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Sample records for modulated transgenomic interactions

  1. Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model

    PubMed Central

    Martin, Francois-Pierre J; Wang, Yulan; Sprenger, Norbert; Yap, Ivan K S; Rezzi, Serge; Ramadan, Ziad; Peré-Trepat, Emma; Rochat, Florence; Cherbut, Christine; van Bladeren, Peter; Fay, Laurent B; Kochhar, Sunil; Lindon, John C; Holmes, Elaine; Nicholson, Jeremy K

    2008-01-01

    Gut microbiome–host metabolic interactions affect human health and can be modified by probiotic and prebiotic supplementation. Here, we have assessed the effects of consumption of a combination of probiotics (Lactobacillus paracasei or L. rhamnosus) and two galactosyl-oligosaccharide prebiotics on the symbiotic microbiome–mammalian supersystem using integrative metabolic profiling and modeling of multiple compartments in germ-free mice inoculated with a model of human baby microbiota. We have shown specific impacts of two prebiotics on the microbial populations of HBM mice when co-administered with two probiotics. We observed an increase in the populations of Bifidobacterium longum and B. breve, and a reduction in Clostridium perfringens, which were more marked when combining prebiotics with L. rhamnosus. In turn, these microbial effects were associated with modulation of a range of host metabolic pathways observed via changes in lipid profiles, gluconeogenesis, and amino-acid and methylamine metabolism associated to fermentation of carbohydrates by different bacterial strains. These results provide evidence for the potential use of prebiotics for beneficially modifying the gut microbial balance as well as host energy and lipid homeostasis. PMID:18628745

  2. Evolutionary transgenomics: prospects and challenges

    PubMed Central

    Correa, Raul; Baum, David A.

    2015-01-01

    Many advances in our understanding of the genetic basis of species differences have arisen from transformation experiments, which allow us to study the effect of genes from one species (the donor) when placed in the genetic background of another species (the recipient). Such interspecies transformation experiments are usually focused on candidate genes – genes that, based on work in model systems, are suspected to be responsible for certain phenotypic differences between the donor and recipient species. We suggest that the high efficiency of transformation in a few plant species, most notably Arabidopsis thaliana, combined with the small size of typical plant genes and their cis-regulatory regions allow implementation of a screening strategy that does not depend upon a priori candidate gene identification. This approach, transgenomics, entails moving many large genomic inserts of a donor species into the wild type background of a recipient species and then screening for dominant phenotypic effects. As a proof of concept, we recently conducted a transgenomic screen that analyzed more than 1100 random, large genomic inserts of the Alabama gladecress Leavenworthia alabamica for dominant phenotypic effects in the A. thaliana background. This screen identified one insert that shortens fruit and decreases A. thaliana fertility. In this paper we discuss the principles of transgenomic screens and suggest methods to help minimize the frequencies of false positive and false negative results. We argue that, because transgenomics avoids committing in advance to candidate genes it has the potential to help us identify truly novel genes or cryptic functions of known genes. Given the valuable knowledge that is likely to be gained, we believe the time is ripe for the plant evolutionary community to invest in transgenomic screens, at least in the mustard family Brassicaceae where many species are amenable to efficient transformation. PMID:26579137

  3. Microbiota-Host Transgenomic Metabolism, Bioactive Molecules from the Inside.

    PubMed

    Turroni, Silvia; Brigidi, Patrizia; Cavalli, Andrea; Candela, Marco

    2017-08-03

    Molecular factors from the gut microbiota provide the host with the right metabolic, immunological, and neurological components to support health and well-being. However, certain circumstances can rupture the mutualistic pact with our intestinal counterpart, pushing the gut microbiome toward a dysbiotic layout, where microbiome-derived molecules may contribute to a disease state. We are now beginning to understand the microbiota-host co-regulated pathways underlying these processes, paving the way for a new era of rational piloting of the gut microbiome functions, through the design of a new generation of microbiome-targeting drugs. Microbiota-derived metabolites are emerging as promising starting hit compounds to modulate human targets, hence triggering certain pharmacological responses. In conclusion, drug discovery targeting the gut microbiota as well as the characterization of microbiota-derived metabolites can represent innovative medicinal chemistry possibilities toward the identification of novel drug candidates, targets, and more in general innovative ways for the treatment of unmet medical needs.

  4. Solving the problem of Trans-Genomic Query with alignment tables.

    PubMed

    Parker, Douglass Stott; Hsiao, Ruey-Lung; Xing, Yi; Resch, Alissa M; Lee, Christopher J

    2008-01-01

    The trans-genomic query (TGQ) problem--enabling the free query of biological information, even across genomes--is a central challenge facing bioinformatics. Solutions to this problem can alter the nature of the field, moving it beyond the jungle of data integration and expanding the number and scope of questions that can be answered. An alignment table is a binary relationship on locations (sequence segments). An important special case of alignment tables are hit tables ? tables of pairs of highly similar segments produced by alignment tools like BLAST. However, alignment tables also include general binary relationships, and can represent any useful connection between sequence locations. They can be curated, and provide a high-quality queryable backbone of connections between biological information. Alignment tables thus can be a natural foundation for TGQ, as they permit a central part of the TGQ problem to be reduced to purely technical problems involving tables of locations.Key challenges in implementing alignment tables include efficient representation and indexing of sequence locations. We define a location datatype that can be incorporated naturally into common off-the-shelf database systems. We also describe an implementation of alignment tables in BLASTGRES, an extension of the open-source POSTGRESQL database system that provides indexing and operators on locations required for querying alignment tables. This paper also reviews several successful large-scale applications of alignment tables for Trans-Genomic Query. Tables with millions of alignments have been used in queries about alternative splicing, an area of genomic analysis concerning the way in which a single gene can yield multiple transcripts. Comparative genomics is a large potential application area for TGQ and alignment tables.

  5. Water-module interaction studies

    NASA Technical Reports Server (NTRS)

    Mon, G.; Wen, L.; Ross, R., Jr.

    1988-01-01

    Mechanisms by which moisture enters photovoltaic modules and techniques for reducing such interactions are reported. Results from a study of the effectiveness of various module sealants are given. Techniques for measuring the rate and quantity of moisture ingress are discussed. It is shown that scribe lines and porous frit bridging conductors provide preferential paths for moisture ingress and that moisture diffusion by surface/interfacial paths is considerably more rapid than diffusion by bulk paths, which implies that thin-film substrate and supersubstrate modules are much more vulnerable to moist environments than are bulk-encapsulated crystalline-silicon modules. Design approaches that reduce moisture entry are discussed.

  6. Applying Economics Using Interactive Learning Modules

    ERIC Educational Resources Information Center

    Goma, Ophelia D.

    2010-01-01

    This article describes the use of web-based, interactive learning modules in the principles of economics course. The learning modules introduce students to important, historical economic events while providing real-world application of the economic theory presented in class. Each module is designed to supplement and complement the economic theory…

  7. Applying Economics Using Interactive Learning Modules

    ERIC Educational Resources Information Center

    Goma, Ophelia D.

    2010-01-01

    This article describes the use of web-based, interactive learning modules in the principles of economics course. The learning modules introduce students to important, historical economic events while providing real-world application of the economic theory presented in class. Each module is designed to supplement and complement the economic theory…

  8. Solar cell modules for plasma interaction evaluation

    NASA Technical Reports Server (NTRS)

    1981-01-01

    A plasma interaction analysis in support of the solar electric propulsion subsystem examined the effects of a large high voltage solar array interacting with an ion thruster produced plasma. Two solar array test modules consisting of 36 large area wraparound contact solar cells welded to a flexible Kapton integrated circuit substrate were abricated. The modules contained certain features of the effects of insulation, din-holes, and bonding of the cell to the substrate and a ground plane. The possibility of a significant power loss occurring due to the collection of charged particles on the solar array interconnects was the focus of the research.

  9. Interactive Astronomy Module for Museums and Schools

    NASA Astrophysics Data System (ADS)

    Smith, I. A.; Reiff, P. H.; Liang, E. P.; Law, C.; Sumners, C.; Sumners, R. W.

    1996-12-01

    To educate visitors about the Earth and Space Sciences, Rice University and the Houston Museum of Natural Sciences have set up interactive computer kiosks in the museum. We developed an astronomy module for this that contains recent and archival astronomical images that we download from sites on the World Wide Web. The main kiosk in the museum has an internet connection to our computers at Rice, allowing us to remotely update it on the same day that new results appear on the WWW. During this year, versions of the whole Earth and Space Sciences project will be made on CD ROMs and distributed to schools. At the meeting, we will display a stand-alone portable kiosk that contains the complete Space Update package. We will also have a laptop dedicated to the astronomy module.

  10. A Usability Study of Interactive Web-Based Modules

    ERIC Educational Resources Information Center

    Girard, Tulay; Pinar, Musa

    2011-01-01

    This research advances the understanding of the usability of marketing case study modules in the area of interactive web-based technologies through the assignment of seven interactive case modules in a Principles of Marketing course. The case modules were provided for marketing students by the publisher, McGraw Hill Irwin, of the…

  11. Interacting Brain Systems Modulate Memory Consolidation

    PubMed Central

    McIntyre, Christa K.; McGaugh, James L.; Williams, Cedric L.

    2011-01-01

    Emotional arousal influences the consolidation of long-term memory. This review discusses experimental approaches and relevant findings that provide the foundation for current understanding of coordinated interactions between arousal activated peripheral hormones and the brain processes that modulate memory formation. Rewarding or aversive experiences release the stress hormones epinephrine (adrenalin) and glucocorticoids from the adrenal glands into the bloodstream. The effect of these hormones on memory consolidation depends upon binding of norepinephrine to beta-adrenergic receptors in the basolateral complex of the amygdala (BLA). Much evidence indicates that the stress hormones influence release of norepinephrine in the BLA through peripheral actions on the vagus nerve which stimulates, through polysynaptic connections, cells of the locus coeruleus to release norepinephrine. The BLA influences memory storage by actions on synapses, distributed throughout the brain, that are engaged in sensory and cognitive processing at the time of amygdala activation. The implications of the activation of these stress-activated memory processes are discussed in relation to stress-related memory disorders. PMID:22085800

  12. Interactive Astronomy Module for Museums and Schools

    NASA Astrophysics Data System (ADS)

    Smith, I. A.; Reiff, P. H.; Law, C.; Liang, E. P.; Sumners, C.

    1998-12-01

    To educate visitors about the Earth and Space Sciences, Rice University and the Houston Museum of Natural Sciences have set up interactive computer kiosks in the museum and in other museums across the country. We developed an astronomy module for this that contains recent and archival astronomical images that we download from sites on the World Wide Web. The main kiosk in the museum has an internet connection to our computers at Rice, allowing us to remotely update it on the same day that new results appear on the WWW. Complete but frozen-in-time versions of the whole Earth and Space Sciences project are made on CD ROMs and distributed to schools and museums: the CD works on both PCs and Macs. Captions and credits with WWW addresses are added to each image so that they can be used as the starting point for further learning later. This project was made possible through NASA grants from the Digital Library Technology Project and the Initiative to Develop Education through Astronomy.

  13. A Transgenomic Cytogenetic Sorghum (Sorghum propinquum) Bacterial Artificial Chromosome Fluorescence in Situ Hybridization Map of Maize (Zea mays L.) Pachytene Chromosome 9, Evidence for Regions of Genome Hyperexpansion

    PubMed Central

    Amarillo, F. Ina E.; Bass, Hank W.

    2007-01-01

    A cytogenetic FISH map of maize pachytene-stage chromosome 9 was produced with 32 maize marker-selected sorghum BACs as probes. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 cM. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole-chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC–FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between cdo17 (at 9L.03) and tda66 (at 9S.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum and creates additional tools and information for understanding the structure and evolution of the maize genome. PMID:17947405

  14. Infant Smiling during Social Interaction: Arousal Modulation or Activation Indicator?

    ERIC Educational Resources Information Center

    Ewy, Richard

    In a study of infant smiling, 20 mother-infant dyads were videotaped in normal face-to-face interaction when the infants were 9 and 14 weeks of age. Videotapes were used to determine which of two classes of smiling behavior models, either arousal modulation or activation indicator, was most supported by empirical data. Arousal modulation models…

  15. Infant Smiling during Social Interaction: Arousal Modulation or Activation Indicator?

    ERIC Educational Resources Information Center

    Ewy, Richard

    In a study of infant smiling, 20 mother-infant dyads were videotaped in normal face-to-face interaction when the infants were 9 and 14 weeks of age. Videotapes were used to determine which of two classes of smiling behavior models, either arousal modulation or activation indicator, was most supported by empirical data. Arousal modulation models…

  16. Online Chemistry Modules: Interaction and Effective Faculty Facilitation

    ERIC Educational Resources Information Center

    Slocum, Laura E.; Towns Marcy Hamby; Zielinski, Theresa Julia

    2004-01-01

    Computer supported collaborative learning, cooperative learning combined with electronic communication, physical chemistry online modules, use of discussion boards, its advantages and limitations are experimented and discussed. The most important finding is the example of effective online faculty facilitation and interaction.

  17. Solar Array Module Plasma Interaction Experiment (SAMPIE): Technical requirements document

    NASA Technical Reports Server (NTRS)

    Hillard, G. Barry; Ferguson, Dale C.

    1992-01-01

    The Solar Array Module Plasma Interactions Experiment (SAMPIE) is a NASA shuttle space flight experiment scheduled for launch in early 1994. The SAMPIE experiment will investigate plasma interactions of high voltage space power systems in low earth orbit. Solar cell modules, representing several technologies, will be biased to high voltages to characterize both arcing and plasma current collection. Other solar modules, specially modified in accordance with current theories of arcing and breakdown, will demonstrate the possibility of arc suppression. Finally, several test modules will be included to study the basic nature of these interactions. The science and technology goals for the project are defined in the Technical Requirements Document (TRD) which is presented here.

  18. Module organization and variance in protein-protein interaction networks

    NASA Astrophysics Data System (ADS)

    Lin, Chun-Yu; Lee, Tsai-Ling; Chiu, Yi-Yuan; Lin, Yi-Wei; Lo, Yu-Shu; Lin, Chih-Ta; Yang, Jinn-Moon

    2015-03-01

    A module is a group of closely related proteins that act in concert to perform specific biological functions through protein-protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores and interface evolution scores to describe the module elements, including core and ring components. Functions of core components were highly correlated with those of essential genes. In comparison with ring components, core proteins/PPIs were conserved across multiple species. Subsequently, protein/module variance of PPI networks confirmed that core components form dynamic network hubs and play key roles in various biological functions. Based on the analyses of gene essentiality, module variance, and gene co-expression, we summarize the observations of module organization and variance as follows: 1) a module consists of core and ring components; 2) core components perform major biological functions and collaborate with ring components to execute certain functions in some cases; 3) core components are more conserved and essential during organizational changes in different biological states or conditions.

  19. Topographic Modulation of Ice-Ocean Interactions

    NASA Astrophysics Data System (ADS)

    Catania, G. A.; Fried, M.; Felikson, D.; Carroll, D.; Bartholomaus, T. C.; Stearns, L. A.; Sutherland, D.; Nash, J. D.; Shroyer, E.

    2016-12-01

    We present a regional synthesis of the oceanic influence on ice dynamics across a suite of outlet glaciers in central west Greenland that range in flux, grounding line depth and catchment area. While far-field atmospheric and oceanographic forcing is uniform, the spatio-temporal response of the ice sheet is highly heterogeneous. We find that the terminus position is significantly influenced by plume-driven submarine melt, resulting from the mixing of buoyant subglacial discharge with deep, warm fjord waters. Further, this plume melting undercuts the glacier terminus and can enhance retreat through calving. Local topography (the presence and height of fjord sills and grounding line depth) modulates the plume structure and melt rate, thereby providing a means for explaining some of the glacier-to-glacier differences in dynamic response. In addition, we find that once retreat is initiated, the amount, duration, rate of retreat and its impact on inland thinning is regulated by local topography of the glacier-fjord system. Glaciers resting on reverse bed slopes experience faster rates of retreat, while those in narrows and/or on positively-sloped beds do not retreat. We also find that the upstream limit to thinning is controlled by glacier geometry. The majority of mass loss occurs downstream from a location where the downstream advective speed is at least four times faster than the upstream diffusive speed of a kinematic wave of thinning initiated by terminus retreat. These observations suggest that while ocean and atmospheric factors provide first-order forcing to glacier dynamics, the response of an individual glacier will be modulated by its inherent and unique topographic state. This suggests the need for improved topographic observations across the ice-ocean boundary and into the ice sheet interior and exploring whether or not these ideas are applicable elsewhere around Greenland.

  20. Interactive online optics modules for the college physics course

    NASA Astrophysics Data System (ADS)

    Hoeling, Barbara M.

    2012-04-01

    A new learning tool for geometrical optics is presented which has been developed for an algebra based introductory college physics course for life science majors. The interactive online learning module contains images, videos of problem solutions, short animated videos, and interactive animations, which allow students to actively explore the physics content beyond the pictures in a textbook. These elements are accompanied by narration and a transcript to guide the students while allowing them to navigate freely between the different parts of the module. The results of student learning, a comparison with a control group, and a survey of student attitudes toward this new instruction method are discussed.

  1. Identification of Topological Network Modules in Perturbed Protein Interaction Networks.

    PubMed

    Sardiu, Mihaela E; Gilmore, Joshua M; Groppe, Brad; Florens, Laurence; Washburn, Michael P

    2017-03-08

    Biological networks consist of functional modules, however detecting and characterizing such modules in networks remains challenging. Perturbing networks is one strategy for identifying modules. Here we used an advanced mathematical approach named topological data analysis (TDA) to interrogate two perturbed networks. In one, we disrupted the S. cerevisiae INO80 protein interaction network by isolating complexes after protein complex components were deleted from the genome. In the second, we reanalyzed previously published data demonstrating the disruption of the human Sin3 network with a histone deacetylase inhibitor. Here we show that disrupted networks contained topological network modules (TNMs) with shared properties that mapped onto distinct locations in networks. We define TMNs as proteins that occupy close network positions depending on their coordinates in a topological space. TNMs provide new insight into networks by capturing proteins from different categories including proteins within a complex, proteins with shared biological functions, and proteins disrupted across networks.

  2. Identification of Topological Network Modules in Perturbed Protein Interaction Networks

    PubMed Central

    Sardiu, Mihaela E.; Gilmore, Joshua M.; Groppe, Brad; Florens, Laurence; Washburn, Michael P.

    2017-01-01

    Biological networks consist of functional modules, however detecting and characterizing such modules in networks remains challenging. Perturbing networks is one strategy for identifying modules. Here we used an advanced mathematical approach named topological data analysis (TDA) to interrogate two perturbed networks. In one, we disrupted the S. cerevisiae INO80 protein interaction network by isolating complexes after protein complex components were deleted from the genome. In the second, we reanalyzed previously published data demonstrating the disruption of the human Sin3 network with a histone deacetylase inhibitor. Here we show that disrupted networks contained topological network modules (TNMs) with shared properties that mapped onto distinct locations in networks. We define TMNs as proteins that occupy close network positions depending on their coordinates in a topological space. TNMs provide new insight into networks by capturing proteins from different categories including proteins within a complex, proteins with shared biological functions, and proteins disrupted across networks. PMID:28272416

  3. Developing Interactive Learning Objects for a Computing Mathematics Module

    ERIC Educational Resources Information Center

    Lim, Cher Ping; Lee, Siew Lie; Richards, Cameron

    2006-01-01

    Based on a case study of the online component of a Computing Mathematics module at a local polytechnic in Singapore, this article provides a descriptive account of the development and employment of interactive learning objects to enhance the learning experiences of the students in the course. The experimented learning objects were branded as…

  4. Protein Interaction Networks—More Than Mere Modules

    PubMed Central

    Pinkert, Stefan; Schultz, Jörg; Reichardt, Jörg

    2010-01-01

    It is widely believed that the modular organization of cellular function is reflected in a modular structure of molecular networks. A common view is that a “module” in a network is a cohesively linked group of nodes, densely connected internally and sparsely interacting with the rest of the network. Many algorithms try to identify functional modules in protein-interaction networks (PIN) by searching for such cohesive groups of proteins. Here, we present an alternative approach independent of any prior definition of what actually constitutes a “module”. In a self-consistent manner, proteins are grouped into “functional roles” if they interact in similar ways with other proteins according to their functional roles. Such grouping may well result in cohesive modules again, but only if the network structure actually supports this. We applied our method to the PIN from the Human Protein Reference Database (HPRD) and found that a representation of the network in terms of cohesive modules, at least on a global scale, does not optimally represent the network's structure because it focuses on finding independent groups of proteins. In contrast, a decomposition into functional roles is able to depict the structure much better as it also takes into account the interdependencies between roles and even allows groupings based on the absence of interactions between proteins in the same functional role. This, for example, is the case for transmembrane proteins, which could never be recognized as a cohesive group of nodes in a PIN. When mapping experimental methods onto the groups, we identified profound differences in the coverage suggesting that our method is able to capture experimental bias in the data, too. For example yeast-two-hybrid data were highly overrepresented in one particular group. Thus, there is more structure in protein-interaction networks than cohesive modules alone and we believe this finding can significantly improve automated function prediction

  5. Interacting Brain Modules for Memory: An Adaptive Representations Architecture

    DTIC Science & Technology

    2008-06-01

    acquired memories for autobiographical events, sometimes collectively called episodic memory (e.g. Squire, 1987; Squire et al., 2004), as well as...AFRL-RI-RS-TR-2008-177 Final Technical Report June 2008 INTERACTING BRAIN MODULES FOR MEMORY : AN ADAPTIVE REPRESENTATIONS...FOR MEMORY : AN ADAPTIVE REPRESENTATIONS ARCHITECTURE 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA8750-05-2-0273 5c. PROGRAM ELEMENT NUMBER 62304F

  6. Novel cholinesterase modulators and their ability to interact with DNA

    NASA Astrophysics Data System (ADS)

    Janockova, Jana; Gulasova, Zuzana; Musilek, Kamil; Kuca, Kamil; Kozurkova, Maria

    2013-11-01

    In the present work, an interaction of four cholinesterase modulators (1-4) with calf thymus DNA was studied via spectroscopic techniques (UV-Vis, fluorescent spectroscopy and circular dichroism). From UV-Vis spectroscopic analysis, the binding constants for DNA-pyridinium oximes complexes were calculated (K = 3.5 × 104 to 1.4 × 105 M-1). All these measurements indicated that the compounds behave as effective DNA-interacting agents. Electrophoretic techniques proved that ligand 2 inhibited topoisomerase I at a concentration 5 μM.

  7. Metal-graphene heterojunction modulation via H2 interaction

    NASA Astrophysics Data System (ADS)

    Cadore, A. R.; Mania, E.; de Morais, E. A.; Watanabe, K.; Taniguchi, T.; Lacerda, R. G.; Campos, L. C.

    2016-07-01

    Combining experiment and theory, we investigate how a naturally created heterojunction (pn junction) at a graphene and metallic contact interface is modulated via interaction with molecular hydrogen (H2). Due to an electrostatic interaction, metallic electrodes induce pn junctions in graphene, leading to an asymmetrical resistance in electronic transport for electrons and holes. We report that the asymmetry in the resistance can be tuned in a reversible manner by exposing graphene devices to H2. The interaction between the H2 and graphene occurs solely at the graphene-contact pn junction and induces a modification on the electrostatic interaction between graphene and metallic contacts. We explain the experimental data with theory providing information concerning the length of the heterojunction and how it changes as a function of H2 adsorption. Our results are valuable for understanding the nature of the metal-graphene interfaces and have potential application for selective sensors of molecular hydrogen.

  8. Inferring modulators of genetic interactions with epistatic nested effects models.

    PubMed

    Pirkl, Martin; Diekmann, Madeline; van der Wees, Marlies; Beerenwinkel, Niko; Fröhlich, Holger; Markowetz, Florian

    2017-04-01

    Maps of genetic interactions can dissect functional redundancies in cellular networks. Gene expression profiles as high-dimensional molecular readouts of combinatorial perturbations provide a detailed view of genetic interactions, but can be hard to interpret if different gene sets respond in different ways (called mixed epistasis). Here we test the hypothesis that mixed epistasis between a gene pair can be explained by the action of a third gene that modulates the interaction. We have extended the framework of Nested Effects Models (NEMs), a type of graphical model specifically tailored to analyze high-dimensional gene perturbation data, to incorporate logical functions that describe interactions between regulators on downstream genes and proteins. We benchmark our approach in the controlled setting of a simulation study and show high accuracy in inferring the correct model. In an application to data from deletion mutants of kinases and phosphatases in S. cerevisiae we show that epistatic NEMs can point to modulators of genetic interactions. Our approach is implemented in the R-package 'epiNEM' available from https://github.com/cbg-ethz/epiNEM and https://bioconductor.org/packages/epiNEM/.

  9. Modulators of 14-3-3 Protein-Protein Interactions.

    PubMed

    Stevers, Loes M; Sijbesma, Eline; Botta, Maurizio; MacKintosh, Carol; Obsil, Tomas; Landrieu, Isabelle; Cau, Ylenia; Wilson, Andrew J; Karawajczyk, Anna; Eickhoff, Jan; Davis, Jeremy; Hann, Michael M; O'Mahony, Gavin; Doveston, Richard G; Brunsveld, Luc; Ottmann, Christian

    2017-10-02

    Direct interactions between proteins are essential for the regulation of their functions in biological pathways. Targeting the complex network of protein-protein interactions (PPIs) has now been widely recognized as an attractive means to therapeutically intervene in disease states. Even though this is a challenging endeavor and PPIs have long been regarded as 'undruggable' targets, the last two decades have seen an increasing number of successful examples of PPI modulators resulting in a growing interest in this field. PPI modulation requires novel approaches and the integrated efforts of multiple disciplines to be a fruitful strategy. This Perspective focuses on the hub protein 14-3-3, which has several hundred identified protein interaction partners and is therefore involved in a wide range of cellular processes and diseases. Here, we aim to provide an integrated overview of the approaches explored for the modulation of 14-3-3 PPIs and review the examples resulting from these efforts in both inhibiting and stabilizing specific 14-3-3 protein complexes by small molecules, peptide-mimetics and natural products.

  10. Class II HLA interactions modulate genetic risk for multiple sclerosis

    PubMed Central

    Dilthey, Alexander T; Xifara, Dionysia K; Ban, Maria; Shah, Tejas S; Patsopoulos, Nikolaos A; Alfredsson, Lars; Anderson, Carl A; Attfield, Katherine E; Baranzini, Sergio E; Barrett, Jeffrey; Binder, Thomas M C; Booth, David; Buck, Dorothea; Celius, Elisabeth G; Cotsapas, Chris; D’Alfonso, Sandra; Dendrou, Calliope A; Donnelly, Peter; Dubois, Bénédicte; Fontaine, Bertrand; Fugger, Lars; Goris, An; Gourraud, Pierre-Antoine; Graetz, Christiane; Hemmer, Bernhard; Hillert, Jan; Kockum, Ingrid; Leslie, Stephen; Lill, Christina M; Martinelli-Boneschi, Filippo; Oksenberg, Jorge R; Olsson, Tomas; Oturai, Annette; Saarela, Janna; Søndergaard, Helle Bach; Spurkland, Anne; Taylor, Bruce; Winkelmann, Juliane; Zipp, Frauke; Haines, Jonathan L; Pericak-Vance, Margaret A; Spencer, Chris C A; Stewart, Graeme; Hafler, David A; Ivinson, Adrian J; Harbo, Hanne F; Hauser, Stephen L; De Jager, Philip L; Compston, Alastair; McCauley, Jacob L; Sawcer, Stephen; McVean, Gil

    2016-01-01

    Association studies have greatly refined the understanding of how variation within the human leukocyte antigen (HLA) genes influences risk of multiple sclerosis. However, the extent to which major effects are modulated by interactions is poorly characterized. We analyzed high-density SNP data on 17,465 cases and 30,385 controls from 11 cohorts of European ancestry, in combination with imputation of classical HLA alleles, to build a high-resolution map of HLA genetic risk and assess the evidence for interactions involving classical HLA alleles. Among new and previously identified class II risk alleles (HLA-DRB1*15:01, HLA-DRB1*13:03, HLA-DRB1*03:01, HLA-DRB1*08:01 and HLA-DQB1*03:02) and class I protective alleles (HLA-A*02:01, HLA-B*44:02, HLA-B*38:01 and HLA-B*55:01), we find evidence for two interactions involving pairs of class II alleles: HLA-DQA1*01:01–HLA-DRB1*15:01 and HLA-DQB1*03:01–HLA-DQB1*03:02. We find no evidence for interactions between classical HLA alleles and non-HLA risk-associated variants and estimate a minimal effect of polygenic epistasis in modulating major risk alleles. PMID:26343388

  11. Apparatus and method for interaction phenomena with world modules in data-flow-based simulation

    DOEpatents

    Xavier, Patrick G.; Gottlieb, Eric J.; McDonald, Michael J.; Oppel, III, Fred J.

    2006-08-01

    A method and apparatus accommodate interaction phenomenon in a data-flow-based simulation of a system of elements, by establishing meta-modules to simulate system elements and by establishing world modules associated with interaction phenomena. World modules are associated with proxy modules from a group of meta-modules associated with one of the interaction phenomenon. The world modules include a communication world, a sensor world, a mobility world, and a contact world. World modules can be further associated with other world modules if necessary. Interaction phenomenon are simulated in corresponding world modules by accessing member functions in the associated group of proxy modules. Proxy modules can be dynamically allocated at a desired point in the simulation to accommodate the addition of elements in the system of elements such as a system of robots, a system of communication terminals, or a system of vehicles, being simulated.

  12. How Auxin and Cytokinin Phytohormones Modulate Root Microbe Interactions

    PubMed Central

    Boivin, Stéphane; Fonouni-Farde, Camille; Frugier, Florian

    2016-01-01

    A large range of microorganisms can associate with plants, resulting in neutral, friendly or hostile interactions. The ability of plants to recognize compatible and incompatible microorganisms and to limit or promote their colonization is therefore crucial for their survival. Elaborated communication networks determine the degree of association between the host plant and the invading microorganism. Central to these regulations of plant microbe interactions, phytohormones modulate microorganism plant associations and coordinate cellular and metabolic responses associated to the progression of microorganisms across different plant tissues. We review here hormonal regulations, focusing on auxin and cytokinin phytohormones, involved in the interactions between plant roots and soil microorganisms, including bacterial and fungi associations, either beneficial (symbiotic) or detrimental (pathogenic). The aim is to highlight similarities and differences in cytokinin/auxin functions amongst various compatible versus incompatible associations. PMID:27588025

  13. Ocean-Atmosphere Interactions Modulate Irrigation's Climate Impacts

    NASA Technical Reports Server (NTRS)

    Krakauer, Nir Y.; Puma, Michael J.; Cook, Benjamin I.; Gentine, Pierre; Nazarenko, Larissa

    2016-01-01

    Numerous studies have focused on the local and regional climate effects of irrigated agriculture and other land cover and land use change (LCLUC) phenomena, but there are few studies on the role of ocean- atmosphere interaction in modulating irrigation climate impacts. Here, we compare simulations with and without interactive sea surface temperatures of the equilibrium effect on climate of contemporary (year 2000) irrigation geographic extent and intensity. We find that ocean-atmosphere interaction does impact the magnitude of global-mean and spatially varying climate impacts, greatly increasing their global reach. Local climate effects in the irrigated regions remain broadly similar, while non-local effects, particularly over the oceans, tend to be larger. The interaction amplifies irrigation-driven standing wave patterns in the tropics and mid-latitudes in our simulations, approximately doubling the global-mean amplitude of surface temperature changes due to irrigation. The fractions of global area experiencing significant annual-mean surface air temperature and precipitation change also approximately double with ocean-atmosphere interaction. Subject to confirmation with other models, these findings imply that LCLUC is an important contributor to climate change even in remote areas such as the Southern Ocean, and that attribution studies should include interactive oceans and need to consider LCLUC, including irrigation, as a truly global forcing that affects climate and the water cycle over ocean as well as land areas.

  14. Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

    PubMed Central

    Doyle, Boryana; Fudenberg, Geoffrey; Imakaev, Maxim; Mirny, Leonid A.

    2014-01-01

    The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently for in silico 3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site. PMID:25340767

  15. Modulation of hydrophobic interactions by proximally immobilized ions.

    PubMed

    Ma, C Derek; Wang, Chenxuan; Acevedo-Vélez, Claribel; Gellman, Samuel H; Abbott, Nicholas L

    2015-01-15

    The structure of water near non-polar molecular fragments or surfaces mediates the hydrophobic interactions that underlie a broad range of interfacial, colloidal and biophysical phenomena. Substantial progress over the past decade has improved our understanding of hydrophobic interactions in simple model systems, but most biologically and technologically relevant structures contain non-polar domains in close proximity to polar and charged functional groups. Theories and simulations exploring such nanometre-scale chemical heterogeneity find it can have an important effect, but the influence of this heterogeneity on hydrophobic interactions has not been tested experimentally. Here we report chemical force microscopy measurements on alkyl-functionalized surfaces that reveal a dramatic change in the surfaces' hydrophobic interaction strengths on co-immobilization of amine or guanidine groups. Protonation of amine groups doubles the strength of hydrophobic interactions, and guanidinium groups eliminate measurable hydrophobic interactions in all pH ranges investigated. We see these divergent effects of proximally immobilized cations also in single-molecule measurements on conformationally stable β-peptides with non-polar subunits located one nanometre from either amine- or guanidine-bearing subunits. Our results demonstrate the importance of nanometre-scale chemical heterogeneity, with hydrophobicity not an intrinsic property of any given non-polar domain but strongly modulated by functional groups located as far away as one nanometre. The judicious placing of charged groups near hydrophobic domains thus provides a strategy for tuning hydrophobic driving forces to optimize molecular recognition or self-assembly processes.

  16. Ocean-atmosphere interactions modulate irrigation's climate impacts

    NASA Astrophysics Data System (ADS)

    Krakauer, Nir Y.; Puma, Michael J.; Cook, Benjamin I.; Gentine, Pierre; Nazarenko, Larissa

    2016-11-01

    Numerous studies have focused on the local and regional climate effects of irrigated agriculture and other land cover and land use change (LCLUC) phenomena, but there are few studies on the role of ocean-atmosphere interaction in modulating irrigation climate impacts. Here, we compare simulations with and without interactive sea surface temperatures of the equilibrium effect on climate of contemporary (year 2000) irrigation geographic extent and intensity. We find that ocean-atmosphere interaction does impact the magnitude of global-mean and spatially varying climate impacts, greatly increasing their global reach. Local climate effects in the irrigated regions remain broadly similar, while non-local effects, particularly over the oceans, tend to be larger. The interaction amplifies irrigation-driven standing wave patterns in the tropics and midlatitudes in our simulations, approximately doubling the global-mean amplitude of surface temperature changes due to irrigation. The fractions of global area experiencing significant annual-mean surface air temperature and precipitation change also approximately double with ocean-atmosphere interaction. Subject to confirmation with other models, these findings imply that LCLUC is an important contributor to climate change even in remote areas such as the Southern Ocean, and that attribution studies should include interactive oceans and need to consider LCLUC, including irrigation, as a truly global forcing that affects climate and the water cycle over ocean as well as land areas.

  17. Modulation of hydrophobic interactions by proximally immobilized ions

    NASA Astrophysics Data System (ADS)

    Ma, C. Derek; Wang, Chenxuan; Acevedo-Vélez, Claribel; Gellman, Samuel H.; Abbott, Nicholas L.

    2015-01-01

    The structure of water near non-polar molecular fragments or surfaces mediates the hydrophobic interactions that underlie a broad range of interfacial, colloidal and biophysical phenomena. Substantial progress over the past decade has improved our understanding of hydrophobic interactions in simple model systems, but most biologically and technologically relevant structures contain non-polar domains in close proximity to polar and charged functional groups. Theories and simulations exploring such nanometre-scale chemical heterogeneity find it can have an important effect, but the influence of this heterogeneity on hydrophobic interactions has not been tested experimentally. Here we report chemical force microscopy measurements on alkyl-functionalized surfaces that reveal a dramatic change in the surfaces' hydrophobic interaction strengths on co-immobilization of amine or guanidine groups. Protonation of amine groups doubles the strength of hydrophobic interactions, and guanidinium groups eliminate measurable hydrophobic interactions in all pH ranges investigated. We see these divergent effects of proximally immobilized cations also in single-molecule measurements on conformationally stable β-peptides with non-polar subunits located one nanometre from either amine- or guanidine-bearing subunits. Our results demonstrate the importance of nanometre-scale chemical heterogeneity, with hydrophobicity not an intrinsic property of any given non-polar domain but strongly modulated by functional groups located as far away as one nanometre. The judicious placing of charged groups near hydrophobic domains thus provides a strategy for tuning hydrophobic driving forces to optimize molecular recognition or self-assembly processes.

  18. Ocean-Atmosphere Interactions Modulate Irrigation's Climate Impacts

    NASA Technical Reports Server (NTRS)

    Krakauer, Nir Y.; Puma, Michael J.; Cook, Benjamin I.; Gentine, Pierre; Nazarenko, Larissa

    2016-01-01

    Numerous studies have focused on the local and regional climate effects of irrigated agriculture and other land cover and land use change (LCLUC) phenomena, but there are few studies on the role of ocean- atmosphere interaction in modulating irrigation climate impacts. Here, we compare simulations with and without interactive sea surface temperatures of the equilibrium effect on climate of contemporary (year 2000) irrigation geographic extent and intensity. We find that ocean-atmosphere interaction does impact the magnitude of global-mean and spatially varying climate impacts, greatly increasing their global reach. Local climate effects in the irrigated regions remain broadly similar, while non-local effects, particularly over the oceans, tend to be larger. The interaction amplifies irrigation-driven standing wave patterns in the tropics and mid-latitudes in our simulations, approximately doubling the global-mean amplitude of surface temperature changes due to irrigation. The fractions of global area experiencing significant annual-mean surface air temperature and precipitation change also approximately double with ocean-atmosphere interaction. Subject to confirmation with other models, these findings imply that LCLUC is an important contributor to climate change even in remote areas such as the Southern Ocean, and that attribution studies should include interactive oceans and need to consider LCLUC, including irrigation, as a truly global forcing that affects climate and the water cycle over ocean as well as land areas.

  19. Eph/ephrin interactions modulate vascular sympathetic innervation.

    PubMed

    Damon, Deborah H; teRiele, Jaclyn A; Marko, Stephen B

    2010-12-08

    Ephs and ephrins are membrane-bound proteins that interact to modulate axon growth and neuronal function. We tested the hypothesis that eph/ephrin interactions affected the growth and function of vascular sympathetic innervation. Using RT-PCR analyses, we detected both classes of ephs (A and B) and both classes of ephrins (A and B) in sympathetic ganglia from neonatal and adult rats. Both classes of ephs (A and B) and both classes of ephrins (A and B) bound to the cell bodies and neurites of dissociated postganglionic sympathetic neurons. Messenger RNAs encoding for both classes of ephs (A and B) and both classes of ephrins (A and B) were also detected in sympathetically innervated arteries from neonatal and adult rats. These data suggest that ephrins/ephs on nerve fibers of postganglionic sympathetic neurons could interact with ephs/ephrins on cells in innervated arteries. We found that ephA4 reduced reinnervation of denervated femoral arteries. Reinnervation in the presence of ephA4-Fc (38.9±6.6%) was significantly less than that in the presence of IgG-Fc (62±10%; n=5; p<0.05; one-tailed unpaired t-test). These data indicate that eph/ephrin interactions modulated the growth of vascular sympathetic innervation. We also found that ephA4 increased basal release of norepinephrine from nerve terminals of isolated tail arteries. These data indicate that eph/ephrin interactions affect the growth and function of vascular sympathetic innervation.

  20. Prion protein self-peptides modulate prion interactions and conversion

    PubMed Central

    2009-01-01

    Background Molecular mechanisms underlying prion agent replication, converting host-encoded cellular prion protein (PrPC) into the scrapie associated isoform (PrPSc), are poorly understood. Selective self-interaction between PrP molecules forms a basis underlying the observed differences of the PrPC into PrPSc conversion process (agent replication). The importance of previously peptide-scanning mapped ovine PrP self-interaction domains on this conversion was investigated by studying the ability of six of these ovine PrP based peptides to modulate two processes; PrP self-interaction and conversion. Results Three peptides (octarepeat, binding domain 2 -and C-terminal) were capable of inhibiting self-interaction of PrP in a solid-phase PrP peptide array. Three peptides (N-terminal, binding domain 2, and amyloidogenic motif) modulated prion conversion when added before or after initiation of the prion protein misfolding cyclic amplification (PMCA) reaction using brain homogenates. The C-terminal peptides (core region and C-terminal) only affected conversion (increased PrPres formation) when added before mixing PrPC and PrPSc, whereas the octarepeat peptide only affected conversion when added after this mixing. Conclusion This study identified the putative PrP core binding domain that facilitates the PrPC-PrPSc interaction (not conversion), corroborating evidence that the region of PrP containing this domain is important in the species-barrier and/or scrapie susceptibility. The octarepeats can be involved in PrPC-PrPSc stabilization, whereas the N-terminal glycosaminoglycan binding motif and the amyloidogenic motif indirectly affected conversion. Binding domain 2 and the C-terminal domain are directly implicated in PrPC self-interaction during the conversion process and may prove to be prime targets in new therapeutic strategy development, potentially retaining PrPC function. These results emphasize the importance of probable PrPC-PrPC and required Pr

  1. Modulation of additive and interactive effects by trial history revisited.

    PubMed

    Masson, Michael E J; Rabe, Maximilian M; Kliegl, Reinhold

    2017-04-01

    Masson and Kliegl (Journal of Experimental Psychology: Learning, Memory, and Cognition, 39, 898-914, 2013) reported evidence that the nature of the target stimulus on the previous trial of a lexical decision task modulates the effects of independent variables on the current trial, including additive versus interactive effects of word frequency and stimulus quality. In contrast, recent reanalyses of previously published data from experiments that, unlike the Masson and Kliegl experiments, did not include semantic priming as a factor, found no evidence for modulation of additive effects of frequency and stimulus quality by trial history (Balota, Aschenbrenner, & Yap, Journal of Experimental Psychology: Learning, Memory, and Cognition, 39, 1563-1571, 2013; O'Malley & Besner, Journal of Experimental Psychology: Learning, Memory, and Cognition, 34, 1400-1411, 2013). We report two experiments that included semantic priming as a factor and that attempted to replicate the modulatory effects found by Masson and Kliegl. In neither experiment was additivity of frequency and stimulus quality modulated by trial history, converging with the findings reported by Balota et al. and O'Malley and Besner. Other modulatory influences of trial history, however, were replicated in the new experiments and reflect potential trial-by-trial alterations in decision processes.

  2. Interactions between modulators of the GABAA receptor: Stiripentol and benzodiazepines

    PubMed Central

    Fisher, Janet L.

    2011-01-01

    Many patients with refractory epilepsy are treated with polytherapy, and nearly 15% of epilepsy patients receive two or more anti-convulsant agents. The anti-convulsant stiripentol is used as an add-on treatment for the childhood epilepsy syndrome known as severe myoclonic epilepsy in infancy (Dravet Syndrome). Stiripentol has multiple mechanisms of action, both enhancing GABAA receptors and reducing activity of metabolic enzymes that break down other drugs. Stiripentol is typically co-administered with other anti-convulsants such as benzodiazepines which also act through GABAA receptor modulation. Stiripentol slows the metabolism of some of these drugs through inhibition of a variety of cytochrome P450 enzymes, but could also influence their effects on GABAergic neurotransmission. Is it rational to co-administer drugs which can act through the same target? To examine the potential interaction between these modulators, we transiently transfected HEK-293T cells to produce α3β3γ2L or α3β3δ recombinant GABAA receptors. Using whole-cell patch clamp recordings, we measured the response to each benzodiazepine alone and in combination with a maximally effective concentration of stiripentol. We compared the responses to four different benzodiazepines: diazepam, clonazepam, clobazam and norclobazam. In all cases we found that these modulators were equally effective in the presence and absence of stiripentol. The δ-containing receptors were insensitive to modulation by the benzodiazepines, which did not affect potentiation by stiripentol. These data suggest that stiripentol and the benzodiazepines act independently at GABAA receptors and that polytherapy could be expected to increase the maximum effect beyond either drug alone, even without consideration of changes in metabolism. PMID:21237147

  3. Quantitative and Qualitative Evaluation of Interactive Videodisk Instructional Modules in Preclinical Neuropathology Education.

    ERIC Educational Resources Information Center

    Lovell, Kathryn L.; And Others

    1993-01-01

    A study evaluated the design and implementation of 10 interactive videodisc instructional modules on neuropathology used in medical instruction at Michigan State University. It investigated levels of student acceptance of the modules, ways in which modules accommodated different learning styles, and modules' facilitation of higher order learning…

  4. Modulators in concert for cognition: modulator interactions in the prefrontal cortex

    PubMed Central

    Briand, Lisa A.; Gritton, Howard; Howe, William M.; Young, Damon A.; Sarter, Martin

    2007-01-01

    Research on the regulation and function of ascending noradrenergic, dopaminergic, serotonergic, and cholinergic systems has focused on the organization and function of individual systems. In contrast, evidence describing co-activation and interactions between multiple neuromodulatory systems has remained scarce. However, commonalities in the anatomical organization of these systems and overlapping evidence concerning the post-synaptic effects of neuromodulators strongly suggest that these systems are recruited in concert; they influence each other and simultaneously modulate their target circuits. Therefore, evidence on the regulatory and functional interactions between these systems is considered essential for revealing the role of neuromodulators. This postulate extends to contemporary neurobiological hypotheses of major neuropsychiatric disorders. These hypotheses have focused largely on aberrations in the integrity or regulation of individual ascending modulatory systems, with little regard for the likely possibility that dysregulation in multiple ascending neuromodulatory systems and their interactions contribute essentially to the symptoms of these disorders. This review will paradigmatically focus on neuromodulator interactions in the PFC and be further constrained by an additional focus on their role in cognitive functions. Recent evidence indicates that individual neuromodulators, in addition to their general state-setting or gating functions, encode specific cognitive operations, further substantiating the importance of research concerning the parallel recruitment of neuromodulator systems and interactions between these systems. PMID:17681661

  5. Modulation of Microtubule Interprotofilament Interactions by Modified Taxanes

    PubMed Central

    Matesanz, Ruth; Rodríguez-Salarichs, Javier; Pera, Benet; Canales, Ángeles; Andreu, José Manuel; Jiménez-Barbero, Jesús; Bras, Wim; Nogales, Aurora; Fang, Wei-Shuo; Díaz, José Fernando

    2011-01-01

    Microtubules assembled with paclitaxel and docetaxel differ in their numbers of protofilaments, reflecting modification of the lateral association between αβ-tubulin molecules in the microtubule wall. These modifications of microtubule structure, through a not-yet-characterized mechanism, are most likely related to the changes in tubulin-tubulin interactions responsible for microtubule stabilization by these antitumor compounds. We have used a set of modified taxanes to study the structural mechanism of microtubule stabilization by these ligands. Using small-angle x-ray scattering, we have determined how modifications in the shape and size of the taxane substituents result in changes in the interprotofilament angles and in their number. The observed effects have been explained using NMR-aided docking and molecular dynamic simulations of taxane binding at the microtubule pore and luminal sites. Modeling results indicate that modification of the size of substituents at positions C7 and C10 of the taxane core influence the conformation of three key elements in microtubule lateral interactions (the M-loop, the S3 β-strand, and the H3 helix) that modulate the contacts between adjacent protofilaments. In addition, modifications of the substituents at position C2 slightly rearrange the ligand in the binding site, modifying the interaction of the C7 substituent with the M-loop. PMID:22208196

  6. Cytoskeletal Modulation of Lipid Interactions Regulates Lck Kinase Activity*

    PubMed Central

    Chichili, Gurunadh R.; Cail, Robert C.; Rodgers, William

    2012-01-01

    The actin cytoskeleton promotes clustering of proteins associated with cholesterol-dependent rafts, but its effect on lipid interactions that form and maintain rafts is not understood. We addressed this question by determining the effect of disrupting the cytoskeleton on co-clustering of dihexadecyl-(C16)-anchored DiO and DiI, which co-enrich in ordered lipid environments such as rafts. Co-clustering was assayed by fluorescence resonance energy transfer (FRET) in labeled T cells, where rafts function in the phosphoregulation of the Src family kinase Lck. Our results show that probe co-clustering was sensitive to depolymerization of actin filaments with latrunculin B (Lat B), inhibition of myosin II with blebbistatin, and treatment with neomycin to sequester phosphatidylinositol 4,5-bisphosphate. Cytoskeletal effects on lipid interactions were not restricted to order-preferring label because co-clustering of C16-anchored DiO with didodecyl (C12)-anchored DiI, which favors disordered lipids, was also reduced by Lat B and blebbistatin. Furthermore, conditions that disrupted probe co-clustering resulted in activation of Lck. These data show that the cytoskeleton globally modulates lipid interactions in the plasma membrane, and this property maintains rafts that function in Lck regulation. PMID:22613726

  7. Effector proteins that modulate plant--insect interactions.

    PubMed

    Hogenhout, Saskia A; Bos, Jorunn I B

    2011-08-01

    Insect herbivores have highly diverse life cycles and feeding behaviors. They establish close interactions with their plant hosts and suppress plant defenses. Chewing herbivores evoke characteristic defense responses distinguishable from general mechanical damage. In addition, piercing-sucking hemipteran insects display typical feeding behavior that suggests active suppression of plant defense responses. Effectors that modulate plant defenses have been identified in the saliva of these insects. Tools for high-throughput effector identification and functional characterization have been developed. In addition, in some insect species it is possible to silence gene expression by RNAi. Together, this technological progress has enabled the identification of insect herbivore effectors and their targets that will lead to the development of novel strategies for pest resistances in plants.

  8. Self, others, objects: how this triadic interaction modulates our behavior.

    PubMed

    Lugli, Luisa; Baroni, Giulia; Gianelli, Claudia; Borghi, Anna M; Nicoletti, Roberto

    2012-11-01

    Two experiments investigated whether the triadic interaction between objects, ourselves and other persons modulates motor system activation during language comprehension. Participants were faced with sentences formed by a descriptive part referring to a positive or negative emotively connoted object and an action part composed of an imperative verb implying a motion toward the self or toward other persons (e.g., "The object is attractive/ugly. Bring it toward you/Give it to another person/Give it to a friend"). Participants judged whether each sentence was sensible or not by moving the mouse toward or away from their body. Findings showed that the simulation of a social context influenced both (1) the motor system and (2) the coding of stimulus valence. Implications of the results for theories of embodied and social cognition are discussed.

  9. Designing high-quality interactive multimedia learning modules.

    PubMed

    Huang, Camillan

    2005-01-01

    Modern research has broadened scientific knowledge and revealed the interdisciplinary nature of the sciences. For today's students, this advance translates to learning a more diverse range of concepts, usually in less time, and without supporting resources. Students can benefit from technology-enhanced learning supplements that unify concepts and are delivered on-demand over the Internet. Such supplements, like imaging informatics databases, serve as innovative references for biomedical information, but could improve their interaction interfaces to support learning. With information from these digital datasets, multimedia learning tools can be designed to transform learning into an active process where students can visualize relationships over time, interact with dynamic content, and immediately test their knowledge. This approach bridges knowledge gaps, fosters conceptual understanding, and builds problem-solving and critical thinking skills-all essential components to informatics training for science and medicine. Additional benefits include cost-free access and ease of dissemination over the Internet or CD-ROM. However, current methods for the design of multimedia learning modules are not standardized and lack strong instructional design. Pressure from administrators at the top and students from the bottom are pushing faculty to use modern technology to address the learning needs and expectations of contemporary students. Yet, faculty lack adequate support and training to adopt this new approach. So how can faculty learn to create educational multimedia materials for their students? This paper provides guidelines on best practices in educational multimedia design, derived from the Virtual Labs Project at Stanford University. The development of a multimedia module consists of five phases: (1) understand the learning problem and the users needs; (2) design the content to harness the enabling technologies; (3) build multimedia materials with web style standards and

  10. BioSIGHT: Interactive Visualization Modules for Science Education

    NASA Technical Reports Server (NTRS)

    Wong, Wee Ling

    1998-01-01

    Redefining science education to harness emerging integrated media technologies with innovative pedagogical goals represents a unique challenge. The Integrated Media Systems Center (IMSC) is the only engineering research center in the area of multimedia and creative technologies sponsored by the National Science Foundation. The research program at IMSC is focused on developing advanced technologies that address human-computer interfaces, database management, and high-speed network capabilities. The BioSIGHT project at is a demonstration technology project in the area of education that seeks to address how such emerging multimedia technologies can make an impact on science education. The scope of this project will help solidify NASA's commitment for the development of innovative educational resources that promotes science literacy for our students and the general population as well. These issues must be addressed as NASA marches toward the goal of enabling human space exploration that requires an understanding of life sciences in space. The IMSC BioSIGHT lab was established with the purpose of developing a novel methodology that will map a high school biology curriculum into a series of interactive visualization modules that can be easily incorporated into a space biology curriculum. Fundamental concepts in general biology must be mastered in order to allow a better understanding and application for space biology. Interactive visualization is a powerful component that can capture the students' imagination, facilitate their assimilation of complex ideas, and help them develop integrated views of biology. These modules will augment the role of the teacher and will establish the value of student-centered interactivity, both in an individual setting as well as in a collaborative learning environment. Students will be able to interact with the content material, explore new challenges, and perform virtual laboratory simulations. The BioSIGHT effort is truly cross

  11. BioSIGHT: Interactive Visualization Modules for Science Education

    NASA Technical Reports Server (NTRS)

    Wong, Wee Ling

    1998-01-01

    Redefining science education to harness emerging integrated media technologies with innovative pedagogical goals represents a unique challenge. The Integrated Media Systems Center (IMSC) is the only engineering research center in the area of multimedia and creative technologies sponsored by the National Science Foundation. The research program at IMSC is focused on developing advanced technologies that address human-computer interfaces, database management, and high- speed network capabilities. The BioSIGHT project at IMSC is a demonstration technology project in the area of education that seeks to address how such emerging multimedia technologies can make an impact on science education. The scope of this project will help solidify NASA's commitment for the development of innovative educational resources that promotes science literacy for our students and the general population as well. These issues must be addressed as NASA marches towards the goal of enabling human space exploration that requires an understanding of life sciences in space. The IMSC BioSIGHT lab was established with the purpose of developing a novel methodology that will map a high school biology curriculum into a series of interactive visualization modules that can be easily incorporated into a space biology curriculum. Fundamental concepts in general biology must be mastered in order to allow a better understanding and application for space biology. Interactive visualization is a powerful component that can capture the students' imagination, facilitate their assimilation of complex ideas, and help them develop integrated views of biology. These modules will augment the role of the teacher and will establish the value of student-centered interactivity, both in an individual setting as well as in a collaborative learning environment. Students will be able to interact with the content material, explore new challenges, and perform virtual laboratory simulations. The BioSIGHT effort is truly cross

  12. BioSIGHT: Interactive Visualization Modules for Science Education

    NASA Technical Reports Server (NTRS)

    Wong, Wee Ling

    1998-01-01

    Redefining science education to harness emerging integrated media technologies with innovative pedagogical goals represents a unique challenge. The Integrated Media Systems Center (IMSC) is the only engineering research center in the area of multimedia and creative technologies sponsored by the National Science Foundation. The research program at IMSC is focused on developing advanced technologies that address human-computer interfaces, database management, and high-speed network capabilities. The BioSIGHT project at is a demonstration technology project in the area of education that seeks to address how such emerging multimedia technologies can make an impact on science education. The scope of this project will help solidify NASA's commitment for the development of innovative educational resources that promotes science literacy for our students and the general population as well. These issues must be addressed as NASA marches toward the goal of enabling human space exploration that requires an understanding of life sciences in space. The IMSC BioSIGHT lab was established with the purpose of developing a novel methodology that will map a high school biology curriculum into a series of interactive visualization modules that can be easily incorporated into a space biology curriculum. Fundamental concepts in general biology must be mastered in order to allow a better understanding and application for space biology. Interactive visualization is a powerful component that can capture the students' imagination, facilitate their assimilation of complex ideas, and help them develop integrated views of biology. These modules will augment the role of the teacher and will establish the value of student-centered interactivity, both in an individual setting as well as in a collaborative learning environment. Students will be able to interact with the content material, explore new challenges, and perform virtual laboratory simulations. The BioSIGHT effort is truly cross

  13. Capacitance-modulated transistor detects odorant binding protein chiral interactions

    PubMed Central

    Mulla, Mohammad Yusuf; Tuccori, Elena; Magliulo, Maria; Lattanzi, Gianluca; Palazzo, Gerardo; Persaud, Krishna; Torsi, Luisa

    2015-01-01

    Peripheral events in olfaction involve odorant binding proteins (OBPs) whose role in the recognition of different volatile chemicals is yet unclear. Here we report on the sensitive and quantitative measurement of the weak interactions associated with neutral enantiomers differentially binding to OBPs immobilized through a self-assembled monolayer to the gate of an organic bio-electronic transistor. The transduction is remarkably sensitive as the transistor output current is governed by the small capacitance of the protein layer undergoing minute changes as the ligand–protein complex is formed. Accurate determination of the free-energy balances and of the capacitance changes associated with the binding process allows derivation of the free-energy components as well as of the occurrence of conformational events associated with OBP ligand binding. Capacitance-modulated transistors open a new pathway for the study of ultra-weak molecular interactions in surface-bound protein–ligand complexes through an approach that combines bio-chemical and electronic thermodynamic parameters. PMID:25591754

  14. Capacitance-modulated transistor detects odorant binding protein chiral interactions

    NASA Astrophysics Data System (ADS)

    Mulla, Mohammad Yusuf; Tuccori, Elena; Magliulo, Maria; Lattanzi, Gianluca; Palazzo, Gerardo; Persaud, Krishna; Torsi, Luisa

    2015-01-01

    Peripheral events in olfaction involve odorant binding proteins (OBPs) whose role in the recognition of different volatile chemicals is yet unclear. Here we report on the sensitive and quantitative measurement of the weak interactions associated with neutral enantiomers differentially binding to OBPs immobilized through a self-assembled monolayer to the gate of an organic bio-electronic transistor. The transduction is remarkably sensitive as the transistor output current is governed by the small capacitance of the protein layer undergoing minute changes as the ligand-protein complex is formed. Accurate determination of the free-energy balances and of the capacitance changes associated with the binding process allows derivation of the free-energy components as well as of the occurrence of conformational events associated with OBP ligand binding. Capacitance-modulated transistors open a new pathway for the study of ultra-weak molecular interactions in surface-bound protein-ligand complexes through an approach that combines bio-chemical and electronic thermodynamic parameters.

  15. Telescience operations with the solar array module plasma interaction experiment

    SciTech Connect

    Wald, L.W.; Bibyk, I.K.

    1995-09-01

    The Solar Array Module Plasma Interactions Experiment (SAMPIE) is a flight experiment that flew on the Space Shuttle Columbia (STS-62) in March 1994, as part of the OAST-2 mission. The overall objective of SAMPIE was to determine the adverse environmental interactions within the space plasma of low earth orbit (LEO) on modern solar cells and space power system materials which are artificially biased to high positive and negative direct current (DC) voltages. The two environmental interactions of interest included high voltage arcing from the samples to the space plasma and parasitic current losses. High voltage arcing can cause physical damage to power system materials and shorten expected hardware life. Parasitic current losses can reduce power system efficiency because electric currents generated in a power system drain into the surrounding plasma via parasitic resistance. The flight electronics included two programmable high voltage DC power supplies to bias the experiment samples, instruments to measure the surrounding plasma environment in the STS cargo bay, and the on-board data acquisition system (DAS). The DAS provided in-flight experiment control, data storage, and communications through the Goddard Space Flight Center (GSFC) Hitchhiker flight avionics to the GSFC Payload Operations Control Center (POCC). The DAS and the SAMPIE POCC computer systems were designed for telescience operations; this paper will focus on the experiences of the SAMPIE team regarding telescience development and operations from the GSFC POCC during STS-62. The SAMPIE conceptual development, hardware design, and system verification testing were accomplished at the NASA Lewis Research Center (LeRC). SAMPIE was developed under the In-Space Technology Experiment Program (IN-STEP), which sponsors NASA, industry, and university flight experiments designed to enable and enhance space flight technology.

  16. Telescience operations with the solar array module plasma interaction experiment

    NASA Technical Reports Server (NTRS)

    Wald, Lawrence W.; Bibyk, Irene K.

    1995-01-01

    The Solar Array Module Plasma Interactions Experiment (SAMPIE) is a flight experiment that flew on the Space Shuttle Columbia (STS-62) in March 1994, as part of the OAST-2 mission. The overall objective of SAMPIE was to determine the adverse environmental interactions within the space plasma of low earth orbit (LEO) on modern solar cells and space power system materials which are artificially biased to high positive and negative direct current (DC) voltages. The two environmental interactions of interest included high voltage arcing from the samples to the space plasma and parasitic current losses. High voltage arcing can cause physical damage to power system materials and shorten expected hardware life. parasitic current losses can reduce power system efficiency because electric currents generated in a power system drain into the surrounding plasma via parasitic resistance. The flight electronics included two programmable high voltage DC power supplies to bias the experiment samples, instruments to measure the surrounding plasma environment in the STS cargo bay, and the on-board data acquisition system (DAS). The DAS provided in-flight experiment control, data storage, and communications through the Goddard Space Flight Center (GSFC) Hitchhiker flight avionics to the GSFC Payload Operations Control Center (POCC). The DAS and the SAMPIE POCC computer systems were designed for telescience operations; this paper will focus on the experiences of the SAMPIE team regarding telescience development and operations from the GSFC POCC during STS-62. The SAMPIE conceptual development, hardware design, and system verification testing were accomplished at the NASA Lewis Research Center (LeRC). SAMPIE was developed under the In-Space Technology Experiment Program (IN-STEP), which sponsors NASA, industry, and university flight experiments designed to enable and enhance space flight technology. The IN-STEP Program is sponsored by the Office of Space Access and Technology (OSAT).

  17. Perilipin polymorphism interacts with dietary carbohydrates to modulate anthropometric traits in Hispanics of Caribbean origin

    USDA-ARS?s Scientific Manuscript database

    Perilipin (PLIN) is the major protein surrounding lipid droplets in adipocytes and regulates adipocyte metabolism by modulating the interaction between lipases and triacylglycerol stores. Associations between PLIN gene polymorphisms and obesity risk have been described, but interactions with die...

  18. The Impact of Interactive, Computerized Educational Modules on Preclinical Medical Education

    ERIC Educational Resources Information Center

    Bryner, Benjamin S.; Saddawi-Konefka, Daniel; Gest, Thomas R.

    2008-01-01

    Interactive computerized modules have been linked to improved retention of material in clinical medicine. This study examined the effects of a new series of interactive learning modules for preclinical medical education, specifically in the areas of quiz performance, perceived difficulty of concepts, study time, and perceived stress level. We…

  19. Modulation and interactions of charged biomimetic membranes with bivalent ions

    NASA Astrophysics Data System (ADS)

    Kazadi Badiambile, Adolphe

    biomolecules in a dynamic environment and the lack of appropriate physical and biochemical tools. In contrast, biomimetic membrane models that rely on the amphiphilic properties of phospholipids are powerful tools that enable the study of these molecules in vitro. By having control over the different experimental parameters such as temperature and pH, reliable and repeatable experimental conditions can be created. One of the key questions I investigated in this thesis is related to the clustering mechanism of PtdIns(4, 5)P2 into pools or aggregates that enable independent cellular control of this species by geometric separation. The lateral aggregation of PtdIns(4, 5)P2 and its underlying physical causes is still a matter of debate. In the first part of this thesis I introduce the general information on lipid membranes with a special focus on the PtdIns family and their associated signaling events. In addition, I explain the Langmuir-Blodgett film balance (LB) system as tool to study lipid membranes and lipid interactions. In the second chapter, I describe my work on the lateral compressibility of PtdIns(4, 5)P2, PtdIns and DOPG monolayers and its modulation by bivalent ions using Langmuir monolayers. In addition, a theoretical framework of compressibility that depends on a surface potential induced by a planar layer of charged molecules and ions in the bulk was provided. In the third part, I present my work on the excess Gibbs free energy of the lipid systems PtdIns(4, 5)P2 --POPC, PtdIns(4, 5)P2, and POPC as they are modulated by bivalent ions. In the fourth part, I report on my foray in engineering a light-based system that relies on different dye properties to simulate calcium induced calcium release (CICR) that occurs in many cell types. In the final chapter, I provide a general conclusion and present directions for future research that would build on my findings.

  20. SAMPIE (Solar Array Module Plasma Interactions Experiment). (Videotape)

    SciTech Connect

    Not Available

    1994-02-01

    SAMPIE is an in-space technology experiment that flew on STS-62. Its intent is to investigate the potentially damaging effects of space plasma (gases) on different types, sizes, and shapes of solar cells, solar modules, and spacecraft materials.

  1. Cross-Modulated Amplitudes and Frequencies Characterize Interacting Components in Complex Systems

    NASA Astrophysics Data System (ADS)

    Gans, Fabian; Schumann, Aicko Y.; Kantelhardt, Jan W.; Penzel, Thomas; Fietze, Ingo

    2009-03-01

    The dynamics of complex systems is characterized by oscillatory components on many time scales. To study the interactions between these components we analyze the cross modulation of their instantaneous amplitudes and frequencies, separating synchronous and antisynchronous modulation. We apply our novel technique to brain-wave oscillations in the human electroencephalogram and show that interactions between the α wave and the δ or β wave oscillators as well as spatial interactions can be quantified and related with physiological conditions (e.g., sleep stages). Our approach overcomes the limitation to oscillations with similar frequencies and enables us to quantify directly nonlinear effects such as positive or negative frequency modulation.

  2. TUNE MODULATION FROM BEAM BEAM INTERACTION AND UNEQUAL RADIO FREQUENCIES IN RHIC.

    SciTech Connect

    FISCHER,W.CAMERON,P.PEGGS,S.SATOGATA,T.

    2003-05-19

    The two RHIC rings have independent rf systems to accommodate different species. Thus, the radio frequencies can differ when the phase and radial loops are closed, and the if frequencies of the two rings are not synchronized. A radio frequency difference leads to longitudinally moving beam crossing points. When the crossing points are between the beam splitting dipoles, the beams experience the beam-beam interaction. Outside the interaction region the beam-beam interaction is switched off. In this way the tune is modulated. A computation of the tune modulation depth, pulse shape and frequency is presented. Tune modulation measurements are shown.

  3. Predictability of Genetic Interactions from Functional Gene Modules

    PubMed Central

    Young, Jonathan H.; Marcotte, Edward M.

    2016-01-01

    Characterizing genetic interactions is crucial to understanding cellular and organismal response to gene-level perturbations. Such knowledge can inform the selection of candidate disease therapy targets, yet experimentally determining whether genes interact is technically nontrivial and time-consuming. High-fidelity prediction of different classes of genetic interactions in multiple organisms would substantially alleviate this experimental burden. Under the hypothesis that functionally related genes tend to share common genetic interaction partners, we evaluate a computational approach to predict genetic interactions in Homo sapiens, Drosophila melanogaster, and Saccharomyces cerevisiae. By leveraging knowledge of functional relationships between genes, we cross-validate predictions on known genetic interactions and observe high predictive power of multiple classes of genetic interactions in all three organisms. Additionally, our method suggests high-confidence candidate interaction pairs that can be directly experimentally tested. A web application is provided for users to query genes for predicted novel genetic interaction partners. Finally, by subsampling the known yeast genetic interaction network, we found that novel genetic interactions are predictable even when knowledge of currently known interactions is minimal. PMID:28007839

  4. A Matlab/Simulink-Based Interactive Module for Servo Systems Learning

    ERIC Educational Resources Information Center

    Aliane, N.

    2010-01-01

    This paper presents an interactive module for learning both the fundamental and practical issues of servo systems. This module, developed using Simulink in conjunction with the Matlab graphical user interface (Matlab-GUI) tool, is used to supplement conventional lectures in control engineering and robotics subjects. First, the paper introduces the…

  5. A Matlab/Simulink-Based Interactive Module for Servo Systems Learning

    ERIC Educational Resources Information Center

    Aliane, N.

    2010-01-01

    This paper presents an interactive module for learning both the fundamental and practical issues of servo systems. This module, developed using Simulink in conjunction with the Matlab graphical user interface (Matlab-GUI) tool, is used to supplement conventional lectures in control engineering and robotics subjects. First, the paper introduces the…

  6. Developing an On-Line Interactive Health Psychology Module

    ERIC Educational Resources Information Center

    Upton, Dominic; Cooper, Carol

    2006-01-01

    On-line teaching material in health psychology was developed which ensured a range of students could access appropriate material for their course and level of study. This material has been developed around the concept of smaller "content chunks" which can be combined into whole units of learning (topics), and ultimately, a module. On the…

  7. Developing an On-Line Interactive Health Psychology Module

    ERIC Educational Resources Information Center

    Upton, Dominic; Cooper, Carol

    2006-01-01

    On-line teaching material in health psychology was developed which ensured a range of students could access appropriate material for their course and level of study. This material has been developed around the concept of smaller "content chunks" which can be combined into whole units of learning (topics), and ultimately, a module. On the…

  8. A unique, interactive and web-based pediatric rheumatology teaching module: residents' perceptions.

    PubMed

    Batthish, Michelle; Bassilious, Ereny; Schneider, Rayfel; Feldman, Brian M; Hyman, Avi; Tse, Shirley Ml

    2013-05-27

    The limited availability of pediatric rheumatologists for teaching in pediatric residency programs negatively impacts resident education about rheumatology. At present, there are no educational websites available for trainees to learn about pediatric rheumatology. We are planning to develop an interactive web-based teaching module to improve resident learning about rheumatology ("POINTER": Pediatric Online INteractive TEaching in Rheumatology). The aim of this study was to perform a needs assessment of pediatric residents who will be using POINTER. Pediatric residents (n = 60) at The Hospital for Sick Children were emailed an online survey. This was designed to assess prior use of online teaching modules, the utility of an online teaching module for rheumatology and which technologies should be included on such a site. Forty-seven residents participated in the survey (78.3% response rate). Ninety-one percent of the respondents thought that an interactive teaching website would enhance their learning and should include case-based teaching modules. Several web-based technologies were felt to be important for inclusion on the teaching modules. These included graphics and animation (86.4%), interactivity (93.2%), pictures (100%), live digital videos (88.9%) and links to articles and research (88.6%). An interactive web-based rheumatology teaching module would be well utilized by pediatric residents. Residents showed preference for case-based teaching modules as well as multimedia modalities for learning a detailed musculoskeletal examination.

  9. Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules

    NASA Astrophysics Data System (ADS)

    Menon, Govind; Krishnan, J.

    2016-07-01

    While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.

  10. Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules.

    PubMed

    Menon, Govind; Krishnan, J

    2016-07-21

    While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.

  11. Topological interactive analysis of power system and its communication module: A complex network approach

    NASA Astrophysics Data System (ADS)

    Hu, Jianqiang; Yu, Jie; Cao, Jinde; Ni, Ming; Yu, Wenjie

    2014-12-01

    Power system and its communication system, which can be called a cyber-physical system, are interconnected and interdependent on each other. This paper considers the interaction problem between power system and its communication module from the perspective of the topological structure. Firstly, some structural properties and centrality measures of complex networks are briefly reviewed. Furthermore, novel interactive measures are proposed to describe the interactive system in terms of topologies. Finally, based on these metrics, the statistical properties and the interactive relationships of the main power system and its communication module (abstracted as two complex heterogeneous networks) of one province in China are investigated.

  12. ModuleRole: a tool for modulization, role determination and visualization in protein-protein interaction networks.

    PubMed

    Li, Guipeng; Li, Ming; Zhang, Yiwei; Wang, Dong; Li, Rong; Guimerà, Roger; Gao, Juntao Tony; Zhang, Michael Q

    2014-01-01

    Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes the PPI network from BioGRID database, finds and visualizes the modules these proteins form, and then defines the role every node plays in this network, based on two topological parameters Participation Coefficient and Z-score. This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. It can be tested online at the website http://www.bioinfo.org/modulerole/index.php, which is free and open to all users and there is no login requirement, with demo data provided by "User Guide" in the menu Help. Non-server application of this program is considered for high-throughput data with more than 200 nodes or user's own interaction datasets. Users are able to bookmark the web link to the result page and access at a later time. As an interactive and highly customizable application, ModuleRole requires no expert knowledge in graph theory on the user side and can be used in both Linux and Windows system, thus a very useful tool for biologist to analyze and visualize PPI networks from databases such as BioGRID. ModuleRole is implemented in Java and C, and is freely available at http://www.bioinfo.org/modulerole/index.php. Supplementary information (user guide, demo data) is also available at this website. API for ModuleRole used for this program can be

  13. Chaotic saddles in nonlinear modulational interactions in a plasma

    SciTech Connect

    Miranda, Rodrigo A.; Rempel, Erico L.; Chian, Abraham C.-L.

    2012-11-15

    A nonlinear model of modulational processes in the subsonic regime involving a linearly unstable wave and two linearly damped waves with different damping rates in a plasma is studied numerically. We compute the maximum Lyapunov exponent as a function of the damping rates in a two-parameter space, and identify shrimp-shaped self-similar structures in the parameter space. By varying the damping rate of the low-frequency wave, we construct bifurcation diagrams and focus on a saddle-node bifurcation and an interior crisis associated with a periodic window. We detect chaotic saddles and their stable and unstable manifolds, and demonstrate how the connection between two chaotic saddles via coupling unstable periodic orbits can result in a crisis-induced intermittency. The relevance of this work for the understanding of modulational processes observed in plasmas and fluids is discussed.

  14. Virtual Reality Simulations and Animations in a Web-Based Interactive Manufacturing Engineering Module

    ERIC Educational Resources Information Center

    Ong, S. K.; Mannan, M. A.

    2004-01-01

    This paper presents a web-based interactive teaching package that provides a comprehensive and conducive yet dynamic and interactive environment for a module on automated machine tools in the Manufacturing Division at the National University of Singapore. The use of Internet technologies in this teaching tool makes it possible to conjure…

  15. Virtual Reality Simulations and Animations in a Web-Based Interactive Manufacturing Engineering Module

    ERIC Educational Resources Information Center

    Ong, S. K.; Mannan, M. A.

    2004-01-01

    This paper presents a web-based interactive teaching package that provides a comprehensive and conducive yet dynamic and interactive environment for a module on automated machine tools in the Manufacturing Division at the National University of Singapore. The use of Internet technologies in this teaching tool makes it possible to conjure…

  16. Perceived live interaction modulates the developing social brain

    PubMed Central

    Rice, Katherine; Moraczewski, Dustin; Redcay, Elizabeth

    2016-01-01

    Although children’s social development is embedded in social interaction, most developmental neuroscience studies have examined responses to non-interactive social stimuli (e.g. photographs of faces). The neural mechanisms of real-world social behavior are of special interest during middle childhood (roughly ages 7–13), a time of increased social complexity and competence coinciding with structural and functional social brain development. Evidence from adult neuroscience studies suggests that social interaction may alter neural processing, but no neuroimaging studies in children have directly examined the effects of live social-interactive context on social cognition. In the current study of middle childhood, we compare the processing of two types of speech: speech that children believed was presented over a real-time audio-feed by a social partner and speech that they believed was recorded. Although in reality all speech was prerecorded, perceived live speech resulted in significantly greater neural activation in regions associated with social cognitive processing. These findings underscore the importance of using ecologically-valid and interactive methods to understand the developing social brain. PMID:27272314

  17. Perceived live interaction modulates the developing social brain.

    PubMed

    Rice, Katherine; Moraczewski, Dustin; Redcay, Elizabeth

    2016-09-01

    Although children's social development is embedded in social interaction, most developmental neuroscience studies have examined responses to non-interactive social stimuli (e.g. photographs of faces). The neural mechanisms of real-world social behavior are of special interest during middle childhood (roughly ages 7-13), a time of increased social complexity and competence coinciding with structural and functional social brain development. Evidence from adult neuroscience studies suggests that social interaction may alter neural processing, but no neuroimaging studies in children have directly examined the effects of live social-interactive context on social cognition. In the current study of middle childhood, we compare the processing of two types of speech: speech that children believed was presented over a real-time audio-feed by a social partner and speech that they believed was recorded. Although in reality all speech was prerecorded, perceived live speech resulted in significantly greater neural activation in regions associated with social cognitive processing. These findings underscore the importance of using ecologically-valid and interactive methods to understand the developing social brain.

  18. Interharmonic modulation products as a means to quantify nonlinear D-region interactions

    NASA Astrophysics Data System (ADS)

    Moore, Robert

    Experimental observations performed during dual beam ionospheric HF heating experiments at the High frequency Active Auroral Research Program (HAARP) HF transmitter in Gakona, Alaska are used to quantify the relative importance of specific nonlinear interactions that occur within the D region ionosphere. During these experiments, HAARP broadcast two amplitude modulated HF beams whose center frequencies were separated by less than 20 kHz. One beam was sinusoidally modulated at 500 Hz while the second beam was sinusoidally modulated using a 1-7 kHz linear frequency-time chirp. ELF/VLF observations performed at two different locations (3 and 98 km from HAARP) provide clear evidence of strong interactions between all field components of the two HF beams in the form of low and high order interharmonic modulation products. From a theoretical standpoint, the observed interharmonic modulation products could be produced by several different nonlinearities. The two primary nonlinearities take the form of wave-medium interactions (i.e., cross modulation), wherein the ionospheric conductivity modulation produced by one signal crosses onto the other signal via collision frequency modification, and wave-wave interactions, wherein the conduction current associated with one wave mixes with the electric field of the other wave to produce electron temperature oscillations. We are able to separate and quantify these two different nonlinearities, and we conclude that the wave-wave interactions dominate the wave-medium interactions by a factor of two. These results are of great importance for the modeling of transioinospheric radio wave propagation, in that both the wave-wave and the wave-medium interactions could be responsible for a significant amount of anomalous absorption.

  19. Interaction between heterogeneously charged surfaces: Surface patches and charge modulation

    NASA Astrophysics Data System (ADS)

    Ben-Yaakov, Dan; Andelman, David; Diamant, Haim

    2013-02-01

    When solid surfaces are immersed in aqueous solutions, some of their charges can dissociate and leave behind charged patches on the surface. Although the charges are distributed heterogeneously on the surface, most of the theoretical models treat them as homogeneous. For overall non-neutral surfaces, the assumption of surface charge homogeneity is rather reasonable since the leading terms of two such interacting surfaces depend on the nonzero average charge. However, for overall neutral surfaces the nature of the surface charge distribution is crucial in determining the intersurface interaction. In the present work we study the interaction between two charged surfaces across an aqueous solution for several charge distributions. The analysis is preformed within the framework of the linearized Poisson-Boltzmann theory. For periodic charge distributions the interaction is found to be repulsive at small separations, unless the two surface distributions are completely out-of-phase with respect to each other. For quenched random charge distributions we find that due to the presence of the ionic solution in between the surfaces, the intersurface repulsion dominates over the attraction in the linear regime of the Poisson-Boltzmann theory. The effect of quenched charge heterogeneity is found to be particularly substantial in the case of large charged domains.

  20. Modulation of short waves by long waves. [ocean wave interactions

    NASA Technical Reports Server (NTRS)

    Reece, A. M., Jr.

    1978-01-01

    Wave-tank experiments were performed to investigate the cyclic short-wave energy changes, related in phase to an underlying long wave, which occur during active generation of the short-wave field by wind. Measurements of time series of the short-wave slope were made by a laser-optical system, where the basic long-wave parameters were controlled and wind speeds were accurately reproducible. The short-wave slope variances were found to exhibit cyclic variations that are related to the phase of the long wave. The variations result from two combined effects: (1) the short wave frequency is varied by the long-wave orbital velocity; (2) the energy of the short waves is modulated by the actions of aerodynamic and hydrodynamic couplings that operate on the short waves in a manner related to the long-wave phase.

  1. Neuroimmune interactions: dendritic cell modulation by the sympathetic nervous system.

    PubMed

    Takenaka, Maisa C; Guereschi, Marcia G; Basso, Alexandre S

    2017-02-01

    Dendritic cells are of paramount importance bridging innate and adaptive immune responses. Depending on the context, after sensing environmental antigens, commensal microorganisms, pathogenic agents, or antigens from the diet, dendritic cells may drive either different effector adaptive immune responses or tolerance, avoiding tissue damage. Although the plasticity of the immune response and the capacity to regulate itself are considered essential to orchestrate appropriate physiological responses, it is known that the nervous system plays a relevant role controlling immune cell function. Dendritic cells present in the skin, the intestine, and lymphoid organs, besides expressing adrenergic receptors, can be reached by neurotransmitters released by sympathetic fibers innervating these tissues. These review focus on how neurotransmitters from the sympathetic nervous system can modulate dendritic cell function and how this may impact the immune response and immune-mediated disorders.

  2. Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

    PubMed Central

    2010-01-01

    Background Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. Results We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy. Conclusions We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy. PMID:20950417

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

    PubMed Central

    Mezhoud, Karim; Sghaier, Haïtham; Barkallah, Insaf

    2009-01-01

    Interactomes of proteins under positive selection from ionizing-radiation-resistant bacteria (IRRB) might be a part of the answer to the question as to how IRRB, particularly Deinococcus radiodurans R1 (Deira), resist ionizing radiation. Here, using the Database of Interacting Proteins (DIP) and the Protein Structural Interactome (PSI)-base server for PSI map, we have predicted novel interactions of orthologs of the 58 proteins under positive selection in Deira and other IRRB, but which are absent in IRSB. Among these, 18 domains and their interactomes have been identified in DNA checkpoint and repair; kinases pathways; energy and nucleotide metabolisms were the important biological processes that were found to be involved. This finding provides new clues to the cellular pathways that can to be important for ionizing-radiation resistance in Deira. PMID:19356244

  4. Spatial coincidence modulates interaction between visual and somatosensory evoked potentials.

    PubMed

    Schürmann, Martin; Kolev, Vasil; Menzel, Kristina; Yordanova, Juliana

    2002-05-07

    The time course of interaction between concurrently applied visual and somatosensory stimulation with respect to evoked potentials (EPs) was studied. Visual stimuli, either in the left or right hemifield, and electric stimuli to the left wrist were delivered either alone or simultaneously. Visual and somatosensory EPs were summed and compared to bimodal EPs (BiEP, response to actual combination of both modalities). Temporal coincidence of stimuli lead to sub-additive or over-additive amplitudes in BiEPs in several time windows between 75 and 275 ms. Additional effects of spatial coincidence (left wrist with left hemifield) were found between 75 and 300 ms and beyond 450 ms. These interaction effects hint at a temporo-spatial pattern of multiple brain areas participating in the process of multimodal integration.

  5. Modulation of molecular interactions and function by rhodopsin palmitylation†

    PubMed Central

    Park, Paul S.-H.; Sapra, K. Tanuj; Jastrzebska, Beata; Maeda, Tadao; Maeda, Akiko; Pulawski, Wojciech; Kono, Masahiro; Lem, Janis; Crouch, Rosalie K.; Filipek, Slawomir; Müller, Daniel J.; Palczewski, Krzysztof

    2009-01-01

    Rhodopsin is palmitylated at two cysteine residues in its carboxyl terminal region. We have looked at the effects of palmitylation on the molecular interactions formed by rhodopsin using single-molecule force spectroscopy and the function of rhodopsin using both in vitro and in vivo approaches. A knockin mouse model expressing palmitate-deficient rhodopsin was used for live animal in vivo studies and to obtain native tissue samples for in vitro assays. We specifically looked at the effects palmitylation has on the chromophore-binding pocket, interactions of rhodopsin with transducin, and molecular interactions stabilizing the receptor structure. The structure of rhodopsin is largely unperturbed by the absence of palmitate linkage. The binding pocket for the chromophore 11-cis-retinal is minimally altered as palmitate-deficient rhodopsin exhibited the same absorbance spectrum as wild-type rhodopsin. Similarly, the rate of release of all-trans-retinal after light activation was the same both in the presence and absence of palmitylation. Significant differences were observed in the rate of transducin activation by rhodopsin and in the force required to unfold the last stable structural segment in rhodopsin at its carboxyl terminal region. A 1.3-fold reduction in the rate of transducin activation by rhodopsin was observed in the absence of palmitylation. Single-molecule force spectroscopy revealed a 2.1-fold reduction in normalized force required to unfold the carboxyl terminal end of rhodopsin. The absence of palmitylation in rhodopsin therefore destabilizes the molecular interactions formed in the carboxyl terminal end of the receptor, which appears to hinder the activation of transducin by light-activated rhodopsin. PMID:19348429

  6. Multi-Omics Studies towards Novel Modulators of Influenza A Virus–Host Interaction

    PubMed Central

    Söderholm, Sandra; Fu, Yu; Gaelings, Lana; Belanov, Sergey; Yetukuri, Laxman; Berlinkov, Mikhail; Cheltsov, Anton V.; Anders, Simon; Aittokallio, Tero; Nyman, Tuula A.; Matikainen, Sampsa; Kainov, Denis E.

    2016-01-01

    Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV–host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 199 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the 665 remains unknown. Studying anti-influenza efficacy and immuno/neuro-modulating properties of these compounds and their combinations as well as potential viral and host resistance to them may lead to the discovery of novel modulators of IAV–host interactions, which might be more effective than the currently available anti-influenza therapeutics. PMID:27690086

  7. Prioritization of gene regulatory interactions from large-scale modules in yeast

    PubMed Central

    Lee, Ho-Joon; Manke, Thomas; Bringas, Ricardo; Vingron, Martin

    2008-01-01

    Background The identification of groups of co-regulated genes and their transcription factors, called transcriptional modules, has been a focus of many studies about biological systems. While methods have been developed to derive numerous modules from genome-wide data, individual links between regulatory proteins and target genes still need experimental verification. In this work, we aim to prioritize regulator-target links within transcriptional modules based on three types of large-scale data sources. Results Starting with putative transcriptional modules from ChIP-chip data, we first derive modules in which target genes show both expression and function coherence. The most reliable regulatory links between transcription factors and target genes are established by identifying intersection of target genes in coherent modules for each enriched functional category. Using a combination of genome-wide yeast data in normal growth conditions and two different reference datasets, we show that our method predicts regulatory interactions with significantly higher predictive power than ChIP-chip binding data alone. A comparison with results from other studies highlights that our approach provides a reliable and complementary set of regulatory interactions. Based on our results, we can also identify functionally interacting target genes, for instance, a group of co-regulated proteins related to cell wall synthesis. Furthermore, we report novel conserved binding sites of a glycoprotein-encoding gene, CIS3, regulated by Swi6-Swi4 and Ndd1-Fkh2-Mcm1 complexes. Conclusion We provide a simple method to prioritize individual TF-gene interactions from large-scale transcriptional modules. In comparison with other published works, we predict a complementary set of regulatory interactions which yields a similar or higher prediction accuracy at the expense of sensitivity. Therefore, our method can serve as an alternative approach to prioritization for further experimental studies. PMID

  8. Nonlinear Optical Systems Interacting with Amplitude-Modulated Optical Fields

    DTIC Science & Technology

    1990-07-01

    results were later confirmed by Harter et al.6 𔄁 using two pulsed dye lasers and a sodium cell . In a later work Gruneisen et al.8 repeated these...experiments in a sodium cell using a pair of cw dye lasers. The3e experiments and the one by Ezekiel3 confirm the physics of the pump-probe interactions quite...Gruneisen et al.4 performed a similar experiment involving a sodium vapor cell and two stabilized dye lasers. In this experiment the effect of varying the

  9. Electro-Optically Modulated Biomolecular-Interaction Analysis Sensor

    DTIC Science & Technology

    2000-07-01

    thn H cN, Laser 0 : 0 0.5 i 1.5 2 2.5 3 3.5 4 k/ko Figure 1: Dispersion relations (eq. 1) of the surface plasmons on Figure 2: Distribution of the...metal thickness decreases, the decoupled surface plasmons interact with each other. Consequently, the degenerate dispersion relations of the surface...as the Kretschmann configuration’ 3 . The plasmons propagate in different speeds with their own dispersion functions. As long as the slab thickness

  10. Task modulated brain connectivity of the amygdala: a meta-analysis of psychophysiological interactions.

    PubMed

    Di, Xin; Huang, Jia; Biswal, Bharat B

    2017-01-01

    Understanding functional connectivity of the amygdala with other brain regions, especially task modulated connectivity, is a critical step toward understanding the role of the amygdala in emotional processes and the interactions between emotion and cognition. The present study performed coordinate-based meta-analysis on studies of task modulated connectivity of the amygdala which used psychophysiological interaction (PPI) analysis. We first analyzed 49 PPI studies on different types of tasks using activation likelihood estimation (ALE) meta-analysis. Widespread cortical and subcortical regions showed consistent task modulated connectivity with the amygdala, including the medial frontal cortex, bilateral insula, anterior cingulate, fusiform gyrus, parahippocampal gyrus, thalamus, and basal ganglia. These regions were in general overlapped with those showed coactivations with the amygdala, suggesting that these regions and amygdala are not only activated together, but also show different levels of interactions during tasks. Further analyses with subsets of PPI studies revealed task specific functional connectivities with the amygdala that were modulated by fear processing, face processing, and emotion regulation. These results suggest a dynamic modulation of connectivity upon task demands, and provide new insights on the functions of the amygdala in different affective and cognitive processes. The meta-analytic approach on PPI studies may offer a framework toward systematical examinations of task modulated connectivity.

  11. Generation of energetic protons in the interaction of Gaussian laser pulses with surface modulated targets

    SciTech Connect

    Wang, W. Q.; Yin, Y. Yu, T. P.; Hu, L. X.; Zhuo, H. B.; Ma, Y. Y.; Shao, F. Q.; Xu, H.

    2014-12-15

    The radiation pressure acceleration of protons in the interaction of Gaussian laser pulses and surface modulated targets is examined by multi-dimensional particle-in-cell simulations. It is shown that strong longitudinal quasi-static magnetic field is generated on the modulated surface of the target, which significantly enhances the transverse diffusion of electrons. This is beneficial for suppressing the transverse Rayleigh-Taylor instability. Finally, the surface of the accelerated proton beams becomes smoother than that in the case of the planar target, and a final mono-energetic proton beam is obtained by using the surface modulated target.

  12. Visual anticipatory information modulates multisensory interactions of artificial audiovisual stimuli.

    PubMed

    Vroomen, Jean; Stekelenburg, Jeroen J

    2010-07-01

    The neural activity of speech sound processing (the N1 component of the auditory ERP) can be suppressed if a speech sound is accompanied by concordant lip movements. Here we demonstrate that this audiovisual interaction is neither speech specific nor linked to humanlike actions but can be observed with artificial stimuli if their timing is made predictable. In Experiment 1, a pure tone synchronized with a deformation of a rectangle induced a smaller auditory N1 than auditory-only presentations if the temporal occurrence of this audiovisual event was made predictable by two moving disks that touched the rectangle. Local autoregressive average source estimation indicated that this audiovisual interaction may be related to integrative processing in auditory areas. When the moving disks did not precede the audiovisual stimulus--making the onset unpredictable--there was no N1 reduction. In Experiment 2, the predictability of the leading visual signal was manipulated by introducing a temporal asynchrony between the audiovisual event and the collision of moving disks. Audiovisual events occurred either at the moment, before (too "early"), or after (too "late") the disks collided on the rectangle. When asynchronies varied from trial to trial--rendering the moving disks unreliable temporal predictors of the audiovisual event--the N1 reduction was abolished. These results demonstrate that the N1 suppression is induced by visual information that both precedes and reliably predicts audiovisual onset, without a necessary link to human action-related neural mechanisms.

  13. An interactive beam line simulator module for RHIC

    SciTech Connect

    MacKay, W.W.

    1997-07-01

    This paper describes the interactive simulation engine, bl, designed for the RHIC project. The program tracks as output to shared memory the central orbit, Twiss and dispersion functions, as well as the 6 x 6 beam hyperellipsoid. Transfer matrices between elements are available via interactive requests. Using a 6-d model, optical elements are modeled with a linear transfer matrix and a vector. The vector allows simulation of misalignments, shifts in field strengths, and beam rigidity. Currently only a linear model is used for elements. In addition to the usual magnets, a foil element is included which can shift the beam`s rigidity (resulting from a change of charge and energy loss), as well as increase the momentum spread and emittance. Running as a Glish client, bl can be interfaced to other programs, such as an orbit plotter and a power supply application to give a quick prediction of the beam orbit from actual operating currents in the accelerator. Various strengths and offsets may be changed by sending Glish events to bl.

  14. Foveal visual acuity is worse and shows stronger contour interaction effects for contrast-modulated than luminance-modulated Cs.

    PubMed

    Hairol, Mohd Izzuddin; Formankiewicz, Monika A; Waugh, Sarah J

    2013-05-01

    Contrast-modulated (CM) stimuli are processed by spatial mechanisms that operate at larger spatial scales than those processing luminance-modulated (LM) stimuli and may be more prone to deficits in developing, amblyopic, and aging visual systems. Understanding neural mechanisms of contour interaction or crowding will help in detecting disorders of spatial vision. In this study, contour interaction effects on visual acuity for LM and CM C and bar stimuli are assessed in normal foveal vision. In Experiment 1, visual acuity is measured for all-LM and all-CM stimuli, at ~3.5× above their respective modulation thresholds. In Experiment 2, visual acuity is measured for Cs and bars of different type (LM C with CM bars and vice versa). Visual acuity is degraded for CM compared with LM Cs (0.46 ± 0.04 logMAR vs. 0.18 ± 0.04 logMAR). With nearby bars, CM acuity is degraded further (0.23 ± 0.01 logMAR or ~2 lines on an acuity chart), significantly more than LM acuity (0.11 ± 0.01 logMAR, ~1 line). Contour interaction for CM stimuli extends over greater distances (arcmin) than it does for LM stimuli, but extents are similar with respect to acuities (~3.5× the C gap width). Contour interaction is evident when the Cs and bars are defined differently: it is stronger when an LM C is flanked by CM bars (0.17 ± 0.03 logMAR) than when a CM C is flanked by LM bars (0.08 ± 0.02 logMAR). Our results suggest that contour interaction for foveally viewed acuity stimuli involves feature integration, such that the outputs of receptive fields representing Cs and bars are combined. Contour interaction operates at LM and CM representational stages, it can occur across stage, and it is enhanced at the CM stage. Greater contour interaction for CM Cs and bars could hold value for visual acuity testing and earlier diagnosis of conditions for which crowding is important, such as in amblyopia.

  15. [Modulation of glucocorticoid receptor interaction with non-steroidal drugs].

    PubMed

    Golikov, P P; Nikolaeva, N Iu

    1993-01-01

    The Scatchard analysis of the specific binding of triamcinolone 3H-acetonide (TA-3HA) to Type II glucocorticoid receptors of cytosol from the liver of female Wistar rats weighing 180-200 g has shown that emoxipin at concentrations of 1 and 2 mM and analgin at concentrations of 5 and 10 mM reduce the density of glucocorticoid receptors and the association constant of a hormone-receptor complex. Analgin, 5 mM, increases the dissociation velocity constant of TA-3HA 5 times the effect of unlabeled triamcinolone acetonide. Emoxipin, 1 mM, produces the same effect on the receptor dissociation velocity constant of TA-3HA as the unlabeled triamcinolone acetonide. The Berke analysis has established that emoxipin and analgin reduce glucocorticoid receptor interactions by uncompetitive inhibition.

  16. A room temperature LSO/PIN photodiode PET detector module that measures depth of interaction

    SciTech Connect

    Moses, W.W.; Derenzo, S.E.; Melcher, C.L.; Manente, R.A.

    1994-11-01

    We present measurements of a 4 element PET detector module that uses a 2{times}2 array of 3 mm square PIN photodiodes to both measure the depth of interaction (DOI) and identify the crystal of interaction. Each photodiode is coupled to one end of a 3{times}3{times}25 mm LSO crystal, with the opposite ends of all 4 crystals attached to a single PMT that provides a timing signal and initial energy discrimination. Each LSO crystal is coated with a {open_quotes}lossy{close_quotes} reflector, so the ratio of light detected in the photodiode and PMT depends on the position of interaction in the crystal, and is used to determine this position on an event by event basis. This module is operated at +25{degrees}C with a photodiode amplifier peaking time of 2 {mu}s. When excited by a collimated beam of 511 keV photons at the photodiode end of the module (i.e. closest to the patient), the DOI resolution is 4 mm fwhm and the crystal of interaction is identified correctly 95% of the time. When excited at the opposite end of the module, the DOI resolution is 13 mm fwhm and the crystal of interaction is identified correctly 73% of the time. The channel to channel variations in performance are minimal.

  17. Structural and functional discussion of the tetra-trico-peptide repeat, a protein interaction module.

    PubMed

    Zeytuni, Natalie; Zarivach, Raz

    2012-03-07

    Tetra-trico-peptide repeat (TPR) domains are found in numerous proteins, where they serve as interaction modules and multiprotein complex mediators. TPRs can be found in all kingdoms of life and regulate diverse biological processes, such as organelle targeting and protein import, vesicle fusion, and biomineralization. This review considers the structural features of TPR domains that permit the great ligand-binding diversity of this motif, given that TPR-interacting partners display variations in both sequence and secondary structure. In addition, tools for predicting TPR-interacting partners are discussed, as are the abilities of TPR domains to serve as protein-protein interaction scaffolds in biotechnology and therapeutics.

  18. Cosmic-ray modulation, merged interaction regions, and multifractals

    NASA Technical Reports Server (NTRS)

    Burlaga, L. F.; Perko, J.; Pirraglia, J.

    1993-01-01

    The large-scale heliospheric magnetic field fluctuations and their effects on cosmic rays are discussed. Voyager 2 observations from 1983.0 to 1989.6 are used as input to the model of Perko and Burlaga (1992) to show that the few largest merged interaction regions (MIRs) provide essential details in the cosmic-ray intensity (CRI) profile. It is demonstrated that the largest MIRs determine the basic structure of the radial gradients of the CRI. It is shown that the magnetic field strength during the period 1983.0-1989.6 does have a multifractal structure, but that there are different multifractal structures in the three intervals 1983.0-1985.0, 1985.0-1987.5, and 1987.5-1989.6. The multifractal structure can be described by simple functions, the multifractal spectra. These analytical descriptions can be used to generate realizations of the heliospheric magnetic field with the same statistical properties as those observed by Voyager 2. Thus, the starting point is provided for realistic global statistical models of the 11-yr variation of the Galactic CRI.

  19. Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.

    PubMed

    Colak, Recep; Moser, Flavia; Chu, Jeffrey Shih-Chieh; Schönhuth, Alexander; Chen, Nansheng; Ester, Martin

    2010-10-25

    Computational prediction of functionally related groups of genes (functional modules) from large-scale data is an important issue in computational biology. Gene expression experiments and interaction networks are well studied large-scale data sources, available for many not yet exhaustively annotated organisms. It has been well established, when analyzing these two data sources jointly, modules are often reflected by highly interconnected (dense) regions in the interaction networks whose participating genes are co-expressed. However, the tractability of the problem had remained unclear and methods by which to exhaustively search for such constellations had not been presented. We provide an algorithmic framework, referred to as Densely Connected Biclustering (DECOB), by which the aforementioned search problem becomes tractable. To benchmark the predictive power inherent to the approach, we computed all co-expressed, dense regions in physical protein and genetic interaction networks from human and yeast. An automatized filtering procedure reduces our output which results in smaller collections of modules, comparable to state-of-the-art approaches. Our results performed favorably in a fair benchmarking competition which adheres to standard criteria. We demonstrate the usefulness of an exhaustive module search, by using the unreduced output to more quickly perform GO term related function prediction tasks. We point out the advantages of our exhaustive output by predicting functional relationships using two examples. We demonstrate that the computation of all densely connected and co-expressed regions in interaction networks is an approach to module discovery of considerable value. Beyond confirming the well settled hypothesis that such co-expressed, densely connected interaction network regions reflect functional modules, we open up novel computational ways to comprehensively analyze the modular organization of an organism based on prevalent and largely available large

  20. Dimethylsulfoxide exposure modulates HL-60 cell rolling interactions.

    PubMed

    Gee, David J; Wright, L Kate; Zimmermann, Jonathan; Cole, Kayla; Soule, Karen; Ubowski, Michelle

    2012-08-01

    Human leukaemic HL-60 cells are widely used for studying interactions involving adhesion molecules [e.g. P-selectin and PSGL-1 (P-selectin glycoprotein ligand-1)] since their rolling behaviour has been shown to mimic the dynamics of leucocyte rolling in vitro. HL-60 cells are neutrophilic promyelocytes that can undergo granulocytic differentiation upon exposure to compounds such as DMSO (dimethylsulfoxide). Using a parallel plate flow chamber functionalized with recombinant P-selectin-Fc chimaera, undifferentiated and DMSO-induced (48, 72 and 96 h) HL-60 cells were assayed for rolling behaviour. We found that depending on P-selectin incubation concentration, undifferentiated cells incurred up to a 6-fold increase in rolling velocity while subjected to an approximately 10-fold increase in biologically relevant shear stress. HL-60 cells exposed to DMSO for up to 72 h incurred up to a 3-fold increase in rolling velocity over the same shear stress range. Significantly, cells exposed for up to 96 h incurred up to a 9-fold decrease in rolling velocity, compared with undifferentiated HL-60 cells. Although cell surface and nuclear morphological changes were evident upon exposure to DMSO, flow cytometric analysis revealed that PSGL-1 expression was unchanged, irrespective of treatment duration. The results suggest that DMSO-treated HL-60 cells may be problematic as a substitute for neutrophils for trafficking studies during advanced stages of the LAC (leucocyte adhesion cascade). We suggest that remodelling of the cell surface during differentiation may affect rolling behaviour and that DMSO-treated HL-60 cells would behave differently from the normal leucocytes during inflammatory response in vivo.

  1. Dimethylsulfoxide exposure modulates HL-60 cell rolling interactions

    PubMed Central

    Gee, David J.; Wright, L. Kate; Zimmermann, Jonathan; Cole, Kayla; Soule, Karen; Ubowski, Michelle

    2012-01-01

    Human leukaemic HL-60 cells are widely used for studying interactions involving adhesion molecules [e.g. P-selectin and PSGL-1 (P-selectin glycoprotein ligand-1)] since their rolling behaviour has been shown to mimic the dynamics of leucocyte rolling in vitro. HL-60 cells are neutrophilic promyelocytes that can undergo granulocytic differentiation upon exposure to compounds such as DMSO (dimethylsulfoxide). Using a parallel plate flow chamber functionalized with recombinant P-selectin–Fc chimaera, undifferentiated and DMSO-induced (48, 72 and 96 h) HL-60 cells were assayed for rolling behaviour. We found that depending on P-selectin incubation concentration, undifferentiated cells incurred up to a 6-fold increase in rolling velocity while subjected to an approximately 10-fold increase in biologically relevant shear stress. HL-60 cells exposed to DMSO for up to 72 h incurred up to a 3-fold increase in rolling velocity over the same shear stress range. Significantly, cells exposed for up to 96 h incurred up to a 9-fold decrease in rolling velocity, compared with undifferentiated HL-60 cells. Although cell surface and nuclear morphological changes were evident upon exposure to DMSO, flow cytometric analysis revealed that PSGL-1 expression was unchanged, irrespective of treatment duration. The results suggest that DMSO-treated HL-60 cells may be problematic as a substitute for neutrophils for trafficking studies during advanced stages of the LAC (leucocyte adhesion cascade). We suggest that remodelling of the cell surface during differentiation may affect rolling behaviour and that DMSO-treated HL-60 cells would behave differently from the normal leucocytes during inflammatory response in vivo. PMID:22494057

  2. Loop electrostatics modulates the intersubunit interactions in ferritin.

    PubMed

    Bernacchioni, Caterina; Ghini, Veronica; Pozzi, Cecilia; Di Pisa, Flavio; Theil, Elizabeth C; Turano, Paola

    2014-11-21

    Functional ferritins are 24-mer nanocages that self-assemble with extended contacts between pairs of 4-helix bundle subunits coupled in an antiparallel fashion along the C2 axes. The largest intersubunit interaction surface in the ferritin nanocage involves helices, but contacts also occur between groups of three residues midway in the long, solvent-exposed L-loops of facing subunits. The anchor points between intersubunit L-loop pairs are the salt bridges between the symmetry-related, conserved residues Asp80 and Lys82. The resulting quaternary structure of the cage is highly soluble and thermostable. Substitution of negatively charged Asp80 with a positively charged Lys in homopolymeric M ferritin introduces electrostatic repulsions that inhibit the oligomerization of the ferritin subunits. D80K ferritin was present in inclusion bodies under standard overexpressing conditions in E. coli, contrasting with the wild type protein. Small amounts of fully functional D80K nanocages formed when expression was slowed. The more positively charged surface results in a different solubility profile and D80K crystallized in a crystal form with a low density packing. The 3D structure of D80K variant is the same as wild type except for the side chain orientations of Lys80 and facing Lys82. When three contiguous Lys groups are introduced in D80KI81K ferritin variant the nanocage assembly is further inhibited leading to lower solubility and reduced thermal stability. Here, we demonstrate that the electrostatic pairing at the center of the L-loops has a specific kinetic role in the self-assembly of ferritin nanocages.

  3. Interactions between alveolar macrophage subpopulations modulate their migratory function.

    PubMed Central

    Laplante, C.; Lemaire, I.

    1990-01-01

    To better understand the mechanisms by which alveolar macrophages (AM) are attracted to local sites in the lung, the locomotion of AM in response to N-formyl-methionyl-leucyl-phenylalanine (FMLP) was investigated. Total bronchoalveolar cells (99% AM) obtained by a nondiscriminating bronchoalveolar lavage procedure migrated toward FMLP over a range of concentrations of 10(-12) M to 10(-6) M. Dose-response experiments showed a biphasic response with two peaks of migration obtained respectively at 5 x 10(-10) M and 10(-8) M. Analysis in the presence and absence of a positive gradient of FMLP revealed that the first peak of migration (5 x 10(-10) M FMLP) corresponded predominantly to chemotactic activity whereas the second peak of migration (10(-8) M FMLP) was associated with chemokinetic activity. To further evaluate these activities of oriented (chemotaxis) vs. random (chemokinesis) migration, AM were separated into two fractions by a two-step bronchoalveolar lavage procedure. Whereas fraction 1 displayed exclusively chemokinesis in response to higher concentrations of FMLP (10(-8) M), fraction 2 was totally unresponsive to FMLP over a wide range of concentrations (5 x 10(-11) M - 10(-7) M). When both fractions were combined, however, the chemotactic response to low concentrations of FMLP (5 x 10(-10) M) was restored. Additional analysis of these two AM fractions indicated that fraction 1 AM had a significantly lower degree of adherence and aggregation than fraction 2 AM. These data suggest that cell-cell cooperation is important for AM chemotactic response to FMLP and that such interaction may involve changes in adherence and aggregation. Images Figure 5 PMID:2297048

  4. Growing functional modules from a seed protein via integration of protein interaction and gene expression data.

    PubMed

    Maraziotis, Ioannis A; Dimitrakopoulou, Konstantina; Bezerianos, Anastasios

    2007-10-23

    Nowadays modern biology aims at unravelling the strands of complex biological structures such as the protein-protein interaction (PPI) networks. A key concept in the organization of PPI networks is the existence of dense subnetworks (functional modules) in them. In recent approaches clustering algorithms were applied at these networks and the resulting subnetworks were evaluated by estimating the coverage of well-established protein complexes they contained. However, most of these algorithms elaborate on an unweighted graph structure which in turn fails to elevate those interactions that would contribute to the construction of biologically more valid and coherent functional modules. In the current study, we present a method that corroborates the integration of protein interaction and microarray data via the discovery of biologically valid functional modules. Initially the gene expression information is overlaid as weights onto the PPI network and the enriched PPI graph allows us to exploit its topological aspects, while simultaneously highlights enhanced functional association in specific pairs of proteins. Then we present an algorithm that unveils the functional modules of the weighted graph by expanding a kernel protein set, which originates from a given 'seed' protein used as starting-point. The integrated data and the concept of our approach provide reliable functional modules. We give proofs based on yeast data that our method manages to give accurate results in terms both of structural coherency, as well as functional consistency.

  5. IIIDB: a database for isoform-isoform interactions and isoform network modules

    PubMed Central

    2015-01-01

    Background Protein-protein interactions (PPIs) are key to understanding diverse cellular processes and disease mechanisms. However, current PPI databases only provide low-resolution knowledge of PPIs, in the sense that "proteins" of currently known PPIs generally refer to "genes." It is known that alternative splicing often impacts PPI by either directly affecting protein interacting domains, or by indirectly impacting other domains, which, in turn, impacts the PPI binding. Thus, proteins translated from different isoforms of the same gene can have different interaction partners. Results Due to the limitations of current experimental capacities, little data is available for PPIs at the resolution of isoforms, although such high-resolution data is crucial to map pathways and to understand protein functions. In fact, alternative splicing can often change the internal structure of a pathway by rearranging specific PPIs. To fill the gap, we systematically predicted genome-wide isoform-isoform interactions (IIIs) using RNA-seq datasets, domain-domain interaction and PPIs. Furthermore, we constructed an III database (IIIDB) that is a resource for studying PPIs at isoform resolution. To discover functional modules in the III network, we performed III network clustering, and then obtained 1025 isoform modules. To evaluate the module functionality, we performed the GO/pathway enrichment analysis for each isoform module. Conclusions The IIIDB provides predictions of human protein-protein interactions at the high resolution of transcript isoforms that can facilitate detailed understanding of protein functions and biological pathways. The web interface allows users to search for IIIs or III network modules. The IIIDB is freely available at http://syslab.nchu.edu.tw/IIIDB. PMID:25707505

  6. Interaction of frequency-modulated light beams in multistage parametric amplifiers at the maximum gain bandwidth

    SciTech Connect

    Vlasov, Sergei N; Koposova, E V; Freidman, Gennadii I

    2009-05-31

    Conditions of the applicability of equations in the quasi-static approximation for studying the parametric interaction of frequency-modulated light beams in multistage amplifiers are considered. This approximation is used to simulate numerically processes in a multistage DKDP crystal amplifier with the output power exceeding 10 PW and suppressed luminescence. (lasers and amplifiers)

  7. Effects of Web-Based Interactive Modules on Engineering Students' Learning Motivations

    ERIC Educational Resources Information Center

    Bai, Haiyan; Aman, Amjad; Xu, Yunjun; Orlovskaya, Nina; Zhou, Mingming

    2016-01-01

    The purpose of this study is to assess the impact of a newly developed modules, Interactive Web-Based Visualization Tools for Gluing Undergraduate Fuel Cell Systems Courses system (IGLU), on learning motivations of engineering students using two samples (n[subscript 1] = 144 and n[subscript 2] = 135) from senior engineering classes. The…

  8. Apollo program soil mechanics experiment. [interaction of the lunar module with the lunar surface

    NASA Technical Reports Server (NTRS)

    Scott, R. F.

    1975-01-01

    The soil mechanics investigation was conducted to obtain information relating to the landing interaction of the lunar module (LM) with the lunar surface, and lunar soil erosion caused by the spacecraft engine exhaust. Results obtained by study of LM landing performance on each Apollo mission are summarized.

  9. The Goals and Development of an Interactive Web Module for a Teacher Education Course.

    ERIC Educational Resources Information Center

    Schnorr, Donna; Bracken, Nicole; Hazari, Sunil

    The World Wide Web has become a promising medium for delivery of instruction. This paper describes a case study in which the Internet was used to supplement teacher education course instruction via an Interactive Web module. The goals of using such a medium for facilitating teaching and enhancing learning are described as they relate to learning…

  10. Probing weak dipole-dipole interaction using phase-modulated nonlinear spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Zeng-Zhao; Bruder, Lukas; Stienkemeier, Frank; Eisfeld, Alexander

    2017-05-01

    Phase-modulated nonlinear spectroscopy with higher harmonic demodulation has recently been suggested to provide information on many-body excitations. In the present work we theoretically investigate the application of this method to infer the interaction strength between two particles that interact via weak dipole-dipole interaction. To this end we use a full numerical solution of the Schrödinger equation with time-dependent pulses. For interpretation purposes we also derive analytical expressions in perturbation theory. We find one can detect dipole-dipole interaction via peak intensities (in contrast to line-shifts which typically are used in conventional spectroscopy). We provide a detailed study on the dependence of these intensities on the parameters of the laser pulse and the dipole-dipole interaction strength. Interestingly, we find that there is a phase between the first and second harmonic demodulated signal whose value depends on the sign of the dipole-dipole interaction.

  11. Development of small molecules designed to modulate protein-protein interactions.

    PubMed

    Che, Ye; Brooks, Bernard R; Marshall, Garland R

    2006-02-01

    Protein-protein interactions are ubiquitous, essential to almost all known biological processes, and offer attractive opportunities for therapeutic intervention. Developing small molecules that modulate protein-protein interactions is challenging, owing to the large size of protein-complex interface, the lack of well-defined binding pockets, etc. We describe a general approach based on the "privileged-structure hypothesis" [Che, Ph.D. Thesis, Washington University, 2003] - that any organic templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as protein-complex antagonists--to address the challenges inherent in the discovery of small-molecule inhibitors of protein-protein interactions.

  12. Modulation of an n→π* interaction with α-fluoro groups.

    PubMed

    Choudhary, Amit; Fry, Charles G; Raines, Ronald T

    2010-07-08

    Noncovalent interactions play an essential role in biological and chemical processes. In the main chain of common protein secondary structures, the lone pair (n) of a carbonyl oxygen is delocalized into the antibonding orbital (π*) of the subsequent carbonyl group. Herein, experimental and computational data reveal that this n→π* interaction can be attenuated by the inductive electron withdrawal of one or two α-fluoro groups in the donor. The steric effect of three α-fluoro groups, however, overcomes the inductive withdrawal. These data evoke a means to modulate the n→π* interaction in peptides, proteins, and other systems.

  13. Reciprocal interactions of Fgf10/Fgfr2b modulate the mouse tongue epithelial differentiation.

    PubMed

    Sohn, Wern-Joo; Jung, Hye-In; Choi, Min-A; Han, Jin-Hyun; Gwon, Gi-Jeong; Yamamoto, Hitoshi; Lee, Sanggyu; Ryoo, Zae Young; Park, Eui-Kyun; Shin, Hong-In; Jung, Han-Sung; Kim, Jae-Young

    2011-08-01

    The molecular mechanisms for epithelial differentiation have been studied by observing skin development in embryogenesis, but the early signaling modulations involved in tongue epithelial differentiation are not completely understood. Based on the gene expression patterns of the Fgf signaling molecules and previous results from Fgf10 and Fgfr2b knockout mice, it was hypothesized that there would be fundamental signaling interactions through the epithelial Fgfr2b and its mesenchymal ligand Fgf10 to regulate tongue epithelium differentiation. To elucidate these reciprocal interactions in tongue epithelial differentiation, this study employed an in vitro tongue organ culture system with antisense-oligodeoxynucleotides (AS-ODNs) and recombinant protein-soaked bead implantation for the loss-of-function and gain-of-function studies. Functional analysis of Fgf signaling revealed precise reciprocal interactions, which showed that mesenchymal Fgf10 rather than Fgf7 modulates tongue epithelial differentiation via Fgfr2b in a temporal- and spatial-specific manner.

  14. Mimosa: Mixture Model of Co-expression to Detect Modulators of Regulatory Interaction

    NASA Astrophysics Data System (ADS)

    Hansen, Matthew; Everett, Logan; Singh, Larry; Hannenhalli, Sridhar

    Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of genes. In particular, when one of the genes is a transcription factor (TF), the co-expression-based interaction is interpreted, with caution, as a direct regulatory interaction. However, any particular TF, and more importantly, any particular regulatory interaction, is likely to be active only in a subset of experimental conditions. Moreover, the subset of expression samples where the regulatory interaction holds may be marked by presence or absence of a modifier gene, such as an enzyme that post-translationally modifies the TF. Such subtlety of regulatory interactions is overlooked when one computes an overall expression correlation. Here we present a novel mixture modeling approach where a TF-Gene pair is presumed to be significantly correlated (with unknown coefficient) in a (unknown) subset of expression samples. The parameters of the model are estimated using a Maximum Likelihood approach. The estimated mixture of expression samples is then mined to identify genes potentially modulating the TF-Gene interaction. We have validated our approach using synthetic data and on three biological cases in cow and in yeast. While limited in some ways, as discussed, the work represents a novel approach to mine expression data and detect potential modulators of regulatory interactions.

  15. In-Depth Study of the Interaction, Sensitivity, and Gating Modulation by PUFAs on K+ Channels; Interaction and New Targets

    PubMed Central

    Moreno, Cristina; de la Cruz, Alicia; Valenzuela, Carmen

    2016-01-01

    Voltage gated potassium channels (KV) are membrane proteins that allow selective flow of K+ ions in a voltage-dependent manner. These channels play an important role in several excitable cells as neurons, cardiomyocytes, and vascular smooth muscle. Over the last 20 years, it has been shown that omega-3 polyunsaturated fatty acids (PUFAs) enhance or decrease the activity of several cardiac KV channels. PUFAs-dependent modulation of potassium ion channels has been reported to be cardioprotective. However, the precise cellular mechanism underlying the cardiovascular benefits remained unclear in part because new PUFAs targets and signaling pathways continue being discovered. In this review, we will focus on recent data available concerning the following aspects of the KV channel modulation by PUFAs: (i) the exact residues involved in PUFAs-KV channels interaction; (ii) the structural PUFAs determinants important for their effects on KV channels; (iii) the mechanism of the gating modulation of KV channels and, finally, (iv) the PUFAs modulation of a few new targets present in smooth muscle cells (SMC), KCa1.1, K2P, and KATP channels, involved in vascular relaxation. PMID:27933000

  16. EPOP Interacts with Elongin BC and USP7 to Modulate the Chromatin Landscape.

    PubMed

    Liefke, Robert; Karwacki-Neisius, Violetta; Shi, Yang

    2016-11-17

    Gene regulatory networks are pivotal for many biological processes. In mouse embryonic stem cells (mESCs), the transcriptional network can be divided into three functionally distinct modules: Polycomb, Core, and Myc. The Polycomb module represses developmental genes, while the Myc module is associated with proliferative functions, and its mis-regulation is linked to cancer development. Here, we show that, in mESCs, the Polycomb repressive complex 2 (PRC2)-associated protein EPOP (Elongin BC and Polycomb Repressive Complex 2-associated protein; a.k.a. C17orf96, esPRC2p48, and E130012A19Rik) co-localizes at chromatin with members of the Myc and Polycomb module. EPOP interacts with the transcription elongation factor Elongin BC and the H2B deubiquitinase USP7 to modulate transcriptional processes in mESCs similar to MYC. EPOP is commonly upregulated in human cancer, and its loss impairs the proliferation of several human cancer cell lines. Our findings establish EPOP as a transcriptional modulator, which impacts both Polycomb and active gene transcription in mammalian cells. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Exploring Space Science Concepts using Interactive Animations and Learning Modules (Invited)

    NASA Astrophysics Data System (ADS)

    Hallau, K.

    2009-12-01

    Many concepts in the planetary sciences can be difficult to teach using traditional or laboratory methods, but interactive media may provide unique opportunities to explore these. Such “interactives” can engage the user by allowing them to manipulate variables, view multiple trials in succession, and explore sophisticated conceptual information within a dynamic graphical interface. In formal educational settings, interactives accompanied by student data sheets can be used to foster and evaluate learning. At Montana State University’s Extended University we have developed interactive animations using Flash® to explore concepts such as gravity assist maneuvers and spin-orbit resonance as part of the education and public outreach efforts for NASA’s MESSENGER and New Horizons missions (to Mercury and Pluto, respectively). Some of theses interactives are paired with standards-based hands-on classroom activities. Here we will demonstrate several interactives and accompanying learning modules.

  18. Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states

    PubMed Central

    LeBon, Lauren; Lee, Tom V; Sprinzak, David; Jafar-Nejad, Hamed; Elowitz, Michael B

    2014-01-01

    The Notch signaling pathway consists of multiple types of receptors and ligands, whose interactions can be tuned by Fringe glycosyltransferases. A major challenge is to determine how these components control the specificity and directionality of Notch signaling in developmental contexts. Here, we analyzed same-cell (cis) Notch-ligand interactions for Notch1, Dll1, and Jag1, and their dependence on Fringe protein expression in mammalian cells. We found that Dll1 and Jag1 can cis-inhibit Notch1, and Fringe proteins modulate these interactions in a way that parallels their effects on trans interactions. Fringe similarly modulated Notch-ligand cis interactions during Drosophila development. Based on these and previously identified interactions, we show how the design of the Notch signaling pathway leads to a restricted repertoire of signaling states that promote heterotypic signaling between distinct cell types, providing insight into the design principles of the Notch signaling system, and the specific developmental process of Drosophila dorsal-ventral boundary formation. DOI: http://dx.doi.org/10.7554/eLife.02950.001 PMID:25255098

  19. Delayed response of a fermion pair condensate to a modulation of the interaction strength

    NASA Astrophysics Data System (ADS)

    Plata, J.

    2009-09-01

    The effect of a sinusoidal modulation of the interaction strength on a fermion pair condensate is analytically studied. The system is described by a generalization of the coupled fermion-boson model that incorporates a time-dependent intermode coupling induced via a magnetic Feshbach resonance. Nontrivial effects are shown to emerge depending on the relative magnitude of the modulation period and the relaxation time of the condensate. Specifically, a nonadiabatic modulation drives the system out of thermal equilibrium: the external field induces a variation of the quasiparticle energies, and, in turn, a disequilibrium of the associated populations. The subsequent relaxation process is studied and an analytical description of the gap dynamics is obtained. Recent experimental findings are explained: the delay observed in the response to the applied field is understood as a temperature effect linked to the condensate relaxation time.

  20. STORMy Interactions: Gaze and the Modulation of Mimicry in Adults on the Autism Spectrum.

    PubMed

    Forbes, Paul A G; Wang, Yin; de C Hamilton, Antonia F

    2016-08-09

    Mimicry involves unconsciously imitating the actions of others and is a powerful and ubiquitous behavior in social interactions. There has been a long debate over whether mimicry is abnormal in people with autism spectrum conditions (ASC) and what the causes of any differences might be. Wang and Hamilton's (2012) social top-down response modulation (STORM) model proposed that people with ASC can and do mimic but, unlike neurotypical participants, fail to modulate their mimicry according to the social context. This study used an established mimicry paradigm to test this hypothesis. In neurotypical participants, direct gaze specifically enhanced congruent hand actions as previously found; in the ASC sample, direct gaze led to faster reaction times in both congruent and incongruent movements. This result shows that mimicry is intact in ASC, but is not socially modulated by gaze, as predicted by STORM.

  1. Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules.

    PubMed

    Ishikawa, Junya; Matsumura, Shigeyoshi; Jaeger, Luc; Inoue, Tan; Furuta, Hiroyuki; Ikawa, Yoshiya

    2009-10-15

    The DSL ribozyme is a class of artificial ligase ribozymes with a highly modular architecture, which catalyzes template-directed RNA ligation on a helical substrate module that can be either covalently connected (cis-DSL) or physically separated (trans-DSL) from the catalytic module. Substrate recognition by the catalytic module is promoted by one or two sets of GNRA/receptor interactions acting as clamps in the cis or trans configurations, respectively. In this study, we have rationally designed and analyzed the catalytic and self-assembly properties of several trans-DSL ribozymes with different sets of natural and artificial GNRA-receptor clamps. Two variants newly designed in this study showed significantly enhanced catalytic properties with respect of the original trans-DSL construct. While this work allows dissection of the turnover and catalytic properties of the trans-DSL ribozyme, it also emphasizes the remarkable modularity of RNA tertiary structure for nano-construction of complex functions.

  2. Temporal development of anticipatory reflex modulation to dynamical interactions during arm movement.

    PubMed

    Kimura, Toshitaka; Gomi, Hiroaki

    2009-10-01

    It is known that somatosensory reflex during voluntary arm movement is modulated anticipatorily according to given tasks or environments. However, when and how reflex amplitude is set remains controversial. Is the reflex modulation completed preparatorily before movement execution or does it vary with the movement? Is the reflex amplitude coded in a temporal manner or in a spatial (or state-dependent) manner? Here we studied these issues while subjects performed planar reaching movements with upcoming opposite (rightward/leftward) directions of force fields. Somatosensory reflex responses of shoulder muscles induced by a small force perturbation were evaluated at several points before the arm encountered predictable force fields after movement start. We found that the shoulder flexor reflex responses were generally higher for the rightward than for the leftward upcoming force fields, whereas the extensor reflex responses were higher for the leftward force field. This reflex amplitude depending on the upcoming force field direction became prominent as the reflex was evoked closer to the force fields, indicating continuous changes in reflex modulation during movement. An additional experiment further showed that the reflex modulation developed as a function of the temporal distance to the force fields rather than the spatial distance. Taken together, the results suggest that, in the force field interaction task, somatosensory reflex amplitude during the course of movement is set anticipatorily on the basis of an estimate of the time-to-contact rather than the state-to-contact, to upcoming dynamical interaction during voluntary movement.

  3. Acceptability of a bilingual interactive computerized educational module in a poor, medically underserved patient population.

    PubMed

    Leeman-Castillo, Bonnie A; Corbett, Kitty K; Aagaard, Eva M; Maselli, Judith H; Gonzales, Ralph; Mackenzie, Thomas D

    2007-01-01

    We evaluated the acceptability and impact of an audiovisual, bilingual, interactive computer module relating to appropriate antibiotic use. In winter 2001, adults seeking urgent care for acute respiratory infections at an inner-city urgent care clinic were invited to complete the computer module and survey (N = 296). After responding to questions about their symptoms, patients were provided information about their illness and appropriate antibiotic use, and then asked several questions about the acceptability of the module. The main outcomes, reflecting qualities known to enhance diffusion of innovations, were "learning something new about colds and flu" and trusting the computer information. Spanish-language respondents (16%) were much less likely to report prior computer experience, more likely to need help, and strongly preferred answering to a person compared with English-language respondents. In multivariable analysis, Spanish-language respondents were more likely to report learning something new (OR = 5.0; 95% CI: 2.0, 12.4) and trusting the information (OR = 2.5; 95% CI: 1.0, 6.0). We conclude that an interactive computer module was well received among a medically underserved urgent care clinic population. Benefits appear greatest among populations having the least experience with this medium.

  4. Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components

    PubMed Central

    Timasheff, Serge N.

    2002-01-01

    Solvent additives (cosolvents, osmolytes) modulate biochemical reactions if, during the course of the reaction, there is a change in preferential interactions of solvent components with the reacting system. Preferential interactions can be expressed in terms of preferential binding of the cosolvent or its preferential exclusion (preferential hydration). The driving force is the perturbation by the protein of the chemical potential of the cosolvent. It is shown that the measured change of the amount of water in contact with protein during the course of the reaction modulated by an osmolyte is a change in preferential hydration that is strictly a measure of the cosolvent chemical potential perturbation by the protein in the ternary water–protein–cosolvent system. It is not equal to the change in water of hydration, because water of hydration is a reflection strictly of protein–water forces in a binary system. There is no direct relation between water of preferential hydration and water of hydration. PMID:12097640

  5. Exponential wave-packet spreading via self-interaction time modulation

    NASA Astrophysics Data System (ADS)

    Zhao, Wen-Lei; Gong, Jiangbin; Wang, Wen-Ge; Casati, Giulio; Liu, Jie; Fu, Li-Bin

    2016-11-01

    The time-periodic modulation of the self-interaction of a Bose-Einstein condensate or a nonlinear optics system has been recognized as an exciting tool to explore interesting physics that was previously unavailable. This tool is exploited here to examine the exotic dynamics of a nonlinear system described by the Gross-Pitaevskii equation. We observe three remarkable and closely related dynamical phenomena, exponentially localized profile of wave functions in momentum space with localization length exponentially increasing in time, exponential wave-packet spreading, and exponential sensitivity to initial conditions. A hybrid quantum-classical theory is developed to partly explain these findings. Time-periodic self-interaction modulation is seen to be a robust method to achieve superfast spreading and induce genuine chaos even in the absence of any external potential.

  6. A New Approach to Developing Interactive Software Modules Through Graduate Education

    NASA Astrophysics Data System (ADS)

    Sanders, Nathan E.; Faesi, Chris; Goodman, Alyssa A.

    2014-06-01

    Educational technology has attained significant importance as a mechanism for supporting experiential learning of science concepts. However, the growth of this mechanism is limited by the significant time and technical expertise needed to develop such products, particularly in specialized fields of science. We sought to test whether interactive, educational, online software modules can be developed effectively by students as a curriculum component of an advanced science course. We discuss a set of 15 such modules developed by Harvard University graduate students to demonstrate various concepts related to astronomy and physics. Their successful development of these modules demonstrates that online software tools for education and outreach on specialized topics can be produced while simultaneously fulfilling project-based learning objectives. We describe a set of technologies suitable for module development and present in detail four examples of modules developed by the students. We offer recommendations for incorporating educational software development within a graduate curriculum and conclude by discussing the relevance of this novel approach to new online learning environments like edX.

  7. Nonlinear modal interaction in HVDC/AC power systems with dc power modulation

    SciTech Connect

    Ni, Y.X.; Vittal, V.; Kliemann, W.; Fouad, A.A.

    1996-11-01

    In this paper investigation of nonlinear modal interaction using the normal form of vector fields technique is extended to HVDC/AC power systems with dc power modulation. The ac-dc interface equations are solved to form a state space model with second order approximation. Using the normal form technique, the system`s nonlinear dynamic characteristics are obtained. The proposed approach is applied to a 4-generator HVDC/AC test power system, and compare with the time domain solution.

  8. Transitive closure and metric inequality of weighted graphs:detecting protein interaction modules using cliques

    SciTech Connect

    Ding, Chris; He, Xiaofeng; Xiong, Hui; Peng, Hanchuan; Holbrook,Stephen R.

    2006-06-02

    We study transitivity properties of edge weights in complex networks. We show that enforcing transitivity leads to a transitivity inequality which is equivalent to ultra-metric inequality. This can be used to define transitive closure on weighted undirected graphs, which can be computed using a modified Floyd-Warshall algorithm. We outline several applications and present results of detecting protein functional modules in a protein interaction network.

  9. Fast Quantum Nondemolition Readout by Parametric Modulation of Longitudinal Qubit-Oscillator Interaction

    NASA Astrophysics Data System (ADS)

    Didier, Nicolas; Bourassa, Jérôme; Blais, Alexandre

    2015-11-01

    We show how to realize fast and high-fidelity quantum nondemolition qubit readout using longitudinal qubit-oscillator interaction. This is accomplished by modulating the longitudinal coupling at the cavity frequency. The qubit-oscillator interaction then acts as a qubit-state dependent drive on the cavity, a situation that is fundamentally different from the standard dispersive case. Single-mode squeezing can be exploited to exponentially increase the signal-to-noise ratio of this readout protocol. We present an implementation of this longitudinal parametric readout in circuit quantum electrodynamics and a possible multiqubit architecture.

  10. TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions.

    PubMed

    Higueruelo, Alicia P; Jubb, Harry; Blundell, Tom L

    2013-01-01

    TIMBAL is a database holding molecules of molecular weight <1200 Daltons that modulate protein-protein interactions. Since its first release, the database has been extended to cover 50 known protein-protein interactions drug targets, including protein complexes that can be stabilized by small molecules with therapeutic effect. The resource contains 14 890 data points for 6896 distinct small molecules. UniProt codes and Protein Data Bank entries are also included. Database URL: http://www-cryst.bioc.cam.ac.uk/timbal

  11. Few-boson tunneling in a double well with spatially modulated interaction

    SciTech Connect

    Chatterjee, Budhaditya; Brouzos, Ioannis; Schmelcher, Peter; Zoellner, Sascha

    2010-10-15

    We study few-boson tunneling in a one-dimensional double well with a spatially modulated interaction. The dynamics changes from Rabi oscillations in the noninteracting case to a highly suppressed tunneling for intermediate coupling strengths followed by a reappearance near the fermionization limit. With extreme interaction inhomogeneity in the regime of strong correlations, we observe tunneling between the higher bands. The dynamics is explained on the basis of the few-body spectrum and stationary eigenstates. For a higher number of particles N{>=}3, it is shown that the inhomogeneity of the interaction can be tuned to generate tunneling resonances. Finally, a tilted double well and its interplay with the interaction asymmetry are discussed.

  12. Ca(2+) modulating α-synuclein membrane transient interactions revealed by solution NMR spectroscopy.

    PubMed

    Zhang, Zeting; Dai, Chenye; Bai, Jia; Xu, Guohua; Liu, Maili; Li, Conggang

    2014-03-01

    α-Synuclein is involved in Parkinson's disease and its interaction with cell membrane is crucial to its pathological and physiological functions. Membrane properties, such as curvature and lipid composition, have been shown to affect the interactions by various techniques, but ion effects on α-synuclein membrane interactions remain elusive. Ca(2+) dynamic fluctuation in neurons plays important roles in the onset of Parkinson's disease and its influx is considered as one of the reasons to cause cell death. Using solution Nuclear Magnetic Resonance (NMR) spectroscopy, here we show that Ca(2+) can modulate α-synuclein membrane interactions through competitive binding to anionic lipids, resulting in dissociation of α-synuclein from membranes. These results suggest a negative modulatory effect of Ca(2+) on membrane mediated normal function of α-synuclein, which may provide a clue, to their dysfunction in neurodegenerative disease. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Metal-graphene heterojunction modulation via H{sub 2} interaction

    SciTech Connect

    Cadore, A. R. E-mail: lccampos@fisica.ufmg.br; Mania, E.; Lacerda, R. G.; Campos, L. C. E-mail: lccampos@fisica.ufmg.br; Morais, E. A. de; Watanabe, K.; Taniguchi, T.

    2016-07-18

    Combining experiment and theory, we investigate how a naturally created heterojunction (pn junction) at a graphene and metallic contact interface is modulated via interaction with molecular hydrogen (H{sub 2}). Due to an electrostatic interaction, metallic electrodes induce pn junctions in graphene, leading to an asymmetrical resistance in electronic transport for electrons and holes. We report that the asymmetry in the resistance can be tuned in a reversible manner by exposing graphene devices to H{sub 2}. The interaction between the H{sub 2} and graphene occurs solely at the graphene-contact pn junction and induces a modification on the electrostatic interaction between graphene and metallic contacts. We explain the experimental data with theory providing information concerning the length of the heterojunction and how it changes as a function of H{sub 2} adsorption. Our results are valuable for understanding the nature of the metal-graphene interfaces and have potential application for selective sensors of molecular hydrogen.

  14. PIPE: a protein–protein interaction passage extraction module for BioCreative challenge

    PubMed Central

    Chu, Chun-Han; Su, Yu-Chen; Chen, Chien Chin; Hsu, Wen-Lian

    2016-01-01

    Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioCreative V (http://www.biocreative.org/) to capture frequent protein-protein interaction (PPI) patterns within text. We also present an interaction pattern tree (IPT) kernel method that integrates the PPI patterns with convolution tree kernel (CTK) to extract PPIs. Methods were evaluated on LLL, IEPA, HPRD50, AIMed and BioInfer corpora using cross-validation, cross-learning and cross-corpus evaluation. Empirical evaluations demonstrate that our method is effective and outperforms several well-known PPI extraction methods. Database URL: PMID:27524807

  15. Spin relaxation rates in quantum dots: Role of the phonon modulated spin orbit interaction

    NASA Astrophysics Data System (ADS)

    Alcalde, A. M.; Romano, C. L.; Marques, G. E.

    2008-11-01

    We calculate the spin relaxation rates in InAs and GaAs parabolic quantum dots due to the interaction of spin carriers with acoustical phonons. We consider a spin relaxation mechanism completely intrinsic to the system, since it is based on the modulation of the spin-orbit interaction by the acoustic phonon potential, which is independent of any structural properties of the confinement potential. The electron-phonon deformation potential and the piezoelectric interaction are described by the Pavlov-Firsov spin-phonon Hamiltonian. Our results demonstrate that, for narrow-gap semiconductors, the deformation potential interaction becomes dominant. This behavior is not observed for wide or intermediate gap semiconductors, where the piezoelectric coupling, in general, governs the relaxation processes. We also demonstrate that the spin relaxation rates are particularly sensitive to values of the Landé g-factor, which depend strongly on the spatial shape of the confinement.

  16. Neuronal and astrocytic interactions modulate brain endothelial properties during metabolic stresses of in vitro cerebral ischemia

    PubMed Central

    2014-01-01

    Neurovascular and gliovascular interactions significantly affect endothelial phenotype. Physiologically, brain endothelium attains several of its properties by its intimate association with neurons and astrocytes. However, during cerebrovascular pathologies such as cerebral ischemia, the uncoupling of neurovascular and gliovascular units can result in several phenotypical changes in brain endothelium. The role of neurovascular and gliovascular uncoupling in modulating brain endothelial properties during cerebral ischemia is not clear. Specifically, the roles of metabolic stresses involved in cerebral ischemia, including aglycemia, hypoxia and combined aglycemia and hypoxia (oxygen glucose deprivation and re-oxygenation, OGDR) in modulating neurovascular and gliovascular interactions are not known. The complex intimate interactions in neurovascular and gliovascular units are highly difficult to recapitulate in vitro. However, in the present study, we used a 3D co-culture model of brain endothelium with neurons and astrocytes in vitro reflecting an intimate neurovascular and gliovascular interactions in vivo. While the cellular signaling interactions in neurovascular and gliovascular units in vivo are much more complex than the 3D co-culture models in vitro, we were still able to observe several important phenotypical changes in brain endothelial properties by metabolically stressed neurons and astrocytes including changes in barrier, lymphocyte adhesive properties, endothelial cell adhesion molecule expression and in vitro angiogenic potential. PMID:24438487

  17. Transcriptional Modulation of Enterotoxigenic Escherichia coli Virulence Genes in Response to Epithelial Cell Interactions

    PubMed Central

    Kansal, Rita; Rasko, David A.; Sahl, Jason W.; Munson, George P.; Roy, Koushik; Luo, Qingwei; Sheikh, Alaullah; Kuhne, Kurt J.

    2013-01-01

    Enterotoxigenic Escherichia coli (ETEC) strains are a leading cause of morbidity and mortality due to diarrheal illness in developing countries. There is currently no effective vaccine against these important pathogens. Because genes modulated by pathogen-host interactions potentially encode putative vaccine targets, we investigated changes in gene expression and surface morphology of ETEC upon interaction with intestinal epithelial cells in vitro. Pan-genome microarrays, quantitative reverse transcriptase PCR (qRT-PCR), and transcriptional reporter fusions of selected promoters were used to study changes in ETEC transcriptomes. Flow cytometry, immunofluorescence microscopy, and scanning electron microscopy were used to investigate alterations in surface antigen expression and morphology following pathogen-host interactions. Following host cell contact, genes for motility, adhesion, toxin production, immunodominant peptides, and key regulatory molecules, including cyclic AMP (cAMP) receptor protein (CRP) and c-di-GMP, were substantially modulated. These changes were accompanied by visible changes in both ETEC architecture and the expression of surface antigens, including a novel highly conserved adhesin molecule, EaeH. The studies reported here suggest that pathogen-host interactions are finely orchestrated by ETEC and are characterized by coordinated responses involving the sequential deployment of multiple virulence molecules. Elucidation of the molecular details of these interactions could highlight novel strategies for development of vaccines for these important pathogens. PMID:23115039

  18. TNF Superfamily Protein–Protein Interactions: Feasibility of Small-Molecule Modulation

    PubMed Central

    Song, Yun; Buchwald, Peter

    2015-01-01

    The tumor necrosis factor (TNF) superfamily (TNFSF) contains about thirty structurally related receptors (TNFSFRs) and about twenty protein ligands that bind to one or more of these receptors. Almost all of these cell surface protein-protein interactions (PPIs) represent high-value therapeutic targets for inflammatory or immune modulation in autoimmune diseases, transplant recipients, or cancers, and there are several biologics including antibodies and fusion proteins targeting them that are in various phases of clinical development. Small-molecule inhibitors or activators could represent possible alternatives if the difficulties related to the targeting of protein-protein interactions by small molecules can be addressed. Compounds proving the feasibility of such approaches have been identified through different drug discovery approaches for a number of these TNFSFR-TNFSF type PPIs including CD40-CD40L, BAFFR-BAFF, TRAIL-DR5, and OX40-OX40L. Corresponding structural, signaling, and medicinal chemistry aspects are briefly reviewed here. While none of these small-molecule modulators identified so far seems promising enough to be pursued for clinical development, they provide proof-of-principle evidence that these interactions are susceptible to small-molecule modulation and can serve as starting points toward the identification of more potent and selective candidates. PMID:25706111

  19. Enumeration of condition-dependent dense modules in protein interaction networks

    PubMed Central

    Georgii, Elisabeth; Dietmann, Sabine; Uno, Takeaki; Pagel, Philipp; Tsuda, Koji

    2009-01-01

    Motivation: Modern systems biology aims at understanding how the different molecular components of a biological cell interact. Often, cellular functions are performed by complexes consisting of many different proteins. The composition of these complexes may change according to the cellular environment, and one protein may be involved in several different processes. The automatic discovery of functional complexes from protein interaction data is challenging. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, constraints from additional information sources such as gene expression and phenotype data can be integrated, so we can systematically mine for dense modules with interesting profiles. Results: Given a weighted protein interaction network, our method discovers all protein sets that satisfy a user-defined minimum density threshold. We employ a reverse search strategy, which allows us to exploit the density criterion in an efficient way. Our experiments show that the novel approach is feasible and produces biologically meaningful results. In comparative validation studies using yeast data, the method achieved the best overall prediction performance with respect to confirmed complexes. Moreover, by enhancing the yeast network with phenotypic and phylogenetic profiles and the human network with tissue-specific expression data, we identified condition-dependent complex variants. Availability: A C++ implementation of the algorithm is available at http://www.kyb.tuebingen.mpg.de/~georgii/dme.html. Contact: koji.tsuda@tuebingen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19213739

  20. General theory of frequency modulated selective reflection. Influence of atom surface interactions

    NASA Astrophysics Data System (ADS)

    Ducloy, M.; Fichet, M.

    1991-12-01

    We calculate the modulation of the reflection coefficient for a frequency-modulated (FM) light beam incident on the interface between a dielectric and an atomic vapor. The vapor is described as a gas of resonant, Doppler-broadened, two-level systems, with transition frequency and linewidth arbitrarily depending on the atom-dielectric distance. The atoms are supposed to get deexcited at collisions with the surface. The transient atomic response is calculated to first order in the incident field, for both incoming and desorbed atoms. The reflection coefficient, evaluated to first order in the vapor dipole polarization, leads to a formal expression of the reflectivity modulation, valid for arbitrary atom-surface interaction potentials. One first discusses the reflection signal in absence of wall interactions, for arbitrary modulation frequencies. At large frequencies, it allows one to monitor both vapor absorption and dispersion. Second, the formal theory is applied to the case of a Van der Waals-London surface attraction exerted on the atomic vapor. Both normal and oblique beam incidences are considered. One shows how the vapor dispersion signal is red-shifted and strongly distorted by the appearance of vapor-surface long-range interactions, and how it can be used to monitor these interactions. At non-normal incidences, the lineshapes get Doppler-broadened. On calcule le coefficient de réflexion d'un faisceau lumineux, modulé en fréquence, incident sur une interface entre un milieu diélectrique et une vapeur atomique. Cette vapeur est décrite comme un ensemble de systèmes à deux niveaux, présentant un élargissement Doppler, et dont la fréquence de transition et la largeur de raie sont supposées dépendre de la distance au milieu diélectrique. On suppose par ailleurs que les atomes sont déexcités sur la paroi. La réponse transitoire des atomes est analysée au premier ordre en fonction du champ électromagnétique incident. Du coefficient de r

  1. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

    PubMed Central

    Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

  2. Controlling Non-Covalent Interactions to Modulate the Dispersion of Fullerenes in Polymer Nanocomposites

    SciTech Connect

    Sumpter, Bobby G

    2011-01-01

    Polymer nanocomposites (PNCs) are materials based on a class of filled plastics that contain relatively small amounts of nanoparticles, which can impart improved structural, mechanical, and thermal properties relative to the neat polymer. However, the homogeneous dispersion of the nanoparticles into a polymer matrix is critical and an impeding factor for the controlled enhancement of PNC properties. In this work, we provide new insight into the importance of polymer chain connectivity and nanoparticle shape and curvature on the formation of noncovalent electron donor-acceptor (EDA) interactions between polymers and nanoparticles. This is accomplished by experimentally monitoring the dispersion of nanoparticles in copolymers containing varying amounts of functional moieties that can form noncovalent interactions with carbon nanoparticles with corroboration through density functional calculations. The results show that the presence of a minority of interacting functional groups within a polymer chain leads to an optimum interaction between the polymer and fullerene. Density functional theory calculations that identify the binding energy and geometry of the interaction between the functional monomers and fullerenes correspond very well with the experimental results. Moreover, comparison of these results to similar studies with single-walled carbon nanotubes (SWNT) indicate a distinct difference in the ability of EDA interactions to improve the dispersion of fullerenes relative to their impact on SWNT. Thus, the polymer chain connectivity, the polymer chain conformation, and size and shape of the nanoparticle modulate the formation of intermolecular interactions and directly impact the dispersion of the resultant nanocomposite.

  3. Cortical and corticospinal output modulations during reaching movements with varying directions and magnitudes of interaction torques.

    PubMed

    Asmussen, M J; Bailey, A Z; Nelson, A J

    2015-12-17

    The neural command required to coordinate a multi-joint movement is inherently complex. During multi-joint movement of the limb, the force created from movement at one joint may create a torque at a second joint known as an interaction torque. Interaction torques may be assistive or resistive thereby aiding or opposing the motion of the second joint, respectively. For movement to be effectively controlled, the central nervous system should modulate neural output to the muscles to appropriately account for interaction torques. The present study examined the neural output from the primary motor cortex before and during reaching movements that required different combinations of assistive and resistive interaction torques occurring at the shoulder and elbow joints. Using transcranial magnetic stimulation to probe neural output from the primary motor cortex, results indicate that corticospinal output controlling the upper arm is related to resistive interaction torques occurring at the shoulder joint. Further, cortical output to bi-articular muscles is associated with interaction torque and this may be driven by the fact that these muscles are in an advantageous position to control torques produced between inter-connection segments. Humans have a tendency to avoid reaching movements that involve resistive interaction torques and this may be driven by the requirement of increased neural output associated with these movements.

  4. Molecular tweezers modulate 14-3-3 protein-protein interactions

    NASA Astrophysics Data System (ADS)

    Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian

    2013-03-01

    Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins—a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)—in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.

  5. Molecular tweezers modulate 14-3-3 protein-protein interactions.

    PubMed

    Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian

    2013-03-01

    Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins--a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)--in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.

  6. Aggregation Modulators Interfere with Membrane Interactions of β2-Microglobulin Fibrils

    PubMed Central

    Sheynis, Tania; Friediger, Anat; Xue, Wei-Feng; Hellewell, Andrew L.; Tipping, Kevin W.; Hewitt, Eric W.; Radford, Sheena E.; Jelinek, Raz

    2013-01-01

    Amyloid fibril accumulation is a pathological hallmark of several devastating disorders, including Alzheimer’s disease, prion diseases, type II diabetes, and others. Although the molecular factors responsible for amyloid pathologies have not been deciphered, interactions of misfolded proteins with cell membranes appear to play important roles in these disorders. Despite increasing evidence for the involvement of membranes in amyloid-mediated cytotoxicity, the pursuit for therapeutic strategies has focused on preventing self-assembly of the proteins comprising the amyloid plaques. Here we present an investigation of the impact of fibrillation modulators upon membrane interactions of β2-microglobulin (β2m) fibrils. The experiments reveal that polyphenols (epigallocatechin gallate, bromophenol blue, and resveratrol) and glycosaminoglycans (heparin and heparin disaccharide) differentially affect membrane interactions of β2m fibrils measured by dye-release experiments, fluorescence anisotropy of labeled lipid, and confocal and cryo-electron microscopies. Interestingly, whereas epigallocatechin gallate and heparin prevent membrane damage as judged by these assays, the other compounds tested had little, or no, effect. The results suggest a new dimension to the biological impact of fibrillation modulators that involves interference with membrane interactions of amyloid species, adding to contemporary strategies for combating amyloid diseases that focus on disruption or remodeling of amyloid aggregates. PMID:23931322

  7. Modulation of CD6 function through interaction with Galectin-1 and -3.

    PubMed

    Escoda-Ferran, Cristina; Carrasco, Esther; Caballero-Baños, Miguel; Miró-Julià, Cristina; Martínez-Florensa, Mario; Consuegra-Fernández, Marta; Martínez, Vanesa G; Liu, Fu-Tong; Lozano, Francisco

    2014-08-25

    CD6 is a lymphocyte glycoprotein receptor that physically associates with the antigen-specific receptor complex at the center of the immunological synapse, where it interacts with its ligand CD166/ALCAM. The present work reports the carbohydrate-dependent interaction of CD6 and CD166/ALCAM with Galectin-1 and -3, two well-known soluble mammalian lectins. Both galectins interfered with superantigen-induced T cell proliferation and cell adhesion phenomena mediated by the CD6-CD166/ALCAM pair, while CD6 expression protected cells from galectin-induced apoptosis. The results suggest that interaction of Galectin-1 and -3 with CD6 and CD166/ALCAM might modulate some relevant aspects of T cell physiology. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  8. The Solar Array Module Plasma Interactions Experiment (SAMPIE): Science and technology objectives

    NASA Technical Reports Server (NTRS)

    Hillard, G. Barry

    1992-01-01

    The Solar Array Module Plasma Interactions Experiment (SAMPIE) is an approved NASA Space Shuttle space flight experiment to be launched in Jul. 1993. The SAMPIE experiment is designed to investigate the interaction of high voltage space power systems with ionospheric plasma. To study the behavior of solar cells, a number of cell coupons, representing technologies of current interest, will be biased to high voltages to characterize both negative potential arcing and positive potential current collection. Additionally, various theories of arc suppression will be tested by including several specially modified cell coupons. Finally, SAMPIE will include experiments to study the basic nature of these interactions. The rationale for a space flight experiment, the measurements to be made, the significance of the expected results, and the current design status of the flight hardware are described.

  9. Ionic interactions. Subnanoscale hydrophobic modulation of salt bridges in aqueous media.

    PubMed

    Chen, Shuo; Itoh, Yoshimitsu; Masuda, Takuya; Shimizu, Seishi; Zhao, Jun; Ma, Jing; Nakamura, Shugo; Okuro, Kou; Noguchi, Hidenori; Uosaki, Kohei; Aida, Takuzo

    2015-05-01

    Polar interactions such as electrostatic forces and hydrogen bonds play an essential role in biological molecular recognition. On a protein surface, polar interactions occur mostly in a hydrophobic environment because nonpolar amino acid residues cover ~75% of the protein surface. We report that ionic interactions on a hydrophobic surface are modulated by their subnanoscale distance to the surface. We developed a series of ionic head groups-appended self-assembled monolayers with C2, C6, C8, and C12 space-filling alkyl chains, which capture a dendritic guest via the formation of multiple salt bridges. The guest release upon protonolysis is progressively suppressed when its distance from the background hydrophobe changes from 1.2 (C2) to 0.2 (C12) nanometers, with an increase in salt bridge strength of ~3.9 kilocalories per mole. Copyright © 2015, American Association for the Advancement of Science.

  10. Design of Protein-Peptide Interaction Modules for Assembling Supramolecular Structures in Vivo and in Vitro.

    PubMed

    Speltz, Elizabeth B; Nathan, Aparna; Regan, Lynne

    2015-09-18

    Synthetic biology and protein origami both require protein building blocks that behave in a reliable, predictable fashion. In particular, we require protein interaction modules with known specificity and affinity. Here, we describe three designed TRAP (Tetratricopeptide Repeat Affinity Protein)-peptide interaction pairs that are functional in vivo. We show that each TRAP binds to its cognate peptide and exhibits low cross-reactivity with the peptides bound by the other TRAPs. In addition, we demonstrate that the TRAP-peptide interactions are functional in many cellular contexts. In extensions of these designs, we show that the binding affinity of a TRAP-peptide pair can be systematically varied. The TRAP-peptide pairs we present thus represent a powerful set of new building blocks that are suitable for a variety of applications.

  11. Structural And Mechanistic Analysis of Protein Interactions in Module 3 of the 6-Deoxyerythronolide B Synthase

    SciTech Connect

    Tang, Y.; Chen, A.Y.; Kim, C.-Y.; Cane, D.E.; Khosla, C.

    2009-06-04

    We report the 2.6 A X-ray crystal structure of a 190 kDa homodimeric fragment from module 3 of the 6-deoxyerthronolide B synthase covalently bound to the inhibitor cerulenin. The structure shows two well-organized interdomain linker regions in addition to the full-length ketosynthase (KS) and acyltransferase (AT) domains. Analysis of the substrate-binding site of the KS domain suggests that a loop region at the homodimer interface influences KS substrate specificity. We also describe a model for the interaction of the catalytic domains with the acyl carrier protein (ACP) domain. The ACP is proposed to dock within a deep cleft between the KS and AT domains, with interactions that span both the KS homodimer and AT domain. In conjunction with other recent data, our results provide atomic resolution pictures of several catalytically relevant protein interactions in this remarkable family of modular megasynthases.

  12. Online Interactive Teaching Modules Enhance Quantitative Proficiency of Introductory Biology Students

    PubMed Central

    Nelson, Kären C.; Marbach-Ad, Gili; Keller, Michael; Fagan, William F.

    2010-01-01

    There is widespread agreement within the scientific and education communities that undergraduate biology curricula fall short in providing students with the quantitative and interdisciplinary problem-solving skills they need to obtain a deep understanding of biological phenomena and be prepared fully to contribute to future scientific inquiry. MathBench Biology Modules were designed to address these needs through a series of interactive, Web-based modules that can be used to supplement existing course content across the biological sciences curriculum. The effect of the modules was assessed in an introductory biology course at the University of Maryland. Over the course of the semester, students showed significant increases in quantitative skills that were independent of previous math course work. Students also showed increased comfort with solving quantitative problems, whether or not they ultimately arrived at the correct answer. A survey of spring 2009 graduates indicated that those who had experienced MathBench in their course work had a greater appreciation for the role of mathematics in modern biology than those who had not used MathBench. MathBench modules allow students from diverse educational backgrounds to hone their quantitative skills, preparing them for more complex mathematical approaches in upper-division courses. PMID:20810959

  13. Online interactive teaching modules enhance quantitative proficiency of introductory biology students.

    PubMed

    Thompson, Katerina V; Nelson, Kären C; Marbach-Ad, Gili; Keller, Michael; Fagan, William F

    2010-01-01

    There is widespread agreement within the scientific and education communities that undergraduate biology curricula fall short in providing students with the quantitative and interdisciplinary problem-solving skills they need to obtain a deep understanding of biological phenomena and be prepared fully to contribute to future scientific inquiry. MathBench Biology Modules were designed to address these needs through a series of interactive, Web-based modules that can be used to supplement existing course content across the biological sciences curriculum. The effect of the modules was assessed in an introductory biology course at the University of Maryland. Over the course of the semester, students showed significant increases in quantitative skills that were independent of previous math course work. Students also showed increased comfort with solving quantitative problems, whether or not they ultimately arrived at the correct answer. A survey of spring 2009 graduates indicated that those who had experienced MathBench in their course work had a greater appreciation for the role of mathematics in modern biology than those who had not used MathBench. MathBench modules allow students from diverse educational backgrounds to hone their quantitative skills, preparing them for more complex mathematical approaches in upper-division courses.

  14. Amplitude-modulated stimuli reveal auditory-visual interactions in brain activity and brain connectivity.

    PubMed

    Laing, Mark; Rees, Adrian; Vuong, Quoc C

    2015-01-01

    The temporal congruence between auditory and visual signals coming from the same source can be a powerful means by which the brain integrates information from different senses. To investigate how the brain uses temporal information to integrate auditory and visual information from continuous yet unfamiliar stimuli, we used amplitude-modulated tones and size-modulated shapes with which we could manipulate the temporal congruence between the sensory signals. These signals were independently modulated at a slow or a fast rate. Participants were presented with auditory-only, visual-only, or auditory-visual (AV) trials in the fMRI scanner. On AV trials, the auditory and visual signal could have the same (AV congruent) or different modulation rates (AV incongruent). Using psychophysiological interaction analyses, we found that auditory regions showed increased functional connectivity predominantly with frontal regions for AV incongruent relative to AV congruent stimuli. We further found that superior temporal regions, shown previously to integrate auditory and visual signals, showed increased connectivity with frontal and parietal regions for the same contrast. Our findings provide evidence that both activity in a network of brain regions and their connectivity are important for AV integration, and help to bridge the gap between transient and familiar AV stimuli used in previous studies.

  15. Amplitude-modulated stimuli reveal auditory-visual interactions in brain activity and brain connectivity

    PubMed Central

    Laing, Mark; Rees, Adrian; Vuong, Quoc C.

    2015-01-01

    The temporal congruence between auditory and visual signals coming from the same source can be a powerful means by which the brain integrates information from different senses. To investigate how the brain uses temporal information to integrate auditory and visual information from continuous yet unfamiliar stimuli, we used amplitude-modulated tones and size-modulated shapes with which we could manipulate the temporal congruence between the sensory signals. These signals were independently modulated at a slow or a fast rate. Participants were presented with auditory-only, visual-only, or auditory-visual (AV) trials in the fMRI scanner. On AV trials, the auditory and visual signal could have the same (AV congruent) or different modulation rates (AV incongruent). Using psychophysiological interaction analyses, we found that auditory regions showed increased functional connectivity predominantly with frontal regions for AV incongruent relative to AV congruent stimuli. We further found that superior temporal regions, shown previously to integrate auditory and visual signals, showed increased connectivity with frontal and parietal regions for the same contrast. Our findings provide evidence that both activity in a network of brain regions and their connectivity are important for AV integration, and help to bridge the gap between transient and familiar AV stimuli used in previous studies. PMID:26483710

  16. MicroRNAs Modulate Interactions between Stress and Risk for Cocaine Addiction

    PubMed Central

    Doura, Menahem B.; Unterwald, Ellen M.

    2016-01-01

    Exposure to stress increases vulnerability to drug abuse, as well as relapse liability in addicted individuals. Chronic drug use alters stress response in a manner that increases drug seeking behaviors and relapse. Drug exposure and withdrawal have been shown to alter stress responses, and corticosteroid mediators of stress have been shown to impact addiction-related brain function and drug-seeking behavior. Despite the documented interplay between stress and substance abuse, the mechanisms by which stress exposure and drug seeking interact remain largely unknown. Recent studies indicate that microRNAs (miRNA) play a significant role in stress modulation as well as addiction-related processes including neurogenesis, synapse development, plasticity, drug acquisition, withdrawal and relapse. MiRNAs are short non-coding RNAs that function as bidirectional epigenetic modulators of gene expression through imperfect sequence targeted degradation and/or translational repression of mRNAs. They serve as dynamic regulators of CNS physiology and pathophysiology, and facilitate rapid and long-lasting changes to complex systems and behaviors. MiRNAs function in glucocorticoid signaling and the mesolimbic dopamine reward system, as well as mood disorders related to drug withdrawal. The literature suggests miRNAs play a pivotal role in the interaction between exposures to stress, addiction-related processes, and negative affective states resulting from extended drug withdrawal. This manuscript reviews recent evidence for the role of miRNAs in the modulation of stress and cocaine responses, and discusses potential mediation of the interaction of these systems by miRNAs. Uncovering the mechanism behind the association of stress and drug taking has the potential to impact the treatment of drug abuse and prevention of relapse. Further comprehension of these complex interactions may provide promising new targets for the treatment of drug addiction. PMID:27303265

  17. Interaction of frequency modulated light pulses with rubidium atoms in a magneto-optical trap

    NASA Astrophysics Data System (ADS)

    Bakos, J. S.; Djotyan, G. P.; Ignácz, P. N.; Kedves, M. Á.; Serényi, M.; Sörlei, Zs.; Szigeti, J.; Tóth, Z.

    2006-07-01

    The spatial displacement of the 85Rb atoms in a Magneto-Optical Trap (MOT) under the influence of series of frequency modulated light pulse pairs propagating opposite to each other is measured as a function of the time elapsed after the start of the pulse train, and compared with the results of simulations. Adiabatic excitation and consecutive de-excitation take place between the ground 52S1/2 (F=3) and the 52P3/2 (F'=2, 3, 4) excited levels as the result of the interaction. The displacement of the 85Rb atoms is calculated as the solution of simple equation of motion where the expelling force is that arising from the action of the frequency modulated light pulses. The restoring and friction forces of the MOT are taken into account also. The system of Bloch equations for the density matrix elements is solved numerically for transitions between six working hyperfine levels of the atom interacting with the sequence of the frequency modulated laser pulses. According to these simulations, the momentum transferred by one pulse pair is always smaller than the expected 2ħk, (1) where ħ is the Plank constant and k=2π/λ where λ is the wavelength, (2) having a maximum value in a restricted region of variation of the laser pulse peak intensity and the chirp.

  18. Modulation of 14-3-3/phosphotarget interaction by physiological concentrations of phosphate and glycerophosphates.

    PubMed

    Sluchanko, Nikolai N; Chebotareva, Natalia A; Gusev, Nikolai B

    2013-01-01

    Molecular mechanisms governing selective binding of a huge number of various phosphorylated protein partners to 14-3-3 remain obscure. Phosphate can bind to 14-3-3 and therefore being present at high intracellular concentration, which undergoes significant changes under physiological conditions, phosphate can theoretically regulate interaction of 14-3-3 with phosphorylated targets. In order to check this hypothesis we analyzed effect of phosphate and other natural abundant anions on interaction of 14-3-3 with phosphorylated human small heat shock protein HspB6 (Hsp20) participating in regulation of different intracellular processes. Inorganic phosphate, glycerol-1-phosphate and glycerol-2-phosphate at physiologically relevant concentrations (5-15 mM) significantly destabilized complexes formed by 14-3-3ζ and phosphorylated HspB6 (pHspB6), presumably, via direct interaction with the substrate-binding site of 14-3-3. Phosphate also destabilized complexes between pHspB6 and 14-3-3γ or the monomeric mutant form of 14-3-3ζ. Inorganic sulfate and pyrophosphate were less effective in modulation of 14-3-3 interaction with its target protein. The inhibitory effect of all anions on pHspB6/14-3-3 interaction was concentration-dependent. It is hypothesized that physiological changes in phosphate anions concentration can modulate affinity and specificity of interaction of 14-3-3 with its multiple targets and therefore the actual phosphointeractome of 14-3-3.

  19. Dynamic flux of microvesicles modulate parasite-host cell interaction of Trypanosoma cruzi in eukaryotic cells.

    PubMed

    Ramirez, M I; Deolindo, P; de Messias-Reason, I J; Arigi, Emma A; Choi, H; Almeida, I C; Evans-Osses, I

    2017-04-01

    Extracellular vesicles released from pathogens may alter host cell functions. We previously demonstrated the involvement of host cell-derived microvesicles (MVs) during early interaction between Trypanosoma cruzi metacyclic trypomastigote (META) stage and THP-1 cells. Here, we aim to understand the contribution of different parasite stages and their extracellular vesicles in the interaction with host cells. First, we observed that infective host cell-derived trypomastigote (tissue culture-derived trypomastigote [TCT]), META, and noninfective epimastigote (EPI) stages were able to induce different levels of MV release from THP-1 cells; however, only META and TCT could increase host cell invasion. Fluorescence resonance energy transfer microscopy revealed that THP-1-derived MVs can fuse with parasite-derived MVs. Furthermore, MVs derived from the TCT-THP-1 interaction showed a higher fusogenic capacity than those from META- or EPI-THP-1 interaction. However, a higher presence of proteins from META (25%) than TCT (12%) or EPI (5%) was observed in MVs from parasite-THP-1 interaction, as determined by proteomics. Finally, sera from patients with chronic Chagas disease at the indeterminate or cardiac phase differentially recognized antigens in THP-1-derived MVs resulting only from interaction with infective stages. The understanding of intracellular trafficking and the effect of MVs modulating the immune system may provide important clues about Chagas disease pathophysiology. © 2016 John Wiley & Sons Ltd.

  20. Calmodulin interacts with Rab3D and modulates osteoclastic bone resorption

    PubMed Central

    Zhu, Sipin; Chim, Shek Man; Cheng, Taksum; Ang, Estabelle; Ng, Benjamin; Lim, Baysie; Chen, Kai; Qiu, Heng; Tickner, Jennifer; Xu, Huazi; Pavlos, Nathan; Xu, Jiake

    2016-01-01

    Calmodulin is a highly versatile protein that regulates intracellular calcium homeostasis and is involved in a variety of cellular functions including cardiac excitability, synaptic plasticity and signaling transduction. During osteoclastic bone resorption, calmodulin has been reported to concentrate at the ruffled border membrane of osteoclasts where it is thought to modulate bone resorption activity in response to calcium. Here we report an interaction between calmodulin and Rab3D, a small exocytic GTPase and established regulator osteoclastic bone resorption. Using yeast two-hybrid screening together with a series of protein-protein interaction studies, we show that calmodulin interacts with Rab3D in a calcium dependent manner. Consistently, expression of a calcium insensitive form of calmodulin (i.e. CaM1234) perturbs calmodulin-Rab3D interaction as monitored by bioluminescence resonance energy transfer (BRET) assays. In osteoclasts, calmodulin and Rab3D are constitutively co-expressed during RANKL-induced osteoclast differentiation, co-occupy plasma membrane fractions by differential gradient sedimentation assay and colocalise in the ruffled border as revealed by confocal microscopy. Further, functional blockade of calmodulin-Rab3D interaction by calmidazolium chloride coincides with an attenuation of osteoclastic bone resorption. Our data imply that calmodulin- Rab3D interaction is required for efficient bone resorption by osteoclasts in vitro. PMID:27897225

  1. Enhanced Ferromagnetic Interaction in Modulation-Doped GaMnN Nanorods

    NASA Astrophysics Data System (ADS)

    Lin, Yuan-Ting; Wadekar, Paritosh Vilas; Kao, Hsiang-Shun; Zheng, Yu-Jung; Chen, Quark Yung-Sung; Huang, Hui-Chun; Cheng, Cheng-Maw; Ho, New-Jin; Tu, Li-Wei

    2017-04-01

    In this report, ferromagnetic interactions in modulation-doped GaMnN nanorods grown on Si (111) substrate by plasma-assisted molecular beam epitaxy are investigated with the prospect of achieving a room temperature ferromagnetic semiconductor. Our results indicate the thickness of GaN layer in each GaN/MnN pair, as well as Mn-doping levels, are essential for suppressing secondary phases as well as enhancing the magnetic moment. For these optimized samples, structural analysis by high-resolution X-ray diffractometry and Raman spectroscopy verifies single-crystalline modulation-doped GaMnN nanorods with Ga sites substituted by Mn atoms. Energy dispersive X-ray spectrometry shows that the average Mn concentration can be raised from 0.4 to 1.8% by increasing Mn fluxes without formation of secondary phases resulted in a notable enhancement of the saturation magnetization as well as coercive force in these nanorods.

  2. ACC-FMD: ant colony clustering for functional module detection in protein-protein interaction networks.

    PubMed

    Ji, Junzhong; Liu, Hongxin; Zhang, Aidong; Liu, Zhijun; Liu, Chunnian

    2015-01-01

    Mining functional modules in Protein-Protein Interaction (PPI) networks is a very important research for revealing the structure-functionality relationships in biological processes. More recently, some swarm intelligence algorithms have been successfully applied in the field. This paper presents a new nature-inspired approach, ACC-FMD, which is based on ant colony clustering to detect functional modules. First, some proteins with the higher clustering coefficients are, respectively, selected as ant seed nodes. And then, the picking and dropping operations based on ant probabilistic models are developed and employed to assign proteins into the corresponding clusters represented by seeds. Finally, the best clustering result in each generation is used to perform the information transmission by updating the similarly function. Experimental results on some benchmarked datasets show that ACC-FMD outperforms the CFinder and MCODE algorithms and has comparative performance with the MINE, COACH, DPClus and Core algorithms in terms of the general evaluation metrics.

  3. Spatial attention modulates center-surround interactions in macaque visual area V4

    PubMed Central

    Sundberg, Kristy A.; Mitchell, Jude F.; Reynolds, John H.

    2010-01-01

    Summary In natural viewing a visual stimulus that is the target of attention is generally surrounded by many irrelevant distracters. Stimuli falling in the receptive field surround can influence the neuronal response evoked by a stimulus appearing within the classical receptive field. Such modulation by task-irrelevant distracters may degrade the target-related neuronal signal. We therefore examined whether directing attention to a target stimulus can reduce the influence of task-irrelevant distracters on neuronal response. We find that in area V4 attention to a stimulus within a neuron’s receptive field filters out a large fraction of the suppression induced by distracters appearing in the surround. When attention is instead directed to the surround stimulus suppression is increased, thereby filtering out part of the neuronal response to the irrelevant distracter positioned within the receptive field. These findings demonstrate that attention modulates the neural mechanisms that give rise to center-surround interactions. PMID:19324003

  4. Coulomb-interaction induced coupling of Landau levels in intrinsic and modulation-doped quantum wells

    NASA Astrophysics Data System (ADS)

    Paul, J.; Stevens, C. E.; Zhang, H.; Dey, P.; McGinty, D.; McGill, S. A.; Smith, R. P.; Reno, J. L.; Turkowski, V.; Perakis, I. E.; Hilton, D. J.; Karaiskaj, D.

    2017-06-01

    We have performed two-dimensional Fourier transform spectroscopy on intrinsic and modulation doped quantum wells in external magnetic fields up to 10 T. In the undoped sample, the strong Coulomb interactions and the increasing separations of the electron and hole charge distributions with increasing magnetic fields lead to a nontrivial in-plane dispersion of the magneto-excitons. Thus, the discrete and degenerate Landau levels are coupled to a continuum. The signature of this continuum is the emergence of elongated spectral line shapes at the Landau level energies, which are exposed by the multidimensional nature of our technique. Surprisingly, the elongation of the peaks is completely absent in the lowest Landau level spectra obtained from the modulation doped quantum well at high fields.

  5. Interaction of dengue virus nonstructural protein 5 with Daxx modulates RANTES production

    SciTech Connect

    Khunchai, Sasiprapa; Junking, Mutita; Suttitheptumrong, Aroonroong; Yasamut, Umpa; Sawasdee, Nunghathai; Netsawang, Janjuree; Morchang, Atthapan; Chaowalit, Prapaipit; Noisakran, Sansanee; Yenchitsomanus, Pa-thai; and others

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer For the first time how DENV NS5 increases RANTES production. Black-Right-Pointing-Pointer DENV NS5 physically interacts with human Daxx. Black-Right-Pointing-Pointer Nuclear localization of NS5 is required for Daxx interaction and RANTES production. -- Abstract: Dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS), caused by dengue virus (DENV) infection, are important public health problems in the tropical and subtropical regions. Abnormal hemostasis and plasma leakage are the main patho-physiological changes in DHF/DSS. A remarkably increased production of cytokines, the so called 'cytokine storm', is observed in the patients with DHF/DSS. A complex interaction between DENV proteins and the host immune response contributes to cytokine production. However, the molecular mechanism(s) by which DENV nonstructural protein 5 (NS5) mediates these responses has not been fully elucidated. In the present study, yeast two-hybrid assay was performed to identify host proteins interacting with DENV NS5 and a death-domain-associate protein (Daxx) was identified. The in vivo relevance of this interaction was suggested by co-immunoprecipitation and nuclear co-localization of these two proteins in HEK293 cells expressing DENV NS5. HEK293 cells expressing DENV NS5-K/A, which were mutated at the nuclear localization sequences (NLS), were created to assess its functional roles in nuclear translocation, Daxx interaction, and cytokine production. In the absence of NLS, DENV NS5 could neither translocate into the nucleus nor interact with Daxx to increase the DHF-associated cytokine, RANTES (CCL5) production. This work demonstrates the interaction between DENV NS5 and Daxx and the role of the interaction on the modulation of RANTES production.

  6. Asbestos modulates thioredoxin-thioredoxin interacting protein interaction to regulate inflammasome activation

    PubMed Central

    2014-01-01

    Background Asbestos exposure is related to various diseases including asbestosis and malignant mesothelioma (MM). Among the pathogenic mechanisms proposed by which asbestos can cause diseases involving epithelial and mesothelial cells, the most widely accepted one is the generation of reactive oxygen species and/or depletion of antioxidants like glutathione. It has also been demonstrated that asbestos can induce inflammation, perhaps due to activation of inflammasomes. Methods The oxidation state of thioredoxin was analyzed by redox Western blot analysis and ROS generation was assessed spectrophotometrically as a read-out of solubilized formazan produced by the reduction of nitrotetrazolium blue (NTB) by superoxide. Quantitative real time PCR was used to assess changes in gene transcription. Results Here we demonstrate that crocidolite asbestos fibers oxidize the pool of the antioxidant, Thioredoxin-1 (Trx1), which results in release of Thioredoxin Interacting Protein (TXNIP) and subsequent activation of inflammasomes in human mesothelial cells. Exposure to crocidolite asbestos resulted in the depletion of reduced Trx1 in human peritoneal mesothelial (LP9/hTERT) cells. Pretreatment with the antioxidant dehydroascorbic acid (a reactive oxygen species (ROS) scavenger) reduced the level of crocidolite asbestos-induced Trx1 oxidation as well as the depletion of reduced Trx1. Increasing Trx1 expression levels using a Trx1 over-expression vector, reduced the extent of Trx1 oxidation and generation of ROS by crocidolite asbestos, and increased cell survival. In addition, knockdown of TXNIP expression by siRNA attenuated crocidolite asbestos-induced activation of the inflammasome. Conclusion Our novel findings suggest that extensive Trx1 oxidation and TXNIP dissociation may be one of the mechanisms by which crocidolite asbestos activates the inflammasome and helps in development of MM. PMID:24885895

  7. The B-box module of CYLD is responsible for its intermolecular interaction and cytoplasmic localization.

    PubMed

    Xie, Songbo; Chen, Miao; Gao, Siqi; Zhong, Tao; Zhou, Peng; Li, Dengwen; Zhou, Jun; Gao, Jinmin; Liu, Min

    2017-02-07

    The tumor suppressor protein cylindromatosis (CYLD), as a microtubule-associated deubiquitinase, plays a pivotal role in a wide range of cellular activities, including innate immunity, cell division, and ciliogenesis. Structural characterization reveals a small zinc-binding B-box inserted within the ubiquitin specific protease (USP) domain of CYLD; however, the exact role for this module remains yet to be elucidated. Here we identify a critical role for the B-box in facilitating the intermolecular interaction and subcellular localization of CYLD. By co-immunoprecipitation assays we uncover that CYLD has the ability to form an intermolecular complex. Native gel electrophoresis analysis and pull down assays show that the USP domain of CYLD is essential for its intermolecular interaction. Further investigation reveals that deletion of the B-box from the USP domain disrupts the intermolecular interaction of CYLD. Importantly, although loss of the B-box has no obvious effect on the deubiquitinase activity of CYLD, it abolishes the USP domain-mediated retention of CYLD in the cytoplasm. Collectively, these data demonstrate an important role for the B-box module of CYLD in mediating its assembly and subcellular distribution, which might be related to the functions of CYLD in various biological processes.

  8. Modulation of fibrin matrix properties via knob:hole affinity interactions using peptide-PEG conjugates

    PubMed Central

    Soon, Allyson S.C.; Lee, Christine S.; Barker, Thomas H.

    2011-01-01

    Fibrin is a widely used biological scaffold in tissue engineering and regenerative medicine. While the polymerization dynamics from its soluble precursor fibrinogen has been studied for decades, few attempts have been made to modulate fibrin network structure through the addition of external agents that actively engage this process. We propose the use of polyethylene glycol (PEG)-based linkers that interact with fibrinogen via knob:hole affinity interactions as a means of controlling thrombin-mediated fibrin polymerization dynamics and resulting network structure. Using bivalent and tetravalent knob-PEG conjugates with sizes ranging from 2 to 20 kDa, we demonstrate that the clotting characteristics of fibrinogen solutions can be altered in a dose-dependent manner, with conjugate size playing a major role in altering fibrin network structure. Interestingly, factor XIIIa-catalyzed fibrin(ogen) crosslinking and plasmin-mediated degradation were not significantly impacted. This work demonstrates the feasibility of modulating fibrin network structure through the addition of knob-PEG conjugates that perturb the polymerization process through non-covalent knob:hole interactions. PMID:21435714

  9. Community Structure Detection for Overlapping Modules through Mathematical Programming in Protein Interaction Networks

    PubMed Central

    Bennett, Laura; Kittas, Aristotelis; Liu, Songsong; Papageorgiou, Lazaros G.; Tsoka, Sophia

    2014-01-01

    Community structure detection has proven to be important in revealing the underlying properties of complex networks. The standard problem, where a partition of disjoint communities is sought, has been continually adapted to offer more realistic models of interactions in these systems. Here, a two-step procedure is outlined for exploring the concept of overlapping communities. First, a hard partition is detected by employing existing methodologies. We then propose a novel mixed integer non linear programming (MINLP) model, known as OverMod, which transforms disjoint communities to overlapping. The procedure is evaluated through its application to protein-protein interaction (PPI) networks of the rat, E. coli, yeast and human organisms. Connector nodes of hard partitions exhibit topological and functional properties indicative of their suitability as candidates for multiple module membership. OverMod identifies two types of connector nodes, inter and intra-connector, each with their own particular characteristics pertaining to their topological and functional role in the organisation of the network. Inter-connector proteins are shown to be highly conserved proteins participating in pathways that control essential cellular processes, such as proliferation, differentiation and apoptosis and their differences with intra-connectors is highlighted. Many of these proteins are shown to possess multiple roles of distinct nature through their participation in different network modules, setting them apart from proteins that are simply ‘hubs’, i.e. proteins with many interaction partners but with a more specific biochemical role. PMID:25412367

  10. GABAergic modulation of human social interaction in a prisoner's dilemma model by acute administration of alprazolam.

    PubMed

    Lane, Scott D; Gowin, Joshua L

    2009-10-01

    Recent work in neuroeconomics has used game theory paradigms to examine neural systems that subserve human social interaction and decision making. Attempts to modify social interaction through pharmacological manipulation have been less common. Here we show dose-dependent modification of human social behavior in a prisoner's dilemma model after acute administration of the γ-aminobutyric acid (GABA)-A modulating benzodiazepine alprazolam. Nine healthy adults received doses of placebo, 0.5, 1.0, and 2.0 mg alprazolam in a counterbalanced within-subject design, while completing multiple test blocks per day on an iterated prisoner's dilemma game. During test blocks in which peak subjective effects of alprazolam were reported, cooperative choices were significantly decreased as a function of dose. Consistent with previous reports showing that high acute doses of GABA-modulating drugs are associated with violence and other antisocial behavior, our data suggest that at sufficiently high doses, alprazolam can decrease cooperation. These behavioral changes may be facilitated by changes in inhibitory control facilitated by GABA. Game theory paradigms may prove useful in behavioral pharmacology studies seeking to measure social interaction, and may help inform the emerging field of neuroeconomics.

  11. Community structure detection for overlapping modules through mathematical programming in protein interaction networks.

    PubMed

    Bennett, Laura; Kittas, Aristotelis; Liu, Songsong; Papageorgiou, Lazaros G; Tsoka, Sophia

    2014-01-01

    Community structure detection has proven to be important in revealing the underlying properties of complex networks. The standard problem, where a partition of disjoint communities is sought, has been continually adapted to offer more realistic models of interactions in these systems. Here, a two-step procedure is outlined for exploring the concept of overlapping communities. First, a hard partition is detected by employing existing methodologies. We then propose a novel mixed integer non linear programming (MINLP) model, known as OverMod, which transforms disjoint communities to overlapping. The procedure is evaluated through its application to protein-protein interaction (PPI) networks of the rat, E. coli, yeast and human organisms. Connector nodes of hard partitions exhibit topological and functional properties indicative of their suitability as candidates for multiple module membership. OverMod identifies two types of connector nodes, inter and intra-connector, each with their own particular characteristics pertaining to their topological and functional role in the organisation of the network. Inter-connector proteins are shown to be highly conserved proteins participating in pathways that control essential cellular processes, such as proliferation, differentiation and apoptosis and their differences with intra-connectors is highlighted. Many of these proteins are shown to possess multiple roles of distinct nature through their participation in different network modules, setting them apart from proteins that are simply 'hubs', i.e. proteins with many interaction partners but with a more specific biochemical role.

  12. Inferring modules of functionally interacting proteins using the Bond Energy Algorithm

    PubMed Central

    Watanabe, Ryosuke LA; Morett, Enrique; Vallejo, Edgar E

    2008-01-01

    Background Non-homology based methods such as phylogenetic profiles are effective for predicting functional relationships between proteins with no considerable sequence or structure similarity. Those methods rely heavily on traditional similarity metrics defined on pairs of phylogenetic patterns. Proteins do not exclusively interact in pairs as the final biological function of a protein in the cellular context is often hold by a group of proteins. In order to accurately infer modules of functionally interacting proteins, the consideration of not only direct but also indirect relationships is required. In this paper, we used the Bond Energy Algorithm (BEA) to predict functionally related groups of proteins. With BEA we create clusters of phylogenetic profiles based on the associations of the surrounding elements of the analyzed data using a metric that considers linked relationships among elements in the data set. Results Using phylogenetic profiles obtained from the Cluster of Orthologous Groups of Proteins (COG) database, we conducted a series of clustering experiments using BEA to predict (upper level) relationships between profiles. We evaluated our results by comparing with COG's functional categories, And even more, with the experimentally determined functional relationships between proteins provided by the DIP and ECOCYC databases. Our results demonstrate that BEA is capable of predicting meaningful modules of functionally related proteins. BEA outperforms traditionally used clustering methods, such as k-means and hierarchical clustering by predicting functional relationships between proteins with higher accuracy. Conclusion This study shows that the linked relationships of phylogenetic profiles obtained by BEA is useful for detecting functional associations between profiles and extending functional modules not found by traditional methods. BEA is capable of detecting relationship among phylogenetic patterns by linking them through a common element shared in

  13. Modulation of the Interaction of Enteric Bacteria with Intestinal Mucosa by Stress-Related Catecholamines.

    PubMed

    Stevens, Mark P

    2016-01-01

    Stress associated with parturition, transport or mixing has long been correlated with enhanced faecal excretion of diarrhoeal zoonotic pathogens in animals such as Salmonella enterica and Escherichia coli. It may also predispose humans to infection and/or be associated with more severe outcomes. One possible explanation for this phenomenon is the ability of enteric bacterial pathogens to sense and respond to host stress-related catecholamines. This article reviews evidence of the ability of catecholamine hormones to modulate interactions between Gram-negative diarrhoeal pathogens and intestinal mucosa, as well as the molecular mechanisms that may be at work.

  14. Photocontrolled Exposure of Pro‐apoptotic Peptide Sequences in LOV Proteins Modulates Bcl‐2 Family Interactions

    PubMed Central

    Mart, Robert J.; Meah, Dilruba

    2015-01-01

    Abstract LOV domains act as biomolecular sensors for light, oxygen or the environment's redox potential. Conformational changes upon the formation of a covalent cysteinyl flavin adduct are propagated through hydrogen‐bonding networks in the core of designed hybrid phototropin LOV2 domains that incorporate the Bcl homology region 3 (BH3) of the key pro‐apoptotic protein BH3‐interacting‐domain death agonist (BID). The resulting change in conformation of a flanking amphiphilic α‐helix creates a light‐dependent optogenetic tool for the modulation of interactions with the anti‐apoptotic B‐cell leukaemia‐2 (Bcl‐2) family member Bcl‐xL. PMID:26493687

  15. Ligand-specific interactions modulate kinetic, energetic and mechanical properties of the human β2 adrenergic receptor

    PubMed Central

    Zocher, Michael; Fung, Juan J; Kobilka, Brian K; Müller, Daniel J

    2015-01-01

    SUMMARY G-protein-coupled receptors (GPCRs) are a class of versatile proteins that transduce signals across membranes. Extracellular stimuli induce inter- and intramolecular interactions that change the functional state of GPCRs and activate intracellular messenger molecules. How these interactions are established and how they modulate the functional state of GPCRs remains to be understood. We used dynamic single-molecule force spectroscopy to investigate how ligand-binding modulates the energy landscape of the human β2 adrenergic receptor (β2AR). Five different ligands representing either agonists, inverse agonists or neutral antagonists established a complex network of interactions that tuned the kinetic, energetic and mechanical properties of functionally important structural regions of β2AR. These interactions were specific to the efficacy profile of the ligands investigated and suggest that the functional modulation of GPCRs follows structurally well-defined interaction patterns. PMID:22748765

  16. BinTree seeking: a novel approach to mine both bi-sparse and cohesive modules in protein interaction networks.

    PubMed

    Jiao, Qing-Ju; Zhang, Yan-Kai; Li, Lu-Ning; Shen, Hong-Bin

    2011-01-01

    Modern science of networks has brought significant advances to our understanding of complex systems biology. As a representative model of systems biology, Protein Interaction Networks (PINs) are characterized by a remarkable modular structures, reflecting functional associations between their components. Many methods were proposed to capture cohesive modules so that there is a higher density of edges within modules than those across them. Recent studies reveal that cohesively interacting modules of proteins is not a universal organizing principle in PINs, which has opened up new avenues for revisiting functional modules in PINs. In this paper, functional clusters in PINs are found to be able to form unorthodox structures defined as bi-sparse module. In contrast to the traditional cohesive module, the nodes in the bi-sparse module are sparsely connected internally and densely connected with other bi-sparse or cohesive modules. We present a novel protocol called the BinTree Seeking (BTS) for mining both bi-sparse and cohesive modules in PINs based on Edge Density of Module (EDM) and matrix theory. BTS detects modules by depicting links and nodes rather than nodes alone and its derivation procedure is totally performed on adjacency matrix of networks. The number of modules in a PIN can be automatically determined in the proposed BTS approach. BTS is tested on three real PINs and the results demonstrate that functional modules in PINs are not dominantly cohesive but can be sparse. BTS software and the supporting information are available at: www.csbio.sjtu.edu.cn/bioinf/BTS/.

  17. A wrench-shaped synthetic molecule that modulates a transcription factor-coactivator interaction.

    PubMed

    Shimogawa, Hiroki; Kwon, Youngjoo; Mao, Qian; Kawazoe, Yoshinori; Choi, Yongmun; Asada, Shinichi; Kigoshi, Hideo; Uesugi, Motonari

    2004-03-24

    Development of synthetic molecules that provide external control over the transcription of a given gene represents a challenge in medicinal and bioorganic chemistry. Here we report design and analysis of wrenchnolol, a wrench-shaped synthetic molecule that impairs the transcription of the Her2 oncogene by disrupting association of transcription factor ESX with its coactivator Sur-2. The "jaw" part of the compound mimics the alpha-helical interface of the activation domain of ESX, and the "handle" region accepts chemical modifications for a range of analysis. A water-soluble handle permitted NMR study in aqueous solution; a biotinylated handle verified the selectivity of the interaction, and a fluorescent handle confirmed the cell permeability of the compound. The case study of wrenchnolol foreshadows the promise and the challenge of targeting protein-protein interactions in the nucleus and may lead to the development of unique synthetic modulators of gene transcription.

  18. Probing interactions between Rydberg atoms with large electric dipole moments in amplitude-modulated electric fields

    NASA Astrophysics Data System (ADS)

    Zhelyazkova, V.; Hogan, S. D.

    2015-07-01

    Dipole-dipole interactions between helium atoms in Rydberg-Stark states with principal quantum number n =53 and approximately linear Stark energy shifts, resulting from induced electric dipole moments of approximately 7900 D, have been investigated experimentally. The experiments were performed in pulsed supersonic metastable helium beams, with particle number densities of up to ˜109cm-3 . In the presence of amplitude-modulated, radio-frequency electric fields, changes in the spectral intensity distributions associated with the transitions to these states that are attributed to dipole-dipole interactions within the ensembles of excited atoms have been observed. The experimental results are in excellent agreement with calculations of the Rydberg energy level structure carried out using Floquet methods, and excitations shared by up to four atoms. The use of these Rydberg-Stark states as sensors for nonresonant broadband radio-frequency electrical noise is also discussed.

  19. Use of live interactive webcasting for an international postgraduate module in ehealth: case study evaluation.

    PubMed

    Jones, Ray B; Maramba, Inocencio; Boulos, Maged N Kamel; Alexander, Tara

    2009-11-13

    Producing "traditional" e-learning can be time consuming, and in a topic such as eHealth, it may have a short shelf-life. Students sometimes report feeling isolated and lacking in motivation. Synchronous methods can play an important part in any blended approach to learning. The aim was to develop, deliver, and evaluate an international postgraduate module in eHealth using live interactive webcasting. We developed a hybrid solution for live interactive webcasting using a scan converter, mixer, and digitizer, and video server to embed a presenter-controlled talking head or copy of the presenter's computer screen (normally a PowerPoint slide) in a student chat room. We recruited 16 students from six countries and ran weekly 2.5-hour live sessions for 10 weeks. The content included the use of computers by patients, patient access to records, different forms of e-learning for patients and professionals, research methods in eHealth, geographic information systems, and telehealth. All sessions were recorded-presentations as video files and the student interaction as text files. Students were sent an email questionnaire of mostly open questions seeking their views of this form of learning. Responses were collated and anonymized by a colleague who was not part of the teaching team. Sessions were generally very interactive, with most students participating actively in breakout or full-class discussions. In a typical 2.5-hour session, students posted about 50 messages each. Two students did not complete all sessions; one withdrew from the pressure of work after session 6, and one from illness after session 7. Fourteen of the 16 responded to the feedback questionnaire. Most students (12/14) found the module useful or very useful, and all would recommend the module to others. All liked the method of delivery, in particular the interactivity, the variety of students, and the "closeness" of the group. Most (11/14) felt "connected" with the other students on the course. Many

  20. Small-molecule modulators of 14-3-3 protein-protein interactions.

    PubMed

    Ottmann, Christian

    2013-07-15

    14-3-3 Proteins are eukaryotic adapter proteins that regulate a plethora of physiological processes by binding to several hundred partner proteins. They play a role in biological activities as diverse as signal transduction, cell cycle regulation, apoptosis, host-pathogen interactions and metabolic control. As such, 14-3-3s are implicated in disease areas like cancer, neurodegeneration, diabetes, pulmonary disease, and obesity. Targeted modulation of 14-3-3 protein-protein interactions (PPIs) by small molecules is therefore an attractive concept for disease intervention. In recent years a number of examples of inhibitors and stabilizers of 14-3-3 PPIs have been reported promising a vivid future in chemical biology and drug development for this remarkable class of proteins. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. Interactions between Starch, Lipids, and Proteins in Foods: Microstructure Control for Glycemic Response Modulation.

    PubMed

    Parada, Javier; Santos, Jose L

    2016-10-25

    In real food, starch is usually forming part of a matrix with lipids and proteins. However, research on this ternary system and interactions between such food components has been scarce so far. The control of food microstructure is crucial to determine the product properties, including sensorial and nutritionals ones. This paper reviews the microstructural principles of interactions between starch, lipids, and proteins in foods as well as their effect on postprandial glycemic response, considering human intrinsic differences on postprandial glycemic responses. Several lines of research support the hypothesis that foods without rapidly digestible starch will not mandatorily generate the lowest postprandial glycemic response, highlighting that the full understanding of food microstructure, which modulates starch digestion, plays a key role on food design from a nutritional viewpoint.

  2. Mesenchymal stem cell interactions with 3D ECM modules fabricated via multiphoton excited photochemistry.

    PubMed

    Su, Ping-Jung; Tran, Quyen A; Fong, Jimmy J; Eliceiri, Kevin W; Ogle, Brenda M; Campagnola, Paul J

    2012-09-10

    To understand complex micro/nanoscale ECM stem cell interactions, reproducible in vitro models are needed that can strictly recapitulate the relative content and spatial arrangement of native tissue. Additionally, whole ECM proteins are required to most accurately reflect native binding dynamics. To address this need, we use multiphoton excited photochemistry to create 3D whole protein constructs or "modules" to study how the ECM governs stem cell migration. The constructs were created from mixtures of BSA/laminin (LN) and BSA alone, whose comparison afforded studying how the migration dynamics are governed from the combination of morphological and ECM cues. We found that mesenchymal stem cells interacted for significantly longer durations with the BSA/LN constructs than pure BSA, pointing to the importance of binding cues of the LN. Critical to this work was the development of an automated system with feedback based on fluorescence imaging to provide quality control when synthesizing multiple identical constructs.

  3. IGF2BP3 modulates the interaction of invasion-associated transcripts with RISC

    PubMed Central

    Ennajdaoui, Hanane; Howard, Jonathan M.; Sterne-Weiler, Timothy; Jahanbani, Fereshteh; Coyne, Doyle J.; Uren, Philip J.; Dargyte, Marija; Katzman, Sol; Draper, Jolene M.; Wallace, Andrew; Cazarez, Oscar; Burns, Suzanne C.; Qiao, Mei; Hinck, Lindsay; Smith, Andrew D.; Toloue, Masoud M.; Blencowe, Benjamin J.; Penalva, Luiz O.F.; Sanford, Jeremy R.

    2016-01-01

    Summary Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) expression correlates with malignancy. But its role(s) in pathogenesis remain enigmatic. Here, we interrogated the IGF2BP3-RNA interaction network in pancreatic ductal adenocarcinoma (PDAC) cells. Using a combination of genome-wide approaches we identify 164 direct mRNA targets of IGF2BP3. These transcripts encode proteins enriched for functions such as cell migration, proliferation and adhesion. Loss of IGF2BP3 reduced PDAC cell invasiveness and remodeled focal adhesion junctions. Individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) revealed significant overlap of IGF2BP3 and miRNA binding sites. IGF2BP3 promotes association of the RNA induced silencing complex (RISC) with specific transcripts. Our results show that IGF2BP3 influences a malignancy-associated RNA regulon by modulating miRNA-mRNA interactions. PMID:27210763

  4. Interactions between target location and reward size modulate the rate of microsaccades in monkeys.

    PubMed

    Joshua, Mati; Tokiyama, Stefanie; Lisberger, Stephen G

    2015-11-01

    We have studied how rewards modulate the occurrence of microsaccades by manipulating the size of an expected reward and the location of the cue that sets the expectations for future reward. We found an interaction between the size of the reward and the location of the cue. When monkeys fixated on a cue that signaled the size of future reward, the frequency of microsaccades was higher if the monkey expected a large vs. a small reward. When the cue was presented at a site in the visual field that was remote from the position of fixation, reward size had the opposite effect: the frequency of microsaccades was lower when the monkey was expecting a large reward. The strength of pursuit initiation also was affected by reward size and by the presence of microsaccades just before the onset of target motion. The gain of pursuit initiation increased with reward size and decreased when microsaccades occurred just before or after the onset of target motion. The effect of the reward size on pursuit initiation was much larger than any indirect effects reward might cause through modulation of the rate of microsaccades. We found only a weak relationship between microsaccade direction and the location of the exogenous cue relative to fixation position, even in experiments where the location of the cue indicated the direction of target motion. Our results indicate that the expectation of reward is a powerful modulator of the occurrence of microsaccades, perhaps through attentional mechanisms. Copyright © 2015 the American Physiological Society.

  5. The interaction between the oxytocin and pain modulation in headache patients.

    PubMed

    Wang, Yong-Liang; Yuan, Yan; Yang, Jun; Wang, Chang-Hong; Pan, Yan-Juan; Lu, Lu; Wu, Yu-Quan; Wang, Da-Xin; Lv, Lu-Xian; Li, Ren-Ren; Xue, Lei; Wang, Xin-Hua; Bi, Jian-Wei; Liu, Xin-Feng; Qian, Yan-Ning; Deng, Zhi-Kuan; Zhang, Zhi-Jian; Zhai, Xin-Huan; Zhou, Xin-Jian; Wang, Guo-Liang; Zhai, Jian-Xin; Liu, Wen-Yan

    2013-04-01

    Oxytocin (OXT), a nonapeptide hormone of posterior pituitary, reaches the central nervous system from systemic blood circulation with a difficulty because of the blood-brain barrier (BBB). The interest has been expressed in the use of the nasal route for delivery of OXT to the brain directly, exploiting the olfactory pathway. Our previous study has demonstrated that OXT in the central nervous system rather than the blood circulation plays an important role in rat pain modulation. The communication tried to investigate the interaction between the OXT and pain modulation in Chinese patients with headache to understand the OXT effect on human pain modulation. The results showed that (1) intranasal OXT could relieve the human headache in a dose-dependent manner; (2) OXT concentration in both plasma and cerebrospinal fluid (CSF) increased significantly in headache patients in relation with the pain level; and (3) there was a positive relationship between plasma and CSF OXT concentration in headache patients. The data suggested that intranasal OXT, which was delivered to the central nervous system through olfactory region, could treat human headache and OXT might be a potential drug of headache relief by intranasal administration.

  6. Magnetic properties of cylindrical diameter modulated Ni80Fe20 nanowires: interaction and coercive fields.

    PubMed

    Salem, Mohamed Shaker; Sergelius, Philip; Corona, Rosa M; Escrig, Juan; Görlitz, Detlef; Nielsch, Kornelius

    2013-05-07

    Magnetic properties of cylindrical Ni80Fe20 nanowires with modulated diameters are investigated theoretically as a function of their geometrical parameters and compared with those produced inside the pores of anodic alumina membranes by pulsed electrodeposition. We observe that the Ni80Fe20 nanowires with modulated diameters reverse their magnetization via the nucleation and propagation of a vortex domain wall. The system begins generating vortex domains in the nanowire ends and in the transition region between the two segments to minimize magnetostatic energy generated by surfaces perpendicular to the initial magnetization of the sample. Besides, we observed an increase of the coercivity for the sample with equal volumes in relation to the sample with equal lengths. Finally, the interaction field is stronger in the case of constant volume segments. These structures could be used to control the motions of magnetic domain walls. In this way, these nanowires with modulated diameters can be an alternative to store information or even perform logic functions.

  7. Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules

    PubMed Central

    Ishikawa, Junya; Matsumura, Shigeyoshi; Jaeger, Luc; Inoue, Tan; Furuta, Hiroyuki; Ikawa, Yoshiya

    2010-01-01

    The DSL ribozyme is a class of artificial ligase ribozymes with a highly modular architecture, which catalyzes template-directed RNA ligation on a helical substrate module that can be either covalently connected (cis-DSL) or physically separated (trans-DSL) from the catalytic module. Substrate recognition by the catalytic module is promoted by one or two sets of GNRA/receptor interactions acting as clamps in the cis or trans configurations, respectively. In this study, we have rationally designed and analyzed the catalytic and self-assembly properties of several trans-DSL ribozymes with different sets of natural and artificial GNRA-receptor clamps. Two variants newly designed in this study showed significantly enhanced catalytic properties with respect of the original trans-DSL construct. While this work allows dissection of the turnover and catalytic properties of the trans-DSL ribozyme, it also emphasizes the remarkable modularity of RNA tertiary structure for nano-construction of complex functions. PMID:19728985

  8. Interactive coding of visual spatial frequency and auditory amplitude-modulation rate.

    PubMed

    Guzman-Martinez, Emmanuel; Ortega, Laura; Grabowecky, Marcia; Mossbridge, Julia; Suzuki, Satoru

    2012-03-06

    Spatial frequency is a fundamental visual feature coded in primary visual cortex, relevant for perceiving textures, objects, hierarchical structures, and scenes, as well as for directing attention and eye movements. Temporal amplitude-modulation (AM) rate is a fundamental auditory feature coded in primary auditory cortex, relevant for perceiving auditory objects, scenes, and speech. Spatial frequency and temporal AM rate are thus fundamental building blocks of visual and auditory perception. Recent results suggest that crossmodal interactions are commonplace across the primary sensory cortices and that some of the underlying neural associations develop through consistent multisensory experience such as audio-visually perceiving speech, gender, and objects. We demonstrate that people consistently and absolutely (rather than relatively) match specific auditory AM rates to specific visual spatial frequencies. We further demonstrate that this crossmodal mapping allows amplitude-modulated sounds to guide attention to and modulate awareness of specific visual spatial frequencies. Additional results show that the crossmodal association is approximately linear, based on physical spatial frequency, and generalizes to tactile pulses, suggesting that the association develops through multisensory experience during manual exploration of surfaces. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Sensing small molecule interactions with lipid membranes by local pH modulation.

    PubMed

    Huang, Da; Zhao, Tao; Xu, Wei; Yang, Tinglu; Cremer, Paul S

    2013-11-05

    Herein, we utilized a label-free sensing platform based on pH modulation to detect the interactions between tetracaine, a positively charged small molecule used as a local anesthetic, and planar supported lipid bilayers (SLBs). The SLBs were patterned inside a flow cell, allowing for various concentrations of tetracaine to be introduced over the surface in a buffer solution. Studies with membranes containing POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) yielded an equilibrium dissociation constant value of Kd = 180 ± 47 μm for this small molecule-membrane interaction. Adding cholesterol to the SLBs decreased the affinity between tetracaine and the bilayers, while this interaction tightened when POPE (1-hexadecanoyl-2-(9-Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine) was added. Studies were also conducted with three negatively charged membrane lipids, POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt)), POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (sodium salt)), and ganglioside GM1. All three measurements gave rise to a similar tightening of the apparent Kd value compared with pure POPC membranes. The lack of chemical specificity with the identity of the negatively charged lipid indicated that the tightening was largely electrostatic. Through a direct comparison with ITC measurements, it was found that the pH modulation sensor platform offers a facile, inexpensive, highly sensitive, and rapid method for the detection of interactions between putative drug candidates and lipid bilayers. As such, this technique may potentially be exploited as a screen for drug development and analysis.

  10. Epistatic interactions between loci of one-carbon metabolism modulate susceptibility to breast cancer.

    PubMed

    Naushad, Shaik Mohammad; Pavani, Addepalli; Digumarti, Raghunadha Rao; Gottumukkala, Suryanarayana Raju; Kutala, Vijay Kumar

    2011-11-01

    In view of growing body of evidence substantiating the role of aberrations in one-carbon metabolism in the pathophysiology of breast cancer and lack of studies on gene-gene interactions, we investigated the role of dietary micronutrients and eight functional polymorphisms of one-carbon metabolism in modulating the breast cancer risk in 244 case-control pairs of Indian women and explored possible gene-gene interactions using Multifactor dimensionality reduction analysis (MDR). Dietary micronutrient status was assessed using the validated Food Frequency Questionnaire. Genotyping was done for glutamate carboxypeptidase II (GCPII) C1561T, reduced folate carrier (RFC)1 G80A, cytosolic serine hydroxymethyltransferase (cSHMT) C1420T, thymidylate synthase (TYMS) 5'-UTR tandem repeat, TYMS 3'-UTR ins6/del6, methylenetetrahydrofolate reductase (MTHFR) C677T, methyltetrahydrofolate-homocysteine methyltransferase (MTR) A2756G, methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR) A66G polymorphisms by using the PCR-RFLP/AFLP methods. Low dietary folate intake (P < 0.001), RFC1 G80A (OR: 1.38, 95% CI 1.06-1.81) and MTHFR C677T (OR: 1.74 (1.11-2.73) were independently associated with the breast cancer risk whereas cSHMT C1420T conferred protection (OR: 0.72, 95% CI 0.55-0.94). MDR analysis demonstrated a significant tri-variate interaction among RFC1 80, MTHFR 677 and TYMS 5'-UTR loci (P (trend) < 0.02) with high-risk genotype combination showing inflated risk for breast cancer (OR 4.65, 95% CI 1.77-12.24). To conclude, dietary as well as genetic factors were found to influence susceptibility to breast cancer. Further, the current study highlighted the importance of multi-loci analyses over the single-locus analysis towards establishing the epistatic interactions between loci of one-carbon metabolism modulate susceptibility to the breast cancer.

  11. Investigating the spatial and temporal modulation of visuotactile interactions in older adults.

    PubMed

    Couth, Samuel; Gowen, Emma; Poliakoff, Ellen

    2016-05-01

    Previous research has shown that spatially and temporally disparate multisensory events are more likely to interact for older adults. For visuotactile interactions, this suggests that the representation of peripersonal space is expanded and temporal perception within this space is less precise. Previously, visuotactile space has been found to expand horizontally into the opposite hemispace, and here we sought to replicate and extend this by exploring both horizontal and vertical space from the hand. Moreover, we investigated whether both spatial and temporal domains are affected for an individual, which have previously been measured using distinct tasks and different participants. We presented a modified cross-modal congruency task (Poole et al. in Multisens Res. doi: 10.1163/22134808-00002475 , 2015a) to thirty older participants (age range 65-85 years), with unisensory tactile performance equated for each individual. For the temporal manipulation, the timings of visual distractors and tactile targets were offset. For the spatial manipulation, visual distractors were presented from multiple positions in ipsilateral and contralateral hemispaces. Whilst the temporal modulation of visuotactile interactions for older adults was equivalent to that observed in young adults, spatial modulation was reduced; significant visuotactile interactions were observed for visual distractors presented in the same and opposite hemispace to the stimulated hand, in the lower visual field. This suggests an expanded representation of visuotactile space surrounding the hand in older adults, which occurs horizontally into the contralateral hemispace only, rather than expanding both vertically and horizontally. This is likely to have consequences for perception of space and goal-directed action in ageing.

  12. An interaction between a neuropeptide Y gene polymorphism and early adversity modulates endocrine stress responses.

    PubMed

    Witt, Stephanie H; Buchmann, Arlette F; Blomeyer, Dorothea; Nieratschker, Vanessa; Treutlein, Jens; Esser, Günter; Schmidt, Martin H; Bidlingmaier, Martin; Wiedemann, Klaus; Rietschel, Marcella; Laucht, Manfred; Wüst, Stefan; Zimmermann, Ulrich S

    2011-08-01

    Interindividual variability in the regulation of the human stress system accounts for a part of the individual's liability to stress-related diseases. These differences are influenced by environmental and genetic factors. Early childhood adversity is a well-studied environmental factor affecting an individual's stress response which has been shown to be modulated by gene-environment interaction (GxE). Neuropeptide Y (NPY) plays a role in stress regulation and genetic variation in NPY may influence stress responses. In this study, we analyzed the association of a common variant in the NPY gene promoter, rs16147, with cortisol and ACTH responses to acute psychosocial stress in young adults from the Mannheim Study of Children at Risk (MARS), an ongoing epidemiological cohort study following the outcome of early adversity from birth into adulthood. We found evidence of a GxE interaction between rs16147 and early adversity significantly affecting HPA axis responses to acute psychosocial stress. These findings suggest that the neurobiological mechanisms linking early adverse experience and later neuroendocrine stress regulation are modulated by a gene variant whose functional relevance is documented by increasing convergent evidence from in vitro, animal and human studies.

  13. Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

    PubMed Central

    Diez, Diego; Hutchins, Andrew Paul; Miranda-Saavedra, Diego

    2014-01-01

    Transcription factors (TFs) combine with co-factors to form transcriptional regulatory modules (TRMs) that regulate gene expression programs with spatiotemporal specificity. Here we present a novel and generic method (rTRM) for the reconstruction of TRMs that integrates genomic information from TF binding, cell type-specific gene expression and protein–protein interactions. rTRM was applied to reconstruct the TRMs specific for embryonic stem cells (ESC) and hematopoietic stem cells (HSC), neural progenitor cells, trophoblast stem cells and distinct types of terminally differentiated CD4+ T cells. The ESC and HSC TRM predictions were highly precise, yielding 77 and 96 proteins, of which ∼75% have been independently shown to be involved in the regulation of these cell types. Furthermore, rTRM successfully identified a large number of bridging proteins with known roles in ESCs and HSCs, which could not have been identified using genomic approaches alone, as they lack the ability to bind specific DNA sequences. This highlights the advantage of rTRM over other methods that ignore PPI information, as proteins need to interact with other proteins to form complexes and perform specific functions. The prediction and experimental validation of the co-factors that endow master regulatory TFs with the capacity to select specific genomic sites, modulate the local epigenetic profile and integrate multiple signals will provide important mechanistic insights not only into how such TFs operate, but also into abnormal transcriptional states leading to disease. PMID:24137002

  14. Extracellular protonation modulates cell-cell interaction mechanics and tissue invasion in human melanoma cells.

    PubMed

    Hofschröer, Verena; Koch, Kevin Alexander; Ludwig, Florian Timo; Friedl, Peter; Oberleithner, Hans; Stock, Christian; Schwab, Albrecht

    2017-02-13

    Detachment of cells from the primary tumour precedes metastatic progression by facilitating cell release into the tissue. Solid tumours exhibit altered pH homeostasis with extracellular acidification. In human melanoma, the Na(+)/H(+) exchanger NHE1 is an important modifier of the tumour nanoenvironment. Here we tested the modulation of cell-cell-adhesion by extracellular pH and NHE1. MV3 tumour spheroids embedded in a collagen matrix unravelled the efficacy of cell-cell contact loosening and 3D emigration into an environment mimicking physiological confinement. Adhesive interaction strength between individual MV3 cells was quantified using atomic force microscopy and validated by multicellular aggregation assays. Extracellular acidification from pHe7.4 to 6.4 decreases cell migration and invasion but increases single cell detachment from the spheroids. Acidification and NHE1 overexpression both reduce cell-cell adhesion strength, indicated by reduced maximum pulling forces and adhesion energies. Multicellular aggregation and spheroid formation are strongly impaired under acidification or NHE1 overexpression. We show a clear dependence of melanoma cell-cell adhesion on pHe and NHE1 as a modulator. These effects are opposite to cell-matrix interactions that are strengthened by protons extruded via NHE1. We conclude that these opposite effects of NHE1 act synergistically during the metastatic cascade.

  15. Geometry and magnetic interaction modulations in dinuclear Dy2 single-molecule magnets.

    PubMed

    Guo, Mei; Xu, Yonghui; Wu, Jianfeng; Zhao, Lang; Tang, Jinkui

    2017-06-27

    Geometry and magnetic interaction modulations in a series of dinuclear dysprosium compounds, [Dy2Lz2(OAc)6]·2CH3OH (1), [Dy2Lz2(C6H5CO2)6]·2CH3CN (2), and [Dy2L2(SO3CF3)4THF4] (3) (Lz = 6-pyridin-2-yl-[1,3,5]triazine-2,4-diamine; L = N-(2,3-dimethylbut-3-en-2-yl)-N-hydroxynitrous amide; THF = tetrahydrofuran), can effectively tune the relaxation dynamics of magnetization. The dysprosium centres of compounds 2 and 3 display a hula hoop-like geometry; however, those in 1 show the monocapped square antiprismatic geometries. Moreover, the Dy2 cores of compounds 1 and 3 were linked by μ2-η(1):η(1) and μ2-η(1):η(2) bridging modes, thus generating shorter intramolecular DyDy distances as compared to those in compound 2. Consequently, these three compounds demonstrate distinct magnetic properties. Compounds 1 and 2 behave as single-molecule magnets (SMMs) under an appropriate static dc field; in addition, 2 displays field-induced multiple relaxation processes under a 1000 Oe dc field. Compound 3 shows a high relaxation energy barrier of 102 K in the zero dc field. These three interesting compounds with Dy2 cores shed light on the coordination geometry and magnetic interactions for the modulation of the properties of SMMs.

  16. Extracellular protonation modulates cell-cell interaction mechanics and tissue invasion in human melanoma cells

    PubMed Central

    Hofschröer, Verena; Koch, Kevin Alexander; Ludwig, Florian Timo; Friedl, Peter; Oberleithner, Hans; Stock, Christian; Schwab, Albrecht

    2017-01-01

    Detachment of cells from the primary tumour precedes metastatic progression by facilitating cell release into the tissue. Solid tumours exhibit altered pH homeostasis with extracellular acidification. In human melanoma, the Na+/H+ exchanger NHE1 is an important modifier of the tumour nanoenvironment. Here we tested the modulation of cell-cell-adhesion by extracellular pH and NHE1. MV3 tumour spheroids embedded in a collagen matrix unravelled the efficacy of cell-cell contact loosening and 3D emigration into an environment mimicking physiological confinement. Adhesive interaction strength between individual MV3 cells was quantified using atomic force microscopy and validated by multicellular aggregation assays. Extracellular acidification from pHe7.4 to 6.4 decreases cell migration and invasion but increases single cell detachment from the spheroids. Acidification and NHE1 overexpression both reduce cell-cell adhesion strength, indicated by reduced maximum pulling forces and adhesion energies. Multicellular aggregation and spheroid formation are strongly impaired under acidification or NHE1 overexpression. We show a clear dependence of melanoma cell-cell adhesion on pHe and NHE1 as a modulator. These effects are opposite to cell-matrix interactions that are strengthened by protons extruded via NHE1. We conclude that these opposite effects of NHE1 act synergistically during the metastatic cascade. PMID:28205573

  17. Oxytocin modulates social interaction but is not essential for sexual behavior in male mice.

    PubMed

    Lazzari, Virgínia Meneghini; Becker, Roberta Ouriques; de Azevedo, Marcia Scherem; Morris, Mariana; Rigatto, Katya; Almeida, Silvana; Lucion, Aldo Bolten; Giovenardi, Márcia

    2013-05-01

    Recently, several studies have shown different conclusions regarding the effect of oxytocin (OT) on the social behaviors of male mice. Most of these studies used exogenous OT, but currently, investigations of the neural bases of social behavior are increasingly employing gene inactivation. This study aimed to analyze the role of OT in the modulation of social behaviors (i.e., sexual and social interaction behaviors) in male mice with selective deletions of the OT gene (OTKO) and the influence of this deletion in basal vasopressin (AVP) plasma concentrations. Our results showed that in the social interaction test, OTKO mice exhibited lower levels of social behaviors and higher levels of non-social behaviors compared to the wild type (WT) group. Additionally, the OTKO group showed a decrease in the number of agonistic behaviors delivered, and consequently, their dominance score was lower than that of the WT group. In the ethological analysis, the OTKO group had a lower aggressive performance and increased social investigation than the WT group. No significant differences were observed in the sexual behavior between groups. Finally, we found lower AVP plasma concentrations in the OTKO compared with the WT group. In conclusion, our data suggest that OT modulates social investigation behavior and the aggressiveness of male mice. The decrease in AVP concentrations in the OTKO group allows us to infer that AVP is physiologically relevant to these behavioral modulations. However, sexual behaviors do not seem to be affected by the lack of OT or by a decrease in the AVP concentration. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Behavior modulation of rats to a robotic rat in multi-rat interaction.

    PubMed

    Shi, Qing; Ishii, Hiroyuki; Tanaka, Katsuaki; Sugahara, Yusuke; Takanishi, Atsuo; Okabayashi, Satoshi; Huang, Qiang; Fukuda, Toshio

    2015-09-28

    In this paper, we study the behavioral response of rats to a robotic rat during multi-rat interaction. Experiments are conducted in an open-field where a robotic rat called WR-5 is put together with three laboratory rats. WR-5 is following one rat (target), while avoiding the other two rats (outside observers) during interaction. The behavioral characteristics of each target rat is evaluated by scoring its locomotor activity and frequencies of performing rearing, body grooming and mounting actions. Additionally, the frequency of being mounted by other rats is also measured. Experimental results show that the target becomes more active after interaction. The rat species, with more active behavioral characteristics, is more susceptible to being adjusted by the robot. The increased time spent by the outside observers in the vicinity of the robot indicates that a biomimetic robot has the promise for modulating rat behavior even without direct interaction. Thus, this study provide a novel approach to shaping the sociality of animals living in groups.

  19. YY1 and GATA-1 interaction modulate the chicken 3'-side alpha-globin enhancer activity.

    PubMed

    Rincón-Arano, Héctor; Valadez-Graham, Viviana; Guerrero, Georgina; Escamilla-Del-Arenal, Martín; Recillas-Targa, Félix

    2005-06-24

    Studying the chicken alpha-globin domain as a model system of gene regulation, we have previously identified contiguous silencer-enhancer elements located on the 3'-side of the domain. To better characterize the enhancer we performed a systematic functional analysis to define its expression influence range and the ubiquitous and stage-specific transcriptional regulators interacting with this control element. In contrast to previous reports, we found that, in addition to a core element that includes three GATA-1 binding sites, the enhancer incorporates a 120 base-pair DNA fragment where EKLF, NF-E2 and a fourth GATA-1 factor could interact. Functional experiments demonstrate that the enhancer activity over the adult alpha(D) promoter is differentially regulated. We found that the transcriptional factor Ying Yang 1 (YY1) binds to the 120 base-pair DNA fragment and its effect over the enhancer activity is GATA-1-dependent. In addition, we characterize a novel physical interaction between GATA-1 and YY1 that influences the enhancer function. Experiments using a histone deacetylation inhibitor indicate that, in pre-erythroblasts, the enhancer down-regulation could be influenced by a closed chromatin conformation. Our observations show that the originally defined enhancer possesses a more complex composition than previously assumed. We propose that its activity is modulated through differential nuclear factor interactions and chromatin modifications at distinct erythroid stages.

  20. Pin1-dependent signalling negatively affects GABAergic transmission by modulating neuroligin2/gephyrin interaction

    PubMed Central

    Antonelli, Roberta; Pizzarelli, Rocco; Pedroni, Andrea; Fritschy, Jean-Marc; Del Sal, Giannino; Cherubini, Enrico; Zacchi, Paola

    2014-01-01

    The cell adhesion molecule Neuroligin2 (NL2) is localized selectively at GABAergic synapses, where it interacts with the scaffolding protein gephyrin in the post-synaptic density. However, the role of this interaction for formation and plasticity of GABAergic synapses is unclear. Here, we demonstrate that endogenous NL2 undergoes proline-directed phosphorylation at its unique S714-P consensus site, leading to the recruitment of the peptidyl-prolyl cis–trans isomerase Pin1. This signalling cascade negatively regulates NL2’s ability to interact with gephyrin at GABAergic post-synaptic sites. As a consequence, enhanced accumulation of NL2, gephyrin and GABAA receptors was detected at GABAergic synapses in the hippocampus of Pin1-knockout mice (Pin1−/−) associated with an increase in amplitude of spontaneous GABAA-mediated post-synaptic currents. Our results suggest that Pin1-dependent signalling represents a mechanism to modulate GABAergic transmission by regulating NL2/gephyrin interaction. PMID:25297980

  1. A functional interaction between ATF7 and TAF12 that is modulated by TAF4.

    PubMed

    Hamard, Pierre-Jacques; Dalbies-Tran, Rozenn; Hauss, Charlotte; Davidson, Irwin; Kedinger, Claude; Chatton, Bruno

    2005-05-12

    The ATF7 proteins, which are members of the cyclic AMP responsive binding protein (CREB)/activating transcription factor (ATF) family of transcription factors, display quite versatile properties: they can interact with the adenovirus E1a oncoprotein, mediating part of its transcriptional activity; they heterodimerize with the Jun, Fos or related transcription factors, likely modulating their DNA-binding specificity; they also recruit to the promoter a stress-induced protein kinase (JNK2). In the present study, we investigate the functional relationships of ATF7 with hsTAF12 (formerly hsTAF(II)20/15), which has originally been identified as a component of the general transcription factor TFIID. We show that overexpression of hsTAF12 potentiates ATF7-induced transcriptional activation through direct interaction with ATF7, suggesting that TAF12 is a functional partner of ATF7. In support of this conclusion, chromatin immunoprecipitation experiments confirm the interaction of ATF7 with TAF12 on an ATF7-responsive promoter, in the absence of any artificial overexpression of both proteins. We also show that the TAF12-dependent transcriptional activation is competitively inhibited by TAF4. Although both TAF12 isoforms (TAF12-1 and -2, formerly TAF(II)20 and TAF(II)15) interact with the ATF7 activation region through their histone-fold domain, only the largest, hsTAF12-1, mediates transcriptional activation through its N-terminal region.

  2. Envelope Interactions in Multi-Channel Amplitude Modulation Frequency Discrimination by Cochlear Implant Users

    PubMed Central

    2015-01-01

    Rationale Previous cochlear implant (CI) studies have shown that single-channel amplitude modulation frequency discrimination (AMFD) can be improved when coherent modulation is delivered to additional channels. It is unclear whether the multi-channel advantage is due to increased loudness, multiple envelope representations, or to component channels with better temporal processing. Measuring envelope interference may shed light on how modulated channels can be combined. Methods In this study, multi-channel AMFD was measured in CI subjects using a 3-alternative forced-choice, non-adaptive procedure (“which interval is different?”). For the reference stimulus, the reference AM (100 Hz) was delivered to all 3 channels. For the probe stimulus, the target AM (101, 102, 104, 108, 116, 132, 164, 228, or 256 Hz) was delivered to 1 of 3 channels, and the reference AM (100 Hz) delivered to the other 2 channels. The spacing between electrodes was varied to be wide or narrow to test different degrees of channel interaction. Results Results showed that CI subjects were highly sensitive to interactions between the reference and target envelopes. However, performance was non-monotonic as a function of target AM frequency. For the wide spacing, there was significantly less envelope interaction when the target AM was delivered to the basal channel. For the narrow spacing, there was no effect of target AM channel. The present data were also compared to a related previous study in which the target AM was delivered to a single channel or to all 3 channels. AMFD was much better with multiple than with single channels whether the target AM was delivered to 1 of 3 or to all 3 channels. For very small differences between the reference and target AM frequencies (2–4 Hz), there was often greater sensitivity when the target AM was delivered to 1 of 3 channels versus all 3 channels, especially for narrowly spaced electrodes. Conclusions Besides the increased loudness, the present results

  3. Modulation of the FGF14:FGF14 homodimer interaction through short peptide fragments

    PubMed Central

    Ali, Syed; Shavkunov, Alexander; Panova, Neli; Stoilova-McPhie, Svetla; Laezza, Fernanda

    2016-01-01

    Fibroblast growth factor 14 (FGF14) is a member of the intracellular FGF (iFGFs) family and a functionally relevant component of the neuronal voltage-gated Na+ (Nav) channel complex. Through a monomeric interaction with the intracellular C-terminus of neuronal Nav channels, FGF14 modulates Na+ currents in an Nav isoform-specific manner serving as a fine-tuning regulator of excitability. Previous studies based on the highly homologous FGF13 homodimer crystal structure have proposed a conserved protein:protein interaction (PPI) interface common to both Nav channel binding and iFGF homodimer formation. This interface could provide a novel target for drug design against neuronal Nav channels. Here, we provide the first in-cell reconstitution of the FGF14:FGF14 protein complex and measure the dimer interaction using the split-luciferase complementation assay (LCA). Based on the FGF14 dimer structure generated in silico, we designed short peptide fragments against the FGF14 dimer interface. One of these fragments, FLPK aligns with the pocket defined by the β12-strand and β8-β9 loop, reducing the FGF14:FGF14 dimer interaction by 25% as measured by LCA. We further compared the relative interaction strength of FGF14 wild type homodimers with FGF14 hetero- and homodimers carrying double N mutations at the Y153 and V155 residues, located at the β8-β9 loop. The Y153N/V155N double mutation counteracts the FLPK effect by increasing the strength of the dimer interaction. These data suggest that the β12 strand of FGF14 might serve as scaffold for drug design against neuronal FGF14 dimers and Nav channels. PMID:25426956

  4. SEROTONIN TRANSPORTER AND INTEGRIN BETA 3 GENES INTERACT TO MODULATE SEROTONIN UPTAKE IN MOUSE BRAIN

    PubMed Central

    Whyte, Alonzo; Jessen, Tammy; Varney, Seth; Carneiro, Ana MD

    2013-01-01

    Dysfunctions in serotonin (5-hydroxytryptamine, 5-HT) systems have been associated with several psychiatric illnesses, including anxiety, depression, obsessive-compulsive disorders and autism spectrum disorders. Convergent evidence from genetic analyses of human subjects has implicated the integrin β3 subunit gene (ITGB3) as a modulator of serotonergic systems via genetic interactions with the 5-HT transporter gene (SLC6A4, SERT). While genetic interactions may result from contributions of each gene at several levels, we hypothesize that ITGB3 modulates the 5-HT system at the level of the synapse, through the actions of integrin αvβ3. Here we utilized a genetic approach in mouse models to examine Itgb3 contributions to SERT function both in the context of normal and reduced SERT expression. As integrin αvβ3 is expressed in postsynaptic membranes, we isolated synaptoneurosomes, which maintain intact pre- and post-synaptic associations. Citalopram binding revealed significant Slc6a4-driven reductions in SERT expression in midbrain synapses, whereas no significant changes were observed in hippocampal or cortical projections. Expecting corresponding changes to SERT function, we also measured 5-HT uptake activity in synaptoneurosomal preparations. Itgb3 single heterozygous mice displayed significant reductions in 5-HT Vmax, with no chages in Km, in midbrain preparations. However, in the presence of both Itgb3 and Slc6a4 heterozygozity, 5-HT uptake was similar to wild-type levels, revealing a significant Slc6a4 by Itgb3 genetic interaction in the midbrain. Similar findings were observed in cortical preparations, whereas in the hippocampus, most Vmax changes were driven solely by Slc6a4. Our findings provide evidence that integrin αvβ3 is involved in the regulation of serotonergic systems in some, but not all 5-HT synapses, revealing novel contributions to synaptic specificity within the central nervous system. PMID:24083985

  5. Serotonin transporter and integrin beta 3 genes interact to modulate serotonin uptake in mouse brain.

    PubMed

    Whyte, Alonzo; Jessen, Tammy; Varney, Seth; Carneiro, Ana M D

    2014-07-01

    Dysfunctions in serotonin (5-hydroxytryptamine, 5-HT) systems have been associated with several psychiatric illnesses, including anxiety, depression, obsessive-compulsive disorders and autism spectrum disorders. Convergent evidence from genetic analyses of human subjects has implicated the integrin β3 subunit gene (ITGB3) as a modulator of serotonergic systems via genetic interactions with the 5-HT transporter gene (SLC6A4, SERT). While genetic interactions may result from contributions of each gene at several levels, we hypothesize that ITGB3 modulates the 5-HT system at the level of the synapse, through the actions of integrin αvβ3. Here we utilized a genetic approach in mouse models to examine Itgb3 contributions to SERT function both in the context of normal and reduced SERT expression. As integrin αvβ3 is expressed in postsynaptic membranes, we isolated synaptoneurosomes, which maintain intact pre- and post-synaptic associations. Citalopram binding revealed significant Slc6a4-driven reductions in SERT expression in midbrain synapses, whereas no significant changes were observed in hippocampal or cortical projections. Expecting corresponding changes to SERT function, we also measured 5-HT uptake activity in synaptoneurosomal preparations. Itgb3 single heterozygous mice displayed significant reductions in 5-HT Vmax, with no changes in Km, in midbrain preparations. However, in the presence of both Itgb3 and Slc6a4 heterozygozity, 5-HT uptake was similar to wild-type levels, revealing a significant Slc6a4 by Itgb3 genetic interaction in the midbrain. Similar findings were observed in cortical preparations, whereas in the hippocampus, most Vmax changes were driven solely by Slc6a4. Our findings provide evidence that integrin αvβ3 is involved in the regulation of serotonergic systems in some, but not all 5-HT synapses, revealing novel contributions to synaptic specificity within the central nervous system.

  6. Neuroticism modulates the effects of intranasal vasopressin treatment on the neural response to positive and negative social interactions.

    PubMed

    Feng, Chunliang; DeMarco, Ashley C; Haroon, Ebrahim; Rilling, James K

    2015-07-01

    Neuroticism is a fundamental personality trait associated with proneness to feel negative affect. Here we ask how Neuroticism influences the neural response to positive and negative social interactions and how Neuroticism modulates the effect of intranasal oxytocin (OT) and vasopressin (AVP) on the neural response to social interactions. In a double-blind, placebo-controlled study, 153 male participants were randomized to receive 24 IU intranasal OT, 20 IU AVP or placebo. Afterwards, they were imaged with fMRI while playing an iterated Prisoner's Dilemma Game. On a different day, subjects completed the NEO personality inventory to measure Neuroticism. Neuroticism was positively correlated with the neural response to negative social interactions in the anterior cingulate cortex/medial prefrontal cortex and with the neural response to positive social interactions in the insula, indicating that Neuroticism modulates neuropsychological processing of both negative and positive social interactions. Neuroticism did not modulate the effect of intranasal OT treatment on the neural response to either positive or negative social interactions. On the other hand, AVP treatment significantly interacted with Neuroticism to modulate the BOLD response to both positive and negative social interactions. Specifically, AVP increased anterior cingulate cortex/medial prefrontal cortex and lateral temporal lobe responses to negative social interactions to a greater extent in participants scoring high rather than low on Neuroticism. AVP also increased the insula response to positive social interactions to a greater extent in participants scoring high rather than low on Neuroticism. These results imply that AVP may increase emotion regulation in response to negative social interactions and the salience of positive social interactions to a greater extent in individuals high compared to low in Neuroticism. The current findings urge caution against uniform clinical application of nonapeptides

  7. Post-transcriptional Modifications Modulate rRNA Structure and Ligand Interactions.

    PubMed

    Jiang, Jun; Seo, Hyosuk; Chow, Christine S

    2016-05-17

    Post-transcriptional modifications play important roles in modulating the functions of RNA species. The presence of modifications in RNA may directly alter its interactions with binding partners or cause structural changes that indirectly affect ligand recognition. Given the rapidly growing list of modifications identified in noncoding and mRNAs associated with human disease, as well as the dynamic control over modifications involved in various physiological processes, it is imperative to understand RNA structural modulation by these modifications. Among the RNA species, rRNAs provide numerous examples of modification types located in differing sequence and structural contexts. In addition, the modified rRNA motifs participate in a wide variety of ligand interactions, including those with RNA, protein, and small molecules. In fact, several classes of antibiotics exert their effects on protein synthesis by binding to functionally important and highly modified regions of the rRNAs. These RNA regions often display conservation in sequence, secondary structure, tertiary interactions, and modifications, trademarks of ideal drug-targeting sites. Furthermore, ligand interactions with such regions often favor certain modification-induced conformational states of the RNA. Our laboratory has employed a combination of biophysical methods such as nuclear magnetic resonance spectroscopy (NMR), circular dichroism, and UV melting to study rRNA modifications in functionally important motifs, including helix 31 (h31) and helix h44 (h44) of the small subunit rRNA and helix 69 (H69) of the large subunit rRNA. The modified RNA oligonucleotides used in these studies were generated by solid-phase synthesis with a variety of phosphoramidite chemistries. The natural modifications were shown to impact thermal stability, dynamic behavior, and tertiary structures of the RNAs, with additive or cooperative effects occurring with multiple, clustered modifications. Taking advantage of the

  8. Quantification of chemical mixture interactions modulating dermal absorption using a multiple membrane fiber array.

    PubMed

    Baynes, Ronald E; Xia, Xin Rui; Imran, Mudassar; Riviere, Jim E

    2008-03-01

    Dermal exposures to chemical mixtures can potentially increase or decrease systemic bioavailability of toxicants in the mixture. Changes in dermal permeability can be attributed to changes in physicochemical interactions between the mixture, the skin, and the solute of interest. These physicochemical interactions can be described as changes in system coefficients associated with molecular descriptors described by Abraham's linear solvation energy relationship (LSER). This study evaluated the effects of chemical mixtures containing either a solvent (ethanol) or a surfactant (sodium lauryl sulfate, SLS) on solute permeability and partitioning by quantifying changes in system coefficients in skin and a three-membrane-coated fiber (MCF) system, respectively. Regression analysis demonstrated that changes in system coefficients in skin were strongly correlated ( R2 = 0.89-0.98) to changes in system coefficients in the three-membrane MCF array with mixtures containing either 1% SLS or 50% ethanol. The PDMS fiber appeared to play a significant role (R2 = 0.84-0.85) in the MCF array in predicting changes in solute permeability, while the WAX fiber appeared to contribute less (R2 = 0.59-0.77) to the array than the other two fibers. On the basis of changes in system coefficients that are part of a LSER, these experiments were able to link physicochemical interactions in the MCF with those interactions in skin when either system is exposed to 1% SLS or 50% ethanol. These experiments further demonstrated the utility of a MCF array to adequately predict changes in dermal permeability when skin is exposed to mixtures containing either a surfactant or a solvent and provide some insight into the nature of the physiochemical interactions that modulate dermal absorptions.

  9. GSTpi modulates JNK activity through a direct interaction with JNK substrate, ATF2

    PubMed Central

    Thévenin, Anastasia F; Zony, Chati L; Bahnson, Brian J; Colman, Roberta F

    2011-01-01

    Human GSTpi, an important detoxification enzyme, has been shown to modulate the activity of JNKs by inhibiting apoptosis and by causing cell proliferation and tumor growth. In this work, we describe a detailed analysis of the interaction in vitro between GSTpi and JNK isoforms (both in their inactive and active, phosphorylated forms). The ability of active JNK1 or JNK2 to phosphorylate their substrate, ATF2, is inhibited by two naturally occurring GSTpi haplotypes (Ile105/Ala114, WT or haplotype A, and Val105/Val114, haplotype C). Haplotype C of GSTpi is a more potent inhibitor of JNK activity than haplotype A, yielding 75–80% and 25–45% inhibition, respectively. We show that GSTpi is not a substrate of JNK, as was earlier suggested by others. Through binding studies, we demonstrate that the interaction between GSTpi and phosphorylated, active JNKs is isoform specific, with JNK1 being the preferred isoform. In contrast, GSTpi does not interact with unphosphorylated, inactive JNKs unless a JNK substrate, ATF2, is present. We also demonstrate, for the first time, a direct interaction: between GSTpi and ATF2. GSTpi binds with similar affinity to active JNK + ATF2 and to ATF2 alone. Direct binding experiments between ATF2 and GSTpi, either alone or in the presence of glutathione analogs or phosphorylated ATF2, indicate that the xenobiotic portion of the GSTpi active site and the JNK binding domain of ATF2 are involved in this interaction. Competition between GSTpi and active JNK for the substrate ATF2 may be responsible for the inhibition of JNK catalysis by GSTpi. PMID:21384452

  10. Transporter modulation by Chinese herbal medicines and its mediated pharmacokinetic herb-drug interactions.

    PubMed

    Wu, Xu; Ma, Jiang; Ye, Yang; Lin, Ge

    2016-07-15

    The increasing use of Chinese herbal medicines (CHMs) as complementary therapy and dietary supplement has been greatly raising the concerns about potential herb-drug interactions (HDIs). HDIs may cause the augmented or antagonized effects of prescription drugs, resulting in unexpected clinical outcomes. Therefore, it is of significance to identify or predict potential HDIs, and to delineate the underlying mechanisms. Drug transporters play key roles in transmembrane passage of a large number of drugs, affecting their absorption, distribution and elimination. Modulation of drug transporters has been recognized as one of the main causes of HDIs. In the last decade, a growing number of Chinese medicinal herbs and their derived phytochemicals have been identified to have modulatory effect toward transporter proteins, leading to pharmacokinetic HDIs when concomitantly used with conventional drugs. Some of these transporter-mediated interactions have already shown clinical significance. This review article focuses on two major transporter superfamilies, the solute carrier (SLC) and the ATP-binding cassette (ABC) transporters, to provide the recent advanced knowledge on CHMs and their inherent phytochemicals that interact with these transporters, and their induced pharmacokinetic HDIs from both preclinical and clinical aspects. In addition, the challenges and strategy for studying HDIs are also discussed.

  11. Protein-protein interactions and protein modules in the control of neurotransmitter release.

    PubMed Central

    Benfenati, F; Onofri, F; Giovedí, S

    1999-01-01

    Information transfer among neurons is operated by neurotransmitters stored in synaptic vesicles and released to the extracellular space by an efficient process of regulated exocytosis. Synaptic vesicles are organized into two distinct functional pools, a large reserve pool in which vesicles are restrained by the actin-based cytoskeleton, and a quantitatively smaller releasable pool in which vesicles approach the presynaptic membrane and eventually fuse with it on stimulation. Both synaptic vesicle trafficking and neurotransmitter release depend on a precise sequence of events that include release from the reserve pool, targeting to the active zone, docking, priming, fusion and endocytotic retrieval of synaptic vesicles. These steps are mediated by a series of specific interactions among cytoskeletal, synaptic vesicle, presynaptic membrane and cytosolic proteins that, by acting in concert, promote the spatial and temporal regulation of the exocytotic machinery. The majority of these interactions are mediated by specific protein modules and domains that are found in many proteins and are involved in numerous intracellular processes. In this paper, the possible physiological role of these multiple protein-protein interactions is analysed, with ensuing updating and clarification of the present molecular model of the process of neurotransmitter release. PMID:10212473

  12. CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

    PubMed Central

    Fiorito, Elisa; Sharma, Yogita; Gilfillan, Siv; Wang, Shixiong; Singh, Sachin Kumar; Satheesh, Somisetty V.; Katika, Madhumohan R.; Urbanucci, Alfonso; Thiede, Bernd; Mills, Ian G.; Hurtado, Antoni

    2016-01-01

    Enhancer regions and transcription start sites of estrogen-target regulated genes are connected by means of Estrogen Receptor long-range chromatin interactions. Yet, the complete molecular mechanisms controlling the transcriptional output of engaged enhancers and subsequent activation of coding genes remain elusive. Here, we report that CTCF binding to enhancer RNAs is enriched when breast cancer cells are stimulated with estrogen. CTCF binding to enhancer regions results in modulation of estrogen-induced gene transcription by preventing Estrogen Receptor chromatin binding and by hindering the formation of additional enhancer-promoter ER looping. Furthermore, the depletion of CTCF facilitates the expression of target genes associated with cell division and increases the rate of breast cancer cell proliferation. We have also uncovered a genomic network connecting loci enriched in cell cycle regulator genes to nuclear lamina that mediates the CTCF function. The nuclear lamina and chromatin interactions are regulated by estrogen-ER. We have observed that the chromatin loops formed when cells are treated with estrogen establish contacts with the nuclear lamina. Once there, the portion of CTCF associated with the nuclear lamina interacts with enhancer regions, limiting the formation of ER loops and the induction of genes present in the loop. Collectively, our results reveal an important, unanticipated interplay between CTCF and nuclear lamina to control the transcription of ER target genes, which has great implications in the rate of growth of breast cancer cells. PMID:27638884

  13. Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modeling.

    PubMed

    Tzul, Franco O; Schweiker, Katrina L; Makhatadze, George I

    2015-01-20

    The kinetics of folding-unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge-charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational model, which incorporates the Debye-Hückel formalism for the electrostatics, was used and found to qualitatively recapitulate the experimental results. Analysis of the energy landscapes of the designed versus wild-type proteins indicates the differences in refolding rates may be correlated with the degree of frustration of their respective energy landscapes. Our simulations indicate that naturally occurring wild-type proteins have frustrated folding landscapes due to the surface electrostatics. Optimization of the surface electrostatics seems to remove some of that frustration, leading to enhanced formation of native-like contacts in the transition-state ensembles (TSE) and providing a less frustrated energy landscape between the unfolded and TS ensembles. Macroscopically, this results in faster folding rates. Furthermore, analyses of pairwise distances and radii of gyration suggest that the less frustrated energy landscapes for optimized variants are a result of more compact unfolded and TS ensembles. These findings from our modeling demonstrates that this simple model may be used to: (i) gain a detailed understanding of charge-charge interactions and their effects on modulating the energy landscape of protein folding and (ii) qualitatively predict the kinetic behavior of protein surface electrostatic interactions.

  14. Tuning Sulfur Oxidation States on Thioether-Bridged Peptide Macrocycles for Modulation of Protein Interactions.

    PubMed

    Perell, Gabriella T; Staebell, Rachel Lynn; Hairani, Mehrdad; Cembran, Alessandro; Pomerantz, William C K

    2017-09-19

    Thioethers, sulfoxides, and sulfonium ions, despite diverse physicochemical properties, all engage in noncovalent interactions with proteins. Thioether-containing macrocycles are also attracting attention as protein-protein interaction (PPI) inhibitors. Here, we used a model PPI between α-helical mixed lineage leukemia (MLL) protein and kinase-inducible domain interacting (KIX) domain to evaluate oxidation effects on sulfurcontaining macrocycle structure, stability, and protein affinity. Desolvation effects from various polarity states were evaluated computationally and experimentally at the side chain, amino acid, and peptide level. Sulfur-containing side chains spanned polarity ranges between all-hydrocarbon and lactam bridges for modulating solubility, cellular uptake, and affinity. Helical propensity studies showed that, although oxidized sulfur-containing side chains could be tolerated, conformational effects were sequence-dependent. In some cases, proteolytic stability, binding capacity with KIX, and increased helicity were obtained as first steps toward developing PPI inhibitors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Interactive Learning Module Improves Resident Knowledge of Risks of Ionizing Radiation Exposure From Medical Imaging.

    PubMed

    Sheng, Alexander Y; Breaud, Alan H; Schneider, Jeffrey I; Kadom, Nadja; Mitchell, Patricia M; Linden, Judith A

    2016-01-01

    Physician awareness of the risks of ionizing radiation exposure related to medical imaging is poor. Effective educational interventions informing physicians of such risk, especially in emergency medicine (EM), are lacking. The SIEVERT (Suboptimal Ionizing Radiation Exposure Education - A Void in Emergency Medicine Residency Training) learning module was designed to improve provider knowledge of the risks of radiation exposure from medical imaging and comfort in communicating these risks to patients. The 1-hour module consists of introductory lecture, interactive discussion, and role-playing scenarios. In this pilot study, we assessed the educational effect using unmatched, anonymous preintervention and postintervention questionnaires that assessed fund of knowledge, participant self-reported imaging ordering practices in several clinical scenarios, and trainee comfort level in discussing radiation risks with patients. All 25 EM resident participants completed the preintervention questionnaire, and 22 completed the postintervention questionnaire within 4 hours after participation. Correct responses on the 14-question learning assessment increased from 6.32 (standard deviation = 2.36) preintervention to 12.23 (standard deviation = 1.85) post-intervention. Overall, 24% of residents were comfortable with discussing the risks of ionizing radiation exposure with patients preintervention, whereas 41% felt comfortable postintervention. Participants ordered fewer computed tomography scans in 2 of the 4 clinical scenarios after attending the educational intervention. There was improvement in EM residents' knowledge regarding the risks of ionizing radiation exposure from medical imaging, and increased participant self-reported comfort levels in the discussion of these risks with patients after the 1-hour SIEVERT learning module. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Environmental factors as modulators of neurodegeneration: insights from gene-environment interactions in Huntington's disease.

    PubMed

    Mo, Christina; Hannan, Anthony J; Renoir, Thibault

    2015-05-01

    Unlike many other neurodegenerative diseases with established gene-environment interactions, Huntington's disease (HD) is viewed as a disorder governed by genetics. The cause of the disease is a highly penetrant tandem repeat expansion encoding an extended polyglutamine tract in the huntingtin protein. In the year 2000, a pioneering study showed that the disease could be delayed in transgenic mice by enriched housing conditions. This review describes subsequent human and preclinical studies identifying environmental modulation of motor, cognitive, affective and other symptoms found in HD. Alongside the behavioral observations we also discuss potential mechanisms and the relevance to other neurodegenerative disorders, including Alzheimer's and Parkinson's disease. In mouse models of HD, increased sensorimotor and cognitive stimulation can delay or ameliorate various endophenotypes. Potential mechanisms include increased trophic support, synaptic plasticity, adult neurogenesis, and other forms of experience-dependent cellular plasticity. Subsequent clinical investigations support a role for lifetime activity levels in modulating the onset and progression of HD. Stress can accelerate memory and olfactory deficits and exacerbate cellular dysfunctions in HD mice. In the absence of effective treatments to slow the course of HD, environmental interventions offer feasible approaches to delay the disease, however further preclinical and human studies are needed in order to generate clinical recommendations. Environmental interventions could be combined with future pharmacological therapies and stimulate the identification of enviromimetics, drugs which mimic or enhance the beneficial effects of cognitive stimulation and physical activity. Copyright © 2015. Published by Elsevier Ltd.

  17. Relativistic Electron Streaming Instabilities Modulate Proton Beams Accelerated in Laser-Plasma Interactions

    NASA Astrophysics Data System (ADS)

    Göde, S.; Rödel, C.; Zeil, K.; Mishra, R.; Gauthier, M.; Brack, F.-E.; Kluge, T.; MacDonald, M. J.; Metzkes, J.; Obst, L.; Rehwald, M.; Ruyer, C.; Schlenvoigt, H.-P.; Schumaker, W.; Sommer, P.; Cowan, T. E.; Schramm, U.; Glenzer, S.; Fiuza, F.

    2017-05-01

    We report experimental evidence that multi-MeV protons accelerated in relativistic laser-plasma interactions are modulated by strong filamentary electromagnetic fields. Modulations are observed when a preplasma is developed on the rear side of a μ m -scale solid-density hydrogen target. Under such conditions, electromagnetic fields are amplified by the relativistic electron Weibel instability and are maximized at the critical density region of the target. The analysis of the spatial profile of the protons indicates the generation of B >10 MG and E >0.1 MV /μ m fields with a μ m -scale wavelength. These results are in good agreement with three-dimensional particle-in-cell simulations and analytical estimates, which further confirm that this process is dominant for different target materials provided that a preplasma is formed on the rear side with scale length ≳0.13 λ0√{a0}. These findings impose important constraints on the preplasma levels required for high-quality proton acceleration for multipurpose applications.

  18. Interaction between personality traits and cerebrospinal fluid biomarkers of Alzheimer's disease pathology modulates cognitive performance.

    PubMed

    Tautvydaitė, Domilė; Kukreja, Deepti; Antonietti, Jean-Philippe; Henry, Hugues; von Gunten, Armin; Popp, Julius

    2017-02-02

    During adulthood, personality characteristics may contribute to the individual capacity to compensate the impact of developing cerebral Alzheimer's disease (AD) pathology on cognitive impairment in later life. In this study we aimed to investigate whether and how premorbid personality traits interact with cerebrospinal fluid (CSF) markers of AD pathology to predict cognitive performance in subjects with mild cognitive impairment or mild AD dementia and in participants with normal cognition. One hundred and ten subjects, of whom 66 were patients with mild cognitive impairment or mild AD dementia and 44 were healthy controls, had a comprehensive medical and neuropsychological examination as well as lumbar puncture to measure CSF biomarkers of AD pathology (amyloid beta1-42, phosphorylated tau and total-tau). Participants' proxies completed the Revised NEO Personality Inventory, Form R to retrospectively assess subjects' premorbid personality. In hierarchical multivariate regression analyses, including age, gender, education, APOEε4 status and cognitive level, premorbid neuroticism, conscientiousness and agreeableness modulated the effect of CSF biomarkers on cognitive performance. Low premorbid openness independently predicted lower levels of cognitive functioning after controlling for biomarker concentrations. Our findings suggest that specific premorbid personality traits are associated with cerebral AD pathology and modulate its impact on cognitive performance. Considering personality characteristics may help to appraise a person's cognitive reserve and the risk of cognitive decline in later life.

  19. Biopolymer-Lipid Bilayer Interaction Modulates the Physical Properties of Liposomes: Mechanism and Structure.

    PubMed

    Tan, Chen; Zhang, Yating; Abbas, Shabbar; Feng, Biao; Zhang, Xiaoming; Xia, Wenshui; Xia, Shuqin

    2015-08-19

    This study was conducted to elucidate the conformational dependence of the modulating ability of chitosan, a positively charged biopolymer, on a new type of liposome composed of mixed lipids including egg yolk phosphatidylcholine (EYPC) and nonionic surfactant (Tween 80). Analysis of the dynamic and structure of bilayer membrane upon interaction with chitosan by fluorescence and electron paramagnetic resonance techniques demonstrated that, in addition to providing a physical barrier for the membrane surface, the adsorption of chitosan extended and crimped chains rigidified the lipid membrane. However, the decrease in relative microviscosity and order parameter suggested that the presence of chitosan coils disturbed the membrane organization. It was also noted that the increase of fluidity in the lipid bilayer center was not pronounced, indicating the shallow penetration of coils into the hydrophobic interior of bilayer. Microscopic observations revealed that chitosan adsorption not only affected the morphology of liposomes but also modulated the particle aggregation and fusion. Especially, a number of very heterogeneous particles were visualized, which tended to confirm the role of chitosan coils as a "polymeric surfactant". In addition to particle deformation, the membrane permeability was also tuned. These findings may provide a new perspective to understand the physiological functionality of biopolymer and design biopolymer-liposome composite structures as delivery systems for bioactive components.

  20. Modulation of Caenorhabditis elegans immune response and modification of Shigella endotoxin upon interaction.

    PubMed

    Kesika, Periyanaina; Prasanth, Mani Iyer; Balamurugan, Krishnaswamy

    2015-04-01

    To analyze the pathogenesis at both physiological and molecular level using the model organism, Caenorhabditis elegans at different developmental stages in response to Shigella spp. and its pathogen associated molecular patterns such as lipopolysaccharide. The solid plate and liquid culture-based infection assays revealed that Shigella spp. infects C. elegans and had an impact on the brood size and pharyngeal pumping rate. LPS of Shigella spp. was toxic to C. elegans. qPCR analysis revealed that host innate immune genes have been modulated upon Shigella spp. infections and its LPS challenges. Non-destructive analysis was performed to kinetically assess the alterations in LPS during interaction of Shigella spp. with C. elegans. The modulation of innate immune genes attributed the surrendering of host immune system to Shigella spp. by favoring the infection. LPS appeared to have a major role in Shigella-mediated pathogenesis and Shigella employs a tactic behavior of modifying its LPS content to escape from the recognition of host immune system.

  1. Norepinephrine versus dopamine and their interaction in modulating synaptic function in the prefrontal cortex.

    PubMed

    Xing, Bo; Li, Yan-Chun; Gao, Wen-Jun

    2016-06-15

    Among the neuromodulators that regulate prefrontal cortical circuit function, the catecholamine transmitters norepinephrine (NE) and dopamine (DA) stand out as powerful players in working memory and attention. Perturbation of either NE or DA signaling is implicated in the pathogenesis of several neuropsychiatric disorders, including attention deficit hyperactivity disorder (ADHD), post-traumatic stress disorder (PTSD), schizophrenia, and drug addiction. Although the precise mechanisms employed by NE and DA to cooperatively control prefrontal functions are not fully understood, emerging research indicates that both transmitters regulate electrical and biochemical aspects of neuronal function by modulating convergent ionic and synaptic signaling in the prefrontal cortex (PFC). This review summarizes previous studies that investigated the effects of both NE and DA on excitatory and inhibitory transmissions in the prefrontal cortical circuitry. Specifically, we focus on the functional interaction between NE and DA in prefrontal cortical local circuitry, synaptic integration, signaling pathways, and receptor properties. Although it is clear that both NE and DA innervate the PFC extensively and modulate synaptic function by activating distinctly different receptor subtypes and signaling pathways, it remains unclear how these two systems coordinate their actions to optimize PFC function for appropriate behavior. Throughout this review, we provide perspectives and highlight several critical topics for future studies. This article is part of a Special Issue entitled SI: Noradrenergic System. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Modulating effect of lipid bilayer-carotenoid interactions on the property of liposome encapsulation.

    PubMed

    Xia, Shuqin; Tan, Chen; Zhang, Yating; Abbas, Shabbar; Feng, Biao; Zhang, Xiaoming; Qin, Fang

    2015-04-01

    Liposomes have become an attractive alternative to encapsulate carotenoids to improve their solubility, stability and bioavailability. The interaction mechanism of carotenoid with lipid bilayer is one of the major concerns in improving the delivery efficiency of liposomes. In this study, the microstructure and carotenoid encapsulation efficiency of liposomes composed of native phospholipid (egg yolk phosphatidylcholine, EYPC) and nonionic surfactant Tween 80 were investigated by atomic force microscopy, dynamic light scattering, and Raman spectroscopy, respectively. Subsequently, the effects of carotenoid incorporation on the physical properties of liposomal membrane were performed by Raman spectroscopy, fluorescence polarization, and electron paramagnetic resonance. Results showed that the incorporation of carotenoids affected the liposomes morphology, size and size distribution to various extents. Analysis on the Raman characteristic peaks of carotenoids revealed that lutein exhibited the strongest incorporating ability into liposomes, followed by β-carotene, lycopene, and canthaxanthin. Furthermore, it was demonstrated that carotenoids modulated the dynamics, structure and hydrophobicity of liposomal membrane, highly depending on their molecular structures and incorporated concentration. These modulations were closely correlated with the stabilization of liposomes, including mediating particle aggregation and fusion. These findings should guide the rationale designing for liposomal encapsulation technology to efficiently deliver carotenoids in pharmaceutics, nutraceuticals and functional foods.

  3. Flavonoids as modulators of memory and learning: molecular interactions resulting in behavioural effects.

    PubMed

    Rendeiro, Catarina; Guerreiro, João D T; Williams, Claire M; Spencer, Jeremy P E

    2012-05-01

    There is considerable interest in the potential of a group of dietary-derived phytochemicals known as flavonoids in modulating neuronal function and thereby influencing memory, learning and cognitive function. The present review begins by detailing the molecular events that underlie the acquisition and consolidation of new memories in the brain in order to provide a critical background to understanding the impact of flavonoid-rich diets or pure flavonoids on memory. Data suggests that despite limited brain bioavailability, dietary supplementation with flavonoid-rich foods, such as blueberry, green tea and Ginkgo biloba lead to significant reversals of age-related deficits on spatial memory and learning. Furthermore, animal and cellular studies suggest that the mechanisms underpinning their ability to induce improvements in memory are linked to the potential of absorbed flavonoids and their metabolites to interact with and modulate critical signalling pathways, transcription factors and gene and/or protein expression which control memory and learning processes in the hippocampus; the brain structure where spatial learning occurs. Overall, current evidence suggests that human translation of these animal investigations are warranted, as are further studies, to better understand the precise cause-and-effect relationship between flavonoid intake and cognitive outputs.

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

    PubMed

    Waller, Jessica A; Nygaard, Sara Holm; Li, Yan; du Jardin, Kristian Gaarn; Tamm, Joseph A; Abdourahman, Aicha; Elfving, Betina; Pehrson, Alan L; Sánchez, Connie; Wernersson, Rasmus

    2017-08-04

    The identification of biomarkers that predict susceptibility to major depressive disorder and treatment response to antidepressants is a major challenge. Vortioxetine is a novel multimodal antidepressant that possesses pro-cognitive properties and differentiates from other conventional antidepressants on various cognitive and plasticity measures. The aim of the present study was to identify biological systems rather than single biomarkers that may underlie vortioxetine's treatment effects. We show that the biological systems regulated by vortioxetine are overlapping between mouse and rat in response to distinct treatment regimens and in different brain regions. Furthermore, analysis of complexes of physically-interacting proteins reveal that biomarkers involved in transcriptional regulation, neurodevelopment, neuroplasticity, and endocytosis are modulated by vortioxetine. A subsequent qPCR study examining the expression of targets in the protein-protein interactome space in response to chronic vortioxetine treatment over a range of doses provides further biological validation that vortioxetine engages neuroplasticity networks. Thus, the same biology is regulated in different species and sexes, different brain regions, and in response to distinct routes of administration and regimens. A recurring theme, based on the present study as well as previous findings, is that networks related to synaptic plasticity, synaptic transmission, signal transduction, and neurodevelopment are modulated in response to vortioxetine treatment. Regulation of these signaling pathways by vortioxetine may underlie vortioxetine's cognitive-enhancing properties.

  5. Modulation of nociceptive ion channels and receptors via protein-protein interactions: implications for pain relief

    PubMed Central

    Rouwette, Tom; Avenali, Luca; Sondermann, Julia; Narayanan, Pratibha; Gomez-Varela, David; Schmidt, Manuela

    2015-01-01

    In the last 2 decades biomedical research has provided great insights into the molecular signatures underlying painful conditions. However, chronic pain still imposes substantial challenges to researchers, clinicians and patients alike. Under pathological conditions, pain therapeutics often lack efficacy and exhibit only minimal safety profiles, which can be largely attributed to the targeting of molecules with key physiological functions throughout the body. In light of these difficulties, the identification of molecules and associated protein complexes specifically involved in chronic pain states is of paramount importance for designing selective interventions. Ion channels and receptors represent primary targets, as they critically shape nociceptive signaling from the periphery to the brain. Moreover, their function requires tight control, which is usually implemented by protein-protein interactions (PPIs). Indeed, manipulation of such PPIs entails the modulation of ion channel activity with widespread implications for influencing nociceptive signaling in a more specific way. In this review, we highlight recent advances in modulating ion channels and receptors via their PPI networks in the pursuit of relieving chronic pain. Moreover, we critically discuss the potential of targeting PPIs for developing novel pain therapies exhibiting higher efficacy and improved safety profiles. PMID:26039491

  6. Development of high-resolution detector module with depth of interaction identification for positron emission tomography

    NASA Astrophysics Data System (ADS)

    Niknejad, Tahereh; Pizzichemi, Marco; Stringhini, Gianluca; Auffray, Etiennette; Bugalho, Ricardo; Da Silva, Jose Carlos; Di Francesco, Agostino; Ferramacho, Luis; Lecoq, Paul; Leong, Carlos; Paganoni, Marco; Rolo, Manuel; Silva, Rui; Silveira, Miguel; Tavernier, Stefaan; Varela, Joao; Zorraquino, Carlos

    2017-02-01

    We have developed a Time-of-flight high resolution and commercially viable detector module for the application in small PET scanners. A new approach to depth of interaction (DOI) encoding with low complexity for a pixelated crystal array using a single side readout and 4-to-1 coupling between scintillators and photodetectors was investigated. In this method the DOI information is estimated using the light sharing technique. The detector module is a 1.53×1.53×15 mm3 matrix of 8×8 LYSO scintillator with lateral surfaces optically depolished separated by reflective foils. The crystal array is optically coupled to 4×4 silicon photomultipliers (SiPM) array and readout by a high performance front-end ASIC with TDC capability (50 ps time binning). The results show an excellent crystal identification for all the scintillators in the matrix, a timing resolution of 530 ps, an average DOI resolution of 5.17 mm FWHM and an average energy resolution of 18.29% FWHM.

  7. The distinctive feature of long time adiabatic modulation in the context of cnoidal wave and Akhmediev breaser interaction

    NASA Astrophysics Data System (ADS)

    Makarov, V. A.; Petnikova, V. M.

    2017-02-01

    For a nonintegrable system of two coupled nonlinear Schrödinger equations the adiabatic approximation is extended for long time interaction. The method enables analytical description of the modulation of a cnoidal wave by Akhmediev breather in an isotropic nonlinear gyrotropic medium with Kerr nonlinearity and second-order group-velocity dispersion. The conditions which must be fulfilled for stable propagation of the obtained solution with amplitude and frequency modulation are determined.

  8. Control-structure interaction study for the Space Station solar dynamic power module

    NASA Technical Reports Server (NTRS)

    Cheng, J.; Ianculescu, G.; Ly, J.; Kim, M.

    1991-01-01

    The authors investigate the feasibility of using a conventional PID (proportional plus integral plus derivative) controller design to perform the pointing and tracking functions for the Space Station Freedom solar dynamic power module. Using this simple controller design, the control/structure interaction effects were also studied without assuming frequency bandwidth separation. From the results, the feasibility of a simple solar dynamic control solution with a reduced-order model, which satisfies the basic system pointing and stability requirements, is suggested. However, the conventional control design approach is shown to be very much influenced by the order of reduction of the plant model, i.e., the number of the retained elastic modes from the full-order model. This suggests that, for complex large space structures, such as the Space Station Freedom solar dynamic, the conventional control system design methods may not be adequate.

  9. Diurnal modulation due to self-interacting mirror and hidden sector dark matter

    SciTech Connect

    Foot, R.

    2012-04-01

    Mirror and more generic hidden sector dark matter models can simultaneously explain the DAMA, CoGeNT and CRESST-II dark matter signals consistently with the null results of the other experiments. This type of dark matter can be captured by the Earth and shield detectors because it is self-interacting. This effect will lead to a diurnal modulation in dark matter detectors. We estimate the size of this effect for dark matter detectors in various locations. For a detector located in the northern hemisphere, this effect is expected to peak in April and can be detected for optimistic parameter choices. The diurnal variation is expected to be much larger for detectors located in the southern hemisphere. In particular, if the CoGeNT detector were moved to e.g. Sierra Grande, Argentina then a 5σ dark matter discovery would be possible in around 30 days of operation.

  10. Features, processing states and heterologous protein interactions in the modulation of the retroviral nucleocapsid protein function

    PubMed Central

    Mirambeau, Gilles; Lyonnais, Sébastien

    2010-01-01

    Nucleocapsid (NC) is central to retroviral replication. Nucleic acid chaperoning is a key function for NC through the action of its conserved basic amino acids and zinc-finger structures. NC manipulates genomic RNA from its packaging in the producer cell to reverse transcription into the infected host cell. This chaperone function, in conjunction with NCs aggregating properties, is up-modulated by successive NC processing events, from the Gag precursor to the fully mature protein, resulting in the condensation of the nucleocapsid within the capsid shell. Reverse transcription also depends on NC processing, whereas this process provokes NC dissociation from double-stranded DNA, leading to a preintegration complex (PIC), competent for host chromosomal integration. In addition NC interacts with cellular proteins, some of which are involved in viral budding, and also with several viral proteins. All of these properties are reviewed here, focusing on HIV-1 as a paradigmatic reference and highlighting the plasticity of the nucleocapsid architecture. PMID:21045549

  11. Observation of interaction-induced modulations of a quantum Hall liquid's area

    PubMed Central

    Sivan, I.; Choi, H. K.; Park, Jinhong; Rosenblatt, A.; Gefen, Yuval; Mahalu, D.; Umansky, V.

    2016-01-01

    Studies of electronic interferometers, based on edge-channel transport in the quantum Hall effect regime, have been stimulated by the search for evidence of abelian and non-abelian anyonic statistics of fractional charges. In particular, the electronic Fabry–Pérot interferometer has been found to be Coulomb dominated, thus masking coherent Aharonov–Bohm interference patterns: the flux trapped within the interferometer remains unchanged as the applied magnetic field is varied, barring unobservable modulations of the interference area. Here we report on conductance measurements indicative of the interferometer's area ‘breathing' with the variation of the magnetic field, associated with observable (a fraction of a flux quantum) variations of the trapped flux. This is the result of partial (controlled) screening of Coulomb interactions. Our results introduce a novel experimental tool for probing anyonic statistics. PMID:27396234

  12. Observation of interaction-induced modulations of a quantum Hall liquid's area

    NASA Astrophysics Data System (ADS)

    Sivan, I.; Choi, H. K.; Park, Jinhong; Rosenblatt, A.; Gefen, Yuval; Mahalu, D.; Umansky, V.

    2016-07-01

    Studies of electronic interferometers, based on edge-channel transport in the quantum Hall effect regime, have been stimulated by the search for evidence of abelian and non-abelian anyonic statistics of fractional charges. In particular, the electronic Fabry-Pérot interferometer has been found to be Coulomb dominated, thus masking coherent Aharonov-Bohm interference patterns: the flux trapped within the interferometer remains unchanged as the applied magnetic field is varied, barring unobservable modulations of the interference area. Here we report on conductance measurements indicative of the interferometer's area `breathing' with the variation of the magnetic field, associated with observable (a fraction of a flux quantum) variations of the trapped flux. This is the result of partial (controlled) screening of Coulomb interactions. Our results introduce a novel experimental tool for probing anyonic statistics.

  13. Radiative forcing by stratospheric aerosol in a CCM with interactive aerosol module

    NASA Astrophysics Data System (ADS)

    Brühl, Christoph; Lelieveld, Jos; Tost, Holger; Steil, Benedikt; Höpfner, Michael

    2013-04-01

    Multiyear studies with the atmospheric chemistry general circulation model EMAC with the aerosol module GMXe demonstrate that stratospheric aerosol formation is controlled by COS oxidation and SO2 injected by low-latitude volcanic eruptions. The model consistently uses the same parameters in the troposphere and stratosphere for 7 aerosol modes applied. Calculated radiative heating by aerosol feeds back to stratospheric dynamics. Radiative forcing by stratospheric aerosol can be diagnosed separately. The simulations include the medium size tropical eruptions in 2003, 2005 and 2006 but also the major eruption of Pinatubo in 1991. We show that calculated radiative forcing by stratospheric aerosol agrees well with the corresponding satellite derived quantity and that the medium size tropical eruptions should not be neglected in climate simulations. Changes in temperature, dynamics and tracer transport due to interactive aerosol will be also presented. We show also that calculated aerosol and SO2 concentrations are consistent with the observations by SAGE and by MIPAS on ENVISAT.

  14. Preliminary results from the flight of the Solar Array Module Plasma Interactions Experiment (SAMPIE)

    NASA Technical Reports Server (NTRS)

    Ferguson, Dale C.; Hillard, G. Barry

    1994-01-01

    SAMPIE, the Solar Array Module Plasma Interactions Experiment, flew in the Space Shuttle Columbia payload bay as part of the Office of Aeronautics and Space Technology-2 (OAST-2) mission on STS-62, March, 1994. SAMPIE biased samples of solar arrays and space power materials to varying potentials with respect to the surrounding space plasma, and recorded the plasma currents collected and the arcs which occurred, along with a set of plasma diagnostics data. A large set of high quality data was obtained on the behavior of solar arrays and space power materials in the space environment. This paper is the first report on the data SAMPIE telemetered to the ground during the mission. It will be seen that the flight data promise to help determine arcing thresholds, snapover potentials, and floating potentials for arrays and spacecraft in LEO.

  15. Modulation of Protein–Protein Interactions for the Development of Novel Therapeutics

    PubMed Central

    Petta, Ioanna; Lievens, Sam; Libert, Claude; Tavernier, Jan; De Bosscher, Karolien

    2016-01-01

    Protein–protein interactions (PPIs) underlie most biological processes. An increasing interest to investigate the unexplored potential of PPIs in drug discovery is driven by the need to find novel therapeutic targets for a whole range of diseases with a high unmet medical need. To date, PPI inhibition with small molecules is the mechanism that has most often been explored, resulting in significant progress towards drug development. However, also PPI stabilization is gradually gaining ground. In this review, we provide a focused overview of a number of PPIs that control critical regulatory pathways and constitute targets for the design of novel therapeutics. We discuss PPI-modulating small molecules that are already pursued in clinical trials. In addition, we review a number of PPIs that are still under preclinical investigation but for which preliminary data support their use as therapeutic targets. PMID:26675501

  16. Protein Interactions of the MLL PHD Fingers Modulate MLL Target Gene Regulation in Human Cells

    PubMed Central

    Fair, Keri; Anderson, Melanie; Bulanova, Elena; Mi, Huaifeng; Tropschug, Maximilian; Diaz, Manuel O.

    2001-01-01

    The PHD fingers of the human MLL and Drosophila trx proteins have strong amino acid sequence conservation but their function is unknown. We have determined that these fingers mediate homodimerization and binding of MLL to Cyp33, a nuclear cyclophilin. These two proteins interact in vitro and in vivo in mammalian cells and colocalize at specific nuclear subdomains. Overexpression of the Cyp33 protein in leukemia cells results in altered expression of HOX genes that are targets for regulation by MLL. These alterations are suppressed by cyclosporine and are not observed in cell lines that express a mutant MLL protein without PHD fingers. These results suggest that binding of Cyp33 to MLL modulates its effects on the expression of target genes. PMID:11313484

  17. Protein interactions of the MLL PHD fingers modulate MLL target gene regulation in human cells.

    PubMed

    Fair, K; Anderson, M; Bulanova, E; Mi, H; Tropschug, M; Diaz, M O

    2001-05-01

    The PHD fingers of the human MLL and Drosophila trx proteins have strong amino acid sequence conservation but their function is unknown. We have determined that these fingers mediate homodimerization and binding of MLL to Cyp33, a nuclear cyclophilin. These two proteins interact in vitro and in vivo in mammalian cells and colocalize at specific nuclear subdomains. Overexpression of the Cyp33 protein in leukemia cells results in altered expression of HOX genes that are targets for regulation by MLL. These alterations are suppressed by cyclosporine and are not observed in cell lines that express a mutant MLL protein without PHD fingers. These results suggest that binding of Cyp33 to MLL modulates its effects on the expression of target genes.

  18. SENP1-modulated sumoylation regulates retinoblastoma protein (RB) and Lamin A/C interaction and stabilization.

    PubMed

    Sharma, P; Kuehn, M R

    2016-12-15

    The retinoblastoma tumor suppressor protein (RB) plays a critical role in cell proliferation and differentiation and its inactivation is a frequent underlying factor in tumorigenesis. While the regulation of RB function by phosphorylation is well studied, proteasome-mediated RB protein degradation is emerging as an important regulatory mechanism. Although our understanding of RB turnover is currently limited, there is evidence that the nuclear lamina filament protein Lamin A/C protects RB from proteasomal degradation. Here we show that SUMO1 conjugation of RB and Lamin A/C is modulated by the SUMO protease SENP1 and that sumoylation of both proteins is required for their interaction. Importantly, this SUMO1-dependent complex protects both RB and Lamin A/C from proteasomal turnover.

  19. Screening of Protein-Protein Interaction Modulators via Sulfo-Click Kinetic Target-Guided Synthesis

    PubMed Central

    Kulkarni, Sameer S.; Hu, Xiangdong; Doi, Kenichiro; Wang, Hong-Gang

    2011-01-01

    Kinetic Target-Guided Synthesis (TGS) and in situ click chemistry are among unconventional discovery strategies having the potential to streamline the development of protein-protein interaction modulators (PPIMs). In kinetic TGS and in situ click chemistry, the target is directly involved in the assembly of its own potent, bidentate ligand from a pool of reactive fragments. Herein, we report the use and validation of kinetic TGS based on the sulfo-click reaction between thio acids and sulfonyl azides as a screening and synthesis platform for the identification of high-quality PPIMs. Starting from a randomly designed library consisting of 9 thio acids and 9 sulfonyl azides leading to 81 potential acylsulfonamides, the target protein, Bcl-XL selectively assembled four PPIMs, acylsulfonamides SZ4TA2, SZ7TA2, SZ9TA1, and SZ9TA5, which have been shown to modulate Bcl-XL/BH3 interactions. To further investigate the Bcl-XL templation effect, control experiments were carried out using two mutants of Bcl-XL. In one mutant, phenylalanine Phe131 and aspartic acid Asp133, which are critical for the BH3 domain binding, have been substituted by alanines, while arginine Arg139, a residue identified to play a crucial role in the binding of ABT-737, a BH3 mimetic, has been replaced by an alanine in the other mutant. Incubation of these mutants with the reactive fragments and subsequent LC/MS-SIM analysis confirmed that these building block combinations yield the corresponding acylsulfonamides at the BH3 binding site, the actual “hot spot” of Bcl-XL. These results validate kinetic TGS using the sulfo-click reaction as a valuable tool for the straightforward identification of high-quality PPIMs. PMID:21506574

  20. A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data*

    PubMed Central

    Aucher, Willy; Becker, Emmanuelle; Ma, Emilie; Miron, Simona; Martel, Arnaud; Ochsenbein, Françoise; Marsolier-Kergoat, Marie-Claude; Guerois, Raphaël

    2010-01-01

    Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at http://biodev.extra.cea.fr/strip/. PMID:20733106

  1. Determining protein function and interaction from genome analysis

    DOEpatents

    Eisenberg, David; Marcotte, Edward M.; Thompson, Michael J.; Pellegrini, Matteo; Yeates, Todd O.

    2004-08-03

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  2. Plume-Free Stream Interaction Heating Effects During Orion Crew Module Reentry

    NASA Technical Reports Server (NTRS)

    Marichalar, J.; Lumpkin, F.; Boyles, K.

    2012-01-01

    During reentry of the Orion Crew Module (CM), vehicle attitude control will be performed by firing reaction control system (RCS) thrusters. Simulation of RCS plumes and their interaction with the oncoming flow has been difficult for the analysis community due to the large scarf angles of the RCS thrusters and the unsteady nature of the Orion capsule backshell environments. The model for the aerothermal database has thus relied on wind tunnel test data to capture the heating effects of thruster plume interactions with the freestream. These data are only valid for the continuum flow regime of the reentry trajectory. A Direct Simulation Monte Carlo (DSMC) analysis was performed to study the vehicle heating effects that result from the RCS thruster plume interaction with the oncoming freestream flow at high altitudes during Orion CM reentry. The study was performed with the DSMC Analysis Code (DAC). The inflow boundary conditions for the jets were obtained from Data Parallel Line Relaxation (DPLR) computational fluid dynamics (CFD) solutions. Simulations were performed for the roll, yaw, pitch-up and pitch-down jets at altitudes of 105 km, 125 km and 160 km as well as vacuum conditions. For comparison purposes (see Figure 1), the freestream conditions were based on previous DAC simulations performed without active RCS to populate the aerodynamic database for the Orion CM. Other inputs to the analysis included a constant Orbital reentry velocity of 7.5 km/s and angle of attack of 160 degrees. The results of the study showed that the interaction effects decrease quickly with increasing altitude. Also, jets with highly scarfed nozzles cause more severe heating compared to the nozzles with lower scarf angles. The difficulty of performing these simulations was based on the maximum number density and the ratio of number densities between the freestream and the plume for each simulation. The lowest altitude solutions required a substantial amount of computational resources

  3. Time-dependent modulation of galactic cosmic rays by merged interaction regions

    NASA Technical Reports Server (NTRS)

    Perko, J. S.

    1993-01-01

    Models that solve the one-dimensional, solar modulation equation have reproduced the 11-year galactic cosmic ray using functional representations of global merged interaction regions (MIRs). This study extends those results to the solution of the modulation equation with explicit time dependence. The magnetometers on Voyagers 1 and 2 provide local magnetic field intensities at regular intervals, from which one calculates the ratio of the field intensity to the average local field. These ratios in turn are inverted to form diffusion coefficients. Strung together in radius and time, these coefficents then fall and rise with the strength of the interplanetary magnetic field, becoming representations of MIRs. These diffusion coefficients, calculated locally, propagate unchanged from approx. 10 AU to the outer boundary (120 AU). Inside 10 AU, all parameters, including the diffusion coefficient are assumed constant in time and space. The model reproduces the time-intensity profiles of Voyager 2 and Pioneer 10. Radial gradient data from 1982-1990 between Pioneer 10 and Voyager 2 are about the same magnitude as those calculated in the model. It is also shows agreement in rough magnitude with the radial gradient between Pioneer 10 and 1 AU. When coupled with enhanced, time-dependent solar wind speed at the probe's high latitude, as measured by independent observers, the model also follows Voyager 1's time-intensity profile reasonably well, providing a natural source the model also follows Voyager 1's time-intensity profile reasonably well, providing a natural source for the observed negative latitudinal gradients. The model exhibits the 11-year cyclical cosmic ray intensity behavior at all radii, including 1 AU, not just at the location of the spacecraft where the magnetic fields are measured. In addition, the model's point of cosmic ray maximum correctly travels at the solar wind speed, illustrating the well-known propagation of modulation. Finally, at least in the inner

  4. Time-dependent modulation of galactic cosmic rays by merged interaction regions

    NASA Technical Reports Server (NTRS)

    Perko, J. S.

    1993-01-01

    Models that solve the one-dimensional, solar modulation equation have reproduced the 11-year galactic cosmic ray using functional representations of global merged interaction regions (MIRs). This study extends those results to the solution of the modulation equation with explicit time dependence. The magnetometers on Voyagers 1 and 2 provide local magnetic field intensities at regular intervals, from which one calculates the ratio of the field intensity to the average local field. These ratios in turn are inverted to form diffusion coefficients. Strung together in radius and time, these coefficents then fall and rise with the strength of the interplanetary magnetic field, becoming representations of MIRs. These diffusion coefficients, calculated locally, propagate unchanged from approx. 10 AU to the outer boundary (120 AU). Inside 10 AU, all parameters, including the diffusion coefficient are assumed constant in time and space. The model reproduces the time-intensity profiles of Voyager 2 and Pioneer 10. Radial gradient data from 1982-1990 between Pioneer 10 and Voyager 2 are about the same magnitude as those calculated in the model. It is also shows agreement in rough magnitude with the radial gradient between Pioneer 10 and 1 AU. When coupled with enhanced, time-dependent solar wind speed at the probe's high latitude, as measured by independent observers, the model also follows Voyager 1's time-intensity profile reasonably well, providing a natural source the model also follows Voyager 1's time-intensity profile reasonably well, providing a natural source for the observed negative latitudinal gradients. The model exhibits the 11-year cyclical cosmic ray intensity behavior at all radii, including 1 AU, not just at the location of the spacecraft where the magnetic fields are measured. In addition, the model's point of cosmic ray maximum correctly travels at the solar wind speed, illustrating the well-known propagation of modulation. Finally, at least in the inner

  5. Cell proliferation and modulation of interaction of estrogen receptors with coregulators induced by ERα and ERβ agonists.

    PubMed

    Evers, Nynke M; van den Berg, Johannes H J; Wang, Si; Melchers, Diana; Houtman, René; de Haan, Laura H J; Ederveen, Antwan G H; Groten, John P; Rietjens, Ivonne M C M

    2014-09-01

    The aim of the present study was to investigate modulation of the interaction of the ERα and ERβ with coregulators in the ligand responses induced by estrogenic compounds. To this end, selective ERα and ERβ agonists were characterized for intrinsic relative potency reflected by EC50 and maximal efficacy towards ERα and ERβ mediated response in ER selective reporter gene assays, and subsequently tested for induction of cell proliferation in T47D-ERβ cells with variable ERα/ERβ ratio, and finally for ligand dependent modulation of the interaction of ERα and ERβ with coregulators using the MARCoNI assay, with 154 unique nuclear receptor coregulator peptides derived from 66 different coregulators. Results obtained reveal an important influence of the ERα/ERβ ratio and receptor selectivity of the compounds tested on induction of cell proliferation. ERα agonists activate cell proliferation whereas ERβ suppresses ERα mediated cell proliferation. The responses in the MARCoNI assay reveal that upon ERα or ERβ activation by a specific agonist, the modulation of the interaction of the ERs with coregulators is very similar indicating only a limited number of differences upon ERα or ERβ activation by a specific ligand. Differences in the modulation of the interaction of the ERs with coregulators between the different agonists were more pronounced. Based on ligand dependent differences in the modulation of the interaction of the ERs with coregulators, the MARCoNI assay was shown to be able to classify the ER agonists discriminating between different agonists for the same receptor, a characteristic not defined by the ER selective reporter gene or proliferation assays. It is concluded that the ultimate effect of the model compounds on proliferation of estrogen responsive cells depends on the intrinsic relative potency of the agonist towards ERα and ERβ and the cellular ERα/ERβ ratio whereas differences in the modulation of the interaction of the ERα and

  6. Interaction between selected bacterial strains and Arabidopsis halleri modulates shoot proteome and cadmium and zinc accumulation.

    PubMed

    Farinati, Silvia; DalCrso, Giovanni; Panigati, Monica; Furini, Antonella

    2011-06-01

    The effects of plant-microbe interactions between the hyperaccumulator Arabidopsis halleri and eight bacterial strains, isolated from the rhizosphere of A. halleri plants grown in a cadmium- and zinc-contaminated site, were analysed for shoot metal accumulation, shoot proteome, and the transcription of genes involved in plant metal homeostasis and hyperaccumulation. Cadmium and zinc concentrations were lower in the shoots of plants cultivated in the presence of these metals plus the selected bacterial strains compared with plants grown solely with these metals or, as previously reported, with plants grown with these metals plus the autochthonous rhizosphere-derived microorganisms. The shoot proteome of plants cultivated in the presence of these selected bacterial strains plus metals, showed an increased abundance of photosynthesis- and abiotic stress-related proteins (e.g. subunits of the photosynthetic complexes, Rubisco, superoxide dismutase, and malate dehydrogenase) counteracted by a decreased amount of plant defence-related proteins (e.g. endochitinases, vegetative storage proteins, and β-glucosidase). The transcription of several homeostasis genes was modulated by the microbial communities and by Cd and Zn content in the shoot. Altogether these results highlight the importance of plant-microbe interactions in plant protein expression and metal accumulation and emphasize the possibility of exploiting microbial consortia for increasing or decreasing shoot metal content.

  7. Phototropism: a "simple" physiological response modulated by multiple interacting photosensory-response pathways.

    PubMed

    Liscum, E; Stowe-Evans, E L

    2000-09-01

    Phototropism is the process by which plants reorient growth of various organs, most notably stems, in response to lateral differences in light quantity and/or quality. The ubiquitous nature of the phototropic response in the plant kingdom implies that it provides some adaptive evolutionary advantage. Upon visual inspection it is tempting to surmise that phototropic curvatures result from a relatively simple growth response to a directional stimulus. However, detailed photophysiological, and more recently genetic and molecular, studies have demonstrated that phototropism is in fact regulated by complex interactions among several photosensory systems. At least two receptors, phototropin and a presently unidentified receptor, appear to mediate the primary photoreception of directional blue light cues in dark-grown plants. PhyB may also function as a primary receptor to detect lateral increases in far-red light in neighbor-avoidance responses of light-grown plants. Phytochromes (phyA and phyB at a minimum) also appear to function as secondary receptors to regulate adaptation processes that ultimately modulate the magnitude of curvature induced by primary photoperception. As a result of the interactions of these multiple photosensory systems plants are able to maximize the adaptive advantage of the phototropic response in ever changing light environments.

  8. Interaction between selected bacterial strains and Arabidopsis halleri modulates shoot proteome and cadmium and zinc accumulation

    PubMed Central

    Panigati, Monica; Furini, Antonella

    2011-01-01

    The effects of plant–microbe interactions between the hyperaccumulator Arabidopsis halleri and eight bacterial strains, isolated from the rhizosphere of A. halleri plants grown in a cadmium- and zinc-contaminated site, were analysed for shoot metal accumulation, shoot proteome, and the transcription of genes involved in plant metal homeostasis and hyperaccumulation. Cadmium and zinc concentrations were lower in the shoots of plants cultivated in the presence of these metals plus the selected bacterial strains compared with plants grown solely with these metals or, as previously reported, with plants grown with these metals plus the autochthonous rhizosphere-derived microorganisms. The shoot proteome of plants cultivated in the presence of these selected bacterial strains plus metals, showed an increased abundance of photosynthesis- and abiotic stress-related proteins (e.g. subunits of the photosynthetic complexes, Rubisco, superoxide dismutase, and malate dehydrogenase) counteracted by a decreased amount of plant defence-related proteins (e.g. endochitinases, vegetative storage proteins, and β-glucosidase). The transcription of several homeostasis genes was modulated by the microbial communities and by Cd and Zn content in the shoot. Altogether these results highlight the importance of plant-microbe interactions in plant protein expression and metal accumulation and emphasize the possibility of exploiting microbial consortia for increasing or decreasing shoot metal content. PMID:21357773

  9. Frequency modulation of stochastic gene expression bursts by strongly interacting small RNAs

    NASA Astrophysics Data System (ADS)

    Kumar, Niraj; Jia, Tao; Zarringhalam, Kourosh; Kulkarni, Rahul V.

    2016-10-01

    The sporadic nature of gene expression at the single-cell level—long periods of inactivity punctuated by bursts of mRNA or protein production—plays a critical role in diverse cellular processes. To elucidate the cellular role of bursting in gene expression, synthetic biology approaches have been used to design simple genetic circuits with bursty mRNA or protein production. Understanding how such genetic circuits can be designed with the ability to control burst-related parameters requires the development of quantitative stochastic models of gene expression. In this work, we analyze stochastic models for the regulation of gene expression bursts by strongly interacting small RNAs. For the parameter range considered, results based on mean-field approaches are significantly inaccurate and alternative analytical approaches are needed. Using simplifying approximations, we obtain analytical results for the corresponding steady-state distributions that are in agreement with results from stochastic simulations. These results indicate that regulation by small RNAs, in the strong interaction limit, can be used to effectively modulate the frequency of bursting. We explore the consequences of such regulation for simple genetic circuits involving feedback effects and switching between promoter states.

  10. Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

    PubMed Central

    Dunipace, Leslie; Ozdemir, Anil; Stathopoulos, Angelike

    2011-01-01

    It has been shown in several organisms that multiple cis-regulatory modules (CRMs) of a gene locus can be active concurrently to support similar spatiotemporal expression. To understand the functional importance of such seemingly redundant CRMs, we examined two CRMs from the Drosophila snail gene locus, which are both active in the ventral region of pre-gastrulation embryos. By performing a deletion series in a ∼25 kb DNA rescue construct using BAC recombineering and site-directed transgenesis, we demonstrate that the two CRMs are not redundant. The distal CRM is absolutely required for viability, whereas the proximal CRM is required only under extreme conditions such as high temperature. Consistent with their distinct requirements, the CRMs support distinct expression patterns: the proximal CRM exhibits an expanded expression domain relative to endogenous snail, whereas the distal CRM exhibits almost complete overlap with snail except at the anterior-most pole. We further show that the distal CRM normally limits the increased expression domain of the proximal CRM and that the proximal CRM serves as a `damper' for the expression levels driven by the distal CRM. Thus, the two CRMs interact in cis in a non-additive fashion and these interactions may be important for fine-tuning the domains and levels of gene expression. PMID:21813571

  11. Hydrophilic-hydrophobic polymer blend for modulation of crystalline changes and molecular interactions in solid dispersion.

    PubMed

    Van Ngo, Hai; Nguyen, Phuc Kien; Van Vo, Toi; Duan, Wei; Tran, Van-Thanh; Tran, Phuong Ha-Lien; Tran, Thao Truong-Dinh

    2016-11-20

    This research study aimed to develop a new strategy for using a polymer blend in solid dispersion (SD) for dissolution enhancement of poorly water-soluble drugs. SDs with different blends of hydrophilic-hydrophobic polymers (zein/hydroxypropyl methylcellulose - zein/HPMC) were prepared using spray drying to modulate the drug crystal and polymer-drug interactions in SDs. Physicochemical characterizations, including power X-ray diffraction and Fourier transform infrared spectroscopy, were performed to elucidate the roles of the blends in SDs. Although hydrophobic polymers played a key role in changing the model drug from a crystal to an amorphous state, the dissolution rate was limited due to the wetting property. Fortunately, the hydrophilic-hydrophobic blend not only reduced the drug crystallinity but also resulted in a hydrogen bonding interaction between the drugs and the polymer for a dissolution rate improvement. This work may contribute to a new generation of solid dispersion using a blend of hydrophilic-hydrophobic polymers for an effective dissolution enhancement of poorly water-soluble drugs.

  12. Posture interacts with arm weight support to modulate corticomotor excitability to the upper limb.

    PubMed

    Runnalls, Keith D; Anson, Greg; Byblow, Winston D

    2017-01-01

    The use of arm weight support (WS) to optimize movement quality may be an avenue for improved upper limb stroke rehabilitation; however, the underlying neurophysiological effects of WS are not well understood. Rehabilitation exercises may be performed when sitting or standing, but the interaction of posture with WS has not been examined until now. We explored the effect of posture with WS on corticomotor excitability (CME) in healthy adults. Thirteen participants performed static shoulder abduction in two postures (sitting and standing) at three levels of WS (0, 45, and 90 % of full support). Transcranial magnetic stimulation of primary motor cortex was used to elicit motor-evoked potentials (MEPs) in eight upper limb muscles. Stimulus-response (SR) curves were fitted to the MEP data using nonlinear regression. Whole-body posture interacted with WS to influence tonic activity and CME in all muscles examined. SR curve parameters revealed greater CME when standing compared to sitting for upper arm muscles, but lower CME to the shoulder, forearm, and hand. Distal to the shoulder, tonic activity and CME were modulated independent of any explicit differences in task requirements. Overall, these results support a model of integrated upper limb control influenced by whole-body posture and WS. These findings have implications for the application of WS in settings such as upper limb rehabilitation after stroke.

  13. Polyglutamine genes interact to modulate the severity and progression of neurodegeneration in Drosophila.

    PubMed

    Lessing, Derek; Bonini, Nancy M

    2008-02-01

    The expansion of polyglutamine tracts in a variety of proteins causes devastating, dominantly inherited neurodegenerative diseases, including six forms of spinal cerebellar ataxia (SCA). Although a polyglutamine expansion encoded in a single allele of each of the responsible genes is sufficient for the onset of each disease, clinical observations suggest that interactions between these genes may affect disease progression. In a screen for modifiers of neurodegeneration due to SCA3 in Drosophila, we isolated atx2, the fly ortholog of the human gene that causes a related ataxia, SCA2. We show that the normal activity of Ataxin-2 (Atx2) is critical for SCA3 degeneration and that Atx2 activity hastens the onset of nuclear inclusions associated with SCA3. These activities depend on a conserved protein interaction domain of Atx2, the PAM2 motif, which mediates binding of cytoplasmic poly(A)-binding protein (PABP). We show here that PABP also influences SCA3-associated neurodegeneration. These studies indicate that the toxicity of one polyglutamine disease protein can be dramatically modulated by the normal activity of another. We propose that functional links between these genes are critical to disease severity and progression, such that therapeutics for one disease may be applicable to others.

  14. Modulation of graft architectures for enhancing hydrophobic interaction of biomolecules with thermoresponsive polymer-grafted surfaces.

    PubMed

    Idota, Naokazu; Kikuchi, Akihiko; Kobayashi, Jun; Sakai, Kiyotaka; Okano, Teruo

    2012-11-01

    This paper describes the effects of graft architecture of poly(N-isopropylacrylamide) (PIPAAm) brush surfaces on thermoresponsive aqueous wettability changes and the temperature-dependent hydrophobic interaction of steroids in silica capillaries (I.D.: 50 μm). PIPAAm brushes were grafted onto glass substrates by surface-initiated atom transfer radical polymerization (ATRP) that is one of the living radical polymerization techniques. Increases in the graft density and chain length of PIPAAm brushes increased the hydration of polymer brushes, resulting in the increased hydrophilic properties of the surface below the transition temperature of PIPAAm at 32 °C. More hydrophobic surface properties were also observed on surfaces modified with the block copolymers of IPAAm and n-butyl methacrylate (BMA) than that with IPAAm homopolymer-grafted surfaces over the transition temperature. Using PBMA-b-PIPAAm-grafted silica capillaries, the baseline separation of steroids was successfully achieved by only changing temperature. The incorporation of hydrophobic PBMA chains in grafted PIPAAm enhanced the hydrophobic interaction with testosterone above the transition temperature. The surface modification of hydrophobicity-enhanced thermoresponsive polymers is a promising method for the preparation of thermoresponsive biointerfaces that can effectively modulated their biomolecule and cell adsorption with the wide dynamic range of hydrophilic/hydrophobic property change across the transition temperature.

  15. Disabled-2 modulates homotypic and heterotypic platelet interactions by binding to sulfatides.

    PubMed

    Welsh, John D; Charonko, John J; Salmanzadeh, Alireza; Drahos, Karen E; Shafiee, Hadi; Stremler, Mark A; Davalos, Rafael V; Capelluto, Daniel G S; Vlachos, Pavlos P; Finkielstein, Carla V

    2011-07-01

    Disabled-2 (Dab2) inhibits platelet aggregation by competing with fibrinogen for binding to the α(IIb) β(3) integrin receptor, an interaction that is modulated by Dab2 binding to sulfatides at the outer leaflet of the platelet plasma membrane. The disaggregatory function of Dab2 has been mapped to its N-terminus phosphotyrosine-binding (N-PTB) domain. Our data show that the surface levels of P-selectin, a platelet transmembrane protein known to bind sulfatides and promote cell-cell interactions, are reduced by Dab2 N-PTB, an event that is reversed in the presence of a mutant form of the protein that is deficient in sulfatide but not in integrin binding. Importantly, Dab2 N-PTB, but not its sulfatide binding-deficient form, was able to prevent sulfatide-induced platelet aggregation when tested under haemodynamic conditions in microfluidic devices at flow rates with shear stress levels corresponding to those found in vein microcirculation. Moreover, the regulatory role of Dab2 N-PTB extends to platelet-leucocyte adhesion and aggregation events, suggesting a multi-target role for Dab2 in haemostasis.

  16. Generalized spin-dependent WIMP-nucleus interactions and the DAMA modulation effect

    SciTech Connect

    Scopel, Stefano; Yoon, Kook-Hyun; Yoon, Jong-Hyun E-mail: koreasds@naver.com

    2015-07-01

    Guided by non-relativistic Effective Field Theory (EFT) we classify the most general spin-dependent interactions between a fermionic Weakly Interacting Massive Particle (WIMP) and nuclei, and within this class of models we discuss the viability of an interpretation of the DAMA modulation result in terms of a signal from WIMP elastic scatterings using a halo-independent approach. We find that, although several relativistic EFT's can lead to a spin-dependent cross section, in some cases with an explicit, non-negligible dependence on the WIMP incoming velocity, three main scenarios can be singled out in the non-relativistic limit which approximately encompass them all, and that only differ by their dependence on the transferred momentum. For two of them compatibility between DAMA and other constraints is possible for a WIMP mass below 30 GeV, but only for a WIMP velocity distribution in the halo of our Galaxy which departs from a Maxwellian. This is achieved by combining a suppression of the WIMP effective coupling to neutrons (to evade constraints from xenon and germanium detectors) to an explicit quadratic or quartic dependence of the cross section on the transferred momentum (that leads to a relative enhancement of the expected rate off sodium in DAMA compared to that off fluorine in droplet detectors and bubble chambers). For larger WIMP masses the same scenarios are excluded by scatterings off iodine in COUPP.

  17. IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC.

    PubMed

    Ennajdaoui, Hanane; Howard, Jonathan M; Sterne-Weiler, Timothy; Jahanbani, Fereshteh; Coyne, Doyle J; Uren, Philip J; Dargyte, Marija; Katzman, Sol; Draper, Jolene M; Wallace, Andrew; Cazarez, Oscar; Burns, Suzanne C; Qiao, Mei; Hinck, Lindsay; Smith, Andrew D; Toloue, Masoud M; Blencowe, Benjamin J; Penalva, Luiz O F; Sanford, Jeremy R

    2016-05-31

    Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) expression correlates with malignancy, but its role(s) in pathogenesis remains enigmatic. We interrogated the IGF2BP3-RNA interaction network in pancreatic ductal adenocarcinoma (PDAC) cells. Using a combination of genome-wide approaches, we have identified 164 direct mRNA targets of IGF2BP3. These transcripts encode proteins enriched for functions such as cell migration, proliferation, and adhesion. Loss of IGF2BP3 reduced PDAC cell invasiveness and remodeled focal adhesion junctions. Individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) revealed significant overlap of IGF2BP3 and microRNA (miRNA) binding sites. IGF2BP3 promotes association of the RNA-induced silencing complex (RISC) with specific transcripts. Our results show that IGF2BP3 influences a malignancy-associated RNA regulon by modulating miRNA-mRNA interactions. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. Applications of snake venom components to modulate integrin activities in cell-matrix interactions

    PubMed Central

    Marcinkiewicz, Cezary

    2013-01-01

    Snake venom proteins are broadly investigated in the different areas of life science. Direct interaction of these compounds with cells may involve a variety of mechanisms that result in diverse cellular responses leading to the activation or blocking of physiological functions of the cell. In this review, the snake venom components interacting with integrins will be characterized in context of their effect on cellular response. Currently, two major families of snake venom proteins are considered as integrin-binding molecules. The most attention has been devoted to the disintegrin family, which binds certain types of integrins through specific motifs recognized as a tri-peptide structurally localized on an integrin-binding loop. Other snake venom integrin-binding proteins belong to the C-type lectin family. Snake venom molecules bind to the cellular integrins resulting in a modulation of cell signaling and in consequence, the regulation of cell proliferation, migration and apoptosis. Therefore, snake venom research on the integrin-binding molecules may have significance in biomedicine and basic cell biology. PMID:23811033

  19. Generalized spin-dependent WIMP-nucleus interactions and the DAMA modulation effect

    NASA Astrophysics Data System (ADS)

    Scopel, Stefano; Yoon, Kook-Hyun; Yoon, Jong-Hyun

    2015-07-01

    Guided by non-relativistic Effective Field Theory (EFT) we classify the most general spin-dependent interactions between a fermionic Weakly Interacting Massive Particle (WIMP) and nuclei, and within this class of models we discuss the viability of an interpretation of the DAMA modulation result in terms of a signal from WIMP elastic scatterings using a halo-independent approach. We find that, although several relativistic EFT's can lead to a spin-dependent cross section, in some cases with an explicit, non-negligible dependence on the WIMP incoming velocity, three main scenarios can be singled out in the non-relativistic limit which approximately encompass them all, and that only differ by their dependence on the transferred momentum. For two of them compatibility between DAMA and other constraints is possible for a WIMP mass below 30 GeV, but only for a WIMP velocity distribution in the halo of our Galaxy which departs from a Maxwellian. This is achieved by combining a suppression of the WIMP effective coupling to neutrons (to evade constraints from xenon and germanium detectors) to an explicit quadratic or quartic dependence of the cross section on the transferred momentum (that leads to a relative enhancement of the expected rate off sodium in DAMA compared to that off fluorine in droplet detectors and bubble chambers). For larger WIMP masses the same scenarios are excluded by scatterings off iodine in COUPP.

  20. CD28–B7 Interaction Modulates Short- and Long-Lived Plasma Cell Function

    PubMed Central

    Njau, Modesta N.; Kim, Jin Hyang; Chappell, Craig P.; Ravindran, Rajesh; Thomas, Leela; Pulendran, Bali; Jacob, Joshy

    2016-01-01

    The interaction of CD28, which is constitutively expressed on T cells, with B7.1/B7.2 expressed on APCs is critical for T cell activation. CD28 is also expressed on murine and human plasma cells but its function on these cells remains unclear. There are two types of plasma cells: short-lived ones that appear in the secondary lymphoid tissue shortly after Ag exposure, and long-lived plasma cells that mainly reside in the bone marrow. We demonstrate that CD28-deficient murine short- and long-lived plasma cells produce significantly higher levels of Abs than do their wild-type counterparts. This was owing to both increased frequencies of plasma cells as well as increased Ab production per plasma cell. Plasma cells also express the ligand for CD28, B7.1, and B7.2. Surprisingly, deficiency of B7.1 and B7.2 in B cells also led to higher Ab levels, analogous to Cd28−/− plasma cells. Collectively, our results suggest that the CD28–B7 interaction operates as a key modulator of plasma cell function. PMID:22908331

  1. Resource availability modulates biodiversity-invasion relationships by altering competitive interactions.

    PubMed

    Yang, Tianjie; Wei, Zhong; Friman, Ville-Petri; Xu, Yangchun; Shen, Qirong; Kowalchuk, George A; Jousset, Alexandre

    2017-02-22

    Community diversity affects the survival of newly introduced species via resource competition. Competitive interactions can be modulated by resource availability and we hypothesised that this may alter biodiversity-invasion relationships. To study this, we assessed the growth of a bacterial invader, Ralstonia solanacearum, when introduced into communities comprised of one to five closely related resident species under different resource concentrations. The invader growth was then examined as a function of resident community richness, species composition and resource availability. We found that the relative density of the invader was reduced by increasing resident community richness and resource availability. Mechanistically, this could be explained by changes in the competitive interactions between the resident species and the invader along the resource availability gradient. At low resource availability, resident species with a high catabolic similarity with the invader efficiently reduced the invader relative density, while at high resource availability, fast-growing resident species became more important for the invader suppression. These results indicate that the relative importance of different resident community species can change dynamically along to resource availability gradient. Diverse communities could be thus more robust to invasions by providing a set of keystone species that can take suppressive roles across different environments. This article is protected by copyright. All rights reserved.

  2. 3D extracellular matrix interactions modulate tumour cell growth, invasion and angiogenesis in engineered tumour microenvironments.

    PubMed

    Taubenberger, Anna V; Bray, Laura J; Haller, Barbara; Shaposhnykov, Artem; Binner, Marcus; Freudenberg, Uwe; Guck, Jochen; Werner, Carsten

    2016-05-01

    Interactions between tumour cells and extracellular matrix proteins of the tumour microenvironment play crucial roles in cancer progression. So far, however, there are only a few experimental platforms available that allow us to study these interactions systematically in a mechanically defined three-dimensional (3D) context. Here, we have studied the effect of integrin binding motifs found within common extracellular matrix (ECM) proteins on 3D breast (MCF-7) and prostate (PC-3, LNCaP) cancer cell cultures, and co-cultures with endothelial and mesenchymal stromal cells. For this purpose, matrix metalloproteinase-degradable biohybrid poly(ethylene) glycol-heparin hydrogels were decorated with the peptide motifs RGD, GFOGER (collagen I), or IKVAV (laminin-111). Over 14days, cancer spheroids of 100-200μm formed. While the morphology of poorly invasive MCF-7 and LNCaP cells was not modulated by any of the peptide motifs, the aggressive PC-3 cells exhibited an invasive morphology when cultured in hydrogels comprising IKVAV and GFOGER motifs compared to RGD motifs or nonfunctionalised controls. PC-3 (but not MCF-7 and LNCaP) cell growth and endothelial cell infiltration were also significantly enhanced in IKVAV and GFOGER presenting gels. Taken together, we have established a 3D culture model that allows for dissecting the effect of biochemical cues on processes relevant to early cancer progression. These findings provide a basis for more mechanistic studies that may further advance our understanding of how ECM modulates cancer cell invasion and how to ultimately interfere with this process. Threedimensional in vitro cancer models have generated great interest over the past decade. However, most models are not suitable to systematically study the effects of environmental cues on cancer development and progression. To overcome this limitation, we have developed an innovative hydrogel platform to study the interactions between breast and prostate cancer cells and

  3. Hsp90 directly interacts, in vitro, with amyloid structures and modulates their assembly and disassembly.

    PubMed

    Schirmer, Claire; Lepvrier, Eléonore; Duchesne, Laurence; Decaux, Olivier; Thomas, Daniel; Delamarche, Christian; Garnier, Cyrille

    2016-11-01

    The 90kDa heat shock protein (Hsp90) participates in regulating the homeostasis of cellular proteins and was considered one of the key chaperones involved in the control and regulation of amyloid deposits. Hsp90 interacts with the amyloid protein tau through tau aggregation-prone regions, including the VQIVYK hexapeptide motif. This hexapeptide, which self-aggregates, forming amyloid fibrils, is widely used to model amyloid formation mechanisms. Despite evidence showing that Hsp90 interacts directly with Ac-VQIVYK-NH2, its role in the hexapeptide fibrillation process and its binding to peptide structures have not yet been determined. Various biochemical and biophysical techniques, including ultracentrifugation, spectrophotometry, spectrofluorimetry, and electron microscopy, were employed to assess the effects of Hsp90 on Ac-VQIVYK-NH2 assembly and disassembly processes. At sub-stoichiometric concentrations, Hsp90 bound directly to Ac-VQIVYK-NH2 amyloid structures in vitro, with each Hsp90 dimer interacting with an amyloid structure made of around 50 hexapeptide subunits. Hsp90 inhibited Ac-VQIVYK-NH2 assembly by increasing the critical concentrations of Ac-VQIVYK-NH2 required for assembly. Hsp90 also inhibited the disassembly of Ac-VQIVYK-NH2 amyloid fibrils and promoted their rescue. A model explaining the dual effect of Hsp90 on the Ac-VQIVYK-NH2 amyloid fibrillation process has been proposed. These in vitro results provide new insights into the possible roles of molecular chaperones in modulating amyloid structures by limiting the spread of toxic species. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Cannabidiol Modulates Fear Memory Formation Through Interactions with Serotonergic Transmission in the Mesolimbic System.

    PubMed

    Norris, Christopher; Loureiro, Michael; Kramar, Cecilia; Zunder, Jordan; Renard, Justine; Rushlow, Walter; Laviolette, Steven R

    2016-11-01

    Emerging evidence suggests that the largest phytochemical component of cannabis, cannabidiol (CBD), may possess pharmacotherapeutic properties in the treatment of neuropsychiatric disorders. CBD has been reported to functionally interact with both the mesolimbic dopamine (DA) and serotonergic (5-HT) receptor systems. However, the underlying mechanisms by which CBD may modulate emotional processing are not currently understood. Using a combination of in vivo electrophysiological recording and fear conditioning in rats, the present study aimed to characterize the behavioral, neuroanatomical, and pharmacological effects of CBD within the mesolimbic pathway, and its possible functional interactions with 5-HT and DAergic transmission. Using targeted microinfusions of CBD into the shell region of the mesolimbic nucleus accumbens (NASh), we report that intra-NASh CBD potently blocks the formation of conditioned freezing behaviors. These effects were challenged with DAergic, cannabinoid CB1 receptor, and serotonergic (5-HT1A) transmission blockade, but only 5-HT1A blockade restored associative conditioned freezing behaviors. In vivo intra-ventral tegmental area (VTA) electrophysiological recordings revealed that behaviorally effective doses of intra-NASh CBD elicited a predominant decrease in spontaneous DAergic neuronal frequency and bursting activity. These neuronal effects were reversed by simultaneous blockade of 5-HT1A receptor transmission. Finally, using a functional contralateral disconnection procedure, we demonstrated that the ability of intra-NASh CBD to block the formation of conditioned freezing behaviors was dependent on intra-VTA GABAergic transmission substrates. Our findings demonstrate a novel NAcVTA circuit responsible for the behavioral and neuronal effects of CBD within the mesolimbic system via functional interactions with serotonergic 5-HT1A receptor signaling.

  5. ABC multidrug transporters: target for modulation of drug pharmacokinetics and drug-drug interactions.

    PubMed

    Marquez, Béatrice; Van Bambeke, Françoise

    2011-05-01

    Nine proteins of the ABC superfamily (P-glycoprotein, 7 MRPs and BCRP) are involved in multidrug transport. Being localised at the surface of endothelial or epithelial cells, they expel drugs back to the external medium (if located at the apical side [P-glycoprotein, BCRP, MRP2, MRP4 in the kidney]) or to the blood (if located at the basolateral side [MRP1, MRP3, MRP4, MRP5]), modulating thereby their absorption, distribution, and elimination. In the CNS, most transporters are oriented to expel drugs to the blood. Transporters also cooperate with Phase I/Phase II metabolism enzymes by eliminating drug metabolites. Their major features are (i) their capacity to recognize drugs belonging to unrelated pharmacological classes, and (ii) their redundancy, a single molecule being possibly substrate for different transporters. This ensures an efficient protection of the body against invasion by xenobiotics. Competition for transport is now characterized as a mechanism of interaction between co-administered drugs, one molecule limiting the transport of the other, potentially affecting bioavailability, distribution, and/or elimination. Again, this mechanism reinforces drug interactions mediated by cytochrome P450 inhibition, as many substrates of P-glycoprotein and CYP3A4 are common. Induction of the expression of genes coding for MDR transporters is another mechanism of drug interaction, which could affect all drug substrates of the up-regulated transporter. Overexpression of MDR transporters confers resistance to anticancer agents and other therapies. All together, these data justify why studying drug active transport should be part of the evaluation of new drugs, as recently recommended by the FDA.

  6. Dia-interacting protein modulates formin-mediated actin assembly at the cell cortex.

    PubMed

    Eisenmann, Kathryn M; Harris, Elizabeth S; Kitchen, Susan M; Holman, Holly A; Higgs, Henry N; Alberts, Arthur S

    2007-04-03

    Mammalian Diaphanous (mDia)-related formins and the N-WASP-activated Arp2/3 complex initiate the assembly of filamentous actin. Dia-interacting protein (DIP) binds via its amino-terminal SH3 domain to the proline-rich formin homology 1 (FH1) domain of mDia1 and mDia2 and to the N-WASp proline-rich region. Here, we investigated an interaction between a conserved leucine-rich region (LRR) in DIP and the mDia FH2 domain that nucleates, processively elongates, and bundles actin filaments. DIP binding to mDia2 was regulated by the same Rho-GTPase-controlled autoinhibitory mechanism modulating formin-mediated actin assembly. DIP was previously shown to interact with and stimulate N-WASp-dependent branched filament assembly via Arp2/3. Despite direct binding to both mDia1 and mDia2 FH2 domains, DIP LRR inhibited only mDia2-dependent filament assembly and bundling in vitro. DIP expression interfered with filopodia formation, consistent with a role for mDia2 in assembly of these structures. After filopodia retraction into the cell body, DIP expression induced excessive nonapoptotic membrane blebbing, a physiological process involved in both cytokinesis and amoeboid cell movement. DIP-induced blebbing was dependent on mDia2 but did not require the activities of either mDia1 or Arp2/3. These observations point to a pivotal role for DIP in the control of nonbranched and branched actin-filament assembly that is mediated by Diaphanous-related formins and activators of Arp2/3, respectively. The ability of DIP to trigger blebbing also suggests a role for mDia2 in the assembly of cortical actin necessary for maintaining plasma-membrane integrity.

  7. Pro-invasive Effect of Proto-oncogene PBF Is Modulated by an Interaction with Cortactin

    PubMed Central

    Watkins, Rachel J.; Imruetaicharoenchoke, Waraporn; Read, Martin L.; Sharma, Neil; Poole, Vikki L.; Gentilin, Erica; Bansal, Sukhchain; Bosseboeuf, Emy; Fletcher, Rachel; Nieto, Hannah R.; Mallick, Ujjal; Hackshaw, Allan; Mehanna, Hisham; Boelaert, Kristien; Smith, Vicki E.

    2016-01-01

    Context: Metastatic disease is responsible for the majority of endocrine cancer deaths. New therapeutic targets are urgently needed to improve patient survival rates. Objective: The proto-oncogene PTTG1-binding factor (PBF/PTTG1IP) is overexpressed in multiple endocrine cancers and circumstantially associated with tumor aggressiveness. This study aimed to understand the role of PBF in tumor cell invasion and identify possible routes to inhibit its action. Design, Setting, Patients, and Interventions: Thyroid, breast, and colorectal cells were transfected with PBF and cultured for in vitro analysis. PBF and cortactin (CTTN) expression was determined in differentiated thyroid cancer and The Cancer Genome Atlas RNA-seq data. Primary Outcome Measure: Pro-invasive effects of PBF were evaluated by 2D Boyden chamber, 3D organotypic, and proximity ligation assays. Results: Our study identified that PBF and CTTN physically interact and co-localize, and that this occurs at the cell periphery, particularly at the leading edge of migrating cancer cells. Critically, PBF induces potent cellular invasion and migration in thyroid and breast cancer cells, which is entirely abrogated in the absence of CTTN. Importantly, we found that CTTN is over-expressed in differentiated thyroid cancer, particularly in patients with regional lymph node metastasis, which significantly correlates with elevated PBF expression. Mutation of PBF (Y174A) or pharmacological intervention modulates the PBF: CTTN interaction and attenuates the invasive properties of cancer cells. Conclusion: Our results demonstrate a unique role for PBF in regulating CTTN function to promote endocrine cell invasion and migration, as well as identify a new targetable interaction to block tumor cell movement. PMID:27603901

  8. Modulation of folding energy landscape by charge–charge interactions: Linking experiments with computational modeling

    PubMed Central

    Tzul, Franco O.; Schweiker, Katrina L.; Makhatadze, George I.

    2015-01-01

    The kinetics of folding–unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge–charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational model, which incorporates the Debye–Hückel formalism for the electrostatics, was used and found to qualitatively recapitulate the experimental results. Analysis of the energy landscapes of the designed versus wild-type proteins indicates the differences in refolding rates may be correlated with the degree of frustration of their respective energy landscapes. Our simulations indicate that naturally occurring wild-type proteins have frustrated folding landscapes due to the surface electrostatics. Optimization of the surface electrostatics seems to remove some of that frustration, leading to enhanced formation of native-like contacts in the transition-state ensembles (TSE) and providing a less frustrated energy landscape between the unfolded and TS ensembles. Macroscopically, this results in faster folding rates. Furthermore, analyses of pairwise distances and radii of gyration suggest that the less frustrated energy landscapes for optimized variants are a result of more compact unfolded and TS ensembles. These findings from our modeling demonstrates that this simple model may be used to: (i) gain a detailed understanding of charge–charge interactions and their effects on modulating the energy landscape of protein folding and (ii) qualitatively predict the kinetic behavior of protein surface electrostatic interactions. PMID:25564663

  9. Interaction between serotonin 5-HT1A receptors and beta-endorphins modulates antidepressant response.

    PubMed

    Navinés, Ricard; Martín-Santos, Rocío; Gómez-Gil, Esther; Martínez de Osaba, María J; Gastó, Cristòbal

    2008-12-12

    Interactions between serotonergic and the endogenous opioid systems have been suggested to be involved in the etiopathogenesis of depression and in the mechanism of action of antidepressants. Activation of serotonin 5-HT1A receptors has been shown to increase plasma beta-endorphin (beta-END) levels in animal studies and in healthy humans. To assess interaction abnormalities between 5-HT1A receptors and the endogenous opioid system in patients with major depression and the possible modulating effect of citalopram. The beta-END response to the 5-HT1A receptor agonist, buspirone (30 mg), was measured in 30 patients with major depression and in 30 age- and sex-matched healthy controls before and after an 8-week treatment with citalopram. Pre-treatment score of the Hamilton Rating Scale for Depression (HRSD) was >or=17. Antidepressant response was defined by a 50% decrease in the HRSD. Pre- and post-treatment maximum peak response (Deltamax) and the area under the curve (AUC) of beta-END response were compared. Three time points were measured (60, 90 and 120 min). We also examined the correlations between the beta-END response and the antidepressant response. Buspirone plasma levels were not measured. At baseline, beta-END response was similar in patients and controls. After 8 weeks of citalopram treatment depressed patients showed a significant decrease in the beta-END response (Deltamax: p<.001; AUC: p<.001). A significant correlation between the beta-END reduction in the response and the reduction in the HRSD score (r=.656; p<.001) was observed. Changes in interaction between 5-HT1A receptor system and the endogenous opioid system may play a role both in the mechanism of action and response to antidepressant drugs.

  10. Interplay of metal node and amine functionality in NH2-MIL-53: modulating breathing behavior through intra-framework interactions.

    PubMed

    Serra-Crespo, Pablo; Gobechiya, Elena; Ramos-Fernandez, Enrique V; Juan-Alcañiz, Jana; Martinez-Joaristi, Alberto; Stavitski, Eli; Kirschhock, Christine E A; Martens, Johan A; Kapteijn, Freek; Gascon, Jorge

    2012-09-04

    A series of amino-functionalized MIL-53 with different metals as nodes has been synthesized. By determining adsorption properties and spectroscopic characterization, we unequivocally show that the interaction between the amines of the organic linker and bridging μ(2)-OH of the inorganic scaffold modulates metal organic framework (MOF) flexibility. The strength of the interaction has been found to correlate with the electropositivity of the metal.

  11. Surfactant-mediated modulation of hydrophobic interactions in associative polymer solutions containing cyclodextrin.

    PubMed

    Talwar, Sachin; Harding, Jonathon; Oleson, Keith R; Khan, Saad A

    2009-01-20

    The ability of nonionic surfactants to modulate the rheological characteristics of comblike hydrophobically modified associative polymer solutions containing cyclodextrin (CD) is examined. Addition of either alpha- or beta-CD to these polymers results in a marked decrease in solution viscosity and viscoelastic properties because of the encapsulation of the polymer hydrophobes by CD. Nonionic surfactants, introduced to such a system, alter the hydrophobic interactions by competing with the polymer hydrophobes for complexation with the CDs. In this regard, nonylphenol ethoxylates (NPe) with different ethylene oxide chain lengths, which determine the hydrophilic-lipophilic balance (HLB) of the surfactant, are used. Our results reveal that the extent and rate of recovery of zero shear viscosity as well as dynamic moduli are strongly influenced by the type of CD (alpha versus beta) as well as the HLB of the surfactant. For polymer solutions containing alpha-CD, recovery is observed solely in the presence of a low-HLB surfactant (NP6 and NP8). Additionally, in the case of NP6, the viscosity increases monotonically above the original hydrophobically modified alkali-soluble emulsion viscosity with surfactant addition, whereas for that of a higher HLB surfactant (NP15), the viscosity shows no appreciable change. In the case of beta-CD, on the other hand, a complete recovery as well as further enhancement of rheological properties is achieved using the above surfactants. However, the trends of viscosity modulation are dissimilar for different surfactants as we witness a monotonous increase in the case of NP6 while a maximum in viscosity is observed in the presence of NP8 and NP15. The contrasting observations can be explained in terms of varying affinities of alpha- and beta-CDs to bind with NP surfactants and the existence of different micellar structures in solution as governed by surfactant HLB. These results are further confirmed by UV/vis spectroscopy and cloud point

  12. REDOX MODULATION OF DIAPHRAGM CONTRACTILITY: INTERACTION BETWEEN DHPR and RyR CHANNELS

    PubMed Central

    Lawler, John M.; Kim, Jong-hee; Kwak, Hyo-Bum; Barnes, William S.

    2010-01-01

    Previous reports indicate that reactive oxygen species (ROS) may modulate contractility in skeletal muscle. Although Ca2+-sensitivity of the contractile apparatus appears to be a primary site of regulation, dihydropyridine receptor (DHPR or L-type Ca2+ channels) and calcium efflux in isolated sarcoplasmic reticulum (SR) vesicles appear to be redox sensitive as well. However, DHPR as a target is poorly understood in intact muscles at body temperature, particularly in the diaphragm, a muscle more dependent on external Ca2+ than locomotor muscles. Previously, we reported that oxidant challenge via xanthine oxidase (XO) alters the K+ contractures in diaphragm fiber bundles, suggestive of a role of L-type Ca2+ channels. Contractility of isolated rat diaphragm fiber bundles revealed a biphasic response to ROS challenge that was dose and time dependent. Potentiation of twitch and low-frequency diaphragm fiber bundle contractility with 0.02 U•ml−1 XO was reversible or partially preventable with washout, dithiothreitol, and the SOD/catalase mimetic EUK-134. The RyR antagonist ruthenium red inhibited xanthine oxidase-induced potentiation, while the RyR agonist caffeine elevated diaphragm twitch and low-frequency tension in a non-additive manner by 55% when introduced simultaneously with ROS challenge. The DHPR antagonist nitrendipine (15 μM) inhibited elevation in low-frequency diaphragm tension produced by ROS challenge. Caffeine threshold tension curves were shifted to the left with 0.02 U•ml−1 XO, but this effect was partially reversed with 15 μM nitrendipine. These results are consistent with the hypothesis that DHPR redox state and RyR function are modulated in an interactive manner, affecting contractility in intact diaphragm fiber bundles. PMID:20920578

  13. Epigenetic Modulation in Periodontitis: Interaction of Adiponectin and JMJD3-IRF4 Axis in Macrophages.

    PubMed

    Xuan, Dongying; Han, Qianqian; Tu, Qisheng; Zhang, Lan; Yu, Liming; Murry, Dana; Tu, Tianchi; Tang, Yin; Lian, Jane B; Stein, Gary S; Valverde, Paloma; Zhang, Jincai; Chen, Jake

    2016-05-01

    Emerging evidence suggests an important role for epigenetic mechanisms in modulating signals during macrophage polarization and inflammation. JMJD3, a JmjC family histone demethylase necessary for M2 polarization is also required for effective induction of multiple M1 genes by lipopolysaccharide (LPS). However, the effects of JMJD3 to inflammation in the context of obesity remains unknown. To address this deficiency, we firstly examined the expression of JMJD3 in macrophage isolated from bone marrow and adipose tissue of diet induced obesity (DIO) mice. The results indicated that JMJD3 was down-regulated in obesity. Adiponectin (APN), a factor secreted by adipose tissue which is down-regulated in obesity, functions to switch macrophage polarization from M1 to M2, thereby attenuating chronic inflammation. Intriguingly, our results indicated that APN contributed to JMJD3 up-regulation, reduced macrophage infiltration in obese adipose tissue, and abolished the up-regulation of JMJD3 in peritoneal macrophages isolated from DIO mice when challenged with Porphyromonas gingivalis LPS (pg.lps). To elucidate the interaction of APN and JMJD3 involved in macrophage transformation in the context of inflammation, we designed the loss and gain-function experiments of APN in vivo with APN(-/-) mice with experimental periodontitis and in vitro with macrophage isolated from APN(-/-) mice. For the first time, we found that APN can help to reduce periodontitis-related bone loss, modulate JMJD3 and IRF4 expression, and macrophage infiltration. Therefore, it can be inferred that APN may contribute to anti-inflammation macrophage polarization by regulating JMJD3 expression, which provides a basis for macrophage-centered epigenetic therapeutic strategies.

  14. Integrating Anatomy Training into Radiation Oncology Residency: Considerations for Developing a Multidisciplinary, Interactive Learning Module for Adult Learners

    ERIC Educational Resources Information Center

    Labranche, Leah; Johnson, Marjorie; Palma, David; D'Souza, Leah; Jaswal, Jasbir

    2015-01-01

    Radiation oncologists require an in-depth understanding of anatomical relationships for modern clinical practice, although most do not receive formal anatomy training during residency. To fulfill the need for instruction in relevant anatomy, a series of four multidisciplinary, interactive learning modules were developed for a cohort of radiation…

  15. Integrating Anatomy Training into Radiation Oncology Residency: Considerations for Developing a Multidisciplinary, Interactive Learning Module for Adult Learners

    ERIC Educational Resources Information Center

    Labranche, Leah; Johnson, Marjorie; Palma, David; D'Souza, Leah; Jaswal, Jasbir

    2015-01-01

    Radiation oncologists require an in-depth understanding of anatomical relationships for modern clinical practice, although most do not receive formal anatomy training during residency. To fulfill the need for instruction in relevant anatomy, a series of four multidisciplinary, interactive learning modules were developed for a cohort of radiation…

  16. Improving Intercultural Interactions. Modules for Cross-Cultural Training Programs. Multicultural Aspects of Counseling Series 3.

    ERIC Educational Resources Information Center

    Brislin, Richard W., Ed.; Yoshida, Tomoko, Ed.

    This book contains modules for use in cross-cultural training programs. A module differs from a chapter in that it is a collection of materials that guide the reader both on the content of a defined unit of training and the method of delivery of that content. The modules are grouped into four sections, three corresponding to organizations in which…

  17. Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming

    PubMed Central

    Tveit, Alexander Tøsdal; Urich, Tim; Frenzel, Peter; Svenning, Mette Marianne

    2015-01-01

    Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH4) in a future warmer climate. How warming affects the complex microbial network decomposing SOC is not understood. We studied CH4 production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH4 production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH4 production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H2-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae. Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH4 is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa. PMID:25918393

  18. Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming.

    PubMed

    Tveit, Alexander Tøsdal; Urich, Tim; Frenzel, Peter; Svenning, Mette Marianne

    2015-05-12

    Arctic permafrost soils store large amounts of soil organic carbon (SOC) that could be released into the atmosphere as methane (CH4) in a future warmer climate. How warming affects the complex microbial network decomposing SOC is not understood. We studied CH4 production of Arctic peat soil microbiota in anoxic microcosms over a temperature gradient from 1 to 30 °C, combining metatranscriptomic, metagenomic, and targeted metabolic profiling. The CH4 production rate at 4 °C was 25% of that at 25 °C and increased rapidly with temperature, driven by fast adaptations of microbial community structure, metabolic network of SOC decomposition, and trophic interactions. Below 7 °C, syntrophic propionate oxidation was the rate-limiting step for CH4 production; above this threshold temperature, polysaccharide hydrolysis became rate limiting. This change was associated with a shift within the functional guild for syntrophic propionate oxidation, with Firmicutes being replaced by Bacteroidetes. Correspondingly, there was a shift from the formate- and H2-using Methanobacteriales to Methanomicrobiales and from the acetotrophic Methanosarcinaceae to Methanosaetaceae. Methanogenesis from methylamines, probably stemming from degradation of bacterial cells, became more important with increasing temperature and corresponded with an increased relative abundance of predatory protists of the phylum Cercozoa. We concluded that Arctic peat microbiota responds rapidly to increased temperatures by modulating metabolic and trophic interactions so that CH4 is always highly produced: The microbial community adapts through taxonomic shifts, and cascade effects of substrate availability cause replacement of functional guilds and functional changes within taxa.

  19. Role of IGF1R+ MSCs in modulating neuroplasticity via CXCR4 cross-interaction

    PubMed Central

    Lee, Hsu-Tung; Chang, Hao-Teng; Lee, Sophie; Lin, Chen-Huan; Fan, Jia-Rong; Lin, Shinn-Zong; Hsu, Chung Y.; Hsieh, Chia-Hung; Shyu, Woei-Cherng

    2016-01-01

    To guide the use of human mesenchymal stem cells (MSCs) toward clinical applications, identifying pluripotent-like-markers for selecting MSCs that retain potent self-renewal-ability should be addressed. Here, an insulin-like growth factor 1 receptor (IGF1R)–expressing sub-population in human dental pulp MSCs (hDSCs), displayed multipotent properties. IGF1R expression could be maintained in hDSCs when they were cultured in 2% human cord blood serum (hUCS) in contrast to that in 10% fetal calf serum (FCS). Cytokine array showed that hUCS contained higher amount of several growth factors compared to FCS, including IGF-1 and platelet-derived growth factor (PDGF-BB). These cytokines modulates the signaling events in the hDSCs and potentially enhances engraftment upon transplantation. Specifically, a bidirectional cross-talk between IGF1R/IGF1 and CXCR4/SDF-1α signaling pathways in hDSCs, as revealed by interaction of the two receptors and synergistic activation of both signaling pathways. In rat stroke model, animals receiving IGF1R+ hDSCs transplantation, interaction between IGF1R and CXCR4 was demonstrated to promote neuroplasticity, therefore improving neurological function through increasing glucose metabolic activity, enhancing angiogenesis and anti-inflammatiory effects. Therefore, PDGF in hUCS-culture system contributed to the maintenance of the expression of IGF1R in hDSCs. Furthermore, implantation of IGF1R+ hDSCs exerted enhanced neuroplasticity via integrating inputs from both CXCR4 and IGF1R signaling pathways. PMID:27586516

  20. Elevated Ozone Modulates Herbivore-Induced Volatile Emissions of Brassica nigra and Alters a Tritrophic Interaction.

    PubMed

    Khaling, Eliezer; Li, Tao; Holopainen, Jarmo K; Blande, James D

    2016-05-01

    Plants damaged by herbivores emit volatile organic compounds (VOCs) that are used by parasitoids for host location. In nature, however, plants are exposed to multiple abiotic and biotic stresses of varying intensities, which may affect tritrophic interactions. Here, we studied the effects of ozone exposure and feeding by Pieris brassicae larvae on the VOCs emitted by Brassica nigra and the effects on oriented flight of the parasitoid Cotesia glomerata. We also investigated the oriented flight of C. glomerata in a wind-tunnel with elevated ozone levels. Herbivore-feeding induced the emission of several VOCs, while ozone alone had no significant effect. However, exposure to 120 ppb ozone, followed by 24 hr of herbivore-feeding, induced higher emissions of all VOCs as compared to herbivore-feeding alone. In accordance, herbivore-damaged plants elicited more oriented flights than undamaged plants, whereas plants exposed to 120 ppb ozone and 24 hr of herbivore-feeding elicited more oriented flights than plants subjected to herbivore-feeding alone. Ozone enrichment of the wind-tunnel air appeared to negatively affect orientation of parasitoids at 70 ppb, but not at 120 ppb. These results suggest that the combination of ozone and P. brassicae-feeding modulates VOC emissions, which significantly influence foraging efficiency of C. glomerata.

  1. Therapeutic design of peptide modulators of protein-protein interactions in membranes.

    PubMed

    Stone, Tracy A; Deber, Charles M

    2017-04-01

    Membrane proteins play the central roles in a variety of cellular processes, ranging from nutrient uptake and signalling, to cell-cell communication. Their biological functions are directly related to how they fold and assemble; defects often lead to disease. Protein-protein interactions (PPIs) within the membrane are therefore of great interest as therapeutic targets. Here we review the progress in the application of membrane-insertable peptides for the disruption or stabilization of membrane-based PPIs. We describe the design and preparation of transmembrane peptide mimics; and of several categories of peptidomimetics used for study, including d-enantiomers, non-natural amino acids, peptoids, and β-peptides. Further aspects of the review describe modifications to membrane-insertable peptides, including lipidation and cyclization via hydrocarbon stapling. These approaches provide a pathway toward the development of metabolically stable, non-toxic, and efficacious peptide modulators of membrane-based PPIs. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.

  2. Hippocampal cannabinoid transmission modulates dopamine neuron activity: impact on rewarding memory formation and social interaction.

    PubMed

    Loureiro, Michael; Renard, Justine; Zunder, Jordan; Laviolette, Steven R

    2015-05-01

    Disturbances in cannabinoid type 1 receptor (CB1R) signaling have been linked to emotional and cognitive deficits characterizing neuropsychiatric disorders, including schizophrenia. Thus, there is growing interest in characterizing the relationship between cannabinoid transmission, emotional processing, and dopamine (DA)-dependent behavioral deficits. The CB1R is highly expressed in the mammalian nervous system, particularly in the hippocampus. Activation of the ventral hippocampal subregion (vHipp) is known to increase both the activity of DAergic neurons located in the ventral tegmental area (VTA) and DA levels in reward-related brain regions, particularly the nucleus accumbens (NAc). However, the possible functional relationship between hippocampal CB1R transmission and VTA DA neuronal activity is not currently understood. In this study, using in vivo neuronal recordings in rats, we demonstrate that activation of CB1R in the vHipp strongly increases VTA DA neuronal firing and bursting activity, while simultaneously decreasing the activity of VTA non-DA neurons. Furthermore, using a conditioned place preference procedure and a social interaction test, we report that intra-vHipp CB1R activation potentiates the reward salience of normally sub-threshold conditioning doses of opiates and induces deficits in natural sociability and social recognition behaviors. Finally, these behavioral effects were prevented by directly blocking NAc DAergic transmission. Collectively, these findings identify hippocampal CB1R transmission as a critical modulator of the mesolimbic DA pathway and in the processing of reward and social-related behavioral phenomena.

  3. CRS-MIS in Candida glabrata: sphingolipids modulate echinocandin-Fks interaction.

    PubMed

    Healey, Kelley R; Katiyar, Santosh K; Raj, Shriya; Edlind, Thomas D

    2012-10-01

    Infections with the azole-refractory yeast Candida glabrata are now commonly treated with the echinocandins caspofungin (CSF) or micafungin (MCF). True resistance (>  32-fold decreased susceptibility) to these lipopeptide inhibitors of cell wall synthesis is rare and strictly associated with mutations in integral membrane proteins Fks1 or Fks2. In contrast, mutants exhibiting 4- to 32-fold CSF reduced susceptibility (CRS) were readily selected in vitro, and surprisingly demonstrated 4- to 32-fold MCF increased susceptibility (MIS). Sequencing and gene deletion demonstrated that CRS-MIS is Fks-independent. To explore alternative mechanisms, we initially employed Saccharomyces cerevisiae, and observed that CRS was conferred by multiple mutations (fen1Δ, sur4Δ, cka2Δ and tsc10-ts) disrupting sphingolipid biosynthesis. Following this lead, C. glabrata fen1Δ and cka2Δ deletants were constructed, and shown to exhibit CRS-MIS. Sphingolipid analysis of CRS-MIS laboratory mutants and clinical isolates demonstrated elevated dihydrosphingosine (DHS) and phytosphingosine (PHS) levels, and consistent with this sequencing revealed fen1, sur4, ifa38 and sur2 mutations. Moreover, exogenous DHS or PHS conferred a CRS-MIS phenotype on wild-type C. glabrata. Exogenous PHS failed, however, to suppress CRS-MIS in a sur2 mutant blocked in conversion of DHS to PHS, implying that accumulation of these intermediates confers CRS-MIS. We conclude that membrane sphingolipids modulate echinocandin-Fks interaction. © 2012 Blackwell Publishing Ltd.

  4. Program EPICP: Electron photon interaction code, photon test module. Version 94.2

    SciTech Connect

    Cullen, D.E.

    1994-09-01

    The computer code EPICP performs Monte Carlo photon transport calculations in a simple one zone cylindrical detector. Results include deposition within the detector, transmission, reflection and lateral leakage from the detector, as well as events and energy deposition as a function of the depth into the detector. EPICP is part of the EPIC (Electron Photon Interaction Code) system. EPICP is designed to perform both normal transport calculations and diagnostic calculations involving only photons, with the objective of developing optimum algorithms for later use in EPIC. The EPIC system includes other modules that are designed to develop optimum algorithms for later use in EPIC; this includes electron and positron transport (EPICE), neutron transport (EPICN), charged particle transport (EPICC), geometry (EPICG), source sampling (EPICS). This is a modular system that once optimized can be linked together to consider a wide variety of particles, geometries, sources, etc. By design EPICP only considers photon transport. In particular it does not consider electron transport so that later EPICP and EPICE can be used to quantitatively evaluate the importance of electron transport when starting from photon sources. In this report I will merely mention where we expect the results to significantly differ from those obtained considering only photon transport from that obtained using coupled electron-photon transport.

  5. Functional interaction between mouse spermatogenic LVA and thapsigargin-modulated calcium channels.

    PubMed

    Stamboulian, Séverine; De Waard, Michel; Villaz, Michel; Arnoult, Christophe

    2002-12-01

    The acrosome reaction in mouse is triggered by a long-lasting calcium signaling produced by a chain of openings of several calcium channels, a low-voltage-activated (LVA) calcium channel, an inositol trisphosphate receptor (IP(3)R), and the store-operated calcium channel TRP2. Since mature sperm cells are refractory to patch clamp experiments, we study the functional interactions among those sperm calcium channels in spermatogenic cells. We have studied the role of cytosolic calcium in voltage-dependent facilitation of low voltage-activated calcium channels. Calcium concentration was modified through the inclusion of the calcium buffers, EGTA and BAPTA, in the recording pipette solution, and by addition of calcium modulators like thapsigargin and the calcium ionophore A23187. We demonstrate that lowering calcium concentration below resting level allows to evidence a voltage-dependent facilitation. We also show that LVA calcium channels present strong voltage-dependent inhibition by thapsigargin. This effect is independent of cytosolic calcium elevation secondary to calcium store depletion and to the activation of TRP channels. Our data evidence an interesting functional relationship, in this cell type, between LVA channels and proteins whose activity is related to calcium filling state of the endoplasmic reticulum (presumably TRP channels and inositol triphosphate receptor). These relationships may contribute to the regulation of calcium signaling during acrosome reaction of mature sperm cell.

  6. Electrostatic interactions at the C-terminal domain of nucleoplasmin modulate its chromatin decondensation activity.

    PubMed

    Hierro, Aitor; Arizmendi, Jesús M; Bañuelos, Sonia; Prado, Adelina; Muga, Arturo

    2002-05-21

    The chromatin decondensation activity, thermal stability, and secondary structure of recombinant nucleoplasmin, of two deletion mutants, and of the protein isolated from Xenopus oocytes have been characterized. As previously reported, the chromatin decondensation activity of recombinant, unphosphorylated nucleoplasmin is almost negligible. Our data show that deletion of 50 residues at the C-terminal domain of the protein, containing the positively charged nuclear localization sequence, activates its chromatin decondensation ability and decreases its stability. Interestingly, both the decondensation activity and thermal stability of this deletion mutant resemble those of the phosphorylated protein isolated from Xenopus oocytes. Deletion of 80 residues at the C-terminal domain, containing the above-mentioned positively charged region and a poly(Glu) tract, inactivates the protein and increases its thermal stability. These findings, along with the effect of salt on the thermal stability of these proteins, suggest that electrostatic interactions between the positive nuclear localization sequence and the poly(Glu) tract, at the C-terminal domain, modulate protein activity and stability.

  7. Fast Quantum Nondemolition Readout by Parametric Modulation of Longitudinal Qubit-Oscillator Interaction

    NASA Astrophysics Data System (ADS)

    Bourassa, Jérôme; Didier, Nicolas; Blais, Alexandre

    For quantum information processing, qubit readout must be fast, of high-fidelity and ideally quantum non-demolition (QND). To rapidly reuse the measured qubit, fast reset of the measurement pointer states is also needed. Combining these characteristics is essential to meet the stringent requirements of fault-tolerant quantum computation. For superconducting qubits, a common strategy is the dispersive readout where the qubit is coupled to an oscillator acting as pointer. In this talk, we present an alternative strategy based on parametric modulation of longitudinal qubit-oscillator interaction. We show that compared to dispersive readout it leads to a faster, high-fidelity and ideally QND qubit readout with a simple reset mechanism. We moreover show how to exponentially improve the signal-to-noise ratio (SNR) of this measurement with the help of single-mode squeezed input state on the oscillator. We present an implementation of this longitudinal parametric readout in circuit quantum electrodynamics along with results using realistic experimental parameters Now at Quantic team, INRIA Paris.

  8. Purification of scatter factor, a fibroblast-derived basic protein that modulates epithelial interactions and movement.

    PubMed Central

    Gherardi, E; Gray, J; Stoker, M; Perryman, M; Furlong, R

    1989-01-01

    Scatter factor is a fibroblast-derived protein that causes separation of contiguous epithelial cells and increased local mobility of unanchored cells. Highly purified scatter factor has been obtained by a combination of ion-exchange and reverse-phase chromatography from serum-free medium conditioned by a ras-transformed clone (D4) of mouse NIH 3T3 fibroblasts. Under nonreducing conditions scatter factor has a pI of approximately 9.5 and migrates in SDS/polyacrylamide gels as a single band at approximately 62 kDa from which epithelial scatter activity can be recovered. Treatment with reducing agents destroys biological activity and is associated with the appearance of two major bands at approximately 57 and approximately 30 kDa. Whether both the 57-kDa and 30-kDa polypeptides are required for biological activity remains to be established. All the activities observed in crude medium conditioned by cells producing scatter factor are retained by highly purified preparations of scatter factor. These include (i) increased local movement, modulation of morphology, and inhibition of junction formation by single epithelial cells and (ii) disruption of epithelial interactions and cell scattering from preformed epithelial sheets. These changes occur with picomolar concentrations of purified scatter factor and without an effect on cell growth. Images PMID:2527367

  9. Interactive Web-based learning module on CT of the temporal bone: anatomy and pathology.

    PubMed

    Phillips, Grace S; LoGerfo, Sung E; Richardson, Michael L; Anzai, Yoshimi

    2012-01-01

    An interactive Web-based learning module on the temporal bone has been developed. It shows normal temporal bone anatomy in four imaging planes: axial, coronal, and parallel and perpendicular to the long axis of the petrous bone. After reviewing the normal anatomy, users should be able to identify key imaging features of pathologic conditions of the temporal bone. Children with congenital abnormalities of the temporal bone may present with conductive or sensorineural hearing loss or both and may have a genetic syndrome. Acute otitis media is the most common infection of the temporal bone and is most prevalent among children. Although imaging is unnecessary in uncomplicated otitis media, it is important for evaluation of infectious complications. Classically, temporal bone fractures were described as longitudinal or transverse with respect to the long axis of the petrous bone. However, it is increasingly recognized that many fractures have both longitudinal and transverse components. Patients with temporal bone fractures may have conductive or sensorineural hearing loss in addition to other complications. The most common tumor of the temporal bone at the cerebellopontine angle is the vestibular schwannoma. Paraganglioma is the second most common tumor of the temporal bone and the most common tumor of the middle ear. Supplemental material available at http://uwmsk.org/temporalbone/atlas.html. RSNA, 2012

  10. Modulation of the Interaction between a Peptide Ligand and a G Protein-Coupled Receptor by Halogen Atoms

    PubMed Central

    2015-01-01

    Systematic halogenation of two native opioid peptides has shown that halogen atoms can modulate peptide–receptor interactions in different manners. First, halogens may produce a steric hindrance that reduces the binding of the peptide to the receptor. Second, chlorine, bromine, or iodine may improve peptide binding if their positive σ-hole forms a halogen bond interaction with negatively charged atoms of the protein. Lastly, the negative electrostatic potential of fluorine can interact with positively charged atoms of the protein to improve peptide binding. PMID:26288687

  11. Modulation of the Interaction between a Peptide Ligand and a G Protein-Coupled Receptor by Halogen Atoms.

    PubMed

    Rosa, Mònica; Caltabiano, Gianluigi; Barreto-Valer, Katy; Gonzalez-Nunez, Verónica; Gómez-Tamayo, José C; Ardá, Ana; Jiménez-Barbero, Jesús; Pardo, Leonardo; Rodríguez, Raquel E; Arsequell, Gemma; Valencia, Gregorio

    2015-08-13

    Systematic halogenation of two native opioid peptides has shown that halogen atoms can modulate peptide-receptor interactions in different manners. First, halogens may produce a steric hindrance that reduces the binding of the peptide to the receptor. Second, chlorine, bromine, or iodine may improve peptide binding if their positive σ-hole forms a halogen bond interaction with negatively charged atoms of the protein. Lastly, the negative electrostatic potential of fluorine can interact with positively charged atoms of the protein to improve peptide binding.

  12. Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.

    PubMed

    Merino, Felipe; Bouvier, Benjamin; Cojocaru, Vlad

    2015-06-01

    Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes. Usually, their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery. Here, we performed unbiased molecular simulations followed by simulations of protein-DNA unbinding and free energy profiling to study the cooperative DNA recognition by OCT4 and SOX2, key components of enhanceosomes in pluripotent cells. We found that SOX2 influences the orientation and dynamics of the DNA-bound configuration of OCT4. In addition SOX2 modifies the unbinding free energy profiles of both DNA-binding domains of OCT4, the POU specific and POU homeodomain, despite interacting directly only with the first. Thus, we demonstrate that the OCT4-SOX2 cooperativity is modulated by an interplay between protein-protein interactions and DNA-mediated allostery. Further, we estimated the change in OCT4-DNA binding free energy due to the cooperativity with SOX2, observed a good agreement with experimental measurements, and found that SOX2 affects the relative DNA-binding strength of the two OCT4 domains. Based on these findings, we propose that available interaction partners in different biological contexts modulate the DNA exploration routes of multi-domain transcription factors such as OCT4. We consider the OCT4-SOX2 cooperativity as a paradigm of how specificity of transcriptional regulation is achieved through concerted modulation of protein-DNA recognition by different types of interactions.

  13. Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery

    PubMed Central

    Merino, Felipe; Bouvier, Benjamin; Cojocaru, Vlad

    2015-01-01

    Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes. Usually, their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery. Here, we performed unbiased molecular simulations followed by simulations of protein-DNA unbinding and free energy profiling to study the cooperative DNA recognition by OCT4 and SOX2, key components of enhanceosomes in pluripotent cells. We found that SOX2 influences the orientation and dynamics of the DNA-bound configuration of OCT4. In addition SOX2 modifies the unbinding free energy profiles of both DNA-binding domains of OCT4, the POU specific and POU homeodomain, despite interacting directly only with the first. Thus, we demonstrate that the OCT4-SOX2 cooperativity is modulated by an interplay between protein-protein interactions and DNA-mediated allostery. Further, we estimated the change in OCT4-DNA binding free energy due to the cooperativity with SOX2, observed a good agreement with experimental measurements, and found that SOX2 affects the relative DNA-binding strength of the two OCT4 domains. Based on these findings, we propose that available interaction partners in different biological contexts modulate the DNA exploration routes of multi-domain transcription factors such as OCT4. We consider the OCT4-SOX2 cooperativity as a paradigm of how specificity of transcriptional regulation is achieved through concerted modulation of protein-DNA recognition by different types of interactions. PMID:26067358

  14. Ion-specific modulation of protein interactions: Anion-induced, reversible oligomerization of a fusion protein

    PubMed Central

    Gokarn, Yatin R; Fesinmeyer, R Matthew; Saluja, Atul; Cao, Shawn; Dankberg, Jane; Goetze, Andrew; Remmele, Richard L; Narhi, Linda O; Brems, David N

    2009-01-01

    Ions can significantly modulate the solution interactions of proteins. We aim to demonstrate that the salt-dependent reversible heptamerization of a fusion protein called peptibody A or PbA is governed by anion-specific interactions with key arginyl and lysyl residues on its peptide arms. Peptibody A, an E. coli expressed, basic (pI = 8.8), homodimer (65.2 kDa), consisted of an IgG1-Fc with two, C-terminal peptide arms linked via penta-glycine linkers. Each peptide arm was composed of two, tandem, active sequences (SEYQGLPPQGWK) separated by a spacer (GSGSATGGSGGGASSGSGSATG). PbA was monomeric in 10 mM acetate, pH 5.0 but exhibited reversible self-association upon salt addition. The sedimentation coefficient (sw) and hydrodynamic diameter (DH) versus PbA concentration isotherms in the presence of 140 mM NaCl (A5N) displayed sharp increases in sw and DH, reaching plateau values of 9 s and 16 nm by 10 mg/mL PbA. The DH and sedimentation equilibrium data in the plateau region (>12 mg/mL) indicated the oligomeric ensemble to be monodisperse (PdI = 0.05) with a z-average molecular weight (Mz) of 433 kDa (stoichiometry = 7). There was no evidence of reversible self-association for an IgG1-Fc molecule in A5N by itself or in a mixture containing fluorescently labeled IgG1-Fc and PbA, indicative of PbA self-assembly being mediated through its peptide arms. Self-association increased with pH, NaCl concentration, and anion size (I− > Br− > Cl− > F−) but could be inhibited using soluble Trp-, Phe-, and Leu-amide salts (Trp > Phe > Leu). We propose that in the presence of salt (i) anion binding renders PbA self-association competent by neutralizing the peptidyl arginyl and lysyl amines, (ii) self-association occurs via aromatic and hydrophobic interactions between the..xx..xxx..xx.. motifs, and (iii) at >10 mg/mL, PbA predominantly exists as heptameric clusters. PMID:19177361

  15. Interactions between endothelial cells and T cells modulate responses to mixed neutron/gamma radiation.

    PubMed

    Cary, Lynnette H; Noutai, Daniel; Salber, Rudolph E; Williams, Margaret S; Ngudiankama, Barbara F; Whitnall, Mark H

    2014-06-01

    Detonation of an improvised nuclear device near a population center would cause significant casualties from the acute radiation syndrome (ARS) due to exposure to mixed neutron/gamma fields (MF). The pathophysiology of ARS involves inflammation, microvascular damage and alterations in immune function. Interactions between endothelial cells (EC) and hematopoietic cells are important not only for regulating immune cell traffic and function, but also for providing the microenvironment that controls survival, differentiation and migration of hematopoietic stem and progenitor cells in blood-forming tissues. Endothelial cells/leukocyte interactions also influence tumor progression and the results of anticancer therapies. In this study, we hypothesized that irradiation of endothelial cells would modulate their effects on hematopoietic cells and vice versa. Human umbilical vein endothelial cells (HUVEC) and immortalized T lymphocytes (Jurkat cells) were cultured individually and in co-culture after exposure to mixed fields. Effects of nonirradiated cells were compared to effects of irradiated cells and alterations in signaling pathways were determined. Mitogen-activated protein kinases (MAPKs) p38 and p44/42 (ERK1/2) in HUVEC exhibited higher levels of phosphorylated protein after exposure to mixed field radiation. IL-6, IL-8, G-CSF, platelet derived growth factor (PDGF) and angiopoietin 2 (ANG2) protein expression were upregulated in HUVEC by exposure to mixed field radiation. PCR arrays using HUVEC mRNA revealed alterations in gene expression after exposure to mixed fields and/or co-culture with Jurkat cells. The presence of HUVEC also influenced the function of Jurkat cells. Nonirradiated Jurkat cells showed an increase in proliferation when co-cultured with nonirradiated HUVEC, and a decrease in proliferation when co-cultured with irradiated HUVEC. Additionally, nonirradiated Jurkat cells incubated in media from irradiated HUVEC exhibited upregulation of activated

  16. Thrombospondin modulates melanoma--platelet interactions and melanoma tumour cell growth in vivo.

    PubMed Central

    Boukerche, H.; Berthier-Vergnes, O.; Tabone, E.; Bailly, M.; Doré, J. F.; McGregor, J. L.

    1995-01-01

    In this study we have investigated the role of thrombospondin (TSP) as a possible ligand playing a key role in human M3Da. melanoma cell interaction with platelets and in tumour growth. TSP is secreted (80 +/- 6 ng TSP 10(-6) cells) and bound to the surface of M3Da. cells via receptors different from CD36, as shown by biosynthetic labelling and immunofluorescence studies. The levels of TSP binding to M3Da. cells evaluated by binding studies, using an anti-TSP monoclonal antibody (MAb) (LYP8), shows 367,000 +/- 58,000 (mean +/- s.d.) LYP8 binding sites per cell with a dissociation constant (Kd) of 67 nM. TSP binding to M3Da. cells shows 400,000 +/- 50,000 TSP binding sites per cell with a Kd of 10 nM. The capacity of anti-TSP MAb (LYP8) to inhibit M3Da.-platelet interactions was followed on an aggregometer and evaluated by electron microscopy studies. The biological role of TSP binding to M3Da. cells was investigated by implanting subcutaneously the M3Da. cell line in nude mice and following the size and time of in vivo tumour growth. Reducing the availability or the functional level of TSP by using an anti-TSP MAb (LYP8) resulted in a significant decrease in platelet aggregates interacting with M3Da. melanoma cells. Using an enzyme-linked immunosorbent assay, purified alpha nu beta 3 was shown to bind TSP. Moreover, LYP8-coated M3Da. cells showed a reduced capacity to form tumours in vivo. M3Da. cells were observed to attach and spread on human platelet TSP-coated plastic wells. This attachment by M3Da. cells was inhibited in a similar way by LYP8 and an anti-alpha nu beta 3 MAb (LYP18). The results obtained in this study show that TSP secreted and bound to the surface of a human melanoma cell line (M3Da.) acts as a link between aggregated platelets and the M3Da. cell surface. Moreover, these results shows that TSP can modulate tumour growth in vivo. Reagents such as MAbs directed against TSP and peptides derived from TSP could not only be used as a new therapeutic

  17. Interaction between total body gamma-irradiation and choline deficiency triggers immediate modulation of choline and choline-containing moieties.

    PubMed

    Batra, Vipen; Kislay, Binita; Devasagayam, Thomas Paul Asir

    2011-12-01

    The objective of this study was to examine the effect of 60Co-gamma (γ) radiation on acute phase modulation, if any, of choline and choline-containing moieties in choline-deficient subjects. Corresponding results could provide information that might be useful in the management of adverse effects of γ-radiation. Male Swiss mice maintained on a choline-sufficient diet (CSD) and choline-free diet (CFD) based on AIN-93M formula, were subjected to whole body γ-irradiation (2-6 Gy). Liver, serum and brain samples from each group were then tested for: (i) Alterations in choline and choline-containing moieties such as phosphatidylcholine (PC) and sphingomyeline (SM); and (ii) modulation of choline profile modulating enzymes such as phospholipase D (PLD) and total sphingomyelinase (t-SMase). Liver and brain samples were also subjected to histo-pathological examinations. No significant changes were observed in folate, choline, choline-containing moieties and choline-modulating enzymes in choline-sufficient mice. In contrast, interaction between cytotoxic effects of γ-radiation and choline deficiency modulated choline and choline-containing moieties. Feeding CFD reduced hepatic concentrations of choline, PC and SM whereas PLD and t-SMase activities were significantly raised. The decrease in liver choline and choline-containing moieties was accompanied by an increase in blood choline concentration. Despite choline deficiency, the level of choline and acetylcholine synthesizing enzyme choline acetyltransfease (ChAT) significantly increased in the brain. We propose that choline deprivation and γ-radiation interact to modulate choline reserves of hepatic tissue, which might release choline to blood. Our studies also clearly showed that interaction between choline deficiency and γ-radiation might substantially enhance liver adipogenesis.

  18. Performance of a PET detector module utilizing an array of silicon photodiodes to identify the crystal of interaction

    SciTech Connect

    Moses, W.W.; Derenzo, S.E. ); Nutt, R.; Digby, W.M.; Williams, C.W.; Andreaco, M. )

    1992-11-01

    We present initial performance results for a new multi-layer PET detector module consisting of an array of 3 mm square by 30 mm deep BGO crystals coupled on one end to a single photomultiplier tube and on the opposite end to an array of 3 mm square silicon photodiodes. The photomultiplier tube provides an accurate timing pulse and energy discrimination for the all the crystals in the module, while the silicon photodiodes identify the crystal of interaction. When a single BGO crystal at +25[degree]C is excited with 511 key photons, we measure a photodiode signal centered at 700 electrons (e[sup [minus

  19. Driving the need to feed: Insight into the collaborative interaction between ghrelin and endocannabinoid systems in modulating brain reward systems.

    PubMed

    Edwards, Alexander; Abizaid, Alfonso

    2016-07-01

    Independent stimulation of either the ghrelin or endocannabinoid system promotes food intake and increases adiposity. Given the similar distribution of their receptors in feeding associated brain regions and organs involved in metabolism, it is not surprising that evidence of their interaction and its importance in modulating energy balance has emerged. This review documents the relationship between ghrelin and endocannabinoid systems within the periphery and hypothalamus (HYP) before presenting evidence suggesting that these two systems likewise work collaboratively within the ventral tegmental area (VTA) to modulate non-homeostatic feeding. Mechanisms, consistent with current evidence and local infrastructure within the VTA, will be proposed.

  20. A "do-it-yourself" interactive bone structure module: development and evaluation of an online teaching resource.

    PubMed

    Rich, Peter; Guy, Richard

    2013-01-01

    A stand-alone online teaching module was developed to cover an area of musculoskeletal anatomy (structure of bone) found to be difficult by students. The material presented in the module was not formally presented in any other way, thus providing additional time for other curriculum components, but it was assessed in the final examination. The module was developed using "in-house" software designed for academics with minimal computer experience. The efficacy and effectiveness of the module was gauged via student surveys, testing student knowledge before and after module introduction, and analysis of final examination results. At least 74% of the class used the module and student responses were positive regarding module usability (navigation, interaction) and utility (learning support). Learning effectiveness was demonstrated by large significant improvements in the post-presentation test scores for "users" compared with "non-users" and by the percentage of correct responses to relevant multiple choice questions in the final examination. Performance on relevant short answer questions in the final examination was, on average, comparable to that for other components. Though limited by study structure, it was concluded that the module produced learning outcomes equivalent to those generated by more traditional teaching methods. This "Do-It-Yourself" e-learning approach may be particularly useful for meeting specific course needs not catered for by commercial applications or where there are cost limitations for generation of online learning material. The specific approaches used in the study can assist in development of effective online resources in anatomy. Copyright © 2012 American Association of Anatomists.

  1. Abscisic acid has a key role in modulating diverse plant-pathogen interactions.

    PubMed

    Fan, Jun; Hill, Lionel; Crooks, Casey; Doerner, Peter; Lamb, Chris

    2009-08-01

    We isolated an activation-tagged Arabidopsis (Arabidopsis thaliana) line, constitutive disease susceptibility2-1D (cds2-1D), that showed enhanced bacterial growth when challenged with various Pseudomonas syringae strains. Systemic acquired resistance and systemic PATHOGENESIS-RELATED GENE1 induction were also compromised in cds2-1D. The T-DNA insertion adjacent to NINE-CIS-EPOXYCAROTENOID DIOXYGENASE5 (NCED5), one of six genes encoding the abscisic acid (ABA) biosynthetic enzyme NCED, caused a massive increase in transcript level and enhanced ABA levels >2-fold. Overexpression of NCED genes recreated the enhanced disease susceptibility phenotype. NCED2, NCED3, and NCED5 were induced, and ABA accumulated strongly following compatible P. syringae infection. The ABA biosynthetic mutant aba3-1 showed reduced susceptibility to virulent P. syringae, and ABA, whether through exogenous application or endogenous accumulation in response to mild water stress, resulted in increased bacterial growth following challenge with virulent P. syringae, indicating that ABA suppresses resistance to P. syringae. Likewise ABA accumulation also compromised resistance to the biotrophic oomycete Hyaloperonospora arabidopsis, whereas resistance to the fungus Alternaria brassicicola was enhanced in cds2-1D plants and compromised in aba3-1 plants, indicating that ABA promotes resistance to this necrotroph. Comparison of the accumulation of salicylic acid and jasmonic acid in the wild type, cds2-1D, and aba3-1 plants challenged with P. syringae showed that ABA promotes jasmonic acid accumulation and exhibits a complex antagonistic relationship with salicylic acid. Our findings provide genetic evidence that the abiotic stress signal ABA also has profound roles in modulating diverse plant-pathogen interactions mediated at least in part by cross talk with the jasmonic acid and salicylic acid biotic stress signal pathways.

  2. Receptor-interacting protein kinases modulate noise-induced sensory hair cell death

    PubMed Central

    Zheng, H-W; Chen, J; Sha, S-H

    2014-01-01

    Receptor-interacting protein (RIP) kinases promote the induction of necrotic cell death pathways. Here we investigated signaling pathways in outer hair cells (OHCs) of adult male CBA/J mice exposed to noise that causes permanent threshold shifts, with a particular focus on RIP kinase-regulated necroptosis. One hour after noise exposure, nuclei of OHCs in the basal region of the cochlea displayed both apoptotic and necrotic features. RIP1 and RIP3 protein levels increased and caspase-8 was activated. Treatment with pan-caspase inhibitor ZVAD blocked the activation of caspase-8 and reduced the number of apoptotic nuclei, while increasing levels of RIP1, RIP3, and necrotic OHCs. Conversely, treatment with necrosis inhibitor necrostatin-1 (Nec-1) or RIP3 siRNA (siRIP3) diminished noise-induced increases in RIP1 and RIP3, and decreased necrotic OHC nuclei. This treatment also increased the number of apoptotic nuclei without increasing activation of caspase-8. Consistent with the elevation of levels of RIP1 and RIP3, noise-induced active AMPKα levels increased with ZVAD treatment, but decreased with Nec-1 and siRIP3 treatment. Furthermore, treatment with siRIP3 did not alter the activation of caspase-8, but instead increased activation of caspase-9 and promoted endonuclease G translocation into OHC nuclei. Finally, auditory brainstem response functional measurements and morphological assessment of OHCs showed that ZVAD treatment reduces noise-induced deficits. This protective function is potentiated when combined with siRIP3 treatment. In conclusion, noise-induced OHC apoptosis and necrosis are modulated by caspases and RIP kinases, respectively. Inhibition of either pathway shifts the prevalence of OHC death to the alternative pathway. PMID:24874734

  3. Stochastic nanoroughness modulates neuron–astrocyte interactions and function via mechanosensing cation channels

    PubMed Central

    Blumenthal, Nils R.; Hermanson, Ola; Heimrich, Bernd; Shastri, V. Prasad

    2014-01-01

    Extracellular soluble signals are known to play a critical role in maintaining neuronal function and homeostasis in the CNS. However, the CNS is also composed of extracellular matrix macromolecules and glia support cells, and the contribution of the physical attributes of these components in maintenance and regulation of neuronal function is not well understood. Because these components possess well-defined topography, we theorize a role for topography in neuronal development and we demonstrate that survival and function of hippocampal neurons and differentiation of telencephalic neural stem cells is modulated by nanoroughness. At roughnesses corresponding to that of healthy astrocytes, hippocampal neurons dissociated and survived independent from astrocytes and showed superior functional traits (increased polarity and calcium flux). Furthermore, telencephalic neural stem cells differentiated into neurons even under exogenous signals that favor astrocytic differentiation. The decoupling of neurons from astrocytes seemed to be triggered by changes to astrocyte apical-surface topography in response to nanoroughness. Blocking signaling through mechanosensing cation channels using GsMTx4 negated the ability of neurons to sense the nanoroughness and promoted decoupling of neurons from astrocytes, thus providing direct evidence for the role of nanotopography in neuron–astrocyte interactions. We extrapolate the role of topography to neurodegenerative conditions and show that regions of amyloid plaque buildup in brain tissue of Alzheimer’s patients are accompanied by detrimental changes in tissue roughness. These findings suggest a role for astrocyte and ECM-induced topographical changes in neuronal pathologies and provide new insights for developing therapeutic targets and engineering of neural biomaterials. PMID:25349433

  4. Genome-Environment Interactions That Modulate Aging: Powerful Targets for Drug Discovery

    PubMed Central

    Wuttke, Daniel; Wood, Shona H.; Plank, Michael; Vora, Chintan

    2012-01-01

    Aging is the major biomedical challenge of this century. The percentage of elderly people, and consequently the incidence of age-related diseases such as heart disease, cancer, and neurodegenerative diseases, is projected to increase considerably in the coming decades. Findings from model organisms have revealed that aging is a surprisingly plastic process that can be manipulated by both genetic and environmental factors. Here we review a broad range of findings in model organisms, from environmental to genetic manipulations of aging, with a focus on those with underlying gene-environment interactions with potential for drug discovery and development. One well-studied dietary manipulation of aging is caloric restriction, which consists of restricting the food intake of organisms without triggering malnutrition and has been shown to retard aging in model organisms. Caloric restriction is already being used as a paradigm for developing compounds that mimic its life-extension effects and might therefore have therapeutic value. The potential for further advances in this field is immense; hundreds of genes in several pathways have recently emerged as regulators of aging and caloric restriction in model organisms. Some of these genes, such as IGF1R and FOXO3, have also been associated with human longevity in genetic association studies. The parallel emergence of network approaches offers prospects to develop multitarget drugs and combinatorial therapies. Understanding how the environment modulates aging-related genes may lead to human applications and disease therapies through diet, lifestyle, or pharmacological interventions. Unlocking the capacity to manipulate human aging would result in unprecedented health benefits. PMID:22090473

  5. Cholesterol modulates the interaction of the islet amyloid polypeptide with membranes.

    PubMed

    Caillon, Lucie; Duma, Luminita; Lequin, Olivier; Khemtemourian, Lucie

    2014-01-01

    The deposition of insoluble amyloid fibrils resulting from the aggregation of the human islet amyloid polypeptide (hIAPP) within the islet of Langerhans is a pathological feature of type 2 diabetes mellitus (T2DM). Increasing evidence indicates that biological membranes play a key role in amyloid aggregation, modulating among others the kinetics of amyloid formation, and being the target of toxic species generated during amyloid formation. In T2DM patients, elevated levels of cholesterol, an important determinant of the physical state of biological membranes, are observed in β-cells and are thought to directly impair β-cell function and insulin secretion. However, it is not known whether cholesterol enhances membrane-interaction or membrane-insertion of hIAPP. In this study, we investigated the effect of cholesterol incorporated in zwitterionic and anionic membranes. Our circular dichroism and liquid state NMR data reveal that 10-30% of cholesterol slightly affects the aggregational and conformational behaviour of hIAPP. Additional fluorescence results indicate that 10 and 20% of cholesterol slightly slow down the kinetics of oligomer and fibril formation while anionic lipids accelerate this kinetics. This behavior might be caused by differences in membrane insertion and therefore in membrane binding of hIAPP. The membrane binding affinity was evaluated using (1)H NMR experiments and our results show that the affinity of hIAPP for membranes containing cholesterol is significantly smaller than that for membranes containing anionic lipids. Furthermore, we found that hIAPP-induced membrane damage is synchronized to fibril formation in the absence and in the presence of cholesterol.

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

    PubMed

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

    2011-07-18

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

  7. Vinexin β Interacts with Hepatitis C Virus NS5A, Modulating Its Hyperphosphorylation To Regulate Viral Propagation

    PubMed Central

    Xiong, Wei; Yang, Jie; Wang, Mingzhen; Wang, Hailong; Rao, Zhipeng; Zhong, Cheng; Xin, Xiu; Mo, Lin; Yu, Shujuan

    2015-01-01

    ABSTRACT Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is essential for HCV genome replication and virion production and is involved in the regulation of multiple host signaling pathways. As a proline-rich protein, NS5A is capable of interacting with various host proteins containing Src homology 3 (SH3) domains. Previous studies have suggested that vinexin, a member of the sorbin homology (SoHo) adaptor family, might be a potential binding partner of NS5A by yeast two-hybrid screening. However, firm evidence for this interaction is lacking, and the significance of vinexin in the HCV life cycle remains unclear. In this study, we demonstrated that endogenously and exogenously expressed vinexin β coimmunoprecipitated with NS5A derived from different HCV genotypes. Two residues, tryptophan (W307) and tyrosine (Y325), in the third SH3 domain of vinexin β and conserved Pro-X-X-Pro-X-Arg motifs at the C terminus of NS5A were indispensable for the vinexin-NS5A interaction. Furthermore, downregulation of endogenous vinexin β significantly suppressed NS5A hyperphosphorylation and decreased HCV replication, which could be rescued by expressing a vinexin β short hairpin RNA-resistant mutant. We also found that vinexin β modulated the hyperphosphorylation of NS5A in a casein kinase 1α-dependent on manner. Taken together, our findings suggest that vinexin β modulates NS5A phosphorylation via its interaction with NS5A, thereby regulating HCV replication, implicating vinexin β in the viral life cycle. IMPORTANCE Hepatitis C virus (HCV) nonstructural protein NS5A is a phosphoprotein, and its phosphorylation states are usually modulated by host kinases and other viral nonstructural elements. Additionally, cellular factors containing Src homology 3 (SH3) domains have been reported to interact with proline-rich regions of NS5A. However, it is unclear whether there are any relationships between NS5A phosphorylation and the NS5A-SH3 interaction, and little is known

  8. Performance of a PET detector module utilizing an array of silicon photodiodes to identify the crystal of interaction

    SciTech Connect

    Moses, W.W.; Derenzo, S.E.; Nutt, R.; Digby, W.M.; Williams, C.W.; Andreaco, M.

    1992-11-01

    We present initial performance results for a new multi-layer PET detector module consisting of an array of 3 mm square by 30 mm deep BGO crystals coupled on one end to a single photomultiplier tube and on the opposite end to an array of 3 mm square silicon photodiodes. The photomultiplier tube provides an accurate timing pulse and energy discrimination for the all the crystals in the module, while the silicon photodiodes identify the crystal of interaction. When a single BGO crystal at +25{degree}C is excited with 511 key photons, we measure a photodiode signal centered at 700 electrons (e{sup {minus}}) with noise of 375 e{sup {minus}} fwhm. When a four crystal / photodiode module is excited with a collimated line source of 511 key photons, the crystal of interaction is correctly identified 82% of the time. The misidentification rate can be greatly reduced and an 8{times}8 crystal / photodiode module constructed by using thicker depletion layer photodiodes or cooling to 0{degrees}C.

  9. SDF-1alpha concentration dependent modulation of RhoA and Rac1 modifies breast cancer and stromal cells interaction.

    PubMed

    Pasquier, Jennifer; Abu-Kaoud, Nadine; Abdesselem, Houari; Madani, Aisha; Hoarau-Véchot, Jessica; Thawadi, Hamda Al; Vidal, Fabien; Couderc, Bettina; Favre, Gilles; Rafii, Arash

    2015-08-01

    The interaction of SDF-1alpha with its receptor CXCR4 plays a role in the occurrence of distant metastasis in many solid tumors. This interaction increases migration from primary sites as well as homing at distant sites. Here we investigated how SDF-1α could modulate both migration and adhesion of cancer cells through the modulation of RhoGTPases. We show that different concentrations of SDF-1α modulate the balance of adhesion and migration in cancer cells. Increased migration was obtained at 50 and 100 ng/ml of SDF-1α; however migration was reduced at 200 ng/ml. The adhesion between breast cancer cells and BMHC was significantly increased by SDF-1α treatment at 200 ng/ml and reduced using a blocking monoclonal antibody against CXCR4. We showed that at low SDF-1α concentration, RhoA was activated and overexpressed, while at high concentration Rac1 was promoting SDF-1α mediating-cell adhesion. We conclude that SDF-1α concentration modulates migration and adhesion of breast cancer cells, by controlling expression and activation of RhoGTPases.

  10. Modulation instability of ion acoustic waves, solitons, and their interactions in nonthermal electron-positron-ion plasmas

    SciTech Connect

    Zhang Jiefang; Wang Yueyue; Wu Lei

    2009-06-15

    The propagation of ion acoustic waves in plasmas composed of ions, positrons, and nonthermally distributed electrons is investigated. By means of the reduction perturbation technique, a nonlinear Schroedinger equation is derived and the modulation instability of ion acoustic wave is analyzed, where the nonthermal parameter is found to be of significant importance. Furthermore, analytical expressions for the bright and dark solitons are obtained, and the interaction of multiple solitons is discussed.

  11. The stress-response factor SigH modulates the interaction between Mycobacterium tuberculosis and host phagocytes.

    PubMed

    Dutta, Noton K; Mehra, Smriti; Martinez, Alejandra N; Alvarez, Xavier; Renner, Nicole A; Morici, Lisa A; Pahar, Bapi; Maclean, Andrew G; Lackner, Andrew A; Kaushal, Deepak

    2012-01-01

    The Mycobacterium tuberculosis stress response factor SigH plays a crucial role in modulating the pathogen's response to heat, oxidative-stress, envelope damage and hypoxia. We hypothesized that the lack of this key stress response factor would alter the interaction between the pathogen and its host cells. We compared the interaction of Mtb, Mtb:Δ-sigH and a strain where the mutation had been genetically complemented (Mtb: Δ-sigH:CO) with primary rhesus macaque bone marrow derived macrophages (Rh-BMDMs). The expression of numerous inducible and homeostatic (CCL) β-chemokines and several apoptotic markers was induced to higher levels in the cells infected with Mtb:Δ-sigH, relative to Mtb or the complemented strain. The differential expression of these genes manifested into functional differences in chemotaxis and apoptosis in cells infected with these two strains. The mutant strain also exhibited reduced late-stage survival in Rh-BMDMs. We hypothesize that the product of one or more SigH-dependent genes may modulate the innate interaction of Mtb with host cells, effectively reducing the chemokine-mediated recruitment of immune effector cells, apoptosis of infected monocytes and enhancing the long-term survival and replication of the pathogen in this milieu The significantly higher induction of Prostaglandin Synthetase 2 (PTGS2 or COX2) in Rh-BMDMs infected with Mtb relative to Mtb: Δ-sigH may explain reduced apoptosis in Mtb-infected cells, as PTGS2 is known to inhibit p53-dependent apoptosis.The SigH-regulon modulates the innate interaction of Mtb with host phagocytes, perhaps as part of a strategy to limit its clearance and prolong its survival. The SigH regulon appears to be required to modulate innate immune responses directed against Mtb.

  12. Corticospinal interaction during isometric compensation for modulated forces with different frequencies.

    PubMed

    Naranjo, José R; Wang, Xi; Schulte-Mönting, Jürgen; Huethe, Frank; Maurer, Christoph; Hepp-Reymond, Marie-Claude; Kristeva, Rumyana

    2010-12-31

    During isometric compensation of modulated low-level forces corticomuscular coherence (CMC) has been shown to occur in high-beta or gamma-range. The influence of the frequency of force modulation on CMC has up to now remained unexplored. We addressed this question by investigating CMC, motor performance, and cortical spectral power during a visuomotor task in which subjects had to compensate a modulated force of 8% of the maximum voluntary contraction exerted on their right index finger. The effect of three frequencies of force modulation (0.6, 1.0 and 1.6 Hz) was tested. EEG, EMG from first dorsal interosseus, hand flexor and extensor muscles, and finger position were recorded in eight right-handed women. Five subjects showed CMC in gamma- (28-45 Hz) and three in beta-range (15-30 Hz). Beta- and gamma-range CMC and cortical motor spectral power were not modulated by the various frequencies. However, a sharp bilateral CMC peak at 1.6 Hz was observed, but only in the five gamma-range CMC subjects. The performance error increased linearly with the frequency. Our findings suggest that the frequency of force modulation has no effect on the beta- and gamma-range CMC during isometric compensation for modulated forces at 8% MVC. The beta- and gamma-range CMC may be related to interindividual differences and possibly to strategy differences.

  13. Corticospinal interaction during isometric compensation for modulated forces with different frequencies

    PubMed Central

    2010-01-01

    Background During isometric compensation of modulated low-level forces corticomuscular coherence (CMC) has been shown to occur in high-beta or gamma-range. The influence of the frequency of force modulation on CMC has up to now remained unexplored. We addressed this question by investigating CMC, motor performance, and cortical spectral power during a visuomotor task in which subjects had to compensate a modulated force of 8% of the maximum voluntary contraction exerted on their right index finger. The effect of three frequencies of force modulation (0.6, 1.0 and 1.6 Hz) was tested. EEG, EMG from first dorsal interosseus, hand flexor and extensor muscles, and finger position were recorded in eight right-handed women. Results Five subjects showed CMC in gamma- (28-45 Hz) and three in beta-range (15-30 Hz). Beta- and gamma-range CMC and cortical motor spectral power were not modulated by the various frequencies. However, a sharp bilateral CMC peak at 1.6 Hz was observed, but only in the five gamma-range CMC subjects. The performance error increased linearly with the frequency. Conclusions Our findings suggest that the frequency of force modulation has no effect on the beta- and gamma-range CMC during isometric compensation for modulated forces at 8% MVC. The beta- and gamma-range CMC may be related to interindividual differences and possibly to strategy differences. PMID:21194447

  14. Interaction between electrical modulation of the brain and pharmacotherapy to control pharmacoresistant epilepsy.

    PubMed

    Rocha, Luisa

    2013-05-01

    In spite of the high success rate of many surgical procedures for pharmacoresistant epilepsy, a substantial number of patients do not become seizure-free. Different strategies for electrical modulation of the brain such as Deep Brain Stimulation, Vagal Nerve Stimulation and Transcraneal Magnetic Stimulation have gained considerable interest in the last decade as alternative therapies for patients with medically refractory epilepsy. Research into the mechanism of action of the strategies for electrical modulation of the brain suggests a crucial role of different molecules and channels such as glutamate, γ-aminobutyric acid, adenosine, brain-derived neurotrophic factor, calcium channels, sodium channels as well as extracellular potassium. Electrical modulation of the brain may reduce the overexpression of P-glycoprotein, a drug efflux transporter that reduces the absorption of antiepileptic drugs. Electrical modulation of the brain induces long-term effects associated with beneficial consequences on clinical symptoms observed during the postictal state. In addition, electrical modulation of the brain might also promote the neurogenesis in subjects with pharmacoresistant epilepsy in whom this process is decreased. Targeting the regulatory pathways in charge of the effects of electrical modulation of the brain is discussed as a means to improve its efficacy. Electrical modulation of the brain combined with pharmacotherapy may represent an innovative approach to avoid epileptogenesis, reduce seizure activity, induce beneficial effects during the postictal state, diminish the amount of antiepileptic drugs, and improve alertness, memory and mood in pharmacoresistant epilepsy.

  15. An interactive computer kiosk module for the treatment of recurrent uncomplicated cystitis in women.

    PubMed

    Aagaard, Eva M; Nadler, Paul; Adler, Joshua; Maselli, Judith; Gonzales, Ralph

    2006-11-01

    To validate and implement a computer module for the management of uncomplicated urinary tract infections (UTI). Women age 18 to 64 years, with a previous UTI, voiding symptoms, and absence of complicating features (comorbidities, vaginal discharge, back pain, emesis, and fever/chills). The computer module was validated against clinician diagnosis and urine culture. Following validation, the module was implemented in the urgent care clinic as a management option for women with suspected UTI; computer-directed therapy (CDT)-eligible women received antibiotic treatment without a clinician examination. Patient satisfaction with the module and return visits for UTI-related complaints were assessed. In the validation study, 18 of 68 women (26%) were CDT-eligible. Clinicians diagnosed 17/18 CDT-eligible women with uncomplicated UTI. Sixty-seven percent of CDT-eligible women had a positive urine culture. Since implementation, 162 women have accessed the module, and 35% have received CDT. Ninety-eight percent (95% confidence interval: 95% to 100%) found the program easy to use and 95% (89% to 100%) would recommend it to friends/family. Two (4%) CDT-treated women had a return visit to our institution for a UTI-related illness within 2 weeks. A computer module accurately identifies women with culture-confirmed, uncomplicated UTIs. Patients are highly satisfied with the module.

  16. An Interactive Computer Kiosk Module for the Treatment of Recurrent Uncomplicated Cystitis in Women

    PubMed Central

    Aagaard, Eva M; Nadler, Paul; Adler, Joshua; Maselli, Judith; Gonzales, Ralph

    2006-01-01

    OBJECTIVE To validate and implement a computer module for the management of uncomplicated urinary tract infections (UTI). PARTICIPANTS Women age 18 to 64 years, with a previous UTI, voiding symptoms, and absence of complicating features (comorbidities, vaginal discharge, back pain, emesis, and fever/chills). MEASUREMENTS The computer module was validated against clinician diagnosis and urine culture. Following validation, the module was implemented in the urgent care clinic as a management option for women with suspected UTI; computer-directed therapy (CDT)-eligible women received antibiotic treatment without a clinician examination. Patient satisfaction with the module and return visits for UTI-related complaints were assessed. RESULTS In the validation study, 18 of 68 women (26%) were CDT-eligible. Clinicians diagnosed 17/18 CDT-eligible women with uncomplicated UTI. Sixty-seven percent of CDT-eligible women had a positive urine culture. Since implementation, 162 women have accessed the module, and 35% have received CDT. Ninety-eight percent (95% confidence interval: 95% to 100%) found the program easy to use and 95% (89% to 100%) would recommend it to friends/family. Two (4%) CDT-treated women had a return visit to our institution for a UTI-related illness within 2 weeks. CONCLUSIONS A computer module accurately identifies women with culture-confirmed, uncomplicated UTIs. Patients are highly satisfied with the module. PMID:16879705

  17. Rosetta stone method for detecting protein function and protein-protein interactions from genome sequences

    DOEpatents

    Eisenberg, David; Marcotte, Edward M.; Pellegrini, Matteo; Thompson, Michael J.; Yeates, Todd O.

    2002-10-15

    A computational method system, and computer program are provided for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins A' and B' have homologs in another organism fused into a single protein chain AB. A trans-genome comparison of sequences can reveal these AB sequences, which are Rosetta Stone sequences because they decipher an interaction between A' and B. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. The profile provides information regarding functional links between different families of proteins. In yet another method a combination of the above two methods is used to predict functional links.

  18. Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions.

    PubMed

    Zhu, Xuefeng; Wirén, Marianna; Sinha, Indranil; Rasmussen, Nina N; Linder, Tomas; Holmberg, Steen; Ekwall, Karl; Gustafsson, Claes M

    2006-04-21

    Mediator exists in a free form containing the Med12, Med13, CDK8, and CycC subunits (the Srb8-11 module) and a smaller form, which lacks these four subunits and associates with RNA polymerase II (Pol II), forming a holoenzyme. We use chromatin immunoprecipitation (ChIP) and DNA microarrays to investigate genome-wide localization of Mediator and the Srb8-11 module in fission yeast. Mediator and the Srb8-11 module display similar binding patterns, and interactions with promoters and upstream activating sequences correlate with increased transcription activity. Unexpectedly, Mediator also interacts with the downstream coding region of many genes. These interactions display a negative bias for positions closer to the 5' ends of open reading frames (ORFs) and appear functionally important, because downregulation of transcription in a temperature-sensitive med17 mutant strain correlates with increased Mediator occupancy in the coding region. We propose that Mediator coordinates transcription initiation with transcriptional events in the coding region of eukaryotic genes.

  19. Drug-Like Protein–Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

    PubMed Central

    Villoutreix, Bruno O; Kuenemann, Melaine A; Poyet, Jean-Luc; Bruzzoni-Giovanelli, Heriberto; Labbé, Céline; Lagorce, David; Sperandio, Olivier; Miteva, Maria A

    2014-01-01

    Fundamental processes in living cells are largely controlled by macromolecular interactions and among them, protein–protein interactions (PPIs) have a critical role while their dysregulations can contribute to the pathogenesis of numerous diseases. Although PPIs were considered as attractive pharmaceutical targets already some years ago, they have been thus far largely unexploited for therapeutic interventions with low molecular weight compounds. Several limiting factors, from technological hurdles to conceptual barriers, are known, which, taken together, explain why research in this area has been relatively slow. However, this last decade, the scientific community has challenged the dogma and became more enthusiastic about the modulation of PPIs with small drug-like molecules. In fact, several success stories were reported both, at the preclinical and clinical stages. In this review article, written for the 2014 International Summer School in Chemoinformatics (Strasbourg, France), we discuss in silico tools (essentially post 2012) and databases that can assist the design of low molecular weight PPI modulators (these tools can be found at www.vls3d.com). We first introduce the field of protein–protein interaction research, discuss key challenges and comment recently reported in silico packages, protocols and databases dedicated to PPIs. Then, we illustrate how in silico methods can be used and combined with experimental work to identify PPI modulators. PMID:25254076

  20. Planetfinder: An Online Interactive Module for Learning How Astronomers Detect Extrasolar Planets

    NASA Astrophysics Data System (ADS)

    McCray, Richard

    Planetfinder is a Web-based module designed to enable undergraduates to learn how astronomers detect extrasolar planets through observations of the Doppler shifts of a star's spectral lines. The module guides students through the process of measuring the masses and orbital parameters of actual extrasolar planets by fitting model Doppler curves to the data. The main goal of the exercise is to give students an understanding of the process of scientific measurement and model fitting. The exercise can be done at various levels of difficulty, ranging from measuring the properties of planetary systems having nearly circular orbits without using algebra, to exploring properties of systems having eccentric orbits and the associated equations of motion. The module is self-checking. Student work is stored in a database that is easily accessible by the instructor. The module has been tested at several institutions and is available for public use.

  1. Observation of relativistic cross-phase modulation in high-intensity laser-plasma interactions.

    PubMed

    Chen, S; Rever, M; Zhang, P; Theobald, W; Umstadter, D

    2006-10-01

    A nonlinear optical phenomenon, relativistic cross-phase modulation, is reported. A relativistically intense light beam (I = 1.3 x 10(18) W cm(-2), lambda = 1.05 microm) is experimentally observed to cause phase modulation of a lower intensity, copropagating light beam in a plasma. The latter beam is generated when the former undergoes the stimulated Raman forward scattering instability. The bandwidth of the Raman satellite is found to be broadened from 3.8-100 nm when the pump laser power is increased from 0.45-2.4 TW. A signature of relativistic cross-phase modulation, namely, asymmetric spectral broadening of the Raman signal, is observed at a pump power of 2.4 TW. The experimental cross-phase modulated spectra compared well with theoretical calculations. Applications to generation of high-power single-cycle pulses are also discussed.

  2. Interaction of acupuncture treatment and manipulation laterality modulated by the default mode network

    PubMed Central

    Niu, Xuan; Zhang, Ming; Liu, Zhenyu; Sun, Chuanzhu; Wang, Shan; Wang, Xiaocui; Chen, Zhen; Chen, Hongyan; Tian, Jie

    2016-01-01

    Appropriate selection of ipsilateral or contralateral electroacupuncture (corresponding to the pain site) plays an important role in reaching its better curative effect; however, the involving brain mechanism still remains unclear. Compared with the heat pain model generally established in previous study, capsaicin pain model induces reversible cutaneous allodynia and is proved to be better simulating aspects of clinical nociceptive and neuropathic pain. In the current study, 24 subjects were randomly divided into two groups with a 2 × 2 factorial design: laterality (ipsi- or contralateral side, inter-subject) × treatment with counter-balanced at an interval of one week (verum and placebo electroacupuncture, within-subject). We observed subjective pain intensity and brain activations changes induced by capsaicin allodynia pain stimuli before and after electroacupuncture treatment at acupoint LI4 for 30 min. Analysis of variance results indicated that ipsilateral electroacupuncture treatment produced significant pain relief and wide brain signal suppressions in pain-related brain areas compared with contralateral electroacupuncture. We also found that verum electroacupuncture at either ipsi- or contralateral side to the pain site exhibited comparable significant magnitudes of analgesic effect. By contrast, placebo electroacupuncture elicited significant pain reductions only on the ipsilateral rather than contralateral side. It was inferred that placebo analgesia maybe attenuated on the region of the body (opposite to pain site) where attention was less focused, suggesting that analgesic effect of placebo electroacupuncture mainly rely on the motivation of its spatial-specific placebo responses via attention mechanism. This inference can be further supported by the evidence that the significant interaction effect of manipulation laterality and treatment was exclusively located within the default mode network, including the bilateral superior parietal

  3. Interaction of acupuncture treatment and manipulation laterality modulated by the default mode network.

    PubMed

    Niu, Xuan; Zhang, Ming; Liu, Zhenyu; Bai, Lijun; Sun, Chuanzhu; Wang, Shan; Wang, Xiaocui; Chen, Zhen; Chen, Hongyan; Tian, Jie

    2017-01-01

    Appropriate selection of ipsilateral or contralateral electroacupuncture (corresponding to the pain site) plays an important role in reaching its better curative effect; however, the involving brain mechanism still remains unclear. Compared with the heat pain model generally established in previous study, capsaicin pain model induces reversible cutaneous allodynia and is proved to be better simulating aspects of clinical nociceptive and neuropathic pain. In the current study, 24 subjects were randomly divided into two groups with a 2 × 2 factorial design: laterality (ipsi- or contralateral side, inter-subject) × treatment with counter-balanced at an interval of one week (verum and placebo electroacupuncture, within-subject). We observed subjective pain intensity and brain activations changes induced by capsaicin allodynia pain stimuli before and after electroacupuncture treatment at acupoint LI4 for 30 min. Analysis of variance results indicated that ipsilateral electroacupuncture treatment produced significant pain relief and wide brain signal suppressions in pain-related brain areas compared with contralateral electroacupuncture. We also found that verum electroacupuncture at either ipsi- or contralateral side to the pain site exhibited comparable significant magnitudes of analgesic effect. By contrast, placebo electroacupuncture elicited significant pain reductions only on the ipsilateral rather than contralateral side. It was inferred that placebo analgesia maybe attenuated on the region of the body (opposite to pain site) where attention was less focused, suggesting that analgesic effect of placebo electroacupuncture mainly rely on the motivation of its spatial-specific placebo responses via attention mechanism. This inference can be further supported by the evidence that the significant interaction effect of manipulation laterality and treatment was exclusively located within the default mode network, including the bilateral superior parietal

  4. A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle

    PubMed Central

    2013-01-01

    Background Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic variability, the genome, and raw phenotypes that are influenced by a large number of environmental effects. The present study combines two concepts, systems biology and metabolic analyses, in an approach without prior functional hypothesis in order to dissect genes and molecular pathways that modulate differential growth at the onset of puberty in male cattle. Furthermore, this integrative strategy was applied to specifically explore distinctive gene interactions of non-SMC condensin I complex, subunit G (NCAPG) and myostatin (GDF8), known modulators of pre- and postnatal growth that are only partially understood for their molecular pathways affecting differential body weight. Results Our study successfully established gene networks and interacting partners affecting growth at the onset of puberty in cattle. We demonstrated the biological relevance of the created networks by comparison to randomly created networks. Our data showed that GnRH (Gonadotropin-releasing hormone) signaling is associated with divergent growth at the onset of puberty and revealed two highly connected hubs, BTC and DGKH, within the network. Both genes are known to directly interact with the GnRH signaling pathway. Furthermore, a gene interaction network for NCAPG containing 14 densely connected genes revealed novel information concerning the functional role of NCAPG in divergent growth. Conclusions Merging both concepts, systems biology and metabolomic analyses, successfully yielded new insights into gene networks and interacting partners affecting growth at the onset of puberty in cattle. Genetic modulation in GnRH signaling was identified as key modifier of differential cattle growth at the onset of puberty. In addition, the benefit of our innovative concept without prior

  5. CD93 interacts with the PDZ domain-containing adaptor protein GIPC: implications in the modulation of phagocytosis.

    PubMed

    Bohlson, Suzanne S; Zhang, Mingyu; Ortiz, Christopher E; Tenner, Andrea J

    2005-01-01

    CD93 was originally identified as a myeloid cell-surface marker and subsequently associated with an ability to modulate phagocytosis of suboptimally opsonized immunoglobulin G and complement particles in vitro. Recent studies using mice deficient in CD93 have demonstrated that this molecule modulates phagocytosis of apoptotic cells in vivo. To investigate signal transduction mechanisms mediated by CD93, CD93 cytoplasmic tail (CYTO)-binding proteins were identified in a yeast two-hybrid screen. Fifteen of 34 positive clones contained a splice variant or a partial cDNA encoding GIPC, a PSD-95/Dlg/ZO-1 (PDZ) domain-containing protein, shown previously to regulate cytoskeletal dynamics. A single clone of the N-terminal kinase-like protein p105 and an uncharacterized stem cell transcript also showed specificity for binding to the CYTO by yeast two-hybrid. Using the yeast two-hybrid system and an in vitro glutathione S-transferase fusion protein-binding assay, the binding of GIPC to the CYTO was shown to involve a newly identified class I PDZ-binding domain in the CD93 carboxyl terminus. Four positively charged amino acids in the juxtamembrane domain of CD93 were shown to be critical in stabilizing these interactions. Treatment of human monocytes with a cell-permeable peptide encoding the C-terminal 11 amino acids of CD93 resulted in an enhancement of phagocytosis, supporting the hypothesis that this protein-protein interaction domain is involved in the modulation of phagocytosis. These protein interactions may participate as molecular switches in modulating cellular phagocytic activity.

  6. General hydrophobic interaction potential for surfactant/lipid bilayers from direct force measurements between light-modulated bilayers

    PubMed Central

    Donaldson, Stephen H.; Lee, C. Ted; Chmelka, Bradley F.; Israelachvili, Jacob N.

    2011-01-01

    We establish and quantify correlations among the molecular structures, interaction forces, and physical processes associated with light-responsive self-assembled surfactant monolayers or bilayers at interfaces. Using the surface forces apparatus (SFA), the interaction forces between adsorbed monolayers and bilayers of an azobenzene-functionalized surfactant can be drastically and controllably altered by light-induced conversion of trans and cis molecular conformations. These reversible conformation changes affect significantly the shape of the molecules, especially in the hydrophobic region, which induces dramatic transformations of molecular packing in self-assembled structures, causing corresponding modulation of electrostatic double layer, steric hydration, and hydrophobic interactions. For bilayers, the isomerization from trans to cis exposes more hydrophobic groups, making the cis bilayers more hydrophobic, which lowers the activation energy barrier for (hemi)fusion. A quantitative and general model is derived for the interaction potential of charged bilayers that includes the electrostatic double-layer force of the Derjaguin–Landau–Verwey–Overbeek theory, attractive hydrophobic interactions, and repulsive steric-hydration forces. The model quantitatively accounts for the elastic strains, deformations, long-range forces, energy maxima, adhesion minima, as well as the instability (when it exists) as two bilayers breakthrough and (hemi)fuse. These results have several important implications, including quantitative and qualitative understanding of the hydrophobic interaction, which is furthermore shown to be a nonadditive interaction. PMID:21896718

  7. Screening for Small-Molecule Modulators of Long Noncoding RNA-Protein Interactions Using AlphaScreen.

    PubMed

    Pedram Fatemi, Roya; Salah-Uddin, Sultan; Modarresi, Farzaneh; Khoury, Nathalie; Wahlestedt, Claes; Faghihi, Mohammad Ali

    2015-10-01

    Long non-protein coding RNAs (lncRNAs) are an important class of molecules that help orchestrate key cellular events. Although their functional roles in cells are not well understood, thousands of lncRNAs and a number of possible mechanisms by which they act have been reported. LncRNAs can exert their regulatory function in cells by interacting with epigenetic enzymes. In this study, we developed a tool to study lncRNA-protein interactions for high-throughput screening of small-molecule modulators using AlphaScreen technology. We tested the interaction of two lncRNAs: brain-derived neurotrophic factor antisense (BDNF-AS) and Hox transcript antisense RNA (HOTAIR), with Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase against a phytochemical library, to look for small-molecule inhibitors that can alter the expression of downstream target genes. We identified ellipticine, a compound that up-regulates BDNF transcription. Our study shows the feasibility of using high-throughput screening to identify modulators of lncRNA-protein interactions and paves the road for targeting lncRNAs that are dysregulated in human disorders using small-molecule therapies. © 2015 Society for Laboratory Automation and Screening.

  8. The in vitro interaction of Sporothrix schenckii with human endothelial cells is modulated by cytokines and involves endothelial surface molecules.

    PubMed

    Figueiredo, Camila Castro; De Lima, Osana Cunha; De Carvalho, Laís; Lopes-Bezerra, Leila Maria; Morandi, Verônica

    2004-04-01

    Sporothrix schenckii is the etiological agent of sporotrichosis, a subcutaneous mycosis that can evolve to systemic complications in immunocompromised patients. Interactions with endothelium are thought to be essential for systemic infections. In the present work, we studied the interaction between S. schenckii and human umbilical vein endothelial cells (HUVECs). S. schenckii interacts with HUVECs in a time-dependent manner. Morphological analysis showed that yeasts locate to interendothelial junctions. Ultrastructural studies showed that internalized yeasts were found inside endocytic vacuoles as early as 2 h, without causing any detectable damage to HUVECs after 24 h of infection. The viability of infected HUVECs was confirmed by the MTT assay. When HUVECs were treated with different concentrations of Interleukin-1beta or transforming growth factor-beta, a significant dose-dependent increase in cell-associated yeasts was observed. The preliminary analysis of the endothelial surface ligands for S. schenckii cells revealed two major molecules, with Mr of approximately 90 and 135 kDa. The interaction of endothelial cell surface molecules with S. schenckii yeast cells was modulated by divalent cations. This is the first demonstration that S. schenckii is able to adhere and invade endothelial cells without significantly affect cellular integrity. Our results suggest the contribution of cytokine-modulated calcium-dependent molecules to this process.

  9. Decoding of lipoprotein – receptor interactions; Properties of ligand binding modules governing interactions with ApoE

    PubMed Central

    Guttman, Miklos; Prieto, J. Helena; Croy, Johnny E.; Komives, Elizabeth A.

    2010-01-01

    Clusters of complement-type ligand binding repeats in the LDL receptor family are thought to mediate the interactions between these receptors and their various ligands. Apolipoprotein E, a key ligand for cholesterol homeostasis, has been shown to interact with LDLR, LRP and VLDLR, through these clusters. LDLR and VLDLR each contain a single ligand-binding repeat cluster, whereas LRP contains three large clusters of ligand binding repeats, each with ligand binding functions. We show that within sLRP3, the three-repeat subcluster CR16-18 recapitulated ligand binding to the isolated receptor binding portion of ApoE (residues 130-149). Binding experiments with LA3-5 of LDLR and CR16-18 showed that a conserved W25/D30 pair appears critical for high affinity binding to ApoE(130-149). The triple repeat LA3-5 showed the expected interaction with ApoE(1-191)•DMPC, but surprisingly CR16-18 did not interact with this form of ApoE. To understand these differences in ApoE binding affinity, we introduced mutations of conserved residues from LA5 into CR18, and produced a CR16-18 variant capable of binding ApoE(1-191)•DMPC. This change cannot fully be accounted for by the interaction with the proposed ApoE receptor binding region, therefore we speculate that LA5 is recognizing a distinct epitope on ApoE that may only exists in the lipid bound form. The combination of avidity effects with this distinct recognition process likely governs the ApoE-LDL receptor interaction. PMID:20030366

  10. Perilipin polymorphism interacts with saturated fat and carbohydrates to modulate insulin resistance

    USDA-ARS?s Scientific Manuscript database

    Macronutrient intakes and genetic variants have been shown to interact to alter insulin resistance, but replications of gene-nutrient interactions across independent populations are rare, despite their critical importance in establishing credibility. We aimed to investigate a previously demonstrated...

  11. Thalamic synaptic transmission of sensory information modulated by synergistic interaction of adenosine and serotonin.

    PubMed

    Yang, Ya-Chin; Hu, Chun-Chang; Huang, Chen-Syuan; Chou, Pei-Yu

    2014-03-01

    The thalamic synapses relay peripheral sensory information to the cortex, and constitute an important part of the thalamocortical network that generates oscillatory activities responsible for different vigilance (sleep and wakefulness) states. However, the modulation of thalamic synaptic transmission by potential sleep regulators, especially by combination of regulators in physiological scenarios, is not fully characterized. We found that somnogen adenosine itself acts similar to wake-promoting serotonin, both decreasing synaptic strength as well as short-term depression, at the retinothalamic synapse. We then combined the two modulators considering the coexistence of them in the hypnagogic (sleep-onset) state. Adenosine plus serotonin results in robust synergistic inhibition of synaptic strength and dramatic transformation of short-term synaptic depression to facilitation. These synaptic effects are not achievable with a single modulator, and are consistent with a high signal-to-noise ratio but a low level of signal transmission through the thalamus appropriate for slow-wave sleep. This study for the first time demonstrates that the sleep-regulatory modulators may work differently when present in combination than present singly in terms of shaping information flow in the thalamocortical network. The major synaptic characters such as the strength and short-term plasticity can be profoundly altered by combination of modulators based on physiological considerations.

  12. MAE-FMD: multi-agent evolutionary method for functional module detection in protein-protein interaction networks.

    PubMed

    Ji, Jun Zhong; Jiao, Lang; Yang, Cui Cui; Lv, Jia Wei; Zhang, Ai Dong

    2014-09-30

    Studies of functional modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in detecting functional modules. We present a new approach using multi-agent evolution for detection of functional modules in PPI networks. The proposed approach consists of two stages: the solution construction for agents in a population and the evolutionary process of computational agents in a lattice environment, where each agent corresponds to a candidate solution to the detection problem of functional modules in a PPI network. First, the approach utilizes a connection-based encoding scheme to model an agent, and employs a random-walk behavior merged topological characteristics with functional information to construct a solution. Next, it applies several evolutionary operators, i.e., competition, crossover, and mutation, to realize information exchange among agents as well as solution evolution. Systematic experiments have been conducted on three benchmark testing sets of yeast networks. Experimental results show that the approach is more effective compared to several other existing algorithms. The algorithm has the characteristics of outstanding recall, F-measure, sensitivity and accuracy while keeping other competitive performances, so it can be applied to the biological study which requires high accuracy.

  13. Affect-modulated startle: interactive influence of catechol-O-methyltransferase Val158Met genotype and childhood trauma.

    PubMed

    Klauke, Benedikt; Winter, Bernward; Gajewska, Agnes; Zwanzger, Peter; Reif, Andreas; Herrmann, Martin J; Dlugos, Andrea; Warrings, Bodo; Jacob, Christian; Mühlberger, Andreas; Arolt, Volker; Pauli, Paul; Deckert, Jürgen; Domschke, Katharina

    2012-01-01

    The etiology of emotion-related disorders such as anxiety or affective disorders is considered to be complex with an interaction of biological and environmental factors. Particular evidence has accumulated for alterations in the dopaminergic and noradrenergic system--partly conferred by catechol-O-methyltransferase (COMT) gene variation--for the adenosinergic system as well as for early life trauma to constitute risk factors for those conditions. Applying a multi-level approach, in a sample of 95 healthy adults, we investigated effects of the functional COMT Val158Met polymorphism, caffeine as an adenosine A2A receptor antagonist (300 mg in a placebo-controlled intervention design) and childhood maltreatment (CTQ) as well as their interaction on the affect-modulated startle response as a neurobiologically founded defensive reflex potentially related to fear- and distress-related disorders. COMT val/val genotype significantly increased startle magnitude in response to unpleasant stimuli, while met/met homozygotes showed a blunted startle response to aversive pictures. Furthermore, significant gene-environment interaction of COMT Val158Met genotype with CTQ was discerned with more maltreatment being associated with higher startle potentiation in val/val subjects but not in met carriers. No main effect of or interaction effects with caffeine were observed. Results indicate a main as well as a GxE effect of the COMT Val158Met variant and childhood maltreatment on the affect-modulated startle reflex, supporting a complex pathogenetic model of the affect-modulated startle reflex as a basic neurobiological defensive reflex potentially related to anxiety and affective disorders.

  14. Siderophore biosynthesis coordinately modulated the virulence-associated interactive metabolome of uropathogenic Escherichia coli and human urine

    PubMed Central

    Su, Qiao; Guan, Tianbing; Lv, Haitao

    2016-01-01

    Uropathogenic Escherichia coli (UPEC) growth in women’s bladders during urinary tract infection (UTI) incurs substantial chemical exchange, termed the “interactive metabolome”, which primarily accounts for the metabolic costs (utilized metabolome) and metabolic donations (excreted metabolome) between UPEC and human urine. Here, we attempted to identify the individualized interactive metabolome between UPEC and human urine. We were able to distinguish UPEC from non-UPEC by employing a combination of metabolomics and genetics. Our results revealed that the interactive metabolome between UPEC and human urine was markedly different from that between non-UPEC and human urine, and that UPEC triggered much stronger perturbations in the interactive metabolome in human urine. Furthermore, siderophore biosynthesis coordinately modulated the individualized interactive metabolome, which we found to be a critical component of UPEC virulence. The individualized virulence-associated interactive metabolome contained 31 different metabolites and 17 central metabolic pathways that were annotated to host these different metabolites, including energetic metabolism, amino acid metabolism, and gut microbe metabolism. Changes in the activities of these pathways mechanistically pinpointed the virulent capability of siderophore biosynthesis. Together, our findings provide novel insights into UPEC virulence, and we propose that siderophores are potential targets for further discovery of drugs to treat UPEC-induced UTI. PMID:27076285

  15. Nonlinear space charge dynamics and modulational instability in the interaction of intense laser pulses with electron-positron plasmas

    NASA Astrophysics Data System (ADS)

    Hashemzadeh, M.; Niknam, A. R.

    2017-06-01

    Nonlinear space charge dynamics and modulational instability in the interaction between ultrashort, intense laser pulses and electron-positron pair plasmas are investigated taking into account the relativistic ponderomotive force and the relativistic mass of electrons and positrons. By coupling Maxwell's equations and hydrodynamic model, the electron and positron density distributions and the dispersion relation for the modulational instability are obtained. Moreover, two coupled nonlinear equations for the scalar and vector potentials are derived and numerically solved. The results show that the growth rate of instability increases with the decrease in the electron and positron temperatures. Moreover, it is shown that when the temperatures of electrons and positrons are not equal to each other, the profiles of scalar potential are similar to bright-like or dark-like solitons.

  16. You Look Human, But Act Like a Machine: Agent Appearance and Behavior Modulate Different Aspects of Human-Robot Interaction.

    PubMed

    Abubshait, Abdulaziz; Wiese, Eva

    2017-01-01

    Gaze following occurs automatically in social interactions, but the degree to which gaze is followed depends on whether an agent is perceived to have a mind, making its behavior socially more relevant for the interaction. Mind perception also modulates the attitudes we have toward others, and determines the degree of empathy, prosociality, and morality invested in social interactions. Seeing mind in others is not exclusive to human agents, but mind can also be ascribed to non-human agents like robots, as long as their appearance and/or behavior allows them to be perceived as intentional beings. Previous studies have shown that human appearance and reliable behavior induce mind perception to robot agents, and positively affect attitudes and performance in human-robot interaction. What has not been investigated so far is whether different triggers of mind perception have an independent or interactive effect on attitudes and performance in human-robot interaction. We examine this question by manipulating agent appearance (human vs. robot) and behavior (reliable vs. random) within the same paradigm and examine how congruent (human/reliable vs. robot/random) versus incongruent (human/random vs. robot/reliable) combinations of these triggers affect performance (i.e., gaze following) and attitudes (i.e., agent ratings) in human-robot interaction. The results show that both appearance and behavior affect human-robot interaction but that the two triggers seem to operate in isolation, with appearance more strongly impacting attitudes, and behavior more strongly affecting performance. The implications of these findings for human-robot interaction are discussed.

  17. You Look Human, But Act Like a Machine: Agent Appearance and Behavior Modulate Different Aspects of Human–Robot Interaction

    PubMed Central

    Abubshait, Abdulaziz; Wiese, Eva

    2017-01-01

    Gaze following occurs automatically in social interactions, but the degree to which gaze is followed depends on whether an agent is perceived to have a mind, making its behavior socially more relevant for the interaction. Mind perception also modulates the attitudes we have toward others, and determines the degree of empathy, prosociality, and morality invested in social interactions. Seeing mind in others is not exclusive to human agents, but mind can also be ascribed to non-human agents like robots, as long as their appearance and/or behavior allows them to be perceived as intentional beings. Previous studies have shown that human appearance and reliable behavior induce mind perception to robot agents, and positively affect attitudes and performance in human–robot interaction. What has not been investigated so far is whether different triggers of mind perception have an independent or interactive effect on attitudes and performance in human–robot interaction. We examine this question by manipulating agent appearance (human vs. robot) and behavior (reliable vs. random) within the same paradigm and examine how congruent (human/reliable vs. robot/random) versus incongruent (human/random vs. robot/reliable) combinations of these triggers affect performance (i.e., gaze following) and attitudes (i.e., agent ratings) in human–robot interaction. The results show that both appearance and behavior affect human–robot interaction but that the two triggers seem to operate in isolation, with appearance more strongly impacting attitudes, and behavior more strongly affecting performance. The implications of these findings for human–robot interaction are discussed. PMID:28878703

  18. The Interaction of Heparin Tetrasaccharides with Chemokine CCL5 Is Modulated by Sulfation Pattern and pH*

    PubMed Central

    Singh, Arunima; Kett, Warren C.; Severin, India C.; Agyekum, Isaac; Duan, Jiana; Amster, I. Jonathan; Proudfoot, Amanda E. I.; Coombe, Deirdre R.; Woods, Robert J.

    2015-01-01

    Interactions between chemokines such as CCL5 and glycosaminoglycans (GAGs) are essential for creating haptotactic gradients to guide the migration of leukocytes into inflammatory sites, and the GAGs that interact with CCL5 with the highest affinity are heparan sulfates/heparin. The interaction between CCL5 and its receptor on monocytes, CCR1, is mediated through residues Arg-17 and -47 in CCL5, which overlap with the GAG-binding 44RKNR47 “BBXB” motifs. Here we report that heparin and tetrasaccharide fragments of heparin are able to inhibit CCL5-CCR1 binding, with IC50 values showing strong dependence on the pattern and extent of sulfation. Modeling of the CCL5-tetrasaccharide complexes suggested that interactions between specific sulfate and carboxylate groups of heparin and residues Arg-17 and -47 of the protein are essential for strong inhibition; tetrasaccharides lacking the specific sulfation pattern were found to preferentially bind CCL5 in positions less favorable for inhibition of the interaction with CCR1. Simulations of a 12-mer heparin fragment bound to CCL5 indicated that the oligosaccharide preferred to interact simultaneously with both 44RKNR47 motifs in the CCL5 homodimer and engaged residues Arg-47 and -17 from both chains. Direct engagement of these residues by the longer heparin oligosaccharide provides a rationalization for its effectiveness as an inhibitor of CCL5-CCR1 interaction. In this mode, histidine (His-23) may contribute to CCL5-GAG interactions when the pH drops just below neutral, as occurs during inflammation. Additionally, an examination of the contribution of pH to modulating CCL5-heparin interactions suggested a need for careful interpretation of experimental results when experiments are performed under non-physiological conditions. PMID:25907556

  19. Interaction between Cannabinoid Type 1 and Type 2 Receptors in the Modulation of Subventricular Zone and Dentate Gyrus Neurogenesis.

    PubMed

    Rodrigues, Rui S; Ribeiro, Filipa F; Ferreira, Filipa; Vaz, Sandra H; Sebastião, Ana M; Xapelli, Sara

    2017-01-01

    Neurogenesis in the adult mammalian brain occurs mainly in two neurogenic niches, the subventricular zone (SVZ) and the subgranular zone (SGZ) of the dentate gyrus (DG). Cannabinoid type 1 and 2 receptors (CB1R and CB2R) have been shown to differently modulate neurogenesis. However, low attention has been given to the interaction between CB1R and CB2R in modulating postnatal neurogenesis (proliferation, neuronal differentiation and maturation). We focused on a putative crosstalk between CB1R and CB2R to modulate neurogenesis and cultured SVZ and DG stem/progenitor cells from early postnatal (P1-3) Sprague-Dawley rats. Data showed that the non-selective cannabinoid receptor agonist WIN55,212-2 promotes DG cell proliferation (measured by BrdU staining), an effect blocked by either CB1R or CB2R selective antagonists. Experiments with selective agonists showed that facilitation of DG cell proliferation requires co-activation of both CB1R and CB2R. Cell proliferation in the SVZ was not affected by the non-selective receptor agonist, but it was enhanced by CB1R selective activation. However, either CB1R or CB2R selective antagonists abolished the effect of the CB1R agonist in SVZ cell proliferation. Neuronal differentiation (measured by immunocytochemistry against neuronal markers of different stages and calcium imaging) was facilitated by WIN55,212-2 at both SVZ and DG. This effect was mimicked by either CB1R or CB2R selective agonists and blocked by either CB1R or CB2R selective antagonists, cross-antagonism being evident. In summary, our findings indicate a tight interaction between CB1R and CB2R to modulate neurogenesis in the two major neurogenic niches, thus contributing to further unraveling the mechanisms behind the action of endocannabinoids in the brain.

  20. Evaluating the Instructional Efficacy of Computer-Mediated Interactive Multimedia: Comparing Three Elementary Statistics Tutorial Modules.

    ERIC Educational Resources Information Center

    Gonzalez, Gerardo M.; Birch, Marc A.

    2000-01-01

    This study evaluated three tutorial modules, equivalent in content but different in mode of presentation, for introducing elementary statistics concepts. Fifty-seven college students participated in one of four randomly assigned conditions: paper-and-pencil, basic computerized, computerized multimedia, or control group. Participant evaluations…

  1. Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

    PubMed Central

    Bai, Qifeng; Yao, Xiaojun

    2016-01-01

    Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing more potential negative allosteric modulator (NAM). Here, we report molecular dynamics simulation studies of the modulation mechanism of FITM on the wild type, T815M and Y805A mutants of mGlu1 through weak interaction analysis and free energy calculation. The weak interaction analysis demonstrates that van der Waals (vdW) and hydrogen bonding play an important role on the dimer packing between six cholesterol molecules and mGlu1 as well as the interaction between allosteric sites T815, Y805 and FITM in wild type, T815M and Y805A mutants of mGlu1. Besides, the results of free energy calculations indicate that secondary binding pocket is mainly formed by the residues Thr748, Cys746, Lys811 and Ser735 except for FITM-bound pocket in crystal structure. Our results can not only reveal the dimer packing and allosteric regulation mechanism, but also can supply useful information for the design of potential NAM of mGlu1. PMID:26887338

  2. Arrangement of scale-interaction and large-scale modulation in high Reynolds number turbulent boundary layers

    NASA Astrophysics Data System (ADS)

    Baars, Woutijn J.; Hutchins, Nicholas; Marusic, Ivan

    2015-11-01

    Interactions between small- and large-scale motions are inherent in the near-wall dynamics of wall-bounded flows. We here examine the scale-interaction embedded within the streamwise velocity component. Data were acquired using hot-wire anemometry in ZPG turbulent boundary layers, for Reynolds numbers ranging from Reτ ≡ δUτ / ν ~ 2800 to 22800. After first decomposing velocity signals into contributions from small- and large-scales, we then represent the time-varying small-scale energy with time series of its instantaneous amplitude and instantaneous frequency, via a wavelet-based method. Features of the scale-interaction are inferred from isocorrelation maps, formed by correlating the large-scale velocity with its concurrent small-scale amplitude and frequency. Below the onset of the log-region, the physics constitutes aspects of amplitude modulation and frequency modulation. Time shifts, associated with the correlation extrema--representing the lead/lag of the small-scale signatures relative to the large-scales--are shown to be governed by inner-scaling. Wall-normal trends of time shifts are explained by considering the arrangement of scales in the log- and intermittent-regions, and how they relate to stochastic top-down and bottom-up processes.

  3. Modulation of pineal melatonin synthesis by glutamate involves paracrine interactions between pinealocytes and astrocytes through NF-κB activation.

    PubMed

    Villela, Darine; Atherino, Victoria Fairbanks; Lima, Larissa de Sá; Moutinho, Anderson Augusto; do Amaral, Fernanda Gaspar; Peres, Rafael; Martins de Lima, Thais; Torrão, Andréa da Silva; Cipolla-Neto, José; Scavone, Cristóforo; Afeche, Solange Castro

    2013-01-01

    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- κ B 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- κ B 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- κ B transcription factor and possibly by subsequent TNF- α release.

  4. Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ.

    PubMed

    Xia, Hongwei; Fu, Hailin; Zhang, Yanfeng; Shih, Kuo-Chih; Ren, Yuan; Anuganti, Murali; Nieh, Mu-Ping; Cheng, Jianjun; Lin, Yao

    2017-08-16

    Supramolecular polymerization or assembly of proteins or large macromolecular units by a homogeneous nucleation mechanism can be quite slow and require specific solution conditions. In nature, protein assembly is often regulated by molecules that modulate the electrostatic interactions of the protein subunits for various association strengths. The key to this regulation is the coupling of the assembly process with a reversible or irreversible chemical reaction that occurs within the constituent subunits. However, realizing this complex process by the rational design of synthetic molecules or macromolecules remains a challenge. Herein, we use a synthetic polypeptide-grafted comb macromolecule to demonstrate how the in situ modulation of interactions between the charged macromolecules affects their resulting supramolecular structures. The kinetics of structural formation was studied and can be described by a generalized model of nucleated polymerization containing secondary pathways. Basic thermodynamic analysis indicated the delicate role of the electrostatic interactions between the charged subunits in the reaction-induced assembly process. This approach may be applicable for assembling a variety of ionic soft matters that are amenable to chemical reactions in situ.

  5. The RecX protein interacts with the RecA protein and modulates its activity in Herbaspirillum seropedicae

    PubMed Central

    Galvão, C.W.; Souza, E.M.; Etto, R.M.; Pedrosa, F.O.; Chubatsu, L.S.; Yates, M.G.; Schumacher, J.; Buck, M.; Steffens, M.B.R.

    2012-01-01

    DNA repair is crucial to the survival of all organisms. The bacterial RecA protein is a central component in the SOS response and in recombinational and SOS DNA repairs. The RecX protein has been characterized as a negative modulator of RecA activity in many bacteria. The recA and recX genes of Herbaspirillum seropedicae constitute a single operon, and evidence suggests that RecX participates in SOS repair. In the present study, we show that the H. seropedicae RecX protein (RecXHs) can interact with the H. seropedicae RecA protein (RecAHs) and that RecAHs possesses ATP binding, ATP hydrolyzing and DNA strand exchange activities. RecXHs inhibited 90% of the RecAHs DNA strand exchange activity even when present in a 50-fold lower molar concentration than RecAHs. RecAHs ATP binding was not affected by the addition of RecX, but the ATPase activity was reduced. When RecXHs was present before the formation of RecA filaments (RecA-ssDNA), inhibition of ATPase activity was substantially reduced and excess ssDNA also partially suppressed this inhibition. The results suggest that the RecXHs protein negatively modulates the RecAHs activities by protein-protein interactions and also by DNA-protein interactions. PMID:23044625

  6. Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

    NASA Astrophysics Data System (ADS)

    Bai, Qifeng; Yao, Xiaojun

    2016-02-01

    Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing more potential negative allosteric modulator (NAM). Here, we report molecular dynamics simulation studies of the modulation mechanism of FITM on the wild type, T815M and Y805A mutants of mGlu1 through weak interaction analysis and free energy calculation. The weak interaction analysis demonstrates that van der Waals (vdW) and hydrogen bonding play an important role on the dimer packing between six cholesterol molecules and mGlu1 as well as the interaction between allosteric sites T815, Y805 and FITM in wild type, T815M and Y805A mutants of mGlu1. Besides, the results of free energy calculations indicate that secondary binding pocket is mainly formed by the residues Thr748, Cys746, Lys811 and Ser735 except for FITM-bound pocket in crystal structure. Our results can not only reveal the dimer packing and allosteric regulation mechanism, but also can supply useful information for the design of potential NAM of mGlu1.

  7. Loss of Cbl-PI3K interaction modulates the periosteal response to fracture by enhancing osteogenic commitment and differentiation.

    PubMed

    Scanlon, Vanessa; Walia, Bhavita; Yu, Jungeun; Hansen, Marc; Drissi, Hicham; Maye, Peter; Sanjay, Archana

    2017-02-01

    The periosteum contains multipotent skeletal progenitors that contribute to bone repair. The signaling pathways regulating the response of periosteal cells to fracture are largely unknown. Phosphatidylinositol-3 Kinase (PI3K), a prominent lipid kinase, is a major signaling protein downstream of several factors that regulate osteoblast differentiation. Cbl is an E3 ubiquitin ligase and a major adaptor protein that binds to the p85 regulatory subunit and modulates PI3K activity. Substitution of tyrosine 737 to phenylalanine (Y737F) in Cbl abolishes the interaction between Cbl and p85 subunit without affecting the Cbl's ubiquitin ligase function. Here, we investigated the role of PI3K signaling during the very early stages of fracture healing using Osterix(RFP) reporter mice. We found that the absence of PI3K regulation by Cbl resulted in robust periosteal thickening, with increased proliferation of periosteal cells. While the multipotent properties of periosteal progenitors to differentiate into chondrocytes and adipocytes did not change, osteogenic differentiation in the absence of Cbl-PI3K interaction was highly augmented. The increased stability and nuclear localization of Osterix observed in periosteal cells lacking Cbl-PI3K interaction may explain this enhanced osteogenic differentiation since the expression of Osterix transcriptional target genes including osteocalcin and BSP are increased in YF cells. Overall, our findings highlight a hitherto unexplored and novel role for Cbl and PI3K in modulating the osteogenic response of periosteal cells during the early stages of fracture repair.

  8. Plasma protein corona modulates the vascular wall interaction of drug carriers in a material and donor specific manner.

    PubMed

    Sobczynski, Daniel J; Charoenphol, Phapanin; Heslinga, Michael J; Onyskiw, Peter J; Namdee, Katawut; Thompson, Alex J; Eniola-Adefeso, Omolola

    2014-01-01

    The nanoscale plasma protein interaction with intravenously injected particulate carrier systems is known to modulate their organ distribution and clearance from the bloodstream. However, the role of this plasma protein interaction in prescribing the adhesion of carriers to the vascular wall remains relatively unknown. Here, we show that the adhesion of vascular-targeted poly(lactide-co-glycolic-acid) (PLGA) spheres to endothelial cells is significantly inhibited in human blood flow, with up to 90% reduction in adhesion observed relative to adhesion in simple buffer flow, depending on the particle size and the magnitude and pattern of blood flow. This reduced PLGA adhesion in blood flow is linked to the adsorption of certain high molecular weight plasma proteins on PLGA and is donor specific, where large reductions in particle adhesion in blood flow (>80% relative to buffer) is seen with ∼60% of unique donor bloods while others exhibit moderate to no reductions. The depletion of high molecular weight immunoglobulins from plasma is shown to successfully restore PLGA vascular wall adhesion. The observed plasma protein effect on PLGA is likely due to material characteristics since the effect is not replicated with polystyrene or silica spheres. These particles effectively adhere to the endothelium at a higher level in blood over buffer flow. Overall, understanding how distinct plasma proteins modulate the vascular wall interaction of vascular-targeted carriers of different material characteristics would allow for the design of highly functional delivery vehicles for the treatment of many serious human diseases.

  9. Definition of EGF-like, closely interacting modules that bear activation epitopes in integrin beta subunits.

    PubMed

    Takagi, J; Beglova, N; Yalamanchili, P; Blacklow, S C; Springer, T A

    2001-09-25

    Integrin beta subunits contain four cysteine-rich repeats in a long extracellular stalk that connects the headpiece to the membrane. Most mAbs to integrin activation epitopes map to these repeats, and they are important in propagating conformational signals from the membrane/cytosol to the ligand-binding headpiece. Sequence analysis of a protein containing only 10 integrin-like, cysteine-rich repeats suggests that these repeats start one cysteine earlier than previously reported. By using the new repeat boundaries, statistically significant sequence homology to epidermal growth factor-like domains is found, and a disulfide bond connectivity of the eight cysteines is predicted that differs in three of four disulfides from a previous prediction of epidermal growth factor-like modules [Berg, R. W., Leung, E., Gough, S., Morris, C., Yao, W.-P., Wang, S.-x., Ni, J. & Krissansen, G. W. (1999) Genomics 56, 169-178]. N-terminally truncated beta2 integrin stalk fragments were well expressed and secreted from 293 T cells when they began at repeat boundaries but not when they began one cysteine earlier or later. Furthermore, peptides that correspond to module 3 or modules 2 + 3 were expressed in bacteria and refolded. The module 2 + 3 fragment was as reactive with three mAbs to activation epitopes as a beta2 fragment expressed in eukaryotic cells, indicating a native fold. Only one residue intervenes between the last cysteine of one module and the first cysteine of the next. This arrangement is consistent with a tight intermodule connection, a prerequisite for signal propagation from the membrane to the ligand binding headpiece.

  10. Dipicrylamine Modulates GABAρ1 Receptors through Interactions with Residues in the TM4 and Cys-Loop Domains.

    PubMed

    Limon, Agenor; Estrada-Mondragón, Argel; Ruiz, Jorge M Reyes; Miledi, Ricardo

    2016-04-01

    Dipicrylamine (DPA) is a commonly used acceptor agent in Förster resonance energy transfer experiments that allows the study of high-frequency neuronal activity in the optical monitoring of voltage in living cells. However, DPA potently antagonizes GABAA receptors that contain α1 and β2 subunits by a mechanism which is not clearly understood. In this work, we aimed to determine whether DPA modulation is a general phenomenon of Cys-loop ligand-gated ion channels (LGICs), and whether this modulation depends on particular amino acid residues. For this, we studied the effects of DPA on human homomeric GABAρ1, α7 nicotinic, and 5-HT3A serotonin receptors expressed in Xenopus oocytes. Our results indicate that DPA is an allosteric modulator of GABAρ1 receptors with an IC50 of 1.6 µM, an enhancer of α7 nicotinic receptors at relatively high concentrations of DPA, and has little, if any, effect on 5-HT3A receptors. DPA antagonism of GABAρ1 was strongly enhanced by preincubation, was slightly voltage-dependent, and its washout was accelerated by bovine serum albumin. These results indicate that DPA modulation is not a general phenomenon of LGICs, and structural differences between receptors may account for disparities in DPA effects. In silico modeling of DPA docking to GABAρ1, α7 nicotinic, and 5-HT3A receptors suggests that a hydrophobic pocket within the Cys-loop and the M4 segment in GABAρ1, located at the extracellular/membrane interface, facilitates the interaction with DPA that leads to inhibition of the receptor. Functional examinations of mutant receptors support the involvement of the M4 segment in the allosteric modulation of GABAρ1 by DPA.

  11. Rab8 Interacts with Distinct Motifs in α2B- and β2-Adrenergic Receptors and Differentially Modulates Their Transport*

    PubMed Central

    Dong, Chunmin; Yang, Lingling; Zhang, Xiaoping; Gu, Hua; Lam, May L.; Claycomb, William C.; Xia, Houhui; Wu, Guangyu

    2010-01-01

    The molecular mechanism underlying the post-Golgi transport of G protein-coupled receptors (GPCRs) remains poorly understood. Here we determine the role of Rab8 GTPase, which modulates vesicular protein transport between the trans-Golgi network (TGN) and the plasma membrane, in the cell surface targeting of α2B- and β2-adrenergic receptors (AR). Transient expression of GDP- and GTP-bound Rab8 mutants and short hairpin RNA-mediated knockdown of Rab8 more potently inhibited the cell surface expression of α2B-AR than β2-AR. The GDP-bound Rab8(T22N) mutant attenuated ERK1/2 activation by α2B-AR, but not β2-AR, and arrested α2B-AR in the TGN compartment. Co-immunoprecipitation revealed that both α2B-AR and β2-AR physically interacted with Rab8 and glutathione S-transferase fusion protein pulldown assays demonstrated that Rab8 interacted with the C termini of both receptors. Interestingly, mutation of the highly conserved membrane-proximal C terminus dileucine motif selectively blocked β2-AR interaction with Rab8, whereas mutation of residues Val431-Phe432-Asn433-Gln434, Pro447-Trp448, Gln450-Thr451, and Trp453 in the C terminus impaired α2B-AR interaction with Rab8. Furthermore, transport inhibition by Rab8(T22N) of a chimeric β2-AR carrying the α2B-AR C terminus was similar to α2B-AR. These data provide strong evidence indicating that Rab8 GTPase interacts with distinct motifs in the C termini of α2B-AR and β2-AR and differentially modulates their traffic from the TGN to the cell surface. PMID:20424170

  12. Mycoplasma fermentans and TNF-β interact to amplify immune-modulating cytokines in human lung fibroblasts

    PubMed Central

    Fabisiak, James P.; Gao, Fei; Thomson, Robyn G.; Strieter, Robert M.; Watkins, Simon C.; Dauber, James H.

    2010-01-01

    Mycoplasma can establish latent infections and are associated with arthritis, leukemia, and chronic lung disease. We developed an experimental model in which lung cells are deliberately infected with Mycoplasma fermentans. Human lung fibroblasts (HLF) were exposed to live M. fermentans and immune-modulating cytokine release was assessed with and without known inducers of cytokine production. M. fermentans increased IL-6, IL-8/CXCL8, MCP-1/CCL2, and Gro-α/CXCL1 production. M. fermentans interacted with TNF-β to release more IL-6, CXCL8, and CXCL1 than predicted by the responses to either stimulus alone. The effects of live infection were recapitulated by exposure to M. fermentans-derived macrophage-activating lipopeptide-2 (MALP-2), a Toll-like receptor-2- and receptor-6-specific ligand. The synergistic effect of combined stimuli was more pronounced with prolonged incubations. Preexposure to TNF-β sensitized the cells to subsequent MALP-2 challenge, but preexposure to MALP-2 did not alter the IL-6 response to TNF-β. Exposure to M. fermentans or MALP-2 did not enhance nuclear localization, DNA binding, or transcriptional activity of NF-κB and did not modulate early NF-κB activation in response to TNF-β. Application of specific inhibitors of various MAPKs suggested that p38 and JNK/stress-activated protein kinase were involved in early IL-6 release after exposure to TNF-β and M. fermentans, respectively. The combined response to M. fermentans and TNF-β, however, was uniquely sensitive to delayed application of SP-600125, suggesting that JNK/stress-activated protein kinase contributes to the amplification of IL-6 release. Thus M. fermentans interacts with stimuli such as TNF-β to amplify lung cell production of immune-modulating cytokines. The mechanisms accounting for this interaction can now be dissected with the use of this in vitro model. PMID:16751226

  13. Early modality-specific somatosensory cortical regions are modulated by attended visual stimuli: interaction of vision, touch and behavioral intent

    PubMed Central

    Staines, W. Richard; Popovich, Christina; Legon, Jennifer K.; Adams, Meaghan S.

    2014-01-01

    Bimodal interactions between relevant visual and tactile inputs can facilitate attentional modulation at early stages in somatosensory cortices to achieve goal-oriented behaviors. However, the specific contribution of each sensory system during attentional processing and, importantly, how these interact with the required behavioral motor goals remains unclear. Here we used electroencephalography and event-related potentials (ERPs) to test the hypothesis that activity from modality-specific somatosensory cortical regions would be enhanced with task-relevant bimodal (visual-tactile) stimuli and that the degree of modulation would depend on the difficulty of the associated sensory-motor task demands. Tactile stimuli were discrete vibrations to the index finger and visual stimuli were horizontal bars on a computer screen, both with random amplitudes. Streams of unimodal (tactile) and crossmodal (visual and tactile) stimuli were randomly presented and participants were instructed to attend to one type of stimulus (unimodal or crossmodal) and responses involved either an indication of the presence of an attended stimulus (detect), or the integration and summation of two stimulus amplitudes using a pressure-sensitive ball (grade). Force-amplitude associations were learned in a training session, and no feedback was provided during the task. ERPs were time-locked to tactile stimuli and extracted for early modality-specific components (P50, P100, N140). The P50 was enhanced with bimodal (visual-tactile) stimuli that were attended to. This was maximal when the motor requirements involved integration of the two stimuli in the grade task and when the visual stimulus occurred before (100 ms) the tactile stimulus. These results suggest that visual information relevant for movement modulates somatosensory processing as early as the primary somatosensory cortex (S1) and that the motor behavioral context influences this likely through interaction of top-down attentional and motor

  14. Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast.

    PubMed

    Zhang, Chi; Liu, Song; Zhou, Yaoqi

    2006-04-01

    Molecular networks in cells are organized into functional modules, where genes in the same module interact densely with each other and participate in the same biological process. Thus, identification of modules from molecular networks is an important step toward a better understanding of how cells function through the molecular networks. Here, we propose a simple, automatic method, called MC(2), to identify functional modules by enumerating and merging cliques in the protein-interaction data from large-scale experiments. Application of MC(2) to the S. cerevisiae protein-interaction data produces 84 modules, whose sizes range from 4 to 69 genes. The majority of the discovered modules are significantly enriched with a highly specific process term (at least 4 levels below root) and a specific cellular component in Gene Ontology (GO) tree. The average fraction of genes with the most enriched GO term for all modules is 82% for specific biological processes and 78% for specific cellular components. In addition, the predicted modules are enriched with coexpressed proteins. These modules are found to be useful for annotating unknown genes and uncovering novel functions of known genes. MC(2) is efficient, and takes only about 5 min to identify modules from the current yeast gene interaction network with a typical PC (Intel Xeon 2.5 GHz CPU and 512 MB memory). The CPU time of MC(2) is affordable (12 h) even when the number of interactions is increased by a factor of 10. MC(2) and its results are publicly available on http://theory.med.buffalo.edu/MC2.

  15. Four imidazolium iodocuprates based on anion-π and π-π interactions: Structural and spectral modulation

    NASA Astrophysics Data System (ADS)

    Liu, Fang; Hao, Pengfei; Yu, Tanlai; Guan, Qi; Fu, Yunlong

    2016-09-01

    Four imidazolium iodocuprates, [(1,3-dimethylimidazole)(Cu2I3)]n (1), [(1,2,3-trimethylimidazole)(Cu2I3)]n (2), [(1,3-dimethylimidazole)(Cu3I5)]n (3) and [(1,3-dimethylbenzimidazole)(CuI2)]n (4) have been solvothermally synthesized and optically characterized. Results exhibit that cationic spatial orientation, anion-π and π-π interactions are beneficial to structural diversity and band gap modulation of iodocuprate hybrids. The UV-vis diffuse reflectance spectra show that compounds 1-4 are potential semiconductor materials.

  16. Endosome–mitochondria interactions are modulated by iron release from transferrin

    PubMed Central

    Nag, Sagarika

    2016-01-01

    Transient “kiss and run” interactions between endosomes containing iron-bound transferrin (Tf) and mitochondria have been shown to facilitate direct iron transfer in erythroid cells. In this study, we used superresolution three-dimensional (3D) direct stochastic optical reconstruction microscopy to show that Tf-containing endosomes directly interact with mitochondria in epithelial cells. We used live-cell time-lapse fluorescence microscopy, followed by 3D rendering, object tracking, and a distance transformation algorithm, to track Tf-endosomes and characterize the dynamics of their interactions with mitochondria. Quenching of iron sensor RDA-labeled mitochondria confirmed functional iron transfer by an interacting Tf-endosome. The motility of Tf-endosomes is significantly reduced upon interaction with mitochondria. To further assess the functional role of iron in the ability of Tf-endosomes to interact with mitochondria, we blocked endosomal iron release by using a Tf K206E/K534A mutant. Blocking intraendosomal iron release led to significantly increased motility of Tf-endosomes and increased duration of endosome–mitochondria interactions. Thus, intraendosomal iron regulates the kinetics of the interactions between Tf-containing endosomes and mitochondria in epithelial cells. PMID:27646275

  17. A conserved patch of hydrophobic amino acids modulates Myb activity by mediating protein-protein interactions.

    PubMed

    Dukare, Sandeep; Klempnauer, Karl-Heinz

    2016-07-01

    The transcription factor c-Myb plays a key role in the control of proliferation and differentiation in hematopoietic progenitor cells and has been implicated in the development of leukemia and certain non-hematopoietic tumors. c-Myb activity is highly dependent on the interaction with the coactivator p300 which is mediated by the transactivation domain of c-Myb and the KIX domain of p300. We have previously observed that conservative valine-to-isoleucine amino acid substitutions in a conserved stretch of hydrophobic amino acids have a profound effect on Myb activity. Here, we have explored the function of the hydrophobic region as a mediator of protein-protein interactions. We show that the hydrophobic region facilitates Myb self-interaction and binding of the histone acetyl transferase Tip60, a previously identified Myb interacting protein. We show that these interactions are affected by the valine-to-isoleucine amino acid substitutions and suppress Myb activity by interfering with the interaction of Myb and the KIX domain of p300. Taken together, our work identifies the hydrophobic region in the Myb transactivation domain as a binding site for homo- and heteromeric protein interactions and leads to a picture of the c-Myb transactivation domain as a composite protein binding region that facilitates interdependent protein-protein interactions of Myb with regulatory proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Endosome-mitochondria interactions are modulated by iron release from transferrin.

    PubMed

    Das, Anupam; Nag, Sagarika; Mason, Anne B; Barroso, Margarida M

    2016-09-26

    Transient "kiss and run" interactions between endosomes containing iron-bound transferrin (Tf) and mitochondria have been shown to facilitate direct iron transfer in erythroid cells. In this study, we used superresolution three-dimensional (3D) direct stochastic optical reconstruction microscopy to show that Tf-containing endosomes directly interact with mitochondria in epithelial cells. We used live-cell time-lapse fluorescence microscopy, followed by 3D rendering, object tracking, and a distance transformation algorithm, to track Tf-endosomes and characterize the dynamics of their interactions with mitochondria. Quenching of iron sensor RDA-labeled mitochondria confirmed functional iron transfer by an interacting Tf-endosome. The motility of Tf-endosomes is significantly reduced upon interaction with mitochondria. To further assess the functional role of iron in the ability of Tf-endosomes to interact with mitochondria, we blocked endosomal iron release by using a Tf K206E/K534A mutant. Blocking intraendosomal iron release led to significantly increased motility of Tf-endosomes and increased duration of endosome-mitochondria interactions. Thus, intraendosomal iron regulates the kinetics of the interactions between Tf-containing endosomes and mitochondria in epithelial cells. © 2016 Das et al.

  19. Do biotic interactions modulate ecosystem functioning along stress gradients? Insights from semi-arid plant and biological soil crust communities

    PubMed Central

    Maestre, Fernando T.; Bowker, Matthew A.; Escolar, Cristina; Puche, María D.; Soliveres, Santiago; Maltez-Mouro, Sara; García-Palacios, Pablo; Castillo-Monroy, Andrea P.; Martínez, Isabel; Escudero, Adrián

    2010-01-01

    Climate change will exacerbate the degree of abiotic stress experienced by semi-arid ecosystems. While abiotic stress profoundly affects biotic interactions, their potential role as modulators of ecosystem responses to climate change is largely unknown. Using plants and biological soil crusts, we tested the relative importance of facilitative–competitive interactions and other community attributes (cover, species richness and species evenness) as drivers of ecosystem functioning along stress gradients in semi-arid Mediterranean ecosystems. Biotic interactions shifted from facilitation to competition along stress gradients driven by water availability and temperature. These changes were, however, dependent on the spatial scale and the community considered. We found little evidence to suggest that biotic interactions are a major direct influence upon indicators of ecosystem functioning (soil respiration, organic carbon, water-holding capacity, compaction and the activity of enzymes related to the carbon, nitrogen and phosphorus cycles) along stress gradients. However, attributes such as cover and species richness showed a direct effect on ecosystem functioning. Our results do not agree with predictions emphasizing that the importance of plant–plant interactions will be increased under climate change in dry environments, and indicate that reductions in the cover of plant and biological soil crust communities will negatively impact ecosystems under future climatic conditions. PMID:20513714

  20. Pharmacokinetic drug interactions of the selective androgen receptor modulator GTx-024(Enobosarm) with itraconazole, rifampin, probenecid, celecoxib and rosuvastatin.

    PubMed

    Coss, Christopher C; Jones, Amanda; Dalton, James T

    2016-08-01

    GTx-024 (also known as enobosarm) is a first in class selective androgen receptor modulator being developed for diverse indications in oncology. Preclinical studies of GTx-024 supported the evaluation of several potential drug-drug interactions in a clinical setting. A series of open-label Phase I GTx-024 drug-drug interaction studies were designed to interrogate potential interactions with CYP3A4 inhibitor (itraconazole), a CYP3A4 inducer (rifampin), a pan-UGT inhibitor (probenecid), a CYP2C9 substrate (celecoxib) and a BCRP substrate (rosuvastatin). The plasma pharmacokinetics of GTx-024, its major metabolite (GTx-024 glucuronide), and each substrate were characterized in detail. Itraconazole administration had no effect on GTx-024 pharmacokinetics. Likewise, GTx-024 administration did not significantly change the pharmacokinetics of celecoxib or rosuvastatin. Rifampin administration had the largest impact on GTx-024 pharmacokinetics of any co-administered agent and reduced the maximal plasma concentration (Cmax) by 23 % and the area under the curve (AUC∞) by 43 %. Probenecid had a complex interaction with GTx-024 whereby both GTx-024 plasma levels and GTx-024 glucuronide plasma levels (AUC∞) were increased by co-administration of the UGT inhibitor (50 and 112 %, respectively). Overall, GTx-024 was well tolerated and poses very little risk of generating clinically relevant drug-drug interactions.

  1. Interaction of G-Protein βγ Complex with Chromatin Modulates GPCR-Dependent Gene Regulation

    PubMed Central

    Bhatnagar, Anushree; Unal, Hamiyet; Jagannathan, Rajaganapathi; Kaveti, Suma; Duan, Zhong-Hui; Yong, Sandro; Vasanji, Amit; Kinter, Michael; Desnoyer, Russell; Karnik, Sadashiva S.

    2013-01-01

    Heterotrimeric G-protein signal transduction initiated by G-protein-coupled receptors (GPCRs) in the plasma membrane is thought to propagate through protein-protein interactions of subunits, Gα and Gβγ in the cytosol. In this study, we show novel nuclear functions of Gβγ through demonstrating interaction of Gβ2 with integral components of chromatin and effects of Gβ2 depletion on global gene expression. Agonist activation of several GPCRs including the angiotensin II type 1 receptor specifically augmented Gβ2 levels in the nucleus and Gβ2 interacted with specific nucleosome core histones and transcriptional modulators. Depletion of Gβ2 repressed the basal and angiotensin II-dependent transcriptional activities of myocyte enhancer factor 2. Gβ2 interacted with a sequence motif that was present in several transcription factors, whose genome-wide binding accounted for the Gβ2-dependent regulation of approximately 2% genes. These findings suggest a wide-ranging mechanism by which direct interaction of Gβγ with specific chromatin bound transcription factors regulates functional gene networks in response to GPCR activation in cells. PMID:23326349

  2. Dual effects of MLS antibiotics: transcriptional modulation and interactions on the ribosome.

    PubMed

    Tsui, Wayne H W; Yim, Grace; Wang, Helena Huimi; McClure, JoAnn E; Surette, Michael G; Davies, Julian

    2004-09-01

    The macrolide-lincosamide-streptogramin (MLS) antibiotics are an important group of translation inhibitors that act on the 50S ribosome. We show that, at subinhibitory concentrations, members of the MLS group modulate specific groups of bacterial promoters, as detected by screening a library of promoter-luxCDABE reporter clones of Salmonella enterica serovar Typhimurium. The patterns of transcription permit identification of classes of promoters having differential responses to antibiotics of related structure and mode-of-action; studies of antibiotic synergy or antagonism showed that eukaryotic translation inhibitors may act on the 50S ribosome. The mechanism of transcriptional modulation is not known but may involve bacterial stress responses and/or the disturbance and subsequent compensation of metabolic networks as a result of subtle interference with ribosome function. Transcriptional patterns detected with promoter-lux clones provide a novel approach to antibiotic discovery and mode-of-action studies.

  3. Target-object integration, attention distribution, and object orientation interactively modulate object-based selection.

    PubMed

    Al-Janabi, Shahd; Greenberg, Adam S

    2016-10-01

    The representational basis of attentional selection can be object-based. Various studies have suggested, however, that object-based selection is less robust than spatial selection across experimental paradigms. We sought to examine the manner by which the following factors might explain this variation: Target-Object Integration (targets 'on' vs. part 'of' an object), Attention Distribution (narrow vs. wide), and Object Orientation (horizontal vs. vertical). In Experiment 1, participants discriminated between two targets presented 'on' an object in one session, or presented as a change 'of' an object in another session. There was no spatial cue-thus, attention was initially focused widely-and the objects were horizontal or vertical. We found evidence of object-based selection only when targets constituted a change 'of' an object. Additionally, object orientation modulated the sign of object-based selection: We observed a same-object advantage for horizontal objects, but a same-object cost for vertical objects. In Experiment 2, an informative cue preceded a single target presented 'on' an object or as a change 'of' an object (thus, attention was initially focused narrowly). Unlike in Experiment 1, we found evidence of object-based selection independent of target-object integration. We again found that the sign of selection was modulated by the objects' orientation. This result may reflect a meridian effect, which emerged due to anisotropies in the cortical representations when attention is oriented endogenously. Experiment 3 revealed that object orientation did not modulate object-based selection when attention was oriented exogenously. Our findings suggest that target-object integration, attention distribution, and object orientation modulate object-based selection, but only in combination.

  4. Short term interactions with long term consequences: modulation of chimeric vessels by neural progenitors.

    PubMed

    Williams, Cicely; Rauch, Millicent Ford; Michaud, Michael; Robinson, Rebecca; Xu, Hao; Madri, Joseph; Lavik, Erin

    2012-01-01

    Vessels are a critical and necessary component of most tissues, and there has been substantial research investigating vessel formation and stabilization. Several groups have investigated coculturing endothelial cells with a second cell type to promote formation and stabilization of vessels. Some have noted that long-term vessels derived from implanted cocultures are often chimeric consisting of both host and donor cells. The questions arise as to whether the coculture cell might impact the chimeric nature of the microvessels and can modulate the density of donor cells over time. If long-term engineered microvessels are primarily of host origin, any impairment of the host's angiogenic ability has significant implications for the long-term success of the implant. If one can modulate the host versus donor response, one may be able to overcome a host's angiogenic impairment. Furthermore, if one can modulate the donor contribution, one may be able to engineer microvascular networks to deliver molecules a patient lacks systemically for long times. To investigate the impact of the cocultured cell on the host versus donor contributions of endothelial cells in engineered microvascular networks, we varied the ratio of the neural progenitors to endothelial cells in subcutaneously implanted poly(ethylene glycol)/poly-L-lysine hydrogels. We found that the coculture of neural progenitors with endothelial cells led to the formation of chimeric host-donor vessels, and the ratio of neural progenitors has a significant impact on the long term residence of donor endothelial cells in engineered microvascular networks in vivo even though the neural progenitors are only present transiently in the system. We attribute this to the short term paracrine signaling between the two cell types. This suggests that one can modulate the host versus donor contributions using short-term paracrine signaling which has broad implications for the application of engineered microvascular networks and

  5. Short Term Interactions with Long Term Consequences: Modulation of Chimeric Vessels by Neural Progenitors

    PubMed Central

    Williams, Cicely; Rauch, Millicent Ford; Michaud, Michael; Robinson, Rebecca; Xu, Hao; Madri, Joseph; Lavik, Erin

    2012-01-01

    Vessels are a critical and necessary component of most tissues, and there has been substantial research investigating vessel formation and stabilization. Several groups have investigated coculturing endothelial cells with a second cell type to promote formation and stabilization of vessels. Some have noted that long-term vessels derived from implanted cocultures are often chimeric consisting of both host and donor cells. The questions arise as to whether the coculture cell might impact the chimeric nature of the microvessels and can modulate the density of donor cells over time. If long-term engineered microvessels are primarily of host origin, any impairment of the host's angiogenic ability has significant implications for the long-term success of the implant. If one can modulate the host versus donor response, one may be able to overcome a host's angiogenic impairment. Furthermore, if one can modulate the donor contribution, one may be able to engineer microvascular networks to deliver molecules a patient lacks systemically for long times. To investigate the impact of the cocultured cell on the host versus donor contributions of endothelial cells in engineered microvascular networks, we varied the ratio of the neural progenitors to endothelial cells in subcutaneously implanted poly(ethylene glycol)/poly-L-lysine hydrogels. We found that the coculture of neural progenitors with endothelial cells led to the formation of chimeric host-donor vessels, and the ratio of neural progenitors has a significant impact on the long term residence of donor endothelial cells in engineered microvascular networks in vivo even though the neural progenitors are only present transiently in the system. We attribute this to the short term paracrine signaling between the two cell types. This suggests that one can modulate the host versus donor contributions using short-term paracrine signaling which has broad implications for the application of engineered microvascular networks and

  6. Systematic expression profiling analysis mines dys-regulated modules in active tuberculosis based on re-weighted protein-protein interaction network and attract algorithm.

    PubMed

    Sun, Ying; Weng, Yan; Zhang, Ying; Yan, Xiang; Guo, Lei; Wang, Jia; Song, Xin; Yuan, Ying; Chang, Fu-Ye; Wang, Chun-Ling

    2017-03-18

    About 90% of tuberculosis (TB) patients latently infected with Mycobacterium tuberculosis (Mtb) show no symptoms, yet have a 10% chance in lifetime to progress active TB. Nevertheless, current diagnosis approaches need improvement in efficiency and sensitivity. The objective of this work was to detect potential signatures for active TB to further improve the understanding of the biological roles of functional modules involved in this disease. First, targeted networks of active TB and control groups were established via re-weighting protein-protein interaction (PPI) networks using Pearson's correlation coefficient (PCC). Candidate modules were detected from the targeted networks, and the modules with Jaccard score >0.7 were defined as attractors. After that, identification of dys-regulated modules was conducted from the attractors using attract method, Subsequently, gene oncology (GO) enrichment analyses were implemented for genes in the dys-regulated modules. We obtained 33 and 65 candidate modules from the targeted networks of control and active TB groups, respectively. Overall, 13 attractors were identified. Using the cut-off criteria of false discovery rate <0.05, there were 4 dys-regulated modules (Module 1, 2, 3, and 4). Based on the GO annotation results, genes in Modules 1, 2 and 4 were only involved in translation. Most genes in Module 1, 2 and 4 were associated with ribosomes. Accordingly, these dys-regulated modules might serve as potential biomarkers of active TB, facilitating the development for a more efficient, and sensitive diagnostic assay for active TB.

  7. Interaction of cannabinoid receptor 2 and social environment modulates chronic alcohol consumption.

    PubMed

    Pradier, Bruno; Erxlebe, Edda; Markert, Astrid; Rácz, Ildikó

    2015-01-01

    Genetic and environmental factors contribute nearly in equal power to the development of alcoholism. Environmental factors, such as negative life events or emotionally disruptive conditions, initiate and promote alcohol drinking and relapse. The endocannabinoid system is involved in hedonic control and modulates stress reactivity. Furthermore, chronic alcohol drinking alters endocannabinoid signalling, which in turn influences the stress reactivity. Recently, it has been shown that CB2 receptor activity influences stress sensitivity and alcohol drinking. We hypothesized that CB2 receptors influence the impact of environmental risk factors on alcohol preference and consumption. Therefore, in this study, we investigated the alcohol-drinking pattern of wild-type and CB2-deficient animals under single- and group-housing conditions using different alcohol-drinking models, such as forced drinking, intermittent forced drinking and two-bottle choice paradigms. Our data showed that CB2 receptor modulates alcohol consumption and reward. Interestingly, we detected that lack of CB2 receptors led to increased alcohol drinking in the intermittent forced drinking paradigm under group-housing conditions. Furthermore, we found that CB2 knockout mice consumed more food and that their body weight gain was modulated by social environment. On the basis of these data, we conclude that social environment critically affects the modulatory function of CB2 receptors, especially in alcohol intake. These findings suggest that a treatment strategy targeting CB2 receptors may have a beneficial effect on pathological drinking, particularly in situations of social stress and discomfort.

  8. Interactive Palliative and End-of-Life Care Modules for Pediatric Residents

    PubMed Central

    Doshi, Ami; Carrasca, London; Pian, Patricia; Auger, JoAnne; Baker, Amira; Proudfoot, James A.; Pian, Mark S.

    2017-01-01

    Background. There is a need for increased palliative care training during pediatric residency. Objective. In this pilot study, we created a comprehensive experiential model to teach palliative care skills to pediatric residents. Our Comfort Care Modules (CCMs) address pediatric palliative care (PPC) topics of breaking bad news, dyspnea, anxiety, pain management, and the dying child. We also evaluated a scoring system and gathered qualitative data. Methods. The CCMs are part of the University of California San Diego pediatric residency's second-year curriculum. Comparisons were made for statistical trends between residents exposed to the modules (n = 15) and those not exposed (n = 4). Results. Nineteen of 36 residents (52%) completed surveys to self-rate their preparedness, knowledge, and confidence about PPC before and after the intervention. Resident scores increased in all areas. All improvements reached statistical significance except confidence when breaking bad news. Overall, the resident feedback about the CCMs was positive. Conclusions. This study demonstrates that the CCMs can be performed effectively in an academic setting and can benefit residents' self-perception of preparedness, confidence, and knowledge about pediatric palliative care. In the future, we plan to implement the modules on a larger scale. We encourage their use in interprofessional settings and across institutions. PMID:28286527

  9. Imaging contrast and tip-sample interaction of non-contact amplitude modulation atomic force microscopy with Q-control

    NASA Astrophysics Data System (ADS)

    Shi, Shuai; Guo, Dan; Luo, Jianbin

    2017-10-01

    Active quality factor (Q) exhibits many promising properties in dynamic atomic force microscopy. Energy dissipation and image contrasts are investigated in the non-contact amplitude modulation atomic force microscopy (AM-AFM) with an active Q-control circuit in the ambient air environment. Dissipated power and virial were calculated to compare the highly nonlinear interaction of tip-sample and image contrasts with different Q gain values. Greater free amplitudes and lower effective Q values show better contrasts for the same setpoint ratio. Active quality factor also can be employed to change tip-sample interaction force in non-contact regime. It is meaningful that non-destructive and better contrast images can be realized in non-contact AM-AFM by applying an active Q-control to the dynamic system.

  10. Exosome engineering for efficient intracellular delivery of soluble proteins using optically reversible protein–protein interaction module

    PubMed Central

    Yim, Nambin; Ryu, Seung-Wook; Choi, Kyungsun; Lee, Kwang Ryeol; Lee, Seunghee; Choi, Hojun; Kim, Jeongjin; Shaker, Mohammed R.; Sun, Woong; Park, Ji-Ho; Kim, Daesoo; Do Heo, Won; Choi, Chulhee

    2016-01-01

    Nanoparticle-mediated delivery of functional macromolecules is a promising method for treating a variety of human diseases. Among nanoparticles, cell-derived exosomes have recently been highlighted as a new therapeutic strategy for the in vivo delivery of nucleotides and chemical drugs. Here we describe a new tool for intracellular delivery of target proteins, named ‘exosomes for protein loading via optically reversible protein–protein interactions' (EXPLORs). By integrating a reversible protein–protein interaction module controlled by blue light with the endogenous process of exosome biogenesis, we are able to successfully load cargo proteins into newly generated exosomes. Treatment with protein-loaded EXPLORs is shown to significantly increase intracellular levels of cargo proteins and their function in recipient cells in vitro and in vivo. These results clearly indicate the potential of EXPLORs as a mechanism for the efficient intracellular transfer of protein-based therapeutics into recipient cells and tissues. PMID:27447450

  11. Unc5B Interacts with FLRT3 and Rnd1 to Modulate Cell Adhesion in Xenopus Embryos

    PubMed Central

    Karaulanov, Emil; Böttcher, Ralph T.; Stannek, Peter; Wu, Wei; Rau, Marlene; Ogata, Souichi; Cho, Ken W. Y.; Niehrs, Christof

    2009-01-01

    The FLRT family of transmembrane proteins has been implicated in the regulation of FGF signalling, neurite outgrowth, homotypic cell sorting and cadherin-mediated adhesion. In an expression screen we identified the Netrin receptors Unc5B and Unc5D as high-affinity FLRT3 interactors. Upon overexpression, Unc5B phenocopies FLRT3 and both proteins synergize in inducing cell deadhesion in Xenopus embryos. Morpholino knock-downs of Unc5B and FLRT3 synergistically affect Xenopus development and induce morphogenetic defects. The small GTPase Rnd1, which transmits FLRT3 deadhesion activity, physically and functionally interacts with Unc5B, and mediates its effect on cell adhesion. The results suggest that FLRT3, Unc5B and Rnd1 proteins interact to modulate cell adhesion in early Xenopus development. PMID:19492039

  12. Role of further-neighbor interactions in modulating the critical behavior of the Ising model with frustration.

    PubMed

    Liu, R M; Zhuo, W Z; Dong, S; Lu, X B; Gao, X S; Qin, M H; Liu, J-M

    2016-03-01

    In this work, we investigate the phase transitions and critical behaviors of the frustrated J(1)-J(2)-J(3) Ising model on the square lattice using Monte Carlo simulations, and particular attention goes to the effect of the second-next-nearest-neighbor interaction J(3) on the phase transition from a disordered state to the single stripe antiferromagnetic state. A continuous Ashkin-Teller-like transition behavior in a certain range of J(3) is identified, while the four-state Potts-critical end point [J(3)/J(1)](C) is estimated based on the analytic method reported in earlier work [Jin, Sen, and Sandvik, Phys. Rev. Lett. 108, 045702 (2012)]. It is suggested that the interaction J(3) can tune the transition temperature and in turn modulate the critical behaviors of the frustrated model. Furthermore, it is revealed that an antiferromagnetic J(3) can stabilize the staggered dimer state via a phase transition of strong first-order character.

  13. Exosome engineering for efficient intracellular delivery of soluble proteins using optically reversible protein-protein interaction module.

    PubMed

    Yim, Nambin; Ryu, Seung-Wook; Choi, Kyungsun; Lee, Kwang Ryeol; Lee, Seunghee; Choi, Hojun; Kim, Jeongjin; Shaker, Mohammed R; Sun, Woong; Park, Ji-Ho; Kim, Daesoo; Heo, Won Do; Choi, Chulhee

    2016-07-22

    Nanoparticle-mediated delivery of functional macromolecules is a promising method for treating a variety of human diseases. Among nanoparticles, cell-derived exosomes have recently been highlighted as a new therapeutic strategy for the in vivo delivery of nucleotides and chemical drugs. Here we describe a new tool for intracellular delivery of target proteins, named 'exosomes for protein loading via optically reversible protein-protein interactions' (EXPLORs). By integrating a reversible protein-protein interaction module controlled by blue light with the endogenous process of exosome biogenesis, we are able to successfully load cargo proteins into newly generated exosomes. Treatment with protein-loaded EXPLORs is shown to significantly increase intracellular levels of cargo proteins and their function in recipient cells in vitro and in vivo. These results clearly indicate the potential of EXPLORs as a mechanism for the efficient intracellular transfer of protein-based therapeutics into recipient cells and tissues.

  14. Use of Live Interactive Webcasting for an International Postgraduate Module in eHealth: Case Study Evaluation

    PubMed Central

    Maramba, Inocencio; Boulos, Maged N Kamel; Alexander, Tara

    2009-01-01

    Background Producing “traditional” e-learning can be time consuming, and in a topic such as eHealth, it may have a short shelf-life. Students sometimes report feeling isolated and lacking in motivation. Synchronous methods can play an important part in any blended approach to learning. Objective The aim was to develop, deliver, and evaluate an international postgraduate module in eHealth using live interactive webcasting. Methods We developed a hybrid solution for live interactive webcasting using a scan converter, mixer, and digitizer, and video server to embed a presenter-controlled talking head or copy of the presenter’s computer screen (normally a PowerPoint slide) in a student chat room. We recruited 16 students from six countries and ran weekly 2.5-hour live sessions for 10 weeks. The content included the use of computers by patients, patient access to records, different forms of e-learning for patients and professionals, research methods in eHealth, geographic information systems, and telehealth. All sessions were recorded—presentations as video files and the student interaction as text files. Students were sent an email questionnaire of mostly open questions seeking their views of this form of learning. Responses were collated and anonymized by a colleague who was not part of the teaching team. Results Sessions were generally very interactive, with most students participating actively in breakout or full-class discussions. In a typical 2.5-hour session, students posted about 50 messages each. Two students did not complete all sessions; one withdrew from the pressure of work after session 6, and one from illness after session 7. Fourteen of the 16 responded to the feedback questionnaire. Most students (12/14) found the module useful or very useful, and all would recommend the module to others. All liked the method of delivery, in particular the interactivity, the variety of students, and the “closeness” of the group. Most (11/14) felt

  15. Dietary fat and fiber interactively modulate apoptosis and mitochondrial bioenergetic profiles in mouse colon in a site-specific manner.

    PubMed

    Fan, Yang-Yi; Vaz, Frederic M; Chapkin, Robert S

    2016-05-10

    We have demonstrated that the combination of bioactive components generated by fish oil (containing n-3 polyunsaturated fatty acids) and fermentable fiber (leading to butyrate production) act coordinately to protect against colon cancer. This is, in part, the result of an enhancement of apoptosis at the base of the crypt across all stages (initiation, promotion, and progression) of colon tumorigenesis. As mitochondria are key organelles capable of regulating the intrinsic apoptotic pathway and mediating programmed cell death, we investigated the effects of diet on mitochondrial function by measuring mucosal cardiolipin composition, mitochondrial respiratory parameters, and apoptosis in isolated crypts from the proximal and distal colon. C57BL/6 mice (n=15/treatment) were fed one of two dietary fats (corn oil and fish oil) and two fibers (pectin and cellulose) for 4 weeks in a 2×2 factorial design. In general, diet modulated apoptosis and the mucosal bioenergetic profiles in a site-specific manner. The fish/pectin diet promoted a more proapoptotic phenotype - for example, increased proton leak (Pinteraction=0.002) - compared with corn/cellulose (control) only in the proximal colon. With respect to the composition of cardiolipin, a unique phospholipid localized to the mitochondrial inner membrane where it mediates energy metabolism, fish oil feeding indirectly influenced its molecular species with a combined carbon number of C68 or greater, suggesting compensatory regulation. These data indicate that dietary fat and fiber can interactively modulate the mitochondrial metabolic profile and thereby potentially modulate apoptosis and subsequent colon cancer risk.

  16. N-cadherin modulates voltage activated calcium influx via RhoA, p120-catenin, and myosinactin interaction

    PubMed Central

    Marrs, Glen S.; Theisen, Christopher S.; Brusés, Juan L.

    2010-01-01

    N-cadherin is a transmembrane adhesion receptor that contributes to neuronal development and synapse formation through homophilic interactions that provide structural-adhesive support to contacts between cell membranes. In addition, N-cadherin homotypic binding may initiate cell signaling that regulates neuronal physiology. In this study, we investigated signaling capabilities of N-cadherin that control voltage activated calcium influx. Using whole-cell voltage clamp recording of isolated inward calcium currents in freshly isolated chick ciliary ganglion neurons we show that the juxtamembrane region of N-cadherin cytoplasmic domain regulates high-threshold voltage activated calcium currents by interacting with p120-catenin and activating RhoA. This regulatory mechanism requires myosin interaction with actin. Furthermore, N-cadherin homophilic binding enhanced voltage activated calcium current amplitude in dissociated neurons that have already developed mature synaptic contacts in vivo. The increase in calcium current amplitude was not affected by brefeldin A suggesting that the effect is caused via direct channel modulation and not by increasing channel expression. In contrast, homotypic N-cadherin interaction failed to regulate calcium influx in freshly isolated immature neurons. However, RhoA inhibitors enhanced calcium current amplitude in these immature neurons, suggesting that the inhibitory effect of RhoA on calcium entry is regulated during neuronal development and synapse maturation. These results indicate that N-cadherin modulates voltage activated calcium entry by a mechanism that involves RhoA activity and its downstream effects on the cytoskeleton, and suggest that N-cadherin provides support for synaptic maturation and sustained synaptic activity by facilitating voltage activated calcium influx. PMID:19162191

  17. 2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein–protein interactions

    PubMed Central

    Basse, Marie-Jeanne; Betzi, Stéphane; Morelli, Xavier; Roche, Philippe

    2016-01-01

    2P2Idb is a hand-curated structural database dedicated to protein–protein interactions with known small molecule orthosteric modulators. It compiles the structural information related to orthosteric inhibitors and their target [i.e. related 3D structures available in the RCSB Protein Data Bank (PDB)] and provides links to other useful databases. 2P2Idb includes all interactions for which both the protein–protein and protein–inhibitor complexes have been structurally characterized. Since its first release in 2010, the database has grown constantly and the current version contains 27 protein–protein complexes and 274 protein–inhibitor complexes corresponding to 242 unique small molecule inhibitors which represent almost a 5-fold increase compared to the previous version. A number of new data have been added, including new protein–protein complexes, binding affinities, molecular descriptors, precalculated interface parameters and links to other webservers. A new query tool has been implemented to search for inhibitors within the database using standard molecular descriptors. A novel version of the 2P2I-inspector tool has been implemented to calculate a series of physical and chemical parameters of the protein interfaces. Several geometrical parameters including planarity, eccentricity and circularity have been added as well as customizable distance cutoffs. This tool has also been extended to protein–ligand interfaces. The 2P2I database thus represents a wealth of structural source of information for scientists interested in the properties of protein–protein interactions and the design of protein–protein interaction modulators. Database URL: http://2p2idb.cnrs-mrs.fr PMID:26980515

  18. Spin relaxation in quantum dots: Role of the phonon modulated spin-orbit interaction

    NASA Astrophysics Data System (ADS)

    Alcalde, A. M.; Romano, C. L.; Sanz, L.; Marques, G. E.

    2010-01-01

    We calculate the spin relaxation rates in a parabolic InSb quantum dots due to the spin interaction with acoustical phonons. We considered the deformation potential mechanism as the dominant electron-phonon coupling in the Pavlov-Firsov spin-phonon Hamiltonian. We analyze the behavior of the spin relaxation rates as a function of an external magnetic field and mean quantum dot radius. Effects of the spin admixture due to Dresselhaus contribution to spin-orbit interaction are also discussed.

  19. Shifting species interaction in soil microbial community and its influence on ecosystem functions modulating.

    PubMed

    Li, Hua; Colica, Giovanni; Wu, Pei-pei; Li, Dunhai; Rossi, Federico; De Philippis, Roberto; Liu, Yongding

    2013-04-01

    The supportive and negative evidence for the stress gradient hypothesis (SGH) led to an ongoing debate among ecologists and called for new empirical and theoretical work. In this study, we took various biological soil crust (BSCs) samples along a spatial gradient with four environmental stress levels to examine the fitness of SGH in microbial interactions and evaluate its influence on biodiversity-function relationships in BSCs. A new assessment method of species interactions within hard-cultured invisible soil community was employed, directly based on denaturing gradient gel electrophoresis fingerprint images. The results showed that biotic interactions in soil phototroph community dramatically shifted from facilitation to dominant competition with the improvement of microhabitats. It offered new evidence, which presented a different perspective on the hypothesis that the relative importance of facilitation and competition varies inversely along the gradient of abiotic stress. The path analysis indicated that influence of biotic interactions (r = 0.19, p < 0.05) on ecosystem functions is lower than other community properties (r = 0.62, p < 0.001), including soil moisture, crust coverage, and biodiversity. Furthermore, the correlation between species interactions and community properties was non-significant with low negative influence (r = -0.27, p > 0.05). We demonstrate that the inversion of biotic interaction as a response to the gradient of abiotic stresses existed not only in the visible plant community but also in the soil microbial community.

  20. Thermal acclimation modulates the impacts of temperature and enrichment on trophic interaction strengths and population dynamics.

    PubMed

    Sentis, Arnaud; Morisson, Julie; Boukal, David S

    2015-09-01

    Global change affects individual phenotypes and biotic interactions, which can have cascading effects up to the ecosystem level. However, the role of environmentally induced phenotypic plasticity in species interactions is poorly understood, leaving a substantial gap in our knowledge of the impacts of global change on ecosystems. Using a cladoceran-dragonfly system, we experimentally investigated the effects of thermal acclimation, acute temperature change and enrichment on predator functional response and metabolic rate. Using our experimental data, we next parameterized a population dynamics model to determine the consequences of these effects on trophic interaction strength and food-chain stability. We found that (1) predation and metabolic rates of the dragonfly larvae increase with acute warming, (2) warm-acclimated larvae have a higher maximum predation rate than cold-acclimated ones, and (3) long-term interaction strength increases with enrichment but decreases with both acclimation and acute temperatures. Overall, our experimental results show that thermal acclimation can buffer negative impacts of environmental change on predators and increase food-web stability and persistence. We conclude that the effect of acclimation and, more generally, phenotypic plasticity on trophic interactions should not be overlooked if we aim to understand the effects of climate change and enrichment on species interaction strength and food-web stability.

  1. Identification of a novel role for dematin in regulating red cell membrane function by modulating spectrin-actin interaction.

    PubMed

    Koshino, Ichiro; Mohandas, Narla; Takakuwa, Yuichi

    2012-10-12

    The membrane skeleton plays a central role in maintaining the elasticity and stability of the erythrocyte membrane, two biophysical features critical for optimal functioning and survival of red cells. Many constituent proteins of the membrane skeleton are phosphorylated by various kinases, and phosphorylation of β-spectrin by casein kinase and of protein 4.1R by PKC has been documented to modulate erythrocyte membrane mechanical stability. In this study, we show that activation of endogenous PKA by cAMP decreases membrane mechanical stability and that this effect is mediated primarily by phosphorylation of dematin. Co-sedimentation assay showed that dematin facilitated interaction between spectrin and F-actin, and phosphorylation of dematin by PKA markedly diminished this activity. Quartz crystal microbalance measurement revealed that purified dematin specifically bound the tail region of the spectrin dimer in a saturable manner with a submicromolar affinity. Pulldown assay using recombinant spectrin fragments showed that dematin, but not phospho-dematin, bound to the tail region of the spectrin dimer. These findings imply that dematin contributes to the maintenance of erythrocyte membrane mechanical stability by facilitating spectrin-actin interaction and that phosphorylation of dematin by PKA can modulate these effects. In this study, we have uncovered a novel functional role for dematin in regulating erythrocyte membrane function.

  2. "iBIM"--internet-based interactive modules: an easy and interesting learning tool for general surgery residents.

    PubMed

    Azer, Nader; Shi, Xinzhe; de Gara, Chris; Karmali, Shahzeer; Birch, Daniel W

    2014-04-01

    The increased use of information technology supports a resident- centred educational approach that promotes autonomy, flexibility and time management and helps residents to assess their competence, promoting self-awareness. We established a web-based e-learning tool to introduce general surgery residents to bariatric surgery and evaluate them to determine the most appropriate implementation strategy for Internet-based interactive modules (iBIM) in surgical teaching. Usernames and passwords were assigned to general surgery residents at the University of Alberta. They were directed to the Obesity101 website and prompted to complete a multiple-choice precourse test. Afterwards, they were able to access the interactive modules. Residents could review the course material as often as they wanted before completing a multiple-choice postcourse test and exit survey. We used paired t tests to assess the difference between pre- and postcourse scores. Out of 34 residents who agreed to participate in the project, 12 completed the project (35.3%). For these 12 residents, the precourse mean score was 50 ± 17.3 and the postcourse mean score was 67 ± 14 (p = 0.020). Most residents who participated in this study recommended using the iBIMs as a study tool for bariatric surgery. Course evaluation scores suggest this novel approach was successful in transferring knowledge to surgical trainees. Further development of this tool and assessment of implementation strategies will determine how iBIM in bariatric surgery may be integrated into the curriculum.

  3. Identification of a Novel Role for Dematin in Regulating Red Cell Membrane Function by Modulating Spectrin-Actin Interaction*

    PubMed Central

    Koshino, Ichiro; Mohandas, Narla; Takakuwa, Yuichi

    2012-01-01

    The membrane skeleton plays a central role in maintaining the elasticity and stability of the erythrocyte membrane, two biophysical features critical for optimal functioning and survival of red cells. Many constituent proteins of the membrane skeleton are phosphorylated by various kinases, and phosphorylation of β-spectrin by casein kinase and of protein 4.1R by PKC has been documented to modulate erythrocyte membrane mechanical stability. In this study, we show that activation of endogenous PKA by cAMP decreases membrane mechanical stability and that this effect is mediated primarily by phosphorylation of dematin. Co-sedimentation assay showed that dematin facilitated interaction between spectrin and F-actin, and phosphorylation of dematin by PKA markedly diminished this activity. Quartz crystal microbalance measurement revealed that purified dematin specifically bound the tail region of the spectrin dimer in a saturable manner with a submicromolar affinity. Pulldown assay using recombinant spectrin fragments showed that dematin, but not phospho-dematin, bound to the tail region of the spectrin dimer. These findings imply that dematin contributes to the maintenance of erythrocyte membrane mechanical stability by facilitating spectrin-actin interaction and that phosphorylation of dematin by PKA can modulate these effects. In this study, we have uncovered a novel functional role for dematin in regulating erythrocyte membrane function. PMID:22927433

  4. The relative vertex clustering value - a new criterion for the fast discovery of functional modules in protein interaction networks

    PubMed Central

    2015-01-01

    Background Cellular processes are known to be modular and are realized by groups of proteins implicated in common biological functions. Such groups of proteins are called functional modules, and many community detection methods have been devised for their discovery from protein interaction networks (PINs) data. In current agglomerative clustering approaches, vertices with just a very few neighbors are often classified as separate clusters, which does not make sense biologically. Also, a major limitation of agglomerative techniques is that their computational efficiency do not scale well to large PINs. Finally, PIN data obtained from large scale experiments generally contain many false positives, and this makes it hard for agglomerative clustering methods to find the correct clusters, since they are known to be sensitive to noisy data. Results We propose a local similarity premetric, the relative vertex clustering value, as a new criterion allowing to decide when a node can be added to a given node's cluster and which addresses the above three issues. Based on this criterion, we introduce a novel and very fast agglomerative clustering technique, FAC-PIN, for discovering functional modules and protein complexes from a PIN data. Conclusions Our proposed FAC-PIN algorithm is applied to nine PIN data from eight different species including the yeast PIN, and the identified functional modules are validated using Gene Ontology (GO) annotations from DAVID Bioinformatics Resources. Identified protein complexes are also validated using experimentally verified complexes. Computational results show that FAC-PIN can discover functional modules or protein complexes from PINs more accurately and more efficiently than HC-PIN and CNM, the current state-of-the-art approaches for clustering PINs in an agglomerative manner. PMID:25734691

  5. Small-molecule modulators of the OX40–OX40 ligand co-stimulatory protein–protein interaction

    PubMed Central

    Song, Yun; Margolles-Clark, Emilio; Bayer, Allison; Buchwald, Peter

    2014-01-01

    Background and Purpose The OX40–OX40L protein–protein interaction (PPI) is an important cell-surface signalling co-stimulatory regulator within the TNFR superfamily (TNFRSF) and a promising therapeutic target for immunomodulation. PPIs are difficult to modulate using small-molecules. Here, we describe the identification of a small-molecule OX40 modulator and confirm its partial agonist character. Experimental Approach Cell-free screening assays were developed and used to identify OX40–OX40L inhibitors. Modified versions of this assay were used to elucidate the binding partner and the binding nature of active compounds. OX40-transfected sensor cells with NF-κB reporters were constructed and used to confirm and characterize activity and specificity. Immunomodulatory activity and partial agonist nature were further confirmed by ex vivo T-cell polarization assays. Key Results Several compounds that concentration-dependently affected OX40-OX40L were identified. Cell assays indicated that they were partial agonists with low micromolar potency and adequate selectivity. Under polarizing conditions based on TGF-β, the most promising compound mimicked the effect of an agonistic anti-OX40 antibody in suppressing regulatory T-cell generation and diverting CD4+CD62L+Foxp3− cells to TH9 phenotype in vitro. Conclusions and Implications We identified, to our knowledge, the first small-molecule compounds able to interfere with OX40–OX40L binding and, more importantly, to act as partial agonists of OX40. This is particularly interesting, as small-molecule agonism or activation of PPIs is considered unusually challenging and there are only few known examples. These results provide proof-of-principle evidence for the feasibility of small-molecule modulation of the OX40–OX40L interaction and for the existence of partial agonists for TNFRSF-PPIs. PMID:24930776

  6. Innate immune interactions within the central nervous system modulate pathogenesis of viral infections

    PubMed Central

    Nair, Sharmila; Diamond, Michael S.

    2015-01-01

    The innate immune system mediates protection against neurotropic viruses that replicate in the central nervous system (CNS). Virus infection within specific cells of the CNS triggers activation of several families of pattern recognition receptors including Toll-like receptors, retinoic acid-inducible gene 1 like receptors, nucleotide-binding oligomerization domain-like receptors, and cytosolic DNA sensors. In this review, we highlight recent advances in our understanding of how cell-intrinsic host defenses within the CNS modulate infection of different DNA and RNA viruses. PMID:26163762

  7. Perilipin polymorphism interacts with saturated fat and carbohydrates to modulate insulin resistance.

    PubMed

    Smith, C E; Arnett, D K; Corella, D; Tsai, M Y; Lai, C Q; Parnell, L D; Lee, Y C; Ordovás, J M

    2012-05-01

    Macronutrient intakes and genetic variants have been shown to interact to alter insulin resistance, but replications of gene-nutrient interactions across independent populations are rare, despite their critical importance in establishing credibility. We aimed to investigate a previously demonstrated saturated fat and carbohydrate interaction for insulin resistance for perilipin (PLIN1), a regulator of adipocyte metabolism. We investigated the previously shown interaction for PLIN1 11482G > A (rs894160) on insulin resistance in US men (n = 462) and women (n = 508) (mean ± SD, 49 ± 16 years). In multivariable linear regression models, we found an interaction (P < 0.05) between the ratio of saturated fat to carbohydrate intake as a continuous variable and PLIN1 11482G > A for HOMA-IR (homeostasis model assessment of insulin resistance) in women. For carriers of the minor allele but not for non-carriers, as the ratio of saturated fat to carbohydrate intake increased, predicted HOMA-IR increased (P = 0.002). By dichotomizing the ratio of saturated fat to carbohydrate intake into high and low, we found significant interaction terms for insulin and HOMA-IR (P < 0.05). When the ratio of saturated fat to carbohydrate was high, insulin and HOMA-IR were higher in minor allele carriers (P = 0.004 and P = 0.003, respectively), but did not differ when the ratio was low. Similar patterns or trends were observed when saturated fat and carbohydrate were dichotomized into high and low as individual macronutrients. Replication of the previously reported interaction between macronutrient intakes and PLIN1 genotype for insulin resistance reinforces the potential usefulness of applying genotype information in the dietary management of insulin resistance. Copyright © 2010. Published by Elsevier B.V.

  8. Interactions Between Anandamide and Corticotropin-Releasing Factor Signaling Modulate Human Amygdala Function and Risk for Anxiety Disorders: An Imaging Genetics Strategy for Modeling Molecular Interactions.

    PubMed

    Demers, Catherine H; Drabant Conley, Emily; Bogdan, Ryan; Hariri, Ahmad R

    2016-09-01

    Preclinical models reveal that stress-induced amygdala activity and impairment in fear extinction reflect reductions in anandamide driven by corticotropin-releasing factor receptor type 1 (CRF1) potentiation of the anandamide catabolic enzyme fatty acid amide hydrolase. Here, we provide clinical translation for the importance of these molecular interactions using an imaging genetics strategy to examine whether interactions between genetic polymorphisms associated with differential anandamide (FAAH rs324420) and CRF1 (CRHR1 rs110402) signaling modulate amygdala function and anxiety disorder diagnosis. Analyses revealed that individuals with a genetic background predicting relatively high anandamide and CRF1 signaling exhibited blunted basolateral amygdala habituation, which further mediated increased risk for anxiety disorders among these same individuals. The convergence of preclinical and clinical data suggests that interactions between anandamide and CRF1 represent a fundamental molecular mechanism regulating amygdala function and anxiety. Our results further highlight the potential of imaging genetics to powerfully translate complex preclinical findings to clinically meaningful human phenotypes. Copyright © 2015 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  9. Queen reproductive state modulates pheromone production and queen-worker interactions in honeybees

    PubMed Central

    Kocher, Sarah D.; Richard, Freddie-Jeanne; Tarpy, David R.

    2009-01-01

    The mandibular glands of queen honeybees produce a pheromone that modulates many aspects of worker honeybee physiology and behavior and is critical for colony social organization. The exact chemical blend produced by the queen differs between virgin and mated, laying queens. Here, we investigate the role of mating and reproductive state on queen pheromone production and worker responses. Virgin queens, naturally mated queens, and queens instrumentally inseminated with either semen or saline were collected 2 days after mating or insemination. Naturally mated queens had the most activated ovaries and the most distinct chemical profile in their mandibular glands. Instrumentally inseminated queens were intermediate between virgins and naturally mated queens for both ovary activation and chemical profiles. There were no significant differences between semen- and saline-inseminated queens. Workers were preferentially attracted to the mandibular gland extracts from queens with significantly more activated ovaries. These studies suggest that the queen pheromone blend is modulated by the reproductive status of the queens, and workers can detect these subtle differences and are more responsive to queens with higher reproductive potential. Furthermore, it appears as if insemination substance does not strongly affect physiological characteristics of honeybee queens 2 days after insemination, suggesting that the insemination process or volume is responsible for stimulating these early postmating changes in honeybee queens. PMID:22476212

  10. The Bacterial Helicase-Primase Interaction: A Common Structural/Functional Module

    PubMed Central

    Soultanas, Panos

    2011-01-01

    The lack of a high-resolution structure for the bacterial helicase-primase complex and the fragmented structural information for the individual proteins have been hindering our detailed understanding of this crucial binary protein interaction. Two new structures for the helicase-interacting domain of the bacterial primases from Escherichia coli and Bacillus stearothermophilus have recently been solved and both revealed a unique and surprising structural similarity to the amino-terminal domain of the helicase itself. In this minireview, the current data are discussed and important new structural and functional aspects of the helicase-primase interaction are highlighted. An attractive structural model with direct biological significance for the function of this complex and also for the development of new antibacterial compounds is examined. PMID:15939015

  11. Reorganization of interaction networks modulates the persistence of species in late successional stages.

    PubMed

    Saavedra, Serguei; Cenci, Simone; Del-Val, Ek; Boege, Karina; Rohr, Rudolf P

    2017-09-01

    Ecological interaction networks constantly reorganize as interspecific interactions change across successional stages and environmental gradients. This reorganization can also be associated with the extent to which species change their preference for types of niches available in their local sites. Despite the pervasiveness of these interaction changes, previous studies have revealed that network reorganizations have a minimal or insignificant effect on global descriptors of network architecture, such as connectance, modularity and nestedness. However, little is known about whether these reorganizations may have an effect on community dynamics and composition. To answer the question above, we study the multi-year dynamics and reorganization of plant-herbivore interaction networks across secondary successional stages of a tropical dry forest. We develop new quantitative tools based on a structural stability approach to estimate the potential impact of network reorganization on species persistence. Then, we investigate whether this impact can explain the likelihood of persistence of herbivore species in the observed communities. We find that resident (early-arriving) herbivore species increase their likelihood of persistence across time and successional stages. Importantly, we demonstrate that, in late successional stages, the reorganization of interactions among resident species has a strong inhibitory effect on the likelihood of persistence of colonizing (late-arriving) herbivores. These findings support earlier predictions suggesting that, in mature communities, changes of species interactions can act as community-control mechanisms (also known as priority effects). Furthermore, our results illustrate that the dynamics and composition of ecological communities cannot be fully understood without attention to their reorganization processes, despite the invariability of global network properties. © 2017 The Authors. Journal of Animal Ecology © 2017 British

  12. Ultrafast spontaneous emission modulation of graphene quantum dots interacting with Ag nanoparticles in solution

    NASA Astrophysics Data System (ADS)

    Zhao, Jianwei; Lu, Jian; Wang, Liang; Tian, Linfan; Deng, Xingxia; Tian, Lijun; Pan, Dengyu; Wang, Zhongyang

    2016-07-01

    We investigated the strong interaction between graphene quantum dots and silver nanoparticles in solution using time-resolved photoluminescence techniques. In solution, the silver nanoparticles are surrounded by graphene quantum dots and interacted with graphene quantum dots through exciton-plasmon coupling. An ultrafast spontaneous emission process (lifetime 27 ps) was observed in such a mixed solution. This ultrafast lifetime corresponds to the emission rate exceeding 35 GHz, with the purcell enhancement by a factor of ˜12. These experiment results pave the way for the realization of future high speed light sources applications.

  13. Ultrafast spontaneous emission modulation of graphene quantum dots interacting with Ag nanoparticles in solution

    SciTech Connect

    Zhao, Jianwei; Lu, Jian Wang, Zhongyang; Wang, Liang; Tian, Linfan; Deng, Xingxia; Tian, Lijun; Pan, Dengyu

    2016-07-11

    We investigated the strong interaction between graphene quantum dots and silver nanoparticles in solution using time-resolved photoluminescence techniques. In solution, the silver nanoparticles are surrounded by graphene quantum dots and interacted with graphene quantum dots through exciton-plasmon coupling. An ultrafast spontaneous emission process (lifetime 27 ps) was observed in such a mixed solution. This ultrafast lifetime corresponds to the emission rate exceeding 35 GHz, with the purcell enhancement by a factor of ∼12. These experiment results pave the way for the realization of future high speed light sources applications.

  14. Phonon modulation of the spin-orbit interaction as a spin relaxation mechanism in quantum dots

    NASA Astrophysics Data System (ADS)

    Romano, C. L.; Marques, G. E.; Sanz, L.; Alcalde, A. M.

    2008-01-01

    We calculate the spin relaxation rates in a parabolic InSb quantum dot due to the spin interaction with acoustical phonons. We considered the deformation potential mechanism as the dominant electron-phonon coupling in the Pavlov-Firsov spin-phonon Hamiltonian. By studying suitable choices of magnetic field and lateral dot size, we determine regions where the spin relaxation rates can be practically suppressed. We analyze the behavior of the spin relaxation rates as a function of an external magnetic field and mean quantum dot radius. Effects of the spin admixture due to Dresselhaus contribution to spin-orbit interaction are also discussed.

  15. Canine Distemper Virus Envelope Protein Interactions Modulated by Hydrophobic Residues in the Fusion Protein Globular Head

    PubMed Central

    Avila, Mislay; Khosravi, Mojtaba; Alves, Lisa; Ader-Ebert, Nadine; Bringolf, Fanny; Zurbriggen, Andreas; Plemper, Richard K.

    2014-01-01

    Membrane fusion for morbillivirus cell entry relies on critical interactions between the viral fusion (F) and attachment (H) envelope glycoproteins. Through extensive mutagenesis of an F cavity recently proposed to contribute to F's interaction with the H protein, we identified two neighboring hydrophobic residues responsible for severe F-to-H binding and fusion-triggering deficiencies when they were mutated in combination. Since both residues reside on one side of the F cavity, the data suggest that H binds the F globular head domain sideways. PMID:25355896

  16. The MIG-2/integrin interaction strengthens cell-matrix adhesion and modulates cell motility.

    PubMed

    Shi, Xiaohua; Ma, Yan-Qing; Tu, Yizeng; Chen, Ka; Wu, Shan; Fukuda, Koichi; Qin, Jun; Plow, Edward F; Wu, Chuanyue

    2007-07-13

    Integrin-mediated cell-matrix adhesion plays an important role in control of cell behavior. We report here that MIG-2, a widely expressed focal adhesion protein, interacts with beta1 and beta3 integrin cytoplasmic domains. Integrin binding is mediated by a single site within the MIG-2 FERM domain. Functionally, the MIG-2/integrin interaction recruits MIG-2 to focal adhesions. Furthermore, using alphaIIbbeta3 integrin-expressing Chinese hamster ovary cells, a well described model system for integrin activation, we show that MIG-2 promotes integrin activation and enhances cell-extracellular matrix adhesion. Although MIG-2 is expressed in many cell types, it is deficient in certain colon cancer cells. Expression of MIG-2, but not of an integrin binding-defective MIG-2 mutant, in MIG-2-null colon cancer cells strengthened cell-matrix adhesion, promoted focal adhesion formation, and reduced cell motility. These results suggest that the MIG-2/integrin interaction is an important element in the cellular control of integrin-mediated cell-matrix adhesion and that loss of this interaction likely contributes to high motility of colon cancer cells.

  17. Phosphomimetic mutations enhance oligomerization of phospholemman and modulate its interaction with the Na/K-ATPase.

    PubMed

    Song, Qiujing; Pallikkuth, Sandeep; Bossuyt, Julie; Bers, Donald M; Robia, Seth L

    2011-03-18

    Na/K-ATPase (NKA) activity is dynamically regulated by an inhibitory interaction with a small transmembrane protein, phospholemman (PLM). Inhibition is relieved upon PLM phosphorylation. Phosphorylation may alter how PLM interacts with NKA and/or itself, but details of these interactions are unknown. To address this, we quantified FRET between PLM and its regulatory target NKA in live cells. Phosphorylation of PLM was mimicked by mutation S63E (PKC site), S68E (PKA/PKC site), or S63E/S68E. The dependence of FRET on protein expression in live cells yielded information about the structure and binding affinity of the PLM-NKA regulatory complex. PLM phosphomimetic mutations altered the quaternary structure of the regulatory complex and reduced the apparent affinity of the PLM-NKA interaction. The latter effect was likely due to increased oligomerization of PLM phosphomimetic mutants, as suggested by PLM-PLM FRET measurements. Distance constraints obtained by FRET suggest that phosphomimetic mutations slightly alter the oligomer quaternary conformation. Photon-counting histogram measurements revealed that the major PLM oligomeric species is a tetramer. We conclude that phosphorylation of PLM increases its oligomerization into tetramers, decreases its binding to NKA, and alters the structures of both the tetramer and NKA regulatory complex.

  18. Interaction of cinnamaldehyde and epicatechin with tau: implications of beneficial effects in modulating Alzheimer's disease pathogenesis.

    PubMed

    George, Roshni C; Lew, John; Graves, Donald J

    2013-01-01

    Abnormal modifications in tau such as hyperphosphorylation, oxidation, and glycation interfere with its interaction with microtubules leading to its dissociation and self-aggregation into neurofibrillary tangles, a hallmark of Alzheimer's disease (AD). Previously we reported that an aqueous extract of cinnamon has the ability to inhibit tau aggregation in vitro and can even induce dissociation of tangles isolated from AD brain. In the present study, we carried out investigations with cinnamaldehyde (CA) and epicatechin (EC), two components of active cinnamon extract. We found that CA and the oxidized form of EC (ECox) inhibited tau aggregation in vitro and the activity was due to their interaction with the two cysteine residues in tau. Mass spectrometry of a synthetic peptide, SKCGS, representing the actual tau sequence, identified the thiol as reacting with CA and ECox. Use of a cysteine double mutant of tau showed the necessity of cysteine for aggregation inhibition by CA. The interaction of CA with tau cysteines was reversible and the presence of CA did not impair the biological function of tau in tubulin assembly in vitro. Further, these compounds protected tau from oxidation caused by the reactive oxygen species, H2O2, and prevented subsequent formation of high molecular weight species that are considered to stimulate tangle formation. Finally, we observed that EC can sequester highly reactive and toxic byproducts of oxidation such as acrolein. Our results suggest that small molecules that form a reversible interaction with cysteines have the potential to protect tau from abnormal modifications.

  19. LEADERSHIP STATUS AS A MODULATOR OF THE DETERMINATION OF SOCIAL INTERACTION BY PRIOR REINFORCEMENT.

    DTIC Science & Technology

    determine degree of shift in judgment. Interaction effects on analysis of variance were significant for leader vs. non-leaders, positive vs. negative ... reinforcement . Thus, leaders are found to respond to cues in the outside world, non-leaders to ’internal’ mediating systems. (Author)

  20. Genetic variants at PSMD3 interact with dietary fat and carbohydrate to modulate insulin resistance

    USDA-ARS?s Scientific Manuscript database

    Proteasome (prosome, macropain) 26S subunit, non-ATPase, 3 (PSMD3) encodes subunit 3 of the 26S proteasome, which is involved in regulating insulin signal transduction. We aimed to investigate the associations of PSMD3 variants with glucose-related traits and the interactions of those variants with ...

  1. Systems with competing interlayer interactions and modulations in one direction: finding their structures.

    PubMed

    Cepič, Mojca

    2014-05-19

    Complex structures in polar smectic systems can be studied within framework of discrete phenomenological models. Considered interactions are usually described by nonlinear trigonometric functions that do not allow for a straightforward search for solutions. The review of three methods reported in the literature are presented and their appropriateness, advantages and disadvantages are discussed. Examples are given as an illustration for each method.

  2. Modulation of Magnetic Heating via Dipolar Magnetic Interactions in Monodisperse and Crystalline Iron Oxide Nanoparticles

    SciTech Connect

    Salas, Gorka; Camarero, Julio; Cabrera, David; Takacs, Hélène; Varela, María; Ludwig, Robert; Dähring, Heidi; Hilger, Ingrid; Miranda, Rodolfo; Morales, María del Puerto; Teran, Francisco Jose

    2014-07-23

    Here, we report on the study of heat dissipation power in monodisperse and crystalline magnetite nanoparticles as function of particle and aggregate sizes, magnetic field frequencies (up to 435 kHz) and amplitudes (up to 50 mT), media viscosity and particle concentration. These nanoparticles display specific absorption rate values of few hundreds of WgFe-1 at moderate frequencies (~100 kHz), increasing up to 3632 WgFe-1 at more extreme field conditions (430 kHz and 40 mT) for the largest size. We have found that Néelian relaxation processes are dominant for all nanoparticle sizes, whereas Brownian contribution dominates only for the largest size (22 nm) at high particle concentrations when dipolar interactions enhance the effective magnetic anisotropy. Besides, the particle concentration dependence of the specific absorption rate reflects the importance of magnetic dipolar interactions which strongly depend on aggregate and particle size. Our results show that dipolar interactions tune the effective magnetic anisotropy determining the Néelian and Brownian contributions into SAR values. The possibility of switching between heating mechanisms via dipolar interactions is of great importance towards controlling the heat exposure supplied by IONP as intracellular heating mediators.

  3. Modulation of Magnetic Heating via Dipolar Magnetic Interactions in Monodisperse and Crystalline Iron Oxide Nanoparticles

    DOE PAGES

    Salas, Gorka; Camarero, Julio; Cabrera, David; ...

    2014-07-23

    Here, we report on the study of heat dissipation power in monodisperse and crystalline magnetite nanoparticles as function of particle and aggregate sizes, magnetic field frequencies (up to 435 kHz) and amplitudes (up to 50 mT), media viscosity and particle concentration. These nanoparticles display specific absorption rate values of few hundreds of WgFe-1 at moderate frequencies (~100 kHz), increasing up to 3632 WgFe-1 at more extreme field conditions (430 kHz and 40 mT) for the largest size. We have found that Néelian relaxation processes are dominant for all nanoparticle sizes, whereas Brownian contribution dominates only for the largest size (22more » nm) at high particle concentrations when dipolar interactions enhance the effective magnetic anisotropy. Besides, the particle concentration dependence of the specific absorption rate reflects the importance of magnetic dipolar interactions which strongly depend on aggregate and particle size. Our results show that dipolar interactions tune the effective magnetic anisotropy determining the Néelian and Brownian contributions into SAR values. The possibility of switching between heating mechanisms via dipolar interactions is of great importance towards controlling the heat exposure supplied by IONP as intracellular heating mediators.« less

  4. A New Approach to Developing Interactive Software Modules through Graduate Education

    ERIC Educational Resources Information Center

    Sanders, Nathan E.; Faesi, Chris; Goodman, Alyssa A.

    2014-01-01

    Educational technology has attained significant importance as a mechanism for supporting experiential learning of science concepts. However, the growth of this mechanism is limited by the significant time and technical expertise needed to develop such products, particularly in specialized fields of science. We sought to test whether interactive,…

  5. Apolipoprotein A5 and lipoprotein lipase interact to modulate anthropometric measures in Hispanics of Caribbean origin

    USDA-ARS?s Scientific Manuscript database

    Apolipoprotein A5 (APOA5) and lipoprotein lipase (LPL) proteins interact functionally to regulate lipid metabolism, and single nucleotide polymorphisms (SNPs) for each gene have also been associated independently with obesity risk. Evaluating gene combinations may be more effective than single SNP a...

  6. Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome.

    PubMed

    Ussar, Siegfried; Griffin, Nicholas W; Bezy, Olivier; Fujisaka, Shiho; Vienberg, Sara; Softic, Samir; Deng, Luxue; Bry, Lynn; Gordon, Jeffrey I; Kahn, C Ronald

    2015-09-01

    Obesity, diabetes, and metabolic syndrome result from complex interactions between genetic and environmental factors, including the gut microbiota. To dissect these interactions, we utilized three commonly used inbred strains of mice-obesity/diabetes-prone C57Bl/6J mice, obesity/diabetes-resistant 129S1/SvImJ from Jackson Laboratory, and obesity-prone but diabetes-resistant 129S6/SvEvTac from Taconic-plus three derivative lines generated by breeding these strains in a new, common environment. Analysis of metabolic parameters and gut microbiota in all strains and their environmentally normalized derivatives revealed strong interactions between microbiota, diet, breeding site, and metabolic phenotype. Strain-dependent and strain-independent correlations were found between specific microbiota and phenotypes, some of which could be transferred to germ-free recipient animals by fecal transplantation. Environmental reprogramming of microbiota resulted in 129S6/SvEvTac becoming obesity resistant. Thus, development of obesity/metabolic syndrome is the result of interactions between gut microbiota, host genetics, and diet. In permissive genetic backgrounds, environmental reprograming of microbiota can ameliorate development of metabolic syndrome. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. PAR3-aPKC regulates Tiam1 by modulating suppressive internal interactions.

    PubMed

    Matsuzawa, Kenji; Akita, Hiroki; Watanabe, Takashi; Kakeno, Mai; Matsui, Toshinori; Wang, Shujie; Kaibuchi, Kozo

    2016-05-01

    Tiam1 is one of the most extensively analyzed activators of the small GTPase Rac. However, fundamental aspects of its regulation are poorly understood. Here we demonstrate that Tiam1 is functionally suppressed by internal interactions and that the PAR complex participates in its full activation. The N-terminal region of Tiam1 binds to the protein-binding and catalytic domains to inhibit its localization and activation. Atypical PKCs phosphorylate Tiam1 to relieve its intramolecular interactions, and the subsequent stabilization of its interaction with PAR3 allows it to exert localized activity. By analyzing Tiam1 regulation by PAR3-aPKC within the context of PDGF signaling, we also show that PAR3 directly binds PDGF receptor β. Thus we provide the first evidence for the negative regulation of Tiam1 by internal interactions, elucidate the nature of Tiam1 regulation by the PAR complex, and reveal a novel role for the PAR complex in PDGF signaling. © 2016 Matsuzawa et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  8. PAR3-aPKC regulates Tiam1 by modulating suppressive internal interactions

    PubMed Central

    Matsuzawa, Kenji; Akita, Hiroki; Watanabe, Takashi; Kakeno, Mai; Matsui, Toshinori; Wang, Shujie; Kaibuchi, Kozo

    2016-01-01

    Tiam1 is one of the most extensively analyzed activators of the small GTPase Rac. However, fundamental aspects of its regulation are poorly understood. Here we demonstrate that Tiam1 is functionally suppressed by internal interactions and that the PAR complex participates in its full activation. The N-terminal region of Tiam1 binds to the protein-binding and catalytic domains to inhibit its localization and activation. Atypical PKCs phosphorylate Tiam1 to relieve its intramolecular interactions, and the subsequent stabilization of its interaction with PAR3 allows it to exert localized activity. By analyzing Tiam1 regulation by PAR3-aPKC within the context of PDGF signaling, we also show that PAR3 directly binds PDGF receptor β. Thus we provide the first evidence for the negative regulation of Tiam1 by internal interactions, elucidate the nature of Tiam1 regulation by the PAR complex, and reveal a novel role for the PAR complex in PDGF signaling. PMID:26941335

  9. Modulation of Additive and Interactive Effects in Lexical Decision by Trial History

    ERIC Educational Resources Information Center

    Masson, Michael E. J.; Kliegl, Reinhold

    2013-01-01

    Additive and interactive effects of word frequency, stimulus quality, and semantic priming have been used to test theoretical claims about the cognitive architecture of word-reading processes. Additive effects among these factors have been taken as evidence for discrete-stage models of word reading. We present evidence from linear mixed-model…

  10. A New Approach to Developing Interactive Software Modules through Graduate Education

    ERIC Educational Resources Information Center

    Sanders, Nathan E.; Faesi, Chris; Goodman, Alyssa A.

    2014-01-01

    Educational technology has attained significant importance as a mechanism for supporting experiential learning of science concepts. However, the growth of this mechanism is limited by the significant time and technical expertise needed to develop such products, particularly in specialized fields of science. We sought to test whether interactive,…

  11. Prothymosin alpha modulates the interaction of histone H1 with chromatin.

    PubMed Central

    Karetsou, Z; Sandaltzopoulos, R; Frangou-Lazaridis, M; Lai, C Y; Tsolas, O; Becker, P B; Papamarcaki, T

    1998-01-01

    Prothymosin alpha (ProTalpha) is an abundant acidic nuclear protein that may be involved in cell proliferation. In our search for its cellular partners, we have recently found that ProTalpha binds to linker histone H1. We now provide further evidence for the physiological relevance of this interaction by immunoisolation of a histone H1-ProTalpha complex from NIH 3T3 cell extracts. A detailed analysis of the interaction between the two proteins suggests contacts between the acidic region of ProTalpha and histone H1. In the context of a physiological chromatin reconstitution reaction, the presence of ProTalpha does not affect incorporation of an amount of histone H1 sufficient to increase the nucleosome repeat length by 20 bp, but prevents association of all further H1. Consistent with this finding, a fraction of histone H1 is released when H1-containing chromatin is challenged with ProTalpha. These results imply at least two different interaction modes of H1 with chromatin, which can be distinguished by their sensitivity to ProTalpha. The properties of ProTalpha suggest a role in fine tuning the stoichiometry and/or mode of interaction of H1 with chromatin. PMID:9628907

  12. Phosphomimetic Mutations Enhance Oligomerization of Phospholemman and Modulate Its Interaction with the Na/K-ATPase*

    PubMed Central

    Song, Qiujing; Pallikkuth, Sandeep; Bossuyt, Julie; Bers, Donald M.; Robia, Seth L.

    2011-01-01

    Na/K-ATPase (NKA) activity is dynamically regulated by an inhibitory interaction with a small transmembrane protein, phospholemman (PLM). Inhibition is relieved upon PLM phosphorylation. Phosphorylation may alter how PLM interacts with NKA and/or itself, but details of these interactions are unknown. To address this, we quantified FRET between PLM and its regulatory target NKA in live cells. Phosphorylation of PLM was mimicked by mutation S63E (PKC site), S68E (PKA/PKC site), or S63E/S68E. The dependence of FRET on protein expression in live cells yielded information about the structure and binding affinity of the PLM-NKA regulatory complex. PLM phosphomimetic mutations altered the quaternary structure of the regulatory complex and reduced the apparent affinity of the PLM-NKA interaction. The latter effect was likely due to increased oligomerization of PLM phosphomimetic mutants, as suggested by PLM-PLM FRET measurements. Distance constraints obtained by FRET suggest that phosphomimetic mutations slightly alter the oligomer quaternary conformation. Photon-counting histogram measurements revealed that the major PLM oligomeric species is a tetramer. We conclude that phosphorylation of PLM increases its oligomerization into tetramers, decreases its binding to NKA, and alters the structures of both the tetramer and NKA regulatory complex. PMID:21220422

  13. Interaction and Modulation of Two Antagonistic Cell Wall Enzymes of Mycobacteria

    PubMed Central

    Rubin, Eric J.

    2010-01-01

    Bacterial cell growth and division require coordinated cell wall hydrolysis and synthesis, allowing for the removal and expansion of cell wall material. Without proper coordination, unchecked hydrolysis can result in cell lysis. How these opposing activities are simultaneously regulated is poorly understood. In Mycobacterium tuberculosis, the resuscitation-promoting factor B (RpfB), a lytic transglycosylase, interacts and synergizes with Rpf-interacting protein A (RipA), an endopeptidase, to hydrolyze peptidoglycan. However, it remains unclear what governs this synergy and how it is coordinated with cell wall synthesis. Here we identify the bifunctional peptidoglycan-synthesizing enzyme, penicillin binding protein 1 (PBP1), as a RipA-interacting protein. PBP1, like RipA, localizes both at the poles and septa of dividing cells. Depletion of the ponA1 gene, encoding PBP1 in M. smegmatis, results in a severe growth defect and abnormally shaped cells, indicating that PBP1 is necessary for viability and cell wall stability. Finally, PBP1 inhibits the synergistic hydrolysis of peptidoglycan by the RipA-RpfB complex in vitro. These data reveal a post-translational mechanism for regulating cell wall hydrolysis and synthesis through protein–protein interactions between enzymes with antagonistic functions. PMID:20686708

  14. Modulation of Additive and Interactive Effects in Lexical Decision by Trial History

    ERIC Educational Resources Information Center

    Masson, Michael E. J.; Kliegl, Reinhold

    2013-01-01

    Additive and interactive effects of word frequency, stimulus quality, and semantic priming have been used to test theoretical claims about the cognitive architecture of word-reading processes. Additive effects among these factors have been taken as evidence for discrete-stage models of word reading. We present evidence from linear mixed-model…

  15. Interdomain Hydrophobic Interactions Modulate the Thermostability of Microbial Esterases from the Hormone-Sensitive Lipase Family*

    PubMed Central

    Li, Ping-Yi; Chen, Xiu-Lan; Ji, Peng; Li, Chun-Yang; Wang, Peng; Zhang, Yi; Xie, Bin-Bin; Qin, Qi-Long; Su, Hai-Nan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Zhang, Xi-Ying

    2015-01-01

    Microbial hormone-sensitive lipases (HSLs) contain a CAP domain and a catalytic domain. However, it remains unclear how the CAP domain interacts with the catalytic domain to maintain the stability of microbial HSLs. Here, we isolated an HSL esterase, E40, from a marine sedimental metagenomic library. E40 exhibited the maximal activity at 45 °C and was quite thermolabile, with a half-life of only 2 min at 40 °C, which may be an adaptation of E40 to the permanently cold sediment environment. The structure of E40 was solved to study its thermolability. Structural analysis showed that E40 lacks the interdomain hydrophobic interactions between loop 1 of the CAP domain and α7 of the catalytic domain compared with its thermostable homologs. Mutational analysis showed that the introduction of hydrophobic residues Trp202 and Phe203 in α7 significantly improved E40 stability and that a further introduction of hydrophobic residues in loop 1 made E40 more thermostable because of the formation of interdomain hydrophobic interactions. Altogether, the results indicate that the absence of interdomain hydrophobic interactions between loop 1 and α7 leads to the thermolability of E40. In addition, a comparative analysis of the structures of E40 and other thermolabile and thermostable HSLs suggests that the interdomain hydrophobic interactions between loop 1 and α7 are a key element for the thermostability of microbial HSLs. Therefore, this study not only illustrates the structural element leading to the thermolability of E40 but also reveals a structural determinant for HSL thermostability. PMID:25771540

  16. Epistatic interactions modulate the evolution of mammalian mitochondrial respiratory complex components

    PubMed Central

    Azevedo, Luísa; Carneiro, João; van Asch, Barbara; Moleirinho, Ana; Pereira, Filipe; Amorim, António

    2009-01-01

    Background The deleterious effect of a mutation can be reverted by a second-site interacting residue. This is an epistatic compensatory process explaining why mutations that are deleterious in some species are tolerated in phylogenetically related lineages, rendering evident that those mutations are, by all means, only deleterious in the species-specific context. Although an extensive and refined theoretical framework on compensatory evolution does exist, the supporting evidence remains limited, especially for protein models. In this current study, we focused on the molecular mechanism underlying the epistatic compensatory process in mammalian mitochondrial OXPHOS proteins using a combination of in-depth structural and sequence analyses. Results Modeled human structures were used in this study to predict the structural impairment and recovery of deleterious mutations alone and combined with an interacting compensatory partner, respectively. In two cases, COI and COIII, intramolecular interactions between spatially linked residues restore the folding pattern impaired by the deleterious mutation. In a third case, intermolecular contact between mitochondrial CYB and nuclear CYT1 encoded components of the cytochrome bc1 complex are likely to restore protein binding. Moreover, we observed different modes of compensatory evolution that have resulted in either a quasi-simultaneous occurrence of a mutation and corresponding compensatory partner, or in independent occurrences of mutations in distinct lineages that were always preceded by the compensatory site. Conclusion Epistatic interactions between individual replacements involving deleterious mutations seems to follow a parsimonious model of evolution in which genomes hold pre-compensating states that subsequently tolerate deleterious mutations. This phenomenon is likely to have been constraining the variability at coevolving sites and shaping the interaction between the mitochondrial and the nuclear genome. PMID

  17. Interactive Learning Modules: Enabling Near Real-Time Oceanographic Data Use In Undergraduate Education

    NASA Astrophysics Data System (ADS)

    Kilb, D. L.; Fundis, A. T.; Risien, C. M.

    2012-12-01

    The focus of the Education and Public Engagement (EPE) component of the NSF's Ocean Observatories Initiative (OOI) is to provide a new layer of cyber-interactivity for undergraduate educators to bring near real-time data from the global ocean into learning environments. To accomplish this, we are designing six online services including: 1) visualization tools, 2) a lesson builder, 3) a concept map builder, 4) educational web services (middleware), 5) collaboration tools and 6) an educational resource database. Here, we report on our Fall 2012 release that includes the first four of these services: 1) Interactive visualization tools allow users to interactively select data of interest, display the data in various views (e.g., maps, time-series and scatter plots) and obtain statistical measures such as mean, standard deviation and a regression line fit to select data. Specific visualization tools include a tool to compare different months of data, a time series explorer tool to investigate the temporal evolution of select data parameters (e.g., sea water temperature or salinity), a glider profile tool that displays ocean glider tracks and associated transects, and a data comparison tool that allows users to view the data either in scatter plot view comparing one parameter with another, or in time series view. 2) Our interactive lesson builder tool allows users to develop a library of online lesson units, which are collaboratively editable and sharable and provides starter templates designed from learning theory knowledge. 3) Our interactive concept map tool allows the user to build and use concept maps, a graphical interface to map the connection between concepts and ideas. This tool also provides semantic-based recommendations, and allows for embedding of associated resources such as movies, images and blogs. 4) Education web services (middleware) will provide an educational resource database API.

  18. Pancortins interact with amyloid precursor protein and modulate cortical cell migration

    PubMed Central

    Rice, Heather C.; Townsend, Matthew; Bai, Jilin; Suth, Seiyam; Cavanaugh, William; Selkoe, Dennis J.; Young-Pearse, Tracy L.

    2012-01-01

    Neuronal precursor cell migration in the developing mammalian brain is a complex process requiring the coordinated interaction of numerous proteins. We have recently shown that amyloid precursor protein (APP) plays a role in migration into the cortical plate through its interaction with two cytosolic signaling proteins, disabled 1 (DAB1) and disrupted in schizophrenia 1 (DISC1). In order to identify extracellular factors that may signal through APP to regulate migration, we performed an unbiased mass spectrometry-based screen for factors that bind to the extracellular domain of APP in the rodent brain. Through this screen, we identified an interaction between APP and pancortins, proteins expressed throughout the developing and mature cerebral cortex. Via co-immunoprecipitation, we show that APP interacts with all four of the mammalian pancortin isoforms (AMY, AMZ, BMY, BMZ). We demonstrate that the BMZ and BMY isoforms of pancortin can specifically reduce β-secretase- but not α-secretase-mediated cleavage of endogenous APP in cell culture, suggesting a biochemical consequence of the association between pancortins and APP. Using in utero electroporation to overexpress and knock down specific pancortin isoforms, we reveal a novel role for pancortins in migration into the cortical plate. Interestingly, we observe opposing roles for alternate pancortin isoforms, with AMY overexpression and BMZ knock down both preventing proper migration of neuronal precursor cells. Finally, we show that BMZ can partially rescue a loss of APP expression and that APP can rescue effects of AMY overexpression, suggesting that pancortins act in conjunction with APP to regulate entry into the cortical plate. Taken together, these results suggest a biochemical and functional interaction between APP and pancortins, and reveal a previously unidentified role for pancortins in mammalian cortical development. PMID:22992957

  19. p16 Modulates VEGF Expression via Its Interaction With HIF-1α in Breast Cancer Cells

    PubMed Central

    Zhang, Jun; Lu, Andrew; Li, Liyuan; Yue, Junming; Lu, Yi

    2010-01-01

    The degree of tumor progression (such as growth, angiogenesis, and metastasis) directly correlates with the expression of vascular endothelial growth factor (VEGF), but inversely correlates with the expression of tumor-suppressor gene p16, therefore we examined whether the restoration of p16 in breast cancer cells would modulate VEGF expression. Adenoviral-mediated p16 expression downregulated VEGF gene expression in breast cancer cells, and inhibited breast cancer cell-induced angiogenesis by a dorsal air sac model in mice. Moreover, p16 appears to form a complex with HIF-1α, the transcription factor for the VEGF gene promoter. Taken together, the binding between p16 and HIF-1α protein may alter HIF-1α’s ability to transactivate VEGF expression. PMID:20307196

  20. Accurate formula for dissipative interaction in frequency modulation atomic force microscopy

    SciTech Connect

    Suzuki, Kazuhiro; Matsushige, Kazumi; Yamada, Hirofumi; Kobayashi, Kei; Labuda, Aleksander

    2014-12-08

    Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve. Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.

  1. Modulating the Delicate Glial-Neuronal Interactions in Neuropathic Pain: Promises and Potential Caveats

    PubMed Central

    Tiwari, Vinod; Guan, Yun; Raja, Srinivasa N.

    2014-01-01

    During neuropathic pain, glial cells (mainly astrocytes and microglia) become activated and initiate a series of signaling cascades that modulate pain processing at both spinal and supraspinal levels. It has been generally accepted that glial cell activation contributes to neuropathic pain because glia release proinflammatory cytokines, chemokines, and factors such as calcitonin gene-related peptide, substance P, and glutamate, which are known to facilitate pain signaling. However, recent research has shown that activation of glia also leads to some beneficial outcomes. Glia release anti-inflammatory factors that protect against neurotoxicity and restore normal pain. Accordingly, use of glial inhibitors might compromise the protective functions of glia in addition to suppressing their detrimental effects. With a better understanding of how different conditions affect glial cell activation, we may be able to promote the protective function of glia and pave the way for future development of novel, safe, and effective treatments of neuropathic pain. PMID:24820245

  2. Modulated interaction in double-layer shape memory-based micro-designed actuators

    PubMed Central

    Crăciunescu, Corneliu; Ercuta, Aurel

    2015-01-01

    The effect of superposed transitions in actuators with layered shape memory alloy (SMA) films undergoing martensitic phase transformation is analyzed in terms of a model developed for two layers of different composition, deposited at the same temperature on a substrate. A significant difference is observed in the actuation versus temperature relationship, depending on the thermal and elastic properties of the SMA layers and their martensitic transformation temperature. The prediction of the actuation is exemplified using a multilayer model and is verified for a cantilever actuator with NiTi and NiMnGa layers deposited on a Si substrate. The model sets the ground for a smart selection of SMAs in order to achieve a modulated actuation. PMID:27877845

  3. An immunomodulatory protein, Ling Zhi-8, facilitates cellular interaction through modulation of adhesion molecules.

    PubMed

    Miyasaka, N; Inoue, H; Totsuka, T; Koike, R; Kino, K; Tsunoo, H

    1992-07-15

    Ling Zhi-8 (LZ-8), a novel immunomodulatory protein, markedly enhanced the expression of CD11b, but not CD11a, CD13, CD14, CD18, CD33 or HLA-DR, on the U937 cell line in a dose-dependent fashion. It also induced ICAM-1 expression on vascular endothelial cells and significantly augmented gamma - interferon-induced cellular binding between vascular endothelial cells and U937. Furthermore, LZ-8 increased the expression of CD2, but not VLA4, VLA5 or LFA3, on MOLT4 and enhanced rosette formation between human T cells and sheep red blood cells. These data suggest that LZ-8 exerts its pharmacological effect by modulating adhesion molecules on immunocompetent cells.

  4. Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules

    PubMed Central

    Bieli, Dimitri; Kanca, Oguz; Requena, David; Hamaratoglu, Fisun; Gohl, Daryl; Schedl, Paul; Affolter, Markus; Slattery, Matthew; Müller, Martin; Estella, Carlos

    2015-01-01

    The subdivision of cell populations in compartments is a key event during animal development. In Drosophila, the gene apterous (ap) divides the wing imaginal disc in dorsal vs ventral cell lineages and is required for wing formation. ap function as a dorsal selector gene has been extensively studied. However, the regulation of its expression during wing development is poorly understood. In this study, we analyzed ap transcriptional regulation at the endogenous locus and identified three cis-regulatory modules (CRMs) essential for wing development. Only when the three CRMs are combined, robust ap expression is obtained. In addition, we genetically and molecularly analyzed the trans-factors that regulate these CRMs. Our results propose a three-step mechanism for the cell lineage compartment expression of ap that includes initial activation, positive autoregulation and Trithorax-mediated maintenance through separable CRMs. PMID:26468882

  5. De novo designed library of linear helical peptides: an exploratory tool in the discovery of protein-protein interaction modulators.

    PubMed

    Bonache, M Ángeles; Balsera, Beatriz; López-Méndez, Blanca; Millet, Oscar; Brancaccio, Diego; Gómez-Monterrey, Isabel; Carotenuto, Alfonso; Pavone, Luigi M; Reille-Seroussi, Marie; Gagey-Eilstein, Nathalie; Vidal, Michel; de la Torre-Martinez, Roberto; Fernández-Carvajal, Asia; Ferrer-Montiel, Antonio; García-López, M Teresa; Martín-Martínez, Mercedes; de Vega, M Jesús Pérez; González-Muñiz, Rosario

    2014-05-12

    Protein-protein interactions (PPIs) have emerged as important targets for pharmaceutical intervention because of their essential role in numerous physiological and pathological processes, but screening efforts using small-molecules have led to very low hit rates. Linear peptides could represent a quick and effective approach to discover initial PPI hits, particularly if they have inherent ability to adopt specific peptide secondary structures. Here, we address this hypothesis through a linear helical peptide library, composed of four sublibraries, which was designed by theoretical predictions of helicity (Agadir software). The 13-mer peptides of this collection fixes either a combination of three aromatic or two aromatic and one aliphatic residues on one face of the helix (Ac-SSEEX(5)ARNX(9)AAX(12)N-NH2), since these are structural features quite common at PPIs interfaces. The 81 designed peptides were conveniently synthesized by parallel solid-phase methodologies, and the tendency of some representative library components to adopt the intended secondary structure was corroborated through CD and NMR experiments. As proof of concept in the search for PPI modulators, the usefulness of this library was verified on the widely studied p53-MDM2 interaction and on the communication between VEGF and its receptor Flt-1, two PPIs for which a hydrophobic α-helix is essential for the interaction. We have demonstrated here that, in both cases, selected peptides from the library, containing the right hydrophobic sequence of the hot-spot in one of the protein partners, are able to interact with the complementary protein. Moreover, we have discover some new, quite potent inhibitors of the VEGF-Flt-1 interaction, just by replacing one of the aromatic residues of the initial F(5)Y(9)Y(12) peptide by W, in agreement with previous results on related antiangiogenic peptides. Finally, the HTS evaluation of the full collection on thermoTRPs has led to a few antagonists of TRPV1 and TRPA

  6. Modulation of diorganoyl dichalcogenides reactivity by non-bonded nitrogen interactions.

    PubMed

    Hassan, Waseem; Narayanaperumal, Senthil; Gul, Kashif; Rahman, Ata Ur; Braga, Antonio L; Rodrigues, Oscar E D; Rocha, João Batista Teixeira

    2012-08-30

    The study was designed to explore the biochemical influence of non bonding nitrogen interactions (N⋯Se/S) on organochalcogens potency. Approximately five and six times higher thiol peroxidase (TPx) like activity was observed for compound (C)-2 than C-1 and C-3, respectively. C-2 also displayed significantly (p<0.05) higher activity in 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging and deoxyribose degradation assays. All compounds, except C-4 and C-6 significantly inhibited Fe (II) and sodium nitroprusside (SNP) induced thiobarbituric acid reactive species (TBARS) production in rat's brain, liver and kidney preparations with highest activity observed for C-2. The highest C-2 activity was attributed to the presence of non-bonded nitrogen interactions which were absent in C-1 and blocked with butoxycarbonyl (BOC group) in C-3. The same structural activity analogy was extended to organosulfur compounds and it was observed that compound with non-bonding nitrogen interactions, i.e. C-5 has significantly (p<0.05) higher TPx like activity than C-6 and C-4. C-5 at the highest tested concentration significantly (p<0.05) protected against Fe (II) and SNP induced TBARS formation in rat's brain, kidney and liver preparations but did not display activity in DPPH and deoxyribose degradation assays. This study confirms the influence of not only N⋯Se interaction but also for the first time the effect of non bonded N⋯S interactions on organochalcogens potency. C-2 (with the highest activity) was also tested in vivo and was administered at three different doses, i.e. 15, 30 and 50 mg/kg to get an exact idea about its interaction with thiol containing molecules (NPSH) and enzyme α-ALA-D (sulfhydryl containing enzyme). Oxidative stress parameters, i.e. free radical concentration by dichlorofluoreseein (DCF) assay, TBARS, ascorbic acid level, hepatic (ALT and AST) and renal (urea and creatinine) toxicity markers were also estimated to get an insight about its possible

  7. Rho activation of mDia formins is modulated by an interaction with inverted formin 2 (INF2)

    PubMed Central

    Sun, Hua; Schlondorff, Johannes S.; Brown, Elizabeth J.; Higgs, Henry N.; Pollak, Martin R.

    2011-01-01

    Inverted formin 2 (INF2) encodes a member of the diaphanous subfamily of formin proteins. Mutations in INF2 cause human kidney disease characterized by focal and segmental glomerulosclerosis. Disease-causing mutations occur only in the diaphanous inhibitory domain (DID), suggesting specific roles for this domain in the pathogenesis of disease. In a yeast two-hybrid screen, we identified the diaphanous autoregulatory domains (DADs) of the mammalian diaphanous-related formins (mDias) mDia1, mDia2, and mDia 3 as INF2_DID-interacting partners. The mDias are Rho family effectors that regulate actin dynamics. We confirmed in vitro INF2_DID/mDia_DAD binding by biochemical assays, confirmed the in vivo interaction of these protein domains by coimmunoprecipitation, and observed colocalization of INF2 and mDias in glomerular podocytes. We investigated the influence of this INF2_DID/mDia_DAD interaction on mDia mediated actin polymerization and on serum response factor (SRF) activation. We find that the interaction of INF2_DID with mDia_DAD inhibited mDia-mediated, Rho-activated actin polymerization, as well as SRF-responsive gene transcriptional changes. Similar assays using the disease-causing E184K and R218Q mutations in INF2_DID showed a decreased effect on SRF activation and gene transcription. The binding of INF2_DID to mDia_DAD may serve as a negative regulatory mechanism for mDias’ function in actin-dependent cell processes. The effects of disease-causing INF2 mutations suggest an important role for this protein and its interaction with other formins in modulating glomerular podocyte phenotype and function. PMID:21278336

  8. APOA5 Gene Variation Interacts with Dietary Fat Intake to Modulate Obesity and Circulating Triglycerides in a Mediterranean Population12

    PubMed Central

    Sánchez-Moreno, Carmen; Ordovás, Jose M.; Smith, Caren E.; Baraza, Juan C.; Lee, Yu-Chi; Garaulet, Marta

    2011-01-01

    APOA5 is one of the strongest regulators of plasma TG concentrations; nevertheless, its mechanisms of action are poorly characterized. Genetic variability at the APOA5 locus has also been associated with increased cardiovascular disease risk; however, this predisposition could be attenuated in the context of a prudent diet as traditionally consumed in the Mediterranean countries. We have investigated the interaction between a single nucleotide polymorphism (SNP) at the APOA5 gene (-1131T > C) and dietary fat that may modulate TG-rich lipoprotein concentrations and anthropometric measures in overweight and obese participants. We recruited 1465 participants from a Spanish population (20–65 y old; BMI 25–40 kg/m2) attending outpatient obesity clinics. Consistent with previous reports, we found an association between the APOA5-1131T > C SNP and TG-rich lipoprotein concentrations that were higher in carriers of the minor allele than in noncarriers (P < 0.001). Moreover, we found a significant genotype-dietary fat interaction for obesity traits. Participants homozygous for the −1131T major allele had a positive association between fat intake and obesity, whereas in those carrying the APOA5−1131C minor allele, higher fat intakes were not associated with higher BMI. Likewise, we found genotype-dietary fat interactions for TG-rich lipoproteins (P < 0.001). In conclusion, we have replicated previous gene-diet interactions between APOA5 -1131T > C SNP and fat intake for obesity traits and detected a novel interaction for TG-rich lipoprotein concentrations. Our data support the hypothesis that the minor C-allele may protect those consuming a high-fat diet from obesity and elevated concentrations of TG-rich lipoproteins. PMID:21209257

  9. Interaction of the Human Papillomavirus E6 Oncoprotein with Sorting Nexin 27 Modulates Endocytic Cargo Transport Pathways

    PubMed Central

    Ganti, Ketaki; Massimi, Paola; Manzo-Merino, Joaquin; Tomaić, Vjekoslav; Pim, David; Playford, Martin P.; Lizano, Marcela; Roberts, Sally; Kranjec, Christian; Doorbar, John; Banks, Lawrence

    2016-01-01

    A subset of high-risk Human Papillomaviruses (HPVs) are the causative agents of a large number of human cancers, of which cervical is the most common. Two viral oncoproteins, E6 and E7, contribute directly towards the development and maintenance of malignancy. A characteristic feature of the E6 oncoproteins from cancer-causing HPV types is the presence of a PDZ binding motif (PBM) at its C-terminus, which confers interaction with cellular proteins harbouring PDZ domains. Here we show that this motif allows E6 interaction with Sorting Nexin 27 (SNX27), an essential component of endosomal recycling pathways. This interaction is highly conserved across E6 proteins from multiple high-risk HPV types and is mediated by a classical PBM-PDZ interaction but unlike many E6 targets, SNX27 is not targeted for degradation by E6. Rather, in HPV-18 positive cell lines the association of SNX27 with components of the retromer complex and the endocytic transport machinery is altered in an E6 PBM-dependent manner. Analysis of a SNX27 cargo, the glucose transporter GLUT1, reveals an E6-dependent maintenance of GLUT1 expression and alteration in its association with components of the endocytic transport machinery. Furthermore, knockdown of E6 in HPV-18 positive cervical cancer cells phenocopies the loss of SNX27, both in terms of GLUT1 expression levels and its vesicular localization, with a concomitant marked reduction in glucose uptake, whilst loss of SNX27 results in slower cell proliferation in low nutrient conditions. These results demonstrate that E6 interaction with SNX27 can alter the recycling of cargo molecules, one consequence of which is modulation of nutrient availability in HPV transformed tumour cells. PMID:27649450

  10. APOA5 gene variation interacts with dietary fat intake to modulate obesity and circulating triglycerides in a Mediterranean population.

    PubMed

    Sánchez-Moreno, Carmen; Ordovás, Jose M; Smith, Caren E; Baraza, Juan C; Lee, Yu-Chi; Garaulet, Marta

    2011-03-01

    APOA5 is one of the strongest regulators of plasma TG concentrations; nevertheless, its mechanisms of action are poorly characterized. Genetic variability at the APOA5 locus has also been associated with increased cardiovascular disease risk; however, this predisposition could be attenuated in the context of a prudent diet as traditionally consumed in the Mediterranean countries. We have investigated the interaction between a single nucleotide polymorphism (SNP) at the APOA5 gene (-1131T > C) and dietary fat that may modulate TG-rich lipoprotein concentrations and anthropometric measures in overweight and obese participants. We recruited 1465 participants from a Spanish population (20-65 y old; BMI 25-40 kg/m(2)) attending outpatient obesity clinics. Consistent with previous reports, we found an association between the APOA5-1131T > C SNP and TG-rich lipoprotein concentrations that were higher in carriers of the minor allele than in noncarriers (P < 0.001). Moreover, we found a significant genotype-dietary fat interaction for obesity traits. Participants homozygous for the -1131T major allele had a positive association between fat intake and obesity, whereas in those carrying the APOA5-1131C minor allele, higher fat intakes were not associated with higher BMI. Likewise, we found genotype-dietary fat interactions for TG-rich lipoproteins (P < 0.001). In conclusion, we have replicated previous gene-diet interactions between APOA5 -1131T > C SNP and fat intake for obesity traits and detected a novel interaction for TG-rich lipoprotein concentrations. Our data support the hypothesis that the minor C-allele may protect those consuming a high-fat diet from obesity and elevated concentrations of TG-rich lipoproteins.

  11. Interaction of multiple networks modulated by the working memory training based on real-time fMRI

    NASA Astrophysics Data System (ADS)

    Shen, Jiahui; Zhang, Gaoyan; Zhu, Chaozhe; Yao, Li; Zhao, Xiaojie

    2015-03-01

    Neuroimaging studies of working memory training have identified the alteration of brain activity as well as the regional interactions within the functional networks such as central executive network (CEN) and default mode network (DMN). However, how the interaction within and between these multiple networks is modulated by the training remains unclear. In this paper, we examined the interaction of three training-induced brain networks during working memory training based on real-time functional magnetic resonance imaging (rtfMRI). Thirty subjects assigned to the experimental and control group respectively participated in two times training separated by seven days. Three networks including silence network (SN), CEN and DMN were identified by the training data with the calculated function connections within each network. Structural equation modeling (SEM) approach was used to construct the directional connectivity patterns. The results showed that the causal influences from the percent signal changes of target ROI to the SN were positively changed in both two groups, as well as the causal influence from the SN to CEN was positively changed in experimental group but negatively changed in control group from the SN to DMN. Further correlation analysis of the changes in each network with the behavioral improvements showed that the changes in SN were stronger positively correlated with the behavioral improvement of letter memory task. These findings indicated that the SN was not only a switch between the target ROI and the other networks in the feedback training but also an essential factor to the behavioral improvement.

  12. Multiaddressable molecular rectangles with reversible host–guest interactions: Modulation of pH-controlled guest release and capture

    PubMed Central

    Chan, Alan Kwun-Wa; Lam, Wai Han; Tanaka, Yuya; Wong, Keith Man-Chung; Yam, Vivian Wing-Wah

    2015-01-01

    A series of multiaddressable platinum(II) molecular rectangles with different rigidities and cavity sizes has been synthesized by endcapping the U-shaped diplatinum(II) terpyridine moiety with various bis-alkynyl ligands. The studies of the host–guest association with various square planar platinum(II), palladium(II), and gold(III) complexes and the related low-dimensional gold(I) complexes, most of which are potential anticancer therapeutics, have been performed. Excellent guest confinement and selectivity of the rectangular architecture have been shown. Introduction of pH-responsive functionalities to the ligand backbone generates multifunctional molecular rectangles that exhibit reversible guest release and capture on the addition of acids and bases, indicating their potential in controlled therapeutics delivery on pH modulation. The reversible host–guest interactions are found to be strongly perturbed by metal–metal and π–π interactions and to a certain extent, electrostatic interactions, giving rise to various spectroscopic changes depending on the nature of the guest molecules. Their binding mode and thermodynamic parameters have been determined by 2D NMR and van’t Hoff analysis and supported by computational study. PMID:25568083

  13. Fragment-based methods for the discovery of inhibitors modulating lysyl-tRNA synthetase and laminin receptor interaction.

    PubMed

    Cho, Hye Young; Kim, Sunghoon; Jeon, Young Ho

    2017-01-15

    Lysyl-tRNA synthetase (KRS) is an enzyme that conjugates lysine to its cognate tRNAs in the process of protein synthesis. In addition to its catalytic function, KRS binds to the 67-kDa laminin receptor (LR) on the cell membrane and facilitates cell migration and metastasis. Modulation of this interaction by small-molecule inhibitors can be exploited to suppress cancer metastasis. In this study, we present fragment-based methods for the identification of inhibitors and monitoring protein-protein interactions between KRS and LR. First, we identified the amino acid residues, located on the KRS anticodon-binding domain, which interact with the C-terminal extension of the LR. One-dimensional (1D) relaxation-edited nuclear magnetic resonance spectroscopy (NMR) and competition experiments were designed and optimized to screen the fragment library. For screening using two-dimensional (2D) NMR, we identified the indicative signals in the KRS anticodon-binding domain and selected inhibitors that bind to KRS and compete with LR at the KRS-LR binding interface. These methods may offer an efficient approach for the discovery of anti-metastatic drugs.

  14. Multiaddressable molecular rectangles with reversible host-guest interactions: modulation of pH-controlled guest release and capture.

    PubMed

    Chan, Alan Kwun-Wa; Lam, Wai Han; Tanaka, Yuya; Wong, Keith Man-Chung; Yam, Vivian Wing-Wah

    2015-01-20

    A series of multiaddressable platinum(II) molecular rectangles with different rigidities and cavity sizes has been synthesized by endcapping the U-shaped diplatinum(II) terpyridine moiety with various bis-alkynyl ligands. The studies of the host-guest association with various square planar platinum(II), palladium(II), and gold(III) complexes and the related low-dimensional gold(I) complexes, most of which are potential anticancer therapeutics, have been performed. Excellent guest confinement and selectivity of the rectangular architecture have been shown. Introduction of pH-responsive functionalities to the ligand backbone generates multifunctional molecular rectangles that exhibit reversible guest release and capture on the addition of acids and bases, indicating their potential in controlled therapeutics delivery on pH modulation. The reversible host-guest interactions are found to be strongly perturbed by metal-metal and π-π interactions and to a certain extent, electrostatic interactions, giving rise to various spectroscopic changes depending on the nature of the guest molecules. Their binding mode and thermodynamic parameters have been determined by 2D NMR and van't Hoff analysis and supported by computational study.

  15. Studies of Peptide:N-glycnase-p97 Interaction Suggest that p97 Phosphorylation Modulates Endoplasmic Reticulum-Associated Degradation

    SciTech Connect

    Zhao,G.; Zhou, X.; Wang, L.; Li, G.; Schindelin, H.; Lennarz, W.

    2007-01-01

    During endoplasmic reticulum-associated degradation, the multifunctional AAA ATPase p97 is part of a protein degradation complex. p97 associates via its N-terminal domain with various cofactors to recruit ubiquitinated substrates. It also interacts with alternative substrate-processing cofactors, such as Ufd2, Ufd3, and peptide:N-glycanase (PNGase) in higher eukaryotes. These cofactors determine different fates of the substrates and they all bind outside of the N-terminal domain of p97. Here, we describe a cofactor-binding motif of p97 contained within the last 10 amino acid residues of the C terminus, which is both necessary and sufficient to mediate interactions of p97 with PNGase and Ufd3. The crystal structure of the N-terminal domain of PNGase in complex with this motif provides detailed insight into the interaction between p97 and its substrate-processing cofactors. Phosphorylation of p97's highly conserved penultimate tyrosine residue, which is the main phosphorylation site during T cell receptor stimulation, completely blocks binding of either PNGase or Ufd3 to p97. This observation suggests that phosphorylation of this residue modulates endoplasmic reticulum-associated protein degradation activity by discharging substrate-processing cofactors.

  16. Spin-wave propagation steered by electric field modulated exchange interaction

    PubMed Central

    Wang, Sheng; Guan, Xiawei; Cheng, Xiaomin; Lian, Chen; Huang, Ting; Miao, Xiangshui

    2016-01-01

    Combined ab initio and micromagnetic simulations are carried out to demonstrate the feasibility on the electrical manipulation of spin-wave propagation in ultrathin Fe films. It is discovered that the exchange interaction can be substantially weakened under the influence of electric field applied perpendicular to the magnetic film surface. Furthermore, we demonstrate that the electric field modified exchange constant could effectively control the propagation of spin waves. To be specific, an external applied electric field of 5 V/nm can effectively weaken exchange interaction by 80% and is sufficient to induce nearly twofold change of the wavenumber. This discovery may open a door to energy-efficient local manipulation of the spin wave propagation utilizing electric fields, which is crucial for both fundamental research and spin wave based logic applications. PMID:27587083

  17. The Role of Through-Space Interactions in Modulating Constructive and Destructive Interference Effects in Benzene.

    PubMed

    Borges, Anders; Xia, Jianlong; Liu, Sheng Hua; Venkataraman, Latha; Solomon, Gemma C

    2017-07-12

    Quantum interference effects, whether constructive or destructive, are key to predicting and understanding the electrical conductance of single molecules. Here, through theory and experiment, we investigate a family of benzene-like molecules that exhibit both constructive and destructive interference effects arising due to more than one contact between the molecule and each electrode. In particular, we demonstrate that the π-system of meta-coupled benzene can exhibit constructive interference and its para-coupled analog can exhibit destructive interference, and vice versa, depending on the specific through-space interactions. As a peculiarity, this allows a meta-coupled benzene molecule to exhibit higher conductance than a para-coupled benzene. Our results provide design principles for molecular electronic components with high sensitivity to through-space interactions and demonstrate that increasing the number of contacts between the molecule and electrodes can both increase and decrease the conductance.

  18. Contrast polarity, chromaticity, and stereoscopic depth modulate contextual interactions in vernier acuity.

    PubMed

    Sayim, Bilge; Westheimer, Gerald; Herzog, Michael H

    2008-06-30

    Vernier alignment thresholds are strongly compromised when the vernier is embedded in an array of equal-length flanking lines. Here, we show that these contextual interactions can be diminished by giving the flanks the opposite contrast polarity, e.g., white flanks surrounding a black vernier. Similar results are obtained for red verniers and equiluminant green flanks and when vernier and flanks have different binocular disparity. Using special flank configurations, we can eliminate location uncertainty as an important factor for this kind of contextual interactions. We interpret these results as evidence that perceptual grouping of the vernier and the flanks plays an important role in the vernier threshold elevation caused by contextual flanks.

  19. Host-Virus Interaction of ZIKA Virus in Modulating Disease Pathogenesis.

    PubMed

    Routhu, Nanda Kishore; Byrareddy, Siddappa N

    2017-03-27

    The Zika virus (ZIKV) is a newly emerging pathogen that has resulted in a worldwide epidemic. It primarily spreads either through infected Aedes aegypti or Aedes albopictus mosquitos leading to severe neurological disorders such as microcephaly and Guillain-Barré syndrome in susceptible individuals. The mode of ZIKV entry into specific cell types such as: epidermal keratinocytes, fibroblasts, immature dendritic cells (iDCs), and stem-cell-derived human neural progenitors has been determined through its major surface envelope glycoprotein. It has been known that oligosaccharides that are covalently linked to viral envelope proteins are crucial in defining host-virus interactions. However, the role of sugars/glycans in exploiting host-immune mechanisms and aiding receptor-mediated virus entry is not well defined. Therefore, this review focuses on host-pathogen interactions to better understand ZIKV pathogenesis.

  20. Context-based retrieval of functional modules in protein-protein interaction networks.

    PubMed

    Dobay, Maria Pamela; Stertz, Silke; Delorenzi, Mauro

    2017-03-27

    Various techniques have been developed for identifying the most probable interactants of a protein under a given biological context. In this article, we dissect the effects of the choice of the protein-protein interaction network (PPI) and the manipulation of PPI settings on the network neighborhood of the influenza A virus (IAV) network, as well as hits in genome-wide small interfering RNA screen results for IAV host factors. We investigate the potential of context filtering, which uses text mining evidence linked to PPI edges, as a complement to the edge confidence scores typically provided in PPIs for filtering, for obtaining more biologically relevant network neighborhoods. Here, we estimate the maximum performance of context filtering to isolate a Kyoto Encyclopedia of Genes and Genomes (KEGG) network Ki from a union of KEGG networks and its network neighborhood. The work gives insights on the use of human PPIs in network neighborhood approaches for functional inference.

  1. Spin-wave propagation steered by electric field modulated exchange interaction

    NASA Astrophysics Data System (ADS)

    Wang, Sheng; Guan, Xiawei; Cheng, Xiaomin; Lian, Chen; Huang, Ting; Miao, Xiangshui

    2016-09-01

    Combined ab initio and micromagnetic simulations are carried out to demonstrate the feasibility on the electrical manipulation of spin-wave propagation in ultrathin Fe films. It is discovered that the exchange interaction can be substantially weakened under the influence of electric field applied perpendicular to the magnetic film surface. Furthermore, we demonstrate that the electric field modified exchange constant could effectively control the propagation of spin waves. To be specific, an external applied electric field of 5 V/nm can effectively weaken exchange interaction by 80% and is sufficient to induce nearly twofold change of the wavenumber. This discovery may open a door to energy-efficient local manipulation of the spin wave propagation utilizing electric fields, which is crucial for both fundamental research and spin wave based logic applications.

  2. Synthetic Nucleosomes Reveal that GlcNAcylation Modulates Direct Interaction with the FACT Complex

    PubMed Central

    Raj, Ritu; Lercher, Lukas; Mohammed, Shabaz

    2016-01-01

    Abstract Transcriptional regulation can be established by various post‐translational modifications (PTMs) on histone proteins in the nucleosome and by nucleobase modifications on chromosomal DNA. Functional consequences of histone O‐GlcNAcylation (O‐GlcNAc=O‐linked β‐N‐acetylglucosamine) are largely unexplored. Herein, we generate homogeneously GlcNAcylated histones and nucleosomes by chemical post‐translational modification. Mass‐spectrometry‐based quantitative interaction proteomics reveals a direct interaction between GlcNAcylated nucleosomes and the “facilitates chromatin transcription” (FACT) complex. Preferential binding of FACT to GlcNAcylated nucleosomes may point towards O‐GlcNAcylation as one of the triggers for FACT‐driven transcriptional control. PMID:27272618

  3. KDM5 Interacts with Foxo to Modulate Cellular Levels of Oxidative Stress

    PubMed Central

    Liu, Xingyin; Greer, Christina; Secombe, Julie

    2014-01-01

    Increased cellular levels of oxidative stress are implicated in a large number of human diseases. Here we describe the transcription co-factor KDM5 (also known as Lid) as a new critical regulator of cellular redox state. Moreover, this occurs through a novel KDM5 activity whereby it alters the ability of the transcription factor Foxo to bind to DNA. Our microarray analyses of kdm5 mutants revealed a striking enrichment for genes required to regulate cellular levels of oxidative stress. Consistent with this, loss of kdm5 results in increased sensitivity to treatment with oxidizers, elevated levels of oxidized proteins, and increased mutation load. KDM5 activates oxidative stress resistance genes by interacting with Foxo to facilitate its recruitment to KDM5-Foxo co-regulated genes. Significantly, this occurs independently of KDM5's well-characterized demethylase activity. Instead, KDM5 interacts with the lysine deacetylase HDAC4 to promote Foxo deacetylation, which affects Foxo DNA binding. PMID:25329053

  4. Modulation of fluorescence signals from biomolecules along nanowires due to interaction of light with oriented nanostructures.

    PubMed

    Frederiksen, Rune S; Alarcon-Llado, Esther; Madsen, Morten H; Rostgaard, Katrine R; Krogstrup, Peter; Vosch, Tom; Nygård, Jesper; Fontcuberta I Morral, Anna; Martinez, Karen L

    2015-01-14

    High aspect ratio nanostructures have gained increasing interest as highly sensitive platforms for biosensing. Here, well-defined biofunctionalized vertical indium arsenide nanowires are used to map the interaction of light with nanowires depending on their orientation and the excitation wavelength. We show how nanowires act as antennas modifying the light distribution and the emitted fluorescence. This work highlights an important optical phenomenon in quantitative fluorescence studies and constitutes an important step for future studies using such nanostructures.

  5. N-cadherin adhesive interactions modulate matrix mechanosensing and fate commitment of mesenchymal stem cells

    NASA Astrophysics Data System (ADS)

    Cosgrove, Brian D.; Mui, Keeley L.; Driscoll, Tristan P.; Caliari, Steven R.; Mehta, Kush D.; Assoian, Richard K.; Burdick, Jason A.; Mauck, Robert L.

    2016-12-01

    During mesenchymal development, the microenvironment gradually transitions from one that is rich in cell-cell interactions to one that is dominated by cell-ECM (extracellular matrix) interactions. Because these cues cannot readily be decoupled in vitro or in vivo, how they converge to regulate mesenchymal stem cell (MSC) mechanosensing is not fully understood. Here, we show that a hyaluronic acid hydrogel system enables, across a physiological range of ECM stiffness, the independent co-presentation of the HAVDI adhesive motif from the EC1 domain of N-cadherin and the RGD adhesive motif from fibronectin. Decoupled presentation of these cues revealed that HAVDI ligation (at constant RGD ligation) reduced the contractile state and thereby nuclear YAP/TAZ localization in MSCs, resulting in altered interpretation of ECM stiffness and subsequent changes in downstream cell proliferation and differentiation. Our findings reveal that, in an evolving developmental context, HAVDI/N-cadherin interactions can alter stem cell perception of the stiffening extracellular microenvironment.

  6. Direct interaction with filamins modulates the stability and plasma membrane expression of CFTR

    PubMed Central

    Thelin, William R.; Chen, Yun; Gentzsch, Martina; Kreda, Silvia M.; Sallee, Jennifer L.; Scarlett, Cameron O.; Borchers, Christoph H.; Jacobson, Ken; Stutts, M. Jackson; Milgram, Sharon L.

    2007-01-01

    The role of the cystic fibrosis transmembrane conductance regulator (CFTR) as a cAMP-dependent chloride channel on the apical membrane of epithelia is well established. However, the processes by which CFTR is regulated on the cell surface are not clear. Here we report the identification of a protein-protein interaction between CFTR and the cytoskeletal filamin proteins. Using proteomic approaches, we identified filamins as proteins that associate with the extreme CFTR N terminus. Furthermore, we identified a disease-causing missense mutation in CFTR, serine 13 to phenylalanine (S13F), which disrupted this interaction. In cells, filamins tethered plasma membrane CFTR to the underlying actin network. This interaction stabilized CFTR at the cell surface and regulated the plasma membrane dynamics and confinement of the channel. In the absence of filamin binding, CFTR was internalized from the cell surface, where it prematurely accumulated in lysosomes and was ultimately degraded. Our data demonstrate what we believe to be a previously unrecognized role for the CFTR N terminus in the regulation of the plasma membrane stability and metabolic stability of CFTR. In addition, we elucidate the molecular defect associated with the S13F mutation. PMID:17235394

  7. HIPK1 interacts with c-Myb and modulates its activity through phosphorylation

    SciTech Connect

    Matre, Vilborg; Nordgard, Oddmund; Alm-Kristiansen, Anne Hege; Ledsaak, Marit; Gabrielsen, Odd Stokke

    2009-10-09

    The transcription factor v-Myb is a potent inducer of myeloid leukaemias, and its cellular homologue c-Myb plays a crucial role in the regulation of haematopoiesis. In a yeast two-hybrid (Y2H) screening we identified the nuclear kinase HIPK1 as an interaction partner for human c-Myb. The interaction involves a C-terminal region of HIPK1, while a bipartite interaction surface was identified in c-Myb, including regions in its N-terminal DNA-binding domain as well as in its C-terminal region. HIPK1 and c-Myb co-localize in distinct nuclear foci upon co-transfection. c-Myb appears to be phosphorylated by HIPK1 in its negative regulatory domain as supported by both in vivo and in vitro data. A functional assay revealed that HIPK1 repressed the ability of c-Myb to activate a chromatin embedded target gene, mim-1, in haematopoetic cells. Our findings point to a novel link between an important kinase and a key regulator of haematopoiesis.

  8. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

    PubMed Central

    Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

    2016-01-01

    Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

  9. N-Cadherin adhesive interactions modulate matrix mechanosensing and fate commitment of mesenchymal stem cells

    PubMed Central

    Cosgrove, Brian D.; Mui, Keeley L.; Driscoll, Tristan P.; Caliari, Steven R.; Mehta, Kush D.; Assoian, Richard K.; Burdick, Jason A.; Mauck, Robert L.

    2016-01-01

    During mesenchymal development, the microenvironment gradually transitions from one that is rich in cell-cell interactions to one that is dominated by cell-extracellular-matrix (ECM) interactions. Because these cues cannot readily be decoupled in vitro or in vivo, how they converge to regulate mesenchymal stem cell (MSC) mechanosensing is not fully understood. Here, we show that a hyaluronic acid hydrogel system enables, across a physiological range of ECM stiffness, the independent co-presentation of the HAVDI adhesive motif from the EC1 domain of N-Cadherin and the RGD adhesive motif from fibronectin. Decoupled presentation of these cues revealed that HAVDI ligation (at constant RGD ligation) reduced the contractile state and thereby nuclear YAP/TAZ localization in MSCs, resulting in altered interpretation of ECM stiffness and subsequent changes in downstream cell proliferation and differentiation. Our findings reveal that, in an evolving developmental context, HAVDI/N-Cadherin interactions can alter stem cell perception of the stiffening extracellular microenvironment. PMID:27525568

  10. Argininosuccinate lyase interacts with cyclin A2 in cytoplasm and modulates growth of liver tumor cells.

    PubMed

    Hung, Yu-Hsuan; Huang, Hau-Lun; Chen, Wei-Ching; Yen, Meng-Chi; Cho, Chien-Yu; Weng, Tzu-Yang; Wang, Chih-Yang; Chen, Yi-Ling; Chen, Li-Tzong; Lai, Ming-Derg

    2017-02-01

    Arginine is a critical amino acid in specific cancer types including hepatocellular carcinoma (HCC) and melanoma. Novel molecular mechanisms and therapeutic targets in arginine metabolism-mediated cancer formation await further identification. Our laboratory has previously demonstrated that arginine metabolic enzyme argininosuccinate lyase (ASL) promoted HCC formation in part via maintenance of cyclin A2 protein expression and arginine production for channeling to nitric oxide synthase. In this study, we investigated the mechanism by which ASL regulates cyclin A2 expression. We found that ASL interacted with cyclin A2 in HCC cells and the localization of their interaction was in the cytoplasm. Mutation of essential residues for enzymatic activity of ASL did not affect the binding of ASL to cyclin A2. Moreover, the mutant ASL retained the ability to restore the decreased tumorigenicity caused by ASL shRNA. Furthermore, overexpression of ASL conferred resistance to arginine deprivation therapy. Finally, the important pathways and potential therapeutic targets in ASL-regulated HCC were identified by bioinformatics analyses with Metacore database and Connectivity Map database. Our analyses suggested that bisoprolol, celecoxib, and ipratropium bromide, are potential therapeutics for ASL-regulated HCC formation. Thus, ASL interacts with cyclin A2 in cytoplasm, and may promote HCC formation through this non-enzymatic function. Overexpression of ASL may be a contributing factor in drug resistance for arginine deprivation therapy.

  11. Nasal priming with immunobiotic Lactobacillus rhamnosus modulates inflammation-coagulation interactions and reduces influenza virus-associated pulmonary damage.

    PubMed

    Zelaya, Hortensia; Tada, Asuka; Vizoso-Pinto, Maria Guadalupe; Salva, Susana; Kanmani, Paulraj; Agüero, Graciela; Alvarez, Susana; Kitazawa, Haruki; Villena, Julio

    2015-08-01

    To evaluate the effect of the nasal administration of live and heat-killed Lactobacillus rhamnosus CRL1505 (Lr1505) on immune-coagulative response during influenza virus (IFV) infection to improve survival and reduce lung injury. Six-week-old BALB/c mice were treated with live or heat-killed Lr1505 by the nasal route during two consecutive days. Treated and untreated control mice were then nasally challenged with IFV. Both viable and non-viable Lr1505 protected infected mice by reducing pulmonary injury and lung viral loads trough several mechanisms: (a) Inflammatory cytokines were efficiently regulated allowing higher clearance of virus and reduction of inflammatory lung tissue damage, associated to higher levels of the regulatory cytokine IL-10. (b) The antiviral immune response was enhanced with improved levels of type I interferons, CD4(+)IFN-γ(+) lymphocytes, and lung CD11c(+)CD11b(low)CD103(+) and CD11c(+)CD11b(high)CD103(-) dendritic cells. (c) The procoagulant state was reversed mainly by down-regulating tissue factor expression and restoring thrombomodulin levels in lung. The capacity of Lr1505 to improve the outcome of IFV infection would be related to its ability to beneficially modulate lung TLR3-triggered immune response. Our work is the first to demonstrate the ability of an immunobiotic strain to beneficially modulate inflammation-coagulation interactions during IFV infection. Interestingly, non-viable L. rhamnosus CRL1505 was as effective as the viable strain to beneficially modulate respiratory antiviral immune response.

  12. Growing evidence suggests WT1 effects in the kidney development are modulated by Hsp70/NO interaction.

    PubMed

    Mazzei, Luciana; Manucha, Walter

    2017-02-01

    The study of kidney development at the cellular and molecular levels remains an active area of nephrology research. The functional integrity of the kidney depends on normal development as well as on physiological cell turnover. Apoptosis induction is essential for these mechanisms. A route to cell death revealed in the past decade shows that heat shock proteins (HSPs) and their cofactors are responsible for regulating the apoptotic pathway. Specifically, heat shock protein 70 (Hsp70), the most ubiquitous and highly conserved HSP, helps proteins adopt native conformation or regain function after misfolding. Hsp70 is an important cofactor for the function of Wilms' tumour 1 (WT1) and suggests a potential role for this chaperone during kidney differentiation. In addition, we have demonstrated that WT1 expression is modulated by nitric oxide (NO) availability and Hsp70 interaction after neonatal unilateral ureteral obstruction. NO has been identified as playing an important role in the developing kidney. These findings suggest that Hsp70 and NO may play a critical and fundamental role in the capacity to modulate both apoptotic pathway and oxidative stress during kidney development. Furthermore, the design of experimental protocols that assess renal epithelial functionality in this context, could contribute to the understanding of renal development and alterations.

  13. Omega-3 fatty acids and cytochrome P450-derived eicosanoids in cardiovascular diseases: Which actions and interactions modulate hemodynamics?

    PubMed

    Bonafini, Sara; Fava, Cristiano

    2017-01-01

    Increasing interest is focused on omega-3 fatty acids (FA) because of their potential beneficial effects, particularly in cardiovascular disease prevention. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), two major omega-3 FA, are mainly consumed through diet, particularly from fish and seafood intake, whereas alpha-linolenic acid (ALA) is present in high amounts in leafy green vegetables, nuts and seeds. The hypothesis of a cardiovascular protective action of omega-3 FA derives mainly from observational studies, whereas the evidence from interventional studies is not always consistent. Nonetheless, clinical trials and meta-analyses indicate a positive action, at minimum on blood pressure (BP). Omega-3 FA may act through different biological pathways; however, in our review, we seek to revisit, most notably, the role of their metabolites via cytochrome P450 (CYP450) in hemodynamic modulation. We emphasize that the effect of omega-3 FA may depend on their balance with other dietary compounds, particularly omega-6 FA, which compete for the same pathways, thus modulating the production of metabolites. Furthermore, the biological activity of omega-3 FA might be better explained by the complex balance and interactions between a variety of nutrients and polymorphisms of genes implicated in specific metabolic pathways.

  14. Low-frequency modulations in the solar microwave radiation as a possible indicator of inductive interaction of coronal magnetic loops

    NASA Astrophysics Data System (ADS)

    Khodachenko, M. L.; Zaitsev, V. V.; Kislyakov, A. G.; Rucker, H. O.; Urpo, S.

    2005-04-01

    Low-frequency (LF) modulations of 37GHz microwave radiation during solar flares, recorded at the Metsähovi Radio Observatory, are considered. A fast Fourier transformation with a sliding window is used to obtain the dynamic spectra of the LF pulsations. We pay attention to the LFdynamic spectra having a specific multi-track structure, which is supposed to be an indication of a complex multi-loop composition of a flaring region. Application of the equivalent electric circuit models of the loops including the effects of electromagnetic inductive interaction in groups of slowly growing current-carrying magnetic loops allows us to explain and reproduce the main dynamical features of the observed LF modulation dynamic spectra. Each loop is considered as an equivalent electric circuit with variable parameters (resistance, capacitance and inductive coefficients) which depend on shape, scale, position of the loop with respect to other loops, as well as on the plasma parameters and value of the total longitudinal current in the magnetic tube.

  15. An artificially evolved albumin binding module facilitates chemical shift epitope mapping of GA domain interactions with phylogenetically diverse albumins.

    PubMed

    He, Yanan; Chen, Yihong; Rozak, David A; Bryan, Philip N; Orban, John

    2007-07-01

    Protein G-related albumin-binding (GA) modules occur on the surface of numerous Gram-positive bacterial pathogens and their presence may promote bacterial growth and virulence in mammalian hosts. We recently used phage display selection to evolve a GA domain, PSD-1 (phage selected domain-1), which tightly bound phylogenetically diverse albumins. With respect to PSD-1's broad albumin binding specificity, it remained unclear how the evolved binding epitope compared to those of naturally occurring GA domains and whether PSD-1's binding mode was the same for different albumins. We investigate these questions here using chemical shift perturbation measurements of PSD-1 with rabbit serum albumin (RSA) and human serum albumin (HSA) and put the results in the context of previous work on structure and dynamics of GA domains. Combined, these data provide insights into the requirements for broad binding specificity in GA-albumin interactions. Moreover, we note that using the phage-optimized PSD-1 protein significantly diminishes the effects of exchange broadening at the binding interface between GA modules and albumin, presumably through stabilization of a ligand-bound conformation. The employment of artificially evolved domains may be generally useful in NMR structural studies of other protein-protein complexes.

  16. A Mitochondrial ATP synthase Subunit Interacts with TOR Signaling to Modulate Protein Homeostasis and Lifespan in Drosophila

    PubMed Central

    Sun, Xiaoping; Wheeler, Charles T.; Yolitz, Jason; Laslo, Mara; Alberico, Thomas; Sun, Yaning; Song, Qisheng; Zou, Sige

    2014-01-01

    SUMMARY Diet composition is a critical determinant of lifespan and nutrient imbalance is detrimental health. However, how nutrients interact with genetic factors to modulate lifespan remains elusive. We investigated how diet composition influences mitochondrial ATP synthase subunit d (ATPsyn-d) in modulating lifespan in Drosophila. ATPsyn-d knockdown extended lifespan in females fed low carbohydrate-to-protein (C:P) diets, but not the high C:P ratio diet. This extension was associated with increased resistance to oxidative stress, transcriptional changes in metabolism, proteostasis and immune genes, reduced protein damage and aggregation, and reduced phosphorylation of S6K and ERK in TOR and MAPK signaling, respectively. ATPsyn-d knockdown did not extend lifespan in females with reduced TOR signaling induced genetically by Tsc2 overexpression or pharmacologically by rapamycin. Our data reveal a link among diet, mitochondria, MAPK and TOR signaling in aging and stresses the importance of considering genetic background and diet composition in implementing interventions for promoting healthy aging. PMID:25220459

  17. Flavonoid Interaction with a Chitinase from Grape Berry Skin: Protein Identification and Modulation of the Enzymatic Activity.

    PubMed

    Filippi, Antonio; Petrussa, Elisa; Rajcevic, Uros; Čurin Šerbec, Vladka; Passamonti, Sabina; Renzone, Giovanni; Scaloni, Andrea; Zancani, Marco; Vianello, Angelo; Braidot, Enrico

    2016-09-28

    In the present study, an antibody raised against a peptide sequence of rat bilitranslocase (anti-peptide Ab) was tested on microsomal proteins obtained from red grape berry skin. Previously, this antibody had demonstrated to recognize plant membrane proteins associated with flavonoid binding and transport. Immuno-proteomic assays identified a number of proteins reacting with this particular antibody, suggesting that the flavonoid binding and interaction may be extended not only to carriers of these molecules, but also to enzymes with very different functions. One of these proteins is a pathogenesis-related (PR) class IV chitinase, whose in vitro chitinolytic activity was modulated by two of the most representative flavonoids of grape, quercetin and catechin, as assessed by both spectrophotometric and fluorimetric assays in grape microsomes and commercial enzyme preparations. The effect of these flavonoids on the catalysis and its kinetic parameters was also evaluated, evidencing that they determine a hormetic dose-dependent response. These results highlight the importance of flavonoids not only as antioxidants or antimicrobial effectors, but also as modulators of plant growth and stress response. Implications of the present suggestion are here discussed in the light of environment and pesticide-reduction concerns.

  18. Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way to Reversibly Concentrate Functionalized Nanoparticles

    PubMed Central

    Villarreal, Oscar D; Chen, Liao Y; Whetten, Robert L; Demeler, Borries

    2015-01-01

    Nanometer-sized gold particles (AuNPs) are of peculiar interest because their behaviors in an aqueous solution are sensitive to changes in environmental factors including the size and shape of the solute ions. In order to determine these important characteristics, we performed all-atom molecular dynamics simulations on the icosahedral Au144 nanoparticles each coated with a homogeneous set of 60 thiolates (4-mercapto-benzoate, pMBA) in eight aqueous solutions having ions of varying sizes and shapes (Na+, K+, tetramethylamonium cation TMA+, trisamonium cation TRS+, Cl−, and OH−). For each solution, we computed the reversible work (potential of mean of force) to bring two nanoparticles together as a function of their separation distance. We found that the behavior of pMBA protected Au144 nanoparticles can be readily modulated by tuning their aqueous environmental factors (pH and solute ion combinations). We examined the atomistic details on how the sizes and shapes of solute ions quantitatively factor in the definitive characteristics of nanoparticle-environment and nanoparticle-nanoparticle interactions. We predict that tuning the concentrations of non-spherical composite ions such as TRS+ in an aqueous solution of AuNPs be an effective means to modulate the aggregation propensity desired in biomedical and other applications of small charged nanoparticles. PMID:26581232

  19. Integrating anatomy training into radiation oncology residency: considerations for developing a multidisciplinary, interactive learning module for adult learners.

    PubMed

    Labranche, Leah; Johnson, Marjorie; Palma, David; D'Souza, Leah; Jaswal, Jasbir

    2015-01-01

    Radiation oncologists require an in-depth understanding of anatomical relationships for modern clinical practice, although most do not receive formal anatomy training during residency. To fulfill the need for instruction in relevant anatomy, a series of four multidisciplinary, interactive learning modules were developed for a cohort of radiation oncology and medical physics residents. Instructional design was based on established learning theories, with the intent of integrating knowledge of specific anatomical regions with radiology and radiation oncology practice. Each session included presentations by a radiologist and a radiation oncologist, as well as hands-on exploration of anatomical specimens with guidance from anatomists. Pre- and post-tests distributed during each session showed significant short-term knowledge retention. According to qualitative surveys and exit interviews, participants felt more comfort' with delineating structures, gross anatomy, and radiograph interpretation at the end of each session. Overall participant experience was positive, and the modules were considered effective for learning radiologic anatomy. Suggestions for future interventions include more time, increased clinical application, additional contouring practice and feedback, and improved coordination between each of the three disciplines. Results and conclusions from this study will be used to inform the design of a future multi-day national workshop for Canadian radiation oncology residents.

  20. Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way To Reversibly Concentrate Functionalized Nanoparticles.

    PubMed

    Villarreal, Oscar D; Chen, Liao Y; Whetten, Robert L; Demeler, Borries

    2015-12-17

    Nanometer-sized gold particles (AuNPs) are of peculiar interest because their behaviors in an aqueous solution are sensitive to changes in environmental factors including the size and shape of the solute ions. In order to determine these important characteristics, we performed all-atom molecular dynamics simulations on the icosahedral Au144 nanoparticles each coated with a homogeneous set of 60 thiolates (4-mercaptobenzoate, pMBA) in eight aqueous solutions having ions of varying sizes and shapes (Na(+), K(+), tetramethylamonium cation TMA(+), tris-ammonium cation TRS(+), Cl(-), and OH(-)). For each solution, we computed the reversible work (potential of mean of force) to bring two nanoparticles together as a function of their separation distance. We found that the behavior of pMBA protected Au144 nanoparticles can be readily modulated by tuning their aqueous environmental factors (pH and solute ion combinations). We examined the atomistic details on how the sizes and shapes of solute ions quantitatively factor in the definitive characteristics of nanoparticle-environment and nanoparticle-nanoparticle interactions. We predict that tuning the concentrations of nonspherical composite ions such as TRS(+) in an aqueous solution of AuNPs be an effective means to modulate the aggregation propensity desired in biomedical and other applications of small charged nanoparticles.

  1. Design and Development of High Voltage Direct Current (DC) Sources for the Solar Array Module Plasma Interaction Experiment

    NASA Technical Reports Server (NTRS)

    Bibyk, Irene K.; Wald, Lawrence W.

    1995-01-01

    Two programmable, high voltage DC power supplies were developed as part of the flight electronics for the Solar Array Module Plasma Interaction Experiment (SAMPIE). SAMPIE's primary objectives were to study and characterize the high voltage arcing and parasitic current losses of various solar cells and metal samples within the space plasma of low earth orbit (LEO). High voltage arcing can cause large discontinuous changes in spacecraft potential which lead to damage of the power system materials and significant Electromagnetic Interference (EMI). Parasitic currents cause a change in floating potential which lead to reduced power efficiency. These primary SAMPIE objectives were accomplished by applying artificial biases across test samples over a voltage range from -600 VDC to +300 VDC. This paper chronicles the design, final development, and test of the two programmable high voltage sources for SAMPIE. The technical challenges to the design for these power supplies included vacuum, space plasma effects, thermal protection, Shuttle vibrations and accelerations.

  2. Social top-down response modulation (STORM): a model of the control of mimicry in social interaction

    PubMed Central

    Wang, Yin; Hamilton, Antonia F. de C.

    2012-01-01

    As a distinct feature of human social interactions, spontaneous mimicry has been widely investigated in the past decade. Research suggests that mimicry is a subtle and flexible social behavior which plays an important role for communication and affiliation. However, fundamental questions like why and how people mimic still remain unclear. In this paper, we evaluate past theories of why people mimic and the brain systems that implement mimicry in social psychology and cognitive neuroscience. By reviewing recent behavioral and neuroimaging studies on the control of mimicry by social signals, we conclude that the subtlety and sophistication of mimicry in social contexts reflect a social top-down response modulation (STORM) which increases one's social advantage and this mechanism is most likely implemented by medial prefrontal cortex (mPFC). We suggest that this STORM account of mimicry is important for our understanding of social behavior and social cognition, and provides implications for future research in autism. PMID:22675295

  3. Tripping the light fantastic: blue-light photoreceptors as examples of environmentally modulated protein-protein interactions.

    PubMed

    Zoltowski, Brian D; Gardner, Kevin H

    2011-01-11

    Blue-light photoreceptors play a pivotal role in detecting the quality and quantity of light in the environment, controlling a wide range of biological responses. Several families of blue-light photoreceptors have been characterized in detail using biophysics and biochemistry, beginning with photon absorption, through intervening signal transduction, to regulation of biological activities. Here we review the light oxygen voltage, cryptochrome, and sensors of blue light using FAD families, three different groups of proteins that offer distinctly different modes of photochemical activation and signal transduction yet play similar roles in a vast array of biological responses. We cover mechanisms of light activation and propagation of conformational responses that modulate protein-protein interactions involved in biological signaling. Discovery and characterization of these processes in natural proteins are now allowing the design of photoregulatable engineered proteins, facilitating the generation of novel reagents for biochemical and cell biological research.

  4. Social top-down response modulation (STORM): a model of the control of mimicry in social interaction.

    PubMed

    Wang, Yin; Hamilton, Antonia F de C

    2012-01-01

    As a distinct feature of human social interactions, spontaneous mimicry has been widely investigated in the past decade. Research suggests that mimicry is a subtle and flexible social behavior which plays an important role for communication and affiliation. However, fundamental questions like why and how people mimic still remain unclear. In this paper, we evaluate past theories of why people mimic and the brain systems that implement mimicry in social psychology and cognitive neuroscience. By reviewing recent behavioral and neuroimaging studies on the control of mimicry by social signals, we conclude that the subtlety and sophistication of mimicry in social contexts reflect a social top-down response modulation (STORM) which increases one's social advantage and this mechanism is most likely implemented by medial prefrontal cortex (mPFC). We suggest that this STORM account of mimicry is important for our understanding of social behavior and social cognition, and provides implications for future research in autism.

  5. UBIQUITIN-SPECIFIC PROTEASE16 interacts with a HEAVY METAL ASSOCIATED ISOPRENYLATED PLANT PROTEIN27 and modulates cadmium tolerance.

    PubMed

    Zhao, Jinfeng; Zhou, Huapeng; Li, Yueyong

    2013-10-01

    Protein ubiquitination and deubiquitination are two reversible processes catalyzed by ubiquitin ligases and deubiquitinating enzymes, respectively. In Arabidopsis, lots of substrates of ubiquitin ligases were found, whereas only a few targets of deubiquitinating enzymes were identified. Recently, we reported that a functional UBIQUITIN-SPECIFIC PROTEASE16 (UBP16) was involved in salt tolerance through positively regulating plasma membrane Na+/H+ antiport activity and at least partially modulating SERINE HYDROXYMETHYLTRANSFERASE1 (SHM 1) stability and activity. Here, we report that UBP16 interacts with HEAVY META L ASSOCIATED ISOPRENYLATED PLANT PROTEIN 27 (HI PP27), a metallochaperone containing a predicted heavy-metal-associated domain, which has been reported to play an important role in cadmium detoxification. Meanwhile, the ubp16 mutant showed more sensitive to cadmium than wild-type. Taken together, HI PP27 may be another target of UBP16 in cadmium response.

  6. Lifetime Modulation of the Pain System via Neuroimmune and Neuroendocrine Interactions

    PubMed Central

    Zouikr, Ihssane; Karshikoff, Bianka

    2017-01-01

    Chronic pain is a debilitating condition that still is challenging both clinicians and researchers. Despite intense research, it is still not clear why some individuals develop chronic pain while others do not or how to heal this disease. In this review, we argue for a multisystem approach to understand chronic pain. Pain is not only to be viewed simply as a result of aberrant neuronal activity but also as a result of adverse early-life experiences that impact an individual’s endocrine, immune, and nervous systems and changes which in turn program the pain system. First, we give an overview of the ontogeny of the central nervous system, endocrine, and immune systems and their windows of vulnerability. Thereafter, we summarize human and animal findings from our laboratories and others that point to an important role of the endocrine and immune systems in modulating pain sensitivity. Taking “early-life history” into account, together with the past and current immunological and endocrine status of chronic pain patients, is a necessary step to understand chronic pain pathophysiology and assist clinicians in tailoring the best therapeutic approach. PMID:28348566

  7. Mycobacterium leprae phenolglycolipid-1 expressed by engineered M. bovis BCG modulates early interaction with human phagocytes.

    PubMed

    Tabouret, Guillaume; Astarie-Dequeker, Catherine; Demangel, Caroline; Malaga, Wladimir; Constant, Patricia; Ray, Aurélie; Honoré, Nadine; Bello, Nana Fatimath; Perez, Esther; Daffé, Mamadou; Guilhot, Christophe

    2010-10-21

    The species-specific phenolic glycolipid 1 (PGL-1) is suspected to play a critical role in the pathogenesis of leprosy, a chronic disease of the skin and peripheral nerves caused by Mycobacterium leprae. Based on studies using the purified compound, PGL-1 was proposed to mediate the tropism of M. leprae for the nervous system and to modulate host immune responses. However, deciphering the biological function of this glycolipid has been hampered by the inability to grow M. leprae in vitro and to genetically engineer this bacterium. Here, we identified the M. leprae genes required for the biosynthesis of the species-specific saccharidic domain of PGL-1 and reprogrammed seven enzymatic steps in M. bovis BCG to make it synthesize and display PGL-1 in the context of an M. leprae-like cell envelope. This recombinant strain provides us with a unique tool to address the key questions of the contribution of PGL-1 in the infection process and to study the underlying molecular mechanisms. We found that PGL-1 production endowed recombinant BCG with an increased capacity to exploit complement receptor 3 (CR3) for efficient invasion of human macrophages and evasion of inflammatory responses. PGL-1 production also promoted bacterial uptake by human dendritic cells and dampened their infection-induced maturation. Our results therefore suggest that M. leprae produces PGL-1 for immune-silent invasion of host phagocytic cells.

  8. Global-Local Interactions Modulate Tropical Moisture Exports to the Ohio River Basin

    NASA Astrophysics Data System (ADS)

    Doss-Gollin, J.; Farnham, D. J.; Lall, U.

    2016-12-01

    Regional-scale extreme rainfall and flooding are temporally and spatially associated with the occurrence of tropical moisture exports (TMEs) in the Ohio River Basin (ORB). TMEs are related to but not synonymous with atmospheric rivers, which refer to specific filiamentary organizational processes. TMEs to the ORB may be driven by strong, persistent ridging over the Eastern United States and troughing over the Central United States, creating favorable conditions for southerly flow and moisture transport from the Gulf of Mexico and Caribbean Sea. However, the strong inter-annual variation in TME activity over the ORB suggests dependence on global-scale features of the atmospheric circulation. We suggest that this synoptic dipole pattern may be viewed as the passage of one or more high-wavenumber, transient Rossby waves. We build a multi-level hierarchical Bayesian model in which the probability distribution of TME entering the ORB is a function of the phase and amplitude of the traveling waves. In turn, the joint distribution of the phase and amplitude of this wave is modulated by hemispheric-scale features of the atmospheric and oceanic circulation, and the amplitude and synchronization of quasi-stationary Rossby waves with wavenumber 1-4. Our approach bridges information about different features of the atmospheric circulation which inform the predictability of TME at multiple time scales and develops existing understanding of the atmospheric drivers of TMEs beyond existing composite and EOF studies.

  9. Prior expectation modulates the interaction between sensory and prefrontal regions in the human brain.

    PubMed

    Rahnev, Dobromir; Lau, Hakwan; de Lange, Floris P

    2011-07-20

    How do expectations about the i