluorescence (SF). It was found that Tb3+ can coordinate with oxygen atoms in carbonyl groups in the peptide chain of HRP, form the complex of Tb3+ and HRP (Tb-HRP), and then lead to the conformation change of HRP. The increase in the random coil content of HRP can disturb the microstructure of the heme active center of HRP, in which the planarity of the porphyrin cycle in the heme group is increased and then the exposure extent of the electrochemical active center is decreased. Thus Tb3+ can inhibit the electrochemical reaction of HRP and its electrocatalytic activity for the reduction of H2O2 at the Au/Cys/GC electrode. The changes in the microstructure of HRP obstructed the electron transfer of Fe(III) in the porphyrin cycle of the heme group, thus HRP catalytic activity is inhibited. The inhibition effect of Tb3+ on HRP catalytic activity is increased with the increasing of Tb3+ concentration. This study would provide some references for better understanding the rare earth elements and heavy metals on peroxidase toxicity in living organisms.

  3. Visual Interactive Analysis

    DEFF Research Database (Denmark)

    Kirchmeier-Andersen, Sabine; Møller Christensen, Jakob; Lihn Jensen, Bente

    2004-01-01

    This article presents the latest version of VIA (version 3.0). The development of the program was initiated by a demand for more systematic training of language analysis in high schools and universities. The system is now web-based, which enables teachers and students to share exercises across th...

  4. Visual Interactive Analysis

    DEFF Research Database (Denmark)

    Kirchmeier-Andersen, Sabine; Møller Christensen, Jakob; Lihn Jensen, Bente

    2004-01-01

    This article presents the latest version of VIA (version 3.0). The development of the program was initiated by a demand for more systematic training of language analysis in high schools and universities. The system is now web-based, which enables teachers and students to share exercises across...... the globe. A new dictionary feature has been added which contains detailed morphological information used by the system to produce intelligent feed-back on student performance. VIA contains more than 1700 exercises for Danish, German, English, Spanish, Latin, French and Italian. For VIA 3.0, a new module...

  5. Surface interactions involved in flashover with high density electronegative gases.

    Energy Technology Data Exchange (ETDEWEB)

    Hodge, Keith Conquest; Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Wallace, Zachariah Red; Lehr, Jane Marie

    2010-01-01

    This report examines the interactions involved with flashover along a surface in high density electronegative gases. The focus is on fast ionization processes rather than the later time ionic drift or thermalization of the discharge. A kinetic simulation of the gas and surface is used to examine electron multiplication and includes gas collision, excitation and ionization, and attachment processes, gas photoionization and surface photoemission processes, as well as surface attachment. These rates are then used in a 1.5D fluid ionization wave (streamer) model to study streamer propagation with and without the surface in air and in SF6. The 1.5D model therefore includes rates for all these processes. To get a better estimate for the behavior of the radius we have studied radial expansion of the streamer in air and in SF6. The focus of the modeling is on voltage and field level changes (with and without a surface) rather than secondary effects, such as, velocities or changes in discharge path. An experiment has been set up to carry out measurements of threshold voltages, streamer velocities, and other discharge characteristics. This setup includes both electrical and photographic diagnostics (streak and framing cameras). We have observed little change in critical field levels (where avalanche multiplication sets in) in the gas alone versus with the surface. Comparisons between model calculations and experimental measurements are in agreement with this. We have examined streamer sustaining fields (field which maintains ionization wave propagation) in the gas and on the surface. Agreement of the gas levels with available literature is good and agreement between experiment and calculation is good also. Model calculations do not indicate much difference between the gas alone versus the surface levels. Experiments have identified differences in velocity between streamers on the surface and in the gas alone (the surface values being larger).

  6. Expert system interaction with existing analysis codes

    Energy Technology Data Exchange (ETDEWEB)

    Ransom, V.H.; Fink, R.K.; Bertch, W.J.; Callow, R.A.

    1986-01-01

    Coupling expert systems with existing engineering analysis codes is a promising area in the field of artificial intelligence. The added intelligence can provide for easier and less costly use of the code and also reduce the potential for code misuse. This paper will discuss the methods available to allow interaction between an expert system and a large analysis code running on a mainframe. Concluding remarks will identify potential areas of expert system application with specific areas that are being considered in a current research program. The difficulty of interaction between an analysis code and an expert system is due to the incompatibility between the FORTRAN environment used for the analysis code and the AI environment used for the expert system. Three methods, excluding file transfer techniques, are discussed to help overcome this incompatibility. The first method is linking the FORTRAN routines to the LISP environment on the same computer. Various LISP dialects available on mainframes and their interlanguage communication capabilities are discussed. The second method involves network interaction between a LISP machine and a mainframe computer. Comparisons between the linking method and networking are noted. The third method involves the use of an expert system tool that is campatible with a FORTRAN environment. Several available tools are discussed. With the interaction methods identified, several potential application areas are considered. Selection of the specific areas that will be developed for the pilot project and applied to a thermal-hydraulic energy analysis code are noted.

  7. Is nonverbal communication disrupted in interactions involving patients with schizophrenia?

    Science.gov (United States)

    Lavelle, Mary; Healey, Patrick G T; McCabe, Rosemarie

    2013-09-01

    Nonverbal communication is a critical feature of successful social interaction and interpersonal rapport. Social exclusion is a feature of schizophrenia. This experimental study investigated if the undisclosed presence of a patient with schizophrenia in interaction changes nonverbal communication (ie, speaker gesture and listener nodding). 3D motion-capture techniques recorded 20 patient (1 patient, 2 healthy participants) and 20 control (3 healthy participants) interactions. Participants rated their experience of rapport with each interacting partner. Patients' symptoms, social cognition, and executive functioning were assessed. Four hypotheses were tested: (1) Compared to controls, patients display less speaking gestures and listener nods. (2) Patients' increased symptom severity and poorer social cognition are associated with patients' reduced gesture and nods. (3) Patients' partners compensate for patients' reduced nonverbal behavior by gesturing more when speaking and nodding more when listening. (4) Patients' reduced nonverbal behavior, increased symptom severity, and poorer social cognition are associated with others experiencing poorer rapport with the patient. Patients gestured less when speaking. Patients with more negative symptoms nodded less as listeners, while their partners appeared to compensate by gesturing more as speakers. Patients with more negative symptoms also gestured more when speaking, which, alongside increased negative symptoms and poorer social cognition, was associated with others experiencing poorer patient rapport. Patients' symptoms are associated with the nonverbal behavior of patients and their partners. Patients' increased negative symptoms and gesture use are associated with poorer interpersonal rapport. This study provides specific evidence about how negative symptoms impact patients' social interactions.

  8. Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate.

    Science.gov (United States)

    Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

    2013-08-01

    Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed.

  9. Do Parentese Prosody and Fathers' Involvement in Interacting Facilitate Social Interaction in Infants Who Later Develop Autism?

    Science.gov (United States)

    Cohen, David; Cassel, Raquel S.; Saint-Georges, Catherine; Mahdhaoui, Ammar; Laznik, Marie-Christine; Apicella, Fabio; Muratori, Pietro; Maestro, Sandra; Muratori, Filippo; Chetouani, Mohamed

    2013-01-01

    Background Whether development of autism impacts the interactive process between an infant and his/her parents remains an unexplored issue. Methodology and Principal Findings Using computational analysis taking into account synchronic behaviors and emotional prosody (parentese), we assessed the course of infants' responses to parents' type of speech in home movies from typically developing (TD) infants and infants who will subsequently develop autism aged less than 18 months. Our findings indicate: that parentese was significantly associated with infant responses to parental vocalizations involving orientation towards other people and with infant receptive behaviours; that parents of infants developing autism displayed more intense solicitations that were rich in parentese; that fathers of infants developing autism spoke to their infants more than fathers of TD infants; and that fathers' vocalizations were significantly associated with intersubjective responses and active behaviours in infants who subsequently developed autism. Conclusion The parents of infants who will later develop autism change their interactive pattern of behaviour by both increasing parentese and father's involvement in interacting with infants; both are significantly associated with infant's social responses. We stress the possible therapeutic implications of these findings and its implication for Dean Falk's theory regarding pre-linguistic evolution in early hominins. PMID:23650498

  10. Kazrin F is involved in apoptosis and interacts with BAX and ARC

    Institute of Scientific and Technical Information of China (English)

    Qiong Wang; Min Liu; Xin Li; Lu Chen; Hua Tang

    2009-01-01

    Kazrin has recently been identified as a functional protein that is involved in cell-cell junctions and in signal transduction. Here, we identified a new isoform, Kazrin F, which is 518 aa in length and has 97 aa unique at the N-terminus. Knockdown of Kazrin F using siRNA caused cell apoptosis and a marked decrease in cell viability measured by MTT and TUNEL assays. Co-immunoprecipitation analysis revealed that Kazrin F interacts with ARC (apoptosis repressor with caspase recruitment domain) and Bas (Bcl-2-associated X protein). Co-localization of Kazriin F with ARC and Bax in the cytoplasm was determined by immunofluorescence analysis. These results suggested that Kazrin F might play an important role in regulating cellular apoptosis by interacting with ARC and Bax.

  11. Similar methodological analysis involving the user experience.

    Science.gov (United States)

    Almeida e Silva, Caio Márcio; Okimoto, Maria Lúcia R L; Tanure, Raffaela Leane Zenni

    2012-01-01

    This article deals with the use of a protocol for analysis of similar methodological analysis related to user experience. For both, were selected articles recounting experiments in the area. They were analyze based on the similar analysis protocol and finally, synthesized and associated.

  12. Analysis of Corynebacterium diphtheriae macrophage interaction: Dispensability of corynomycolic acids for inhibition of phagolysosome maturation and identification of a new gene involved in synthesis of the corynomycolic acid layer.

    Science.gov (United States)

    Ott, Lisa; Hacker, Elena; Kunert, Timo; Karrington, Ian; Etschel, Philipp; Lang, Roland; Wiesmann, Veit; Wittenberg, Thomas; Singh, Albel; Varela, Cristian; Bhatt, Apoorva; Sangal, Vartul; Burkovski, Andreas

    2017-01-01

    Corynebacterium diphtheriae is the causative agent of diphtheria, a toxin mediated disease of upper respiratory tract, which can be fatal. As a member of the CMNR group, C. diphtheriae is closely related to members of the genera Mycobacterium, Nocardia and Rhodococcus. Almost all members of these genera comprise an outer membrane layer of mycolic acids, which is assumed to influence host-pathogen interactions. In this study, three different C. diphtheriae strains were investigated in respect to their interaction with phagocytic murine and human cells and the invertebrate infection model Caenorhabditis elegans. Our results indicate that C. diphtheriae is able to delay phagolysosome maturation after internalization in murine and human cell lines. This effect is independent of the presence of mycolic acids, as one of the strains lacked corynomycolates. In addition, analyses of NF-κB induction revealed a mycolate-independent mechanism and hint to detrimental effects of the different strains tested on the phagocytic cells. Bioinformatics analyses carried out to elucidate the reason for the lack of mycolates in one of the strains led to the identification of a new gene involved in mycomembrane formation in C. diphtheriae.

  13. Human macrophage differentiation involves an interaction between integrins and fibronectin

    Energy Technology Data Exchange (ETDEWEB)

    Laouar, A.; Chubb, C.B.H.; Collart, F.; Huberman, E.

    1997-03-14

    The authors have examined the role of integrins and extracellular matrix (ECM) proteins in macrophage differentiation of (1) human HL-60 myeloid leukemia cells induced by phorbol 12-myristate 13-acetate (PMA) and (2) human peripheral blood monocytes induced by either PMA or macrophage-colony stimulating factor (M-CSF). Increased {beta}{sub 1} integrin and fibronectin (FN) gene expression was observed in PMA-treated HL-60 cells and PMA- or M-CSF-treated monocytes, even at a time preceding the manifestation of macrophage markers. Treated HL-60 cells and monocytes also released and deposited FN on the culture dishes. An HL-60 cell variant, HL-525, which is deficient in protein kinase C {beta} (PKC{beta}) and resistant to PMA-induced differentiation, failed to express FN after PMA treatment. Restoration of PKC{beta} resulted in PMA-induced FN gene expression and macrophage differentiation. The macrophage phenotype induced in HL-60 cells or monocytes was attenuated by anti-{beta}{sub 1} integrin or anti-FN MAbs. The authors suggest that macrophage differentiation involves activation of PKC and expression of specific integrins and ECM proteins. The stimulated cells, through their integrins, attach and spread on these substrates by binding to the deposited ECM proteins. This attachment and spreading in turn, through integrin signaling, leads to the macrophage phenotype.

  14. Integrative computational in-depth analysis of dysregulated miRNA-mRNA interactions in drug-resistant pediatric acute lymphoblastic leukemia cells: an attempt to obtain new potential gene-miRNA pathways involved in response to treatment.

    Science.gov (United States)

    Mesrian Tanha, Hamzeh; Mojtabavi Naeini, Marjan; Rahgozar, Soheila; Moafi, Alireza; Honardoost, Mohammad Amin

    2016-06-01

    Acute lymphoblastic leukemia (ALL) is the major neoplasia type among children. Despite the tremendous success of current treatment strategies, drug resistance still remains a major cause of chemotherapy failure and relapse in pediatric patients. Overwhelming evidence illustrates that microRNAs (miRNAs) act as post-transcriptional regulators of drug-resistance-related genes. The current study was aimed at how dysregulated miRNA-mRNA-signaling pathway interaction networks mediate resistance to four commonly used chemotherapy agents in pediatric ALL, including asparaginase, daunorubicin, prednisolone, and vincristine. Using public expression microarray datasets, a holistic in silico approach was utilized to investigate candidate drug resistance miRNA-mRNA-signaling pathway interaction networks in pediatric ALL. Our systems biology approach nominated significant drug resistance and cross-resistance miRNAs, mRNAs, and cell signaling pathways based on anti-correlative relationship between miRNA and mRNA expression pattern. To sum up, our systemic analysis disclosed either a new potential role of miRNAs, or a possible mechanism of cellular drug resistance, in chemotherapy resistance of pediatric ALL. The current study may shed light on predicting drug response and overcoming drug resistance in childhood ALL for subsequent generations of chemotherapies.

  15. Comparative genomics of plant-asssociated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions

    NARCIS (Netherlands)

    Loper, J.E.; Hassan, K.A.; Mavrodi, D.V.; Davis II, E.W.; Lim, C.K.; Shaffer, B.T.; Elbourne, L.D.H.; Stockwell, V.O.; Hartney, S.L.; Breakwell, K.; Henkels, M.D.; Tetu, S.G.; Rangel, L.I.; Kidarsa, T.A.; Wilson, N.L.; Mortel, van de J.E.; Song, C.; Blumhagen, R.; Radune, D.; Hostetler, J.B.; Brinkac, L.M.; Durkin, A.C.; Kluepfel, D.A.; Wechter, W.P.; Anderson, A.J.; Kim, Y.C.; Pierson III, L.S.; Pierson, E.A.; Lindow, S.E.; Kobayashi, D.Y.; Raaijmakers, J.; Weller, D.M.; Thomashow, L.S.; Allen, A.E.; Paulsen, I.T.

    2012-01-01

    We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multi

  16. The effects of interactive (TIPS) homework on family involvement and science achievement of middle grade students

    Science.gov (United States)

    van Voorhis, Frances Landis

    The purpose of the study was to investigate the effects of interactive and non-interactive science homework assignments on family involvement in homework, homework completion and accuracy, student science achievement, and student and parent attitudes about science. Most previous research on homework has examined what parental involvement results naturally, without prompts or instruction from teachers. In contrast, this study experimentally examined the effects of teacher prompts to parents for involvement in their children's homework. Two hundred and fifty-three students from 10 classes of sixth and eighth grade students participated in the study that lasted 18 weeks of the school year. Six classes of students completed the TIPS (Teachers Involve Parents In Schoolwork) interactive homework assignments, and four classes completed the non-interactive assignments that contained the same content and questions as the TIPS assignments. TIPS students received instructions to involve a parent or other family partner in certain sections of the homework assignment. ATIPS students received the same assignment with no instruction to involve another person. Results indicated that TIPS students more often involved parents in their science homework assignments than ATIPS students. However, TIPS science students reported no more parental involvement in homework than ATIPS students in subjects not assigning interactive homework. Therefore, the TIPS instructions elicited more parental involvement in homework than the ATIPS assignments. TIPS students did not differ from ATIPS students in the percent of homework returned or accuracy. Students who rated the homework more positively and involved families regularly returned more homework assignments than students who did not do so. TIPS students did earn significantly higher science report card grades than ATIPS students after controlling for background variables, teacher effects, and percent of homework returned. Exploratory analyses of

  17. DFT study and crystal structure analysis of a new nano-structure five coordinated Hg(II) complex involving C-H⋯O, N⋯O and π⋯π interactions in a supra-molecular structure.

    Science.gov (United States)

    Montazerozohori, M; Musavi, S A; Masoudiasl, A; Hojjati, A; Assoud, A

    2015-08-05

    In this research, template synthesis and crystal structure of a new HgLI₂ complex are presented (L=N(1)-(4-nitrobenzylidene)-N(2)-(2-((E)-(4-nitrobenzylidene)amino)ethyl)ethane-1,2-diamine). The mercury complex crystallizes in the triclinic system with space group of P1¯. The crystal structure of the complex shows a distorted trigonal bipyramidal geometry around the mercury(II) center; including two I and an N atoms of Schiff base ligand in equatorial plane and two iminic N atoms in axial positions. Two five membered mercury containing rings [Hg(-N-C-C-N-)] are found in the structure. Some C-H⋯O, N⋯O and π⋯π intermolecular interactions causes a supra-molecular network in the solid-state. In addition to crystal structure analysis, density functional theory (DFT) study at the B3LYP/LanL2DZ level of theory has been also performed on the structure. Thereafter some theoretical structural and spectral data were compared with experimental results. Furthermore, total energy levels of HOMO and LUMO orbitals, molecular electrostatic potential, Mullikan atomic charges, thermodynamic and polarizability properties of the complex were calculated. Finally the mercury complex was prepared in nano-structure size confirmed by SEM and XRD analyses. The particles size of the titled complex was evaluated under 40 nm based on Sherrer's formula.

  18. Interfacial interactions involved in the biological assembly of Chandipura virus nucleocapsid protein.

    Science.gov (United States)

    Sreejith, R; Gulati, Sahil; Gupta, Sanjay

    2013-06-01

    The biological assembly of Chandipura virus nucleocapsid (N) protein has been modeled and the amino acid residues involved in specific intermolecular interactions among N monomers during oligomerisation have been predicted.

  19. Genes related to antioxidant metabolism are involved in Methylobacterium mesophilicum-soybean interaction.

    Science.gov (United States)

    Araújo, Welington Luiz; Santos, Daiene Souza; Dini-Andreote, Francisco; Salgueiro-Londoño, Jennifer Katherine; Camargo-Neves, Aline Aparecida; Andreote, Fernando Dini; Dourado, Manuella Nóbrega

    2015-10-01

    The genus Methylobacterium is composed of pink-pigmented methylotrophic bacterial species that are widespread in natural environments, such as soils, stream water and plants. When in association with plants, this genus colonizes the host plant epiphytically and/or endophytically. This association is known to promote plant growth, induce plant systemic resistance and inhibit plant infection by phytopathogens. In the present study, we focused on evaluating the colonization of soybean seedling-roots by Methylobacterium mesophilicum strain SR1.6/6. We focused on the identification of the key genes involved in the initial step of soybean colonization by methylotrophic bacteria, which includes the plant exudate recognition and adaptation by planktonic bacteria. Visualization by scanning electron microscopy revealed that M. mesophilicum SR1.6/6 colonizes soybean roots surface effectively at 48 h after inoculation, suggesting a mechanism for root recognition and adaptation before this period. The colonization proceeds by the development of a mature biofilm on roots at 96 h after inoculation. Transcriptomic analysis of the planktonic bacteria (with plant) revealed the expression of several genes involved in membrane transport, thus confirming an initial metabolic activation of bacterial responses when in the presence of plant root exudates. Moreover, antioxidant genes were mostly expressed during the interaction with the plant exudates. Further evaluation of stress- and methylotrophic-related genes expression by qPCR showed that glutathione peroxidase and glutathione synthetase genes were up-regulated during the Methylobacterium-soybean interaction. These findings support that glutathione (GSH) is potentially a key molecule involved in cellular detoxification during plant root colonization. In addition to methylotrophic metabolism, antioxidant genes, mainly glutathione-related genes, play a key role during soybean exudate recognition and adaptation, the first step in

  20. Analysis of bilinear stochastic systems. [involving multiplicative noise processes

    Science.gov (United States)

    Willsky, A. S.; Marcus, S. I.; Martin, D. N.

    1974-01-01

    Analysis of stochastic dynamical systems that involve multiplicative (bilinear) noise processes is considered. After defining the systems of interest, the evolution of the moments of such systems, the question of stochastic stability, and estimation for bilinear stochastic systems are discussed. Both exact and approximate methods of analysis are introduced, and, in particular, the uses of Lie-theoretic concepts and harmonic analysis are discussed.

  1. Digraph matrix analysis applications to systems interactions

    Energy Technology Data Exchange (ETDEWEB)

    Alesso, H.P.; Altenbach, T.; Lappa, D.; Kimura, C.; Sacks, I.J.; Ashmore, B.C.; Fromme, D.; Smith, C.F.; Williams, W.

    1984-01-01

    Complex events such as Three Mile Island-2, Brown's Ferry-3 and Crystal River-3 have demonstrated that previously unidentified system interdependencies can be important to safety. A major aspect of these events was dependent faults (common cause/mode failures). The term systems interactions has been introduced by the Nuclear Regulatory Commission (NRC) to identify the concepts of spatial and functional coupling of systems which can lead to system interdependencies. Spatial coupling refers to dependencies resulting from a shared environmental condition; functional coupling refers to both dependencies resulting from components shared between safety and/or support systems, and to dependencies involving human actions. The NRC is currently developing guidelines to search for and evaluate adverse systems interactions at light water reactors. One approach utilizes graph theoretical methods and is called digraph matrix analysis (DMA). This methodology has been specifically tuned to the systems interaction problem. The objective of this paper is to present results from two DMA applications and to contrast them with the results from more traditional fault tree approaches.

  2. The Data Party: Involving Stakeholders in Meaningful Data Analysis

    Science.gov (United States)

    Franz, Nancy K.

    2013-01-01

    A hallmark of Extension includes the involvement of stakeholders in research and program needs assessment, design, implementation, evaluation, and reporting. A data party can be used to enhance this stakeholder involvement specifically in data analysis. This type of event can not only increase client participation in Extension programming and…

  3. The Data Party: Involving Stakeholders in Meaningful Data Analysis

    Science.gov (United States)

    Franz, Nancy K.

    2013-01-01

    A hallmark of Extension includes the involvement of stakeholders in research and program needs assessment, design, implementation, evaluation, and reporting. A data party can be used to enhance this stakeholder involvement specifically in data analysis. This type of event can not only increase client participation in Extension programming and…

  4. DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction.

    Science.gov (United States)

    K, Muhammed Jamsheer; Laxmi, Ashverya

    2014-01-01

    Zinc fingers are a ubiquitous class of protein domain with considerable variation in structure and function. Zf-FCS is a highly diverged group of C2-C2 zinc finger which is present in animals, prokaryotes and viruses, but not in plants. In this study we identified that a plant specific domain of unknown function, DUF581 is a zf-FCS type zinc finger. Based on HMM-HMM comparison and signature motif similarity we named this domain as FCS-Like Zinc finger (FLZ) domain. A genome wide survey identified that FLZ domain containing genes are bryophytic in origin and this gene family is expanded in spermatophytes. Expression analysis of selected FLZ gene family members of A. thaliana identified an overlapping expression pattern suggesting a possible redundancy in their function. Unlike the zf-FCS domain, the FLZ domain found to be highly conserved in sequence and structure. Using a combination of bioinformatic and protein-protein interaction tools, we identified that FLZ domain is involved in protein-protein interaction.

  5. DUF581 is plant specific FCS-like zinc finger involved in protein-protein interaction.

    Directory of Open Access Journals (Sweden)

    Muhammed Jamsheer K

    Full Text Available Zinc fingers are a ubiquitous class of protein domain with considerable variation in structure and function. Zf-FCS is a highly diverged group of C2-C2 zinc finger which is present in animals, prokaryotes and viruses, but not in plants. In this study we identified that a plant specific domain of unknown function, DUF581 is a zf-FCS type zinc finger. Based on HMM-HMM comparison and signature motif similarity we named this domain as FCS-Like Zinc finger (FLZ domain. A genome wide survey identified that FLZ domain containing genes are bryophytic in origin and this gene family is expanded in spermatophytes. Expression analysis of selected FLZ gene family members of A. thaliana identified an overlapping expression pattern suggesting a possible redundancy in their function. Unlike the zf-FCS domain, the FLZ domain found to be highly conserved in sequence and structure. Using a combination of bioinformatic and protein-protein interaction tools, we identified that FLZ domain is involved in protein-protein interaction.

  6. Integrative analysis for finding genes and networks involved in diabetes and other complex diseases

    DEFF Research Database (Denmark)

    Bergholdt, R.; Størling, Zenia, Marian; Hansen, Kasper Lage;

    2007-01-01

    identified a number of new protein network modules and novel candidate genes/proteins for type 1 diabetes. We propose this type of integrative analysis as a general method for the elucidation of genes and networks involved in diabetes and other complex diseases.......We have developed an integrative analysis method combining genetic interactions, identified using type 1 diabetes genome scan data, and a high-confidence human protein interaction network. Resulting networks were ranked by the significance of the enrichment of proteins from interacting regions. We...

  7. Neural mirroring and social interaction: Motor system involvement during action observation relates to early peer cooperation.

    Science.gov (United States)

    Endedijk, H M; Meyer, M; Bekkering, H; Cillessen, A H N; Hunnius, S

    2017-04-01

    Whether we hand over objects to someone, play a team sport, or make music together, social interaction often involves interpersonal action coordination, both during instances of cooperation and entrainment. Neural mirroring is thought to play a crucial role in processing other's actions and is therefore considered important for social interaction. Still, to date, it is unknown whether interindividual differences in neural mirroring play a role in interpersonal coordination during different instances of social interaction. A relation between neural mirroring and interpersonal coordination has particularly relevant implications for early childhood, since successful early interaction with peers is predictive of a more favorable social development. We examined the relation between neural mirroring and children's interpersonal coordination during peer interaction using EEG and longitudinal behavioral data. Results showed that 4-year-old children with higher levels of motor system involvement during action observation (as indicated by lower beta-power) were more successful in early peer cooperation. This is the first evidence for a relation between motor system involvement during action observation and interpersonal coordination during other instances of social interaction. The findings suggest that interindividual differences in neural mirroring are related to interpersonal coordination and thus successful social interaction. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  8. An Ehrlichia chaffeensis tandem repeat protein interacts with multiple host targets involved in cell signaling, transcriptional regulation, and vesicle trafficking.

    Science.gov (United States)

    Wakeel, Abdul; Kuriakose, Jeeba A; McBride, Jere W

    2009-05-01

    Ehrlichia chaffeensis is an obligately intracellular bacterium that exhibits tropism for mononuclear phagocytes forming cytoplasmic membrane-bound microcolonies called morulae. To survive and replicate within phagocytes, E. chaffeensis exploits the host cell by modulating a number of host cell processes, but the ehrlichial effector proteins involved are unknown. In this study, we determined that p47, a secreted, differentially expressed, tandem repeat (TR) protein, interacts with multiple host proteins associated with cell signaling, transcriptional regulation, and vesicle trafficking. Yeast two-hybrid analysis revealed that p47 interacts with polycomb group ring finger 5 (PCGF5) protein, Src protein tyrosine kinase FYN (FYN), protein tyrosine phosphatase non-receptor type 2 (PTPN2), and adenylate cyclase-associated protein 1 (CAP1). p47 interaction with these proteins was further confirmed by coimmunoprecipitation assays and colocalization in HeLa cells transfected with p47-green fluorescent fusion protein (AcGFP1-p47). Moreover, confocal microscopy demonstrated p47-expressing dense-cored (DC) ehrlichiae colocalized with PCGF5, FYN, PTPN2, and CAP1. An amino-terminally truncated form of p47 containing TRs interacted only with PCGF5 and not with FYN, PTPN2, and CAP1, indicating differences in p47 domains that are involved in these interactions. These results demonstrate that p47 is involved in a complex network of interactions involving numerous host cell proteins. Furthermore, this study provides a new insight into the molecular and functional distinction of DC ehrlichiae, as well as the effector proteins involved in facilitating ehrlichial survival in mononuclear phagocytes.

  9. Hamiltonian analysis of interacting fluids

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, Rabin; Mitra, Arpan Krishna [S. N. Bose National Centre for Basic Sciences, Kolkata (India); Ghosh, Subir [Indian Statistical Institute, Kolkata (India)

    2015-05-15

    Ideal fluid dynamics is studied as a relativistic field theory with particular stress on its hamiltonian structure. The Schwinger condition, whose integrated version yields the stress tensor conservation, is explicitly verified both in equal-time and light-cone coordinate systems. We also consider the hamiltonian formulation of fluids interacting with an external gauge field. The complementary roles of the canonical (Noether) stress tensor and the symmetric one obtained by metric variation are discussed. (orig.)

  10. Pyoverdine and PQS Mediated Subpopulation Interactions Involved in Pseudomonas aeruginosa Biofilm Formation

    DEFF Research Database (Denmark)

    Yang, Liang; Nilsson, Martin; Gjermansen, Morten;

    2009-01-01

    Using flow chamber-grown Pseudomonas aeruginosa biofilms as model system, we show in the present study that formation of heterogeneous biofilms may occur through mechanisms that involve complex subpopulation interactions. One example of this phenomenon is expression of the iron...

  11. Interactions between membrane-bound cellulose synthases involved in the synthesis of the secondary cell wall

    NARCIS (Netherlands)

    Timmers, J.F.P.; Vernhettes, S.; Desprez, T.; Vincken, J.P.; Visser, R.G.F.; Trindade, L.M.

    2009-01-01

    It has not yet been reported how the secondary CESA (cellulose synthase) proteins are organized in the rosette structure. A membrane-based yeast two-hybrid (MbYTH) approach was used to analyze the interactions between the CESA proteins involved in secondary cell wall synthesis of Arabidopsis and the

  12. Skill versus luck: A motivational analysis of gambling involvement.

    Science.gov (United States)

    Chantal, Y; Vallerand, R J

    1996-12-01

    The purpose of the present investigation was to test the skill/luck distinction among gambling games by comparing the motivations underlying participation in a skill (horse racing) and a luck (lottery) betting activity. Predictions were made using Self-Determination Theory (Deci & Ryan, 1985, 1991). It was predicted that self-determined motivations (intrinsic motivation and identified regulation) would be more prominent for the skill game because it is conducive to optimal challenges, fun, and self-involvement. Conversely, the non self-determined forms of motivation (especially external regulation) should be more important for the game of luck because the luck dimension precludes true involvement of the self and orients the individual towards material gains. Results from a hierarchical discriminant function analysis, with 120 gamblers predominantly involved in one of the two betting activities, supported these hypotheses. These results highlight the relevance of a motivational analysis for a better understanding of the inherent properties of gambling games.

  13. DYNAMIC SIMULATION OF FLUID-STRUCTURE INTERACTION PROBLEMS INVOLVING LARGE-AMPLITUDE SLOSHING

    Institute of Scientific and Technical Information of China (English)

    Chen Jianping; Zhou Rurong; Wu Wenlong

    2004-01-01

    An effective computational method is developed for dynamic analysis of fluid-structure interaction problems involving large-amplitude sloshing of the fluid and large-displacement motion of the structure.The structure is modeled as a rigid container supported by a system consisting of springs and dashpots.The motion of the fluid is decomposed into two parts: the large-displacement motion with the container and the large-amplitude sloshing relative to the container.The former is conveniently dealt with by defining a container-fixed noninertial local frame, while the latter is easily handled by adopting an ALE kinematical description.This leads to an easy and accurate treatment of both the fluid-structure interface and the fluid free surface without producing excessive distortion of the computational mesh.The coupling between the fluid and the structure is accomplished through the coupling matrices that can be easily established.Two numerical examples, including a TLD-structure system and a simplified liquid-loaded vehicle system, are presented to demonstrate the effectiveness and reliability of the proposed method.The present work can also be applied to simulate fluid-structure problems incorporating multibody systems and several fluid domains.

  14. Proteins involved in motility and sperm-egg interaction evolve more rapidly in mouse spermatozoa.

    Science.gov (United States)

    Vicens, Alberto; Lüke, Lena; Roldan, Eduardo R S

    2014-01-01

    Proteomic studies of spermatozoa have identified a large catalog of integral sperm proteins. Rapid evolution of these proteins may underlie adaptive changes of sperm traits involved in different events leading to fertilization, although the selective forces underlying such rapid evolution are not well understood. A variety of selective forces may differentially affect several steps ending in fertilization, thus resulting in a compartmentalized adaptation of sperm proteins. Here we analyzed the evolution of genes associated to various events in the sperm's life, from sperm formation to sperm-egg interaction. Evolutionary analyses were performed on gene sequences from 17 mouse strains whose genomes have been sequenced. Four of these are derived from wild Mus musculus, M. domesticus, M. castaneus and M. spretus. We found a higher proportion of genes exhibiting a signature of positive selection among those related to sperm motility and sperm-egg interaction. Furthermore, sperm proteins involved in sperm-egg interaction exhibited accelerated evolution in comparison to those involved in other events. Thus, we identified a large set of candidate proteins for future comparative analyses of genotype-phenotype associations in spermatozoa of species subjected to different sexual selection pressures. Adaptive evolution of proteins involved in motility could be driven by sperm competition, since this selective force is known to increase the proportion of motile sperm and their swimming velocity. On the other hand, sperm proteins involved in gamete interaction could be coevolving with their egg partners through episodes of sexual selection or sexual conflict resulting in species-specific sperm-egg interactions and barriers preventing interspecies fertilization.

  15. Adverse drug interactions involving common prescription and over-the-counter analgesic agents.

    Science.gov (United States)

    Hersh, Elliot V; Pinto, Andres; Moore, Paul A

    2007-01-01

    Eight analgesic preparations with approved indications for acute pain were among the top 200 drugs prescribed in the United States in 2006. In addition, an estimated 36 million Americans use over-the-counter (OTC) analgesics daily. Given this volume of use, it is not surprising that a number of drug interactions involving analgesic drugs have been reported. This article examines the pharmacologic factors that enhance the clinical relevance of potential drug interactions and reviews the literature on drug interactions involving the most commonly used analgesic preparations in the United States. A PubMed search was conducted for English-language articles published between January 1967 and July 2007. Among the search terms were drug interactions, acetaminophen, aspirin, ibuprofen, naproxen, celecoxib, NSAIDs, hydrocodone, oxycodone, codeine, tramadol, OTC analgesics, alcohol, ethanol, antihypertensive drugs, methotrexate, warfarin, SSRIs, paroxetine, fluoxetine, sertraline, citalopram, serotonin syndrome, MAOIs, and overdose. Controlled clinical trials, case-control studies, and case reports were included in the review. A number of case reports and well-controlled clinical trials were identified that provided evidence of the relatively well known drug-drug interactions between prescription/OTC NSAIDs and alcohol, antihypertensive drugs, high-dose methotrexate, and lithium, as well as between frequently prescribed narcotics and other central nervous system depressants. In contrast, the ability of recent alcohol ingestion to exacerbate the hepatotoxic potential of therapeutic doses of acetaminophen is not supported by either case reports or clinical research. Use of ibuprofen according to OTC guidelines in patients taking cardioprotective doses of aspirin does not appear to interfere with aspirin's antiplatelet activity, whereas chronic prescription use of ibuprofen and other NSAIDs may interfere. Low-dose aspirin intake appears to abolish the gastroprotective effects

  16. Development of a Chemoenzymatic-like and Photoswitchable Method for the High-Throughput creation of Protein Microarrays. Application to the Analysis of the Protein/Protein Interactions Involved in the YOP Virulon from Yersinia pestis.

    Energy Technology Data Exchange (ETDEWEB)

    Camarero, J A

    2006-12-07

    Protein arrays are ideal tools for the rapid analysis of whole proteomes as well as for the development of reliable and cheap biosensors. The objective of this proposal is to develop a new ligand assisted ligation method based in the naturally occurring protein trans-splicing process. This method has been used for the generation of spatially addressable arrays of multiple protein components by standard micro-lithographic techniques. Key to our approach is the use of the protein trans-splicing process. This naturally occurring process allows the development of a truly generic and highly efficient method for the covalent attachment of proteins through its C-terminus to any solid support. This technology has been used for the creation of protein chips containing several virulence factors from the human pathogen Y. pestis.

  17. Accelerator physics analysis with interactive tools

    Energy Technology Data Exchange (ETDEWEB)

    Holt, J.A.; Michelotti, L.

    1993-05-01

    Work is in progress on interactive tools for linear and nonlinear accelerator design, analysis, and simulation using X-based graphics. The BEAMLINE and MXYZPTLK class libraries, were used with an X Windows graphics library to build a program for interactively editing lattices and studying their properties.

  18. Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence.

    Science.gov (United States)

    Quinn, Robert A; Vermeij, Mark J A; Hartmann, Aaron C; Galtier d'Auriac, Ines; Benler, Sean; Haas, Andreas; Quistad, Steven D; Lim, Yan Wei; Little, Mark; Sandin, Stuart; Smith, Jennifer E; Dorrestein, Pieter C; Rohwer, Forest

    2016-04-27

    Holobionts are assemblages of microbial symbionts and their macrobial host. As extant representatives of some of the oldest macro-organisms, corals and algae are important for understanding how holobionts develop and interact with one another. Using untargeted metabolomics, we show that non-self interactions altered the coral metabolome more than self-interactions (i.e. different or same genus, respectively). Platelet activating factor (PAF) and Lyso-PAF, central inflammatory modulators in mammals, were major lipid components of the coral holobionts. When corals were damaged during competitive interactions with algae, PAF increased along with expression of the gene encoding Lyso-PAF acetyltransferase; the protein responsible for converting Lyso-PAF to PAF. This shows that self and non-self recognition among some of the oldest extant holobionts involve bioactive lipids identical to those in highly derived taxa like humans. This further strengthens the hypothesis that major players of the immune response evolved during the pre-Cambrian.

  19. The required interactions among institutions involved with Research and Development in the power sector

    Energy Technology Data Exchange (ETDEWEB)

    Vieira Filho, X.; Medeiros, J.C.; Szechtman, M. [Centro de Pesquisas de Energia Eletrica (CEPEL), Rio de Janeiro, RJ (Brazil)

    1994-12-31

    This paper presents the form which CEPEL (Brazilian Federal Research Center in Electric Energy) works for the Brazilian electric system, the interaction with associates, especially with ELETROBRAS (the Federal holding company in Brazil), the modern way of CEPEL operation and interactions with clients, the partnership in Research and Development, the CEPEL philosophy of transferring technology to its clients, and the cost-benefit analysis of Research and Development activities. (author) 2 refs., 4 figs., 1 tab.

  20. Moving shape analysis and control applications to fluid structure interactions

    CERN Document Server

    Moubachir, Marwan

    2006-01-01

    Problems involving the evolution of two- and three-dimensional domains arise in many areas of science and engineering. Emphasizing an Eulerian approach, Moving Shape Analysis and Control: Applications to Fluid Structure Interactions presents valuable tools for the mathematical analysis of evolving domains. The book illustrates the efficiency of the tools presented through different examples connected to the analysis of noncylindrical partial differential equations (PDEs), such as Navier-Stokes equations for incompressible fluids in moving domains. The authors first provide all of the details of existence and uniqueness of the flow in both strong and weak cases. After establishing several important principles and methods, they devote several chapters to demonstrating Eulerian evolution and derivation tools for the control of systems involving fluids and solids. The book concludes with the boundary control of fluid-structure interaction systems, followed by helpful appendices that review some of the advanced m...

  1. Interactions among stakehoklders involved in return to work after sick leave due to mental disorders: a meta-ethnography.

    Science.gov (United States)

    Neves, Robson da Fonseca; Nunes, Mônica de Oliveira; Magalhães, Lilian

    2015-11-01

    Mental disorders cause impact in the work environment. Investigations of interaction among stakeholders who are involved in the return to work are scarce. Meta-ethnography serves to synthesize qualitative studies by means of ongoing interpretation and comparison of the ideas presented in the articles. The goal of this study is to present a meta-ethnography of the interactions among the stakeholders involved in the return to work process after leave of absence due to mental disorders. It aims: (1) to investigate the interactions among stakeholders involved in return to work; (2) to identify enablers or obstacles for the return to work. The database search found 619 articles, 16 of which met the inclusion criteria. Analysis of the articles revealed six second-order concepts that resulted in two syntheses. The first is about performance ethos in the return to work, and the second shows return to work as a catalyst of new life styles. Models that favor the worker's performance ethos, as well as a perspective oriented by psychosocial aspects may enable return to work practices after leave of absence due to mental disorders.

  2. Involvement of Apoptosis in Host-Parasite Interactions in the Zebra Mussel

    OpenAIRE

    Laëtitia Minguez; Nelly Brulé; Bénédicte Sohm; Simon Devin; Laure Giambérini

    2013-01-01

    International audience; The question of whether cell death by apoptosis plays a biological function during infection is key to understanding host-parasite interactions. We investigated the involvement of apoptosis in several host-parasite systems, using zebra mussels Dreissena polymorpha as test organisms and their micro-and macroparasites. As a stress response associated with parasitism, heat shock proteins (Hsp) can be induced. In this protein family, Hsp70 are known to be apoptosis inhibit...

  3. A Conformal Mapping Suitable for Problems Involving Interaction Between Given Geometries and Known Far Fields.

    Science.gov (United States)

    1984-09-01

    A conformal transformation formula using Riemann-Stieltjes integrals is derived for use with problems involving the interaction between a given finite-sized geometry and a known far field. The derivative of this transformation is non-singular in the domain considered and tends to one at infinity. A formula is derived for transformation from the unit circle to the exterior of an arbitrarily given continuous curve with bounded variation . A special case of the transformation is very similar

  4. The nature and limits of interactive communication: A philosophical analysis

    Directory of Open Access Journals (Sweden)

    Halvor Nordby

    2011-04-01

    Full Text Available In many modern study programs, teachers and students communicate via internet and other interactive communicative channels. What is the essential nature of this communication? How does interactive communication differ from ordinary face-to-face communication in the most fundamental sense? The article uses conceptual analysis as a philosophical method to explore the intrinsic nature of the concept interactive communication. The aim of this method is to develop a concept definition that matches shared linguistic beliefs about informative examples from internet based communication and information exchange that is central in electronic teaching courses. The article examines several concept definitions and argues in favor of a philosophical information processing analysis of interactive communication. The significance of this analysis has two dimensions. First, it can give teachers and others who are involved in interactive communication a better understanding of the essential differences between interactive and face-toface communication. Second, the analysis can stimulate pedagogical and critical reflection on the nature and limits of internet based communication and electronic teaching tools.

  5. Mass spectrometric analysis of protein interactions

    DEFF Research Database (Denmark)

    Borch, Jonas; Jørgensen, Thomas J. D.; Roepstorff, Peter

    2005-01-01

    Mass spectrometry is a powerful tool for identification of interaction partners and structural characterization of protein interactions because of its high sensitivity, mass accuracy and tolerance towards sample heterogeneity. Several tools that allow studies of protein interaction are now...... available and recent developments that increase the confidence of studies of protein interaction by mass spectrometry include quantification of affinity-purified proteins by stable isotope labeling and reagents for surface topology studies that can be identified by mass-contributing reporters (e.g. isotope...... labels, cleavable cross-linkers or fragment ions. The use of mass spectrometers to study protein interactions using deuterium exchange and for analysis of intact protein complexes recently has progressed considerably....

  6. Influence of external inputs and asymmetry of connections on information-geometric measures involving up to ten neuronal interactions.

    Science.gov (United States)

    Nie, Yimin; Fellous, Jean-Marc; Tatsuno, Masami

    2014-10-01

    The investigation of neural interactions is crucial for understanding information processing in the brain. Recently an analysis method based on information geometry (IG) has gained increased attention, and the property of the pairwise IG measure has been studied extensively in relation to the two-neuron interaction. However, little is known about the property of IG measures involving more neuronal interactions. In this study, we systematically investigated the influence of external inputs and the asymmetry of connections on the IG measures in cases ranging from 1-neuron to 10-neuron interactions. First, the analytical relationship between the IG measures and external inputs was derived for a network of 10 neurons with uniform connections. Our results confirmed that the single and pairwise IG measures were good estimators of the mean background input and of the sum of the connection weights, respectively. For the IG measures involving 3 to 10 neuronal interactions, we found that the influence of external inputs was highly nonlinear. Second, by computer simulation, we extended our analytical results to asymmetric connections. For a network of 10 neurons, the simulation showed that the behavior of the IG measures in relation to external inputs was similar to the analytical solution obtained for a uniformly connected network. When the network size was increased to 1000 neurons, the influence of external inputs almost disappeared. This result suggests that all IG measures from 1-neuron to 10-neuron interactions are robust against the influence of external inputs. In addition, we investigated how the strength of asymmetry influenced the IG measures. Computer simulation of a 1000-neuron network showed that all the IG measures were robust against the modulation of the asymmetry of connections. Our results provide further support for an information-geometric approach and will provide useful insights when these IG measures are applied to real experimental spike data.

  7. Interactive Data Analysis. Development of an Interactive Data Manipulation System.

    Science.gov (United States)

    1984-06-01

    8217 .°- .. .’". .. ....... ... . ., . . .’.’_. _ .. _. Aplication L a -iza e S iulIa tinet. 1st programs Ianalys’.s.. steo 2nd Results on r RqAWr step disK storage DAAfor data K...1 and 21; (b) the IDA from SPSS (Interactive Data Analysis from the Software Package for Social Sciences); and (c) the presented system, IDAMAN. 14...are the Bio- MeDical Package (BMDP, 1981), and the Statistical Package for the Social Sciences ( SPSS , 1983). 16 BMDP and SPSS are comnlete statistical

  8. Evolution of the interaction between Runx2 and VDR, two transcription factors involved in osteoblastogenesis

    Directory of Open Access Journals (Sweden)

    Barriga Elias H

    2010-03-01

    Full Text Available Abstract Background The mineralized skeleton is a major evolutionary novelty that has contributed to the impressive morphological diversifications of the vertebrates. Essential to bone biology is the solidified extracellular matrix secreted by highly specialized cells, the osteoblasts. We now have a rather complete view of the events underlying osteogenesis, from a cellular, molecular, genetic, and epigenetic perspective. Because this knowledge is still largely restricted to mammals, it is difficult, if not impossible, to deduce the evolutionary history of the regulatory network involved in osteoblasts specification and differentiation. In this study, we focused on the transcriptional regulators Runx2 and VDR (the Vitamin D Receptor that, in mammals, directly interact together and stabilize complexes of co-activators and chromatin remodellers, thereby allowing the transcriptional activation of target genes involved in extracellular matrix mineralization. Using a combination of functional, biochemical, and histological approaches, we have asked if the interaction observed between Runx2 and VDR represents a recent mammalian innovation, or if it results from more ancient changes that have occurred deep in the vertebrate lineage. Results Using immunohistochemistry and in situ hybridization in developing embryos of chick, frog and teleost fishes, we have revealed that the co-expression of Runx2 and VDR in skeletal elements has been particularly strengthened in the lineage leading to amniotes. We show that the teleost Runx2 orthologue as well as the three mammalian Runx1, Runx2 and Runx3 paralogues are able to co-immunoprecipitate with the VDR protein present in nuclear extracts of rat osteoblasts stimulated with 1α,25-dihydroxyvitamin D3. In addition, the teleost Runx2 can activate the transcription of the mammalian osteocalcin promoter in transfection experiments, and this response can be further enhanced by 1α,25-dihydroxyvitamin D3. Finally

  9. Identification of Protein-Protein Interactions Involved in Pectin Biosynthesis in the golgi Apparatus

    DEFF Research Database (Denmark)

    Lund, Christian Have

    GALACTURONOSYLTRANSFERASE1 (GAUT1) and GAUT7 has beesn identified and is essential for pectin biosynthesis. Interestingly, GAUT1 has been shown to be proteolytic processed from its transmembrane anchor domain and its catalytic domain is retained by GAUT7, thus ensuring biosynthesis of HG in the Golgi apparatus. Many...... methods exist in identifying protein-protein interaction (PPI) but many of these are developed for other organisms than plants and are most applicable for PPI detection in other organelles than the Golgi apparatus where pectin biosynthesis occurs. In this work, different PPI detection methods are examined...... for their ability to detect PPI inside the Golgi lumen. The first method tested was the commercially available splitubiquitin system from Dualsystems Biotech AG. This was applied to test binary interactions between proteins involved in HG and Rhamnogalacturonan I (RG-I) biosynthesis (see Manuscript II...

  10. Novel protein-protein interaction family proteins involved in chloroplast movement response.

    Science.gov (United States)

    Kodama, Yutaka; Suetsugu, Noriyuki; Wada, Masamitsu

    2011-04-01

    To optimize photosynthetic activity, chloroplasts change their intracellular location in response to ambient light conditions; chloroplasts move toward low intensity light to maximize light capture, and away from high intensity light to avoid photodamage. Although several proteins have been reported to be involved in the chloroplast photorelocation movement response, any physical interaction among them was not found so far. We recently found a physical interaction between two plant-specific coiled-coil proteins, WEB1 (Weak Chloroplast Movement under Blue Light 1) and PMI2 (Plastid Movement Impaired 2), that were identified to regulate chloroplast movement velocity. Since the both coiled-coil regions of WEB1 and PMI2 were classified into an uncharacterized protein family having DUF827 (DUF: Domain of Unknown Function) domain, it was the first report that DUF827 proteins could mediate protein-protein interaction. In this mini-review article, we discuss regarding molecular function of WEB1 and PMI2, and also define a novel protein family composed of WEB1, PMI2 and WEB1/PMI2-like proteins for protein-protein interaction in land plants.

  11. Proteomic analysis of proteins involved in spermiogenesis in mouse.

    Science.gov (United States)

    Guo, Xuejiang; Shen, Jian; Xia, Zhengrong; Zhang, Rui; Zhang, Ping; Zhao, Chun; Xing, Jun; Chen, Ling; Chen, Wen; Lin, Min; Huo, Ran; Su, Bing; Zhou, Zuomin; Sha, Jiahao

    2010-03-05

    Spermiogenesis is a unique process in mammals during which haploid round spermatids mature into spermatozoa in the testis. Its successful completion is necessary for fertilization and its malfunction is an important cause of male infertility. Here, we report the high-confidence identification of 2116 proteins in mouse haploid germ cells undergoing spermiogenesis: 299 of these were testis-specific and 155 were novel. Analysis of these proteins showed many proteins possibly functioning in unique processes of spermiogenesis. Of the 84 proteins annotated to be involved in vesicle-related events, VAMP4 was shown to be important for acrosome biogenesis by in vivo knockdown experiments. Knockdown of VAMP4 caused defects of acrosomal vesicle fusion and significantly increased head abnormalities in spermatids from testis and sperm from the cauda epididymis. Analysis of chromosomal distribution of the haploid genes showed underrepresentation on the X chromosome and overrepresentation on chromosome 11, which were due to meiotic sex chromosome inactivation and expansion of testis-expressed gene families, respectively. Comparison with transcriptional data showed translational regulation during spermiogenesis. This characterization of proteins involved in spermiogenesis provides an inventory of proteins useful for understanding the mechanisms of male infertility and may provide candidates for drug targets for male contraception and male infertility.

  12. Informational analysis involving application of complex information system

    Science.gov (United States)

    Ciupak, Clébia; Vanti, Adolfo Alberto; Balloni, Antonio José; Espin, Rafael

    The aim of the present research is performing an informal analysis for internal audit involving the application of complex information system based on fuzzy logic. The same has been applied in internal audit involving the integration of the accounting field into the information systems field. The technological advancements can provide improvements to the work performed by the internal audit. Thus we aim to find, in the complex information systems, priorities for the work of internal audit of a high importance Private Institution of Higher Education. The applied method is quali-quantitative, as from the definition of strategic linguistic variables it was possible to transform them into quantitative with the matrix intersection. By means of a case study, where data were collected via interview with the Administrative Pro-Rector, who takes part at the elaboration of the strategic planning of the institution, it was possible to infer analysis concerning points which must be prioritized at the internal audit work. We emphasize that the priorities were identified when processed in a system (of academic use). From the study we can conclude that, starting from these information systems, audit can identify priorities on its work program. Along with plans and strategic objectives of the enterprise, the internal auditor can define operational procedures to work in favor of the attainment of the objectives of the organization.

  13. Generalized Structured Component Analysis with Latent Interactions

    Science.gov (United States)

    Hwang, Heungsun; Ho, Moon-Ho Ringo; Lee, Jonathan

    2010-01-01

    Generalized structured component analysis (GSCA) is a component-based approach to structural equation modeling. In practice, researchers may often be interested in examining the interaction effects of latent variables. However, GSCA has been geared only for the specification and testing of the main effects of variables. Thus, an extension of GSCA…

  14. Representation of analysis results involving aleatory and epistemic uncertainty.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Jay Dean (ProStat, Mesa, AZ); Helton, Jon Craig (Arizona State University, Tempe, AZ); Oberkampf, William Louis; Sallaberry, Cedric J.

    2008-08-01

    Procedures are described for the representation of results in analyses that involve both aleatory uncertainty and epistemic uncertainty, with aleatory uncertainty deriving from an inherent randomness in the behavior of the system under study and epistemic uncertainty deriving from a lack of knowledge about the appropriate values to use for quantities that are assumed to have fixed but poorly known values in the context of a specific study. Aleatory uncertainty is usually represented with probability and leads to cumulative distribution functions (CDFs) or complementary cumulative distribution functions (CCDFs) for analysis results of interest. Several mathematical structures are available for the representation of epistemic uncertainty, including interval analysis, possibility theory, evidence theory and probability theory. In the presence of epistemic uncertainty, there is not a single CDF or CCDF for a given analysis result. Rather, there is a family of CDFs and a corresponding family of CCDFs that derive from epistemic uncertainty and have an uncertainty structure that derives from the particular uncertainty structure (i.e., interval analysis, possibility theory, evidence theory, probability theory) used to represent epistemic uncertainty. Graphical formats for the representation of epistemic uncertainty in families of CDFs and CCDFs are investigated and presented for the indicated characterizations of epistemic uncertainty.

  15. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    Science.gov (United States)

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations.

  16. VIGS for dissecting mechanisms involved in the symbiotic interaction of microbes with plants

    DEFF Research Database (Denmark)

    Grønlund, Mette

    2015-01-01

    Virus-induced gene silencing (VIGS) is an alternative reverse genetics tool for silencing of genes in some plants which are difficult to transform. The pea early browning virus (PEBV) has been developed as a VIGS vector and used in pea for functional analysis of several genes. Here, a PEBV-VIGS p......-VIGS protocol is described which is suitable for reverse genetics studies in pea for genes involved in the symbiosis with arbuscular mycorrhizal fungi and Rhizobium....

  17. SpecViz: Interactive Spectral Data Analysis

    Science.gov (United States)

    Earl, Nicholas Michael; STScI

    2016-06-01

    The astronomical community is about to enter a new generation of scientific enterprise. With next-generation instrumentation and advanced capabilities, the need has arisen to equip astronomers with the necessary tools to deal with large, multi-faceted data. The Space Telescope Science Institute has initiated a data analysis forum for the creation, development, and maintenance of software tools for the interpretation of these new data sets. SpecViz is a spectral 1-D interactive visualization and analysis application built with Python in an open source development environment. A user-friendly GUI allows for a fast, interactive approach to spectral analysis. SpecViz supports handling of unique and instrument-specific data, incorporation of advanced spectral unit handling and conversions in a flexible, high-performance interactive plotting environment. Active spectral feature analysis is possible through interactive measurement and statistical tools. It can be used to build wide-band SEDs, with the capability of combining or overplotting data products from various instruments. SpecViz sports advanced toolsets for filtering and detrending spectral lines; identifying, isolating, and manipulating spectral features; as well as utilizing spectral templates for renormalizing data in an interactive way. SpecViz also includes a flexible model fitting toolset that allows for multi-component models, as well as custom models, to be used with various fitting and decomposition routines. SpecViz also features robust extension via custom data loaders and connection to the central communication system underneath the interface for more advanced control. Incorporation with Jupyter notebooks via connection with the active iPython kernel allows for SpecViz to be used in addition to a user’s normal workflow without demanding the user drastically alter their method of data analysis. In addition, SpecViz allows the interactive analysis of multi-object spectroscopy in the same straight

  18. Hypersensitivity reactions to fluoroquinolones: analysis of the factors involved.

    Science.gov (United States)

    Blanca-López, N; Ariza, A; Doña, I; Mayorga, C; Montañez, M I; Garcia-Campos, J; Gomez, F; Rondón, C; Blanca, M; Torres, M J

    2013-05-01

    Hypersensitivity reactions to fluoroquinolones seem to be on the increase, especially immediate type reactions. The aim of this study was to determine whether several conditions, including gender, age, type of reaction, time interval between the reaction and the study, type of symptoms, the specific fluoroquinolone involved in the reaction and previous confirmed hypersensitivity to betalactams or to other drugs were factors contributing to the development of hypersensitivity to fluoroquinolones. We analysed retrospectively all patients attending our allergy department between January 2005 and December 2010 because of a reaction associated with fluoroquinolone administration. The diagnosis was confirmed by basophil activation test or drug provocation tests. In accordance with the results, patients were then classified as having hypersensitivity or non-hypersensitivity to fluoroquinolones. A group of 218 patients was evaluated; 69 were confirmed as having hypersensitivity, 146 as non-hypersensitivity and 3 were excluded. Comparisons between groups showed that the allergic patients more often had a previous confirmed hypersensitivity to betalactams (P = 0.029), immediate reactions (P = 0.001) and anaphylaxis (P = 0.000), and moxifloxacin was the fluoroquinolone most frequently involved (P = 0.027). The logistic regression analysis showed three factors associated with the diagnosis of hypersensitivity reactions to fluoroquinolones: previous hypersensitivity to betalactams (OR: 4.571; 95% CI: 0.987-21.171; adjusted OR: 23.654; 95% CI: 1.529-365.853), immediate reactions (OR: 17.333; 95% CI: 4.374-68.691; adjusted OR: 52.493; 95% CI: 6.621-416.200) and reactions induced by moxifloxacin (OR: 3.091; 95% CI: 1.160-8.239; adjusted OR: 13.610; 95% CI: 2.419-76.565). In patients who develop reactions to fluoroquinolones, hypersensitivity is more often confirmed in those with immediate reactions and when moxifloxacin is involved. Moreover, patients with hypersensitivity to

  19. A Computational Study of the Interaction and Polarization Effects of Complexes Involving Molecular Graphene and C60 or a Nucleobases.

    Science.gov (United States)

    Avramopoulos, Aggelos; Otero, Nicolás; Karamanis, Panaghiotis; Pouchan, Claude; Papadopoulos, Manthos G

    2016-01-21

    A systematic analysis of the molecular structure, energetics, electronic (hyper)polarizabilities and their interaction-induced counterparts of C60 with a series of molecular graphene (MG) models, CmHn, where m = 24, 84, 114, 222, 366, 546 and n = 12, 24, 30, 42, 54, 66, was performed. All the reported data were computed by employing density functional theory and a series of basis sets. The main goal of the study is to investigate how alteration of the size of the MG model affects the strength of the interaction, charge rearrangement, and polarization and interaction-induced polarization of the complex, C60-MG. A Hirshfeld-based scheme has been employed in order to provide information on the intrinsic polarizability density representations of the reported complexes. It was found that the interaction energy increases approaching a limit of -26.98 kcal/mol for m = 366 and 546; the polarizability and second hyperpolarizability increase with increasing the size of MG. An opposite trend was observed for the dipole moment. Interestingly, the variation of the first hyperpolarizability is relatively small with m. Since polarizability is a key factor for the stability of molecular graphene with nucleobases (NB), a study of the magnitude of the interaction-induced polarizability of C84H24-NB complexes is also reported, aiming to reveal changes of its magnitude with the type of NB. The binding strength of C84H24-NB complexes is also computed and found to be in agreement with available theoretical and experimental data. The interaction involved in C60 B12N12H24-NB complexes has also been considered, featuring the effect of contamination on the binding strength between MG and NBs.

  20. The Longitudinal Process of Early Parent Involvement on Student Achievement: A Path Analysis.

    Science.gov (United States)

    Hayakawa, Momoko; Englund, Michelle M; Warner-Richter, Mallory N; Reynolds, Arthur J

    2013-01-01

    This longitudinal study investigated the process whereby early parent involvement in preschool effects student achievement from kindergarten through 6(th) grade. Participants were 1,539 low-income, mainly African American children and their mothers, in the Chicago Longitudinal Study. Program children (N = 989) received one or two years of the Child-Parent Center (CPC) program - a preschool intervention that strongly promoted parents' development of parent involvement skills within the school and at home. Children from similar backgrounds who did not attend the CPC, but participated in available local resources (e.g. day care), were obtained as a comparison group (N = 550). Path analysis revealed an interactive process between parent involvement, academic achievement, and children's motivation. Early parent involvement directly influenced kindergarten achievement, which in turn influenced first grade student motivation. Highly motivated children then encouraged parents to continue involvement. The cyclic nature of this process across elementary school was observed. The model accounted for 61% of the variance in 6(th) grade achievement. Findings suggest that early parent involvement promoted in the CPC program, sets the stage for subsequent parent involvement, student motivation, and academic achievement throughout early and middle childhood.

  1. Interactions involving ozone, Botrytis cinerea, and B. squamosa on onion leaves

    Energy Technology Data Exchange (ETDEWEB)

    Rist, D.L.

    1983-01-01

    Interactions involving Botrytis cinerea Pers., B. squamosa Walker, and ozone on onion (alium cepae L.) were investigated. Initially, threshold dosages of ozone required to predispose onion leaves to greater infection by B. cinerea and B. squamosa were determined under controlled conditions in an ozone-exposure chamber. Subsequent experiments supported the hypothesis that nutrients leaking out of ozone-injured cells stimulated lesion production by B. cinerea. The electrical conductivity of, and carbohydrate concentration in, dew collected from leaves of onion plants which had been exposed to ozone were greater than the electrical conductivity of, and carbohydrate concentration in, dew collected from leaves of other, non-exposed onion plants. When conidia of B. cinerea were suspended in dew collected from leaves of plants which had been exposed to ozone and the resulting suspension atomized onto leaves of non-exposed plants, more lesions were induced than on leaves of other non-exposed plants inoculated with conidia suspended in dew collected from plants which had not been exposed to ozone. EDU protected onion leaves from ozone-induced predisposition to these fungi under controlled conditions. Experiments designed to detect interaction between B. cinerea and B. squamosa in onion leaf blighting indicated that such interaction did not occur. Leaves were blighted rapidly when inoculated with B. squamosa whether B. cinerea was present or absent.

  2. An Atomic Force Microscopy Study of the Interactions Involving Polymers and Silane Networks

    Directory of Open Access Journals (Sweden)

    Rodrigo L. Oréfice

    1998-12-01

    Full Text Available ABSTRACT: Silane coupling agents have been frequently used as interfacial agents in polymer composites to improve interfacial strength and resistance to fluid migration. Although the capability of these agents in improving properties and performance of composites has been reported, there are still many uncertainties regarding the processing-structure-property relationships and the mechanisms of coupling developed by silane agents. In this work, an Atomic Force Microscope (AFM was used to measure interactions between polymers and silica substrates, where silane networks with a series of different structures were processed. The influence of the structure of silane networks on the interactions with polymers was studied and used to determine the mechanisms involved in the coupling phenomenon. The AFM results showed that phenomena such as chain penetration, entanglements, intersegment bonding, chain conformation in the vicinities of rigid surfaces were identified as being relevant for the overall processes of adhesion and adsorption of polymeric chains within a silane network. AFM adhesion curves showed that penetration of polymeric chains through a more open silane network can lead to higher levels of interactions between polymer and silane agents.

  3. Bifidobacterial enolase, a cell surface receptor for human plasminogen involved in the interaction with the host.

    Science.gov (United States)

    Candela, Marco; Biagi, Elena; Centanni, Manuela; Turroni, Silvia; Vici, Manuela; Musiani, Francesco; Vitali, Beatrice; Bergmann, Simone; Hammerschmidt, Sven; Brigidi, Patrizia

    2009-10-01

    The interaction with the host plasminogen/plasmin system represents a novel component in the molecular cross-talk between bifidobacteria and human host. Here, we demonstrated that the plasminogen-binding bifidobacterial species B. longum, B. bifidum, B. breve and B. lactis share the key glycolytic enzyme enolase as a surface receptor for human plasminogen. Enolase was visualized on the cell surface of the model strain B. lactis BI07. The His-tagged recombinant protein showed a high affinity for human plasminogen, with an equilibrium dissociation constant in the nanomolar range. By site-directed mutagenesis we demonstrated that the interaction between the B. lactis BI07 enolase and human plasminogen involves an internal plasminogen-binding site homologous to that of pneumococcal enolase. According to our data, the positively charged residues Lys-251 and Lys-255, as well as the negatively charged Glu-252, of the B. lactis BI07 enolase are crucial for plasminogen binding. Acting as a human plasminogen receptor, the bifidobacterial surface enolase is suggested to play an important role in the interaction process with the host.

  4. Management of the Benefits on the Client's Involvement on Ergonomic Analysis

    Science.gov (United States)

    Loureiro, Isabel F.; Leão, Celina P.; Arezes, Pedro

    Nowadays, market trade economy is witnessing to a continuous development and transformation. The organizations come to be seen as sociotechnical systems with new ergonomic contexts. Various types of relationships can be established. From the ergonomic analysis point of view, it is necessary to understand all the mechanisms that regulate these relationships. The interaction between clients and professionals (workers) reproduce a relationship that can be important to the ergonomic analysis. This paper allows a better comprehension of the relationship in the effective's ergonomic intervention. A case study was analyzed in a private health sector using the Ergonomic Three-dimension Analysis as an ergonomic approach. This analysis is made by three different but related dimensions: analyst, professional and client. The results show that that clients' involvement in the ergonomic analysis will benefit the ergonomic intervention and consequently the professional environment.

  5. Involvement of apoptosis in host-parasite interactions in the zebra mussel.

    Science.gov (United States)

    Minguez, Laëtitia; Brulé, Nelly; Sohm, Bénédicte; Devin, Simon; Giambérini, Laure

    2013-01-01

    The question of whether cell death by apoptosis plays a biological function during infection is key to understanding host-parasite interactions. We investigated the involvement of apoptosis in several host-parasite systems, using zebra mussels Dreissena polymorpha as test organisms and their micro- and macroparasites. As a stress response associated with parasitism, heat shock proteins (Hsp) can be induced. In this protein family, Hsp70 are known to be apoptosis inhibitors. Mussels were diagnosed for their respective infections by standard histological methods; apoptosis was detected using the TUNEL methods on paraffin sections and Hsp70 by immunohistochemistry on cryosections. Circulating hemocytes were the main cells observed in apoptosis whereas infected tissues displayed no or few apoptotic cells. Parasitism by intracellular bacteria Rickettsiales-like and the trematode Bucephalus polymorphus were associated with the inhibition of apoptosis whereas ciliates Ophryoglena spp. or the trematode Phyllodistomum folium did not involve significant differences in apoptosis. Even if some parasites were able to modulate apoptosis in zebra mussels, we did not see evidence of any involvement of Hsp70 on this mechanism.

  6. Involvement of apoptosis in host-parasite interactions in the zebra mussel.

    Directory of Open Access Journals (Sweden)

    Laëtitia Minguez

    Full Text Available The question of whether cell death by apoptosis plays a biological function during infection is key to understanding host-parasite interactions. We investigated the involvement of apoptosis in several host-parasite systems, using zebra mussels Dreissena polymorpha as test organisms and their micro- and macroparasites. As a stress response associated with parasitism, heat shock proteins (Hsp can be induced. In this protein family, Hsp70 are known to be apoptosis inhibitors. Mussels were diagnosed for their respective infections by standard histological methods; apoptosis was detected using the TUNEL methods on paraffin sections and Hsp70 by immunohistochemistry on cryosections. Circulating hemocytes were the main cells observed in apoptosis whereas infected tissues displayed no or few apoptotic cells. Parasitism by intracellular bacteria Rickettsiales-like and the trematode Bucephalus polymorphus were associated with the inhibition of apoptosis whereas ciliates Ophryoglena spp. or the trematode Phyllodistomum folium did not involve significant differences in apoptosis. Even if some parasites were able to modulate apoptosis in zebra mussels, we did not see evidence of any involvement of Hsp70 on this mechanism.

  7. Interaction analysis and psychology: a dialogical perspective.

    Science.gov (United States)

    Grossen, Michèle

    2010-03-01

    Interaction analysis is not a prerogative of any discipline in social sciences. It has its own history within each disciplinary field and is related to specific research objects. From the standpoint of psychology, this article first draws upon a distinction between factorial and dialogical conceptions of interaction. It then briefly presents the basis of a dialogical approach in psychology and focuses upon four basic assumptions. Each of them is examined on a theoretical and on a methodological level with a leading question: to what extent is it possible to develop analytical tools that are fully coherent with dialogical assumptions? The conclusion stresses the difficulty of developing methodological tools that are fully consistent with dialogical assumptions and argues that there is an unavoidable tension between accounting for the complexity of an interaction and using methodological tools which necessarily "monologise" this complexity.

  8. Analysis of Human-Spacesuit Interaction

    Science.gov (United States)

    Thomas, Neha

    2015-01-01

    Astronauts sustain injuries of various natures such as finger delamination, joint pain, and redness due to their interaction with the space suit. The role of the Anthropometry and Biomechanics Facility is to understand the biomechanics, environmental variables, and ergonomics of the suit. This knowledge is then used to make suggestions for improvement in future iterations of the space suit assembly to prevent injuries while allowing astronauts maneuverability, comfort, and tactility. The projects I was involved in were the Extravehicular Mobility Unit (EMU) space suit stiffness study and the glove feasibility study. The EMU project looked at the forces exerted on the shoulder, arm, and wrist when subjects performed kinematic tasks with and without a pressurized suit. The glove study consisted of testing three conditions - the Series 4000 glove, the Phase VI glove, and the no glove condition. With more than forty channels of sensor data total, it was critical to develop programs that could analyze data with basic descriptive statistics and generate relevant graphs to help understand what happens within the space suit and glove. In my project I created a Graphical User Interface (GUI) in MATLAB that would help me visualize what each sensor was doing within a task. The GUI is capable of displaying overlain plots and can be synchronized with video. This was helpful during the stiffness testing to visualize how the forces on the arm acted while the subject performed tasks such as shoulder adduction/abduction and bicep curls. The main project of focus, however, was the glove comparison study. I wrote MATLAB programs which generated movies of the strain vectors during specific tasks. I also generated graphs that summarized the differences between each glove for the strain, shear and FSR sensors. Preliminary results indicate that the Phase VI glove places less strain and shear on the hand. Future work includes continued data analysis of surveys and sensor data. In the end

  9. Identification of sequence motifs involved in Dengue virus-host interactions.

    Science.gov (United States)

    Asnet Mary, J; Paramasivan, R; Shenbagarathai, R

    2016-01-01

    Dengue fever is a rapidly spreading mosquito-borne virus infection, which remains a serious global public health problem. As there is no specific treatment or commercial vaccine available for effective control of the disease, the attempts on developing novel control strategies are underway. Viruses utilize the surface receptor proteins of host to enter into the cells. Though various proteins were said to be receptors of Dengue virus (DENV) using Virus Overlay Protein Binding Assay, the precise interaction between DENV and host is not explored. Understanding the structural features of domain III envelope glycoprotein would help in developing efficient antiviral inhibitors. Therefore, an attempt was made to identify the sequence motifs present in domain III envelope glycoprotein of Dengue virus. Computational analysis revealed that the NGR motif is present in the domain III envelope glycoprotein of DENV-1 and DENV-3. Similarly, DENV-1, DENV-2 and DENV-4 were found to contain Yxxphi motif which is a tyrosine-based sorting signal responsible for the interaction with a mu subunit of adaptor protein complex. High-throughput virtual screening resulted in five compounds as lead molecules based on glide score, which ranges from -4.664 to -6.52 kcal/Mol. This computational prediction provides an additional tool for understanding the virus-host interactions and helps to identify potential targets in the host. Further, experimental evidence is warranted to confirm the virus-host interactions and also inhibitory activity of reported lead compounds.

  10. Characterization of aid1, a novel gene involved in Fusobacterium nucleatum interspecies interactions.

    Science.gov (United States)

    Kaplan, Aida; Kaplan, Christopher W; He, Xuesong; McHardy, Ian; Shi, Wenyuan; Lux, Renate

    2014-08-01

    The oral opportunistic pathogen Fusobacterium nucleatum is known to interact with a large number of different bacterial species residing in the oral cavity. It adheres to a variety of Gram-positive bacteria, including oral streptococci via the arginine-inhibitable adhesin RadD. In this study, we describe a novel protein encoded by the predicted open reading frame FN1253 that appears to play a role in interspecies interactions of F. nucleatum, particularly with oral streptococci and related Gram-positive species. We designated FN1253 as aid1 (Adherence Inducing Determinant 1). Expression analyses demonstrated that this gene was induced in F. nucleatum single species biofilms, while the presence of representative members of the oral microbiota known to adhere to F. nucleatum triggered its suppression. Inactivation as well as overexpression of aid1 affected the ability of F. nucleatum to coaggregate with oral streptococci and the closely related Enterococcus faecalis, but not other Gram-positive oral species tested. Furthermore, overexpression of aid1 led to a drastic change in the structure of dual species biofilms of F. nucleatum with oral streptococci. Aid1 function was abolished in the presence of arginine and found to be dependent on RadD. Interestingly, differential expression of aid1 did not affect messenger RNA and protein levels of RadD. These findings indicate that RadD-mediated adhesion to oral streptococci involves more complex cellular processes than the simple interaction of adhesins on the surface of partner strains. Aid1 could potentially play an important role in facilitating RadD-mediated interaction with oral streptococci by increasing binding specificity of F. nucleatum to other microbial species.

  11. Thermodynamic Analysis of Interacting Nucleic Acid Strands

    OpenAIRE

    Dirks, Robert M.; Bois, Justin S.; Schaeffer, Joseph M.; Winfree, Erik; Pierce, Niles A.

    2007-01-01

    Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed...

  12. Proteomic analysis of SETD6 interacting proteins.

    Science.gov (United States)

    Cohn, Ofir; Chen, Ayelet; Feldman, Michal; Levy, Dan

    2016-03-01

    SETD6 (SET-domain-containing protein 6) is a mono-methyltransferase that has been shown to methylate RelA and H2AZ. Using a proteomic approach we recently identified several new SETD6 substrates. To identify novel SETD6 interacting proteins, SETD6 was immunoprecipitated (IP) from Human erythromyeloblastoid leukemia K562 cells. SETD6 binding proteins were subjected to mass-spectrometry analysis resulting in 115 new SETD6 binding candidates. STRING database was used to map the SETD6 interactome network. Network enrichment analysis of biological processes with Gene Ontology (GO) database, identified three major groups; metabolic processes, muscle contraction and protein folding.

  13. Low cost real time interactive analysis system

    Science.gov (United States)

    Stetina, F.

    1988-01-01

    Efforts continue to develop a low cost real time interactive analysis system for the reception of satellite data. A multi-purpose ingest hardware software frame formatter was demonstrated for GOES and TIROS data and work is proceeding on extending the capability to receive GMS data. A similar system was proposed as an archival and analysis system for use with INSAT data and studies are underway to modify the system to receive the planned SeaWiFS (ocean color) data. This system was proposed as the core of a number of international programs in support of U.S. AID activities. Systems delivered or nearing final testing are listed.

  14. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma.

    Science.gov (United States)

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

  15. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma

    Science.gov (United States)

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite; Dos Santos, Laurita; Martin, Airton Abrahão; Rogatto, Silvia Regina; De Azevedo Canevari, Renata

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study was to determine whether protein phosphatase Mg2+/Mn2+ dependent 1D, β-1,3-N-acetylglucosaminyltransferase, neural precursor cell expressed, developmentally down-regulated 9, prohibitin, phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5), phosphatidylinositol-5-phosphate 4-kinase type IIα, TRF1-interacting ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse transcription-quantitative polymerase chain reaction analysis was performed on primary breast tumor tissues from women with negative lymph node involvement (n=27) compared with primary tumor tissues from women with positive lymph node involvement (n=23), and was also performed on primary tumors and paired lymph node metastases (n=11). For all genes analyzed, only the PIK3R5 gene exhibited differential expression in samples of primary tumors with positive lymph node involvement compared with primary tumors with negative lymph node involvement (P=0.0347). These results demonstrate that the PIK3R5 gene may be considered predictive of lymph node involvement in breast carcinoma. Although the other genes evaluated in the present study have been previously characterized to be involved with

  16. Molecular Basis of Gene-Gene Interaction: Cyclic Cross-Regulation of Gene Expression and Post-GWAS Gene-Gene Interaction Involved in Atrial Fibrillation.

    Directory of Open Access Journals (Sweden)

    Yufeng Huang

    2015-08-01

    Full Text Available Atrial fibrillation (AF is the most common cardiac arrhythmia at the clinic. Recent GWAS identified several variants associated with AF, but they account for <10% of heritability. Gene-gene interaction is assumed to account for a significant portion of missing heritability. Among GWAS loci for AF, only three were replicated in the Chinese Han population, including SNP rs2106261 (G/A substitution in ZFHX3, rs2200733 (C/T substitution near PITX2c, and rs3807989 (A/G substitution in CAV1. Thus, we analyzed the interaction among these three AF loci. We demonstrated significant interaction between rs2106261 and rs2200733 in three independent populations and combined population with 2,020 cases/5,315 controls. Compared to non-risk genotype GGCC, two-locus risk genotype AATT showed the highest odds ratio in three independent populations and the combined population (OR=5.36 (95% CI 3.87-7.43, P=8.00×10-24. The OR of 5.36 for AATT was significantly higher than the combined OR of 3.31 for both GGTT and AACC, suggesting a synergistic interaction between rs2106261 and rs2200733. Relative excess risk due to interaction (RERI analysis also revealed significant interaction between rs2106261 and rs2200733 when exposed two copies of risk alleles (RERI=2.87, P<1.00×10-4 or exposed to one additional copy of risk allele (RERI=1.29, P<1.00×10-4. The INTERSNP program identified significant genotypic interaction between rs2106261 and rs2200733 under an additive by additive model (OR=0.85, 95% CI: 0.74-0.97, P=0.02. Mechanistically, PITX2c negatively regulates expression of miR-1, which negatively regulates expression of ZFHX3, resulting in a positive regulation of ZFHX3 by PITX2c; ZFHX3 positively regulates expression of PITX2C, resulting in a cyclic loop of cross-regulation between ZFHX3 and PITX2c. Both ZFHX3 and PITX2c regulate expression of NPPA, TBX5 and NKX2.5. These results suggest that cyclic cross-regulation of gene expression is a molecular basis for gene

  17. Mapping of the molecular determinants involved in the interaction between eps15 and AP-2

    DEFF Research Database (Denmark)

    Iannolo, G; Salcini, A E; Gaidarov, I

    1997-01-01

    domain, located in its NH2-terminal region. In addition, a proline-rich region, located in the COOH-terminal portion of eps15, can bind to the Src homology 3 domain of the crk proto-oncogene product in vitro. Recently, coimmunoprecipitation between eps15 and AP-2, a major component of coated pits......, was reported. Here, we characterize the molecular determinants of the eps15/AP-2 interaction. The AP-2 binding region of eps15 is localized in its COOH-terminal region and spans approximately 80 amino acids. At least three molecular determinants, located at residues 650-660, 680-690, and 720-730, are involved...... in the binding. AP-2 binds to eps15 through its alpha subunit (alpha-adaptin); in particular, the COOH-terminal region of alpha-adaptin, the so-called alpha-ear, contains the eps15 binding region....

  18. Involvement of lipid-protein complexes in plant-microorganism interactions

    Directory of Open Access Journals (Sweden)

    Blein Jean-Pierre

    2002-01-01

    Full Text Available Increasing concerns about the environmental impact of modern agricultural have prompted research for alternate practices to pesticide treatments, notably using plant defense mechanisms. Thus, isolation and characterization of plant defense elicitors have been the main step of studies in many groups. Moreover, in the global concept of interactions between organisms and their environment, a major concern is to discriminate recognition between exogenous and endogenous signals, notably during pathogenic or allergenic interactions involving small proteins, such as elicitins or lipid transfer proteins (LTPs. Elicitins and lipid transfer proteins (LTP are both able to load and transfer lipidic molecules and share some structural and functional properties. While elicitins are known as elicitors of plant defense mechanisms, the biological function of LTPs is still an enigma. They are ubiquitous plant proteins able to load and transfer hydrophobic molecules such as fatty acids or phospholipids. Among them, LTPs1 (type 1 lipid transfer proteins constitute a multigenic family of secreted plant lipid binding proteins that are constitutively expressed in specific tissues and/or induced in response to biotic and abiotic stress (for reviews [1-4]. Their biological function is still unknown, even if some data provide arguments for a role of these proteins in the assembly of extracellular hydrophobic polymers (i.e., cutin and suberin [2, 4] and/or in plant defense against fungal pathogens [1, 3]. Beside their involvement in plant defense, LTPs1 are also known to be pan-allergens of plant-derived foods [5]. Finally, the discovery of the sterol carrier-properties of elicitins has opened new perspectives dealing with the relationship between this function and the elicitor activity of these small cystein-rich proteins. Nevertheless, this elicitor activity is restrained to few plant species, and thus does not appear in accordance with a universal lipid transfer

  19. Interactions between salinity and boron toxicity in tomato plants involve apoplastic calcium.

    Science.gov (United States)

    Bastías, Elizabeth; Alcaraz-López, Carlos; Bonilla, Ildefonso; Martínez-Ballesta, M Carmen; Bolaños, Luis; Carvajal, Micaela

    2010-01-01

    The lack of consensus about the mutual relations between salinity and boron (B) toxicity with respect to the physiological response of plants necessitates investigation of the interactions of soluble B with salinity. In this investigation, the effect of B was compared with Ca in order to elucidate whether the two nutrients have similar effects and/or to elucidate a relationship under salinity. Following addition of B or Ca, salinity was applied to tomato plants and the cell wall and plasma membrane permeability, measured as water permeability and electrolyte leakage, in relation to amino acid and ion cell wall composition, were determined. As the relationship between B and salinity was complex, several hypotheses are established. The increase of aquaporin functionality due to the presence of B and Ca compared with NaCl-treated plants could be the most feasible, whereas there is currently no satisfactory explanation for the results for the cell wall amino acid composition. In addition, the elemental composition results revealed that, in addition the known interactions between B and Ca with respect to cell wall stability, Mg and Mn were also increased in NaCl+B and NaCl+Ca treatments, suggesting their possible involvement in the cell wall function necessary for plant growth.

  20. Salmonella biofilm formation on Aspergillus niger involves cellulose--chitin interactions.

    Directory of Open Access Journals (Sweden)

    Maria T Brandl

    Full Text Available Salmonella cycles between host and nonhost environments, where it can become an active member of complex microbial communities. The role of fungi in the environmental adaptation of enteric pathogens remains relatively unexplored. We have discovered that S. enterica Typhimurium rapidly attaches to and forms biofilms on the hyphae of the common fungus, Aspergillus niger. Several Salmonella enterica serovars displayed a similar interaction, whereas other bacterial species were unable to bind to the fungus. Bacterial attachment to chitin, a major constituent of fungal cell walls, mirrored this specificity. Pre-incubation of S. Typhimurium with N-acetylglucosamine, the monomeric component of chitin, reduced binding to chitin beads by as much as 727-fold and inhibited attachment to A. niger hyphae considerably. A cellulose-deficient mutant of S. Typhimurium failed to attach to chitin beads and to the fungus. Complementation of this mutant with the cellulose operon restored binding to chitin beads to 79% of that of the parental strain and allowed for attachment and biofilm formation on A. niger, indicating that cellulose is involved in bacterial attachment to the fungus via the chitin component of its cell wall. In contrast to cellulose, S. Typhimurium curli fimbriae were not required for attachment and biofilm development on the hyphae but were critical for its stability. Our results suggest that cellulose-chitin interactions are required for the production of mixed Salmonella-A. niger biofilms, and support the hypothesis that encounters with chitinaceous alternate hosts may contribute to the ecological success of human pathogens.

  1. University Physics Students' Use of Models in Explanations of Phenomena Involving Interaction between Metals and Electromagnetic Radiation.

    Science.gov (United States)

    Redfors, Andreas; Ryder, Jim

    2001-01-01

    Examines third year university physics students' use of models when explaining familiar phenomena involving interaction between metals and electromagnetic radiation. Concludes that few students use a single model consistently. (Contains 27 references.) (DDR)

  2. Training in Compensatory Strategies Enhances Rapport in Interactions Involving People with Möbius Syndrome

    Directory of Open Access Journals (Sweden)

    John eMichael

    2015-10-01

    Full Text Available In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius Syndrome (MS to increase the use of alternative communication strategies (e.g. gestures to compensate for their lack of facial expressiveness. Specifically, we expected the intervention to increase the level of rapport experienced in social interactions by our participants. In addition, we aimed to identify the mechanisms responsible for any such increase in rapport. In the study, five teenagers with MS interacted with three naïve participants without MS before the intervention, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual nonverbal behavior was assessed via behavioral coders, while verbal behavior was automatically extracted from the sound files. Alignment was assessed using cross recurrence quantification analysis and mixed effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased in participants with and without MS, while overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact nonverbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing, while decreasing alignment.

  3. Training in Compensatory Strategies Enhances Rapport in Interactions Involving People with Möbius Syndrome

    Science.gov (United States)

    Michael, John; Bogart, Kathleen; Tylén, Kristian; Krueger, Joel; Bech, Morten; Østergaard, John Rosendahl; Fusaroli, Riccardo

    2015-01-01

    In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius syndrome (MS) to increase the use of alternative communication strategies (e.g., gestures) to compensate for their lack of facial expressivity. Specifically, we expected the intervention to increase the level of rapport experienced in social interactions by our participants. In addition, we aimed to identify the mechanisms responsible for any such increase in rapport. In the study, five teenagers with MS interacted with three naïve participants without MS before the intervention, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual non-verbal behavior was assessed via behavioral coders, whereas verbal behavior was automatically extracted from the sound files. Alignment was assessed using cross recurrence quantification analysis and mixed-effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased in participants with and without MS, whereas overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact non-verbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing, while decreasing alignment. PMID:26500605

  4. Training in Compensatory Strategies Enhances Rapport in Interactions Involving People with Möbius Syndrome.

    Science.gov (United States)

    Michael, John; Bogart, Kathleen; Tylén, Kristian; Krueger, Joel; Bech, Morten; Østergaard, John Rosendahl; Fusaroli, Riccardo

    2015-01-01

    In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius syndrome (MS) to increase the use of alternative communication strategies (e.g., gestures) to compensate for their lack of facial expressivity. Specifically, we expected the intervention to increase the level of rapport experienced in social interactions by our participants. In addition, we aimed to identify the mechanisms responsible for any such increase in rapport. In the study, five teenagers with MS interacted with three naïve participants without MS before the intervention, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual non-verbal behavior was assessed via behavioral coders, whereas verbal behavior was automatically extracted from the sound files. Alignment was assessed using cross recurrence quantification analysis and mixed-effects models. The results showed that observer-coded rapport was greater after the intervention, whereas self-reported rapport did not change significantly. Observer-coded gesture and expressivity increased in participants with and without MS, whereas overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact non-verbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing, while decreasing alignment.

  5. Interactive analysis of geodata based intelligence

    Science.gov (United States)

    Wagner, Boris; Eck, Ralf; Unmüessig, Gabriel; Peinsipp-Byma, Elisabeth

    2016-05-01

    When a spatiotemporal events happens, multi-source intelligence data is gathered to understand the problem, and strategies for solving the problem are investigated. The difficulties arising from handling spatial and temporal intelligence data represent the main problem. The map might be the bridge to visualize the data and to get the most understand model for all stakeholders. For the analysis of geodata based intelligence data, a software was developed as a working environment that combines geodata with optimized ergonomics. The interaction with the common operational picture (COP) is so essentially facilitated. The composition of the COP is based on geodata services, which are normalized by international standards of the Open Geospatial Consortium (OGC). The basic geodata are combined with intelligence data from images (IMINT) and humans (HUMINT), stored in a NATO Coalition Shared Data Server (CSD). These intelligence data can be combined with further information sources, i.e., live sensors. As a result a COP is generated and an interaction suitable for the specific workspace is added. This allows the users to work interactively with the COP, i.e., searching with an on board CSD client for suitable intelligence data and integrate them into the COP. Furthermore, users can enrich the scenario with findings out of the data of interactive live sensors and add data from other sources. This allows intelligence services to contribute effectively to the process by what military and disaster management are organized.

  6. The Prediction of Key Cytoskeleton Components Involved in Glomerular Diseases Based on a Protein-Protein Interaction Network.

    Directory of Open Access Journals (Sweden)

    Fangrui Ding

    Full Text Available Maintenance of the physiological morphologies of different types of cells and tissues is essential for the normal functioning of each system in the human body. Dynamic variations in cell and tissue morphologies depend on accurate adjustments of the cytoskeletal system. The cytoskeletal system in the glomerulus plays a key role in the normal process of kidney filtration. To enhance the understanding of the possible roles of the cytoskeleton in glomerular diseases, we constructed the Glomerular Cytoskeleton Network (GCNet, which shows the protein-protein interaction network in the glomerulus, and identified several possible key cytoskeletal components involved in glomerular diseases. In this study, genes/proteins annotated to the cytoskeleton were detected by Gene Ontology analysis, and glomerulus-enriched genes were selected from nine available glomerular expression datasets. Then, the GCNet was generated by combining these two sets of information. To predict the possible key cytoskeleton components in glomerular diseases, we then examined the common regulation of the genes in GCNet in the context of five glomerular diseases based on their transcriptomic data. As a result, twenty-one cytoskeleton components as potential candidate were highlighted for consistently down- or up-regulating in all five glomerular diseases. And then, these candidates were examined in relation to existing known glomerular diseases and genes to determine their possible functions and interactions. In addition, the mRNA levels of these candidates were also validated in a puromycin aminonucleoside(PAN induced rat nephropathy model and were also matched with existing Diabetic Nephropathy (DN transcriptomic data. As a result, there are 15 of 21 candidates in PAN induced nephropathy model were consistent with our predication and also 12 of 21 candidates were matched with differentially expressed genes in the DN transcriptomic data. By providing a novel interaction network and

  7. Pleiotropic effect of disrupting a conserved sequence involved in a long-range compensatory interaction in the Drosophila Adh gene.

    Science.gov (United States)

    Baines, John F; Parsch, John; Stephan, Wolfgang

    2004-01-01

    Recent advances in experimental analyses of the evolution of RNA secondary structures suggest a more complex scenario than that typically considered by Kimura's classical model of compensatory evolution. In this study, we examine one such case in more detail. Previous experimental analysis of long-range compensatory interactions between the two ends of Drosophila Adh mRNA failed to fit the classical model of compensatory evolution. To further investigate and verify long-range pairing in Drosophila Adh with respect to models of compensatory evolution and its potential functional role, we introduced site-directed mutations in the Drosophila melanogaster Adh gene. We explore two alternative hypotheses for why previous analysis of long-range compensatory interactions failed to fit the classical model. Specifically, we investigate whether the disruption of a conserved short-range pairing within Adh exon 2 has an effect on Adh expression or if there is a dual functional role of a conserved sequence in the 3'-UTR in both long-range pairing and the negative regulation of Adh expression. We find that a classical result was not observed due to the pleiotropic effect of changing a nucleotide involved in both long-range base pairing and the negative regulation of gene expression. PMID:15020421

  8. Transcriptome analysis of monocyte-HIV interactions

    Directory of Open Access Journals (Sweden)

    Tran Huyen

    2010-06-01

    /macrophage dysfunction is involved may only now be emerging or remain yet to be discovered, in particular in view of the limited number of studies focussing on the monocyte response to ART 32. In order to generate novel hypotheses rather than test pre-existing ones in the context of monocyte-HIV interactions, we performed a transcriptome analysis on monocyte samples from patients in different stages of HIV infection and/or combination ART treatment, using a parallel approach of genome-wide microarray analysis and focused gene expression profiling to identify broad areas of monocyte dysfunction and to pinpoint genes which are potentially involved in one or several of these dysfunctions. In particular the factors which are exploited by the monocyte/macrophage to communicate with and/or modulate other immune cells were of interest, as they represent a particularly relevant population 3334 which is a primary target for intervention.

  9. Analysis of the promoters involved in enterocin AS-48 expression.

    Directory of Open Access Journals (Sweden)

    Rubén Cebrián

    Full Text Available The enterocin AS-48 is the best characterized antibacterial circular protein in prokaryotes. It is a hydrophobic and cationic bacteriocin, which is ribosomally synthesized by enterococcal cells and post-translationally cyclized by a head-to-tail peptide bond. The production of and immunity towards AS-48 depend upon the coordinated expression of ten genes organized in two operons, as-48ABC (where genes encoding enzymes with processing, secretion, and immunity functions are adjacent to the structural as-48A gene and as-48C1DD1EFGH. The current study describes the identification of the promoters involved in AS-48 expression. Seven putative promoters have been here amplified, and separately inserted into the promoter-probe vector pTLR1, to create transcriptional fusions with the mCherry gene used as a reporter. The activity of these promoter regions was assessed measuring the expression of the fluorescent mCherry protein using the constitutive pneumococcal promoter PX as a reference. Our results revealed that only three promoters PA, P2(2 and PD1 were recognized in Enterococcus faecalis, Lactococcus lactis and Escherichia coli, in the conditions tested. The maximal fluorescence was obtained with PX in all the strains, followed by the P2(2 promoter, which level of fluorescence was 2-fold compared to PA and 4-fold compared to PD1. Analysis of putative factors influencing the promoter activity in single and double transformants in E. faecalis JH2-2 demonstrated that, in general, a better expression was achieved in presence of pAM401-81. In addition, the P2(2 promoter could be regulated in a negative fashion by genes existing in the native pMB-2 plasmid other than those of the as-48 cluster, while the pH seems to affect differently the as-48 promoter expression.

  10. Involvement of hepatitis B X-interacting protein (HBXIP) in proliferation regulation of cells

    Institute of Scientific and Technical Information of China (English)

    Feng-ze WANG; Li SHA; Wei-ying ZHANG; Lian-ying WU; Ling QIAO; Nan LI; Xiao-dong ZHANG; Li-hong YE

    2007-01-01

    Aim: To investigat the effect of Hepatitis B X-interacting protein (HBXIP) on cell proliferation. Methods: A rabbit antibody against HBXIP was generated. The RNA interference (RNAi) fragment of the HBXIP gene was constructed in the pSilencer-3.0-H1 vector termed pSilencer-hbxip. Plasmids of the pcDNA3-hbxip encoding HBXIP gene and pSilencer-hbxip were transfected into human breast carcinoma MCF-7 cells, hepatoma H7402 cells, and the normal human hepatic cell line L-O2, respectively. 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bro- mide (MTT) assay and 5-bromo-2-deoxyuridine incorporation assay were applied to detect cell proliferation. MCF-7 cells and L-O2 cells in the cell cycle were examined by flow cytometry. The proteins involved in cell proliferation and cell cycle were investigated by Western blot. Results: Overexpression of HBXIP resulted in the promotion of proliferation of MCF-7, H7402, and L-O2 cells. Flow cytometry showed that the overexpression of HBXIP promoted the cell prolifera-tion of MCF-7 and L-O2 cells, and led to an increased cell proliferative index in MCF-7 cells (from 46.25% to 58.28%) and L-O2 cells (from 29.62% to 35.54%). Western blot showed that expression levels of c-Myc, Bcl-2, and proliferating cell nuclear antigen were upregulated in MCF-7, H7402, or L-O2 cells, whereas that of p27 was downregulated. However, the RNAi of HBXIP brought opposite results.Conclusion: One of the functions of HBXIP is its involvement in cell proliferation.

  11. Interactions involved in pH protection of the alphavirus fusion protein

    Energy Technology Data Exchange (ETDEWEB)

    Fields, Whitney; Kielian, Margaret, E-mail: margaret.kielian@einstein.yu.edu

    2015-12-15

    The alphavirus membrane protein E1 mediates low pH-triggered fusion of the viral and endosome membranes during virus entry. During virus biogenesis E1 associates as a heterodimer with the transmembrane protein p62. Late in the secretory pathway, cellular furin cleaves p62 to the mature E2 protein and a peripheral protein E3. E3 remains bound to E2 at low pH, stabilizing the heterodimer and thus protecting E1 from the acidic pH of the secretory pathway. Release of E3 at neutral pH then primes the virus for fusion during entry. Here we used site-directed mutagenesis and revertant analysis to define residues important for the interactions at the E3–E2 interface. Our data identified a key residue, E2 W235, which was required for E1 pH protection and alphavirus production. Our data also suggest additional residues on E3 and E2 that affect their interacting surfaces and thus influence the pH protection of E1 during alphavirus exit.

  12. Interactions involved in pH protection of the alphavirus fusion protein.

    Science.gov (United States)

    Fields, Whitney; Kielian, Margaret

    2015-12-01

    The alphavirus membrane protein E1 mediates low pH-triggered fusion of the viral and endosome membranes during virus entry. During virus biogenesis E1 associates as a heterodimer with the transmembrane protein p62. Late in the secretory pathway, cellular furin cleaves p62 to the mature E2 protein and a peripheral protein E3. E3 remains bound to E2 at low pH, stabilizing the heterodimer and thus protecting E1 from the acidic pH of the secretory pathway. Release of E3 at neutral pH then primes the virus for fusion during entry. Here we used site-directed mutagenesis and revertant analysis to define residues important for the interactions at the E3-E2 interface. Our data identified a key residue, E2 W235, which was required for E1 pH protection and alphavirus production. Our data also suggest additional residues on E3 and E2 that affect their interacting surfaces and thus influence the pH protection of E1 during alphavirus exit. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Mark 3 interactive data analysis system

    Science.gov (United States)

    Ryan, J. W.; Ma, C.; Schupler, B. P.

    1980-01-01

    The interactive data analysis system, a major subset of the total Mark 3 very long baseline interferometry (VLBI) software system is described. The system consists of two major and a number of small programs. These programs provide for the scientific analysis of the observed values of delay and delay rate generated by the VLBI data reduction programs and product the geophysical and astrometric parameters which are among the ultimate products of VLBI. The two major programs are CALC and SOLVE. CALC generates the theoretical values of VLBI delay rate as well as partial derivatives based on apriori values of the geophysical and astronometric parameters. SOLVE is a least squares parameters estimation program which yields the geophysical and astrometric parameters using the observed values by the data processing system and theoretical values and partial derivatives provided by CALC. SOLVE is a highly interactive program in which the user selects the exact form of the recovered parameters and the data to be accepted into the solution.

  14. Interatomic Coulombic Decay Effects in Theoretical DNA Recombination Systems Involving Protein Interaction Sites

    Science.gov (United States)

    Vargas, E. L.; Rivas, D. A.; Duot, A. C.; Hovey, R. T.; Andrianarijaona, V. M.

    2015-03-01

    DNA replication is the basis for all biological reproduction. A strand of DNA will ``unzip'' and bind with a complimentary strand, creating two identical strands. In this study, we are considering how this process is affected by Interatomic Coulombic Decay (ICD), specifically how ICD affects the individual coding proteins' ability to hold together. ICD mainly deals with how the electron returns to its original state after excitation and how this affects its immediate atomic environment, sometimes affecting the connectivity between interaction sites on proteins involved in the DNA coding process. Biological heredity is fundamentally controlled by DNA and its replication therefore it affects every living thing. The small nature of the proteins (within the range of nanometers) makes it a good candidate for research of this scale. Understanding how ICD affects DNA molecules can give us invaluable insight into the human genetic code and the processes behind cell mutations that can lead to cancer. Authors wish to give special thanks to Pacific Union College Student Senate in Angwin, California, for their financial support.

  15. Dimensions of Human-Work Domain Interaction: A Preliminary Analysis for the Design of a Corporate Digital Library.

    Science.gov (United States)

    Xie, Hong

    2003-01-01

    Applies the cognitive system engineering approach to investigate human-work interaction at a corporate setting. Reports preliminary analysis of data collected from diary analysis and interview of 20 subjects. Results identify three dimensions for each of four interactive activities involved in human-work interaction and their relationships.…

  16. Parent involvement and student academic performance: a multiple mediational analysis.

    Science.gov (United States)

    Topor, David R; Keane, Susan P; Shelton, Terri L; Calkins, Susan D

    2010-01-01

    Parent involvement in a child's education is consistently found to be positively associated with a child's academic performance. However, there has been little investigation of the mechanisms that explain this association. The present study examines two potential mechanisms of this association: the child's perception of cognitive competence and the quality of the student-teacher relationship. This study used a sample of 158 seven-year-old participants, their mothers, and their teachers. Results indicated a statistically significant association between parent involvement and a child's academic performance, over and above the impact of the child's intelligence. A multiple mediation model indicated that the child's perception of cognitive competence fully mediated the relation between parent involvement and the child's performance on a standardized achievement test. The quality of the student-teacher relationship fully mediated the relation between parent involvement and teacher ratings of the child's classroom academic performance. Limitations, future research directions, and implications for public policy initiatives are discussed.

  17. Cardiovascular involvement by osteosarcoma: an analysis of 20 patients

    Energy Technology Data Exchange (ETDEWEB)

    Yedururi, Sireesha; Morani, Ajaykumar C.; Gladish, Gregory W. [The University of Texas MD Anderson Cancer Center, Department of Diagnostic Radiology, Houston, TX (United States); Vallabhaneni, Srilakshmi [Medstar Harbor Hospital, Department of Internal Medicine, Baltimore, MD (United States); Anderson, Peter M. [Levine Children' s Hospital/Levine Cancer Institute, Department of Pediatrics Hematology/Oncology/BMT, Carolinas Healthcare System, Charlotte, NC (United States); Hughes, Dennis; Daw, Najat C. [The University of Texas MD Anderson Cancer Center, Division of Pediatrics, Houston, TX (United States); Wang, Wei-Lien [The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, TX (United States)

    2016-01-15

    Although hematogenous spread of osteosarcoma is well known, the imaging findings of cardiovascular involvement by osteosarcoma are seldom reported and can be difficult to recognize. The enhanced resolution of modern CT and MRI scanners may lead to better detection of cardiovascular involvement. To describe the key imaging findings and clinical behavior of cardiovascular involvement by osteosarcoma. We retrospectively reviewed the imaging findings and clinical characteristics of 20 patients with cardiovascular involvement by osteosarcoma identified by two pediatric radiologists from a review of imaging studies at our institution from 2007 to 2013. At initial diagnosis, the median age of the patients was 15.1 years (range 4.8-24.6 years), and 7 (35%) patients had detectable metastases. Median time to detection of cardiovascular metastases was 1.8 years (range 0-7.3 years). Sixteen patients died of disease; 4 have survived a median of 7.4 years since initial diagnosis. The sites of cardiovascular involvement were the systemic veins draining the primary and metastatic osteosarcoma, pulmonary arteries, pulmonary veins draining the pulmonary metastases, and heart. A dilated and mineralized terminal pulmonary arteriole is an early sign of metastatic osteosarcoma in the lung. Unfamiliarity with the imaging features resulted in under-recognition and misinterpretation of intravascular tumor thrombus as bland thrombus. Knowledge of imaging findings in the era of modern imaging modalities has enhanced our ability to detect cardiovascular involvement and lung metastases early and avoid misinterpreting tumor thrombus in draining systemic veins or pulmonary arteries as bland thrombus. (orig.)

  18. Cardiovascular involvement by osteosarcoma: an analysis of 20 patients.

    Science.gov (United States)

    Yedururi, Sireesha; Morani, Ajaykumar C; Gladish, Gregory W; Vallabhaneni, Srilakshmi; Anderson, Peter M; Hughes, Dennis; Wang, Wei-Lien; Daw, Najat C

    2016-01-01

    Although hematogenous spread of osteosarcoma is well known, the imaging findings of cardiovascular involvement by osteosarcoma are seldom reported and can be difficult to recognize. The enhanced resolution of modern CT and MRI scanners may lead to better detection of cardiovascular involvement. To describe the key imaging findings and clinical behavior of cardiovascular involvement by osteosarcoma. We retrospectively reviewed the imaging findings and clinical characteristics of 20 patients with cardiovascular involvement by osteosarcoma identified by two pediatric radiologists from a review of imaging studies at our institution from 2007 to 2013. At initial diagnosis, the median age of the patients was 15.1 years (range 4.8-24.6 years), and 7 (35%) patients had detectable metastases. Median time to detection of cardiovascular metastases was 1.8 years (range 0-7.3 years). Sixteen patients died of disease; 4 have survived a median of 7.4 years since initial diagnosis. The sites of cardiovascular involvement were the systemic veins draining the primary and metastatic osteosarcoma, pulmonary arteries, pulmonary veins draining the pulmonary metastases, and heart. A dilated and mineralized terminal pulmonary arteriole is an early sign of metastatic osteosarcoma in the lung. Unfamiliarity with the imaging features resulted in under-recognition and misinterpretation of intravascular tumor thrombus as bland thrombus. Knowledge of imaging findings in the era of modern imaging modalities has enhanced our ability to detect cardiovascular involvement and lung metastases early and avoid misinterpreting tumor thrombus in draining systemic veins or pulmonary arteries as bland thrombus.

  19. A decision analysis framework for stakeholder involvement and learning in groundwater management

    Directory of Open Access Journals (Sweden)

    T. P. Karjalainen

    2013-07-01

    Full Text Available Multi-criteria decision analysis (MCDA methods are increasingly used to facilitate both rigorous analysis and stakeholder involvement in natural and water resource planning. Decision making in that context is often complex and multi-faceted with numerous trade-offs between social, environmental and economic impacts. However, practical applications of decision-support methods are often too technically oriented and hard to use, understand or interpret for all participants. The learning of participants in these processes is seldom examined, even though successful deliberation depends on learning. This paper analyzes the potential of an interactive MCDA framework, the decision analysis interview (DAI approach, for facilitating stakeholder involvement and learning in groundwater management. It evaluates the results of an MCDA process in assessing land-use management alternatives in a Finnish esker aquifer area where conflicting land uses affect the groundwater body and dependent ecosystems. In the assessment process, emphasis was placed on the interactive role of the MCDA tool in facilitating stakeholder participation and learning. The results confirmed that the structured decision analysis framework can foster learning and collaboration in a process where disputes and diverse interests are represented. Computer-aided interviews helped the participants to see how their preferences affected the desirability and ranking of alternatives. During the process, the participants' knowledge and preferences evolved as they assess their initial knowledge with the help of fresh scientific information. The decision analysis process led to the opening of a dialogue, showing the overall picture of the problem context, and the critical issues for the further process.

  20. IAA8 involved in lateral root formation interacts with the TIR1 auxin receptor and ARF transcription factors in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Fumi Arase

    Full Text Available The expression of auxin-responsive genes is regulated by the TIR1/AFB auxin receptor-dependent degradation of Aux/IAA transcriptional repressors, which interact with auxin-responsive factors (ARFs. Most of the 29 Aux/IAA genes present in Arabidopsis have not been functionally characterized to date. IAA8 appears to have a distinct function from the other Aux/IAA genes, due to its unique transcriptional response to auxin and the stability of its encoded protein. In this study, we characterized the function of Arabidopsis IAA8 in various developmental processes governed by auxin and in the transcriptional regulation of the auxin response. Transgenic plants expressing estrogen-inducible IAA8 (XVE::IAA8 exhibited significantly fewer lateral roots than the wild type, and an IAA8 loss-of-function mutant exhibited significantly more. Ectopic overexpression of IAA8 resulted in abnormal gravitropism. The strong induction of early auxin-responsive marker genes by auxin treatment was delayed by IAA8 overexpression. GFP-fusion analysis revealed that IAA8 localized not only to the nucleus, but, in contrast to other Aux/IAAs, also to the cytosol. Furthermore, we demonstrated that IAA8 interacts with TIR1, in an auxin-dependent fashion, and with ARF proteins, both in yeast and in planta. Taken together, our results show that IAA8 is involved in lateral root formation, and that this process is regulated through the interaction with the TIR1 auxin receptor and ARF transcription factors in the nucleus.

  1. Ligand requirements for involvement of PKCε in synergistic analgesic interactions between spinal μ and δ opioid receptors

    Science.gov (United States)

    Schuster, D J; Metcalf, M D; Kitto, K F; Messing, R O; Fairbanks, C A; Wilcox, G L

    2015-01-01

    BACKGROUND AND PURPOSE We recently found that PKCε was required for spinal analgesic synergy between two GPCRs, δ opioid receptors and α2A adrenoceptors, co-located in the same cellular subpopulation. We sought to determine if co-delivery of μ and δ opioid receptor agonists would similarly result in synergy requiring PKCε. EXPERIMENTAL APPROACH Combinations of μ and δ opioid receptor agonists were co-administered intrathecally by direct lumbar puncture to PKCε-wild-type (PKCε-WT) and -knockout (PKCε-KO) mice. Antinociception was assessed using the hot-water tail-flick assay. Drug interactions were evaluated by isobolographic analysis. KEY RESULTS All agonists produced comparable antinociception in both PKCε-WT and PKCε-KO mice. Of 19 agonist combinations that produced analgesic synergy, only 3 required PKCε for a synergistic interaction. In these three combinations, one of the agonists was morphine, although not all combinations involving morphine required PKCε. Morphine + deltorphin II and morphine + deltorphin I required PKCε for synergy, whereas a similar combination, morphine + deltorphin, did not. Additionally, morphine + oxymorphindole required PKCε for synergy, whereas a similar combination, morphine + oxycodindole, did not. CONCLUSIONS AND IMPLICATIONS We discovered biased agonism for a specific signalling pathway at the level of spinally co-delivered opioid agonists. As the bias is only revealed by an appropriate ligand combination and cannot be accounted for by a single drug, it is likely that the receptors these agonists act on are interacting with each other. Our results support the existence of μ and δ opioid receptor heteromers at the spinal level in vivo. LINKED ARTICLES This article is part of a themed section on Opioids: New Pathways to Functional Selectivity. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue-2 PMID:24827408

  2. Automatic quantitative morphological analysis of interacting galaxies

    CERN Document Server

    Shamir, Lior; Wallin, John

    2013-01-01

    The large number of galaxies imaged by digital sky surveys reinforces the need for computational methods for analyzing galaxy morphology. While the morphology of most galaxies can be associated with a stage on the Hubble sequence, morphology of galaxy mergers is far more complex due to the combination of two or more galaxies with different morphologies and the interaction between them. Here we propose a computational method based on unsupervised machine learning that can quantitatively analyze morphologies of galaxy mergers and associate galaxies by their morphology. The method works by first generating multiple synthetic galaxy models for each galaxy merger, and then extracting a large set of numerical image content descriptors for each galaxy model. These numbers are weighted using Fisher discriminant scores, and then the similarities between the galaxy mergers are deduced using a variation of Weighted Nearest Neighbor analysis such that the Fisher scores are used as weights. The similarities between the ga...

  3. The Interaction between Personality, Social Network Position and Involvement in Innovation Process

    NARCIS (Netherlands)

    E. Dolgova; W. van Olffen (Woody); F.A.J. van den Bosch (Frans); H.W. Volberda (Henk)

    2010-01-01

    textabstractAbstract This dissertation proposal investigates how personality and individuals’ social network position affect individuals’ involvement into the innovation process. It posits that people would feel inclined to become involved into the different phases of the innovation process dependin

  4. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions.

    Science.gov (United States)

    Loper, Joyce E; Hassan, Karl A; Mavrodi, Dmitri V; Davis, Edward W; Lim, Chee Kent; Shaffer, Brenda T; Elbourne, Liam D H; Stockwell, Virginia O; Hartney, Sierra L; Breakwell, Katy; Henkels, Marcella D; Tetu, Sasha G; Rangel, Lorena I; Kidarsa, Teresa A; Wilson, Neil L; van de Mortel, Judith E; Song, Chunxu; Blumhagen, Rachel; Radune, Diana; Hostetler, Jessica B; Brinkac, Lauren M; Durkin, A Scott; Kluepfel, Daniel A; Wechter, W Patrick; Anderson, Anne J; Kim, Young Cheol; Pierson, Leland S; Pierson, Elizabeth A; Lindow, Steven E; Kobayashi, Donald Y; Raaijmakers, Jos M; Weller, David M; Thomashow, Linda S; Allen, Andrew E; Paulsen, Ian T

    2012-07-01

    We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to

  5. Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions.

    Directory of Open Access Journals (Sweden)

    Joyce E Loper

    2012-07-01

    Full Text Available We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45-52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring

  6. Parent Involvement and Science Achievement: A Latent Growth Curve Analysis

    Science.gov (United States)

    Johnson, Ursula Yvette

    2011-01-01

    This study examined science achievement growth across elementary and middle school and parent school involvement using the Early Childhood Longitudinal Study-Kindergarten Class of 1998-1999 (ECLS-K). The ECLS-K is a nationally representative kindergarten cohort of students from public and private schools who attended full-day or half-day…

  7. Analysis of a distributed neural system involved in spatial information, novelty, and memory processing.

    Science.gov (United States)

    Menon, V; White, C D; Eliez, S; Glover, G H; Reiss, A L

    2000-10-01

    Perceiving a complex visual scene and encoding it into memory involves a hierarchical distributed network of brain regions, most notably the hippocampus (HIPP), parahippocampal gyrus (PHG), lingual gyrus (LNG), and inferior frontal gyrus (IFG). Lesion and imaging studies in humans have suggested that these regions are involved in spatial information processing as well as novelty and memory encoding; however, the relative contributions of these regions of interest (ROIs) are poorly understood. This study investigated regional dissociations in spatial information and novelty processing in the context of memory encoding using a 2 x 2 factorial design with factors Novelty (novel vs. repeated) and Stimulus (viewing scenes with rich vs. poor spatial information). Greater activation was observed in the right than left hemisphere; however, hemispheric effects did not differ across regions, novelty, or stimulus type. Significant novelty effects were observed in all four regions. A significant ROI x Stimulus interaction was observed - spatial information processing effects were largest effects in the LNG, significant in the PHG and HIPP and nonsignificant in the IFG. Novelty processing was stimulus dependent in the LNG and stimulus independent in the PHG, HIPP, and IFG. Analysis of the profile of Novelty x Stimulus interaction across ROIs provided evidence for a hierarchical independence in novelty processing characterized by increased dissociation from spatial information processing. Despite these differences in spatial information processing, memory performance for novel scenes with rich and poor spatial information was not significantly different. Memory performance was inversely correlated with right IFG activation, suggesting the involvement of this region in strategically flawed encoding effort. Stepwise regression analysis revealed that memory encoding accounted for only a small fraction of the variance (temporal lobe activation. The implications of these results for

  8. Yeast Two-Hybrid Studies on Interaction of Proteins Involved in Regulation of Nitrogen Fixation in the Phototrophic Bacterium Rhodobacter capsulatus

    OpenAIRE

    Pawlowski, Alice; Riedel, Kai-Uwe; Klipp, Werner; Dreiskemper, Petra; Groß, Silke; Bierhoff, Holger; Drepper, Thomas; Masepohl, Bernd

    2003-01-01

    Rhodobacter capsulatus contains two PII-like proteins, GlnB and GlnK, which play central roles in controlling the synthesis and activity of nitrogenase in response to ammonium availability. Here we used the yeast two-hybrid system to probe interactions between these PII-like proteins and proteins known to be involved in regulating nitrogen fixation. Analysis of defined protein pairs demonstrated the following interactions: GlnB-NtrB, GlnB-NifA1, GlnB-NifA2, GlnB-DraT, GlnK-NifA1, GlnK-NifA2, ...

  9. Hydrophilic interaction chromatographic analysis of anthocyanins.

    Science.gov (United States)

    Willemse, Chandré M; Stander, Maria A; de Villiers, André

    2013-12-06

    Hydrophilic interaction chromatography (HILIC) provides an alternative separation mode for the analysis of phenolic compounds, in which aqueous-organic mobile phases with polar stationary phases are used. This paper reports the evaluation of HILIC for the analysis of the natural pigments anthocyanins, which are of importance because of their chromophoric properties and a range of health benefits associated with their consumption. Several HILIC stationary phases (silica, diol, amine, cyanopropyl and amide) and mobile phase combinations were evaluated, with the latter proving particularly important due to the distinctive chromatographic behaviour of anthocyanins. Diode array detection was used for selective detection of anthocyanins, while high resolution quadrupole-time-of-flight mass spectrometry (Q-TOF-MS) was used for compound identification. The potential of HILIC separation is demonstrated for a range of anthocyanins varying in glycosylation and acylation patterns found in blueberries, grape skins, black beans, red cabbage and red radish. HILIC is shown to be a complementary separation method to reversed phase liquid chromatography (RP-LC) due to the alternative retention mechanism.

  10. Drug interactions involving antiepileptic drugs: assessment of the consistency among three drug compendia and FDA-approved labels.

    Science.gov (United States)

    Ekstein, Dana; Tirosh, Matanya; Eyal, Yonatan; Eyal, Sara

    2015-03-01

    Interactions of antiepileptic drugs (AEDs) with other substances may lead to adverse effects and treatment failure. To avoid such interactions, clinicians often rely on drug interaction compendia. Our objective was to compare the concordance for twenty-two AEDs among three drug interaction compendia (Micromedex, Lexi-Interact, and Clinical Pharmacology) and the US Food and Drug Administration-approved product labels. For each AED, the overall concordance among data sources regarding existence of interactions and their classification was poor, with less than twenty percent of interactions listed in all four sources. Concordance among the three drug compendia decreased with the fraction of the drug excreted unchanged and was greater for established inducers of hepatic drug-metabolizing enzymes than for the drugs that are not inducers (R-square=0.83, P<0.01). For interactions classified as contraindications, major, and severe, concordance among the four data sources was, in most cases, less than 30%. Prescribers should be aware of the differences between drug interaction sources of information for both older AEDs and newer AEDs, in particular for those AEDs which are not involved in hepatic enzyme-mediated interactions.

  11. Involvement of platelet-tumor cell interaction in immune evasion. Potential role of podocalyxin-like protein 1

    Directory of Open Access Journals (Sweden)

    Laura eAmo

    2014-09-01

    Full Text Available Besides their essential role in hemostasis and thrombosis, platelets are involved in the onset of cancer metastasis by interacting with tumor cells. Platelets release secretory factors that promote tumor growth, angiogenesis, and metastasis. Furthermore, the formation of platelet-tumor cell aggregates in the bloodstream provides cancer cells with an immune escape mechanism by protecting circulating malignant cells from immune-mediated lysis by natural killer (NK cells. Platelet-tumor cell interaction is accomplished by specific adhesion molecules, including integrins, selectins, and their ligands. Podocalyxin-like protein 1 (PCLP1 is a selectin ligand protein which overexpression has been associated with several aggressive cancers. PCLP1 expression enhances cell adherence to platelets in an integrin-dependent process and through the interaction with P-selectin expressed on activated platelets. However, the involvement of PCLP1-induced tumor-platelet interaction in tumor immune evasion still remains unexplored. The identification of selectin ligands involved in the interaction of platelets with tumor cells may provide help for the development of effective therapies to restrain cancer cell dissemination. This article summarizes the current knowledge on molecules that participate in platelet-tumor cell interaction as well as discusses the potential role of PCLP1 as a molecule implicated in tumor immune evasion.

  12. Interaction involving the thymus and the hypothalamus-pituitary axis, immunomodulation by hormones

    Directory of Open Access Journals (Sweden)

    Marković Ljiljana 2

    2004-01-01

    Full Text Available Perfectly projected and impeccably created, the endocrine system precisely regulates the most delicate immune processes. The immune and neuroendocrine systems are two essential physiological components of mammalian organisms important for protection from the infection and disease on one hand, and on the other, for regulation of metabolism and other physiological activities; namely, the evidence has been found indicating that there is active and dynamic collaboration of these systems in the execution of their designated functions [1, 2,4]. These interactions occur at many stages of embryonic and neonatal development, and they are a continual part of normal homeostatic balance necessary to preserve health. There is communication between neuroendocrine and immune system via cytokines, neurotransmitters and peptide hormones which act, in both systems, through the same receptor molecules (Scheme 1. Many investigators have reported the increased thymic weight in experimental animals due to both castration and adrenalectomy [4]. The discovery from 1898 revealing that thymus was enlarged in castrated rabbits has been considered the embryo of hybrid medical discipline, i.e. the immunoendocrinology [1]. In the actual literature, at least in that available to us, it has not been noted that the appearance of the eunuchs, i.e. the castrates, stimulated the analytical approach to this phenomenon. Endocrine influences appear to be a part of bidirectional circuitry, namely, thymic hormones also regulate the release of hormones from the pituitary gland. Physiologically, thymus is under neuroendocrine control. It is apparent that the circulating levels of distinct peptide hormones are necessary to maintain a series of biological functions related both to micro environmental and lymphoid cells of the organ. The neuroendocrine control of the thymus appears to be extremely complex, with apparent presence of complete intrathymic biological circuitry involving the

  13. Protein-protein interaction network analysis of cirrhosis liver disease.

    Science.gov (United States)

    Safaei, Akram; Rezaei Tavirani, Mostafa; Arefi Oskouei, Afsaneh; Zamanian Azodi, Mona; Mohebbi, Seyed Reza; Nikzamir, Abdol Rahim

    2016-01-01

    Evaluation of biological characteristics of 13 identified proteins of patients with cirrhotic liver disease is the main aim of this research. In clinical usage, liver biopsy remains the gold standard for diagnosis of hepatic fibrosis. Evaluation and confirmation of liver fibrosis stages and severity of chronic diseases require a precise and noninvasive biomarkers. Since the early detection of cirrhosis is a clinical problem, achieving a sensitive, specific and predictive novel method based on biomarkers is an important task. Essential analysis, such as gene ontology (GO) enrichment and protein-protein interactions (PPI) was undergone EXPASy, STRING Database and DAVID Bioinformatics Resources query. Based on GO analysis, most of proteins are located in the endoplasmic reticulum lumen, intracellular organelle lumen, membrane-enclosed lumen, and extracellular region. The relevant molecular functions are actin binding, metal ion binding, cation binding and ion binding. Cell adhesion, biological adhesion, cellular amino acid derivative, metabolic process and homeostatic process are the related processes. Protein-protein interaction network analysis introduced five proteins (fibroblast growth factor receptor 4, tropomyosin 4, tropomyosin 2 (beta), lectin, Lectin galactoside-binding soluble 3 binding protein and apolipoprotein A-I) as hub and bottleneck proteins. Our result indicates that regulation of lipid metabolism and cell survival are important biological processes involved in cirrhosis disease. More investigation of above mentioned proteins will provide a better understanding of cirrhosis disease.

  14. Children's Responses to the Interactivity of Storybook Apps in Family Shared Reading Events Involving the iPad

    Science.gov (United States)

    Aliagas, Cristina; Margallo, Ana María

    2017-01-01

    This paper reports on some data on the effects of screen-based interactivity on children's engagement with storybook apps during family shared book reading that were gathered in a 2-year, small-scale ethnographic case study in Spain. Data analysis focuses on the complex interplay between the storybook app's interactive features and the children's…

  15. Impeller-diffuser interaction: analysis of the unsteady flow structures based on their direction of propagation

    Institute of Scientific and Technical Information of China (English)

    N. Bulot; I. Trébinjac

    2007-01-01

    The present study is focused on the analysis of the deterministic fluctuations arising from the rotor-stator interaction within a transonic centrifugal compressor stage. A spectral analysis applied to the unsteady flow field leads to the values of the rotation speed of most energetic modes. From these values, the various structures are classified according to their direction of propagation which leads to a comprehensive description of the underlying mechanisms involved in the interaction.

  16. Hydrophobic Interactions Involved in Attachment of a Baculovirus to Hydrophobic Surfaces

    OpenAIRE

    Small, Deirdre A.; Moore, Norman F.; Entwistle, Philip F.

    1986-01-01

    The hydrophobic interactions of Trichoplusia ni nuclear polyhedrosis virus were characterized by hydrophobic interaction chromatography. The determination of the hydrophobic force and some of the factors that influence its size is discussed in relation to the attachment to leaf surfaces of polyhedra during their use as biological control agents against insect pests.

  17. Mapping of the regions involved in self-interaction of rice stripe virus P3 protein.

    Science.gov (United States)

    Zhao, S L; Hao, J H; Xue, Y N; Liang, C Y

    2016-03-01

    Rice stripe virus (RSV) protein P3 is a suppressor of RNA silencing in plants. P3 has been shown by biomolecular fluorescence complementation assay to self-interact in planta but the regions responsible for homotypic interaction have not been determined. Here we analyzed the domains for the self-interaction of P3 by using yeast two-hybrid, co-immunoprecipitation and fluorescence experiments. The results showed that P3 was also able to interact with itself in yeast and insect cells. The domain responsible for P3-P3 interaction was mapped to amino acids 15-30 at the N-terminal region of P3. Furthermore, subcellular localization suggested that the homo-oligomerization was the prerequisite for P3 to form larger protein aggregates in the nucleus of insect cell.

  18. Metabolomic profiling identifies potential pathways involved in the interaction of iron homeostasis with glucose metabolism

    Directory of Open Access Journals (Sweden)

    Lars Stechemesser

    2017-01-01

    Conclusions: Our data suggest that high serum ferritin concentrations are linked to impaired glucose homeostasis in subjects with the MetS. Iron excess is associated to distinct changes in the serum concentrations of phosphatidylcholine subsets. A pathway involving sarcosine and citrulline also may be involved in iron-induced impairment of glucose metabolism.

  19. Are glutathione S transferases involved in DNA damage signalling? Interactions with DNA damage and repair revealed from molecular epidemiology studies

    Energy Technology Data Exchange (ETDEWEB)

    Dusinska, Maria, E-mail: Maria.DUSINSKA@nilu.no [CEE-Health Effects Group, NILU - Norwegian Institute for Air Research, Kjeller (Norway); Staruchova, Marta; Horska, Alexandra [Department of Experimental and Applied Genetics, Slovak Medical University, Bratislava (Slovakia); Smolkova, Bozena [Laboratory of Cancer Genetics, Cancer Research Institute of the Slovak Academy of Sciences, Bratislava (Slovakia); Collins, Andrew [Department of Nutrition, Faculty of Medicine, University of Oslo (Norway); Bonassi, Stefano [Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana, Rome (Italy); Volkovova, Katarina [Department of Experimental and Applied Genetics, Slovak Medical University, Bratislava (Slovakia)

    2012-08-01

    Glutathione S-transferases (GSTs) are members of a multigene family of isoenzymes that are important in the control of oxidative stress and in phase II metabolism. Acting non-enzymically, GSTs can modulate signalling pathways of cell proliferation, cell differentiation and apoptosis. Using a molecular epidemiology approach, we have investigated a potential involvement of GSTs in DNA damage processing, specifically the modulation of DNA repair in a group of 388 healthy adult volunteers; 239 with at least 5 years of occupational exposure to asbestos, stone wool or glass fibre, and 149 reference subjects. We measured DNA damage in lymphocytes using the comet assay (alkaline single cell gel electrophoresis): strand breaks (SBs) and alkali-labile sites, oxidised pyrimidines with endonuclease III, and oxidised purines with formamidopyrimidine DNA glycosylase. We also measured GST activity in erythrocytes, and the capacity for base excision repair (BER) in a lymphocyte extract. Polymorphisms in genes encoding three GST isoenzymes were determined, namely deletion of GSTM1 and GSTT1 and single nucleotide polymorphism Ile105Val in GSTP1. Consumption of vegetables and wine correlated negatively with DNA damage and modulated BER. GST activity correlated with oxidised bases and with BER capacity, and differed depending on polymorphisms in GSTP1, GSTT1 and GSTM1. A significantly lower BER rate was associated with the homozygous GSTT1 deletion in all asbestos site subjects and in the corresponding reference group. Multifactorial analysis revealed effects of sex and exposure in GSTP1 Ile/Val heterozygotes but not in Ile/Ile homozygotes. These variants affected also SBs levels, mainly by interactions of GSTP1 genotype with exposure, with sex, and with smoking habit; and by an interaction between sex and smoking. Our results show that GST polymorphisms and GST activity can apparently influence DNA stability and repair of oxidised bases, suggesting a potential new role for these

  20. Interaction between the cytoplasmic domains of HIV-1 Vpu and CD4: role of Vpu residues involved in CD4 interaction and in vitro CD4 degradation.

    Science.gov (United States)

    Margottin, F; Benichou, S; Durand, H; Richard, V; Liu, L X; Gomas, E; Benarous, R

    1996-09-15

    The Vpu and CD4 cytoplasmic domains were found, by using a two-hybrid assay in yeast, to interact in the absence of their membrane anchor domains. Studies on several deletion and point mutants revealed that the overall structure of the Vpu cytoplasmic domain is required for this interaction. The Vpu amino acid residues involved in the interaction with CD4 were identified. Deletion of the C-terminal residues of Vpu, required for CD4 degradation, as well as the double mutation on the casein kinase II phosphorylation sites S52N-S56N, also involved in CD4 degradation, resulted in the loss of interaction with CD4 and in the inability to induce CD4 degradation. These results suggest that the ability of Vpu to mediate the degradation of CD4 is linked to its capacity to physically interact with CD4. However, additional mutagenesis on the S52 site revealed that the interaction between the cytoplasmic domains of Vpu and CD4 is not sufficient for in vitro Vpu-mediated CD4 degradation.

  1. Exclusively visual analysis of classroom group interactions

    Science.gov (United States)

    Tucker, Laura; Scherr, Rachel E.; Zickler, Todd; Mazur, Eric

    2016-12-01

    Large-scale audiovisual data that measure group learning are time consuming to collect and analyze. As an initial step towards scaling qualitative classroom observation, we qualitatively coded classroom video using an established coding scheme with and without its audio cues. We find that interrater reliability is as high when using visual data only—without audio—as when using both visual and audio data to code. Also, interrater reliability is high when comparing use of visual and audio data to visual-only data. We see a small bias to code interactions as group discussion when visual and audio data are used compared with video-only data. This work establishes that meaningful educational observation can be made through visual information alone. Further, it suggests that after initial work to create a coding scheme and validate it in each environment, computer-automated visual coding could drastically increase the breadth of qualitative studies and allow for meaningful educational analysis on a far greater scale.

  2. A Meta-Analysis of Father Involvement in Parent Training

    Science.gov (United States)

    Lundahl, Brad W.; Tollefson, Derrik; Risser, Heather; Lovejoy, M. Christine

    2008-01-01

    Objective: Investigate (a) whether including fathers in parent training enhances outcomes and (b) whether mothers and fathers benefit equally from parent training. Method: Using traditional meta-analysis methodology, 26 studies that could answer the research questions were identified and meta-analyzed. Results: Studies that included fathers,…

  3. Toward Interactive Scenario Analysis and Exploration

    Energy Technology Data Exchange (ETDEWEB)

    Gayle, Thomas R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Interactive Systems, Simulations, and Analysis; Summers, Kenneth Lee [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Interactive Systems, Simulations, and Analysis; Jungels, John [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Interactive Systems, Simulations, and Analysis; Oppel III, Fred J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Interactive Systems, Simulations, and Analysis

    2015-01-01

    As Modeling and Simulation (M&S) tools have matured, their applicability and importance have increased across many national security challenges. In particular, they provide a way to test how something may behave without the need to do real world testing. However, current and future changes across several factors including capabilities, policy, and funding are driving a need for rapid response or evaluation in ways that many M&S tools cannot address. Issues around large data, computational requirements, delivery mechanisms, and analyst involvement already exist and pose significant challenges. Furthermore, rising expectations, rising input complexity, and increasing depth of analysis will only increase the difficulty of these challenges. In this study we examine whether innovations in M&S software coupled with advances in ''cloud'' computing and ''big-data'' methodologies can overcome many of these challenges. In particular, we propose a simple, horizontally-scalable distributed computing environment that could provide the foundation (i.e. ''cloud'') for next-generation M&S-based applications based on the notion of ''parallel multi-simulation''. In our context, the goal of parallel multi- simulation is to consider as many simultaneous paths of execution as possible. Therefore, with sufficient resources, the complexity is dominated by the cost of single scenario runs as opposed to the number of runs required. We show the feasibility of this architecture through a stable prototype implementation coupled with the Umbra Simulation Framework [6]. Finally, we highlight the utility through multiple novel analysis tools and by showing the performance improvement compared to existing tools.

  4. Immunohistochemical analysis of small plaque parapsoriasis: involvement of dendritic cells.

    Science.gov (United States)

    Zeybek, N Dilara; Asan, Esin; Erbil, A Hakan; Dagdeviren, Attila

    2008-01-01

    Small plaque parapsoriasis (SPP) is one of the cutaneous T-cell lymphoproliferative disorders. The aim of the present study was to show the antigenic profile of a subset of dendritic cells and lymphocytes in SPP in comparison with normal cells to provide data on the role of these two cell types in the pathogenesis of SPP. Skin biopsy specimens of lesions were obtained from 8 patients with SPP. Biopsies of the healthy skin from 9 control individuals were also analyzed. Immunohistochemistry was performed on the frozen tissue sections to reveal binding of anti-HLA Class II, anti-CD1a, anti-CD4, anti-CD8, anti-CD44, anti-CD45, and anti-CD68 monoclonal antibodies. There was a statistically significant increase in the number of CD1a(+), Langerhans cells (LCs), HLA-DR-immunoreactive and, CD1a-positive dermal dendritic cells and CD68(+) macrophages in the SPP group (p=0.008, 0.008, 0.002 and <0.0009, respectively). The number of lymphocytes positive for CD4, CD8 and CD45 was significantly higher than normal in the SPP group (p=0.015, <0.0009 and <0.0009, respectively). Our study demonstrates that both peptide- and lipid-based antigens are involved in the persistent antigenic exposure in SPP. Dendritic cells play a pivotal role in SPP by presenting antigens by both LC and dermal dendritic cells via MHC Class II and CD1a molecules. The CD68(+) macrophages are thought to be involved in the immune response in this pathology as an antigen-presenting cell.

  5. Graph theory and stability analysis of protein complex interaction networks.

    Science.gov (United States)

    Huang, Chien-Hung; Chen, Teng-Hung; Ng, Ka-Lok

    2016-04-01

    Protein complexes play an essential role in many biological processes. Complexes can interact with other complexes to form protein complex interaction network (PCIN) that involves in important cellular processes. There are relatively few studies on examining the interaction topology among protein complexes; and little is known about the stability of PCIN under perturbations. We employed graph theoretical approach to reveal hidden properties and features of four species PCINs. Two main issues are addressed, (i) the global and local network topological properties, and (ii) the stability of the networks under 12 types of perturbations. According to the topological parameter classification, we identified some critical protein complexes and validated that the topological analysis approach could provide meaningful biological interpretations of the protein complex systems. Through the Kolmogorov-Smimov test, we showed that local topological parameters are good indicators to characterise the structure of PCINs. We further demonstrated the effectiveness of the current approach by performing the scalability and data normalization tests. To measure the robustness of PCINs, we proposed to consider eight topological-based perturbations, which are specifically applicable in scenarios of targeted, sustained attacks. We found that the degree-based, betweenness-based and brokering-coefficient-based perturbations have the largest effect on network stability.

  6. Microarray analysis of human epithelial cell responses to bacterial interaction.

    Science.gov (United States)

    Mans, Jeffrey J; Lamont, Richard J; Handfield, Martin

    2006-09-01

    Host-pathogen interactions are inherently complex and dynamic. The recent use of human microarrays has been invaluable to monitor the effects of various bacterial and viral pathogens upon host cell gene expression programs. This methodology has allowed the host response transcriptome of several cell lines to be studied on a global scale. To this point, the great majority of reports have focused on the response of immune cells, including macrophages and dendritic cells. These studies revealed that the immune response to microbial pathogens is tailored to different microbial challenges. Conversely, the paradigm for epithelial cells has--until recently--held that the epithelium mostly served as a relatively passive physical barrier to infection. It is now generally accepted that the epithelial barrier contributes more actively to signaling events in the immune response. In light of this shift, this review will compare transcriptional profiling data from studies that involved host-pathogen interactions occurring with epithelial cells. Experiments that defined both a common core response, as well as pathogen-specific host responses will be discussed. This review will also summarize the contributions that transcriptional profiling analysis has made to our understanding of bacterial physio-pathogensis of infection. This will include a discussion of how host transcriptional responses can be used to infer the function of virulence determinants from bacterial pathogens interacting with epithelial mucosa. In particular, we will expand upon the lessons that have been learned from gastro-intestinal and oral pathogens, as well as from members of the commensal flora.

  7. Regional repression of a Drosophila POU box gene in the endoderm involves inductive interactions between germ layers.

    Science.gov (United States)

    Affolter, M; Walldorf, U; Kloter, U; Schier, A F; Gehring, W J

    1993-04-01

    An induction process occurring between the mesodermal and the endodermal germ layers has recently been described in the regulation of the Drosophila homeotic gene labial (lab). We report here that proper spatial regulation of the Drosophila POU box gene pdm-1 products also involves interaction between these two germ layers. pdm-1 transcripts are initially present in both the anterior and the posterior endodermal midgut primordia. Upon fusion of the two primordia, transcripts disappear from two regions in the endoderm, a central domain and an anterior domain. The anterior repression domain of pdm-1 is independent of the expression of known homeotic genes and genes encoding secreted signalling molecules in the visceral mesoderm, both for its positioning and its repression. Repression in the central domain requires both the homeotic gene Ultrabithorax (Ubx) and the decapentaplegic (dpp) gene, which encodes a secreted protein. Both of these genes are also required for lab induction. However, the analysis of pdm-1 expression in various mutant backgrounds indicates that the regulation of lab and pdm-1 across germ layers is controlled by different genetic cascades. Our study indicates that dpp is not the signal that dictates central pdm-1 repression across germ layers and suggests that in the same midgut region, different signalling pathways result in the differential activation or repression of potential transcription factors.

  8. Collaboratives for Wildlife-Wind Turbine Interaction Research: Fostering Multistakeholder Involvement (Poster)

    Energy Technology Data Exchange (ETDEWEB)

    Sinclair, K.

    2013-04-01

    This poster highlights the various wildlife-wind collaboratives (specific to wildlife-wind turbine interaction research) that currently exist. Examples of collaboratives are included along with contact information, objectives, benefits, and ways to advance the knowledge base.

  9. Phenomenological analysis of the interacting boson model

    Science.gov (United States)

    Hatch, R. L.; Levit, S.

    1982-01-01

    The classical Hamiltonian of the interacting boson model is defined and expressed in terms of the conventional quadrupole variables. This is used in the analyses of the dynamics in the various limits of the model. The purpose is to determine the range and the features of the collective phenomena which the interacting boson model is capable of describing. In the commonly used version of the interacting boson model with one type of the s and d bosons and quartic interactions, this capability has certain limitations and the model should be used with care. A more sophisticated version of the interacting boson model with neutron and proton bosons is not discussed. NUCLEAR STRUCTURE Interacting bosons, classical IBM Hamiltonian in quadrupole variables, phenomenological content of the IBM and its limitations.

  10. In silico Analysis of Candidate Genes Involved in Sanfilippo Syndrome

    Directory of Open Access Journals (Sweden)

    Mehreen Zaka

    2015-04-01

    Full Text Available Sanfilippo syndrome is an autosomal recessive lysosomal storage disorder, caused by the deficiency of enzymes that play an important role in degradation of glycosaminoglycans and also called mucopolysaccharidosis III. Mucopolysaccharidosis is genetic disorder. Here, we searched the candidate genes for Sanfilippo syndrome by using BLAST with the query sequence. As no suitable homology was found against the query sequence we moved towards threading approach. The threading approach was carried out by employing online CPH models and LOMETS tools. Through present research, domains of the proteins were predicted by utilizing the Domain Sweep tools, GNS and two domains were reported. Motif search reported the maximum number of motifs for Type D protein as compared to other types. All four proteins were totally soluble proteins and no transmembrane domains were found. In future, these results and predicted 3D structures can be used for the molecular docking studies, binding activities and protein-protein interactions for all the four types of Sanfilippo syndrome.

  11. Interaction Pattern Analysis in cMOOCs Based on the Connectivist Interaction and Engagement Framework

    Science.gov (United States)

    Wang, Zhijun; Anderson, Terry; Chen, Li; Barbera, Elena

    2017-01-01

    Connectivist learning is interaction-centered learning. A framework describing interaction and cognitive engagement in connectivist learning was constructed using logical reasoning techniques. The framework and analysis was designed to help researchers and learning designers understand and adapt the characteristics and principles of interaction in…

  12. Dynamic Stall Analysis Utilizing Interactive Computer Graphics

    Science.gov (United States)

    1988-03-01

    Blade-Vortex Interaction (BV[) studies. solkes the two-dimen i,)nal, unsteady, compressible Euler and Napier -Stokes equations in strong conservation...requirements, interactive computer graphics workstations have been evolved to complement the super -computer. Workstation capabilities, in terms of

  13. Effect of metal ions on some pharmacologically relevant interactions involving fluoroquinolone antibiotics.

    Science.gov (United States)

    Seedher, Neelam; Agarwal, Pooja

    2010-01-01

    Complexation of five metal cations, Fe(3+), Al(3+), Zn(2+), Cu(2+) and Mg(2+) with four fluoroquinolones, levofloxacin, sparfloxacin, ciprofloxacin hydrochloride and enrofloxacin and human serum albumin (HSA) has been studied for better understanding of bioavailability of drugs interacting with metals and proteins. The binding parameters have been determined using fluorescence and ultraviolet absorption spectroscopic techniques. The effect of metal cations on the interaction of fluoroquinolones with HSA has also been investigated. The association constants were of the order of 10(2)-10(4) for the fluoroquinolone-metal ion interaction. For a given drug, the chelation potential of Al(3+) was highest, whereas that of Mg(2+) was lowest. At a metal ion/drug ratio of 1:1, approximately 50%-73% of metal ion was bound per mole drug in most cases. In the case of HSA-metal ion interaction, for Fe(3+) and Zn(2+) ions, there was only one class of binding site, whereas for Al(3+) and Cu(2+) ions, two types of binding sites were found. The relative affinity of various metal ions was found to vary as Al(3+)>Cu(2+)>Zn(2+)>Fe(3+). The extent of binding was found to be independent of the charge on the ion. Owing to very weak quenching of fluorescence, the association constant for the interaction of Mg(2+) ion could not be determined by this technique. The binding affinity of all the fluoroquinolones to HSA was found to increase in the presence of Cu(2+) ions, whereas all other metal ions decreased the binding -affinity with the exception of levofloxacin in the presence of Zn(2+) and Al(3+) ions. Increase in the binding affinity indicated that the metal ions facilitate HSA-fluoroquinolone interaction and fluoroquinolones probably interact with HSA via a metal ion bridge. Decrease in the binding affinity, by contrast, can either be due to the fact that fluoroquinolone-metal ion complex inhibits fluoroquinolone-HSA interaction or metal ions produce conformational changes in the HSA

  14. Disrupting the Acyl Carrier Protein/SpoT interaction in vivo: identification of ACP residues involved in the interaction and consequence on growth.

    Directory of Open Access Journals (Sweden)

    Sandra Angelini

    Full Text Available In bacteria, Acyl Carrier Protein (ACP is the central cofactor for fatty acid biosynthesis. It carries the acyl chain in elongation and must therefore interact successively with all the enzymes of this pathway. Yet, ACP also interacts with proteins of diverse unrelated function. Among them, the interaction with SpoT has been proposed to be involved in regulating ppGpp levels in the cell in response to fatty acid synthesis inhibition. In order to better understand this mechanism, we screened for ACP mutants unable to interact with SpoT in vivo by bacterial two-hybrid, but still functional for fatty acid synthesis. The position of the selected mutations indicated that the helix II of ACP is responsible for the interaction with SpoT. This suggested a mechanism of recognition similar to one used for the enzymes of fatty acid synthesis. Consistently, the interactions tested by bacterial two-hybrid of ACP with fatty acid synthesis enzymes were also affected by the mutations that prevented the interaction with SpoT. Yet, interestingly, the corresponding mutant strains were viable, and the phenotypes of one mutant suggested a defect in growth regulation.

  15. A novel mechanism of hippocampal LTD involving muscarinic receptor-triggered interactions between AMPARs, GRIP and liprin-α

    Directory of Open Access Journals (Sweden)

    Dickinson Bryony A

    2009-06-01

    Full Text Available Abstract Background Long-term depression (LTD in the hippocampus can be induced by activation of different types of G-protein coupled receptors, in particular metabotropic glutamate receptors (mGluRs and muscarinic acethycholine receptors (mAChRs. Since mGluRs and mAChRs activate the same G-proteins and isoforms of phospholipase C (PLC, it would be expected that these two forms of LTD utilise the same molecular mechanisms. However, we find a distinct mechanism of LTD involving GRIP and liprin-α. Results Whilst both forms of LTD require activation of tyrosine phosphatases and involve internalisation of AMPARs, they use different molecular interactions. Specifically, mAChR-LTD, but not mGluR-LTD, is blocked by peptides that inhibit the binding of GRIP to the AMPA receptor subunit GluA2 and the binding of GRIP to liprin-α. Thus, different receptors that utilise the same G-proteins can regulate AMPAR trafficking and synaptic efficacy via distinct molecular mechanisms. Conclusion Our results suggest that mAChR-LTD selectively involves interactions between GRIP and liprin-α. These data indicate a novel mechanism of synaptic plasticity in which activation of M1 receptors results in AMPAR endocytosis, via a mechanism involving interactions between GluA2, GRIP and liprin-α.

  16. Functional interactions within 23S rRNA involving the peptidyltransferase center

    DEFF Research Database (Denmark)

    Douthwaite, S

    1992-01-01

    A molecular genetic approach has been employed to investigate functional interactions within 23S rRNA. Each of the three base substitutions at guanine 2032 has been made. The 2032A mutation confers resistance to the antibiotics chloramphenicol and clindamycin, which interact with the 23S r...... that also confer antibiotic resistance. Both the domain II deletion and the 2057A mutation relieve the hypersensitive effect of the 2032A mutation, producing an erythromycin-resistant phenotype; in addition, the combination of the 2032A and 2057A mutations confers a higher level of chloramphenicol...... and chloramphenicol. Introduction of the domain II deletion into these double-mutation constructs gives rise to erythromycin resistance. The results are interpreted as indicating that position 2032 interacts with the peptidyltransferase loop and that there is a functional connection between domains II and V....

  17. The role of hydrogen atoms in interactions involving imidazolium-based ionic liquids

    Science.gov (United States)

    Kempter, V.; Kirchner, B.

    2010-05-01

    In the first part of this report experimental results are discussed which focus onto the importance of hydrogen atoms in the interaction of imidazolium-based ionic liquids. These include examples for the cation-anion interaction in neat ionic liquids as well as the interactions between ionic liquids and their molecular environment, water in particular. Most of the studies emphasize the importance of the C(2)-H group of the imidazolium ring for the intra- and intermolecular interactions; commonly, the interactions of the type C-H … X (X =: O, halide) are attributed to "hydrogen bonding". In the second part it is analyzed whether these interactions and their consequences fulfill the criteria set by standard definitions of hydrogen bonding. Two cation-anion co-conformations at the C(2)-H group are found. One co-conformer (in-plane) often resembles a hydrogen bond while the other one (on-top) points to a non-hydrogen bonding behavior. Furthermore, the degree of hydrogen bonding for the in-plane structure is very dependent on the anion. Spatial distribution functions show that, in general, both co-conformations are occupied. However, the question of how long a particular co-conformer is populated in the liquid state has yet to be answered. Therefore, it is concluded that the term "hydrogen bond" should, at present, be treated with care to characterize the cation-anion contacts, because of the above-mentioned difficulties. Once more it must be stressed that oversimplifications and generalizations, even for this subclass of ionic liquids have to be avoided, because these liquids are more complicated than it appears from first sight.

  18. Advanced Seismic Fragility Modeling using Nonlinear Soil-Structure Interaction Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bolisetti, Chandu [Idaho National Lab. (INL), Idaho Falls, ID (United States); Coleman, Justin [Idaho National Lab. (INL), Idaho Falls, ID (United States); Talaat, Mohamed [Simpson-Gupertz & Heger, Waltham, MA (United States); Hashimoto, Philip [Simpson-Gupertz & Heger, Waltham, MA (United States)

    2015-09-01

    The goal of this effort is to compare the seismic fragilities of a nuclear power plant system obtained by a traditional seismic probabilistic risk assessment (SPRA) and an advanced SPRA that utilizes Nonlinear Soil-Structure Interaction (NLSSI) analysis. Soil-structure interaction (SSI) response analysis for a traditional SPRA involves the linear analysis, which ignores geometric nonlinearities (i.e., soil and structure are glued together and the soil material undergoes tension when the structure uplifts). The NLSSI analysis will consider geometric nonlinearities.

  19. Compatible and Incompatible Interactions in Wheat Involving the Bt-10 Gene for Resistance to Tilletia tritici, the Common Bunt Pathogen.

    Science.gov (United States)

    Gaudet, Denis A; Lu, Zhen-Xiang; Leggett, Frances; Puchalski, Bryan; Laroche, André

    2007-11-01

    ABSTRACT The infection of wheat lines Neepawa (susceptible), and its sib BW553 that is nearly isogenic for the Bt-10 resistance gene by differentially virulent races T1 and T27 of common bunt (Tilletia tritici), was followed for 21 days following seeding (dfs) using fluorescence and confocal microscopy. Spore germination was nonsynchronous and all spore stages including germination were observed 5 to 21 dfs. Initial host perception of pathogen invasion, based on autofluorescence in epidermal cells adjacent to the appressoria, was similar in both compatible and incompatible interactions, and occurred as early as 5 to 6 dfs. The total number of sites on a 1-cm segment of coleoptile adjacent to the seed that exhibited autofluorescence was similar in both the compatible and incompatible interactions and rose to a maximum of 35 to 40 per 1 cm length of coleoptile following 17 dfs, although new infection events were observed as late as 21 dfs. In the compatible interaction, the autofluorescence became more diffuse 10 to 12 dfs, emanating in all directions in association with fungal spread. In the incompatible interaction, autofluorescence remained restricted to a small area surrounding the penetration site. Two different reaction zones that extended further in tissues surrounding the penetration point in the incompatible interaction compared with the compatible interaction were identified. The accumulation of callose around invading fungal hyphae was observed during both the compatible and incompatible interactions from 8 to 21 dfs. While callose accumulation was more extensive and widespread in the incompatible interaction, it was clearly present in compatible interactions, particularly in treatments involving BW553. These results were confirmed by expression of callose synthase transcripts that were more abundant in BW553 than in Neepawa and were upregulated during pathogen infection in both compatible and incompatible interactions.

  20. A Meta-Analysis: The Relationship Between Parental Involvement and Latino Student Outcomes

    Science.gov (United States)

    Jeynes, William H.

    2017-01-01

    This meta-analysis of 28 studies examines the relationship between parental involvement and the academic achievement and school behavior of Latino pre-kindergarten-college-age children. Analyses determined the effect sizes for parental involvement overall and specific categories of involvement. Results indicate a significant relationship between…

  1. A Meta-Analysis: The Relationship between Father Involvement and Student Academic Achievement

    Science.gov (United States)

    Jeynes, William H.

    2015-01-01

    A meta-analysis was undertaken, including 66 studies, to determine the relationship between father involvement and the educational outcomes of urban school children. Statistical analyses were done to determine the overall impact and specific components of father involvement. The possible differing effects of paternal involvement by race were also…

  2. A typology of affordances: untangling sociomaterial interactions through video analysis

    NARCIS (Netherlands)

    van Osch, W.; Mendelson, O.

    2011-01-01

    In this study we untangle the sociomaterial interactions between developers, users, and artifacts by analyzing what types of affordances occur in the interactions between actors and artifacts in the context of group generativity. Hereto, we conducted an in-depth ethnographic and interaction analysis

  3. Interaction of targeted liposomes with primary cultured hepatic stellate cells : Involvement of multiple receptor systems

    NARCIS (Netherlands)

    Adrian, Joanna Ewa; Poelstra, Klaas; Scherphof, Gerrit; Molema, Ingrid; Meijer, D.K F; Reker-Smit, Catharina; Morselt, Henriette; Kamps, Jan

    2006-01-01

    Background/Aims: In designing a versatile liposomal drug carrier to hepatic stellate cells (HSC), the interaction of mannose 6-phosphate human serum albumin (M6P-HSA) liposomes with cultured cells was studied. Methods: M6P-HSA was covalently coupled to the liposomal surface and the uptake and bindin

  4. Microbial interactions involving sulfur bacteria : implications for the ecology and evolution of bacterial communities

    NARCIS (Netherlands)

    Overmann, J; van Gemerden, H

    2000-01-01

    A major goal of microbial ecology is the identification and characterization of those microorganisms which govern transformations in natural ecosystems. This review summarizes our present knowledge of microbial interactions in the natural sulfur cycle. Central to the discussion is the recent progres

  5. Microbial interactions involving sulfur bacteria : implications for the ecology and evolution of bacterial communities

    NARCIS (Netherlands)

    Overmann, J; van Gemerden, H

    2000-01-01

    A major goal of microbial ecology is the identification and characterization of those microorganisms which govern transformations in natural ecosystems. This review summarizes our present knowledge of microbial interactions in the natural sulfur cycle. Central to the discussion is the recent

  6. Language learning, recasts, and interaction involving AAC: background and potential for intervention.

    Science.gov (United States)

    Clarke, Michael T; Soto, Gloria; Nelson, Keith

    2017-03-01

    For children with typical development, language is learned through everyday discursive interaction. Adults mediate child participation in such interactions through the deployment of a range of co-constructive strategies, including repeating, questioning, prompting, expanding, and reformulating the child's utterances. Adult reformulations of child utterances, also known as recasts, have also been shown to relate to the acquisition of linguistic structures in children with language and learning disabilities and children and adults learning a foreign language. In this paper we discuss the theoretical basis and empirical evidence for the use of different types of recasts as a major language learning catalyst, and what may account for their facilitative effects. We consider the occurrence of different types of recasts in AAC-mediated interactions and their potential for language facilitation, within the typical operational and linguistic constraints of such interactions. We also consider the benefit of explicit and corrective forms of recasts for language facilitation in conversations with children who rely on AAC. We conclude by outlining future research directions.

  7. Analysis of crucial molecules involved in herniated discs and degenerative disc disease

    Directory of Open Access Journals (Sweden)

    Zhigang Qu

    2013-01-01

    Full Text Available OBJECTIVES: Herniated discs and degenerative disc disease are major health problems worldwide. However, their pathogenesis remains obscure. This study aimed to explore the molecular mechanisms of these ailments and to identify underlying therapeutic targets. MATERIAL AND METHODS: Using the GSE23130 microarray datasets downloaded from the Gene Expression Omnibus database, differentially co-expressed genes and links were identified using the differentially co-expressed gene and link method with a false discovery rate ,0.25 as a significant threshold. Subsequently, the underlying molecular mechanisms of the differential co-expression of these genes were investigated using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, the transcriptional regulatory relationship was also investigated. RESULTS: Through the analysis of the gene expression profiles of different specimens from patients with these diseases, 539 differentially co-expressed genes were identified for these ailments. The ten most significant signaling pathways involving the differentially co-expressed genes were identified by enrichment analysis. Among these pathways, apoptosis and extracellular matrix-receptor interaction pathways have been reported to be related to these diseases. A total of 62 pairs of regulatory relationships between transcription factors and their target genes were identified as critical for the pathogenesis of these diseases. CONCLUSION: The results of our study will help to identify the mechanisms responsible for herniated discs and degenerative disc disease and provides a theoretical basis for further therapeutic study.

  8. Relationship of Purchasing, Brand, and Self Involvement with Advertising Interactions and Beliefs among Malaysian Students.

    Science.gov (United States)

    Ramaprasad, Jyotika

    A study examined Malaysian students' involvement with purchasing, with branded products, and with themselves as well as their responses to and beliefs about advertising, by ethnic group. Subjects, 387 students at a university in Penang, Malaysia, completed questionnaires measuring their responses to advertising. Results indicated a relatively high…

  9. The Interactive Effects of Perceived Parental Involvement and Personality on Teacher Satisfaction

    Science.gov (United States)

    Li, Chung-Kai; Hung, Chia-Hung

    2012-01-01

    Purpose: This study aims to examine the relations between teachers' perception of parental involvement and teacher satisfaction. It further aims to investigate how this relationship may be moderated by interpersonal personality traits. Design/methodology/approach: A questionnaire was conducted; participants were 572 classroom teachers who teach at…

  10. Identification of Protein-Protein Interactions Involved in Pectin Biosynthesis in the golgi Apparatus

    DEFF Research Database (Denmark)

    Lund, Christian Have

    for instance as food additives, nutraceutical, for paper and energy production. Pectin is a cell wall glycan that crucial for every plant growing on land. Pectin is said to be one of the most complex glycans on earth and it is hypothesized that at least 67 enzymatic reactions are involved in its biosynthesis...

  11. Analysis of Protein-Membrane Interactions

    DEFF Research Database (Denmark)

    Kemmer, Gerdi Christine

    Cellular membranes are complex structures, consisting of hundreds of different lipids and proteins. These membranes act as barriers between distinct environments, constituting hot spots for many essential functions of the cell, including signaling, energy conversion, and transport. These functions...... are implemented by soluble proteins reversibly binding to, as well as by integral membrane proteins embedded in, cellular membranes. The activity and interaction of these proteins is furthermore modulated by the lipids of the membrane. Here, liposomes were used as model membrane systems to investigate...... interactions between proteins and lipids. First, interactions of soluble proteins with membranes and specific lipids were studied, using two proteins: Annexin V and Tma1. The protein was first subjected to a lipid/protein overlay assay to identify candidate interaction partners in a fast and efficient way...

  12. Molecular Analysis of Rice CIPKs Involved in Both Biotic and Abiotic Stress Responses

    Institute of Scientific and Technical Information of China (English)

    CHEN Xi-feng; Gu Zhi-min; LIU Feng; MA Bo-jun; ZHANG Hong-sheng

    2011-01-01

    Plant calcineurin B-like (CBL) proteins have been proposed as important Ca2+ sensors and specifically interact with CBL-interacting protein kinases (CIPKs) in plant-specific calcium signaling.Here,we identified and isolated 15 CIPK genes in a japonica rice variety Nipponbare based on the predicted sequences of rice CIPK gene family.Gene structure analysis showed that these 15 genes were divided into intron-less and intron-rich groups,and OsCIPK3 and OsCIPK24 exhibited alternative splicing in their mature process.The phylogenetic analyses indicated that rice CIPKs shared an ancestor with Arabidopsis and poplar CIPKs.Analyses of gene expression showed that these OsCIPK genes were differentially induced by biotic stresses such as bacterial blight and abiotic stresses (heavy metal such as Hg2+,high salinity,cold and ABA).Interestingly,five OsCIPK genes,OsCIPK1,2,10,11 and 12,were transcriptionally up-regulated after bacterial blight infection whereas four OsCIPK genes,OsCIPK2,10,11 and 14,were induced by all treatments,indicating that some of OsCIPK genes are involved in multiple stress response pathways in plants.Our finding suggests that CIPKs play a key role in both biotic and abiotic stress responses.

  13. Comparative Proteomic Analysis Reveals Proteins Putatively Involved in Toxin Biosynthesis in the Marine Dinoflagellate Alexandrium catenella

    Directory of Open Access Journals (Sweden)

    Da-Zhi Wang

    2013-01-01

    Full Text Available Alexandrium is a neurotoxin-producing dinoflagellate genus resulting in paralytic shellfish poisonings around the world. However, little is known about the toxin biosynthesis mechanism in Alexandrium. This study compared protein profiles of A. catenella collected at different toxin biosynthesis stages (non-toxin synthesis, initial toxin synthesis and toxin synthesizing coupled with the cell cycle, and identified differentially expressed proteins using 2-DE and MALDI-TOF-TOF mass spectrometry. The results showed that toxin biosynthesis of A. catenella occurred within a defined time frame in the G1 phase of the cell cycle. Proteomic analysis indicated that 102 protein spots altered significantly in abundance (P < 0.05, and 53 proteins were identified using database searching. These proteins were involved in a variety of biological processes, i.e., protein modification and biosynthesis, metabolism, cell division, oxidative stress, transport, signal transduction, and translation. Among them, nine proteins with known functions in paralytic shellfish toxin-producing cyanobacteria, i.e., methionine S-adenosyltransferase, chloroplast ferredoxin-NADP+ reductase, S-adenosylhomocysteinase, adenosylhomocysteinase, ornithine carbamoyltransferase, inorganic pyrophosphatase, sulfotransferase (similar to, alcohol dehydrogenase and arginine deiminase, varied significantly at different toxin biosynthesis stages and formed an interaction network, indicating that they might be involved in toxin biosynthesis in A. catenella. This study is the first step in the dissection of the behavior of the A. catenella proteome during different toxin biosynthesis stages and provides new insights into toxin biosynthesis in dinoflagellates.

  14. Identification of novel GAPDH-derived antimicrobial peptides secreted by Saccharomyces cerevisiae and involved in wine microbial interactions

    DEFF Research Database (Denmark)

    Branco, Patrícia; Francisco, Diana; Chambon, Christophe

    2014-01-01

    a wide variety of wine-related yeasts (e.g. Dekkera bruxellensis) and bacteria (e.g. Oenococcus oeni). Mass spectrometry analyses revealed that these AMPs correspond to fragments of the S. cerevisiae glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein. The involvement of GAPDH-derived peptides...... in wine microbial interactions was further sustained by results obtained in mixed cultures performed with S. cerevisiae single mutants deleted in each of the GAPDH codifying genes (TDH1-3) and also with a S. cerevisiae mutant deleted in the YCA1 gene, which codifies the apoptosis-involved enzyme...... metacaspase. These findings are discussed in the context of wine microbial interactions, biopreservation potential and the role of GAPDH in the defence system of S. cerevisiae....

  15. Calculation of the matrix elements of the Coulomb interaction involving relativistic hydrogenic wave functions

    Science.gov (United States)

    Sarkadi, L.

    2017-03-01

    The program MTRDCOUL [1] calculates the matrix elements of the Coulomb interaction between a charged particle and an atomic electron, ∫ ψf∗ (r) ∣ R - r∣-1ψi(r) d r. Bound-free transitions are considered, and relativistic hydrogenic wave functions are used. In this revised version a bug discovered in the F3Y CPC Program Library subprogram [2] is fixed.

  16. Supramolecular assembly of 2,4,5-trifluorobenzoate complex based on weak interactions involving fluorine atoms

    Institute of Scientific and Technical Information of China (English)

    Chun-Hua Ge; Rui Zhang; Ping Fan; Xiang-Dong Zhang; Li-Juan Wang; Fang-Fang Wang

    2013-01-01

    The complex [Cd(tfbz)2(phen)]2 (1) (tfbz =2,4,5-trifluorobenzoate,phen =1,10-phenanthro-line) was synthesized using trifluorobenzoic acid ligand.The single-crystal structure of 1 has been determined by X-ray crystallography.The packing structure is characterized by the formation of an intricate three-dimensional supramolecular network that depends on the C-H…F,F…F, F(lp)…π (lp =lone pair) interactions.

  17. The effect of diet and opponent size on aggressive interactions involving caribbean crazy ants (Nylanderia fulva).

    Science.gov (United States)

    Horn, Katherine C; Eubanks, Micky D; Siemann, Evan

    2013-01-01

    Biotic interactions are often important in the establishment and spread of invasive species. In particular, competition between introduced and native species can strongly influence the distribution and spread of exotic species and in some cases competition among introduced species can be important. The Caribbean crazy ant, Nylanderia fulva, was recently introduced to the Gulf Coast of Texas, and appears to be spreading inland. It has been hypothesized that competition with the red imported fire ant, Solenopsis invicta, may be an important factor in the spread of crazy ants. We investigated the potential of interspecific competition among these two introduced ants by measuring interspecific aggression between Caribbean crazy ant workers and workers of Solenopsis invicta. Specifically, we examined the effect of body size and diet on individual-level aggressive interactions among crazy ant workers and fire ants. We found that differences in diet did not alter interactions between crazy ant workers from different nests, but carbohydrate level did play an important role in antagonistic interactions with fire ants: crazy ants on low sugar diets were more aggressive and less likely to be killed in aggressive encounters with fire ants. We found that large fire ants engaged in fewer fights with crazy ants than small fire ants, but fire ant size affected neither fire ant nor crazy ant mortality. Overall, crazy ants experienced higher mortality than fire ants after aggressive encounters. Our findings suggest that fire ant workers might outcompete crazy ant workers on an individual level, providing some biotic resistance to crazy ant range expansion. However, this resistance may be overcome by crazy ants that have a restricted sugar intake, which may occur when crazy ants are excluded from resources by fire ants.

  18. The Interaction between Pesticide Use and Genetic Variants Involved in Lipid Metabolism on Prostate Cancer Risk

    Directory of Open Access Journals (Sweden)

    Gabriella Andreotti

    2012-01-01

    Full Text Available Background. Lipid metabolism processes have been implicated in prostate carcinogenesis. Since several pesticides are lipophilic or are metabolized via lipid-related mechanisms, they may interact with variants of genes in the lipid metabolism pathway. Methods. In a nested case-control study of 776 cases and 1444 controls from the Agricultural Health Study (AHS, a prospective cohort study of pesticide applicators, we examined the interactions between 39 pesticides (none, low, and high exposure and 220 single nucleotide polymorphisms (SNPs in 59 genes. The false discovery rate (FDR was used to account for multiple comparisons. Results. We found 17 interactions that displayed a significant monotonic increase in prostate cancer risk with pesticide exposure in one genotype and no significant association in the other genotype. The most noteworthy association was for ALOXE3 rs3027208 and terbufos, such that men carrying the T allele who were low users had an OR of 1.86 (95% CI = 1.16–2.99 and high users an OR of 2.00 (95% CI = 1.28–3.15 compared to those with no use of terbufos, while men carrying the CC genotype did not exhibit a significant association. Conclusion. Genetic variation in lipid metabolism genes may modify pesticide associations with prostate cancer; however our results require replication.

  19. Hydrophobic interactions are involved in the inhibition of human leukocyte elastase by alkyltrimethylammonium salts.

    Science.gov (United States)

    Kouadri-Boudjelthia, A; Wallach, J M

    1997-02-01

    Electrostatic forces and hydrophobic interactions had been suggested to modify the adsorption of elastases onto insoluble fibrous elastin, which is the initial stage of elastolysis, but conflicting results had been obtained, and comparison between compounds with different structures was difficult. In order to explore these observations, we have studied the effect of six alkyltrimethylammonium bromides, with alkyl chain length ranging from six to 16 carbon atoms, on human leucocyte elastase activities, either with a synthetic substrate or with insoluble elastin. The enzymatic studies were performed either spectrophotometrically or using conductimetry, and direct binding on to elastin was conductimetrically measured. Binding of the alkyltrimethylammonium salts is increasing with alkyl chain length and we could demonstrate a cooperative binding for tetra- and hexadecyl chains. No effect of the six compounds could be evidenced on hydrolysis of a specific synthetic substrate. With insoluble elastin, elastolysis inhibition could be demonstrated for alkyl chain longer than ten carbon atoms, the effect increasing with chain length. A similar inhibition was observed with the soluble kappa-elastin, but it was less effective. The study shows that the interaction between the alkyltrimethylammonium salts and elastin plays a major role in the inhibitory potency of these molecules. As this effect is enhanced with alkyl chain length, it was concluded that hydrophobic interactions favour their binding, protecting elastin against elastase adsorption.

  20. Transgenerational interactions involving parental age and immune status affect female reproductive success in Drosophila melanogaster.

    Science.gov (United States)

    Nystrand, M; Dowling, D K

    2014-11-07

    It is well established that the parental phenotype can influence offspring phenotypic expression, independent of the effects of the offspring's own genotype. Nonetheless, the evolutionary implications of such parental effects remain unclear, partly because previous studies have generally overlooked the potential for interactions between parental sources of non-genetic variance to influence patterns of offspring phenotypic expression. We tested for such interactions, subjecting male and female Drosophila melanogaster of two different age classes to an immune activation challenge or a control treatment. Flies were then crossed in all age and immune status combinations, and the reproductive success of their immune- and control-treated daughters measured. We found that daughters produced by two younger parents exhibited reduced reproductive success relative to those of other parental age combinations. Furthermore, immune-challenged daughters exhibited higher reproductive success when produced by immune-challenged relative to control-treated mothers, a pattern consistent with transgenerational immune priming. Finally, a complex interplay between paternal age and parental immune statuses influenced daughter's reproductive success. These findings demonstrate the dynamic nature of age- and immune-mediated parental effects, traceable to both parents, and regulated by interactions between parents and between parents and offspring.

  1. Biomembrane models and drug-biomembrane interaction studies: Involvement in drug design and development

    Directory of Open Access Journals (Sweden)

    R Pignatello

    2011-01-01

    Full Text Available Contact with many different biological membranes goes along the destiny of a drug after its systemic administration. From the circulating macrophage cells to the vessel endothelium, to more complex absorption barriers, the interaction of a biomolecule with these membranes largely affects its rate and time of biodistribution in the body and at the target sites. Therefore, investigating the phenomena occurring on the cell membranes, as well as their different interaction with drugs in the physiological or pathological conditions, is important to exploit the molecular basis of many diseases and to identify new potential therapeutic strategies. Of course, the complexity of the structure and functions of biological and cell membranes, has pushed researchers toward the proposition and validation of simpler two- and three-dimensional membrane models, whose utility and drawbacks will be discussed. This review also describes the analytical methods used to look at the interactions among bioactive compounds with biological membrane models, with a particular accent on the calorimetric techniques. These studies can be considered as a powerful tool for medicinal chemistry and pharmaceutical technology, in the steps of designing new drugs and optimizing the activity and safety profile of compounds already used in the therapy.

  2. Coil–globule transition of a polymer involved in excluded-volume interactions with macromolecules

    Energy Technology Data Exchange (ETDEWEB)

    Odagiri, Kenta [School of Network and Information, Senshu University, Kawasaki 214-8580 (Japan); Seki, Kazuhiko, E-mail: k-seki@aist.go.jp [National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 5, Tsukuba, Ibaraki 305-8565 (Japan)

    2015-10-07

    Polymers adopt extended coil and compact globule states according to the balance between entropy and interaction energies. The transition of a polymer between an extended coil state and compact globule state can be induced by changing thermodynamic force such as temperature to alter the energy/entropy balance. Previously, this transition was theoretically studied by taking into account the excluded-volume interaction between monomers of a polymer chain using the partition function. For binary mixtures of a long polymer and short polymers, the coil-globule transition can be induced by changing the concentration of the shorter polymers. Here, we investigate the transition caused by short polymers by generalizing the partition function of the long polymer to include the excluded-volume effect of short polymers. The coil-globule transition is studied as a function of the concentration of mixed polymers by systematically varying Flory’s χ-parameters. We show that the transition is caused by the interplay between the excluded-volume interaction and the dispersion state of short polymers in the solvent. We also reveal that the same results can be obtained by combining the mixing entropy and elastic energy if the volume of a long polymer is properly defined.

  3. Thermodynamic and Acoustic Study on Molecular Interactions in Certain Binary Liquid Systems Involving Ethyl Benzoate

    Directory of Open Access Journals (Sweden)

    B. Nagarjun

    2013-01-01

    Full Text Available Speeds of sound and density for binary mixtures of ethyl benzoate (EB with N,N-dimethylformamide (NNDMF, N,N-dimethyl acetamide (NNDMAc, and N,N-dimethylaniline (NNDMA were measured as a function of mole fraction at temperatures 303.15, 308.15 K, 313.15 K, and 318.15 K and atmospheric pressure. From the experimental data, adiabatic compressibility (βad, intermolecular free length (Lf, and molar volume (V have been computed. The excess values of the above parameters were also evaluated and discussed in light of molecular interactions. Deviation in adiabatic compressibilities and excess intermolecular free length (LfE are found to be negative over the molefraction of ethyl benzoate indicating the presence of strong interactions between the molecules. The negative excess molar volume VE values are attributed to strong dipole-dipole interactions between unlike molecules in the mixtures. The binary data of Δβad, VE, and LfE were correlated as a function of molefraction by using the Redlich-Kister equation.

  4. A receptionist robot for Brazilian people: study on interaction involving illiterates

    Directory of Open Access Journals (Sweden)

    Trovato Gabriele

    2017-04-01

    Full Text Available The receptionist job, consisting in providing useful indications to visitors in a public office, is one possible employment of social robots. The design and the behaviour of robots expected to be integrated in human societies are crucial issues, and they are dependent on the culture and society in which the robot should be deployed. We study the factors that could be used in the design of a receptionist robot in Brazil, a country with a mix of races and considerable gaps in economic and educational level. This inequality results in the presence of functional illiterate people, unable to use reading, writing and numeracy skills. We invited Brazilian people, including a group of functionally illiterate subjects, to interact with two types of receptionists differing in physical appearance (agent v mechanical robot and in the sound of the voice (human like v mechanical. Results gathered during the interactions point out a preference for the agent, for the human-like voice and a more intense reaction to stimuli by illiterates. These results provide useful indications that should be considered when designing a receptionist robot, as well as insights on the effect of illiteracy in the interaction.

  5. A novel statistic for genome-wide interaction analysis.

    Science.gov (United States)

    Wu, Xuesen; Dong, Hua; Luo, Li; Zhu, Yun; Peng, Gang; Reveille, John D; Xiong, Momiao

    2010-09-23

    Although great progress in genome-wide association studies (GWAS) has been made, the significant SNP associations identified by GWAS account for only a few percent of the genetic variance, leading many to question where and how we can find the missing heritability. There is increasing interest in genome-wide interaction analysis as a possible source of finding heritability unexplained by current GWAS. However, the existing statistics for testing interaction have low power for genome-wide interaction analysis. To meet challenges raised by genome-wide interactional analysis, we have developed a novel statistic for testing interaction between two loci (either linked or unlinked). The null distribution and the type I error rates of the new statistic for testing interaction are validated using simulations. Extensive power studies show that the developed statistic has much higher power to detect interaction than classical logistic regression. The results identified 44 and 211 pairs of SNPs showing significant evidence of interactions with FDRanalysis is a valuable tool for finding remaining missing heritability unexplained by the current GWAS, and the developed novel statistic is able to search significant interaction between SNPs across the genome. Real data analysis showed that the results of genome-wide interaction analysis can be replicated in two independent studies.

  6. Aetiology of SMON may involve an interaction between clioquinol and environmental metals

    Energy Technology Data Exchange (ETDEWEB)

    Tjaelve, H.

    1984-11-01

    Clioquinol can increase the penetration of metallic cations through cellular membranes by forming lipophilic metal-chelates. It is suggested that the pathogenesis of SMON may involve an accumulation of injurious metals in nervous tissues due to facilitated uptake by complex formation with clioquinol. The Japanese have been more heavily exposed to metals by environmental pollution than the inhabitants of other countries, which may explain the prevalent occurrence of SMON in Japan.

  7. Identification of genes involved in radioresistance of nasopharyngeal carcinoma by integrating gene ontology and protein-protein interaction networks.

    Science.gov (United States)

    Guo, Ya; Zhu, Xiao-Dong; Qu, Song; Li, Ling; Su, Fang; Li, Ye; Huang, Shi-Ting; Li, Dan-Rong

    2012-01-01

    Radioresistance remains one of the important factors in relapse and metastasis of nasopharyngeal carcinoma. Thus, it is imperative to identify genes involved in radioresistance and explore the underlying biological processes in the development of radioresistance. In this study, we used cDNA microarrays to select differential genes between radioresistant CNE-2R and parental CNE-2 cell lines. One hundred and eighty-three significantly differentially expressed genes (pgenes were upregulated and 45 genes were downregulated in CNE-2R. We further employed publicly available bioinformatics related software, such as GOEAST and STRING to examine the relationship among differentially expressed genes. The results show that these genes were involved in type I interferon-mediated signaling pathway biological processes; the nodes tended to have high connectivity with the EGFR pathway, IFN-related pathways, NF-κB. The node STAT1 has high connectivity with other nodes in the protein-protein interaction (PPI) networks. Finally, the reliability of microarray data was validated for selected genes by semi-quantitative RT-PCR and Western blotting. The results were consistent with the microarray data. Our study suggests that microarrays combined with gene ontology and protein interaction networks have great value in the identification of genes of radioresistance in nasopharyngeal carcinoma; genes involved in several biological processes and protein interaction networks may be relevant to NPC radioresistance; in particular, the verified genes CCL5, STAT1-α, STAT2 and GSTP1 may become potential biomarkers for predicting NPC response to radiotherapy.

  8. Information Retrieval Interaction: an Analysis of Models

    Directory of Open Access Journals (Sweden)

    Farahnaz Sadoughi

    2012-03-01

    Full Text Available Information searching process is an interactive process; thus users has control on searching process, and they can manage the results of the search process. In this process, user's question became more mature, according to retrieved results. In addition, on the side of the information retrieval system, there are some processes that could not be realized, unless by user. Practically, this issue, is egregious in “Interaction” -i.e. process of user connection to other system elements- and in “Relevance judgment”. This paper had a glance to existence of “Interaction” in information retrieval, in first. Then the tradition model of information retrieval and its strenght and weak points were reviewed. Finally, the current models of interactive information retrieval includes: Belkin episodic model, Ingwersen cognitive model, Sarasevic stratified model, and Spinks interactive feedback model were elucidated.

  9. Analysis of Interaction Factors Between Two Piles

    Institute of Scientific and Technical Information of China (English)

    CAO Ming; CHEN Long-zhu

    2008-01-01

    A rigorous analytical method is presented for calculating the interaction factor between two identical piles subjected to vertical loads. Following the technique proposed by Muki and Sternberg, the problem is decomposed into an extended soil mass and two fictitious piles characterized respectively by Young's modulus of the soil and that of the difference between the pile and soil. The unknown axial forces along fictitious piles are determined by solving a Fredholm integral equation of the second kind, which imposes the compatibility condition that the axial strains of the fictitious piles are equal to those corresponding to the centroidal axes of the extended soil. The real pile forces and displacements can subequally be calculated based on the determined fictitious pile forces, and finally, the desired pile interaction factors may be obtained. Results confirm the validity of the proposed approach and portray the influence of the governing parameters on the pile interaction.

  10. Combinatorial analysis of interacting RNA molecules

    CERN Document Server

    Li, Thomas J X

    2010-01-01

    Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.

  11. A novel statistic for genome-wide interaction analysis.

    Directory of Open Access Journals (Sweden)

    Xuesen Wu

    2010-09-01

    Full Text Available Although great progress in genome-wide association studies (GWAS has been made, the significant SNP associations identified by GWAS account for only a few percent of the genetic variance, leading many to question where and how we can find the missing heritability. There is increasing interest in genome-wide interaction analysis as a possible source of finding heritability unexplained by current GWAS. However, the existing statistics for testing interaction have low power for genome-wide interaction analysis. To meet challenges raised by genome-wide interactional analysis, we have developed a novel statistic for testing interaction between two loci (either linked or unlinked. The null distribution and the type I error rates of the new statistic for testing interaction are validated using simulations. Extensive power studies show that the developed statistic has much higher power to detect interaction than classical logistic regression. The results identified 44 and 211 pairs of SNPs showing significant evidence of interactions with FDR<0.001 and 0.001interacting pairs of SNPs in genes LST1/NCR3, CXCR5/BCL9L, and GLS2, some of which were located in the target sites of miR-324-3p, miR-433, and miR-382, as well as 15 pairs of interacting SNPs that had nonsynonymous substitutions. Our results demonstrated that genome-wide interaction analysis is a valuable tool for finding remaining missing heritability unexplained by the current GWAS, and the developed novel statistic is able to search significant interaction between SNPs across the genome. Real data analysis showed that the results of genome-wide interaction analysis can be replicated in two independent studies.

  12. A Fortran program to calculate the matrix elements of the Coulomb interaction involving hydrogenic wave functions

    Science.gov (United States)

    Sarkadi, L.

    2017-03-01

    The program MTRXCOUL [1] calculates the matrix elements of the Coulomb interaction between a charged particle and an atomic electron, ∫ ψf∗ (r) | R - r | - 1ψi(r) d r. Bound-free transitions are considered, and non-relativistic hydrogenic wave functions are used. In this revised version a bug discovered in the F3Y CPC Program Library (PL) subprogram [2] is fixed. Furthermore, the COULCC CPC PL subprogram [3] applied for the calculations of the radial wave functions of the free states and the Bessel functions is replaced by the CPC PL subprogram DCOUL [4].

  13. Features of an interactive writing discourse: conversational involvement, conventional knowledge, and internalization in "Morning Message".

    Science.gov (United States)

    Mariage, T V

    2001-01-01

    This study describes how meaning potentials were constructed in the literacy event known as Morning Message. Morning Message provided teachers and students with opportunities to construct a written text around the experiences of one student. This discourse of writing allowed for the examination of how meaning was orchestrated and scaffolded between the teacher and her students. Three findings are discussed, including the function of a series of conversational involvement moves utilized by the teacher, the specific writing conventions and metamessages afforded in the Morning Message dialogue, and an examination of how the social dialogues of Morning Message may have come to guide independent action as internalized processes on several transfer measures.

  14. Quantitative timed analysis of interactive Markov chains

    NARCIS (Netherlands)

    Guck, Dennis; Han, Tingting; Katoen, Joost-Pieter; Neuhausser, M.

    2012-01-01

    This paper presents new algorithms and accompanying tool support for analyzing interactive Markov chains (IMCs), a stochastic timed 1 1/2-player game in which delays are exponentially distributed. IMCs are compositional and act as semantic model for engineering formalisms such as AADL and dynamic fa

  15. Interactive Graphics Analysis for Aircraft Design

    Science.gov (United States)

    Townsend, J. C.

    1983-01-01

    Program uses higher-order far field drag minimization. Computer program WDES WDEM preliminary aerodynamic design tool for one or two interacting, subsonic lifting surfaces. Subcritical wing design code employs higher-order far-field drag minimization technique. Linearized aerodynamic theory used. Program written in FORTRAN IV.

  16. Mutual Group Hypnosis: A Social Interaction Analysis.

    Science.gov (United States)

    Sanders, Shirley

    Mutual Group Hypnosis is discussed in terms of its similarity to group dynamics in general and in terms of its similarity to a social interaction program (Role Modeling) designed to foster the expression of warmth and acceptance among group members. Hypnosis also fosters a regression to prelogical thought processes in the service of the ego. Group…

  17. Mutual Group Hypnosis: A Social Interaction Analysis.

    Science.gov (United States)

    Sanders, Shirley

    Mutual Group Hypnosis is discussed in terms of its similarity to group dynamics in general and in terms of its similarity to a social interaction program (Role Modeling) designed to foster the expression of warmth and acceptance among group members. Hypnosis also fosters a regression to prelogical thought processes in the service of the ego. Group…

  18. Molecular players involved in the interaction between beneficial bacteria and the immune system

    Directory of Open Access Journals (Sweden)

    Arancha eHevia

    2015-11-01

    Full Text Available The human gastrointestinal tract is a very complex ecosystem, in which there is a continuous interaction between nutrients, host cells, and microorganisms. The gut microbiota comprises trillions of microbes that have been selected during evolution on the basis of their functionality and capacity to survive in, and adapt to, the intestinal environment. Host bacteria and our immune system constantly sense and react to one another. In this regard, commensal microbes contribute to gut homeostasis, whereas the necessary responses are triggered against enteropathogens. Some representatives of our gut microbiota have beneficial effects on human health. Some of the most important roles of these microbes are to help to maintain the integrity of the mucosal barrier, to provide nutrients such as vitamins, or to protect against pathogens. In addition, the interaction between commensal microbiota and the mucosal immune system is crucial for proper immune function. This process is mainly performed via the pattern recognition receptors of epithelial cells, such as Toll-like or Nod-like receptors, which are able to recognize the molecular effectors that are produced by intestinal microbes. These effectors mediate processes that can ameliorate certain inflammatory gut disorders, discriminate between beneficial and pathogenic bacteria, or increase the number of immune cells or their pattern recognition receptors. This review intends to summarize the molecular players produced by probiotic bacteria, notably Lactobacillus and Bifidobacterium strains, but also other very promising potential probiotics, which affect the human immune system.

  19. Anion-π interactions involving [MX(n)](m-) anions: a comprehensive theoretical study.

    Science.gov (United States)

    Estarellas, Carolina; Quiñonero, David; Deyà, Pere M; Frontera, Antonio

    2013-01-14

    In this manuscript we perform a systematic study on the geometric and energetic features of anion-π complexes, wherein the anion is a metal complex of variable shapes and charges. Such a study is lacking in the literature. For the calculations we used the ab initio RI-MP2/def2-TZVPP level of theory. A search in the Cambridge Structural Database (CSD) provides the experimental starting point that inspired the subsequent theoretical study. The influence of [MX(n)](m-) on the anion-π interaction was analyzed in terms of energetic, geometric, and charge transfer properties and Bader's theory of "atom-in-molecules" (AIM). The binding energy depends on the coordination index, geometric features and different orientations adopted by the metallic anion. The binding mode resembling a stacking interaction for linear, trigonal planar and square-planar anions is the most favorable. For tetrahedral and octahedral anions the most favorable orientation is the one with three halogen atoms pointing to the ring.

  20. Bench to Bed Evidences for Pharmacokinetic and Pharmacodynamic Interactions Involving Oseltamivir and Chinese Medicine

    Science.gov (United States)

    Chang, Qi; Wo, Siukwan; Ngai, Karry L. K.; Wang, Xiaoan; Fok, Benny; Ngan, Teresa M.; Wong, Vivian T.; Chan, Thomas Y. K.; Lee, Vincent H. L.; Tomlinson, Brian; Chan, Paul K. S.; Chow, Moses S. S.; Zuo, Zhong

    2014-01-01

    Oseltamivir (OA), an ethyl ester prodrug of oseltamivir carboxylate (OC), is clinically used as a potent and selective inhibitor of neuraminidase. Chinese medicines have been advocated to combine with conventional drug for avian influenza. The current study aims to investigate the potential pharmacokinetic and pharmacodynamic interactions of a Chinese medicine formula, namely, Yin Qiao San and Sang Ju Yin (CMF1), commonly used for anti-influenza in combination with OA in both rat and human, and to reveal the underlined mechanisms. It was found that although Cmax, AUC and urinary recovery of OC, as well as metabolic ratio (AUCOC/AUCOA), were significantly decreased in a dose-dependent manner following combination use of CMF1 and OA in rat studies (P < 0.01), such coadministration in 14 healthy volunteers only resulted in a trend of minor decrease in the related parameters. Further mechanistic studies found that although CMF1 could reduce absorption and metabolism of OA, it appears to enhance viral inhibition of OA (P < 0.01). In summary, although there was potential interaction between OA and CMF1 found in rat studies, its clinical impact was expected to be minimal. The coadministration of OA and CMF1 at the clinical recommended dosages is, therefore, considered to be safe. PMID:24527044

  1. Bench to Bed Evidences for Pharmacokinetic and Pharmacodynamic Interactions Involving Oseltamivir and Chinese Medicine

    Directory of Open Access Journals (Sweden)

    Qi Chang

    2014-01-01

    Full Text Available Oseltamivir (OA, an ethyl ester prodrug of oseltamivir carboxylate (OC, is clinically used as a potent and selective inhibitor of neuraminidase. Chinese medicines have been advocated to combine with conventional drug for avian influenza. The current study aims to investigate the potential pharmacokinetic and pharmacodynamic interactions of a Chinese medicine formula, namely, Yin Qiao San and Sang Ju Yin (CMF1, commonly used for anti-influenza in combination with OA in both rat and human, and to reveal the underlined mechanisms. It was found that although Cmax, AUC and urinary recovery of OC, as well as metabolic ratio (AUCOC/AUCOA, were significantly decreased in a dose-dependent manner following combination use of CMF1 and OA in rat studies (P<0.01, such coadministration in 14 healthy volunteers only resulted in a trend of minor decrease in the related parameters. Further mechanistic studies found that although CMF1 could reduce absorption and metabolism of OA, it appears to enhance viral inhibition of OA (P<0.01. In summary, although there was potential interaction between OA and CMF1 found in rat studies, its clinical impact was expected to be minimal. The coadministration of OA and CMF1 at the clinical recommended dosages is, therefore, considered to be safe.

  2. Designing Progressive and Interactive Analytics Processes for High-Dimensional Data Analysis.

    Science.gov (United States)

    Turkay, Cagatay; Kaya, Erdem; Balcisoy, Selim; Hauser, Helwig

    2017-01-01

    In interactive data analysis processes, the dialogue between the human and the computer is the enabling mechanism that can lead to actionable observations about the phenomena being investigated. It is of paramount importance that this dialogue is not interrupted by slow computational mechanisms that do not consider any known temporal human-computer interaction characteristics that prioritize the perceptual and cognitive capabilities of the users. In cases where the analysis involves an integrated computational method, for instance to reduce the dimensionality of the data or to perform clustering, such non-optimal processes are often likely. To remedy this, progressive computations, where results are iteratively improved, are getting increasing interest in visual analytics. In this paper, we present techniques and design considerations to incorporate progressive methods within interactive analysis processes that involve high-dimensional data. We define methodologies to facilitate processes that adhere to the perceptual characteristics of users and describe how online algorithms can be incorporated within these. A set of design recommendations and according methods to support analysts in accomplishing high-dimensional data analysis tasks are then presented. Our arguments and decisions here are informed by observations gathered over a series of analysis sessions with analysts from finance. We document observations and recommendations from this study and present evidence on how our approach contribute to the efficiency and productivity of interactive visual analysis sessions involving high-dimensional data.

  3. Quantitative proteomic analysis of mice corneal tissues reveals angiogenesis-related proteins involved in corneal neovascularization.

    Science.gov (United States)

    Shen, Minqian; Tao, Yimin; Feng, Yifan; Liu, Xing; Yuan, Fei; Zhou, Hu

    2016-07-01

    Corneal neovascularization (CNV) was induced in Balb/c mice by alkali burns in the central area of the cornea with a diameter of 2.5mm. After fourteen days, the cornea from one eye was collected for histological staining for CNV examination, while the cornea from the other eye of the same mouse was harvested for proteomic analysis. The label-free quantitative proteomic approach was applied to analyze five normal corneal tissues (normal group mice n=5) and five corresponding neovascularized corneal tissues (model group mice n=5). A total of 2124 proteins were identified, and 1682 proteins were quantified from these corneal tissues. Among these quantified proteins, 290 proteins were significantly changed between normal and alkali burned corneal tissues. Of these significantly changed proteins, 35 were reported or predicted as angiogenesis-related proteins. Then, these 35 proteins were analyzed using Ingenuity Pathway Analysis Software, resulting in 26 proteins enriched and connected to each other in the protein-protein interaction network, such as Lcn-2, αB-crystallin and Serpinf1 (PEDF). These three significantly changed proteins were selected for further Western blotting validation. Consistent with the quantitative proteomic results, Western blotting showed that Lcn-2 and αB-crystallin were significantly up-regulated in CNV model, while PEDF was down-regulated. This study provided increased understanding of angiogenesis-related proteins involved in corneal vascular development, which will be useful in the ophthalmic clinic of specifically target angiogenesis.

  4. Analysis of Presenilin 1 and 2 interacting proteins in mouse cerebral cortex during development.

    Science.gov (United States)

    Kumar, Ashish; Thakur, M K

    2014-11-01

    In our previous report, we showed that Presenilin (PS)1 and 2 have differential expression profile from early embryonic stages till adulthood in mouse cerebral cortex, suggesting that both of these proteins are crucial for brain development. Genetic manipulation studies have also shown the involvement of PS1 in brain development, but PS2 remains largely unexplored. In order to understand how PS1 and 2 mediate developmental functions, we have investigated the interaction of PS1 and 2 with proteins of mouse cerebral cortex during development. Co-immunoprecipitation (Co-IP) combined with MALDI-MS/MS analysis revealed 12 interacting partners of PS1 and 11 partners of PS2. The interacting proteins were different for PS1 and 2, and involved in cell division, glycolysis, cell adhesion and protein trafficking. Densitometric analysis of protein bands visualized after SDS-PAGE separation of Co-IP proteins revealed variation in their amount and degree of interaction during different developmental stages of mice. Further, immunoblot based validation of PS1 interacting protein Notch-1 showed maximum interaction at embryonic day (E) 12.5, decline at E18.5, upregulation from postnatal day 0 (P0) to P20 and thereafter reduction at P45 and 20 weeks. In-silico analysis of PS and its interacting proteins indicated conformation based interaction through common type of secondary structures having alpha helical, extended beta strand and random coil, and CK2, PKC phosphorylation and myristoylation motifs. Taken together, our study showed that PS1 and PS2 interact to varying extent with different proteins of mouse cerebral cortex and suggests their interaction based on specific conformation and involvement in diverse functions essential for the brain development.

  5. Nutrient analysis explained for non-chemists by using interactive e-learning material

    NARCIS (Netherlands)

    Busstra, M.C.; Hulshof, P.J.M.; Houwen, J.; Elburg, L.; Hollman, P.C.H.

    2012-01-01

    The diverse educational and professional background of individuals involved in food composition data work presents challenges in their training. In particular, it is difficult to explain chemical analysis of nutrients to individuals lacking a background in chemistry. Therefore an interactive e-learn

  6. Realtime Interaction Analysis of Social Interplay in a Multimodal Musical-Sonic Interaction Context

    DEFF Research Database (Denmark)

    Hansen, Anne-Marie

    2010-01-01

    This paper presents an approach to the analysis of social interplay among users in a multimodal interaction and musical performance situation. The approach consists of a combined method of realtime sensor data analysis for the description and interpretation of player gestures and video micro......-analysis methods used to describe the interaction situation and the context in which the social interplay takes place. This combined method is used in an iterative process, where the design of interactive games with musical-sonic feedback is improved according to newly discovered understandings and interpretations...

  7. Analysis of regulatory network involved in mechanical induction of embryonic stem cell differentiation.

    Directory of Open Access Journals (Sweden)

    Xinan Zhang

    Full Text Available Embryonic stem cells are conventionally differentiated by modulating specific growth factors in the cell culture media. Recently the effect of cellular mechanical microenvironment in inducing phenotype specific differentiation has attracted considerable attention. We have shown the possibility of inducing endoderm differentiation by culturing the stem cells on fibrin substrates of specific stiffness. Here, we analyze the regulatory network involved in such mechanically induced endoderm differentiation under two different experimental configurations of 2-dimensional and 3-dimensional culture, respectively. Mouse embryonic stem cells are differentiated on an array of substrates of varying mechanical properties and analyzed for relevant endoderm markers. The experimental data set is further analyzed for identification of co-regulated transcription factors across different substrate conditions using the technique of bi-clustering. Overlapped bi-clusters are identified following an optimization formulation, which is solved using an evolutionary algorithm. While typically such analysis is performed at the mean value of expression data across experimental repeats, the variability of stem cell systems reduces the confidence on such analysis of mean data. Bootstrapping technique is thus integrated with the bi-clustering algorithm to determine sets of robust bi-clusters, which is found to differ significantly from corresponding bi-clusters at the mean data value. Analysis of robust bi-clusters reveals an overall similar network interaction as has been reported for chemically induced endoderm or endodermal organs but with differences in patterning between 2-dimensional and 3-dimensional culture. Such analysis sheds light on the pathway of stem cell differentiation indicating the prospect of the two culture configurations for further maturation.

  8. Training in Compensatory Strategies Enhances Rapport in Interactions Involving People with Möbius Syndrome

    DEFF Research Database (Denmark)

    Michael, John; Bogart, Kathleen; Tylén, Kristian

    2015-01-01

    In the exploratory study reported here, we tested the efficacy of an intervention designed to train teenagers with Möbius Syndrome (MS) to increase the use of alternative communication strategies (e.g. gestures) to compensate for their lack of facial expressivity. Specifically, we expected......, and with three different naïve participants without MS after the intervention. Rapport was assessed by self-report and by behavioral coders who rated videos of the interactions. Individual nonverbal behavior was assessed via behavioral coders, while verbal behavior was automatically extracted from the sound...... in participants with and without MS, while overall linguistic alignment decreased. Fidgeting and repetitiveness of verbal behavior also decreased in both groups. In sum, the intervention may impact nonverbal and verbal behavior in participants with and without MS, increasing rapport as well as overall gesturing...

  9. Interactive tutorial to improve student understanding of single photon experiments involving a Mach-Zehnder interferometer

    Science.gov (United States)

    Marshman, Emily; Singh, Chandralekha

    2016-03-01

    We have developed and evaluated a quantum interactive learning tutorial (QuILT) on a Mach-Zehnder interferometer with single photons to expose upper-level students in quantum mechanics courses to contemporary quantum optics applications. The QuILT strives to help students develop the ability to apply fundamental quantum principles to physical situations in quantum optics and explore the differences between classical and quantum ideas. The QuILT adapts visualization tools to help students build physical intuition about counter-intuitive quantum optics phenomena with single photons including a quantum eraser setup and focuses on helping them integrate qualitative and quantitative understanding. We discuss findings from in-class evaluations.

  10. Interactive tutorial to improve student understanding of single photon experiments involving a Mach-Zehnder Interferometer

    CERN Document Server

    Marshman, Emily

    2016-01-01

    We have developed and evaluated a Quantum Interactive Learning Tutorial (QuILT) on a Mach-Zehnder Interferometer with single photons to expose upper-level students in quantum mechanics courses to contemporary quantum optics applications. The QuILT strives to help students develop the ability to apply fundamental quantum principles to physical situations in quantum optics and explore the differences between classical and quantum ideas. The QuILT adapts visualization tools to help students build physical intuition about counter-intuitive quantum optics phenomena with single photons including a quantum eraser setup and focuses on helping them integrate qualitative and quantitative understanding. We discuss findings from in-class evaluations.

  11. Involvement of the histaminergic system on appetitive learning and its interaction with haloperidol in goldfish.

    Science.gov (United States)

    Medalha, Carla Christina; Mattioli, Rosana

    2007-05-17

    This study investigated the actions of the histaminergic system on appetitive learning and memory, and its interaction with the dopaminergic system in goldfish. It consisted of nine sessions, in which fish were tested in a four-arm tank. On day 1, the animals were habituated for 10 min. On day 2, they were placed in one arm and had to find food at the left or the right arm. Time to begin feeding was recorded, and the procedure repeated for more 3 days (training phase). On training day 4, seven groups were injected with saline, seven with haloperidol (2.0 mg/kg) and one with DMSO solution before training and after feeding, three groups received saline, six chlorpheniramine (CPA) (1.0, 4.0 and 8.0 mg/kg), and six l-histidine (LH) (25, 50 and 100 mg/kg). Saline groups were considered as control of CPA and LH treated groups and DMSO as control of haloperidol. A non-injected group was also included. Testing occurred after 24 h. A reversal procedure was conducted 24h after testing and repeated for 3 days. The groups receiving CPA at 1.0 and 8.0 mg/kg and LH at 25, 50 and 100 mg/kg differed between Test and Reversal day 1. Pre-treatment with haloperidol plus 8.0 mg/kg of CPA and 25 and 50 mg/kg of LH reverted the treatment effect. However, in the groups treated with 1.0 mg/kg of CPA and 100 mg/kg of LH, the difference remained. This study confirmed the interaction between the histaminergic and the dopaminergic systems on memory process in goldfish.

  12. Secretomics identifies Fusarium graminearum proteins involved in the interaction with barley and wheat

    DEFF Research Database (Denmark)

    Yang, Fen; Jensen, Jens D.; Svensson, Birte;

    2012-01-01

    of cell walls, starch and proteins. Of these proteins, 35% had not been identified in previous in planta or in vitro studies, 70% were predicted to contain signal peptides and a further 16% may be secreted in a nonclassical manner. Proteins identified in the 72 spots showing differential appearance...... between wheat and barley flour medium were mainly involved in fungal cell wall remodelling and the degradation of plant cell walls, starch and proteins. The in planta expression of corresponding F. graminearum genes was confirmed by quantitative reverse transcriptase‐polymerase chain reaction in barley...... and wheat spikelets harvested at 2−6 days after inoculation. In addition, a clear difference in the accumulation of fungal biomass and the extent of fungal‐induced proteolysis of plant β‐amylase was observed in barley and wheat. The present study considerably expands the current database of F. graminearum...

  13. Analysis of Protein-Membrane Interactions

    DEFF Research Database (Denmark)

    Kemmer, Gerdi Christine

    Cellular membranes are complex structures, consisting of hundreds of different lipids and proteins. These membranes act as barriers between distinct environments, constituting hot spots for many essential functions of the cell, including signaling, energy conversion, and transport. These functions....... Discovered interactions were then probed on the level of the membrane using liposome-based assays. In the second part, a transmembrane protein was investigated. Assays to probe activity of the plasma membrane ATPase (Arabidopsis thaliana H+ -ATPase isoform 2 (AHA2)) in single liposomes using both giant...... are implemented by soluble proteins reversibly binding to, as well as by integral membrane proteins embedded in, cellular membranes. The activity and interaction of these proteins is furthermore modulated by the lipids of the membrane. Here, liposomes were used as model membrane systems to investigate...

  14. Facilitating Discourse Analysis with Interactive Visualization.

    Science.gov (United States)

    Zhao, Jian; Chevalier, F; Collins, C; Balakrishnan, R

    2012-12-01

    A discourse parser is a natural language processing system which can represent the organization of a document based on a rhetorical structure tree-one of the key data structures enabling applications such as text summarization, question answering and dialogue generation. Computational linguistics researchers currently rely on manually exploring and comparing the discourse structures to get intuitions for improving parsing algorithms. In this paper, we present DAViewer, an interactive visualization system for assisting computational linguistics researchers to explore, compare, evaluate and annotate the results of discourse parsers. An iterative user-centered design process with domain experts was conducted in the development of DAViewer. We report the results of an informal formative study of the system to better understand how the proposed visualization and interaction techniques are used in the real research environment.

  15. Interactive visualization and analysis of transitional flow.

    Science.gov (United States)

    Johnson, Gregory P; Calo, Victor M; Gaither, Kelly P

    2008-01-01

    A stand-alone visualization application has been developed by a multi-disciplinary, collaborative team with the sole purpose of creating an interactive exploration environment allowing turbulent flow researchers to experiment and validate hypotheses using visualization. This system has specific optimizations made in data management, caching computations, and visualization allowing for the interactive exploration of datasets on the order of 1TB in size. Using this application, the user (co-author Calo) is able to interactively visualize and analyze all regions of a transitional flow volume, including the laminar, transitional and fully turbulent regions. The underlying goal of the visualizations produced from these transitional flow simulations is to localize turbulent spots in the laminar region of the boundary layer, determine under which conditions they form, and follow their evolution. The initiation of turbulent spots, which ultimately lead to full turbulence, was located via a proposed feature detection condition and verified by experimental results. The conditions under which these turbulent spots form and coalesce are validated and presented.

  16. Interaction Analysis through Proteomic Phage Display

    Directory of Open Access Journals (Sweden)

    Gustav N. Sundell

    2014-01-01

    Full Text Available Phage display is a powerful technique for profiling specificities of peptide binding domains. The method is suited for the identification of high-affinity ligands with inhibitor potential when using highly diverse combinatorial peptide phage libraries. Such experiments further provide consensus motifs for genome-wide scanning of ligands of potential biological relevance. A complementary but considerably less explored approach is to display expression products of genomic DNA, cDNA, open reading frames (ORFs, or oligonucleotide libraries designed to encode defined regions of a target proteome on phage particles. One of the main applications of such proteomic libraries has been the elucidation of antibody epitopes. This review is focused on the use of proteomic phage display to uncover protein-protein interactions of potential relevance for cellular function. The method is particularly suited for the discovery of interactions between peptide binding domains and their targets. We discuss the largely unexplored potential of this method in the discovery of domain-motif interactions of potential biological relevance.

  17. Analysis of interactions among barriers in project risk management

    Science.gov (United States)

    Dandage, Rahul V.; Mantha, Shankar S.; Rane, Santosh B.; Bhoola, Vanita

    2017-06-01

    In the context of the scope, time, cost, and quality constraints, failure is not uncommon in project management. While small projects have 70% chances of success, large projects virtually have no chance of meeting the quadruple constraints. While there is no dearth of research on project risk management, the manifestation of barriers to project risk management is a less dwelt topic. The success of project management is oftentimes based on the understanding of barriers to effective risk management, application of appropriate risk management methodology, proactive leadership to avoid barriers, workers' attitude, adequate resources, organizational culture, and involvement of top management. This paper represents various risk categories and barriers to risk management in domestic and international projects through literature survey and feedback from project professionals. After analysing the various modelling methods used in project risk management literature, interpretive structural modelling (ISM) and MICMAC analysis have been used to analyse interactions among the barriers and prioritize them. The analysis indicates that lack of top management support, lack of formal training, and lack of addressing cultural differences are the high priority barriers, among many others.

  18. A C-code for the double folding interaction potential for reactions involving deformed target nuclei

    Science.gov (United States)

    Gontchar, I. I.; Chushnyakova, M. V.

    2013-01-01

    We present a C-code designed to obtain the interaction potential between a spherical projectile nucleus and an axial-symmetrical deformed target nucleus and in particular to find the Coulomb barrier, by using the double folding model (DFM). The program calculates the nucleus-nucleus potential as a function of the distance between the centers of mass of colliding nuclei as well as of the angle between the axis of symmetry of the target nucleus and the beam direction. The most important output parameters are the Coulomb barrier energy and the radius. Since many researchers use a Woods-Saxon profile for the nuclear term of the potential we provide an option in our code for fitting the DFM potential by such a profile near the barrier. Program summaryProgram title: DFMDEF Catalogue identifier: AENI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2245 No. of bytes in distributed program, including test data, etc.: 215442 Distribution format: tar.gz Programming language: C. Computer: PC, Mac. Operating system: Windows XP (with the GCC-compiler version 2), MacOS, Linux. RAM: 100 MB with average parameters set Classification: 17.9. Nature of problem: The code calculates in a semimicroscopic way the bare interaction potential between a spherical projectile nucleus and a deformed but axially symmetric target nucleus as a function of the center of mass distance as well as of the angle between the axis of symmetry of the target nucleus and the beam direction. The height and the position of the Coulomb barrier are found. The calculated potential is approximated by a conventional Woods-Saxon profile near the barrier. Dependence of the barrier parameters upon the characteristics of the effective NN forces (like, e

  19. The involvement of proteoglycans in the human plasma prekallikrein interaction with the cell surface.

    Directory of Open Access Journals (Sweden)

    Camila Lopes Veronez

    Full Text Available INTRODUCTION: The aim of this work was to evaluate the role of human plasma prekallikrein assembly and processing in cells and to determine whether proteoglycans, along with high molecular weight kininogen (H-kininogen, influence this interaction. METHODS: We used the endothelial cell line ECV304 and the epithelial cell lines CHO-K1 (wild type and CHO-745 (deficient in proteoglycans. Prekallikrein endocytosis was studied using confocal microscopy, and prekallikrein cleavage/activation was determined by immunoblotting using an antibody directed to the prekallikrein sequence C364TTKTSTR371 and an antibody directed to the entire H-kininogen molecule. RESULTS: At 37°C, prekallikrein endocytosis was assessed in the absence and presence of exogenously applied H-kininogen and found to be 1,418.4±0.010 and 1,070.3±0.001 pixels/cell, respectively, for ECV304 and 1,319.1±0.003 and 631.3±0.001 pixels/cell, respectively, for CHO-K1. No prekallikrein internalization was observed in CHO-745 in either condition. Prekallikrein colocalized with LysoTracker in the absence and presence of exogenous H-kininogen at levels of 76.0% and 88.5%, respectively, for ECV304 and at levels of 40.7% and 57.0%, respectively, for CHO-K1. After assembly on the cell surface, a plasma kallikrein fragment of 53 kDa was predominant in the incubation buffer of all the cell lines studied, indicating specific proteolysis; plasma kallikrein fragments of 48-44 kDa and 34-32 kDa were also detected in the incubation buffer, indicating non-specific cleavage. Bradykinin free H-kininogen internalization was not detected in CHO-K1 or CHO-745 cells at 37°C. CONCLUSION: The prekallikrein interaction with the cell surface is temperature-dependent and independent of exogenously applied H-kininogen, which results in prekallikrein endocytosis promoted by proteoglycans. Prekallikrein proteolysis/activation is influenced by H-kininogen/glycosaminoglycans assembly and controls plasma kallikrein

  20. PIC. Profile of Interaction in the Classroom. A Quick Feedback of Interaction Analysis.

    Science.gov (United States)

    Brunner, Ellen

    The Profile of Interaction in the Classroom (PIC) is a short-cut method of interaction analysis that can provide the quick feedback essential to effective supervision of instruction. And because the PIC contains a record of all the behaviors that occurred in the classroom, as well as the sequence, the data may be used to build a traditional…

  1. Modulation of Pineal Melatonin Synthesis by Glutamate Involves Paracrine Interactions between Pinealocytes and Astrocytes through NF-κB Activation

    Directory of Open Access Journals (Sweden)

    Darine Villela

    2013-01-01

    Full Text Available The glutamatergic modulation of melatonin synthesis is well known, along with the importance of astrocytes in mediating glutamatergic signaling in the central nervous system. Pinealocytes and astrocytes are the main cell types in the pineal gland. The objective of this work was to investigate the interactions between astrocytes and pinealocytes as a part of the glutamate inhibitory effect on melatonin synthesis. Rat pinealocytes isolated or in coculture with astrocytes were incubated with glutamate in the presence of norepinephrine, and the melatonin content, was quantified. The expression of glutamate receptors, the intracellular calcium content and the NF-κB activation were analyzed in astrocytes and pinealocytes. TNF-α's possible mediation of the effect of glutamate was also investigated. The results showed that glutamate's inhibitory effect on melatonin synthesis involves interactions between astrocytes and pinealocytes, possibly through the release of TNF-α. Moreover, the activation of the astrocytic NF-κB seems to be a necessary step. In astrocytes and pinealocytes, AMPA, NMDA, and group I metabotropic glutamate receptors were observed, as well as the intracellular calcium elevation. In conclusion, there is evidence that the modulation of melatonin synthesis by glutamate involves paracrine interactions between pinealocytes and astrocytes through the activation of the astrocytic NF-κB transcription factor and possibly by subsequent TNF-α release.

  2. Involvement of breast cancer resistance protein (BCRP/ABCG2) in the secretion of danofloxacin into milk: interaction with ivermectin.

    Science.gov (United States)

    Real, R; Egido, E; Pérez, M; González-Lobato, L; Barrera, B; Prieto, J G; Alvarez, A I; Merino, G

    2011-08-01

    Danofloxacin, a veterinary fluoroquinolone antimicrobial drug, is actively secreted into milk by an as yet unknown mechanism. One of the main determinants of active drug secretion into milk is the transporter (BCRP/ABCG2). The main purpose was to determine whether danofloxacin is an in vitro substrate for Bcrp1/BCRP and to assess its involvement in danofloxacin secretion into milk. In addition, the role of potential drug-drug interactions in this process was assessed using ivermectin. Danofloxacin was transported in vitro by Bcrp1/BCRP, and ivermectin efficiently blocked this transport. Experiments with Bcrp1(-/-) mice showed no evidence of the involvement of Bcrp1 in plasma pharmacokinetics of danofloxacin. However, the milk concentration and milk-to-plasma ratio of danofloxacin were almost twofold higher in wild-type compared with Bcrp1(-/-) mice. The in vivo interaction with ivermectin was studied in sheep after co-administration of danofloxacin (1.25 mg/kg, i.m.) and ivermectin (0.2 mg/kg, s.c.). Ivermectin had no significant effect on the plasma levels of danofloxacin but significantly decreased danofloxacin concentrations in milk by almost 40%. Concomitant administration of multiple drugs, often used in veterinary therapy, may not only affect their pharmacological activity but also their secretion into milk, because of potential drug-drug interactions mediated by BCRP.

  3. BIP, a BRAM-interacting protein involved in TGF-beta signalling, regulates body length in Caenorhabditis elegans.

    Science.gov (United States)

    Sugawara, K; Morita, K; Ueno, N; Shibuya, H

    2001-07-01

    The TGF-beta superfamily has diverse biological activities and is involved in the early development of animals. We previously identified a novel family member, BMP receptor associated molecule (BRAM), which binds to the intracellular domain of BMP type IA receptor and is involved in the BMP signalling pathway. To identify novel molecules involved in TGF-beta signalling pathways, we performed yeast two-hybrid screening using BRAM as bait. From a Xenopus cDNA library, we cloned a cDNA encoding 693 amino acids and containing the motif for an oxysterol binding protein (OSBP), which we designated BRAM interacting protein (BIP). We then isolated a BIP homologue from the Caenorhabditis elegans that encodes 733 amino acids and also contains the OSBP-like motif. Immunoprecipitation and Western blotting studies revealed that C. elegans BIP could interact with the C. elegans BRAM homologues BRA-1 and BRA-2. C. elegans BIP was expressed in pharyngeal muscle, hypodermis and several neuronal cells, an expression pattern overlaps with those of BRA-1 and BRA-2. Finally, we found that inhibition of BIP expression in C. elegans by double stranded RNA interference produces a Sma phenotype. BIP was isolated using the yeast two-hybrid systems. BIP may function in the TGF-beta pathway and regulate body length in C. elegans.

  4. The dual role of autophagy under hypoxia-involvement of interaction between autophagy and apoptosis.

    Science.gov (United States)

    Li, Mengmeng; Tan, Jin; Miao, Yuyang; Lei, Ping; Zhang, Qiang

    2015-06-01

    Hypoxia is one of severe cellular stress and it is well known to be associated with a worse outcome since a lack of oxygen accelerates the induction of apoptosis. Autophagy, an important and evolutionarily conserved mechanism for maintaining cellular homeostasis, is closely related to the apoptosis caused by hypoxia. Generally autophagy blocks the induction of apoptosis and inhibits the activation of apoptosis-associated caspase which could reduce cellular injury. However, in special cases, autophagy or autophagy-relevant proteins may help to induce apoptosis, which could aggravate cell damage under hypoxia condition. In addition, the activation of apoptosis-related proteins-caspase can also degrade autophagy-related proteins, such as Atg3, Atg4, Beclin1 protein, inhibiting autophagy. Although the relationship between autophagy and apoptosis has been known for rather complex for more than a decade, the underlying regulatory mechanisms have not been clearly understood. This short review discusses and summarizes the dual role of autophagy and the interaction and molecular regulatory mechanisms between autophagy and apoptosis under hypoxia.

  5. Using Social Media Sentiment Analysis for Interaction Design Choices

    DEFF Research Database (Denmark)

    McGuire, Mark; Kampf, Constance Elizabeth

    2015-01-01

    Social media analytics is an emerging skill for organizations. Currently, developers are exploring ways to create tools for simplifying social media analysis. These tools tend to focus on gathering data, and using systems to make it meaningful. However, we contend that making social media data...... meaningful is by nature a human-computer interaction problem. We examine this problem around the emerging field of sentiment analysis, exploring criteria for designing sentiment analysis systems based in Human Computer interaction, HCI. We contend that effective sentiment analysis affects audience analysis...

  6. Using Social Media Sentiment Analysis for Interaction Design Choices

    DEFF Research Database (Denmark)

    McGuire, Mark; Kampf, Constance Elizabeth

    2015-01-01

    Social media analytics is an emerging skill for organizations. Currently, developers are exploring ways to create tools for simplifying social media analysis. These tools tend to focus on gathering data, and using systems to make it meaningful. However, we contend that making social media data...... meaningful is by nature a human-computer interaction problem. We examine this problem around the emerging field of sentiment analysis, exploring criteria for designing sentiment analysis systems based in Human Computer interaction, HCI. We contend that effective sentiment analysis affects audience analysis......, and can serve as a basis for communication design choices that support strategic relationship goals for organizations....

  7. The mechanism of sperm-egg interaction and the involvement of IZUMO1 in fusion.

    Science.gov (United States)

    Inoue, Naokazu; Ikawa, Masahito; Okabe, Masaru

    2011-01-01

    An average human ejaculate contains over 100 million sperm, but only a few succeed in accomplishing the journey to an egg by migration through the female reproductive tract. Among these few sperm, only one participates in fertilization. There might be an ingenious molecular mechanism to ensure that the very best sperm fertilize an egg. However, recent gene disruption experiments in mice have revealed that many factors previously described as important for fertilization are largely dispensable. One could argue that the fertilization mechanism is made robust against gene disruptions. However, this is not likely, as there are already six different gene-disrupted mouse lines (Calmegin, Adam1a, Adam2, Adam3, Ace and Pgap1), all of which result in male sterility. The sperm from these animals are known to have defective zona-binding ability and at the same time lose oviduct-migrating ability. Concerning sperm-zona binding, the widely accepted involvement of sugar moiety on zona pellucida 3 (ZP3) is indicated to be dispensable by gene disruption experiments. Thus, the landscape of the mechanism of fertilization is revolving considerably. In the sperm-egg fusion process, CD9 on egg and IZUMO1 on sperm have emerged as essential factors. This review focuses on the mechanism of fertilization elucidated by gene-manipulated animals.

  8. The mechanism of sperm-egg interaction and the involvement of IZUM01 in fusion

    Institute of Scientific and Technical Information of China (English)

    Naokazu Inoue; Masahito Ikawa; Masaru Okabe

    2011-01-01

    An average human ejaculate contains over 100 million sperm,but only a few succeed in accomplishing the journey to an egg by migration through the female reproductive tract.Among these few sperm,only one participates in fertilization.There might be an ingenious molecular mechanism to ensure that the very best sperm fertilize an egg.However,recent gene disruption experiments in mice have revealed that many factors previously described as important for fertilization are largely dispensable.One could argue that the fertilization mechanism is made robust against gene disruptions.However,this is not likely,as there are already six different gene-disrupted mouse lines (Calmegin,Adam1a,Adam2,Adam3,Aceand Pgap1),all of which result in male sterility.The sperm from these animals are known to have defective zona-binding ability and at the same time lose oviduct-migrating ability.Concerning spermzona binding,the widely accepted involvement of sugar moiety on zona pellucida 3 (ZP3) is indicated to be dispensable by gene disruption experiments.Thus,the landscape of the mechanism of fertilization is revolving considerably.In the sperm-egg fusion process,CD9 on egg and IZUM01 on sperm have emerged as essential factors.This review focuses on the mechanism of fertilization elucidated by gene-manipulated animals.

  9. Identification of CXCL5/ENA-78 as a factor involved in the interaction between cholangiocarcinoma cells and cancer-associated fibroblasts.

    Science.gov (United States)

    Okabe, Hirohisa; Beppu, Toru; Ueda, Mitsuharu; Hayashi, Hiromitsu; Ishiko, Takatoshi; Masuda, Toshiro; Otao, Ryu; Horlad, Hasita; Mima, Kosuke; Miyake, Keisuke; Iwatsuki, Masaaki; Baba, Yoshifumi; Takamori, Hiroshi; Jono, Hirofumi; Shinriki, Satoru; Ando, Yukio; Baba, Hideo

    2012-11-15

    Knowledge of tumor-stromal interactions is essential for understanding tumor development. We focused on the interaction between cholangiocarcinoma and cancer-associated fibroblasts (CAFs) in intrahepatic cholangiocarcinoma and reported their positive interaction in vitro and in vivo. The aim of this study is to identify the key protein involved in the interaction between cholangiocarcinoma cells and CAFs and its role on cholangiocarcinoma progression. Using the conditioning medium from cholangiocarcinoma cells, hepatic stellate cells and coculture of them, Protein-Chip analysis with SELDI-TOF-MS showed that the peak of an 8,360-Da protein remarkably increased in the coculture medium. This protein was identified as CXCL5/ENA78, epithelial cell-derived neutrophil-activating peptide-78, by q-TOF/MS/MS analysis. Two cholangiocarcinoma cell lines, HuCCT1 and RBE, produced CXCL5 that promoted their invasion and migration in an autocrine fashion. These effects of CXCL5 significantly decreased by inhibition of CXC-receptor 2, which is the receptor for CXCL5. In addition, IL-1β produced by hepatic stellate cells induced the expression of CXCL5 in cholangiocarcinoma cells. In human tissue samples, a significant correlation was observed between CAFs and CXCL5 produced by cholangiocarcinoma cells in intrahepatic cholangiocarcinoma (p = 0.0044). Furthermore, the high-CXCL5-expression group exhibited poor overall survival after curative hepatic resection (p = 0.027). The presence of tumor-infiltrating neutrophils expressing CD66b was associated with CXCL5 expression in tumor cells (p < 0.0001). These data suggest that CXCL5 is important for the interaction between cholangiocarcinoma and CAFs, and inhibition of tumor-stromal interactions may be a useful therapeutic approach for cholangiocarcinoma.

  10. Plasma diagnostics surface analysis and interactions

    CERN Document Server

    Auciello, Orlando

    2013-01-01

    Plasmas and their interaction with materials have become subjects of major interest because of their importance in modern forefront technologies such as microelectronics, fusion energy, and space. Plasmas are used in microelectronics to process semiconductors (etching of patterns for microcircuits, plasma-induced deposition of thin films, etc.); plasmas produce deleterious erosion effects on surfaces of materials used for fusion devices and spaceships exposed to the low earth environment.Diagnostics of plasmas and materials exposed to them are fundamental to the understanding of the physical a

  11. Involvement of the carboxyl-terminal region of the yeast peroxisomal half ABC transporter Pxa2p in its interaction with Pxa1p and in transporter function.

    Directory of Open Access Journals (Sweden)

    Cheng-Yi Chuang

    Full Text Available BACKGROUND: The peroxisome is a single membrane-bound organelle in eukaryotic cells involved in lipid metabolism, including β-oxidation of fatty acids. The human genetic disorder X-linked adrenoleukodystrophy (X-ALD is caused by mutations in the ABCD1 gene (encoding ALDP, a peroxisomal half ATP-binding cassette [ABC] transporter. This disease is characterized by defective peroxisomal β-oxidation and a large accumulation of very long-chain fatty acids in brain white matter, adrenal cortex, and testis. ALDP forms a homodimer proposed to be the functional transporter, whereas the peroxisomal transporter in yeast is a heterodimer comprising two half ABC transporters, Pxa1p and Pxa2p, both orthologs of human ALDP. While the carboxyl-terminal domain of ALDP is engaged in dimerization, it remains unknown whether the same region is involved in the interaction between Pxa1p and Pxa2p. METHODS/PRINCIPAL FINDINGS: Using a yeast two-hybrid assay, we found that the carboxyl-terminal region (CT of Pxa2p, but not of Pxa1p, is required for their interaction. Further analysis indicated that the central part of the CT (designated CT2 of Pxa2p was indispensable for its interaction with the carboxyl terminally truncated Pxa1_NBD. An interaction between the CT of Pxa2p and Pxa1_NBD was not detected, but could be identified in the presence of Pxa2_NBD-CT1. A single mutation of two conserved residues (aligned with X-ALD-associated mutations at the same positions in ALDP in the CT2 of the Pxa2_NBD-CT protein impaired its interaction with Pxa1_NBD or Pxa1_NBD-CT, resulting in a mutant protein that exhibited a proteinase K digestion profile different from that of the wild-type protein. Functional analysis of these mutant proteins on oleate plates indicated that they were defective in transporter function. CONCLUSIONS/SIGNIFICANCE: The CT of Pxa2p is involved in its interaction with Pxa1p and in transporter function. This concept may be applied to human ALDP studies

  12. Investigating the biogeochemical interactions involved in simultaneous TCE and Arsenic in situ bioremediation

    Science.gov (United States)

    Cook, E.; Troyer, E.; Keren, R.; Liu, T.; Alvarez-Cohen, L.

    2016-12-01

    The in situ bioremediation of contaminated sediment and groundwater is often focused on one toxin, even though many of these sites contain multiple contaminants. This reductionist approach neglects how other toxins may affect the biological and chemical conditions, or vice versa. Therefore, it is of high value to investigate the concurrent bioremediation of multiple contaminants while studying the microbial activities affected by biogeochemical factors. A prevalent example is the bioremediation of arsenic at sites co-contaminated with trichloroethene (TCE). The conditions used to promote a microbial community to dechlorinate TCE often has the adverse effect of inducing the release of previously sequestered arsenic. The overarching goal of our study is to simultaneously evaluate the bioremediation of arsenic and TCE. Although TCE bioremediation is a well-understood process, there is still a lack of thorough understanding of the conditions necessary for effective and stable arsenic bioremediation in the presence of TCE. The objective of this study is to promote bacterial activity that stimulates the precipitation of stable arsenic-bearing minerals while providing anaerobic, non-extreme conditions necessary for TCE dechlorination. To that end, endemic microbial communities were examined under various conditions to attempt successful sequestration of arsenic in addition to complete TCE dechlorination. Tested conditions included variations of substrates, carbon source, arsenate and sulfate concentrations, and the presence or absence of TCE. Initial arsenic-reducing enrichments were unable to achieve TCE dechlorination, probably due to low abundance of dechlorinating bacteria in the culture. However, favorable conditions for arsenic precipitation in the presence of TCE were eventually discovered. This study will contribute to the understanding of the key species in arsenic cycling, how they are affected by various concentrations of TCE, and how they interact with the key

  13. EptC of Campylobacter jejuni Mediates Phenotypes Involved in Host Interactions and Virulence

    Science.gov (United States)

    Cullen, Thomas W.; O'Brien, John P.; Hendrixson, David R.; Giles, David K.; Hobb, Rhonda I.; Thompson, Stuart A.; Brodbelt, Jennifer S.

    2013-01-01

    Campylobacter jejuni is a natural commensal of the avian intestinal tract. However, the bacterium is also the leading cause of acute bacterial diarrhea worldwide and is implicated in development of Guillain-Barré syndrome. Like many bacterial pathogens, C. jejuni assembles complex surface structures that interface with the surrounding environment and are involved in pathogenesis. Recent work in C. jejuni identified a gene encoding a novel phosphoethanolamine (pEtN) transferase, EptC (Cj0256), that plays a promiscuous role in modifying the flagellar rod protein, FlgG; the lipid A domain of lipooligosaccharide (LOS); and several N-linked glycans. In this work, we report that EptC catalyzes the addition of pEtN to the first heptose sugar of the inner core oligosaccharide of LOS, a fourth enzymatic target. We also examine the role pEtN modification plays in circumventing detection and/or killing by host defenses. Specifically, we show that modification of C. jejuni lipid A with pEtN results in increased recognition by the human Toll-like receptor 4–myeloid differentiation factor 2 (hTLR4-MD2) complex, along with providing resistance to relevant mammalian and avian antimicrobial peptides (i.e., defensins). We also confirm the inability of aberrant forms of LOS to activate Toll-like receptor 2 (TLR2). Most exciting, we demonstrate that strains lacking eptC show decreased commensal colonization of chick ceca and reduced colonization of BALB/cByJ mice compared to wild-type strains. Our results indicate that modification of surface structures with pEtN by EptC is key to its ability to promote commensalism in an avian host and to survive in the mammalian gastrointestinal environment. PMID:23184526

  14. Linguistic feature analysis for protein interaction extraction

    Directory of Open Access Journals (Sweden)

    Cornelis Chris

    2009-11-01

    Full Text Available Abstract Background The rapid growth of the amount of publicly available reports on biomedical experimental results has recently caused a boost of text mining approaches for protein interaction extraction. Most approaches rely implicitly or explicitly on linguistic, i.e., lexical and syntactic, data extracted from text. However, only few attempts have been made to evaluate the contribution of the different feature types. In this work, we contribute to this evaluation by studying the relative importance of deep syntactic features, i.e., grammatical relations, shallow syntactic features (part-of-speech information and lexical features. For this purpose, we use a recently proposed approach that uses support vector machines with structured kernels. Results Our results reveal that the contribution of the different feature types varies for the different data sets on which the experiments were conducted. The smaller the training corpus compared to the test data, the more important the role of grammatical relations becomes. Moreover, deep syntactic information based classifiers prove to be more robust on heterogeneous texts where no or only limited common vocabulary is shared. Conclusion Our findings suggest that grammatical relations play an important role in the interaction extraction task. Moreover, the net advantage of adding lexical and shallow syntactic features is small related to the number of added features. This implies that efficient classifiers can be built by using only a small fraction of the features that are typically being used in recent approaches.

  15. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.

    Science.gov (United States)

    Teimouri, Hamid; Kolomeisky, Anatoly B; Mehrabiani, Kareem

    2015-02-13

    Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  16. Interpersonal Communication Skills: The Marriage of Interaction Analysis and Microcounseling

    Science.gov (United States)

    Bradley, Curtis H.

    1976-01-01

    Describes microcounseling and interaction analysis, provides a reationale for the "marriage" of these two successful innovations, and demonstrates how the combination can provide an objective and systematic technology for the development of effective interpersonal communication skills.

  17. Analysis of nitrated proteins in Saccharomyces cerevisiae involved in mating signal transduction.

    Science.gov (United States)

    Kang, Jeong Won; Lee, Na Young; Cho, Kyung-Cho; Lee, Min Young; Choi, Do-Young; Park, Sang-Hyun; Kim, Kwang Pyo

    2015-01-01

    Protein tyrosine nitration (PTN) is a PTM that regulates signal transduction and inflammatory responses, and is related to neurodegenerative and cardiovascular diseases. The cellular function of PTN remains unclear because the low stoichiometry of PTN limits the identification and quantification of nitrated peptides. Effective enrichment is an important aspect of PTN analysis. In this study, we analyzed the in vivo nitroproteome elicited by mating signal transduction in Saccharomyces cerevisiae using a novel chemical enrichment method followed by LC-MS/MS. Nitroproteome profiling successfully identified changes in the nitration states of 14 proteins during mating signal transduction in S. cerevisiae, making this the first reported in vivo nitroproteome in yeast. We investigated the biological functions of these nitroproteins and their relationships to mating signal transduction in S. cerevisiae using a protein-protein interaction network. Our results suggest that PTN and denitration may be involved in nonreactive nitrogen species-mediated signal transduction and can provide clues for understanding the functional roles of PTN in vivo.

  18. A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process.

    Science.gov (United States)

    Bruni, Roberto; Costantino, Angela; Tritarelli, Elena; Marcantonio, Cinzia; Ciccozzi, Massimo; Rapicetta, Maria; El Sawaf, Gamal; Giuliani, Alessandro; Ciccaglione, Anna Rita

    2009-07-29

    The E1 protein of Hepatitis C Virus (HCV) can be dissected into two distinct hydrophobic regions: a central domain containing an hypothetical fusion peptide (FP), and a C-terminal domain (CT) comprising two segments, a pre-anchor and a trans-membrane (TM) region. In the currently accepted model of the viral fusion process, the FP and the TM regions are considered to be closely juxtaposed in the post-fusion structure and their physical interaction cannot be excluded. In the present study, we took advantage of the natural sequence variability present among HCV strains to test, by purely sequence-based computational tools, the hypothesis that in this virus the fusion process involves the physical interaction of the FP and CT regions of E1. Two computational approaches were applied. The first one is based on the co-evolution paradigm of interacting peptides and consequently on the correlation between the distance matrices generated by the sequence alignment method applied to FP and CT primary structures, respectively. In spite of the relatively low random genetic drift between genotypes, co-evolution analysis of sequences from five HCV genotypes revealed a greater correlation between the FP and CT domains than respect to a control HCV sequence from Core protein, so giving a clear, albeit still inconclusive, support to the physical interaction hypothesis.The second approach relies upon a non-linear signal analysis method widely used in protein science called Recurrence Quantification Analysis (RQA). This method allows for a direct comparison of domains for the presence of common hydrophobicity patterns, on which the physical interaction is based upon. RQA greatly strengthened the reliability of the hypothesis by the scoring of a lot of cross-recurrences between FP and CT peptides hydrophobicity patterning largely outnumbering chance expectations and pointing to putative interaction sites. Intriguingly, mutations in the CT region of E1, reducing the fusion process in

  19. Possible mechanism of psoralen phototoxicity not involving direct interaction with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Laskin, J.D.; Lee, E.; Yurkow, E.J.; Laskin, D.L.; Gallo, M.A.

    1985-09-01

    Psoralens in combination with ultraviolet light (UVA; 320-400 nm) are used in the photochemical treatment of a variety of skin diseases including vitiligo, a skin depigmentational disorder, and psoriasis, a disease of accelerated epidermal cell proliferation. Although it is generally assumed that the major site of action of the psoralens is DNA, the authors have obtained evidence that another site may be the primary target for these compounds. They have identified specific, saturable, high-affinity binding sites for 8-methoxypsoralen on HeLa cells and have detected specific binding of 8-methoxypsoralen to four other human cell lines and five mouse cell lines. In HeLa cells, specific binding is reversible and independent of the ability of the compound to intercalate into DNA. In addition, binding sites become covalently modified by the psoralen after UVA exposure. Specific binding of 8-(methyoxy-/sup 3/H)methoxypsoralen constitutes 79% of the label bound to the cells. Scatchard analysis indicated two classes of psoralen binding sites. Based on these findings, the authors hypothesize that specific binding sites for psoralens on mammalian cells mediate, at least in part, psoralen-induced phototoxicity.

  20. Early canine plaque biofilms: characterization of key bacterial interactions involved in initial colonization of enamel.

    Directory of Open Access Journals (Sweden)

    Lucy J Holcombe

    Full Text Available Periodontal disease (PD is a significant problem in dogs affecting between 44% and 63.6% of the population. The main etiological agent for PD is plaque, a microbial biofilm that colonizes teeth and causes inflammation of the gingiva. Understanding how this biofilm initiates on the tooth surface is of central importance in developing interventions against PD. Although the stages of plaque development on human teeth have been well characterized little is known about how canine plaque develops. Recent studies of the canine oral microbiome have revealed distinct differences between the canine and human oral environments and the bacterial communities they support, particularly with respect to healthy plaque. These differences mean knowledge about the nature of plaque formation in humans may not be directly translatable to dogs. The aim of this study was to identify the bacterial species important in the early stages of canine plaque formation in vivo and then use isolates of these species in a laboratory biofilm model to develop an understanding of the sequential processes which take place during the initial colonization of enamel. Supra-gingival plaque samples were collected from 12 dogs at 24 and 48 hour time points following a full mouth descale and polish. Pyrosequencing of the 16S rDNA identified 134 operational taxonomic units after statistical analysis. The species with the highest relative abundance were Bergeyella zoohelcum, Neisseria shayeganii and a Moraxella species. Streptococcal species, which tend to dominate early human plaque biofilms, had very low relative abundance. In vitro testing of biofilm formation identified five primary colonizer species, three of which belonged to the genus Neisseria. Using these pioneer bacteria as a starting point, viable two and three species communities were developed. Combining in vivo and in vitro data has led us to construct novel models of how the early canine plaque biofilm develops.

  1. Localization of CD9 Molecule on Bull Spermatozoa: Its Involvement in the Sperm-Egg Interaction.

    Science.gov (United States)

    Antalíková, J; Jankovičová, J; Simon, M; Cupperová, P; Michalková, K; Horovská, Ľ

    2015-06-01

    Tetraspanin CD9 is one of the egg membrane proteins known to be essential in fertilization process. The presence and localization of CD9 molecule in spermatozoa and its possible function in reproduction are still unclear. In our study, we describe the localization of CD9 on bull spermatozoa. In the immunofluorescence assay, the positive signal has been observed in the high proportion of sperm cells as a fine grains either on the apical part or through the entire anterior region of sperm head. CD9 recognized by monoclonal antibody IVA-50 was detected on freshly ejaculated (83.4 ± 3.7%) and frozen-thawed (84.3 ± 2.3%) sperm. The same reaction pattern was observed on sperm capacitated for 1 h, 2 h, 3 h and 4 h (83.6 ± 2.0%; 84.0 ± 1.5%; 85.7 ± 0.8%; 77.5 ± 10.8%). The presence of CD9 exclusively on plasma membrane of the bovine sperm has been detected by Western blot analysis of the protein fractions after the discontinuous sucrose gradient fractionation of the bull sperm. Moreover, probable role of the sperm CD9 molecule in fertilization process of cattle has been suggested as sperm treatment with anti-CD9 antibody significantly reduced (by 25%, p ≤ 0.001) the number of fertilized oocytes compared to control group in fertilization assay in vitro.

  2. Analysis of Multi-Stakeholder Requirements Using Requirement Interaction Matrix

    Directory of Open Access Journals (Sweden)

    Rohayanti Hassan

    2017-09-01

    Full Text Available Software requirements engineering is an imperative phase in the software development life cycle in every project regardless of the project size. In a project, different people are involved in the requirements engineering process, including requirement engineers, stakeholders, end users, and system designers. Amongst them, stakeholders play an essential role. Differences in goals and priorities of multiple stakeholders would make requirements management complex and difficult, which is a huge challenge for requirement engineers. From time to time, new requirements emerge and existing requirements need changes to fulfil stakeholders’ goals. Thus, such situation leads to high requirements volatility and low stability which causes overlapping and conflicting of requirements. The correctness and validity of requirements are of paramount importance as they are the key factors toward a successful system. A deep understanding of requirement management technique that conforms to users’ needs is crucial. Such technique of the concept is applied to the Labour Management System. In this study, we have discussed the implementation of analysis of multi-stakeholder requirements using requirement interaction matrix in the f. The study used real requirements to yield a solid and dependable result. We have documented the requirements using a template and assessed their respective volatility level. An algorithm is constructed to   show   that   the   technique has managed to minimize   the time   used   when   checking requirements.

  3. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    Directory of Open Access Journals (Sweden)

    Venkatesha R. Hathwar

    2015-09-01

    Full Text Available Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

  4. Molecular genetic analysis of activation-tagged transcription factors thought to be involved in photomorphogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Neff, Michael M.

    2011-06-23

    This is a final report for Department of Energy Grant No. DE-FG02-08ER15927 entitled “Molecular Genetic Analysis of Activation-Tagged Transcription Factors Thought to be Involved in Photomorphogenesis”. Based on our preliminary photobiological and genetic analysis of the sob1-D mutant, we hypothesized that OBP3 is a transcription factor involved in both phytochrome and cryptochrome-mediated signal transduction. In addition, we hypothesized that OBP3 is involved in auxin signaling and root development. Based on our preliminary photobiological and genetic analysis of the sob2-D mutant, we also hypothesized that a related gene, LEP, is involved in hormone signaling and seedling development.

  5. Brain regions involved in human movement perception: a quantitative voxel-based meta-analysis.

    Science.gov (United States)

    Grosbras, Marie-Hélène; Beaton, Susan; Eickhoff, Simon B

    2012-02-01

    Face, hands, and body movements are powerful signals essential for social interactions. In the last 2 decades, a large number of brain imaging studies have explored the neural correlates of the perception of these signals. Formal synthesis is crucially needed, however, to extract the key circuits involved in human motion perception across the variety of paradigms and stimuli that have been used. Here, we used the activation likelihood estimation (ALE) meta-analysis approach with random effect analysis. We performed meta-analyses on three classes of biological motion: movement of the whole body, hands, and face. Additional analyses of studies of static faces or body stimuli and sub-analyses grouping experiments as a function of their control stimuli or task employed allowed us to identify main effects of movements and forms perception, as well as effects of task demand. In addition to specific features, all conditions showed convergence in occipito-temporal and fronto-parietal regions, but with different peak location and extent. The conjunction of the three ALE maps revealed convergence in all categories in a region of the right posterior superior temporal sulcus as well as in a bilateral region at the junction between middle temporal and lateral occipital gyri. Activation in these regions was not a function of attentional demand and was significant also when controlling for non-specific motion perception. This quantitative synthesis points towards a special role for posterior superior temporal sulcus for integrating human movement percept, and supports a specific representation for body parts in middle temporal, fusiform, precentral, and parietal areas.

  6. Involving people with dementia in developing an interactive web tool for shared decision-making: experiences with a participatory design approach.

    Science.gov (United States)

    Span, Marijke; Hettinga, Marike; Groen-van de Ven, Leontine; Jukema, Jan; Janssen, Ruud; Vernooij-Dassen, Myrra; Eefsting, Jan; Smits, Carolien

    2017-03-12

    The aim of this study was at gaining insight into the participatory design approach of involving people with dementia in the development of the DecideGuide, an interactive web tool facilitating shared decision-making in their care networks. An explanatory case study design was used when developing the DecideGuide. A secondary analysis focused on the data gathered from the participating people with dementia during the development stages: semi-structured interviews (n = 23), four focus group interviews (n = 18), usability tests (n = 3), and a field study (n = 4). Content analysis was applied to the data. Four themes showed to be important regarding the participation experiences of involving people with dementia in research: valuable feedback on content and design of the DecideGuide, motivation to participate, perspectives of people with dementia and others about distress related to involvement, and time investment. People with dementia can give essential feedback and, therefore, their contribution is useful and valuable. Meaningful participation of people with dementia takes time that should be taken into account. It is important for people with dementia to be able to reciprocate the efforts others make and to feel of significance to others. Implications for Rehabilitation People with dementia can contribute meaningfully to the content and design and their perspective is essential for developing useful and user-friendly tools. Participating in research activities may contribute to social inclusion, empowerment, and quality of life of people with dementia.

  7. Reflections on Practical Approaches to Involving Children and Young People in the Data Analysis Process

    Science.gov (United States)

    Coad, Jane; Evans, Ruth

    2008-01-01

    This article reflects on key methodological issues emerging from children and young people's involvement in data analysis processes. We outline a pragmatic framework illustrating different approaches to engaging children, using two case studies of children's experiences of participating in data analysis. The article highlights methods of…

  8. Reflections on Practical Approaches to Involving Children and Young People in the Data Analysis Process

    Science.gov (United States)

    Coad, Jane; Evans, Ruth

    2008-01-01

    This article reflects on key methodological issues emerging from children and young people's involvement in data analysis processes. We outline a pragmatic framework illustrating different approaches to engaging children, using two case studies of children's experiences of participating in data analysis. The article highlights methods of…

  9. Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.

    Directory of Open Access Journals (Sweden)

    Susan Khor

    Full Text Available Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains.

  10. Adding Graphical Interactive FITS Image Interaction to Data Analysis in IPython Notebooks

    Science.gov (United States)

    Jeschke, E.

    2014-05-01

    IPython notebooks are becoming a popular and viable approach for documenting data analysis procedures and helping produce open, reproducible science. Recent developments in the IPython project allow notebooks to be published and viewed on the web, providing a nearly seamless transition from data analysis to publication. In this talk we will review and demonstrate the ipython notebook as a data analysis tool, and show how graphical FITS image interaction can be integrated in the workflow to simplify some cumbersome tasks.

  11. Proteomic tools for the analysis of transient interactions between metalloproteins.

    Science.gov (United States)

    Martínez-Fábregas, Jonathan; Rubio, Silvia; Díaz-Quintana, Antonio; Díaz-Moreno, Irene; De la Rosa, Miguel Á

    2011-05-01

    Metalloproteins play major roles in cell metabolism and signalling pathways. In many cases, they show moonlighting behaviour, acting in different processes, depending on the physiological state of the cell. To understand these multitasking proteins, we need to discover the partners with which they carry out such novel functions. Although many technological and methodological tools have recently been reported for the detection of protein interactions, specific approaches to studying the interactions involving metalloproteins are not yet well developed. The task is even more challenging for metalloproteins, because they often form short-lived complexes that are difficult to detect. In this review, we gather the different proteomic techniques and biointeractomic tools reported in the literature. All of them have shown their applicability to the study of transient and weak protein-protein interactions, and are therefore suitable for metalloprotein interactions.

  12. Tim50a, a nuclear isoform of the mitochondrial Tim50, interacts with proteins involved in snRNP biogenesis

    Directory of Open Access Journals (Sweden)

    Robinson Melvin L

    2005-07-01

    Full Text Available Abstract Background The Cajal body (CB is a nuclear suborganelle involved in the biogenesis of small nuclear ribonucleoproteins (snRNPs, which are vital for pre-mRNA splicing. Newly imported Sm-class snRNPs traffic through CBs, where the snRNA component of the snRNP is modified, and then target to other nuclear domains such as speckles and perichromatin fibrils. It is not known how nascent snRNPs localize to the CB and are released from this structure after modification. The marker protein for CBs, coilin, may play a role in snRNP biogenesis given that it can interact with snRNPs and SMN, the protein mutated in Spinal Muscular Atrophy. Loss of coilin function in mice leads to significant viability and fertility problems and altered CB formation. Results In this report, we identify a minor isoform of the mitochondrial Tim50, Tim50a, as a coilin interacting protein. The Tim50a transcript can be detected in some cancer cell lines and normal brain tissue. The Tim50a protein differs only from Tim50 in that it contains an additional 103 aa N-terminal to the translation start of Tim50. Importantly, a putative nuclear localization signal is found within these 103 residues. In contrast to Tim50, which localizes to the cytoplasm and mitochondria, Tim50a is strictly nuclear and is enriched in speckles with snRNPs. In addition to coilin, Tim50a interacts with snRNPs and SMN. Competition binding experiments demonstrate that coilin competes with Sm proteins of snRNPs and SMN for binding sites on Tim50a. Conclusion Tim50a may play a role in snRNP biogenesis given its cellular localization and protein interaction characteristics. We hypothesize that Tim50a takes part in the release of snRNPs and SMN from the CB.

  13. The neutrino interaction analysis chain in OPERA

    CERN Document Server

    Rescigno, Regina

    Th e aim of the OPERA experiment i s to provide a “smoking - gun” proof of neutrino oscillation s, through the detecti on of the appearance signal of ν τ ’s in an initially pure ν μ beam. The beam is produced at CERN, 732 Km fa r from the detector , which is located underground in t he Gran Sasso laboratory. The evidence of the appearance signal will be provided by the detection of the daughter particles produced in the decay of the τ lepton. A micro - metric spatial resolution is needed in order to measure a nd study the topology of the ν τ - induced events. With this goal, n uclear emulsions, the highest resolution tracking detector , were chosen to be the core of the OPERA apparatus. The analysis of the large amount of nuclear emulsions used in the OPERA experime n t has required the development of a new generation of fast automatic mi croscopes , featuring a scanning speed more than one order of magnitude hi g h er than in p...

  14. Traf2- and Nck-interacting kinase (TNIK) is involved in the anti-cancer mechanism of dovitinib in human multiple myeloma IM-9 cells.

    Science.gov (United States)

    Chon, Hae Jung; Lee, Yura; Bae, Kyoung Jun; Byun, Byung Jin; Kim, Soon Ae; Kim, Jiyeon

    2016-07-01

    Traf2- and Nck-interacting kinase (TNIK) is a member of the germinal center kinase family. TNIK was first identified as a kinase that is involved in regulating cytoskeletal organization in many types of cells, and it was recently proposed as a novel therapeutic target in several types of human cancers. Although previous studies suggest that TNIK plays a pivotal role in cancer cell survival and prognosis, its function in hematological cancer cell survival has not been investigated. Here we investigated the relationship between TNIK function and cell viability in multiple myeloma IM-9 cells using TNIK small interfering RNA (siRNA) transfection and dovitinib treatment. Treatment of IM-9 cells with TNIK siRNA and dovitinib treatment reduced cell proliferation. The ATP competing kinase assay and western blot analysis showed that dovitinib strongly inhibited both the interaction of TNIK with ATP (K i, 13 nM) and the activation of Wnt signaling effectors such as β-catenin and TCF4. Dovitinib also induced caspase-dependent apoptosis in IM-9 cells without significant cytotoxicity in PBMCs. Our results provide new evidence that TNIK may be involved in the proliferation of multiple myeloma IM-9 cells and in the anti-cancer activity of dovitinib via inhibition of the endogenous Wnt signaling pathway.

  15. Analysis of Pumphouse RCC Frame Structure for Soil Structure Interaction

    Directory of Open Access Journals (Sweden)

    Mr A.S. Thombare

    2016-06-01

    Full Text Available When structure is built on ground some elements of structure are direct contact with soil. When loads are applied on structure internal forces are developed in both the structure as well as in soil. It results in deformation of both the components which are independent to each other. This are called soil structure interaction. The analysis is done by using (Bentley STAAD.Pro V8i Version 2007 software. The analysis carried out been pump house structure R.C.C. frame structure find out shear force Z direction fixed support and fixed but support for different soil. It concluded that soil structure interaction more affected on fixed base. So overcome the effects of the soil structure interaction on the soft soil, it is important to design the structure to standard loading condition and interaction forces. Thus here concluded that pump house building should be design resist the maximum shear force in fixed base

  16. Employee Involvement, Technology, and Evolution in Job Skills: A Task-Based Analysis

    OpenAIRE

    Francis Green

    2012-01-01

    The author investigates the evolution of job skill distribution using task data derived from the U.K. Skills Surveys of 1997, 2001, and 2006, and the 1992 Employment Survey in Britain. He determines the extent to which employee involvement in the workplace and computer technologies promote the use of higher order cognitive and interactive skills. He finds that literacy, other communication tasks, and self-planning skills have grown especially fast. Numerical and problem-solving skills have al...

  17. Coaggregation of Streptococcus salivarius with periodontopathogens: evidence for involvement of fimbriae in the interaction with Prevotella intermedia.

    Science.gov (United States)

    Lévesque, C; Lamothe, J; Frenette, M

    2003-10-01

    Streptococcus salivarius is divided into two serological subgroups that carry either fibrils or fimbriae. Although fimbriae have been observed on up to 50% of S. salivarius strains in the human oral cavity, no function has yet been assigned to them. To determine whether S. salivarius fimbriae have a role in adhesion, we examined the ability of S. salivarius to coaggregate with selected microorganisms involved in periodontal diseases. Our results show that S. salivarius coaggregated with Fusobacterium nucleatum, Porphyromonas gingivalis, and Prevotella intermedia. However, only fimbriated S. salivarius cells were able to coaggregate with P. intermedia, suggesting a specific role for these structures in the interaction. Heat treatment, sensitivity to sugars, amino acids, and EDTA, as well as protease treatment were also used to further characterize coaggregation between S. salivarius and periodontopathogens.

  18. Analysis of nodulation kinetics in Frankia-Discaria trinervis symbiosis reveals different factors involved in the nodulation process.

    Science.gov (United States)

    Gabbarini, Luciano Andrés; Wall, Luis Gabriel

    2008-08-01

    The induction of root nodule development in actinorhizal symbiosis would depend on the concentration of factors produced by the bacteria and the plant. A detailed analysis of nodulation description parameters revealed different factors related to the nodulation process. The initial time for nodulation (t(0)), the initial nodulation rate (v(0)) and the total time of nodule development (t(NOD)) were defined and consequently quantified in different experimental conditions: co-inoculation of Discaria trinervis with increasing concentrations of different non-infective bacteria together with the full compatible infective Frankia strain (the indicator strain) used at a limiting concentration or by changing plant factor(s) concentration. All the above nodulation parameters were modified by changing doses of full compatibility infective strain Frankia BCU110501; v(0) appears to be an expression of symbiotic recognition between partners as only fully symbiotic indicator Frankia BCU110501 was able to change it; t(0) seems not to reflect symbiotic recognition because it can also be modified by non-infective Frankia but suggest the existence of a basic level of plant microbe recognition. The initial time for nodulation t(0), reflecting the time required for the early interactions toward nodulation, is an inverse measure of the ability to establish early interactions toward nodulation. The increase in plant factors concentration also reduces t(0) values, suggesting that a plant factor is involved and favors very early interactions. Increases in plant factors concentration also modify the final number of nodules per plant and the nodule cluster profile along the taproot as an expression of the autoregulation phenomenon. Meanwhile, Frankia inoculums' concentration, either infective or not, modified t(NOD) in an opposite way plant factors did. In conclusion, the analysis of nodulation kinetics appears to be an appropriate tool to investigate factors involved in the symbiotic

  19. Analysis and Verification of Service Interaction Protocols - A Brief Survey

    CERN Document Server

    Salaün, Gwen

    2010-01-01

    Modeling and analysis of interactions among services is a crucial issue in Service-Oriented Computing. Composing Web services is a complicated task which requires techniques and tools to verify that the new system will behave correctly. In this paper, we first overview some formal models proposed in the literature to describe services. Second, we give a brief survey of verification techniques that can be used to analyse services and their interaction. Last, we focus on the realizability and conformance of choreographies.

  20. Phase space analysis of some interacting Chaplygin gas models

    Energy Technology Data Exchange (ETDEWEB)

    Khurshudyan, M. [Academy of Sciences of Armenia, Institute for Physical Research, Ashtarak (Armenia); Tomsk State University of Control Systems and Radioelectronics, Laboratory for Theoretical Cosmology, Tomsk (Russian Federation); Tomsk State Pedagogical University, Department of Theoretical Physics, Tomsk (Russian Federation); Myrzakulov, R. [Eurasian National University, Eurasian International Center for Theoretical Physics, Astana (Kazakhstan)

    2017-02-15

    In this paper we discuss a phase space analysis of various interacting Chaplygin gas models in general relativity. Linear and nonlinear sign changeable interactions are considered. For each case appropriate late time attractors of field equations are found. The Chaplygin gas is one of the dark fluids actively considered in modern cosmology due to the fact that it is a joint model of dark energy and dark matter. (orig.)

  1. Proteomic analysis reveals metabolic and regulatory systems involved the syntrophic and axenic lifestyle of Syntrophomonas wolfei.

    Directory of Open Access Journals (Sweden)

    Jessica Rhea Sieber

    2015-02-01

    Full Text Available Microbial syntrophy is a vital metabolic interaction necessary for the complete oxidation of organic biomass to methane in all-anaerobic ecosystems. However, this process is thermodynamically constrained and represents an ecosystem-level metabolic bottleneck. To gain insight into the physiology of this process, a shotgun proteomic approach was used to quantify the protein landscape of the model syntrophic metabolizer, Syntrophomonas wolfei, grown axenically and syntrophically with Methanospirillum hungatei. Remarkably, the abundance of most proteins as represented by normalized spectral abundance factor (NSAF value changed very little between the pure and coculture growth conditions. Among the most abundant proteins detected were GroEL and GroES chaperonins, a small heat shock protein, and proteins involved in electron transfer, beta-oxidation, and ATP synthesis. Several putative energy conservation enzyme systems that utilize NADH and ferredoxin were present. The abundance of an EtfAB2 and the membrane-bound iron-sulfur oxidoreductase (Swol_0698 gene product delineated a potential conduit for electron transfer between acyl-CoA dehydrogenases and membrane redox carriers. Proteins detected only when S. wolfei was grown with M. hungatei included a zinc-dependent dehydrogenase with a GroES domain, whose gene is present in genomes in many organisms capable of syntrophy, and transcriptional regulators responsive to environmental stimuli or the physiological status of the cell. The proteomic analysis revealed an emphasis macromolecular stability and energy metabolism to S. wolfei and presence of regulatory mechanisms responsive to external stimuli and cellular physiological status.

  2. The cyanobacterial Fluorescence Recovery Protein has two distinct activities: Orange Carotenoid Protein amino acids involved in FRP interaction.

    Science.gov (United States)

    Thurotte, Adrien; Bourcier de Carbon, Céline; Wilson, Adjélé; Talbot, Léa; Cot, Sandrine; López-Igual, Rocio; Kirilovsky, Diana

    2017-04-01

    To deal with fluctuating light condition, cyanobacteria have developed a photoprotective mechanism which, under high light conditions, decreases the energy arriving at the photochemical centers. It relies on a photoswitch, the Orange Carotenoid Protein (OCP). Once photoactivated, OCP binds to the light harvesting antenna, the phycobilisome (PBS), and triggers the thermal dissipation of the excess energy absorbed. Deactivation of the photoprotective mechanism requires the intervention of a third partner, the Fluorescence Recovery Protein (FRP). FRP by interacting with the photoactivated OCP accelerates its conversion to the non-active form and its detachment from the phycobilisome. We have studied the interaction of FRP with free and phycobilisome-bound OCP. Several OCP variants were constructed and characterized. In this article we show that OCP amino acid F299 is essential and D220 important for OCP deactivation mediated by FRP. Mutations of these amino acids did not affect FRP activity as helper to detach OCP from phycobilisomes. In addition, while mutated R60L FRP is inactive on OCP deactivation, its activity on the detachment of the OCP from the phycobilisomes is not affected. Thus, our results demonstrate that FRP has two distinct activities: it accelerates OCP detachment from phycobilisomes and then it helps deactivation of the OCP. They also suggest that different OCP and FRP amino acids could be involved in these two activities.

  3. [Involvement of soluble mediators of inflammation in the pathogenic agent interaction--immune system in acute bacterial meningitis].

    Science.gov (United States)

    Lerescu, L; Tucureanu, C; Caraş, Iuliana; Pitica, Ramona; Ungureanu, Vasilica; Sălăgeanu, Aurora

    2008-01-01

    Acute Bacterial Meningitis is a medical emergency, which warrants early diagnosis and aggressive therapy, which in most cases must be initiated as an "empirical" treatment. Such an approach needs permanent epidemiological surveillance due to the major variability of the etiological agents depending upon time, geographical areas and demographic characteristics of the population. A program for the surveillance of meningitis is in progress in Romania, but the available clinical inbformation is incomplete and not well documented by paraclinical data, poorly reflecting the real incidence of the disease. The specific anatomic localization of the disease has major influences on the antiinfectious immune response. Inflammation is involved in the disease pathogenesis, especially in promotion and evolution of neurological sequelae (neuronal demyelinisation and degeneration) even in case of pathogen clearance following antimicrobial therapy. Activation of the immune response in a immunologically "privileged "region can lead to the break of tolerance and induction of autoimmunity (neuronal degenerescence). On the other hand, an efficient immune response is necessary for the clearance of pathogenic agents. A detailed investigation of the interaction between pathogenic agents and the immune system in relation to the particular meningeal localization and also a study on the involvement of soluble mediators of inflammation (cytokines, chemokines) in the pathogenesis of meningitis might prove useful for differential diagnosis (viral or "aseptic" meningitis) and also for elucidating the mechanisms which that underlie the disease pathogenesis/neurological complications.

  4. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus.

    Science.gov (United States)

    Lund, Christian H; Bromley, Jennifer R; Stenbæk, Anne; Rasmussen, Randi E; Scheller, Henrik V; Sakuragi, Yumiko

    2015-01-01

    A growing body of evidence suggests that protein-protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. Our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta.

  5. Prevalence and type of drug-drug interactions involving antiretrovirals in patients attending a specialist outpatient clinic in Kampala, Uganda

    Directory of Open Access Journals (Sweden)

    K Seden

    2012-11-01

    Full Text Available Scale-up of HIV services in countries such as Uganda has resulted in a rapid increase in facilities offering antiretrovirals (ARVs and an increase in healthcare workers trained to deliver care. Consequently, evaluating medication safety is increasingly important in these settings. Data from developed countries suggest that drug-drug interactions (DDIs involving ARVs are common, occurring at rates of 14–58%. Few data are available from low resource settings, however a study of 996 Kenyan patients found that 33.5% were at risk of clinically significant DDIs. We evaluated the prevalence and type of ARV DDIs and the patients most at risk in an African outpatient setting. A random sample of patients taking current ARVs and accessing care at the Infectious Diseases Institute, Makerere University, Kampala was selected from the clinic database. The most recent prescription for each patient was screened for DDIs using www.hiv-druginteractions.org. Clinical significance of DDIs was assessed by two of us using a previously developed technique evaluating: likelihood of interaction, therapeutic index of affected drug and severity of potential adverse effect. From 1000 consecutive patients 99.6% were taking≥1 co-medication alongside their ARV regimen (mean 1.89. 24.5% had≥1 potential DDI, with a total of 335 DDIs observed. Of these, 255 DDIs were considered clinically significant, affecting 18.8% of patients. Only 0.3% of DDIs involved a contraindicated combination. There was a higher rate of potential DDIs observed in patients taking TB treatment (p=0.0047, who were WHO stage 3 or 4 (p=0.001, or patients taking ≥2 co-medications alongside ARVs (p<0.0001 (Fishers exact test. Patient age, gender, CD4 count and weight did not affect risk for DDIs. Co-medications commonly associated with potential DDIs were antibiotics (6.2% of 1000 patients, anthelminthics (4.6% and antifungals (3.5%. Potential DDIs involving ARVs occur at similar rates in resource

  6. GUN1 Controls Accumulation of the Plastid Ribosomal Protein S1 at the Protein Level and Interacts with Proteins Involved in Plastid Protein Homeostasis.

    Science.gov (United States)

    Tadini, Luca; Pesaresi, Paolo; Kleine, Tatjana; Rossi, Fabio; Guljamow, Arthur; Sommer, Frederik; Mühlhaus, Timo; Schroda, Michael; Masiero, Simona; Pribil, Mathias; Rothbart, Maxi; Hedtke, Boris; Grimm, Bernhard; Leister, Dario

    2016-03-01

    Developmental or metabolic changes in chloroplasts can have profound effects on the rest of the plant cell. Such intracellular responses are associated with signals that originate in chloroplasts and convey information on their physiological status to the nucleus, which leads to large-scale changes in gene expression (retrograde signaling). A screen designed to identify components of retrograde signaling resulted in the discovery of the so-called genomes uncoupled (gun) mutants. Genetic evidence suggests that the chloroplast protein GUN1 integrates signals derived from perturbations in plastid redox state, plastid gene expression, and tetrapyrrole biosynthesis (TPB) in Arabidopsis (Arabidopsis thaliana) seedlings, exerting biogenic control of chloroplast functions. However, the molecular mechanism by which GUN1 integrates retrograde signaling in the chloroplast is unclear. Here we show that GUN1 also operates in adult plants, contributing to operational control of chloroplasts. The gun1 mutation genetically interacts with mutations of genes for the chloroplast ribosomal proteins S1 (PRPS1) and L11. Analysis of gun1 prps1 lines indicates that GUN1 controls PRPS1 accumulation at the protein level. The GUN1 protein physically interacts with proteins involved in chloroplast protein homeostasis based on coimmunoprecipitation experiments. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation experiments suggest that GUN1 might transiently interact with several TPB enzymes, including Mg-chelatase subunit D (CHLD) and two other TPB enzymes known to activate retrograde signaling. Moreover, the association of PRPS1 and CHLD with protein complexes is modulated by GUN1. These findings allow us to speculate that retrograde signaling might involve GUN1-dependent formation of protein complexes.

  7. Gene network and familial analyses uncover a gene network involving Tbx5/Osr1/Pcsk6 interaction in the second heart field for atrial septation.

    Science.gov (United States)

    Zhang, Ke K; Xiang, Menglan; Zhou, Lun; Liu, Jielin; Curry, Nathan; Heine Suñer, Damian; Garcia-Pavia, Pablo; Zhang, Xiaohua; Wang, Qin; Xie, Linglin

    2016-03-15

    Atrial septal defects (ASDs) are a common human congenital heart disease (CHD) that can be induced by genetic abnormalities. Our previous studies have demonstrated a genetic interaction between Tbx5 and Osr1 in the second heart field (SHF) for atrial septation. We hypothesized that Osr1 and Tbx5 share a common signaling networking and downstream targets for atrial septation. To identify this molecular networks, we acquired the RNA-Seq transcriptome data from the posterior SHF of wild-type, Tbx5(+/) (-), Osr1(+/-), Osr1(-/-) and Tbx5(+/-)/Osr1(+/-) mutant embryos. Gene set analysis was used to identify the Kyoto Encyclopedia of Genes and Genomes pathways that were affected by the doses of Tbx5 and Osr1. A gene network module involving Tbx5 and Osr1 was identified using a non-parametric distance metric, distance correlation. A subset of 10 core genes and gene-gene interactions in the network module were validated by gene expression alterations in posterior second heart field (pSHF) of Tbx5 and Osr1 transgenic mouse embryos, a time-course gene expression change during P19CL6 cell differentiation. Pcsk6 was one of the network module genes that were linked to Tbx5. We validated the direct regulation of Tbx5 on Pcsk6 using immunohistochemical staining of pSHF, ChIP-quantitative polymerase chain reaction and luciferase reporter assay. Importantly, we identified Pcsk6 as a novel gene associated with ASD via a human genotyping study of an ASD family. In summary, our study implicated a gene network involving Tbx5, Osr1 and Pcsk6 interaction in SHF for atrial septation, providing a molecular framework for understanding the role of Tbx5 in CHD ontogeny.

  8. Polymorphism Interaction Analysis (PIA: a method for investigating complex gene-gene interactions

    Directory of Open Access Journals (Sweden)

    Chanock Stephen J

    2008-03-01

    Full Text Available Abstract Background The risk of common diseases is likely determined by the complex interplay between environmental and genetic factors, including single nucleotide polymorphisms (SNPs. Traditional methods of data analysis are poorly suited for detecting complex interactions due to sparseness of data in high dimensions, which often occurs when data are available for a large number of SNPs for a relatively small number of samples. Validation of associations observed using multiple methods should be implemented to minimize likelihood of false-positive associations. Moreover, high-throughput genotyping methods allow investigators to genotype thousands of SNPs at one time. Investigating associations for each individual SNP or interactions between SNPs using traditional approaches is inefficient and prone to false positives. Results We developed the Polymorphism Interaction Analysis tool (PIA version 2.0 to include different approaches for ranking and scoring SNP combinations, to account for imbalances between case and control ratios, stratify on particular factors, and examine associations of user-defined pathways (based on SNP or gene with case status. PIA v. 2.0 detected 2-SNP interactions as the highest ranking model 77% of the time, using simulated data sets of genetic models of interaction (minor allele frequency = 0.2; heritability = 0.01; N = 1600 generated previously [Velez DR, White BC, Motsinger AA, Bush WS, Ritchie MD, Williams SM, Moore JH: A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Genet Epidemiol 2007, 31:306–315.]. Interacting SNPs were detected in both balanced (20 SNPs and imbalanced data (case:control 1:2 and 1:4, 10 SNPs in the context of non-interacting SNPs. Conclusion PIA v. 2.0 is a useful tool for exploring gene*gene or gene*environment interactions and identifying a small number of putative associations which may be investigated further using other

  9. Ethylene-responsive transcription factors interact with promoters of ADH and PDC involved in persimmon (Diospyros kaki) fruit de-astringency.

    Science.gov (United States)

    Min, Ting; Yin, Xue-ren; Shi, Yan-na; Luo, Zheng-rong; Yao, Yun-cong; Grierson, Donald; Ferguson, Ian B; Chen, Kun-song

    2012-11-01

    The persimmon fruit is a particularly good model for studying fruit response to hypoxia, in particular, the hypoxia-response ERF (HRE) genes. An anaerobic environment reduces fruit astringency by converting soluble condensed tannins (SCTs) into an insoluble form. Although the physiology of de-astringency has been widely studied, its molecular control is poorly understood. Both CO(2) and ethylene treatments efficiently removed the astringency from 'Mopan' persimmon fruit, as indicated by a decrease in SCTs. Acetaldehyde, the putative agent for causing de-astringency, accumulated during these treatments, as did activities of the key enzymes of acetaldehyde synthesis, alcohol dehydrogenase (ADH), and pyruvate decarboxylase (PDC). Eight DkADH and DkPDC genes were isolated, and three candidates for a role in de-astringency, DkADH1, DkPDC1, and DkPDC2, were characterized by transcriptional analysis in different tissues. The significance of these specific isoforms was confirmed by principal component analysis. Transient expression in leaf tissue showed that DkPDC2 decreased SCTs. Interactions of six hypoxia-responsive ERF genes and target promoters were tested in transient assays. The results indicated that two hypoxia-responsive ERF genes, DkERF9 and DkERF10, were involved in separately regulating the DkPDC2 and DkADH1 promoters. It is proposed that a DkERF-DkADH/DkPDC cascade is involved in regulating persimmon de-astringency.

  10. Analysis of a signal transduction pathway involved in leaf epidermis differentiation.

    Energy Technology Data Exchange (ETDEWEB)

    Philip W. Becraft

    2005-05-23

    The major objective of this study was to identify and analyze signal transduction factors that function with the CR4 receptor kinase. We pursued this analysis in Arabidopsis. Analysis of other members of the ACR4 related receptor (CRR) family produced biochemical evidence consistent with some of them functioning in ACR4 signal transduction. Yeast 2-hybrid identified six proteins that interact with the cytoplasmic domain of ACR4, representing putative downstream signal transduction components. The interactions for all 6 proteins were verified by in vitro pull down assays. Five of the interacting proteins were phosphorylated by ACR4. We also identified candidate interactors with the extracellular TNFR domain. We hypothesize this may be the ligand binding domain for ACR4. In one approach, yeast 2-hybrid was again used and five candidate proteins identified. Nine additional candidates were identified in a genome wide scan of Arabidopsis amino acid sequences that threaded onto the TNF structure.

  11. Distributed and interactive visual analysis of omics data.

    Science.gov (United States)

    Farag, Yehia; Berven, Frode S; Jonassen, Inge; Petersen, Kjell; Barsnes, Harald

    2015-11-01

    The amount of publicly shared proteomics data has grown exponentially over the last decade as the solutions for sharing and storing the data have improved. However, the use of the data is often limited by the manner of which it is made available. There are two main approaches: download and inspect the proteomics data locally, or interact with the data via one or more web pages. The first is limited by having to download the data and thus requires local computational skills and resources, while the latter most often is limited in terms of interactivity and the analysis options available. A solution is to develop web-based systems supporting distributed and fully interactive visual analysis of proteomics data. The use of a distributed architecture makes it possible to perform the computational analysis at the server, while the results of the analysis can be displayed via a web browser without the need to download the whole dataset. Here the challenges related to developing such systems for omics data will be discussed. Especially how this allows for multiple connected interactive visual displays of omics dataset in a web-based setting, and the benefits this provide for computational analysis of proteomics data.This article is part of a Special Issue entitled: Computational Proteomics.

  12. Mental health policy and mental health service user perspectives on involvement: a discourse analysis.

    Science.gov (United States)

    Hui, Ada; Stickley, Theodore

    2007-08-01

    This paper is a report of an exploration of the concept of service user involvement in mental health nursing using a discourse analysis approach. Service user involvement has come to be expected in mental health nursing policy and practice. This concept, however, is often applied somewhat ambiguously and some writers call for a clearer understanding of what service users actually want. A Foucauldian discourse analysis was conducted in 2005, examining literature and health policies published by the United Kingdom government and service users. The discursive perspectives of both were explored and conceptual themes were generated from the data. Concepts occurring within government discourse include language relating to service users, the notion of service user involvement and power. Concepts from the service user discourse include power, change and control, theory, policy and practice, and experiential expertise. Differences in perspectives were found within these themes which distinguished government from service user discourses. Greater flexibility in ideas and perspectives was demonstrated by service users, with a seemingly greater range of theoretical underpinnings. Greater awareness is needed of the significance of language, of how subtle inferences may be drawn from the rhetorical language of policies, of how these might affect the involvement of service users, and of the implications for the role of mental health nurses. Nurses need to be aware of these tensions and conflicts in managing their practice and in creating a mental health nursing philosophy of 'involvement'. If true 'involvement' is to ensue, nurses may also need to consider the transfer of power to service users.

  13. In silico analysis suggests interaction between Ebola virus and the extracellular matrix

    Directory of Open Access Journals (Sweden)

    Veljko eVeljkovic

    2015-02-01

    Full Text Available The worst Ebola virus (EV outbreak in history has hit Liberia, Sierra Leone and Guinea hardest and the trendlines in this crisis are grave, and now represents global public health threat concern. Limited therapeutic and/or prophylactic options which are available for humans suffering from Ebola virus disease (EVD further complicate situation. Previous studies suggested that the EV glycoprotein (GP is the main determinant causing structural damage of endothelial cells that triggers the hemorrhagic diathesis, but molecular mechanisms underlying this phenomenon remains elusive. Using the informational spectrum method (ISM, a virtual spectroscopy method for analysis of the protein-protein interactions, the interaction of GP with endothelial extracellular matrix (ECM was investigated. Presented results of this in silico study suggest that Elastin Microfibril Interface Located Proteins (EMILINs are involved in interaction between GP and ECM. This finding could contribute to better understanding of EV/endothelium interaction and its role in pathogenesis, prevention and therapy of EVD.

  14. Recent applications of hydrophilic interaction liquid chromatography in pharmaceutical analysis.

    Science.gov (United States)

    Zhang, Qian; Yang, Feng-Qing; Ge, Liya; Hu, Yuan-Jia; Xia, Zhi-Ning

    2017-01-01

    Hydrophilic interaction liquid chromatography, an alternative liquid chromatography mode, is of particular interest in separating hydrophilic and polar ionic compounds. Compared with traditional liquid chromatography techniques, hydrophilic interaction liquid chromatography offers specific advantages mainly including: (1) relatively green and water-soluble mobile phase composition, which enhances the solubility of hydrophilic and polar ionic compounds; (2) no need for ion-pairing reagents and high content of organic solvent, which benefits mass spectrometry detection; (3) high orthogonality to reverse-phase liquid chromatography, well adapted to two-dimensional liquid chromatography for complicated samples. Therefore, hydrophilic interaction liquid chromatography has been rapidly developed in many areas over the past decades. This review summarizes the recent progress (from 2012 to July 2016) of hydrophilic interaction liquid chromatography in pharmaceutical analysis, with the focus on detecting chemical drugs in various matrices, charactering active compounds of natural products and assessing biotherapeutics through typical structure unit. Moreover, the retention mechanism and behavior of analytes in hydrophilic interaction liquid chromatography as well as some novel hydrophilic interaction liquid chromatography columns used for pharmaceutical analysis are also described.

  15. Analysis of factors associated with injury severity in crashes involving young New Zealand drivers

    DEFF Research Database (Denmark)

    Weiss, Harold B.; Kaplan, Sigal; Prato, Carlo Giacomo

    2014-01-01

    Young people are a risk to themselves and other road users, as motor vehicle crashes are the leading cause of their death. A thorough understanding of the most important factors associated with injury severity in crashes involving young drivers is important for designing well-targeted restrictive...... measures within youth-oriented road safety programs. The current study estimates discrete choice models of injury severity of crashes involving young drivers conditional on these crashes having occurred. The analysis examined a comprehensive set of single-vehicle and two-vehicle crashes involving at least...... fit than a binary and a generalized ordered logit. Results show that the young drivers’ behavior, the presence of passengers and the involvement of vulnerable road users were the most relevant factors associated with higher injury severity in both single-vehicle and two-vehicle crashes. Seatbelt non...

  16. Clinicopathological Features Analysis of 86 Endometrial Endometrioid Adenocarcinoma Patients with Adnexal Involvement.

    Science.gov (United States)

    Zuo, Jing; Cheng, Min; Song, Yan; Li, Zhuo; Zhang, Rong; Li, Bin; Wu, Lingying

    2017-06-20

    To investigate the clinicopathological features of endometrial endometrioid adenocarcinoma(EEA)with adnexal involvement.Methods The clinicopathological data of 86 EEA patients who underwent surgical treatment at our center from January 2000 to December 2015 were analyzed retrospectively.The clinicopathological features were compared between patients with occult adnexal involvement and those with gross adnexal involvement.Results A total of 86 EEA patients with adnexal involvement(mean age:58.1 years)were included in this study,accounting for 5.4%(86/1592)of the EEA patients during the same period.Among these 86 patients,there were 13 premenopausal patients(15.1%)including 2 premenopausal patients aged under 40 years.Gross adnexal involvement was found in 47 patients(54.7%),while occult adnexal involvement was found in 39 patients(45.3%)in pathology evaluation.Ovarian metastasis was found in 34 patients(39.5%),followed by both ovarian and tubal metastasis in 19 patients(22.1%)and tubal metastasis in 33 patients(38.4%).The expressionss of estrogen receptor(χ(2)=8.086,P=0.042)and progesterone receptor(PR)(χ(2)=9.149,P=0.026)were significantly different between gross adnexal involvement group and occult adnexal involvement group,whereas no significant difference was found in other clinicopathological features(all P>0.05).The non-conditional Logistic regression analysis showed that,compared with PR no-expression group,the rate of occult microscopic adnexal involvement in PR low-expression group was 6.375 times of that of the gross adnexal involvement(P=0.005,95%CI:1.768-22.976),and the rate of occult microscopic adnexal involvement in the PR high-expression group was 3.719 times of that of gross adnexal involvement(P=0.048,95%CI:1.009-13.702). Conclusion PR expression level is remarkably lower in EEA patients with gross adnexal involvement than those with occult adenxal involvement.

  17. Isobolographic analysis of the antinociceptive interactions between ketoprofen and paracetamol.

    Science.gov (United States)

    Qiu, Hai-Xia; Liu, Jin; Kong, Hui; Liu, Yan; Mei, Xing-Guo

    2007-02-28

    The present study was undertaken to evaluate the antinociceptive interaction between paracetamol and ketoprofen. The antinociceptive effect of oral administration of the drugs alone or in combination was evaluated using the mouse abdominal constriction test. The data were interpreted by isobolographic analysis to establish the nature of the interaction. The effective dose that produced 50% antinociception (ED(50,mix)) was calculated from the log dose-response curve of fixed-ratio combinations of paracetamol with ketoprofen. This ED(50,mix) was compared to the theoretical additive ED(50,add) by isobolographic analysis. The experimental ED(50,mix) was found to be significantly smaller than the theoretically calculated ED(50,add), indicating a synergistic antinociceptive interaction between ketoprofen and paracetamol. Pharmacokinetic studies were carried out with mice treated with combined ketoprofen (12 mg/kg) and paracetamol (36 mg/kg). Plasma levels of ketoprofen were not changed by concurrent paracetamol treatment, and similarly no statistically significant difference was observed between paracetamol alone and the combination with ketoprofen. The pharmacokinetic analysis revealed that the combination of ketoprofen with paracetamol exerted a synergistic (supra-additive) interaction that was not associated with a pharmacokinetic interaction. The results of this study demonstrate significant synergism between ketoprofen and paracetamol.

  18. A Meta-Analysis of Parent-Involved Treatment for Child Sexual Abuse

    Science.gov (United States)

    Corcoran, Jacqueline; Pillai, Vijayan

    2008-01-01

    Sexual abuse in children not only occurs with alarming frequency, it also potentially leads to deleterious consequences for victims. Previous narrative reviews have touted the benefits of including the nonoffending caregiver in child sexual treatment. Objective: A meta-analysis is conducted to determine the effects of parent-involved treatment in…

  19. A Meta-Analysis of Parent-Involved Treatment for Child Sexual Abuse

    Science.gov (United States)

    Corcoran, Jacqueline; Pillai, Vijayan

    2008-01-01

    Sexual abuse in children not only occurs with alarming frequency, it also potentially leads to deleterious consequences for victims. Previous narrative reviews have touted the benefits of including the nonoffending caregiver in child sexual treatment. Objective: A meta-analysis is conducted to determine the effects of parent-involved treatment in…

  20. Criminal Justice System Involvement and Continuity of Youth Crime: A Longitudinal Analysis

    Science.gov (United States)

    Johnson, Lee Michael; Simons, Ronald L.; Conger, Rand D.

    2004-01-01

    Studies of criminal careers reveal several possible factors associated with persistent offending. This analysis examines the part that criminal justice system involvement plays in persistent offending. Seven waves of data collected on 153 boys as part of the Iowa Youth and Families Project were used to test a structural equation model…

  1. Impact of Incredible Years® on teacher perceptions of parental involvement: A latent transition analysis.

    Science.gov (United States)

    Thompson, Aaron M; Herman, Keith C; Stormont, Melissa A; Reinke, Wendy M; Webster-Stratton, Carolyn

    2017-06-01

    The purpose of the present study was to examine the impact of the Incredible Years® Teacher Classroom Management (IY TCM) training on teacher perceptions of parental involvement. A cluster randomized design was used to assign 42 classroom teachers to either an IY TCM training (n=19) or a control condition (n=23). Teachers rated parental involvement (i.e., bonding with teacher, parental involvement at school) for the families of 805 low income students (IY TCM=504, control=301). A latent profile transition analysis framework was used to model the effect of IY TCM on teacher perceptions of parental involvement from pre to posttest. Four profiles consisting of various patterns of high, medium, and low teacher perceptions of bonding with and involvement of parents emerged. Analyses of teacher profiles at baseline revealed teachers who felt parental involvement and bonding was low were also likely to rate students as having more externalizing behaviors, fewer social competencies, more attention deficit symptoms, and disruptive behaviors towards adults and peers compared to teachers with more adaptive profiles. Further analysis revealed that parents of teachers randomly assigned to IY TCM were more likely to transition to a more adaptive view of parental involvement at follow-up compared to teachers in the control condition. Because teacher perceptions of parental involvement may adversely impact teacher attitudes towards difficult students, findings from the present study support the promise of teacher training as an avenue for conferring protections for struggling students. Copyright © 2017 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  2. An Analysis of Interaction Patterns in the Focus Group Interview

    Directory of Open Access Journals (Sweden)

    Gavora Peter

    2015-12-01

    Full Text Available This paper is based on the analysis of a focus group interview of a moderator and a group of undergraduate students on the topic of self-regulation of learning. The purpose of the investigation was to identify interaction patterns that appeared in the talk of participants and the moderator. In the stream of communication two rudimentary interaction patterns were recognized. The first pattern was named the Catalogue. It consists of a sequence of turns of participants who respond to a request of the moderator and who provide their answers, one by one, without reacting on the content of the previous partner(s talk. The other interaction pattern was called the Domino. In this pattern participants respond to each other. The Catalogue pattern prevailed in the interview. Alongside with identification of patterns of interaction the study demonstrated the functions of the common ground and its accomplishment in the talk of the moderator and participants.

  3. Morphological Analysis and Interaction of Chlorophyll and BSA

    Directory of Open Access Journals (Sweden)

    Filipe D. S. Gorza

    2014-01-01

    Full Text Available Interactions between proteins and drugs, which can lead to formation of stable drug-protein complexes, have important implications on several processes related to human health. These interactions can affect, for instance, free concentration, biological activity, and metabolism of the drugs in the blood stream. Here, we report on the UV-Visible spectroscopic investigation on the interaction of bovine serum albumin (BSA with chlorophyll (Chl in aqueous solution under physiological conditions. Binding constants at different temperatures—obtained by using the Benesi-Hildebrand equation—were found to be of the same order of magnitude (~104 M−1 indicating low affinity of Chl with BSA. We have found a hyperchromism, which suggested an interaction between BSA and Chl occurring through conformational changes of BSA caused by exposition of tryptophan to solvent. Films from BSA and Chl obtained at different Chl concentrations showed fractal structures, which were characterized by fractal dimension calculated from microscopic image analysis.

  4. Identification of calgranulin B interacting proteins and network analysis in gastrointestinal cancer cells

    Science.gov (United States)

    Yoo, Byong Chul

    2017-01-01

    Calgranulin B is known to be involved in tumor development, but the underlying molecular mechanism is not clear. To gain insight into possible roles of calgranulin B, we screened for calgranulin B-interacting molecules in the SNU-484 gastric cancer and the SNU-81 colon cancer cells. Calgranulin B-interacting partners were identified by yeast two-hybrid and functional information was obtained by computational analysis. Most of the calgranulin B-interacting partners were involved in metabolic and cellular processes, and found to have molecular function of binding and catalytic activities. Interestingly, 46 molecules in the network of the calgranulin B-interacting proteins are known to be associated with cancer and FKBP2 was found to interact with calgranulin B in both SNU-484 and SNU-81 cells. Polyubiquitin-C encoded by UBC, which exhibited an interaction with calgranulin B, has been associated with various molecules of the extracellular space and plasma membrane identified in our screening, including Na-K-Cl cotransporter 1 and dystonin in SNU-484 cells, and ATPase subunit beta-1 in SNU-81 cells. Our data provide novel insight into the roles of calgranulin B of gastrointestinal cancer cells, and offer new clues suggesting calgranulin B acts as an effector molecule through which the cell can communicate with the tumor microenvironment via polyubiquitin-C. PMID:28152021

  5. Weighted protein interaction network analysis of frontotemporal dementia\\ud

    OpenAIRE

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

    2016-01-01

    The genetic analysis of complex disorders has undoubtedly led to the identification of a wealth of associations between genes and specific traits. However, moving from genetics to biochemistry one gene at a time has, to date, rather proved inefficient and under-powered to comprehensively explain the molecular basis of phenotypes. Here we present a novel approach, weighted protein−protein\\ud interaction network analysis (W-PPI-NA), to highlight key functional players within relevant biological...

  6. Prolactin Regulatory Element Binding Protein Is Involved in Hepatitis C Virus Replication by Interaction with NS4B

    Science.gov (United States)

    Kong, Lingbao; Fujimoto, Akira; Nakamura, Mariko; Aoyagi, Haruyo; Matsuda, Mami; Watashi, Koichi; Suzuki, Ryosuke; Arita, Minetaro; Yamagoe, Satoshi; Dohmae, Naoshi; Suzuki, Takehiro; Sakamaki, Yuriko; Ichinose, Shizuko; Suzuki, Tetsuro; Wakita, Takaji

    2016-01-01

    ABSTRACT It has been proposed that the hepatitis C virus (HCV) NS4B protein triggers the membranous HCV replication compartment, but the underlying molecular mechanism is not fully understood. Here, we screened for NS4B-associated membrane proteins by tandem affinity purification and proteome analysis and identified 202 host proteins. Subsequent screening of replicon cells with small interfering RNA identified prolactin regulatory element binding (PREB) to be a novel HCV host cofactor. The interaction between PREB and NS4B was confirmed by immunoprecipitation, immunofluorescence, and proximity ligation assays. PREB colocalized with double-stranded RNA and the newly synthesized HCV RNA labeled with bromouridine triphosphate in HCV replicon cells. Furthermore, PREB shifted to detergent-resistant membranes (DRMs), where HCV replication complexes reside, in the presence of NS4B expression in Huh7 cells. However, a PREB mutant lacking the NS4B-binding region (PREBd3) could not colocalize with double-stranded RNA and did not shift to the DRM in the presence of NS4B. These results indicate that PREB locates at the HCV replication complex by interacting with NS4B. PREB silencing inhibited the formation of the membranous HCV replication compartment and increased the protease and nuclease sensitivity of HCV replicase proteins and RNA in DRMs, respectively. Collectively, these data indicate that PREB promotes HCV RNA replication by participating in the formation of the membranous replication compartment and by maintaining its proper structure by interacting with NS4B. Furthermore, PREB was induced by HCV infection in vitro and in vivo. Our findings provide new insights into HCV host cofactors. IMPORTANCE The hepatitis C virus (HCV) protein NS4B can induce alteration of the endoplasmic reticulum and the formation of a membranous web structure, which provides a platform for the HCV replication complex. The molecular mechanism by which NS4B induces the membranous HCV replication

  7. Computer-Based Interaction Analysis with DEGREE Revisited

    Science.gov (United States)

    Barros, B.; Verdejo, M. F.

    2016-01-01

    We review our research with "DEGREE" and analyse how our work has impacted the collaborative learning community since 2000. Our research is framed within the context of computer-based interaction analysis and the development of computer-supported collaborative learning (CSCL) tools. We identify some aspects of our work which have been…

  8. Interaction Analysis in Foreign Language Teaching: A Rationale.

    Science.gov (United States)

    Swanson, Maria Antonieta Medina

    A system for observing and coding verbal interchanges between the teacher and his pupils, at all instructional levels, is described in this study. The system, widely known as the Flanders System of Interaction Analysis, is reviewed in terms of its effect on the classroom behavior of teachers and on student attitudes. The application of the…

  9. Interactive exploratory data analysis tool in Alzheimer’s disease

    Directory of Open Access Journals (Sweden)

    Diana Furcila

    2015-04-01

    Thus, MorExAn provide us the possibility to relate histopathological data with neuropsychological and clinical variables. The aid of this interactive visualization tool brings us the possibility to find unexpected conclusions beyond the insight provided by simple statistics analysis, as well as to improve neuroscientists’ productivity.

  10. Semiparametric bayesian analysis of gene-environment interactions

    OpenAIRE

    Lobach, I.

    2010-01-01

    A key component to prevention and control of complex diseases, such as cancer, diabetes, hypertension, is to analyze the genetic and environmental factors that lead to the development of these complex diseases. We propose a Bayesian approach for analysis of gene-environment interactions that efficiently models information available in the observed data and a priori biomedical knowledge.

  11. Pomeron-Odderon Interactions: A Functional RG Flow Analysis

    CERN Document Server

    Vacca, Gian Paolo

    2016-01-01

    In the quest for an effective field theory which could help to understand some non perturbative feature of the QCD in the Regge limit, we consider a Reggeon Field Theory (RFT) for both Pomeron and Odderon interactions and perform an analysys of the critical theory using functional renormalization group techniques, unveiling a novel symmetry structure.

  12. Stochastic Process Analysis of Interactive Discourse in Early Counseling Interviews.

    Science.gov (United States)

    Friedlander, Myrna L.; Phillips, Susan D.

    1984-01-01

    Examined patterns of interactive discourse to suggest how client and counselor establish a working alliance in their early interviews. Based on classification of 312 conversational turns from 14 dyads, a stochastic analysis was conducted. Results showed the sequences of talk were highly stable and predictable. (JAC)

  13. I PASS: an interactive policy analysis simulation system.

    Science.gov (United States)

    Doug Olson; Con Schallau; Wilbur Maki

    1984-01-01

    This paper describes an interactive policy analysis simulation system(IPASS) that can be used to analyze the long-term economic and demographic effects of alternative forest resource management policies. The IPASS model is a dynamic analytical tool that forecasts growth and development of an economy. It allows the user to introduce changes in selected parameters based...

  14. Evidence that intramolecular interactions are involved in masking the activation domain of transcriptional activator Leu3p.

    Science.gov (United States)

    Wang, D; Hu, Y; Zheng, F; Zhou, K; Kohlhaw, G B

    1997-08-01

    The Leu3 protein of Saccharomyces cerevisiae regulates the expression of genes involved in branched chain amino acid biosynthesis and in ammonia assimilation. It is modulated by alpha-isopropylmalate, an intermediate in leucine biosynthesis. In the presence of alpha-isopropylmalate, Leu3p is a transcriptional activator. In the absence of the signal molecule, the activation domain is masked, and Leu3p acts as a repressor. The recent discovery that Leu3p retains its regulatory properties when expressed in mammalian cells (Guo, H., and Kohlhaw, G. B. (1996) FEBS Lett. 390, 191-195) suggests that masking and unmasking of the activation domain occur without the participation of auxiliary proteins. Here we present experimental support for this notion and address the mechanism of masking. We show that modulation of Leu3p is exceedingly sensitive to mutations in the activation domain. An activation domain double mutant (D872N/D874N; designated Leu3-dd) was constructed that has the characteristics of a permanently masked activator. Using separately expressed segments containing either the DNA binding domain-middle region or the activation domain of wild type Leu3p (or Leu3-dd) in a modified yeast two-hybrid system, we provide direct evidence for alpha-isopropylmalate-dependent interaction between these segments. Finally, we use the phenotype of Leu3-dd-containing cells (slow growth in the absence of added leucine) to select for suppressor mutations that map to the middle region of Leu3-dd. The properties of nine such suppressors further support the idea that masking is an intramolecular process and suggest a means for mapping the surface involved in masking.

  15. Hybrid transfinite element modeling/analysis of nonlinear heat conduction problems involving phase change

    Science.gov (United States)

    Tamma, Kumar K.; Railkar, Sudhir B.

    1988-01-01

    The present paper describes the applicability of hybrid transfinite element modeling/analysis formulations for nonlinear heat conduction problems involving phase change. The methodology is based on application of transform approaches and classical Galerkin schemes with finite element formulations to maintain the modeling versatility and numerical features for computational analysis. In addition, in conjunction with the above, the effects due to latent heat are modeled using enthalpy formulations to enable a physically realistic approximation to be dealt computationally for materials exhibiting phase change within a narrow band of temperatures. Pertinent details of the approach and computational scheme adapted are described in technical detail. Numerical test cases of comparative nature are presented to demonstrate the applicability of the proposed formulations for numerical modeling/analysis of nonlinear heat conduction problems involving phase change.

  16. Qualitative analysis of factors that increase and reduce involvement in gambling

    Directory of Open Access Journals (Sweden)

    Egidijus

    2015-12-01

    Full Text Available During the rapid development of gambling business, the number of pathological gamblers is increasing as well. The problem of pathological gambling is just as important as alcoholism or drug addiction. However, there is a lack of information and research of this topicin Lithuania. The aim of work: to investigate and analyse the factors that increase or reduce involvement in gambling. Research questions: 1 What factors increase involvement in gambling? 2 What factors reduce involvement in gambling? Critical case sampling was used for selection of the participants. Subjects were required to a have experience of involvement in gambling for at least one year; b have experience of negative impact of gambling on quality of life; c have at least 6 months of gambling abstinence. Five individuals participated in the research; all of them were males who live in Vilnius. Age of the participants varied from 19 to 45. Semi-structured interviews were used to collect data. Interviews were recorded and transcribed verbatim. The matic analysis of the data led to the identification of four major the matic categories: psychological factors; social relations; material well being; quality of life. There search results show that negatyve childhood experience, gambling friends, escaping from various troubles, disputes in family and high financial needs can increase involvement in gambling. Factors that reduce involvement in gambling are: feeling support of social environment, proper evaluation of financial position, awareness of one‘s own addiction to gambling and desire to change life.

  17. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

    Institute of Scientific and Technical Information of China (English)

    Yonglong Yu; Dong Zhu; Chaoying Ma; Hui Cao; Yaping Wang; Yanhao Xu; Wenying Zhang; Yueming Yan

    2016-01-01

    Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20) during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA) was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further informa-tion about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  18. Transcriptome analysis reveals key differentially expressed genes involved in wheat grain development

    Directory of Open Access Journals (Sweden)

    Yonglong Yu

    2016-04-01

    Full Text Available Wheat seed development is an important physiological process of seed maturation and directly affects wheat yield and quality. In this study, we performed dynamic transcriptome microarray analysis of an elite Chinese bread wheat cultivar (Jimai 20 during grain development using the GeneChip Wheat Genome Array. Grain morphology and scanning electron microscope observations showed that the period of 11–15 days post-anthesis (DPA was a key stage for the synthesis and accumulation of seed starch. Genome-wide transcriptional profiling and significance analysis of microarrays revealed that the period from 11 to 15 DPA was more important than the 15–20 DPA stage for the synthesis and accumulation of nutritive reserves. Series test of cluster analysis of differential genes revealed five statistically significant gene expression profiles. Gene ontology annotation and enrichment analysis gave further information about differentially expressed genes, and MapMan analysis revealed expression changes within functional groups during seed development. Metabolic pathway network analysis showed that major and minor metabolic pathways regulate one another to ensure regular seed development and nutritive reserve accumulation. We performed gene co-expression network analysis to identify genes that play vital roles in seed development and identified several key genes involved in important metabolic pathways. The transcriptional expression of eight key genes involved in starch and protein synthesis and stress defense was further validated by qRT-PCR. Our results provide new insight into the molecular mechanisms of wheat seed development and the determinants of yield and quality.

  19. Cep57 is a Mis12-interacting kinetochore protein involved in kinetochore targeting of Mad1–Mad2

    Science.gov (United States)

    Zhou, Haining; Wang, Tianning; Zheng, Tao; Teng, Junlin; Chen, Jianguo

    2016-01-01

    The spindle assembly checkpoint (SAC) arrests cells in mitosis by sensing unattached kinetochores, until all chromosomes are bi-oriented by spindle microtubules. Kinetochore accumulation of the SAC component Mad1–Mad2 is crucial for SAC activation. However, the mechanism by which Mad1–Mad2 accumulation at kinetochores is regulated is not clear. Here we find that Cep57 is localized to kinetochores in human cells, and binds to Mis12, a KMN (KNL1/Mis12 complex/Ndc80 complex) network component. Cep57 also interacts with Mad1, and depletion of Cep57 results in decreased kinetochore localization of Mad1–Mad2, reduced SAC signalling and increased chromosome segregation errors. We also show that the microtubule-binding activity of Cep57 is involved in the timely removal of Mad1 from kinetochores. Thus, these findings reveal that the KMN network-binding protein Cep57 is a mitotic kinetochore component, and demonstrate the functional connection between the KMN network and the SAC. PMID:26743940

  20. Circular Dichroism for the Analysis of Protein-DNA Interactions.

    Science.gov (United States)

    Scarlett, Garry; Siligardi, Giuliano; Kneale, Geoffrey G

    2015-01-01

    The aim of this chapter is to provide information on the practical aspects of circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) in protein-nucleic acids interaction solution studies. The chapter will describe the guidelines appropriate to designing experiments and conducting correct data interpretation, the use of both benchtop and synchrotron CD approaches is discussed and the advantages of SRCD outlined. Further information and a good general review of the field a can be found in Gray (Circular Dichroism of protein-nucleic acid interactions. In: Fasman GD (ed) Circular dichroism and the conformational analysis of biomolecules. Plenum Press, New York. pp 469-500, 1996).

  1. Biospecific protein immobilization for rapid analysis of weak protein interactions using self-interaction nanoparticle spectroscopy.

    Science.gov (United States)

    Bengali, Aditya N; Tessier, Peter M

    2009-10-01

    "Reversible" protein interactions govern diverse biological behavior ranging from intracellular transport and toxic protein aggregation to protein crystallization and inactivation of protein therapeutics. Much less is known about weak protein interactions than their stronger counterparts since they are difficult to characterize, especially in a parallel format (in contrast to a sequential format) necessary for high-throughput screening. We have recently introduced a highly efficient approach of characterizing protein self-association, namely self-interaction nanoparticle spectroscopy (SINS; Tessier et al., 2008; J Am Chem Soc 130:3106-3112). This approach exploits the separation-dependent optical properties of gold nanoparticles to detect weak self-interactions between proteins immobilized on nanoparticles. A limitation of our previous work is that differences in the sequence and structure of proteins can lead to significant differences in their affinity to adsorb to nanoparticle surfaces, which complicates analysis of the corresponding protein self-association behavior. In this work we demonstrate a highly specific approach for coating nanoparticles with proteins using biotin-avidin interactions to generate protein-nanoparticle conjugates that report protein self-interactions through changes in their optical properties. Using lysozyme as a model protein that is refractory to characterization by conventional SINS, we demonstrate that surface Plasmon wavelengths for gold-avidin-lysozyme conjugates over a range of solution conditions (i.e., pH and ionic strength) are well correlated with lysozyme osmotic second virial coefficient measurements. Since SINS requires orders of magnitude less protein and time than conventional methods (e.g., static light scattering), we envision this approach will find application in large screens of protein self-association aimed at either preventing (e.g., protein aggregation) or promoting (e.g., protein crystallization) these

  2. An in silico analysis of the key genes involved in flavonoid biosynthesis in Citrus sinensis

    Directory of Open Access Journals (Sweden)

    Adriano R. Lucheta

    2007-01-01

    Full Text Available Citrus species are known by their high content of phenolic compounds, including a wide range of flavonoids. In plants, these compounds are involved in protection against biotic and abiotic stresses, cell structure, UV protection, attraction of pollinators and seed dispersal. In humans, flavonoid consumption has been related to increasing overall health and fighting some important diseases. The goals of this study were to identify expressed sequence tags (EST in Citrus sinensis (L. Osbeck corresponding to genes involved in general phenylpropanoid biosynthesis and the key genes involved in the main flavonoids pathways (flavanones, flavones, flavonols, leucoanthocyanidins, anthocyanins and isoflavonoids. A thorough analysis of all related putative genes from the Citrus EST (CitEST database revealed several interesting aspects associated to these pathways and brought novel information with promising usefulness for both basic and biotechnological applications.

  3. EST analysis of Prorocentrum donghaiense with emphasis on genes involved in PCD

    Institute of Scientific and Technical Information of China (English)

    Zhang Xiufang; Liu Yongjian; Yang Guanpin; Zhu Mingyuan; Li Ruixiang

    2009-01-01

    Prorocentrum donghaiense has caused large-scale red tides off the Chinese coast in recent years. Expressed sequence tag (EST) analysis was carried out for this dinoflagellate in order to identify the functional genes involved in its biological processes. A cDNA library was constructed for P. donghaiense at exponential growth phase, and 565 usable sequencing reads were obtained from 700 clones selected randomly. Messenger RNA corresponding reads were clustered into 36 contigs and 272 singletons (EST groups). Twenty-two EST groups were found to tag the genes involved in diverse biological processes including programmed cell death (PCD). Two EST groups showed significant homologies with the encoding genes of cysteine protease (caspase) and proliferating cell nuclear antigen, respectively, two key proteins involved in PCD.

  4. Dynamical analysis of yeast protein interaction network during the sake brewing process.

    Science.gov (United States)

    Mirzarezaee, Mitra; Sadeghi, Mehdi; Araabi, Babak N

    2011-12-01

    Proteins interact with each other for performing essential functions of an organism. They change partners to get involved in various processes at different times or locations. Studying variations of protein interactions within a specific process would help better understand the dynamic features of the protein interactions and their functions. We studied the protein interaction network of Saccharomyces cerevisiae (yeast) during the brewing of Japanese sake. In this process, yeast cells are exposed to several stresses. Analysis of protein interaction networks of yeast during this process helps to understand how protein interactions of yeast change during the sake brewing process. We used gene expression profiles of yeast cells for this purpose. Results of our experiments revealed some characteristics and behaviors of yeast hubs and non-hubs and their dynamical changes during the brewing process. We found that just a small portion of the proteins (12.8 to 21.6%) is responsible for the functional changes of the proteins in the sake brewing process. The changes in the number of edges and hubs of the yeast protein interaction networks increase in the first stages of the process and it then decreases at the final stages.

  5. Analysis of Patterns of Interaction and Knowledge Construction in On-Line Learning Environments: A Methodological Strategy

    Directory of Open Access Journals (Sweden)

    Benilde García Cabrero

    2008-05-01

    Full Text Available A model of analysis of interaction and construction of knowledge in educational environments based on computer-mediated communication (CMC is proposed. This proposal considers: 1 the contextual factors that constitute the input and the scenario of interaction, 2 the interaction processes: types of interaction and its contents (Garrison, Anderson and Archer, 2000 as well as the discursive strategies (Lemke, 1997, and 3 learning results that involve the quality of the knowledge constructed by the participants (Gunawardena, Lowe and Anderson, 1997. This model was applied to the analysis of the interaction among a group of participants in two web forums (with or without the presence of a teacher, during the teaching of a PhD in Psychology program. The results show evidence of the model’s viability to describe the patterns of interaction and the levels of construction of knowledge in web forums.

  6. Transcriptomic analysis of the interactions between Agaricus bisporus and Lecanicillium fungicola.

    Science.gov (United States)

    Bailey, Andy M; Collopy, Patrick D; Thomas, D John; Sergeant, Martin R; Costa, Ana M S B; Barker, Gary L A; Mills, Peter R; Challen, Michael P; Foster, Gary D

    2013-06-01

    Agaricus bisporus is susceptible to a number of diseases, particularly those caused by fungi, with Lecanicillium fungicola being the most serious. Control of this disease is important for the security of crop production, however given the lack of knowledge about fungal-fungal interactions, such disease control is rather limited. Exploiting the recently released genome sequence of A. bisporus, here we report studies simultaneously investigating both the host and the pathogen, focussing on transcriptional changes associated with the cap spotting lesions typically seen in this interaction. Forward-suppressive subtractive hybridisation (SSH) analysis identified 68 A. bisporus unigenes induced during infection. Chitin deacetylase showed the strongest response, with almost 1000-fold up-regulation during infection, so was targeted for down-regulation by silencing to see if it was involved in defence against L. fungicola. Transgenic lines were made expressing hairpin RNAi constructs, however no changes in susceptibility to L. fungicola were observed. Amongst the other up-regulated genes there were none with readily apparent roles in resisting infection in this susceptible interaction. Reverse-SSH identified 72 unigenes from A. bisporus showing reduced expression, including two tyrosinases, several genes involved in nitrogen metabolism and a hydrophobin. The forward-SSH analysis of infected mushrooms also yielded 64 unigenes which were not of A. bisporus origin and thus derived from L. fungicola. An EST analysis of infection-mimicking conditions generated an additional 623 unigenes from L. fungicola including several oxidoreductases, cell wall degrading enzymes, ABC and MFS transporter proteins and various other genes believed to play roles in other pathosystems. Together, this analysis shows how both the pathogen and the host modify their gene expression during an infection-interaction, shedding some light on the disease process, although we note that some 40% of unigenes

  7. Social network extraction and analysis based on multimodal dyadic interaction.

    Science.gov (United States)

    Escalera, Sergio; Baró, Xavier; Vitrià, Jordi; Radeva, Petia; Raducanu, Bogdan

    2012-01-01

    Social interactions are a very important component in people's lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times' Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links' weights are a measure of the "influence" a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network.

  8. Social Network Extraction and Analysis Based on Multimodal Dyadic Interaction

    Directory of Open Access Journals (Sweden)

    Bogdan Raducanu

    2012-02-01

    Full Text Available Social interactions are a very important component in people’s lives. Social network analysis has become a common technique used to model and quantify the properties of social interactions. In this paper, we propose an integrated framework to explore the characteristics of a social network extracted from multimodal dyadic interactions. For our study, we used a set of videos belonging to New York Times’ Blogging Heads opinion blog. The Social Network is represented as an oriented graph, whose directed links are determined by the Influence Model. The links’ weights are a measure of the “influence” a person has over the other. The states of the Influence Model encode automatically extracted audio/visual features from our videos using state-of-the art algorithms. Our results are reported in terms of accuracy of audio/visual data fusion for speaker segmentation and centrality measures used to characterize the extracted social network.

  9. Review of Treating chronic depression with disciplined personal involvement: Cognitive behavioral analysis system of psychotherapy (CBASP).

    Science.gov (United States)

    Hellerstein, David J

    2008-09-01

    Reviews the book, Treating chronic depression with disciplined personal involvement: Cognitive behavioral analysis system of psychotherapy (CBASP) by James P. McCullough Jr. (see record 2006-11486-000). The premise of this book is that therapeutic neutrality does not apply to the psychotherapy of chronically depressed individuals, and that disciplined personal involvement is an efficacious and perhaps necessary component of their treatment. Cognitive behavioral analysis system of psychotherapy (CBASP) is a learning model, in which the therapist focuses on teaching patients to recognize the consequences of their behavior. McCullough addresses practical and theoretical objections to this therapeutic approach, which include fears of overinvolvement, and inappropriate behavior, and clinical risks of flooding patients with excessively personal information and content. Ultimately, most readers will finish reading this volume with many open questions, some specific to McCullough's approach, others related to the challenging condition of chronic depression itself. (PsycINFO Database Record (c) 2010 APA, all rights reserved).

  10. Molecular change signal-to-noise criteria for interpreting experiments involving exposure of biological systems to weakly interacting electromagnetic fields.

    Science.gov (United States)

    Vaughan, Timothy E; Weaver, James C

    2005-05-01

    We describe an approach to aiding the design and interpretation of experiments involving biological effects of weakly interacting electromagnetic fields that range from steady (dc) to microwave frequencies. We propose that if known biophysical mechanisms cannot account for an inferred, underlying molecular change signal-to-noise ratio, (S/N)gen, of a observed result, then there are two interpretation choices: (1) there is an unknown biophysical mechanism with stronger coupling between the field exposure and the ongoing biochemical process, or (2) the experiment is responding to something other than the field exposure. Our approach is based on classical detection theory, the recognition that weakly interacting fields cannot break chemical bonds, and the consequence that such fields can only alter rates of ongoing, metabolically driven biochemical reactions, and transport processes. The approach includes both fundamental chemical noise (molecular shot noise) and other sources of competing chemical change, to be compared quantitatively to the field induced change for the basic case that the field alters a single step in a biochemical network. Consistent with pharmacology and toxicology, we estimate the molecular dose (mass associated with field induced molecular change per mass tissue) resulting from illustrative low frequency field exposures for the biophysical mechanism of voltage gated channels. For perspective, we then consider electric field-mediated delivery of small molecules across human skin and into individual cells. Specifically, we consider the examples of iontophoretic and electroporative delivery of fentanyl through skin and electroporative delivery of bleomycin into individual cells. The total delivered amount corresponds to a molecular change signal and the delivery variability corresponds to generalized chemical noise. Viewed broadly, biological effects due to nonionizing fields may include animal navigation, medical applications, and environmental

  11. A Physics-driven Neural Networks-based Simulation System (PhyNNeSS) for multimodal interactive virtual environments involving nonlinear deformable objects.

    Science.gov (United States)

    De, Suvranu; Deo, Dhannanjay; Sankaranarayanan, Ganesh; Arikatla, Venkata S

    2011-08-01

    BACKGROUND: While an update rate of 30 Hz is considered adequate for real time graphics, a much higher update rate of about 1 kHz is necessary for haptics. Physics-based modeling of deformable objects, especially when large nonlinear deformations and complex nonlinear material properties are involved, at these very high rates is one of the most challenging tasks in the development of real time simulation systems. While some specialized solutions exist, there is no general solution for arbitrary nonlinearities. METHODS: In this work we present PhyNNeSS - a Physics-driven Neural Networks-based Simulation System - to address this long-standing technical challenge. The first step is an off-line pre-computation step in which a database is generated by applying carefully prescribed displacements to each node of the finite element models of the deformable objects. In the next step, the data is condensed into a set of coefficients describing neurons of a Radial Basis Function network (RBFN). During real-time computation, these neural networks are used to reconstruct the deformation fields as well as the interaction forces. RESULTS: We present realistic simulation examples from interactive surgical simulation with real time force feedback. As an example, we have developed a deformable human stomach model and a Penrose-drain model used in the Fundamentals of Laparoscopic Surgery (FLS) training tool box. CONCLUSIONS: A unique computational modeling system has been developed that is capable of simulating the response of nonlinear deformable objects in real time. The method distinguishes itself from previous efforts in that a systematic physics-based pre-computational step allows training of neural networks which may be used in real time simulations. We show, through careful error analysis, that the scheme is scalable, with the accuracy being controlled by the number of neurons used in the simulation. PhyNNeSS has been integrated into SoFMIS (Software Framework for Multimodal

  12. Analysis on liquid metal corrosion-oxidation interactions

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Jinsuo [International and Nuclear System Engineering, MS K-575, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)], E-mail: jszhang@lanl.gov; Li Ning [International and Nuclear System Engineering, MS K-575, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

    2007-11-15

    The interaction between growing surface oxides and flowing liquid metals is of importance in many high temperature applications such as coolant systems using liquid lead or lead bismuth eutectic (LBE) in advanced nuclear energy systems. The impact of flow can manifest through particle erosion, mass transfer corrosion, stress scrape, etc. In the present study, we consider the continuous flow-induced corrosion by dissolution of steel components or dissociation of surface oxides. In oxygen controlled liquid lead or LBE systems, steels exposed to the liquid metals are subject to both oxidation and flow-induced corrosion. It is necessary and important to understand the corrosion-oxidation interactions for selecting structural materials and optimizing operating conditions. A comprehensive theoretical analysis of the key corrosion-oxidation interactions is presented here. Possible corrosion-oxidation mechanisms are considered and the corrosion-oxidation interactions are classified into different regimes. In each regime, a theoretical model is given. Based on the analysis, corrosion-oxidation maps are developed for selecting and optimizing the operation conditions for liquid lead-alloy systems.

  13. Stability and modal analysis of shock/boundary layer interactions

    Science.gov (United States)

    Nichols, Joseph W.; Larsson, Johan; Bernardini, Matteo; Pirozzoli, Sergio

    2016-06-01

    The dynamics of oblique shock wave/turbulent boundary layer interactions is analyzed by mining a large-eddy simulation (LES) database for various strengths of the incoming shock. The flow dynamics is first analyzed by means of dynamic mode decomposition (DMD), which highlights the simultaneous occurrence of two types of flow modes, namely a low-frequency type associated with breathing motion of the separation bubble, accompanied by flapping motion of the reflected shock, and a high-frequency type associated with the propagation of instability waves past the interaction zone. Global linear stability analysis performed on the mean LES flow fields yields a single unstable zero-frequency mode, plus a variety of marginally stable low-frequency modes whose stability margin decreases with the strength of the interaction. The least stable linear modes are grouped into two classes, one of which bears striking resemblance to the breathing mode recovered from DMD and another class associated with revolving motion within the separation bubble. The results of the modal and linear stability analysis support the notion that low-frequency dynamics is intrinsic to the interaction zone, but some continuous forcing from the upstream boundary layer may be required to keep the system near a limit cycle. This can be modeled as a weakly damped oscillator with forcing, as in the early empirical model by Plotkin (AIAA J 13:1036-1040, 1975).

  14. Interaction Analysis of a Two-Component System Using Nanodiscs.

    Directory of Open Access Journals (Sweden)

    Patrick Hörnschemeyer

    Full Text Available Two-component systems are the major means by which bacteria couple adaptation to environmental changes. All utilize a phosphorylation cascade from a histidine kinase to a response regulator, and some also employ an accessory protein. The system-wide signaling fidelity of two-component systems is based on preferential binding between the signaling proteins. However, information on the interaction kinetics between membrane embedded histidine kinase and its partner proteins is lacking. Here, we report the first analysis of the interactions between the full-length membrane-bound histidine kinase CpxA, which was reconstituted in nanodiscs, and its cognate response regulator CpxR and accessory protein CpxP. Using surface plasmon resonance spectroscopy in combination with interaction map analysis, the affinity of membrane-embedded CpxA for CpxR was quantified, and found to increase by tenfold in the presence of ATP, suggesting that a considerable portion of phosphorylated CpxR might be stably associated with CpxA in vivo. Using microscale thermophoresis, the affinity between CpxA in nanodiscs and CpxP was determined to be substantially lower than that between CpxA and CpxR. Taken together, the quantitative interaction data extend our understanding of the signal transduction mechanism used by two-component systems.

  15. Stability and modal analysis of shock/boundary layer interactions

    Science.gov (United States)

    Nichols, Joseph W.; Larsson, Johan; Bernardini, Matteo; Pirozzoli, Sergio

    2017-02-01

    The dynamics of oblique shock wave/turbulent boundary layer interactions is analyzed by mining a large-eddy simulation (LES) database for various strengths of the incoming shock. The flow dynamics is first analyzed by means of dynamic mode decomposition (DMD), which highlights the simultaneous occurrence of two types of flow modes, namely a low-frequency type associated with breathing motion of the separation bubble, accompanied by flapping motion of the reflected shock, and a high-frequency type associated with the propagation of instability waves past the interaction zone. Global linear stability analysis performed on the mean LES flow fields yields a single unstable zero-frequency mode, plus a variety of marginally stable low-frequency modes whose stability margin decreases with the strength of the interaction. The least stable linear modes are grouped into two classes, one of which bears striking resemblance to the breathing mode recovered from DMD and another class associated with revolving motion within the separation bubble. The results of the modal and linear stability analysis support the notion that low-frequency dynamics is intrinsic to the interaction zone, but some continuous forcing from the upstream boundary layer may be required to keep the system near a limit cycle. This can be modeled as a weakly damped oscillator with forcing, as in the early empirical model by Plotkin (AIAA J 13:1036-1040, 1975).

  16. Visual exploration and analysis of human-robot interaction rules

    Science.gov (United States)

    Zhang, Hui; Boyles, Michael J.

    2013-01-01

    We present a novel interaction paradigm for the visual exploration, manipulation and analysis of human-robot interaction (HRI) rules; our development is implemented using a visual programming interface and exploits key techniques drawn from both information visualization and visual data mining to facilitate the interaction design and knowledge discovery process. HRI is often concerned with manipulations of multi-modal signals, events, and commands that form various kinds of interaction rules. Depicting, manipulating and sharing such design-level information is a compelling challenge. Furthermore, the closed loop between HRI programming and knowledge discovery from empirical data is a relatively long cycle. This, in turn, makes design-level verification nearly impossible to perform in an earlier phase. In our work, we exploit a drag-and-drop user interface and visual languages to support depicting responsive behaviors from social participants when they interact with their partners. For our principal test case of gaze-contingent HRI interfaces, this permits us to program and debug the robots' responsive behaviors through a graphical data-flow chart editor. We exploit additional program manipulation interfaces to provide still further improvement to our programming experience: by simulating the interaction dynamics between a human and a robot behavior model, we allow the researchers to generate, trace and study the perception-action dynamics with a social interaction simulation to verify and refine their designs. Finally, we extend our visual manipulation environment with a visual data-mining tool that allows the user to investigate interesting phenomena such as joint attention and sequential behavioral patterns from multiple multi-modal data streams. We have created instances of HRI interfaces to evaluate and refine our development paradigm. As far as we are aware, this paper reports the first program manipulation paradigm that integrates visual programming

  17. Interacting Ghost Dark Energy Model: Dynamical System Analysis

    CERN Document Server

    Golchin, Hanif; Ebrahimi, Esmaeil

    2016-01-01

    We study the impacts of interaction between dark matter and dark energy in the context of ghost dark energy model. Using the dynamical system analysis, we obtain the fixed points of the system for different types of interactions while the universe is filled with radiation, matter (including dark matter and luminous matter) and dark energy components. We consider the stability of the fixed points in details for different cases. In all cases there is an unstable matter dominated epoch and a stable late time dark energy dominated phase. However, we find that adding the linear interaction, the evolution of ghost dark energy model does not contain the radiation dominated epoch in the early times which is a necessary point in any cosmic model. This failure resolved when we add the non-linear interaction to the model. We also find an upper bound for the value of the coupling constant of the interaction between dark matter and dark energy as b < 0.57 . This bound is necessary to have a decelerating and unstable ma...

  18. Nexus analysis and interaction in healthcare educational practices

    DEFF Research Database (Denmark)

    Kjær, Malene

    practice. Thus a thorough insight into the field is necessary in order to change it. Using nexus analysis (Scollon & Scollon, 2004, 2007) as an ethnographic framework a study of the development of a professional identity among student nurses in Denmark was conducted. Scollon and Scollon’s notions...... on 'navigate' and 'engage' in the field provided a frame to combine both discourse (Edley, 2014) document (Prior, 2003) and interaction analysis (Jordan & Henderson, 1995; Sacks, 1992) in order to grasp the crucial social actors (nurses, students, patients, relatives) and their daily routinized practice....... The paper shows how a combination of (video) observations, written interviews and workshops can be a way to obtain knowledge about the practice that consists of members generalizations, neutral observations, individual experiences and interaction with members (Scollon & Scollon 2004, p. 158)...

  19. Analysis of linear and nonlinear genotype × environment interaction

    Directory of Open Access Journals (Sweden)

    Rong-Cai eYang

    2014-07-01

    Full Text Available The usual analysis of genotype × environment interaction (GxE is based on the linear regression of genotypic performance on environmental changes (e.g., classic stability analysis. This linear model may often lead to lumping together of the nonlinear responses to the whole range of environmental changes from suboptimal and superoptimal conditions, thereby lowering the power of detecting GxE variation. On the other hand, the GxE is present when the magnitude of the genetic effect differs across the range of environmental conditions regardless of whether the response to environmental changes is linear or nonlinear. The objectives of this study are: (i explore the use of four commonly used nonlinear functions (logistic, parabola, normal and Cauchy functions for modeling nonlinear genotypic responses to environmental changes and (ii to investigate the difference in the magnitude of estimated genetic effects under different environmental conditions. The use of nonlinear functions was illustrated through the analysis of one data set taken from barley cultivar trials in Alberta, Canada (Data A and the examination of change in effect sizes is through the analysis another data set taken from the North America Barley Genome Mapping Project (Data B. The analysis of Data A showed that the Cauchy function captured an average of >40% of total GxE variation whereas the logistic function captured less GxE variation than the linear function. The analysis of Data B showed that genotypic responses were largely linear and that strong QTL × environment interaction existed as the positions, sizes and directions of QTL detected differed in poor vs. good environments. We conclude that (i the nonlinear functions should be considered when analyzing multi-environmental trials with a wide range of environmental variation and (ii QTL × environment interaction can arise from the difference in effect sizes across environments.

  20. Physiologically Based Pharmacokinetic Modeling to Predict Drug-Drug Interactions with Efavirenz Involving Simultaneous Inducing and Inhibitory Effects on Cytochromes.

    Science.gov (United States)

    Marzolini, Catia; Rajoli, Rajith; Battegay, Manuel; Elzi, Luigia; Back, David; Siccardi, Marco

    2017-04-01

    Antiretroviral drugs are among the therapeutic agents with the highest potential for drug-drug interactions (DDIs). In the absence of clinical data, DDIs are mainly predicted based on preclinical data and knowledge of the disposition of individual drugs. Predictions can be challenging, especially when antiretroviral drugs induce and inhibit multiple cytochrome P450 (CYP) isoenzymes simultaneously. This study predicted the magnitude of the DDI between efavirenz, an inducer of CYP3A4 and inhibitor of CYP2C8, and dual CYP3A4/CYP2C8 substrates (repaglinide, montelukast, pioglitazone, paclitaxel) using a physiologically based pharmacokinetic (PBPK) modeling approach integrating concurrent effects on CYPs. In vitro data describing the physicochemical properties, absorption, distribution, metabolism, and elimination of efavirenz and CYP3A4/CYP2C8 substrates as well as the CYP-inducing and -inhibitory potential of efavirenz were obtained from published literature. The data were integrated in a PBPK model developed using mathematical descriptions of molecular, physiological, and anatomical processes defining pharmacokinetics. Plasma drug-concentration profiles were simulated at steady state in virtual individuals for each drug given alone or in combination with efavirenz. The simulated pharmacokinetic parameters of drugs given alone were compared against existing clinical data. The effect of efavirenz on CYP was compared with published DDI data. The predictions indicate that the overall effect of efavirenz on dual CYP3A4/CYP2C8 substrates is induction of metabolism. The magnitude of induction tends to be less pronounced for dual CYP3A4/CYP2C8 substrates with predominant CYP2C8 metabolism. PBPK modeling constitutes a useful mechanistic approach for the quantitative prediction of DDI involving simultaneous inducing or inhibitory effects on multiple CYPs as often encountered with antiretroviral drugs.

  1. Graph spectral analysis of protein interaction network evolution

    OpenAIRE

    Thorne, Thomas; Stumpf, Michael P. H.

    2012-01-01

    We present an analysis of protein interaction network data via the comparison of models of network evolution to the observed data. We take a Bayesian approach and perform posterior density estimation using an approximate Bayesian computation with sequential Monte Carlo method. Our approach allows us to perform model selection over a selection of potential network growth models. The methodology we apply uses a distance defined in terms of graph spectra which captures the network data more natu...

  2. Analysis of protein interactions at native chloroplast membranes by ellipsometry.

    Directory of Open Access Journals (Sweden)

    Verena Kriechbaumer

    Full Text Available Membrane bound receptors play vital roles in cell signaling, and are the target for many drugs, yet their interactions with ligands are difficult to study by conventional techniques due to the technical difficulty of monitoring these interactions in lipid environments. In particular, the ability to analyse the behaviour of membrane proteins in their native membrane environment is limited. Here, we have developed a quantitative approach to detect specific interactions between low-abundance chaperone receptors within native chloroplast membranes and their soluble chaperone partners. Langmuir-Schaefer film deposition was used to deposit native chloroplasts onto gold-coated glass slides, and interactions between the molecular chaperones Hsp70 and Hsp90 and their receptors in the chloroplast membranes were detected and quantified by total internal reflection ellipsometry (TIRE. We show that native chloroplast membranes deposited on gold-coated glass slides using Langmuir-Schaefer films retain functional receptors capable of binding chaperones with high specificity and affinity. Taking into account the low chaperone receptor abundance in native membranes, these binding properties are consistent with data generated using soluble forms of the chloroplast chaperone receptors, OEP61 and Toc64. Therefore, we conclude that chloroplasts have the capacity to selectively bind chaperones, consistent with the notion that chaperones play an important role in protein targeting to chloroplasts. Importantly, this method of monitoring by TIRE does not require any protein labelling. This novel combination of techniques should be applicable to a wide variety of membranes and membrane protein receptors, thus presenting the opportunity to quantify protein interactions involved in fundamental cellular processes, and to screen for drugs that target membrane proteins.

  3. A Multimodal Data Analysis Approach for Targeted Drug Discovery Involving Topological Data Analysis (TDA).

    Science.gov (United States)

    Alagappan, Muthuraman; Jiang, Dadi; Denko, Nicholas; Koong, Albert C

    2016-01-01

    In silico drug discovery refers to a combination of computational techniques that augment our ability to discover drug compounds from compound libraries. Many such techniques exist, including virtual high-throughput screening (vHTS), high-throughput screening (HTS), and mechanisms for data storage and querying. However, presently these tools are often used independent of one another. In this chapter, we describe a new multimodal in silico technique for the hit identification and lead generation phases of traditional drug discovery. Our technique leverages the benefits of three independent methods-virtual high-throughput screening, high-throughput screening, and structural fingerprint analysis-by using a fourth technique called topological data analysis (TDA). We describe how a compound library can be independently tested with vHTS, HTS, and fingerprint analysis, and how the results can be transformed into a topological data analysis network to identify compounds from a diverse group of structural families. This process of using TDA or similar clustering methods to identify drug leads is advantageous because it provides a mechanism for choosing structurally diverse compounds while maintaining the unique advantages of already established techniques such as vHTS and HTS.

  4. Deformed Gaussian Orthogonal Ensemble Analysis of the Interacting Boson Model

    CERN Document Server

    Pato, M P; Lima, C L; Hussein, M S; Alhassid, Y

    1994-01-01

    A Deformed Gaussian Orthogonal Ensemble (DGOE) which interpolates between the Gaussian Orthogonal Ensemble and a Poissonian Ensemble is constructed. This new ensemble is then applied to the analysis of the chaotic properties of the low lying collective states of nuclei described by the Interacting Boson Model (IBM). This model undergoes a transition order-chaos-order from the $SU(3)$ limit to the $O(6)$ limit. Our analysis shows that the quantum fluctuations of the IBM Hamiltonian, both of the spectrum and the eigenvectors, follow the expected behaviour predicted by the DGOE when one goes from one limit to the other.

  5. Structural mode significance using INCA. [Interactive Controls Analysis computer program

    Science.gov (United States)

    Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

    1990-01-01

    Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

  6. Structural mode significance using INCA. [Interactive Controls Analysis computer program

    Science.gov (United States)

    Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

    1990-01-01

    Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

  7. Data Analysis through a Generalized Interactive Computer Animation Method (DATICAM)

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, J.N.; Schweider, D.H.

    1983-01-01

    DATICAM is an interactive computer animation method designed to aid in the analysis of nuclear research data. DATICAM was developed at the Idaho National Engineering Laboratory (INEL) by EG and G Idaho, Inc. INEL analysts use DATICAM to produce computer codes that are better able to predict the behavior of nuclear power reactors. In addition to increased code accuracy, DATICAM has saved manpower and computer costs. DATICAM has been generalized to assist in the data analysis of virtually any data-producing dynamic process.

  8. Data analysis through interactive computer animation method (DATICAM)

    Energy Technology Data Exchange (ETDEWEB)

    Curtis, J.N.; Schwieder, D.H.

    1983-01-01

    DATICAM is an interactive computer animation method designed to aid in the analysis of nuclear research data. DATICAM was developed at the Idaho National Engineering Laboratory (INEL) by EG and G Idaho, Inc. INEL analysts use DATICAM to produce computer codes that are better able to predict the behavior of nuclear power reactors. In addition to increased code accuracy, DATICAM has saved manpower and computer costs. DATICAM has been generalized to assist in the data analysis of virtually any data-producing dynamic process.

  9. Interactive Safety Analysis Framework of Autonomous Intelligent Vehicles

    Directory of Open Access Journals (Sweden)

    Cui You Xiang

    2016-01-01

    Full Text Available More than 100,000 people were killed and around 2.6 million injured in road accidents in the People’s Republic of China (PRC, that is four to eight times that of developed countries, equivalent to 6.2 mortality per 10 thousand vehicles—the highest rate in the world. There are more than 1,700 fatalities and 840,000 injuries yearly due to vehicle crashes off public highways. In this paper, we proposed a interactive safety situation and threat analysis framework based on driver behaviour and vehicle dynamics risk analysis based on ISO26262…

  10. Analysis of the interaction of participants freight forwarding system

    Directory of Open Access Journals (Sweden)

    Pavlo Popovych

    2016-12-01

    Full Text Available Main goal of this work is the analysis of the interaction of participants of freight forwarding activities. Research methods included analysis of scientific literature, theory of systems and systems analysis, methods of induction and deduction. As sources of information used and applied work of fundamental importance known foreign and local scientists and regulatory and legislative documents of Ukraine for the state transport policy. In the article the basic interactions of participants of freight forwarding activities. Classified components freight forwarding services. Assign the concept freight forwarding system and its aim. Established element and forms of cooperation in the freight forwarding system. The main task of forwarding companies are organizing, coordinating and ensuring the delivery from shipper to consignee. Freight forwarding company responsible for the timely delivery of the goods on the condition of preservation of the quantity and quality specified time conditions. Currently used methods are uneffective decision-making, leading to losses. These circumstances require improvement methodology management of freight forwarding companies. This is possible only using modern mathematical methods and information technologies that will improve the operation of freight forwarding companies. The article presents a theoretical exposition of the basic processes of interaction between participants in freight forwarding system. The article may be of interest to specialists of freight forwarding companies.

  11. Probability and sensitivity analysis of machine foundation and soil interaction

    Directory of Open Access Journals (Sweden)

    Králik J., jr.

    2009-06-01

    Full Text Available This paper deals with the possibility of the sensitivity and probabilistic analysis of the reliability of the machine foundation depending on variability of the soil stiffness, structure geometry and compressor operation. The requirements to design of the foundation under rotating machines increased due to development of calculation method and computer tools. During the structural design process, an engineer has to consider problems of the soil-foundation and foundation-machine interaction from the safety, reliability and durability of structure point of view. The advantages and disadvantages of the deterministic and probabilistic analysis of the machine foundation resistance are discussed. The sensitivity of the machine foundation to the uncertainties of the soil properties due to longtime rotating movement of machine is not negligible for design engineers. On the example of compressor foundation and turbine fy. SIEMENS AG the affectivity of the probabilistic design methodology was presented. The Latin Hypercube Sampling (LHS simulation method for the analysis of the compressor foundation reliability was used on program ANSYS. The 200 simulations for five load cases were calculated in the real time on PC. The probabilistic analysis gives us more complex information about the soil-foundation-machine interaction as the deterministic analysis.

  12. Genotype-Based Bayesian Analysis of Gene-Environment Interactions with Multiple Genetic Markers and Misclassification in Environmental Factors

    OpenAIRE

    Iryna Lobach; Ruzong Fan

    2012-01-01

    A key component to understanding etiology of complex diseases, such as cancer, diabetes, alcohol dependence, is to investigate gene-environment interactions. This work is motivated by the following two concerns in the analysis of gene-environment interactions. First, multiple genetic markers in moderate linkage disequilibrium may be involved in susceptibility to a complex disease. Second, environmental factors may be subject to misclassification. We develop a genotype based Bayesian pseudolik...

  13. Genome-wide interaction-based association analysis identified multiple new susceptibility Loci for common diseases.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2011-03-01

    Full Text Available Genome-wide interaction-based association (GWIBA analysis has the potential to identify novel susceptibility loci. These interaction effects could be missed with the prevailing approaches in genome-wide association studies (GWAS. However, no convincing loci have been discovered exclusively from GWIBA methods, and the intensive computation involved is a major barrier for application. Here, we developed a fast, multi-thread/parallel program named "pair-wise interaction-based association mapping" (PIAM for exhaustive two-locus searches. With this program, we performed a complete GWIBA analysis on seven diseases with stringent control for false positives, and we validated the results for three of these diseases. We identified one pair-wise interaction between a previously identified locus, C1orf106, and one new locus, TEC, that was specific for Crohn's disease, with a Bonferroni corrected P < 0.05 (P = 0.039. This interaction was replicated with a pair of proxy linked loci (P = 0.013 on an independent dataset. Five other interactions had corrected P < 0.5. We identified the allelic effect of a locus close to SLC7A13 for coronary artery disease. This was replicated with a linked locus on an independent dataset (P = 1.09 × 10⁻⁷. Through a local validation analysis that evaluated association signals, rather than locus-based associations, we found that several other regions showed association/interaction signals with nominal P < 0.05. In conclusion, this study demonstrated that the GWIBA approach was successful for identifying novel loci, and the results provide new insights into the genetic architecture of common diseases. In addition, our PIAM program was capable of handling very large GWAS datasets that are likely to be produced in the future.

  14. Texture analysis of CT images in the characterization of oral cancers involving buccal mucosa

    Science.gov (United States)

    Raja, JV; Khan, M; Ramachandra, VK; Al-Kadi, O

    2012-01-01

    Objective The aim of this study was to investigate the usefulness of texture analysis in the characterization of oral cancers involving the buccal mucosa and to assess its effectiveness in differentiating between the various grades of the tumour. Methods Contrast enhanced CT examination was carried out in 21 patients with carcinoma of the buccal mucosa who had consented to retrospective analysis during a research study that was approved by the institutional review board. Two regions of interest (ROIs) were created, one at the site of the lesion and the other at the contralateral normal side. Texture analysis measures of fractal dimension (FD), lacunarity and grey level co-occurrence matrix (GLCM) were computed for each ROI. The numeric data from the two ROIs were compared and were correlated with the tumour grade as confirmed by biopsy. Results The difference between the mean FD and GLCM parameters of the lesion vs the normal ROI were statistically significant (p 0.05). Conclusion Texture analysis on CT images is a potential method in the characterization of oral cancers involving the buccal mucosa and deserves further investigation as a predictor of tumour aggression. PMID:22241875

  15. Metabonomic analysis of potential biomarkers and drug targets involved in diabetic nephropathy mice.

    Science.gov (United States)

    Wei, Tingting; Zhao, Liangcai; Jia, Jianmin; Xia, Huanhuan; Du, Yao; Lin, Qiuting; Lin, Xiaodong; Ye, Xinjian; Yan, Zhihan; Gao, Hongchang

    2015-07-07

    Diabetic nephropathy (DN) is one of the lethal manifestations of diabetic systemic microvascular disease. Elucidation of characteristic metabolic alterations during diabetic progression is critical to understand its pathogenesis and identify potential biomarkers and drug targets involved in the disease. In this study, (1)H nuclear magnetic resonance ((1)H NMR)-based metabonomics with correlative analysis was performed to study the characteristic metabolites, as well as the related pathways in urine and kidney samples of db/db diabetic mice, compared with age-matched wildtype mice. The time trajectory plot of db/db mice revealed alterations, in an age-dependent manner, in urinary metabolic profiles along with progression of renal damage and dysfunction. Age-dependent and correlated metabolite analysis identified that cis-aconitate and allantoin could serve as biomarkers for the diagnosis of DN. Further correlative analysis revealed that the enzymes dimethylarginine dimethylaminohydrolase (DDAH), guanosine triphosphate cyclohydrolase I (GTPCH I), and 3-hydroxy-3-methylglutaryl-CoA lyase (HMG-CoA lyase) were involved in dimethylamine metabolism, ketogenesis and GTP metabolism pathways, respectively, and could be potential therapeutic targets for DN. Our results highlight that metabonomic analysis can be used as a tool to identify potential biomarkers and novel therapeutic targets to gain a better understanding of the mechanisms underlying the initiation and progression of diseases.

  16. Large-scale screening of transcription factor-promoter interactions in spruce reveals a transcriptional network involved in vascular development.

    Science.gov (United States)

    Duval, Isabelle; Lachance, Denis; Giguère, Isabelle; Bomal, Claude; Morency, Marie-Josée; Pelletier, Gervais; Boyle, Brian; MacKay, John J; Séguin, Armand

    2014-06-01

    This research aimed to investigate the role of diverse transcription factors (TFs) and to delineate gene regulatory networks directly in conifers at a relatively high-throughput level. The approach integrated sequence analyses, transcript profiling, and development of a conifer-specific activation assay. Transcript accumulation profiles of 102 TFs and potential target genes were clustered to identify groups of coordinately expressed genes. Several different patterns of transcript accumulation were observed by profiling in nine different organs and tissues: 27 genes were preferential to secondary xylem both in stems and roots, and other genes were preferential to phelloderm and periderm or were more ubiquitous. A robust system has been established as a screening approach to define which TFs have the ability to regulate a given promoter in planta. Trans-activation or repression effects were observed in 30% of TF-candidate gene promoter combinations. As a proof of concept, phylogenetic analysis and expression and trans-activation data were used to demonstrate that two spruce NAC-domain proteins most likely play key roles in secondary vascular growth as observed in other plant species. This study tested many TFs from diverse families in a conifer tree species, which broadens the knowledge of promoter-TF interactions in wood development and enables comparisons of gene regulatory networks found in angiosperms and gymnosperms.

  17. Metarhizium anisopliae host-pathogen interaction: differential immunoproteomics reveals proteins involved in the infection process of arthropods.

    Science.gov (United States)

    Santi, Lucélia; Silva, Walter O B; Pinto, Antônio F M; Schrank, Augusto; Vainstein, Marilene H

    2010-04-01

    Metarhizium anisopliae is an entomopathogenic fungus well characterized for the biocontrol of a wide range of plagues. Its pathogenicity depends on the secretion of hydrolytic enzymes that degrade the host cuticle. To identify proteins involved in the infection process and in host specify, immunoproteomic analysis was performed using antiserum produced against crude extract of M. anisopliae cultured in the presence of Rhipicephalus (Boophilus) microplus and Dysdercus peruvianus cuticles. Spots detected using antisera produced against M. anisopliae cultured in cuticles and spore surface proteins, but not with antiserum against M. anisopliae cultured in glucose, were identified so as to give insights about the infection process. An MS/MS allowed the identification of proteases, like elastase, trypsin, chymotrypsin, carboxypeptidase and subtilisin (Pr1A, Pr1I and PR1J), chitinases, DNase I and proline-rich protein. Chymotrypsin and Pr1I were inferred as host specific, being recognized in D. peruvianus infection only. This research represents an important contribution to the understanding the adaptation mechanisms of M. anisopliae to different hosts.

  18. Analysis and interpretation of RNA splicing alterations in genes involved in genetic disorders.

    Science.gov (United States)

    Vreeswijk, Maaike P G; van der Klift, Heleen M

    2012-01-01

    Germ line mutations in genes involved in hereditary cancer syndromes, such as BRCA1 and BRCA2 in breast cancer and MSH2, MSH6, MLH1, and PSM2 in hereditary nonpolyposis colorectal cancer (HNPCC, more recently indicated as Lynch syndrome), confer a high risk to develop cancer. Mutation analysis in these genes has resulted in the identification of a large number of sequence variants, of which mutations causing frame shifts and nonsense codons are considered undoubtedly to be pathogenic. Many variants, however, cannot be classified as either disease-causing mutations or neutral variants and are therefore called unclassified variants (UVs). A subset of these variants may have an effect on RNA splicing. Appropriate RNA analysis will enable the characterization of the exact molecular nature of this effect and hence, is essential to determine the clinical relevance of the genomic variant. This chapter describes the design and implementation of RNA analysis as an indispensible tool in today's clinical diagnostic setting.

  19. Interaction and kinetic analysis for coal and biomass co-gasification by TG-FTIR.

    Science.gov (United States)

    Xu, Chaofen; Hu, Song; Xiang, Jun; Zhang, Liqi; Sun, Lushi; Shuai, Chao; Chen, Qindong; He, Limo; Edreis, Elbager M A

    2014-02-01

    This study aims to investigate the interaction and kinetic behavior of CO2 gasification of coal, biomass and their blends by thermogravimetry analysis (TG). The gas products evolved from gasification were measured online with Fourier Transform Infrared Spectroscopy (FTIR) coupled with TG. Firstly, TG experiments indicated that interaction between the coals and biomasses mainly occurred during co-gasification process. The most significant synergistic interaction occurred for LN with SD at the blending mass ratio 4:1. Furthermore, thermal kinetic analysis indicated that the activation energy involved in co-gasification decreased as the SD content increased until the blending ratio of SD with coal reached 4:1. The rise of the frequency factor indicated that the increase of SD content favored their synergistic interaction. Finally, FTIR analysis of co-gasification of SD with LN indicated that except for CO, most gases including CH3COOH, C6H5OH, H2O, etc., were detected at around 50-700°C. Copyright © 2014. Published by Elsevier Ltd.

  20. A Hybrid Artificial Reputation Model Involving Interaction Trust, Witness Information and the Trust Model to Calculate the Trust Value of Service Providers

    Directory of Open Access Journals (Sweden)

    Gurdeep Singh Ransi

    2014-02-01

    Full Text Available Agent interaction in a community, such as the online buyer-seller scenario, is often uncertain, as when an agent comes in contact with other agents they initially know nothing about each other. Currently, many reputation models are developed that help service consumers select better service providers. Reputation models also help agents to make a decision on who they should trust and transact with in the future. These reputation models are either built on interaction trust that involves direct experience as a source of information or they are built upon witness information also known as word-of-mouth that involves the reports provided by others. Neither the interaction trust nor the witness information models alone succeed in such uncertain interactions. In this paper we propose a hybrid reputation model involving both interaction trust and witness information to address the shortcomings of existing reputation models when taken separately. A sample simulation is built to setup buyer-seller services and uncertain interactions. Experiments reveal that the hybrid approach leads to better selection of trustworthy agents where consumers select more reputable service providers, eventually helping consumers obtain more gains. Furthermore, the trust model developed is used in calculating trust values of service providers.

  1. Supporting secure programming in web applications through interactive static analysis.

    Science.gov (United States)

    Zhu, Jun; Xie, Jing; Lipford, Heather Richter; Chu, Bill

    2014-07-01

    Many security incidents are caused by software developers' failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE) and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases.

  2. Supporting secure programming in web applications through interactive static analysis

    Directory of Open Access Journals (Sweden)

    Jun Zhu

    2014-07-01

    Full Text Available Many security incidents are caused by software developers’ failure to adhere to secure programming practices. Static analysis tools have been used to detect software vulnerabilities. However, their wide usage by developers is limited by the special training required to write rules customized to application-specific logic. Our approach is interactive static analysis, to integrate static analysis into Integrated Development Environment (IDE and provide in-situ secure programming support to help developers prevent vulnerabilities during code construction. No additional training is required nor are there any assumptions on ways programs are built. Our work is motivated in part by the observation that many vulnerabilities are introduced due to failure to practice secure programming by knowledgeable developers. We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. Our evaluations also suggest that false positives may be limited to a very small class of use cases.

  3. DOSCHEDA: a web application for interactive chemoproteomics data analysis

    Directory of Open Access Journals (Sweden)

    Bruno Contrino

    2017-08-01

    Full Text Available Background Mass Spectrometry (MS based chemoproteomics has recently become a main tool to identify and quantify cellular target protein interactions with ligands/drugs in drug discovery. The complexity associated with these new types of data requires scientists with a limited computational background to perform systematic data quality controls as well as to visualize the results derived from the analysis to enable rapid decision making. To date, there are no readily accessible platforms specifically designed for chemoproteomics data analysis. Results We developed a Shiny-based web application named DOSCHEDA (Down Stream Chemoproteomics Data Analysis to assess the quality of chemoproteomics experiments, to filter peptide intensities based on linear correlations between replicates, and to perform statistical analysis based on the experimental design. In order to increase its accessibility, DOSCHEDA is designed to be used with minimal user input and it does not require programming knowledge. Typical inputs can be protein fold changes or peptide intensities obtained from Proteome Discover, MaxQuant or other similar software. DOSCHEDA aggregates results from bioinformatics analyses performed on the input dataset into a dynamic interface, it encompasses interactive graphics and enables customized output reports. Conclusions DOSCHEDA is implemented entirely in R language. It can be launched by any system with R installed, including Windows, Mac OS and Linux distributions. DOSCHEDA is hosted on a shiny-server at https://doscheda.shinyapps.io/doscheda and is also available as a Bioconductor package (http://www.bioconductor.org/.

  4. Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation

    DEFF Research Database (Denmark)

    Nandy, Subir Kumar; Jouhten, Paula; Nielsen, Jens

    2010-01-01

    proteins. Despite the value of BioGRID for studying protein-protein interactions, there is a need for manual curation of these interactions in order to remove false positives. RESULTS: Here we describe an annotated reconstruction of the protein-protein interactions around four key nutrient......-sensing and metabolic regulatory signal transduction pathways (STP) operating in Saccharomyces cerevisiae. The reconstructed STP network includes a full protein-protein interaction network including the key nodes Snf1, Tor1, Hog1 and Pka1. The network includes a total of 623 structural open reading frames (ORFs......) and for all the interactions between them (edges). The annotated information is readily available utilizing the functionalities of network modelling tools such as Cytoscape and CellDesigner. CONCLUSIONS: The reported fully annotated interaction model serves as a platform for integrated systems biology studies...

  5. Mother-child and father-child interaction with their 24-month-old children during feeding, considering paternal involvement and the child's temperament in a community sample.

    Science.gov (United States)

    Cerniglia, Luca; Cimino, Silvia; Ballarotto, Giulia

    2014-01-01

    The article aims to study mother-child and father-child interactions with 24-month-old children during feeding, considering the possible influence of time spent by the parent with the child, the infantile temperament, and the parental psychological profile. The families were recruited from 12 preschools in Italy (N = 77 families). Through an observation of the feeding [Scala di Valutazione dell'Interazione Alimentare (SVIA - Feeding Scale; I. Chatoor et al., ; L. Lucarelli et al., )], self-reporting [Symptom Checklist-90-Revised (SCL-90-R; L.R. Derogatis, ), and report-form questionnaires [Italian Questionnaires on Temperament (QUIT; G. Axia, )], and information provided by the parents about the amount of time spent with their children, results showed that the overall quality of father-child interactions during feeding is lower than that of mother-child interactions. Fathers showed higher psychological symptoms than did mothers. No associations were found between the fathers' psychopathological risk and the quality of interactions with their children during feeding. Mothers' psychopathological risks predicted less contingent exchanges interactions with their children during feeding. Children's temperaments significantly influence mother-child interactions, but no association exists between maternal involvement and the quality of interactions with their children. Paternal involvement predicts a better quality of father-infant interactions when associated with a child's higher scores on Social Orientation. The quality of parents' interactions with their children during feeding are impacted by different issues originating from the parent's psychological profile, the degree of involvement, and from the child's temperament. © 2014 Michigan Association for Infant Mental Health.

  6. Automatic Feature Interaction Analysis in PacoSuite

    Directory of Open Access Journals (Sweden)

    Wim Vanderperren

    2004-10-01

    Full Text Available In this paper, we build upon previous work that aims at recuperating aspect oriented ideas into component based software development. In that research, a composition adapter was proposed in order to capture crosscutting concerns in the PacoSuite component based methodology. A composition adapter is visually applied onto a given component composition and the changes it describes are automatically applied. Stacking multiple composition adapters onto the same component composition can however lead to unpredictable and undesired side-effects. In this paper, we propose a solution for this issue, widely known as the feature interaction problem. We present a classification of different interaction levels among composition adapters and the algorithms required to verify them. The proposed algorithms are however of exponential nature and depend on both the composition adapters and the component composition as a whole. In order to enhance the performance of our feature interaction analysis, we present a set of theorems that define the interaction levels solely in terms of the properties of the composition adapters themselves.

  7. Police involvement in child protective services investigations: literature review and secondary data analysis.

    Science.gov (United States)

    Cross, Theodore P; Finkelhor, David; Ormrod, Richard

    2005-08-01

    This article examines the relationship of police and child protective services (CPS) coinvolvement to the outcomes of child maltreatment investigations. It reviews practice and empirical literature and conducts a secondary analysis of a national CPS data set. Most sources argue that coordination of the two agencies improves investigations and benefits children and families. Yet, sources also report friction between these agencies, interference with each other's job, and concerns that police involvement increases child removal. In the CPS case data, allegations were more likely to be judged credible when police also investigated and families were also more likely to receive various services. For neglect cases, multi-disciplinary decision making, but not police involvement per se, was linked to child removal. Across studies, police do not appear to hinder CPS effectiveness and may actually promote it. Their investigations should be coordinated in every community.

  8. Analysis of human emotion in human-robot interaction

    Science.gov (United States)

    Blar, Noraidah; Jafar, Fairul Azni; Abdullah, Nurhidayu; Muhammad, Mohd Nazrin; Kassim, Anuar Muhamed

    2015-05-01

    There is vast application of robots in human's works such as in industry, hospital, etc. Therefore, it is believed that human and robot can have a good collaboration to achieve an optimum result of work. The objectives of this project is to analyze human-robot collaboration and to understand humans feeling (kansei factors) when dealing with robot that robot should adapt to understand the humans' feeling. Researches currently are exploring in the area of human-robot interaction with the intention to reduce problems that subsist in today's civilization. Study had found that to make a good interaction between human and robot, first it is need to understand the abilities of each. Kansei Engineering in robotic was used to undergo the project. The project experiments were held by distributing questionnaire to students and technician. After that, the questionnaire results were analyzed by using SPSS analysis. Results from the analysis shown that there are five feelings which significant to the human in the human-robot interaction; anxious, fatigue, relaxed, peaceful, and impressed.

  9. Analysis of molecular markers as predictive factors of lymph node involvement in breast carcinoma

    DEFF Research Database (Denmark)

    Paula, Luciana Marques; De Moraes, Luis Henrique Ferreira; Do Canto, Abaeté Leite

    2017-01-01

    Nodal status is the most significant independent prognostic factor in breast cancer. Identification of molecular markers would allow stratification of patients who require surgical assessment of lymph nodes from the large numbers of patients for whom this surgical procedure is unnecessary, thus...... leading to a more accurate prognosis. However, up to now, the reported studies are preliminary and controversial, and although hundreds of markers have been assessed, few of them have been used in clinical practice for treatment or prognosis in breast cancer. The purpose of the present study...... ankyrin-related ADP-ribose polymerase 2, BCL2 associated agonist of cell death, G2 and S-phase expressed 1 and PAX interacting protein 1 genes, described as prognostic markers in breast cancer in a previous microarray study, are also predictors of lymph node involvement in breast carcinoma Reverse...

  10. Association analysis of schizophrenia on 18 genes involved in neuronal migration

    DEFF Research Database (Denmark)

    Kähler, Anna K; Djurovic, Srdjan; Kulle, Bettina

    2008-01-01

    Several lines of evidence support the theory of schizophrenia (SZ) being a neurodevelopmental disorder. The structural, cytoarchitectural and functional brain abnormalities reported in patients with SZ, might be due to aberrant neuronal migration, since the final position of neurons affects...... neuronal function, morphology, and formation of synaptic connections. We have investigated the putative association between SZ and gene variants engaged in the neuronal migration process, by performing an association study on 839 cases and 1,473 controls of Scandinavian origin. Using a gene-wide approach......, tagSNPs in 18 candidate genes have been genotyped, with gene products involved in the neuron-to-glial cell adhesion, interactions with the DISC1 protein and/or rearrangements of the cytoskeleton. Of the 289 markers tested, 19 markers located in genes MDGA1, RELN, ITGA3, DLX1, SPARCL1, and ASTN1...

  11. Improved statistics for genome-wide interaction analysis.

    Science.gov (United States)

    Ueki, Masao; Cordell, Heather J

    2012-01-01

    Recently, Wu and colleagues [1] proposed two novel statistics for genome-wide interaction analysis using case/control or case-only data. In computer simulations, their proposed case/control statistic outperformed competing approaches, including the fast-epistasis option in PLINK and logistic regression analysis under the correct model; however, reasons for its superior performance were not fully explored. Here we investigate the theoretical properties and performance of Wu et al.'s proposed statistics and explain why, in some circumstances, they outperform competing approaches. Unfortunately, we find minor errors in the formulae for their statistics, resulting in tests that have higher than nominal type 1 error. We also find minor errors in PLINK's fast-epistasis and case-only statistics, although theory and simulations suggest that these errors have only negligible effect on type 1 error. We propose adjusted versions of all four statistics that, both theoretically and in computer simulations, maintain correct type 1 error rates under the null hypothesis. We also investigate statistics based on correlation coefficients that maintain similar control of type 1 error. Although designed to test specifically for interaction, we show that some of these previously-proposed statistics can, in fact, be sensitive to main effects at one or both loci, particularly in the presence of linkage disequilibrium. We propose two new "joint effects" statistics that, provided the disease is rare, are sensitive only to genuine interaction effects. In computer simulations we find, in most situations considered, that highest power is achieved by analysis under the correct genetic model. Such an analysis is unachievable in practice, as we do not know this model. However, generally high power over a wide range of scenarios is exhibited by our joint effects and adjusted Wu statistics. We recommend use of these alternative or adjusted statistics and urge caution when using Wu et al

  12. Global Interactions Analysis of Epileptic ECoG Data

    Science.gov (United States)

    Ortega, Guillermo J.; Sola, Rafael G.; Pastor, Jesús

    2007-05-01

    Localization of the epileptogenic zone is an important issue in epileptology, even though there is not a unique definition of the epileptic focus. The objective of the present study is to test ultrametric analysis to uncover cortical interactions in human epileptic data. Correlation analysis has been carried out over intraoperative Electro-Corticography (ECoG) data in 2 patients suffering from temporal lobe epilepsy (TLE). Recordings were obtained using a grid of 20 electrodes (5×4) covering the lateral temporal lobe and a strip of either 4 or 8 electrodes at the mesial temporal lobe. Ultrametric analysis was performed in the averaged final correlation matrices. By using the matrix of linear correlation coefficients and the appropriate metric distance between pairs of electrodes time series, we were able to construct Minimum Spanning Trees (MST). The topological connectivity displayed by these trees gives useful and valuable information regarding physiological and pathological information in the temporal lobe of epileptic patients.

  13. A Meta-Analysis of the Efficacy of Different Types of Parental Involvement Programs for Urban Students

    Science.gov (United States)

    Jeynes, William

    2012-01-01

    This meta-analysis of 51 studies examines the relationship between various kinds of parental involvement programs and the academic achievement of pre-kindergarten-12th-grade school children. Analyses determined the effect sizes for various parental involvement programs overall and subcategories of involvement. Results indicate a significant…

  14. Economics of alcohol-involved traffic crashes in the USA: an input-output analysis.

    Science.gov (United States)

    Zaloshnja, Eduard; Miller, Ted R; Lawrence, Bruce A

    2016-02-01

    Preventing traffic crashes reduces crash costs paid by employers and employees. The related savings filter through the economy, impacting its performance. This study is the first to measure the impact of traffic crash reduction on a national economy. It focuses on impaired driving crashes. We analysed the impact of the almost 50% alcohol-involved driving crash rate reduction from 1984-1986 to 2010 and the impact if such crashes in 2010 had not occurred. The analysis entered published estimates of costs that employers, consumers and governments paid because of US impaired-driving crashes as production costs and demand changes in Rutgers University's input-output model of the US economy. For example, reducing medical costs paid by employers lowers the cost of labour inputs to production while reducing vehicle repairs raises demand for other goods. Running the model at current and alternative crash rates revealed the impacts of crash reductions on economic output, gross domestic product (GDP), national income and employment. Alcohol-involved crash reductions since 1984-1986 increased economic output in 2010 by an estimated $20 billion, raised GDP by $10 billion, increased US income by $6.5 billion, and created 215 000 jobs. GDP gains from alcohol-involved crash reduction contributed 5% of the $200 million compounded average annual growth in US GDP from 1985 to 2013. Eliminating remaining alcohol-involved crashes would result in similar economic gains. Alcohol-involved crashes drag down the US economy. On average, each of the 25.5 billion miles Americans drove impaired in 2010 reduced economic output by $0.80. Those losses are preventable. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  15. Dynamic Analysis of Wind Turbines Including Soil-Structure Interaction

    DEFF Research Database (Denmark)

    Harte, M.; Basu, B.; Nielsen, Søren R.K.

    2012-01-01

    This paper investigates the along-wind forced vibration response of an onshore wind turbine. The study includes the dynamic interaction effects between the foundation and the underlying soil, as softer soils can influence the dynamic response of wind turbines. A Multi-Degree-of-Freedom (MDOF...... rotational speed (3P effects). The effect of dynamic soil-structure interaction on the rotation of the foundation has also been investigated.......) horizontal axes onshore wind turbine model is developed for dynamic analysis using an Euler–Lagrangian approach. The model is comprised of a rotor blade system, a nacelle and a flexible tower connected to a foundation system using a substructuring approach. The rotor blade system consists of three rotating...

  16. Analysis of crease-wrinkle interaction for thin sheets

    Energy Technology Data Exchange (ETDEWEB)

    Woo, Kyeong Sik [Chungbuk National University, Cheongju (Korea, Republic of); Jenkins, Christopher H. [Montana State University, Bozeman (United States)

    2012-03-15

    In this paper, geometrically non-linear post-buckling analyses were performed to study the effect of sheet thickness, deployment angle, and load ratio on the crease-wrinkle interaction. A square sheet configuration with a single transverse crease was modeled using thin shell elements. The analysis proceeded by initially providing a realistic deployed state of a creased membrane sheet. Then an uneven corner loading was applied to introduce wrinkling. The effects of the induced anisotropy from the crease on the fine-scale detail of the wrinkle evolution, as a function of sheet thickness, loading, and crease deployment angle were systematically investigated. Significant differences were found in sheet compliance and crease-wrinkle interaction as these parameters were varied.

  17. Mouse Social Interaction Test (MoST): a quantitative computer automated analysis of behavior.

    Science.gov (United States)

    Thanos, Panayotis K; Restif, Christophe; O'Rourke, Joseph R; Lam, Chiu Yin; Metaxas, Dimitris

    2017-01-01

    Rodents are the most commonly used preclinical model of human disease assessing the mechanism(s) involved as well as the role of genetics, epigenetics, and pharmacotherapy on this disease as well as identifying vulnerability factors and risk assessment for disease critical in the development of improved treatment strategies. Unfortunately, the majority of rodent preclinical studies utilize single housed approaches where animals are either entirely housed and tested in solitary environments or group housed but tested in solitary environments. This approach, however, ignores the important contribution of social interaction and social behavior. Social interaction in rodents is found to be a major criterion for the ethological validity of rodent species-specific behavioral characteristics (Zurn et al. 2007; Analysis 2011). It is also well established that there is significant and growing number of reports, which illustrates the important role of social environment and social interaction in all diseases, with particularly significance in all neuropsychiatric diseases. Thus, it is imperative that research studies be able to add large-scale evaluations of social interaction and behavior in mice and benefit from automated tracking of behaviors and measurements by removing user bias and by quantifying aspects of behaviors that cannot be assessed by a human observer. Single mouse setups have been used routinely, but cannot be easily extended to multiple-animal studies where social behavior is key, e.g., autism, depression, anxiety, substance and non-substance addictive disorders, aggression, sexual behavior, or parenting. While recent efforts are focusing on multiple-animal tracking alone, a significant limitation remains the lack of insightful measures of social interactions. We present a novel, non-invasive single camera-based automated tracking method described as Mouse Social Test (MoST) and set of measures designed for estimating the interactions of multiple mice at the

  18. Computing and Visualizing Log-linear Analysis Interactively

    Directory of Open Access Journals (Sweden)

    Pedro M. Valero-Mora

    2002-09-01

    Full Text Available The purpose of this paper is to describe a simple program for computing log-linear analysis based on a direct manipulation interface that emphasizes the use of plots for guiding the analysis and evaluating the results obtained. The program described here works as a plugin for ViSta (Young 1997 and receives the name of LoginViSta (for Log-linear analysis in ViSTa. ViSta is a statistical package based on Lisp-Stat. Lisp-Stat is a statistical programming environment developed by Luke Tierney (1990 that features an object-oriented approach for statistical computing and one that allows for The purpose of this paper is to describe a simple program for computing log-linear analysis based on a direct manipulation interface that emphasizes the use of plots for guiding the analysis and evaluating the results obtained. The program described here works as a plugin for ViSta (Young 1997 and receives the name of LoginViSta (for Log-linear analysis in ViSTa. ViSta is a statistical package based on Lisp-Stat. Lisp-Stat is a statistical programming environment developed by Luke Tierney (1990 that features an object-oriented approach for statistical computing and one that allows for Computing and Visualizing Pedro Valero-Mora and Forrest W. Young interactive and dynamic graphs.

  19. Basic helix-loop-helix transcription factor Bmsage is involved in regulation of fibroin H-chain gene via interaction with SGF1 in Bombyx mori.

    Science.gov (United States)

    Zhao, Xiao-Ming; Liu, Chun; Li, Qiong-Yan; Hu, Wen-Bo; Zhou, Meng-Ting; Nie, Hong-Yi; Zhang, Yin-Xia; Peng, Zhang-Chuan; Zhao, Ping; Xia, Qing-You

    2014-01-01

    Silk glands are specialized in the synthesis of several secretory proteins. Expression of genes encoding the silk proteins in Bombyx mori silk glands with strict territorial and developmental specificities is regulated by many transcription factors. In this study, we have characterized B. mori sage, which is closely related to sage in the fruitfly Drosophila melanogaster. It is termed Bmsage; it encodes transcription factor Bmsage, which belongs to the Mesp subfamily, containing a basic helix-loop-helix motif. Bmsage transcripts were detected specifically in the silk glands of B. mori larvae through RT-PCR analysis. Immunoblotting analysis confirmed the Bmsage protein existed exclusively in B. mori middle and posterior silk gland cells. Bmsage has a low level of expression in the 4th instar molting stages, which increases gradually in the 5th instar feeding stages and then declines from the wandering to the pupation stages. Quantitative PCR analysis suggested the expression level of Bmsage in a high silk strain was higher compared to a lower silk strain on day 3 of the larval 5th instar. Furthermore, far western blotting and co-immunoprecipitation assays showed the Bmsage protein interacted with the fork head transcription factor silk gland factor 1 (SGF1). An electrophoretic mobility shift assay showed the complex of Bmsage and SGF1 proteins bound to the A and B elements in the promoter of fibroin H-chain gene(fib-H), respectively. Luciferase reporter gene assays confirmed the complex of Bmsage and SGF1 proteins increased the expression of fib-H. Together, these results suggest Bmsage is involved in the regulation of the expression of fib-H by being together with SGF1 in B. mori PSG cells.

  20. Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

    Directory of Open Access Journals (Sweden)

    Vicente Martí-Centelles

    2012-01-01

    competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

  1. Proteomic analysis of pathways involved in estrogen-induced growth and apoptosis of breast cancer cells.

    Directory of Open Access Journals (Sweden)

    Zhang-Zhi Hu

    Full Text Available BACKGROUND: Estrogen is a known growth promoter for estrogen receptor (ER-positive breast cancer cells. Paradoxically, in breast cancer cells that have been chronically deprived of estrogen stimulation, re-introduction of the hormone can induce apoptosis. METHODOLOGY/PRINCIPAL FINDINGS: Here, we sought to identify signaling networks that are triggered by estradiol (E2 in isogenic MCF-7 breast cancer cells that undergo apoptosis (MCF-7:5C versus cells that proliferate upon exposure to E2 (MCF-7. The nuclear receptor co-activator AIB1 (Amplified in Breast Cancer-1 is known to be rate-limiting for E2-induced cell survival responses in MCF-7 cells and was found here to also be required for the induction of apoptosis by E2 in the MCF-7:5C cells. Proteins that interact with AIB1 as well as complexes that contain tyrosine phosphorylated proteins were isolated by immunoprecipitation and identified by mass spectrometry (MS at baseline and after a brief exposure to E2 for two hours. Bioinformatic network analyses of the identified protein interactions were then used to analyze E2 signaling pathways that trigger apoptosis versus survival. Comparison of MS data with a computationally-predicted AIB1 interaction network showed that 26 proteins identified in this study are within this network, and are involved in signal transduction, transcription, cell cycle regulation and protein degradation. CONCLUSIONS: G-protein-coupled receptors, PI3 kinase, Wnt and Notch signaling pathways were most strongly associated with E2-induced proliferation or apoptosis and are integrated here into a global AIB1 signaling network that controls qualitatively distinct responses to estrogen.

  2. Intervention or Involvement

    DEFF Research Database (Denmark)

    Liebst, Lasse Suonperä; Ejbye-Ernst, Peter; Heinskou, Marie Bruvik

    patrons plays in bouncers’ use of violence. To address this gap, we offer a micro-interactional analysis of violent behavior of bouncers. We observed video surveillance footage of naturally occurring barroom conflicts involving bouncers. A quantitative analysis shows that violence is relatively uncommon......, and when it occurs, it is associated with interactions where bouncers are a party to the conflict, compared to situations where they intervene as a third party. Further, a visual analysis of emotional cues identifies anger as a plausible mechanism leading bouncers to practice violent aggression. Thus......, adding to the situational and cultural interpretations in the literature, this study highlights interactional structures as a feature influencing the likelihood of violent bouncer behavior. In considering the implications of our study, we discuss strengths and weaknesses of applying video data analysis...

  3. Fixed point sensitivity analysis of interacting structured populations.

    Science.gov (United States)

    Barabás, György; Meszéna, Géza; Ostling, Annette

    2014-03-01

    Sensitivity analysis of structured populations is a useful tool in population ecology. Historically, methodological development of sensitivity analysis has focused on the sensitivity of eigenvalues in linear matrix models, and on single populations. More recently there have been extensions to the sensitivity of nonlinear models, and to communities of interacting populations. Here we derive a fully general mathematical expression for the sensitivity of equilibrium abundances in communities of interacting structured populations. Our method yields the response of an arbitrary function of the stage class abundances to perturbations of any model parameters. As a demonstration, we apply this sensitivity analysis to a two-species model of ontogenetic niche shift where each species has two stage classes, juveniles and adults. In the context of this model, we demonstrate that our theory is quite robust to violating two of its technical assumptions: the assumption that the community is at a point equilibrium and the assumption of infinitesimally small parameter perturbations. Our results on the sensitivity of a community are also interpreted in a niche theoretical context: we determine how the niche of a structured population is composed of the niches of the individual states, and how the sensitivity of the community depends on niche segregation.

  4. ESTs analysis reveals putative genes involved in symbiotic seed germination in Dendrobium officinale.

    Directory of Open Access Journals (Sweden)

    Ming-Ming Zhao

    Full Text Available Dendrobiumofficinale (Orchidaceae is one of the world's most endangered plants with great medicinal value. In nature, D. officinale seeds must establish symbiotic relationships with fungi to germinate. However, the molecular events involved in the interaction between fungus and plant during this process are poorly understood. To isolate the genes involved in symbiotic germination, a suppression subtractive hybridization (SSH cDNA library of symbiotically germinated D. officinale seeds was constructed. From this library, 1437 expressed sequence tags (ESTs were clustered to 1074 Unigenes (including 902 singletons and 172 contigs, which were searched against the NCBI non-redundant (NR protein database (E-value cutoff, e(-5. Based on sequence similarity with known proteins, 579 differentially expressed genes in D. officinale were identified and classified into different functional categories by Gene Ontology (GO, Clusters of orthologous Groups of proteins (COGs and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways. The expression levels of 15 selected genes emblematic of symbiotic germination were confirmed via real-time quantitative PCR. These genes were classified into various categories, including defense and stress response, metabolism, transcriptional regulation, transport process and signal transduction pathways. All transcripts were upregulated in the symbiotically germinated seeds (SGS. The functions of these genes in symbiotic germination were predicted. Furthermore, two fungus-induced calcium-dependent protein kinases (CDPKs, which were upregulated 6.76- and 26.69-fold in SGS compared with un-germinated seeds (UGS, were cloned from D. officinale and characterized for the first time. This study provides the first global overview of genes putatively involved in D. officinale symbiotic seed germination and provides a foundation for further functional research regarding symbiotic relationships in orchids.

  5. Functional involvement of proteins, interacting with sphingolipids, in sphingolipid transport to the canalicular membrane in the human hepatocytic cell line, HepG2?

    NARCIS (Netherlands)

    Zegers, MMP; Zaal, KJM; Hoekstra, D

    A photoreactive sphingolipid precursor was used to investigate the potential involvement of protein-lipid interactions that may convey specificity to sphingolipid transport in the human hepatoma cell line, HepG2, A I-125-labeled, photoreactive ceramide, I-125-N-3-Cer, was incubated with the cells

  6. Prevalence and type of drug–drug interactions involving ART in patients attending a specialist HIV outpatient clinic in Kampala, Uganda

    Science.gov (United States)

    Seden, K.; Merry, C.; Hewson, R.; Siccardi, M.; Lamorde, M.; Byakika-Kibwika, P.; Laker, E.; Parkes-Ratanshi, R.; Back, D. J.; Khoo, S. H.

    2015-01-01

    Objectives Scale-up of HIV services in sub-Saharan Africa has rapidly increased, necessitating evaluation of medication safety in these settings. Drug–drug interactions (DDIs) involving antiretrovirals (ARVs) in sub-Saharan Africa are poorly characterized. We evaluated the prevalence and type of ARV DDIs in Ugandan outpatients and identified the patients most at risk. Methods A total of 2000 consecutive patients receiving ARVs at the Infectious Diseases Institute, Kampala were studied. The most recent prescription for each patient was screened for clinically significant DDIs using www.hiv-druginteractions.org. Univariable and multivariable logistic regression were used to identify risk factors for DDIs. A screening tool was developed using significant risk factors and tested in a further 500 patients. Results Clinically significant DDIs were observed in 374 (18.7%) patients, with a total of 514 DDIs observed. Only 0.2% of DDIs involved a contraindicated combination. Comedications commonly associated with DDIs were antibiotics (4.8% of 2000 patients), anthelmintics (2.2%) and antifungals (3.5%). Patient age, gender, CD4 count and weight did not affect risk of DDIs. In multivariable analysis, the patient factors that independently increased risk of DDIs were two or more comedications (P < 0.0001), a PI-containing ARV regimen (P < 0.0001), use of an anti-infective (P < 0.0001) and WHO clinical stage 3–4 (P = 0.04). A scoring system based on having at least two of these risk factors identified between 75% and 90% of DDIs in a validation cohort. Conclusions Significant ARV DDIs occur at similar rates in resource-limited settings and developed countries; however, the comedications frequently causing DDIs differ. Development of tools that are relevant to particular settings should be a priority to assist with prevention and management of DDIs. PMID:26286575

  7. Interaction between international trade and economic growth: evidence from qualitative comparative analysis

    Directory of Open Access Journals (Sweden)

    Asli Seda Bilman

    2014-12-01

    Full Text Available The relationship between international trade and growth is one of the most popular debates in international economics literature. Although there are numerous theoretical approaches and empirical studies about the issue, the direction of the causality and the magnitude of the interaction still remain unclear. In this study, qualitative comparative analysis introduced by Ragin (1987 is applied, different from the previous empirical studies on the topic. The results present the conditions for growth in the country groups involved. The findings imply that trade policy is still of great importance in terms of stimulating growth in developing countries, while it has little importance in developed countries.

  8. ANALYSIS OF THE KQML MODEL IN MULTI-AGENT INTERACTION

    Institute of Scientific and Technical Information of China (English)

    刘海龙; 吴铁军

    2001-01-01

    Our analysis of the KQML(Knowledge Query and Manipulation Language) model yielded some conclusions on the knowledge level of communication in agent-oriented program. First, the agent state and transition model were given for analyzing the necessary conditions for interaction with the synchronal and asynchronous KQML model respectively. Second, we analyzed the deadlock and starvation problems in the KQML communication, and gave the solution. At last, the advantages and disadvantages of the synchronal and asynchronous KQML model were listed respectively, and the choosing principle was given.

  9. Interactive facades analysis and synthesis of semi-regular facades

    KAUST Repository

    AlHalawani, Sawsan

    2013-05-01

    Urban facades regularly contain interesting variations due to allowed deformations of repeated elements (e.g., windows in different open or close positions) posing challenges to state-of-the-art facade analysis algorithms. We propose a semi-automatic framework to recover both repetition patterns of the elements and their individual deformation parameters to produce a factored facade representation. Such a representation enables a range of applications including interactive facade images, improved multi-view stereo reconstruction, facade-level change detection, and novel image editing possibilities. © 2013 The Author(s) Computer Graphics Forum © 2013 The Eurographics Association and Blackwell Publishing Ltd.

  10. Distributed Parallel Interactive Data Analysis Using the Proof System

    Institute of Scientific and Technical Information of China (English)

    ReneBrun; FonsRademakers

    2001-01-01

    The only way Terabytes of data can be processed and analyzed in a reasonable time is by using parallel processing architectures.The Paralle ROOT Facility,PROOF,is s system for the parallel interactive analysis of such datasets on clusters of heterogeneous computers.Early prototypes have confirmed the validity of the basic PROOF architecture However,some important work still has to be done before PROOF can be used as a production facility.The basic architecture and the planned developments are described in this paper.

  11. Using role analysis to plan for stakeholder involvement: a Wyoming case study

    Science.gov (United States)

    Burkardt, Nina; Ponds, Phadrea D.

    2006-01-01

    Prior to implementing laws and policies regulating water, wildlife, wetlands, endangered species, and recreation, natural resource managers often solicit public input. Concomitantly, managers are continually seeking more effective ways to involve stakeholders. In the autumn of 1999, the Wyoming Game and Fish Department sought to develop a state management plan for its portion of the Yellowstone grizzly bear (Ursus arctos horribilis) population if it was removed from the federal threatened species list. A key aspect of developing this plan was the involvement of federal, state, and local agencies, representatives from nongovernmental organizations, and citizens. Wyoming wildlife managers asked researchers from the United States Geological Survey to demonstrate how the Legal-Institutional Analysis Model could be used to initiate this process. To address these needs, we conducted similar workshops for a group of state and federal managers or staffers and a broad group of stakeholders. Although we found similarities among the workshop groups, we also recorded differences in perspective between stakeholder groups. The managers group acknowledged the importance of varied stakeholders but viewed the grizzly bear planning process as one centered on state interests, influenced by state policies, and amenable to negotiation. The other workshops identified many stakeholders and viewed the decision process as diffuse, with many opportunities for entry into the process. These latter groups were less certain about the chance for a successful negotiation. We concluded that if these assumptions and differences were not reconciled, the public involvement effort was not likely to succeed.

  12. A quantitative analysis of the reactions involved in stratospheric ozone depletion in the polar vortex core

    Directory of Open Access Journals (Sweden)

    I. Wohltmann

    2017-09-01

    Full Text Available We present a quantitative analysis of the chemical reactions involved in polar ozone depletion in the stratosphere and of the relevant reaction pathways and cycles. While the reactions involved in polar ozone depletion are well known, quantitative estimates of the importance of individual reactions or reaction cycles are rare. In particular, there is no comprehensive and quantitative study of the reaction rates and cycles averaged over the polar vortex under conditions of heterogeneous chemistry so far. We show time series of reaction rates averaged over the core of the polar vortex in winter and spring for all relevant reactions and indicate which reaction pathways and cycles are responsible for the vortex-averaged net change of the key species involved in ozone depletion, i.e., ozone, chlorine species (ClOx, HCl, ClONO2, bromine species, nitrogen species (HNO3, NOx and hydrogen species (HOx. For clarity, we focus on one Arctic winter (2004–2005 and one Antarctic winter (2006 in a layer in the lower stratosphere around 54 hPa and show results for additional pressure levels and winters in the Supplement. Mixing ratios and reaction rates are obtained from runs of the ATLAS Lagrangian chemistry and transport model (CTM driven by the European Centre for Medium-Range Weather Forecasts (ECMWF ERA-Interim reanalysis data. An emphasis is put on the partitioning of the relevant chemical families (nitrogen, hydrogen, chlorine, bromine and odd oxygen and activation and deactivation of chlorine.

  13. Interaction of activity involvement and recreational location selection behavior in Lowland City: A case study of public parks in Saga City, Japan

    Institute of Scientific and Technical Information of China (English)

    IAMTRAKUL Pawinee; TEKNOMO Kardi; GE Jian; HOKAO Kazunori

    2005-01-01

    Public parks provide many benefits to the community as the representatives of green area. The allocation of public places plays an extremely important role in the daily lives of inhabitants especially for recreational use that could enhance the quality of life of residents in the vicinity. To understand park users' behavior is one of the most important prerequisites for assessing the participation in public service from the park users' point of view. The pattern of park utilization on location and activity selection are important elements in behavioral study, while the public parks topograph may also influence the typical user's behavior. Questionnaire survey on park utilization was used to investigate the interaction between activity involvement and recreational location with the use of linear discriminant analysis (LDA) model. The study found that public park users' behavior is influenced not only by social characteristics but also by the recreational activities and their specific location characteristics. We found that about 45 percent of park visitors are local residents living within a radius of 3 km preferred travel to parks near their residential area. This implies that location selection behavior is correlated with travel distance, travel time and travel cost. Visit frequencies and on site expenditures reflect the recreation behavior for different type of activities. The overall information can be usefully applied by decision makers to launch appropriate public policy in consistence with the useful results of this study.

  14. Asymmetrical peer interaction and formal operational development: Dialogue dimensions analysis

    Directory of Open Access Journals (Sweden)

    Stepanović-Ilić Ivana

    2015-01-01

    Full Text Available The main goal of the study is to define dialogue dimensions in order to describe the interaction within peer dyads and potentially connect them with formal operations development in the less competent participants. Its significance is related to rare investigations of this subject in the context of formal operations development and to practical implications regarding peer involvement in education process. The sample included 316 students aged 12 and 14. The research had an experimental design: pre-test, intervention and post-test. In the pre-test and the post-test phases students solved the formal operations test BLOT. According to the pre-test results, 47 dyads were formed where less and more competent students jointly solved tasks from BLOT. Their dialogues were coded by 14 dimensions operationalized for this purpose. Correlations between the dialogue dimensions indicate clearly distinguished positive and negative interaction patterns. There are no connections between dialogue dimensions and progress of less competent adolescents on BLOT in the entire sample, but several are found in the subsamples. Arguments exchange seems to be the most encouraging dialogue feature regarding formal operations development, particularly in older students. This confirms relevant research data and the expectations about peers’ constructive role in fostering cognitive development. [Projekat Ministarstva nauke Republike Srbije, br. 179018: Identification, measurement and development of cognitive and emotional competences important for a society oriented towards European integrations

  15. Isobolographic analysis of interactions: an update on applications and utility.

    Science.gov (United States)

    Gessner, P K

    1995-12-28

    Isobolographic analysis provides a fundamental basis for assessing whether biological responses induced by mixtures of agents are greater, equal or smaller than would have been expected on the basis of the individual activities of the component agents and the concept of dose additivity. Limited in its direct application to binary mixtures, isobolographic analysis provides a conceptual framework and an unambiguous terminology, as well as an algebraic paradigm for the analysis of the interaction of ternary and higher order mixtures. A library of examples generously illustrated graphically is provided to facilitate the understanding of the methodology and serve as a guide for investigators who are unfamiliar with the approach. Also discussed are the theoretical derivation of the isobologram, the representation of various dosage combinations, the derivation of the principle of dose additivity, supra-additivity, infra-additivity, antagonism, the methods for probit analysis of mixture potency, effect addition and the consequences of peak effect coincidence in time or lack thereof, and the role of isobolographic analysis in the various aspects of dose-response surface methodology.

  16. Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae)

    Science.gov (United States)

    Vongsangnak, Wanwipa; Chumnanpuen, Pramote

    2016-01-01

    Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system. PMID:27761329

  17. Transcriptome Analysis Reveals Putative Genes Involved in Iridoid Biosynthesis in Rehmannia glutinosa

    Directory of Open Access Journals (Sweden)

    Xianen Li

    2012-10-01

    Full Text Available Rehmannia glutinosa, one of the most widely used herbal medicines in the Orient, is rich in biologically active iridoids. Despite their medicinal importance, no molecular information about the iridoid biosynthesis in this plant is presently available. To explore the transcriptome of R. glutinosa and investigate genes involved in iridoid biosynthesis, we used massively parallel pyrosequencing on the 454 GS FLX Titanium platform to generate a substantial EST dataset. Based on sequence similarity searches against the public sequence databases, the sequences were first annotated and then subjected to Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG based analysis. Bioinformatic analysis indicated that the 454 assembly contained a set of genes putatively involved in iridoid biosynthesis. Significantly, homologues of the secoiridoid pathway genes that were only identified in terpenoid indole alkaloid producing plants were also identified, whose presence implied that route II iridoids and route I iridoids share common enzyme steps in the early stage of biosynthesis. The gene expression patterns of four prenyltransferase transcripts were analyzed using qRT-PCR, which shed light on their putative functions in tissues of R. glutinosa. The data explored in this study will provide valuable information for further studies concerning iridoid biosynthesis.

  18. Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses

    Science.gov (United States)

    2014-01-01

    Background Phenotypic plasticity in defensive traits occurs in many species when facing heterogeneous predator regimes. The waterflea Daphnia is well-known for showing a variety of these so called inducible defences. However, molecular mechanisms underlying this plasticity are poorly understood so far. We performed proteomic analysis on Daphnia magna exposed to chemical cues of the predator Triops cancriformis. D. magna develops an array of morphological changes in the presence of Triops including changes of carapace morphology and cuticle hardening. Results Using the 2D-DIGE technique, 1500 protein spots could be matched and quantified. We discovered 179 protein spots with altered intensity when comparing Triops exposed animals to a control group, and 69 spots were identified using nano-LC MS/MS. Kairomone exposure increased the intensity of spots containing muscle proteins, cuticle proteins and chitin-modifying enzymes as well as enzymes of carbohydrate and energy metabolism. The yolk precursor protein vitellogenin decreased in abundance in 41 of 43 spots. Conclusion Identified proteins may be either directly involved in carapace stability or reflect changes in energy demand and allocation costs in animals exposed to predator kairomones. Our results present promising candidate proteins involved in the expression of inducible defences in Daphnia and enable further in depth analysis of this phenomenon. PMID:24762235

  19. Expert Involvement Predicts mHealth App Downloads: Multivariate Regression Analysis of Urology Apps

    Science.gov (United States)

    Osório, Luís; Cavadas, Vitor; Fraga, Avelino; Carrasquinho, Eduardo; Cardoso de Oliveira, Eduardo; Castelo-Branco, Miguel; Roobol, Monique J

    2016-01-01

    Background Urological mobile medical (mHealth) apps are gaining popularity with both clinicians and patients. mHealth is a rapidly evolving and heterogeneous field, with some urology apps being downloaded over 10,000 times and others not at all. The factors that contribute to medical app downloads have yet to be identified, including the hypothetical influence of expert involvement in app development. Objective The objective of our study was to identify predictors of the number of urology app downloads. Methods We reviewed urology apps available in the Google Play Store and collected publicly available data. Multivariate ordinal logistic regression evaluated the effect of publicly available app variables on the number of apps being downloaded. Results Of 129 urology apps eligible for study, only 2 (1.6%) had >10,000 downloads, with half having ≤100 downloads and 4 (3.1%) having none at all. Apps developed with expert urologist involvement (P=.003), optional in-app purchases (P=.01), higher user rating (P<.001), and more user reviews (P<.001) were more likely to be installed. App cost was inversely related to the number of downloads (P<.001). Only data from the Google Play Store and the developers’ websites, but not other platforms, were publicly available for analysis, and the level and nature of expert involvement was not documented. Conclusions The explicit participation of urologists in app development is likely to enhance its chances to have a higher number of downloads. This finding should help in the design of better apps and further promote urologist involvement in mHealth. Official certification processes are required to ensure app quality and user safety. PMID:27421338

  20. A genome-wide analysis of gene-caffeine consumption interaction on basal cell carcinoma.

    Science.gov (United States)

    Li, Xin; Cornelis, Marilyn C; Liang, Liming; Song, Fengju; De Vivo, Immaculata; Giovannucci, Edward; Tang, Jean Y; Han, Jiali

    2016-12-01

    Animal models have suggested that oral or topical administration of caffeine could inhibit ultraviolet-induced carcinogenesis via the ataxia telangiectasia and rad3 (ATR)-related apoptosis. Previous epidemiological studies have demonstrated that increased caffeine consumption is associated with reduced risk of basal cell carcinoma (BCC). To identify common genetic markers that may modify this association, we tested gene-caffeine intake interaction on BCC risk in a genome-wide analysis. We included 3383 BCC cases and 8528 controls of European ancestry from the Nurses' Health Study and Health Professionals Follow-up Study. Single nucleotide polymorphism (SNP) rs142310826 near the NEIL3 gene showed a genome-wide significant interaction with caffeine consumption (P = 1.78 × 10(-8) for interaction) on BCC risk. There was no gender difference for this interaction (P = 0.64 for heterogeneity). NEIL3, a gene belonging to the base excision DNA repair pathway, encodes a DNA glycosylase that recognizes and removes lesions produced by oxidative stress. In addition, we identified several loci with P value for interaction caffeine consumption-related SNPs reported by previous genome-wide association studies and risk of BCC, both individually and jointly, but found no significant association. In sum, we identified a DNA repair gene that could be involved in caffeine-mediated skin tumor inhibition. Further studies are warranted to confirm these findings. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Analysis of the Human Interaction with a Wearable Lower-Limb Exoskeleton

    Directory of Open Access Journals (Sweden)

    Juan C. Moreno

    2009-01-01

    Full Text Available The design of a wearable robotic exoskeleton needs to consider the interaction, either physical or cognitive, between the human user and the robotic device. This paper presents a method to analyse the interaction between the human user and a unilateral, wearable lower-limb exoskeleton. The lower-limb exoskeleton function was to compensate for muscle weakness around the knee joint. It is shown that the cognitive interaction is bidirectional; on the one hand, the robot gathered information from the sensors in order to detect human actions, such as the gait phases, but the subjects also modified their gait patterns to obtain the desired responses from the exoskeleton. The results of the two-phase evaluation of learning with healthy subjects and experiments with a patient case are presented, regarding the analysis of the interaction, assessed in terms of kinematics, kinetics and/or muscle recruitment. Human-driven response of the exoskeleton after training revealed the improvements in the use of the device, while particular modifications of motion patterns were observed in healthy subjects. Also, endurance (mechanical tests provided criteria to perform experiments with one post-polio patient. The results with the post-polio patient demonstrate the feasibility of providing gait compensation by means of the presented wearable exoskeleton, designed with a testing procedure that involves the human users to assess the human-robot interaction.

  2. Dynamics of Disagreement: Large-Scale Temporal Network Analysis Reveals Negative Interactions in Online Collaboration

    Science.gov (United States)

    Tsvetkova, Milena; García-Gavilanes, Ruth; Yasseri, Taha

    2016-11-01

    Disagreement and conflict are a fact of social life. However, negative interactions are rarely explicitly declared and recorded and this makes them hard for scientists to study. In an attempt to understand the structural and temporal features of negative interactions in the community, we use complex network methods to analyze patterns in the timing and configuration of reverts of article edits to Wikipedia. We investigate how often and how fast pairs of reverts occur compared to a null model in order to control for patterns that are natural to the content production or are due to the internal rules of Wikipedia. Our results suggest that Wikipedia editors systematically revert the same person, revert back their reverter, and come to defend a reverted editor. We further relate these interactions to the status of the involved editors. Even though the individual reverts might not necessarily be negative social interactions, our analysis points to the existence of certain patterns of negative social dynamics within the community of editors. Some of these patterns have not been previously explored and carry implications for the knowledge collection practice conducted on Wikipedia. Our method can be applied to other large-scale temporal collaboration networks to identify the existence of negative social interactions and other social processes.

  3. Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment.

    Science.gov (United States)

    Varn, Frederick S; Wang, Yue; Mullins, David W; Fiering, Steven; Cheng, Chao

    2017-03-15

    With the recent advent of immunotherapy, there is a critical need to understand immune cell interactions in the tumor microenvironment in both pan-cancer and tissue-specific contexts. Multidimensional datasets have enabled systematic approaches to dissect these interactions in large numbers of patients, furthering our understanding of the patient immune response to solid tumors. Using an integrated approach, we inferred the infiltration levels of distinct immune cell subsets in 23 tumor types from The Cancer Genome Atlas. From these quantities, we constructed a coinfiltration network, revealing interactions between cytolytic cells and myeloid cells in the tumor microenvironment. By integrating patient mutation data, we found that while mutation burden was associated with immune infiltration differences between distinct tumor types, additional factors likely explained differences between tumors originating from the same tissue. We concluded this analysis by examining the prognostic value of individual immune cell subsets as well as how coinfiltration of functionally discordant cell types associated with patient survival. In multiple tumor types, we found that the protective effect of CD8(+) T cell infiltration was heavily modulated by coinfiltration of macrophages and other myeloid cell types, suggesting the involvement of myeloid-derived suppressor cells in tumor development. Our findings illustrate complex interactions between different immune cell types in the tumor microenvironment and indicate these interactions play meaningful roles in patient survival. These results demonstrate the importance of personalized immune response profiles when studying the factors underlying tumor immunogenicity and immunotherapy response. Cancer Res; 77(6); 1271-82. ©2017 AACR.

  4. SWAN: a Service for Interactive Analysis in the Cloud

    CERN Document Server

    Piparo, Danilo; Mato, Pere; Mascetti, Luca; Moscicki, Jakub; Lamanna, Massimo

    2016-01-01

    SWAN (Service for Web based ANalysis) is a platform to perform interactive data analysis in the cloud. SWAN allows users to write and run their data analyses with only a web browser, leveraging on the widely-adopted Jupyter notebook interface. The user code, executions and data live entirely in the cloud. SWAN makes it easier to produce and share results and scientific code, access scientific software, produce tutorials and demonstrations as well as preserve analyses. Furthermore, it is also a powerful tool for non-scientific data analytics. This paper describes how a pilot of the SWAN service was implemented and deployed at CERN. Its backend combines state-of-the-art software technologies with a set of existing IT services such as user authentication, virtual computing infrastructure, mass storage, file synchronisation and sharing, specialised clusters and batch systems. The added value of this combination of services is discussed, with special focus on the opportunities offered by the CERNBox service and it...

  5. Interactive Building Design Space Exploration Using Regionalized Sensitivity Analysis

    DEFF Research Database (Denmark)

    Jensen, Rasmus Lund; Maagaard, Steffen; Østergård, Torben

    2017-01-01

    Monte Carlo simulations combined with regionalized sensitivity analysis provide the means to explore a vast, multivariate design space in building design. Typically, sensitivity analysis shows how the variability of model output relates to the uncertainties in models inputs. This reveals which...... in combination with the interactive parallel coordinate plot (PCP). The latter is an effective tool to explore stochastic simulations and to find high-performing building designs. The proposed methods help decision makers to focus their attention to the most important design parameters when exploring...... a multivariate design space. As case study, we consider building performance simulations of a 15.000 m² educational centre with respect to energy demand, thermal comfort, and daylight....

  6. A novel comparative molecule/pseudo receptor interaction analysis

    Institute of Scientific and Technical Information of China (English)

    ZHOU Peng; TONG Jianbo; TIAN Feifei; LI Zhiliang

    2006-01-01

    Comparative molecule/pseudo receptor interaction analysis (CoMPIA) is developed as a novel 3D-QSAR method by adding postulated pseudo receptor and GA-optimized probe into comparative molecular field analysis (CoMFA). CoMPIA is used to find the pseudo receptor mode by optimizing probe distributions and to establish the optimal model of high qualities and good interpretations. Correlative coefficient R2, cross-validated correlative coefficient Q2 and root mean square error RMSEP of the resulting model are 0.940, 0.868 and 0.502, respectively by applying CoMPIA to quantitative structure-activity relationship (QSAR) of 31 classical steroids.

  7. Interactive Correspondence Analysis in a Dynamic Object-Oriented Environment

    Directory of Open Access Journals (Sweden)

    Jason Bond

    1997-11-01

    Full Text Available A highly interactive, user-friendly object-oriented software package written in LispStat is introduced that performs simple and multiple correspondence analysis, and profile analysis. These three techniques are integrated into a single environment driven by a user-friendly graphical interface that takes advantage of Lisp-Stat's advanced graphical capabilities. Techniques that assess the stability of the solution are also introduced. Some of the features of the package include colored graphics, incremental graph zooming capabilities, manual point separation to determine identities of overlapping points, and stability and fit measures. The features of the package are used to show some interesting trends in a large educational dataset.

  8. The interaction between the hepatitis C proteins NS4B and NS5A is involved in viral replication.

    Science.gov (United States)

    David, Naama; Yaffe, Yakey; Hagoel, Lior; Elazar, Menashe; Glenn, Jeffrey S; Hirschberg, Koret; Sklan, Ella H

    2015-01-15

    Hepatitis C virus (HCV) replicates in membrane associated, highly ordered replication complexes (RCs). These complexes include viral and host proteins necessary for viral RNA genome replication. The interaction network among viral and host proteins underlying the formation of these RCs is yet to be thoroughly characterized. Here, we investigated the association between NS4B and NS5A, two critical RC components. We characterized the interaction between these proteins using fluorescence resonance energy transfer and a mammalian two-hybrid system. Specific tryptophan residues within the C-terminal domain (CTD) of NS4B were shown to mediate this interaction. Domain I of NS5A, was sufficient to mediate its interaction with NS4B. Mutations in the NS4B CTD tryptophan residues abolished viral replication. Moreover, one of these mutations also affected NS5A hyperphosphorylation. These findings provide new insights into the importance of the NS4B-NS5A interaction and serve as a starting point for studying the complex interactions between the replicase subunits.

  9. The multiple imputation method: a case study involving secondary data analysis.

    Science.gov (United States)

    Walani, Salimah R; Cleland, Charles M

    2015-05-01

    To illustrate with the example of a secondary data analysis study the use of the multiple imputation method to replace missing data. Most large public datasets have missing data, which need to be handled by researchers conducting secondary data analysis studies. Multiple imputation is a technique widely used to replace missing values while preserving the sample size and sampling variability of the data. The 2004 National Sample Survey of Registered Nurses. The authors created a model to impute missing values using the chained equation method. They used imputation diagnostics procedures and conducted regression analysis of imputed data to determine the differences between the log hourly wages of internationally educated and US-educated registered nurses. The authors used multiple imputation procedures to replace missing values in a large dataset with 29,059 observations. Five multiple imputed datasets were created. Imputation diagnostics using time series and density plots showed that imputation was successful. The authors also present an example of the use of multiple imputed datasets to conduct regression analysis to answer a substantive research question. Multiple imputation is a powerful technique for imputing missing values in large datasets while preserving the sample size and variance of the data. Even though the chained equation method involves complex statistical computations, recent innovations in software and computation have made it possible for researchers to conduct this technique on large datasets. The authors recommend nurse researchers use multiple imputation methods for handling missing data to improve the statistical power and external validity of their studies.

  10. Ferrocene Orientation Determined Intramolecular Interactions Using Energy Decomposition Analysis

    Directory of Open Access Journals (Sweden)

    Feng Wang

    2015-11-01

    Full Text Available Two very different quantum mechanically based energy decomposition analyses (EDA schemes are employed to study the dominant energy differences between the eclipsed and staggered ferrocene conformers. One is the extended transition state (ETS based on the Amsterdam Density Functional (ADF package and the other is natural EDA (NEDA based in the General Atomic and Molecular Electronic Structure System (GAMESS package. It reveals that in addition to the model (theory and basis set, the fragmentation channels more significantly affect the interaction energy terms (ΔE between the conformers. It is discovered that such an interaction energy can be absorbed into the pre-partitioned fragment channels so that to affect the interaction energies in a particular conformer of Fc. To avoid this, the present study employs a complete fragment channel—the fragments of ferrocene are individual neutral atoms. It therefore discovers that the major difference between the ferrocene conformers is due to the quantum mechanical Pauli repulsive energy and orbital attractive energy, leading to the eclipsed ferrocene the energy preferred structure. The NEDA scheme further indicates that the sum of attractive (negative polarization (POL and charge transfer (CL energies prefers the eclipsed ferrocene. The repulsive (positive deformation (DEF energy, which is dominated by the cyclopentadienyle (Cp rings, prefers the staggered ferrocene. Again, the cancellation results in a small energy residue in favour of the eclipsed ferrocene, in agreement with the ETS scheme. Further Natural Bond Orbital (NBO analysis indicates that all NBO energies, total Lewis (no Fe and lone pair (LP deletion all prefer the eclipsed Fc conformer. The most significant energy preferring the eclipsed ferrocene without cancellation is the interactions between the donor lone pairs (LP of the Fe atom and the acceptor antibond (BD* NBOs of all C–C and C–H bonds in the ligand, LP(Fe-BD*(C–C & C

  11. Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease

    DEFF Research Database (Denmark)

    Jensen, Majken Karoline; Pers, Tune Hannes; Dworzynski, Piotr

    2011-01-01

    Background-Network-based approaches may leverage genome-wide association (GWA) analysis by testing for the aggregate association across several pathway members. We aimed to examine if networks of genes that represent experimentally determined protein-protein interactions (PPIs) are enriched...... are involved in abnormal cardiovascular system physiological features based on knockout mice (4-fold enrichment; Fisher exact test, P = 0.006). Ingenuity pathway analysis revealed that canonical pathways, especially related to blood pressure regulation, were significantly enriched in the genes from the top...... complex. Conclusions-The integration of a GWA study with PPI data successfully identifies a set of candidate susceptibility genes for incident CHD that would have been missed in single-marker GWA analysis. (Circ Cardiovasc Genet. 2011; 4:549-556.)...

  12. VALIDATION OF CRACK INTERACTION LIMIT MODEL FOR PARALLEL EDGE CRACKS USING TWO-DIMENSIONAL FINITE ELEMENT ANALYSIS

    Directory of Open Access Journals (Sweden)

    R. Daud

    2013-06-01

    Full Text Available Shielding interaction effects of two parallel edge cracks in finite thickness plates subjected to remote tension load is analyzed using a developed finite element analysis program. In the present study, the crack interaction limit is evaluated based on the fitness of service (FFS code, and focus is given to the weak crack interaction region as the crack interval exceeds the length of cracks (b > a. Crack interaction factors are evaluated based on stress intensity factors (SIFs for Mode I SIFs using a displacement extrapolation technique. Parametric studies involved a wide range of crack-to-width (0.05 ≤ a/W ≤ 0.5 and crack interval ratios (b/a > 1. For validation, crack interaction factors are compared with single edge crack SIFs as a state of zero interaction. Within the considered range of parameters, the proposed numerical evaluation used to predict the crack interaction factor reduces the error of existing analytical solution from 1.92% to 0.97% at higher a/W. In reference to FFS codes, the small discrepancy in the prediction of the crack interaction factor validates the reliability of the numerical model to predict crack interaction limits under shielding interaction effects. In conclusion, the numerical model gave a successful prediction in estimating the crack interaction limit, which can be used as a reference for the shielding orientation of other cracks.

  13. Identification and functional analysis of a potential key lncRNA involved in fat loss of cancer cachexia.

    Science.gov (United States)

    Liu, Huiquan; Zhou, Ting; Wang, Bangyan; Li, Lu; Ye, Dawei; Yu, Shiying

    2017-08-07

    Cancer cachexia is a devastating, multifactorial, and irreversible syndrome characterized by skeletal muscle reduction with or without fat loss. Although much attention has been focused on muscle wasting, fat loss may occur earlier and accelerate muscle wasting in cachexia. The cause of 20% of cancer related death makes it urgent to discover molecular mechanisms behind cancer cachexia. Here we applied weighted gene co-expression network analysis (WGCNA) to identify cachexia related gene modules using differentially expressed 3289 genes and 59 long non-coding RNAs based on microarray data of cachectic and non-cachectic subcutaneous adipose tissue. Subsequently, 16 independent modules were acquired and GSAASeqSP Toolset confirmed that black module was significantly associated with fat loss in cancer cachexia. Top 50 hub-genes in black module contained only one lncRNA, VLDLR antisense RNA 1 (VLDLR-AS1). We then explored the function of black module from the view of VLDLR-AS1-connected genes in the network. GO enrichment and KEGG pathways analysis revealed LDLR-AS1-connected genes were involved in Wnt signaling pathway, small GTPase mediated signal transduction, epithelial-mesenchymal transition and so on. Through construction of competing endogenous RNAs (ceRNAs) regulation network, we showed that VLDLR-AS1 may function with hsa-miR-600 to regulate gene GOLGA3, DUSP14, and UCHL1, or interact with hsa-miR-1224-3p to modulate the expression of gene GOLGA3, ZNF219, RNF141, and CALU. After literature validation, we predicted that VLDLR-AS1 most likely interacted with miR-600 to regulate UCH-L1 through Wnt/β-catenin signaling pathway. However, further experiments are still required to validate mechanisms of VLDLR-AS1 in fat reduction of cancer cachexia. © 2017 Wiley Periodicals, Inc.

  14. Quantitative proteomic analysis of the interaction between the endophytic plant-growth-promoting bacterium Gluconacetobacter diazotrophicus and sugarcane.

    Science.gov (United States)

    Lery, Letícia M S; Hemerly, Adriana S; Nogueira, Eduardo M; von Krüger, Wanda M A; Bisch, Paulo M

    2011-05-01

    Gluconacetobacter diazotrophicus is a plant-growth-promoting bacterium that colonizes sugarcane. In order to investigate molecular aspects of the G. diazotrophicus-sugarcane interaction, we performed a quantitative mass spectrometry-based proteomic analysis by (15)N metabolic labeling of bacteria, root samples, and co-cultures. Overall, more than 400 proteins were analyzed and 78 were differentially expressed between the plant-bacterium interaction model and control cultures. A comparative analysis of the G. diazotrophicus in interaction with two distinct genotypes of sugarcane, SP70-1143 and Chunee, revealed proteins with fundamental roles in cellular recognition. G. diazotrophicus presented proteins involved in adaptation to atypical conditions and signaling systems during the interaction with both genotypes. However, SP70-1143 and Chunee, sugarcane genotypes with high and low contribution of biological nitrogen fixation, showed divergent responses in contact with G. diazotrophicus. The SP70-1143 genotype overexpressed proteins from signaling cascades and one from a lipid metabolism pathway, whereas Chunee differentially synthesized proteins involved in chromatin remodeling and protein degradation pathways. In addition, we have identified 30 bacterial proteins in the roots of the plant samples; from those, nine were specifically induced by plant signals. This is the first quantitative proteomic analysis of a bacterium-plant interaction, which generated insights into early signaling of the G. diazotrophicus-sugarcane interaction.

  15. Detailed analysis of distraction induced by in-vehicle verbal interactions on visual search performance

    Directory of Open Access Journals (Sweden)

    Kazumitsu Shinohara

    2010-07-01

    Full Text Available We examined the negative effect of in-vehicle verbal interaction on visual search performance. Twenty participants performed a primary visual search task and a secondary verbal interaction task concurrently. We found that visual search performance deteriorated when the secondary task involving memory retrieval and speech production was performed concurrently. Moreover, a detailed analysis of the reaction time as a function of set size revealed that the increased reaction time was attributed not to the slowing of inspecting each item but to the increased processing time other than the inspection of each visual item, possibly due to task switching between the primary visual search task and the secondary verbal task. These findings have implications for providing information from in-vehicle information devices while reducing the risk of driver distraction.

  16. Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

    Science.gov (United States)

    Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

    2016-05-01

    Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

  17. Roles of rifampicin in drug-drug interactions: underlying molecular mechanisms involving the nuclear pregnane X receptor

    Directory of Open Access Journals (Sweden)

    Raymond Kenneth

    2006-02-01

    Full Text Available Abstract Rifampicin, an important drug in the treatment of tuberculosis, is used extensively despite its broad effects on drug-drug interactions, creating serious problems. The clinical importance of such interactions includes autoinduction leading to suboptimal or failed treatment. The concomitantly administered effects of rifampicin on other drugs can result in their altered metabolism or transportation that are metabolised by cytochromes P450 or transported by p-glycoprotein in the gastrointestinal tract and liver. This review paper summarises recent findings with emphases on the molecular mechanisms used to explain these broad drug-drug interactions. In general, rifampicin can act on a pattern: rifampicin activates the nuclear pregnane X receptor that in turn affects cytochromes P450, glucuronosyltransferases and p-glycoprotein activities. This pattern of action may explain many of the rifampicin inducing drug-drug interactions. However, effects through other mechanisms have also been reported and these make any explanation of such drug-drug interactions more complex.

  18. Changes in oxidative enzyme activity during interspecific mycelial interactions involving the white-rot fungus Trametes versicolor.

    Science.gov (United States)

    Hiscox, Jennifer; Baldrian, Petr; Rogers, Hilary J; Boddy, Lynne

    2010-06-01

    Interspecific fungal antagonism leads to biochemical changes in competing mycelia, including up-regulation of oxidative enzymes. Laccase, manganese peroxidase (MnP), manganese-repressed peroxidase (MRP) and lignin peroxidase (LiP) gene expression and enzyme activity were compared during agar interactions between Trametes versicolor and five other wood decay fungi resulting in a range of interaction outcomes from deadlock to replacement of one fungus by another. Increased laccase and Mn-oxidising activities were detected at all interaction zones, but there were few changes in activity in regions away from the interaction zone in T. versicolor mycelia compared to self-pairings. Whilst no LiP activity was detected in any pairing, low level LiP gene expression was detected. MnP activity was detected but not expression of MnP genes; instead, MRP could explain the observed activity. No relationship was found between extent of enzyme activity increase and interaction outcome. Similarities between patterns of gene expression and enzyme activity are discussed.

  19. Interaction of human mitochondrial transcription factor A in mitochondria: its involvement in the dynamics of mitochondrial DNA nucleoids.

    Science.gov (United States)

    Kasashima, Katsumi; Endo, Hitoshi

    2015-12-01

    Mitochondrial transcription factor A (TFAM) is a key regulator of mitochondrial DNA (mtDNA). TFAM interacts with itself and forms dimers; however, the precise interaction domain in vivo has not yet been determined. We herein showed that human TFAM formed oligomers in mitochondria by in situ chemical cross-linking. We used the separated fluorescent protein, monomeric Kusabira-Green, as a reporter to monitor their self-association in mitochondria. This reporter successfully detected the TFAM-TFAM interaction in cells as fluorescent signals on mitochondria. We also found that the N-terminal high-mobility group box domain was sufficient for this interaction. The expression of the dimer-defective mutant induced enlarged mtDNA nucleoids, suggesting the importance of dimerization in the distribution of mtDNA. The reporter system also supported the association and mixture between independent nucleoids through TFAM by a cell fusion assay using hemagglutinating virus of Japan. We here, for the first time, visualized the interaction of TFAM molecules in mitochondria and proposed its implications for the dynamics of mtDNA nucleoids.

  20. Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis

    Directory of Open Access Journals (Sweden)

    Ueki Masao

    2012-05-01

    Full Text Available Abstract Background Genome-wide gene-gene interaction analysis using single nucleotide polymorphisms (SNPs is an attractive way for identification of genetic components that confers susceptibility of human complex diseases. Individual hypothesis testing for SNP-SNP pairs as in common genome-wide association study (GWAS however involves difficulty in setting overall p-value due to complicated correlation structure, namely, the multiple testing problem that causes unacceptable false negative results. A large number of SNP-SNP pairs than sample size, so-called the large p small n problem, precludes simultaneous analysis using multiple regression. The method that overcomes above issues is thus needed. Results We adopt an up-to-date method for ultrahigh-dimensional variable selection termed the sure independence screening (SIS for appropriate handling of numerous number of SNP-SNP interactions by including them as predictor variables in logistic regression. We propose ranking strategy using promising dummy coding methods and following variable selection procedure in the SIS method suitably modified for gene-gene interaction analysis. We also implemented the procedures in a software program, EPISIS, using the cost-effective GPGPU (General-purpose computing on graphics processing units technology. EPISIS can complete exhaustive search for SNP-SNP interactions in standard GWAS dataset within several hours. The proposed method works successfully in simulation experiments and in application to real WTCCC (Wellcome Trust Case–control Consortium data. Conclusions Based on the machine-learning principle, the proposed method gives powerful and flexible genome-wide search for various patterns of gene-gene interaction.

  1. Identification and expression analysis of MATE genes involved in flavonoid transport in blueberry plants.

    Directory of Open Access Journals (Sweden)

    Li Chen

    Full Text Available Multidrug and toxic compound extrusion (MATE proteins are the most recently identified family of multidrug transporters. In plants, this family is remarkably large compared to the human and bacteria counterpart, highlighting the importance of MATE proteins in this kingdom. Here 33 Unigenes annotated as MATE transporters were found in the blueberry fruit transcriptome, of which eight full-length cDNA sequences were identified and cloned. These proteins are composed of 477-517 residues, with molecular masses ~54 kDa, and theoretical isoelectric points from 5.35 to 8.41. Bioinformatics analysis predicted 10-12 putative transmembrane segments for VcMATEs, and localization to the plasma membrane without an N-terminal signal peptide. All blueberry MATE proteins shared 32.1-84.4% identity, among which VcMATE2, VcMATE3, VcMATE5, VcMATE7, VcMATE8, and VcMATE9 were more similar to the MATE-type flavonoid transporters. Phylogenetic analysis showed VcMATE2, VcMATE3, VcMATE5, VcMATE7, VcMATE8 and VcMATE9 clustered with MATE-type flavonoid transporters, indicating that they might be involved in flavonoid transport. VcMATE1 and VcMATE4 may be involved in the transport of secondary metabolites, the detoxification of xenobiotics, or the export of toxic cations. Real-time quantitative PCR demonstrated that the expression profile of the eight VcMATE genes varied spatially and temporally. Analysis of expression and anthocyanin accumulation indicated that there were some correlation between the expression profile and the accumulation of anthocyanins. These results showed VcMATEs might be involved in diverse physiological functions, and anthocyanins across the membranes might be mutually maintained by MATE-type flavonoid transporters and other mechanisms. This study will enrich the MATE-based transport mechanisms of secondary metabolite, and provide a new biotechonology strategy to develop better nutritional blueberry cultivars.

  2. Identification and expression analysis of MATE genes involved in flavonoid transport in blueberry plants.

    Science.gov (United States)

    Chen, Li; Liu, Yushan; Liu, Hongdi; Kang, Limin; Geng, Jinman; Gai, Yuzhuo; Ding, Yunlong; Sun, Haiyue; Li, Yadong

    2015-01-01

    Multidrug and toxic compound extrusion (MATE) proteins are the most recently identified family of multidrug transporters. In plants, this family is remarkably large compared to the human and bacteria counterpart, highlighting the importance of MATE proteins in this kingdom. Here 33 Unigenes annotated as MATE transporters were found in the blueberry fruit transcriptome, of which eight full-length cDNA sequences were identified and cloned. These proteins are composed of 477-517 residues, with molecular masses ~54 kDa, and theoretical isoelectric points from 5.35 to 8.41. Bioinformatics analysis predicted 10-12 putative transmembrane segments for VcMATEs, and localization to the plasma membrane without an N-terminal signal peptide. All blueberry MATE proteins shared 32.1-84.4% identity, among which VcMATE2, VcMATE3, VcMATE5, VcMATE7, VcMATE8, and VcMATE9 were more similar to the MATE-type flavonoid transporters. Phylogenetic analysis showed VcMATE2, VcMATE3, VcMATE5, VcMATE7, VcMATE8 and VcMATE9 clustered with MATE-type flavonoid transporters, indicating that they might be involved in flavonoid transport. VcMATE1 and VcMATE4 may be involved in the transport of secondary metabolites, the detoxification of xenobiotics, or the export of toxic cations. Real-time quantitative PCR demonstrated that the expression profile of the eight VcMATE genes varied spatially and temporally. Analysis of expression and anthocyanin accumulation indicated that there were some correlation between the expression profile and the accumulation of anthocyanins. These results showed VcMATEs might be involved in diverse physiological functions, and anthocyanins across the membranes might be mutually maintained by MATE-type flavonoid transporters and other mechanisms. This study will enrich the MATE-based transport mechanisms of secondary metabolite, and provide a new biotechonology strategy to develop better nutritional blueberry cultivars.

  3. Identification and analysis of signaling networks potentially involved in breast carcinoma metastasis to the brain.

    Directory of Open Access Journals (Sweden)

    Feng Li

    Full Text Available Brain is a common site of breast cancer metastasis associated with significant neurologic morbidity, decreased quality of life, and greatly shortened survival. However, the molecular and cellular mechanisms underpinning brain colonization by breast carcinoma cells are poorly understood. Here, we used 2D-DIGE (Difference in Gel Electrophoresis proteomic analysis followed by LC-tandem mass spectrometry to identify the proteins differentially expressed in brain-targeting breast carcinoma cells (MB231-Br compared with parental MDA-MB-231 cell line. Between the two cell lines, we identified 12 proteins consistently exhibiting greater than 2-fold (p<0.05 difference in expression, which were associated by the Ingenuity Pathway Analysis (IPA with two major signaling networks involving TNFα/TGFβ-, NFκB-, HSP-70-, TP53-, and IFNγ-associated pathways. Remarkably, highly related networks were revealed by the IPA analysis of a list of 19 brain-metastasis-associated proteins identified recently by the group of Dr. A. Sierra using MDA-MB-435-based experimental system (Martin et al., J Proteome Res 2008 7:908-20, or a 17-gene classifier associated with breast cancer brain relapse reported by the group of Dr. J. Massague based on a microarray analysis of clinically annotated breast tumors from 368 patients (Bos et al., Nature 2009 459: 1005-9. These findings, showing that different experimental systems and approaches (2D-DIGE proteomics used on brain targeting cell lines or gene expression analysis of patient samples with documented brain relapse yield highly related signaling networks, suggest strongly that these signaling networks could be essential for a successful colonization of the brain by metastatic breast carcinoma cells.

  4. A statistical mechanical calculation of the thermodynamic properties of interstitial solid solutions involving second nearest neighbor interactions.

    Science.gov (United States)

    Alex, K.; Mclellan, R. B.

    1971-01-01

    A previous calculation of the thermodynamic properties of interstitial solid solutions based on the technique of Kirkwood expansions has been extended to include the effects of second nearest neighbor solute atom mutual interactions. The error inherent in the first order (or quasi-chemical) counting of the degeneracy of the solution crystal is avoided. It is shown that, at high temperatures, even strong second nearest neighbor solute mutual interactions have a negligible effect on the entropy of the solution and a small, temperature-dependent effect on the solute partial enthalpy.

  5. Prediction of drug-drug interactions from chemogenomic and gene-gene interactions and analysis of drug-drug interactions

    OpenAIRE

    2013-01-01

    The interactions between multiple drugs administered to an organism concurrently, whether in the form of synergy or antagonism, are of clinical relevance. Moreover, un-derstanding the mechanisms and nature of drug-drug interactions is of great practical and theoretical interest. Work has previously been done on gene-gene and gene-drug interactions, but the prediction and rationalization of drug-drug interactions from this data is not straightforward. We present a strategy for attacking this p...

  6. Transcriptome analysis in Ceratitis capitata to unveil genes involved in ageing-maturation process

    Directory of Open Access Journals (Sweden)

    V. San Andrés

    2013-07-01

    Full Text Available The sterile insect technique (SIT is widely used in integrated programmes against the Mediterranean fruit fly, Ceratitis capitata (Wiedemann (Diptera: Tephritidae. Information on the age distribution of insects, and more particularly, the knowledge of wild female reproductive status (mature or not at the time of the sterile male release is one of the key factors for the success of the SIT. In recent years, sequencing analysis has become an important tool in molecular biology. In this work we present a genome-wide expression analysis based on SSH (substractive sequence hybridization and EST (expressed sequence tag sequencing and macroarray expression analysis to identify signature genes related to the ageing-maturing process in C. capitata, leading to the successful identification of new putative candidate genes of reproductive status in medfly that would serve as molecular markers for ageing. We have sorted out 94 unigenes from 873 single-pass ESTs, of which 57% have homology with known genes. Ageing-maturing process in C. capitata presents a marked expression pattern accompanied by the increase of transcription level of genes involved in reproduction (vitellogenins, chorion proteins and male-specific serum proteins. Other identified cDNAs (43% with a differential expression pattern would be also candidates but deserve further studies, as they belong to the unknown function class.

  7. Proteomic Analysis Reveals Proteins Involved in Seed Imbibition under Salt Stress in Rice.

    Science.gov (United States)

    Xu, Enshun; Chen, Mingming; He, Hui; Zhan, Chengfang; Cheng, Yanhao; Zhang, Hongsheng; Wang, Zhoufei

    2016-01-01

    Enhancement of salinity tolerance during seed germination is very important for direct seeding in rice. In this study, the salt-tolerant japonica landrace Jiucaiqing was used to determine the regulators that are involved in seed imbibition under salt stress. Briefly, the comparative proteomic analysis was conducted between dry (0 h) and imbibed (24 h) seeds with 150 mM NaCl. Under salt stress, the uptake of water increased rapidly before 24 h imbibition (Phase I), followed by a plateau of seed imbibition from 24 to 96 h imbibition (Phase II). We identified 14 proteins involved in seed imbibition, in which the majority of these proteins were involved in energy supply and storage protein. The early imbibition process was mediated by protein catabolism; the most of proteins were down-regulated after 24 h imbibition. Eleven genes in salt stress treated seeds were expressed early during the seed imbibition in comparison to control seeds. By comparison, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (BPM), glutelin (GLU2.2 and GLU2.3), glucose-1-phosphate adenylyltransferase large subunit (GAS8), and cupin domain containing protein (CDP3.1 and CDP3.2) were near the regions of quantitative trait loci (QTLs) for seed dormancy, seed reserve utilization, and seed germination in Jiucaiqing. In particular, CDP3.1 was co-located in the region of qIR-3 for imbibition rate, and qGP-3 for germination percentage. The role of CDP3.1 was verified in enhancing seed germination under salt stress using T-DNA mutant. The identified proteins might be applicable for the improvement of seed germination under salt stress in rice.

  8. Clinical analysis of neuropsychiatric systemic lupus erythematosus involving the central nervous system

    Directory of Open Access Journals (Sweden)

    YANG Huan

    2013-01-01

    Full Text Available Background Neuropsychiatric systemic lupus erythematosus (NP-SLE presents with a wide variety of clinical manifestations, which is often difficult to diagnose with a high mortality. This study aims to investigate the clinical features of NP-SLE involving the central nervous system (CNS and the differential diagnoses between CNS NP-SLE and intracranial infections. Methods The clinical manifestations, serum immunological features, cerebrospinal fluid (CSF examinations (including intracranial pressure, leukocyte count, protein, glucose and chloride, CT and (or MRI and electroencephalogram (EEG data of 23 NP-SLE patients with CNS involved were retrospectively reviewed. Results Nine patients presented with diffuse manifestations, while 14 patients presented with focal manifestations. Serum analysis showed the positive rates of immunoglobulins anti-nuclear antibody (ANA, anti-double stranded DNA antibody (dsDNA, anti-Sm, anti-ribosmal P protein, anti-SSA and anti-SSB antibodies were 21/22, 7/22, 1/14, 2/14, 9/14 and 3/14 respectively. Patients with decreased serum C3 accounted for 14/20 while patients with decreased serum C4 accounted for 5/20. Besides, patients with increased CSF leukocyte count and microalbumin took up 5/12 and 7/12, while patients with decreased glucose and chloride levels took up 5/12 and 6/12. All 23 patients presented abnormal CT and (or MRI and 6 patients presented abnormal EEG. Conclusion Serum immunological levels, CT and (or MRI and EEG examinations contributed to the diagnosis of NP-SLE involving CNS. Although CSF analyses were slightly abnormal, the increase of leukocyte count and average microalbumin was not obvious, and the mean values of glucose and chloride were in the normal range, suggesting that the CSF examinations were helpful for the differential diagnoses from intracranial infections. Glucocorticoids and immunosuppressive drugs were remarkably effective for CNS NP-SLE patients.

  9. Identification and expression analysis of candidate genes involved in carotenoid biosynthesis in chickpea seeds

    Directory of Open Access Journals (Sweden)

    Mohammad Kazem Rezaei

    2016-12-01

    Full Text Available Plant carotenoids have a key role in preventing various diseases in human because of their antioxidant and provitamin A properties. Chickpea is a good source of carotenoid among legumes and its diverse germplasm and genome accessibility makes it a good model for carotenogenesis studies. The structure, location and copy numbers of genes involved in carotenoid biosynthesis were retrieved from the chickpea genome. The majority of the single nucleotide polymorphism (SNPs within these genes across five diverse chickpea cultivars was synonymous mutation. We examined the expression of the carotenogenesis genes and their association with carotenoid concentration at different seed development stages of five chickpea cultivars. Total carotenoid concentration ranged from 22 μg g-1 in yellow cotyledon kabuli to 44 μg g-1 in green cotyledon desi at 32 days post anthesis (DPA. The majority of carotenoids in chickpea seeds consists of lutein and zeaxanthin. The expression of the selected 19 genes involved in carotenoid biosynthesis pathway showed common pattern across five cultivars with higher expression at 8 and/or 16 DPA then dropped considerably at 24 and 32 DPA. Almost all genes were up-regulated in CDC Jade cultivar. Correlation analysis between gene expression and carotenoid concentration showed that the genes involved in the primary step of carotenoid biosynthesis pathway including carotenoid desaturase and isomerase positively correlated with various carotenoid components in chickpea seeds. A negative correlation was found between hydroxylation activity and provitamin A concentration in the seeds. The highest provitamin A concentration including β-carotene and β-cryptoxanthin were found in green cotyledon chickpea cultivars.

  10. Transcriptome analysis identifies genes involved in ethanol response of Saccharomyces cerevisiae in Agave tequilana juice.

    Science.gov (United States)

    Ramirez-Córdova, Jesús; Drnevich, Jenny; Madrigal-Pulido, Jaime Alberto; Arrizon, Javier; Allen, Kirk; Martínez-Velázquez, Moisés; Alvarez-Maya, Ikuri

    2012-08-01

    During ethanol fermentation, yeast cells are exposed to stress due to the accumulation of ethanol, cell growth is altered and the output of the target product is reduced. For Agave beverages, like tequila, no reports have been published on the global gene expression under ethanol stress. In this work, we used microarray analysis to identify Saccharomyces cerevisiae genes involved in the ethanol response. Gene expression of a tequila yeast strain of S. cerevisiae (AR5) was explored by comparing global gene expression with that of laboratory strain S288C, both after ethanol exposure. Additionally, we used two different culture conditions, cells grown in Agave tequilana juice as a natural fermentation media or grown in yeast-extract peptone dextrose as artificial media. Of the 6368 S. cerevisiae genes in the microarray, 657 genes were identified that had different expression responses to ethanol stress due to strain and/or media. A cluster of 28 genes was found over-expressed specifically in the AR5 tequila strain that could be involved in the adaptation to tequila yeast fermentation, 14 of which are unknown such as yor343c, ylr162w, ygr182c, ymr265c, yer053c-a or ydr415c. These could be the most suitable genes for transforming tequila yeast to increase ethanol tolerance in the tequila fermentation process. Other genes involved in response to stress (RFC4, TSA1, MLH1, PAU3, RAD53) or transport (CYB2, TIP20, QCR9) were expressed in the same cluster. Unknown genes could be good candidates for the development of recombinant yeasts with ethanol tolerance for use in industrial tequila fermentation.

  11. Interaction between the FTO gene, body mass index and depression: meta-analysis of 13701 individuals.

    Science.gov (United States)

    Rivera, Margarita; Locke, Adam E; Corre, Tanguy; Czamara, Darina; Wolf, Christiane; Ching-Lopez, Ana; Milaneschi, Yuri; Kloiber, Stefan; Cohen-Woods, Sara; Rucker, James; Aitchison, Katherine J; Bergmann, Sven; Boomsma, Dorret I; Craddock, Nick; Gill, Michael; Holsboer, Florian; Hottenga, Jouke-Jan; Korszun, Ania; Kutalik, Zoltan; Lucae, Susanne; Maier, Wolfgang; Mors, Ole; Müller-Myhsok, Bertram; Owen, Michael J; Penninx, Brenda W J H; Preisig, Martin; Rice, John; Rietschel, Marcella; Tozzi, Federica; Uher, Rudolf; Vollenweider, Peter; Waeber, Gerard; Willemsen, Gonneke; Craig, Ian W; Farmer, Anne E; Lewis, Cathryn M; Breen, Gerome; McGuffin, Peter

    2017-08-01

    BackgroundDepression and obesity are highly prevalent, and major impacts on public health frequently co-occur. Recently, we reported that having depression moderates the effect of the FTO gene, suggesting its implication in the association between depression and obesity.AimsTo confirm these findings by investigating the FTO polymorphism rs9939609 in new cohorts, and subsequently in a meta-analysis.MethodThe sample consists of 6902 individuals with depression and 6799 controls from three replication cohorts and two original discovery cohorts. Linear regression models were performed to test for association between rs9939609 and body mass index (BMI), and for the interaction between rs9939609 and depression status for an effect on BMI. Fixed and random effects meta-analyses were performed using METASOFT.ResultsIn the replication cohorts, we observed a significant interaction between FTO, BMI and depression with fixed effects meta-analysis (β = 0.12, P = 2.7 × 10(-4)) and with the Han/Eskin random effects method (P = 1.4 × 10(-7)) but not with traditional random effects (β = 0.1, P = 0.35). When combined with the discovery cohorts, random effects meta-analysis also supports the interaction (β = 0.12, P = 0.027) being highly significant based on the Han/Eskin model (P = 6.9 × 10(-8)). On average, carriers of the risk allele who have depression have a 2.2% higher BMI for each risk allele, over and above the main effect of FTOConclusionsThis meta-analysis provides additional support for a significant interaction between FTO, depression and BMI, indicating that depression increases the effect of FTO on BMI. The findings provide a useful starting point in understanding the biological mechanism involved in the association between obesity and depression. © The Royal College of Psychiatrists 2017.

  12. Association between the Interaction of Key Genes Involved in Effector T-Cell Pathways and Susceptibility to Develop allergic Rhinitis: A Population-Based Case-Control Association Study.

    Directory of Open Access Journals (Sweden)

    Yuan Zhang

    Full Text Available Evidence suggests that interaction between key genes mediating signaling and transcriptional networks involving effector T-cell responses may influence an individual's susceptibility to develop allergic rhinitis(AR.The aim of this study was todetermine whether specific interactions between key genes involved in effector T-cell pathways are associated with an individual's susceptibility to develop AR in Han Chinese subjects.A cohort of 489 patients with AR and 421 healthy controls was enrolled from the Han Chinese population in Beijing, China. AR was established by questionnaire and clinical examination, and peripheral blood was drawn from all subjects for DNA extraction. A total of 96 single nucleotide polymorphisms (SNPs in 26 reprehensive candidate genes involved in T helper 1 (Th1, Th2, Th17, Th9 and T regulatory cell pathways were selected from the International Haplotype Mappingdatabase for Han Chinese in Beijing (CHB population, and IlluminaGoldenGate assay was conducted for SNP genotyping. The PLINK software package was used to perform statistical analyses.Simple SNP-phenotype association analysis using logistic regression showed SNP rs8193036 in IL17A gene, rs2569254 in IL-12 and rs1898413 in RORα weresignificantlyassociatedwith AR.Simple SNP-phenotype association analysis with genetic models demonstrated thatrs2569254 in IL-12, rs1031508 in STAT4, and rs3741809 in IL-26 were likely to be recessive, rs8193036 in IL17A allelic, rs897200in STAT4 genotypic, and rs1898413 in RORα dominant. Epistasis analyses exhibited that 83 SNPs in 23 genes were significantly interactive; of which 59 interactions/SNP pairs demonstrated OR values higher than 2 or lower than 0.5, and 12 interactions/SNP pairs OR values higher than 4 or lower than 0.25. STAT3, RORα and IL-26, involved in Th17 pathway,were the mostfrequentlyinteractive genes.This study suggests that interactions between several SNPs in key genes involved in effector T-cell pathways are

  13. The involvement of girls and boys with bullying: an analysis of gender differences.

    Science.gov (United States)

    Silva, Marta Angélica Iossi; Pereira, Beatriz; Mendonça, Denisa; Nunes, Berta; de Oliveira, Wanderlei Abadio

    2013-12-05

    This exploratory and cross-sectional study aimed to identify the prevalence of bullying in a group of students and analyze the data regarding the gender of those involved in the violence. A questionnaire adapted from Olweus was applied in seven elementary education schools in Portugal. The sample consisted of 387 students between 7 and 14 years old. Data are presented in terms of descriptive statistics and differences between proportions were analyzed using chi-square tests. The gender analysis of victimization and aggression shows that boys and girls are both victims and aggressors, and there are significant differences in involvement in bullying between genders and the roles played. Boys are victims more often when considering different types of bullying, although significant differences were only found for physical aggression. Strategies that include gender roles are a priority for prevention and careful attention to this phenomenon in the school context. The questions addressed contribute to a broader understanding of the phenomenon, emphasizing the differential participation of boys and girls in bullying.

  14. The Involvement of Girls and Boys with Bullying: An Analysis of Gender Differences

    Directory of Open Access Journals (Sweden)

    Marta Angélica Iossi Silva

    2013-12-01

    Full Text Available This exploratory and cross-sectional study aimed to identify the prevalence of bullying in a group of students and analyze the data regarding the gender of those involved in the violence. A questionnaire adapted from Olweus was applied in seven elementary education schools in Portugal. The sample consisted of 387 students between 7 and 14 years old. Data are presented in terms of descriptive statistics and differences between proportions were analyzed using chi-square tests. The gender analysis of victimization and aggression shows that boys and girls are both victims and aggressors, and there are significant differences in involvement in bullying between genders and the roles played. Boys are victims more often when considering different types of bullying, although significant differences were only found for physical aggression. Strategies that include gender roles are a priority for prevention and careful attention to this phenomenon in the school context. The questions addressed contribute to a broader understanding of the phenomenon, emphasizing the differential participation of boys and girls in bullying.

  15. Lateral and perpendicular interaction forces involved in mobile and immobile adhesion of microorganism on model solid surfaces

    NARCIS (Netherlands)

    Busscher, HJ; Poortinga, AT; Bos, R.R.M.

    1998-01-01

    Gliding and near-surface swimming of microorganisms are described as a mobile form of microbial adhesion that need not necessarily be reversible. It is argued that the reversibility of microbial adhesion depends on the depth of the secondary interaction minimum, calculated from the forces between an

  16. The uses of overlap: carer-child interaction involving a nine-year-old boy with auditory neuropathy.

    Science.gov (United States)

    Anstey, Julie; Wells, Bill

    2013-01-01

    The subject of this single case study, Ricky, is a nine-year-old boy with a profound hearing loss arising from auditory neuropathy. Despite cochlear implantation at the age of two, his receptive language skills remain very restricted and his speech is unintelligible. Techniques of interactional linguistics are used to analyse recordings of Ricky and his mother during shared book reading. Both participants display competences in managing turn-taking and overlapping talk that enable them to progress the book-reading activity, to talk spontaneously on topically related matters and also to handle issues of phonetic and linguistic repair. Instances of both competitive and non-competitive overlap reveal that Ricky has access to interactionally important prosodic skills. The study thus reinforces the need, when assessing a child's potential to understand and use spoken language, to examine the child's talk from an interactional perspective. It further indicates that overlapping talk is not necessarily a problem; indeed it can be part of a solution to issues of interpersonal understanding that routinely arise in the course of talk-in-interaction.

  17. Interactions of plasminogen activator inhibitor-1 with vitronectin involve an extensive binding surface and induce mutual conformational rearrangements

    DEFF Research Database (Denmark)

    Blouse, Grant E; Dupont, Daniel Miotto; Schar, Christine R

    2009-01-01

    full-length vitronectin is present. Nonetheless, in all cases, the initial fast interaction is followed by slower fluorescence changes attributed to a conformational change in PAI-1. Complementary experiments using an engineered, fluorescently silent PAI-1 with non-natural amino acids showed...

  18. Methodology for Design and Analysis of Reactive Distillation Involving Multielement Systems

    DEFF Research Database (Denmark)

    Jantharasuk, Amnart; Gani, Rafiqul; Górak, Andrzej;

    2011-01-01

    A new methodology for design and analysis of reactive distillation has been developed. In this work, the elementbased approach, coupled with a driving force diagram, has been extended and applied to the design of a reactive distillation column involving multielement (multicomponent) systems....... The transformation of ordinary systems to element-based ones and the aggregation of non-key elements allow the important design parameters, such as the number of stages, feed stage and minimum reflux ratio, to be determined by using simple diagrams similar to those regularly employed for non-reactive systems...... consisting of two components. Based on this methodology, an optimal design configuration is identified using the equivalent binary-element-driving force diagram. Two case studies of methyl acetate (MeOAc) synthesis and methyl-tert-butyl ether (MTBE) synthesis have been considered to demonstrate...

  19. Evidence that the pathway of disulfide bond formation in Escherichia coli involves interactions between the cysteines of DsbB and DsbA.

    OpenAIRE

    Guilhot, C; Jander, G.; Martin, N L; Beckwith, J

    1995-01-01

    Disulfide bond formation is catalyzed in the periplasm of Escherichia coli. This process involves at least two proteins: DsbA and DsbB. Recent evidence suggests that DsbA, a soluble periplasmic protein directly catalyzes disulfide bond formation in proteins, whereas DsbB, an inner membrane protein, is involved in the reoxidation of DsbA. Here we present direct evidence of an interaction between DsbA and DsbB. (Kishigami et al. [Kishigami, S., Kanaya, E., Kikuchi, M. & Ito, K. (1995) J. Biol. ...

  20. Identification and analysis of novel genes involved in gravitropism of Arabidopsis thaliana.

    Science.gov (United States)

    Morita, Miyo T.; Tasaka, Masao; Masatoshi Taniguchi, .

    2012-07-01

    Gravitropism is a continuous control with regard to the orientation and juxtaposition of the various parts of the plant body in response to gravity. In higher plants, the relative directional change of gravity is mainly suscepted in specialized cells called statocytes, followed by signal conversion from physical information into physiological information within the statocytes. We have studied the early process of shoot gravitropism, gravity sensing and signaling process, mainly by molecular genetic approach. In Arabidopsis shoot, statocytes are the endodermal cells. sgr1/scarcrow (scr) and sgr7/short-root (shr) mutants fail to form the endodermis and to respond to gravity in their inflorescence stems. Since both SGR1/SCR and SGR7/SHR are transcriptional factors, at least a subset of their downstream genes can be expected to be involved in gravitropism. In addition, eal1 (endodermal-amyloplast less 1), which exhibits no gravitropism in inflorescence stem but retains ability to form endodermis, is a hypomorphic allele of sgr7/shr. Take advantage of these mutants, we performed DNA microarray analysis and compared gene expression profiles between wild type and the mutants. We found that approx. 40 genes were commonly down-regulated in these mutants and termed them DGE (DOWN-REGULATED GENE IN EAL1) genes. DGE1 has sequence similarity to Oryza sativa LAZY1 that is involved in shoot gravitropism of rice. DGE2 has a short region homologous to DGE1. DTL (DGE TWO-LIKE}) that has 54% identity to DGE2 is found in Arabidopsis genome. All three genes are conserved in angiosperm but have no known functional domains or motifs. We analyzed T-DNA insertion for these genes in single or multiple combinations. In dge1 dge2 dtl triple mutant, gravitropic response of shoot, hypocotyl and root dramatically reduced. Now we are carrying out further physiological and molecular genetic analysis of the triple mutant.

  1. Functional analysis of soybean genes involved in flavonoid biosynthesis by virus-induced gene silencing.

    Science.gov (United States)

    Nagamatsu, Atsushi; Masuta, Chikara; Senda, Mineo; Matsuura, Hideyuki; Kasai, Atsushi; Hong, Jin-Sung; Kitamura, Keisuke; Abe, Jun; Kanazawa, Akira

    2007-11-01

    Virus-induced gene silencing (VIGS) is a powerful tool for functional analysis of genes in plants. A wide-host-range VIGS vector, which was developed based on the Cucumber mosaic virus (CMV), was tested for its ability to silence endogenous genes involved in flavonoid biosynthesis in soybean. Symptomless infection was established using a pseudorecombinant virus, which enabled detection of specific changes in metabolite content by VIGS. It has been demonstrated that the yellow seed coat phenotype of various cultivated soybean lines that lack anthocyanin pigmentation is induced by natural degradation of chalcone synthase (CHS) mRNA. When soybean plants with brown seed coats were infected with a virus that contains the CHS gene sequence, the colour of the seed coats changed to yellow, which indicates that the naturally occurring RNA silencing is reproduced by VIGS. In addition, CHS VIGS consequently led to a decrease in isoflavone content in seeds. VIGS was also tested on the putative flavonoid 3'-hydroxylase (F3'H) gene in the pathway. This experiment resulted in a decrease in the content of quercetin relative to kaempferol in the upper leaves after viral infection, which suggests that the putative gene actually encodes the F3'H protein. In both experiments, a marked decrease in the target mRNA and accumulation of short interfering RNAs were detected, indicating that sequence-specific mRNA degradation was induced. The present report is a successful demonstration of the application of VIGS for genes involved in flavonoid biosynthesis in plants; the CMV-based VIGS system provides an efficient tool for functional analysis of soybean genes.

  2. Moroccan Mothers' Involvement in Dialogic Literary Gatherings in a Catalan Urban Primary School: Increasing Educative Interactions and Improving Learning

    Science.gov (United States)

    de Botton, Lena; Girbés, Sandra; Ruiz, Laura; Tellado, Itxaso

    2014-01-01

    This article analyses a case study on Moroccan mothers' involvement in the Dialogic Literary Gathering (DLG) in an urban primary school in Catalonia (Spain). DLG is a dialogic learning environment that improves reading skills and communicative abilities and promotes school-community links. This activity has been identified in previous European…

  3. Egalitarianism and Achievement in the Involvement of Others in Consumer Decisions: A Functional Analysis.

    Science.gov (United States)

    Miller, Duane I.

    1980-01-01

    Studied how egalitaranism and success through individual achievement, were expressed in the involvement of others in consumer decisions. Results found egalitarians involved others in seeking more information. Individual achievement subjects delegated more decision responsibility for non-ego involving decisions. Suggests involvement of others could…

  4. Interactive flutter analysis and parametric study for conceptual wing design

    Science.gov (United States)

    Mukhopadhyay, Vivek

    1995-01-01

    An interactive computer program was developed for wing flutter analysis in the conceptual design stage. The objective was to estimate the flutter instability boundary of a flexible cantilever wing, when well defined structural and aerodynamic data are not available, and then study the effect of change in Mach number, dynamic pressure, torsional frequency, sweep, mass ratio, aspect ratio, taper ratio, center of gravity, and pitch inertia, to guide the development of the concept. The software was developed on MathCad (trademark) platform for Macintosh, with integrated documentation, graphics, database and symbolic mathematics. The analysis method was based on nondimensional parametric plots of two primary flutter parameters, namely Regier number and Flutter number, with normalization factors based on torsional stiffness, sweep, mass ratio, aspect ratio, center of gravity location and pitch inertia radius of gyration. The plots were compiled in a Vaught Corporation report from a vast database of past experiments and wind tunnel tests. The computer program was utilized for flutter analysis of the outer wing of a Blended Wing Body concept, proposed by McDonnell Douglas Corporation. Using a set of assumed data, preliminary flutter boundary and flutter dynamic pressure variation with altitude, Mach number and torsional stiffness were determined.

  5. Virus host protein interaction network analysis reveals that the HEV ORF3 protein may interrupt the blood coagulation process.

    Directory of Open Access Journals (Sweden)

    Yansheng Geng

    Full Text Available Hepatitis E virus (HEV is endemic worldwide and a major cause of acute liver disease in developing countries. However, the molecular mechanisms of liver pathology and clinical disease are not well understood for HEV infection. Open reading frame 3 (ORF3 of HEV encodes a small phosphoprotein, which is assumed to be involved in liver pathology and clinical disease. In this study, the interactions between the HEV ORF3 protein and human proteins were investigated using a stringent, high-throughput yeast two-hybrid (Y2H analysis. Thirty two proteins were shown to interact with genotype 1 ORF3, 28 of which have not been reported previously. These novel interactions were evaluated by coimmunoprecipitation of protein complexes from transfected cells. We found also that the ORF3 proteins of genotype 4 and rabbit HEV interacted with all of the human proteins identified by the genotype 1 ORF3 protein. However, the putative ORF3 protein derived from avian HEV did not interact with the majority of these human proteins. The identified proteins were used to infer an overall interaction map linking the ORF3 protein with components of the host cellular networks. Analysis of this interaction map, based on functional annotation with the Gene Ontology features and KEGG pathways, revealed an enrichment of host proteins involved in complement coagulation, cellular iron ion homeostasis and oxidative stress. Additional canonical pathway analysis highlighted the enriched biological pathways relevant to blood coagulation and hemostasis. Consideration of the clinical manifestations of hepatitis E reported previously and the results of biological analysis from this study suggests that the ORF3 protein is likely to lead to an imbalance of coagulation and fibrinolysis by interacting with host proteins and triggering the corresponding pathological processes. These results suggest critical approaches to further study of the pathogenesis of the HEV ORF3 protein.

  6. Cytoplasmic- and extracellular-proteome analysis of Diplodia seriata: a phytopathogenic fungus involved in grapevine decline

    Directory of Open Access Journals (Sweden)

    Cobos Rebeca

    2010-09-01

    Full Text Available Abstract Background The phytopathogenic fungus Diplodia seriata, whose genome remains unsequenced, produces severe infections in fruit trees (fruit blight and grapevines. In this crop is recognized as one of the most prominent pathogens involved in grapevine trunk disease (or grapevine decline. This pathology can result in the death of adult plants and therefore it produces severe economical losses all around the world. To date no genes or proteins have been characterized in D. seriata that are involved in the pathogenicity process. In an effort to help identify potential gene products associated with pathogenicity and to gain a better understanding of the biology of D. seriata, we initiated a proteome-level study of the fungal mycelia and secretome. Results Intracellular and secreted proteins from D. seriata collected from liquid cultures were separated using two-dimensional gel electrophoresis. About 550 cytoplasmic proteins were reproducibly present in 3 independent extractions, being 53 identified by peptide mass fingerprinting and tandem mass spectrometry. The secretome analysis showed 75 secreted proteins reproducibly present in 3 biological replicates, being 16 identified. Several of the proteins had been previously identified as virulence factors in other fungal strains, although their contribution to pathogenicity in D. seriata remained to be analyzed. When D. seriata was grown in a medium supplemented with carboxymethylcellulose, 3 proteins were up-regulated and 30 down-regulated. Within the up-regulated proteins, two were identified as alcohol dehydrogenase and mitochondrial peroxyrredoxin-1, suggesting that they could play a significant role in the pathogenicity process. As for the 30 down-regulated proteins, 9 were identified being several of them involved in carbohydrate metabolism. Conclusions This study is the first report on proteomics on D. seriata. The proteomic data obtained will be important to understand the pathogenicity

  7. Understanding metallic bonding: Structure, process and interaction by Rasch analysis

    Science.gov (United States)

    Cheng, Maurice M. W.; Oon, Pey-Tee

    2016-08-01

    This paper reports the results of a survey of 3006 Year 10-12 students on their understandings of metallic bonding. The instrument was developed based on Chi's ontological categories of scientific concepts and students' understanding of metallic bonding as reported in the literature. The instrument has two parts. Part one probed into students' understanding of metallic bonding as (a) a submicro structure of metals, (b) a process in which individual metal atoms lose their outermost shell electrons to form a 'sea of electrons' and octet metal cations or (c) an all-directional electrostatic force between delocalized electrons and metal cations, that is, an interaction. Part two assessed students' explanation of malleability of metals, for example (a) as a submicro structural rearrangement of metal atoms/cations or (b) based on all-directional electrostatic force. The instrument was validated by the Rasch Model. Psychometric assessment showed that the instrument possessed reasonably good properties of measurement. Results revealed that it was reliable and valid for measuring students' understanding of metallic bonding. Analysis revealed that the structure, process and interaction understandings were unidimensional and in an increasing order of difficulty. Implications for the teaching of metallic bonding, particular through the use of diagrams, critiques and model-based learning, are discussed.

  8. An interactive system for analysis of global cloud imagery

    Science.gov (United States)

    Woodberry, Karen; Tanaka, Ken; Hendon, Harry; Salby, Murry

    1991-01-01

    Synoptic images of the global cloud pattern composited from six contemporaneous satellites provide an unprecedented view of the global cloud field. Having horizontal resolution of about 0.5 deg and temporal resolution of 3 h, the global cloud imagery (GCI) resolves most of the variability of organized convection, including several harmonics of the diurnal cycle. Although the GCI has these attractive features, the dense and 3D nature of that data make it a formidable volume of information to treat in a practical and efficient manner. An interactive image-analysis system (IAS) has been developed to investigate the space-time variability of global cloud behavior. In the IAS, data, hardware, and software are integrated into a single system providing a variety of space-time covariance analyses in a menu-driven format. Owing to its customized architecture and certain homogeneous properties of the GCI, the IAS calculates such quantities effectively. Many covariance statistics are derived from 3D data with interactive speed, allowing the user to interrogate the archive iteratively in a single session. The 3D nature of those analyses and the speed with which they are performed distinguish the IAS from conventional image processing of 2D data.

  9. Isobolographic analysis of the analgesic interactions between ketamine and tramadol.

    Science.gov (United States)

    Chen, Yong; Chan, Sui Y; Ho, Paul C

    2002-05-01

    Owing to different mechanisms of analgesia, we hypothesized that the combination of ketamine and tramadol could produce synergistic or additive antinociceptive effects. Swiss albino mice were administered intraperitoneally with ketamine, tramadol, a combination of ketamine and tramadol, or saline, and the resulting antinociceptive effects were tested in the mouse tail-flick and formalin tests. The potencies of the two drugs alone or in combination were obtained by fitting data to the Sigmoid Emax equation. Isobolographic analysis was performed to evaluate the interaction. CNS depression was also monitored. Results showed that tramadol exhibited apparent dose-dependent effects in the tail-flick test, and in phase 1 and phase 2 of the formalin test. Ketamine dose-dependently inhibited the phase 2 responses, but failed to modify the phase 1 and tail-flick responses. Combination of tramadol and ketamine produced significant synergistic interactions only in phase 2 of the formalin test (P < 0.05). The synergistic combinations also displayed less CNS depression than when an equianalgesic dose of ketamine was administered alone. We conclude that in the acute thermal or chemical pain model, ketamine is not effective and the net effect of ketamine and tramadol in combination was simply additive after systemic administration. However, the coadministration produced synergistic antinociception in the chemical-induced persistent pain model.

  10. Major component analysis of dynamic networks of physiologic organ interactions

    Science.gov (United States)

    Liu, Kang K. L.; Bartsch, Ronny P.; Ma, Qianli D. Y.; Ivanov, Plamen Ch

    2015-09-01

    The human organism is a complex network of interconnected organ systems, where the behavior of one system affects the dynamics of other systems. Identifying and quantifying dynamical networks of diverse physiologic systems under varied conditions is a challenge due to the complexity in the output dynamics of the individual systems and the transient and nonlinear characteristics of their coupling. We introduce a novel computational method based on the concept of time delay stability and major component analysis to investigate how organ systems interact as a network to coordinate their functions. We analyze a large database of continuously recorded multi-channel physiologic signals from healthy young subjects during night-time sleep. We identify a network of dynamic interactions between key physiologic systems in the human organism. Further, we find that each physiologic state is characterized by a distinct network structure with different relative contribution from individual organ systems to the global network dynamics. Specifically, we observe a gradual decrease in the strength of coupling of heart and respiration to the rest of the network with transition from wake to deep sleep, and in contrast, an increased relative contribution to network dynamics from chin and leg muscle tone and eye movement, demonstrating a robust association between network topology and physiologic function.

  11. Multi-scale analysis for random quantum systems with interaction

    CERN Document Server

    Chulaevsky, Victor

    2014-01-01

    The study of quantum disorder has generated considerable research activity in mathematics and physics over past 40 years. While single-particle models have been extensively studied at a rigorous mathematical level, little was known about systems of several interacting particles, let alone systems with positive spatial particle density. Creating a consistent theory of disorder in multi-particle quantum systems is an important and challenging problem that largely remains open. Multi-scale Analysis for Random Quantum Systems with Interaction  presents the progress that had been recently achieved in this area.   The main focus of the book is on a rigorous derivation of the multi-particle localization in a strong random external potential field. To make the presentation accessible to a wider audience, the authors restrict attention to a relatively simple tight-binding Anderson model on a cubic lattice Zd.   This book includes the following cutting-edge features: * an introduction to the state-of-the-art single-...

  12. Interactive Visual Analysis of High Throughput Text Streams

    Energy Technology Data Exchange (ETDEWEB)

    Steed, Chad A [ORNL; Potok, Thomas E [ORNL; Patton, Robert M [ORNL; Goodall, John R [ORNL; Maness, Christopher S [ORNL; Senter, James K [ORNL; Potok, Thomas E [ORNL

    2012-01-01

    The scale, velocity, and dynamic nature of large scale social media systems like Twitter demand a new set of visual analytics techniques that support near real-time situational awareness. Social media systems are credited with escalating social protest during recent large scale riots. Virtual communities form rapidly in these online systems, and they occasionally foster violence and unrest which is conveyed in the users language. Techniques for analyzing broad trends over these networks or reconstructing conversations within small groups have been demonstrated in recent years, but state-of- the-art tools are inadequate at supporting near real-time analysis of these high throughput streams of unstructured information. In this paper, we present an adaptive system to discover and interactively explore these virtual networks, as well as detect sentiment, highlight change, and discover spatio- temporal patterns.

  13. Functional phylogenetic analysis of LGI proteins identifies an interaction motif crucial for myelination.

    Science.gov (United States)

    Kegel, Linde; Jaegle, Martine; Driegen, Siska; Aunin, Eerik; Leslie, Kris; Fukata, Yuko; Watanabe, Masahiko; Fukata, Masaki; Meijer, Dies

    2014-04-01

    The cellular interactions that drive the formation and maintenance of the insulating myelin sheath around axons are only partially understood. Leucine-rich glioma-inactivated (LGI) proteins play important roles in nervous system development and mutations in their genes have been associated with epilepsy and amyelination. Their function involves interactions with ADAM22 and ADAM23 cell surface receptors, possibly in apposing membranes, thus attenuating cellular interactions. LGI4-ADAM22 interactions are required for axonal sorting and myelination in the developing peripheral nervous system (PNS). Functional analysis revealed that, despite their high homology and affinity for ADAM22, LGI proteins are functionally distinct. To dissect the key residues in LGI proteins required for coordinating axonal sorting and myelination in the developing PNS, we adopted a phylogenetic and computational approach and demonstrate that the mechanism of action of LGI4 depends on a cluster of three amino acids on the outer surface of the LGI4 protein, thus providing a structural basis for the mechanistic differences in LGI protein function in nervous system development and evolution.

  14. Toward Molecular Magnets of Organic Origin via Anion-π Interaction Involving m-Aminyl Diradical: A Theoretical Study

    DEFF Research Database (Denmark)

    Bhattacharya, Debojit; Shil, Suranjan; Misra, Anirban;

    2016-01-01

    Here we study a set of novel magnetic organic molecular species with different halide ions (fluoride, chloride, bromide) absorbed ∼2 Å above or below the center of an aromatic π-ring in an m-aminyl diradical. Focus is on the nature of anion-π interaction and its impact on magnetic properties......, specifically on magnetic anisotropy and on intramolecular magnetic exchange coupling. In the development of single molecule magnets, magnetic anisotropy is considered to be the most influential factor. A new insight regarding the magnetic anisotropy that determines the barrier height for relaxation...... of magnetization of m-aminyl diradical-derived anionic complexes is obtained from calculations of the axial zero-field-splitting (ZFS) parameter D. The noncovalent anion-π interaction strongly influences magnetic anisotropy in m-aminyl-halide diradical complexes. In particular, the change of D values from positive...

  15. The telomeric protein AKTIP interacts with A- and B-type lamins and is involved in regulation of cellular senescence

    Science.gov (United States)

    Burla, Romina; Carcuro, Mariateresa; Torre, Mattia La; Fratini, Federica; Crescenzi, Marco; D'Apice, Maria Rosaria; Spitalieri, Paola; Raffa, Grazia Daniela; Astrologo, Letizia; Lattanzi, Giovanna; Cundari, Enrico; Raimondo, Domenico; Biroccio, Annamaria; Gatti, Maurizio

    2016-01-01

    AKTIP is a shelterin-interacting protein required for replication of telomeric DNA. Here, we show that AKTIP biochemically interacts with A- and B-type lamins and affects lamin A, but not lamin C or B, expression. In interphase cells, AKTIP localizes at the nuclear rim and in discrete regions of the nucleoplasm just like lamins. Double immunostaining revealed that AKTIP partially co-localizes with lamin B1 and lamin A/C in interphase cells, and that proper AKTIP localization requires functional lamin A. In mitotic cells, AKTIP is enriched at the spindle poles and at the midbody of late telophase cells similar to lamin B1. AKTIP-depleted cells show senescence-associated markers and recapitulate several aspects of the progeroid phenotype. Collectively, our results indicate that AKTIP is a new player in lamin-related processes, including those that govern nuclear architecture, telomere homeostasis and cellular senescence. PMID:27512140

  16. Light-regulated stapled peptides to inhibit protein-protein interactions involved in clathrin-mediated endocytosis.

    Science.gov (United States)

    Nevola, Laura; Martín-Quirós, Andrés; Eckelt, Kay; Camarero, Núria; Tosi, Sébastien; Llobet, Artur; Giralt, Ernest; Gorostiza, Pau

    2013-07-22

    Control of membrane traffic: Photoswitchable inhibitors of protein-protein interactions were applied to photoregulate clathrin-mediated endocytosis (CME) in living cells. Traffic light (TL) peptides acting as "stop" and "go" signals for membrane traffic can be used to dissect the role of CME in receptor internalization and in cell growth, division, and differentiation. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Assembly of the U1 snRNP involves interactions with the backbone of the terminal stem of U1 snRNA

    OpenAIRE

    McConnell, Timothy S.; Lokken, R. Peter; Steitz, Joan A.

    2003-01-01

    Nucleotide analog interference mapping (NAIM) is a powerful method for identifying RNA functional groups involved in protein–RNA interactions. We examined particles assembled on modified U1 small nuclear RNAs (snRNAs) in vitro and detected two categories of interferences. The first class affects the stability of two higher-order complexes and comprises changes in two adenosines, A65 and A70, in the loop region previously identified as the binding site for the U1 small nuclear ribonucleoprotei...

  18. The Thymic Orchestration Involving Aire, miRNAs, and Cell-Cell Interactions during the Induction of Central Tolerance.

    Science.gov (United States)

    Passos, Geraldo Aleixo; Mendes-da-Cruz, Daniella Arêas; Oliveira, Ernna Hérida

    2015-01-01

    Developing thymocytes interact sequentially with two distinct structures within the thymus: the cortex and medulla. Surviving single-positive and double-positive thymocytes from the cortex migrate into the medulla, where they interact with medullary thymic epithelial cells (mTECs). These cells ectopically express a vast set of peripheral tissue antigens (PTAs), a property termed promiscuous gene expression that is associated with the presentation of PTAs by mTECs to thymocytes. Thymocyte clones that have a high affinity for PTAs are eliminated by apoptosis in a process termed negative selection, which is essential for tolerance induction. The Aire gene is an important factor that controls the expression of a large set of PTAs. In addition to PTAs, Aire also controls the expression of miRNAs in mTECs. These miRNAs are important in the organization of the thymic architecture and act as posttranscriptional controllers of PTAs. Herein, we discuss recent discoveries and highlight open questions regarding the migration and interaction of developing thymocytes with thymic stroma, the ectopic expression of PTAs by mTECs, the association between Aire and miRNAs and its effects on central tolerance.

  19. I’m Sorry I Don’t Have a Story: An Essay Involving Interactive Documentary, Bristol and Hypertext

    Directory of Open Access Journals (Sweden)

    Adrian Miles

    2016-12-01

    Full Text Available From the Introduction:I don’t know what this is, which is a strange place from which to begin. This is unsettling, for as an academic I am trained and acculturated to displaying a certainty of manner — a certainty that many of my students and conference colleagues would attest I have down pat. It begins from Bristol. It begins from Alisa Lebow’s presentation at the 2016 i–Docs conference about her interactive documentary Filming Revolution. It begins from what I was reading during my thirty hours of travel between Melbourne and Bristol. It begins from the question that gnawed and nagged at me after Alisa’s keynote in Bristol. It begins in my body. Not much of an introduction, is it? This writing reintroduces hypertext as a specific and material way of making and performing knowledge and proposes it as a valuable precursor to interactive documentary and what I am describing as computational nonfiction. What I say here about hypertext, Filming Revolution as an interactive documentary, and story, are a prolegomena toward what computational nonfiction might be as a broader field that might encompass computers, technodigital practice, and networks. Oh, it was originally written as hypertext, and translating it into something more linear and sequential sees its looping rhythms, redundancies, and recursiveness become clumsy stutterings and repetitions.  

  20. Older adults catch up to younger adults on a learning and memory task that involves collaborative social interaction.

    Science.gov (United States)

    Derksen, B J; Duff, M C; Weldon, K; Zhang, J; Zamba, K D; Tranel, D; Denburg, N L

    2015-01-01

    Learning and memory abilities tend to decline as people age. The current study examines the question of whether a learning situation that emphasises collaborative social interaction might help older persons overcome age-related learning and memory changes and thus perform similarly to younger persons. Younger and Older participants (n = 34 in each group) completed the Barrier Task (BT), a game-like social interaction where partners work together to develop labels for a set of abstract tangrams. Participants were also administered standard clinical neuropsychological measures of memory, on which the Older group showed expected inferiority to the Younger group. On the BT, the Older group performed less well than the Younger group early on, but as the task progressed, the performance of the Older group caught up and became statistically indistinguishable from that of the Younger group. These results can be taken to suggest that a learning milieu characterised by collaborative social interaction can attenuate some of the typical memory disadvantages associated with being older.

  1. Parallel analysis of tagged deletion mutants efficiently identifies genes involved in endoplasmic reticulum biogenesis.

    Science.gov (United States)

    Wright, Robin; Parrish, Mark L; Cadera, Emily; Larson, Lynnelle; Matson, Clinton K; Garrett-Engele, Philip; Armour, Chris; Lum, Pek Yee; Shoemaker, Daniel D

    2003-07-30

    Increased levels of HMG-CoA reductase induce cell type- and isozyme-specific proliferation of the endoplasmic reticulum. In yeast, the ER proliferations induced by Hmg1p consist of nuclear-associated stacks of smooth ER membranes known as karmellae. To identify genes required for karmellae assembly, we compared the composition of populations of homozygous diploid S. cerevisiae deletion mutants following 20 generations of growth with and without karmellae. Using an initial population of 1,557 deletion mutants, 120 potential mutants were identified as a result of three independent experiments. Each experiment produced a largely non-overlapping set of potential mutants, suggesting that differences in specific growth conditions could be used to maximize the comprehensiveness of similar parallel analysis screens. Only two genes, UBC7 and YAL011W, were identified in all three experiments. Subsequent analysis of individual mutant strains confirmed that each experiment was identifying valid mutations, based on the mutant's sensitivity to elevated HMG-CoA reductase and inability to assemble normal karmellae. The largest class of HMG-CoA reductase-sensitive mutations was a subset of genes that are involved in chromatin structure and transcriptional regulation, suggesting that karmellae assembly requires changes in transcription or that the presence of karmellae may interfere with normal transcriptional regulation.

  2. Multivariate analysis of variance of designed chromatographic data. A case study involving fermentation of rooibos tea.

    Science.gov (United States)

    Marini, Federico; de Beer, Dalene; Walters, Nico A; de Villiers, André; Joubert, Elizabeth; Walczak, Beata

    2017-03-17

    An ultimate goal of investigations of rooibos plant material subjected to different stages of fermentation is to identify the chemical changes taking place in the phenolic composition, using an untargeted approach and chromatographic fingerprints. Realization of this goal requires, among others, identification of the main components of the plant material involved in chemical reactions during the fermentation process. Quantitative chromatographic data for the compounds for extracts of green, semi-fermented and fermented rooibos form the basis of preliminary study following a targeted approach. The aim is to estimate whether treatment has a significant effect based on all quantified compounds and to identify the compounds, which contribute significantly to it. Analysis of variance is performed using modern multivariate methods such as ANOVA-Simultaneous Component Analysis, ANOVA - Target Projection and regularized MANOVA. This study is the first one in which all three approaches are compared and evaluated. For the data studied, all tree methods reveal the same significance of the fermentation effect on the extract compositions, but they lead to its different interpretation.

  3. Microbial community analysis involved in the aerobic/extended-idle process performing biological phosphorus removal.

    Science.gov (United States)

    Zeng, Tian-jing; Yang, Guo-jing; Wang, Dong-bo; Li, Xiao-ming; Zheng, Wei; Yang, Qi; Zeng, Guang-ming

    2013-01-01

    Recently, it has been found that biological phosphorus removal can be achieved in an aerobic/extended-idle (AEI) process using both glucose and acetate as the sole substrate. However, the microbial consortiums involved in glucose-fed and acetate-fed systems have not yet been characterized. Thus the aims of this paper were to investigate the diversities and dynamics of bacterial communities during the acclimation period, and to quantify polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) in the systems. The phylogenetic analysis showed that the microbial communities were mainly composed of phylum Proteobacteria, Bacteroidetes, Chlorobi and another six kinds of unclassified bacteria. Fluorescence in-situ hybridization (FISH) analysis revealed that PAOs and GAOs accounted for 43 ± 7 and 16 ± 3% of all bacteria in the glucose-fed system, and 19 ± 4 and 35 ± 5% of total bacteria in the acetate-fed system, respectively. The results showed that the conventional PAOs could thrive in the AEI process, and a defined anaerobic zone was not necessarily required for putative PAOs growth.

  4. Bioinformatics Analysis for Coding SNPs of the HLADQA1 Gene Involved in Susceptibility to Cervical Cancer

    Institute of Scientific and Technical Information of China (English)

    Yanyun Li; Jun Xing; Linsheng Zhao; Yanni Li; Yuchuan Wang; Weiming Zhang

    2006-01-01

    OBJECTIVE To analyze coding SNPs of the HLA-DQA1 gene involved in susceptibility for cervical cancer by a bioinformatics approach, and to choose some SNPs that may have an association with cervical cancer.METHODS By a SNPper tool we extracted SNPs from a public database (dbSNP), exporting them in FASTA formats suitable for subsequent use.Then we used PARSESNP as a tool for the analysis of the cSNPs.RESULTS In the cSNPs of the HLA-DQA1 gene, we find that rs9272693and rs9272703, are made up of missense mutations which convert a codon for one amino acid into a codon for a different amino acid. We chose a PSSM Difference >10 as a lower level for the scores of changes predicted to be deldterious.CONCLUSION We used a bioinformatics approach for cSNPs analysis of the HLA-DQA1 gene. This method can select the variants in a conserved region, and give a PSSM Difference score. But the results need to be verified in cervical cancer patients and a control population.

  5. Screening and identification of microRNA involved in unstable angina using gene-chip analysis

    Science.gov (United States)

    Li, Si; Sun, Ya-Nan; Zhou, Yun-Tao; Zhang, Chun-Lai; Lu, Feng; Liu, Jia; Shang, Xiao-Ming

    2016-01-01

    Increasing evidence has suggested that microRNA (miRNA) may play a role in the pathogenesis of cardiovascular disease, which has led to a greater understanding of the complex pathophysiological processes underlying unstable angina (UA). The present study aimed to investigate changes in the miRNA expression profiles of patients with UA using gene-chip analysis, in order to further elucidate the pathogenesis of UA. Total RNA was extracted and purified from plasma samples collected from patients with UA and healthy controls. The samples underwent microarray analysis using an Exiqon miRCURY LNA™ microRNA Array. Differentially expressed miRNAs were identified by volcano plot filtering, and were validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). In addition, functional annotation of the differentially expressed miRNAs involved gene ontology analyses. Among the 212 miRNAs differentially expressed between the two groups, 82 were upregulated and 130 were downregulated. Notably, the results of the RT-qPCR were consistent with the gene-chip results. The miRNAs identified in the present study may be potential novel biomarkers for the prevention and early diagnosis of UA. Furthermore, the results of the present study suggested that UA occurs as a result of complex and dynamic processes regulated by numerous factors, including multiple miRNAs.

  6. Proteomic analysis of male 4C germ cell proteins involved in mouse meiosis.

    Science.gov (United States)

    Guo, Xuejiang; Zhang, Ping; Qi, Yujuan; Chen, Wen; Chen, Xiangxiang; Zhou, Zuomin; Sha, Jiahao

    2011-01-01

    Male meiosis is a specialized type of cell division that gives rise to sperm. Errors in this process can result in the generation of aneuploid gametes, which are associated with birth defects and infertility in humans. Until now, there has been a lack of a large-scale identification of proteins involved in male meiosis in mammals. In this study, we report the high-confidence identification of 3625 proteins in mouse male germ cells with 4C DNA content undergoing meiosis I. Of these, 397 were found to be testis specific. Bioinformatics analysis of the proteome led to the identification of 28 proteins known to be essential for male meiosis in mice. We also found 172 proteins that had yeast orthologs known to be essential for meiosis. Chromosome distribution analysis of the proteome showed underrepresentation of the identified proteins on the X chromosome, which may be due to meiotic sex chromosome inactivation. Characterization of the proteome of 4C germ cells from mouse testis provides an inventory of proteins, which is useful for understanding meiosis and the mechanisms of male infertility.

  7. Recent insights into plant-virus interactions through proteomic analysis.

    Science.gov (United States)

    Di Carli, Mariasole; Benvenuto, Eugenio; Donini, Marcello

    2012-10-05

    Plant viruses represent a major threat for a wide range of host species causing severe losses in agricultural practices. The full comprehension of mechanisms underlying events of virus-host plant interaction is crucial to devise novel plant resistance strategies. Until now, functional genomics studies in plant-virus interaction have been limited mainly on transcriptomic analysis. Only recently are proteomic approaches starting to provide important contributions to this area of research. Classical two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) is still the most widely used platform in plant proteome analysis, although in the last years the application of quantitative "second generation" proteomic techniques (such as differential in gel electrophoresis, DIGE, and gel-free protein separation methods) are emerging as more powerful analytical approaches. Apparently simple, plant-virus interactions reveal a really complex pathophysiological context, in which resistance, defense and susceptibility, and direct virus-induced reactions interplay to trigger expression responses of hundreds of genes. Given that, this review is specifically focused on comparative proteome-based studies on pathogenesis of several viral genera, including some of the most important and widespread plant viruses of the genus Tobamovirus, Sobemovirus, Cucumovirus and Potyvirus. In all, this overview reveals a widespread repression of proteins associated with the photosynthetic apparatus, while energy metabolism/protein synthesis and turnover are typically up-regulated, indicating a major redirection of cell metabolism. Other common features include the modulation of metabolisms concerning sugars, cell wall, and reactive oxigen species as well as pathogenesis-related (PR) proteins. The fine-tuning between plant development and antiviral defense mechanisms determines new patterns of regulation of common metabolic pathways. By offering a 360-degree view of protein modulation

  8. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry.

    Science.gov (United States)

    Ito, Jun; Herter, Thomas; Baidoo, Edward E K; Lao, Jeemeng; Vega-Sánchez, Miguel E; Michelle Smith-Moritz, A; Adams, Paul D; Keasling, Jay D; Usadel, Björn; Petzold, Christopher J; Heazlewood, Joshua L

    2014-03-01

    Understanding the intricate metabolic processes involved in plant cell wall biosynthesis is limited by difficulties in performing sensitive quantification of many involved compounds. Hydrophilic interaction liquid chromatography is a useful technique for the analysis of hydrophilic metabolites from complex biological extracts and forms the basis of this method to quantify plant cell wall precursors. A zwitterionic silica-based stationary phase has been used to separate hydrophilic nucleotide sugars involved in cell wall biosynthesis from milligram amounts of leaf tissue. A tandem mass spectrometry operating in selected reaction monitoring mode was used to quantify nucleotide sugars. This method was highly repeatable and quantified 12 nucleotide sugars at low femtomole quantities, with linear responses up to four orders of magnitude to several 100pmol. The method was also successfully applied to the analysis of purified leaf extracts from two model plant species with variations in their cell wall sugar compositions and indicated significant differences in the levels of 6 out of 12 nucleotide sugars. The plant nucleotide sugar extraction procedure was demonstrated to have good recovery rates with minimal matrix effects. The approach results in a significant improvement in sensitivity when applied to plant samples over currently employed techniques.

  9. Functional and Structural Analysis of a β-Glucosidase Involved in β-1,2-Glucan Metabolism in Listeria innocua.

    Directory of Open Access Journals (Sweden)

    Masahiro Nakajima

    Full Text Available Despite the presence of β-1,2-glucan in nature, few β-1,2-glucan degrading enzymes have been reported to date. Recently, the Lin1839 protein from Listeria innocua was identified as a 1,2-β-oligoglucan phosphorylase. Since the adjacent lin1840 gene in the gene cluster encodes a putative glycoside hydrolase family 3 β-glucosidase, we hypothesized that Lin1840 is also involved in β-1,2-glucan dissimilation. Here we report the functional and structural analysis of Lin1840. A recombinant Lin1840 protein (Lin1840r showed the highest hydrolytic activity toward sophorose (Glc-β-1,2-Glc among β-1,2-glucooligosaccharides, suggesting that Lin1840 is a β-glucosidase involved in sophorose degradation. The enzyme also rapidly hydrolyzed laminaribiose (β-1,3, but not cellobiose (β-1,4 or gentiobiose (β-1,6 among β-linked gluco-disaccharides. We determined the crystal structures of Lin1840r in complexes with sophorose and laminaribiose as productive binding forms. In these structures, Arg572 forms many hydrogen bonds with sophorose and laminaribiose at subsite +1, which seems to be a key factor for substrate selectivity. The opposite side of subsite +1 from Arg572 is connected to a large empty space appearing to be subsite +2 for the binding of sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc in spite of the higher Km value for sophorotriose than that for sophorose. The conformations of sophorose and laminaribiose are almost the same on the Arg572 side but differ on the subsite +2 side that provides no interaction with a substrate. Therefore, Lin1840r is unable to distinguish between sophorose and laminaribiose as substrates. These results provide the first mechanistic insights into β-1,2-glucooligosaccharide recognition by β-glucosidase.

  10. Functional analysis of a cinnamyl alcohol dehydrogenase involved in lignin biosynthesis in wheat.

    Science.gov (United States)

    Ma, Qing-Hu

    2010-06-01

    Cinnamyl alcohol dehydrogenase (CAD) catalyses the final step in the biosynthesis of monolignols. In the present study, a cDNA encoding a CAD was isolated from wheat, designated as TaCAD1. A genome-wide data mining in the wheat EST database revealed another 10 CAD-like homologues, namely TaCAD2 to TaCAD11. A phylogenetic analysis showed that TaCAD1 belonged to the bona fide CAD group involved in lignin synthesis. Two other putative CADs from the wheat genome (TaCAD2 and TaCAD4) also belonged to this group and were very close to TaCAD1, but lacked C-terminal domain, suggesting that they are pseudogenes. DNA gel blot analysis for the wheat genome showed two to three copies of CAD related to TaCAD1, but RNA gel blot analysis revealed only single band for TaCAD1, which was highly expressed in stem, with quite low expression in leaf and undetectable expression in root. The predicted three-dimension structure of TaCAD1 resembled that of AtCAD5, but two amino acid substitutions were identified in the substrate binding region. Recombinant TaCAD1 protein used coniferyl aldehyde as the most favoured substrate, also showed high efficiencies toward sinapyl and p-coumaryl aldehydes. TaCAD1 was an enzyme being pH-dependent and temperature-sensitive, and showing a typical random catalysing mechanism. At the milky stage of wheat, TaCAD1 mRNA abundance, protein level and enzyme activity in stem tissues were higher in a lodging-resistant cultivar (H4546) than in lodging-sensitive cultivar (C6001). These properties were correlated to the lignin contents and lodging indices of the two cultivars. These data suggest that TaCAD1 is the predominant CAD in wheat stem for lignin biosynthesis and is critical for lodging resistance.

  11. Histone modifications involved in cassette exon inclusions: a quantitative and interpretable analysis.

    Science.gov (United States)

    Liu, Hui; Jin, Ting; Guan, Jihong; Zhou, Shuigeng

    2014-12-19

    Chromatin structure and epigenetic modifications have been shown to involve in the co-transcriptional splicing of RNA precursors. In particular, some studies have suggested that some types of histone modifications (HMs) may participate in the alternative splicing and function as exon marks. However, most existing studies pay attention to the qualitative relationship between epigenetic modifications and exon inclusion. The quantitative analysis that reveals to what extent each type of epigenetic modification is responsible for exon inclusion is very helpful for us to understand the splicing process. In this paper, we focus on the quantitative analysis of HMs' influence on the inclusion of cassette exons (CEs) into mature RNAs. With the high-throughput ChIP-seq and RNA-seq data obtained from ENCODE website, we modeled the association of HMs with CE inclusions by logistic regression whose coefficients are meaningful and interpretable for us to reveal the effect of each type of HM. Three type of HMs, H3K36me3, H3K9me3 and H4K20me1, were found to play major role in CE inclusions. HMs' effect on CE inclusions is conservative across cell types, and does not depend on the expression levels of the genes hosting CEs. HMs located in the flanking regions of CEs were also taken into account in our analysis, and HMs within bounded flanking regions were shown to affect moderately CE inclusions. Moreover, we also found that HMs on CEs whose length is approximately close to nucleosomal-DNA length affect greatly on CE inclusion. We suggested that a few types of HMs correlate closely to alternative splicing and perhaps function jointly with splicing machinery to regulate the inclusion level of exons. Our findings are helpful to understand HMs' effect on exon definition, as well as the mechanism of co-transcriptional splicing.

  12. IgG4-related epididymo-orchitis associated with bladder cancer: possible involvement of BAFF/BAFF-R interaction in IgG4-related urogenital disease.

    Science.gov (United States)

    Migita, Kiyoshi; Miyashita, Taiichiro; Mizuno, Aya; Jiuchi, Yuka; Ito, Masahiro; Matsuo, Manabu; Izumi, Yasumori; Takeoka, Atsushi; Nishino, Ayako; Hayashi, Mikio

    2014-01-01

    We describe herein a patient who presented with immunoglobulin G4-related disease (IgG4-RD) involving the testis and prostate as well as the submandibular glands. Massive infiltration of IgG4-expressing plasma cells was observed in testis and prostate tissues. Serum concentrations of B cell activating factor belonging to the tumor necrosis factor family (BAFF) were elevated in parallel with serum IgG4 concentrations, and infiltration of BAFF-receptor (BAFF-R)-expressing B cells and BAFF-expressing lymphoid cells was observed around the ectopic lymphoid foci in the affected urogenital tissues. To date, testicular involvement in a patient diagnosed with IgG4-RD had not been reported, making this the first reported case of IgG4-related epididymo-orchitis. These findings suggest that the immune mechanism underlying ectopic lymphoneogenesis in IgG4-RD may involve enhanced BAFF/BAFF-R interactions among lymphoid cells.

  13. Proteomic analysis of HIV-T cell interaction: an update.

    Directory of Open Access Journals (Sweden)

    Dave eSpeijer

    2012-07-01

    Full Text Available This mini-review summarizes techniques applied in, and results obtained with, proteomic studies of HIV-1 T cell interaction. Our group previously reported on the use of two-dimensional differential gel electrophoresis (2D-DIGE coupled to MALDI-TOF peptide mass fingerprint analysis, to study T cell responses upon HIV-1 infection. Only one in three differentially expressed proteins could be identified using this experimental setup. Here we report on our latest efforts to test models generated by this data set and extend its analysis by using novel bioinformatic algorithms. The 2D-DIGE results are compared with other studies including a pilot study using one-dimensional peptide separation coupled to MSE, a novel mass spectrometric approach. It can be concluded that although the latter method detects fewer proteins, it is much faster and less labor intensive. Last but not least, recent developments and remaining challenges in the field of proteomic studies of HIV-1 infection and proteomics in general are discussed.

  14. Toward Molecular Magnets of Organic Origin via Anion-π Interaction Involving m-Aminyl Diradical: A Theoretical Study.

    Science.gov (United States)

    Bhattacharya, Debojit; Shil, Suranjan; Misra, Anirban; Bytautas, Laimutis; Klein, Douglas J

    2016-11-17

    Here we study a set of novel magnetic organic molecular species with different halide ions (fluoride, chloride, bromide) absorbed ∼2 Å above or below the center of an aromatic π-ring in an m-aminyl diradical. Focus is on the nature of anion-π interaction and its impact on magnetic properties, specifically on magnetic anisotropy and on intramolecular magnetic exchange coupling. In the development of single molecule magnets, magnetic anisotropy is considered to be the most influential factor. A new insight regarding the magnetic anisotropy that determines the barrier height for relaxation of magnetization of m-aminyl diradical-derived anionic complexes is obtained from calculations of the axial zero-field-splitting (ZFS) parameter D. The noncovalent anion-π interaction strongly influences magnetic anisotropy in m-aminyl-halide diradical complexes. In particular, the change of D values from positive (for the m-aminyl diradical, m-aminyl diradical/fluoride, and m-aminyl diradical/chloride complexes) to negative D-values in m-aminyl diradical complexes containing bromide signals a change from oblate to prolate type of spin-density distribution. Furthermore, the noncovalent halide-π interactions lead to large values of intramolecular magnetic exchange coupling coefficients J exhibiting a ferromagnetic sign. The magnitude of J steadily increases going from anionic complexes containing fluoride to chloride and then to bromide. Relations are sought between the magnetic exchange coupling coefficients J and aromaticity, namely structural HOMA (harmonic oscillator model of aromaticity) and magnetic NICS (nucleus independent chemical shift) aromaticity indices, in particular, the NICSzz(+1) component. Finally, possible numerical checks on the conditions relating to validity of the well-known Yamaguchi's formula for calculating the exchange coupling coefficient J in diradical systems are discussed.

  15. Transcription of human resistin gene involves an interaction of Sp1 with peroxisome proliferator-activating receptor gamma (PPARgamma.

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    Anil K Singh

    Full Text Available BACKGROUND: Resistin is a cysteine rich protein, mainly expressed and secreted by circulating human mononuclear cells. While several factors responsible for transcription of mouse resistin gene have been identified, not much is known about the factors responsible for the differential expression of human resistin. METHODOLOGY/PRINCIPAL FINDING: We show that the minimal promoter of human resistin lies within approximately 80 bp sequence upstream of the transcriptional start site (-240 whereas binding sites for cRel, CCAAT enhancer binding protein alpha (C/EBP-alpha, activating transcription factor 2 (ATF-2 and activator protein 1 (AP-1 transcription factors, important for induced expression, are present within sequences up to -619. Specificity Protein 1(Sp1 binding site (-276 to -295 is also present and an interaction of Sp1 with peroxisome proliferator activating receptor gamma (PPARgamma is necessary for constitutive expression in U937 cells. Indeed co-immunoprecipitation assay demonstrated a direct physical interaction of Sp1 with PPARgamma in whole cell extracts of U937 cells. Phorbol myristate acetate (PMA upregulated the expression of resistin mRNA in U937 cells by increasing the recruitment of Sp1, ATF-2 and PPARgamma on the resistin gene promoter. Furthermore, PMA stimulation of U937 cells resulted in the disruption of Sp1 and PPARgamma interaction. Chromatin immunoprecipitation (ChIP assay confirmed the recruitment of transcription factors phospho ATF-2, Sp1, Sp3, PPARgamma, chromatin modifier histone deacetylase 1 (HDAC1 and the acetylated form of histone H3 but not cRel, C/EBP-alpha and phospho c-Jun during resistin gene transcription. CONCLUSION: Our findings suggest a complex interplay of Sp1 and PPARgamma along with other transcription factors that drives the expression of resistin in human monocytic U937 cells.

  16. Mining genes involved in insecticide resistance of Liposcelis bostrychophila Badonnel by transcriptome and expression profile analysis.

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    Wei Dou

    Full Text Available BACKGROUND: Recent studies indicate that infestations of psocids pose a new risk for global food security. Among the psocids species, Liposcelis bostrychophila Badonnel has gained recognition in importance because of its parthenogenic reproduction, rapid adaptation, and increased worldwide distribution. To date, the molecular data available for L. bostrychophila is largely limited to genes identified through homology. Also, no transcriptome data relevant to psocids infection is available. METHODOLOGY AND PRINCIPAL FINDINGS: In this study, we generated de novo assembly of L. bostrychophila transcriptome performed through the short read sequencing technology (Illumina. In a single run, we obtained more than 51 million sequencing reads that were assembled into 60,012 unigenes (mean size = 711 bp by Trinity. The transcriptome sequences from different developmental stages of L. bostrychophila including egg, nymph and adult were annotated with non-redundant (Nr protein database, gene ontology (GO, cluster of orthologous groups of proteins (COG, and KEGG orthology (KO. The analysis revealed three major enzyme families involved in insecticide metabolism as differentially expressed in the L. bostrychophila transcriptome. A total of 49 P450-, 31 GST- and 21 CES-specific genes representing the three enzyme families were identified. Besides, 16 transcripts were identified to contain target site sequences of resistance genes. Furthermore, we profiled gene expression patterns upon insecticide (malathion and deltamethrin exposure using the tag-based digital gene expression (DGE method. CONCLUSION: The L. bostrychophila transcriptome and DGE data provide gene expression data that would further our understanding of molecular mechanisms in psocids. In particular, the findings of this investigation will facilitate identification of genes involved in insecticide resistance and designing of new compounds for control of psocids.

  17. Comparative Genome Analysis of Trichophyton rubrum and Related Dermatophytes Reveals Candidate Genes Involved in Infection

    Science.gov (United States)

    Martinez, Diego A.; Oliver, Brian G.; Gräser, Yvonne; Goldberg, Jonathan M.; Li, Wenjun; Martinez-Rossi, Nilce M.; Monod, Michel; Shelest, Ekaterina; Barton, Richard C.; Birch, Elizabeth; Brakhage, Axel A.; Chen, Zehua; Gurr, Sarah J.; Heiman, David; Heitman, Joseph; Kosti, Idit; Rossi, Antonio; Saif, Sakina; Samalova, Marketa; Saunders, Charles W.; Shea, Terrance; Summerbell, Richard C.; Xu, Jun; Young, Sarah; Zeng, Qiandong; Birren, Bruce W.; Cuomo, Christina A.; White, Theodore C.

    2012-01-01

    ABSTRACT The major cause of athlete’s foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response. PMID:22951933

  18. Evidence that inhibition of BAX activation by BCL-2 involves its tight and preferential interaction with the BH3 domain of BAX

    Institute of Scientific and Technical Information of China (English)

    Bonsu Ku; Chengyu Liang; Jae U Jung; Byung-Ha Oh

    2011-01-01

    Interactions between the BCL-2 family proteins determine the cell's fate to live or die. How they interact with each other to regulate apoptosis remains as an unsettled central issue. So far, the antiapoptotic Bc1-2 proteins are thought to interact with BAX weakly, but the physiological significance of this interaction has been vague.Herein, we show that recombinant BCL-2 and BCL-w interact potently with a BCL-2 homology (BH) 3 domain-containing peptide derived from BAX, exhibiting the dissociation constants of 15 and 23 nM, respectively. To clarify the basis for this strong interaction, we determined the three-dimensional structure of a complex of BCL-2 with a BAX peptide spanning its BH3 domain. It revealed that their interactions extended beyond the canonical BH3 domain and involved three nonconserved charged residues of BAX. A novel BAX variant, containing the alanine substitution of these three residues, had greatly impaired affinity for BCL-2 and BCL-w, hut was otherwise indistinguishable from wild-type BAX. Critically, the apoptotic activity of the BAX variant could not be restrained by BCL-2 and BCL-w, pointing that the observed tight interactions are critical for regulating BAX activation. We also comprehensively quantified the binding affinities between the three BCL-2 subfamily proteins. Collectively, the data show that due to the high affinity of BAX for BCL-2, BCL-w and A1, and of BAK for BCL-XL, MCL-1 and A1, only a subset of BH3-only proteins, commonly including BIM, BID and PUMA, could he expected to free BAX or BAK from the antiapoptotic BCL-2 proteins to elicit apoptosis.

  19. Analysis of Metabolites in Stem Parasitic Plant Interactions: Interaction of Cuscuta–Momordica versus Cassytha–Ipomoea

    Directory of Open Access Journals (Sweden)

    Takeshi Furuhashi

    2016-12-01

    Full Text Available Cuscuta and Cassytha are two well-known stem parasitic plant genera with reduced leaves and roots, inducing haustoria in their stems. Their similar appearance in the field has been recognized, but few comparative studies on their respective plant interactions are available. To compare their interactions, we conducted a metabolite analysis of both the Cassytha–Ipomoea and the Cuscuta–Momordica interaction. We investigated the energy charge of the metabolites by UFLC (ultra-high performance liquid chromatography, and conducted GC-MS (gas chromatography-mass spectrometry analysis for polar metabolites (e.g., saccharides, polyols and steroids. The energy charge after parasitization changed considerably in Cassytha but not in Cusucta. Cuscuta changed its steroid pattern during the plant interaction, whereas Cassytha did not. In the polar metabolite analysis, the laminaribiose increase after parasitization was conspicuous in Cuscuta, but not in Cassytha. This metabolite profile difference points to different lifestyles and parasitic strategies.

  20. Analysis of Metabolites in Stem Parasitic Plant Interactions: Interaction of Cuscuta–Momordica versus Cassytha–Ipomoea

    Science.gov (United States)

    Furuhashi, Takeshi; Nakamura, Takemichi; Iwase, Koji

    2016-01-01

    Cuscuta and Cassytha are two well-known stem parasitic plant genera with reduced leaves and roots, inducing haustoria in their stems. Their similar appearance in the field has been recognized, but few comparative studies on their respective plant interactions are available. To compare their interactions, we conducted a metabolite analysis of both the Cassytha–Ipomoea and the Cuscuta–Momordica interaction. We investigated the energy charge of the metabolites by UFLC (ultra-high performance liquid chromatography), and conducted GC-MS (gas chromatography-mass spectrometry) analysis for polar metabolites (e.g., saccharides, polyols) and steroids. The energy charge after parasitization changed considerably in Cassytha but not in Cusucta. Cuscuta changed its steroid pattern during the plant interaction, whereas Cassytha did not. In the polar metabolite analysis, the laminaribiose increase after parasitization was conspicuous in Cuscuta, but not in Cassytha. This metabolite profile difference points to different lifestyles and parasitic strategies. PMID:27941603

  1. Interactive Correlation Analysis and Visualization of Climate Data

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Kwan-Liu [Univ. of California, Davis, CA (United States)

    2016-09-21

    The relationship between our ability to analyze and extract insights from visualization of climate model output and the capability of the available resources to make those visualizations has reached a crisis point. The large volume of data currently produced by climate models is overwhelming the current, decades-old visualization workflow. The traditional methods for visualizing climate output also have not kept pace with changes in the types of grids used, the number of variables involved, and the number of different simulations performed with a climate model or the feature-richness of high-resolution simulations. This project has developed new and faster methods for visualization in order to get the most knowledge out of the new generation of high-resolution climate models. While traditional climate images will continue to be useful, there is need for new approaches to visualization and analysis of climate data if we are to gain all the insights available in ultra-large data sets produced by high-resolution model output and ensemble integrations of climate models such as those produced for the Coupled Model Intercomparison Project. Towards that end, we have developed new visualization techniques for performing correlation analysis. We have also introduced highly scalable, parallel rendering methods for visualizing large-scale 3D data. This project was done jointly with climate scientists and visualization researchers at Argonne National Laboratory and NCAR.

  2. Rice–arsenate interactions in hydroponics: whole genome transcriptional analysis

    Science.gov (United States)

    Norton, Gareth J.; Lou-Hing, Daniel E.; Meharg, Andrew A.; Price, Adam H.

    2008-01-01

    Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 μM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the Bala×Azucena mapping population. PMID:18453530

  3. Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis.

    Science.gov (United States)

    Norton, Gareth J; Lou-Hing, Daniel E; Meharg, Andrew A; Price, Adam H

    2008-01-01

    Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 muM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the BalaxAzucena mapping population.

  4. Guide to IDAP, Version 2: an interactive decision analysis procedure

    Energy Technology Data Exchange (ETDEWEB)

    Jusko, M.J.; Whitfield, R.G.

    1980-11-01

    This document is intended to serve as both a programmer's and user's guide to the current version of the IDAP; and to prompt interested individuals into making suggestions for the future development of IDAP. The majority of the sections pertain to the main IDA program rather than to the IDAIN procedure. A brief discussion is presented of the theory of decision analysis. The aspects of decision analysis that are relevant to the IDAP are discussed. A complete list and description of the commands used in the IDAP program is provided and, including three complete examples. This section may be considered a user's guide to the IDAP. The programmer's guide to the IDAP discusses the various technical aspects of the programs, and may be skipped by users not involved with programming the IDAP. A list of the error messages generated by the IDAP is presented. As the program is developed, error handling and messages will improve.

  5. The pragmatic language abilities of children with ADHD following a play-based intervention involving peer-to-peer interactions.

    Science.gov (United States)

    Cordier, Reinie; Munro, Natalie; Wilkes-Gillan, Sarah; Docking, Kimberley

    2013-08-01

    Children with Attention Deficit Hyperactivity Disorder (ADHD) commonly experience significant pragmatic language deficits which put them at risk of developing emotional and social difficulties. This study aimed to examine the pragmatic language exhibited in a peer-to-peer interaction between the children with ADHD and their playmates following a pilot play-based intervention. Participants were children (aged 5-11 years) diagnosed as having ADHD (n = 14) and their self-selected typically-developing playmate. Pragmatic language was measured using the Pragmatic Protocol (PP) and the Structured Multidimensional Assessment Profiles (S-MAPs). Children's structural language was also screened and compared against their pragmatic language skills pre-post play-based intervention. The pragmatic language of children with ADHD improved significantly from pre-post intervention as measured by both the PP and S-MAPs. Both children with and without structural language difficulties improved significantly from pre- to post-intervention using S-MAPs; only children with structural language difficulties improved significantly using PP. The findings support the notion that pragmatic skills may improve following a play-based intervention that is characterized by didactic social interaction. As pragmatic language is a complex construct, it is proposed that clinicians and researchers reconsider the working definition of pragmatic language and the operationalization thereof in assessments.

  6. Optimization of photosynthesis by multiple metabolic pathways involving interorganelle interactions: resource sharing and ROS maintenance as the bases.

    Science.gov (United States)

    Sunil, Bobba; Talla, Sai K; Aswani, Vetcha; Raghavendra, Agepati S

    2013-11-01

    The bioenergetic processes of photosynthesis and respiration are mutually beneficial. Their interaction extends to photorespiration, which is linked to optimize photosynthesis. The interplay of these three pathways is facilitated by two major phenomena: sharing of energy/metabolite resources and maintenance of optimal levels of reactive oxygen species (ROS). The resource sharing among different compartments of plant cells is based on the production/utilization of reducing equivalents (NADPH, NADH) and ATP as well as on the metabolite exchange. The responsibility of generating the cellular requirements of ATP and NAD(P)H is mostly by the chloroplasts and mitochondria. In turn, besides the chloroplasts, the mitochondria, cytosol and peroxisomes are common sinks for reduced equivalents. Transporters located in membranes ensure the coordinated movement of metabolites across the cellular compartments. The present review emphasizes the beneficial interactions among photosynthesis, dark respiration and photorespiration, in relation to metabolism of C, N and S. Since the bioenergetic reactions tend to generate ROS, the cells modulate chloroplast and mitochondrial reactions, so as to ensure that the ROS levels do not rise to toxic levels. The patterns of minimization of ROS production and scavenging of excess ROS in intracellular compartments are highlighted. Some of the emerging developments are pointed out, such as model plants, orientation/movement of organelles and metabolomics.

  7. The Association between Gene-Environment Interactions and Diseases Involving the Human GST Superfamily with SNP Variants

    Directory of Open Access Journals (Sweden)

    Antoinesha L. Hollman

    2016-03-01

    Full Text Available Exposure to environmental hazards has been associated with diseases in humans. The identification of single nucleotide polymorphisms (SNPs in human populations exposed to different environmental hazards, is vital for detecting the genetic risks of some important human diseases. Several studies in this field have been conducted on glutathione S-transferases (GSTs, a phase II detoxification superfamily, to investigate its role in the occurrence of diseases. Human GSTs consist of cytosolic and microsomal superfamilies that are further divided into subfamilies. Based on scientific search engines and a review of the literature, we have found a large amount of published articles on human GST super- and subfamilies that have greatly assisted in our efforts to examine their role in health and disease. Because of its polymorphic variations in relation to environmental hazards such as air pollutants, cigarette smoke, pesticides, heavy metals, carcinogens, pharmaceutical drugs, and xenobiotics, GST is considered as a significant biomarker. This review examines the studies on gene-environment interactions related to various diseases with respect to single nucleotide polymorphisms (SNPs found in the GST superfamily. Overall, it can be concluded that interactions between GST genes and environmental factors play an important role in human diseases.

  8. Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum).

    Science.gov (United States)

    Tokala, Ranjeet K; Strap, Janice L; Jung, Carina M; Crawford, Don L; Salove, Michelle Hamby; Deobald, Lee A; Bailey, J Franklin; Morra, M J

    2002-05-01

    A previously undescribed plant-microbe interaction between a root-colonizing Streptomyces species, S. lydicus WYEC108, and the legume Pisum sativum is described. The interaction is potentially of great importance to the health and growth in nature of this nodulating legume. The root-colonizing soil actinomycete S. lydicus WYEC108 influences pea root nodulation by increasing root nodulation frequency, possibly at the level of infection by Rhizobium spp. S. lydicus also colonizes and then sporulates within the surface cell layers of the nodules. Colonization leads to an increase in the average size of the nodules that form and improves the vigor of bacteroids within the nodules by enhancing nodular assimilation of iron and possibly other soil nutrients. Bacteroid accumulation of the carbon storage polymer, poly-beta-hydroxybutyrate, is reduced in colonized nodules. Root nodules of peas taken from agricultural fields in the Palouse hills of northern Idaho were also found to be colonized by actinomycete hyphae. We hypothesize that root and nodule colonization is one of several mechanisms by which Streptomyces acts as a naturally occurring plant growth-promoting bacterium in pea and possibly other leguminous plants.

  9. Assembly of ROMK1 (Kir 1.1a) inward rectifier K+ channel subunits involves multiple interaction sites.

    Science.gov (United States)

    Koster, J C; Bentle, K A; Nichols, C G; Ho, K

    1998-04-01

    The ROMK1 (Kir 1.1a) channel is formed by a tetrameric complex of subunits, each characterized by cytoplasmic N- and C-termini and a core region of two transmembrane helices flanking a pore-forming segment. To delineate the general regions mediating the assembly of ROMK1 subunits we constructed epitope-tagged N-terminal, C-terminal, and transmembrane segment deletion mutants. Nonfunctional subunits with N-terminal, core region, and C-terminal deletions had dominant negative effects when coexpressed with wild-type ROMK1 subunits in Xenopus oocytes. In contrast, coexpression of these nonfunctional subunits with Kv 2.1 (DRK1) did not suppress Kv 2.1 currents in control oocytes. Interactions between epitope-tagged mutant and wild-type ROMK1 subunits were studied in parallel by immunoprecipitating [35S]-labeled oocyte membrane proteins. Complexes containing both wild-type and mutant subunits that retained H5, M2, and C-terminal regions were coimmunoprecipitated to a greater extent than complexes consisting of wild-type and mutant subunits with core region and/or C-terminal deletions. The present findings are consistent with the hypothesis that multiple interaction sites located in the core region and cytoplasmic termini of ROMK1 subunits mediate homomultimeric assembly.

  10. Intermolecular interactions involving C-H bonds, 3, Structure and energetics of the interaction between CH{sub 4} and CN{sup {minus}}

    Energy Technology Data Exchange (ETDEWEB)

    Novoa, J.J.; Whangbo, Myung-Hwan [North Carolina State Univ., Raleigh, NC (United States). Dept. of Chemistry; Williams, J.M. [Argonne National Lab., IL (United States)

    1991-12-31

    On the basis of SCF and single reference MP2 calculations, the full potential energy surface of the interaction between CH{sub 4} and CN{sup {minus}} was studied using extended basis sets of up to near Hartree-Fock limit quality. Colinear arrangements C-N{sup {minus}}{hor_ellipsis}H-CH{sub 3} and N-C{sup {minus}}{hor_ellipsis}H-CH{sub 3} are found to be the only two energy minima. The binding energies of these two structures are calculated to be 2.5 and 2.1 kcal/mol, respectively, at the MP2 level. The full vibrational analyses of two structures show a red shift of about 30 cm{sup {minus}1} for the v{sub s} C-H stretching.

  11. Social Network Analysis to Examine Interaction Patterns in Knowledge Building Communities

    Science.gov (United States)

    Philip, Donald N.

    2010-01-01

    This paper describes use of social network analysis to examine student interaction patterns in a Grade 5/6 Knowledge Building class. The analysis included face-to-face interactions and interactions in the Knowledge Forum[R] Knowledge Building environment. It is argued that sociogram data are useful to reveal group processes; in sociological terms,…

  12. Types of parental involvement in CBT with anxious youth : A preliminary meta-analysis

    NARCIS (Netherlands)

    Manassis, Katharina; Lee, Trevor Changgun; Bennett, Kathryn; Zhao, Xiu Yan; Mendlowitz, Sandra; Duda, Stephanie; Saini, Michael; Wilansky, Pamela; Baer, Susan; Barrett, Paula; Bodden, Denise; Cobham, Vanessa E; Dadds, Mark R; Flannery-Schroeder, Ellen; Ginsburg, Golda; Heyne, David; Hudson, Jennifer L; Kendall, Philip C; Liber, Juliette; Masia-Warner, Carrie; Nauta, Maaike H; Rapee, Ronald M; Silverman, Wendy; Siqueland, Lynne; Spence, Susan H; Utens, Elisabeth; Wood, Jeffrey J

    2014-01-01

    OBJECTIVE: Meta-analytic studies have not confirmed that involving parents in cognitive behavior therapy (CBT) for anxious children is therapeutically beneficial. There is also great heterogeneity in the type of parental involvement included. We investigated parental involvement focused on contingen

  13. Resident Black Fathers' Involvement: A Comparative Analysis of Married and Unwed, Cohabitating Fathers

    Science.gov (United States)

    Perry, Armon R.; Harmon, Dana K.; Leeper, James

    2012-01-01

    Increasing fathers' involvement with their children has become a priority in recent years. Marriage promotion programs have been offered as the primary vehicles for increasing paternal involvement. Although marriage is likely to provide fathers with increased access and opportunity for paternal involvement, much less is known about the ways in…

  14. A rigid surface boundary element for soil-structure interaction analysis in the direct time domain

    Science.gov (United States)

    Rizos, D. C.

    Many soil-structure interaction problems involve studies of single or multiple rigid bodies of arbitrary shape and soil media. The commonly used boundary element methods implement the equations of the rigid body in a form that depends on the particulars of the geometry and requires partitioning and condensation of the associated algebraic system of equations. The present work employs the direct time domain B-Spline BEM for 3D elastodynamic analysis and presents an efficient implementation of rigid bodies of arbitrary shape in contact with, or embedded in, elastic media. The formulation of a rigid surface boundary element introduced herein is suitable for direct superposition in the BEM system of algebraic equations. Consequently, solutions are computed in a single analysis step, eliminating, thus, the need for partitioning of the system of equations. Computational efficiency is also achieved due to the extremely sparse form of the associated coefficient matrices. The proposed element can be used for the modeling of single or multiple rigid bodies of arbitrary shape within the framework of the BEM method. The efficiency and general nature of the proposed element is demonstrated through applications related to the dynamic analysis of rigid surface and embedded foundations and their interaction with embedded rigid bodies of arbitrary shape.

  15. Integrating R and Java for Enhancing Interactivity of Algorithmic Data Analysis Software Solutions

    Directory of Open Access Journals (Sweden)

    Titus Felix FURTUNĂ

    2016-06-01

    Full Text Available Conceiving software solutions for statistical processing and algorithmic data analysis involves handling diverse data, fetched from various sources and in different formats, and presenting the results in a suggestive, tailorable manner. Our ongoing research aims to design programming technics for integrating R developing environment with Java programming language for interoperability at a source code level. The goal is to combine the intensive data processing capabilities of R programing language, along with the multitude of statistical function libraries, with the flexibility offered by Java programming language and platform, in terms of graphical user interface and mathematical function libraries. Both developing environments are multiplatform oriented, and can complement each other through interoperability. R is a comprehensive and concise programming language, benefiting from a continuously expanding and evolving set of packages for statistical analysis, developed by the open source community. While is a very efficient environment for statistical data processing, R platform lacks support for developing user friendly, interactive, graphical user interfaces (GUIs. Java on the other hand, is a high level object oriented programming language, which supports designing and developing performant and interactive frameworks for general purpose software solutions, through Java Foundation Classes, JavaFX and various graphical libraries. In this paper we treat both aspects of integration and interoperability that refer to integrating Java code into R applications, and bringing R processing sequences into Java driven software solutions. Our research has been conducted focusing on case studies concerning pattern recognition and cluster analysis.

  16. Interactive retinal blood flow analysis of the macular region.

    Science.gov (United States)

    Tian, Jing; Somfai, Gábor Márk; Campagnoli, Thalmon R; Smiddy, William E; Debuc, Delia Cabrera

    2016-03-01

    The study of retinal hemodynamics plays an important role to understand the onset and progression of diabetic retinopathy. In this work, we developed an interactive retinal analysis tool to quantitatively measure the blood flow velocity (BFV) and blood flow rate (BFR) in the macular region using the